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Delbert Bagwell U.S. Army ERDC Jaroslav Burda Charles University in Prague 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 Alan L. Middleton U.S. Army ERDC W. Andrzej Sokalski Wroclaw University of Technology

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Shonda Allen Hill Jackson State University Olexandr Isayev Jackson State University Debra Jackson Jackson State University Ami Mehta Jackson State University Yevgeniy Podolyan Jackson State University

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National Science Foundation (CREST Program) U.S. Army Engineer Research and Development Center Department of Defense (Chemical Materials and Computational Modeling (CMCM) Project) through ERDC 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 2005 November 4-5, 2005 Jackson, Miss.

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Conference on Current Trends in Computational Chemistry 2005 November 4-5, 2005 Jackson, Miss.

5 Schedule of Events Conference on Current Trends in Computational Chemistry 2005

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7:30 – 9:00 Continental Breakfast 8:00 – 12:00 Registration 9:00 – 9:30 Opening Ceremony 9:30 – 10:30 1st Session (S1) Parrinello 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

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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 – 5:30 6th Session (S6) 2 Talks 5:30 – 7:30 Third Poster Session (P3) 8:00 – 8:30 Cocktails 8:30 – 11:00 Banquet Speaker: Dr. John Parmentola Best Student Poster Award Director for Research and Laboratory Presentation Management, US Army

7 Invited Presentations Conference on Current Trends in Computational Chemistry 2005

Session Chairman: Frank Hagelberg Parrinello Lecture Jackson State University Michele Parrinello New Strategies for Large Scale Atomistic Modeling Swiss Federal Institute of Technology Zurich

Session Chairman: Frances Hill 2nd Session Army High Performance Computing Research Center Axel D. Becke Van der Waals Interactions from the Exchange Hole Dipole Queen's University Moment Wim Klopper Current Trends in Explicitly Correlated Coupled Cluster Theory Universität Karlsruhe

Session Chairman: Peter Pulay 3rd Session University of Arkansas Helena Dodziuk Modelling the Structure of Fullerenes and their Endohedral Polish Academy of Sciences Complexes with Nontrivial Topological Properties Andrzej Wierzbicki Combining Computational and Experimental Techniques to Study University of South Alabama Complex Interfacial Adsorption Phenomena Jack C. Wells Searching for Nanowire Candidates among Synthetic Nucleic Oak Ridge National Laboratory Acids

Session Chairman: Jaroslav Burda 4th Session Charles University in Prague Stephen L. Mayo Modulation and De Novo Design of Protein-Protein Interactions California Institute of Technology Jiali Gao Dynamics, Pathways, and Tunneling – A Computational University of Minnesota Perspective of Enzyme Catalysis

Session Chairman: Jane Murray 5th Session University of New Orleans David M. Close The Accurate Calculations of Hyperfine Couplings with Density East Tennessee State University Functional Theory Jiří Šponer Structure, Dynamics and Molecular Interactions of Functional Academy of Sciences of the Czech RNAs. Advanced Computational Studies Republic

Session Chairman: Peter Politzer 6th Session University of New Orleans Hans Lischka Ab Initio Theory and On-The-Fly Dynamics: The Photochemistry University of Vienna of the C=C Bond and Excited-State Proton Transfer

C. David Sherrill Energy Landscapes from π-Stacking to Bond-Breaking Georgia Institute of Technology

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Conference on Current Trends in Computational Chemistry 2005 November 4-5, 2005 Jackson, Miss.

Contents for Abstracts Conference on Current Trends in Computational Chemistry 2005 11

Session† Presentation Page

P1 Electronic Charge Distribution in Methylamines: a New Look 19 on the Gas-Phase Basicity Descriptors Dmitriy Y. Afanasyev and Alexander V. Prosyanik

P1 The Regiochemical Outcomes in the Hydrolysis of Assymetric Diester: Studies of 21 the Hydrolysis of Methyl-4-Acetoxybenzoate Lovell Agwaramgbo, Tishina Okegbe, Glake Hill, Jerzy Leszczynski, Tiffarah Cline

P1 Examination of the Structure & Thermodynamic Properties 22 of Silyl and Non-Silyl Epoxides Lovell Agwaramgbo, Glake Hill, and Chi-Cobi Speaks

P1 Ab Initio Insight on the Interaction of Ascorbate with Li+, Na+, K+, Be2+, Mg2+and 23 Ca2+ Metal Cations Reeshemah N. Allen, M.K. Shukla, and Jerzy Leszczynski

P1 HCl Dissociation in Small Water Clusters: A Study with New PM3-MAIS 24 Parameters O. I. Arillo-Flores, M. F. Ruiz-López and M. I. Bernal-Uruchurtu

P1 Rare Gas Insertion Compounds of Perfluorobenzene: Aromaticity of Some 27 Unstable Species Jon Baker, Patrick W. Fowler, Alessandro Soncini and Mark Lillington

P3 Film Formation from Dispersion of Heterogeneous Colloidal Particulates with 28 Fluorinated Markers in Aqueous Solution - Experimental Observations and Computer Simulation Modeling Samuel Bateman, Adam Seyfarth, R.B. Pandey, and Marek W. Urban

S2 Van der Waals Interactions from the Exchange Hole Dipole Moment 29 Axel D. Becke and Erin R. Johnson

P1 Stepwise Hydration of Organic Acids. Test of PM3-PIF as a Model for Hydrated 30 Systems M. I. Bernal-Uruchurtu, W. Harb and M. F. Ruiz-López

P1 Effect of Solvent Polarity on First Order Nonlinear Optical Properties of 32 Zwitterionic Merocyanine Dyes P. Bonifassi, J. Leszczynski and P. C. Ray

P1 The Gauss-Bessel Quadrature: A Tool for the Evaluation of Barnett- 35 Coulson/Löwdin Functions Ahmed Bouferguene, Hassan Safouhi

P1 A Computational Study of Four Sulfur Oxo Acids and Related Species 38 Judge Brown and John D. Watts

P1 Comparison between Folding Conformations of Met-Enkephaline and Morphine 39 Deborah J. Bryan and Jesse Edwards

P1 Computational Study on the DNA Bases Interactions with Dinuclear 40 Rh(II)Tetraacetyl Complex Jaroslav V. Burda, Jiande Gu, and Jerzy Leszczynski

P1 Analysis of a Promiscuous Alu Subfamily, Yj7, within Homo sapiens and Pan 41 troglodytes Marion L. Carroll, Toye Metoyer, Algernon Kelly, Thuy Lee, April Holmes, Endia Ford, Shemika Sample and R. D. Morris 12 Conference on Current Trends in Computational Chemistry 2005 Contents for Abstracts

P1 Computational Studies on Stable Triplet States of Metallaacetylenes and the 44 Effects of Halogen Substituents Mu-Jeng Cheng and San-Yan Chu

P1 Investigating Ring Current Effects around a Benzene Ring 45 Anthony Chuma

P1 The Influence of Microhydration on the Ionization Energy Thresholds of Cytosine 46 David M. Close

P1 Analysis of the C-O bond in Diphenyl Ether Using Computational Chemistry 47 Sherrita M. Cooks and Melissa S. Reeves

P1 Stone-Wales Defect Formation in (5,5) Armchair Single-walled Carbon Nanotube 48 T. C. Dinadayalane and Jerzy Leszczynski

P1 Interaction of Li+, Na+ and K+ with Novel Cup-shaped Molecules: Effect of Ring 50 Annelation to Benzene and Cavity Selectivity T. C. Dinadayalane, Dmitriy Afanasiev and Jerzy Leszczynski

P1 Energetic and Structural Comparison of Cisplatin and Analogs from DFT 52 Calculations LaTanya Dixon, Jo-Lyque Turner, Glake A. Hill, Jerzy Leszczynski

S3 Modelling the Structure of Fullerenes and their Endohedral Complexes with 53 Nontrivial Topological Properties Helena Dodziuk

P1 Theoretical Studies on the Effect of Protonation on C-P bond Cleavage of 55 Pyridylmethyl-(amino)phosphonates Marek Doskocz, Devashis Majumdar, Szczepan Roszak Roman Gancarz, and Jerzy Leszczynski

P1 Prediction of Excited States for Carbon, Nitrogen and Oxygen Systems Using 57 Quantum Monte Carlo Floyd Fayton, Jr., John A.W. Harkless, and Ainsley Gibson

P1 Identifying Potential LPA3 Antagonists Using in Silico Screening 58 James I. Fells and Abby L. Parrill

P1 Development of Array Files for Computational Chemistry 59 Alan Ford and Peter Pulay

P1 Theoretical Conformational Studies of Parathion 60 Jason Ford-Green, D. Majumdar, Jerzy Leszczynski

P1 Enthalpies of Formation for Thio Ethers by Isodesmic and Homodesmotic 61 Reactions Ryan Fortenberry and David H. Magers

P1 Relative Energies of 2-Pyrimidinethiol and 2-Pyrimidinethione and Their Dimers: 62 Effect of Theoretical Levels Fillmore Freeman and Henry N. Po

P1 Hydrogen Cyanide Covalent Dimers and Reactions of Aminocyanocarbene: A 64 Computational Study Fillmore Freeman and Mahshid Gomarooni

P1 Ab Initio Molecular Dynamics Study: Statistical Analysis of Structural 65 Nonrigidity of DNA Bases Al’ona Furmanchuk, Olexandr Isayev, Oleg Sukhanov, Oleg Shishkin Leonid Gorb, and Jerzy Leszczynski Contents for Abstracts Conference on Current Trends in Computational Chemistry 2005 13

S4 Dynamics, Pathways, and Tunneling – A Computational Perspective of Enzyme 67 Catalysis Jiali Gao

P1 A Theoretical Study on the Reactivity and Regioselectivity of Cycloadditions of 68 Phospholes G. Gayatri, T. C. Dinadayalane, and Jerzy Leszczynski and G. Narahari Sastry

P1 Computational Study of Structure-Activity Relationships for β-Lactam Antibiotics 70 against PBP5 Xiaoxia Ge, John Buynak

P1 Quantum Monte Carlo Results for the Ionization Potentials, Electron and Proton 72 Affinities of the 3d-Block Transition Metals Ainsley A. Gibson, Floyd A. Fayton, Gordon J. P. Taylor, Jose Gonzalez and John A. W. Harkless

P2 Conformational Studies of di-tert-Butylcyclohexanes 73 Gurvinder Gill, Diwakar M. Pawar, and Eric A Noe

P2 Conformational Study of Propynoic Anhydride by Computational Methods 74 Gurvinder Gill and Eric A. Noe

P2 A Computer Study of Point Defects in the RDX Crystal 75 Matthew Gravelle and Sylke Boyd

P2 A Possible Nature of Hot and Cold Spots of UV-Mutagenesis 78 H. A. Grebneva

P2 Derivation of a QSAR Model for Anandamide Based on Quantum Molecular 82 Descriptors Ming-Ju Huang

P2 Can Gibbs Free Energy for Intermolecular Complexes be Predicted Accurately at 83 the MP2 and the DFT Levels of Theory? Olexandr Isayev, Al’ona Furmanchuk, Leonid Gorb and Jerzy Leszczynski

P2 Parallel Calculation of Coupled Cluster Energies on Distributed Memory 84 Workstations Tomasz Janowski and Peter Pulay

3 1 P2 Computational Study of Carbon Atom ( P and D) Reaction with CH2O: 86 1 1 Theoretical Evidence of B1 Methylene Production by C ( D) Atom Hyun Joo, Philip B. Shevlin and Michael L. McKee

P2 The Conformational Analysis of CL-20. A DFT Study 87 Yana Kholod, Sergiy Okovytyy, Leonid Gorb, Mohammad (Mo) Qasim, John Furey, Herbert Fredrickson and Jerzy Leszczynski

P2 Extraordinary Optical Transmission through Subwavelength Hole Arrays 88 Arman S. Kirakosyan, Tigran V. Shahbazyan

S2 Current Trends in Explicitly Correlated Coupled Cluster Theory 89 Wim Klopper, Heike Fliegl, Christof Hättig, Christian Neiss, David P. Tew

P2 Tautomeric Transitions in 2′-Deoxy-Guanosine-Monophosphate 90 Dmytro Kosenkov, Leonid Gorb, Yevgeniy Podolyan and Jerzy Leszczynski

P2 Catalytic Strategies of the Hepatitis Delta Virus Ribozyme as Probed by 91 Molecular Dynamics Simulations Maryna V. Krasovska Jana Sefcikova, Nils G. Walter and Jiri Sponer 14 Conference on Current Trends in Computational Chemistry 2005 Contents for Abstracts

P2 Computational Chemistry as a Tool for Scientific Predictions of Chemical 92 Reaction Mechanisms V. Kukueva

P2 Transferable Force Fields of Some Polycyclic Molecules 96 G.M. Kuramshina, Yu.A. Pentin, D.A. Sharapov, S.A. Sharapova, V.K. Matveev

P2 Effects of Peripheral Substituents and Axial Ligands on the Electronic Structure 100 and Properties of Cobalt Porphyrins Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang

S6 Ab Initio Theory and on-the-fly Dynamics: the Photochemistry of the C=C Bond 101 and Excited-State Proton Transfer Hans Lischka

P2 Relationship between Structural Stability and Cage – Core Interaction for 105 Sc3@C82 and Sc2@C84 Dan Liu and Frank Hagelberg

P2 Comparison of Reaction Pathways of Acetylcholine and Sarin in the 106 Acetylcholinesterase Adduct Christa Loar and E. Johnson

P2 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of 107 Carbon and Silicon Brandon Magers, Harley McAlexander, Crystal B. Coghlan, and David H. Magers

S4 Modulation and De Novo Design of Protein-Protein Interactions 108 Stephen L. Mayo

P2 Conventional Strain Energy in Boracyclobutane and Diboracyclobutane 109 Harley McAlexander, Brandon Magers, Crystal B. Coghlan, and David H. Magers

P2 Ab Initio Studies of Boron Carbonyl Molecules 110 James L. Meeks

P2 Theoretical Study of Adsorption of Sarin and Soman on Tetrahedral Edge Clay 111 Surfaces A. Michalkova, J. Martinez, O. A. Zhikol, L. Gorb, J. Leszczynski

P2 What is Halogen Bonding? 113 Jane S. Murray, Pat Lane, Monica C. Concha, Tim Clark and Peter Politzer

P2 Chemistry of Hydrated Cations: I. Ab Initio and QTAIM Calculations on 114 + [Li(H2O)n] , n=1,2,3 Jamshid Najafpour, Abdolreza Sadjadi

P2 Theoretical Studies of AZT and AZT Analogues 116 Edmund Moses N. Ndip

P2 Understanding Binding of Phosphates to Sevelamar Hydrochloride through 117 Molecular Dynamics and Thermodynamic Modeling R. Parker, J. Edwards, D. Fisher, A. A. Odukale, C. Batich, and E. Ross

S1 New Strategies for Large Scale Atomistic Modeling 118 Michele Parrinello

P2 Theoretical Studies on the Conformational and Electrostatic Properties of Tabun 119 to Probe its Cholinesterase Inhibition Characteristics Yuliya Paukku, Devashis Majumdar, Andrea Michalkova, and Jerzy Leszczynski Contents for Abstracts Conference on Current Trends in Computational Chemistry 2005 15

P2 Theoretical Study of the Adsorption of Tabun on Calcium Oxide 120 Y. Paukku, A. Michalkova, D. Majumdar, and J. Leszczynski

P2 Structure – Hepatotropic Activity Relationship Study of Sesquiterpene Lactones: 122 A QSAR Analysis Yuliya Paukku, Bakhtiyor Rasulev and Jerzy Leszczynski

P2 Conformational Study of HCO2C(CF3)2OH by Dynamic NMR Spectroscopy and 123 Computational Methods Diwakar M. Pawar, Eric A. Noe

P2 Quantum-Chemical and NMR Spectral Investigation of Products of Amidoacids of 124 Norbornene Row Oxidation T. Petrova, S. Okovytyy, I.N. Tarabara, V.A. Palchikov, L.I. Kasyan, J. Leszczynski

P2 Microscopic Theory of Fluorescent Resonance Energy Transfer for Molecules 125 Adsorbed at Noble-Metal Nanoparticles V. N. Pustovit and T. V. Shahbazyan

P2 RNA Kink-turns as Flexible Molecular Hinges of the Ribosomal “LEGO”. The Role 126 of Aecond A-minor Motif and Nominally Unpaired Bases Filip Razga, Jaroslav Koca, Neocles B.Leontis and Jiri Sponer

P2 The Effect of Multiple Substituents in π-π Interactions: Sandwich and T-shaped 127 Configurations Ashley L. Ringer, Mutasem O. Sinnokrot, Ryan P. Lively, and C. David Sherrill

P2 Adsorption of Thymine on the Surface of Dickite: An ab Initio Study 129 T. L. Robinson, A. Michalkova, L. Gorb, and J. Leszczynski

S5 The Accurate Calculations of Hyperfine Couplings with Density Functional Theory 131 David M. Close

P3 Vibrational Dynamic (hyper)Polarizability of Push-Pull Organic Molecules: A 133 Quantum Chemistry Study Amar Saal and Ourida Ouamerali

P3 Full Accuracy Local MP2 134 Svein Saebo, and Peter Pulay

P3 Extrapolation Methods for Improving Convergence of Coulomb Integrals over 135 Slater type Functions Hassan Safouhi and Ahmed Bouferguene

P3 Mass Spectrometric and Theoretical Studies of the NaCl-SnCl2 Quasi-Binary 138 System Julia Saloni, Szczepan Roszak, and Jerzy Leszczynski

P3 Nonlinear Optical Properties of Zwitterionic Merocyanine Aggregates: Role of 139 Intermolecular Interaction and Solvent Polarity Zuhail Sansudeen and Paresh Chandra Ray

P3 Theoretical Studies of Dissociation of Perfluorohydroxylamine (F2NOF) 140 Hasan Sayin and Michael L. McKee

P3 Theoretical Study on the Regioselectivity of the Cycloaddition Reaction between 141 Cyclopentadiene and Methyleneketene Yinghong Sheng and Jerzy Leszczynski

S6 Energy Landscapes from π-Stacking to Bond-Breaking 142 C. David Sherrill 16 Conference on Current Trends in Computational Chemistry 2005 Contents for Abstracts

P3 Quantum Chemical Investigation of the Excited State Proton Transfer in Guanine 143 M.K. Shukla and Jerzy Leszczynski

P3 Probing the Physico-Chemical and Structural Requirements among 3-Anilino-4- 145 arylmaleimides for GSK-3α Inhibitory Activity Enhancement through 2D and 3D QSAR Investigations Prasanna Sivaprakasam, Pankaj R. Daga, Aihua Xie, Robert J. Doerksen

P1 Quantitative Structure-Activity Relationships of Anti-Inflammatory Agents: A 147 Study of a Series of Sesquiterpene Lactone Austricine Derivatives Using Descriptors Derived From 3D Structures Talibah Smith, Bakhtiyor Rasulev, Jerzy Leszczynski

P3 A DFT Study of the Singlet Oxygen Activation by Unique Transition-Metal Ion 148 Structures in Fe(2+)/ZSM-5 and Zn(2+)/ZSM-5 Zeolites: Formation of the Sigma-Complex between Activated Oxygen and Benzene Vitaly Solkan and Jerzy Leszczynski

P3 A DFT Study of the Ethane Activation by Unique Metal Ion Structures in O=Ga- 151 O-Ga=O oxide and O=Ga(1+)/ZSM-5 Zeolites: Formation of the Ethene and Ethanol Vitaly Solkan

P3 A DFT Study of the NO Activation by Unique Transition-Metal Ion Structures in 154 Co(1+)/ZSM-5 and Ni(1+)/ZSM-5 Zeolites Vitaly Solkan and Jerzy Leszczynski

P3 A DFT Study of the Transition Metal Clusters Co4 , Rh4 , Pd4 , and Pt4 in ZSM-5 158 Zeolite. Does Exist Transition Metal-Proton Adducts in High-Silica Zeolite ZSM-5? Vitaly Solkan

P3 Enthalpies of Formation of TNT Derivatives by Isodesmic Reactions 161 Amika Sood, Patricia Honea, and David H. Magers

P3 Side-Chain Mobility and Binding Selectivity of Naphthylquinoline Derivatives: 162 Correlation of Conformational Energetics with Thermodynamic Binding Energies Angela Sood, M. Jeanann Lovell, G. Reid Bishop, and David H. Magers

S5 Structure, Dynamics and Molecular Interactions of Functional RNAs. Advanced 164 Computational Studies Jiri Sponer

P3 Accurate Interaction Energies of Base Pairing and Base Stacking 166 Jiri Sponer, Petr Jurecka and Pavel Hobza

P3 Principles of RNA Base Pairing 167 Judit E. Sponer, Jerzy Leszczynski and Jiri Sponer

P3 Anharmonic Calculations of CH3-nClnSiF3 (n=0-3) Molecules 168 S.V. Syn’ko, G.M. Kuramshina, Yu.A. Pentin

P3 The Influence of the Microsolvation on the Proton Affinity of Ammonia 170 Jaroslaw J. Szymczak, Jan Urban, Szczepan Roszak, and Jerzy Leszczynski

