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Delbert Bagwell U.S. Army ERDC Cary F. Chabalowski U.S. Army Research Laboratory Glake Hill Jackson State University William A. Lester, Jr. University of California at Berkeley Jerzy Leszczynski (Chairman) Jackson State University David Magers Mississippi College Gerald Maggiora Pfizer, Inc. Alan L. Middleton U.S. Army Engineer Research and Development Center Donald G. Truhlar University of Minnesota

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Shonda Allen Jackson State University Olexandr Isayev Jackson State University Debra Jackson Jackson State University Tracye Lewis Jackson State University Yevgeniy Podolyan Jackson State University Ilya Yanov Jackson State University

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National Science Foundation (CREST Program) U.S. Army Engineer Research and Development Center Army High Performance Computing Research Center Office of Vice President for Research and Strategic Initiatives, JSU National Institutes of Health (RCMI Program) Parallel Quantum Solutions

Conference on Current Trends in Computational Chemistry 2004 November 12-13, 2004 Jackson, Miss.

5 Schedule of Events Conference on Current Trends in Computational Chemistry 2004

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7:30 – 9:00 Continental Breakfast 8:00 – 12:00 Registration 9:00 – 9:30 Opening Ceremony Mary Ware Interim Assistant Commissioner Institutions of Higher Learning Ronald Mason Jackson State University, President Deborah Dent U.S. Army Engineer Research and Development Center, Deputy Director 9:30 – 10:30 1st Session (S1) Pulay lecture 10:30 – 10:40 Group photo 10:40 – 11:10 Coffee Break 11:10 – 12:40 2nd Session (S2) 2 Talks 12:40 – 2:00 Lunch 2:00 – 4:15 3rd Session (S3) 3 Talks 4:15 – 4:30 Coffee Break 4:30 – 6:30 First Poster Session (P1) 7:00 – 10:00 Dinner After-dinner Noble Lecture Series Speaker: Dr. William Lester, Jr. University of California, Berkeley

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8:00 – 9:00 Continental Breakfast 8:30 – 11:00 Registration 9:00 – 10:30 4th Session (S4) 2 Talks 10:30 – 11:00 Coffee Break 11:00 – 1:00 Second Poster Session (P2) 1:00 – 2:00 Lunch 2:00 – 3:30 5th Session (S5) 2 Talks 3:30 – 4:00 Coffee Break 4:00 – 6:15 6th Session (S6) 3 Talks 6:15 – 8:00 Third Poster Session (P3) 8:00 – 8:30 Cocktails 8:30 – 11:00 Banquet Speaker: Dr. Joseph Bordogna Best Student Poster Award National Science Foundation Presentation

7 Invited Presentations Conference on Current Trends in Computational Chemistry 2004

Session Chairman: Svein Saebo Pulay Lecture Mississippi State University Peter Pulay Density Functional and Configuration-based Methods for Large University of Arkansas Systems: The Fourier Transform Coulomb Method and Full- accuracy Local MP2

nd Session Chairman: William Adams 2 Session Rutgers University Mattanjah S. de Vries Gas Phase Spectroscopy of Biomolecular Building Blocks: University of California at Santa Interplay between Theory and Experiment Barbara Alejandro Toro-Labbé Toward the Characterization of Mechanisms of Chemical Pontificia Universidad Católica de Reactions: The Role of the Reaction Force Profiles Chile

rd Session Chairman: Szczepan Roszak 3 Session Wroclaw University of Technology Samuel B. Trickey Prediction of Materials Properties via Gaussian Orbital DFT University of Florida Methods Lars G. M. Pettersson Water in the Bulk and at Interfaces Stockholm University Richard Jaffe Applications of Quantum Chemistry to the Study of Carbon NASA Ames Research Center Nanotubes

th Session Chairman: Andrzej Wierzbicki 4 Session University of South Alabama Richard Lavery Nucleic Acid Recognition Institut de Biologie Physico- Chimique Gregory A. Voth Proton Solvation and Transport in Aqueous and Biomolecular University of Utah Environments

th Session Chairman: James L. Meeks 5 Session West Kentucky Commun. & Technical College Hiroshi Nakatsuji Solving the Schrödinger Equation: Analytical Wave Functions of Kyoto University Atoms and Molecules Grzegorz Chalasinski Pre-Reactive Complexes of Open-Shell Atom + Molecule University of Warsaw Interactions: An ab Initio Study

th Session Chairman: Marek W. Urban 6 Session University of Southern Mississippi Tim Clark Towards a Next-Generation Semiempirical MO-Technique Friedrich-Alexander-Universität Erlangen-Nürnberg Paul L. A. Popelier Towards a Force Field via Quantum Chemical Topology University of Manchester Ursula Röthlisberger Some Challenges in First-Principles Based Simulations of Swiss Federal Institute of Biological Systems Technology of Lausanne

Contents for Abstracts Conference on Current Trends in Computational Chemistry 2004 11

Session† Presentation Page

P1 Theoretical Study of the Interaction of Urate with Li+, Na+, K+, Cu+ and Mg2+ 19 Metal Cations Reeshemah N. Allen, M.K. Shukla, and Jerzy Leszczynski

P1 Density Functional Study of the Structural Properties of Ascorbic Acid (Vitamin C) 20 R.N. Allen, M.K. Shukla, Demarcio Reed and Jerzy Leszczynski

P1 Experimental and Ab Initio Study of Mechanochemical Reactions of Chromium, 21 Molybdenum and Tungsten Carbonyls with 3,6-di-tert-butyl-o-quinone Sabrina Arrington-Peet and Rakhim Rakhimov

P1 A Parallel Implementation of Hartree-Fock and Density Functional Theory 22 Analytical Second Derivatives Jon Baker, Krzysztof Wolinski, Massimo Malagoli and Peter Pulay

P1 Film Formation from a Multi-component System with Evaporating Aqueous 23 Solution: A Monte Carlo Simulation Sam Bateman

P1 Modified Genetic Algorithms for Medium-size Silicon Clusters 24 Victor E. Bazterra, Ofelia Oña, María C. Caputo, Marta B. Ferraro, Patricio Fuentealba and Julio C. Facelli

P1 The Accurate Calculation of Ro-Vibrational Eigenenergies of Hydrogen Cyanide 26 Joseph A. Bentley and Jennifer L. Curry

P1 Activation Barriers and Rate Constants for Hydration of Platinum and Palladium 27 Square Complexes: An ab Initio and DFT Calculations with Inclusion of PCM – COSMO Model Jaroslav Burda, Michal Zeizinger, and Jerzy Leszczynski

P1 Structure and 1H NMR Chemical Shifts of к-Hefutoxin a Novel Toxin from the 28 Scorpion Heterometrus fulvipes with Unique Structure and Function. Experimental and Computational Approaches Anthony Chuma, Vaithiyalingam Sivaraja, Chin Yu, and Peter Pulay

S6 Towards a Next-Generation Semiempirical MO-Technique 29 Tim Clark

P1 Effects of the First Hydration Shell on the Ionization Potentials of the Pyrimidine 30 Bases David M. Close

P1 Conventional Strain Energy in Small Heterocycles of Carbon and Silicon 31 Crystal B. Coghlan and David H. Magers

P1 Towards Accurate Ionization Energy Thresholds for the DNA and the RNA 34 Nucleosides: A First Principles Study in Gas and in Aqueous Phase Carlos E. Crespo-Hernández, Rafael Arce, Leonid Gorb, and Jerzy Leszczynski

P1 Point Defects in Silicon Oxynitride: A Study of Magnetic and Optical Properties 35 Lonnie D. Crosby and Henry A. Kurtz

P2 Molecular Dynamics Simulation Studies of the Effect Phosphocitrate on Crystal- 36 Induced Membranolysis Pranav Dalal, Kimberely Zannotti, Andrzej Wierzbicki, Jeffry D. Madura, and Herman S. Cheung 12 Conference on Current Trends in Computational Chemistry 2004 Contents for Abstracts

P1 Second-order Nonlinear Optical Time Dependent Hartree–Fock Computations for 37 Functionalized Thiophenes. Acceptor Group and Conjugation Lenght Effect Y. Daoudi, P.J. Bonifassi

P1 Quantum Chemical Investigation of a Dinuclear Iridium Porphyrin and its π-cation 40 Biradical Yuanjian Deng and Ming-Ju Huang

P1 A Density Functional Theory Study on the Diels-Alder Reactions of Phospholes 42 with Butadiene T. C. Dinadayalane, G. Narahari Sastry and Jerzy Leszczynski

P1 A Theoretical Study on the Interactions of CnH4 and CnH2 (n=8, 6, 4 and 2) with a 44 Single Walled Carbon Nanotube C60H20 T. C. Dinadayalane, Leonid Gorb, Helena Dodziuk and Jerzy Leszczynski

P1 Computational Approach to Controlling the Conformation of Antimicrobial 46 Oligomers Robert J. Doerksen

P1 Molecular Structure of Queuosine: A DFT Study 47 Galina I. Dovbeshko, Oleg V. Shishkin, Leonid Gorb, Jerzy Leszczynski, Roman I. Zubatyuk and Dmitriy V. Kosenkov

P1 Effects of Solvent on HIV Protease Folding 49 Claudia D. Eybl, Jesse Edwards

P1 Computational Studies of Agonist Selectivity at the S1P4 Receptor 50 James Fells, Abby L. Parrill

P1 A Theoretical Model of Proton Pumping in the Bacteriorhodopsin Photocycle 51 Antonio M. Ferreira and Donald E. Bashford

P1 Deformation Specific Frequency Scaling Factors for Polycyclic Aromatic 52 Hydrocarbons Alan Ford and Peter Pulay

P1 DFT Study on the Reaction Mechanism of the 1,3-Dipolar Cyloaddition between 53 Ethene and Nitrile Oxide Jason Ford-Green, Ayourinde Hassan, Yinghong Sheng

P1 Relative Energies of Conformations, Sulfonium Ylide, and Transition States in the 54 Sila-Pummerer Rearrangement of Axial 3,3-Dimethyl-3-Silathiacyclohexane 1- Oxide Fillmore Freeman, Svetlana V. Kirpichenko and Bagrat A. Shainyan

P1 Ab Initio Molecular Dynamics Study on Structural Nonrigidity of Nucleic Acid 55 Bases Al’ona Furmanchuk, Olexandr Isayev, Oleg Sukhanov, Oleg Shishkin, Leonid Gorb, and Jerzy Leszczynski

P1 Electronic Properties the 3d-block Transition Metals Using Hartree-Fock, Post 57 Hartree-Fock, Density Functional Theory and Quantum Monte Carlo Methods Ainsley Gibson, Gordon Taylor and John Harkless

P1 Conformational Study of Thioformic Anhydride by Computational Methods 58 Gurvinder Gill and Eric A. Noe

P1 Conformational Study of Cyclic Dienes and Cycloalkynes by Computational 59 Methods Gurvinder Gill, Jose Luis Moncada, Diwakar Pawar and Eric A. Noe Contents for Abstracts Conference on Current Trends in Computational Chemistry 2004 13

P1 Conformational Studies of Propynoic Acid and Related Compounds By Ab Initio 60 Calculations Gurvinder Gill, Diwakar Pawar, and Eric A. Noe

P1 Dynamic NMR Spectroscopy and Computational Methods 61 Gurvinder Gill, Diwakar Pawar, and Eric A. Noe

P1 DNA Bases in Rare Tautomeric Forms, which are not the Components of Dimers 62 or Modified Bases, as one of the Reasons of an Untargeted Mutagenesis H. A. Grebneva

S2 The Role of the Reaction Force to Characterize the Hydrogen Transfer between 66 Sulfur and Oxygen Atoms Soledad Gutiérrez-Oliva, Bárbara Herrera and Alejandro Toro-Labbé

P1 Carbon Nanotube Growth on Iron Catalysts from Carbon Monoxide Feedstock 67 G. L. Gutsev, M. D. Mochena, C. W. Bauschlicher, Jr.

P1 How Do Organophosphates Bind to Acetylcholinesterase? 68 Steven R. Gwaltney

P1 Theoretical and Experimental Studies toward the Synthesis of Potential Estrogen 69 Mimics Ashton T. Hamme, Jun Wang, Erick Ellis, Tiffany Cook, and Tom Wiese

P1 The Stabilities and Geometries of Six(x=12,16,20,24,28,32,36,40,44,60) 70 Fullerenes Doped with an Re Atom: A Theoretical Investigation Ju-Guang Han, Ming-Ju Huang

P1 Stopped-Flow and UV-VIS Spectrophotometric Studies of the Transformation of 71 CL-20 Patricia L. Honea, Mohammad (Mo) Qasim, Herbert L. Fredrickson, John Furey, S. Okovytyy, Y. Kholod, J. Leszczynski

P1 Polyhedral Oligomeric Silsesquioxanes (POSS) Cages with Atomic Alkali, Noble 74 Gas and Halogen Impurities Delwar Hossain, Charles U. Pittman, Jr., Svein Saebo, Sung Soo Park, Chuanyun Xiao, and Frank Hagelberg

P1 Molecular Dynamics Simulation of E-coli Dihydrofolate Reductase’s Circular 76 Permuted Variants Zengjian Hu, Buyong Ma, Ruth Nussinov, Donnel Bowen, and William M. Southerland

P2 Nuclear Magnetic Resonance Spectral Analysis and Molecular Properties of 79 Berberine Ming-Ju Huang, Ken S. Lee, and Sharon J. Hurley

P2 Theoretical Studies of Quantum-like Optimization Principle for 3-D Conformation 80 of Complex Molecular Systems Xiaofei Huang

P2 Effects of Positional Isomers on Polyimide Properties 84 Danielle L. Hudson, Jeffrey A. Hinkley, Thomas C. Clancy, Melissa S. Reeves

P2 Transfer Hamiltonian: An Independent Particle Model with Correlation via the 86 Exact Coupled Cluster Equations Thomas F. Hughes and Rodney J. Bartlett

P2 Pathways of Nitrobenzene Reduction by Iron (II) Compounds. A DFT Study 87 Olexandr Isayev, Leonid Gorb, Igor Zilberberg, and Jerzy Leszczynski 14 Conference on Current Trends in Computational Chemistry 2004 Contents for Abstracts

P2 Comparison of Basis-set and Method Dependence of Ground- and Excited-State 88 Calculations for Cytosine and 5-methyl-cytosine in an Excited-state Quantum Chemical Investigation Mark Jack, Manoj Shukla, and Jerzy Leszczynski

S3 Applications of Quantum Chemistry to the Study of Carbon Nanotubes 89 Richard L. Jaffe

P2 Thiotepa Antitumor Drug: Theoretical Study for Predicting its Biological Activity, 90 IR and Raman Vibrational Spectra D. Kheffache, O. Ouamerali

P2 Coherent Oscillations of Vibrational Modes in Metal Nanoshells 91 Arman S. Kirakosyan, Tigran V. Shahbazyan

S5 Pre-Reactive Complexes of Open-Shell Atom + Molecule Interactions: An ab 92 Initio Study J. Klos, J. E. Rode, M. M. Szczesniak, and G. Chalasinski

P2 Catalytic Strategies of the Hepatitis Delta Virus Ribozyme as Probed by Molecular 93 Dynamics Simulations Maryna V. Krasovska, Jana Sefcikova, Nada Spakova, Nils G. Walter, and Jiri Sponer

P2 Theoretical Studies of Pyridoxal-5’-Phosphate Methylamine Schiff Base Isomers 94 G. M. Kuramshina and H. Takahashi

P2 Predicting Vibrational Spectra of Large Molecules within Combined Approach 96 Based on the Joint Use of Theoretical and Empirical Methods G.M. Kuramshina, E. Ōsawa

P2 An ECP Basis Set for Accurate Polarizability Calculations 100 Nicholas P. Labello, Antonio M. Ferreira, Henry A. Kurtz

S4 Nucleic Acid Recognition 101 Richard Lavery

P2 Ambiguity of Definition of Atomic Charges in Cytizine Molecule 102 M.G. Levkovich

P2 Electronic Structure, Bonding, and Properties of Unligated and Ligated 104 ManganeseII Porphyrins and -Phthalocyanines Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang

P2 Efficient Implementation of Effective Core Potentials and COSMO Solvation Model 107 for the Parallel Calculation of NMR Chemical Shift within the GIAO Method Massimo Malagoli, Jon Baker, and Krzysztof Wolinski

P2 The Transfer Hamiltonian: Application to Energetic Materials 108 Joshua J. McClellan and Rodney J. Bartlett

P2 The Molecular Geometry of Boron Tetracyclo (6.1.0.02,4.05,7) Nonane Using 109 Gaussian 2003 James L. Meeks, Harry B. Fannin

P2 Theoretical Study of Adsorption of 1-Methylcytosine on Substituted and Hydrated 110 Surface of Dickite A. Michalkova, A. D. Fortner, L. Gorb, J. Leszczynski

P2 A Simple Calculational Model for Predicting the Site for Nucleophilic Substitution 112 in Aromatic Perfluorocarbons Max Muir and Jon Baker Contents for Abstracts Conference on Current Trends in Computational Chemistry 2004 15

S5 Solving the Schrödinger Equation: Analytical Wave Functions of Atoms and 113 Molecules Hiroshi Nakatsuji

P2 Theoretical Studies of Prototypical Thiyl Peroxyl, Sulfonyl, and Sulfonyl Peroxyl 114 Radicals Brian Napolion and John D. Watts

P2 Conventional Strain Energy in the Thiazetidines and the Thiadiazetidines 115 Adria Neely and David H. Magers

P2 Post Hartree Fock Study of the Structure, Vibrational Spectra, and Energetics of 117 XBr and XBr+ (X=H, F, Cl, Br) Paul Nkansah, V. R. Morris, J. S. Francisco, J. Edwards

P2 The Theoretical Investigation of Potential Energy Surface of CL-20 Degradation 118 Process S. Okovytyy, Y. Kholod, M. Qasim, H. Fredrickson and J. Leszczynski

P2 Aminolysis of Succinic Anhydride by Methylamine. Density Functional Theory and 119 Intrinsic Reaction Coordinate Study S. Okovytyy, T. Petrova

P2 The Mechanism of Amine-Catalyzed Ethylene Epoxidation. A Computational DFT 122 study S. Okovytyy, Y. Kholod and J. Leszczynski

P2 Quantum-well Magnetoexciton with Spin-orbit Interaction 123 O. Olendski and T. V. Shahbazyan

P2 Sphingosine 1-Phosphate (S1P) Receptor Selectivity for an Aromatic 124 Immunosuppressant Daniel A. Osborne, James I. Fells, Yongmei Wang, Yuko Fujiwara, Sandor Cseh, Gabor Tigyi, and Abby L. Parrill

P2 Determination of Charges of Ions by Means of Graphs Theory 125 Valentin V. Oshchapovsky

P2 Electronic Transport in Nanoscale Systems from First-principles using 126 GAUSSIAN03 J. J. Palacios, A. J. Pérez-Jiménez, E. Louis, E. SanFabián, and J. A. Vergés

P2 Interacting Clay Sheet in an Effective Solvent Medium: Conformation and 127 Dynamics by Monte Carlo Simulation Ras B. Pandey, Kelly L. Anderson, Hendrik Heinz, B.L. Farmer

P2 Hydrogen Bonding in Phenol, Water and Mixed Phenol-Water Clusters: From 128 Electron Density Perspective R. Parthasarathi, V. Subramanian and N. Sathyamurthy

S3 Water in the Bulk and at Interfaces 130 Lars G.M. Pettersson

P2 Prototropic Tautomerism in a Nucleic Acid Base Analog: ab Initio MP2 and DFT 131 Study Yevgeniy Podolyan, Leonid Gorb, Jerzy Leszczynski

P2 Towards a Precise ab Initio Accuracy in Molecular Mechanics Computations for 132 Nucleic Acids. I. Cytosine Structure and Energy Variations V.I. Poltev, E. Gonzalez, A.S. Deriabina, L. Lozano, A. Martinez, T. Robinson, L. Gorb, J. Leszczynski 16 Conference on Current Trends in Computational Chemistry 2004 Contents for Abstracts

P2 Conformational Studies of Rotationally Hindered Retinoids 134 Morgan S. Ponder, Tracy P. Hamilton, and Donald D. Muccio

S6 Towards a Force Field via Quantum Chemical Topology 135 P. Popelier, M. Devereux, S. Liem and M. Leslie

P2 Structure, Bonding, and Solvation of Dilithiodiamines 139 Lawrence M. Pratt and R. Mu

P2 Theoretical Studies on Z,E-Isomerization of HN- and N-Alkylimines 141 A.V. Prosyanik, D. Yu. Afanasiev, D. V. Fedoseyenko

S1 Density Functional and Configuration-based Methods for Large Systems: The 145 Fourier Transform Coulomb Method and Full-accuracy Local MP2 Peter Pulay

P2 Microscopic Theory of Surface-enhanced Raman Scattering from Molecules 146 Adsorbed at Noble-metal Nanoparticles V. N. Pustovit, K. Walker, and T. V. Shahbazyan

P2 Inhibition CETP activity of (R)-Chiral Halogenated Substituted N-Benzyl-N-Phenyl 148 Aminoalcohol Compounds: A QSAR Study Bakhtiyor Rasulev, Ashton T. Hamme, Jerzy Leszczynski

P3 Molecular Design for Octupolar Nonlinear Optical Systems: Structure-Function 149 Relationship and Solvent Effects Paresh Chandra Ray and Jerzy Leszczynski

P3 Ribosomal RNA Kink-turn Motif – A Flexible Molecular Hinge 150 Filip Razga, Nada Spackova, Kamila Reblova, Jaroslav Koca, Neocles B. Leontis and Jiri Sponer

P3 Conformational Study of Cyclic Dienes and Cycloalcaines by Computational 151 Method Jose Luis Moncada Reyes, Dewakar M. Pawar, Erick A. Noe

P3 Calculated Surface Electrostatic Potential Maxima as Measures of the Stabilities of 152 Carbocations Adele M. Robbins, Ping Jin, Jane S. Murray and Peter Politzer

P3 An Attempt to Bridge the Gap between Computation and Experiment for 153 Nonlinear Optical Properties Zuhail Sainudeen and Paresh Chandra Ray

P3 Ab Initio Density Functional Theory via Second-Order Perturbation Theory: 154 Energies, Exchange-Correlation Potentials, Dipole Moments, and Ionization Potentials Igor V. Schweigert, Victor F. Lotrich, and Rodney J. Bartlett

P3 Soft Film Growth: Density Profile and Roughness by Kinetic Monte Carlo 155 Simulation Adam Seyfarth, Ras Pandey and Ray Seyfarth

P3 UV-Induced DNA Damage: A Theoretical Investigation on Guanine Base under 156 Different Hydrogen Bonding Environments M.K. Shukla and Jerzy Leszczynski

P3 Time-Dependent Density Functional Theory (TDDFT) Investigation on Electronic 158 Transitions of Thiouracils in the Gas Phase and in Solutions M.K. Shukla and Jerzy Leszczynski Contents for Abstracts Conference on Current Trends in Computational Chemistry 2004 17

P3 Atom-Like Building Blocks for Nanotechnology Fullerene Molecules with 160 Substitutions T. M. Simeon, I. Yanov, and J. Leszczynski

P3 Interactions of Isoniazid and Its Derivatives with Mycobacterium Tuberculosis 161 Susceptible Enzyme: Molecular Modeling and Docking Studies K.Q. Sohail, I. Pazilah, A.W. Habibah

P3 A DFT Study of the Methane Activation by Unique Transition-Metal Ion Structures 162 in Co(1+)/ZSM-5, Ni(1+)/ ZSM-5 AND Cu(1+)/ZSM-5 Zeolites Vitali Solkan, Aleksandr Serykh, and Jerzy Leszczynski

P3 A DFT Study of the Dihydrogen Activation by Unique Transition-Metal Ion 165 Structures in Co(1+)/ZSM-5 and Ni(1+)/ZSM-5 Zeolites Vitali Solkan and Jerzy Leszczynski

P3 An ab Initio Studies of Donor-Acceptor Complexes for Several Alkyl Fluorides with 168 BF3 in HF-Superacid Medium Taking Into Account the Solvation Effects Vitali Solkan and Jerzy Leszczynski

P3 Is the R-N=N=O+ Ion Stable? 169 Vitali N. Solkan, Aleksandr M. Churakov

P3 Theoretical Study of Dihydrogen Adsorption on Zn(II) Exchanged ZSM-5 Zeolites 172 Using DFT/B3LYP Vitali Solkan

P3 Correlation of Conformational Energetics of Naphthylquinolines with 174 Thermodynamic Binding Energies Angela Sood, M. Jeanann Lovell, G. Reid Bishop, and David H. Magers

P3 Non–Watson–Crick Base Pairing in RNA. Quantum-Chemical Analysis of the cis- 176 W.C. /Sugar Edge Base Pair Family Judit E. Sponer, Jerzy Leszczynski and Jiří Šponer

P3 Interactions between Guanine and Amino Acids: A Theoretical Study 177 Andrea Sterling, Jing Wang, Jerzy Leszczynski

P3 Effects of Axial Ligands on the Structure and Electronic Properties of Metal 178 Porphyrins and Phthalocyanines Nicole M. Strauss and William A. Parkinson

P3 Theoretical Study of the Effect of Some Metal Clusters on the Conductance of 179 Benzene using Various Alligator Clips (As, P, S, O, Se, Te) Krzysztof Tajchert, Devashis Majumdar, Szczepan Roszak, Jerzy Leszczynski

P3 Proton Affinities of Some Ketones, Vicinal Diketones and α-Keto Esters: A 180 Computational Study Antti Taskinen, Ville Nieminen, Esa Toukoniitty, Dmitry Yu. Murzin, and Matti Hotokka

P3 Frozen Natural Orbitals: A Systematic Method of Basis Set Truncation 181 Andrew G. Taube and Rodney J. Bartlett

P3 A DFT/TDDFT Study of Excitation Spectrum of Dibenzoborole Containing π- 182

electron Systems: “on/off” Fluorescence Device Can be Controlled by Changing pπ –π* Conjugation Kanchana S. Thanthiriwatte and Steven R. Gwaltney

S3 Prediction of Materials Properties via Gaussian Orbital DFT Methods 184 S.B. Trickey 18 Conference on Current Trends in Computational Chemistry 2004 Contents for Abstracts

P3 Molecular Modelling and QSAR Studies of Aconitum and Delphinium Alkaloids 185 Having Antagonist Actions at Voltage-Gated Sodium Channels Malakhat A. Turabekova

P3 Structure Analysis of Oligopeptides by Means of Quantum Chemical Calculations 189 Zoltán Varga and Attila Kovács

P3 Structure of the HMT-CDA 1:1 Adduct: Crystal Structure, IR Spectroscopy and 190 DFT Approach Ramaiyer Venkatraman, Paresh Chandra Ray, and Frank R Fronczek

S4 Proton Solvation and Transport in Aqueous and Biomolecular Environments 191 Gregory A. Voth

S2 Gas Phase Spectroscopy of Biomolecular Building Blocks: Interplay between 192 Theory and Experiment Mattanjah S. de Vries

P3 Cooperativity Effects in the Interactions between Fas2 Loop1 and AChE: A 193 Theoretical Study Jing Wang, Jiande Gu, and Jerzy Leszczynski

P3 Theoretical Study of Interactions of Guanine with Na+ Cation and Water Molecule 194 C. C. Watts, A. Michalkova, J. Leszczynski

- - P3 Coupled-Cluster Analyses of the Photoelectron Spectra of FeCl3 and FeBr3 196 John D. Watts

P3 Molecular Properties of Protonated Oxygen Clusters 197 Mary La’Françes Williams, and Jaroslaw Szymczak

P3 Computational Investigation of Small Si Clusters on a Graphite Substrate 198 Jianhua Wu, Jian-Ge Zhou, and Frank Hagelberg

P3 Quantum Transport in Porphyrin 199 Ilya Yanov and Jerzy Leszczynski

P3 Density Functional Theory Study of Vibrational Properties of the 3,4,9,10- 200 Perylene Tetracarboxylic Dianhydride (PTCDA) Molecule: IR, Raman and UV-vis Spectra N.U. Zhanpeisov, S. Nishio and H. Fukumura

P3 The Origin of IR and Raman Band Shifts in H-bond Complexes of Triethylamine 201 with Water: Density Functional Theory Study N.U. Zhanpeisov, K. Ohta, S. Kajimoto, J. Hobley, K. Hatanaka, and H. Fukumura

P3 Adsorption of 1-Propanol on the Si(100) Surface 202 Jian-Ge Zhou and Frank Hagelberg

P3 Analysis of the Unrestricted Solutions in the Basis of Paired Orbitals 203 Igor Zilberberg, Sergey Ph. Ruzankin, Sergey Malykhin

P3 Concerted vs. Diradical Pathways for Reactions of Fluorinated Allenes 204 Robert W. Zurales

†S* – Oral presentation (* denotes session number); P* – Poster presentation (* denotes poster session number) Conference on Current Trends in Computational Chemistry 2004 19

Theoretical Study of the Interaction of Urate with Li+, Na+, K+, Cu+ and Mg2+ Metal Cations

Reeshemah N. Allen, M.K. Shukla, and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University 1400 J.R. Lynch Street, Jackson, MS 39217

The geometries and energetics of complexes of urate and Li+, Na+, K+, Cu+ and Mg2+ metal cations were studied. The complexes were fully optimized utilizing density functional level theory employing the B3LYP exchange correlation functional and 6-311++G(d,p) basis set. The interactions on the different binding sites of urate were considered. The influence of aqueous solvent on the relative stability of different complexes has been examined using the Tomasi’s polarized continuum model. A variation-perturbation energy decomposition scheme defining sequence of approximate intramolecular interaction energy model was employed for the most stable metal complexes. The basis set superposition error (BSSE) corrected interaction energy was also computed for the complexes. The charge distribution analysis and molecular electrostatic potential mapping were also performed.

20 Conference on Current Trends in Computational Chemistry 2004

Density Functional Study of the Structural Properties of Ascorbic Acid (Vitamin C)

R.N. Allen, M.K. Shukla, Demarcio Reed and Jerzy Leszczynski

Jackson State University1400 J.R. Lynch Street, Jackson, MS 39217 Computational Center for Molecular Structure and Interactions Department of Chemistry

The radical electronic structure is of great interest since herein lies the inherit information relevant to the protective capacity of the ascorbic acid. The geometries of the neutral tautomeric and anionic species of AA were optimized at the Density Functional Theory level using the B3LYP method. The radical species were evaluated using the unrestricted B3LYP method. Single point energy calculations were also performed using the MP2 and UMP2 method for all species. All calculation utilized the 6-311++G(d,p) basis set. Nature of stationary points on the potential energy surfaces (PESs) was ascertained by harmonic vibrational frequency analysis; all structures were found minima. The Tomasi’s polarized continuum model was used to examine the effects of aqueous solvation on the relative stability of interested species. The species obtained by the deprotonation of the O3 site is the most stable monoanion of AA in gas and aqueous medium. For the radical species, it appears that the dehydrogenation of the O3 site is the most stable radical formation in both gas phase and aqueous medium. Among the radical anions, the species obtained by the dehydrogenation of the O3 and the deprotonation of the O2 is the most stable in gas phase and aqueous medium which is conclusive with the spin density population which lies between the O2 and O3 sites. The electronic charge distribution, molecular electrostatic potential, ionization potential and electron affinity are reported.

Ascorbic Acid

Conference on Current Trends in Computational Chemistry 2004 21

Experimental and Ab Initio Study of Mechanochemical Reactions of Chromium, Molybdenum and Tungsten Carbonyls with 3,6-di-tert- butyl-o-quinone

Sabrina Arrington-Peet and Rakhim Rakhimov

Center for Materials Research and Department of Chemistry, Norfolk State University, Norfolk, Virginia 23504

Using a shock wave technique, electron paramagnetic resonance (EPR) method and ab initio quantum-mechanical analysis, we have quantitatively described mechanochemical reactions of metal carbonyls Cr(CO)6, Mo(CO)6, and W(CO)6 with 3,6-di-tert-butyl-o-quinone (Q). These reactions lead to the formation of metal complexes with paramagnetic 3,6-di-tert-butyl-o- semiquinone ligand, a reduced form of Q. The structure of paramagnetic products and the reaction yield were determined from EPR spectra. The reaction yield G was measured as a function of pressure P in the shock wave and we found that it has a threshold character. After the threshold point the reaction yield G rapidly increases with the pressure increase and reaches its maximum value Gmax at P = Pmax. At P > Pmax we observed no further increase in the reaction product yield. The values of Pmax and Gmax were considered as experimental parameters that describe mechanochemical reactivity of metal carbonyls towards organic acceptor molecule Q. For the group of metal carbonyls we found that mechanochemical reactivity decreases from Cr(CO)6 to Mo(CO)6 and W(CO)6. This was seen from our experiments that showed the increase of Pmax and decrease of Gmax in this sequence of metal carbonyls. Based on the density functional theory we performed ab initio calculations of the metal carbonyls in order to obtain their electronic chemical potential µ, molecular hardness η and dissociation energy of the metal- carbon chemical bond in metal carbonyls DM−C, which were used as theoretical parameters that describe mechanochemical reactivity of metal carbonyls. We found the relation of experimental values (Pmax, Gmax ) vs. theoretical values (µ, η, DM−C), which presents a possible way towards quantitative description of mechanochemical reactions and their mechanisms. 22 Conference on Current Trends in Computational Chemistry 2004

A Parallel Implementation of Hartree-Fock and Density Functional Theory Analytical Second Derivatives

Jon Baker1,2, Krzysztof Wolinski1,3, Massimo Malagoli1 and Peter Pulay2

1Parallel Quantum Solutions, 2013 Green Acres Road, Suite A Fayetteville, Arkansas 72703 2Department of Chemistry, University of Arkansas, Fayetteville, Arkansas 72701 3Department of Chemistry , Maria Curie-Sklodowska University, Lublin, Poland

We present an efficient, parallel implementation for the calculation of Hartree-Fock and Density Functional Theory analytical Hessian (force constant, nuclear second derivative) matrices. These are important for the determination of harmonic vibrational frequencies, and to classify stationary points on potential energy surfaces. Our program is designed for modest parallelism (4-16 CPUs) as exemplified by our standard 8-processor QuantumCube™. We can routinely handle systems with up to 100+ atoms and 1000+ basis functions using under 0.5 GB of RAM memory per CPU. Timings are presented for several systems, ranging in size from aspirin (C9H8O4) to nickel octaethylporphyrin (C36H44N4Ni). Conference on Current Trends in Computational Chemistry 2004 23

Film Formation from a Multi-component System with Evaporating Aqueous Solution: A Monte Carlo Simulation

Sam Bateman

Using a computer simulation model, film formation on an absorbing substrate is studied on a simple three-dimensional lattice Lx*Ly*Lz. We consider a mixture of components A, B, and C in an effective solvent medium. Interactions among the constituent particles, solvent, and the substrate, their molecular weight, and temperate orchestrate the stochastic motion of particles by the Metropolis algorithm. A periodic boundary condition is used along the transverse direction and open boundary conditions along the longitudinal directions. Due to impenetrable substrate at the bottom, the aqueous constituents are allowed to evaporate only from the top; B and C components cannot escape the lattice. Unlike a choice of very limited hopping sites, i.e., six nearest neighbor sites on a cubic lattice, in the traditional lattice simulations, the degrees of freedom for hopping these particles is considerably enhanced to 26 here. On average, each particle (selected randomly) attempts to move once to one of these randomly selected neighboring sites in one Monte Carlo step (MCS) time. Particles gravitate and film grows from the substrate during the course of simulation time steps. How the constituent particles distribute and equilibrate to provide a film with specific surface characteristics is our primary objective. Growth of the interface width and roughness of the film will be examined as a function of the concentration of its constituents. 24 Conference on Current Trends in Computational Chemistry 2004

Modified Genetic Algorithms for Medium-size Silicon Clusters

Victor E. Bazterra,a,b Ofelia Oña,b María C. Caputo,b Marta B. Ferraro,b Patricio Fuentealbac and Julio C. Facellia,∗

a Center for High Performance Computing, University of Utah, 155 South 1452 East Rm 405, Salt Lake City, UT 84112-0190, b Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. I (1428), Buenos Aires, Argentina and c Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago 1, Chile.

The study of the structure and physical properties of atomic and molecular clusters is an extremely active area of research due to their importance, both in fundamental science and in applied technology.1 Existing experimental methods for structural determination seldom can obtain the structure of atomic clusters directly. Therefore the calculation, using theoretical structures and comparison with experimental values of their physical and optical properties is the most common way to obtain structural information about their structures. Clusters with up to ~10 atoms can be modeled using standard geometry optimization techniques in conjunction with quantum chemical methods, like DFT, MP2, coupled clusters, etc. Otherwise, a systematic and global geometry optimizations of larger clusters is complex and time-consuming task due to the large number of possible structures,6 the time required for the calculation of their total energies and the lack of efficient methods to perform global searches. Nowadays, the global optimization of clusters with ~20 atoms is almost an intractable problem and inconsistent results on the structures of Sin, 10≤n≤30 clusters have been reported in the literature.2-10 For these medium to large size clusters the option of using ab initio or DFT methods to calculate the cluster energies is limited to the study of a few plausible configurations. This is the case of the comprehensive study of one of the largest silicon clusters studied by ab 9 initio methods: Si36. For this system, it was used the strategy of locally optimized several plausible structures of Si36 that were constructed by introducing small modifications into several common structural motifs observed in nanostructures: cages, wires and fullerenes. This strategy use a reduced number of structures and therefore reducing the high cost of the ab initio calculations. However, this is not exhaustive study of the structural parameter space, leaving open the possibility that geometries quite different from those derived from the selected motifs may be valid candidates for stable isomers of this species. Very recently,16 we report the use of a Parallel Genetic Algorithm (PGA) to predict the structure of medium size silicon clusters using a semiempirical molecular orbital program, MSINDO,11-13 to evaluate the energy of the clusters in the global search using the GA. This was combined with a Density Functional Theory (DFT) method to refine those more promising ones by performing a local optimization of the best structures found by the GA. Two sets of structures were presented, one on small silicon clusters, Sin (n=4-14 and 16) to demonstrate the validity of the method in silicon clusters with structures that are well characterized using DFT methods,4, 13- 15 and a second set on Si36, one of the largest silicon clusters previously studied by ab initio methods. In this presentation, we show the preliminary results of to apply this methodology to include Sin (n=16-21, 24, 26, 28, 32). These structures plus those previously published partially

∗ Corresponding author at the University of Utah. E-mail: [email protected] Conference on Current Trends in Computational Chemistry 2004 25

complete the series of silicon cluster up to 36. The geometries of these series are compared with others that were produced through the use of other methodologies. Furthermore, electronic properties as binding energies; energy gaps and polarizability are calculated and compared. From this comparison the advantages and problems between different strategies are found and analyzed.

1 U. Landman, R. N. Barnett, A. G. Scherbakov, and P. Avouris, Phys. Rev. Lett. 85, 1958 (2000). 2 S. Yoo, X. C. Zeng, X. Zhu, and J. Bai, J. Am. Chem. Soc. 125, 13318 (2003). 3 L. R. Marim, M. R. Lemes, and A. Dal Pino, Jr., Phys. Rev. A 67, 033203 (2003). 4 M. R. Lemes, L. R. Marim, and A. Dal Pino, Jr., Phys. Rev. A 66, 023203 (2002). 5 K. Jackson, M. Pederson, C. Z. Wang, and K. M. Ho, Phys. Rev. A 59, 3685 (1999). 6 K. M. Ho, A. A. Shvartsburg, B. Pan, Z.Yi Lu, C. Z. Wang, J. G. Wacker, J. L. Fye, and M. F. Jarrold, Nature 392, 582 (1998). 7 A. Sieck, D. Porezag, Th. Frauenheim, M. R. Pederson, and K. Jackson, Phys. Rev. A 56, 4890 (1997). 8 C. Xiao, F. Hagelberg, and W. A. Lester, Jr., Phys. Rev. B 66, 075425 (2002). 9 Q. Sun, Q. Wang, P. Jena, S. Waterman, and Y. Kawazoe, Phys. Rev. A 67, 063201 (2003). 10 I. Rata, A. A. Shvartsburg, M. Horoi, T. Frauenheim, K. W. M. Siu, and K. A. Jackson, Phys. Rev. Lett. 85, 546 (2000). 11 B. Ahlswede and K. Jug, J. Comp. Chem. 20, 563 (1999). 12 B. Ahlswede and K. Jug, J. Comp. Chem. 20, 572 (1999). 13 T. Bredow, G. Geudtner, and K. Jug, J. Comp. Chem. 22, 861 (2001). 14 B. Liu, Z. Y. Lu, B. Pan, C. Z. Wang, and K. M. Ho , J. Chem. Phys. 109, 9401 (1998). 15 J. C. Grossman and L. Mitás, Phys. Rev. B 52, 16735 (1995). 16 V. E. Bazterra, O. Oña, M. C. Caputo, M. B. Ferraro, P. Fuentealba and J.C. Facelli, Phys. Rev. A 69, 053202 (2004).

26 Conference on Current Trends in Computational Chemistry 2004

The Accurate Calculation of Ro-Vibrational Eigenenergies of Hydrogen Cyanide

Joseph A. Bentley and Jennifer L. Curry

Division of Biological and Physical Sciences, Delta State University, Cleveland, MS 38733

A methodology for accurately calculating the quantal ro-vibrational energies of light-heavy- heavy (LHH) triatomic molecules is presented. Calculated ro-vibrational energies of the ground electronic state of HCN are given for J ≤ 2 . The discrete variable representation (DVR) [J. C. Light and T. Carrington, Jr., Adv. Chem. Phys. 114, 263 (2000)] is used as a basis set for radial coordinates. An angular basis set is used which diagonalizes the rotational ( J ≥ 0 ) part of the total kinetic energy. It is shown how this basis is contracted through a series of diagonalizations of smaller Hamiltonian matrices. The final basis set is a direct product of these contracted angular functions and the primitive radial DVRs.

Conference on Current Trends in Computational Chemistry 2004 27

Activation Barriers and Rate Constants for Hydration of Platinum and Palladium Square Complexes: An ab Initio and DFT Calculations with Inclusion of PCM – COSMO Model

Jaroslav Burdaa, Michal Zeizingera, and Jerzy Leszczynskib

aDepartment of Chemical Physics and Optics, Faculty of Mathematics and Physics,Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic bDepartment of Chemistry, Jackson State University, 1325 J. R. Lynch Street, Jackson, Mississippi 39217-0510, USA

In present work, ab initio study on hydration of cis- and transplatin and several analogues was performed within a neutral pseudomolecule approach (e.g., metal-complex + water as reactant complex). Subsequent replacement of two ligands was considered. Optimizations were performed at MP2 and DFT/6-31+G(d) levels with single-point energy evaluation using the CCSD(T)/6-31++G(d,p) approach. Gas phase calculations were compared with estimations in aqua solutions employing COSMO – PCM methodology. For the obtained structures of reactants, transition states (TS), and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (rate constants) characteristics were estimated. It was found that all the hydration processes are mildly endothermic reactions. Corresponding energies for cispalladium and transpalladium (gas phase only) were also determined. Based on vibrational analyses, TST rate constants were computed for all the hydration reactions. A qualitative agreement between the predicted (in solution) and known experimental data was achieved. It was also found that the close similarities in reaction thermodynamics of both Pd(II) and Pt(II) complexes (average difference for all the hydration reactions ca 1.8 kcal/mol) do not correspond to the TS characteristics. The TS energies for examined Pd(II) complexes are about 9.7 kcal/mol lower in 6 comparison with the Pt-analogues. This leads to 10 times faster reaction course in the Pd cases. This is by 1 or 2 orders of magnitude more than the results based on experimental measurements. 28 Conference on Current Trends in Computational Chemistry 2004

Structure and 1H NMR Chemical Shifts of к-Hefutoxin a Novel Toxin from the Scorpion Heterometrus fulvipes with Unique Structure and Function. Experimental and Computational Approaches

Anthony Chuma, Vaithiyalingam Sivaraja, Chin Yu, and Peter Pulay

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701-1201

There are ~1500 distinct species of scorpions around the world, and their venoms are rich sources of toxins that affect the ion channel functions of excitable and nonexcitable cells (2–4). Scorpion toxins are classified into four groups according to their effects on specific ion channels, such as Na+, K+, Ca2-, and Cl-. к-Hefutoxin 1 is a 22-residue peptide with two disulfide bridges, the shortest scorpion toxin reported so far, and possesses a unique three-dimensional structure and biological activity. Based on the presence of the functional diad (Tyr5/Lys19) at a distance (6.0±1.0 Å) comparable with other potassium channel toxins, its function was hypothesized (1) as a potassium channel toxin. к -Hefutoxin 1 not only blocks the voltage-gated K+-channels, Kv1.3 and Kv1.2, but also slows the activation kinetics of Kv1.3 currents, a novel feature of к- hefutoxin 1, unlike other scorpion toxins, which are considered solely pore blockers. The chemical shifts and structure were first obtained using a DMX 600-MHz spectrometer in 90% H O, 10% D O at pH 4.0 and a temperature of 25 °C. The two-dimensional experiments included TOCSY (18), NOESY (18), DQF-COSY (18), and E-COSY (19) experiments with 4094 data points in the f2 dimension and 512 increments in the f1 dimension over a spectral width corresponding to 12 ppm. The structures were calculated using the standard simulated annealing and energy minimization protocols using distance constraints and coupling constants from the above experiments. Two calculations were then performed using this structure. In one the torsional angles were then taken as constraints for an ab initio calculation, and all the other coordinates (bond lengths and angles) were left to optimize (using 6- 31G*/BLYP) to their ideal values. In the other the forcefield structure was retained (all coordinates were constrained). The chemical shifts were calculated (using 6-311G**/BLYP) in both cases and compared to the experimental shifts. The ab initio structure was found to reproduce the experimental shifts more accurately and hence a better representation of the actual structure of the molecule. Conference on Current Trends in Computational Chemistry 2004 29

Towards a Next-Generation Semiempirical MO-Technique

Tim Clark

Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg Nägelsbachstraße 25, 91052 Erlangen, Germany

Current semiempirical methods all have more or less significant weaknesses for use in investigating biological systems. MNDO and MNDO/d do not reproduce hydrogen bonds at all. AM1 gives hydrogen bonds with the wrong geometry, whereas PM3 gives the correct geometry but hydrogen bonds that are too weak. MNDO, MNDO/d and PM3 all suffer from very severely underestimated rotation barriers for bonds in conjugated systems and no current method can reproduce van der Waals’ interactions. We have therefore started to develop a “next-generation” method that attempts to avoid these problems. As a first step, we have parameterized a AM1 for Al, Si, P, S, Cl, Ti and Zr using d-orbitals in order to improve performance for these elements. In a further, more important step, we have investigated a number of factors that influence the accuracy of current parameterizations and have developed a dispersion treatment based on the variational technique for calculating the molecular electronic polarizability first introduced by Jean-Louis Rivail. The requirements and probable features of the next generation of semiempirical MO techniques will be discussed. 30 Conference on Current Trends in Computational Chemistry 2004

Effects of the First Hydration Shell on the Ionization Potentials of the Pyrimidine Bases

David M. Close

Department of Physics, East Tennessee State University, Johnson City, TN, 37414

Two previous studies have dealt with calculating the ionization potentials (IP’s) of the DNA and RNA bases in the gas phase and in aqueous medium.1,2 In aqueous medium the ordering of the vertical and adiabatic IP’s is the same as in the gas phase (U>T>C>A>G). Both previous studies neglected the influence of the first hydration shell on these IP calculations. In the present study the IP’s of the bases have been calculated with 1-4 water molecules placed in the first hydration shell. Then PCM calculations were performed on the bases with the first hydration shell included. The advantage of this “supermolecular” approach is the ability to account for the specific effects of hydrogen bonding of the solvated molecule and the molecules of the solvent. The procedure for building a complex of a base with water molecules is to determine the structure of all possible monohydrated complexes. The complex with the lowest energy is chosen. A second water molecule is added, and the dihydrated complex with the lowest energy is selected. A third water molecule is added and the process is repeated. All steps are shown in tables that contain the thermodynamic parameters relevant to the formation of each cluster. Attempts are made to use the Gibbs free energies for each structure to ascertain the optimal placements of the water molecules in each step of hydration. The calculated IP’s can be compared with experimental values in the literature. In some cases the agreement is very good. In cases where isomers of the bases are likely present in the experiments, the agreement is not very good. These cases will be discussed.

1) Crespo-Hernandez, C.E. et al, J. Phys. Chem. A, 2004, 108, 6373. 2) Close, D.M., J. Phys. Chem. A, in press.

Conference on Current Trends in Computational Chemistry 2004 31

Conventional Strain Energy in Small Heterocycles of Carbon and Silicon

Crystal B. Coghlan and David H. Magers

Computational Chemistry Group, Mississippi College Department of Chemistry and Biochemistry, Clinton, Mississippi

The conventional strain energies for three- and four-membered heterocycles of carbon and silicon are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include silacyclopropane (Figure 1.), disilacyclopropane (Figure 2.), silacyclobutane (Figure 3.), 1,2-disilacyclobutane (Figure 4.), 1,3-disilacyclobutane (Figure 5.), and trisilacyclobutane (Figure 6.). Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation.

Figure 1. Silacyclopropane Figure 2. Disilacyclopropane

Figure 3. Silacyclobutane 32 Conference on Current Trends in Computational Chemistry 2004

Figure 4. Figure 5. 1,2-disilacyclobutane 1,3-disilacyclobutane

Figure 6. Trisilacyclobutane

Results indicate that silicon reduces the conventional strain energy of cyclobutane, most likely because the Baeyer strain is reduced since the silicon can accommodate a small bond angle more easily than carbon. However, silicon substitution increases the conventional strain energy in cyclopropane, perhaps by destroying the stabilizing factor of sigma delocalization. Finaly, the conventional strain energy for cyclotrisilane (Figure 7.) is computed to determine if the stability returns when the three-membered ring is again a homocycle and for cyclotetrasilane (Figure 8.) to see if additional substitution of silicon for carbon continues to reduce the strain energy in the four-membered system. We gratefully acknowledge support from NSF EPSCoR (EPS- 0132618).