P3 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of 171 Carbon and Germanium Lyssa Taylor, Crystal B. Coghlan, and David H. Magers

P3 The Excitation Spectra of Dibenzoborole Containing π-electron Systems: 172 * Controlling the Electronic Spectra by Changing the pπ – π Conjugation Kanchana S. Thanthiriwatte and Steven R. Gwaltney Contents for Abstracts Conference on Current Trends in Computational Chemistry 2005 17

P3 Aconitum and Delphinium sp. Alkaloids as Antagonist Modulators of Voltage- 173 Gated Na+ Channels. AM1/DFT Electronic Structure Investigations and QSAR Studies Malakhat A. Turabekova, Bakhtiyor F. Rasulev, and Mikhail G. Levkovich and Jerzy Leszczynski

P3 Electron Impact Ionization of Hydrocarbons and Amino Acids – A Theoretical 174 Study J. Urban, P. Mach and M. Probst

P3 Endohedral Carbon in Single-Wall Carbon Nanotubes 175 R. K. Vadapalli and J. W. Mintmire

P3 Computational Study of Phosphonylation Mechanisms between Sarin and 178 Acetylcholinesterase Jing Wang, Jiande Gu, and Jerzy Leszczynski

P3 Coupled-Cluster Studies of Photoelectron Spectra of Transition-Metal Halide 179 Anions John D. Watts

S3 Searching for Nanowire Candidates among Synthetic Nucleic Acids 180 Jack C. Wells and Miguel Fuentes-Cabrera

S3 Combining Computational and Experimental Techniques to Study Complex 181 Interfacial Adsorption Phenomena Andrzej Wierzbicki

P3 Chemical Reaction Pathway for the Phosphonylation of Serine 182 Adrian Wilson, Gregory Woodall, Elijah Johnson, and Jerzy Leszczynski

P3 Equilibrium Geometries of Mixed Metal-Semiconductor Clusters from Global 183 Optimization and Associated Electronic Properties Jianhua Wu and Frank Hagelberg

P3 CoMFA Studies of Antimalarial Compounds Based on 2,5-Diaminobenzophenone 184 Scaffold Aihua Xie, Prasanna Sivaprakasam, Robert J. Doerksen

P3 Film Formation from Reactive Aqueous Solutions Containing Hydrophobic and 185 Polar Groups: A Computer Simulation Model Shihai Yang, Sam Bateman, Adam Seyfarth, Erik Heidenreich, Ras Pandey, Marek Urban

P3 Fragmentation Dynamics of Organic Species Deposited on a Semiconductor 186 Substrate Jian-Ge Zhou and Frank Hagelberg

P3 Chemisorption of Alkanethiols on Au(111): Is It Dissociative or Nondissociative? 187 Jian-Ge Zhou and Frank Hagelberg

†S* – Oral presentation (* denotes session number); P* – Poster presentation (* denotes poster session number)

Conference on Current Trends in Computational Chemistry 2005 19

Electronic Charge Distribution in Methylamines: a New Look on the Gas-Phase Basicity Descriptors

Dmitriy Y. Afanasyev and Alexander V. Prosyanik

Department of Organic Chemistry, Ukrainian State Chemical Technology University, 8 Gagarin ave., Dnepropetrovsk, 49005, Ukraine

Electronic structure of simple amines NH3, CH3NH2, (CH3)2NH and (CH3)3N has been studied [1] using Weinhold’s natural bond orbital techniques. NAO, PNBO and NBO orthonormal localized sets of one-electron functions for analysis of one-electron density matrix and energetic analysis of the Fock operator have been obtained from DZ and TZ polarized non- orthogonal Gaussian AO sets in HF approximation. Total atomic electronic occupancies of the nitrogen atom determined by means of NAO population analysis which corrects many of the deficiencies of the Mulliken population analysis are found to decrease in the abovementioned series of amines in contrast to organic chemistry’s well-known “inductive effect” and increasing gas-phase basicity. Occupancy of bond orbital (NBO) corresponding to the classical “lone pair” of nitrogen atom is also found to decrease in this series. Such behavior of the nitrogen atom electronic occupancy is found to be in agreement with more rigorous integrated atomic electronic occupancies obtained by means of quantum-chemical topology (AIM) even at correlated levels of theory [2]. Observed decrease in total and “lone pair” electronic occupancies, as well as increase in hybrid p-character of “lone pair” NBO (table 1) is found to be due to the important role of negative hyperconjugation of nitrogen’s “lone pair” with antibonding orbitals of CH3 group. Thus, as clearly can be seen from the table 1, methyl group in amines exhibits electron withdrawing properties.

Table 1. Partial NPA charges, qN, total atomic (Ntot) and “lone pair” (NLP) electronic populations of nitrogen atom, “lone pair” energies (E(nσN)), hybrid p-characters of “lone pair” orbital (% p-char), and experimental ΔGB values for investigated amines. All theoretical values obtained at HF/TZP level.

E(n N), ΔG , qN, е Ntot, е NLP, е σ % p-char. B Molecule a.u. kcal/mol NH3 -1.020 8.020 1.997 -0.4973 79.98 0.0 CH3NH2 -0.817 7.817 1.968 -0.4739 80.95 9.1 (CH3)2NH -0.631 7.631 1.930 -0.4480 82.90 15.15 (CH3)3N -0.473 7.473 1.890 -0.4251 84.89 20.0

In general, such quantitative hyperconjugation picture corresponds to intramolecular charge- transfer interaction between bonding (lone pair) and antibonding (sigma star C-H) NBOs (see picture).

20 Conference on Current Trends in Computational Chemistry 2005

Procedure of zeroing specific Fock matrix elements in NBO basis ( i Fˆ j * ) combined with numerical EF geometry optimization was recently used for detailed analysis of molecular and electronic structure of amines [1]. Importance of nitrogen hyperconjugation in determining molecular geometry was also pointed out earlier [3]. Increase of the gas-phase basicity of alkylamines is thus not due to increase of the total electronic occupancy and “lone pair” occupancy of the nitrogen atom. Correspondingly, textbooks’ classical “inductive electron-donating effect” of alkyl groups (at least of methyl group) is not responsible for the increase of the gas-phase basicity of alkylamines. Perfect correlation between experimental ΔGB values and calculated nitrogen’s “lone pair” NBO energy eigenvalues (table 1) allows assuming that characteristics of this orbital (energy and spatial form) are responsible for the gas-phase basicity and factors that control these characteristics (mostly hyperconjugation and Pauli “steric” repulsion) constitute real origin of gas-phase basicity changes observed.

Literature

[1] D. Y. Afanasyev, D. V. Fedoseyenko and A. V. Prosyanik ARKIVOC, 2005, part (VIII) (http://www.arkat-usa.org/ark/ARKIVOC/), submitted (invited article). [2] D. Y. Afanasyev et al J. Org. Chem., in preparation. [3] D. Y. Afanasyev, A. V. Prosyanik J. Mol. Struct. (Theochem) 730 (2005) p. 45.

Acknowledgements

D.Y.A. gratefully acknowledges helpful discussions with Professors Frank A. Weinhold and Paul L. A. Popelier. D.Y.A. is also thankful to Professor Jerzy Leszczynski, especially for the opportunity to visit JSU this summer.

Conference on Current Trends in Computational Chemistry 2005 21

The Regiochemical Outcomes in the Hydrolysis of Assymetric Diester: Studies of the Hydrolysis of Methyl-4-Acetoxybenzoate

Lovell Agwaramgbo1, Tishina Okegbe1, Glake Hill2, Jerzy Leszczynski2, Tiffarah Cline2

1Dillard University,Department of Chemistry, New Orleans, La 70122 2CCMSI, Jackson State University, Jackson, MS 39217

Ester hydrolysis has been extensively studied in term of the mechanism and kinetics. In solution, ester hydrolysis can occur via O-alkyl or O-Acyl cleavage. In solution chemistry and in normal hydrolysis reactions, the mode of cleavage is determined by the stability of the leaving group and the strength of the nucleophile. This is usually the O-acyl cleavage. Although some studies have been conducted on some simple esters in terms of substituent effects on the rate of hydrolysis, yet no gas phase studies have been done on systems containing two different leaving groups. This project examined the regiochemical outcome and product distribution in the experimental and Ab initio quantum mechanics studies of the hydrolysis of the Methyl Acetoxybenzoate below. The di-ester was hydrolyzed under acidic & basic conditions. The structures of the starting isomeric diesters and their expected products were optimized using 6- 311G basis set and Hartree Fork, B3LYP, and MP2 methods. The results of the investigations will be discussed.

This Presentation is dedicated to my Dillard University HBCUUP & Research Scholars displaced by the hurricane. I thank Jackson State University, JSU Chemistry Dept, & JSU CCMSI, Shonda Allen, Reeshemah Allen & Dr. G. Hill’s graduate students for their support 22 Conference on Current Trends in Computational Chemistry 2005

Examination of the Structure & Thermodynamic Properties of Silyl and Non-Silyl Epoxides

Lovell Agwaramgbo1, Glake Hill2, and Chi-Cobi Speaks2

1Dillard University,Department of Chemistry, New Orleans, La 70122 2CCMSI, Jackson State University, Jackson, MS 39217

The rate and pathway of many reactions depend on the structure of the reacting substrates. Whether a reaction will be thermodynamically or kinetically controlled depends in part on the nature of substrates, solvent, etc. Substituents can greatly control the outcome of a reaction, not only on product distribution, but also on the regio and stereo chemistry. We therefore wanted to evaluate the DFT calculations of substituted epoxides in an effort to look for thermodynamic marker/s that can predict not only the stability of the epoxides but also the regiochemistry of the epoxide ring-opening.

O O O Z Z

Z Z Z Z 1 2 3

Z = SiH3, CH3; Me3Si-, Me3C-

The results suggest that for compounds with Z = Me3Si group, compound 3 was more stable than compound 2 which is more stable than compound 1. Other aspects of this project will be discussed. Conference on Current Trends in Computational Chemistry 2005 23

Ab Initio Insight on the Interaction of Ascorbate with Li+, Na+, K+, Be2+, Mg2+and Ca2+ 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 of the interaction of ascorbate with Li+, Na+, K+, Be2+, Mg2+and Ca2+ metal cations were studied at the density functional level theory employing the B3LYP exchange correlation functional and the 6-311++G (d,p) basis set. The interactions of the metal cations at the different binding sites of ascorbate were considered. Tomasi’s polarized continuum model was used to evaluate the influence of aqueous solvent on the relative stability of different complexes. The interaction energy was corrected for the complexes utilizing basis set superposition error (BSSE) method. The AIM theory was used to characterize the electron density distribution involved in the binding interaction between ascorbate and the metal cations. In the gas phase, the most preferred position for the interaction of urate with Li+, Na+, and K+ 2+ 2+ 2+ cations is between the O2 and O3 sites, while all divalent cations Be , Mg , and Ca prefer binding between the O1 and O2 sites of urate. However, all of the metal cations exhibit the strongest binding energy at the O6 and O7 sites.

24 Conference on Current Trends in Computational Chemistry 2005

HCl Dissociation in Small Water Clusters: A Study with New PM3-MAIS Parameters

O. I. Arillo-Flores1, M. F. Ruiz-López2 and M. I. Bernal-Uruchurtu1

1Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, 62209 Cuernavaca, México. 2Laboratoire de Chimie et Biochimie théorique, UMR 7565 CNRS - Université Henri Poincaré, Nancy 1, France.

One of the most fundamental processes in nature is acid dissociation. For long time it has been an interesting subject for fundamental research, both with experimental and theoretical techniques. In this work, we present a semiempiric model specially designed for studying the dissociation of acids in water, here we will describe the methodology and some results concerning the behavior of HCl in water clusters. The PM3-PIF method was recently developed as a correction of the well known problems standard PM3 has for describing non bonded interactions. This was accomplished by substitution of the Gaussian Correction Function (GCF) in the core-core term of PM3 by a Parametrized Interaction Function (PIF) defined for non-bonded atoms.1 The new function, fitted to reproduce highly refined ab initio calculated potential energy surfaces, has proven to overcome the known PM3 problems in the description of H-bonds.1, 2 ... In this case, the model system used for the parameterization is the HCl H2O dimer. Four relative orientations between monomers were scanned as a function of r(Cl-O) distance and the O-Cl-H angle. In particular, special care was taken for conformations coming from the global minimum, hb, with water molecule acting as the hydrogen bond acceptor and ha structure, where the acid molecule acts as the acceptor. The PES for the rigid dimer was calculated using MP2/aug-cc-pVTZ. Parameters for the Cl-O and Cl-H interaction were optimized using the Levenber-Marquardt method and parameters for the O-O, O-H and H-H pairs were taken from a previous work for water.1 As it can be seen in Fig. 1, the interaction energies predicted with PM3-PIF are in much better agreement with the MP2 values than the standard PM3 ones. Standard PM3 interaction energies are not attractive enough for H-bonded conformations and also, it is not repulsive enough for non favorable geometries.

Conference on Current Trends in Computational Chemistry 2005 25

The overall improvement for the PES description can be seen in terms of the correlation coefficient for the interaction energies of the whole PES, 0.674 with PM3 and 0.842 with PM3- PIF. PM3-PIF can be safely used for optimizing molecular geometries. The optimized structures of the HCl-H2O dimer in the ha and hb conformation are shown in Figure 2. The structural parameters of both structures are also in better agreement with MP2 than those from PM3

However, in order to design a model able to describe acid dissociation it is necessary to have a continuous treatment of A-B interactions, i. e. a single g(A,B) function in the core-core term, able to reproduce covalent bond as well as non bonded interactions. With that purpose, the PM3- MAIS model was developed,3 in it the original GCF and the PIF were united in a single, continuous function. The advantage of PM3-MAIS is that it holds the intramolecular description of GCF’s and the intermolecular behavior of PIF, making it capable for studying the process of breaking and forming chemical bonds. In this case, it was needed to build a Cl-O and Cl-H MAIS function. The parameters obtained for these atoms pairs were thoroughly tested to ensure that no artifacts appeared in the short or long range interactions. Once this was done, we undertook the study of HCl-(H2O)n clusters. ... The interaction energies of HCl (H2O)n clusters with n=2-4 are presented in Table I. PM3- MAIS reduces the absolute error in average by 15.5 % over the PM3 results. An improvement in the structural parameters for these structures was also found.

... TABLE I. Interaction energies in kcal/mol for HCl (H2O)n n MP2 PM3 PM3-MAIS 2 -14.89 -12.47 -15.27 3 -26.07 -19.30 -26.89 4 -35.27 -24.84 -38.47

It has been observed that as the number of water molecules augments around the HCl molecule, the Cl-H distance also increases, as a precondition for the acid dissociation.4 26 Conference on Current Trends in Computational Chemistry 2005

Larger clusters of this system were also studied using direct molecular dynamics, i. e. the semiempirical PM3-MAIS forces acting on each nucleus were computed “on the fly” as the molecular dynamics trajectory was generated. Systems with HCl:H2O ratios of 1:7 and 1:15 were studied. Comparison is made with the results from standard PM3 and some CP-MD calculations on the deuterated system.5 We will discuss the capability of the proposed model to give insight into the process of acid dissociation at an affordable computational cost.

1. Bernal-Uruchurtu M. I., M.-C. M. T. C., Millot C. and Ruiz-López M. F., Improving Description of Hydrogen Bonds at the Semiempirical Level: Water-Water Interactions as Test Case. J. Comput. Chem 2000, 21, (7), 572-581. 2. W. Harb, M. I. Bernal-Uruchurtu, M. F. Ruiz-López, An improved semiempirical method for hydrated systems. Theor Chem Acc 2004, 112, 204-216. 3. Ruíz-López, M. I. Bernal-Uruchurtu a. M. F., Basic ideas for the correction of semiempirical methods describing H-bonded systems. Chem. Phys. Lett 2000, 330, 118- 124. 4. Cabaleiro-Lago E. M., Hermida-Ramon J. M., and Rodríguez-Otero J., Computational Study of the Dissociation of H-X acids (X=F, Cl, Br, I) in Water Clusters. J. Chem. Phys. 2002, 117, 3160-3168. 5. Laasonen K. E. and Klein M. L., Ab initio Study of Aqueous Hydrochloric Acid. J. Phys. Chem. A, 1997, 101, 98-102.

Conference on Current Trends in Computational Chemistry 2005 27

Rare Gas Insertion Compounds of Perfluorobenzene: Aromaticity of Some Unstable Species

Jon Baker1,2, Patrick W. Fowler,3 Alessandro Soncini4 and Mark Lillington3

1Department of Chemistry, University of Arkansas Fayetteville, Arkansas 72701 2Parallel Quantum Solutions, 2013 Green Acres Road, Suite A Fayetteville, Arkansas 72703 3Department of Chemistry, University of Exeter, Exeter, UK 4Dipartimento di Chimica, Universitá degli Studi di Modena e Reggio Emilia, via G. Campi 183, I-41100 Modena, ITALY

Calculations on the novel argon insertion compounds C6F6Arn, n=1,6, where the argon atoms are inserted into the six C-F bonds in perfluorobenzene, suggest that all possible species, with from one to six inserted atoms, are minima on their respective potential energy surfaces. Ring-current plots using the ipsocentric model indicate that there is no disruption of the aromatic π system upon argon insertion, and consequently all insertion compounds are aromatic according to the magnetic criterion. The barrier height for decomposition of the single-insertion compound, C6F6Ar, into C6F6 + Ar is 19.5 kcal/mol at HF/6-311G* and 29.5 kcal/mol at B3LYP/6-311G*, suggesting that – although clearly thermodynamically unstable – argon-perfluorobenzene insertion compounds may be stable kinetically. Preliminary calculations indicate that other rare gas-perfluorobenzene insertion compounds may also be metastable. Both C6F6Ne and C6F6He are predicted to be minima on their respective potential energy surfaces.

28 Conference on Current Trends in Computational Chemistry 2005

Film Formation from Dispersion of Heterogeneous Colloidal Particulates with Fluorinated Markers in Aqueous Solution - Experimental Observations and Computer Simulation Modeling

Samuel Bateman, Adam Seyfarth, R.B. Pandey, and Marek W. Urban

University of Southern Mississippi, Hattiesburg, MS

A computer simulation model is introduced to understand the film formation recently studied experimentally (Macromolecules 38, 2205 (2005)) from the dispersion of particulates on an impenetrable substrate on a discrete lattice. A heterogeneous colloidal particulate, i.e., a blob of size ni is modeled by a cluster of ni particles bonded together by covalent bonds. Each flexible bond fluctuates within a minimum and a maximum limits. A fraction of the surface particles of each blob are further bonded by no particles or chains to describe fluorinated component of assembled composite particulate (ACP). A number (nb) of ACPs are randomly dispersed on the lattice along with a random distribution of ns solvent particles. Each constituent of different components, i.e., interior colloid, exterior marker, and solvent is characterized by their molecular weight. Solvent constituents and particles of each ACP interact and execute their stochastic movement with the Metropolis algorithm within the limit of their bond-fluctuations. Interior colloid constituents are more mobile than that of exterior markers in this study, a constraint imposed by laboratory observation. The size of ACP and its mobility depend on ni, no, their interactions, and temperature. Since ACPs are relatively massive (in this study), they seem to deposit on impenetrable substrate at the bottom. Distribution of the interior (bulk) constituents and surface markers of ACPs are examined by analyzing their density profiles at different temperatures. Film thickness and its roughness are also studied. Distribution of ACPs seems to suggest seggregation of surface markers at least at some temperatures and marker concentration. Thus, the surface markers play important role in orchestrating the film morphology, an important feature found in experimental observations.

Conference on Current Trends in Computational Chemistry 2005 29

Van der Waals Interactions from the Exchange Hole Dipole Moment

Axel D. Becke and Erin R. Johnson

Department of Chemistry, Queen’s University Kingston, ON K7L 3N6 Canada

Despite its importance in chemistry, the Van der Waals (or dispersion) interaction is difficult to model accurately. Standard Density Functional Theory (DFT) methods, very popular in computational chemistry today, do not include the necessary physics. This often leads to qualitatively incorrect predictions when DFT is applied to dispersion-bound systems. The dispersion interaction between molecules arises when an instantaneous dipole moment in one molecule induces a dipole moment in another. What, however, is the source of these instantaneous dipole moments? We have proposed a novel post-Hartree-Fock dispersion model in which the source is the position-dependent dipole moment of the exchange hole. This model is very economical and yields remarkably accurate C6 and higher-order C8 and C10 dispersion coefficients of intermolecular complexes. Intermonomer separations and binding energies are well predicted also.

30 Conference on Current Trends in Computational Chemistry 2005

Stepwise Hydration of Organic Acids. Test of PM3-PIF as a Model for Hydrated Systems

M. I. Bernal-Uruchurtu1, W. Harb2 and M. F. Ruiz-López3

1Centro de Investigaciones Químicas, UAEM, Morelos, México; 2 Universite de Kaslik, Beyrouth, Lebanon; 3Laboratoire de Chimie et Biochimie théorique, UMR 7565, CNRS - Université Henri Poincaré, Nancy 1, France.

Hydrogen bonding is a key feature in many chemical and biochemical processes as well as in hydration phenomena. It has been shown that description of hydrogen bonds by standard semiempirical methods is rather inaccurate and contains serious nonphysical artifacts. We have recently suggested a scheme to overcome this important limitation.1 Basically, we have proposed to replace the Gaussian correction function (GCF) in the core-core interaction term of standard Austin model 1 (AM1) or parameterized model 3 (PM3) methods by a suitable function that is parameterized to correctly reproduce the long-range behavior of the interaction potential. This parameterizable interaction function (PIF) is a sum of atom – atom contributions of the form:

inter inter χ δ ε PIF = g()A,B = α _β ABRAB + AB + AB + AB ∑ ∑ AB e 6 8 10 A,B A,B RAB RAB RAB

where αAB, β AB, χ AB, δ AB and ε AB are adjustable parameters depending on (A, B) atom types. Each g(A, B) replaces the corresponding GCF for the (A, B) intermolecular pair in the AM1 or PM3 nuclear repulsion function. On its first stage this approach provided a very good description of hydrogen bonding in water, from small clusters to liquid water,2 thus stimulating an extension of the model to the case of solute-solvent interactions of organic molecules in aqueous solution.3 Compared with the standard method, the PM3-PIF approach leads to a better agreement with high-level ab initio results for both interaction energies and geometrical parameters of dimers formed with the training set molecules (water, methane, methanol, formic acid, hydrocyanic acid and ammonia). In atmospheric chemistry it is of great interest the actual behavior of volatile organic chemicals. And, since an important amount of water might be also participating in the reactive processes occurring in the atmosphere, we would like to look into the hydrated structures of some small volatile organic compounds as a way of building a more realistic picture of the participating moieties in reactive processes. We have applied the PM3-PIF model in the current study to investigate he relative stability and structure of clusters [A(H2O)n] with n=2-6. In this case, A was chosen to be four different organic acids: formic acid, acetic acid, hydrocyanic acid and phenol. Due to the importance of these molecules in the gas phase, it is possible to find ab initio predictions for some small structures, comparison with those studies shows that the method is performing fairly well. The lowest energy structures for a given number of water molecules were used for estimating the relative abundance of each in gas phase. Due to the low computational cost of this method it was possible to explore several different conformations and the paths interconnecting them.

Conference on Current Trends in Computational Chemistry 2005 31

References:

1. Bernal-Uruchurtu M. I., M.-C. M. T. C., Millot C. and Ruiz-López M. F., Improving Description of Hydrogen Bonds at the Semiempirical Level: Water-Water Interactions as Test Case. J. Comput. Chem 2000, 21, (7), 572-581. 2. G. Monard, M. I. B.-U., A. van der Vaart, K. M. Merz Jr. and M. F. Ruiz-López, Simulation of Liquid Water Using Semiempirical Hamiltonians and the Divide and Conquer Approach. J. Phys. Chem. A 2005, 109, 3425-3432. 3. W. Harb, M. I. B.-U., M. F. Ruiz-López, An improved semiempirical method for hydrated systems. Theor Chem Acc 2004, 112, 204-216.

32 Conference on Current Trends in Computational Chemistry 2005

Effect of Solvent Polarity on First Order Nonlinear Optical Properties of Zwitterionic Merocyanine Dyes

P. Bonifassi, J. Leszczynski and P. C. Ray

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

We present a quantum-chemical analysis of the solvent effect on first hyperpolarizabilities of a series of Zwitterionic Merocyanine dyes (Fig 1). The molecular geometries are obtained via BL3YP/6-31G (d,p) level optimization including SCRF/PCM approach, while the dynamic NLO properties are calculated with the ZINDO/CV method including solvent effects. The effect of donor or acceptor substitution and elongation of the conjugation path length are established to demonstrate the engineering guidelines for enhancing molecular optical non-linearities. It is found that solvents play a remarkable role on the structure and first hyperpolarizabilities of merocyanine dyes. Changing the solvent from low to high dielectric causes not only an increase in magnitude of dynamic hyperpolarizability β but also a change in sign, therefore passing through zero at intermediate dielectric. Concerning the static hyperpolarizabilities βtot the chart 1 shows that βtot increases when the dielectric constant increases because the zwitterionic character becomes predominant. The best way to visualize the strongly solvent-dependent molecular properties is to plot the dipole moment µ values against the solvent’s dielectric constant ε (Chart 2). Two regions of ε values are identified : 1)a large range (7 < ε < 78) of dielectric constants in which µ values are very large and do not vary significantly between 30 and 78 and where the structures have a predominant zwitterionic character. 2) A much smaller ε range (1 < ε < 7) in which the dipole moments increases very slowly from ε =1 to 7 and where the quinoid structures are predominant. The computed solvent-dependent Mulliken acceptor and donor charge distributions in each medium are shown on the Chart 3 where the charges are increasing when the dielectric constant ε is increasing Importances of our results on the design of NLO device will be discussed.

SOLVENT EFFECT on TOTAL STATIC HYPERPOLARIZABILITY

200000 Merocyan1 150000 Merocyan2

total Merocyan3 100000 ⎯ Merocyan4 50000 Merocyan5

0

dielectric constant

Chart 1 Conference on Current Trends in Computational Chemistry 2005 33

Solvent effect on dipol moment

45

40

35 Merocyan1 30 Merocyan2 Merocyan3 25 Merocyan4 Merocyan5 20

dipol moment(debye) 15

10 0 1020304050607080 dielectric constant

Chart 2

Solvent effect on donor and acceptor charges

0.80

0.70

0.60

0.50 merocyan1 0.40 merocyan1 0.30 merocyan2 0.20 merocyan2 0.10 merocyan3 0.00 0 1020304050607080 merocyan3

Charges -0.10 merocyan4 -0.20 merocyan4 -0.30 merocyan5 -0.40 merocyan5 -0.50

-0.60

-0.70

-0.80 dielectric constant

Chart 3

34 Conference on Current Trends in Computational Chemistry 2005

CN

H3C N CN

Merocyan1 Ph C N

C C CN

H3C N S

CN Merocyan2 O C4H9 C N

C C O

H3C N CN C H O 4 9 Merocyan3b

NC CN

C C

NC HC CNCH3 Merocyan4

C2H5

N C H NC 2 5

C C

NC CN

Merocyan5

FIGURE 1

Conference on Current Trends in Computational Chemistry 2005 35

The Gauss-Bessel Quadrature: A Tool for the Evaluation of Barnett-Coulson/Löwdin Functions

Ahmed Bouferguene and Hassan Safouhi

Campus Saint-Jean/Univ. of Alberta, 8406 – 91Street, T6C 4G9, Edmonton, Canada

In the past few years, scientists have taken the challenge of elaborating numerical algorithms geared to make usage of Slater Type Orbitals~(STOs)[1] as the basis of choice for molecular structure determination. The arguments in favor of such functions rely on two fundamental properties that have to be satisfied by the solutions of the Schrödinger equation. On the one hand, a cusp on the origin [2] and on the other hand an exponential decrease at infinity [3]. Because Exponentially Type Functions (ETFs) satisfy both criteria they fall in the category of admissible functions to be used as part of the trial wave function when a method such as the variational procedure is used to build approximates to the solutions of the Schrödinger equation. As a consequence, number of scientists (the first of whom were the very pioneers of quantum chemistry) have devoted some of their work setting up mathematical tools that can be used to handle efficiently the basic building blocks of ab initio quantum chemical procedures, i.e. multi- center integrals over ETFs of which STOs are a special case. The attempts of the pioneers of quantum chemistry to incorporate ETFs as part of an operational and routine framework for quantum chemistry calculations did not fully succeed mainly because modern numerical analysis was in its infancy owing to the limitations of the hardware and software of the time. Consequently, Gaussian Type Orbitals (GTOs) [4] took over the field of quantum chemistry since they allowed cost efficient numerical procedures to be developed for multi-center integrals. GTOs owe their success to one very important feature: their multiplication theorem [4, 5 (p. 154)] allowing a product of two such orbitals centered on two arbitrary points defined by a and b to be written as, ⎡ G G 2 ⎤ G G 2 G G 2 ⎛ α α G G 2 ⎞ G α a + α b exp(−α r − a ) exp(−α r − b ) = exp⎜ 1 2 a − b ⎟ exp⎢− (α + α ) r − 1 2 ⎥ 1 2 ⎜α + α ⎟ ⎢ 1 2 α + α ⎥ ⎝ 1 2 ⎠ ⎣ 1 2 ⎦ To within a constant, the result is obviously a new Gaussian centered on the center of "mass" (barycenter) of the two initial centers. Such a specific property yields tremendous simplifications in multi-center integral formulae and hence in the leading computational algorithms. Consequently, even though GTOs violated the fundamental behavioral properties of the Schrödinger eigenfunctions, they have been and still are at the heart of most operational quantum chemistry packages such as PolyAtom, Gaussian suite which started as Gaussian-70 and Hondo to name few. In addition, the success of GTOs has encouraged an extensive intellectual production which contributed to increase our insight into the limitations of GTOs as applied in quantum chemistry but more importantly to propose work arounds where problems are potentially to occur. To name few instances one may consider, • the systematic procedure which was proposed to generate automatically large basis sets that could approach to any degree of accuracy the original STO [6] • to compensate for the drawbacks of GTOs at the origin, use of correlated orbitals was proposed and satisfactory results has been obtained especially for light atoms and small molecules [7] However, in spite of all the qualities that made GTOs so successful and perhaps the only path leading to routine simulations on molecules of practical interest, the challenge of using STOs is 36 Conference on Current Trends in Computational Chemistry 2005

still an active and open problem responsible for numerous contributions every year. Whether STOs will prove to be superior in practice than GTOs, i.e. computational time vs accuracy, that is yet to be seen but this does not seem to be the main driving force as much it is to solve the problem. Indeed, as early as 1981, during the first international conference on Exponential Type Orbitals~(ETOs) [8], devoted exclusively to examine the state of the art around the methods that could potentially be used to tackle the problem of multi-center integrals over STOs, Milan Randic [9] proposed to elevate such a long standing unsolved problem to the status of a conjecture,

The four center conjecture: Two electron four center STO molecular integrals can be solved analytically

Although from a practical standpoint, having an analytical form for multi-center integrals over STOs is not as crucial as having a numerically stable and fast algorithm, the above conjecture nonetheless expresses the strong will of some scientists not only to solve the problem but also to do it with some mathematical elegance (as can be suggested by the word "analytically"). As for practical applications of STOs in the field of quantum chemistry, one must recognize that recently even I. Shavitt [10], one of the pioneers in the field, has questioned the usefulness of STOs as a basis of choice in quantum chemistry. One of the arguments of Shavitt in favor of GTOs is that a tail that is too long (as is the case for STOs compared to GTOs) cannot be easily removed by improving the basis set. Hopefully, some future investigation will bring a counter argument which will show that improving a diffused STO basis set could be as easy as in the case of GTOs. In the present work, we examine the evaluation of Barnett-Coulson/Löwdin Functions (BCLFs) by means of a tailored Gauss quadrature, referred to as Gauss-Bessel. Indeed, when multi-center integrals over STFs are evaluated within the single center two-range expansion method, one ends up with an infinite series involving BCLFs which need to be evaluated efficiently. In our previous investigation [11], it was shown that closed analytical forms of BCLFs were numerically unstable while their infinite series expansions were slowly convergent [12]. Fortunately it turns out that BCLFs can be represented by a semi-infinite integral involving a function of the form z r+1/ 2 exp(−σ / z −τ z ) which after investigation appears to be an admissible weight function. The remaining part of the integrand being close to a polynomial, it is therefore expected that Gauss-Bessel quadrature (built using the abovementioned weight functions) should allow one to evaluate BCLFs accurately and quickly (as compared to other approaches). As a last remark, it is important to note that the single center expansion method can is a general purpose method which can be used beyond the scope of multi-center integrals. In such cases and for the sake of efficiency, it may be beneficial to consider a method in the same line as that developed in the present work.

[1] J. C. Slater, Phys. Rev. 36, 57 (1930). [2] T. Kato, Commun. Pure. Appl. Math 10, 151 (1957). [3] S. Agmon, Lectures on Exponential Decay of Solutions of Second-Order Elliptic Equations : Bound on Eigenfunctions of N-Body Schr odinger Operators, Princeton University, Princeton, NJ, 1982. [4] S. F. Boys, Proc. Roy. Soc. A200, 542 (1950). [5] A. Szabo and N. Ostlund, Modern quantum chemistry, Mc Graw-Hill Publishing Company, New York, First (revised) edition, 1989. [6] S. Wilson, J. Phys. B: At. Mol. Opt. Phys. 28, L495 (1995). [7] K. Pachucki and J. Komasa, Chem. Phys. Lett. 389, 209 (2004). Conference on Current Trends in Computational Chemistry 2005 37

[8] C. A. Weatherford and H. W. Jones, editors, Dordrecht, Holland, 1982, D. Reidel Publishing Company. [9] M. Randic, On auxiliary functions in molecular integrals, In Weatherford and Jones [12], pages 141-155. [10] I. Shavitt, Int. J. Quantum Chem. 100, 105 (2004). [11] A. Bouferguene and D. Rinaldi, Int. J. Quantum Chem. 50, 21 (1994). [12] A. Bouferguene, J. Phys. A: Math and Gen., 38(13), 2899-2916, 2005

38 Conference on Current Trends in Computational Chemistry 2005

A Computational Study of Four Sulfur Oxo Acids and Related Species

Judge Brown and John D. Watts

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

The ground-state geometries, dipole moments, vibrational frequencies, relative energies and enthalpies of formation have been calculated for the “simplest” sulfenic and sulfinic acids along with their associated esters using high-level ab initio (MP2) and density functional (B3LYP) methods. The conformational flexibility of sulfinic acid, methanesulfinic acid and methyl sulfinate under rotation of the S−O bond was investigated. Two conformations of C1 symmetry are predicted for each of the aforementioned species with free energy differences of 0.2, 0.6, and 1.1 kcal/mol, respectively, at the MP2/6-311++G(3df,3pd) level. Using the isodesmic reaction procedure, the MP2 (B3LYP) enthalpies of formation for HSOH, HSO2H, CH3SOH, CH3OSH, CH3SO2H, and HSO2CH3 are calculated to be -24.7(-28.8), -59.9(-64.3), -32.1(-34.8), -20.1 (-24.2), -76.3(-78.7), and -56.8(-61.7) kcal/mol, respectively. These results are in reasonable agreement with available experimental and theoretical measurements.

Conference on Current Trends in Computational Chemistry 2005 39

Comparison between Folding Conformations of Met-Enkephaline and Morphine

Deborah J. Bryan and Jesse Edwards III

Department of Chemistry, Florida A & M University Tallahassee, FL 32307

The objective of this work is to generate folding conformations of Met-Enkephaline through molecular dynamics (MD) and compare them with morphine structure. Met-Enkephaline (MEK), a linear pentapeptide, is hypothesized to fold similarly to tetracyclic morphine. Using the molecular mechanics package AMBER, an initially extended structure of MEK was relaxed by MD to folded structures. MD simulations of morphine were also carried out. Partial charges were assigned by AMBER default values to MEK, while the semi-empirical PM3 method, was used for morphine. MD simulations were conducted in both vacuum and water for 1ns at 300K. Several conformations were selected from equilibrium regions for comparison. Morphine conformations were insensitive to thermal agitations both in vacuum and in water due to its ring structure; whereas, MEK was found to be flexible as compared to morphine. To compare folding conformations of MEK with morphine, corresponding atomic pairs were selected, and the root- mean square deviation (RMS) of the interatomic distances were calculated.

40 Conference on Current Trends in Computational Chemistry 2005

Computational Study on the DNA Bases Interactions with Dinuclear Rh(II)Tetraacetyl Complex

Jaroslav V. Burda,1 Jiande Gu2, and Jerzy Leszczynski3

1Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic. 2Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China. 3Department of Chemistry, Jackson State University, 1325 J.R. Lynch Street, Jackson, Mississippi 39217-0510 U.S.A.

In the study the thermodynamic behavior were determined for the replacement reaction of one and two acetyl-ligands from diaqua-tetrakis-μ-acetatodirhodium complex by purine DNA bases. The complexes were optimized at the DFT level with the B3LYP functional. Stuttgart/Dresden pseudopotentials were treated for the description of Rh atoms. All the replacement reactions are midly exothermic, ΔG is up to 12 kcal/mol for first acetyl-ligand and up to 8 kcal/mol for the second ligand replacement. For all explored complexes, stabilization and bond dissociation energies were computed together with selected electronic properties. Adenine base coordinates to dirhodium complex slightly more firmly than guanine. In head-to-tail conformation the two guanines are better stabilized (by about 8 kcal/mol) than in head-to-head arrangement due to minimization of sterical repulsion of both bases. It was shown the bond dissociation energy of axial water ligands is very small (up to 13 kcal/mol), resembling more or less H-bonds than dative coordination.

Conference on Current Trends in Computational Chemistry 2005 41

Analysis of a Promiscuous Alu Subfamily, Yj7, within Homo sapiens and Pan troglodytes

Marion L. Carroll, Toye Metoyer, Algernon Kelly#, Thuy Lee, April Holmes, Endia Ford, Shemika Sample and R. D. Morris

Xavier University of Louisiana, Department of Chemistry, New Orleans, LA and the Center for Biomodular and Multi-scaled Systems, Louisiana State University, Baton Rouge, LA. #Louisiana State University, Department of Chemistry, Baton Rouge, LA.

Alu repetitive mobile DNA elements are the most abundant Short INterspersed Elements (SINEs) reaching a copy number of over one million in the human genome, making them the mobile element with the highest copy number. Alu elements compose greater than 10% of the mass of the human genome. Full length Alu elements are approximately 300 base pairs in length and are commonly found in introns, 3’ untranslated regions of genes, and intergenic genomic regions. Amplification and insertion of Alu elements occurs through the reverse transcription of RNA in a process termed retroposition.

Alu elements have no open reading frames, so they are thought to parasitize the required factors for their amplification from Long Interspersed Elements (LINEs). Although the human genome contains over one million Alu elements, only a few Alu elements, termed “Master” or source genes, are retroposition competent. The crucial factor(s) that determine an Alu as a functional source gene or “Master” are not fully known. Several factors that may influence the amplification process include transcriptional capacity, priming or self priming for reverse transcription and length of poly-A tail. Alu mobile elements first evolved in the primate genomes over 65 mya (million years ago). Since then, the amplification of Alu elements determined within the human genome has been punctuated, with the current rate being at least 100 fold slower than the initial rate of Alu expansion within primate genomes. Throughout Alu evolution, the source gene will accumulate mutations that are incorporated into the new copies made, creating new Alu subfamilies. Therefore, the Alu family is composed of a number of distinct subfamilies characterized by a hierarchical series of mutations that result in a series of subfamilies of different evolutionary ages arrising over the past 20 million years. Of these subfamilies, almost all of the recently integrated Alu elements characterized within the human genome belong to one of several closely related “young” Alu subfamilies: Ya5, Ya8,Ya5a2, Yb8, Yb9, Yc1, Yc2, Yd, Ye, Yg, Yh, and Yi with the majority being Ya5 and Yb8 subfamily members. The vast majority of data 42 Conference on Current Trends in Computational Chemistry 2005

accumulated on the archeology of these mobile elements find that the youngest Alu subfamilies mark the divergence of humans and great apes between 5-7 million years ago. Alu Y are the family of Alu elements that have amplified within the primate lineage beginning 20-30 mya. As a consequence all catarrhini genomes contain the Alu Y family. Pan troglodytes or the common chimpanzee is believed to be one of the closest living ancestors to humans. Its genome averages to be 95-99% identical to the human genome and is a likely place to find clues to the dynamics of Alu insertion and evidence of the influence of Alu retroposition in chimp and human genome structure and gene distribution. Several Alu subfamilies have been identified within the human genome and have become useful markers in population genetic studies, forensics and primate divergence studies. In expanding our understanding of the influence of Alu insertions on primate genomes it is wise to consider evidence of unique patterns of Alu amplification and the significance of these patterns in human-chimp divergence.

We have employed a computational genomic survey of the Pan troglodytes and Homo sapiens genome sequence databases to determine the distribution of unique recently integrated mobile DNA sequences among the Alu Y family. Our search begins first in the USCS Genome Browser then with a sequence alignment of elements found using the InfoMax VectorNTI Advance software suite and DNAstar Expert DNA sequence analysis tools. BEAUti and the BEAST are sequence analysis software tools we are using to rigorously determine phylogenetic relationships within the sequences aligned. PCR functions to empirically establish the allelic character of our Alu insertions within genomic DNA of humans and chimps. We have focused our efforts on the chimpanzee genome to identify unique subfamilies and compare their structure to the thoroughly analyzed human-specific Alu subfamily structure. By comparing sequence alignments of several hundred Alu Y elements from a chimp genome-wide survey we directly establish subfamilies base on local nucleotide sequence similarity (diagnostic mutations). Most recent insertions in the chimp chromosomes would be marked by intact target- site duplications and few random mutations making elements at least 95-98% similar to the Alu Y family consensus sequence. We have described what we have termed a “promiscuous” Master or source gene in both the human and chimpanzee genomes yet absent from their common ancestor. This Master has actively propagated the identical subfamily in both primate lineages over different periods of time, 4.7 mya in chimpanzee and 2.7 mya in humans. Ages have been established base on the neutral rate of intergenic non-CpG mutation accumulation and by using BEAST (Bayesian evolutionary analysis sampling trees) for evolutionary inference from molecular sequences. Conference on Current Trends in Computational Chemistry 2005 43

Yj7 Human Yj7 Chimp

2.7 mya to ancestor

4.7 mya to ancestor

Y The Alu subfamily we term AluYj7, to follow the standard Alu nomenclature, was tested by PCR using the Dimorphic Alu Insertion Assay for the presence or absence of Yj7 in 20 individual unrelated chimp whole blood genomic DNA isolates and 20 Asian genomic DNA samples isolated from peripheral blood lymphocytes.