Conference on Current Trends in Computational Chemistry 2004 33

Figure 7. Cyclotrisilane

Figure 8. Cyclotetrasilane

34 Conference on Current Trends in Computational Chemistry 2004

Towards Accurate Ionization Energy Thresholds for the DNA and the RNA Nucleosides: A First Principles Study in Gas and in Aqueous Phase

Carlos E. Crespo-Hernández1,2, Rafael Arce1, Leonid Gorb3, and Jerzy Leszczynski3

1 Department of Chemistry, University of Puerto Rico, San Juan, PR 2 Departments of Chemistry, The Ohio State University, Columbus, Ohio 3 Computational Center for Molecular Modeling Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS

The determination of the ionization energy thresholds (IET) for the nucleic acid constituents is one of the vexing issues of DNA/RNA photophysics and photobiology. Proper evaluation of IET is not straightforward and there still are doubts in the literature concerning their values [Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247]. Their determination is of fundamental importance not only to understand electron/charge transfer processes along DNA double helix, but essential for a better understanding of electronic influences on DNA biochemistry. Recently, we show that corrections of the radical cations for contamination by higher spin states significantly improve the calculated IET of the DNA/RNA bases [Crespo-Hernández et al. J. Phys. Chem. B 2004, 108, 6373]. This correction provides practically experimental accuracy into calculated IET. Herein, a comprehensive report on the IET for a wide range of the DNA and RNA nucleosides conformations is presented, both in the gas and in the aqueous phase. The measurements are performed at B3LYP and MP2 levels of theory and using the standard 6- 31++G(d,p) basis set. To model water solvent, the self-consistent isodensity polarizable continuum model, as implemented in Gaussian98, is used. It is shown that long-range bulk polarization interactions have a significant role in the stabilization of the first vertical and adiabatic IET for the DNA and the RNA nucleosides. Our results also show that formation of the N-glycosidic bond lower the IET of the bases by as much as 0.4 eV in the gas and 0.2 eV in the aqueous phase. Substitution of deoxyribose by ribose sugar has only a small effect on the IET for the nucleosides (≤ 0.1 eV). Surprisingly, both DFT and MP2 methods suggest that the IET for the cytosine and the adenine nucleosides is very similar in aqueous solutions, whereas in the gas phase cytosine shows a ~ 0.3 eV higher IET than adenine. The reliability of our calculations is confirmed by the good agreement with existing experimental data. In addition, the advantages and limitations of B3LYP and MP2 theoretical methods to estimate the IET will be briefly discuss. Conference on Current Trends in Computational Chemistry 2004 35

Point Defects in Silicon Oxynitride: A Study of Magnetic and Optical Properties

Lonnie D. Crosby and Henry A. Kurtz

Department of Chemistry, University of Memphis, Memphis, TN 38152

Silicon dioxide is used in the manufacturing of transistors for integrated circuits. This material is nitrated to form silicon oxynitride and serves as the dielectric layer in metal oxide semiconductor field effect transistors (MOSFETs). Defects present in these materials have the potential to adversely affect the operation of such devices. Paramagnetic defects are generally detectable via electron spin resonance (ESR) spectroscopy. Other spectroscopic methods such as FT-IR, UV-VIS, and photoluminescence provide means to detect diamagnetic defects. This study consists of ab initio quantum mechanical calculations aimed toward quantifying the magnetic and optical properties of these defects. A family of E’ like paramagnetic defects fitting the form O3-nNn≡Si↑, {0 ≤ n ≤ 3}, have been studied using cluster models. The isotropic hyperfine coupling constants due to 29Si and 14N have been calculated at the DFT level of theory and compared to experiment. Various diamagnetic defects present in silicon dioxide and silicon oxynitride materials have also been studied. The transition energies and probabilities related to absorption and emission between low lying electronic states of these defects were calculated at various levels of theory including MCSCF, MRCI, MRPT, and TDDFT. 36 Conference on Current Trends in Computational Chemistry 2004

Molecular Dynamics Simulation Studies of the Effect Phosphocitrate on Crystal-Induced Membranolysis

Pranav Dalal1, Kimberely Zannotti1, Andrzej Wierzbicki2, Jeffry D. Madura1, and Herman S. Cheung3

1Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282 2Department of Chemistry, University of South Alabama, Mobile, Alabama 36688 3Department of Biomedical Engineering, University of Miami, and Geriatric Research, Education, and Clinical Center, V.A. Medical Center, Miami, Florida 33135

In this study, following our earlier work on Calcium Pyrophosphate Dihydrate (CPPD) crystal-induced membranolysis, we demonstrate, using the CHARMM method of molecular dynamics simulation, the protective role of phosphocitrate (PC) against solvated Dimirystoyl phosphatiadylcholine (DMPC) phospholipid bilayer disintegration on contact with the CPPD crystal. Our molecular dynamics simulations studies show that coverage of the CPPD crystal with a layer of phosphocitrate molecules results in the conservation of phospholipid bilayer integrity. We show that the rupture of the lipid bilayer in the presence of CPPD and the protective effect of PC are primarily due to electrostatic interactions. The protective role of phosphocitrate, which may also play an important and potentially therapeutic function against crystal-induced membranolysis is also discussed.

Conference on Current Trends in Computational Chemistry 2004 37

Second-order Nonlinear Optical Time Dependent Hartree–Fock Computations for Functionalized Thiophenes. Acceptor Group and Conjugation Lenght Effect

Y. Daoudia, P.J. Bonifassib

a) Institut de chimie industrielle, Université des Sciences et de la Technologie Houari Boumédienne, Bab Ezzouar, Alger, Algérie. b) Laboratoire de synthèse organique, Faculté des sciences, Université du Maine, Avenue Olivier Messiaen, Le Mans, 72017, France

Molecules studied and discussion.

The molecules studied THIO1AL(1,2,3,4,5), THIO2AL(1), THIO3AL(1),THIO4AL((3,5,6) have the acceptor group in alpha position of the sulphur atom and we know the βµ product at 1907 nm by EFISH measurement found in the references below. These 4 structures can be shown in the figure 1 and the experimental values of β, and βµ are shown in the tables 1 and 2 For the other molecules , THIO1BETA,THIO2BETA and THIO3BETA with the acceptor group in beta position of the sulphur atom, we have no experiment values because in this work we have tried to see if we obtain a significant variation in the first hyperpolarizabilities TDHF computations and we can see in the table 1 a large decreasing of these non linear optical properties for the beta connection of the acceptor group. In the table 2, we have for the EFISH experimental values : βµTHIO3AL > βµTHIO2AL > βµTHIO4AL > βµTHIO1AL and for the theoretical values of the first hyperpolarizabilities by second harmonic generation calculations with Mopac93 or Gamess with semiempirical AM1 hamiltonian : βµTHIO3AL > βµTHIO2AL > βµTHIO4AL > βµTHIO1AL It seems that the relative correlation between EFISH results and calculations is acceptable althought we notice some absolute difference in particular for THIO2AL and THIO3AL structures.For the calculations concerning THIO1BETA , THIO2BETA and THIO3BETA structures, we find the same theoretical order : βµTHIO3BETA > βµTHIO2BETA > βµTHIO4BETA > βµTHIO1BETA. but, we remark that the non linear optical properties seem very low by breakdown of the conjugation along the structure in the case of acceptor group in ortho position of the sulfur atom.

References: V.P.Rao,A.K.Jen,K.Y.Wong and K.J.Drost , J.Chem.Soc.Commun,(1993) 1118-1120. K.Y.Wong, A.K.Jen ,V.P.Rao, , and K.J.Drost , J.Chem.phys, 100, 9, (1994) 6818-6825. A.K.Jen ,K.Y.Wong, ,V.P.Rao, , and K.J.Drost , Mat.Res.Symp.Proc, vol 247, (1992) 59-64. V.P.Rao,A.K.Jen,K.Y.Wong , K.J.Drost and R.M.Mininni , S.P.I.E, vol 1775, (1992) 32-42. A.K.Jen, V.P.Rao, ,K.Y.Wong and K.J.Drost, J.Chem.Soc.Commun, (1993) 90-92. K.Y.Wong, A.K.Jen ,V.P.Rao, K.J.Drost and R.M.Mininni, S.P.I.E, vol 1775, 64-84.

Acknowledgements. We acknowledge P.Delage, S.Bourdais, L.Calvayrac and S.Binois for assistance in order to resolve graphics, printing, computer connection and other system problems, as welle as for an unlimited access to the CeTiC computers and Beowulf cluster linux system. 38 Conference on Current Trends in Computational Chemistry 2004

Table 1 Hyperpolarizabilities TDHF SHG Calculations for an incident wave length of 1907nm for the laser beam

MOLECULE Dipol moment Dynamic Static STUDIED µ Hyperpolarizability Hyperpolarizability (debyes) β in10-30 esu β0 in 10-30 esu THIO1AL 9,18 205 128 THIO2AL 10,16 315 181 THIO3AL 11,09 477 263 THIO4AL 7,99 369 200 THIO1BETA 6,61 61 45 THIO2BETA 8,04 75 55 THIO3BETA 9,85 119 82

THIO1AL,THIO2AL,THIO3AL and THIO4AL : acceptor group in alpha position on the thiophen ring

THIO1BETA,THIO2BETA and THIO3BETA : acceptor group in beta position on the thiophen ring

Table 2

Theoretical TDHF SHG result for βµ Experimental result of βµ and β0µ for a 1907 nm wave length and β0µ EFISH values measured at 1907 nm of wave length with MOLECULE βµ β0µ an incident laser beam STUDIED in10-48 esu in10-48 esu βµ β0µ in10-48 esu in10-48 esu THIO1AL 1888 1173 1300 857 THIO2AL 3203 1839 6200 3023 THIO3AL 5285 2914 9100 4146 THIO4AL 3573 1974 2330 3469 THIO1BETA 485 361 THIO2BETA 496 366 THIO3BETA 954 660

Conference on Current Trends in Computational Chemistry 2004 39

H3C N CH R S 1 H3C HC C

C CN NC R1 =H THIO1AL Structure

R1 =CN THIO2AL Structure

H3C N CH H H C CN 3 HC C S C C THIO3AL Structure H C CN NC H3C N CH S H3C HC CH

HC R2 H S R2 = C THIO4AL Structure C CN NC

For THIO1A1,THIO2AL,THIO3AL and THIO4AL : Cyano acceptor group Conected in ALPHA POSITION on the THIOPHEN RING

H3C N CH S H3C HC CN C C R=H THIO1BETA Structure CN R R=CN THIO2BETA Structure

THIO3BETA Structure is THIO3AL Structure with BETA POSITION for the connection of CYANO Acceptor Group R2 on THIOPHEN RING

Figure 1 40 Conference on Current Trends in Computational Chemistry 2004

Quantum Chemical Investigation of a Dinuclear Iridium Porphyrin and its π-cation Biradical

Yuanjian Deng1 and Ming-Ju Huang2*

1 Department of Chemistry, Texas Southern University, 3100 Cleburne Avenue, Houston, Texas 77004. 2 Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P. O. Box 17910, 1325 J.R. Lynch Street, Jackson, Mississippi 39217

The main thrust of the initial studies on metalloporphyrins arises from the biological functions of cytochrome P450 enzymes that contain an iron porphyrin unit and are present in most organisms. The iron porphyrin compounds play important roles as an oxygen transfer and storage agent in hemoglobin and myoglobin and as an electron carrier in the cytochrome. Metalloporphyrins have a square-planar geometry in which a metal ion is chelated by the four nitrogens of a porphine ring with open coordination sites for axial ligation. The biological significance and rich chemistry of these compounds have promoted extensive research on model metalloporphyrins. The models most frequently selected have been the naturally occurring porphyrins such as chlorophylls, green pigments found in plants, and synthetic metalloporphyrins by varying side chains, metal ions, and surrounding species. The vast majority of metalloporphyrins are mononuclear compounds and contain iron. Metalloporphyrins containing other metals such as platinum and polynuclear metalloporphyrins have also been synthesized and characterized. Although most of the synthetic metalloporphyrins have no direct applications to biological systems, the studies on the model compounds will help scientists to gain a fundamental understanding of the molecular mechanism and related chemistry in biological reactions. Metalloporphyrins also find other applications as sensors for vapor detection, catalysts in organic synthesis, and nonlinear optical materials. Oxidation of metalloporphyrins can occur at two sites: the aromatic porphyrin ring and the central metal ion. Extraction of one electron from a porphyrin ring results in the formation of porphyrin π-cation radicals. Under proper experimental conditions, the mononuclear porphyrin π-cation radical crystallizes as a cofacial π-π dimer. It has long been observed that in these dimeric π-cation radicals, the bond distance values in the inner 16-membered ring showed an unexpected alternating pattern, and reduced symmetry. In a recent review, Scheidt has discussed factors, such as the relative ring orientation and pseudo-Jahn-Teller distortion, that cause structural deformations and bond length alternation in porphyrin π-cation radicals [1]. At the end of the review, Scheidt raised the issue as to whether all π-cation derivatives have bond alternation patterns. It is noteworthy that one of the common features of the dimers investigated is the lack of a bridging ligand between the two porphyrin rings. Whether a similar pattern is present in other bridged dinuclear metalloporphyrins has not been addressed in the literature. In the present research we have performed quantum chemical calculations on a dinuclear iridium porphyrin and its π-cation biradical at both HF/6-31G and B3LYP/6-31G levels using the Gaussian03 program package. The dimer consists of two units of iridium octaethylporphyrin ring with axial chlorine and a bridging ligand, 1,2-bis(diphenylphosphino)ethane [2]. The optimized geometry of the dimer is shown below with hydrogens omitted for clarity. A comparison between the theoretical calculations and the experimental results shows excellent agreement. Conference on Current Trends in Computational Chemistry 2004 41

Cl

N N N Ir N

P

P

N

N Ir N N

Cl

References: 1. Scheidt, W.R. Structural deformations and bond length alternation in porphyrin π-cation radicals, J. Biol. Inorg. Chem. 2001, 6, 727-732. 2. Kadish, K.M.; Deng, Y.J.; Korp, J.D. Synthesis, X-ray structure, and characterization of [(OEP)IrCl]2dppe, where OEP is the dianion of octaethylporphryin and deep is 1,2- bis(diphenylphosphino)ethane, Inorg. Chem. 1990, 29, 1036-1042.

42 Conference on Current Trends in Computational Chemistry 2004

A Density Functional Theory Study on the Diels-Alder Reactions of Phospholes with Butadiene

T. C. Dinadayalane,a G. Narahari Sastry*,b and Jerzy Leszczynski*,a

aComputational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA bMolecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Hyderabad – 500 007, India.

Thermally allowed [4+2] Diels-Alder reactions between phospholes (1H-, 2H- and 3H- phospholes) and butadiene have been explored using density functional theory B3LYP/6-31G(d) method. The calculations have also been performed for the cycloaddition reactions between cyclopentadiene and butadiene for comparison. Two pathways are examined with butadiene as diene and dienophile parts in the cycloadditions with each of the five membered rings considered. Only trans-1,3-butadiene is used in the case of butadiene to model the dienophile part. Although both concerted and stepwise mechanisms are possible in these thermal cyclocaddition reactions, only concerted mechanism is explored in all the cases. All the reactions considered in the present study are depicted in Scheme 1. Both exo and endo products are possible for each of the reactant pairs in the twin pathways, paths A and B explored in the study. One of the reactants in each pair exists as a diene rather than a dienophile. Thus, the results of the present study are systematically examined to identify which of the two reactants prefers to be a diene in each reactant pair. Eight products in the reaction of 1H-phosphole (1P) with butadiene (BD) were obtained. All the possible cycloadducts in the reactions of 2H-phosphole (2P) with butadiene and 3H-phosphole (3P) with butadiene were optimized and characterized. The transition state corresponding to each of the cycloadduct has been obtained and all the transition states possess one imaginary frequency whose normal mode corresponds to the concerted [4+2] cycloaddition. Computed activation energies are used to predict which of the two pathways is more favored. Reaction energies indicate that the reactions are thermodynamically controlled when the butadiene acts as a diene with each of the five membered rings considered. The less stability of bicyclo[2.2.1] systems over bicyclo[4.3.0] species may be traced to the high strain in the former. In general, the exo transition states are slightly lower (or almost) in energy compared to the corresponding endo transition states for the cycloaddition reactions with BD as dienophile component. On the other hand, the endo transition states lie lower in energy than the corresponding exo when BD acts as a diene and the five memebered rings as a dienophile, which can be directly traced to secondary orbital interactions. In the case of the reaction between CP and BD, the activation energies indicate that both paths A and B are highly competitive. However, path B in which CP and BD are diene and dienophile respectively is slightly more preferred over path A. In contrast, the activation barriers for the reactions of 1P as dienophile (path A) are lower in energy than for path B. This indicates that 1H-phosphole is preferred to act as a dienophile rather than a diene. The reactions of BD and 1P corresponding to diene and dienophile are both kinetically as well as thermodynamically controlled. Similar to the reactions involving CP, paths A and B are highly competitive in case of 2P but path B is predicted to be slightly more favored over path A particularly when C=P is the dienophile part. The reactions of BD with C=P of 3P as a dienophile part require activation energies of about 13-14 kcal/mol, which are about 8-12 kcal/mol less than the barriers for other reactions involving 3P. Conference on Current Trends in Computational Chemistry 2004 43

Path A Path B

BDCP-ex-Pr BDCP-ex-TS CPBD-ex-TS CPBD-ex-Pr

CP BD

BDCP-en-Pr BDCP-en-TS CPBD-en-TS CPBD-en-Pr

H H P P

HP HP s/a-BD1P-ex-Pr s/a-BD1P-ex-TS s/a-1PBD-ex-TS s/a-1PBD-ex-Pr

H P P H H P 1P BD

HP HP s/a-BD1P-en-Pr s/a-BD1P-en-TS s/a-1PBD-en-TS s/a-1PBD-en-Pr

Y Y X X X X Y Y BD2P1-ex-Pr X=P, Y=CH BD2P1-ex-TS X=P, Y=CH 2P1BD-ex-TS 2P1BD-ex-Pr BD2P3-ex-Pr X=CH, Y=P BD2P3-ex-TS X=CH, Y=P 2P2BD-ex-TS 2P2BD-ex-Pr P

2P BD Y Y

Y Y X X X X BD2P1-en-Pr X=P, Y=CH BD2P1-en-TS X=P, Y=CH 2P1BD-en-TS 2P1BD-en-Pr BD2P3-en-Pr X=CH, Y=P BD2P3-en-TS X=CH, Y=P 2P2BD-en-TS 2P2BD-en-Pr

X Y Y X Y Y X X

BD3P1-ex-Pr X=P, Y=CH BD3P1-ex-TS P X=P, Y=CH 3P1BD-ex-TS 3P1BD-ex-Pr BD3P2-ex-Pr X=CH, Y=P BD3P2-ex-TS X=CH, Y=P 3P2BD-ex-TS 3P2BD-ex-Pr

3P BD Y Y Y X Y X X X

BD3P1-en-Pr X=P, Y=CH BD3P1-en-TS X=P, Y=CH 3P1BD-en-TS 3P1BD-en-Pr BD3P2-en-Pr X=CH, Y=P BD3P2-en-TS X=CH, Y=P 3P2BD-en-TS 3P2BD-en-Pr

The cyclodimerizations of the reactants cannot be ruled out in the reactions considered. Thus, the feasibility of the cyclodimerizations will also be examined by comparing the activation barriers calculated for the reactions considered with the reported values for the cyclodimerizations.

References: (1) Dinadayalane, T. C.; Sastry, G. N. Organometallics 2003, 22, 5526. (2) Dinadayalane, T. C.; Geetha, K.; Sastry, G. N. J. Phys. Chem. A 2003, 107, 5479.

44 Conference on Current Trends in Computational Chemistry 2004

A Theoretical Study on the Interactions of CnH4 and CnH2 (n=8, 6, 4 and 2) with a Single Walled Carbon Nanotube C60H20

a a b ,a T. C. Dinadayalane, Leonid Gorb, Helena Dodziuk and Jerzy Leszczynski*

aComputational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA bInstitute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Kasprzaka 44, Poland.

The present study examines the structures and interaction energies of the complexes of armchair (5, 5) nanotube C60H20 with linear hydrocarbons CnH4 and CnH2 (n = 8, 6, 4 and 2) (Scheme 1). Semiempirical (AM1, MNDO and PM3), ab initio (HF and MP2), density functional theory (B3LYP) methods were employed to assess how the interaction energies vary for these complexes. The study is also aimed to propose the method of choice for calculating the interaction energies for these types of systems. The linear hydrocarbons CnH4 and CnH2 (n = 8, 6 and 4) possess contiguous double bonds and alternate triple bonds, respectively. The linear hydrocarbons are placed only in the center of the nanotube. The results at semiemprical (AM1, MNDO and PM3) levels as well as at HF and B3LYP methods with STO-3G and 3-21G basis sets indicate that the interaction between the hydrocarbons and the carbon nanotube is highly repulsive, while the MP2 method with a double-ζ basis set shows attractive interaction. Thus, the present study indicates that the calculations at MP2 level with at least a 3-21G basis set is necessary to obtain reliable results in these types of complexes with π-π interaction. For obvious reason, the interaction energy decreases gradually as the number of carbon atoms in the linear hydrocarbon chain is smaller. We found that the binding of allenes CnH4 is stronger than that of the corresponding acetylenes CnH2.

1

Conference on Current Trends in Computational Chemistry 2004 45

H H H H

CCC C C C C C CCC C C C

H 23H H H

H H H H

CCC C CC

H 45H H H

H CCC C C C C C H H CCC C C C H 67

H CCC C H H CCH 89

46 Conference on Current Trends in Computational Chemistry 2004

Computational Approach to Controlling the Conformation of Antimicrobial Oligomers

Robert J. Doerksen

Department of Medicinal Chemistry, University of Mississippi University, MS, 38677-1848, USA

A combined computational and experimental approach was used to design, synthesize and test a series of novel oligomers and polymers which mimic the facial amphiphilicity of natural antimicrobial peptides such as magainin. Density-functional theory computations of geometries, torsional potentials, and chemical shifts showed the effects of modified structure on torsional potentials and the role of intramolecular hydrogen-bonding on conformation. The resulting compounds feature a variety of chemical formulae but have the general feature of an extended conformation with cationic, hydrophilic groups aligned on one side of the backbone while the other side is lined with hydrophobic groups. The novel compounds show excellent activity against a broad range of gram-positive and gram-negative bacteria; and some of the compounds are highly selective to kill bacterial not human cells.

References

R.J. Doerksen; B. Chen; D. Liu; G.N. Tew; W.F. DeGrado; M.L. Klein "Controlling the conformation of arylamides: Computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers," Chemistry: A European Journal 10, yyy-zzz (2004). In press.

D. Liu; S. Choi; B. Chen; R.J. Doerksen; D.J. Clements; J.D. Winkler; M.L. Klein; W.F. DeGrado "Nontoxic membrane-active antimicrobial arylamide oligomers," Angewandte Chemie International Edition 43, 1158-1162 (2004). Conference on Current Trends in Computational Chemistry 2004 47

Molecular Structure of Queuosine: A DFT Study

Galina I. Dovbeshko1, Oleg V. Shishkin 2, Leonid Gorb3, Jerzy Leszczynski3, Roman I. Zubatyuk2 and Dmitriy V. Kosenkov1,4

1) Department of Physics of Biological Systems, Institute of Physics of National Academy of Sciences of Ukraine, 46 Prospkt Nauki, Kiev 02038, Ukraine 2) Institute for Scintillation Materials, National Academy of Sciences of Ukraine, 60 Lenina ave., Kharkiv 61001, Ukraine, 3) Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217 4) Radiophysical Faculty, National Taras Shevchenko University of Kiev, 46 Vladimirskaya St, Kiev 01001, Ukraine

OH The molecular structure and relative stability (1Q) (5Q) of conformers of hyper-modified nucleoside Q H

(queuosine) [7-(4, 5-cis-dihydroxy-1- (2Q) (4Q) OH cyclopentene-3-ylaminomethyl)-7- (3Q) H deazaguanosine] [1] (Fig. 1) and corresponding (11) NH nucleotide pQ (queuosine 5’-monophospahte) have O been obtained and analyzed at the DFT/B3LYP (10) H2C level using the 6-31++G(d, p) basis set. Bader’s (1) (5) C (7) HN (6) (8) Atoms in Molecules (AIM) theory [2] have been (1P) O (3) applied for analysis of intramolecular hydrogen (2) (4) N H2N N (9) bonds. HO P O We have considered north and south (5') (5') (4') OH O conformations of ribose ring and syn and anti (4') H H (1') orientations of base with respect to sugar in the (3') (2') H H nucleoside Q and nucleotide pQ. OH OH On the basis of calculation we suppose that Fig. 1 Structural formula of pQ queuosine north (C(3')-endo) conformation of ribose ring is [7-(4,5-cis-dihydroxy-1-cyclopentene-3- stabilized by O(3')···H-O(2') bond and south (C(2')- ylaminomethyl)-7-deazaguanosine]-5'- endo) is stabilized by O(2')···H-O(3') bond. monophosphate. In syn orientation N(3) atom of the 7- deazaguanine is the acceptor of the hydrogen bond when the atoms of sugar ring and phosphate group in nucleotide appears as donors. In anti conformation C(8) appears in hydrogen bond as a donor and atoms of the sugar ring as acceptors. We found that cyclopentene ring nonplanarity caused by O(4Q)···H-O(5Q) and N(11)···H-O(4Q) hydrogen bonds. The arrangement of the (1-cyclopentene-3-ylaminomethyl) group respect to 7- deazaguanine is determined by O(6)···H-N(11) hydrogen bond. The group is extended outwards and possibly has minor influence on the base pairing of queuosine. Orientation (syn, anti) of 7-deazaguanine respect to sugar ring and presence of 5'- monophosphate group in pQ nucleotide leads to changes in pyramidality of N(2)H2 amino group of 7-deazaguanine. Especially in the case of syn- orientation of 7-deazaguanine when amino 48 Conference on Current Trends in Computational Chemistry 2004

group is closely located to phosphate. It has been observed significant pyramidality of N(11)H (ylamino) group of queuosine. The structure of queuosine are characterized by presence (1-cyclopentene-3- ylaminomethyl) group witch has not significant influence on base pairing of queuosine. However this group could form additional hydrogen bonds between queuosine and neighboring bases in RNA. Inramolecular hydrogen bonds of queuosine increase rigidity of the structure.

References

[1] Yokoyama S. et al. Three-dimensional structure of hyper-modified nucleoside Q located in the wobbling position of tRNA, Nature 282, pp107-109, 1979 [2] Bader, R. W. F. Atoms in Molecules: A Quantum Theory; Oxford University Press: Oxford, U.K., 1990. Conference on Current Trends in Computational Chemistry 2004 49

Effects of Solvent on HIV Protease Folding

Claudia D. Eybl1, Jesse Edwards2

1Florida A & M University College of Pharmacy and Pharmaceutical Sciences, Tallahassee, Florida; 2Florida A & M University Department of Chemistry, Tallahassee, Florida

Folding and binding of HIV protease are essential for its catalytic activity. Atomic-level understanding of the monomeric and dimeric folding may suggest an alternative approach for design of more powerful inhibitors. Here, we study the kinetics of folding of HIV-1 PR using molecular dynamics techniques with explicit and implicit solvent models. We compare resulting globular structures with X-ray structures and examine how well each model describes folding of HIV-PR. 50 Conference on Current Trends in Computational Chemistry 2004

Computational Studies of Agonist Selectivity at the S1P4 Receptor

James Fells, Abby L. Parrill

Department of Chemistry and Computational Research on Materials Institute, The University of Memphis, Memphis, TN 38152

Sphingosine 1-phosphate (S1P) is a phospholipid that functions as both an extracellular signaling molecule through five integral membrane receptors, S1P1-5, and as an intracellular second messenger. S1P affects numerous biological responses including cell death, cell migration, cell division, and cell differentiation. Receptor-selective agonists are of interest both as potential therapeutic leads and as pharmacological probes to study the physiological role of individual receptors. The relatively low affinity of S1P for S1P4 relative to other S1P receptors limits use of S1P as a model for novel agonists targeting this receptor. Several other agonists have shown better activity than S1P at S1P4, namely phytosphingosine 1-phosphate (PS1P) and dihydrosphingosine 1-phosphate(DhS1P). DhS1P and PS1P both have similar structures as S1P. Figure 1 shows that the former has an additional hydroxyl at C4 and lacks the C4-C5 double bond. The latter differs from S1P only in the lack of the C4-C5 double bond. Published experimental studies show that PS1P binds more than 70 times better to S1P4 than S1P, thus providing an important guide to improving S1P4 affinity in novel compounds. Our studies computationally explore the source of the S1P4 receptor selectivity for DhS1P and PS1P over S1P. Both qualitative and quantitative methods have been applied to better understand agonist selectivity at S1P4. The Autodock program was used to generate complexes of S1P, DhS1P, and PS1P with an S1P4 receptor model. In our qualitative search we were able to point out several key interaction differences that are consistent with the observed selectivity. Molecular dynamics simulations coupled with Poisson Boltzmann calculations provide the electrostatic component of the binding free energy difference. Poisson Boltzmann data is consistent with experimental data. PS1P and DhS1P are both binding better in comparison of S1P to S1P4. OH O P OH O O- S1P NH3+

OH O P OH O O- OH NH3+ PS1P OH O P OH O O- NH + DhS1P 3

Conference on Current Trends in Computational Chemistry 2004 51

A Theoretical Model of Proton Pumping in the Bacteriorhodopsin Photocycle

Antonio M. Ferreira and Donald E. Bashford

Hartwell Center for Bioinformatics and Biotechnology St. Jude Children’s Research Hospital 332 N. Lauderdale Street, Memphis, Tennessee 38105

Describing the binding of protons or other ligands to biological macromolecules is a challenging problem because these molecules typically have multiple potential binding sites. Additionally, such macromolecules tend to be flexible, which means that the binding properties are energetically coupled to the available set of conformers. We present a general formalism that describes both the equilibrium binding states and the time evolution of these states. The bacteriorhodopsin (bR) photocycle has been chosen as a test case of this methodology for several reasons: (1) bR is the smallest known autonomous photo-activated proton pump, (2) a wealth of experimental information exists for this system, including the time evolution and structure of the intermediate states, and (3) using protons as the ligands allows for simplifications in the description of ligand binding. However, it is important to note that these restrictions do not affect the ansatz we present and the method is applicable to the description of any ligand binding to a macromolecule. Our theoretical treatment correctly reproduces the time-ordered sequence of events in the bR photocycle and provides insights into the microstate interactions involved in the proton- pumping process. We describe the potential numerical problems that must be overcome when large numbers of microstates are involved and discuss the pitfalls of using energy cutoffs to reduce the number of microstates included in the analysis. Finally, we present an analysis of the proton flux through bR (i.e. - across a membrane) using our model and investigate the efficiency of this system in the absence of a pH gradient. Further refinements and extension to the method are also presented.

52 Conference on Current Trends in Computational Chemistry 2004

Deformation Specific Frequency Scaling Factors for Polycyclic Aromatic Hydrocarbons

Alan Ford and Peter Pulay

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous carcinogens that are produced by the incomplete combustion of hydrocarbons. In the environment, they contaminate the air and water. For example, tobacco smoke is known to be riddled with PAHs. As well, PAHs have been shown to exist in several objects of our Solar System. The detection and analysis of PAHs, especially in extraterrestrial areas, usually involves vibrational (i.e. infrared) spectroscopy. Several IR studies have already obtained gas phase and pellet spectra for many PAHs, and highly resolved matrix isolated spectra down to 400 cm-1 have been collected by Hudgins.1-3 The vibrational spectra indicate that each PAH has characteristic intensities and frequencies that allow them to be distinguished. Consequently, it could be possible to determine the components of a mixture of PAHs by using IR spectroscopy if the spectra can be interpreted with the aid of spectra obtained by theory. From a theoretical standpoint, Langhoff4 provides one of the earliest and most thorough computational approaches into the interpretation of the experimental vibrational PAH spectra, in which he calculated frequencies and intensities for a wide variety of PAHs. For most of his work, he uses a 4-31G* basis with the B3LYP functional. Although the basis is quite small, the theoretical frequencies give good general agreement with experiment when they are scaled by a single scaling factor. However, many frequencies have errors of more than 10 cm-1 when compared to the spectra of Hudgins. Although using a single scaling factor as in Langhoff’s work is the simplest approach to improving the accuracy of the frequencies, the best scaling factors for a set of related compounds like PAHs are specific to stretching, bending, etc.5-7 Unfortunately, deformation specific scaling factors require a transformation of the molecular force field into internal coordinates, so that the scaling factors can no longer be applied directly to the frequencies. However, the demanding process of transforming the molecular force field and generating the scaled frequencies and intensities has been overcome by the use of the (scaled quantum mechanical) SQM force field module developed by PQS.8 Recently, deformation specific scaling factors have been determined for a wide variety of PAHs. Theoretical frequencies and intensities have been obtained using the B3LYP and B3PW91 methods with a 6-311G** basis. Experimental data has also been acquired from the matrix isolated work of Hudgins and from solution phase IR spectra taken at the University of Arkansas. Using the square root of the experimental intensities as statistical weights, the theoretical frequencies have been fitted against the experimental frequencies with SQM to yield scaling factors for the various types of molecular vibrations.

1. Hudgins, D. M., Sandford, S. A. J. Phys. Chem. A, 102, 1998, 329. 2. Hudgins, D. M., Sandford, S. A. J. Phys. Chem. A, 102, 1998, 344. 3. Hudgins, D. M., Sandford, S. A. J. Phys. Chem. A, 102, 1998, 353. 4. Langhoff, S. R. J. Chem. Phys. 100, 1996, 2819. 5. Blom, C. E., Altona, C. Mol. Phys. 31, 1976, 1377. 6. Blom, C. E., Otto, L. P., Altona, C. Mol. Phys. 32, 1976, 1137. 7. Blom, C. E., Altona, C. Mol. Phys. 33, 1977, 875. 8. PQS version 2.5, Parallel Quantum Solutions, 2013 Green Acres Road, Fayetteville, Arkansas 72703. Conference on Current Trends in Computational Chemistry 2004 53

DFT Study on the Reaction Mechanism of the 1,3-Dipolar Cyloaddition between Ethene and Nitrile Oxide

1Jason Ford-Green, 2Ayourinde Hassan,3Yinghong Sheng

1Department of Chemistry,Jackson State University,Jackson,MS 39217; 2Department of Chemistry,Rust College,Holly Springs, MS 38635; 3Department of Chemistry,Jackson State University, Jackson, MS 39217

Two reaction mechanisms of the 1,3-dipolar cycloaddition between ethene and nitrile oxide have been studied at the B3LYP/6-31G(d) level. One is the concerted reaction, the other is a two- step reaction which contains an intermediate. The concerted reaction mechanism is found to be favorable over the step-wise one. The preference of the reaction mechanisms are explained in terms of the molecular orbital interactions and the Mulliken charge distribution. 54 Conference on Current Trends in Computational Chemistry 2004

Relative Energies of Conformations, Sulfonium Ylide, and Transition States in the Sila-Pummerer Rearrangement of Axial 3,3-Dimethyl-3-Silathiacyclohexane 1-Oxide

Fillmore Freemana, Svetlana V. Kirpichenkob and Bagrat A. Shainyanb

Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025 A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of Science, 1 Favorsky Street, 664033, Irkutsk, Russian Federation

The thermal rearrangement of axial 3,3-dimethyl-3-silathiacyclohexane 1-oxide (1) to 4,4- dimethyl-3-oxa-4-silathiacycloheptane (2) is the first example of a ring expansion in the sila- 1 Pummerer rearrangement of a cyclic organosilicon sulfoxide (eq 1). B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p) calculations located two transition state structures (TS-1, TS-2) and a 2 sulfonium ylide intermediate (3) along the reaction path. TS-1 lies on the way from 1 to 3 and TS-2 on the way from 3 to 2. The B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p) calculated energy differences between 1 and transition state TS-1 are 25.97 and 23.06 kcal/mol, respectively, and between 1 and transition state TS-2 are 26.36 and 22.86 kcal/mol, respectively. The calculated structural features and relative energies of the conformers of the product, sulfonium ylide, and transitions states involved in the rearrangement will be discussed.

O S CH3 CH3 Si S Si (1) CH3 CH3 O

1 2

CH 2 CH2 O Me S Me Si O S S O Si Si Me Me CH CH 2 3 CH3 TS-1 TS-2 3

1. Kirpichenko, S. V.; Suslova, E. N.; Albanov, A. I.; Shainyan, B. A. Tetrahedron Lett. 1999, 40, 185-188. 2. Shainyan, B. A; Kirpichenko, S. V.; Freeman, F. J. Am. Chem. Soc. 2004, 126, 11456- 11457. Conference on Current Trends in Computational Chemistry 2004 55

Ab Initio Molecular Dynamics Study on Structural Nonrigidity of Nucleic Acid Bases

Al’ona Furmanchuka, Olexandr Isayeva Oleg Sukhanovb, Oleg Shishkinb, Leonid Gorba, and Jerzy Leszczynskia

aComputational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217 bInstitute for Scintillation Materials, National Academy of Science of Ukraine., 60 Lenina Ave., Kharkiv 61072, Ukraine

Recently [1] we have introduced a theoretical approach to perform an analysis of ring conformational flexibility of DNA bases which is based on the combined analyses of the shape of the relaxed potential surface, the normal out-of-plane frequencies, and the amplitudes of the corresponding vibrations.

The proposed approach includes the following steps:

The calculation of the frequencies of the vibrations in cartesian coordinates and the location of so called low-frequency vibrations which are located in the area below 200 cm-1. A vibrational analysis of the internal coordinates of every low-frequency vibration in order to locate the internal coordinates which have a maximum amplitude for each vibration. A scan of the potential energy using the internal coordinates determined from step 2. The calculation of the population of the excited vibrational levels for every mode. This allows an estimation of the fraction of molecules which are non-planar at certain temperatures.

The use of this approach at the MP2 and DFT levels of theory to nucleobases enable us to conclude that all molecules of nucleic acid bases have at least one easy deformable torsion coordinate which suggest that the molecular geometry of them should be considered as structurally non-rigid. Since the proposed picture of the DNA bases behavior has rather dynamic nature, it is very desirable to investigate the described phenomenon by the computational methods which directly include the dynamic effects. Therefore, we present the results of ab initio simulation of DNA bases non-rigidity obtained at the Carr - Parinello molecular dynamic level. We have analyzed the percent distribution of torsion angles which each DNA bases posses during the time of CPMD simulation.

The most important conclusion is the following.

The CPMD simulation confirms significant structural non-rigidity of all DNA bases. It results in presence not one, as it been shown previously, but numerous of soft torsion coordinates of pyrimidine ring. To illustrate the described phenomenon, we present below the distribution of the torsion angles which characterize out-of-plane vibration in guanine.

56 Conference on Current Trends in Computational Chemistry 2004

Distribution of torsion angles % Vibration Angles (0±5) (±5±10) (±10±15) (±15±20) Remainder

C(4)-C(5)-C(6)-N(1) 44.1 32.8 15.4 6.1 1.6 C(5)-C(6)-N(1)-C(2) 36.7 31.2 19.3 7.9 4.9 N(1) out- C(6)-N(1)-C(2)-N(3) 38.9 31.8 18.9 7.7 2.7 of-plane, 151 cm-1 C(2)-N(3)-C(4)-N(9) 52.7 31.7 13 2.2 0.2 N(3)-C(4)-N(9)-C(8) 52.4 32.8 12.2 1.9 0.6 O(11)-C(6)-C(5)-(4) 41.7 31.5 17.7 6 3.2

References 1 a)O.V. Shishkin, L. Gorb, P.Hobza, J. Leszczynski, Int. J. Quant. Chem, 80(2000), 1116; b)O.V. Shishkin, L. Gorb, J. Leszczynski, Chem. Phys. Lett., 330(2000), 603.

Conference on Current Trends in Computational Chemistry 2004 57

Electronic Properties the 3d-block Transition Metals Using Hartree- Fock, Post Hartree-Fock, Density Functional Theory and Quantum Monte Carlo Methods

Ainsley Gibson, Gordon Taylor and John Harkless

Department of Chemistry, Howard University, Washington DC 20059

In an effort to show that quantum Monte Carlo methods can be used to accurately describe difficult systems, we carried out comparative studies of the performance of Hartree-Fock; post Hartree-Fock, Density Functional and Quantum Monte Carlo methods. Both variational and perturbative methods [MP2, CCSD, CCSD (T), MRCI, CISD, QCISD, CASPT (2), and MCSCF] are used, along with DFT [BPW91, B3PW91, BLYP, B3LP, B3PW98, B3P86, and B1B96] and Variational Monte Carlo (VMC) and fixed-node Diffusion Monte Carlo (DMC). Electron affinities (EA) and ionization potentials (IP) are used as benchmark parameters for the study. For the ionization potentials, the theoretical values obtained are compared to the experimental values published by the National Institute of Standards and Technology (NIST). The study is expected to show that the level of accuracy in the calculation of each parameter increases as one moves from HF to Quantum Monte Carlo.

58 Conference on Current Trends in Computational Chemistry 2004

Conformational Study of Thioformic Anhydride by Computational Methods

Gurvinder Gill and Eric A. Noe

Department of Chemistry, Jackson State University, Jackson, MS 39217

The conformations of thioformic anhydride have been studied at the HF and MP2 levels with the Gaussian 98 program. The optimized geometries, relative free energies, dipole moments and free-energy barriers were obtained for the EZ, EE, and ZZ conformations and their corresponding transition states at various levels of theory. At the MP2/6-311++G(2d,2p) level, the EE conformation is higher in free energy relative to the most stable ( EZ ) conformation by 1.02 kcal/mol. Both the EZ and the EE conformations are nearly planar. A third conformer, ZZ, has optimized OCSC dihedral angles of 9.6 and a relative free energy of 3.6 kcal/mol. The free- energy barriers leading to topomerization of the EZ conformation were 6.7 and 8.6 kcal/mol, depending on the pathway. The dipole moments of the EE, EZ and ZZ conformations were 2.16, 2.90, and 4.14 D, respectively. This work was supported by NSF - CREST Grant No. HRD- 9805465. Conference on Current Trends in Computational Chemistry 2004 59

Conformational Study of Cyclic Dienes and Cycloalkynes by Computational Methods

Gurvinder Gill, Jose Luis Moncada, Diwakar Pawar and Eric A. Noe

Department of Chemistry, Jackson State University, Jackson, MS 39217

The conformational space was searched for cyclooctyne (1), cyclononyne (2), cyclodecyne (3), cycloundecyne (4), 1,2 - cycloctadiene (5), 1,2 - cyclodecadiene (6), and 1,2 - cyclododecadiene (7) with Allinger’s MM3 molecular mechanics program, and free energies were obtained at two different temperatures. Calculations were repeated for low - energy conformations with ab initio methods until the HF/6-311G(d) level was reached. The results obtained at this level were compared with the MM3 results. For example, MM3 predicts conformer 1a of cyclooctyne to be lower in strain energy and free energy than 1b by 6.578 and 6.978 kcal/mol (25 oC), and the ab initio calculations predict a free-energy difference of 4.086 kcal/mol at the HF/6-311G(d) level. Molecular symmetries, relative strain energies, and relative free energies for conformations of compounds 1 - 7 will be presented. Experimental work is in progress. This work was supported by NSF - CREST Grant No. HRD - 980 5465. 60 Conference on Current Trends in Computational Chemistry 2004

Conformational Studies of Propynoic Acid and Related Compounds By Ab Initio Calculations

Gurvinder Gill, Diwakar Pawar, and Eric A. Noe

Department of Chemistry, Jackson State University, Jackson, MS 39217

A free-energy difference of 3.46 kcal/mol at 25 0C was calculated for the E and Z conformations of propynoic acid (1) at the MP2/6-311++G(df, pd) level. This O O

C C H C O C O C C H H H

E Z

difference is smaller than the literature value for acetic acid, which may be related to the smaller equatorial preference for ethynylcyclohexane, in comparison to methylcyclohexane. Dipole moments, frequencies, T∆S, and ∆H were also calculated for 1, and the results of an experimental study will be described. Calculations will also be reported for 3-fluoropropynoic acid, 2-butynoic acid, the methyl ester of 1, and the compound derived from 1 by replacing the ethynyl group by cyano. This work was supported by NIH - SCORE Grant No. S06GM008047. Conference on Current Trends in Computational Chemistry 2004 61

Dynamic NMR Spectroscopy and Computational Methods

Gurvinder Gill, Diwakar Pawar, and Eric A. Noe

Department of Chemistry, Jackson State University, Jackson, MS 39217

The twist-boat conformation of cyclohexane is about 5.5 kcal/mol higher in energy than the chair, but in cis–1, 4 -di–tert-butylcyclohexane (1), the chair is destabilized by the presence of an axial tert-butyl group, and we have found signals in the low-temperature 13C NMR spectra of 1 for the chair (1a) and twist-boat (1b) conformations. 13C NMR signals were assigned to specific carbons based on the different populations, different symmetries (time-averaged CS for 1a and time-averaged C2V for 1b), and calculated chemical shifts (GIAO, HF/6-311+G(d)). In addition to slow ring inversion and interconversion of the chair and twist-boat conformations, slow rotation of the tert-butyl groups was found. Most of the expected 13C peaks were observed. Free- energy barriers of 6.35 and 6.82 kcal/mol were found for interconversion of 1a (minor) and 1b (major) at – 149.1 0C. Conformational space was searched with Allinger’s MM3 program, and free energies were obtained for several low-energy conformations. Calculations were repeated with ab initio methods for several conformations, including 1a, 1b, and a second TB conformation. Calculations were also done for a boat conformation (transition state with C2V symmetry). The HF/6-311+G(d) level was reached, and molecular symmetries, relative free energies, relative enthalpies and entropies, and frequencies were obtained in addition to the NMR chemical shifts. This work was supported by NSF – CREST grant No. HRD – 9805465.

62 Conference on Current Trends in Computational Chemistry 2004

DNA Bases in Rare Tautomeric Forms, which are not the Components of Dimers or Modified Bases, as one of the Reasons of an Untargeted Mutagenesis

H. A. Grebneva

Donetsk Physical and Technical Institute, NAS of Ukraine 83114 Donetsk, Ukraine

In a number of papers it is shown that rare tautomeric forms of nucleotide bases are not so rare [1-3]. DNA bases can change their tautomeric state as a result of interaction with water molecules [1,2], under the influence of heavy metals [3], ultraviolet light [4], free radicals [5], etc. It is commonly concluded, basing on Watson and Crick’s paradigm, that such bases being in rare tautomeric forms result in mutations [1]. However, the experiment shows that upon the action of ultraviolet light the pyrimidine dimers are the main source of mutations [4], for spontaneous mutagenesis, under the action of ionizing radiation and free radicals these are modified bases [5]. At present, the mutagenesis under the ultraviolet (UV) irradiation of double-stranded DNA is investigated the best. Thus the basic photodamages are cyclobutane pyrimidine dimers and (6- 4)-adducts resulting in base-replacement mutations and frame shift mutations. As a rule, mutations are formed at the sites of dimers. By word "dimer" we mean both the cyclobutane pyrimidine dimers and the (6-4)-adducts. Such mutagenesis is termed targeted mutagenesis. Sometimes mutations are formed in a small neighborhood of a dimer, this is an untargeted mutagenesis [7]. It is known that the mutations occur at SOS-replication or SOS-reparation. However, their mechanisms remain in many respects unclear [4, 7]. At present, the generally accepted hypothesis, in its various modifications [8], relates the nature of a mutagenesis exclusively to properties of a DNA-polymerase, which sometimes wrongly incorporates accidental nucleotide bases opposite the dimers instead of correct ones [7]. At thus present, the situation is thus paradoxical. There are two practically independent trends in investigation of mutagenesis. Physicists and chemists admitting the role of enzymes, as a rule, practically ignore it and rely solely on Watson and Crick’s paradigm [3]. While biologists are citing the idea of Watson and Crick [6], but do their research work in the spirit of Bresler’s paradigm [8]. In [4] it was shown that the hypothesis [8] contradicts a series of the experimental data and is unable to explain some features of UV-mutagenesis, in particular, an untargeted mutagenesis. There are endeavors to consolidate these trends [9]. It was shown that as a result of deexcitation of the UV-quantum of energy, in pairs of the bases there is a change in their tautomeric state [4]. It turned out [10] that in bases pairs are not included in dimers, and only rare tautomeric state, in which atoms of hydrogen of the guanine- cytosine pairs H′4 and Н1 were simultaneously sent to the partners on Н-bonds (fig. 1b) will be stable. Apparently similar situation is with pairs adenine-thymine. In other words, a rare tautomeric state of A-T pair, with hydrogen atoms H′6 and H3 have simultaneously passed to their partners in hydrogen bonds, will, apparently, be stable. It would be interesting to have potential-energy surfaces for adenine-thymine pair for various tautomeric states and to check whether this is true. In [11] double-proton transfer in adenine-thymine and guanine-cytosine base pairs in gas phase at room temperature has been investigated. Rare А*-Т* base pair has local unstable minimum. It was found that the interaction with Na cation results in stabilization of the rare А*-Т* form. Conference on Current Trends in Computational Chemistry 2004 63

Let us assume that a change in tautomeric state has occurred in DNA base adjoining the dimer. As in a close vicinity of dimer the DNA strand becomes curved [12], then, consequently, the hydrogen bonds between bases of that strand and complementary bases of another strand are broken. In this case, the newly formed rare tautomeric states of bases will be stable. New possible forms of thymines, have been obtained [4]. It would be interesting to study the problem in more detail. In particular, to find out whether the hydrogen bonds are broken, at what distances to dimers the stabilization of different rare tautomeric states are happen, and so on. We study the role of such damages in mutagenesis. As a rule, the mutations occur as a result of SOS-system induction [4]. Therefore we first see what is the difference between SOS- synthesis and error-free DNA synthesis.

Some features of the SOS-synthesis of DNA

As a rule, the DNA synthesis is a high-perfect process. Such fidelity is because the DNA- polymerase controls the regularity of template bases and that of the incorporated bases. It controls the dimension of the newly formed pair. It incorporates only such bases which are capable of forming the hydrogen bonds between template bases and incorporated bases [13]. It is known that the DNA-polymerase acts usually in complex with another enzymes and proteins. If during the replication process an erroneous base has been incorporated, it is usually removed by 3′ → 5′ -exonuclease . After a mistake has been made, the 3′ -OH end DNA- polymerase dissociates from DNA, then the exonuclease center of the same or another molecule associates with it. Then the erroneous nucleotides may be removed by 3′ → 5′ -exonucleases of DNA-polymerase. Having removed the unpaired nucleotide, the 3′ → 5′ -exonuclease separates soon from the DNA and the polymerase synthesis recommences [14]. The processiveness factor, i. e. subunit β, plays a decisive part in controlling the ratio between the polymerase and the proof-reading activity of DNA-polymerase III of E.coli. Its molecules form a ring-like moving platform or a “sliding clamp” which is moving along the DNA. In the central part of the clamp, there is a hole for the double-stranded DNA. It retains the DNA-polymerase III on the template and ensures a high-processive synthesis of DNA. A similar mechanism is with mammals [15]. So, first, during SOS-system induction, the control ever the bases of template DNA becomes weaker, and the nucleotide bases are incorporated opposite the dimers. Second, even if an erroneous pair has been formed, the “sliding clamp” mechanism presses the DNA-polymerase against the template and prevents the 3′ → 5′ -exonuclease from removing the “improper base”. Depending on degree of DNA damage, there may be a several times variation in the synthesis rate and the efficiency of 3′ → 5′ -exonuclease operation. [15]. We see that there are no grounds to believe that this is not so with SOS-synthesis. In other respects, the SOS-synthesis of the DNA containing dimers is like the conventional one. That is, first, the structure of incorporated bases is controlled. This means that the canonical bases are incorporated. Second, the bases which can form hydrogen bonds with template-DNA bases are incorporated. Third, control of another types is carried out as far as possible.

Possible mechanisms of formation of untargeted mutations at SOS-replication

Let in a small (10-15 bases) neighborhood of dimer or modified base the Watson-Crick pairs of the bases C-G and A-T have changed their tautomeric state such, that the pairs of the bases C*-G *, G*-C* both Т*-А* and А*-Т* were formed, where C*, G* correspond to the bases in fig. 1b. Let the given DNA site be synthesized as a result of SOS-replication. In this case, the dimer (or modified base)-containing site is not cut out and the nucleotide bases are incorporated 64 Conference on Current Trends in Computational Chemistry 2004

opposite them. This is only possible when the DNA-polymerase is pressed by the “sliding clamp” such that this obstructs the operation of exonucleases. As a result, the dimer (or modified base) itself and a small (12-15) DNA site near it become inaccessible to 3′ → 5′ -exonucleases. Let us see, what may happen when opposite such bases there will be incorporated canonical bases of DNA capable of forming the hydrogen bonds with template bases. The molecule С* can not form hydrogen bonds with guanine or thymine which are in the canonical tautomeric forms. Therefore DNA-polymerase will not incorporate guanine or thymine opposite С*. Adenine can form two hydrogen bonds with С* (fig. 1c). Therefore opposite С* the DNA-polymerase can incorporate adenine, that will cause transition G-C→A-T. The canonical tautomeric form of cytosine can form two hydrogen bonds with С* (fig. 1d). Therefore the modified DNA-polymerase can incorporate cytosine opposite С*, cytosine is in the canonical tautomeric form, thus the resulting is the homologous transversion G-C→C-G. The guanine G* can not form Н-bonds with cytosine, guanine and adenine, which are in the canonical tautomeric form. Hence, DNA-polymerase can not incorporate cytosine, guanine or adenine opposite G*. G* can form three hydrogen bonds with thymine (fig. 1e). Hence, the DNA-polymerase can incorporate thymine opposite guanine G*, that will cause the transition G- С→A-T. We stress that everywhere the question is about checking an opportunity of formation of the hydrogen bonds. As the bases, which are in the rare tautomeric forms, are posed in a small neighborhood of dimer (10-15 bases) [7], it is quite probable, that at SOS-replication the hydrogen bonds between template bases and incorporated bases are not, as a matter of fact, formed because of a DNA strand deformation in the neighborhood of dimer [12]. It is shown that in this case one of possible sources of untargeted mutations are pairs of the bases in rare tautomeric forms and not included in dimers. Such state is the stable one when in G-C pair H′4 and Н1 or H′6 and Н3 in A-T pair simultaneously transfer to the partners in hydrogen bonds. If such pairs are not far from dimers it can cause transitions A-T→G-C, G- C→A-T or homologous transversions A-T→T-A, G-C→C-G.

Acknowledgment. This work was facilitated by The State Fund for Fundamental Research of Ukraine. (Grant No 5.7.249).

1. L. Gorb, Y. Podolyan, J. Leszczynski, W. Siebrand, A. Fernandez-Ramos, Z. Smedarchina, Biopolymers (Nucl. Acid. Sci.) 61 (2002) 77. 2. L. Gorb, Y. Podolyan, J. Leszczynski, J. Mol. Struct. (Theochem) 487 (1999) 47. 3. J. Sponer, M. Sabat, L. Gorb, J. Leszczynski, B. Lippert, P. Hobza, J. Phys. Chem. B 104 (2000) 7535. 4. H. A. Grebneva, J. Mol. Struct. 645 (2003) 133. 5. H. A. Grebneva, 10th Current Trends in Computational Chemistry, Vicksburg (2001) 89. 6. J. D. Watson, F. H. C. Crick, Cold Spring Harbor Symp. Quant Biol. 18 (1953) 123. 7. U. Hagen, Experientia 45 (1989) 7. 8. S. Bresler, Mut. Res. 29 (1975) 467. 9. V. H. Harris, C. L. Smith, W. J. Cummins, A. L. Hamilton, H. Adams, M. Dickman, D. P. Hornby, D. M. Williams, J. Mol. Biol. 326 (2003) 1389. 10. E .Clementi, G. Corongiu, J. Detrich, S. Chin, J. Domingo, Int. J. Quant. Chem.: Quantum Chemistry Symposium 18 (1984) 601. 11. L. Gorb, Y. Podolyan, P. Dziekonski, W. A. Sokalski, J. Leszczynski, J. Am. Chem. Soc. 126 (2004) 10119. 12. G. Raghunathan, T. Kieber-Emmons, R. Rein, J. L. Alderfer, J. Biomol. Struct. and Dyn. 7 (1990) 899. Conference on Current Trends in Computational Chemistry 2004 65

13. V. I. Poltev, N. V. Shulyupina, V. I. Bruskov, Molecular Biology 32 (1998) 268. 14. V. M. Krutyakov, Molecular Biology 32 (1998) 229. 15. V. S. Mikhailov, Molecular Biology 33 (1999) 567.

H4 H4 O6 O6 H4C H8 H4 H8 N4 N4 N7 N7 H C8 H5 C8 5 C5 C6 C5 C6 N9 C4 C5 N9 C4 C5 C4 C4 N1 N1 N3 N3 H C6 H C6 9 H1 H6 9 H1G H6 N3 C2 N3 C2 C2 N1 C2 N1

H2 H2 N2 N2 O O2 2 H1 H1 H2 H2

H4 H6 H4 H4 H6 N N4 H N4 4 5 H4 H N6 H5 5

H8 N7 C6 C4 C5 C4 C4 C5 C8 C5 C5 N1 N3 N3 N3 N9 C6 H6 C6 C6 H C4 H1G H6 H1G 6 C2 N1 C2 C2 N1 N3 C2 N1 H9 H2 O O2 O2 2 H1 H1 H1

H5 H5 H4C H4 O6 H4C H4 H8 O4 H5 H8 O6 C Me N4 N7 N7 H C8 C8 5 C5 C6 C 4 C 5 C5 C6 N9 N9 C4 C5 C4 C4 N1 N1 N3 C 6 H N3 6 H C6 H9 H3 9 H6 N3 C2 N3 C2 C2 N1 C2 N1

H2 N2 N2 O2 H1 O2 H2 H1 H2 H2

1. The possible versions of the pairs of the bases: a) G-C in the canonic tautomeric form; b) G*-C* in the rare stable tautomeric form; c) C*-A; d) C*-C; e) T-G*. 66 Conference on Current Trends in Computational Chemistry 2004

The Role of the Reaction Force to Characterize the Hydrogen Transfer between Sulfur and Oxygen Atoms

Soledad Gutiérrez-Oliva, Bárbara Herrera and Alejandro Toro-Labbé

Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile

The role of the reaction force to characterize the mechanisms of intramolecular hydrogen transfer is analyzed stressing the fact that the force profile gives elements to define different regions along the reaction coordinate where different steps of the reactions operates. These steps are characterized by amounts of work that are calculated by integrating the force profile within the region where the specific process take place. In this way a partition of the potential energy barriers is obteined and used to characterize the energetic cost of the different local processes.

In this work the 1,3 intramolecular hydrogen transfer reactions HSNO↔SNOH and HSCH(O) ↔(S)CHOH are studied with the aim of comparing the hydrogen donor and/or acceptor capability of oxygen and sulfur. DFT/B3LYP/6-311G** calculations indicate that even though the barrier for hydrogen transfer from sulfur to oxygen are higher than those from oxygen to sulfur, the oxigen is still a better hydrogen acceptor than sulfur. This becomes evident from the analysis of the regions that involves only the hydrogenic motion.

Acknowledgements. This work was supported by FONDECYT through Project No.1020534. Conference on Current Trends in Computational Chemistry 2004 67

Carbon Nanotube Growth on Iron Catalysts from Carbon Monoxide Feedstock

G. L. Gutsev,1 M. D. Mochena,1 C. W. Bauschlicher, Jr.2

1Department of Physics, Florida A & M University, Tallahassee, Florida 32307 2Mail Stop 230-3 NASA Ames Research Center, Moffett Field, CA 94035

Carbon single-walled nanotubes (SWNT) exhibit many unique physical and chemical properties and are prospective in various technological applications such as sensors, composite materials, hydrogen storages, computer memories, etc. In particular, composite materials might be used as lighter personal armors, conducting carbon nanotubes are potential candidates for chemical and biological sensors, while nanoelectronics is expected to have lower power consumption that should reduce the battery weights. In order to obtain a notion about micro- processes involved in the SWNT growth, we performed calculations of neutral and singly

charged clusters FenC [1], FenCO [2] (n=1-6). Fe4C2, Fe4C(CO), Fe4(CO)2, Fe4C2CO, Fe4C(CO)2, Fe4C3, and Fe4(CO)3 [3] using all-electron density functional theory with the generalized gradient corrections. We estimated the Fen–C and Fen–CO binding energies, as well as the energetics of the FenCO+CO → FenC + CO2 and Fe4Ci(CO)j → Fe4Ci+1(CO)j-1 + CO2 Boudouard reactions. Some of these reactions are found to be exothermic, which may appear surprising because it requires 11.1 eV to break the bond in the gas-phase CO molecule. Our results are in good

agreement with experimental binding energies and vibrational frequencies measured for Fe2CO and FeCO. We found [4] that the use of CO as feedstock helps removing oxygen from iron clusters by converting surface oxygen into CO2; that is, the iron clusters sustain a full catalytic cycle of carbon monoxide oxidation. In addition, we explore [5] interactions of water with iron clusters since water may degrade the iron catalyst.

References

- [1] Gutsev G. L. and Bauschlicher C. W., Jr. Interaction of carbon atoms with Fen, Fen , and + Fen clusters (n=1–6),: Chem. Phys. 291, 27 (2003). [2] Gutsev G. L. and Bauschlicher C.W.,Jr., Structure of neutral and charged FenCO clusters (n=1-6) and energetics of the FenCO +CO → FenC +CO2 reaction, J. Chem. Phys. 119, 3681 (2003). [3] Gutsev G. L., Mochena M.D., and Bauschlicher C.W., Jr., Structure and properties of Fe4 with different coverage by C and CO, J. Phys. Chem. A 000, 000 (2004). [4] Gutsev G. L. and Bauschlicher C.W., Jr., Oxidation of carbon monoxide on small iron clusters, Chem. Phys. Lett. 380, 435 (2003). [5] Gutsev G. L., Mochena M.D., and Bauschlicher C.W., Jr., in preparation. 68 Conference on Current Trends in Computational Chemistry 2004

How Do Organophosphates Bind to Acetylcholinesterase?

Steven R. Gwaltney

Department of Chemistry and ERC Center for Computational Sciences Mississippi State University Mississippi State, MS 39762

The effects of organophosphate (OP) insecticide exposure on human health are currently of significant concern. Organophosphates make up the largest by volume class of insecticides in use today. At high enough doses, acute exposure to OP agents can lead to vomiting, muscle twitches, convulsions, and even death. 1 The primary route of organophosphate toxicity is phosphorylation of the enzyme acetylcholinesterase (AChE). The role of AChE is to degrade the neurotransmitter acetylcholine, which is involved in signaling between nerve cells and from nerves to muscles.2 In order to better elucidate the chemical mechanism by which the phosphorylation occurs, we have performed a series of protein docking and molecular dynamics calculations. We started with a structure of mouse AChE (PDB structure 1J06). For the OP we have been studying paraoxon, the active metabolite of parathion. It is well known that the phosphorylation reaction involves forming a bond between the hydroxyl oxygen on Ser203 and the phosphorus atom in paraoxon. However, automated docking of a conformationally flexible paraoxon model into a fixed AChE structure gave the preferred structure as one with the NO2 moiety of paraoxon located next to the Ser203, not the P atom. Initial results of molecular mechanics minimizations and molecular dynamics simulations have strongly suggested that, in fact, the paraoxon does not prefer to bind initially in a reactive conformation. If true, this greatly complicates what has until now been assumed to be a relatively simple protein-substrate chemical reaction.

1 H. W. Chambers, “Organophosphorus Compounds: An Overview,” in Organophosphates: Chemistry, Fate, and Effects, edited by J. E. Chambers and P. E. Levi (Academic Press, San Diego, 1992), pp. 3-17. 2 T. Shen, K. Tai, R. H. Henchman, and J. A. McCammon, “Molecular Dynamics of Acetylcholinesterase,” Acc. Chem. Res. 35, 332 (2002).

Conference on Current Trends in Computational Chemistry 2004 69

Theoretical and Experimental Studies toward the Synthesis of Potential Estrogen Mimics

Ashton T. Hamme1, Jun Wang1, Erick Ellis1, Tiffany Cook1, and Tom Wiese2

1Department of Chemistry, Jackson State University 2Department of Pharmacy, Xavier UniversityNaturally occurring compounds such as flavanoids and isoflavones, which are found in green tea, soybeans, and fish, have been shown to be beneficial in breast cancer treatment through binding to estrogen receptors. Other natural products such as 11-deoxyfistualrin-3 are cytotoxic against estrogen dependant MCF-7 breast cancer tissue.1 The investigation of 11-deoxyfistularin-3, and the synthesis of closely related analogues, can determine if this compound is an estrogen mimic, and which functional groups may be responsible for the biological response. The purpose of this project was to model 11- deoxyfistualrin-3 with known breast cancer pharmaceutical compounds, such as Raloxifene2, to determine if there is any overlap of the functional groups in the estrogen receptor active site. If any overlap is present between the two compounds, then analogues of the natural product would be synthesized for invitro estrogen receptor binding studies. FlexS and FlexX molecular modeling programs were used to study the natural product and the pharmaceutical compound. The synthesis of the 4,5-dihydroisoxazole precursor to an analogue of 11-deoxfistularin-3 was accomplished by using 1,3-dipolar cycloaddition with a functionalized enone. The cycloaddition of Methyl 2-(bromomethyl)acrylate with (4-Methoxyphenyl)hydroximoyl chloride using triethylamine in chloroform afforded only the 5,5 disubstituted 4,5-dihydroisoxazole regioisomer. The 1,3-dipolar cycloaddition of 3- chloro-2-chloromethyl propene with aromatic hydroximoyl chlorides also gave rise to one regioisomeric cycloadduct. Both of these compounds will be used as precursors to 11-deoxyfistularin-3 analogues. 70 Conference on Current Trends in Computational Chemistry 2004

The Stabilities and Geometries of Six(x=12,16,20,24,28,32,36,40,44,60) Fullerenes Doped with an Re Atom: A Theoretical Investigation

Ju-Guang Hana,b), Ming-Ju Huanga)*

a) Department of Chemistry, Jackson State University, Jackson, MS 39217, U.S.A. b) National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230026, People’s Republic of China

Geometry optimizations of mixed SixRe(x=12,16,20,24,28,32,36,40,44,60) cages with doublet, quartet, and sextet spin configurations are carried out systematically at the HF/LanL2DZ level, together with a vibrational frequency analysis. Equilibrium structures, total energies, stabilities, Mulliken atomic net population of the Re atom and HOMO-LUMO gaps of ReSix cages are presented and discussed. Theoretical results show that all ReSix cages of maximum symmetry undergo slight distortion into much more stable structures of lower symmetry; the most stable cage corresponds to the lower symmetry. The Re atom in ReSix (x=12, 16, 20, 24, 28, 32, 36, 40, 44, 60) cages deviates from the center site of Six fullerenes and acts as an acceptor of charges. Charge-transfer between Re and Si atoms makes a contribution to the stability of Six fullerenes. It should be mentioned that the Egap of ReSix cages is about 5.0 — 6.0 eV, which is larger than those of Si bulk or small Si clusters. Conference on Current Trends in Computational Chemistry 2004 71

Stopped-Flow and UV-VIS Spectrophotometric Studies of the Transformation of CL-20

Patricia L. Honea,1 Mohammad (Mo) Qasim,1 Herbert L. Fredrickson,1 John Furey,1 S. Okovytyy,2,3 Y. Kholod,2,3 J. Leszczynski3

1ERDC-EL, MS, Vicksburg, MS 39180 USA 2Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 3Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217 USA

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) is a cage cyclic nitramine used for military purposes. A DFT study of the decomposition of CL-20 has been completed and found to occur via several types of reactions, with the preferred pathway being identified. The computational study of the unimolecular decomposition of CL-20 was completed by S. Okovytyy et al, as a collaboration with our ongoing study of the alkaline hydrolysis of CL- 20. The final product in the degradation of CL-20 via alkaline hydrolysis was identified as 1,5- dihydrodiimidazo[4,5-b:4'5'-e]pyrazine, an aromatic, recalcitrant product (Figure 1). The current study is an attempt to follow the results of the computational study via experimental data obtained from UV-VIS and Stopped-Flow spectroscopy, combined with data collected from a monochromatic irradiation system as well as FTIR data. The course of degradation of CL-20 was followed through alkaline hydrolysis using the aforementioned experimental methods. Various concentrations of NaOH were added to CL-20. The results imply that competing mechanisms occur, according to the concentration of base used, with different carbon-carbon bonds of CL-20 breaking. The preferred pathway as predicted by Okovytyy et al is the cleavage of the attic C-C bond, which confirms our prediction of the ultimate formation of a recalcitrant, toxic product. The formation of this recalcitrant aromatic compound can be seen clearly in the UV-VIS data collected, as a peak at 370 nm. Upon addition of more base, UV spectra reveals a shift of the peak towards a longer wavelength, possibly due to the stepwise removal of the nitro groups. As CL-20 is transformed, the conjugation of the system is extended as nitro groups are removed, resulting in a lower energy and higher wavelength for the subsequent intermediates. At even higher concentrations of base, or, alternatively, as time elapses, the UV spectra shifts back to a shorter wavelength. The sample of CL-20 treated with base was placed in a monochromatic irradiation system and irradiated at appropriate absorption bands. Monochromatic irradiation at 370 nm causes a photo-induced free radical reaction to occur, thereby eliminating the final aromatic product. Disappearance of the band at 370 nm suggests that the product formed from the transformation of CL-20 is degraded (Figure 2). Our stopped-flow data follows the rate of the transformation of CL-20 by alkaline hydrolysis. This data was collected in three regions: at 236 nm, where CL-20 itself absorbs; at 370 nm, where the aromatic intermediate absorbs; and around 420 nm, where the absorption peak shifts as nitro groups are peeled off (Figure 3). The kinetics of the mechanism has been studied through fitting the rate equations obtained from the stopped-flow data. The data demonstrates the appearance and disappearance of intermediates, throughout the reaction, as well as a competition of reactions. Stopped-Flow data shows, just as other experimental data showed, that at low concentrations of base, different products are forming than at high concentrations. This project demonstrates how computational chemistry can be used to predict preferred degradation pathways, as verified by experimental data. 72 Conference on Current Trends in Computational Chemistry 2004

O O O O - + NO O N + 2 NO N+ N 2 N N + O- H N H O- N N N N - N O H H

N N N N N O- O H H + N+ N NO O2N 2 NO2 - O O

N H N N H H

N N H N

Figure 1. Decomposition of CL-20 by alkaline hydrolysis to give recalcitrant product.

UV/Vis Data of 55 mg/L CL-20 in MeOH with 0.05 N NaOH Before and After Irradiation at 368 nm 4

3.5 55 mg/ L CL-20 in 0.05 N NaOH af t er one day, bef ore 3 irradiat ion

2.5 55 mg/ L CL-20 in 0.05 N NaOH af t er 30 min irradiat ion 2 55 mg/ L CL-20 in 0.05 N NaOH af t er 1 hr irradiat ion

1.5

1

0.5

0 200 250 300 350 400 450 500 550

Wavelength

Figure 2. Monochromatic irradiation degrades recalcitrant product at 368 nm.

Conference on Current Trends in Computational Chemistry 2004 73

Stopped Flow: 55 mg/L CL-20 in MeOH w/ various NaOH concentrations at 236 nm

2.2 2 0.01 N NaOH

e 0.05 N NaOH 1.8 0.1 N NaOH 1.6 0.25 N NaOH 0.35 N NaOH 1.4 Absorbanc 0.5 N NaOH 1.2 1 N NaOH 1 0.001 0.01 0.1 1 10 100 1000 Time (sec) - Log Based

Stopped Flow: 55 mg/L CL-20 in MeOH w/ various NaOH concentrations at 370 nm

0.5

0.4

0.3

0.2 0.01 N NaOH 0.05 N NaOH 0.1 0.1 N NaOH 0.25 N NaOH 0 0.35 N NaOH 0.001 0.01 0.1 1 10 100 1000 0.5 N NaOH Time (sec) - Log Based 1 N NaOH

Stopped Flow: 55 mg/L CL-20 in MeOH w/ various NaOH concentrations at 410 nm

0.5

0.4 0.01 N NaOH 0.3 0.05 N NaOH 0.1 N NaOH 0.2 0.25 N NaOH Absorbance 0.1 0.35 N NaOH 0.5 N NaOH 0 0.001 0.1 10 1000 1 N NaOH

Time (sec) - Log Based

Stopped Flow: 55 mg/L CL-20 in MeOH w/ various NaOH concentrations at 430 nm

0.7 0.01 N NaOH 0.6 0.05 N NaOH e 0.5 0.1 N NaOH 0.4 0.25 N NaOH 0.3 0.35 N NaOH Absorbanc 0.2 0.5 N NaOH 0.1 1 N NaOH 0 0.001 0.01 0.1 1 10 100 1000 Time (sec) - Log Based

Figure 3. Stopped-Flow graphs of CL-20 treated with various concentrations of NaOH at various wavelengths.

74 Conference on Current Trends in Computational Chemistry 2004

Polyhedral Oligomeric Silsesquioxanes (POSS) Cages with Atomic Alkali, Noble Gas and Halogen Impurities

a a a b Delwar Hossain , Charles U. Pittman , Jr., Svein Saebo , Sung Soo Park , Chuanyun Xiaob, and Frank Hagelbergb

aDepartment of Chemistry, Mississippi State University Mississippi State, MS 39762 bComputational Center for Molecular Structures and Interactions Department of Physics, Atmospheric Sciences, and General Science Jackson State University, Jackson, MS 39217

Octahydridosilsesquioxane, (HSiO3/2)8, or Polyhedral Oligomeric Silsesquioxane (POSS) T8 1 cage systems and its derivatives have attracted considerable interest. The POSS monomer T8 cage consists of silicon atoms occupying the vertices of a cube, and oxygen atoms bridging each pair of silicon atoms. In the parent octahydridosilsesquioxane a single hydrogen atom is attached to each silicon atom. In general, POSS derivatives exhibit the composition (RSiO3/2)2n, where R denotes an organic ligand. POSS derivatives incorporated into organic polymers, dendrimers, and zeolites have found substantial attention due to their applications in material science and catalysis.1 One interesting feature of these cages is that atoms or ions can be encapsulated into them, and several studies, including our own, have focused on this property. Most experimental and theoretical studies2 reported in the literature have focused on the pure or metal-substituted parent POSS cage with or without encapsulated species. We will comment on endohedral [X@(HAO3/2)8] and exohedral [X(HAO3/2)8] T8 cages, as shown in Figure 1, and also include preliminary results on the corresponding T10 units.

X

A A A = [ C, Si, Ge ] and AA A A TS + He, Ne, Ar, X X = Li+, Na+, K+, A A A A F-, Cl-, Br- A A

(a) (b) (c) (d) (e)

Figure 1. Schematic representation of host cage species with D4R units and impurities; (a) Host cage with Oh or Th symmetries, (b) specification of vertex atoms (A) and impurities (X), (c) exohedral species and (e) endohedral species are connected by a transition state (d).

Investigations have been carried out on T8 cages complexed with the atomic or ionic species: Li+, Na+, K+, F-, Cl-, Br-, He, Ne, Ar have been investigated at the B3LYP/6-31G* and B3LYP/6-311++G** levels. Geometric, electronic and energetic properties were obtained. For the endohedral complexes the noble gas atoms (X = He, Ne and Ar) inside the cage cause the Conference on Current Trends in Computational Chemistry 2004 75

cages to expand, and the extent of the expansion depends on the size of the included atom. Endohedral alkali ions, in contrast, exhibit both attractive and repulsive interactions with the cage atoms. The cage expands when X = K+ and contracts when X = Li+ or Na+ for A = Si, Ge, and for A=C, the cage expands for all three ions. Encapsulation of the halide ions results in cage expansion throughout. Furthermore, the symmetry of the endohedral complexes when X is a cation depends critically on the relative cation and cage sizes. The binding energies of the endohedral and exohedral complexes document a clear preference for the latter, except for halides, where the endohedral complexes are more stable. The stability of endohedral complexes containing the isoelectronic species X = Na+, Ne, F- is determined by the charge transfer to the A–O cage bonding sites. The formation of the endohedral complexes is discussed in terms of transition states that connect the exohedral and endohedral minima, as well as the activation barriers for insertion of the guest into the cage. Our studies predict that a fluoride anion can - penetrate into the (HAO3/2)8 cage without destroying it. For X = Cl , in contrast, the cage ruptures upon insertion of the impurity.

References. (1) (a) Brown, J. F., Jr.; Vogt, L. H., Jr. J. Am. Chem. Soc. 1965, 87, 4313-4317. (b) Lamm, M.H.; Chen, T.; Glotzer, S.C. Nano Lett. 2003, 3, 989. (c) Li, G.-Z.; Wang, L., Ni, H.; Pittman, Jr., C. U., J. Inorg. And Organometal. Polym., 2001, 11(3) 123. (d) Li, G.-Z.; Wang, Li.; Toghiani, H.; Pittman, Jr., C. U.; Daulton, T. L., Polymer, 2002, 43(15), 4167. (2) (a) Feher, F.J.; Newman, D.A.; Walzer, J.F. J. Am. Chem. Soc. 1989, 111, 1741 (b) Maxim, N.; Overweg, A.; Kooyman, P.J.; Wolput, J.H.M.C.v.; Hanssen, R.W.J.M.; Santen, R.A.v.; Abbenhuis, H.C.L. J. Phys. Chem. B 2002, 106, 2203. (c) Murugavel, R.; Davis, P.; Shete, V.S. Inorg. Chem. 2003, 42, 4696. 76 Conference on Current Trends in Computational Chemistry 2004

Molecular Dynamics Simulation of E-coli Dihydrofolate Reductase’s Circular Permuted Variants

Zengjian Hu1, Buyong Ma3, Ruth Nussinov3, Donnel Bowen2, and William M. Southerland1

1 Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Washington, DC 20059, 2 Department of Pharmacology, Howard University College of Medicine, Washington, DC 20059, 3 Laboratory of Experimental and Computational Biology, Basic Research Program, SAIC, NCI-FCRDC, Frederick, MD 21702

Understanding the factors which influence protein folding will have a significant impact on protein structure prediction and protein design. Recently, essential folding sequences of the native E coli dihydrofolate reductase protein were detected. Molecular dynamics simulations of the native E coli DHFR and several of its circular permuted variants have been carried out in order to correlate folded stabilities among these variants. Here we reported our initial results about the significant difference in structural stability between amino acid sequences identified as folding sequences and those not identified as folding sequences.

Introduction Circular permutation analysis, in which the original N and C termini of a protein are connected by an appropriate linker and new termini are created at a position of interest, has reveals the essential folding elements in DHFR of E coli by systematically constructing all 158 permutants of the 159-residue DHFR. We have carried out a systematic analysis of the native DHFR from Escherichia coli and several of its circular permuted variants using molecular dynamics simulations at different temperatures in order to reveal the distribution of the folding elements within the primary structure and to study their relative stabilities.

Materials and methods Protein. The structure of DHFR of E. coli was taken from the protein data bank. Both crystallographic waters and substrates were deleted. Circular permutation of a protein consists of connecting the native N- and C-termini covalently with a peptide linker and cleaving the peptide backbone at one specific site. Because a five-glycine peptide had been shown to be the most favorable linker in the circularly permutation analysis, this peptide linker was employed in all variants in our study. Simulation procedure. For all computations the CHARMM program (version 30b1) was used. The native DHFR and its circular permuted variants were simulated in a 60 x 60 x 60 Å3 explicitly solvated periodic box. Water molecules were introduced as TIP3P waters. Each simulation was initialized with Adopted Basis Newton-Raphson (ABNR) minimization followed by 3-psec of system heating and 17-psec of system equilibration. The average Cα RMSD at the end of the initialization was ~1 Å. A 2.5-nsec simulation was then carried out for each of the protein structures described above at 300, 350, 400, 450 K respectively at 1-fsec time steps. Analysis of trajectories. The structure of the native protein, derived from the X-ray structure, was used as reference. The Cα RMSD of each simulation trajectory, recorded at 1-psec time interval, was evaluated after superimposing all of the Cα atoms with the reference.

Conference on Current Trends in Computational Chemistry 2004 77

Results Permutant models. Two permutant models have been used based on the breaking the backbone connnectivity (Fig. 1). Model A breaks the peptide bond in the ‘folding element’ region while model B breaks the bond outside the region.

A B Fig. 1. Permutant models used in the simulation

2 Root-mean-square deviations (RMSD) of all the Cα atoms vs time

Fig. 2. RMSD of all the Cα atoms vs time Fig. 3. RMSD of all the Cα atoms vs time for for model A at 300K (in red) and model B at 300K (in red), 350K (in 350K (in green). green), 400K (in blue), and 450K (in magenta).

3 Comparison of RMSD vs time of model A and that of model B (all the Cα atoms)

Fig. 4. RMSD vs time of model A and Fig. 5. RMSD vs time of both model A and model B at 300K (in red) and 350K model B at 300K (in red) and 350K (in green), respectively. (in green), respectively.

78 Conference on Current Trends in Computational Chemistry 2004

4 Comparison of RMSD fluctuations (RMSF) of model A and model B

Fig. 6. Comparison of RMSF for model A (in red) and model B (in green) at 350K .

Conclusions • MD simulations show the different stabilities for the permutated mutants, in agreement with experimental results. • For the two mutants reported here, it seems that the stability of local interaction is decisive. As show in Fig 7, the break of folding element region leads to the large fluctuation around breaking point first, while the breaking in the nonfolding element region does not affect the local (breaking point stability). Folding element has two roles: (1)to provide stability for the local region, and (2)acting as folding neucleis to affect global stability. • Large scale MD simulation will provide more complete folding feature of the DHFR permutation mutants.

Reference • Iwakura M, Nakamura T, Yamane C, Maki K. Systematic circular permutation of an entire protein reveals essential folding elements. Nat Struct Biol. 2000; 7: 580-5. • Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002; 9: 646-52.

Acknowledgments. This work is supported by grant RCMI-NIH 2G12RR03048, grant MCB030037P from Pittsburg Supercomputing Center, and by NCI Advanced Biomedical Computing Center Conference on Current Trends in Computational Chemistry 2004 79

Nuclear Magnetic Resonance Spectral Analysis and Molecular Properties of Berberine

Ming-Ju Huang, Ken S. Lee, and Sharon J. Hurley

The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P. O. Box 17910, 1400 J. R. Lynch Street, Jackson, MS 39217

Berberine (see figure) is a plant yellow quaternary protoberberine alkaloid and has been used in Ayurvedic and Chinese medicine for at least 3000 years. The quaternary protoberberine is the iminium cation derived from 5,6-dihydrodibenzo[a,g]quinolizinium. Berberine is a tetrasubstituted alkaloid with a methylenedioxy group at C28 and C29, and two methoxy groups at C3 and C6. Berberine alkaloid is found in the roots, rhizomes, and stem bark of Berberis vulgaris L. plants and has demonstrated significant antimicrobial activity against a variety of organisms such as bacteria, viruses, fungi, protozoans, and chlamydia. In addition, berberine displays a great variety of biological and pharmacological activities. It has also been reported that berberine possesses anti-tumor properties, and the 3-position in berberine analogues is an important determinant of DNA topoisomerase II inhibition. Currently, the predominant clinical uses of berberine include bacterial diarrhea, intestinal parasite infections, and ocular trachoma infections. The chemistry of berberine and related alkaloids may deal either with side chain alterations to form structural analogs or with nucleophilic attack on the iminium C=N+ bond. As far as we know, no ab initio molecular orbital calculations have been applied to berberine and its derivatives. Investigations of three aspects of berberine were undertaken in these studies: (a) structural comparisons of two crystalline berberine derivatives, berberine azide and berberine thiocyanate with the corresponding ab initio and density-functional theory optimized geometries with and without solvent effects; (b) comparison of experimental 1H and 13C NMR chemical shifts of berberine with calculated results by using GIAO (with and without solvent effects), CSGT, and IGAIM methods; (c) harmonic vibrational frequency calculations were performed at the B3LYP/6-311G** level.

80 Conference on Current Trends in Computational Chemistry 2004

Theoretical Studies of Quantum-like Optimization Principle for 3-D Conformation of Complex Molecular Systems

Xiaofei Huang

UCLVenture Foster City, CA 94404, USA

The 3-D conformation of a complex molecular system, such as protein folding, can be thought as a process of minimizing some free energy associated with the system. The native 3-D structure of a molecular system is assumed to be at the global minimum of the free energy surface of the system. Understanding such a process is important to biochemistry and life sciences. It might hold the key to the secret of life because it will tell us how living things, consisted of different proteins, are created by the DNA codes. Up to now, however, we are still lack of a proper theory for understanding such a process so that we can predict the protein structures from their DNA codes.

A New Principle for Global Optimization The cooperative optimization is a new way of optimization. It is more general in principle than classic ones, such as gradient descent. It is based on a system of multiple dynamic agents working together in an interactive and cooperative way to minimize an objective function associated with the system. Under the new cooperative optimization principle, different cooperation schemes can be defined among the agents. They lead to different computational behaviors of the system. Gradient descent is a special case when the cooperation level is at the strongest [1]. In this case, the system can have many equilibriums, each one corresponding to a local optimum of the objective function associated with the system. If the level of cooperation is just at a certain moderate level, then the system has a unique equilibrium and it converges to it with an exponential rate regardless of initial conditions and perturbations. The unique equilibrium is the global optimum of the objective function in many important cases, though not guaranteed. Otherwise, NP=P.

Newtonian Dynamics, and Local Minimum In the language of physics, given a system of multiple particles, we can treat each particle as an agent. In the classical Newtonian dynamics, each particle accelerates in response to applied forces, or in general, it picks out the path with minimum in the action (Hamilton principle). This kind of dynamics can be described by the multi-agent system with the cooperation scheme corresponding to gradient descent. When proteins fold, they are, at most of the time, within an open system where they interact with each other and molecules of solvents. As a consequence, both energy and momentum are not conserved. However, we can still assume that each amino acid in a protein’s polypeptide chain moves in response to applied forces to minimize the potential energy of the protein. Therefore, it picks out the path that minimizes the potential energy. The fundamental is the same as the Hamilton principle. In this case, the potential energy corresponds to the work.

Conference on Current Trends in Computational Chemistry 2004 81

Initial point

Trajectory

Local Minimum

Fig. 1. With the point of view of the classical dynamics, a molecular system evolves from a initial point in the configuration space, follows a trajectory that minimizes the potential energy, and lands in a station point which is a local minimum of the potential energy function.

The classical dynamics works quite well to describe motions from stars, planets in heaven, to rocks and applies on earth. However, it doesn’t seem to be a right model to describe the conformation process of complex molecular systems. In nature, molecules form clusters easily and a protein, a polypeptide chain of amino acids, is able to fold to a relatively fixed three- dimensional structure, or conformation, which is thought to correspond to the global optimum of the system free energy. However, the dynamics defined by the classic model converges to a local optimum of the free energy, not the global one. It predicts much more conformation structures, in contrary to the reality.

Quantum Dynamics, and Global Minimum Can we find a better model to describe the dynamics at the molecular world? As mentioned before, the classical Newtonian dynamics can be described by the multi-agent system with a cooperation scheme corresponding to gradient descent. With this scheme, the system has a large number of equilibriums, corresponding to the local minima of the system objective function (energy). If we change the cooperation scheme by adjusting the cooperation level, the number of equilibriums can be reduced significantly. They can be reduced to one equilibrium only, which corresponds to the global optimum of the system energy. In the language of physics, this requires us to change the way to treat particles in the system. Each particle, instead of being treated to have a definite position in 3-D space at any given time, should be viewed to have simultaneously many possible positions spread within a certain range in space at any given time. If the possible positions of each particle are spread more in space, then the dynamic system has less number of equilibriums. Under certain conditions, the system has one and only one equilibrium. If the possible positions of each particle shrink more in space, the system has more equilibriums. If they are shrink to a point in space at any given time, the dynamic system falls back to the classical Newtonian dynamics, which has lots of local minima. The new dynamics defined by the cooperation scheme assigns a real value for each possible position of a particle. It describes the likelihood of finding the particle at that position. However, does this have any physical meaning in the real world? The new mathematical requirement for viewing particles in a system seems to match perfectly with those required by quantum physics. In quantum physics, a subatomic particle in micro-world, such as electron or nuclei, can no longer be viewed to have a definite position any given time due to the Heisenberg uncertainty principle. Instead, it has wave-like nature, governed by the wave equation proposed by Erwin Schrödinger. Physicist Max Born proposed a probability interpretation of the Schrödinger equation, which is mathematically same as the likelihood of finding a particle at a certain position, required by the cooperative optimization to make the system having less number of equilibriums and being more stable. 82 Conference on Current Trends in Computational Chemistry 2004

Based on this quantum dynamics, each particle in a molecular system, such as an amino acid in a polypeptide chain, spreads in space as a wave from its initial position pi, say Si, instead of having a definition position pi in space. In total, they form a space, S1xS2x…xSn, which is a subspace of the configuration space, instead of a point in the configuration space, p1 x p2 x …x pn , in the classical dynamics. The quantum dynamics enables the molecular system to find the local minimum within the subspace S1 x S2 x…x Sn, jump to it and spread as waves again so that the system can find the new local minimum within the new subspace. Figure 2 illustrates such a quantum dynamics for the 3-D conformation of a molecular system.

Initial

Spreading

Jump to the minimum

Fig. 2.With the point of view of the quantum dynamics, a molecular system evolves from initial point in the configuration space, expands its configuration point into a subspace by spreading each particle’s position in space as a quantum wave, jump (tunnel) to the lowest energy state in the subspace, and repeat such a spreading and jumping process until the system lands into a configuration with an energy state which is also the minimum in the subspace spread from it.

Such a quantum dynamic model for the 3-D conformation of molecular systems suggests that not any randomly chosen amino acid sequence for a protein folds into its native structure except when its free energy has a funnel-like landscape. Unlike the classic dynamics, the quantum dynamics, because of its spreading-and-jumping characteristic, enables the system to find the native structure even if the funnel-like landscape is textured with enormous number of local minima. This requirement is the same as Leopold, Montal, and Onuchic’s proposal in [2] for the energy landscape of a natural protein, but with different principles to understand the conformation process. Their principle is based on the thermodynamics and this paper is based on the quantum dynamics. The former doesn’t have a theoretical foundation to guarantee the convergence to the global optimum in general, and it requires much longer time to converge than the physiological timescales (~m sec) under typical biochemical conditions. It plays an important role in protein folding, but it looks like to the author that it is the quantum dynamics that plays the major role (It has been found that cooperative optimization is much more efficient and has much better performance than simulated annealing in solving hard optimization problems from visual perception, such as shape from stereo [4]).

A Case Study of Lennard-Jones Clusters To demonstrate the behavior of the quantum dynamics in energy minimization, we use the potential energy of a cluster of particles which have pair-wise interactions defined by the Lennard-Jones (L-J) potential. It is a well-studied, difficult optimization problem. This problem is important because the L-J energy is a special case of the general Van der Waals interaction which acts between pairs of non bonded atoms in complex molecular systems, like in proteins. The performances of gradient descent and cooperative optimization are evaluated for L-J clusters of size 10, 15, and 20, respectively. Gradient descent is a special case of the cooperative optimization (CO) with no spreading of particle positions in space. Computer simulated the Conference on Current Trends in Computational Chemistry 2004 83

spreading of particle positions with two different space ranges by sampling the 3-D space with 5x5x5 and 7x7x7 grids, plus the no spreading (gradient descent). For each cluster size, 20 runs were executed and the average of the final energies are listed in the following table. In the experiments, significant improvement in solution qualities were achieved by spreading particle positions. The effect of spreading from 5x5x5 to 7x7x7 is not so significant. But it becomes more obvious with the increase of cluster sizes. Cluster size Gradient Descent CO with 5x5x5 spreading CO with 7x7x7 spreading 10 -16.27807 -27.41539 27.45702 15 -44.81970 -50.06841 -50.81305 20 -63.21395 -73.51386 -74.39001

The 20 runs for L-J clusters of size 15 and 20 are given in the following the figure. The fluctuation of the energy states found by gradient descent is more significant than those found by cooperative optimization.

20 runs for L-J clusters of size 15 20 runs for L-J clusters of size 20 -30 0 1 3 5 7 9 1 3 5 7 9 11 13 15 17 19

11 13 15 17 19 -10 -35 -20 -30 -40 -40

energy -45 -50 energy -60 -50 -70 -80 -55 -90 Gradient Descent Cooperative (5x5x5) Gradient Descent Cooperative (5x5x5) Cooperative (7x7x7) Cooperative (7x7x7)

Conclusions More than 50 years again, Erwin Schrödinger made the startling proposal that life is based on quantum-mechanical principles. If the native structure of a protein corresponds to the global minimum of its free energy, the classical Newtonian dynamics is not suitable in explaining the conformation process because it has too many equilibriums, corresponding to local minima of the energy function, even if we add the statistical laws into it. The quantum dynamics, which requires spreading the positions of particles of a molecular system in space, has much more computational power in finding the global minimum of the system’s energy. Both of them can be understood and unified as a multi-agent system, where agents interact with each other governed by the dynamics defined by a new optimization principle, called cooperative optimization. Different cooperation schemes corresponds to different dynamics and lead to the different computational behaviors of the system. With the classical Newtonian dynamics tends to find local minima and the quantum dynamics tends to discover global minima through quantum tunneling. References [1] X. Huang, “Cooperative Optimization for Solving Large Scale Combinatorial Problems”, Theory and Algorithms for Cooperative Systems, World Scientific (2004). [2] P. E. Leopold, M. Montal, and J.N. Onuchic, Proc. Natl. Acad. Sci. USA 89, 8721 (1992). [3] E.Nelson, P.Wolynes, J. Onuchic, “An approach to detect the dominant folds of pretein like heterropolymers from the statistics of a homopolymeric chain”, Optimization in Computational Chemistry and Molecular Biology, Kluwer Academic Publisher, (2000). [4] X. Huang, “Cooperative optimization for energy minimization in computer vision: a case study of stereo matching”, Proceedings of 26th DAGM Symposium, Springer (2004). 84 Conference on Current Trends in Computational Chemistry 2004

Effects of Positional Isomers on Polyimide Properties

Danielle L. Hudson1, Jeffrey A. Hinkley2, Thomas C. Clancy3, Melissa S. Reeves1

1Tuskegee University Department of Chemistry Tuskegee, Alabama 2Advanced Materials and Processing Branch NASA Langley Research Center 3National Institute of Aerospace, Hampton, VA

Polyimides (PIs) are an important class of materials because of their many desirable characteristics: excellent mechanical properties, low dielectric constant, low relative permittivity, high breakdown voltage, low losses over a wide rage of frequency, good planarization, wear resistance, radiation resistance, inertness to solvents, good adhesion properties, low thermal expansion, good hydrolytic stability, and long-term stability. Because of these traits, PIs have found applications in many technologies such as inter-metal dielectric materials, high temperature adhesives, photoresist materials, nonlinear optical materials, membranes, and Langmuir-Blodgett(L-B) films. These applications can be found in industries ranging from aerospace to microelectronics to optoelectronics to composites to fiber optics. In this study, diffusion of small gas penetrants, structural and mechanical properties, and flexibility of three related PIs were studied to determine correlations between these properties and structural differences. The related PIs, all biphenyl dianhydride (BPDA) asymmetric PIs, differ in the connections among phenyl rings in diamine portion. PI-1 has a meta-meta-meta connection, PI-2 has a para-para-para, and PI-3 has a para-meta-para connection. (See Figure 1.)

O O O

N (A) (C) O (B) O N

n O Figure 1. Repeat unit for polyimides in this study where positional differences occur at rings A, B, and C. Relatively few molecular dynamics (MDs) studies have been reported on PIs, partially because the rigid aromatic rings can be difficult to model. Coarse-grain reverse mapping techniques1 were used to produce well-equilibrated amorphous structures while avoiding catenation and spearing. The amorphous cell (AC) contained seven chains with ten repeat units on each chain and periodic boundary conditions. The cubic cell was 36Å on a side with a density of 1.4x 103 kg m-3 and contained ~ 4230 atoms. In this study, Materials Studio (MS) and InsightII, commercial software programs from Accelrys Inc., were used to simulate equilibrated structures of the PIs, as well as of penetrants, helium (He), hydrogen molecule (H2), and argon (Ar) diffusing through these PIs at 500K. MDs were run for 300ps for penetrants He and H2. However, for Ar, 500ps were necessary to reach an equilibrated cell for PIs 1 and 3, and 1100ps for PI-2. Structural and mechanical properties were studied using an equilibrated cell without penetrants from the last 100ps of dynamics. Structural properties were calculated using the full 100ps trajectory, and mechanical properties were calculated using the lowest energy frame. In order to determine the flexibility of the PIs, a single chain with three repeat units was minimized, then subjected to 4.0 ns of MD at 300K with a time step of 0.5 fs. The torsional energy maps of the PIs were calculated relative to an all-trans conformation of each PI. Several different Conference on Current Trends in Computational Chemistry 2004 85

dihedral angles were defined and dihedral mapping was calculated with and without a rigid rotor assumption. The structural properties studied were length and angle distributions, pair correlations and free volume. Analysis of the length distribution was performed to determine if the head-to-tail length of each monomer on the polymer chain had an effect on the properties. The head-to-tail length distributions of the pure PIs from the single frame did show significant differences. The monomer in PI-1 was shorter in length than those in PIs 2 and 3. A similar trend was seen with the head-to-tail length distributions for the PIs over the entire trajectory. The angle distributions for the carbon-ether oxygen-carbon bond were studied to determine if there were any differences in this angle among the PIs. In the trajectory, PI-1 has 6.36% of the angles peak at 115°, PI-2 has 6.38% of angles peak at 114° and PI-3 has 6.22% of the angles peak at 117°. The free volume in the pure polymer was measured through Voronoi tessellation to determine differences among the free volumes in the polymers. The free volumes for the pure polymers in this study did not show significant differences. Pair correlation functions were calculated for He and H2 penetrants with selected atoms in the PIs, the ether oxygen (EO), carbonyl oxygen (CO), and nitrogen (N). He and H2 did show some association with the CO and N but not the EO. The EOs are surrounded by bulky phenyl rings and are not exposed to the penetrants. The mechanical properties studied were Young’s, bulk, and shear moduli along with Poisson’s ratio. These properties determine how “stiff” or “rigid” a polymeric material will be on the macroscopic level. PI-1 that had the most flexible single-chain architecture also proved to have the lowest tensile modulus and the highest compressibility (See Table 1).

Table 1. Mechanical properties from Synthia (Syn), Molecular Mechanics (MM), & Experimental (Exp)2 Polymer Young’s modulus Bulk modulus Shear modulus (GPa) (GPA) (GPa) MM Syn Exp MM Syn MM Syn PI-1 3.43 3.32 3.48 6.09 5.80 1.22 1.18 PI-2 4.84 3.54 4.10 7.90 5.98 1.73 1.26 PI-3 5.52 3.80 3.57 8.66 5.92 1.98 1.36

The positions of the penetrant atoms as a function of time were used to determine the diffusion coefficient of the penetrants in BPDA PIs. Penetrant atoms diffused the fastest through the PI with meta-meta-meta connections (PI-1) (See Table 2).

Table 2. Diffusion coefficient (cm2 s-1) for various penetrants in PIs at 500 K ± 10.

Polymer DH2 DHe DAr DH2/H2 DH2/He DH2/Ar PI-1 16.8 x 10-6 6.2 x 10-6 . 11x10-6 1 2.7 151 PI-2 10.1 x 10-6 3.9 x 10-6 .065x10-6 1 2.6 157 PI-3 6.6 x 10-6 2.3 x 10-6 .038x10-6 1 2.9 171

The positions of connections of the aromatic rings have been shown to have an effect on structural and mechanical properties and on diffusion.

1. Clancy, T. C.; Jang, J. H.; Dhinojwala, A.; Mattice, W. L. J. Phys. Chem. 2001 105 11493 2. Hergenrother, P. M. et al. Polymer, 2002, 43(19),5077-5093. 86 Conference on Current Trends in Computational Chemistry 2004

Transfer Hamiltonian: An Independent Particle Model with Correlation via the Exact Coupled Cluster Equations

Thomas F. Hughes and Rodney J. Bartlett

Quantum Theory Project, Department of Chemistry and Physics University of Florida, Gainesville, FL 32611

In order to simulate materials accurately in molecular dynamics we need to account for electron correlation which can significantly change the shape of the potential energy surface and therefore the forces which govern bond breaking and other critical events. The goal is to treat very large (~103) systems with little geometric symmetry but with memory requirements comparable to independent particle theories. We argue that the wave operator ansatz from Coupled Cluster theory gives a naturally advantageous representation of such a Hamiltonian, called the Transfer Hamiltonian (TH), which contains a correlation operator. As opposed to treating such systems by popular conventions such as NDDO Hamiltonians where correlation is trapped in parametrizations of coulomb and exchange terms, the TH offers the exact correlation contribution and therefore predicts bulk properties of target simulations.

Despite common criticism, Dewar type theories have been supported for over forty years and are said to rival high-level ab initio theories because by introducing the concept of a parameter fit one can approach the exact experimental result with arbitrary accuracy. In modeling the TH we adopt multipole expansions in the same way as semi-empirical theory and work in a two-center atomic orbital based framework, indicative of diatomics-in-molecules, to ensure a very fast (O(N3) or faster) method. We consider the large system as composed of repeated units and parametrize the correlation operator of the monomer to reproduce forces, ionization potentials, geometries, etc. We demonstrate that for weakly interacting systems the changes in parameters upon monomeric addition to an existing cluster go to zero for relatively small clusters. Applications include parametrizations for clusters of water and of high energy materials such as nitromethane and fox. Conference on Current Trends in Computational Chemistry 2004 87

Pathways of Nitrobenzene Reduction by Iron (II) Compounds. A DFT Study

Olexandr Isayev, Leonid Gorb, Igor Zilberberg† and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217 †Boreskov Institute of Catalysis, Novosibirsk 630090, Russia.

Selective reduction of nitrobenzene (NB) by ferrous iron has relevance to many areas. One application of this reaction is related to the synthesis from nitrosobenzene of various industrial products such as antioxidants, insecticides and photolacquers.1 Transition metals and particularly iron oxides are known to exhibit catalytic activity in this process.2 Another application concerns the development of cleanup technologies for a disposal of nitroaromatics (NACs). This is a challenge for environmental science. Such development involves the coordination of experimental and theoretical investigations to integrate both technological and fundamental aspects of key process. The iron oxo-species are one of the most attractive NACs-reducing agents being extremely cheap and environmentally clean. Although the major processes affecting the iron treatment of NACs have been investigated qualitatively, many issues regarding a reaction mechanism remain unsolved.3 The Following model reactions has been calculated:

1) C6H5NO2 + FeO C6H5NO + FeO2

2) C6H5NO2 + Fe(OH)2 C6H5OH + HOFeONO

All interactions are studied at UDFT level using the hybrid B3LYP and gradient-corrected local-density functionals BLYP and BPW91. The standard 6-311++G(d,p) basis set was employed. The local minima and transition states were verified by frequency analysis. All minima have also been checked for SCF instability to ensure that all obtained solutions are stable. On the basis of our calculations mechanism of studied reactions was proposed. The thermodynamics both of considered processes is determined by the ability of ferrous iron to compensate the energy necessary to brake the N-O bond by the formation of the oxo ferrous-iron bond. The reduction of nitrosobenzene by FeO seems to be possible at the elevated temperatures because of “effective activation barrier” is almost zero. In contrast, Fe(OH)2 can not compensate such energy gap. So, the fate of nucleophiclic substitution is yet unclear. As our study of the initial stage of the nitrobenzene-iron oxo-species interaction reveals, there is a non-barrier one-electron transfer from the d shell of iron into the anti-bonding LUMO localized mostly on the nitro group of nitrobenzene. Hybrid functional (B3LYP) have the strong tendency to underestimate of the bond energy between FeO and O revealed by the hybrid DFT as compared with the pure DFT methods. And vice versa in the case of Fe(OH)2.