18 unrelated Asian DNA Chimp DNA samples

500 bp

150 bp

These and other new identical by decent dimorphic Alu insertions will be useful markers for comparing and contrasting Alu sequence evolution, for studying amplification mechanisms among similar mobile elements, as new reagents for forensic analysis, for studying primate divergence and evolution and for mapping population dynamics among primates species worldswide.

44 Conference on Current Trends in Computational Chemistry 2005

Computational Studies on Stable Triplet States of Metallaacetylenes and the Effects of Halogen Substituents

Mu-Jeng Cheng and San-Yan Chu

National Tsing Hua University, Hsinchu 30013, Taiwan

This paper describes theoretical studies of halogen-substituted metallaacetylenes (XC≡MY, M = Si, Ge, and Sn; X, Y = H, Cl, and F) performed at the QCISD(T)/6-311G**//QCISD/6- 31G* and QCISD(T)//QCISD/3-21G* levels of theory. The electronegative halogen substituents destabilize the singlet state such that the triplet state becomes more favorable. The triplet state has the bifunctional electronic structure of a triplet carbene joined to a heavy singlet carbene. We found that the substituents effectively reduce the energy of the donor–acceptor interactions (ED-A) between the two in-plane lone pairs of electrons of the singlet state; therefore, the remaining π bond is less favorable energetically than is the triplet state with a σ bond. A related phenomenon occurs for the homonuclear heavy acetylenes in which the lead compound RPbPbR switches to a Pb–Pb bond from the bonds observed for the lighter acetylenes. Furthermore, we performed a study on the insertion of HCMH into a C–H bond of CH4 to interpret the carbene- like reaction mode that Sakamoto, Kira, and coworkers observed for stannaacetylenes.

Conference on Current Trends in Computational Chemistry 2005 45

Investigating Ring Current Effects around a Benzene Ring

Anthony Chuma

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

Aromatic rings have strongly anisotropic magnetizability attributed to ring currents induced by the magnetic field. This affects the chemical shifts of neighboring nuclei. The simplest treatment of this effect, the McConnell equation1 treats the magnetized group as a point dipole. Modern ab initio methods can directly calculate the effect of aromatic ring currents on the isotropic chemical shifts. A major advantage of such calculations is that they can determine induced chemical shifts at arbitrary positions, not only at the positions of the nuclei, an approach pioneered by Schleyer2 and independently by Wolinski3. The Nuclear Independent Chemical Shifts (NICS) have been nicely used to assess the aromatic character of molecules. Less work has been done on characterizing the effect of anisotropic functional groups, in particular aromatic residues, on chemical shifts, apart from application of the McConnell equation. It is important to account for the effects of aromatic residues in modeling the NMR shifts of large molecules, for instance proteins where the calculations are necessarily limited to smaller fragments. We have calculated both NICS and chemical shift changes in nearby molecules using the PQS suite of programs and compared the results with the McConnell model. Our aim is to develop a simple, accurate model for the ring current effects on NMR shifts, particularly in proteins.

1 H. M. McConnell, J. Chem. Phys. (1956), 24 (2), 460-467 2 P. v. R. Schleyer, C. Maerker, A. Dransfeld, H. Jiao, and N. J. R. v. E. Hommes, J. Am. Chem. Soc. (1996), 118, 6317-6318 3 K. Wolinski, J. Chem. Phys. (1667), 106 (14), 6061-6067 46 Conference on Current Trends in Computational Chemistry 2005

The Influence of Microhydration on the Ionization Energy Thresholds of Cytosine

David M. Close

Department of Physics, East Tennessee State University, Johnson City, TN, 37614

In the present study the Ionization Energy Thresholds (IET) of cytosine have been calculated (with the B3LYP, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with 1-3 water molecules placed in the first hydration shell. Calculations show there is very little effect of microhydration on the IET’s of cytosine. Placing the microhydrated structures of cytosine in a PCM cavity was also seen to make very little difference in the IET’s when compared to the IET of ordinary cytosine in a PCM cavity. The implications are that accurate calculations of the IET of cytosine can be obtained by simply considering long-range solvation effects. This holds for the present case because for the cytosine cations + nH2O there is very little delocalization of charge or spin onto the waters.

B3LYP Energies and IET’s for Cytosine + nH2O Structures

E(B3LYP)1 Vert. IE Vert. IE Dipole Moments C + nH O 2 (Hartrees) (eV) PCM (eV) μ(Debye)2 Cytosine -394.9633498 8.69 6.51 6.86, 6.81: 9.49, 10.90 C1 -471.4169950 8.75 6.57 3.78, 4.59: 5.16, 5.76 C2 -471.4158149 8.82 6.55 4.96, 7.94: 6.92, 10.4 C3 -471.40995923 8.98 6.55 4.73, 7.95: 6.27, 10.2 C11 -547.8717402 8.69 6.59 5.30, 7.83: 7.46, 12.81 C13 -547.8691212 8.64 6.60 5.17, 7.07: 7.06, 11.08 C33 -547.8699243 8.85 6.54 5.88, 9.24: 7.96, 13.71 C23 -547.8678241 8.78 6.56 5.44, 7.94: 7.28, 13.46 C111 -624.3205934 8.89 6.65 5.56, 9.65: 7.32, 15.02 C113 -624.3238709 8.88 6.61 4.46, 6.99: 7.05, 13.39 C133 -624.3230761 8.80 6.56 4.53, 7.89: 6.18, 11.33

1Calculated at the B3LYP/6-31++G(d,p) level. 2Notation. (neutral, cation in gas phase):(neutral, cation in PCM cavity). 3C3 does not appear to form H-bonds with water in this position at least with the diffuse functions used in this study.

Conference on Current Trends in Computational Chemistry 2005 47

Analysis of the C-O bond in Diphenyl Ether Using Computational Chemistry

Sherrita M. Cooks and Melissa S. Reeves

Department of Chemistry, Armstrong Hall Room 102, Tuskegee University, Tuskegee, AL 36088-1645.

The diphenyl ether group appears in many polyimide structures, providing flexibility (and therefore processability) to these stiff polymer systems. In this work, the bonding properties of the ether linkage in diphenyl ether were investigated using computational chemistry. The goals were to determine why the accepted bond angle of 121° differs from the bond angle found in diethyl ether (112°) and how their bonding correlates with that of an “intermediate” molecule of ethyl phenyl ether. We investigated the bond properties using ab initio computational chemistry. Results from Gaussian98 for Windows show that MP2/6-311+g** calculations and B3LYP/6- 311+g* calculations both confirm the X-ray diffraction value of approximately 121° for diphenyl ether and give a similar value for ethyl phenyl ether. Comparison of the electron density and the molecular orbitals for diethyl ether and diphenyl ether demonstrate a qualitative difference in the electron density surrounding the oxygen. A quartic angle-bending potential was calculated which could be used to modify current force fields for polymer modeling.

48 Conference on Current Trends in Computational Chemistry 2005

Stone-Wales Defect Formation in (5,5) Armchair Single-walled Carbon Nanotube

T. C. Dinadayalane and Jerzy Leszczynski*

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

Hartree-Fock, B3LYP and MP2 calculations have been performed to examine the formation energy of a single Stone-Wales defect at different locations and the different orientation in the (5,5) single-walled carbon nanotube. Single-walled carbon nanotubes called ‘buckytubes’ can be thought of a single graphene sheet that is wrapped into a seamless cylinder. Carbon nanotubes are not found to be as perfect as they seem due to the presence of defects such as vacancies, Stone-Wales defects, pentagons, heptagons and dopants as demonstrated by recent experimental and theoretical studies.1-3 The imperfections in the nanotubes are likely to occur through defects introduced either during the synthesis or due to stress applied. Stone-Wales defect is one of the most important defects in the nanotubes. A dipole consisting of two pentagon-heptagon pairs can be created by rotation of a C-C bond in the hexagonal network of the carbon nanotube by 90˚. Such a dipole was later called a Stone-Wales defect, which appears to be the lowest energy defect possible in a perfect nanotube.4 The two distinct C-C bonds such as axial and circumferential bonds in the carbon nanotubes can be rotated 90˚ independently to generate the Stone-Wales defects in the nanotubes with different orientations (Scheme 1). The structures and reactivities of the nanotubes with a single Stone-Wales defect are compared with the corresponding defect-free single-walled carbon nanotube. The computed formation energies at the B3LYP/6-31G(d) are in good agreement with those obtained at the MP2/6-31G(d). The present study clearly indicates that the HF method, in general, overestimates the formation energies compared to B3LYP or MP2. The formation energy for the Stone-Wales defect to occur at the edge of the nanotube with ten atom layer is significantly lower compared to that locates near the center of the nanotube indicating that the Stone-Wales defect need not always form at the middle of the nanotube. The computed pyramidalization angles for the carbons and the measured -orbital misalignment angles5,6 of the perfect nanotube and the Stone-Wales defect region were critically analyzed to correlate the reactivity of the sites and the local curvature. Band gap values obtained for the defect and defect-free nanotubes were compared.

References: (1) Hashimoto, A.; Suenaga, K.; Gloter, A.; Urita, K.; Iijima, S. Nature 2004, 430, 870. (2) Lu, A.; Pan, B. C. Phys. Rev. Lett. 2004, 92, 105504. (3) Rossato, J.; Baierle, R. J.; Fazzio, A.; Mota, R. Nano Lett. 2005, 5, 197. (4) Stone, A. J.; Wales, D. J. Chem. Phys. Lett. 1986, 128, 501. (5) Haddon, R. C. J. Phys. Chem. A 2001, 105, 4164. (6) Niyogi, S.; Hamon, M. A.; Hu, H.; Zhao, B.; Bhowmik, P.; Sen, R.; Itkis, M. E.; Haddon, R. C.; Acc. Chem. Res. 2002, 35, 1105.

Conference on Current Trends in Computational Chemistry 2005 49

Rotation about Rotation about circumferential bond axial bond 1, D5d

1a, Cs 1a’, C2

Scheme 1

50 Conference on Current Trends in Computational Chemistry 2005

Interaction of Li+, Na+ and K+ with Novel Cup-shaped Molecules: Effect of Ring Annelation to Benzene and Cavity Selectivity

T. C. Dinadayalane,1 Dmitriy Afanasiev1,2 and Jerzy Leszczynski*,1

1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217, USA 2Ukrainian State Chemical Technology University, Gagarin av., 8, Dnepropetrovsk, 49005, Ukraine.

The hybrid density functional theory (B3LYP) and Moller-Plesset perturbation (MP2) method using 6-31G(d) basis set have been employed to study the interactions of the alkali metal cations Li+, Na+ and K+ with the novel cup-shaped molecule tri-7-azanorbornadiene annelated benzene and the corresponding hydrocarbon analog (III), benzene (I), trindene and tri- azatrindene (II) systems. The geometries and the binding energies obtained for the cup-shaped system (III) were compared with the results for the benzene (I), trindene and tri-azatrindene (II) systems as host molecules to examine the effect of annelation to benzene on structural and binding affinities. The cup-shaped molecule tri-7-azanorbornadiene annelated benzene has been synthesized recently.1 The cation-π interaction is a predominant source in molecular recognition and has been observed in many biological systems.2,3 The interactions of cations with the aromatic compounds and the aromatic rings of the amino acids are the recent theoretical interests.4-7 The cup-shaped molecules exhibit two faces (top and bottom). Our results indicate that the metal ions under study highly prefer to bind bottom face (13, 17 and 19 kcal/mol for Li+, Na+ and K+ respectively) rather than top face for tri-7-azanorbornadiene annelated benzene system when the lone pair electrons of nitrogen atoms interact with metal ions. The bottom face selectivity could be ascribed to the combined effect of the cation-lone pair and cation-π interactions. For the hydrocarbon system as well as the nitrogen lone pair electrons that are prevented from interaction with metal ions, the preference is shown for top face due to the strong interaction of the cation with the π-cloud not only from the central ring of benzene but also from the π-orbitals of annelated rings. The present study indicates that cation-lone pair interaction is much stronger than the cation-π interaction. The host molecule becomes deeper bowl when the lone pair electrons of nitrogen involved with cation binding; this is evidenced from the significant pyramidalization at the sp2 carbons of central benzene ring annleated by three 7- azanorbornadiene. The deeper bowl structure is due to the effective cation-lone pair interaction otherwise not possible. Tri-annelation to the benzene significantly increases the binding of alkali metal cations. The present study suggests that the novel cup-shaped molecules could serve as potential cavities for many cations and anions, and the studied cation bound complexes may be realized experimentally. M M M

x x x X X X M x x x Bottom face Top face I II III + + + Where X = CH2 and NH; M = Li , Na and K .

Conference on Current Trends in Computational Chemistry 2005 51

References: (7) Zonta, C.; Fabris, F.; De Lucchi, O. Org. Lett. 2005, 7, 1003. (8) Dougherty, D. A. Science 1996, 271, 163. (9) Ma, J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303. (10) Tsuzuki, S.; Yoshida, M.; Uchimaru, T.; Mikami, M. J. Phys. Chem. A 2001, 105, 769. (11) Kim, D.; Hu, S.; Tarakeshwar, P.; Kim, K. S.; Lisy, J. M. J. Phys. Chem. A 2003, 107, 1228. (12) Reddy, A. S.; Sastry, G. N. J. Phys. Chem. A 2005, 109, 8893. (13) Ruan, C.; Rodgers, M. T. J. Am. Chem. Soc. 2004, 126, 14600.

52 Conference on Current Trends in Computational Chemistry 2005

Energetic and Structural Comparison of Cisplatin and Analogs from DFT Calculations

LaTanya Dixon, Jo-Lyque Turner, Glake A. Hill, Jerzy Leszczynski

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

There have been many developments in the effectiveness of cisplatin since its discovery in the late 1960s. Analogs of cisplatin have been developed to decrease toxicity, cell resistance, and discomfort in drug administration. Cisplatin analogs such as carboplatin, oxaliplatin, and nedaplatin have surpassed cisplatin in some efficacy while analogs such as ormaplatin exhibit oral activity. However, the mechanism of cisplatin and its analog has been elusive to date. Thus, a qualitative and quantitative comparison of cisplatin and four analogs is presented utilizing theoretical methods. A Density Functional Theory method (B3LYP) and 6-31G* basis set was used for all calculations. LanL2DZ pseudopotential was applied to account for the effective core potential of platinum. Geometric and population analysis provided insight into bonding and charge distribution in the antitumor compounds. Many similarities and differences existed among the platinum compounds. A thorough comparison will be discussed.

Conference on Current Trends in Computational Chemistry 2005 53

Modelling the Structure of Fullerenes and their Endohedral Complexes with Nontrivial Topological Properties

Helena Dodziuk

Institute of Physical Chemistry, Polish Academy of Sciences 01-224 Warsaw, Kasprzaka 44/52, Poland http://ichf.edu.pl/person/dodziuk.htm

For more than 100 years chemists considered topology as playing ground for mathematicians unrelated to their activities [1] and the first paper by van Gullick on the possibility of synthesis of molecules having nontrivial topology was rejected by one of the most respectable chemical journals Tetrahedron in 1960 as too speculative. However, the first synthesis of a catenane (link) was published in the same year [2] while the van Gullick work appeared 30 years later [3]. Several catenanes, like schematically shown 1, rotaxanes 2 (which at that time have not been considered to be topologically nontrivial species), and a molecule mimicking Möbius strip 3 have been synthesized but a real bust allowing chemists not only to increase reaction yields but also to obtain much more complicated structures like olympiadane 4 and knot 5 resulted from the development of supramolecular chemistry by making use of preorganization phenomenon [1]. Another major factor in the history of topological chemistry was the finding that circular DNAs, which themselves are nontrivial topological objects, can form in addition catenated and knotted structures maling use of special enzymes - topoisomerases [4, 5]. The latter property may have practical consequences. Later we have shown that rotaxanes 2, 'in' and 'out' isomers of hypothetical hydrogenated fullerenes like 6 and well known endohedral fullerene complexes like 7 are also systems with nontrivial topological properties [6]. It should be stressed that 6 and 7 are very difficult to study theoretically since they are very big systems. In addition, nonbonding interactions which are of importance in them can be correctly described only at a very high level of theory. Moreover, the guest molecules or ions inside the relatively rigid fullerene cages are known to be highly mobile. For + + instance, in La @C80, two La cations have been shown to rapidly move inside the fullerene cage by means of 13C and 139La NMR technique [7]. It should be stressed that among numerous practical applications of fullerenes foreseen in late 1980-ties endohedral fullerene complexes played an important role. In this talk I would like 1. to report our model molecular mechanics calculations for "in" and "out" isomers of perhydrogenated fullerenes [8, 9] and for endohedral complexes of fullerenes with small molecules [10, 11] and nested fullerenes [12]. In particular, the prospects of obtaining the endohedral complexes with molecules inside allowing for practical applications will be presented. 2. To discuss the literature data on unreasonable applications of semiempirical quantum calculations for these systems [13, 14]. 3. To put a general question and initiate a discussion on the future of the modeling of such complicated systems as those discussed here.

54 Conference on Current Trends in Computational Chemistry 2005

O

C CHOH

C63H34D5 (CH2)32

1 2 3

4 5

La

H H H H

La

6a 6b 7

References

1. H. Dodziuk, "Introduction to Supramolecular Chemistry", Kluwer, Dordrecht, 2002, Sects. 2.3 and 8.2. 2. E. Wasserman, J. Am. Chem. Soc., 1960, 82, 4433. 3. N. van Gulick, New J. Chem., 1993, 17, 619. 4. E. M. Shektman, S. A. Wasserman, N. Cozarelli, M. J. Solomon, New J. Chem., 1993, 17, 757. 5. J. M. Berger, S. J. Gamblin, S. C. Harrison, J. C. Wang, Nature, 1996, 379, 225. 6. H. Dodziuk, K. S. Nowiński, Tetrahedron, 1998, 54, 2917. 7. T. Akasaka, S. Nagase, K. Kobayashi, M. Wälchli, K. Yamamoto, H. Funasaka, M. Kako, T. Hoshino, T. Erata, Angew. Chem. Int. Ed. Engl., 1997, 36, 1643. 8. H. Dodziuk, K. Nowiński, Chem. Phys. Lett., 1996, 249, 406. 9. H. Dodziuk, O. Lukin, K. S. Nowiński, Pol. J. Chem., 1999, 73, 299. 10. H. Dodziuk, G. Dolgonos, O. Lukin, Carbon, 2001, 39, 1907. 11. H. Dodziuk, Chem. Phys. Lett., 2005, 410, 39-41. 12. H. Dodziuk, G. Dolgonos, O. Lukin, Chem. Phys. Lett., 2000, 329, 351. 13. S. Erkoc, L. Turker, J. Mol. Struct. (THEOCHEM), 2003, 640. 57. 14. L. Turker, S. Erkoc, J. Mol. Struct. (THEOCHEM), 2003, 638, 37. Conference on Current Trends in Computational Chemistry 2005 55

Theoretical Studies on the Effect of Protonation on C-P bond Cleavage of Pyridylmethyl-(amino)phosphonates

Marek Doskocza,c, Devashis Majumdarc, Szczepan Roszakb,c Roman Gancarza, and Jerzy Leszczynskic

aDepartment of Organic Chemistry, Faculty of Chemistry Wroclaw University of Technology, Wyb. Wyspianskiego 27; 50-370 Wroclaw, Poland bInstitute of Physical and Theoretical Chemistry Wroclaw University of Technology, Wyb. Wyspianskiego 27; 50-370 Wroclaw, Poland cThe Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University; P.O. Box 17910 J.R. Lynch Street; Jackson, Mississippi 39217 USA

Pyridylmethyl-(amino)phosphonic acid and their esters are interesting for their diverse biological and biochemical properties. These compounds could be used as antibacterial agents, plant growth, and calcium metabolism receptors and inhibitors of various enzymatic processes [1,2]. They also have neuro-toxic properties since they can act either as agonists of neuronal receptors or exhibit antagonist activity depending upon their structures [3]. The cleavage mechanism of the C-P bond of such molecules has recently drawn interest as it could be a way of detoxification of such compounds [4,5,6]. The C-P bond cleavage of aminophosphonic acids depend on the acidic pH of the medium and thus the protonation of the pyridine as well as the amino groups are quite important in such cleavage mechanism. In the present work we have studied the cleavage mechanism of pyridylmethyl-(amino)phosphonic [Fig. 1] at the density functional (DFT) and Moller-Plessett second order perturbation (MP2) level of theories.