1. Zengel, H. G. Chem. Ing.-Tech. 1983, 55, 962. 2. Maltha A.; Vanwermeskerken Sc.; Brunet, B.; Ponec, V. J. Mol. Catal. 1994, 93, 305. 3. Klausen, J.; Troeber, S. P.; Haderlein, S. B.; Schwarzenbach R. P. Environ. Sci. Technol. 1995, 29, 2396. 88 Conference on Current Trends in Computational Chemistry 2004

Comparison of Basis-set and Method Dependence of Ground- and Excited-State Calculations for Cytosine and 5-methyl-cytosine in an Excited-state Quantum Chemical Investigation

Mark Jacka, Manoj Shuklab, and Jerzy Leszczynskib

aFlorida A&M University, Dept. of Physics, Tallahassee, FL 33207 bJackson State University, CCMSI, Dept. of Chemistry, Jackson, MS 39217

A detailed computational study is performed on the molecular geometry and electronic spectra of cytosine and 5-methyl-cytosine. Ground-state geometries are optimized and compared for each molecule for three different theoretical methods: Harttree-Fock theory (HF), density functional theory (DFT/B3YLP) and Moller-Plesset perturbation theory (MP2). For each method, the molecular ground-state energies and harmonic vibrational frequencies are calculated using four different basis set, 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p), and 6-311++G(d,p), in order to study the basis-set dependence of the calculated observables. For the optimized ground-state geometries the vertical transition energies to the (non-optimized) excited states are computed in each individual case using time- dependent density functional theory (TDDFT). The calculations for cytosine are again performed for the four different basis sets. For 5-methyl-cytosine in comparison, only the basis set, which yielded the most accurate result for cytosine, is employed. These studies are conducted both for the gas phase and with water as a solvent in order to study the effects of hydration theoretically using different basis functions and methods.

Cytosine as constituent nucleic acid base forms next to the molecules adenine, guanine, and thymine one of the four fundamental building blocks of the DNA molecule as nucleic acid polymer. Effects of hydration on the geometries and spectra of the cytosine molecule are important to study the structural stabilization and electronic excitations of DNA in water compared to the gas phase for theoretical predictions under realistic environmental conditions. Due to the lack of direct experimental methods to study excited-state geometries of cytosine, a detailed study of the dependence of geometric and spectral observables on the choice of basis functions and methods is necessary in order to obtain reliable theoretical predictions. Such a study is especially crucial in the light of providing with TDDFT a fast and precise computational alternative to the more accurate but computationally much more intensive coupled-cluster methods (CCSD(T)). All calculations on geometries, frequencies and spectra are done with the suites of the program Gaussian 03. The analysis of the molecular orbital transitions is done with the help of the molecular viewing program Molden, which also provides the initial molecule structures of cytosine and 5-bmethyl-cytosine as input for Gaussian. Conference on Current Trends in Computational Chemistry 2004 89

Applications of Quantum Chemistry to the Study of Carbon Nanotubes

Richard L. Jaffe

Nanotechnology Branch NASA Ames Research Center Moffett Field, CA 94035

For several years, scientists at NASA Ames have been studying the properties of carbon nanotubes using various experimental and computational methods. In this talk, I will compare different strategies for using quantum chemistry calculations to describe the electronic structure, deformation and chemical functionalization of single wall carbon nanotubes (SWNT) and the physisorption of small molecules on nanotube surfaces. The SWNT can be treated as an infinite (periodic) or finite length carbon cylinder or as a polycyclic aromatic hydrocarbon (PAH) molecule with an imposed curvature maintained by external constraints (as if it were cut out of the SWNT surface). Calculations are carried out using DFT and MP2 methods and a variety of atomic orbital basis sets from minimal (STO-3G) to valence triple zeta. The optimal approach is based on the particular SWNT property of interest. Examples to be discussed include: nanotube fluorination and other functionalization reactions; coating of nanotubes by water vapor and low- molecular weight organic molecules; and the nature of the interface between SWNT and liquids such as water and amines. In many cases, the quantum chemistry calculations are used to parameterize or validate force fields for molecular dynamics simulations. The results of these calculations have helped explain experimental data and contributed to the design of novel materials and sensors based on carbon nanotubes. Some of this research is described in the following papers: "Carbon nanotubes in water: structural characteristics and energetics”, J.H. Walther, R. L. Jaffe, T. Halicioglu and P. Koumoutsakos, J. Phys. Chem. B 105, 9980 (2001). “On the water-Carbon Interaction for Use in MD Simulations of graphite and Carbon Nanotubes”, T. Werder, J. H. Walther, R. L. Jaffe, T. Halicioglu and P. Koumoutsakos, J. Phys. Chem. B 107, 1345 (2003). “Quantum chemistry study of fullerene and carbon nanotube fluorination”, R. L. Jaffe, J. Phys. Chem. B 107, 10378 (2003). “Hydrophobic hydration of C60 and carbon nanotubes”, J.H. Walther, R. L. Jaffe, E. Kotsalis, T. Werder, T. Halicioglu and P. Koumoutsakos, Carbon 42, 1185 (2004). “Hydrodynamic Properties of Carbon Nanotubes”, J. H. Walther, T. Werder, R. L. Jaffe and P. Koumoutsakos, Phys. Rev. E 69, 062201 (2004). “Water-Carbon Interactions 3: The Influence of Surface and Fluid Impurities”, J. H. Walther, T. Werder, R. L. Jaffe, P. Gonnet, M. Bergdorf, U. Zimmerli and P. Koumoutsakos, Phys. Chem. Chem. Phys. 6, 1988 (2004). 90 Conference on Current Trends in Computational Chemistry 2004

Thiotepa Antitumor Drug: Theoretical Study for Predicting its Biological Activity, IR and Raman Vibrational Spectra

D. Kheffache, O. Ouamerali

Laboratoire de Chimie Théorique et Informatique, Faculté de Chimie USTHB, BP 32 El alia Bab Ezzouar

The area of quantum chemistry has developed considerably over the last decades, due to both increased computer power and efficient implementation of quantum chemical methods in computer programs. Consequently, accurate computational techniques can now be applied to much larger molecular system than before. Accurate calculations on biologically active compounds are very important in the search of the correlation between the structure and physical chemical and biological properties of such system. In this study we will present recent computational work on thiotepa drug of general formula (C2H4N)3PS. Thiotepa drug is an alkylating agent whose antitumor action consist essentially in alkylating the N7 position of guanine base in DNA. The alkylating drug thiotepa have been the subject of just few theoretical studies. The aim of the latter studies was to clarify the molecular structure of thiotepa. Kosvich et al [1] have noted a discrepancy between molecular structure in solid state (X-ray study ) and the MNDO optimized structure. Kosvich et al [1] did not specify molecular symmetry of thuiotepa. Igore Novak et al [2] reported the ab initio calculation with full geometry optimization suggesting that the molecular structures resemble a “windmill” shape corresponding to C3v symmetry with Nitrogen ion pairs (Nip) in the Trans conformation conformation vs PS bond. Another conformer with C3 symmetry have a gauche arrangement of the Nitrogen ion pair were found higher in energy than C3v. Igore Novak et al [2] have also carried out semi-empirical calculations (AM1, PM3, MNDO), all of them suggest C3 symmetry as the conformation with minimum energy. It is important to not that in the literature the crystal structure indicate the existence of distored C3 symmetry with each <(Nip)PS angle slightly different. In the present investigation a detailed theoretical study of thiotepa drug by performing ab initio and density functional type calculations utilizing 6-31G* basis set to obtain several descriptors of the electronic charge distribution such as dipole moment as well as electrostatic potential charge. A biological activity of thiotepa have been studied using the computed highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy value. The application of IR and Raman spectroscopy in structural studies of biologically active compounds is widely used. In this purpose, theoretical investigation have been made to develop an understanding of normal co- ordinates associated with the vibrational mode of thiotepa and to simulate IR and Raman spectra of thiotepa.

References [1] Marina V. Kosevixh, Vadim S. Shelkovsky, Stepan G. Stepanian., Biophysical Chemistry. 1996, 57, 123. [2] Igor Novak and Anthony W. Potts., J.Org. Chem. 1999, 64, 4201 Conference on Current Trends in Computational Chemistry 2004 91

Coherent Oscillations of Vibrational Modes in Metal Nanoshells

Arman S. Kirakosyan, Tigran V. Shahbazyan

Department of Physics, Jackson State University, Jackson, MS 39217

When laser rapidly hits nanoparticle, it launches impulsive excitation of acoustic vibrational modes. These breathing modes can be observed and monitored by using of pump-probe spectroscopy as a modulation in time of the surface plasmon (SP) resonance energy position [1, 2]. The oscillations originate from radial contractions and expansions of a nanoparticle around a new equilibrium position, while energy transfer to the surrounding dielectric matrix leads to the damping of oscillations. In solid spherical nanoparticles eigenfrequencies and decay rate inversely proportional to the nanoparticle size, although in small nanoparticles laser predominantly excites the lowest (n=0) radial mode. It can be accounted for the fact that the lowest fundamental breathing mode has best matching with initial thermal sphere expansion. In contrast to solid particles, nanoshells have two metal surfaces. This leads to a substantially different energy spectrum of acoustic vibrations. We found that two lowest modes of a nanoshell are excited by the pump pulse. These modes correspond to in-phase (n=0) and anti-phase (n=1) contractions of shell-core and shell-matrix interfaces respectively. We calculated the energy spectrum as well as the damping of nanoshell vibrational modes for stress- free metal boundaries, and found that the size-dependence of in-phase and anti-phase modes are different. In particular, in a wide range of aspect ratios, the frequency of the n=1 mode is inversely proportional to the nanoshell thickness while the lowest mode frequency is nearly independent of it, resulting in significantly longer period of the in-phase mode. We have also shown that the amplitude of the coherent oscillations is much larger in nanoshells as compared to solid particles due to a strong dependence of the SP energy to nanoshell aspect ratio.

Supported by NSF under grants DMR-0305557 and NUE-0407108, by NIH under grant 5 SO6 GM008047-31, and by ARL under grant DAAD19-01-2-0014.

References 1. N. Del Fatti et al., J. Chem. Phys. 110, 11484 (1999). 2. J . Hodak et al., J. Chem. Phys. 111, 8613 (1999). 92 Conference on Current Trends in Computational Chemistry 2004

Pre-Reactive Complexes of Open-Shell Atom + Molecule Interactions: An ab Initio Study

J. Klos,1,2 J. E. Rode,1 M. M. Szczesniak,1 and G. Chalasinski1,2

1Department of Chemistry, Oakland University, Rochester, MI 48309 2Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszawa, Poland.

The reactions of open-shell, non-zero angular momentum (2P, 3P) atoms with polar, closed shell molecules are represented by coupled potential energy surfaces with differing shapes. The long-range forces that govern remote regions of the potential energy surfaces give rise to pre- reactive van der Waals complexes. These complexes can profoundly affect the fate of chemical reactions. We have examined a number of such complexes at the ab initio level. The treatment of these systems will be described on the basis of the three paradigm systems: Cl(2P) + HCl, Br(2P) + HBr, and O(3P) + HCl. In this group of systems, the separation of adiabatic states is fairly strong due to a relatively strong quadrupole (atom) - dipole (molecule) interactions. This permits the calculations of the three lowest adiabatic surfaces using a coupled-cluster approach. Only the nonadiabatic coupling term requires the application of a multi-reference CI approach. The transformation to diabatic representation is carried out by 2x2 rotation using the transformation angle derived from calculations of the transition moment of the electronic angular momentum. All the adiabatic PESs are also properly corrected for the basis set superposition error (BSSE). The long range of the PESs, where the adiabats are nearly degenerate and no ab initio treatment is sufficiently accurate to discern among them, are described by the multipole electrostatics. The complexes of this kind necessitate the inclusion of spin-orbit coupling. Based on the recent evidence, such treatment can safely assume that the SO coupling is constant with respect to geometrical parameters. The SO coupling has profound effects on the interactions in all the three complexes. For example, the well-depths of their lowest SO-adiabats are decreased by about one half. It is concluded that the spin-free picture of these complexes (in terms of energetics, structure, zero-point motions, etc.) is incorrect and can be misleading. Conference on Current Trends in Computational Chemistry 2004 93

Catalytic Strategies of the Hepatitis Delta Virus Ribozyme as Probed by Molecular Dynamics Simulations

Maryna V. Krasovska,1 Jana Sefcikova,2 Nada Spakova, 1 Nils G. Walter,2 and Jiri Sponer1

1Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, 2Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109-1055

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme involved in the replication of a human pathogen, the hepatitis delta virus. Recent crystal structures of precursor and product forms of catalysis, together with detailed kinetic analyses, have led to hypotheses on the catalytic strategies employed by the HDV ribozyme. We have performed nine molecular dynamics (MD) simulations (~120 ns total simulation time) to test the plausibility of these hypotheses at atomic resolution. Site-specific self-cleavage requires a cytidine in position 75 (C75). Precursor simulation with unprotonated C75 reveals a rather weak dynamical binding of C75 in the catalytic pocket with spontaneous temporary formation of a H-bond between U- 1(2’OH) and C75(N3). This H-bond would be consistent with C75 acting as the general base. Upon protonation in the precursor, C75H+ moves towards its product location and establishes firm H-bonding with the catalytic pocket. However, the C75H+ – G1(O5’) H-bond that would be expected for C75 acting as the general acid was precluded, at least at the present simulation timescale. The adjacent loop L3 appears to serve as a flexible structural element, possibly gated by a G:U base pair, to facilitate this C75H+ induced conformational switch. L3 also controls the electrostatic environment of the catalytic core, which in turn likely modulates metal ion binding and C75 base strength. We find that a distant RNA tertiary interaction involving a protonated cytidine (C41) is instable when unprotonated, leading to detrimental conformational rearrangements in the catalytic core. Initially, a Na+ attempts to compensate for the loss of the protonated hydrogen bond, however, the Na+ insertion is not stable. The observed structural dynamics of the HDV ribozyme is complemented by a network of cation binding sites and a wide range of structurally important long-residency hydration sites, many of them occurring in the area of the catalytic pocket. 94 Conference on Current Trends in Computational Chemistry 2004

Theoretical Studies of Pyridoxal-5’-Phosphate Methylamine Schiff Base Isomers

G. M. Kuramshinaa and H. Takahashib

aFaculty of Chemistry, Moscow State University (M.V.Lomonosov)Moscow 119992, Russia bDepartment of Chemistry, School of Science and Engineering, Waseda University, Tokyo 160-8555, Japan

An interest to the structure of the pyridoxal-5’-phosphate (PLP) itself and its derivatives (Vitamin 6 analogs) is initiated by the breakthrough role of this compound in the biological processes where it acts as coenzyme catalyzing different reactions involved in the metabolism of amino acids. Among possible derivatives the most interesting is the PLP methylamine Schiff base as a final product of the releasing of the amino group of the Lys residue. Application of the photochemistry to the investigation of PLP methylamine leads to the photoreactions which yield the transients of the unknown structure. The knowledge on the structure and relative stability of possible PLP methylamine Schiff base isomers is necessary for the identification of such photoreaction products as well as for clarification of the mechanism for the transamination reaction. However, to our knowledge, complete vibrational studies of this compound have not been reported and no quantum mechanical predictions of the vibrational spectra of PLP methylamine Schiff base isomers have been carried out. The goal of this work was to carry out modern level quantum mechanical calculations of different stable isomers of PLP methylamine for determining the stable configurations, their relative stability energies and structural and spectral features of different conformations which can be associated with resonance Raman spectra components and can be used for the assignment of the PLP methylamine photoreaction products. Molecular orbital calculations were carried out using the Gaussian 94 and Gaussian 03 program systems. The fully optimized geometries for six isomers I-VI (I – trans-enol form, II- cis(a)-enol form, III- cis(b)-enol form(b), IV – keto(+)-form, V – keto(-)-form, VI – zwitterionic form) of PLP methylamine were calculated with the 6-31G*, 6-31+G* and 6-31+G** basis sets at the HF and B3LYP levels of theory. The minima of the potential surface were found by relaxing the geometric parameters with the standard optimization methods. Analytical force constants were derived and harmonic vibrational frequencies were calculated using all investigated theoretical levels. The optimized conformations and their relative energies (in kcal/mol) with corresponding dipole moments (in D) are shown in Figure 1.

I: 0.0 (µ=2.576) IV: 2.60 (µ=4.467) Conference on Current Trends in Computational Chemistry 2004 95

II: 14.26 (µ=0.744) V: 13.60 (µ=5.152)

III: 16.20 (µ=3.021) VI: 13.00 (µ=4.735)

Figure 1. Optimized B3LYP/6-31 G* structures of PLP methylamine, their relative energies (in kcal/mol) and dipole moments (in D).

Acknowledgement. Support from the exchange program between Waseda and Moscow State Universities is gratefully acknowledged. GMK thanks the RFBR-YUGRA grant No 03-07-96842 for partial financial support. 96 Conference on Current Trends in Computational Chemistry 2004

Predicting Vibrational Spectra of Large Molecules within Combined Approach Based on the Joint Use of Theoretical and Empirical Methods

G.M. Kuramshinaa, E. Ōsawab

aFaculty of Chemistry, Moscow State University (M.V.Lomonosov) Moscow 119992, Russia bNanoCarbon Research Institute, 1080 Yabutsuka, Chosei-mura, Chosei-gun Chiba 299-4395, Japan

The importance of large molecular systems (biological objects, polymers, giant aggregates etc.) stimulates the development of special approaches for (the) describing their physicochemical properties such as molecule geometry, vibrational frequencies, and thermodynamic functions (etc). Fast growing computational resources and numerical methods leads to the great advantage of modern methods of quantum chemistry for the solving many problems of structural chemistry in application to the large molecular systems. But there are also existed obvious severe limitations of using purely ab initio methods for the analysis of molecular systems consisting of a few hundred atoms. In cases where such systems are organized from separate smaller size units the most successful approaches for their analysis are as a rule based on the joint use of theoretical results (e.g. ab initio or DFT data obtained for these chosen unites) with some empirical approach (e.g. molecular mechanics) and in many cases result in good descriptions of investigated systems. Solving such problems require the knowledge of molecular force fields which can be obtained as within purely empirical approach based on experimental frequencies so within the joint treatment of quantum mechanical and experimental data using some force field model. At the present one of the most popular force field models is based on the introducing the scaling factors. Otherwise it is also possible to use some modification of harmonic force constant matrix. While the problem of finding the force constants or scaling factors is formulated as fitting the experimental frequencies it leads to the solving the inverse vibrational problem, which belongs to a class of nonlinear ill-posed problems. The modern numerical methods for solving such problems are based on the theory of regularization [1] and as the result we have so-called regularized quantum mechanical force field (RQMFF) or regularized scaled quantum mechanical force field (RSQMFF). Here we demonstrate the application of this approach to the normal coordinate analysis of C240 fullerene molecule (Ih symmetry) presented in Fig. 1. Conference on Current Trends in Computational Chemistry 2004 97

Figure 1. Schematic illustration of C240 molecule

The molecular geometry of C240 was optimized at the HF/STO-3G level. The equilibrium configuration of the icosahedral (Ih) symmetry molecule C240 is completely defined by five bond lengths shown in the figure 2. Their optimized values are given in a Table 1 in comparison with experimental data on corannulene C20H10 and fullerene C60.

E D C

B

A

: Figure 2. Five types of bond lengths in C240.

This geometry was used for the normal coordinate analysis of C240. To perform the calculations for this molecule we introduced 1080 of internal coordinates consisting of 360 bond- stretching coordinates and 720 bond angles. Altogether 1080 redundant coordinates were introduced, only 714 of them being independent. Internal coordinates were optimized automatically with the help of special utility in the SPECTRUM program package [1], which now is a part of the developing data base [2] The list of 90 different force constants for C240 were extended by certain model assumptions on intraball forces on a base transferred from the regularized force constant matrices (RQMFF) of C60 and corannulene molecules. 98 Conference on Current Trends in Computational Chemistry 2004

Table 1. Optimized geometry parameters of C240. C240 C60 C20H10 Bond (Å) HF/STO-3G X-Raya X-Rayb EDc B3LYP/6-31G*c a R(A) 1.4336 1.432 1.419 1.410 1.417 R(B) 1.3685 1.388 1.396 1.408 1.385 R(C) 1.4581 1.441 1.448 R(D) 1.4132 1.444 1.374 1.390 R(E) 1.4320

a J.M.Hawkins et al. Science 1991, 252, 312. b J.C.Hanson, C.E.Nordman. Acta Crystallogr. 1976, B32, 1147. c L. Hedberg et al. J. Phys. Chem. A 2000, 104, 7689

The 714 normal vibrations of C240 are distributed by irreducible representations as

7Ag + 5Au + 16F1g + 18F1u + 17F2g + 19F2u + 24Gg + 24Gu + 31Hg + 29Hu

The symmetry properties allow one to reduce the complete force constant matrix of C240 into 10 blocks with orders varying from 6 to 48 in redundant symmetry coordinates. Symmetry coordinates were run by means of the SYMM program included into the SPECTRUM program package. The vibrational density plots (a distribution of calculated frequencies by a wavenumber scale) for fullerene C240 are presented in Fig. 3. There are two plots for vibrations with different inversion symmetry (g and u), one referring to the total number of frequencies active in the Raman spectrum, while the other to frequencies active in the infrared absorption spectrum. These frequencies were used for the calculation of the thermodynamic functions of C240 in the 100- 2000 K temperature region (Table 2).

→ ω, cm-1 Fig. 3. Vibrational state density for C240 molecule in the infrared absorption region between 100 and 1650 cm-1. Conference on Current Trends in Computational Chemistry 2004 99

Table 2. Thermodynamic properties of C240

T K C J/(K*mol) F J/(K*mol) S J/(K*mol) HT-H0 kJ/mol 100.00 812.643 451.228 744.299 29.307 200.00 1764.340 814.276 1619.183 160.981 300.00 2535.696 1227.608 2483.138 376.659 400.00 3220.793 1645.542 3308.904 665.345 500.00 3787.296 2057.205 4090.837 1016.816 600.00 4229.931 2457.823 4822.236 1418.648 700.00 4567.916 2844.693 5500.847 1859.308 800.00 4825.301 3216.448 6128.385 2329.550 900.00 5022.748 3572.650 6708.622 2822.375 1000.00 5175.961 3913.459 7246.090 3332.631 1100.00 5296.468 4239.391 7745.288 3856.486 1200.00 5392.495 4551.151 8210.409 4391.109 1300.00 5469.990 4849.536 8645.200 4934.363 1400.00 5533.287 5135.373 9052.969 5484.634 1500.00 5585.555 5409.460 9436.560 6040.651 1600.00 5629.157 5672.572 9798.486 6601.463 1700.00 5665.872 5925.432 10140.879 7166.260 1800.00 5697.063 6168.723 10465.637 7734.446 1900.00 5723.743 6403.061 10774.385 8305.515 2000.00 5746.747 6629.033 11068.569 8879.072

Acknowledgement. GMK thanks the RFBR-YUGRA grant No 03-07-96842 for partial financial support.

References 2. A.G.Yagola, I.V.Kochikov, G.M.Kuramshina, Yu.A.Pentin. Inverse problems of Vibrational Spectroscopy. VSP. Zeist, The Netherlands, 1999. 3. I.V.Kochikov, G.M.Kuramshina, L.M.Samkov. A hybrid database on spectral data: reference and research tool. In 20th Austin Symposium on Molecular Structure, Austin, March 7-9, 2004, p.100. 100 Conference on Current Trends in Computational Chemistry 2004

An ECP Basis Set for Accurate Polarizability Calculations

Nicholas P. Labello, Antonio M. Ferreira, Henry A. Kurtz

Department of Chemistry, University Of Memphis, Memphis TN 38152

Effective core potentials (ECPs) are often used for molecular geometry optimizations and energy calculations when the equivalent all-electron studies are difficult or impossible due to high computational cost. The SBKJC1 ECP and basis set is an example of a small valence basis set that utilizes relativistic ECPs to model core electrons and is optimized to give good energies and geometries. The aim of this work is to extend the capabilities of the SBKJC basis set to optical calculations by developing an appropriate augmentation scheme. Basis set selection is extremely important for accurate non-linear optics (NLO) calculations. The necessary characteristics of a basis set used for determining NLO properties differ from those for energy and geometry calculations2. Diffuse and polarization functions are needed to describe the response of an electron to an electrical field. Polarization functions allow symmetry breaking, whereas diffuse functions allow for redistribution of the electron density3. The Sadlej4 basis set is a very effective basis that builds both of these properties into an implementation capable of quantitatively matching experimental results for polarizabilities and some hyperpolarizability properties. It is often used in benchmarking polarizability calculations. Our goal is to produce a basis set capable of Sadlej-quality polarizability results that requires one to several orders of magnitude less CPU time. Target atoms include 90+ elements (H – Rn, La – Lu, Ac – U). TDHF polarizability calculations have been performed with both the Sadlej and new polarized ECP basis set for molecules where both basis sets are available. The polarizabilities are found to be in excellent agreement, while taking a fraction of the time with our new basis set. These calculations and a full comparison of results will be presented along with additional methodological details.

References [1] W. J. Stevens, H. Basch, M. Krauss, J. Chem. Phys., 81, 6026 (1984). [2] H. A. Kurtz, D. S. Dudis, “Reviews in Computational Chemistry”, 12, 241 (1998). [3] A. M. Ferreira, “Theoretical Investigations of the Structure and Properties of Point Defects in Amorphous Silicon Dioxide”, The University of Memphis, (2000). [4] A. J. Sadlej, Collec. Czech. Chem. Commun. 53, 1995 (1988). Conference on Current Trends in Computational Chemistry 2004 101

Nucleic Acid Recognition

Richard Lavery

Laboratoire de Biochimie Théorique CNRS UPU 9080 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie, France 75005

Molecular modeling and simulation have provided new insights into the way base sequence affects not only the structure, but also the mechanics of the DNA double helix. This information, which is difficult to obtain experimentally, is important in understanding how DNA is recognized by other biological molecules and, most notably, by proteins. In order to test how local mechanics can be exploited by proteins, we have developed a modeling technique related to the sequence threading algorithms used in identifying protein folds. This approach enables us to estimate protein binding energies for millions of base sequences with little computational effort and to generate consensus sequences which agree well with experiment. A more detailed analysis of the results for a wide variety of complexes leads to a new classification of recognition mechanisms and also points to weaknesses in current methods for searching for protein binding sites within genome sequences. 102 Conference on Current Trends in Computational Chemistry 2004

Ambiguity of Definition of Atomic Charges in Cytizine Molecule

M.G. Levkovich

Institute of the Chemistry of Plant Substances, Academy of Sciences, 700170, Tashkent, H. Abdullaev st., 77 Uzbekistan

The properties of each molecule must be formed by simple physical parameter set, which characterise the structure of a molecule. The simplest parameter is the electric atomic charge. This notion is very wide-spread in chemistry. However, it still doesn’t have any clear definition. It is impossible to measure it by experiment. Quantum calculation results are also ambiguous. The application of molecular modelling methods for definition of atomic charges indicates essential divergence. In this work we have calculated the atomic charges in cytizine molecule, which is the typical alkaloid molecule. We used six most modern methods of calculating of charges: Mulliken population analysis (MPA), NPA, CHELP, CHELPG, Merz-Singh-Kollmann and AIM. The calculation was performed in gas phase at ab initio level applying B3LYP/6-311+G (2d, p)//HF/3-21G (d) basis set.

The results showed considerable dispersion of the results. It is interesting, that not only heteroatoms were difficult for calculation, but some carbon atoms too. The selection of the Conference on Current Trends in Computational Chemistry 2004 103

optimal method for classic chemical purposes was made from comparison of our results and typical properties of cytizine. From our investigation we are able to make the following conclusions. At first, it is important to differentiate the notion of atomic charge for physical or chemical purposes. For physical purposes the topologic distribution of electron density inside the molecule is more important. Hence the optimal method is AIM technology. However, for chemical problems the condition of external electrostatic fields is essential. This represents the external face of the molecule. In this case electrostatic methods give the best results. Thus for calculations of atomic charges in alkaloid molecules for typical chemical purposes we recommend the CHELPG- method as the best one. Secondly, we have established that is better to calculate the hard-atomic charge as the sum of both hard-atoms’ and attached hydrogen atoms’ charges. 104 Conference on Current Trends in Computational Chemistry 2004

Electronic Structure, Bonding, and Properties of Unligated and Ligated ManganeseII Porphyrins and -Phthalocyanines

Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang*

Department of Chemistry, P.O. Box 17910 Jackson State University Jackson, MS 39217

Metal porphyrins (MPors) are interesting species because of their great biological importance and the unique nature of their coordination chemistry. As the active centers or prosthetic groups of hemoproteins, iron porphyrins have been extensively studied, both experimentally and theoretically. In the meantime, much experimental work has now been done for the analogous manganese complexes. MnPors have been of particular interest in many fields concerning, for example, NMR image enhancement agents, nonlinear optical materials, DNA binding and cleavage agents, radio-diagnostic agents, foodstuff anti-oxidants, and P-450 cytochrome mimics. In contrast to iron porphyrins, there have been rather few theoretical studies of manganese complexes. The electronic structure of the MnII porphyrins is not well understood yet. From early EHMO calculations [1], a free MnPor molecule is predicted to have a quartet ground state. However, a solid sample of manganese tetraphenylporphine (MnTPP) [2] has a magnetic susceptibility indicative of a high-spin configuration (effective magnetic moment µeff = 6.2 µB). Since the EHMO method is rather approximate and only limited to a qualitative analysis based on orbital energies, we think that more accurate calculations on MnPor are most desirable. Metal phthalocyanines (MPcs) are another class of fascinating compounds that have found important applications in many fields of science and technology. One of the more interesting scientific applications of MPcs is the modeling of biologically important porphyrin-like species. In this regard, MnPc is particularly useful. Although it is generally thought that MPors and MPcs show closely similar behavior, they have many important differences which are exhibited in a striking fashion by the manganese complexes [3]. One major difference between MnPor and MnPc is related to the different spin states of both complexes: the phthalocyanine forms an intermediate-spin four-coordinate planar complex, while the porphyrin is a high-spin complex that is most likely non-planar. It would be of interest to make a comparison between MnPors and MnPcs. On the other hand, some issues and fine details remain to be addressed with MnPcs. From early magnetic susceptibility measurements of MnPc in a crystal [4], the four-coordinate 4 2 2 1 complex has predominantly a A2g ground state arising from the (b2g/dxy) (eg/dπ) (a1g/dz2) configuration. But later magnetic circular dichroism (MCD) and ultraviolet-visible (UV-Vis) 4 spectroscopy measurements of MnPc in an argon matrix [5] indicated a Eg ground state that 1 3 1 4 corresponds to the (dxy) (dπ) (dz2) configuration. A A2g ground state for MnPc was suggested to be a consequence of intermolecular interactions in the crystal [6]. There is also a question as to the electronic structure of the six-coordinate complex of MnPc with pyridine (py), MnPc(py)2. Recently, Janczak et al. [7] reported an X-ray determination of solid MnPc(py)2 and performed a magnetic susceptibility measurement. They argue that their evaluated effective magnetic moment µeff of ~3.62 µB indicates three unpaired electrons (S = 3/2) and they assign MnPc(py)2 a 2 2 1 (dxy) (dπ) (dz2) ground state configuration. This is different from the results of electron spin resonance (ESR) and magnetic measurements [8], which “unequivocally” show the complex to be low spin (where µeff = 1.6 µB). We note that the axial bond length Mn-N(ax) in solid MnPc(py)2 is only 2.114 Å, much smaller than the Co-N(ax) bond length (2.340 Å) in CoPc(py)2 Conference on Current Trends in Computational Chemistry 2004 105

[7], where an unpaired electron in the 3dz2 orbital is responsible for the rather long Co-N(ax) bond. The observed Mn-N(ax) bond length in MnPc(py)2 argues strongly against occupation of the σ-antibonding 3dz2; i.e. an intermediate-spin ground state is incompatible with the observed Mn-N(ax) bond length in MnPc(py)2, which requires a low-spin ground state. The nature of the reduced products of MnPc(py)2 also remains unclear. The electrochemistry of manganese phthalocyanines has received a good deal of attention and may involve both the central metal and the Pc ring [8-11]. The electronic structures of the oxidized and reduced species were analyzed through their optical spectra [8-11], but no definite conclusions could be drawn about the ground state configurations of some of the ions. We have therefore performed a detailed DFT study of unligated as well as ligated MnII porphyrins and -phthalocyanines. The following main conclusions can be drawn from the results:

(1) While MnTPP in the crystal structure is high spin (S = 5/2) with the MnII atom out of the porphyrin plane [2], the free MnPor molecule has no obvious tendency to distort from planarity even in the high-spin state. The ground state of the planar structure is an intermediate-spin (S = 3/2) state, as previous EHMO calculations suggested [1]. It is possible that the high-spin state of MnTPP in the crystal is induced by significant intermolecular interactions which effectively change the coordination number of the metal and also draw the metal out of the porphyrin plane. 4 (2) The free MnPc molecule is calculated to have a Eg ground state arising from the 1 3 1 (dxy) (dπ) (dz2) configuration, in agreement with the more recent MCD and UV-Vis measurements of MnPc in a argon matrix [5], but different from the early magnetic 4 measurements of crystal MnPc [4] which yielded a A2g ground state arising from the 2 2 1 (dxy) (dπ) (dz2) configuration. Since in the crystal, there are N-atoms of adjacent parallel molecules lying ∼3.4 Å above and below the metal atom, this was suggested to be the reason for 4 a A2g ground state in the crystal. A calculation on a model system MnPc⋅⋅⋅(HCN)2 shows that 4 weak axial ligation indeed lowers the relative energy of A2g notably, but is not able to change 4 4 the energy order between the Eg and A2g states. Other intermolecular effects may also need to be considered in order to account for the ground state of solid MnPc. (3) The first oxidation of MnPc occurs at the central metal, in contrast to the macro-ring oxidation in the FePc analog. The electronic properties of MnPc differ somewhat from those of MnPor due to the presence of benzo groups and shorter Mn-N(eq) bond lengths in the former molecule. (4) Upon complexation of two axial py ligands to MnPor/Pc, the MnII ion becomes low spin 1 4 (S = 1/2), having a ground state configuration of (dxy) (dπ) . The calculated geometry parameters in MnPc(py)2 at this low-spin state are in good agreement with the X-ray crystal structure data 2 2 1 [7]. The recent assignment of this complex as an intermediate-spin (dxy) (dπ) (dz2) ground state [7] is questionable. − (5) The [MnPor/Pc(py)2] ion results from the addition of an electron to a d-orbital of the metal, and so it is a closed-shell system. This result is consistent with the ESR measurement [8], and argues against the first reduced product of MnPc(py)2 involving reduction of the Pc ring [8]. (6) When one py is removed from MnPor/Pc(py)2, the other py then “pulls” the metal out of the plane toward itself in order to avoid strong repulsion forces with the P/Pc nitrogen atoms. In this case the Mn dx2-y2 and dz2 orbital energy levels are lowered significantly. For MnPor, the dx2-y2 orbital is lowered enough to be occupied, and so this five-coordinate molecule becomes high spin. But the smaller core size of Pc results in less lowering of the dx2-y2 energy level, and so MnPc(py) is an intermediate-spin system. (7) While the MnPor−py bond strength [in MnPor(py)] is comparable to that of MnPc−py, the MnPor−(py)2 binding energy is notably smaller than that of MnPc−(py)2. This may be one of 106 Conference on Current Trends in Computational Chemistry 2004

the reasons why in solution, MnPc picks up two solvent molecules (L) to form a six-coordinate II MnPc(L)2 complex, while five-coordination of Mn prevails for manganese porphyrins [2].

References [1] Zerner, M.; Gouterman, M. Theoret. Chim. Acta 1966, 4, 44. [2] Gonzalez, B.; Kouba, J.; Yee, S.; Reed, C. A.; Kirner, J. F.; Scheidt, W. R. J. Am. Chem. Soc. 1975, 97, 3247. [3] Boucher, L. J. Coord. Chem. Rev. 1972, 7, 289. [4] Barraclough, C. G.; Martin, R. L.; Mitra, S.; Sherwood, R. C. J. Chem. Phys. 1970, 53. [5] Williamson, B. E.; VanCott, T. C.; Boyle, M. E.; Misener, G. C.; Stillman, M. J.; Schatz, P. N. J. Am. Chem. Soc. 1992, 114, 2412. [6] Reynolds, P. A.; Figgis, B. N. Inorg. Chem. 1991, 30, 2294. [7] Janczak, J.; Kubiak, R.; Śledź, M.; Borrmann, H.; Grin, Y. Polyhedron 2003, 22, 2689. [8] Lever, A. B. P.; Minor, P. C.; Wilshire, J. P. Inorg. Chem. 1981, 20, 2550. [9] Clack, D. W.; Yandle, J. R. Inorg. Chem. 1972, 11, 1738. [10] Minor, P. C.; Gouterman, M.; Lever, A. B. P. Inorg. Chem. 1985, 24, 1894. [11] Lin, C.-L.; Lee, C.-C.; Ho, K.-C. J. Electroanal. Chem. 2002, 524, 81. Conference on Current Trends in Computational Chemistry 2004 107

Efficient Implementation of Effective Core Potentials and COSMO Solvation Model for the Parallel Calculation of NMR Chemical Shift within the GIAO Method

Massimo Malagoli,1 Jon Baker,1 and Krzysztof Wolinski1,2

1Parallel Quantum Solutions, 2013 Green Acres Road Suite A, Fayetteville, Arkansas 72703 2Department of Chemistry, Maria Curie-Sklodowska University, Lublin, Poland

We have recently extended the capabilities of the PQS ab-initio software to include Effective Core Potentials (ECP) and the COSMO solvation model. In addition to the calculation of molecular energies, geometries, and vibrational frequencies, these methods can also be used to compute the NMR chemical shift within the Gauge-Including Atomic Orbital (GIAO) framework. Calculations can be performed at the Hartree-Fock or at the Density Functional Theory level using a variety of functionals.

The computation of the COSMO contributions to energy, gradient and NMR chemical shift is fully parallelized. This, in addition to the customary parallelilazion of the HF and DFT steps, improves the speed and the efficiency of the algorithm. Our implementation is designed for low parallelism (4-16 CPUs), and can routinely handle systems with up to 100+ atoms and 1000+ basis functions.

Results are presented for a variety of systems, including organic molecules, organometallics and transition metal complexes. 108 Conference on Current Trends in Computational Chemistry 2004

The Transfer Hamiltonian: Application to Energetic Materials

Joshua J. McClellan and Rodney J. Bartlett

Quantum Theory Project, University of Florida Gainesville, Florida 32611-8435, USA

Using semi-empirical neglect of diatomic differential overlap (NDDO) methods, such as AM1 and PM3, in non-equilibrium cases gives incorrect behavior for energies, forces, and geometries. Therefore the use of such techniques to do molecular dynamics (MD) can and will lead to incorrect results. Alternatively, one may perform high level ab initio calculations and obtain forces that give correct behavior, but, these methods are too expensive and therefore currently impractical for MD. It is possible to build a NDDO transfer Hamiltonian that reproduces a set of reference properties, such as forces, calculated from high level ab initio theory. The transfer Hamiltonian method gives credence to the fact that a one-particle reference method, e.g. NDDO, DFT, etc., can reproduce the correct answer given that a proper Hamiltonian is found.

The current implementation of the transfer Hamiltonian involves a quasi-Newton optimization algorithm used in tandem with a genetic algorithm to fit NDDO parameters to reproduce the forces determined at the coupled cluster level of theory. Presented in this poster will be the application of this procedure to energetic materials. Parameter sets were trained using nitromethane and dimethylnitramine as the fundamental units. These new parameter sets reproduce the reference CCSD/DZP forces for C-N and N-N bond breaking well. These new NDDO parameterizations will allow for unprecedented accuracy in MD simulations for these systems, as well as systems for which they are major components. Conference on Current Trends in Computational Chemistry 2004 109

The Molecular Geometry of Boron Tetracyclo (6.1.0.02,4.05,7) Nonane Using Gaussian 2003

James L. Meeksa, Harry B. Fanninb

aWest Kentucky Community & Technical College, Department of Physics PO Box 7380 Paducah, Kentucky 42002-7380, bDepartment of Chemistry Murray State University Murray KY 42071

The insertion of a Boron atom into tetracyclo (6.1.0.02,4.05,7) nonane gives a “caged” molecule with the Boron atom in the center of the molecule, s-C9H9B. The s-C9H9B molecule with the use of the symmetry option keeps the starting geometry of the model. When the symmetry function is not used, the s-C9H9B (D3h) molecule undergoes a molecular rearrangement into a non-symmetrical molecule, n-C9H9B of C2v symmetry with the ab initio computations of Gaussian 2003.

The RHF/6-31G** and B3LYP /6-31G** basis sets of Gaussian 2003 were used for final optimizations. The geometries of both molecules, s-C9H9B and n-C9H9B, will be discussed. The changes of the molecular energies, bond distances and angles are compared with computations of Gaussian 98.

110 Conference on Current Trends in Computational Chemistry 2004

Theoretical Study of Adsorption of 1-Methylcytosine on Substituted and Hydrated Surface of Dickite

A. Michalkova, A. D. Fortner, L. Gorb, J. Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA

Methyl-cytosine (MeC) is a molecule that could mimic the corresponding nucleotide in DNA or RNA molecules. It is a pyrimidine derivative consisting of a single six member ring, containing both nitrogen and carbon atom, and an amino group. The presence of methylcytosine in human DNA has genetic and epigenetic effects on cellular development, differentiation, and neoplastic transformation. Methylcytosine differs from cytosine by the presence of a methyl group at the position of the pyrimidine ring. Methylcytosine is formed after replication by addition of a methyl group to a cytosine already present in the DNA strand. It is known that the conformational behavior and function of DNA are often influenced by the presence of metal ions. Cation-base interactions are involved in many important biophysical processes such as the stabilization of DNA triple and quadruple helices. Recent data suggest that ionization may be relevant in determining mutagenic properties of analogues of nucleic acid bases. The stability and conformational integrity of nucleic acids are largely controlled by the interactions with surrounding water molecules. Previous studies using X-ray diffraction and infrared and ultraviolet spectroscopy have shown that hydration water is necessary for maintaining the structural integrity of the DNA molecule. It was found that the interactions of cytosine with water change the order of the relative stability of cytosine tautomers and results in significant changes of geometry. Dickite, a chosen model of clay minerals, has the same formula as kaolinite, nacrite and halloysite Al2Si2O5(OH)4 but a different crystal structure. It is a kaolinite polymorph and, as such, is a 1:1 aluminous dioctahedral phyllosilicate (clay) mineral. The adsorption of 1-methylcytosine on the hydrated octahedral and tetrahedral surface of dickite was studied using the density functional theory in conjunction with the B3LYP functional applying the 6-31G(d) basis set. The models of dickite consist of one fragment of the 1:1 layer of dickite having one silicon-oxygen ring from the tetrahedral sheet or one aluminum-oxygen ring from the octahedral sheet. Dangling bonds of the mineral fragment were saturated by hydrogen atoms. The Na+ cation was placed above the ring to compensate the negative charge which arises as a consequence of the substitution of Si atom for Al atom in the tetrahedral sheet and of Al atom by Mg atom in the octahedral sheet of dickite. The MeC molecule was fully optimized while the geometry of the tetrahedral mineral part was kept frozen. In the case of the adsorption on the octahedral surface the target molecule and six hydrogen atoms of the surface hydroxyls were allowed to relax. We have calculated the interaction energy corrected by the basis set superposition error. We have studied the interactions between MeC and the mineral, changes in the geometrical parameters and electron density during the adsorption. The topological characteristics of the electron density distribution were obtained following Bader’s “Atoms in Molecules” approach (AIM). We have found the position and orientation of MeC on the surface of dickite in the presence of the cation and water molecule. The target molecule is almost parallel with the surface plane. MeC is mostly stabilized on the surface by the ion-dipole interactions between the cation and the oxygen atom of MeC. Hydrogen bonds formed between the target and water molecule provide an Conference on Current Trends in Computational Chemistry 2004 111

additional stabilization of this molecule on the surface. The adsorption of MeC on the surface of dickite results in changes of the geometry and polarization of MeC.

Figure 1. The structure of 1-methylcytosine adsorbed on the substituted tetrahedral surface of dickite in the presence of water molecule and the Na+ cation. 112 Conference on Current Trends in Computational Chemistry 2004

A Simple Calculational Model for Predicting the Site for Nucleophilic Substitution in Aromatic Perfluorocarbons

Max Muir1 and Jon Baker2,3

1FQubed, 6330 Nancy Ridge Drive, Suite 107, San Diego California 92121 2Department of Chemistry, University of Arkansas Fayetteville, Arkansas 72701 3Parallel Quantum Solutions, 2013 Green Acres Road, Suite A Fayetteville, Arkansas 72703

We present a simple model for predicting the principal site for nucleophilic substitution in aromatic perfluorocarbons. Our model is based on the relative stabilities of the Meisenheimer complexes as calculated using density functional theory with a modest basis set. (Hartree-Fock theory will do just as well.) Although such calculations were essentially impossible to carry out when early theoretical work on this topic was undertaken in the mid-1960s and early 1970s, they are now routine and full geometry optimization for any of the systems studied in this work can be completed in a matter of minutes with modern quantum chemistry programs and computational hardware. Predictions from our model agree with experimental observations for 16 aromatic perfluorocarbons, and – together with additional NMR calculations - lead us to conclude that the earlier prediction that perfluoroanthracene undergoes nucleophilic substitution in the 2-position is incorrect, and is based on a misinterpretation of the experimental 19F NMR spectrum. Conference on Current Trends in Computational Chemistry 2004 113

Solving the Schrödinger Equation: Analytical Wave Functions of Atoms and Molecules

Hiroshi Nakatsuji

Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano-Nishihiraki-cho, Sakyou-ku, Kyoto 606-8103, Japan

To develop a general theory of solving the Schrödinger equation is a central theme of theoretical chemistry: it has a huge scientific and practical importance. Since 2000, we have investigated the structure of the exact wave functions and proposed the methods of solving the Schrödinger equation. For analytical solutions, the singularity problem caused by the nuclear and electron potentials was solved by introducing the scaled Schrödinger equation. We formulate the ICI (iterative CI) method as a general systematic method of calculating the exact wave functions of atoms and molecules in analytical forms. Applications to several atoms and molecules are satisfactory, showing a high potentiality of the proposed method.

References [1] H. Nakatsuji, J. Chem. Phys. 113, 2949 (2000). [2] H. Nakatsuji and E. R. Davidson, J. Chem. Phys. 115, 2000 (2001). [3] H. Nakatsuji, J. Chem. Phys. 115, 2465 (2001). [4] H. Nakatsuji, J. Chem. Phys. 116, 1811 (2002). [5] H. Nakatsuji and M. Ehara, J. Chem. Phys. 117, 9 (2002). [6] H. Nakatsuji, Phys. Rev. A 65, 052122 (2002). [7] H. Nakatsuji, Phys. Rev. Lett. 93, 030403 (2004). 114 Conference on Current Trends in Computational Chemistry 2004

Theoretical Studies of Prototypical Thiyl Peroxyl, Sulfonyl, and Sulfonyl Peroxyl Radicals†

Brian Napolion and John D. Watts

Department of Chemistry and Center for Molecular Structure and Interactions P. O. Box 17910, Jackson State University, Jackson, MS 39217

Thiols (RSH) serve as antioxidants in biological systems by reacting with a variety of free radicals. These reactions produce thiyl radicals, which themselves must be quickly removed. Otherwise, thiyl radicals might generate a series of potentially cytotoxic oxygen, sulfur, and oxysulfur radicals. These include thiyl peroxyl radicals (RSOO), sulfonyl radicals (RSO2), and the sulfonyl peroxyl radicals (RSO2OO). Reaction schemes for the production of these species have been proposed, although the presence of these radicals in biological systems has not been established. Thiyl peroxyl and sulfonyl radicals may also play a role in atmospheric chemistry. For example, species with R = H may be relevant to reactions of SH and O2. Since experimental studies of these radicals are difficult, we are applying ab initio quantum chemical methods in order to obtain structural, energetic, and other properties of the aforementioned radicals with R = H and CH3. These studies are seeking to provide reliable characterizations of the radicals, particularly thermodynamic and kinetic data that will help us to assess the viability of these species. The initial focus is on the smaller species, for which calculations with coupled-cluster methods, particularly CCSD(T), are possible. As well as unrestricted Hartree-Fock reference determinants, restricted open-shell Hartree-Fock reference determinants are being used. Density- functional theory calculations are also being performed for comparison, since DFT methods may be applied to larger, more representative systems.

† This work is supported by the Louis Stokes Mississippi Access to Minorities Program (LS- MAMP) and the National Institutes of Health (S06 GM08047). Conference on Current Trends in Computational Chemistry 2004 115

Conventional Strain Energy in the Thiazetidines and the Thiadiazetidines

Adria Neely and David H. Magers

Computational Chemistry Group Mississippi College Department of Chemistry and Biochemistry Clinton, Mississippi

The conventional strain energies of 1,2-thiazetidine (Figure 1), 1,3-thiazetidine (Figure 2), cis-1,2,3-thidiazetidine (Figure 3.), trans-1,2,3-thiadiazetidine (Figure 4.), cis-1,2,4- thiadiazetidine (Figure 5.), and trans-1,2,4-thiadiazetidine (Figure 6.) are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory (DFT). The DFT functional employed is Becke’s three parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple-zeta quality on valence electrons, are employed: 6-311G(d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Finally, the calculated strain energies are compared to those of cyclopropane, cyclobutane, the oxazetidines, and the oxadiazetidines. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).

Figure 1. 1,2-thiazetidine Figure 2. 1,3-thiazetidine

116 Conference on Current Trends in Computational Chemistry 2004

Figure 3. cis-1,2,3-thiadiazetidine Figure 4. trans-1,2,3-thiadiazetidine

Figure 5. cis-1,2,4-thiadiazetidine Figure 6. trans-1,2,4-thiadiazetidine Conference on Current Trends in Computational Chemistry 2004 117

Post Hartree Fock Study of the Structure, Vibrational Spectra, and Energetics of XBr and XBr+ (X=H, F, Cl, Br)

Paul Nkansah,1 V. R. Morris2, J. S. Francisco,3 J. Edwards4

1Department of Chemical Engineering, Howard University, Washington, DC 20059-0001 2Department of Chemistry, Howard University, Washington, DC 20059-0001, 3Department of Chemistry, Purdue University, West Lafayette, IN 47907-1393, 4Department of Chemistry Florida A&M University, Tallahassee, Florida 32307.