H2N O

P OCH3 N H3CO

Figure 1

The particular molecular system that is studied here has the pyridylmethyl- (amino)phosphonic group at the para position with respect to the pyridine nitrogen. Although there are some experimental studies on the amino-phosphonic acid systems, these amino- phosphonates are relatively less studied. The alternative protonation sites which might affect the C-P cleavage are the pyridine nitrogen, amino nitrogen of the side change and the phosphoryl oxygen. Extensive proton affinity calculations on these sites have been carried out at the DFT and MP2 levels to get an insight into the effect of protonation on the C-P cleavage. Various low energy conformers of this molecule have been used for such a calculation. The solvation corrections to the reaction path analyses and the proton affinity studies have been made at the DFT and MP2 levels using polarized continuum model with the conductor like reaction field (COSMO) approach. Our results show that the proton affinity of the different sites as well as the 56 Conference on Current Trends in Computational Chemistry 2005

conformation of the protonated pyridylmethyl-(amino)phosphonic group has direct influence on the C-P cleavage mechanism.

References [1] R. Lipinski, L. Chruscinski, P. Mlynarz, B. Boduszek, and H. Kozlowski, Inorg. Chim. Acta (2001), 322, 157. [2] B. Boduszek, Syn. Commun. (2003), 33, 4087. [3] K. Chruszcza, M. Baranska, K. Czarniecki, L. M. Proniewicz, J. Mol. Struc. (2003), 651– 653, 729–737. [4] M. Lim and C. J. Cramer, J. Phys. Org. Chem. (1998), 11, 149. [5] B. Boduszek PhD disseration, Wroclaw University of Technology 1978. [4] R. Gancarz PhD disseration, Wroclaw University of Technology 1977.

Conference on Current Trends in Computational Chemistry 2005 57

Prediction of Excited States for Carbon, Nitrogen and Oxygen Systems Using Quantum Monte Carlo

Floyd Fayton, Jr., John A.W. Harkless, and Ainsley Gibson

Department of Chemistry, Howard University, 525 College St., NW, Washington, DC 20059

Quantum Monte Carlo (QMC) refers to a class of ab initio methods that use a stochastic simulation to solve the many-body Schrödinger equation. These QMC methods are applied to elucidate the thermodynamic and electronic properties of nitrogen plasma, reacting with carbon in an oxygenated environment. Excited states of the atomic and binary compounds of carbon, nitrogen, and oxygen were observed in order to illustrate the ability to accurately describe the range of reactions that may occur. These structures include, CN, NO, CO, N2, O2, C2, CNO, OCN, and selected excited states of each element. In order to show the accuracy of the QMC method, our values and B3LYP/6-31G*, MP2/6-31G*, and CI values are compared against experiment.

58 Conference on Current Trends in Computational Chemistry 2005

Identifying Potential LPA3 Antagonists Using in Silico Screening

James I. Fells and Abby L. Parrill

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

The World Health Organization has reported that 16.7 million deaths annually are attributed to cardiovascular disease. Lysophosphatidic acid(LPA) is one of the causes of cardiovascular disease. LPA responses are mediated by its G-protein coupled receptors(GPCR), LPA1-3. LPA promotes platelet and neointima formation; which in turn can cause plaque rupture and thrombus formation. LPA1 and LPA3 antagonists both inhibit platelet shape change. Identification of selective LPA3 antagonists has the potential to aid the development of new leads for further understanding LPA’s role in disease. Due to the vast number of potential lead compounds available, high throughput screening is a key instrument in rational drug design. These potential leads can be selectively screened further using a pharmacophore model. In our current study we have developed a pharmacophore model to identify potential LPA3 antagonists. This pharmacophore model has been used to mine databases for readily available compounds. These compounds can then be tested by in silico screening using rigid docking. Pharmacophores typically identify elements needed for activity rather than potency, using in silico screening we can optimize which compounds should further be tested experimentally. Several non-lipid antagonists with sub-micromolar potency have been identified.

Conference on Current Trends in Computational Chemistry 2005 59

Development of Array Files for Computational Chemistry

Alan Ford and Peter Pulay

Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701

In the current work, a simple message passing implementation of a shared disk system for Unix/Linux clusters termed Array Files (AF) is described. It greatly facilitates the parallelization of scientific programs that must handle large amounts of data and are consequently dependent on secondary (disk) storage. The version described in the present work is aimed specifically for computational chemistry problems, in particular to large-scale electron correlation calculations, although it should be useful also in other disciplines. It uses the PVM1 message-passing library. However, it would be straightforward to create versions for other message-passing libraries like MPI, and we have plans to do that. The application presented in the current work is the calculation of second order Møller-Plesset perturbation theory energies. Though MP2 energies are a relatively simple problem, they can be straightforwardly implemented in parallel using explicit message passing 2,3. Thus, the efficiency of the current implementation can be compared with hand-coded message passing implementations. More complex tasks, like Coupled Cluster (CC) energies and MP2 gradients, are very tedious to implement in parallel, and Array Files, or a similar tool, become almost indispensable. Parallel CC energies (at the singles and doubles level, CCSD) and a number of similar methods (QCISD, CISD, MP4(SDQ) etc.) have already been implemented using AF. They will be described in a forthcoming paper 4. Implementation of parallel MP2 gradients with AF is also currently underway.

1. Geist, A.; Beguelin, A.; Dongarra, J.; Jiang, W.; Manchek, R.; Sunderam, V. PVM: Parallel Virtual Machine. A Users’ Guide and Tutorial for Networked Parallel Computing; MIT Press: Cambridge, 1994. 2. Baker, J.; Pulay, P. J Comput Chem 2002, 23, 1150. 3. Ishimura, K.; Pulay, P.; Nagase, S. J Comput Chem, submitted. 4. Janowski, T.; Pulay, P., to be submitted. 60 Conference on Current Trends in Computational Chemistry 2005

Theoretical Conformational Studies of Parathion

Jason Ford-Green, D. Majumdar, Jerzy Leszczcynski

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

Theoretical conformational analyses have been carried out on a highly toxic pesticide parathion (O,O-diethyl O-(4-Nitrophenyl) phosphorothioate) at the density functional (DFT) and Moller-Plessett second order perturbation (MP2) level of theories. The pesticide activity of parathion and other organophosphorus pesticides has been found to be through the inhibition of the enzyme acetylcholinesterase (ACHE). The mechanism of the toxic action of these organophosphorus nerve agents has been interpreted as the blockage of hydrolysis of the neurotransmitter molecule, acetylcholine (ACH), through competetive binding with the active part of the cholinesterase enzyme. The organo- phosphorus pesticides have long-term toxic effects on various organisms via oral, inhalation, and dermal contact by causation of the build up of acetylcholine in the synaptic cleft. Since ACH adapts a specific conformation while binding with the active ACHE site, it could be imagined that parathion and similar organo-phosphorus pesticides would adapt similar conformation during the competetive binding process. The conformational studies of parathion is thus extremely important to understand its’ ACHE inhibition. Different conformers of parathion have been taken into account during the conformational analyses and the aqueous solvation of this molecule has been studied at the DFT level using the polarized continuum model with a conductor like reaction field (COSMO) approach. The results show that parathion has quite high conformational fexibility in both gas-phase and aqueous medium because of the low transition barriers. The electrostatic properties of the different conformers have studied through generation of molecular electrostatic potential surfaces and have been used to interpret its ACHE inhibition property.

Conference on Current Trends in Computational Chemistry 2005 61

Enthalpies of Formation for Thio Ethers by Isodesmic and Homodesmotic Reactions

Ryan Fortenberry and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

Recently, the study of thio ethers (or simply, sulfides) in polymer chemistry has been rekindled in the field of ultraviolet-curable resins. Different thiols are allowed to react with different alkenes to form thio ethers that serve as precursors to polymerization. Conjectural applications for these polymers include printing plates, coatings for electronics, and enhancing film. In an effort to judge the relative stability of these thio ethers, the current study focuses on the computation of their standard enthalpies of formation by isodesmic and homdesmotic reactions. Isodesmic reactions are reactions in which the number of each type of bond is conserved. Homodesmotic reactions not only conserve bond number and type, but bonding environments are also conserved. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and enthalpies 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. Basis sets of at least triple-zeta quality on valence electrons are employed. We gratefully acknowledge support from NSF EPSCoR (EPS- 0132618). 62 Conference on Current Trends in Computational Chemistry 2005

Relative Energies of 2-Pyrimidinethiol and 2-Pyrimidinethione and Their Dimers: Effect of Theoretical Levels

Fillmore Freeman1, Henry N. Po2

1Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025 2Department of Chemistry and Biochemistry, California State University, Long Beach, CA 9084

Density functional theory (BLYP, B3P86, B3LYP, B3PW91) with the 6-31+G(d,p), 6- 311+G(d,p), 6-311+G(3d,2p), and cc-pVTZ basis sets have been used to calculate structural parameters, relative energies, and vibrational spectra of 2-pyrimidinethiol (1) and 2(1H)- ‡ pyrimidinethione (2). Their hydrogen-bonded homodimers (C2 3, C2h [4] , C2h 5), heterodimer (6) and possible transition state structures involved in the tautomerization process have also been examined. At the B3PW91/6-311+G(d,p)//B3PW91/6-31+G(d,p) level 2-pyrimidinethiol (1) is 3.41 kcal/mol more stable (Erel) than 2(1H)-pyrimidinethione (2) in the gas phase and 2 is 6.47 kcal/mol more stable than 1 in aqueous medium. 2-Pyrimidinethiol---H2O and 2-pyrimidinethiol- --2H2O are predicted to be 1.27 and 3.54 kcal/mol, respectively, higher in energy than 2(1H)- pyrimidinethione---H2O and 2(1H)-pyrimidinethione---2H2O. The previously proposed strained planar four-membered intramolecular transition state (TS1) for the tautomerization of 1 and 2 lies 29.07 kcal/mol higher in energy than 2-pyrimidinethiol (1). Water promoted tautomerization via transition states involving one water molecule (TS---H2O) and two water molecules (TS--- 2H2O) lie 10.56 and 13.94 kcal/mol, respectively, higher in energy than 2-pyrimidinethiol---H2O and 2-pyrimidinethiol---2H2O. The 2-pyrimidinethiol C2 dimer (3) is 5.26 kcal/mol lower in ‡ energy than the dimeric C2 transition state structure ([C2 dimer] ) that connects dimers 3 and 4. ‡ The dimeric transition state [C2 dimer] provides a facile pathway for tautomerization between 1 and 2 (monomer-dimer promoted tautomerization). Conference on Current Trends in Computational Chemistry 2005 63

1.345 H S S 94.3 82.0 1.766 1.660 2.690 124.4 119.3 114.7 118.3 2.506 1.337 1.338 1.372 1.401 H 1.013 119.3 N 127.0 N N N 115.7 119.5 1.333 115.9 1.311124.3 1.350 122.7 1.335 125.0 122.6 119.1 116.0 115.7 1.089 H 1.090 H H 1.393 1.392 H 1.088 1.421 1.367 1.085

H H 1.084 1.082

1 2

S 1.703 1.718 H 1.335 1.320 1.375 N N 1.329 1.335

H 1.086 H 1.089 1.392 1.400

H 1.083

TS1

S 1.089 H 1.332 N 1.340 1.365 H

1.757 H 2.084 1.394 1.342 H 1.084 N 129.3 N 122.6 H 167.3 1.390 1.335 119.1 H

H 96.2 116.4 H N 1.089 S

τ = N1-C2-N1'-C2' = 16.6 °

τ = C2-S7-C2'-S7' = 16.9 °

3 64 Conference on Current Trends in Computational Chemistry 2005

Hydrogen Cyanide Covalent Dimers and Reactions of Aminocyanocarbene: A Computational Study

Fillmore Freeman and Mahshid Gomarooni

Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025

Hydrogen cyanide (HCN) and its covalent dimers, trimers, tetramers, pentamers, and polymers are of profound interest owing to their possible involvement in prebiotic chemistry on primitive Earth. An understanding of the chemistry of covalent HCN dimers and their isomers will provide insight into their modern chemistry as well as into the preferred pathways for prebiotic and extraterrestrial chemistry. Intramolecular and intermolecular insertion reactions, rearrangements, and 1,2-cyclo- addition reactions to alkenes of aminocyanocarbene (N≡C—C—NH2) have been studied using restricted and unrestricted CCD, CCSD, QCISD, B3LYP, and MP2 methods with the 6-31G(d), 6-311+G(d,p), 6-311+G(3d,2p), cc-pVDZ, and cc-pVTZ basis sets. Although HCCN has a triplet ground state, HCNH2, NCCNH2, NCCN(CH3)2, and NCCN(CF3)2 have singlet ground states. (Z)-C-cyanomethanimine is lower in energy than (E)-C-cyanomethanimine and N- cyanomethanimine (2). The transition state TS1 connecting the E and Z isomers is 29.54 kcal/mol higher in energy than the Z isomer. QCISD/cc-pVTZ predicts that (Z)-C- cyanomethanimine is 28.30 and 57.35 kcal/mol, respectively, more stable than singlet (S-3) and triplet (T-3) aminocyanocarbene and that the singlet form (S-3) is 29.05 kcal/mol lower in energy than the triplet form (T-3). The transition state structure TS2 for isomerization of singlet aminocyanocarbene (S-3) to C-cyanomethanimine lies 55.7 kcal/mol above singlet aminocyanocarbene. The transition state structure TS2 has the migrating hydrogen roughly symmetrically disposed between the carbon and nitrogen involved in the 1,2-shift. The singlet— triplet gaps (S—T, ∆EST) for substituted aminocyanocarbenes have been calculated as well as the philicity of aminocyanocarbene (S-3).

N N N 1.154 1.155 1.159 120.5° H ° ° 125.2 H 120.6 1.444 1.094 1.447 1.092 1.338 N N N 1.031 1.281 1.094 1.270 1.090 1.089 1.276 H H H H

(E)-1 (Z)-1 2

1.335 1.186 N 1.443 1.411 1.358

1.170 H N 1.014 140.2 123.1° N ° N H H 1.032 H S-3 T-3

Conference on Current Trends in Computational Chemistry 2005 65

Ab Initio Molecular Dynamics Study: Statistical Analysis of Structural Nonrigidity of DNA Bases

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

aComputational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217 bSTC “Institute for Single Crystals”, National Academy of Science of Ukraine., 60 Lenina Ave., Kharkiv, Ukraine 61001 cInstitute of Molecular Biology and Genetics, Dept. of Molecular Biophysics, National Academy of Sciences, 150 Zabolotnoho, Kiev, Ukraine 03143

The results of recent accurate ab initio quantum-chemical calculations suggest that isolated molecules of DNA bases are significantly softer than it was expected before. The formal indication of such a property is a presence of low frequency vibrations which correspond to out- of-plane pyrimidine ring deformation [1, 2]. In practice it results in easy deformation of that rings: transition of pyrimidine ring in uracil, thymine, cytosine, and guanine molecules from a planar equilibrium conformation to a non-planar one with a relevant torsion angle of ±20o entails an increase in energy of less than 1.5 kcal/mol. Taking into account that described above phenomenon will be modeled much more adequately at molecular dynamics level, we have performed a CPMD study of the of the gas phase nonrigidity of DNA bases. The Car–Parrinello molecular dynamics simulations were performed with the CPMD program using a plane-wave basis and hybrid BLYP functional. The wave function was expanded at the point in a plane-wave basis set with the kinetic energy cutoff of 70 Ry. The Kleinman and Bylander nonlocal pseudopotential was employed, and the core electrons were described by the pseudopotentials of Trouiller and Martins. To illustrate the obtained results, we present in Figure below the histogram of the puckering degree distribution using Zefirov-Palyulin-Dashevskaya puckering parameters [3] for thymine. Value of puckering degree less than 0.1 corresponds to a planar or almost planar ring.

The data presented on the histogram suggest the following: 66 Conference on Current Trends in Computational Chemistry 2005

1. The amount of plane structures does not exceed 12%. This is even less than we obtained in previous static ab initio calculations. 2. The distribution of the conformers looks as following:

TOTAL BOAT-LIKE CONFORMATIONS: 11.99% TOTAL TWIST-BOAT-LIKE CONFORMATIONS: 28.99% TOTAL CHAIR-LIKE CONFORMATIONS: 7.51% TOTAL HALF-CHAIR-LIKE CONFORMATIONS: 27.92% SOFA: 11.74% PLANARCONFORMATION 11.85%

This means that at the room temperature the thymine molecules oscillate mostly between twist-boat and half-chair-like conformations rather than being planar. Similar data have been obtained for other DNA bases and will be presented on the poster.

1. O. V. Shishkin, L. Gorb, J. Leszczynski, Chem. Phys. Lett.330 (2000) 603. 2. O.V.Shishkin, L. Gorb, P. Hobza, J. Leszczynski, Int. J. Quantum Chem. 80 (2000) 1116. 3. N. S. Zefirov, V. A. Palyulin, E. E. Dashevskaya, J.Phys.Org.Chem., 3 (1990) 147. Conference on Current Trends in Computational Chemistry 2005 67

Dynamics, Pathways, and Tunneling – A Computational Perspective of Enzyme Catalysis

Jiali Gao

Department of Chemistry, University of Minnesota, Minneapolis, MN 55455

A great challenge in molecular biology is to elucidate the enormous power of enzyme’s ability to catalyze chemical reactions. This requires a detailed analysis of factors that may contribute to the lowering of the free energy of activation. These include protein dynamics, transition state stabilization and reactant state destabilization, solvation and desolvation, and quantum mechanical tunneling among other factors. In enzyme kinetics modeling, there are three main ways in which quantum mechanics should be included. First, the electronic structure of the reactant system must be treated quantum mechanically. Second, the discrete nature of quantum mechanical vibrational energies should be incorporated in the description of nuclear motion for computing the potential of mean force. Finally, quantum mechanical tunneling should be considered, particularly for reactions involving hydrogen transfer. I will use the hydride transfer reaction catalyzed by dihydrofolate reductase as an example to illustrate the necessity of including these quantum mechanical treatments to determine the free energy of activation and the significance of dynamics, tunneling, and barrier lowering factors on catalysis. Furthermore, I will also present simulation results that help to understand the experimental observation of temperature-independence of kinetic isotope effects. In addition, I will discuss recent studies of the reaction mechanism of cysteine proteases, in particular, the SARS main protease. Our computational study provides insight into substrate-enzyme binding and interactions that can be useful in drug design 68 Conference on Current Trends in Computational Chemistry 2005

A Theoretical Study on the Reactivity and Regioselectivity of Cycloadditions of Phospholes

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

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

Cycloaddition reactions of phospholes have been employed to access novel polycyclic organophosphorous compounds. Many of the phosphorous containing cycloadducts have promising applications in the fields of homogeneous catalysis and molecular materials. The cyclcoaddition reactions of phospholes have been our recent theoretical interests.1-5 The objective of the current study is to assess the competitive Diels-Alder reactions between phospholes and butadiene. Elaborate computational studies were carried out at CCSD(T) and B3LYP levels to delineate the reaction paths depicted in Scheme 1. Products Path 2A 5-mem. ring trans-BD BD as diene Products as dienophile Path 1 cis-BD BD as dienophile Path 2B Products 5-mem. ring: P P P H Scheme 1 A total of 42 [4+2] cycloaddition possibilities for the reactions, that were divided into two categories path 1 and path 2 (A and B) depending on whether butadiene acts as diene or dienophile respectively, were considered. Activation barriers show that cyclopentadiene prefers to be a diene rather than a dienophile, indicating the formation of products via path 2. Pathways 1 and 2 (A and B) corresponding to the butadiene as the diene and dienophile are predicted to be highly competitive in the case of 1H- phosphole. The reactions require lower activation energy when the conversion of weak C=P to C–P occurs in the case of 2H- and 3H-phospholes. The transition state geometries reveal that many of the transition states are highly asynchronous, although the reactions are concerted. In all the systems, the reaction pathway 1, wherein butadiene acts as diene and cyclic five membered rings act as dienophile, is thermodynamically controlled. Although the diene and dienophile are clearly distinguishable in most reactions, some transition states are bispericyclic. The bispericyclic transition state structures can occur in the reactions where the reactants act as both diene and dienophile. In the reactions of BD as the diene, endo transition states are more stable compared to the corresponding exo. There is only negligible energy difference between the endo and exo transition states in the case of path 2 where BD acts as a dienophile. Secondary orbital interactions and also the preferable bispericyclic nature of the transition states are responsible for the stability of these endo Conference on Current Trends in Computational Chemistry 2005 69

transition states. IRC calculations were done on all the transition states. The IRC calculations indicate that all the transition states are true except the three transition states that are bispericyclic in nature, where one of the forming C…C bonds is almost formed, have not connected to the reactants. The high stability of the products resulting via path 1 can be attributed to the less strain in the bicyclo[4.3.0]nonadiene skeleton compared to the norbornene derivatives obtained from path 2. In the case of reactions of BD acts as dienophile, Cp, 2P and 3P show more stability of endo products than those of exo while 1P indicates the stability of exo products. Except for the bispericyclic transition states, butadiene prefers to be in trans conformation rather than cis conformation. Activation and reaction energy values for these Diels-Alder reaction pathways are compared with the values reported for the [4+2] cyclodimerizations of each of the reactants to examine the likelihood of cyclodimerizations along these pathways.2 FMO and conceptual DFT descriptors were used to correlate computational results. Our systematic computational studies account for several interesting observations made in Mathey’s group.6 We feel that the present study helps in devising feasible synthetic pathways to access novel polycyclic phosphorous containing compounds.