The geometrical structures and vibrational frequencies of HBr, FBr, ClBr, and Br2 and their corresponding cations have been computed using fourth-order Møller-Plesset perturbation theory, coupled-cluster methods (CCSD, CCSDT), and quadratic configuration interaction (QCISDT and QCISDTQ) with extensive basis sets. The overall root-mean square deviation from the experimental bond lengths is 0.02Å. Although the CCSD/6-311+G (3df) results are found to yield the best agreement for both geometrical and vibrational frequencies, the MP4 and CCSD(T) methods are found to give better general agreement with experiment. 118 Conference on Current Trends in Computational Chemistry 2004

The Theoretical Investigation of Potential Energy Surface of CL-20 Degradation Process

S. Okovytyy,1,2 Y. Kholod,1,2 M. Qasim,3 H. Fredrickson3 and J. Leszczynski2

1Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 2Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA 3US Army ERDC, Vicksburg, Mississippi, 39180, USA

High-energy density materials play an important role in aeronautics, the weapons industry and other high-tech fields in which cage structural compounds have generated popular interest due to their high density, high energy and high tension. Hexanitrohexaazaisowurtzitane (HNIW, CL-20, 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane, 2,4,6,8,10,12-hexanitro- 2,4,6,8,10,12-hexaazatetracyclo[5.5.0.05,9.03,11]dodecane) (1) has become the new focus of energetic materials.

NO2

N NO2 N

NO2 N N NO2

N N NO2

NO2 1

An understanding of the complex chemical processes and an estimation of the influence of different factors on the reactivity of the titled explosive are essential for the design of efficient techniques for CL-20 utilization. In the present work a quantum-chemical investigation of potential energy surface of CL-20 unimolecular degradation process has been carried out. Geometry optimization of all minima and transition states structures has been performed at the B3LYP/6-31G(d) level of theory. Energies of all systems have been computed using the B3LYP/cc-pVTZ level of theory. The following three types of reactions for cyclic nitroamines decomposition have been defined: 1) homolytic cleavage of an N–N bond accompanied by the elimination of the NO2-group (TS1); 2) the elimination of the NO2-group accompanied by H atom migration from the C atom to the N atom (TS2); 3) ring opening reactions accompanied by an C–N bond cleavage (TS3); 4) ring opening reactions accompanied by an C–C bond cleavage (TS4); 5) HONO elimination (TS5).

O O CH CH O N N O N H O N O N H N N N CH N C CH CH CH CH N C

TS1 TS2 TS3 TS4 TS5 Conference on Current Trends in Computational Chemistry 2004 119

Aminolysis of Succinic Anhydride by Methylamine. Density Functional Theory and Intrinsic Reaction Coordinate Study

S. Okovytyy, T. Petrova

Dnepropetrovsk National University, Dnepropetrovsk, Ukraine

The aminolysis of anhydrides is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles which leads to formation of peptide bonds. More complete knowledge of the mechanisms of this reaction should provide useful insights into chemical and biochemical processes and could be of great importance to develop new and more efficient antibacterial drugs. The present investigation examines the mechanism of uncatalyzed succinic anhydride aminolysis (reaction 1) in gas phase and with taking into account solvent influence, general base catalytic effect by the methylamine molecule has also been studied (reaction 2). H O O O H NCH3 C N CH C C 3 3 2 (1) O H O 4 O C + H2N CH3 C 1 C H O O O 1 2 3

O O H O NCH H C C 3 C N CH 3 H 3 O 2 4 (2) O 2 H N CH O - H N CH C + 2 3 C 1 H NCH 2 3 C H 5 3 O O 6 H O 4 5 6 The theoretical calculations have been performed at the B3LYP/6-31G(d) levels of theory. The effects of solvent have been predicted by using the Polarized Continuum Model (PCM). Single point PCM/B3LYP/6-31G(d) calculations have been performed for estimating the change in energetics of the reaction in the presence of the aprotic neutral solvent benzene. Because of the large structural differences between transition structures, reactants and products, IRC paths have been determined to establish connectivities. The computations have been carried out with the Gaussian 03 program package. The general anhydride aminolysis mechanism usually begins with the formation of a substrate-nucleophile agent intermediate. This intermediate subsequently undergoes the cleavage of the C-О bond and the transfer of hydrogen atom from nitrogen atom of methylamine to the anhydride oxygen (2). In the case of uncatalyzed reaction activation barriers for processes in gas phase and in solution are equal to 29.40 and 23.00 kcal/mol, correspondingly. Plots of the changes in the internal coordinates along the IRC path is shown in Figure 1. According to the calculations the lowest energy pathway involves two distinct steps. The first step, rupture of the anhydride ring and C2-N3 bond formation, is followed by a second step, proton H4 migration, a process not commenced until breaking of the C2-O1 and formation of C2-N3 bond is complete. The combination of these two steps defines a concerted asynchronous pathway. It follows from Figure 1 that the C2-O1 and C2-N3 bond lengths smoothly change during reaction, while O1-H4 1/2 and N3-H4 bonds undergo remarkable changes in the interval 0.0-2.0 amu Bohr. 120 Conference on Current Trends in Computational Chemistry 2004

1.598

1.527 2.239 1.060 2.075 1.280 1.669

1.331 1.832 1.037

(O1-C2) 3,0 (O1-H4) 3,0 (C2-N3) (N3-H4) 2,8 2,5 2,6

2,4 2,0 2,2

2,0 1,5 1,8

1,6 1,0 Bond lengths(Angstroms) Bond

1,4 lengths(Angstroms) Bond

-10 -8 -6 -4 -2 0 2 4 6 -10 -8 -6 -4 -2 0 2 4 6 Reaction coordinate Reaction coordinate

Figure 1. Evolution of the internal coordinates along the IRC for the uncatalyzed aminolysis of succinic anhydride by methylamine

General base-catalyzed attack of succinic anhydride modeled by the addition of the second methylamine molecule leads to noticeably decreasing of the activation barrier to 17.11 and 13.29 kcal/mol for processes in gas phase and in solution, correspondingly. In this case the 1/2 consecutive protons transfer takes place: in transition state (at 0.0 amu Bohr) H4 proton migrates from atom N3 of attacking nucleophile to N5 atom of catalytic methylamine molecule, 1/2 while H6 proton migrates from N5 to O1 atom at 5.5 amu Bohr. Conference on Current Trends in Computational Chemistry 2004 121

(N3-H4) 2,6 3,0 (O1-H6) (H4-N5) 2,4 (N5-H6) 2,2 2,5

2,0

1,8 2,0

1,6

1,4 1,5

1,2

1,0

1,0 lengths(Angstroms) Bond Bond lengths(Angstroms) Bond 0,8 -10 -5 0 5 10 15 -10 -5 0 5 10 15 Reaction coordinate Reaction coordinate (O1-C2)

2,8 (C2-N3)

2,6

2,4

2,2

2,0 1,8

1,6

Bond lengths(Angstroms) Bond 1,4 -10 -5 0 5 10 15 Reaction coordinate

Figure 2. Evolution of the internal coordinates along the IRC for the catalyzed aminolysis of succinic anhydride

In summary, the results of this study reveal that aminolysis of succinic anhydride is an asynchronous but concerted reaction. Taking into account of the base catalysis and solvent effects leads to significant decreasing of activation barrier of reaction. 122 Conference on Current Trends in Computational Chemistry 2004

The Mechanism of Amine-Catalyzed Ethylene Epoxidation. A Computational DFT study

S. Okovytyy,1,2 Y. Kholod 1,2 and J. Leszczynski 2

1Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 2Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA

The process of alkenes epoxidation, using salts of the monoperoxysulphuric acid as an oxidant, catalyzed by simple amines is attractively simple and requires readily available cheap reagents in environmentally friendly solvents. This method, which does not require the using of transition metal catalysts, utilizes Oxone (2KHSO5+KHSO4+K2SO4) in MeCN:H2O mixture as a solvent. Till present time the mechanism of the titled reaction has not been studied. In the present work a quantum-chemical investigation of the potential energy surface (PES) – of ethylene epoxidation process with the HSO5 anion as an oxygen donor without catalysts and with different amines (diethylamine, pyrrolidine, piperidine and N-methylpyrrolidine) as catalysts has been carried out. Geometry optimizations of all minima and transition states structures have been performed at the B3LYP/6-31G(d) level of theory using the Gaussian 98 program. An influence of a solvent has been considered using the macroscopic PCM approach. We have located points TS1-TS5 which correspond to transition states at PES of abovementioned reactions.

All transition states can be characterized as symmetric spiro-structures with closed-shell character of wave function. According to the calculations all of studied amines catalyze the epoxidation process. It means that protonated amines are intimately involved in the oxygen transfer process, but not only as phase-transfer. The most efficient catalysts are pyrrolidine and piperidine. Diethylamine and N-methylpyrrolidine own less catalytic activity. Conference on Current Trends in Computational Chemistry 2004 123

Quantum-well Magnetoexciton with Spin-orbit Interaction

O. Olendski and T. V. Shahbazyan

Department of Physics, Jackson State University, P.O. Box 17660, Jackson, MS 39217 USA

We study theoretically two-dimensional electron-hole pair in the magnetic field which is tilted with respect to the exciton confining plane. In addition, electron Rashba [1] and Dresselhaus [2] spin-orbit interactions are taken into account. We find that, in the presence of an in-plane field component, the interplay between Zeeman and spin-orbit terms leads to a drastic change in the magnetoexciton energy spectrum. When separation between adjacent Landau levels with opposite spins becomes of the order of the magnetoexciton binding energy, the bright and dark exciton dispersions exhibit anticrossing, resulting in a pronounced minimum at finite momentum for the higher-energy eigenstate. With varying in-plane field, the anticrossing moves to zero momentum leading to a spin-orbit-induced splitting of the excitonic absorption spectrum. For zero exciton momentum these results allow to calculate optical absorption. Using algebra of exciton creation and annihilation operators, matrix elements of the Hamiltonian are calculated exactly in the basis of one-exciton wavefunctions [3]. For strong field, the full matrix reduces to the 4X4 form describing interaction between relevant spin-split Landau levels, and the excitonic spectrum near the anticrossing can be calculated analytically. Comparative analysis of Rashba and Dresselhaus terms is performed, and their relative weights in the full interaction are discussed. Effects of in-plane electric field in the fine tuning of the absorption spectrum are calculated too.

Supported by NSF under grants DMR-0304036, DMR-0305557 and HRD-0318519, and by ARO under grant DAAD19-01-2-0014.

References 1. E.I. Rashba, Fiz. Tverd. Tela 2, 1224 (1960) [Sov. Phys. Solid State 2, 1109 (1960)]; Y.A. Bychkov and E.I. Rashba, J. Phys. C 17, 6039 (1984). 2. G. Dresselhaus, Phys. Rev. 100, 580 (1955). 3. C. Kallin and B.I. Halperin, Phys. Rev. B 30, 5655 (1984).

124 Conference on Current Trends in Computational Chemistry 2004

Sphingosine 1-Phosphate (S1P) Receptor Selectivity for an Aromatic Immunosuppressant

Daniel A. Osborne*, James I. Fells*, Yongmei Wang*, Yuko Fujiwara**, Sandor Cseh**, Gabor Tigyi**, and Abby L. Parrill*

*Department of Chemistry and Computational Research on Materials Institute, The University of Memphis, Memphis, TN 38152, and **Department of Physiology, The University of Tennessee Health Sciences, Memphis, TN, 38163

Sphingosine-1-phosphate (S1P) is a lysophospholipid that stimulates multiple signaling pathways, giving a variety of biological responses. These cellular functions are mediated by the binding of S1P to cell surface G protein-coupled receptors (S1P1-S1P5). Numerous S1P receptor agonists with varying degrees of selectivity have been characterized. S1P agonists are promising leads as immunosuppressives and to protect against oocyte apoptosis during cancer chemotherapy. FTY720 is a novel immunosuppressant that prevents graft rejection without the major side effects associated with many currently marketed therapies. FTY720 activates all S1P receptors except S1P2, and the molecular basis of this experimentally-observed selectivity has proven elusive [efforts aren’t elusive, the basis for selectivity is]. A computational model has been developed that identifies several residues that appear to impart the observed selectivity and as a result provides a molecular basis for the activation of the S1P receptors by aromatic S1P agonists. Additionally, a quantitative computational model has been developed that identifies estimates the binding free energy due to electrostatic interactions between ligand and receptor via the Poisson-Boltzmann methodology. This work provides key structural information regarding S1P receptor agonism, in addition to yielding insight into the mechanism by which the ligand binds to the receptor.

Conference on Current Trends in Computational Chemistry 2004 125

Determination of Charges of Ions by Means of Graphs Theory

Valentin V. Oshchapovsky

Lviv State Institute of Fire Safety, P.O.Box 10676, Lvov, 79000, Ukraine

On the basis of the mathematical theory of graphs the expression for calculation of ionic crystals lattice energy was received [1]. In this case a molecule (the formula unit of MeX crystal) was presented in the form of complete and finite graph. It allowed to infer the equations for a priori calculation of the internuclear distances R12, as well as the values of ions radii depending on their oxidation number only. According to the assumption that: 1) molecules of all types are ionic compounds with any arbitrary (including fractional) oxidation numbers in framework of “octets”; 2) charges on atoms are “instantaneous” quantities of electron substance, which were lost by a cation and gain by an anion during the overlapping of electron clouds and the formation of chemical bond – the reverse task is solved: the method of calculation of the effective charges on atoms of gaseous molecules (when crystalline field action is absent), as well as in crystals is proposed. Given method of effective charges determination is based only on the values of the radii of ions and atoms (for metals), potentials of ionization of atoms, as well as experimentally determined magnitudes of internuclear distances in the molecules (in crystals) and does not need any other arbitrary quantities (constants). The system of ions radii of Shannon was used. The values δ for the alkali metals halides in crystalline and gaseous forms were calculated.

Crystal: Li+0.966F–0.966 ; Na+1.00Cl–1.00 . Gas: Li+0.863F–0.863 ; Na+1.00Cl–1.00.

The preliminary analysis of obtained mathematical expressions gives certain reasons to assume that on micro-level the metrics of space (intra-molecular and intra-atomic) is changed. Obviously, this space is described with the laws of multidimensional geometry.

References [1] Oshchapovsky V.V. "Scientific Israel – technological advantages", 1999, Vol.1, No 2, pp.37-40. 126 Conference on Current Trends in Computational Chemistry 2004

Electronic Transport in Nanoscale Systems from First-principles using GAUSSIAN03

J. J. Palacios*, A. J. Pérez-Jiménez**, E. Louis*, E. SanFabián**, and J. A. Vergés***

* Departamento de Física Aplicada , Universidad de Alicante, San Vicente del Raspeig, Alicante 03690, Spain. ** Departamento de Química-Física, Universidad de Alicante, San Vicente del Raspeig, Alicante 03690, Spain. *** Instituto de Ciencia de Materiales (CSIC), Campus de Cantoblanco, 28049 Madrid.

Mastering the flow of electrical current at the nanoscale lies at the heart of nanotechnology. In a foreseeable future, the functionality of electronic devices will rely on the conduction properties of molecules or nanoscopic regions comprised of a surprisingly small number of atoms. Over the past ten years various experimental groups have developed different techniques to connect two large metallic electrodes by just an atom or a chain of atoms. These systems receive different names such as atomic contacts or nanocontacts1. They are not expected to have any practical technological application, but are an excellent test bed to learn about electrical transport at the atomic scale. A more promising and interesting version of these nanoscopic bridges can be realized when organic molecules are deposited in the vicinity of the junction. With the appropriate end groups these molecules can bind themselves to the electrodes and form fairly stable molecular bridges. These techniques open the possibility of building a molecular transistor which may serve as the basis for molecular electronics2. Magnetism, not less important when it comes to device functionality at the nanoscale, has begun to attract due theoretical and experimental attention. While a large amount of experimental work has been done in large area magnetic junctions and magnetic multilayers due to the huge technological impact of these systems3, a deep theoretical understanding is still lacking. Magnetic nanocontacts, in turn, exhibit a very rich and complex behavior which, at this moment, is far from being understood4. Even nonmagnetic material nanocontacts are expected to exhibit some sort of magnetism due to the lowest coordination of the atoms at the junction5. Magnetic molecules like Mn12 or ferrocenes are also being the subject of several experimental studies of transport6. First-principles calculations of electrical transport that can explicitly take into account the spin degree of freedom are a major challenge. Here we show how to make use of Gaussian03 to calculate electrical transport in this framework7.

1) N. Agrait, A. Levy-Yeyati, and J. M. van Ruitenbeek, Physics Reports 377 (2003) 81. 2) A. Nitzan and M. Ratner, Science 300 (2003) 1384. 3) T. H. Kim and J. S. Moodera, Phys. Rev. B 69 (2004) 020403. 4) M. Viret et al. Phys. Rev. B 66 (2002) 220401. 5) A. Delin and E. Tosatti, Phys. Rev. B 68 (2003) 144434. 6) J. Park et al. Nature (London) 417 (2002) 722. 7) J. J. Palacios et al., Phys. Rev. B 64, 115411 (2001), J. J. Palacios et al., Phys. Rev. B 66, 035322 (2002), E. Louis et al., Phys. Rev. B 67, 155321 (2003); J. J. Palacios et al., Phys. Rev. Lett. 90, 106801 (2003), Y. García et al., Phys. Rev. B 69, 041402

Conference on Current Trends in Computational Chemistry 2004 127

Interacting Clay Sheet in an Effective Solvent Medium: Conformation and Dynamics by Monte Carlo Simulation

Ras B. Pandey1, Kelly L. Anderson2, Hendrik Heinz3, B.L. Farmer2

1Department of Physics and Astronomy University of Southern Mississippi, Hattiesburg, MS 39406-5046 2Materials and Manufacturing Directorate Air Force Research Laboratory, Wright Patterson Air Force Base, OH 45433 3Department of Mechanical and Materials Engineering Wright State University, Dayton, OH 45435

A parametric study of the effect of temperature and solvent affinity of a deformable clay 2 3 sheet, comprised of a set of Ls nodes connected by flexible bonds on a L lattice, is presented. Each node is connected by its four nearest neighbors, except those along the boundaries with three neighbors and at the corners with two neighbors. The shape and size of the sheet change via stochastic movements of nodes. The bond length varies between 2 and √(10) in units of the lattice constant. Apart from excluded volume interactions, each node interacted with its neighboring nodes and effective solvent medium within a range r (i.e., r = 4, 6). In addition to the constraints on the bond length, the interaction energy and temperature determine the motion of a node with the Metropolis Monte Carlo algorithm. Relaxation of the sheet is studied for a range of temperatures with the range of interaction extending up to r = 6. Variation of the mean square displacements of the center node of the sheet and its center of mass with the time steps are being examined in detail. Attempts are made to identify the power-law dependence in short and long time regimes. Scaling of the radius of gyration of the sheet with its molecular weight is also currently under study. Results from these data (subject to availability) will be presented. 128 Conference on Current Trends in Computational Chemistry 2004

Hydrogen Bonding in Phenol, Water and Mixed Phenol-Water Clusters: From Electron Density Perspective

R. Parthasarathia, V. Subramaniana* and N. Sathyamurthyb*

aChemical Laboratory, Central Leather Research Institute, Adyar, Chennai, India 600 020 and bDepartment of Chemistry, Indian Institute of Technology, Kanpur, India, 208 016

Studies on the structure and stability of clusters are very important in order to understand the solvation phenomenon. The hydrogen bonding (H-bonding) is a key interaction in molecular solvation and recognition. The theory of atoms in molecules (AIM) offers rigorous ways of looking H-bonding interactions in clusters by considering the gradient vector field of its electron density. By means of topological features of electron density (ρ(r)), it is possible to gain more insight into the H-bonded systems. In this investigation an attempt has been made to characterize the structure, stability and H-bonding interaction of phenol (P), water (W) and mixed phenol- water (PW) clusters using conventional ab initio and density functional theory (DFT) methods and also using various topological properties of ρ(r). The structure, stability and AIM topographical features of PmWn (m = 1-3, n = 1-3, m+n ≤ 4) clusters have been computed and compared with the corresponding geometries for W2, W3, W4, P2, P3 and P4. The molecular graphs of phenol, water and mixed phenol-water clusters illustrating H-bonding interaction are depicted in Figure. 1.

Figure 1. Molecular Topography of Phenol Tetramer, Water Tetramer and Mixed Phenol- Water Clusters Obtained from Theoretical Charge Density. Bond Critical Points are denoted by Red Dots and Yellow Dots denotes the Ring Critical Point.

Calculated interaction energy for the clusters with similar hydrogen bonding pattern reveal that hydrogen bonding in water clusters is stronger than in phenol clusters. However, fusion of phenol and water clusters in tetrameric ring arrangements leads to stability that is akin to that of 2 W 4. The presence of hydrogen bond critical points (HBCP) and the values of ρ(rc) and ∇ ρ(rc) at the HBCPs provide an insight into the nature of closed shell interaction in the hydrogen-bonded 2 clusters. It is found that the sums of the electron density ( ∑ ρ(rc)) and its Laplacian ( ∑ ∇ ρ(rc)) at all HBCPs bear a linear relationship with the stabilization energy for all the hydrogen-bonded clusters as illustrated in Figure 2. The linear regression analyses yields

Interaction Energy = -213.96 ∑ ρ(rc ) at HBCP + 0.127 R= -0.997 (1) 2 Interaction Energy = -253.62 ∑ ∇ ρ(rc ) at HBCP + 0.426 R= -0.995 (2)

Conference on Current Trends in Computational Chemistry 2004 129

The correlation coefficient is nearly unity in both cases. It can be seen from Figure 2 that the hydrogen bonded clusters having SE in the range of -5 to -25 kcal/mole show three clusters 3 in the density region between 0.020 to 0.125 e/a0 .

-5 -5

-10 -10

-15 -15

-20 -20 Interaction Energy (kcal/mol) Interaction Energy (kcal/mol) -25 -25

0.02 0.04 0.06 0.08 0.10 0.12 0.02 0.04 0.06 0.08 0.10 3 2 5 Total ρ(r ) in (e/a ) Total ∇ ρ (r ) in (e/a ) c 0 c 0

(a) (b)

Figure 2. (a) Relationship between Interaction energy and Total ρ(rc) (b) Interaction energy and 2 Total ∇ ρ(rc) of the Phenol, Water and mixed Phenol-Water clusters 130 Conference on Current Trends in Computational Chemistry 2004

Water in the Bulk and at Interfaces

Lars G.M. Pettersson

FYSIKUM, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden

We have investigated the electronic structure of water and ice using a combination of experimental and theoretical techniques [1]. Measurements have been performed on the liquid using both X-ray Absorption (XAS) and X-ray Raman Spectroscopy. The spectrum of the liquid is distinctly different from that of the bulk ice, where the liquid shows a distinct pre-edge feature and a strong enhancement of the intensity at the edge. Through spectrum simulations and model experiments (bulk and surface of ice) we show that the specific features in the liquid spectrum are due exclusively to asymmetric configurations with only two strong hydrogen bonds: one donating and one accepting, indicating that the liquid is dominated by rings or chains embedded in a disordered H-bond network [1]. Current molecular dynamics techniques fail to predict these new experimental data. We have furthermore investigated the bonding of water at metallic interfaces, where, for Pt(111), we find a wetting layer where all molecules bind to the surface either through the oxygen or through a hydrogen, i.e. the buckled bilayer model is not correct [2]. Comparison of the contact layer on the noble metal copper with that on Pt(111) and Ru(001) leads to an atomistic picture of wetting.

References [1] Wernet et al, Science 304, 995-999 (2004) [2] Ogasawara et al, Phys. Rev. Letters 89, 276102 (2002) Conference on Current Trends in Computational Chemistry 2004 131

Prototropic Tautomerism in a Nucleic Acid Base Analog: ab Initio MP2 and DFT Study

Yevgeniy Podolyan, Leonid Gorb, Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Jackson State University, Department of Chemistry, 1325 Lynch St., Jackson, MS 39127

The nucleoside analog dP (6-(2-deoxy-β-D-rybofuranosyl)-3,4-dihydro-6H,8H- pyrimido[4,5-c][1,2]oxazin-2-one) has been recently incorporated into the DNA. The former can display ambivalent hydrogen bonding characteristics. For example, the imino tautomer of P can form a complementary pair with adenine, while the amino tautomer can form a pair with guanine. The ambivalence such as this one in the natural bases can lead to point mutations. The experimental results have shown that in the aqueous solution the N-methyl-P (Figure 1), a model compound of nucleoside dP, exists predominantly as its imino tautomer with a ratio of the imino to amino form of 11:1. In this work we have studied the proton transfer in the N-methyl-P molecule. The geometry optimizations of the local minima and transition states have been performed at the MP2/cc- pVDZ and B3LYP/cc-pVDZ levels of theory without symmetry restrictions. The effects of the water have been accounted for by using PCM solvation model as well as the explicit inclusion of a limited amount of water molecules. The results have shown that the imino form is significantly more stable than the amino form in the gas phase. However, the influence of the polar surrounding significantly decreases the difference in the tautomer stability. Thus, the difference becomes smaller while adding explicit water molecules and comes close to 1 kcal/mol when PCM solvation model is employed.

H O O N N H N N

O N O N

Me Me a) b)

Figure 1. Structures of the a) amino and b) imino tautomers of the N-methyl-P. 132 Conference on Current Trends in Computational Chemistry 2004

Towards a Precise ab Initio Accuracy in Molecular Mechanics Computations for Nucleic Acids. I. Cytosine Structure and Energy Variations

V.I. Poltev1,2, E. Gonzalez1, A.S. Deriabina1, L. Lozano1, A. Martinez1, T. Robinson3, L. Gorb3, J. Leszczynski3

1Physics and Mathematics Department, Puebla Autonomous University, Puebla, 72570, Mexico 2Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia 3Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, 39217 MS

Molecular mechanics method is a powerful tool for description and prediction of three- dimensional structure, dynamics and biological functioning of nucleic acids and all the biomolecules. This method is essentially a semi-empirical one, and its force fields depend on experimental data used and theoretical assumptions. In order to construct more detailed molecular models of nucleic acids and their complexes, it is necessary to refine permanently or regularly the method and force fields, using new data, both experimental and theoretical. Achievements in quantum theory and in computers allow to predict from rigorous ab initio computations structure and energy of the monomers and their small complexes with an accuracy of the most reliable experimental studies. We are using such calculations for a refinement of molecular mechanics force fields for nucleic acids. Some results of rigorous quantum chemistry calculations, namely, the data describing a phenomenon of nonplanarity and conformational flexibility of base amine groups, cannot be reproduced by existing force fields of molecular mechanics. Detailed quantum mechanics study of this phenomenon, approximation of the results by sufficiently simple formulae, and inclusion of appropriate terms into force fields will enable us to combine molecular mechanics simplicity with exactness of rigorous quantum mechanics methods. We are performing ab initio MP2/6-31G(d,p) level computations of base energy and structure as functions of amine group parameters. The detailed results will be presented here for cytosine. First of all we calculated dependencies of cytosine energy and structure on each of the three amine group torsions with all the other variables being free. Rather simple dependencies of energy for torsions describing amine hydrogen positions were obtained with two symmetrically arranged minima separated by a maximum. These dependences can be approximated by superposition of two nearly parabolic curves. The minima correspond to displacements of the hydrogens in one direction out of ring plane, and the nitrogen has less pronounced displacement in the opposite direction. The maximum for both torsions corresponds to the planar arrangement of all the atoms in a base ring plane. Dependence of N4 torsion is more complicated, and contains two curves, corresponding to two minima with the same energy value and the same structure as those obtained for the minima for amine hydrogen torsions. The energies and structures predicted for each N4 torsion value being dependent on direction of its changes. The maximum of this dependence corresponds to position of the nitrogen in base ring plane, amine hydrogens being displaced from this plane; as a result energy barrier between two minima is smaller. Similar dependences were obtained for these torsions, when one or two of other torsions are fixed in positions of minima or of planar structure. The calculations of dependences Conference on Current Trends in Computational Chemistry 2004 133

demonstrate, that energy changes, caused by the torsion variations, cannot be approximated by a sum of items corresponding to variation of each of three torsions. It means, that such dependences are not sufficient to describe possible changes of cytosine energy and molecular structure. As a next step to such description, we performed calculations for extended set of values for pairs of torsions describing positions of two amine hydrogens. This set includes all the pair-wise combinations of the hydrogen torsions within the regions of 800 with an interval of 10, the planar structure being in the center. This network of energy and geometry parameters enables us to construct two-dimensional energy map in a space of two torsions, and such maps for all the geometry parameters of the molecule. We suggest approximating the energy map by analytical formula and using this formula as an additional term in molecular mechanics computations. Dependences for all other geometry parameters will be calculated from the maps constructed. As we concluded, the energy dependence cannot be approximated by usual formulae of molecular mechanics. The dependence is more complicated, and we are searching for most simple expressions for its description. Several trial relationships have been examined, but a choice of final expression is in progress yet. Some semi-quantitative conclusions can be made from the results obtained. Base ring retains practically planar structure for wide range of variations of amine group torsions. All the bond lengths and bond angles of the base ring as well as those of C=O, C-H and N1-H bonds undergo changes in rather narrow range (0.01Å and 1º respectively). On the other hand, C-N bond length of amine group as well as its C-N-H and H- N-H bond angles fluctuate substantially with the variation of any torsion. These changes cannot be reproduced by canonical formulae of molecular mechanics, and should be approximated using ab initio data. Trial dependences for these parameters obtained from the two-dimensional maps are tested as well. Similar calculations and analytical approximations for guanine and adenine are in progress now. After their completion, the MP2/6-31G(d,p) level computations of base-base interactions for various mutual positions of bases will be performed and compared with improved molecular mechanics computations. This comparison should enable us to modify the formulae and to obtain exact numerical values of the coefficients in the formulae. More rigorous ab initio computations for restricted set of configurations will be performed as a final step in force field improvement.

Authors are thankful for financial support from NIH SCORE grant #3 S06 GM008047- 31S1, from CONACYT, Mexico (project No. 41885F), and from VIEP BUAP (project II 28- 04/EXC/G). 134 Conference on Current Trends in Computational Chemistry 2004

Conformational Studies of Rotationally Hindered Retinoids

Morgan S. Ponder1, Tracy P. Hamilton2, and Donald D. Muccio2

1Department of Chemistry, Samford University, Birmingham, AL 35229-2236 2Department of Chemistry, University of Alabama in Birmingham, Birmingham, Alabama 35294-1240

Retinoic acid is a member of the Vitamin A family, collectively known as the retinoids. Many of the retinoids have shown encouraging experimental and clinical activity in cancer chemoprevention. However, use of the retinoids is limited by their toxicity and their potential role in the development of tumors. These side effects may result from the ability of an individual retinoid to activate more than one retinoid receptor. This ability to activate more than one receptor may be due to the large degree of rotational freedom about the single bonds in the side chain. If this rotational freedom can be reduced, the resulting compounds may activate only a single retinoid receptor and consequently may exhibit improved therapeutic ability and increased clinical utility.

The purpose of this work was to investigate the conformations of retinoids in which rotation about the 6-7 single bond is hindered. This restriction in rotational freedom was achieved by using a one-, two-, or three-carbon bridge between carbons 18 and 7. The cyclohexenyl ring was replaced by various functional groups. Both 9-cis and 9-trans compounds were studied; all other double bonds were trans. The effects of these structural changes on the conformation of the resulting compounds will be discussed. Conference on Current Trends in Computational Chemistry 2004 135

Towards a Force Field via Quantum Chemical Topology

P. Popelier1, M. Devereux1, S. Liem1 and M. Leslie2

1 School of Chemistry, University of Manchester, Manchester M60 1QD, Great Britain 2 Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD, Great Britain

The theory of Quantum Chemical Topology (QCT)[1,2] was introduced by Bader and co- workers with an eye on generalising quantum mechanics to subspaces. QCT uses so-called zero- flux surfaces to partition a molecule into (topological) atoms. As a corollary QCT also unambiguously partitions a cluster of molecules into molecules. Here we focus on how topological atoms can be employed to construct intermolecular potentials and in a further stage to provide transferable units for the design of a novel force field including intra-molecular terms. The latter part of the project is in the initial stages of construction and will not be explicitly talked about here. We now discuss the title project in a number of key steps.

"Atomic partitioning of Molecular Electrostatic Potentials" [3] First we focused on the electrostatic component of intermolecular interaction given its importance in biological systems. An understanding of the convergence of the electrostatic multipole expansion was vital to make solid progress. The electrostatic potential was chosen as a starting point because it is a special case of electrostatic interaction, where one of the interacting partners is just a proton. In this work we have computed for the first time the exact electrostatic potential generated by an AIM atomic fragment, called the AEP. The premise that the multipole expansion associated with bounded fragments in real space, such as AIM atoms, has poor convergence proves to be wrong. In summary, this study demonstrates that we do not need an excessively large number of multipoles to reproduce the exact ab initio molecular electrostatic potentials within the AIM theory. This work makes clear that the atomic population (or rank-zero multipole moment) is just one term of the expansion of a physically observable quantity, namely the electrostatic potential. Hence the AIM populations cannot be judged on their reproduction of the electrostatic potential. Instead, they must be seen in the context of a multipole expansion of the AEP. Finally we computed the exact AEP and its value obtained via multipole expansion for molecules including molecular nitrogen, water, ammonia, imidazole, alanine and valine.

Fig.2 The deviations in the exact AEP and the AEP obtained from the multipole

moments up to the octupole (A=3) for the Cα

atoms in alanine. The part of the picture in front of the plotting plane is deleted in order to show the interior of the object. The Fig.1 Since topological largest deviations occur near the cusp-like atoms are finite it is possible edges of the atom and the region of closest to monitor their formal proximity. Color code (in kJ/mol): convergence. white<0.1

136 Conference on Current Trends in Computational Chemistry 2004

"Convergence of the Multipole Expansion for Electrostatic Potentials of finite Topological Atoms" [4] We then tried to understand the cause of the excellent convergence. How can it be compatible with the admittedly highly non-spherical shape of the topological atoms? The answer lies in the exponentially decaying electron density. The convergence behaviour of the actual electron density inside an atomic basin is due to its decay rather than to the atom’s shape. Indeed when the atom is filled with a uniform density the convergence worsens often by more than an order of magnitude. AIM multipole moments are adequate for the modeling of both inter- and in principle intramolecular interactions in force field (non-bonded terms). In summary we confirm that finite atomic shapes have undesirable convergence properties but that this phenomenon is in practice not relevant due to the profile of the actual electron density inside.

"Atom-atom Partitioning of molecular Coulomb Energy" [5] Then we focused on the Coulomb energy between atoms in supermolecules. We proposed coul an atom-atom partitioning of the Coulomb interaction, denoted by E AB , based on the topology of the electron density. Our atom-atom Coulomb interaction energy should not be confused with the electrostatic component of the intermolecular interaction defined within the perturbation approach. Instead we introduce an atom-atom Coulomb interaction energy that uses the total molecular or supermolecular electron density as its input. Atom-atom contributions to the molecular intra-and intermolecular Coulomb energy are computed exactly, i.e. via a double integration over atomic basins, and by means of the spherical tensor multipole expansion, up to

rank L=AA+AB+1=5. The convergence of the multipole expansion is able to reproduce the exact interaction energy with an accuracy of 0.1-2.3 kJ/mol at L=5 for atom pairs, each atom belonging to a different molecule constituting a van der Waals complex, and for non-bonded atom-atom interactions in single molecules. The atom-atom contributions do not show a significant basis set dependence (3%) provided electron correlation and polarisation basis functions are included. The proposed atom-atom Coulomb interaction energy can be used both with post-Hartree-Fock wave functions, without recourse to the Hilbert space of basis functions, and experimental charge densities in principle. We provide computational details of this method and apply it to (C2H2)2 ; (HF)2 ; (H2O)2 ; butane ; 1,3,5-hexatriene ; acrolein and urocanic acid, thereby covering a cross section of hydrogen bonds, and covalent bonds with and without charge transfer. The Coulomb interaction energy between two molecules in a van der Waals complex can be computed by summing the additive atom-atom contributions between the molecules. Our method is able to extract from the supermolecule wavefunction an estimate of the molecular interaction energy in a complex, without invoking the reference state of free non-interacting molecules. Provided quadrupole-quadrupole interactions are included the convergence is adequate between atoms belonging to different interacting molecules. Within a single molecule the convergence is reasonable except for bonded neighbours.

Fig.3 Coordinate system used in the description of the Coulomb interaction between two topological atoms ΩA and ΩB.

Conference on Current Trends in Computational Chemistry 2004 137

“The Convergence of the Electrostatic Interaction based on topological Atoms”[6] Here we focus on a topological intermolecular potential without the perturbation approach. We are interested in a careful test of this proposal in the context of the successful Buckingham- Fowler model, using improved algorithms. Particular attention was paid to the convergence of both the energy and the geometry of a set of van der Waals complexes, with respect to the rank L of the multipole expansion. For the first time this convergence behaviour has been contrasted with exact values, obtained without multipole expansion, via 6D integration over two atomic basins. We find that, although the AIM results converge more slowly than the DMA results, excellent agreement is obtained between the two methods at high rank (L=6), both for geometry as well as intermolecular electrostatic interaction energy. This is the first time that a direct, complete and explicit comparison between AIM and Distributed Multipole Analysis (DMA) has been made. Contrary to views expressed before in the literature this work opens an avenue to introduce the topological approach in the construction of an accurate intermolecular force field. It is here that the high degree of transferability of the functional groups defined by AIM will be extremely useful.

“Improved Convergence of the Atoms in Molecules multipole expansion of electrostatic interaction.” [7] In this paper we continue our study of the convergence properties of multipolar expansions of topological atoms. To assess the quality and the speed of this convergence we made systematic comparisons with an accurate and well-known anisotropic electrostatic model called DMA. A set of small van der Waals systems was investigated as well as a set of much larger DNA base pairs. Based on a clearly made distinction between partitioning and distribution it is shown for the first time how topological multipole moments can be distributed to off-nuclear sites. The introduction of extra sites improves the convergence of AIM without detracting from the way it partitions molecular information among atoms. In the AIM context the addition of extra sites is more beneficial to the convergence of the electrostatic interaction energy of small systems. However for large systems excellent convergence is found with AIM without the introduction of extra sites. This advantage further encourages the development of a topological intermolecular force field.

“DNA base pairing : towards a topological intermolecular force field for biological systems”[8] Following the success of the topological electrostatic model on van der Waals complexes we assessed its performance on the important biological problem of DNA base-pairing. Geometries and intermolecular interaction energies predicted by AIM supplemented with a hard-sphere or the Lennard-Jones potential have been compared with other methods in two stages. First with supermolecular HF, MP2 and B3LYP calculations at 6-31G(d,p) level and then with other potentials such as MK, NPA and DMA at 6-311+G(2d,p) level. The geometries for all 27 base pairs predicted by AIM and B3LYP differ by 0.08Å and 3.50 for 55 selected intermolecular geometrical parameters, while the energies show an average discrepancy of 6 kJ/mol. The B3LYP functional proves to be a reliable alternative to MP2 since their energies are in excellent agreement (~1 kJ/mol). Globally the AIM interaction energy curve follows the same pattern as that of MK, NPA and DMA. The MK model systematically underestimates the interaction energy and NPA shows undesirable fluctuations. Surprisingly the convergence of the AIM multipole expansion is somewhat better than that of DMA, but both have similar basis set dependence. A test of AIM on a DNA tetrad suggests that it is able to predict geometries of more complex nucleic acid oligomers than base pairs. Our work clearly demonstrates that the electrostatic description dominates DNA base pair patterns but more work is needed to predict the three most stable base pairs better. A current 138 Conference on Current Trends in Computational Chemistry 2004

inadequacy of our AIM potential is that it is combined with empirical potentials, and hence not completely derived from ab initio calculations. Ultimately the AIM potential should draw all its information from ab initio calculations on monomers. Given the success of topological distributed polarisabilities induction energies could be included next, while work on the modeling of exchange-repulsion is warranted. A similar analysis (to be submitted) was performed for water clusters and a selection of hydrated amino acids.

“Simulation of liquid water using a high rank quantum topological electrostatic potential"[9] For the first time[7] a QCT potential based on high-rank atomic MMs was used in a molecular dynamics simulation. Other than the parameter L, which keeps track of the rank of the electrostatic interaction, this potential contains only two adjustable parameters of the Lennard– Jones type. A system of 216 water molecules was simulated including long-range interactions represented by a high rank multipolar Ewald summation. High-order multipolar interactions are essential to recover the typical features of a liquid-like structure. Liquid simulations at five different temperatures showed a maximum in the density and a temperature profile that agrees fairly well with experiment. The density of simulated water at 300 K and 1 atm is about 0.1% off the experimental value, while the calculated potential energy of the liquid is within 3% of the experimental result. The experimental value of the self-diffusion coefficient is underestimated by 35%. The value of the heat capacity Cp is overestimated by 40% and the thermal expansion coefficient by 37%. The calculated correlation coefficients between the calculated QCT profile and the experimental profile of gOO(r), gOH(r), and gHH(r) are 0.976, 0.970, and 0.972, respectively. Finally, in preparation of the peptide/protein fore field we computed atom types[10-12] via a cluster analysis on 760 atoms drawn from amino acids and derived molecules.

References 1. Bader, R. F. W. Atoms in Molecules. A Quantum Theory; Oxford Univ. Press: Oxford, GB, 1990. 2. Popelier, P. L. A. Atoms in Molecules. An Introduction.; Pearson Education: London, GB, 2000. 3. Kosov, D. S., Popelier, P. L. A. J. Phys. Chem. A, 104 (2000) 7339. 4. Kosov, D. S., Popelier, P. L. A. J.Chem.Phys., 113 (2000) 3969. 5. Popelier, P. L. A., Kosov, D. S. J.Chem.Phys., 114 (2001) 6539. 6. Popelier, P. L. A.,Joubert, L., Kosov, D. S. J.Phys.Chem.A, 105 (2001) 8254. 7. Joubert, L., Popelier, P. L. A. Molec.Phys., 100 (2002) 3357. 8. Joubert, L., Popelier, P. L. A. Phys.Chem.Chem.Phys., 4 (2002) 4353. 9. Liem, S.,Popelier, P. L. A., Leslie, M. Int.J.of Quant.Chem., 99 (2004) 685. 10. Popelier, P. L. A., Aicken, F. M. J.Am.Chem.Soc., 125 (2003) 1284. 11. Popelier, P. L. A., Aicken, F. M. ChemPhysChem, 4 (2003) 824. 12. Popelier, P. L. A., Aicken, F. M. Chemistry. A European Journal, 9 (2003) 1207.

Conference on Current Trends in Computational Chemistry 2004 139

Structure, Bonding, and Solvation of Dilithiodiamines

Lawrence M. Pratta and R. Mub

Departments of Chemistry and Physics Fisk University, Nashville, TN 37209 a. Department of Chemistry b. Department of Physics

Lithium dialkylamides are used extensively in organic synthesis for the formation of enolates. The structure of these bases is of interest because the reactivity and stereoselectivity of enolization is dependent on the lithium amide structure, solvent, and the formation of mixed aggregates. Mixed aggregates between the lithium amide and butyllithium are often formed by addition of an excess of butyllithium to the amine to ensure complete deprotonation. Lithium dialkylamide mixed aggregates are also formed with the newly generated lithium enolate in deprotonation reactions, and these mixed aggregates often reduce the enolization stereoselectivity. Dilithiodiamines were initially investigated as potential bases for ketone enolization with high stereoselectivity because it was anticipated that they would resist mixed aggregate formation due to the formation of energetically favorable intramolecular dimers. Although the stereoselectivity of dilithio-N,N'-dimethyl-1,3-diaminopropane suggests that mixed aggregates are formed even with this system, the structure and bonding in dilithiodiamines remains of interest. In particular, this paper investigates the energy of cyclization of dilithiodiamines in the gas phase and the effects of temperature, solvation, and chain length on the cyclization energy. The cyclic intramolecular dimer gives rise to new vibrational frequencies corresponding to Li-N motions in the bridged structure. Solvent effects are very important in organolithium chemistry. They dramatically influence the aggregation state and reactivity of alkyllithiums, lithium dialkylamides, and other organolithium compounds. Hydrocarbon solvents involve little or no coordination to the lithium atoms, and the associated solvent effects consist primarily of dielectric polarization, dispersion interactions, and cavitation. Hexamethylphosphoramide (HMPA) is at the other extreme, coordinating so strongly to lithium that two-bond NMR spin coupling can be observed between lithium and phosphorous. Ethereal solvents such as tetrahydrofuran (THF) are intermediate in their binding affinity for lithium. Rapid exchange of THF ligands prevents the observation of lithium-carbon spin coupling, although coordination of several ethers to lithium dialkylamides has been observed indirectly. A common solvation model for lithium compounds is microsolvation by explicit coordinating ligands such as THF, dimethyl ether, or trimethylamine. The resulting "supermolecules" are presumed to serve as good models for the solution behavior of organolithium compounds. The choice of ligands is often determined by the computational cost and chemical intuition. For example, dimethyl ether is sometimes used in place of THF because of the lower computational cost. Both ligands have similar dielectric constants and have similar steric bulk in the vicinity of the coordinated lithium atom. Although water has been occasionally used as a model ligand, it is a poor choice because of the higher dielectric constant, and because of computational artifacts resulting from hydrogen bonding. Microsolvation with dimethyl ether instead of THF makes the calculations more tractable with ab initio methods, and microsolvation captures a portion of the solvent dielectric effects. Although several continuum solvation models are available, their use alone (e. g., without microsolvation) is questionable because they may not reproduce the steric effects and specific interactions of coordinated ether ligands. A critical 140 Conference on Current Trends in Computational Chemistry 2004

missing element in the use of these solvation models in organolithium chemistry to date is the systematic testing and validation against experiment. Therefore, the dimerization energies were calculated for lithium diisopropylamide (LDA) and lithium tetramethylpiperidide (LiTMP) for comparison to the dilithiodiamines, as the aggregation states for both of those compounds are known experimentally. The cyclization energy of diamines 1-4 were examined in the gas phase at the B3LYP/6- 31+G(d) level, as shown in Scheme 1. The calculations were repeated for the microsolvated structures in Scheme 2, both with and without use of the IEFPCM continuum solvent model.

(CH2)n n=2 1a n=2 1b n=3 2a n=3 2b N (CH2)n N N n=4 3a n=4 3b N Li Li Li Li n=5 4a n=5 4b

Scheme 1. Cyclization of dilithiodiamines.

E=Me O E=THF E=Me2O E=THF (CH2)n 2 n=2 1g 1h -2 E n=2 1c 1d N N (CH )n N n=3 2g 2h n=3 2c 2d 2 N Li Li n=4 3g 3h Li Li n=4 3c 3d EEEE n=5 4g 4h EEn=5 4c 4d

Scheme 2. Cyclization of solvated dilithiodiamines.

The calculations indicated that the dilithiodiamines exist as bridged intramolecular dimers in THF solution provided that they are soluble. The three solvation models used were the IEFPCM continuum model alone, microsolvation by dimethyl ether or THF, and the combined microsolvation and continuum models. Based on a comparison with the calculated dimerization energies of LDA and LiTMP, the microsolvation model with THF ligands appears to generate free energies in best agreement with the available experimental data. Increasing the temperature makes the dilithiodiamine cyclization slightly less exergonic in the gas phase, but more exergonic in solution. This may be due to the increase in entropy of two THF molecules as they are bonded to lithium in the acyclic form but free in the cyclic form. The vibrational frequencies were calculated at the B3LYP/MIDI! level of theory on structures that were optimized with the same basis set. The infrared spectrum of dilithio-N,N'- dimethyl-1,3-propanediamine is consistent with the cyclic intramolecular dimer, which is soluble in THF, and inconsistent with the hypothetical open chain form. The calculated frequencies for vibrations involving significant Li-N movement, such as ring breathing, were dependent on the presence or absence of THF, with microsolvation lowering the calculated frequencies. Conference on Current Trends in Computational Chemistry 2004 141

Theoretical Studies on Z,E-Isomerization of HN- and N-Alkylimines

A.V. Prosyanik, D. Yu. Afanasiev, D. V. Fedoseyenko

Ukrainian State University of Chemical Technology 49005 Dnepropetrovsk, Gagarina, av. 8, Ukraine

Z,E-Isomerization of imines is realized by rotation around C=N bond or by inversion of nitrogen atom. To investigate the mechanism of isomerization of imines we conducted ≠ ≠ calculations of inversion (∆GI ) and rotation (∆GR ) barriers of compounds I-X (table) using 6- 31+G(d) basis set at BH&HLYP (А) and MP2(full) (B) levels. Stationary points on potential energy surfaces of investigated structures are found under full geometry optimizations (for transition state rotation angle C-N-R was assumed to be equal to angle in ground state). Zero- point energies and free energies are obtained by vibrational frequencies calculations; wave functions analysis was conducted by Natural Bond Orbitals (NBO) method.