References: 1. Dinadayalane, T. C.; Gayatri, G.; Sastry, G. N.; Leszczynski, J. J. Phys. Chem. A, 2005, 109, 0000. 2. Dinadayalane, T. C.; Sastry, G. N. Organometallics 2003, 22, 5526. 3. Geetha, K.; Dinadayalane, T. C.; Sastry, G. N. J. Phys. Org. Chem. 2003, 16, 298. 4. Dinadayalane, T. C.; Geetha, K.; Sastry, G. N. J. Phys. Chem. A 2003, 107, 5479. 5. Geetha, K.; Sastry, G. N. Indian J. Chem. 2003, 42A, 11. 6. Mathey, F. Acc. Chem. Res. 2004, 37, 954.

70 Conference on Current Trends in Computational Chemistry 2005

Computational Study of Structure-Activity Relationships for β-Lactam Antibiotics against PBP5

Xiaoxia Ge,a John Buynakb

aWeill Graduate School of Medical Science, Cornell University, New York, NY bDepartment of Chemistry, Southern Methodist University, Dallas, TX

Bacterial Penicillin Binding proteins (PBPs) are members of the penicilloyl serine transferase family of enzymes [1]. PBPs catalyze the essential reactions in the biosynthesis of cell wall peptidoglycan from glycopeptides precursors [2]. β-lactam antibiotics inactivate PBPs and interfere with the process of transpeptidation by forming an ester bond between the active site serine and the carbonyl carbon of β-lactam. Based on PBP5 wild type and drug-resistant mutant structures, computational study was carried out to understand the kinetics of this interaction. Structure-activity relationships study shows that the rate of formation of the acyl- enzyme is an essential factor determining the efficacy of a β-lactam, and suggests that the specific side chain interactions of β-lactams could be modified to improve inactivation of resistant PBPs.

The binding modes and affinities of various β-lactams were predicted by multiple computational modeling approaches. The results are fully in agreement with the experimental data (Table 1)

Table 1. β-lactams inhibitions to PBP5 Inhibitors IC50 / μM Ki / μM T-core / kJ·mol-1 C-score Azlocillin 25 7+0.3 -26.6 4 Pipercillin 80 36+3 -23.6 4 Ampicillin 125 51+10 -19.4 4

The inhibitor structures were built and minimized energetically with program Sybyl. FlexX [7] was used for flexible inhibitors docking to the wild type protein structure (1NZO in PDB). Relative binding affinities of different inhibitors were inferred by their binding free energy and consensus scores (C-score) [3]. GOLD [4] was chosen to study ligand-binding mode in the flexible protein active site.

Hydroxamide inhibitors were designed based on the binding site structure, showing higher theoretical binding affinity (Figure 1). More important interactions form between ligand and protein in these cases.

Conference on Current Trends in Computational Chemistry 2005 71

Figure1 Hydroxamide Inhibitors Improved Binding Affinity

Chart

0 -5

-10 T-Score -15 (k J/mol) -20 Amides Hydroxamide -25 -30 -35 Az Pi Am

Inhibitor

Reference: [1] Ghuysen, J. M. TrendsMicrobiol, 1994, 2:372-380. [2] Hujer, A. M. Ge, X. et al. Antimicrobial Agents and Chemotherapy, 2005, 49 (2): 612-618. [3] Clark, R. D. et al. J. Mol. Graphics and Modelling, 2002, 20: 281-295. [4] Jones, G. et al. J. Mol. Biol., 1997, 267: 727-748. 72 Conference on Current Trends in Computational Chemistry 2005

Quantum Monte Carlo Results for the Ionization Potentials, Electron and Proton Affinities of the 3d-Block Transition Metals

Ainsley A. Gibson, Floyd A. Fayton, Gordon J. P. Taylor, Jose Gonzalez and John A. W. Harkless

Department of Chemistry, Howard University, Washington DC 20059

The difficulty in determining the electronic structure properties of transition metal systems is well known. This study presents ionization potentials, electron affinities and proton affinities of the 3d-block transition metals. These benchmark quantities will be used to determine the suitability of methods for further elucidation of the electronic structure of the 3d-block transition metals. The methods used include Hartree-Fock(HF), post Hartree-Fock[CISD, CCSD(T), CASSCF, MP2], Density Functional Theory[B3LYP], Variational Monte Carlo(VMC) and Diffusion Monte Carlo(DMC) with the AhlrichsTZV basis set. Emphasis is placed on the performance the quantum Monte Carlo methods and the ability to obtain results within a statistical error of 0.05 eV when compared with experimental data. Conference on Current Trends in Computational Chemistry 2005 73

Conformational Studies of di-tert-Butylcyclohexanes

Gurvinder Gill, Diwakar M. Pawar, and Eric A Noe

Department of Chemistry, Jackson State University, Jackson, MS, 39217 - 0510.

Conformational space was searched for 1,1-di-tert-butylcyclohexane (1), trans-1,2-di-tert- butylcyclohexane (2), and trans-1,3-di-tert-butylcyclohexane (3) with Allinger's molecular mechanics programs (MM3 and MM4), and free energies were obtained at various temperatures. Calculations were repeated for low - energy conformations with ab initio methods at the HF/6- 31G* and HF/6-311+G* levels. Ab initio calculations for 1 and 3 predict that twist - boat conformation is lower in free energy than the equatorial, axial chair conformation, and the diaxial chair form is found to be more stable for 2. Molecular mechanics calculations are in qualitative agreement with ab initio calculations except for 1, the chair conformation of which is predicted to be more stable by MM3 and MM4 free energies. Structural parameters, symmetries, relative strain energies, relative free energies, and calculated (GIAO) chemical shifts for compounds 1 - 3 will be presented. Literature studies for compounds 2 and 3 will be summarized. Experimental work is in progress.

This work was supported by NSF - CREST Grant No. HRD-9805465.

74 Conference on Current Trends in Computational Chemistry 2005

Conformational Study of Propynoic Anhydride by Computational Methods

Gurvinder Gill and Eric A. Noe

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

The conformations of propynoic anhydride have been studied at the HF and MP2 levels with the Gaussian 03 program. The optimized geometries, relative free energies, dipole moments and the free-energy barriers were obtained for the ZZ, EZ and EE conformations and their corresponding transition states at various levels of theory. At the MP2/6-31G* level, the EZ conformation is higher in free energy relative to the most stable ( ZZ ) conformation by 0.72 kcal/mol and EE is 3.95 kcal/mol higher in relative free energy. All three conformations are nonplanar. The free-energy barriers leading to topomerization of the EZ conformation were 2.2 and 5.4 kcal/mol, depending on the pathway. The dipole moments of the ZZ, EZ and EE conformations were 4.92, 4.15, and 5.65 D, respectively.

This work was supported by NSF - CREST Grant No. HRD-9805465.

Conference on Current Trends in Computational Chemistry 2005 75

A Computer Study of Point Defects in the RDX Crystal

Matthew Gravelle and Sylke Boyd

University of Minnesota-Morris

Defects in a crystalline energetic compound are incorporated during the crystal growth from solution [1]. It has been shown that they are crucial in the early stages of detonation [1-4]. Their energetically exposed position changes the local electronic structure, thus facilitating the initial bond breaking process. The initial energy release then propagates the reaction to the surrounding lattice. While extended defects such as dislocations may play a role [4], vacancies and vacancy clusters have been identified as possible candidates since they allow for significant motion during the passing of a compression wave. Therefore, the properties and incorporation mechanisms of these defects are interesting with regard to our ability to control their presence. Model: We are presenting results concerning vacancies, vacancy pairs and orientational defects within the crystal lattice with respect to their energetic, geometric, and diffusion properties, respectively. Based on a recently developed computer model of RDX [5], a 216- molecule periodic model serves as the matrix for these defects. The crystal symmetry is Pbca, which corresponds to an orthorhombic cell containing 8 molecules. The model therefore includes 3×3×3 elementary cells. The molecular dynamics (MD) simulations use an Andersen/Berendsen thermo- and barostat allowing response of the box dimensions to the required pressure settings. All of our MD simulations have been performed at a pressure of 1 atm. Typical time steps lie between 0.5 and 0.8 fs, while typical MD sampling runs have durations between 0.5 and 2.0 ns. Geometry optimizations are performed using a simulated annealing technique in order to adjust the box dimensions for the ground state geometry, followed by a conjugate gradient process at constant box dimensions. The intramolecular forces are modeled using a force field reminiscent of a traditional molecular mechanics force field. The intermolecular forces are separated into Van der Waals and electrostatic interactions. The potential parameters for both parts have recently been refined or newly fitted in order to stabilize the α modification of the RDX crystal. The force field yields very good agreement for the ground state crystal symmetry with 0-K lattice parameters of 12.901 Å, 11.167 Å, and 10.705 Å, which is within less than 4% of the experimental values. The binding energy of 27.2 kcal/mol is very close to the sublimation energy of RDX of 31.1 kcal/mol; the model gives a bulk modulus of 18.0 GPa. In molecular dynamics simulations performed at constant pressure and temperature, the correct crystal symmetry is stable without constraints, and the expansion coefficient is in excellent agreement with experiment. The model disintegrates at a temperature of 650 K. Vacancy: The formation energy of the isolated vacancy has been determined to be 51.2 kcal/mol in our force field. This is in very good accord with other theoretical results [kukl99]. The relaxation of the lattice surrounding the vacancy is minimal and consists mainly of an adjustment of the nitro groups. Constant-temperature MD yields interesting observations about the thermal stability of the vacancy’s position. The simulations were continued for up to 5 ns. In cumulative projections of the vacancy's center in the three principal directions we can observe a temperature-related broadening of the location. The overall size of the vacancy increases with temperature from a radius of 5.6 Å at 300 K to 5.8 Å at 600 K.. The intermolecular forces are mainly of electrostatic and Van der Waals type. Diffusion is limited mainly by the bulk size of the molecules and geometric constraints. At temperatures close to the 76 Conference on Current Trends in Computational Chemistry 2005

disintegration temperature of the model we observe a number of diffusion steps or attempted diffusion steps, possible mechanisms for which will be presented. Divacancy: The diffusion of vacancies can lead to the formation of vacancy clusters, the simplest of which would be a divacancy. In order to study the influence of a vacancy in close vicinity to another vacancy we modeled systems in which deliberately two molecules have been removed. Two vacancies can be arranged in a variety of ways. We chose to vary the separation distance, selecting molecules from neighbor shells with increasing distance from the first vacancy. Eighteen vacancy pairs with separations between 4.1 Å and 14.5 Å have been created and subjected to an energy minimization. The binding energy of the two vacancies can then be derived as the energy difference between the formation energy of two isolated vacancies and the formation energy observed for a divacancy of a distinct separation distance. Such a binding energy arises from a combination of the lattice distortions around both of the vacancies. We observe the binding energy to be -21 kcal/mol for a distance of 4.5 Å between the centers of the vacancies, and the quickly converge toward zero for distances around 14 Å. We also attempted long constant-temperature and constant-pressure MD simulations in order to observe possible clustering behavior of the divacancy. Results on the dependence of the formation energy on separation, and on the diffusion behavior will be presented. Orientational defects refer to misoriented or non-conforming molecules, hence breaking the local symmetry. In order to identify stable defects in this category, an ideal crystal is modified by rotating a single molecule in the order x, y and z axis, in increments of 45º. This results in 64 different initial structures which subsequently have been geometry optimized to the nearest minimum in potential energy. While most of the perturbed molecules simply flipped back into the ideal crystal position, we found four situations in which the system found a metastable position. The formation energies of the four orientational defects are between 36 and 60 kcal/mol. All these defects are characterized by misorientations of the average plane of the ring structure, and a change in conformation. The conformational change affects changes in the axial and equatorial positioning of the nitro groups, as well as the change from chair to twist conformation of the ring. The defects have been studied with respect to their stability under thermal conditions, based on constant-temperature molecular dynamics simulations. Since we are interested in identifying these types of defects in long MD simulations, we had to seek a criterion to distinguish such perturbed molecules and identify their type. This criterion would not sufficiently be defined by the orientation of the molecule, since the orientations of “ideal” molecules will exhibit a distribution of increasing width with higher temperature. The defect ID of a molecule is defined upon three things: (i) the orientation of the normal ring axis; (ii) the angle of the nitro side groups with respect to the ring normal axis; and (iii) the effective ring volume, signifying chair or twist conformation. We follow the time-development of these three characteristics as well as their combination (the defect ID) over the run of long (>2 ns) constant- temperature MD runs. This provides us with information about the diffusion and healing behavior of this type of defects. This investigation is not quite concluded at time of abstract submission; however the results are expected to be available at the time of the conference. Preliminary results indicate that defects arising from perturbed conformation or orientation tend to heal fast when the model temperature is raised above 400 K. In summary, a computer model of RDX has been used to identify a variety of point defects such as vacancies, divacancies and orientational defects. The formation energy, geometric properties and diffusion behavior have been studied. We have found evidence for vacancy diffusion in our MD simulations, and will present results on observed diffusion mechanisms. The divacancy has been investigated in terms of eighteen different possible arrangements of the two vacancies. The binding energy of the two vacancies in dependence on their distance is found to rapidly change from -21 kcal/mol at 4.5 Å to zero at 14 Å. Several metastable orientational defects have been identified, with formation energies between 36 kcal/mol and 60 kcal/mol. The Conference on Current Trends in Computational Chemistry 2005 77

orientational defects show rapid healing for temperatures above 400 K. We hope to gain insight into the incorporation mechanisms and stability in relation to thermodynamic conditions. The results of this study will be used in Monte Carlo growth simulations of the RDX crystal.

References: [1]. Van der Heijden, A. E. D. M.; Bouma, R. H. B. Crystal Growth & Design 2004, 4, 999. [2] Ershov, A. P.; Satonkina, N. P.; Ivanov, G. M. Tech. Phys. Lett. 2004, 30, 63. [3] Kuklja, M. M. ACS Conf. Proc., Shock Compression of Cond. Matt., ed. M. D. Furnish, N. N. Thadhami, Y. Horie, 2001, 620, 454. [4] Kuklja, M. M. Appl. Phys. Lett. A 2003, 76, 359. [5] S. Boyd, M. Gravelle, and P. Politzer, in preparation for JPC; please contact the authors for a copy

78 Conference on Current Trends in Computational Chemistry 2005

A Possible Nature of Hot and Cold Spots of UV-Mutagenesis

H. A. Grebneva

Donetsk Physics and Technology Institute of the NAS of Ukraine 83114 Donetsk, Ukraine

The irradiation of DNA molecule with ultraviolet light promotes the formation of cyclobutane pyrimidine dimers and (6-4) adducts. In replication or reparation processes they can result in mutations. The UV light – induced mutations are non-uniformly distributed in DNA molecule. Mostly they are concentrated in the so-called hot spots. At some sites they are never met – these are cold spots of mutagenesis [1, 2]. Thymine dimers are most frequently formed, nevertheless the cytosine dimers result in mutations more often as compared to the thymine ones. The hot spots coincide, as a rule, with the CT dimers. It is shown that cytosine substitution by thymine at the hot spot of CT transforms the same into the cold one. Moreover, a single substitution of the base not coinciding with the hot spot can transform it into the cold one and vice versa [1]. The generally accepted theory of the UV-mutagenesis rests upon the hypothesis that mutations are exceptionally due to accidental errors of DNA polymerases, while there is no difference in dimers resulting in mutations and nonmutational dimers. At present, the nature of hot and cold spots of mutagenesis are explained within this paradigm. That is, it is assumed that sites of a specific nucleotide composition are repaired better (or worse) than others, and so on. It is, however, well known that the phenomenon has not been yet explained satisfactorily [2]. It has been shown that upon dimerization there may be changes in the tautomeric state of constituent bases. The mutagenous are dimers in which the tautomeric state of constituent bases has changed [3]. Such dimers may give transitions or transversions under SOS-replication and post-replication SOS-reparation [4]. A mechanism of changes in the tautomeric state of bases in double-stranded DNA has been developed [3]. Let us try to explain some peculiarities in the formation of hot and cold spots of mutagenesis by using our model. First of all we see what happens when the DNA molecule absorbs the UV- quantum of energy which is as a rule localized on one of the bases. This energy may remain at that base or pass to neighbor bases as an exciton or by energy transfer in parts [5]. To study the fate of the UV-quantum, the relationship between energies of singlet and triplet energy levels for different DNA bases should be known. They are illustrated in Fig. 1 [6]. The singlet (resolved energy level has the lifetime of the order of 10-12 s). There the most probable process is energy radiation. It is clear that no changes in DNA structure will occur in that case. The lifetime of triplet (forbidden) energy level is of about 10-6 s. For this level, the transformation of the UV-quantum energy into the energy of neighbor atom oscillation is the most probable process [7]. There the strong forced oscillations are the first stage of pyrimidine formation and changes in the tautomeric state of constituent pyrimidine dimers [3]. Thermal deexcitation from the triplet energy level is the main reason of DNA damages induced by UV- light. Now we try to answer some questions resting on the above data.

1. Why are thymine dimers most frequently formed?.

It is seen (Fig. 1) that among the whole of bases the thymine triplet energy level is the lowest in contrast to cytosine with the highest triplet energy level. Thus, the energy will more frequently sink and localize at thymine than at cytosine. Moreover, as shown, in the process of Conference on Current Trends in Computational Chemistry 2005 79

formation of premutagenous changes in DNA structure there is the stage of semiopen metastable states [3]. For the A-T pair the probability formation of such states is much more higher than for the G-C pair [8]. Because of the two reasons the formation of thymine dimers is of a higher probability as compared to cytosine or thymine – cytosine dimers.

2. Why do cytosine dimers result in mutations more frequently than thymine dimers? Capacity to changing the tautomeric state was shown to be the main cause of premutagenous changes in DNA [3]. It is known that in G-C pairs the tautomeric state changes more easily than in A-T pairs [9]. This is evidently due to the properties of hydrogen bonds between paired bases and, in particular, the shape potential energy surface for hydrogen bonds. In addition, the analysis of different premutagenous tautomeric states for A-T and G-C pairs shows that in G-C pairs the percentage of possible new tautomeric states that results in base substitution mutations is higher. Wave numbers , nm

S 1 T 1 36 A G, T C 30 C G A T

26 the ground state S 0 Fig. 1. Energy band diagram for different DNA bases [6]. S1 – the lowest singlet level, T1 – the lowest triplet level.

3. Why are TC dimers most frequently happen to be hot spots ? Apparently, among the stages of dimer formation is the formation of eximer when the energy absorbed by a base becomes a property common of the two. Each of the bases contributes to mutagenesis. Thymine provides capture of the UV-quantum energy, cytosine – changes in the tautomeric state and, as a consequence, the formation of premutagenous changes. It is known that in T-C dimer the base substitution mutations are, as a rule, formed opposite cytosine [1]. Now consider a DNA site with hot and cold spots of UV-mutagenesis.

4. Why dimer C150T151 in supF [1] is a cold spot of mutagenesis ? Consider a coding strand of the DNA encoding the suppressor tyrosyl tRNA, supF [1]. There is a strong hot spot – dimer C156T157 which has generated 11% mutations on the spot DNA site studied (№№ 100-180) and has induced 14 transitions of the G-C→A-T type. At the same time, similar dimer C150T151 has given no mutation. This site was called a cold spot of UV- mutagenesis [1]. As the premutagenous changes in DNA structure occur during a thermal deexcitation of the UV-quantum from the triplet energy level of one of the bases, we consider the energy levels of that base together with the neighbor ones. The absorbed energy quantum is always at the singlet level. Radiation of UV-quantum energy is the process most probable for the singlet level. However, to a probability other than zero the energy can pass to the triplet level, thus showing the difference in the energy (forbidden transition). This is the basic mechanism of triplet level population [7]. In addition, a partial energy transfer to a neighbor base of a lower energy level is possible. In the absence of data for comparing the probabilities of those processes we will, in a first approximation, assume that passage from the singlet level to the triplet one is a partial 80 Conference on Current Trends in Computational Chemistry 2005

energy transfer from the singlet level to the singlet one or from the triplet level to the triplet one are of approximately the same probability. We try to estimate roughly a probability to which the UV-quantum energy can sink from neighbor bases to triplet levels of C150 and T151 forming the dimer, which on DNA site of Fig. 2 is a cold UV-mutagenesis spot. Let W(CT150) be a probability of thermal deexcitation of the energy UV-quantum from the triplet level of cytosine C150. Imagine that cytosine C150 absorbed the UV-quantum and, as a result, localized at the singlet level. Moreover, we assume that the energy has passed to the

E

pSP189 SupF

A S

G S , TS

C S

C T

G T

A T

T T Coding strand 145 150 155 160 165 170 № bases Bases C AAGGTTG C AA GGGC TTTTC C A AACC

Fig. 2. DNA site of the supF marker gene [1]. Bases and their numbers are plotted on the abscissa, on the ordinate – their triplet and singlet energy levels.

triplet level. It can deexcitatize and result in oscillations of atoms on C150 or can sink portion-wise to G149 or T151. Since we assume those processes to be of equal probability, it is believed that on C150 the energy is of weight 1/3. We further assume that the UV-quantum has absorbed guanine G149. The energy can pass from singlet level to the triplet one or sink to C150. It follows that ½ of GS149 energy on the average will sink to CS150 and 1/6GS149 will be added to 1/3CS150, then W(CT150) = 1/3(CS150 + 1/2GS149). We write GS149 for singlet – level energy of the energy of guanine in position 149, and so on. Let the UV-quantum be localized at the singlet level of adenine A148. It can pass to the triplet level or sink to T147 or A148. Then W(CT150) = 1/3(GS150 + 1/2(GS149 + 1/3AS148)). As seen in Fig. 2, no portion of energy can sink from T147 to C150. After similar considerations we have W(CT150) = 1/3(CS150 + ½(GS149 + 1/3AS148) + 1/3(TS151 + ½(GS152 + 1/3(AS153 + 1/3AS154)))) = 1/3CS150 +1/6GS149 + 1/18AS148 + 1/9TS151 + 1/18GS152 + 1/54AS153 + 1/112AS154. Considering in the first approximation that all the energies are equal to E, we have W(CT150) = 0.750. For the case of thymine T151 we have W(TT151) = 1/3(TS151 + ½(GS152 + 1/3(AS153 + 1/3AS154)) + 1/3(CT150 + ½(GS149 +1/2AS148))) = 1/3TS151 + 1/6GS152 + 1/18AS153 + 1/54AS154 + 1/9CT150 1/18GS149 + 1/36AS148. Assuming the energies to be equal, we have W(TT151) = 0.769. At dimer C150T151 the total energy is W(C150T151) = 1.519. Conference on Current Trends in Computational Chemistry 2005 81

To estimate the resulting values it is necessary to compare them with those obtained by the same procedure for the hot spot of exactly the same dimer CT. Consider now dimer C156T157 which at the DNA site coding a supF is the strong hot spot of the UV-mutagenesis.