Table. Barriers of isomerization of imines calculated using ab initio methods, kcal/mol

R1 R BH&HLYP/6- MP2(full)/6- N № 31+G(d) 31+G(d) R2 1 2 ≠ ≠ ≠ ≠ R R R ∆GI ∆GR ∆GI ∆GR I H H H 27.02 49.21 28.52 51.04

II Me H H 27.39 52.22 30.75 53.79 III t-Bu H H 25.78 47.88 27.56 50.54 IV H Me Me 27.21 44.94 29.23 46.86 V Me Me Me 26.45 43.15 26.99 45.52 VI t-Bu Me Me 19.53 34.28 22.05 36.05 Z-VII H Me H 26.54 45.31 27.55 47.06 E-VII H H Me 27.37 46.14 28.65 48.15 Z-VIII Me Me H 24.44 47.36 27.14 48.78 E-VIII Me H Me 28.36 51.29 31.36 52.99

IX Me CO2Me CO2Me 22.51 45.55 - -

X COMe CO2Me CO2Me 10.56 28.95 - -

≠ Calculated ∆Gi values are in close fit with experimental values of imines isomerization barriers I (25-27 kcal/mol [1]), II (25-27 kcal/mol [1]), Z-VII (27.3 kcal/mol [2]), IX (24.9 kcal/mol) и X (11.7 kcal/mol), that indicates on the one hand inversion mechanism of 142 Conference on Current Trends in Computational Chemistry 2004

isomerization of all investigated imines I-X, and on the other hand — reliability of conducted calculations. Analysis of found values of imines isomerization barriers I-VIII shows: 1. Inversion barrier of nitrogen atom decreases when the size of N substituent increases (imines II, III; IV-VI и Z-VII, Z-VIII), that corresponds to known regularities for inversion [3]. ≠ Exception from this rule is ∆GI values for some HN-imines and corresponding MeN-derivatives ≠ - when going from imine I to imine II ∆GI increases by 0.37 (A) and 2.23 (B) kcal/mol, from ≠ imine E-VII to imine E-VIII ∆GI increases by 0.99 (A) and 2.71 (B) kcal/mol, whereas going ≠ from NH-imine IV to MeN-derivative V ∆GI decreases by 0.76 (A) and 2.24 (B) kcal/mol. ≠ Anomalous ∆GI increasing in imine II and E-VII can be stipulated by dominating contribution of rising σ-electron withdrawal of N-substituent [3] in the presence of actual constancy of steric interactions of cis-located substituents in H-C=N-H and H-C=N-Me fragments. Reduction of negative charge on N atom when going from HN-imines to MeN-imines [ – 0.6503) (I) and –0.452е (II), –0.679 (IV) and –0.494е (V), -0.664 (Z-VII) and -0.478e (Z-VIII), - 0.677 (E-VII) and -0.478e (E-VIII), respectively] under actual equality of charges on the atom C= in the compared imines [-0.081 (I) and –0.090 (II), 0.297 (IV) and 0.297 (V), 0.116 (Z-VII) and 0.116 (Z-VII), 0.122 (E-VII) and 0.120е (E-VIII), respectively] indicates greater electron withdrawal of Me group in comparison with H. Observed reduction of negative charge on atom N in MeN-imines II, V, Z-VIII and E-VIII is determined by interaction of unshared electron pair * * of nitrogen atom (nσN) with antibonding orbitals (σ NC-H) and Rydberg orbitals (X ) of N-Me- group, that are absent in HN-imines I, IV, Z-VII and E-VII. At the same time for ground state * b) (GS) of imines II, V, Z-VIII and E-VIII energy of interaction nσN-σ NC-H (8.76 , 10.27, 7.80 and * 8.67 kcal/mol, respectively) is higher than energy of “reverse interaction” σNC-H-N (3.99, 5.03, * * 4.31 and 4.48 kcal/mol, respectively), while sum of interaction energies nσN-C , nσN-H and core orbital of atom N with Rydberg orbitals C* (5.49, 5.08, 4.72 and 5.43 kcal/mol, respectively) is higher than sum of interaction energies of core orbital of atom C with Rydberg orbitals N* (0.87, 0.73, 1.68 and 0.71 kcal/mol, respectively). Indirectly equality of valent angles H-N=C in model HN-imines I, IV, Z-VII and E-VII (111.3о3), 111.1о, 111.1о and 111.3о, respectively) that contain cis-located substituents in H-C=N- H and Me-C=N-H fragments indicates approximate constancy of steric interactions of cis-located substituents – H-C=N-H and H-C=N-Me. Therefore, introducing cis-MeC-group does not affect relatively labile valent angle C=N-H. Direct comparison of valent angles C=N-H and C=N-Me in similar imines I and II, Z-VII and Z-VIII, E-VII and E-VIII is not correct because of their lability and dependence from N atom inversion barrier value. In such a way, angle C=N-R increases abruptly in the imine series I, IV (R=H), II, V (R=Me) and III, VI (R=t-Bu), amounting respectively to 111.3о, 111.1о; 118.2о, 121.3о; 122.0о, 126.9о whereas angle N=C-R1 for these imines I-III and IV, V practically does not depend on substituent at N atom, amounting respectively to 124.7о, 123.3о; 124.9о, 125.0о; 125.9о. Similarly, angles C=N-R in imines Z-VII and Z-VIII, E-VII and E-VIII are respectively 111.1о and 120.0о, 111.3о and 118.5о, whereas angles N=C-R1 for these imines amount to 127.8оand 129.2о, 122.3о and 121.0о respectively. Direct estimation of contribution of steric interaction of cis-located substituents at C=N ≠ fragment on the value ∆GI shows that in isomeric imines Z-VII and E-VII trans-location of MeC- and HN-groups is more favorable only by 1.1 kcal/mol than cis-location. At the same time, replacing HN- by MeN group results in ground state destabilization of imine Z-VIII in comparison with E-isomer by 4.22 kcal/mol. Comparable results are obtained when estimating full steric energy by molecular mechanics method MMFF94 for imines Z-VII and Z-VIII, E-VII and E-VIII (6.96 and 11.58, 6.44 and 9.09 kJ/mol. On the whole contribution of steric constituent

3) data calculated by BH&HLYP method b) data obtained by NBO analysis Conference on Current Trends in Computational Chemistry 2004 143

≠ in ∆GI value increases sharply with increasing of total volume of interacting substituents. ≠ Thereafter, observed decreasing of ∆GI values in the imines series IV, V or Z-VII, Z-VIII is determined by dominating contribution of steric interactions of cis-located substituents. 2. Inversion barriers of N atom decrease as it was expected [3] with increasing of C- substituent size (imines II, V; III, VI; II, Z-VIII; E-VII, Z-VII and E-VIII, Z-VIII). At the same ≠ time for HN-imines ∆GI grows when the size of C-substituent increases (imines I, IV; I, E-VII; Z-VII, IV). Barrier increases even for MeN-imines when going from imine II to imine E-VIII. ≠ Anomalous ∆GI increasing in imine IV (as has been stated above) is stipulated by dominating contribution of rising σ-electron withdrawal of C-substituent – in the presence of actual constancy of steric interactions of cis located substituents. Reduction of negative charge on C= atom when going from HC-imines to MeC-imines [–0.081а) (I) and 0.297е (IV); -0.081 (I) and 0.122e (E-VII); 0.116 (Z-VII) and 0.297e (IV); –0.090 (II) and 0.120 (E-VIII)] under actual equality of charges on the atom N in the compared imines [-0.650 (I) and -0.679е (IV); -0.650 (II) and –0.677е (E-VII); -0.664 (Z-VII) and –0.679е (IV); -0.452 (II) and –0.478e (E-VIII)]. As ≠ it was expected σ-electron withdrawal of C-substituents exerts smaller influence on ∆GI than ≠ σ-electron withdrawal of N-substituents. ∆GI value for isomeric MeN- and MeC-imines that have comparable steric contributions of cis located groups in MeN=CH and HN=CMe fragments, is considerably higher for MeN-derivatives [30.75c) (II) and 27.55 (Z-VII), 31.36 (E- VIII) and 29.23 (IV) kcal/mol]. Thus, analysis of calculated inversion barriers values requires separate consideration of HN- imines and N-alkylimines. 3. Rotation barrier around С=N bond decreases with growth of N-substituent size (imines II, III; IV-VI). At the same time when going from HN-imines to corresponding MeN-imines inversion barriers increase (imines I, II; Z-VII, Z-VIII and E-VII, E-VIII); exception is passage from imine IV to imine V. Thus in concerned imines change of N substituent volume equally influences on the values of rotation (p.3) and inversion (p.1) barriers. Thereafter, factors, that determine the changing of these barriers are identical as well. It should only be noted that despite mechanism differences of inversion and rotation and differences in transition states of these ≠ ≠ processes, observed analogy of changing ∆GI и ∆GR is determined probably by relative stabilization of imines ground state when going from HN- to MeN-derivatives. 4. Rotation barriers around С=N bond decrease with growth of C-substituent size (imines I, ≠ IV; II, V; III, VI; E-VII, Z-VII and E-VIII, Z-VIII). In this connection values ∆∆GR (difference ≠ between ∆GR values of HC- and MeC-imines with the same N-substituents) increase with ≠ growth of N-substituent size. In symmetrically C-substituted imines ∆∆GR values are: in HN- imines I, IV - 4.18c), in MeN-imines II, V - 8.27, in t-BuN-imines III, VI - 14.49 kcal/mol; in ≠ non-symmetrically C-substituted imines ∆∆GR values are considerably less than in similar C- substituted ones: in HN-imines E-VII, Z-VII – 1.09, in MeN-imines E-VIII, Z-VIII – 4.21 ≠ kcal/mol. Thus in contrast to influence of C-substituent size on ∆GI (p.2), increase of C- ≠ substituent size always results in decrease of ∆GR . This probably is a consequence of difference between transition states of inversion and rotation and indicates on stabilization of rotation transition state by introduced MeC-group. Analysis of NPA charges on the C and N atoms of GS and TS of stated above imines shows that π-C=N bond is broken heterolytically during rotation resulting in formation of carbocatione center which stabilizes rotational TS. As follows from above stated, observed reduction of inversion and rotation barriers with increasing of N and/or C-substituents size is determined mainly by increasing of steric strain in ground states of concerned imines, i.e. relative increase of their energies and as a result by approaching of ground state to transition one. Thus, the study of steric influence of non-

c) data calculated by MP2(full) method 144 Conference on Current Trends in Computational Chemistry 2004

conjugated with C=N group substituent on Z, E-isomerization barriers of imines does not permit to establish mechanism of isomerization.

References 1) Gordon M.S., Fischer H. J. Am. Chem. Soc., 1968, vol. 90, p. 2471 2) Josefredo R. Pliego Jr. et. al. J. Braz. Chem. Soc., 1999, vol. 10, №5, 381-388 3) J.M. Lehn Topics in Current Chemistry, 1970, Band 15, Heft 3, p. 311- 377

Acknowledgement. D. Yu. Afanasiev would like to thank Dr. Jerzy Leszczynski for his help and interest in the topic. Conference on Current Trends in Computational Chemistry 2004 145

Density Functional and Configuration-based Methods for Large Systems: The Fourier Transform Coulomb Method and Full- accuracy Local MP2

Peter Pulay

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA

Several new methods, intended for efficient calculations on large molecules, and implemented recently our laboratory, will be described. The Fourier Transform Coulomb (FTC) method [1] uses an intermediate plane wave expansion for the calculation of the Coulomb term in density functional calculations. Compared to the Density Fitting (DF) method (also called RI, Resolution of Identity), it yields microhartree accuracy and linear scaling. Our program shares the goals and the basic techniques of the GAPW method pioneered by the Parrinello group [2] but aims at higher precision and full compatibility with the usual Gaussian programs. Efforts to remove the remaining major bottlenecks in DFT calculations, primarily the evaluation of the exchange-correlations term, as well as parallel implementation on distributed-memory computers [3], will be discussed. Second-order many-body perturbation theory with the Møller-Plesset partitioning (MP2) is the simplest and most widely used configuration-based correlation theory, and is superior to DFT when dispersion forces are important. Our recent work in this area includes an efficient parallel canonical MP2 [4,5] that can be applied to systems with over a hundred atoms and 2000 basis functions, dual-basis MP2 [6], full accuracy local MP2 [7], and atomic orbital formulated MP2 gradients [8]. Generalization to higher order (Coupled Cluster, CC) methods will be discussed in connection with the Array Files middleware [9]. This software allows transparent parallel disk storage of, and efficient access to intermediate arrays in CC and similar calculations.

References L. Füsti-Molnár and P. Pulay, The Fourier Transform Coulomb Method: Efficient and Accurate Calculation of the Coulomb Operator in a Gaussian Basis, J. Chem. Phys., 2002, 117, 7827. M. Krack and M. Parrinello, All-electron ab initio Molecular Dynamics, Phys. Chem. Chem. Phys. 2000, 2, 2105. J. Baker, L. Fusti-Molnar, and P. Pulay, Parallel Density Functional Theory Energies using the Fourier Transform Coulomb Method, J. Phys. Chem. A. 2004, 108, 3040. P. Pulay, S. Saebo, and K. Wolinski, Efficient Calculation of Canonical MP2 Energies, Chem. Phys. Lett. 2001, 344, 543. J. Baker and P. Pulay, An Efficient Parallel Algorithm for the Calculation of Canonical MP2 Energies, J. Comput. Chem. 2002, 23, 1150. K. Wolinski and P. Pulay, Second-Order Møller-Plesset Calculations with Dual Basis Sets, J. Chem. Phys., 118, 9497-9503 (2003). S. Saebo and P. Pulay, A Low-Scaling Method for Second-Order Moller-Plesset Calculations, J. Chem. Phys. 2001, 115, 3975. S. Saebo, J. Baker, K. Wolinski and P. Pulay, An Efficient Atomic Orbital Based Second-Order Møller-Plesset Gradient Program, J. Chem. Phys. 2004, 120, 11423. Y. Zhang, A. Apon, and P. Pulay, File Arrays for Out-of-Core Computations , Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, Las Vegas, Nevada, June, 2003. 146 Conference on Current Trends in Computational Chemistry 2004

Microscopic Theory of Surface-enhanced Raman Scattering from Molecules Adsorbed at Noble-metal Nanoparticles

V. N. Pustovit, K. Walker, and T. V. Shahbazyan

Department of Physics, Jackson State University, P.O. Box 17660, Jackson, Mississippi 39217 USA

Surface-enhanced Raman scattering (SERS) from molecules adsorbed on small metal particles has attracted increasing interest during past two decades. The main SERS mechanism has electromagnetic (EM) origin and is due to the strong surface plasmon (SP) local field near the metal surface [1] (see also [2] for review of all SERS mechanisms). Recent observations of enormous (up to 1015) enhancement of single-molecule Raman scattering [3] as well as emerging possibilities of nanoparticle-based Raman sensors [4] have prompted a new interest in single particle SERS and, in particular, in finite-size effects in small nanoparticles. Although classical EM enhancement is size-independent, quantum corrections due to the discreteness of the electron spectrum result a weaker enhancement in small nanoparticles. Here we describe a novel finite-size quantum-mechanical mechanism that leads to a relative increase of SERS in small noble-metal particles. This mechanism stems from different effect that the confining potential has on s-band and d-band electrons. Namely, the spillout of delocalized s- electrons beyond the classical nanoparticle boundary results in an incomplete embedding of sp- electron distribution in the background of localized d-electrons whose density profile follows more closely the classical shape. In the absence of d-electron population in the nanoparticle surface layer, the effective dielectric constant is reduced relative to the bulk, giving rise to a blue shift of the SP resonance in Ag nanoparticles [5]. Specifically, we performed calculations of the local field and Raman enhancement factor, based on time-dependent local-density approximation, in small Ag nanoparticles. We found that, the effect of underscreening of s-electrons by d-electrons in the surface layer leads to a stronger SP local field acting on a molecule located in a close proximity to the metal surface. This results in an additional enhancement of the Raman signal. Importantly, such an enhancement becomes more pronounced for small nanoparticles due to the larger volume of surface layer.

Supported by NSF under grants DMR-0305557 and NUE-0407108, by NIH under grant 5 SO6 GM008047-31, and by ARO under grant DAAD19-01-2-0014.

References [1] G. C. Schatz and R. P. Van Duyne, in “Handbook of Vibrational Spectroscopy”, J. J. Chalmers and P. R. Griffiths, eds., (Wiley, 2002). [2] K. Kneipp, H. Kneipp, I. Itzkan, R. R. Dasari, and M. S. Feld, Chem. Rev. 99, 2957 (1999). [3] S. Nie and S. R. Emory, Science 275, 1102 (1997). [4] Y. C. Cao, R. Jin, and C. A. Mirkin, Science 297, 1536 (2002). [5] A. Liebsch, Phys. Rev. 48, 11317 (1993).

Conference on Current Trends in Computational Chemistry 2004 147

Figure 1. Calculated absorption spectrum of Ag nanoparticles for surface layer without (solid line) and with surface layer with thickness 2 a.u. (dashed line) and 4 a.u. (dotted line). With increasing thickness, the blueshift is accompanied by an increase in amplitude indicating an enhancement of the SP local field.

Figure 2. Calculated size-dependence of SERS for various surface layer thicknesses. For finite thickness, the relative increase in SERS for small nanoparticles is stronger due to larger volume fraction of underscreened region. 148 Conference on Current Trends in Computational Chemistry 2004

Inhibition CETP activity of (R)-Chiral Halogenated Substituted N- Benzyl-N-Phenyl Aminoalcohol Compounds: A QSAR Study

Bakhtiyor Rasulev, Ashton T. Hamme, Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Jackson State University, 1325 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi, 39217-0510, USA

Elevated lipid level is supposed to be one of the main risk factors of atherosclerosis and subsequent cardiovascular disease. A lipid lowering is one of the major tasks in cardiovascular disease treatment and prevention. Therefore, there is a great necessity to acquire activity of the drugs inhibiting cholesteryl ester transfer. The present work is devoted to identification of the structural features, which determine the inhibition cholesteryl ester transfer protein (CETP) activity. A Quantitative Structure-Activity Analysis (QSAR) has been performed for dataset of 39 compounds. Investigated compounds have been showed a good CETP activity for the species in which (R)-Chiral halogenated substituted N-benzyl-N-phenyl aminoalcohol compounds exists. For these compounds a large set of the theoretical descriptors (2D, 3D, constitutional, topological and etc), including quantum- chemical parameters have been calculated. The quantum-chemical descriptors have been obtained from ab initio calculations at the DFT B3LYP/6-31G(d,p) level of theory. Combining obtained data (descriptors) we constructed activity profile using Genetic Algorithm variable selection method with Multiple Linear Regression Analysis QSAR approach.

We gratefully acknowledge the support of National Science Foundation RISE grant No.HRD-0401730. Conference on Current Trends in Computational Chemistry 2004 149

Molecular Design for Octupolar Nonlinear Optical Systems: Structure-Function Relationship and Solvent Effects

Paresh Chandra Ray and Jerzy Leszczynski

Department of Chemistry, Jackson State University, Jackson, MS, USA, 39217

We present a quantum-chemical analysis of the molecular structure and first hyperpolarizabilities of a series of push-pull octupolar nonlinear optical systems. Ab initio coupled perturbed Hatree-Fock (CPHF) calculations using 6-31G** basis set have been performed to investigate the static first hyperpolarizabilities (β0) of those NLO chromophores. The effect of donor or acceptor substitution and also elongation of the conjugation path length are established to demonstrate the engineering guidelines for enhancing molecular optical non- linearities. The solvent induced effects on the NLO properties are studied by using the self- consistent reaction field (SCRF) method. Dynamic first hyperpolarizability (β) was investigated using ZINDO/SOS method including solvent effects. Theoretical results will be compared with the experimental values wherever available in the literature and the results are evaluated in detail about the agreements and disagreements between theoretical and experimental findings. 150 Conference on Current Trends in Computational Chemistry 2004

Ribosomal RNA Kink-turn Motif – A Flexible Molecular Hinge

Filip Razga1, Nada Spackova2, Kamila Reblova1, Jaroslav Koca1, Neocles B. Leontis3 and Jiri Sponer2

1National Centre for Biomolecular Research, Kotlarska 2, 61137 Brno, Czech Republic, 2Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic, 3Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403

Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in “V” shaped structures, recurrently observed in ribosomes and showing high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their x-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behaviour of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is it ability to investigate the region immediately around their ribosomal-like geometries. This part of the conformational space is not well characterised by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large– scale motions or they can allow a smooth assembling of the other parts of the ribosome. Conference on Current Trends in Computational Chemistry 2004 151

Conformational Study of Cyclic Dienes and Cycloalcaines by Computational Method

Jose Luis Moncada Reyes, Dewakar M. Pawar, Erick A. Noe

Jackson State University, Department of Chemistry, 1400 J. R. Lynch Street, Jackson, MS 39217-0510

The conformational space was searched for cyclooctyne (1), cyclononyne (2), cyclodecyne (3), cycloundecyne (4), 1,2 - cycloctadiene (5), 1,2-cyclodecadiene (6), and 1,2 - cyclododecadiene (7) with Allinger's MM3 molecular mechanics programs, and free energies were obtained at two different temperatures. Calculations were repeated for low - energy conformation with ab initio methods until HF/6-311G(d) level was reached. The results obtained at this level were compared with MM3 results. For example, MM3 predicts conformer 1a of cyclooctyne to be lower in strain energy and free energy than 1b by 6.578 and 6.978 kcal/mol (25°C), and the ab initio calculations predict a free-energy difference of 4.086 kcal/mol at the HF/6-311G(d) level. Molecular symmetries, relative strain energies, and relative free energies for conformations of compounds 1-7 will by presented. Experimental work is in progress.

This work was supported by NSF - CREST Grant No. HRD - 980 5465. 152 Conference on Current Trends in Computational Chemistry 2004

Calculated Surface Electrostatic Potential Maxima as Measures of the Stabilities of Carbocations

Adele M. Robbins, Ping Jin, Jane S. Murray and Peter Politzer

Department of Chemistry University of New Orleans New Orleans, LA 70148

When a hydrocarbon or substituted hydrocarbon loses a hydride ion, it becomes positively charged and is referred to as a carbocation. Carbocations are important in organic chemistry, both as intermediates in reactions, such as nucleophilic substitution reactions, and as components of compounds containing highly polar C+C− linkages. The stability of any particular carbocation is viewed as being determined by how well its molecular framework can delocalize the positive charge on the system; that stability decreases in the order 3° > 2° > 1° > methyl is a general rule of thumb learned by every student in the first semester of organic chemistry. The purpose of this work has been to investigate whether the computed electrostatic potential V(r) might prove to be an indicator of how well the positive charge in a carbocation is delocalized. In this poster, we demonstrate for a series of carbocations that the computed surface electrostatic potential maxima, VS,max, associated with the carbons that have lost the hydride ions correlate with their relative stabilities, with stability increasing as VS,max decreases. We have computed optimized geometries and electrostatic potentials at the HF/6-31G* level. Our surfaces are defined as the 0.001 electrons/bohr3 contour of the electronic density. Conference on Current Trends in Computational Chemistry 2004 153

An Attempt to Bridge the Gap between Computation and Experiment for Nonlinear Optical Properties

Zuhail Sainudeen and Paresh Chandra Ray

Department of Chemistry, Jackson State University, Jackson, MS, USA, 39217.

We present a quantum-chemical analysis of the influence of solvents on the first hyperpolarizability of nonlinear optical (NLO) molecules. The molecular geometries are obtained via BL3YP/6-31G** optimization. The effect of several type of interaction between solute and surrounding solvent molecules are established to demonstrate the engineering guidelines for enhancing molecular optical non-linearities. The solvent induced effects on the structure and NLO properties are studied by using the self-consistent reaction field (SCRF) / polarizable Continium model (PCM) method. Dynamic first hyperpolarizability (β) was investigated using ZINDO/SOS method including solvent effects. Theoretical results will be compared with the experimental values wherever available in the literature . 154 Conference on Current Trends in Computational Chemistry 2004

Ab Initio Density Functional Theory via Second-Order Perturbation Theory: Energies, Exchange-Correlation Potentials, Dipole Moments, and Ionization Potentials

Igor V. Schweigert, Victor F. Lotrich, and Rodney J. Bartlett

Quantum Theory Project, Department of Chemistry University of Florida, Gainesville, FL 32611-8435

Ab initio Density Functional Theory uses wave-function-based many-body methods to construct the exchange-correlation functional, the cornerstone of DFT methods. In this approach, the exchange functional is exact since the exchange energy is known in terms of orbitals. The correlation functional can be obtained, for example, via finite-order perturbation theory, as originally proposed by Görling and Levy [1]. The resulting exchange-correlation functional implicitly depends on the density via orbitals and the corresponding local potential is obtained using the Optimized Effective Potential method. Our implementation of the second-order OEP method [2] improves upon the original Görling-Levy scheme by exploiting the freedom in partitioning of the Hamiltonian for the perturbative expansion. While the Görling-Levy scheme significantly overestimates correlation effects, a particular choice of the partitioning provides a balanced description of the correlation at the second-order level. As we demonstrate in applications to a large set of closed-shell molecules, the OEP2 method goes far beyond conventional Kohn-Sham DFT and improves upon Møller-Plesset perturbation theory, at the price of an iterative second-order scheme. To assess the quality of the OEP2 energy functional and associated density we compare the total energies and dipole moments calculated with the OEP2, MP2, several density-dependent DFT functionals, and Coupled Cluster methods. We also demonstrate that, unlike any density-dependent functionals, the ab initio exchange-correlation functional corresponds to a qualitatively correct potential. We also demonstrate that the OEP2 method results in improved single-electron spectra, with the occupied orbital energies giving reasonable estimation of the ionization potentials.

References [1] A. Görling and M. Levy, Phys. Rev. A 50, 196 (1994) [2] R.J. Bartlett, V.F. Lotrich, and I.V. Schweigert, J. Chem. Phys. (submitted) Conference on Current Trends in Computational Chemistry 2004 155

Soft Film Growth: Density Profile and Roughness by Kinetic Monte Carlo Simulation

Adam Seyfarth, Ras Pandey and Ray Seyfarth

Mobile constituents (monomer particles for the film fabrication) of molecular weight Mp and covalent functionality f are initially placed randomly on a fraction p of the lattice Lx*Ly*Lz. A particle occupies a unit cube (i.e., eight sites) and a lattice site cannot be shared by more than one particle due to excluded volume. Particles interact with neighboring particles and empty sites (the effective medium) with a certain range. The Metropolis algorithm is used to move particles energetically using Boltzmann distribution to one of their 26 neighboring sites. When a particle is next to the absorbing substrate, a bond is formed between them. Bonded particles are still mobile as long as the bond length stays within certain limits (2 and sqrt(10) with an exception of sqrt(8) ). A Monte Carlo time step is defined by the number of attempts to move each particle once. After each hopping attempt, a particle reacts with one of its neighboring monomers by forming a covalent bond with a probability P_B subject to

(i) availability of reactive bonds in each functional group with at least (ii) one of the two monomers having already reacted at least once.

The constituents hop and bond as the reaction proceeds from the substrate. The growth of the density profile and the interface width with time are evaluated as a function of monomer concentration (p) and reaction probability P_B. Analysis of the interface growth and roughness will be presented as the data becomes available. 156 Conference on Current Trends in Computational Chemistry 2004

UV-Induced DNA Damage: A Theoretical Investigation on Guanine Base under Different Hydrogen Bonding Environments

M.K. Shukla and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University 1400 J.R. Lynch Street, Jackson, MS 39217 (USA)

The phenomena of hydrogen bonding are ubiquitous. H-bonds may be classified in the following way: those for which H-bond energies are about 15-40 kcal/mol are known as strong ones; the range of 4-15 kcal/mol is for moderate H-bonds and 1-4 kcal/mol for weak ones. Guanine is an important brick of building blocks of nucleic acids. It is hydrogen bonded with cytosine with three hydrogen bonds. It shows the maximum tautomeric activity among the natural nucleic acid bases. Recent experimental investigations in supersonic beam show that guanine can have four tautomeric forms (keto-N9H, keto-N7H, enol-N9H, enol-N7H). Ab initio computational study was performed to study effect of hydrogen bonding on the ground and lowest singlet ππ* excited state geometry of guanine. The studied systems consisted of isolated guanine, guanine complexed with three, five and six-water molecules in the first solvation shell, guanine-cytosine base pair and guanine-guanine base pair with two different hydrogen bonded orientations (GG16 and GG17). Ground state geometries were optimized at the Hartree-Fock level while excited state geometries were optimized at the CIS level. The 6- 311G(d,p) basis set was used in all calculations. The nature of potential energy surfaces was ascertained via the harmonic vibrational frequency analysis; all structures were found minima at the respective potential energy surfaces. It was found that while the ground state ring geometry of guanine is planar, the excited state geometry was found to be deformed in the N1C2N3 part of the ring in all cases except that of GG16 base pair. In the case of GG16 base pair, geometry of guanine was revealed to be planar; while both monomers were slightly folded along the perpendicular direction of hydrogen bonds. The change in hydrogen bond strngths and different stretching modes of guanine consequent to hydrogen bonding and electronic excitations are also discussed. Conference on Current Trends in Computational Chemistry 2004 157

GG16

GG17

G

G+3W

G+5W

G+6W

GC

Figure. Geometry of guanine and its different complexes in the lowest singlet ππ* excited state.

Acknowledgement. Authors are thankful for NSF-CREST grant No. HRD-0318519, ONR grant No. N00034-03-1-0116, NIH-SCORE grant No. 3-S06 GM008047 31S1 and NSF-EPSCoR grant No. 02-01-0067-08/MSU for financial assistance. Authors are also thankful to Mississippi Center for Supercomputing Research (MCSR) for the generous computational facility. 158 Conference on Current Trends in Computational Chemistry 2004

Time-Dependent Density Functional Theory (TDDFT) Investigation on Electronic Transitions of Thiouracils in the Gas Phase and in Solutions

M.K. Shukla and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University 1400 J.R. Lynch Street, Jackson, MS 39217 (USA)

Significant changes in the photophysical properties of molecules are revealed when the carbonyl groups are substituted by thiocarbonyl groups. Consequently, the lowest singlet ππ* and nπ* states of thiocarbonyl containing molecules have significantly lower energy than the corresponding carbonyl containing molecules. The thio analogs of uracil, namely, 2-thiouracil (2TU), 4-thiouracil (4TU) and 2,4-dithiouracil (DTU) have been found to possess notable biological and pharmacological activities. The thio analogs of uracil, namely, 2TU, 4TU and DTU have been the subject of several experimental and theoretical studies. All theoretical investigations have suggested that these molecules exist in the keto-thione (dithione in the case of DTU) form, both in the gas phase and in aqueous solution. However, in experimental studies the observed electronic transitions for 2TU and DTU were explained in terms of the thione-thiol tautomeric forms. Therefore, this work was undertaken to resolve existing ambiguity regarding the existence of different tautomers of thiouracils in different solutions. The ground state geometries of different tautomers were optimized at the B3LYP level using the 6-311++G(d,p) basis set. Single point energy calculations were performed at the MP2/cc- pVTZ level using the B3LYP/6-311++G(d,p) geometries. Geometry optimizations for the most stable tautomers of each species were also performed at the MP2/cc-pVTZ level. Vertical electronic transition energies were computed at the time-dependent density functional theory level (TDDFT) using the B3LYP functional and the 6-311++G(d,p) basis set and utilizing the B3LYP/6-311++G(d,p) geometries. The effect of water and acetonitrile solutions on the ground and excited states were computed using the Polarizable Continuum Model (PCM).

Figure 1. General structure and atomic X4 numbering scheme of uracil (X2=X4=O), H5 2TU (X2=S, X4=O), 4TU (X2=O, X4=S) C4 and DTU (X2=X4=S). The N1 and N3 methyl derivatives can be obtained by the N3 C5 H3 substitution of methyl group at the relevant site of the corresponding molecule. C2 C6 H6 X2 N1

H1

Conference on Current Trends in Computational Chemistry 2004 159

5.5 B C 5.0 D E F 4.5 G H I 4.0

3.5

3.0 Excitation Energy (eV) Energy Excitation 2.5

2.0 U 2TU 4TU DTU

Figure 2. Variation of computed transition energies of uracil and thiouracils; B: 3ππ* in gas, C: 3ππ* in water, D: 3nπ* in gas, E: 3nπ* in water, F: 1ππ* in gas, G: 1ππ* in water, H: 1nπ* in gas, and I: 1nπ* in water.

It was revealed that all thiouracils, namely, 2TU, 4TU and DTU studied here would be present in the keto-thione (dithione in case of DTU) tautomeric form in the gas phase and in water and acetonitrile solutions. The TDDFT computed transition energies are generally in good agreement with the corresponding experimental data. In the case of 2,4-dithiouracil, an anionic form of the molecule obtained by the deprotonation of the N1H site may also be present in the water and acetonitrile solutions. Further, the spectral features of DTU were found to be complex. Uracil and all thiouracils studied here have the ππ* type of the lowest triplet state in the gas phase and in water and acetonitrile solutions. In going from uracil to mono-thio substituted uracil, the computed lowest singlet nπ* and triplet ππ* and nπ* transition energies were found to decrease linearly, the transition energies for 2TU were found to be in between the transition energies of uracil and 4TU. Further, the transition energies of 4TU and DTU were found similar. In the case of the lowest singlet ππ* transition, the transition energy for 2TU and 4TU is similar, although, it is decreased in going from uracil to mono-thio substituted uracil. The di-thiouracil has the lowest transition energy.

Acknowledgement. Authors are thankful for NSF-CREST grant No. HRD-0318519, ONR grant No. N00034-03-1-0116, NIH-SCORE grant No. 3-S06 GM008047 31S1 and NSF-EPSCoR grant No. 02-01-0067-08/MSU for financial assistance. Authors are also thankful to Mississippi Center for Supercomputing Research (MCSR) for the generous computational facility. 160 Conference on Current Trends in Computational Chemistry 2004

Atom-Like Building Blocks for Nanotechnology Fullerene Molecules with Substitutions

T. M. Simeon, I. Yanov, and J. Leszczynski

Computational Center for Molecular Structure and Interactions Jackson State University 1400 J.R. Lynch Street, Jackson, MS 39217

Introducing heteroatoms into the frame of fullerene (C60) brings up new and fascinating properties of this compound and raises new fundamental questions about their stability, structure and chemical behavior. The unique properties of these molecules allow for the assumption that in the future they will be widely used for the creation of new materials. Another important member of the fullerene family C50, is quite possibly the most stable fullerene with n<60, but the theoretical information on C50 is very limited [1]. Bakowies et. al provided structures for 30 polyhedral carbon clusters and provided their structures, heats of formation and orbital energies. C50 is one of these cages and several symmetries of C50 were proposed [2]. The fullerene C50 has scarcely been studied and the properties of these systems need to be further explored. The purpose of this study is to elucidate and compare the physical and chemical properties of modified C60 and C50 and its derivatives. Their electronic structure and properties will be discussed in detailed.

References [1]. Q.S. Li, Y. Wang and W. G. Xu, Journal of Molecular Structure, 531(2000) 119-125. [2]. D. Bakowies, W. Thiel, Journal American Chemical Society, 113(1991) 3704. Conference on Current Trends in Computational Chemistry 2004 161

Interactions of Isoniazid and Its Derivatives with Mycobacterium Tuberculosis Susceptible Enzyme: Molecular Modeling and Docking Studies

K.Q. Sohail, I. Pazilah, A.W. Habibah

School of Pharmaceutical Sciences, University Sains Malaysia, 11800 USM. Penang. Malaysia.

In this study, the molecular basis of resistance in Mycobacterium tuberculosis was analyzed and the susceptibility of mycobacterium to isoniazid was compared with its derivatives. The main emphasis was to compute the atomic and molecular interactions associated with the binding of antitubercular drugs with InhA, an enzyme involved in the biosynthesis of mycolic acids in Mycobacterium tuberculosis. Fourteen ligand molecules were studied. The ligands were isoniazid and its derivatives and I-NADH. Molecular docking technique was used to generate the docked complexes of each ligand with InhA. In order to find the cause of resistance developed in mutant strains, the docked conformations of I-NADH were compared with the wild-type and the mutant-type InhA. The major structural difference found was the repositioning of adenine ring instead of its original position in the wild-type InhA that cause a decrease in affinity with phenylalanine 41 and an increased interactions from the mutant residue alanine 94, thus drifting from its ideal position. This drift in the position of phenylalanine 41 due to mutant alanine 94 may have altered the direction and position of isonicotinic acyl group attached to NADH at the other end facing amino acid phenylalanine 149. The study suggests that this particular change in the structure of I-NADH with respect to InhA could be the major cause of resistance developed in Mycobacterium tuberculosis. In the case of derivatives, INH14 (1-isonicotinyl-2-tetradecanoyl hydrazine) and INH16 (1-isonicotinyl-2-hexadecanoyl hydrazine) showed marked increase in binding affinity compared to isoniazid. Further studies on derivatives could prove useful in the design of a new generation of antitubercular drugs. 162 Conference on Current Trends in Computational Chemistry 2004

A DFT Study of the Methane Activation by Unique Transition-Metal Ion Structures in Co(1+)/ZSM-5, Ni(1+)/ ZSM-5 AND Cu(1+)/ZSM-5 Zeolites

Vitali Solkan, Aleksandr Serykh, and Jerzy Leszczynski

N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr.47, Russian Federation Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Str., Jackson, MS 39217, USA.

The Cu ion exchanged zeolites, in particular Cu-ZSM-5, exhibit high activity for the catalytic decomposition of NO [1] and for selective catalytic reduction of NO by C3 and C4 hydrocarbons in excess of oxygen. High-silica zeolites ZSM-5 containing Co (2+) and Ni(2+) cations are known to be active catalysts for selective catalytic reduction (SCR) of NO by methane [2-5] and for N2O decomposition to nitrogen and oxygen. However, as a rule, SCR catalysts contain alter-valent cations [6-7]. Hence, one can expect that reduced cobalt and nickel sites in Co-ZSM-5 or Ni-ZSM-5 could play an important role in some reaction stages. A peculiarity of Co-ZSM-5 is that it is an active catalyst for reduction of NO with methane even in absence of oxygen. Thus, we could speculate that, under these reaction conditions, cobalt ions in Co-ZSM-5 would change their oxidation state between Co(2+) and Co(1+). The electronic properties of TM-ions vary, depending on the coordination environment. Therefore, the TM ability to bind methane can strongly depend on the TM-cation sitting site. FTIR studies of the interaction of these sites with CH4 probe molecules are common in the literature. The shift in C- H bond stretching frequency, upon complexation with the TM ions exchanged in high-silica zeolites such as ZSM-5, can be used as a measure of the activation strength. Theoretical attempts to reflect the experimental frequency shifts using Hartree-Fock theory have been very limited in their success. More resent studies at the MP2 and density functional level have shown improvement when compared to experimental data. We present herein a density functional study of the interaction of methane with Cu(1+)(3d10), Co(1+) (3d74s1), and Ni(1+) (3d84s1), exchanged zeolite ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 3T-cluster and 5T-ring, 6T-ring, and 10T-ring (T denoted tetrahedral Al and Si atoms), where there are single framework Al atom in rings containing five, six or ten T atoms, one of which is Al atom. The largest cluster, [AlSi9O16H20](1-) M(1+), is a complete 10- membered-ring cluster of the main channel of ZSM-5. The T3-cluster ((SiH3)-O-Al(OH)2-O- - (SiH3)) is picked out from the 10-ring structure of the ZSM-5 zeolite. The Si atom of the central tetrahedral site (T-12 site) is substituted with an Al atom and the terminal dangling bonds are satisfied by H atoms. This model size is chosen because it is regarded as the smallest limit that guarantees a realistic description of the surface complex for the case of H-form zeolite. All the calculations were performed using nonlocal hybrid density functional theory (B3LYP functional). The Gaussian 98 program package was used in this study. For practical purpose, we employed a larger basis set only for the active site region, namely, the 6-311++G(d, p) basis set for CH4 molecule; the 6-31G(d) or CEP-31G basis sets for O, Si, Al, Cu, Co and Ni atoms; the 3- 21G basis set for hydrogen atoms. The TM-ions are the most exposed to probe molecule CH4 when sitting in “10T-ring” and on 3T-cluster. We report in detail the calculated results for CH4- TM(1+)- T3-clusters. In case of T3-cluster we employed a larger basis set only for the active site region, namely, the 6-311++G(d, p) basis set for CH4 molecule; the 6-311G(d) for Cu, Co and Ni Conference on Current Trends in Computational Chemistry 2004 163

atoms, and 6-31G(d, p) basis sets for H, O, Si, Al atoms. The geometry optimization of the studied CH4-TM(1+)-T3-clusters has been performed with no constraints imposed by the molecular symmetry. In accordance with DFT calculations, CH4 is bound on TM(1+)-ions in T3- cluster in a 2-fold configuration (figures 1-3). The calculated vibrational frequencies of adsorbed methane on 3T-cluster are presented in Table 1. A comparison of calculated vibrational frequencies for free methane and methane adsorbed on TM(1+)-T3-clusters indicates the strong perturbation of adsorbed methane. Comparing the red-shift of the C-H stretching modes caused by Co(1+) and Ni(1+) , one can see that the influence of Co(1+) is much stronger than that of Ni(1+). The results presented in Table 1 indicate the unusual activation power of the Cu(1+), Co(1+), and Ni(1+) ions adsorbed on 3T-cluster. The TM-ion activation of methane results in a weakening of the C-H bonds and hence can facilitate the dissociation of methane along a possible “alkyl path” at elevated temperatures [8]. One of the unique properties of these active sites is the changeable oxidation state. Another key property is the ability to activate C-H bonds, resulted in lowering of their stretching frequencies. Although Gaussian 98 evaluates only the harmonic vibration frequencies, the comparison of such values with experimental results proved very useful to analyze the induced changes in the IR spectra of the adsorbed probe molecules. Very recently it was found than a part of Cu(1+) ions in Cu-ZSM-5 unusually strongly adsorb and perturb molecular hydrogen [9] and methane [10].

Table 1. The calculated vibrational frequencies (units in cm-1) at B3LYP/6-311++G(d, p) level for adsorbed methane molecules on TM(+1)-T3-cluster. CH4 CH4…Co(1+)ZSM-5 CH4…Ni(1+)ZSM-5 CH4…Cu(1+)ZSM-5 1340 1204 1248 1253 1340 1406 1394 1385 1340 1441 1413 1427 1558 1495 1518 1525 1558 1672 1653 1679 3025 2583 2748 2634 3130 2814 2830 2942 3130 3102 3112 3116 3130 3162 3176 3179

The DRIFT-spectra of methane adsorbed at different pressures on Cu-ZSM-5 show two broad and very intense bands from adsorbed methane with extremely low-frequency maxima at -1 -1 2660 cm and 2616 cm [10], which was ascribed to ν1 vibration of strongly perturbed methane molecules adsorbed on two different Cu(+1) sites. The calculated frequency corresponding to ν1 vibration in CH4-Cu(1+)-T3-cluster is in agreement with the observed spectra. One should note that the similar low-frequency shift of ν1 vibrations of the adsorbed methane molecules has never been previously reported for CH4 adsorbed on any cationic forms of zeolites. 164 Conference on Current Trends in Computational Chemistry 2004

References

1. Y. Li and K. Hall, J. Catal., 1991, 129, 202. 2. X. Wang, H. Y. Chen, and W. M. H. Sachtler, J. Catal., 2001, 197, 281. 3. J. Tang et all. Catal. Lett. 2001, 73 193. 4. K. Hadjiivanov et all. Phys. Chem. Chem. Phys. 1999, 1, 4521. 5. S. K. Park, H. Choo, L. Kevan. Phys. Chem. Chem. Phys. 2001, 3, 3247. 6. K. Hadjiivanov, H. Knozinger, and M. Mihailovl. J. Phys. Chem. B 2002, 106, 2618. 7. K. Hadjiivanov et all. Phys. Chem. Chem. Phys. 2003, 5, 243. 8. M. V. Frash and R. A. van Santen, Phys. Chem. Chem. Phys. 2000, 2, 1085. 9. A. I. Serykh and V. B. Kazansky, Phys. Chem. Chem. Phys. 2004, 6, . 10. A. I. Serykh (unpublished results)

Figure 1 Figure 2

Figure 3 Conference on Current Trends in Computational Chemistry 2004 165

A DFT Study of the Dihydrogen Activation by Unique Transition- Metal Ion Structures in Co(1+)/ZSM-5 and Ni(1+)/ZSM-5 Zeolites

Vitali Solkan and Jerzy Leszczynski

N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr.47, Russian Federation Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Str., Jackson, MS 39217, USA.

Transition-metal (TM) ions exchanged in high-silica zeolites such as ZSM-5 and mordenite have recently attracted great attention as active sites for several selective redox reactions. High- silica zeolites modified by transition metal cations possess unusual catalytic properties. The Cu ion exchanged zeolites, in particular Cu-ZSM-5, exhibit high activity for the catalytic decomposition of NO [1] and for selective catalytic reduction of NO by C3 and C4 hydrocarbons in excess of oxygen. The activity of Cu ions differs for Si/Al ratios and Cu loading. High-silica zeolites ZSM-5 containing Co(2+) and Ni(2+) cations are known to be active catalysts for selective catalytic reduction (SCR) of NO by methane [2-5] and for N2O decomposition to nitrogen and oxygen. A peculiarity of Co-ZSM-5 is that it is an active catalyst for reduction of NO with methane even in absence of oxygen. However, as a rule, SCR catalysts contain alter- valent cations [6-7]. Hence, one can expect that reduced cobalt and nickel sites in Co-ZSM-5 or Ni-ZSM-5 could play an important role in some reaction stages. The electronic properties of TM-ions vary, depending on the coordination environment. Therefore, the TM ability to bind dihydrogen can strongly depend on the TM-cation sitting site. FTIR studies of the interaction of these sites with H2 probe molecules are common in the literature. The shift in H-H bond stretching frequency, upon complexation with the TM ions exchanged in high-silica zeolites such as ZSM-5, can be used as a measure of the activation strength. We present herein a density functional study of the interaction of dihydrogen with Co(1+) (3d74s1), and Ni(1+) (3d84s1)- exchanged zeolite ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 5T-ring, 6T-ring, and 10T-ring (T denoted tetrahedral Al and Si atoms), where there are single framework Al atom in rings containing five, six or ten T atoms, one of which is Al atom. The 10T-ring , [AlSi9O16H20](1-) M(1+), is a complete 10-membered- ring cluster of the main channel of ZSM-5. The largest 20T-cluster is picked out from the main channel of the ZSM-5 zeolite. The Si atom of the central tetrahedral site (T-12 site) is substituted with an Al atom, and the terminal dangling bonds are satisfied by H atoms. All the calculations were performed using nonlocal hybrid density functional theory (B3LYP functional). The Gaussian-98 program package was used in this study. For practical purpose, we employed a larger basis set only for the active site region, namely, the 6-31G(d, p) basis set for H2 molecule; the 6-31G(d) basis set for O, Si, Al, Co and Ni atoms; the 3-21G basis set for hydrogen atoms. We report in detail the calculated results for H2 TM(1+)-20T-clusters. The geometry optimization of the studied H2-TM(1+)-20T-clusters has been performed only for active site. In accordance with DFT calculations H2 is bound on TM(1+)-ions in 20T-cluster in a 2-fold configuration (figures 1-2). The calculated vibrational frequencies of adsorbed dihydrogen on 20T cluster are presented in Table 1. A comparison of calculated vibrational frequencies for free dihydrogen and H2 adsorbed on TM(1+)-20T-clusters indicates the strong perturbation of adsorbed H2. Comparing the red-shift of the H-H stretching mode caused by Co(1+) and Ni(1+) , one can see that the influence of Co(1+) is less stronger than that of Ni(1+).

166 Conference on Current Trends in Computational Chemistry 2004

Table 1. The calculated vibrational frequencies (units in cm-1) at B3LYP/6-31G(d, p) level for adsorbed H2 molecules on TM(+1)-20T-cluster. H2 H2 Co(1+)-20T-cluster (ZSM-5) H2 Ni(1+)-20T-cluster (ZSM-5) 4445 3636 3590

The results presented in Table 1 indicate the unusual activation power of the Co(1+), and Ni(1+) TM ions adsorbed on 20T-cluster. The TM-ion activation of dihydrogen results in a weakening of the H-H bond and hence can facilitate the dissociation of H2 at elevated temperatures. One of the unique properties of these active sites is the changeable oxidation state. Another key property is the ability to activate H-H bond, which resulted in lowering of its stretching frequency. Although Gaussian 98 evaluates only the harmonic vibration frequencies, the comparison of such values with experimental results proved very useful to analyze the induced changes in the IR spectra of the adsorbed probe molecules. Very recently it was found than a part of Cu(1+) ions in Cu-ZSM-5 unusually strongly adsorb and perturb molecular hydrogen [8]. The DRIFT spectra of H2 adsorbed at different pressures on Cu-ZSM-5 show two broad and very intense bands from adsorbed dihydrogen with extremely low-frequency maxima -1 -1 at 3075 cm and 3125 cm [8], which was ascribed to the stretching mode of a H2 molecules adsorbed on two different Cu(+1) sites. The calculated frequency corresponding to H-H stretching vibrations of adsorbed hydrogen molecule in H2-Co(1+)-20T-cluster is in agreement with the observed spectra. One should note that the similar low-frequency shift of H-H stretching vibrations of the adsorbed hydrogen molecules has never been previously reported for H2 adsorbed on cationic forms of zeolites.

References 1. Y. Li and K. Hall, J. Catal., 1991, 129, 202. 2. X. Wang, H. Y. Chen, and W. M. H. Sachtler, J. Catal., 2001, 197, 281. 3. J. Tang et al., Catal. Lett. 2001, 73, 193. 4. K. Hadjiivanov et al., Phys. Chem. Chem. Phys. 1999, 1, 4521. 5. S. K. Park, H. Choo, L. Kevan. Phys. Chem. Chem. Phys. 2001, 3, 3247. 6. K. Hadjiivanov, H. Knozinger, and M. Mihailovl. J. Phys. Chem. B 2002, 106, 2618. 7. K. Hadjiivanov et al., Phys. Chem. Chem. Phys. 2003, 5, 243. 8. A. I. Serykh and V. B. Kazansky, Phys. Chem. Chem. Phys. 2004, 6.

Conference on Current Trends in Computational Chemistry 2004 167

Figure 1.

Figure 2. 168 Conference on Current Trends in Computational Chemistry 2004

An ab Initio Studies of Donor-Acceptor Complexes for Several Alkyl Fluorides with BF3 in HF-Superacid Medium Taking Into Account the Solvation Effects

Vitali Solkan and Jerzy Leszczynski

N. D. Zelinski Institute of Organic Chemistry, Russian Academy of Science, 119991 Moscow, Leninskii pr.47, Russian Federation Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Str., Jackson, MS 39217, USA.

Friedel-Crafts reactions comprise a wide variety of synthetically useful processes, of which the BF3-catalyzed alkylation of aromatics is a well-known example. When the source of alkyl group is the corresponding alkyl fluoride, these reactions proceed via the formation of donor- acceptor intermediates (Alk-F---BF3). Even in the non-ionic intermediates, the alkyl group appears to be an effective electrophile, suggesting a significant perturbation of the carbon- fluorine bond, and in turn, a significantly developed B—F dative bond. In light of the importance of these systems we have performed the theoretical studies on HF-BF3 and related alkyl fluoride- BF3 complexes. The system HF/BF3 is frequently used as a Friedel-Crafts catalyst in reactions, which require a proton source to proceed. In the particular case of HF-BF3 complex, the formation of BF4(-)H(+) leaves behind a bare proton, and this may be too energetically costly to occur without the formation of a genuine bond to a proton acceptor. The solvation of BF3 in HF is described by : BF3+ 2HF <=> BF4(-) + H2F(+) +2.26 kcal/mol at MP4/6-311++G**//MP2/6- 31+G* level. The structures, frequencies, and interaction energies of small donor-acceptor clusters ([FH]n + BF3), n=1,2,3,4,5,6; (CH3F + BF3+[FH]n ), (C2H5F + BF3+ [FH]n), (iso- C3H7F + BF3+[FH]n), and (tr-C4H9F + BF3+[FH]n), n=0,3; were calculated by Hartree-Fock and DFT/B3LYP methods with medium-sized (6-31++G** and 6-311++G**) basis sets. Stationary points have been also relocated at the MP2/6-31+G* level. The electron correlation has been estimated at the MP4/6-311++G** level. The contribution of superacidic environment to an electrostatic solvation free energy for these clusters are included at HF/6-31++G** and B3LYP/6-31++G** levels by means of a polarizable continuum model (PCM). The only minimum found on the potential surfaces of clusters (alkyl fluorides +BF3) is a weakly bound complex, with a B---F distance in ranges 2.27-2,31 A at the MP2/6-31+G* level of theory. The calculated binding energies of clusters (alkyl fluorides +BF3) fall in ranges 5.5-7.2 kcal/mol at the MP4/6-311++G** level with optimized MP2/6-31+G* geometries. In light of the weak interaction and the poorly defined equilibrium structures, the potential energy surface of clusters (alkyl fluorides +BF3) was systematically searched for other possible minima. In particular, the existence of a Alk(+)…BF4(-) structures as suggested in previous theoretical work was throughly investigated. But, these calculations do not rigorously point to formation of carbocation tetrafluoroborates. Based on the results of the calculations, a quantitative estimation of the catalytic activity of BF3 is given with an explicit consideration of solvation with HF- molecules. Possibility of the application of the hybrid model being developed to calculation of spectral parameters of donor-acceptor clusters was shown as well. Conference on Current Trends in Computational Chemistry 2004 169

Is the R-N=N=O+ Ion Stable?

Vitali N. Solkan, Aleksandr M. Churakov

N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, 119991 Moscow, Russian Federation

The high-nitrogen chains stabilized with alternating N-oxide substituents are of high interest, especially when this chain is a part of conjugated cyclic system. Compounds with such fragments could be potential high energy density materials (HEDM).