5. Why is dimer C156T157 a hot spot of the UV-mutagenesis at DNA site encoding supF? Let us try to understand why could dimer C156T157 result in the formation of 14 transitions. How it differs from nonmutagenous dimer C150T151? Having considered all variants for the triplet level of cytosine CT156, we have W(CT156) = 1/3CT156 + 1/6GS155 + 1/18AS154 + 1/54AS153 + 1/3TS157 + 1/9TS158. In the first approximation, taking the energies to be equal to E, we obtain W(CT156) = 1.019 In the same way, after examining the triplet level of the thymine TT158, we have W(TT157) = 1/3TS157 + 1/3TS158 + 1/3CT156 + 1/6GS155 + 1/18AS154 + 1/54AS153 + 1/8GS159 + 1/16CS160 + 1/54AS161 + 1/162AS161 + 1/24CS160 + 1/72AS161 + 1/216AS162. Assuaging that all the energies are equal to E we have W(TT157) = 1.758. With the total energy at the dimer C156T157 W(C156T157) = 2.777. It is thus seen that there is energy from seven and thirteen bases sunken to thymines T151 and T157, respectively, and there is much more sunken energy at thymine T157 than at T161. We see that though the cold and hot spots are dimers CT, much more energy can be sunken to dimer C156T157, especially to thymine T157. and since the rest above – described properties are identical the latter fact explains the “neighbor effect”, i. e. the influence of neighboring bases on mutation probability of the base. Of course, this is a very rough estimate. It is aimed at determining reasons of the formation of UV-mutagenesis hot and cold spots. This important and interesting phenomenon needs a detailed experimental and theoretical study.

The study was supported by the Ukrainian State Fund for Fundamental Research (Grant No Ф7-208/2004).

1. C. N. Parris, D. D. Levy, J. Jessee, M. Seidman, J. Mol. Biol. 236 (1994) 491-502. 2. K. A. Canella, M. M. Seidman, Mutation Research 450 (2000) 61-73. 3. H. A. Grebneva, J. Mol. Struct. 645 (2003) 133. 4. H. A. Grebneva, Biopolym. Cell 17 (2001) 487-500. (Ukraine). 5. N. L. Vekshin, Results of Science and Technology, Radiation Chemistry, Photochemistry, vol. 7, VINITI,, Moskow, 1089. Russ. ed., 164p. 6. A. A. Lamola, T. Gamane, Proc. Natl. Acad. Sci. USA 58 (1967) 443-446. 7. J. A. Barltrop, J. D. Coyle, Excited States in Organic Chemistry, Wiley, New York, 1978, p. 446. 8. M. D. Frank-Kamenetskii, Mol. Biol. 29 (1983) 639. 9. M. J. Novak, L. Lapinski, J. S. Kwiatkowski, J. Leszczynski, in: J. Leszczynski Ed., Current Trend in Computational Chemistry, vol. 2, Wold Scientific Publishing Co. Pte. Ltd, River Edge, NJ, 1997, 140 p. 82 Conference on Current Trends in Computational Chemistry 2005

Derivation of a QSAR Model for Anandamide Based on Quantum Molecular Descriptors

Ming-Ju Huang

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

Arachidonylethanolamide (named anandamide on the basis of the Sanskrit word “ananda”, meaning “bliss”), the first putative endogenous ligand for cannabinoid receptors, was originally discovered in porcine brain. Anandamide is comprised of arachidonyl and ethanolamide moieties. The structure of anandamide differs drastically from the tricyclic structure of Δ9- tetrahydrocannabinol (Δ9-THC) and other naturally occuring cannabinoids present in marijuana plants. Unlike the long-acting classical cannabinoids, anandamide has a much shorter duration of action due to its rapid metabolism by fatty acid and amide hydrolase. A quantitative structure-activity relationship (QSAR) model for the binding activity of anandamide analogs (anandamide and a series of anandamide analogs with modification of either ethanolamide or arachidonyl moieties) at the CB1 receptor was developed by correlating activity with the physical-chemical properties. The physico-chemical properties of each of the anadamide analogs consisted of the computed molecular electronic descriptors, hydrophobic/hydrophilic descriptors, and geometric descriptors from the quantum mechanical ab initio Hartree-Fock 6-31G** optimized structure. Systematic regression analysis using a self- written computer program has been performed.

11

9 10 OH O 7 8 5 1 1' 1 2' OH N O 3 20 1' 5' 11 14

Δ9-T H C Arachidonylethanolamide (anandamide) Conference on Current Trends in Computational Chemistry 2005 83

Can Gibbs Free Energy for Intermolecular Complexes be Predicted Accurately at the MP2 and the DFT Levels of Theory?

Olexandr Isayev1, Al’ona Furmanchuk1, Leonid Gorb1,2 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217 2Institute of Molecular Biology and Genetics, Department of Molecular Biophysics, National Academy of Sciences, 150 Zabolotnoho, Kiev, Ukraine 03143

The study has been performed to refine the procedure for calculation of Gibbs free energy with relative accuracy less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and DFT (BLYP, B3LYP) theories augmented by Dannenberg’s correlation-consisted basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed and results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anaharmonicity to the ZPE and TΔSint values is fairly small. The new, quite economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. Proposed model has been verified on extended set of 15 intermolecular complexes. In addition, interaction energy (De) and free energy change ( A) for considered species evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and conventional BLYP- plane waves calculations. The free energy change along the reaction paths were determined by the thermodynamic integration / “Blue Moon Ensemble” technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. The results show that CPMD technique is capable reproduce interaction and free energy with accuracy 1 kcal/mol and 2-3 kcal/mol respectively.

84 Conference on Current Trends in Computational Chemistry 2005

Parallel Calculation of Coupled Cluster Energies on Distributed Memory Workstations

Tomasz Janowski and Peter Pulay

Department of Chemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA

We have recently implemented the parallel calculation of coupled cluster singles and doubles (CCSD) energies for a closed-shell reference in the PQS suite of programs. Energies and wavefunctions can also be calculated using related methods: Singles and Doubles CI (CISD), Quadratic CI (QCISD), the Coupled Electron Pair Approximation (CEPA-0 and CEPA-2), and perturbative methods (MP4-SDQ, MP3). Our target hardware is small and moderate size PC and workstation clusters. Our implementation is based on the efficient matrix formulation of the singles and doubles correlation problem, the Self-Consistent Electron Pair theory1. We use the Generator State spin adaptation2. This reduces the flop count by a factor of 2 for the pair coupling terms compared to orthogonal spin adaptation, and significantly simplifies the formulas. For instance, the CCD residuum formula is only a few lines long. The matrix formulation is ideal for modern workstations and PCs because they can perform matrix multiplications much faster than other related operations, e.g. long dot products (DDOT), and vector linear combinations (DAXPY). E.g., the Intel Nocona processor runs for a 1000×1000 matrix multiplication at 5128 Mflops/s while its performance for a 1,000,000 long dot product is only 465 Mflops/s and for a DAXPY 307 Mflops/s, over 15 times slower. It is important to reformulate all operation to run as matrix multiplications. For instance, the contribution of four virtual orbitals is one of the most computationally demanding parts of the calculation. To avoid the need for a full integral transformation, we carry out this part in atomic orbital (AO) basis, as ij ij K(T )pr=∑qs (pq|rs)(T )qs where p,q,r,s are AOs. In the simplest formulation, this is a dot product but by treating together a modest number of pr and ij indices, we can achieve near-limiting performance. E.g. the best BLAS library routine performs a 40×500000×40 matrix multiplication at ~3300 Mflops/s, about 2/3rd of the peak performance. We have parallelized the code using Array Files3, a middleware allowing transparent access to distributed disk storage on clusters. Currently, both Array Files and other parts of the program use PVM as the basic message-passing software. Parallel scaling is satisfactory, for instance the speed-up from 2 to 10 processors is 4.00 . Both canonical and localized occupied orbitals can be used. While canonical orbitals show slightly better convergence, localized orbitals allow the treatment of weak pairs at a reduced level (MP2), leading to potentially large savings for larger molecules, without restricting the correlation basis to local domains4 as in local correlation theory. The performance of the program will be demonstrated on several examples, mostly at the QCISD level, including The binding energy of the adenine-thymine base pair, using a triple-zeta, 2df basis The binding energy of the benzene dimer, using cc-pVDZ, TZ and QZ basis sets Nitroglycerine using the 6-31G* and 6-311G** and the cc-pVDZ/TZ basis sets. With the capability of performing large basis QCISD/CCSD calculations on relatively large systems (e.g. the benzene dimer, nitroglycerine), we can evaluate the accuracy of schemes that extrapolate high-level (CCSD) energies from small to large basis sets based on MP2 energies. Conference on Current Trends in Computational Chemistry 2005 85

These schemes assume the additivity of higher order correlation and basis set contributions, according to E(CC,large basis) ≈ E(CC,small basis) + E(MP2, large basis) – E(MP2,small basis) Our preliminary results show that the additivity assumption generally overestimates the absolute value of the correlation energy. Current work is aimed at improving the efficiency of the method by using sparsity and localization, including symmetry, and adding triple substitutions.

W. Meyer, J. Chem. Phys. 1976, 64, 2901. P. Pulay, S. Saebo and W. Meyer, J. Chem. Phys. 1984, 81, 1901. A. R. Ford and P. Pulay, to be published. S. Saebo and P. Pulay, J. Chem. Phys. 1987, 86, 914. 86 Conference on Current Trends in Computational Chemistry 2005

Computational Study of Carbon Atom (3P and 1D) Reaction 1 with CH2O: Theoretical Evidence of B1 Methylene Production by C (1D) Atom

Hyun Joo, Philip B. Shevlin and Michael L. McKee

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849

The reaction of singlet (1D) and triplet (3P) C atom with formaldehyde was studied by using PBE1PBE, CASSCF, and MCQDPT2 methods with moderate size basis sets. The most favorable reaction path is C atom addition to the C-O double bond for reactions on both singlet and triplet surfaces. On the triplet potential energy surface, the lowest energy isomer is a 3A” 3 bent ketene and the free energy of dissociation of lowest triplet compound to CO + CH2 ( B1) is calculated as 12.9 kcal/mol. Direct hydrogen abstraction from formaldehyde by C (3P) is a non- 1 spontaneous reaction by 4.1 kcal/mol. Ketene ( A1) is the global minimum on the CH2CO 1 potential energy surface and its formation from C ( D) and CH2O is highly exothermic (ΔH298 = - 1 180.1 kcal/mol). Two possible pathways to form B1 methylene are found. One is direct 1 1 1 1 deoxygenation by C ( D) along the Sr7 ( A2) - S7 ( A”) - S7p ( A”) path, which is spontaneous 1 1 by –75.1 kcal/mol, and the other is crossing from the A1 surface to the B1 surface. Calculated thermodynamic data is in very good agreement with available experimental data.

Sr7 1 H A2 COC 0.0 H C (1D) + OC H CH2O C

H S7p 1 A" -45.4 -50.1 OC H C S7 -75.1 1 H CH2 ( B1) + CO Conference on Current Trends in Computational Chemistry 2005 87

The Conformational Analysis of CL-20. A DFT Study

Yana Kholod,1,2 Sergiy Okovytyy,1,2 Leonid Gorb,1,3 Mohammad (Mo) Qasim,3 John Furey,3 Herbert Fredrickson3 and Jerzy Leszczynski1

1 Jackson State University, Jackson, Mississippi, 39217, USA 2Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 3US Army ERDC, Vicksburg, Mississippi, 39180, USA

We present here the results of conformational analysis of 2,4,6,8,10,12-hexanitro- 2,4,6,8,10,12-hexaazaisowurtzitane (CL-20). This high-energetic material was recently developed for military and industrial applications. The basic structure of CL-20 consists of a rigid isowurtzitane cage, which includes two five- member rings (FMRs) and a six-member ring (SMR). The CL20 molecule has six nitro groups attached to each of the six bridging nitrogen atoms in the cage. Both spatial orientations of these nitro groups with respect to the FMRs and SMR in the cage, and the differences in crystal lattice packing (as well as the number of molecules per unit cell) define four polymorphs: α-, β-, γ- and ε-CL-20, isolated experimentally. The structures of these polymorphs correspond to: α,γ(II), β(IV), and ε(III). In addition, a high pressure ζ-phase was discovered arising from a reversible transition from γ-phase; however it was not yet identified by X-ray measurements. The structure (I) is presumed to correspond to ζ-CL-20. It was shown, the stability of isolated polymorphic forms decreases in the range ε>γ>α>β (no data about stability of ζ- CL-20 is available). To clarify the mechanism of conformational transformations and to reveal features of IR spectral behaviors we carried out quantum-chemical investigation.

O2N NO2 N N -1 ΔEact=2.36 kcal·mol O N NO O2N N N NO2 O N NO2 2 2 -1 2 ΔEact=1.67 kcal·mol N N N N O2N N N NO2 -1 ΔEact=1.20 kcal·mol O N N N NO (III) O2N N N NO2 2 2 -1 ΔEact=2.36 kcal·mol O2N

N N O2N N N N N NO2 NO -1 O2N NO2 2 ΔEact=2.90 kcal·mol O2N N N NO2 (II) -1 (I) ΔEact=4.03 kcal·mol

O2N N N

NO2 (IV) DFT calculations were performed with the program GAUSSIAN03. The fully optimized geometries of conformers (I)-(IV) were calculated with at the B3LYP/6-31G(d) and B3LYP/6- 311++G(d,p) levels of theory. It was revealed, the stability of conformers decreases in the range (IV)>(II)>(III)>(I). The transition states points on the potential energy surface (PES), which correspond to transformations (I) (II), (II) (III) and (II) (IV) were located. Activation energies of direct and reverse reactions are shown in the figure. Analytical force constants of conformers (I)-(IV) were derived at all employed theoretical levels. The predicted vibrational modes were used for comparison with the experimental quantities. Based on the results of this theoretical study the mechanism of conformational transformations was proposed and complete assignment of IR spectra of the studied compound was done. 88 Conference on Current Trends in Computational Chemistry 2005

Extraordinary Optical Transmission through Subwavelength Hole Arrays

Arman S. Kirakosyan, Tigran V. Shahbazyan

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

When light propagates through small apertures such as subwavelength hole array in metal film, standard aperture theory predicts rather low transmission of light. In the experiment real transmission can be orders of magnitude larger [1]. This mystery can be resolved by understanding of extremely important role playing by surface plasmon polaritons (SPP) in this process. This extraordinary transmission effect can be interpreted as a result of the SPP enhancement of the fields associated with the evanescent waves. Enhanced transmission naturally occurs when coupling conditions allow SPP to be excited on both metal surfaces. In this case transmission resonances can occur due to tunnel coupling between photons and SPP on the opposite interfaces. At excitation of SPP in nanohole array the main contribution in the transmission comes from the evanescent wave with largest spatial extension. This SPP mode wave vector was calculated by reducing of 2d nanoholes array to 1d grating [2]. We develop analytical for the transmission change as well as numerical approach based on hybrid two-temperature model and Boltzmann equation for the electron distribution function. The damping in Drude formula for the dielectric function of metal depends linearly on the lattice temperature. This change produces the change of the transmission measured by pump-probe ultrafast spectroscopy technique. Experimental data for Aluminium are in excellent agreement with numerically simulated results for the differential transmission both versus pump-probe time delay and probe wavelength.

1. T. W. Ebbesen et al., Nature 391 (1998). 2. S. A. Darmanyan et al. Phys. Rev. B 67, 035424 (2003). Conference on Current Trends in Computational Chemistry 2005 89

Current Trends in Explicitly Correlated Coupled Cluster Theory

Wim Klopper,1,2 Heike Fliegl,1 Christof Hättig,2 Christian Neiss,2 David P. Tew1

1Institute of Physical Chemistry, University of Karlsruhe (TH), D-76128 Karlsruhe, Germany 2Institute of Nanotechnology, Forschungszentrum Karlsruhe, P.O. Box 3640, D-76021 Karlsruhe, Germany

The quantum chemical methods that expand the electronic wave function in terms of products of one-particle basis functions converge very slowly with the size of the one-particle basis. Basis set errors in correlation energies that are computed using Dunning’s correlation consistent basis sets (cc-pVXZ) only decrease as X−3 with the cardinal number X [1]. This is a very slow rate of convergence in view of the fact that the computational effort of correlated wave function methods increases as X12 when cc-pVXZ basis sets are used. The reason for the slow convergence is that the products of one-particle basis functions are unable to describe the cusps in the wave function that appear at the coalescence of two electronic coordinates. In the R12 methods, additional two-particle basis functions are used to expand the correlated electronic wave function. These two-particle functions depend explicitly (and linearly) on the interparticle distance r12 and describe the electronic cusps efficiently. By adding the two-particle functions to the standard coupled cluster methods CC2, CCSD and CCSD(T), the explicitly correlated coupled cluster methods CC2-R12, CCSD-R12 and CCSD(T)-R12 are obtained. These methods have been used successfully to compute highly accurate total energies and heats of formation of small molecules. For example, accurate CCSD(T)-R12 calculations have been performed on molecules such as OH, FO, H2O, HOF and F2O [2], yielding theoretical values for their heats of formation that rival or even surpass the accuracy of experimental measurements. In this lecture, we shall address current trends in R12 theory. First, the explicitly correlated linear response coupled cluster theory for the computation of vertical electronic excitation energies at the CC2 level will be discussed, and preliminary results will be presented. Second, a simplified R12 approach, which is denoted CCSD(R12)(T), will be discussed. This new approach is obtained by identifying those linear and quadratic terms in the coupled cluster amplitudes equations of the full CCSD-R12(T) theory that can be neglected without significant loss in accuracy [3]. Third, we shall discuss the perspectives of using new correlation factors in place of the linear r12-term of R12 theory. It was recently proposed to use Slater-type geminals of the form exp(−ζr12) [4,5], and we have investigated this correlation factor as well as others [6].

References

1. T. Helgaker, W. Klopper, H. Koch and J. Noga, J. Chem. Phys. 106, 9639 (1997). 2. W. Klopper and J. Noga, ChemPhysChem 4, 32 (2003). 3. H. Fliegl, W. Klopper and C. Hättig, J. Chem. Phys. 122, 084107 (2005). 4. S. Ten-no, Chem. Phys. Lett. 398, 56 (2004). 5. A.J. May, E. Valeev, R. Polly and F.R. Manby, Phys. Chem. Chem. Phys. 7, 2710 (2005). 6. D.P. Tew and W. Klopper, J. Chem. Phys. 123, 074101 (2005). 90 Conference on Current Trends in Computational Chemistry 2005

Tautomeric Transitions in 2′-Deoxy-Guanosine-Monophosphate

Dmytro Kosenkov1, Leonid Gorb1,2, Yevgeniy Podolyan1 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217 2Institute of Molecular Biology and Genetics, Dept. of Molecular Biophysics, National Academy of Sciences, 150 Zabolotnoho, Kiev, Ukraine 03143

The mechanism of spontaneous mutations in DNA could be understood by studying the proton transitions that result in the formation of ‘rare’ tautomeric forms of DNA bases. These computational studies had been performed quite often by using isolated and hydrated DNA bases. However, DNA building blocks consist of nucleobase, 2′-deoxyribose ring, and phosphate group. In addition the DNA phosphate unit forms the complex with hydrated metal cations. We expect that the presence of phosphate unit along with hydrated metal cation could lead to change in thermodynamic and kinetic characteristics of proton transfer in the nucleobase and therefore shift tautomeric equilibrium in nucleotide in comparison with free nucleobase. To verify this hypothesis we have studied tautomeric transitions that occur in 2′-deoxy-guanosine- monophosphate possessing syn-south, syn-north, anti-south and anti-north conformations. The study has been performed at the B3LYP/cc-pVDZ and MP2/cc-pVDZ levels of theory.