OO OO NNNN NNNN One of the possible synthetic routes to this chain is a reaction of the oxodiazonium ion (R– N=N=O+) with the tert-butyl-NNO-azoxy group followed by elimination of the tert-butyl cation. The intramolecular variant of this reaction, presumably, took place in the synthesis of benzo- 1,2,3,4-tetrazine 1,3-dioxides [1]. However, the oxodiazonium ion has never been directly observed by spectral methods and thus it remains a hypothetical species. The aim of this study is to analyze the possible degradation pathways of oxodiazonium ions + R–N=N=O with R = tBu, Ph, Me2N. Geometries of the stationary points have been optimized at the B3LYP/6-311++G** level. The stationary points have been further characterized by vibrational frequency analysis at the same level of theory. The combination of Becke's three parameters mixing of exchange and the Lee-Yang-Parr correlation functional has been shown to provide accurate geometries and reaction energies for nitrogen and oxygen containing molecules [1]. Solvation energies have been calculated using the polarizable continuum model (PCM). The solvent parameters, including dielectric constant, were the same, as those implemented for water in the Gaussian-98 program. The final free energies in solution were calculated by adding the solvation energies to the computed gas-phase free energies. The degradation of oxodiazonium ion could proceed in two main directions. The first one + could involve the cleavage of C–N bond with formation of cation R and N2O (path a). The second one could involve the cleavage of the N–N bond with formation of nitrene and nitrosonium ion (path b).

a b RN2O R NNO R N NO For tBu–N=N=O+ ion, it has not been possible to obtain the minimum on the potential energy surface even at high levels of theory. It decomposes in accordance with path a to give the stabilized tert-butyl cation and N2O (fig. 1, the complex on the potential energy surface). The + Me2N–N=N=O ion is also unstable. It decomposes in accordance with path b to give the stabilized nitrene Me2N–N: and nitrosonium ion (fig. 2, the complex on the potential energy surface). In contrast, Ph–N=N=O+ ion proved to be rather stable species (fig.3). Both degradation pathways, a and b, were analyzed in gas phase and in solvution. 170 Conference on Current Trends in Computational Chemistry 2004

E PhN (T) NO kcal/mol (gas phase) ∆H = 81.71 ∆G = 70.96

PhN (T) NO (solvated) ∆H = 59.51 ∆G = 48.76

b Ph N2O (solvated) ∆H = 33.29 ∆G = 26.76

a Ph N2O (gas phase) ∆H = 30.46 ∆G = 23.93

Ph N N O

Scheme 1. The calculated gas phase free energies indicates that the Ph-N=N=O+ ion is strongly stabilized relative to the degradation products. The reactions energies are highly endothermic (+26.8 kcal/mol, path a, + 48.8, path b,) and However, after considering solvent effects we find that the The activation free energy for pathway a is higher than 26.8 kcal/mol, which means that no detectable amount of the N2O could form at room temperature. The activation free energy for path b is much higher. Thus, there is not thermodynamic driving force for dissociation of Ph- N=N=O+ ion. The data obtained show that this cation could be stable enough for its spectral observation at room temperature or for its separation in pure state as a salt with the appropriate non- – nucleophilic anion, e.g., BF4 .

Figure 1. The complex on the potential energy surface. Conference on Current Trends in Computational Chemistry 2004 171

Figure 2. The complex on the potential energy surface

Figure 3.

References 1. A. M. Churakov, V. A. Tartakovsky, Progress in 1,2,3,4-Tetrazine Chemistry. Chem. Rev. 2004, 104, 2601–2616.. 2. V. N. Solkan (in preparation) 172 Conference on Current Trends in Computational Chemistry 2004

Theoretical Study of Dihydrogen Adsorption on Zn(II) Exchanged ZSM-5 Zeolites Using DFT/B3LYP

Vitali Solkan

N. D. Zelinski Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Leninskii pr.47, Russian Federation

Zn and Ga zeolites have been used to promote the aromatization of alkanes and shown to exhibit a very high activity [1-2]. Several studies have been performed to understand the catalytic effect of these active sites [3-4]. The adsorption of small molecules in combination with vibrational spectroscopy has been widely used to provide information on the adsorption mechanism. FTIR spectroscopy study with use of H2 probe molecules is a powerful method for identification and structural investigation of active sites in Zn/HZSM-5 zeolites [5]. Unfortunately, this method did not provide any information on the local geometry of the Zn ion environment. Such information can be obtained only from comparison of results of the ab initio calculations of IR spectra for adsorbed H2 probe molecule at different cationic sites in ZSM-5 with the experimentally measured IR H-H stretching frequencies. We present herein new theoretical results, regarding the molecular hydrogen adsorption on Zn2+ (3d10)-exchanged zeolite ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 4T-ring, 5T-ring (Fig. 1), 6T-ring (Fig. 2), and 10T-ring (T denoted tetrahedral Al and Si atoms), where there are two framework Al atoms present at next nearest- 2- 2+ neighbor T position. The cluster, [Al2Si8O16H20] Zn , is a complete 10-membered-ring cluster of the main channel of ZSM-5. To mimic the rigidity of the zeolite lattice, the dangling OH- 2- 2+ groups in largest cluster [Al2Si8O16H20] Zn , were kept fixed. They were built using experimental crystal data. No symmetry constraints were used for 4T-ring model. For the 5T- ring and 6T-ring models, a full optimization predicted a non-realistic geometry for the adsorption of dihydrogen on the Zn(2+) site; therefore, some constraints were used to keep the ring shape of the clusters as in zeolite framework.(see Fig. 1 and Fig. 2). The hybrid B3LYP functional was used in this work as implemented in Gaussian 98 code. All the calculations for 4T –6T ring models were performed using the 6-31G(d,p) basis set. Firstly the Zn(II) bonding in the 4T-6T- rings was studied. The cation is located in a tetracoordinated configuration, in which the Zn-O distances are 2.03 A. In the 5T-ring model, a different trend is observed: the Zn2+ cation is located in the same plane as the oxygen atoms. The difference in the structural position has a 2+ direct effect on the interaction between the Zn cation and the H2 molecule. The value of adsorption energy of dihydrogen on these sites show the same trend, decreasing from 4T-ring to 2- 2+ 6T-rings; only the largest ring [Al2Si8O16H20] Zn H2 breaks the general trend found for other complexes. The calculated shift for the ν(H-H) stretching frequency mode was, at maximum, equal to 192 cm-1 for Zn2+-4T ring and at minimum, equal to 124 cm-1 for Zn2+-6T ring. In case of 5T ring the calculated shift for the ν(H-H) stretching frequency mode is equal to 160 cm-1. So far we have demonstrated that the main spectroscopic features of hydrogen adsorbed on ZSM-5 containing Zn(II) [5] can be satisfactorily reproduced by employing 5T-ring, and 6T-ring models. The theoretical calculations have provided more insight into the adsorption of H2 on Zn2+ containing ZSM-5 zeolites in term of the local geometry, strength of the interaction between cation and H2, and charge transfer from H2 to active site.

Conference on Current Trends in Computational Chemistry 2004 173

References 1. Y. Ono, Catal. Rev. Sci. Eng., 1992, 34, 179. 2. N. Kumar and L.-E. Lindfors, Catal. Lett., 1996, 38, 239. 3. M. V. Frash and R. A. van Santen, Phys. Chem. Chem. Phys., 2000, 2, 1085. 4. L. A. M. M. Barbosa, G. M. Zhidomirov, and R. A. van Santen, Phys., Chem. Chem. Phys., 2000, 2, 3909. 5. V. B. Kazansky, A. I. Serykh, and R. A. van Santen. Catal. Lett., 2003, 88, 211.

Figure 1

Figure 2 174 Conference on Current Trends in Computational Chemistry 2004

Correlation of Conformational Energetics of Naphthylquinolines with Thermodynamic Binding Energies

Angela Sood, M. Jeanann Lovell, G. Reid Bishop, and David H. Magers

Mississippi College Department of Chemistry and Biochemistry Clinton, Mississippi

A library of naphthylquinoline derivatives satisfying hypothesized structural criteria for triplex DNA selectivity have been designed and synthesized by Dr. Lucjan Strekowski of Georgia State University. Proposed structural characteristic criteria promoting intercalation between bases of triplex DNA include a large aromatic surface area, an unfused flexible ring system, and a crescent shape. High-throughput competition dialysis experiments among fourteen of these test compounds demonstrated that the replacement of the secondary amine function found in LS8 (Figure 1.) with an ether oxygen producing MHQ12 (Figure 2.) greatly increased selectivity towards triplex DNA over the more common duplex DNA. Preliminary semi- empirical studies showed a correlation of enhanced triplex DNA selectivity with an increase in rotational flexibility of the side chain of the derivative compound.

Figure 1. LS8 – amine linkage Figure 2. MHQ12 – ether linkage

The binding study has been extended to include two additional compounds, OZ121 (Figure 3.) and G106 (Figure 4.). OZ121 is identical to the highly selective MHQ12 except that a sulfur atom replaces the ether oxygen. G106 contains an amide linkage between the naphthylquinoline and the side chain. Here we present results from computational studies designed to examine the dynamic flexibility of the naphthylquinoline side-chain for the four compounds containing amine, ether, thiol, or amide linkages. Calculations are performed to determine the energy of each compound with varying dihedral angles between the side chain and the naphthylquinoline. Beginning from optimized geometries, the specific dihedral angle is frozen at 5-degree increments for values between 0 and 360 degrees and the rest of the structure is reoptimized to yield the energy barrier of the side-chain rotation and the approximate dihedral angle at which the top of the barrier lies. Calculations are performed using SCF theory and density functional theory with various basis sets. Conference on Current Trends in Computational Chemistry 2004 175

Figure 3. OZ121 – thiol linkage

Figure 4. G106 – amide linkage

Results from these computational studies of all four derivatives are coupled with results from thermodynamic binding studies to determine if any informative correlations can be made. We gratefully acknowledge the support of NSF EPSCoR (EPS-0132618). 176 Conference on Current Trends in Computational Chemistry 2004

Non–Watson–Crick Base Pairing in RNA. Quantum-Chemical Analysis of the cis-W.C. /Sugar Edge Base Pair Family

Judit E. Sponer,1 Jerzy Leszczynski2 and Jiří Šponer1,2

1 Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic 2Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, USA

In the present study, we fill the gap that presently exists in the literature on RNA base pairing. The non-WC base pairs were characterized through x-ray and database studies, however, such studies provide a purely geometrical information with no insights into the energetics of the interactions. In contrast to the experimental structural studies, QM computations characterize simultaneously the molecular structures and base-pairing energies. We investigate one of the key families of RNA base pairing, i.e., the cis-Watson Crick/Sugar Edge base pairs. The main aim is to complement the available structural information by evaluating the energies of the interactions. In the cis-Watson Crick/Sugar Edge X/Y base pairs, the base X is involved in the base pairing via its Watson Crick edge while nucleotide Y participates through its sugar edge with the O2`H hydroxyl group H-bonded with the base X. There are 16 possible base-pair members of this family while 13 of them were already seen in RNA structures. It is thus one of the biologically most relevant RNA base pairing families with no counterpart in DNA. The cis-WC/SE interactions play essential role in building up the modular three dimensional structures of large RNA molecules. Conference on Current Trends in Computational Chemistry 2004 177

Interactions between Guanine and Amino Acids: A Theoretical Study

Andrea Sterling, Jing Wang, Jerzy Leszczynski*

Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University, Jackson, MS 39217 U. S. A.

Hydrogen-bonding interactions often make substantial contributions to the specificity of the protein-nucleic acid complexes. Such interactions could be used to uniquely distinguish the backbone structures. In the present study, the interactions between amino acids and the nucleic base Guanine(G) are investigated through sixteen models, including the interactions between G and amino acids arginine, lysine, asparagines/glutamine, aspartic acid/glutamic acid, and serine/threonine, respectively. The fully optimized structures were located using three different density functional theory levels, B3LYP/6-311G (d,p), MPW1PW91/6-311G (d,p), and KMLYP/6-311G (d,p). Frequency analysis results suggest that the obtained species are the local energy minima on the potential surface. The H-bonds in the interactive models of Guanine with the amino acids are characterized by the BCPs density and the Laplacian of density via atoms-in-molecules (AIM) approach.

G_arg1 G_ arg 2 G_ arg 3 G_ arg 4

G_ arg 6 G_ arg 5 G_ser/thr_1 G_ ser/thr_2

G_lys G_asp/glu_1 G_ asp/glu_2 G_ asp/glu_3

G_ asn/gln_1 G_ asn/gln_2 G_ asn/gln_3 G_asn/gln_4

178 Conference on Current Trends in Computational Chemistry 2004

Effects of Axial Ligands on the Structure and Electronic Properties of Metal Porphyrins and Phthalocyanines

Nicole M. Strauss and William A. Parkinson

Department of Chemistry and Physics, Southeastern Louisiana University, Hammond LA 70401

Calculations of the electronic structure and properties of porphyrin and phthalocyanine molecules have been conducted since the early days of computational chemistry. Recently there has been renewed interest in this topic, owing to the application of these molecules as photosensitizers in the cancer treatment known as photodynamic therapy. Upon irradiation, effective photosensitizers produce a large quantum yield of singlet oxygen in cancerous tissues as they phosphoresce. Metalation of the ring systems enhances this process, and predicting the electronic spectra of such species has accordingly drawn much attention. Recent calculations have demonstrated good agreement with gas phase uv-visible spectra. In addition to binding the ring system equatorially as a tetravalent ligand, most metals also incorporate one or possibly two axial ligands. This is particularly likely in vivo, with water acting as a hard (electron pair donating) ligand. Axial ligation dramatically affects symmetry, in most instances drawing the metal from the ring plane and/or puckering the ring system. This disruption could possibly alter ring conjugation, the property which gives porphyrins and phtalocyanines their remarkable absorption characteristics. Using DFT and TDDFT, this study examines the change in geometry and its effect on the predicted electronic spectra of axially-ligated zinc and magnesium porphyrins and phthalocyanines. Conference on Current Trends in Computational Chemistry 2004 179

Theoretical Study of the Effect of Some Metal Clusters on the Conductance of Benzene using Various Alligator Clips (As, P, S, O, Se, Te)

Krzysztof Tajchert1, Devashis Majumdar2, Szczepan Roszak1,2, Jerzy Leszczynski2

1Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland 2Computational Center for Molecular Structure and Interactions Department of Chemistry Jackson State University 1400 J. R. Lynch St., Jackson, MS 39217

The precise determination of the characteristics of metal-molecule interface is a key factor in molecular electronics. Most of theoretical approaches so far made in this area, are based on the gold cluster as an electrode. The cluster is being attached to the molecular system through the S linkage (called alligator clip). Before designing any molecular circuit, the problem of metal- surface linkage has to be fully resolved, especially from the viewpoint of efficiency. With this goal in mind, we have, in the present work, tried to study Ga, In, W, Rh and Pd clusters as electrodes. As, P, O, S, Se and Te atoms are being used as alligator clips. In this preliminary study, we have investigated the nature of metal-molecule interaction using benzene as the conducting molecule. The calculations are done at the density functional level using B2PW91 functional and LANL2DZ effective core potential basis sets. Since the HOMO-LUMO gap in the main criteria for the molecular conductance, we have calculated this parameter for various metal- molecule systems and compared with the available results. 180 Conference on Current Trends in Computational Chemistry 2004

Proton Affinities of Some Ketones, Vicinal Diketones and α-Keto Esters: A Computational Study

Antti Taskinen1, Ville Nieminen2, Esa Toukoniitty2, Dmitry Yu. Murzin2, and Matti Hotokka1

1Department of Physical Chemistry, Åbo Akademi University, FIN-20500 Turku-Åbo, Finland 2Laboratory of Industrial Chemistry, Process Chemistry Centre, Åbo Akademi University, FIN- 20500 Turku-Åbo, Finland

Due to the importance of asymmetric synthesis and catalysis in chemistry, hydrogenation of activated ketones over cinchonidine modified Pt catalysts (Fig. 1) has been actively investigated [1] by groups working in the field of catalysis, organic chemistry, surface science and quantum chemistry. The main focus of today’s research is in understanding of the enantiodifferentiation mechanism on catalytically active surfaces. H H O O O

O O Pt, H2 + O N (R)-product (S)-product N H OH (major) (minor)

cinchonidine

Figure 1. A simplified reaction scheme of asymmetric hydrogenation of a vicinal diketone. Hydrogenation of 1-phenyl-1,2-propanedione over cinchonidine modified platinum catalyst yields enantiomeric excess of (R)-1-hydroxy-1-phenylpropan-2-one.

Solvent effects on the enantiomeric purity of hydrogenated ketones obtained in the catalytic reactions have been widely studied but not completely understood. In some cases the relative amount of the major enantiomer seems to depend considerably on whether the solvent is aprotic or protic. At least in theory, the protonation of the substrate molecules is possible in protic solvents and at its worst it could disturb the enantiodifferentiation process. Therefore, it is important to know the ability of these molecules to accept a proton, i.e., their proton affinity. In this study the gas phase proton affinities of acetophenone, 2,2,2-trifluoro-acetophenone, 2,3-butadione, 1-phenyl-1,2-propanedione, methyl pyruvate, ethylbenzoyl-formate and ketopantolactone were determined using density functional theory with the B3LYP functional and some ab initio post-Hartree−Fock methods (MP2, MP4 and CCSD). The above-mentioned compounds are among the frequently used substrates in the investigation of the enantioselective hydrogenation over chirally modified platinum catalysts. Since proton affinities have previously been determined experimentally for three of these compounds, not only the theoretical results could be compared with the experimental ones but also new physicochemical data was gained. [1] M. Studer, H.-U. Blaser, C. Exner, Adv. Synth. Catal. 345 (2003) 45 and references therein. Conference on Current Trends in Computational Chemistry 2004 181

Frozen Natural Orbitals: A Systematic Method of Basis Set Truncation

Andrew G. Taube and Rodney J. Bartlett

Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, FL 32611

To overcome the undesirable scaling of coupled cluster theory with increasing basis sets, a new method of basis set truncation is developed, implemented and evaluated. Truncating the exact natural orbitals (eigenfunctions of the one-particle reduced density matrix) best approximates the expectation value of a bounded operator. Because the determination of the exact natural orbitals requires the solution of the Full Configuration Interaction problem, approximate natural orbitals are constructed. The virtual-virtual block of the MBPT(2) density matrix is diagnolized yielding the so-called “Frozen Natural Orbitals.” The least occupied of these orbitals are removed, and the Hartree-Fock solution is constructed in the truncated space. A coupled cluster calculation is then performed based on this reference function. Results for a series of small diatomic and triatomic test molecules were performed, verifying the quality of this truncation. Truncation of 60% of the virtual space recovered greater than 90% of the correlation energy of the full basis set for CCSD and CCSD(T) calculations. The dependence of the truncated results on geometry and different starting basis sets was also determined. Results of molecules of experimental interest are reported, as well as the formalism and implementation of gradients for coupled-cluster methods based on the frozen natural orbitals. 182 Conference on Current Trends in Computational Chemistry 2004

A DFT/TDDFT Study of Excitation Spectrum of Dibenzoborole Containing π-electron Systems: “on/off” Fluorescence Device Can * be Controlled by Changing pπ –π Conjugation

Kanchana S. Thanthiriwatte and Steven R. Gwaltney

Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762

The growth of molecular-scale optoelectronic information processing systems requires a variety of molecular devices1 such as wires, switches, logic gates, memories and input-output components, which can be designed for use in photonic, electronic, and optoelectronic systems.2,3 Boron-containing pi-conjugate extended systems have been investigated both experimentally and theoretically because of their tremendous applications in optoelectronic and materials science which can be used in information processing.4,5 Some of them show remarkable fluoresce phenomena, recently used in the fabrication of molecular switches.6,7 These systems are widely investigated in view of their design, synthesis, and characterization for materials and technological applications.

R R D B B

mode A mode B

Figure 1. The “on/off” control of the pπ – π* conjugation in the LUMO of borole.

We report a first-principles theoretical calculation of the structural properties and excited electronic spectrum for a series of 5H-Dibenzoborole derivatives. Three coordinated 5H- Dibenzoborole (Borole) and four coordinated 5H-Fluoro-5H-dibenzoborole ion (fluoroborole) are considered as basic skeleton structures. The three coordinated and four coordinated borole compounds exhibit remarkable fluorescence changes which can be employed as an “on/off” fluorescence device and can be controlled by changing the pπ–π* conjugation. The pπ←–π* * conjugation of the vacant pz orbital on three coordinated boron atom with the π orbital of attached carbon π-conjugated moieties is responsible for this unique property.8,9 In this system, the “on/off” control of the pπ–π* conjugation by the addition of a donor molecule would change the LUMO delocalization mode from “mode A” to “mode B”, as shown in Figure 1. This change significantly increases the HOMO – LUMO gap and causes a hypsochromic shift in the absorption and fluorescence. However, the resulting LUMO in mode B is still delocalized over the carbon framework as in a normal π– conjugated system. Density functional theory (DFT) was the method that we chose to use our study. All calculations were executed using Q-Chem 2.1.10 All geometry optimizations of the ground states of borole and fluoroborole derivatives were performed by using B3LYP, which has been shown Conference on Current Trends in Computational Chemistry 2004 183

to be effective at accurately predicting structures and energies. The geometry optimization of the dibenzoborole derivatives have been carried out using the 6-31G* basis set, which we feel provides a good compromise of accuracy and efficiency, given the size of these molecules. After these optimized structures are obtained, vibrational frequencies are calculated, and TDDFT excited state spectra are calculated, all using the same level of theory and basis set. There are few experimental results available for borole compound’s absorption spectra11 and the fluorescence properties of borole compounds.5 Experimental results and calculations are compared.

References 1. Carroll, R. L.; Gorman, B. C. Angew. Chem., Int. Ed. 2002, 41, 4378. 2. Ziessel, R.; Harriman, A. Coord. Chem. Rev. 1998, 171, 331. 3. de Silva, A. P.; McClenaghan, N. D. J. Am. Chem. Soc. 2000, 122, 3965. 4. Yamaguchi, S.; Shirasaka, T.; Tamao, K. Org. Lett. 2000, 2, 4129. 5. Yamaguchi, S.; Shirasaka, T.; Akiyama, A, Tamao, K. J. Am. Chem. Soc. 2002, 124, 8816. 6. Rurack, K.; Kollmannsberger, M.; Daub, Angew. Chem., Int. Ed. 2001, 40, 385. 7. Franzen, S.; Ni, W.; Wang, B. J. Phys. Chem. B 2003, 107, 12942. 8. Sugihara, Y.; Yagi, T.; Murata, I.; Imamura, A. J. Am. Chem. Soc. 1992, 114, 1479. 9. Salzner, U.; Lagowski, J. B.; Pickup, P. G.; Poirier, R. A. Synth. Met. 1998, 96, 177. 10. Kong, J.; White, C. A.; Krylov, A. I.; Sherrill, D.; Adamson, R. D.; Furlani, T. R.; Lee, M. S.; Lee, A. M.; Gwaltney, S. R.; Adams, T. R.; Ochsenfeld, C.; Gilbert, A. T. B.; Kedziora, G. S.; Rassolov, V. A.; Maurice, D. R.; Nair, N,; Shao, Y.; Besley, N. A.; Maslen, P. E.; Dombroski, J. P.; Daschel, H.; Zhang, W.; Korambath, P. P.; Baker, J.; Byrd, E. F. C.; Van Voorhis, T.; Oumi, M.; Hirata, S.; Hsu, C. -P.; Ishikawa, N.; Florian, J.; Warshel, A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M.; Pople, J. A. Q-Chem 2.0: a high- performance ab initio electronic structure program package. J. Comp. Chem. 2000, 21, 1532. 11. Chase, P. A.; Piers, W. E.; Partrick, B. O. J. Am. Chem. Soc. 2000, 122, 12911. 184 Conference on Current Trends in Computational Chemistry 2004

Prediction of Materials Properties via Gaussian Orbital DFT Methods

S.B. Trickey

Quantum Theory Project, Department of Physics and Department of Chemistry, P.O.Box 118435, University of Florida, Gainesville FL 32611-8435

Computational prediction and characterization of the structure, energetics, and properties of material systems is a non-trivial task. This is especially true for ordered surfaces and ultra-thin films, which lack both the localization of molecules and the 3-dimensional periodicity of perfect crystals. Predictive electronic structure treatment of these systems nevertheless has been pursued vigorously because of the great potential payoffs in helping focus experimental efforts and in obtaining results in physical regimes inaccessible to experiment. Over roughly the last three decades, much progress has been made. I will give a brief review of the main methodological approaches (DFT vs. wavefunction, all-electron vs. pseudopotential, plane-wave vs. gaussian vs. numerical basis sets) to highlight their essential strengths and limitations. Then I will focus on Gaussian Orbital methods, with particular emphasis on the all-electron, DFT methodology in the code GTOFF (S.B. Trickey, J.A. Alford, and J.C. Boettger, in \Computational Materials Science", vol. 15 of Theoretical and Computational Chemistry, J. Leszczynski ed. (Elsevier, Amsterdam, 2004)) 171-228] as well as a summary of the main features of Hirata's POLYMER code. Some illustrative results will be given, with emphasis on quantum size effects in ultra-thin films. The talk will conclude with a status summary of recent work to develop Current Density Functional Theory to handle external magnetic fields and the complete redevelopment of GTOFF in modern, object-oriented C++ software.

[Thanks for key contributions go to J.C. Boettger, N. Rosch, J.R. Sabin, J.W. Mintmire, J.A. Alford, U. Birkenheuer, R.J. Mathar, and Wuming Zhu. Work supported by US National Science Foundation ITR grants DMR-0218957 and DMR-0325553]. Conference on Current Trends in Computational Chemistry 2004 185

Molecular Modelling and QSAR Studies of Aconitum and Delphinium Alkaloids Having Antagonist Actions at Voltage-Gated Sodium Channels

Malakhat A. Turabekova

Department of Chemistry, National University of Uzbekistan named after Mirzo Ulugbek, Vuzgorodok, Tashkent, 700174, Uzbekistan

Voltage-gated sodium channels are transmembrane proteins responsible for signal transduction and amplification, and are primary molecular targets for several groups of naturally occurring neurotoxins and a number of drugs. One of these groups is represented by lipid-soluble neurotoxins targeting type 2 receptor site on voltage-gated Na+ channels. Site 2 toxins are of very diverse chemical structures and a number of studies on mechanisms of action suggest that they promote Na+ channel opening by indirect allosteric interactions. The recent investigations showed that receptor site of these neurotoxins appears to be adjacent to or overlap with that for sodium channel blockers (anticonvulsant, antidepressant, local anaesthetics, antiarrhythmic etc. therapeutic drugs).[1] Diterpene alkaloids isolated from Delphinium and Aconitum plant species are targets of considerable interest and studies as they belong to site 2 neurotoxins. Paradoxically, despite of similar molecular structures these alkaloids exhibit antagonistic alteration of sodium channel function and therefore different therapeutic action. Thus, as it was demonstrated earlier, arrhythmogenic effect of aconitine can quickly be reversed by antiarrhythmic agent lappaconitine. The interesting fact about these two alkaloids is that they both belong to the subgroup comprised of molecules with lycoctonine skeleton [2,3]. As it was reported elsewhere [3], there are 4 active regions in a molecule: nitrogen atom of lycoctonine skeleton that acquires a strong positive charge when protonated in a solution, and three functional residues (hydroxyl group at C13, benzoylester group at C14 and acetyl group at C8) playing a crucial role for exhibiting channel opening properties (Fig.1). Interestingly, the absence of any of functional groups mentioned results in blockade of sodium ion channel.

Figure 1. Aconitine alkaloid molecule (A) with three functional residues responsible for the sodium channel opening activity and its antagonist Lappaconitine alkaloid molecule (B)

186 Conference on Current Trends in Computational Chemistry 2004

These reports inspired us for detailed investigations of Delphinium and Aconitum alkaloids in order to trace structure-activity(toxicity) relationship at electronic structure level. Selection of diterpene alkaloids for quantum-chemical investigations has been performed ensuring an equal number of channel blockers and openers in a series (Fig. 2). Moreover, structures maximally related to aconitine alkaloid but with various combinations of three crucial residues were of the first choice. HO H O OCOC H OCH 6 5 O 3 O OCH3 OH N OCH 3 OCH N OH 3 OH CH3 CH3 N OCOC6H5 OH 6-benzoylheteratizine (b) 1-benzoylnapelline (b) O OCH3 OCH3

OCH OCH3 3 OH OCOC6H5 O

NHCOCH3 N N " OH OH lappaconitine (b)

OCH OCH3 3

talatisamine (b) 14-benzoyltalatisamine (b)

OR5 OCH3

OCH3 R4 OR6 R

R8 N OR7 OR R1 3

OCH R2 3 Figure 2. A series of Aconitum and Delphinium alkaloids studied. Compound name Functional groups

aconine (b) R1=OH; R2=OCH3; R8=C2H5 aenzoylaconine (b) R1=OH; R2=OCH3; R6=COC6H5; R8=C2H5 3,13,15-threeacetylaconitine (b) R1=OCOCH3; R2=OCH3; R3=R5=R7=COCH3; R6=COC6H5; R8=C2H5 aconitine (o) R1=OH; R2=OCH3; R3=COCH3; R6=COC6H5; R8=C2H5 aconiphine (o) R1=R4=OH; R2=OCH3; R3=COCH3; R6=COC6H5; R8=C2H5 altaconitine (o) R=R1=OH; R2=OCH3; R3=COCH3; R6=COC6H5; R8=C2H5 mesaconitine (o) R1=OH; R2=OCH3; R3=COCH3; R6=COC6H5; R8=CH3 noraconitine (o) R1=OH; R2=OCH3; R3=COCH3; R6=COC6H5; R8=H hyppaconitine (o) R2=OCH3; R3=COCH3; R6=COC6H5; R8=CH3 3-monoacetylaconitine (o) R1=OCOCH3; R2=OCH3; R3=COCH3; R6=COC6H5; R8=C2H5 3,15-diacetylaconitine (o) R1=OCOCH3; R2=OCH3; R3=R7=COCH3; R6=COC6H5; R8=C2H5 (b) – sodium channel blocker; (o) – sodium channel opener

The molecular modelling studies included molecular mechanics and semi-empirical calculations: To start with, Molecular Mechanics (MM+) force field was applied for preliminary structure optimisation and study of the conformational behaviour of each alkaloid. Next, the MM+ optimised structures were re-optimised y applying PM3 semi-empirical method in order to obtain an accurate charge distribution and quantum-chemical characteristics for each compound in the series. Conference on Current Trends in Computational Chemistry 2004 187

Aiming to identify which of quantum-chemical characteristics (Heat of formation, Energy of HOMO, Energy of LUMO, HOMO and LUMO energy gap, dipole moment contributors) correlates best with toxicity data we built several QSAR models. As a result, HOMO-LUMO energy gap and energy of LUMO well correlated with toxicity. A statistical fit of the models have considerably been improved after the blockers and the openers of sodium ion channels were studied independently from each other. Next, detailed investigations of HOMO and LUMO were carried out in order to reveal whether electronic features of a molecule would depend on the modulation effect nature of particular alkaloid. Molecular orbitals analysis showed, the HOMO of each alkaloid was mainly represented by contributions of lycoctonine carcass nitrogen atom orbitals. This confirms the nitrogen atom being the most active region and after its protonation playing the role of a primary anchor which helps each alkaloid to stabilise within the receptor site. In contrast to HOMO, LUMO appeared to be linearly dependent on toxicity (for both types of modulators), but again no substantial features have been identified that would help to distinguish whether particular structure is activator or blocker of Na+ channels. The picture below with LUMOs plotted for aconine, benzoylaconine, aconitine and lappaconitine clearly demonstrates that three essential functional groups (Fig.1) do not participate altogether in this molecular orbital formation except benzoylester group which only contribution is not enough for opening the sodium ion channels.

Figure 3. LUMO isosurfaces of aconine (A), benzoylaconine (B), aconitine (C) and lappaconitine (D)

The latter observations have shown, that antagonist modulating action of Aconitum and Delphinium diterpene alkaloids cannot be completely explained by analysing solely HOMOs and LUMOs. The next approach to be applied was QSAR analysis for which we have selected 104 alkaloids that belong to the same class of compounds. Several runs of GA-MLRA implemented in a programm BuildQSAR have selected descriptor MR (Molecular Refractivity) as the one correlating best with toxicity. 188 Conference on Current Trends in Computational Chemistry 2004

−1 Log( LD50 ) = +0.02264(±0.00496) MR +1.18750(±0.655547) (n=104; r=0.663; s=0.654; F=80.033; Q2=0.406; SPRESS=0.673) (1)

Figure 4. Correlation of Predicted versus Experimental toxicities for model (1)

On a figure 4 the red points correspond to arrhythmogenic alkaloids that cause persistent activation of sodium channel, whereas the blue ones correspond to antiarrhythmic alkaloids that block sodium channels. MR descriptor used accounts for two main characteristics of a molecule – its both polarizability and molecular volume. Next, the series of 104 compounds was divided into two groups (in accordance with the alkaloids nature) that were studied separately and QSARs obtained for both type of alkaloids were compared (Equations 2 and 3). The latter work is in progress.

For 9 arrhythmogenics: −1 Log( LD50 ) = -0.02904(±0.01737) MR +10.95811(±2.901921) (n=009; r=0.825; s=0.446; F=14.873; Q2=0.312; SPRESS=0.654) (2)

For 88 antiarrhythmics (with 7 being exluded from the list): −1 Log( LD50 ) = +0.02225(±0.00284) MR +1.17966(±0.358091) (n=088; r=0.860; s=0.289; F=243.708; Q2=0.172; SPRESS=0.515) (3)

References 1.W.A.Catterall, Neuron, 2000, Vol. 26, 13–25 2.Ameri A. Prog. Neurobiol., 1998, 56, 211 3.Dzhakhangirov, F. N.; Sultankhodzhaev, M. N.; Tashkhodzhaev, B.; Salimov, B. T. Chem. Nat. Comp., 1997, 33, 190 Conference on Current Trends in Computational Chemistry 2004 189

Structure Analysis of Oligopeptides by Means of Quantum Chemical Calculations

Zoltán Varga1 and Attila Kovács2

1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson MS 39217, USA 2Hungarian Academy of Sciences – Budapest University of Technology and Economics, Research Group of Technical Analytical Chemistry, H-1111 Budapest, Hungary

The secondary structure of proteins is of primary importance in the biological functions of these molecules. Our present knowledge on the characteristics of the secondary structures stems from X-ray and NMR studies as well as from low-level molecular modelling. Each listed method has its deficiencies, due to that our information on the exact character of the interactions stabilising the secondary structures is still incomplete. Sophisticated quantum chemical calculations are well suited to study weak molecular interactions, hence to explore the nature of the secondary structures of oligopeptides. The goal of our present study was to elucidate the role of hydrogen bonds in various oligopeptide conformers, viz., β-sheet, 27-ribbon, 310-helix, α- helix, π-helix, β-turn II and γ-turn. For the present calculations hexapeptides of glicine, alanine, valine and serine were selected. The effect of solvent (water) was investigated using the COSMO model.

The above listed secondary structures were optimised at the B3-LYP/6-31G** level. The strongest intramolecular hydrogen bonds have been obtained in the 27-ribbon structure among the investigated conformers. However, we did not find a straight correlation between the number/strength of the hydrogen bonds and the relative stability of the secondary structures. This indicates, that the dipole-dipole interactions and steric effects play a role in magnitude similar to that of hydrogen bonding in stabilising the conformers. The energy ordering obtained in vacuo is disturbed upon the effect of water: most noteworthy is the strong stabilization of α-helix with respect to the other conformers. We determined the geometrical characteristics of the various secondary structures: this included the range of φ and ψ torsion angles, the charateristic lengthening of the C=O and N–H bonds involved in hydrogen bonding and the shortening of the C–N bonds. An excellent correlation was found between the lenghening of the N–H bonds and the lengths of the hydrogen bonds. The correlation is much poorer with the lengthening of the C=O bonds, which has a strong effect also from hyperconjugation interactions. 190 Conference on Current Trends in Computational Chemistry 2004

Structure of the HMT-CDA 1:1 Adduct: Crystal Structure, IR Spectroscopy and DFT Approach

Ramaiyer Venkatramana, Paresh Chandra Raya, and Frank R Fronczekb

aDepartment of Chemistry, Jackson State University, Jackson, MS, USA. bDepartment of Chemistry, Louisiana State University, Baton Rouge, La.

We present a quantum chemical analysis, crystal structure and IR spectroscopic investigation of self-assembly between hexamethylenetramine (HMT) and trans-1,2- cyclohexanedicarboxilic acid (CDA) .Equimolar amounts of hexamethylenetramine (HMT) and trans-1,2-cyclohexanedicarboxilic acid (CDA) formed a 1:1 adduct through a hydrogen bonding network. Room temperature single crystal diffraction studies and FTIR spectroscopy of the system indicated adduct formation between HMT and CDA. Ab-initio Density Functional Theory (DFT) calculations, using the 6-31G(d,p) basis set, have been performed to investigate the gas phase structure and IR frequencies. The theoretical parameters (geometry and vibrational frequencies) predicted DFT methods for the adduct are in good agreement with the experimental data. Conference on Current Trends in Computational Chemistry 2004 191

Proton Solvation and Transport in Aqueous and Biomolecular Environments

Gregory A. Voth

Department of Chemistry and Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, UT, 84112, USA

The solvation and transport of excess protons in several important systems will be described using the multi-state empirical valence (MS-EVB) approach combined with large scale molecular dynamics (MD) simulation. The MS-EVB approach allows for the treatment of explicit proton shuttling (dynamical bond-breaking), which, in turn, strongly influences the properties of excess protons in various aqueous environments. Proton solvation and transport in bulk water, water clusters, the water liquid-vacuum interface, and water-filled biological proton channels will be discussed. 192 Conference on Current Trends in Computational Chemistry 2004

Gas Phase Spectroscopy of Biomolecular Building Blocks: Interplay between Theory and Experiment

Mattanjah S. de Vries

Department of Chemistry and Biochemistry, University of California Santa Barbara, California 93106, U.S.A.

We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. A prime motivation is the need to provide gas phase data for comparison with the latest high level computations. An additional motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment as well as understanding interactions that may have played a role in the early stages of life. We use a combination of laser desorption and double resonant laser spectroscopy, applied to DNA bases, nucleosides, small peptides and their clusters with each other and with water. We compare results from IR-UV hole burning spectroscopy with ab initio calculations, both to analyze our findings and to provide calibration for computations in other groups, with which we collaborate.

Conference on Current Trends in Computational Chemistry 2004 193

Cooperativity Effects in the Interactions between Fas2 Loop1 and AChE: A Theoretical Study

Jing Wang,a Jiande Gu,b and Jerzy Leszczynskia*

aComputational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217 U. S. A. bDrug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 P. R. China

Noncovalent interactions, including hydrogen bonding, dispersion interactions, electrostatic interactions, hydrophobic interactions, charge-transfer interactions, and ion-mediated interactions, play a dominant role in protein conformation and the folding process. Among them, hydrogen bonding has been recognized as one of the most important phenomena. The coexistence of several pairs of H-bonds is common in protein-protein complexes. Due to the coupling between H-bonds, cooperativity becomes a feature of primary importance. Cooperativity effects of H-bonding have been found to directly tighten or loosen the bound protein complexes by increasing or decreasing the individual H-bonding interactions. In the present study, the cooperativity effects for the interactions between Fas2 Loop1 and AChE have been theoretically investigated. Fas2 residues from Thr8 through Ala12 were selected to represent the subset of Loop1. Four binding sites were identified for AChE as residues of Glu73, Ser81-Asn85, Tyr70-Val71, and Asp276, respectively. Interactions between these four AChE fragments and the subset of Fas2 Loop1 were explored, including four dimers, six trimers, four tetramers, and one full pentamer models. The B3LYP/6-311G(d,p) theoretical level was applied in this study. The atoms-in-molecules (AIM) approach was employed to characterize the corresponding noncovalent hydrogen bonds through the densities and the Laplacian of electron densities at the bond critical points (BCPs).

Loop III

Loop I

Loop II

194 Conference on Current Trends in Computational Chemistry 2004

Theoretical Study of Interactions of Guanine with Na+ Cation and Water Molecule

C. C. Watts, A. Michalkova, J. Leszczynski

Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA

The interactions of guanine (G) and its tautomeric forms (GT) with the non-hydrated and hydrated Na+ cation by one water molecule have been studied. Guanine is an organic compound belonging to the purine group, a class of compounds with a characteristic two-ringed structure, composed of carbon and nitrogen atoms. These compounds are occurring free or combined in such diverse natural sources as guano (the accumulated excrement and dead bodies of birds, bats, and seals), sugar beets, yeast, and fish scales. Guanine is a component of nucleic acids. On one hand, metal cations determine the structure and function of many biological macromolecules. Because of that, the study of the structure and intrinsic reactivity of the basic constituents of biological macromolecules when interacting with metal cations or upon ionization is of great interest and has received considerable attention in the last years. Accurate quantum chemical calculations will provide important insights to the interactions of guanine base and its tautomers of nucleic acids with cations and water. This work can help to understand the aspects of nucleic bases tautomerism and their mutagenic properties in the presence of cations and water molecule. The interactions of G and its tautomers with the Na+ cation and one water molecule have been investigated using the density functional theory in conjunction with the B3LYP functional and second order of the Møller-Plesset perturbation theory in conjunction with the at 6-31G(d) basis set. Several initial positions of the cation and water molecule around guanine and its tautomeric forms were tested to find the most stable complexes. Four stable systems of G and GT with the cation and one water molecule were found. The optimized structure of guanine interacting with the Na+ cation and the water molecule is presented in Figure 1. The presence of the cation and water molecule changes the order of the relative stability of tautomers of guanine. The regular guanine forms the most stable system with the cation in comparison with its tautomers. However, based on values of the interaction energies we concluded that the selected tautomers of guanine interact more strongly with the Na+ cation than with regular guanine. The values of the interaction energies are decreased by the addition of water. It means that the presence of water weakens the interactions of guanine and its tautomers with the Na+ cation. These less strong interactions correspond with longer Na-O and Na-N distances. The interactions of guanine and its tautomers with cation and water result in changes of the geometry and polarization of the target molecules. All atomic charges of interacting guanine are enlarged in comparison with the atomic charges of isolated guanine. The atomic charge is changed the most significantly for the oxygen atom. Biological significance of this study is in finding that the presence of cations and water molecules affects significantly the properties and stability of guanine and its tautomers.

Conference on Current Trends in Computational Chemistry 2004 195

Figure 1. The optimized structure of guanine interacting with the sodium cation and the water molecule. 196 Conference on Current Trends in Computational Chemistry 2004

Coupled-Cluster Analyses of the Photoelectron Spectra of – – † FeCl3 and FeBr3

John D. Watts

Department of Chemistry and Computational Center for Molecular Structure and Interactions P. O. Box 17910 Jackson State University Jackson, MS 39217

- - Photoelectron spectra of FeCl3 , FeBr3 , and several other transition metal halide complexes have recently been obtained (X. Yang, X. B. Wang, L. S. Wang, S. Niu, and T. Ichiye, J. Chem. Phys. 119, 8311-8320 (2003)). We are applying coupled-cluster methods including connected triple excitations (CCSD(T)) along with atomic natural orbital basis sets to calculate the electron - detachment energies of these complexes and interpret the photoelectron spectra. For FeCl3 , energies of six bands in the photoelectron spectrum have been reported. Our calculated data closely correspond to the observed energies. In order of increasing energy, the six observed bands are labeled as X, A, B, C, D, and E. The energies (in eV) of these bands are as follows: 4.46, 5.69, 6.31, 6.72, 7.27, and 7.62, with uncertainties of 0.08 eV. The calculations assign the 6 X band to the formation of the A1″ state of FeCl3. The calculated vertical electron detachment 4 energy (VEDE) is 4.32 eV. The A band is assigned to the E′ state of FeCl3. The VEDE is 5.83 eV. According to the calculations, the B band could arise from the formation of either the 4E″ 6 state (the VEDE is 6.46 eV) or the A2′ state (the VEDE is 6.24 eV) of FeCl3. The C band is calculated to arise from the formation of the 6E″ state of FeCl3 (the VEDE is 6.80 eV). For the D band there are again two possible assignments, the formation of the 6E′ state (the VEDE is 7.07 6 6 eV) or the A2″ state (the VEDE is 7.01 eV). The E band is assigned to a higher E′ state (the VEDE is 7.60 eV).

† This work is supported by the National Science Foundation (grant numbers HRD01256 and NSF300423-190200-21000). Conference on Current Trends in Computational Chemistry 2004 197

Molecular Properties of Protonated Oxygen Clusters

Mary La’Françes Williamsa,b, and Jaroslaw Jerzy Szymczaka,c

aThe Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217 USA; bCenter for Materials Research, Norfolk State University, Norfolk, VA 23504 cInstitute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland

+ Ab initio calculations were used to study the molecular structures and stability of H (O2)n + (n=1-6) clusters. The structures of H (O2)n were determined at the HF/6-31G(d) and MP2/6- 311++G(d,p) level of theory. The frequency analysis was performed to ensure presence of true minima and CCSD(T) single point (with structure optimized at MP2/6-311++G(d,p) level) calculations were carried to obtain more accurate energetical results. The thermochemical data were compared to available experimental findings.

References S. Yamabe and K. Hirao, J. Am. Chem. Soc. 1981, 103, 2176-2179. S. G. Lias, J. F. Liebman, and R. D. Levin, J. Phys. Chem. Ref. Data. 1984, 13, 695. K. Hiraoka and T. Mori, Chemical Physics, 1989, 137, 345. S. N. Ketkar, A. D. Scott, Jr., E. J. Hunter, International J. Mass Spec., 2001, 206, 7. I. Kaplan, J. Murrell, S. Roszak, and J. Leszczynski, Molecular Physics, 2002, 100, 843. J. Szymczak, S. Roszak, and R. Gora, J. Chem. Phys. 2003, 119, 6560. S. Roszak and J. Leszczynski, J. Phys. Chem., 2003, 107, 949-955. 198 Conference on Current Trends in Computational Chemistry 2004

Computational Investigation of Small Si Clusters on a Graphite Substrate

Jianhua Wu, Jian-Ge Zhou, and Frank Hagelberg

Computational Center for Molecular Structure and Interactions, Department of Physics, Atmospheric Sciences and General Sciences, Jackson State University, Jackson, MS 39217

The structures and electronic properties of small Sin (n=1,2,3) clusters adsorbed on the graphite (0001) surface are studied by Density Functional Theory and with periodic boundary conditions. A 5-layer graphite slab is used to represent the graphite substrate. For the two top layers, allowance is made for geometric relaxation while the three bottom layers are kept fixed with structural parameters equal to the bulk values. The surface energy of graphite is about 4meV, i.e., the interlayer interaction of graphite is sufficiently small to justify a treatment of the graphite substrate as two-dimensional system.1 Various cases of adsorption are considered. The most stable one is associated with Si atom adsorption on the β site above the graphite surface (see Fig.1). It differs from the case of sodium 2 clusters on a graphite surface. The coverage of Sin clusters is considered by using different sizes of supercells (p(1x1), p( 3 × 3 )R300, and p(3x3)). The obtained adsorption energy is much larger than that of sodium clusters. A covalent bond between Si atoms and C atoms on the surface is observed in most cases of adsorption. The structure of pure Sin clusters is found to be altered as a result of the strong interaction between Si atoms and the graphite surface. The deformations of Sin clusters from their pure cases are endothermic, while the bond formation between Si and C atoms on the graphite is exothermic. The equilibrium structures identified for the adsorbed Sin clusters on graphite are the lowest energy structures emerging from the competition of these two processes. For particle adsorption (Si atoms located on the α and β sites in Fig.1), the structures of Sin clusters deviate from the respective pure cases to match the surface structure of graphite. The densities of states (DOS) of pure and deformed Sin clusters are quite different. The energy gaps of pure Si3 clusters is about 1.0eV, while that of the deformed Si3 becomes 0.5 eV. Thus, the interaction between the graphite substrate and the Si adsorbate are of considerable impact on the properties of the Si clusters.3,4

Fig.1. The 5-layer graphite structure with particle sites being marked. .

Reference 1. K.R. Kganyago and P.E. Ngoepe, Phys. Rev. B 68, 205111 (2003). 2. K. Rytkoenen, J. Akola, and M. Manninen, Phys. Rev. B 69, 205404 (2004). 3. B. Marsen, M. Lonfat, P. Scheier, and K. Sattler, Phys. Rev. B 62, 6892 (2000). 4. F. Hagelberg, C. Xiao, B. Marsen, M. Lonfat, P. Scheier, and K. Sattler, Eur. Phys. J. D 16, 37 (2001). Conference on Current Trends in Computational Chemistry 2004 199

Quantum Transport in Porphyrin

Ilya Yanov and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions (CCMSI) Department of Chemistry, Jackson State University

Recent developments in nanotechnology open the possibility for production of nanoscale sensors which provide instant and inexpensive way to monitor environmental conditions and to diagnose chemical and biological hazards. One of the widely proposed molecules for design of nanosensors is the porphyrin (e.g. US Pat. No. 5,981,202; 6,402,0376; 6,488,891; 6,495,102). Porphyrins are nitrogen-containing compounds derived from the parent molecule tetrapyrroleporphin. Utilization of the porphyrin complexes as the sensor is based on the fact that the absorbance spectrum of metallo-porphyrins are affected by neighboring molecules. [1-3]. A perspective new way of design of nanosensors is to incorporate porphyrin molecules in electric circuits and obtain information amperometrically. The main feature of electronic devices is that they are open systems with respect to electron flow. A theoretical consideration of such devices should be done in terms of statistically mixed states which address the problem to quantum kinetic theory. We present here the results of ab initio non-equilibrium Green’s function study of the electron transport properties of porphyrin molecules. Comparison with the available experimental and theoretical data is provided.

References 1. Igarashi, S. and Yotsuyanagi,T. (1993) Analytica Chimica Acta. 281,347-351. 2. Mauzerall, D. (1965) Biohem. 4, 1801-1810. 3. Karasevich, I.E., Anisomova, B. L., Rubailo, V.L., and Shilov, A.E. (1993) Kinetics and Catalysis 34, 651-657. 200 Conference on Current Trends in Computational Chemistry 2004

Density Functional Theory Study of Vibrational Properties of the 3,4,9,10-Perylene Tetracarboxylic Dianhydride (PTCDA) Molecule: IR, Raman and UV-vis Spectra

N.U. Zhanpeisov,a S. Nishiob and H. Fukumuraa

aDepartment of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan bDepartment of Applied Chemistry, Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan

Recent developments in molecular beam deposition techniques and especially in pulsed laser deposition made enormous progress in the growth of well-ordered organic thin films on different metals and inorganic substrates. Among these organic molecules, 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) is one of the most intensively studied classical perylene derivatives. The graphite-like films can be obtained via removing functional carboxylic as well as anhydride groups from both side-ends of PTCDA while perylene monomer polymerizes to polyperinaphthalene (PPN) nanoparticles. PTCDA is also an interesting model system to study the influence of intermolecular interactions on the structural, optical and electronic properties. Especially, vibrational spectra obtained by Raman and infrared spectroscopy often provide indispensable information on the chemical composition and the crystalline quality of films that reveal important aspects for device performances. In this our work, we present the vibrational properties of PTCDA obtained within the DFT method at B3LYP/6-31G* level. Especially, the assignment of IR bands given by Kobitski et al.1 have been critically reconsidered because of the presence of substantial deviations for some set of estimated IR vibrations. In addition, our estimated Raman frequencies as well as UV-vis properties of PTCDA would be compared with those observed experimentally. Moreover, some potential derivatives of PTCDA modified via replacing of its two anhydride groups by N, B, S and Se-containing fragments and their spectroscopic properties would be further presented and discussed. ______1 Kobitski, A.Yu.; Scholz, R.; Zahn, D.R.T. J. Mol. Struct. (Theochem) 2003, 625, 39 Conference on Current Trends in Computational Chemistry 2004 201

The Origin of IR and Raman Band Shifts in H-bond Complexes of Triethylamine with Water: Density Functional Theory Study

N.U. Zhanpeisova,*, K. Ohtab ,S. Kajimotoa ,J. Hobleya , K. Hatanakaa, and H. Fukumuraa,*

aDepartment of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan bPhotonics Research Institute, National Institute of Advanced Industrial Science and Technology, Kansai Center, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan

In recent paper of our group1, we have reported on phase change following a nanosecond laser-induced temperature jump (T-jump) in classic triethylamine-water (TEA/H2O) system. We have introduced a sensitive Raman detection scheme which allows one more precisely and quantitatively determine the ratio of solute molecules solvated with solvent molecules, and in particular, TEA with water in diluted solutions. This scheme were further applied for spinodal demixing for yet another binary system of 2-butoxyethanol/water with an electrolyte KCl.2 Based on time-resolved Raman spectroscopy data we have shown that after phase splitting of binary TEA/H2O mixture, a clear red shift occurs to the methylene νC-H mode at around 2800 cm-1. The present paper discusses the results of density functional calculations obtained using the B3LYP functional and the standard 6-31G* basis sets for mono,- di- and triethylamines (MEA, DEA and TEA, respectively) and their H-bonded complexes with water molecules. Especially, the origin of the observed experimentally clear red shift for methylene νC-H mode due to nanosecond laser T-jump in TEA/H2O system is theoretically validated by explicit consideration of related IR and Raman peaks appeared at the C-H absorbance region. All theoretical calculations were performed with full geometry optimizations without imposing any constraints and followed by direct harmonic frequency calculations. The effects of non-specific and specific solvations were accounted for using simple Onsager model and explicit water molecules. It was shown that the former continuum model does not strongly perturbs the observed spectral changes in the C-H region because of shallow potential energy surface for the interacting subsystems. Both the structural changes in geometry and electron redistributions as a result of H-bonding were found to be main factors to explain the observed experimental spectral changes in IR and Raman spectra. ______1Hobley, J.; Kajimoto, S.; Takamizawa, A.; Ohta, K.; Tran-Cong, Q.; Fukumura, H. J. Phys. Chem. B 2003, 107, 11411. 2Takamizawa, A.; Kajimoto, S.; Hobley, J.; Fukumura, H. Phys. Rev. E 2003, 68, 020501R. 202 Conference on Current Trends in Computational Chemistry 2004

Adsorption of 1-Propanol on the Si(100) Surface

Jian-Ge Zhou and Frank Hagelberg

Computational Center for Molecular Structure and Interactions, Department of Physics, Atmospheric Sciences and General Science, Jackson State University, Jackson, MS 39217, US

The chemisorption of organic molecules on silicon surfaces is attracting much interest. This can be attributed to both the fundamental nature of this problem, involving the interaction between finite units and periodic substrates, but also to its relevance to various areas of current technology, such as insulator films, resistance of nanolithography, chemical and biological sensors, and molecular electronics. Guided by this motivation, we studied the adsorption of 1-propanol on Si(100)-(2X1) surface from the first principles calculations by using a slab approach. We use the VASP code [1] to carry out our calculations, where the electron-ion interaction is described by the projector augmented-wave (PAW) method. Our slab consists of five Si layers and one passivating H layer. The top four Si layers are relaxed while the bottom layer Si atoms and passivating H atoms are kept fixed to simulate bulk termination. Our results show that the 1-propanol molecule initially interacts with the Si surface through formation of a dative bond. Subsequently the physisorbed 1- propanol molecule reacts with the surface by cleavage of either the O-C or the O-H bond. We find that the O-C bond cleavage is thermodynamically stable, but the O-H bond cleavage is kinetically favored. Our calculation results match exactly with the experimental data [2], and show significant improvement over previous calculations where a simplified cluster model was used [2].

References

1. [1] G. Kresse and J. Hafner, Phys. Rev. B47, R558 (1993); G. Kresse and J. Furtmuller, Phys. Rev. B54, 11169 (1996). 2. [2] L. Zhang, A. Carman and S. Casey, J. Phys. Chem. B107, 8424 (2003). Conference on Current Trends in Computational Chemistry 2004 203

Analysis of the Unrestricted Solutions in the Basis of Paired Orbitals

Igor Zilberberg, Sergey Ph. Ruzankin, Sergey Malykhin

Boreskov Institute of Catalysis, Novosibirsk 630090, Russian Federation

Wide use of unrestricted density functional theory (UDFT) for various open-shell systems like transition-metal compounds revived the problem of spin-mixture contained in the U α unrestricted determinant (Ψ ) constructed from non-orthogonal orbitals {ψ i,i=1,n} and β U {ψ i,i=1,m}. Analysis of spin-mixture contained in Ψ can be in general carried out using projection technique which is though rarely applied in practice due to its complexity. In the present work such analysis is performed using “paired” or “corresponding” orbitals {ar,r=1,n} and {bs,s=1,m} for α and β spin, respectively, which are all orthogonal except for m pairs: =Trδrs. Paired orbitals can be always obtained by means of separate unitary α β transformations of “raw” orbitals ψ i and ψ j. The orbital space determined by paired orbitals is divided into the subspaces of completely, partially and non-overlapping orbitals having Tr = 1.0, 0.0 equal to 0, 1, 2,…,k they allow one to obtain a transparent assignment of the effective electron configuration(s) responsible for given unrestricted solution. Developed approach is especially useful in treating broken-symmetry solutions for systems with antiferromagnetically coupled paramagnetic centers. 204 Conference on Current Trends in Computational Chemistry 2004

Concerted vs. Diradical Pathways for Reactions of Fluorinated Allenes

Robert W. Zurales

Southeastern Louisiana University, Hammond, LA 70402

We used B3LYP/6-31G(d) density functional theory to obtain good agreement between predicted and experimental product distributions for the concerted and diradical reactions of butadiene and 1,1-difluoroallene. We also obtained good agreement for reactions of methylcyclopentadiene dimer with 1-chloro-3,3-difluoropropyne. We now predict the product distributions for the reactions of cyclopentadiene and methylcyclopentadiene with 3-chloro-1,1- difluroallene. This includes analysis of the competition between concerted and diradical pathways with dimerization of the reactants.

List of Participants Conference on Current Trends in Computational Chemistry 2004 207

William Adams Jon Baker Rutgers University Parallel Quantum Solutions 1208 Ursulines Ave. 2013 Green Acres Road, Suite A New Orleans, LA 70116 U.S.A. Fayetteville, AR 72703 U.S.A. Tel: 504-561-0128 Tel: (479) 521-5118 Email: [email protected] Fax: (479) 521-5167 Email: [email protected]

Dmitriy Afanasiev Anu Bamgbelu Ukrainian State University Norfolk State University of Chemical Technology Attn: Center for Materials Research NIL BAV, r. 206, 223 700 Park Ave. Dnepropetrovsk, 49005 Ukraine Norfolk, VA 23504 U.S.A Tel: (80562)477478 Tel: 757-515-5258 Fax: (80562)371890 Email: [email protected] Email: [email protected]

M. Mohamed Naseer Ali Victor Bazterra Department of Physics 155 S 1452 E RM 405 Bharathidasan University Salt Lake City, UT 84112 U.S.A. Tiruchirappalli, 620024 India Tel: (801) 585-0003 Tel: +91-431-5504785 Fax: (801) 585-5366 Fax: +91-431-2407045 Email: [email protected] Email: [email protected]

Reeshemah Allen Joseph Bentley Jackson State University Delta State University Department of Chemistry PO Box 3262-DSU 1325 Lynch St. Cleveland, MS 38733 U.S.A. Jackson, MS 39217 U.S.A. Tel: 662.846.4482 Tel: 601 979-3979 Email: [email protected] Fax: 601 979-7823 Email: [email protected]

Shonda Allen Pierre Bonifassi Jackson State University Avenue Olivier Messiaen Department of Chemistry Laboratoire synthèse organique 1325 Lynch St. Université du Mans Jackson, MS 39217 U.S.A. Le Mans, Sarthe72085 France Phone: (601) 979-6865 or 3981 Tel: 06 16 24 82 43 Fax: (601) 979-6865 Email: [email protected] E-mail: [email protected]

Sabrina Arrington-Peet Joseph Bordogna 815 Pecan Point Road Apt. #15 National Science Foundation Norfolk, VA 23502 U.S.A. Office of Legislative and Public Affairs Tel: (757) 461-1946 4201 Wilson Boulevard Email: [email protected] Arlington, VA 22230 U.S.A. Tel: 703-292-8070

Delbert Bagwell Rudolf Burcl Information Technology Laboratory Marshall University Engineer Research and Development Department of Chemistry Center, 3909 Halls Ferry Road Huntington, WV 25755 U.S.A. Vicksburg, MS 39180-9981 U.S.A. Tel: (304) 696-4808 Tel: (601) 634-4057 Fax: (304) 696-3243 Fax: (601) 634-2236 Email: [email protected] [email protected]

208 Conference on Current Trends in Computational Chemistry 2004 List of Participants

Jaroslav Burda Crystal Coghlan Ke Karlovu 3 Mississippi College Prague 2, 12116 Czech Republic Department of Chemistry & Biochemistry Tel: +420221911246 200 South Capitol St. Fax: +420221911249 Clinton, MS 39058 U.S.A. Email: [email protected] Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Louis Carlacci Lonnie Crosby Network CS Inc The University of Memphis 32 Clearwater Ct Department of Chemistry Damascus, MD 20872 U.S.A. 213 Smith Chemistry Building Tel: (301)253-6184 Memphis, TN 38152-3550 U.S.A. Email: [email protected] Tel: 901-678-4429 Fax: 901-678-3447 Email: [email protected]

Grzegorz Chalasinski Yuanjian Deng Department of Chemistry Texas Southern University University of Warsaw Department of Chemistry 1 Pasteura Street 3100 Cleburne Ave. Warsaw, 02-093 Poland Houston, TX 77004 U.S.A. Tel: +4822 8220211 Tel: 713-313-1917 Email: Grzegorz.Chalasinski@tiger. Fax: 713-313-7824 chem.uw.edu.pl Email: [email protected]

Rozlyn Chambliss Deborah Dent Department of Chemistry Deputy Director Armstrong Hall Room 102 U.S. Army Engineer Research and Tuskegee University Development Center Tuskegee, AL 36088-1645 U.S.A. ATTN: CEERD-IV-A Tel: 334-727-8878 3909 Halls Ferry Road Fax: 334-724-4492 Vicksburg, MS 39180-9981 U.S.A. Email: [email protected] Tel: 601-634-3455

Anthony Chuma LaTanya Dixon Chem 101 Jackson State University Department of Chemistry & Biochemistry Department of Chemistry University of Arkansas 1325 Lynch St. Fayetteville, AR 72701 U.S.A. Jackson, MS 39217 U.S.A. Tel: (479)575-5080 Tel: 601-624-5260 Email: [email protected] Email: [email protected]

Tim Clark Robert Doerksen Computer Chemie Centrum University of Mississippi Friedrich-Alexander-Universität Department of Medicinal Chemistry Erlangen, Nägelsbachstraße 25 421 Faser Hall Erlangen, 91052 Germany University, MS 38677-1848 U.S.A. Tel: +49(0)9131-85-22948 Tel: 6628016222 Fax: +49(0)9131-85-26565 Fax: 6629155638 Email: [email protected] Email: [email protected]

David Close David Doherty Physics Dept. Box 70652 Army High Performance Computing East Tennessee State University Research Center Johnson City, TN 37614 U.S.A. 1200 Washington Ave. S. Tel: 423-439-5646 Minneapolis, MN 55415 U.S.A. Fax: 423-439-6905 Tel: 612-337-3425 Email: [email protected] Fax: 612-337-3400 Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2004 209

Jesse Edwards Ryan Fortenberry 219 Jones Hall Mississippi College Chemistry Department Department of Chemistry & Biochemistry Florida A&M University 200 South Capitol St. Tallahassee, FL 32307 U.S.A. Clinton, MS 39058 U.S.A. Tel: 850-599-3638 Tel: 601-925-3852 Fax: 850-561-2388 Fax: 601-925-3933 Email: [email protected] Email: [email protected]

Claudia Eybl Fillmore Freeman Florida A & M University Department of Chemistry 109 Jones Hall University of California, Irvine Tallahassee, FL 32301 U.S.A. Irvine, CA 92697-2025 U.S.A. Tel: 850-321-6556 Tel: 949-824-6501 Email: [email protected] Fax: 949-824-2210 Email: [email protected]

James Fells Al'ona Furmanchuk 111 S. Highland #324 Jackson State University Memphis, TN 38111 U.S.A. Department of Chemistry Tel: (901)678-6968 1325 Lynch St. Email: [email protected] Jackson, MS 39217 U.S.A. Tel: 601-979-1134 Fax: 601-979-7823 Email: [email protected]

Marta Ferraro Luis Galiano Dpto. de Fisica 2300 New Physics Building #92 Ciudad Universitaria. Pab. I PO Box 118435 Buenos Aires, 1428 Argentina Gainesville, FL 32611 U.S.A. Tel: 54-11-45763353 Tel: (352)392-6365 Fax: 54-11-45763357 Email: [email protected] Email: [email protected]

Antonio Ferreira Ainsley Gibson Hartwell Center Howard University St. Jude Children's Research Hospital Department of Chemistry Mail Stop 312, 332 N. Lauderdale St. 525 College Street NW Memphis, TN 38105 U.S.A. Washington, DC 20059 U.S.A. Tel: (901) 495-4624 Tel: 240-353-5750 Fax: (901) 495-2945 Fax: 202-806-5442 Email: [email protected] Email: [email protected]

Alan Ford Gurvinder Gill University of Arkansas Jackson State University Department of Chemistry & Biochemistry Department of Chemistry CHEM 101 1325 Lynch St. Fayetteville, AR 72701 U.S.A. Jackson, MS 39217 U.S.A. Tel: (479) 251-8130 Tel: 601-979-2922 Email: [email protected] Fax: 601-979-3674 Email: [email protected]

Jason Ford-Green Leonid Gorb Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 Lynch St. 1325 Lynch St. Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: (850)443-9233 Tel: 6019792213 Email: [email protected] Email: [email protected]

210 Conference on Current Trends in Computational Chemistry 2004 List of Participants

Helen Grebneva John Harkless Luxemburg str., 72 Howard University Donetsk, 83114 Ukraine 525 College St., NW Tel: +3806223048121 Washington, DC 20059 U.S.A. Email: [email protected] Tel: 202-806-6899 Fax: 202-806-5442 Email: [email protected]

Jiande Gu Frances Hill Shanghai Institute of Materia Medica Network Computing Services, Inc/AHPCRC Chinese Academy of Sciences 1200 Washington Ave S Shanghai, 201203 P. R. China Minneapolis, MN 55415 U.S.A. Tel: 086-21-50806720 Tel: 612-337-3569 Email: [email protected] Fax: 612-337-3400 Email: [email protected]

Gennady Gutsev Glake Hill Department of Physics Jackson State University Florida A&M University Department of Chemistry Tallahassee, FL 32307 U.S.A. 1325 Lynch St. Tel: (850) 599-3783 Jackson, MS 39217 U.S.A. Fax: (850) 599-3577 Tel: 601-979-1699 Email: [email protected] Email: [email protected]

Steven Gwaltney Patricia Honea Mississippi State University US Army Engineer Research and Box 1593 Development Center Department of Chemistry 3909 Halls Ferry Rd Mississippi State, MS 39762 U.S.A. Vicksburg, MS 39180 U.S.A. Tel: 662-325-7602 Tel: 601-634-2070 Fax: 662-323-1618 [email protected] Email: [email protected]

Frank Hagelberg Delwar Hossain Jackson State University Chemistry Department Department of Physics Mississippi State University 1325 Lynch St. Mississippi State, MS 39762 U.S.A. Jackson, MS 39217 U.S.A. Tel: 662-325-1378 Tel: 601 979 3633 Email: [email protected] Fax: 601 979 3630 [email protected]

Ju-Guang Han Pamela Howell Jackson State University 11 Bloomingdale Dr. Department of Chemistry Hillsborough, NJ 08844 U.S.A. 1325 Lynch St. Tel: 908-500-1326 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979 3714 Email: [email protected]

Zengjian Hu Mark G. Hardy 520 West Street, NW Associate Dean, College of Science, Howard University College of Medicine Engineering, and Technology Room 324 Jackson State University Washington, DC 20059 U.S.A. Jackson, MS 39217 Tel: 202-806-9714 Tel: 601-979-3449 Fax: 202-806-9714 Email: [email protected] Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2004 211

Ming-Ju Huang Angela Jackson Department of Chemistry 520 West Street NW Jackson State University Howard University College of Medicine P. O. Box 17910 Washington, DC 20059 U.S.A. Jackson, MS 39217 U.S.A. Tel: 202-726-4499 Tel: 601-979-3492 Fax: 202-806-5784 Fax: 601-979-3674 Email: [email protected] Email: [email protected]

Xiaofei Huang Debra Jackson Blythe Street Department of Chemistry Foster City, CA 94404 U.S.A. Jackson State University Tel: (650)578-9582 P. O. Box 17910 Fax: (650)578-9582 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979-3303 Email: [email protected]

Danielle Hudson Richard L. Jaffe Department of Chemistry NASA Ames Research Center Armstrong Hall Room 102 Computational Chemistry Branch Tuskegee University Mail Stop 230-3 Tuskegee, AL 36088-1645 U.S.A. Moffett Field, CA 94035 U.S.A. Tel: 334-727-8878 Tel: 650-604-4444 Fax: 334-724-4492 Email: [email protected] Email: [email protected]

Thomas Hughes Valentin Karasiev Univ. of FL Quantum Theory Project Centro de Quimica 2217 New Physics Building IVIC PO Box 118435 Apartado 21827 Gainesville, FL 32601 U.S.A. Caracas, 1020-A Venezuela Tel: 352-392-6365 Tel: +58(212)504-1356 Email: [email protected] Fax: +58(212)504-1350 Email: [email protected]

Shelley Huskey Arman Kirakosyan Mississippi College Jackson State University Department of Chemistry & Biochemistry Department of Physics 200 South Capitol St. 1325 Lynch St. Clinton, MS 39058 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-925-3852 Tel: 601 979 1391 Fax: 601-925-3933 Fax: 601 979 6998 Email: [email protected] Email: [email protected]

Olexandr Isayev Dmitriy Kosenkov Jackson State University Kiev National University Department of Chemistry 46, Prospekt Nauky 1325 Lynch St. Kiev, 03028 Jackson, MS 39217 U.S.A. Ukraine Tel: 601 9791134 Tel: +38(044)2659851 Fax: 601 9797823 Fax: +38(044)2651589 Email: [email protected] Email: [email protected]

Mark Jack Vitalina Kukueva Florida A&M University, Dept. of Physics Onoprienko, 8 1500 Wahnish Way Cherkassy, 18034 Ukraine 205 Jones Hall Tel: 8067-90-20-135 Tallahassee, FL 32307 U.S.A. Fax: 804729-45-61-57 Tel: 8505998457 Email: [email protected] Fax: 8505993577 Email: [email protected]

212 Conference on Current Trends in Computational Chemistry 2004 List of Participants

Gulnara Kuramshina Michail Levkovich Department of Physical Chemistry Institute of Plant Substances Chemistry Faculty of Chemistry Kh.Abdullaev Str., 77 Moscow State University Tashkent, 700170 Uzbekistan Moscow, 119992 Russia Tel: (998 71) 1627897 Tel: 7(095)9392950 Fax: (998 71) 1206475 Fax: 7(095)9328846 Email: [email protected] Email: [email protected]

Nicholas Labello Meng-Sheng Liao The University of Memphis Jackson State University Department of Chemistry Department of Chemistry 213 Smith Chemistry Building 1325 Lynch St. Memphis, TN 38152 U.S.A. Jackson, MS 39217 U.S.A. Tel: (901) 678-4429 Tel: (601)979-3714 Fax: (901) 678-3447 Fax: (601)979-3674 Email: [email protected] Email: [email protected]

Richard Lavery Dan Liu Laboratoire de Biochimie Théorique Jackson State University Institut de Biologie Physico-Chimique Department of Chemistry 13, rue Pierre et Marie Curie 1325 Lynch St. Paris, F-75005 France Jackson, MS 39217 U.S.A. Tel: +33(0)1 58 415 016 Tel: 601-979-3640 Fax: +33(0)1 58 415 026 Email: [email protected] Email: [email protected]

Christopher Lee David Magers 3630 Rainey Road Apt. #26 Mississippi College Moss Point, MS 39212 U.S.A. Department of Chemistry & Biochemistry Tel: 228-990-1932 200 South Capitol St. Email: [email protected] Clinton, MS 39058 U.S.A. Tel: 601-925-3851 Fax: 601-925-3933 Email: [email protected]

William A. Lester, Jr. Devashis Majumdar University of California, Berkeley Jackson State University Department of Chemistry Department of Chemistry Berkeley, CA 94720-1460 U.S.A. 1325 Lynch St. Tel: 510-643-9590 Jackson, MS 39217 U.S.A. Fax: 510-642-1088 Tel: (601)-979-9801 Email: [email protected] Fax: (601)-979-7823 Email: [email protected]

Danuta Leszczynska Massimo Malagoli FAMU-FSU College of Engineering Parallel Quantum Solutions Department of Civil Engineering 2013 Green Acres Road, Suite A 2525 Pottsdamer Str. Fayetteville, AR 72703 U.S.A. Tallahassee, FL 32310 U.S.A. Tel: (479) 521-5118 Tel: 904-487-6137 Fax: (479) 521-5167 Fax: 904-487-6142 Email: malagoli@pqs-chem.com Email: [email protected]

Jerzy Leszczynski Ronald Mason Jackson State University President, Jackson State University Department of Chemistry 1400 Lynch St. 1325 Lynch St. Jackson, MS 39217-0280 USA Jackson, MS 39217 U.S.A. Tel: 601.979.2323 Tel: 601-979-7824 Fax: 601.979.2948 Fax: 601-979-7823 E-mail: [email protected] Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2004 213

Joshua McClellan Jane Murray Quantum Theory Project Department of Chemistry University of Florida University of New Orleans 2301 NPB #92 Kenner, LA 70124 U.S.A. P.O. Box 118435 Tel: 504-280-3250 Gainesville, FL 32611-8435 U.S.A. Fax: 504-280-6860 Tel: (352)392-6713 Email: [email protected] Email: [email protected]

James L. Meeks Hiroshi Nakatsuji West Kentucky Comm & Tech College Fukui Institute for Fundamental Chemistry, Department of Physics Kyoto University PO BOX 7380 34-4 Takano-Nishihiraki-cho, Sakyou-ku Paducah, KY 42002-7380 U.S.A. Kyoto 606-8103, Japan Tel: 270 534 3137 Tel: 81-75-383-2738 Fax: 270 534 6291 Fax: 81-75-383-2741 Email: [email protected] Email: [email protected]

Andrea Michalkova Brian Napolion Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 Lynch St. 1325 Lynch St. Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-9791041 Tel: 601 979 2171 Fax: 601-9797823 Fax: 601 979 3674 Email: [email protected] Email: [email protected]

Alan L. Middleton Edmund Moses Ndip Information Technology Laboratory Hampton University Engineer Research and Development East Queen & Tyler Streets Center, 3909 Halls Ferry Road Hampton, VA 23668 U.S.A. Vicksburg, MS 39180-9981 U.S.A. Tel: 757 727 5043 Tel: (601) 634-4057 Fax: 757 727 5604 Fax: (601) 634-2236 Email: [email protected] [email protected]

Abdul K. Mohamed Adria Neely Dean, College of Science, Engineering & Mississippi College Technology Department of Chemistry & Biochemistry Jackson State University 200 South Capitol St. Jackson, MS 39217 USA Clinton, MS 39058 U.S.A. Tel: 601-979-2153 Tel: 601-925-3852 Email: [email protected] Fax: 601-925-3933 Email: [email protected]

Regina Monaco Eric Noe NASA Ames Research Center Jackson State University MS 239-4 Department of Chemistry Moffett Field, CA 94035 U.S.A. 1325 Lynch St. Tel: 925 3524590 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979-2922 Fax: 601-979-3674 Email: [email protected]

Jose Moncada Felix Okojie Av. Vicuna Mackenna 4860 Vice President for Research Facultad de Quimica and Strategic Initiatives Lab. Quimica Teorica Computacional Jackson State University Santiago, Santiago782-0436 Chile Jackson, MS 39217 USA Tel: (56-2)6865474 Tel: 601-979-2931 Fax: (56-2)6864744 Fax: 601-979-3664 Email: [email protected] Email: [email protected]

214 Conference on Current Trends in Computational Chemistry 2004 List of Participants

Sergiy Okovytyy William Parkinson Dnepropetrovsk National University Southeastern Louisiana University Department of Chemistry Hammond, LA 70401 U.S.A. Nauchny St. 13 Tel: 9855495124 Dnepropetrovsk, 49625 Ukraine Fax: 9855495126 Tel: +(380562)463143 Email: [email protected] Email: [email protected]

Oleg Olendski Yuliya Paukku Jackson State University Jackson State University Department of Physics Department of Chemistry 1325 Lynch St. 1325 Lynch St. Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-979-1391 Tel: 601-979-7824 Fax: 601-979-6998 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Daniel Osborne Diwakar Pawar The University of Memphis Jackson State University 425 J.M. Smith Hall Department of Chemistry Memphis, TN 38152 U.S.A. 1325 Lynch St. Tel: 901-678-4425 Jackson, MS 39217 U.S.A. Fax: 901-678-3447 Tel: 601-979-2922 Email: [email protected] Fax: 601-979-3674 Email: [email protected]

Valentin Oshchapovsky James Perkins Kleparivska, 35 Jackson State University Lvov, 79007 Ukraine Office of Research, Industrial and Tel: 38 032 233 02 02 Community Relations, Director Fax: 38 032 233 00 88 Tel: (601) 979-2024/76 Email: [email protected] Email: [email protected]

Ourida Ouamerali Lars G. M. Pettersson Lab. de PhysicoChimie Theorique et Chimi, Stockholm University Faculte de Chimie USTHB Albanova University Center BPN032 El Alia Bab Ezzouar FYSIKUM Algiers, 16111 Algeria Stockholm, S-106 91 Sweden Tel: +(213) 21 247 950 Tel: +46(8)5537 8712 Fax: +(213) 21 247 311 Fax: +46(8)5537 8442 Email: [email protected] Email: [email protected]

Juan Palacios Yevgeniy Podolyan Dept. Fisica Aplicada Jackson State University Universidad de Alicante Department of Chemistry Campus de San Vicente del Raspeig 1325 Lynch St. Alicante, Alicante03690 Spain Jackson, MS 39217 U.S.A. Tel: 34965909630 Tel: 601-979-4114 Fax: 34965909726 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Ras Pandey Peter Politzer University of Southern Mississippi Department of Chemistry Dept. of Physics & Astronomy University of New Orleans Box 5046 New Orleans, LA 70148 U.S.A. Hattiesburg, MS 39406 U.S.A. Tel: 504-280-6850 Tel: 601 266 4485 Fax: 504-280-6860 Fax: 601 266 5149 Email: [email protected] Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2004 215

Valeri Poltev Sohail Qamar Physics and Mathematics Department University Sains Malaysia Puebla Autonomous University School of Pharmacy Puebla, 72570, Mexico Penang, Penang11800 Malaysia Puebla, Puebla72570 Mexico Tel: 60-04-6577888 Tel: 52 2222295522 2154 Email: [email protected] Email: [email protected]

Morgan Ponder Mohammad Qasim Samford University US Army Engineer Research and Department of Chemistry Development Center Birmingham, AL 35222-2236 U.S.A. 3909 Halls Ferry Rd Tel: 205-726-2680 Vicksburg, MS 39180 U.S.A. Fax: 205-726-2479 Tel: 601-634-3422 Email: [email protected] Email: [email protected]

Paul Popelier N. Radhakrishnan Department of Chemistry North Carolina Agricultural and Technical University of Manchester State University Manchester, M60 1QD, Great Britain 1601 East Market St. Tel: +44-161-2004511 Greensboro, NC 27411 U.S.A. Fax: +44-161-2004559 Tel: 336-334-7995 Email: [email protected] Fax: 336-334-7086 Email: [email protected]

Lawrence Pratt Parthasarathi Ramakrishnan Fisk University Senior Research Fellow Nashville, TN 37208 U.S.A. Chemical Laboratory, Tel: 615-329-8559 Central Leather ResearchInstitute, Adyar Fax: 615-329-8634 Chennai, Tamil Nadu 600020 India Email: [email protected] Tel: +91-44-24411630 Fax: +91-44-24411630 Email: [email protected]

Rita Presley Bakhtiyor Rasulev Director, Office of Sponsored Programs Jackson State University Jackson State University Department of Chemistry Jackson, MS 39217 USA 1325 Lynch St. Phone: 601.979.2457 Jackson, MS 39217 U.S.A. E-mail: [email protected] Tel: 601-979-6716 Fax: 601-979-7823 Email: [email protected]

Peter Pulay Paresh Ray Department of Chemistry & Biochemistry Jackson State University University of Arkansas Department of Chemistry 348 Arkansas Avenue 1325 Lynch St. Fayetteville, AR 72701 U.S.A. Jackson, MS 39217 U.S.A. Tel: (479) 575-6612 Tel: 6019793487 Fax: (479) 575-4049 Fax: 6019793674 Email: [email protected] Email: [email protected]

Vitaliy Pustovit Melissa Reeves Jackson State University Department of Chemistry Department of Physics Armstrong Hall Room 102 1325 Lynch St. Tuskegee University Jackson, MS 39217 U.S.A. Tuskegee, AL 36088-1645 U.S.A. Tel: 6019791391 Tel: 334-727-8327 Fax: 6019796998 Fax: 334-724-4492 Email: [email protected] Email: [email protected]

216 Conference on Current Trends in Computational Chemistry 2004 List of Participants

Teri Robinson Yinghong Sheng Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 Lynch St. 1325 Lynch St. Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-979-3981 Tel: 6019791219 Fax: 601-979-7824 Fax: 6019797823 Email: [email protected] Email: [email protected]

Szczepan Roszak Manoj Shukla Wroclaw University of Technology Jackson State University Wyb. Wyspianskiego 27 Department of Chemistry Wroclaw, 50370 Poland 1325 Lynch St. Tel: 48 71 3202675 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: 601-979-1136 Fax: 601-979-7823 Email: [email protected]

Ursula Röthlisberger Tomekia Simeon Institute of Chemical Sci. & Engineering Jackson State University Laboratory of Computational Chemistry & Department of Chemistry Biochemistry 1325 Lynch St. Lausanne, CH-1015 Switzerland Jackson, MS 39217 U.S.A. Tel: +41 (0)21 693 03 25 Tel: 601-979-3979 Fax: +41 (0)21 693 03 20 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Zuhail Sainudeen Vitali Solkan Jackson State University N.D. Zelinsky Institute of Organic Department of Chemistry Chemistry, RAS. Leninskii pr-t 47 1325 Lynch St. Moscow, 119991 Russia Jackson, MS 39217 U.S.A. Tel: 7(095)1356425 Tel: 601-979-3487 Fax: 7(095)1355328 Email: [email protected] Email: [email protected]

Julia Saloni Angela Sood Jackson State University Mississippi College Department of Chemistry Department of Chemistry & Biochemistry 1325 Lynch St. 200 South Capitol St. Jackson, MS 39217 U.S.A. Clinton, MS 39058 U.S.A. Tel: 601-979-7824 Tel: 601-925-3852 Fax: 601-979-7823 Fax: 601-925-3933 Email: [email protected] Email: [email protected]

Igor Schweigert William Southerland University of Florida 520 West Street NW 2300 New Physics Building #92 Howard University College of Medicine PO Box 118435 Washington, DC 20059 U.S.A. Gainesville, FL 32611-8435 U.S.A. Tel: 202-806-9711 Tel: (352) 392-6365 Fax: 202-588-9330 Fax: (352) 392-8722 Email: [email protected] Email: [email protected]

Adam Seyfarth Jiri Sponer Computer Science Institute of Biophysics The University of Southern Mississippi Academy of Sciences of the CR 118 College Drive #5106 Kralovopolska 135 Hattiesburg, MS 39406-5106 U.S.A. Brno, 612 65 Czech Republic Tel: 601-266-4949 Tel: +420 5415 17133 Fax: 601-266-6452 Fax: +420 5412 12179 Email: [email protected] Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2004 217

Andrea Sterling Andrew Taube Jackson State University University of Florida Department of Chemistry 2217 New Physics Building 1325 Lynch St. P.O. Box 118435 Jackson, MS 39217 U.S.A. Gainesville, FL 32611 U.S.A. Tel: (601)979-7250 Tel: (352) 392-6365 Fax: Email: [email protected] Email: [email protected]

Jaroslaw Szymczak Gordon Taylor Jackson State University 2251 Sherman Ave, NW Department of Chemistry Apt. 443W 1325 Lynch St. Washington, DC 20001 U.S.A. Jackson, MS 39217 U.S.A. Tel: 202-612-9686 Tel: 601-979-7824 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

Krzysztof Tajchert Lyssa Taylor Jackson State University Mississippi College Department of Chemistry Department of Chemistry & Biochemistry 1325 Lynch St. 200 South Capitol St. Jackson, MS 39217 U.S.A. Clinton, MS 39058 U.S.A. Tel: 601-979-7824 Tel: 601-925-3852 Fax: 601-979-7823 Fax: 601-925-3933 Email: [email protected] Email: [email protected]

Genzo Tanaka Tamara Taylor NCSI/AHPCRC Jackson State University 205 Jones Hall, FAMU Department of Chemistry Tallahassee, FL 32307 U.S.A. 1325 Lynch St. Tel: 850-599-3666 Jackson, MS 39217 U.S.A. Fax: 850-599-3953 Tel: (601)454-0052 Email: [email protected] Email: [email protected]

Dinadayalane Tandabany Kanchana Thanthiriwatte Jackson State University Department of Chemistry Department of Chemistry Mississippi State University 1325 Lynch St. Box 9573 Jackson, MS 39217 U.S.A. Mississippi State , MS 39762 U.S.A. Tel: 601-979-7824 Tel: (662) 325-9562 Fax: 601-979-7823 Fax: (662) 325-1618 Email: [email protected] Email: [email protected]

Shauna Tanner Alejandro Toro-Labbe 131 Colony Square Pontificia Universidad Catolica de Chile Jackson, MS 39204 U.S.A. QTC, Facultad de Quimica, Tel: 601-372-1817 V. Mackenna 4860, Macul Email: [email protected] Santiago, 6904411 Chile Tel: 56-2-686 4746 Fax: 56-2-686 4744 Email: [email protected]

Antti Taskinen Samuel Trickey Åbo Akademi University Quantum Theory Project Department of Physical Chemistry University of Florida Porthaninkatu 3-5 Box 118435 Turku, FIN-20500 Finland Gainesville , FL 32611-8435 U.S.A. Tel: +358-2-2154951 Tel: 352-392-1597 Fax: +358-2-2154706 Fax: 352-392-8722 Email: [email protected] Email: [email protected]

218 Conference on Current Trends in Computational Chemistry 2004 List of Participants

Malakhat Turabekova Jing Wang National University of Uzbekistan Jackson State University Vuzgorodok Department of Chemistry Tashkent, 700174 Uzbekistan 1325 Lynch St. Tel: 00998712-460788 Jackson, MS 39217 U.S.A. Fax: 0099871-1447728 Tel: 601-9791159 Email: [email protected] Fax: 601-9797823 Email: [email protected]

Jan Urban Mary Ware Faculty of Mathematics, Physics and Interim Assistant Commissioner Informatics, Comenius University Academic Affairs Mlynska dolina F1 Institutions of Higher Learning Bratislava, 842 48 Slovakia 3825 Ridgewood Road Tel: ++421 2 602 95 111 Jackson, MS 39211-6453 Fax: ++421 2 654 26 720 Tel: 601-432-6501 Email: [email protected] Fax: 601-432-6978

Marek W. Urban Courtney Watts The University of Southern Mississippi Jackson State University Department of Polymer Science Department of Chemistry Box 10076 1325 Lynch St. Hattiesburg, MS 39406-0076 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-266-6868/6454 Tel: 601-9791041 Fax: 601-266-5635 Fax: 601-9797823 Email: [email protected] Email: [email protected]

Ravi Vadapalli John Watts 145 Physical Sciences Jackson State University Oklahoma State University Department of Chemistry Stillwater, OK 74078 U.S.A. 1325 Lynch St. Tel: 405-744-3857 Jackson, MS 39217 U.S.A. Fax: 405-744-6811 Tel: 601 979 3488 Email: [email protected] Fax: 601 979 3674 Email: [email protected]

Zoltan Varga Robert W. Whalin Institute of General and Analytical Associate Dean, College of Science, Chemistry Engineering & Technology Budapest University of Technology and Jackson State University Economics Jackson, MS 39217 USA Szt. Gellért tér 4 Tel: 601-979-4043 Budapest, H-1111 Hungary Email: [email protected] Email: [email protected]

Gregory Voth Andrzej Wierzbicki Department of Chemistry Department of Chemistry University of Utah University of South Alabama 315 S. 1400 E. Rm 2020 Mobile, AL 36688 U.S.A. Salt Lake City, UT 84112-0850 U.S.A. Tel: (251) 460-7436 Tel: (801) 581-5419 Fax: (251) 460-7359 Fax: (801) 581-4353 Email: [email protected] Email: [email protected]

Mattanjah S. de Vries Mary La'Françes Williams Department of Chemistry & Biochemistry Norfolk State University University of California at Santa Barbara Attn: Center for Materials Research Santa Barbara, CA 93106 U.S.A. 700 Park Ave. Tel: (805) 893-5921 Norfolk, VA 23504 U.S.A. Fax: (805) 893-4120 Tel: (757)823 2153 / 8403 Email: [email protected] Fax: (757)823 9054 Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2004 219

Shi'Nitta Woulard Nurbosyn U. Zhanpeisov P.O. Box 190269 Department of Chemistry Jackson, MS 39217 U.S.A. Graduate School of Science Tel: 601-454-4185 Tohoku University Email: [email protected] Sendai, 980-8578 Japan Tel: 81-22-217-6568 Fax: 81-22-217-6570 [email protected]

Nydeia Wright Lijiao Zhao Department of Chemistry Pingleyuan NO.100 Armstrong Hall Room 102 Chaoyang District Tuskegee University Beijing University of Technology Tuskegee, AL 36088-1645 U.S.A. Beijing, Beijing 100022 China Tel: 334-727-8878 Tel: 0086-010-67396211 Fax: 334-724-4492 Fax: 0086-010-67392001 Email: [email protected] Email: [email protected]

Jianhua Wu Jian-Ge Zhou Jackson State University Jackson State University Department of Physics Department of Physics 1400 Lynch St. 1400 Lynch St. Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-979-3640 Tel: 1-601-9696890 Email: [email protected] Email: [email protected]

Albert Wynn III Igor Zilberberg Florida A&M University Lavrentieva 5 205 Jones Hall Novosibirsk, 630090 Russia Tallahassee, FL 32307 U.S.A. Tel: 7-3832-341064 Tel: 850-599-3642 Fax: 7-3832-343056 Fax: 850-599-3953 Email: [email protected] Email: [email protected]

Ilya Yanov Robert Zurales Jackson State University Southeastern Louisiana University Department of Chemistry SLU 10878 1325 Lynch St. Hammond, LA 70402 U.S.A. Jackson, MS 39217 U.S.A. Tel: 985-549-3480 Tel: (601)979-4136 Fax: 985-549-5126 Fax: (601)979-7823 Email: [email protected] Email: [email protected]

Hongtao Yu Jackson State University Department of Chemistry 1325 Lynch St. Jackson, MS 39217 U.S.A. Tel: (601)979-2174 Fax: (601)979-3674 Email: [email protected]

220 Conference on Current Trends in Computational Chemistry 2004 Author Index

Author Index

Afanasiev, D.Yu...... 141 Fortner, A.D...... 110 Allen, Reeshemah N...... 19,20 Francisco, J.S...... 117 Anderson, Kelly L...... 127 Fredrickson, Herbert L...... 71,118 Arce, Rafael ...... 34 Freeman, Fillmore...... 54 Arrington-Peet, Sabrina ...... 21 Fronczek, Frank R ...... 190 Baker, Jon ...... 22,107,112 Fuentealbac, Patricio ...... 24 Bartlett, Rodney J...... 86,108,154,181 Fujiwara, Yuko ...... 124 Bashford, Donald E...... 151 Fukumura, H...... 200,201 Bateman, Sam ...... 23 Furey, John...... 71 Bauschlicher, C.W...... 67 Furmanchuk, Al'ona ...... 55 Bazterra, Victor E...... 24 Gibson, Ainsley...... 57 Bentley, Joseph A...... 26 Gill, Gurvinder...... 58,59,60,61 Bishop, G. Reid...... 174 Gonzalez, E...... 132 Bonifassi, P.J...... 37 Gorb, Leonid ...... 34,44,47,55,87,110,131,132 Bowen, Donnel ...... 76 Grebneva, H.A...... 62 Burda, Jaroslav...... 27 Gu, Jiande ...... 193 Caputo, M.C...... 24 Gutierrez-Oliva, Soledad ...... 66 Chalasinski, G...... 92 Gutsev, G.L...... 67 Cheung, Herman S...... 36 Gwaltney, Steven R...... 68,182 Chuma, Anthony...... 28 Habibah, A.W...... 161 Churakov, Aleksandr M...... 169 Hagelberg, Frank ...... 74,198,202 Clancy, Thomas C...... 84 Hamilton, Tracy P...... 134 Clark, Tim...... 29 Hamme, Ashton T...... 69,148 Close, David M...... 30 Han, Ju-Guang ...... 70 Coghlan, Crystal B...... 31 Harkless, John...... 57 Cook, Tiffany...... 69 Hassan, Ayourinde ...... 53 Crespo-Hernandez, Carlos E...... 34 Hatanaka, K...... 201 Crosby, Lonnie D...... 35 Heinz, Hendrik...... 127 Cseh, Sandor ...... 124 Herrera, Barbara ...... 66 Curry, Jennifer L...... 26 Hinkley, Jeffrey A...... 84 Dalal, Pranav ...... 36 Hobley, J...... 201 Daoudi, Y...... 37 Honea, Patricia L...... 71 Deng, Yuanjian...... 40 Hossain, Delwar...... 74 Deriabina, A.S...... 132 Hu, Zengjian ...... 76 Devereux, M...... 135 Huang, Ming-Ju ...... 40,70,79,104 Dinadayalane, T.C...... 42,44 Huang, Xiaofei...... 80 Dodziuk, Helena ...... 44 Hudson, Danielle L...... 84 Doerksen, Robert J...... 46 Hughes, Thomas F...... 86 Dovbeshko, Galina I...... 47 Hurley, Sharon J...... 79 Edwards, Jesse...... 49,117 Isayev, Olexandr ...... 55,87 Ellis, Erick...... 69 Jack, Mark ...... 88 Eybl, Claudia D...... 49 Jaffe, Richard L...... 89 Facelli, Julio C...... 24 Jin, Ping ...... 152 Fannin, Harry B...... 109 Kajimoto, S...... 201 Farmer, B.L...... 127 Kheffache, D...... 90 Fedoseyenko, D.V...... 141 Kholod, Y...... 71,118,122 Fells, James I...... 50,124 Kirakosyan, Arman S...... 91 Ferraro, Marta B...... 24 Kirpichenko, Svetlana V...... 54 Ferreira, Antonio M...... 51,100 Klos, J...... 92 Ford, Alan...... 52 Koca, Jaroslav ...... 150 Ford-Green, Jason ...... 53 Kosenkov, Dmitriy V...... 47 Author Index Conference on Current Trends in Computational Chemistry 2004 221

Kovacs, Attila ...... 189 Ouamerali, O...... 90 Krasovska, Maryna V...... 93 Palacios, J.J...... 126 Kuramshina, G.M...... 94,96 Pandey, Ras B...... 127,155 Kurtz, Henry A...... 35,100 Park, Sung Soo...... 74 Labello, Nicholas P...... 100 Parkinson, William A...... 178 Lavery, Richard ...... 101 Parrill, Abby L...... 50,124 Lee, Ken S...... 79 Parthasarathi, R...... 128 Leontis, Neocles B...... 150 Pawar, Dewakar M...... 59,60,61,151 Leslie, M...... 135 Pazilah, I...... 161 Leszczynski, Jerzy.19,20,27,34,42,44,47,55,71 Perez-Jimenez, A.J...... 126 87,88,110,118,120,131,132,148,149,156,158 Petrova, T...... 119 160,162,165,168,176,177,179,193,194,199 Pettersson, Lars G.M...... 130 Levkovich, M.G...... 102 Pittman, Charles U...... 74 Liao, Meng-Sheng ...... 104 Podolyan, Yevgeniy ...... 131 Liem, S...... 135 Politzer, Peter...... 152 Lotrich, Victor F...... 154 Poltev, V.I...... 132 Louis, E...... 126 Ponder, Morgan S...... 134 Lovell, M. Jeanann ...... 174 Popelier, P...... 135 Lozano, L...... 132 Pratt, Lawrence M...... 139 Ma, Buyong...... 76 Prosyanik, A.V...... 141 Madura, Jeffry D...... 36 Pulay, Peter ...... 22,28,52,145 Magers, David H...... 31,115,174 Pustovit, V.N...... 146 Majumdar, Devashis...... 179 Qasim, Mohammad ...... 71,118 Malagoli, Massimo...... 22,107 Rakhimov, Rakhim ...... 21 Malykhin, Sergey ...... 203 Rasulev, Bakhtiyor ...... 148 Martinez, A...... 132 Ray, Paresh Chandra ...... 149,153,190 Matti, Hotokka...... 180 Razga, Filip ...... 150 McClellan, Joshua J...... 108 Reblova, Kamila...... 150 Meeks, James L...... 109 Reed, Demarcio ...... 20 Michalkova, A...... 110,194 Reeves, Melissa S...... 84 Mochena, M.D...... 67 Reyes, Moncada ...... 151 Moncada, Jose Luis ...... 59,151 Robbins, Adele M...... 152 Morris, V.R...... 117 Robert, W. Zurales...... 204 Mu, R...... 139 Robinson, T...... 132 Muccio, Donald D...... 134 Rode, J.E...... 92 Muir, Max ...... 112 Roszak, Szczepan ...... 179 Murray, Jane S...... 152 Ruzankin, Sergey Ph...... 203 Murzin, Dmitry Yu...... 180 Saebo, Svein...... 74 Nakatsuji, Hiroshi ...... 113 Sainudeen, Zuhail ...... 153 Napolion, Brian...... 114 SanFabian, E...... 126 Neely, Adria ...... 115 Sastry, G. Narahari ...... 42 Nieminen, Ville ...... 180 Sathyamurthy, N...... 128 Nishio, S...... 200 Schweigert, Igor V...... 154 Nkansah, Paul ...... 117 Sefcikova, Jana ...... 93 Noe, Eric A...... 58,59,60,61,151 Serykh, Aleksandr...... 162 Nussinov, Ruth ...... 76 Seyfarth, Adam ...... 155 Ohta, K...... 201 Seyfarth, Ray ...... 155 Okovytyy, S...... 71,118,119,122 Shahbazyan, Tigran V...... 91,123,146 Olendski, O...... 123 Shainyan, Bagrat A...... 54 Ona, Ofelia ...... 24 Sheng, Yinghong ...... 53 Osawa, E...... 96 Shishkin, Oleg ...... 47,55 Osborne, Daniel A...... 124 Shukla, M.K...... 19,20,88,156,158 Oshchapovsky, Valentin V...... 125 Simeon, T.M...... 160 222 Conference on Current Trends in Computational Chemistry 2004 Author Index

Sivaraja, Vaithiyalingam ...... 28 Sohail, K.Q...... 161 Solkan, Vitali N...... 162,165,168,169,172 Sood, Angela...... 174 Southerland, William M...... 76 Spackova, Nada...... 93,150 Sponer, Jiri ...... 93,150,176 Sponer, Judit E...... 176 Sterling, Andrea ...... 177 Strauss, Nicole M...... 178 Subramanian, V...... 128 Sukhanov, Oleg ...... 55 Szczesniak, M.M...... 92 Szymczak, J...... 197 Tajchert, Krzysztof...... 179 Takahashi, H...... 94 Taskinen, Antti ...... 180 Taube, Andrew G...... 181 Taylor, Gordon ...... 57 Thanthiriwatte, Kanchana S...... 182 Tigyi, Gabor ...... 124 Toro-Labbe, Alejandro ...... 66 Toukoniitty, Esa...... 180 Trickey, S.B...... 184 Turabekova, Malakhat A...... 185 Varga, Zoltan ...... 189 Venkatraman, Ramaiyer ...... 190 Verges, J.A...... 126 Voth, Gregory A...... 191 de Vries, Mattanjah S...... 192 Walker, K...... 146 Walter, Nils G...... 93 Wang, Jing...... 177,193 Wang, Jun ...... 69 Wang, Yongmei ...... 124 Watts, C.C...... 194 Watts, John D...... 104,114,196 Wierzbicki, Andrzej ...... 36 Wiese, Tom...... 69 Williams, Mary La'Frances ...... 197 Wolinski, Krzysztof...... 22,107 Xiao, Chuanyun ...... 74 Yanov, Ilya ...... 160,199 Yu, Chin ...... 28 Zannotti, Kimberely ...... 36 Zeizinger, Michal...... 27 Zhanpeisov, N.U...... 200,201 Zhou, Jian-Ge ...... 198,202 Zilberberg, Igor ...... 87,203 Zubatyuk, Roman I...... 47

Conference on Current Trends in Computational Chemistry 2004 223

Some Challenges in First-Principles Based Simulations of Biological Systems

Ute Röhrig, Anatole von Lilienfeld, Leonardo Guidoni, Ivano Tavernelli, and Ursula Rothlisberger

Laboratory of Computational Chemistry and Biochemistry, Federal Institute of Technology, 1015 Lausanne, Switzerland

Mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations based on density functional theory have become a useful tool for the investigation of complex biological systems. However, biological problems still pose severe challenges in terms of characteristic time scales and required accuracy of the underlying quantum chemical method. In this paper, we will discuss some of the problems encountered in (TD)DFT/MM simulations. In particular, we will discuss a novel approach to treat dispersion interactions within DFT calculations based on purely local approximations to the exchange-correlation functional [1,2] and we will also outline some of the problems encountered in TDDFT-based simulations of photoactive proteins [3,4].

[1] A. vonLilienfeld, I. Tavernelli, D. Sebastiani, and U. Rothlisberger, Phys. Rev. Lett. 93, No.153004 (2004) [2] A. vonLilienfeld, I. Tavernelli, D. Sebastiani, and U. Rothlisberger, J. Phys. Chem. (in press) [3] U. Röhrig. I. Tavernelli, and U. Rothlisberger, Mol. Phys. (in press) [4] U. Röhrig, L. Guidoni, and U. Rothlisberger, J. Am. Chem. Soc. (in press)