Fig.1 Molecular structure of syn-hydroxo-amino 2′-deoxy-guanosine-monophosphate coordi- nated by hydrated Mg2+ cation.

Conference on Current Trends in Computational Chemistry 2005 91

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

Maryna V. Krasovska1,2 Jana Sefcikova,3 Nils G. Walter3* and Jiri Sponer1*

1Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic 2 National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic 3Department 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 the precursor and product of self-cleavage, together with detailed kinetic analyses, have led to hypotheses on the catalytic strategies employed by the HDV ribozyme. We report molecular dynamics (MD) simulations (~200 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). A precursor simulation with unprotonated C75 reveals a rather weak dynamic binding of C75 in the catalytic pocket with spontaneous, transient formation of a H-bond between U-1(O2’) and C75(N3). This H-bond is consistent with C75 acting as the general base. Upon protonation in the precursor, C75H+ moves towards its product location and establishes a firm H-bonding network within the catalytic pocket. However, a C75H+(N3)-G1(O5’) H-bond, which would be expected if C75 acted as a general acid catalyst, was not observed on the present simulation timescale. The adjacent loop L3 may serve as a flexible structural element, possibly gated by the closing U20·G25 wobble base pair, to facilitate the conformational switch induced by a protonated C75H+. L3 also controls the electrostatic environment of the catalytic core, which in turn likely modulates C75 base strength and metal ion binding. We find that a distant RNA tertiary interaction involving a protonated cytidine (C41) is instable when unprotonated, leading to detrimental conformational rearrangements adjacent to the catalytic core.

References

M. V. Krasovska, J. Sefcikova, N. Spackova, J. Sponer and N G. Walter: Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations. J. Mol. Biol.351, 731-748 (2005).

* To whom correspondence should be addressed. Phone: +420 5415 17133. Fax: +420 5412 12179. E-mail: [email protected] and Phone: (734) 615-2060. Fax: (734) 647-4865. E-mail: [email protected].

92 Conference on Current Trends in Computational Chemistry 2005

Computational Chemistry as a Tool for Scientific Predictions of Chemical Reaction Mechanisms

V. Kukueva

Fire Safety Institute, Onoprienko str. 8, Cherkassy, Ukraine, 18034

Computational chemistry is a new discipline. Its advent and popularity have paralleled improvements in computing power during the last several decades. As with other disciplines in chemistry, computational chemistry uses tools to understand chemical reactions and processes. Scientists use computer software to gain insight into chemical processes. Although computational chemists frequently develop and refine software tools, their primary interest is in applying software tools to enhance chemical knowledge. The challenges for computational chemistry are to characterize and predict the structure and stability of chemical systems, to estimate energy difference between different states, and to explain reaction pathways and mechanisms at the atomic level. Meeting these challenges could eliminate time-consuming experiments. Software tools for computational chemistry are often based on empirical information. To use these tools, you need to understand how the technique is implemented and the nature of the database used to parameterize the method. The development of theoretical tools to describe and understand adsorption and reactions at surfaces has been quite parallel to the experimental one. A number of useful concepts have been introduced to describe the electronic structure, the interaction energies and the dynamics of adsorbents on surfaces. It is now possible to describe at a semi-quantitative level the electronic structure and energetic of adsorption on metal surfaces. The accuracy is still not sufficient to calculate rates of chemical reactions, but it is sufficient for a semi-quantitative description of adsorption and reaction processes, and in particular for comparing different systems. The latter is particularly important if one wants theoretical input into a search for surfaces with a desired activity or selectivity for a given chemical reaction. Even if we are at a point where bond energies and activation energies can be calculated for the simplest systems with a reasonable accuracy, there is a strong need for models and simplified theories of binding. The large scale calculations can be viewed as computer experiments and just as for real experiments we need a conception framework for an understanding or rationalization of the results. If we are for instance interested in finding new alloy surfaces with a particular reactivity or bond strength towards a certain molecule it would be extremely helpful with an understanding of the most important factors determining the ability of a surface to bind or react with the molecule in question. What determines the catalytic activity of a given surface for a given chemical reaction? One of the aspects about solid surfaces that have the largest fundamental and technical importance is the way in which chemical reactions are affected by the presence of a surface. Many catalytic reactions are structure sensitive, meaning that the rate depends on the geometrical structure of the surface. Almost all of them proceed with rates that are much larger at a surface than in the gas or liquid phase. For reactions with more than one possible product the presence of a surface can change the selectivity [1]. On the other side, the poisoning and promoting effect that co- adsorbates can have on the rate of a reaction for a fixed surface structure of the catalyst is ascribed to an electronic factor [2]. These principles are used extensively in all industrial production of chemicals. At the most general level the role of the surface can often be regarded as a means of stabilizing intermediates in the reaction. Such effects are all demonstrations of a dependence of Conference on Current Trends in Computational Chemistry 2005 93

the potential energy surface (PES) on which the catalytic reaction proceeds on the position and kind of atoms in the surroundings. The potential energy surface is given by the electronic structure of the system and even differences in activity between different facets of same metal are due to differences in the electronic structure of the system and are thus electronic in nature. The starting point is the understanding is much larger for metal surfaces than for oxides, so even though oxides are at least as important catalysts as metal, the present paper will be restricted to deal with metallic surfaces almost exclusively. The chemisorption of a gas atom like H, O, C, or N on a metal surface is accompanied by the formation of very strong bonds. For H results for the 4d and 5d series have been described [2], and it is seen that the trend is exactly the same as for 3d’s. It is clear that the number of d-electrons of the surface is more important in determining the binding energy that other factors such as lattice constant or whether the d-electrons are 3d, 4d, or 5d. The synthesis of NH3 directly from N2 and H2, for instance, is extremely slow in the gas phase because it requires a prohibitively large energy to break the N-N bond. At a metal surface the N atoms are stabilized by the chemisorption bond to the surface and this means that the reactions can proceed with a reasonable activation energy [1]. The quantum-chemical calculation has been provided to illustrate the possibilities of theoretical interpretation and prediction of catalytic reaction pathway. As an object of research the oxydation of NH3 on the Fe surface have been choused. We will the kinetics developed for the ammonia oxydation to explain: if the molecular either atomic oxygen co-adsorbtion more preferable for this reaction. The calculation of elementary interaction of ammonium molecule with atomic and molecular oxygen in presence ferrum atom by quantum-chemical method MNDO have been provided in this paper. The model of ammonia with clear Fe surface interaction has been investigated at first. Ammonia on the Fe forms the one layer adsorption region, where the binding power can be increased at the co-adsorption with atomic and molecular oxygen. Then the research has been devoted to calculation of the ammonia on the Fe in presence atomic and molecular oxygen accordingly. The activation energy barrier and total energy have been presented for each stage.

0. 0 0

E , eV

-4 . 0 0

-8 . 0 0

-1 2 . 0 0

1. 0 0 1. 5 0 2. 0 0 2. 5 0 3. 0 0 R, A

. . 0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 Distance NH3 from Fe surface, R, Å Distance atom from surface, R, Å a b

Fig. 1 a. The calculated the interaction potential of collision complex NH3…Fe by the MNDO method. b. Schematic picture of the potential a simple gas atom feels outside a metal.

The collision complexes: Fe…NH3, Fe…O2, Fe…O have been calculated for evidence of the first stage of catalytic transformation, namely – particles adsorption on the metal surface. The Fe … NH3 collision complex has been calculated at the distance between particles from 1 till 3.2Å. The calculation of ammonium molecule on the clear Fe shows the insignificant interaction. We can see it by small energy minima at the distance equal to R = 1.9Å (fig. 1 a). We also 94 Conference on Current Trends in Computational Chemistry 2005

presented the Lennard-Jones [3] potential curve of interaction two particles for comparison (fig. 1b). As we can see the calculation result almost repeats the shape of classical interaction potential curve. This result proofs the first stage of catalytic interaction – molecular adsorption. The activation energy of this interaction not high Eact= 4.03 eВ. This is can be explained by the presence of vacant d-оrbitals of Fe and ammonia electron pair. The adsorption energy [4] equal to ΔΕаds= ΔΕ1е + ΔΕel, where ΔΕ1е – one electron energy, ΔΕel – electrostatic interaction energy of interatomic interaction. Specifically for this calculation the absolute energy value corresponds to total interaction energy, which coincides with potential energy minimum. The collision complexes between Fe and atomic and between Fe and molecular oxygen have been calculated. It is interesting to note that there is potential minimum at the almost the same distances between Fe atom and both particles. It can be interpreted as equal interaction probabilities for all investigated particles. But the comparison activation energy shows that the less barrier is for ammonia and molecular oxygen adsorption (Еаct = 4.03 eV and Еаct = 4.45 eV, accordingly). For atomic oxygen adsorption the activation energy has some more value Еаct = 6.74 eV. It is necessary to note, that there is attraction between atomic oxygen and Fe. According to calculation results we have classical potential curve, to evidence even molecule formation. It gives us right to suppose that atomic oxygen influents not at the ammonia oxidation but at the catalyst oxidation. The activation energy analysis of investigated adsorption complexes (table 1) shows that almost at the same distance between particles (R = 1.9 Å) the activation barrier of Fe…O complex some exceed the analogical values for other interacting components. Therefore at the adsorption stage in the competition between particles the molecular oxygen is predominating. It is coincide with experiments [5]. It is also agreed with suggested explanation of molecular oxygen participation in the formation complexes at the surface due to particularities of it electronic structure (the triplet ground state with two unpaired electrons).

Results of MNDO calculations of the processes on the Fe catalyst during ammonia oxidation. Table 1.

Collision complexes NH3…Fe O2…Fe O…Fe Fe…O2…NH3 Fe...O...NH3 Total energy -350,689 -745,635 -427,04 -989,23 -668,7 Еtot eV Heat of formation 164,77 72,00 29,216 211,19 219,94 0 ΔΗ 298, kcal/mol Dist. betw. particles 1,9 1,95 1,9 2,05 1,75 and Fe, R, Å The activation 4,03 4,45 6,74 1,16 4,2 energy, Eact

The next research stage is calculation of ammonia with Fe interaction at the presence molecular or atomic oxygen. As for as NH3…O…Fe collision complex shows considerable interaction and energy minimum at R = 1.8 Å. According to electronic density distribution analysis we can see that oxygen atom almost “seat” on the d-orbitals of iron. There is weak overlapping between ammonia molecular orbitals and oxygen atomic orbitals. Besides, there is significant interaction of the oxygen p-orbitals and iron d-orbitals. It can be explained by more strong influence atomic oxygen on the Fe, than on the NH3. The deep potential minimum had confirmed this supposition. As mentioned above the chemisorption’s analyses have demonstrated the same conclusion. But the calculation of all collision complexes confirmed significantly deep interaction between ammonia and atomic oxygen at the presence of Fe catalyst. The potential curve of the NH3…O2…Fe has small energy minimum, in spite of the activation energy much Conference on Current Trends in Computational Chemistry 2005 95

less, then for atomic oxygen. Therefore it is necessary to admit that atomic oxygen can be more active in the ammonia oxidation on the Fe surface. It is agreed with traditional point of view on the ammonia oxidation mechanism. But we can’t underestimate the molecular oxygen presence, because as experiments have showed [5] and our calculations confirmed, the molecular oxygen has formed the complexes on the catalyst surface. It is probable would be useful to use ferrum oxide and catalysis could be carried out in the molecular oxygen presence. So, the calculated activation energies and potential curves analysis allows say about predominant flowing one or another stage of complicated chemical transformation in the catalytic reaction process. It was proofed, that atomic oxygen has more influence on the catalyst surface, than on the ammonium oxidation process. The predicted formation of adsorbed complexes between molecular oxygen and catalyst surface to be obtained by experiments has been confirmed by calculations. Accordingly calculation results the participation of atomic oxygen in the ammonia oxidation is substantially too.

References 1. Theretical aspects of surface reactions, J.K.Norskov and P.Stolze, Surface Science, 189/190, 91-105 (1987) 2. North-Holland, Amsterdam, J.K.Norskov, Progress in Surface Science, V. 38, №2, 1991 3. S.Holloway and J.K.Norskov, Surface science lecture notes, 1991, Liverpool University press 4. Van Santen Rutger A, and Neurock, Catal. Rev.-sci.eng., 1995, 37 (4), 557-698 5. C.T.Au and M.W.Roberts, Nature, 319, 206 (1986) 96 Conference on Current Trends in Computational Chemistry 2005

Transferable Force Fields of Some Polycyclic Molecules

G.M. Kuramshinaa, Yu.A. Pentina, D.A. Sharapovb, S.A. Sharapovab, V.K. Matveeva

aFaculty of Chemistry, bFaculty of Physics Moscow State University (M.V.Lomonosov), Moscow 119992, Russia

Rapid progress in quantum mechanical calculations of harmonic force fields for rather large molecular systems with inclusion of electron correlation at MP2 and DFT levels with sufficiently developed basis sets provide possibilities for analysis of form and view of molecular force fields, finding peculiarities in values of force constants, etc. These data can be used for the formulation of limitations on force constant values in solving inverse vibrational problem [1]. Another very important aspect of using theoretical data is a possibility of inclusion them in force constant databases and consequent application for prediction of vibrational spectra of large size molecules, e.g. DNA fragments, polymers, clusters, etc. within different so-called empirical models. It is a transferability of force constants in a series of related molecules should be in the foundation of such calculations. In turn quantum mechanical calculations give a nice possibility for determining transferable force fields. In this work we consider results of quantum mechanical calculations of conformational stabilities, optimized geometries and harmonic force fields of 5H-dibenz[b,f]azepine and 5H- dibenzo[a,d]cyclohepten-5-ol axial and equatorial conformations (Figure 1) with a goal to find trends in their molecular force fields. These molecules with a central seven-member part have similar benzene-like fragments. Theoretical (B3LYP/6-31G*) harmonic frequencies and force constants of these parts were compared to the corresponding data for the benzene molecule. Additionally, there were calculated the scaling factors of benzene molecule on a base of complete set of its fundamentals [2]. A set of scaling factors were found within the posing of inverse vibrational problem proposed elsewhere [1,3] : we consider a solution of inverse vibrational problem when a priory constraint set D is specified as: D={F: F=BFoB}, B=diag{β1,…,βn), βi are the scaling parameters. Solution of this problem is found as a force constant matrix F that is the nearest (in a sense of Euclidian norm) to a given quantum mechanical force constant matrix Fo and reproduces the set of experimental data Λδ within given error level δ≥0 by means of regularizing algorithms [1]. Calculations were done using redundant internal coordinates set. Experimental error δ was chosen as equal to ±3 cm-1 for each frequency. Optimized values of benzene scaling factors (CC=0.9327, CH=0.9177, CCC=0.9804, CCH=0.9443, CH-out-of-plane=0.9724, torsion=0.9440) were used for the correction of theoretical B3LYP/6-31G* frequencies of 5H-dibenz[b,f]azepine and 5H- dibenzo[a,d]cyclohepten-5-ol isomers (Table 1). The comparison of observed and fitted frequencies of benzene is presented in Table 1, where also these data are compared to the corresponding frequencies of investigated molecules related with benzene-like modes.

Conference on Current Trends in Computational Chemistry 2005 97

5H-dibenzo[b,f]azepine

NH-equatorial conformation NH-axial conformation

5H-dibenz[a,d]cyclohepten-5-ol

CH-equatorial conformation CH-axial conformation

Figure 1. Stable conformations of investigated molecules

Theoretical results show that for the considered molecules there is observed the closeness of corresponding frequencies of benzene ring in benzene itself and in and 5H-dibenzo[b,f]azepine (see the diagrams presented below, Figure 2). These characteristic properties of vibrational modes is reflected in the closeness of corresponding force constants. 98 Conference on Current Trends in Computational Chemistry 2005

Table 1. Observed and calculated at the B3LYP/6-31G* theoretical level frequencies (cm-1) of benzene in comparison with calculated similar modes of 5H-dibenzo[a,d]cyclohepten-5-ol and 5H-dibenzo[b,f]azepine Benzene 5H-dibenzo[a,d]cyclohepten-5-ol 5H-dibenzo[b,f]azepine CH-equatorial CH-axial NH-equatorial NH-axial sym mode Exp B3LYP/6-31G* A’ A” A’ A” A’ A” A’ A” [1] Theor. Scaled Scaled Scaled Scaled Scaled Scaled Scaled Scaled Scaled a1g 2 3074 3211 3076 3074 3074 3080 3080 3076 3076 3080 3080 1 993 1021 986 1042 1044 1045 1052 1042 1050 1032 1033 a2g 3 1350 1387 1348 1301 1236 1293 1265 1294 1244 1274 1254 a2u 11 674 692 682 772 767 731 743 753 759 754 768 b1u 13 3057 3175 3051 3044 3043 3045 3045 3035 3036 3044 3043 12 1010 1020 1006 846 906 1105 891 868 907 822 903 b2g 5 990 1009 993 970 969 968 967 953 951 971 968 4 707 717 706 575 582 697 584 598 582 618 584 b2u 14 1309 1357 1312 1326 1308 1321 1317 1324 1310 1315 1298 15 1150 1187 1151 1162 1163 1165 1162 1161 1158 1160 1156 e1g 10a 847 863 850 ------10b ------e1u 20a 3047 3200 3065 3061 3061 3070 3070 3060 3060 3055 3055 20b ------19b 1484 1532 1487 1484 1496 1486 1488 1507 1515 1477 1485 19a 1442 1464 1444 1462 1440 1469 1446 1465 18b 1038 1070 1037 1172 1196 1175 1205 1156 1196 1092 1033 18a ------e2g 7b 3057 3185 3051 ------7a 3048 3047 3056 3056 3047 3047 3069 3069 8b 1601 1657 1605 1607 1609 1609 1608 1605 1612 1608 1608 8a 1562 1577 1570 1577 1588 1585 1559 1574 9b 1178 1209 1172 1104 1113 1158 1106 1114 1113 1148 1106 9a ------6a 608 623 614 666 626 642 619 696 612 700 599 6b 531 472 566 526 552 479 552 475 e2u 17a 967 966 952 882 879 889 867 851 852 861 875 17b 937 938 934 932 920 920 946 937 16a 398 413 406 386 394 434 388 445 390 449 396 16b 135 100 125 95 154 95 153 91

Conference on Current Trends in Computational Chemistry 2005 99

For instance, the CC force constant of benzene is equal to 5.31 mdyn/Å (for canonical model of force constants matrix [1]). For 5H-dibenzo[b,f]azepine the force constans of CC-stretchings in benzene-like parts are within the interval 5.52-5.65 for both isomers and for 5H- dibenzo[a,d]cyclohepten-5-ol those are within 5.56-5.66. There are observed the similar trends and closeness of other diagonal and off-diagonal force constants of benzene and benzene-like fragments.

3500

3000

2500 CH-eq 2000 CH-ax

1500 NH-eq NH-ax 1000 Benzene 500

0 12345678

1,2 – A1g; 3 –A2g; 4- A2u; 5,6 –B1u; 7,8 –B2u vibrations (benzene notations)

3500

3000

2500

2000

1500

1000

500

0 123456789

1-6 – E1u; 7-9 – E2u vibrations (benzene notations) Figure 2. The distribution of normal modes of benzene and benzene-like fragments

Acknowledgement. Authors thank the RFBR grant No 05-03-32135 and the RFBR-OB’ grant No 05-07-96842 for partial financial support.

References

1. I.V.Kochikov, G.M.Kuramshina, Yu.a.Pentin, A.G.Yagola. Inverse Problems of Vibrational Spectroscopy. VSP Scientific Publishers: Zeist, 1999. 2. L.Goodman, A.G.Ozkabak and S.N.Thakur, J. Phys. Chem., 95 (1991) 9044. 3. I.V. Kochikov, G.M. Kuramshina, A.V.Stepanova, A.G. Yagola. Numerical aspects of the calculation of scaling factors from experimental data. Numerical Methods and Programming, 2004, v. 5, pp. 281-290. 100 Conference on Current Trends in Computational Chemistry 2005

Effects of Peripheral Substituents and Axial Ligands on the Electronic Structure and Properties of Cobalt Porphyrins

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

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

The effects of peripheral substituents and axial ligands (L) on the electronic structure and properties of cobalt tetraphenylporphyrin CoTPP have been studied using DFT methods. Various density functionals were tested and the ground state of each system was determined by considering several possible low-lying states. The ground states of the fully fluorinated 4 CoTPPF28(L)2 complexes with L = THF, Py, and Im were identified to be high spin ( Eg) by the meta-GGA functional τ-HCTH which contains the kinetic energy density τ, in agreement with experimental measurements. All the pure GGA functionals, including the recently developed mPBE, OPBE, and HCTH/407, show more or less overestimation of the relative energies of the 2 4 high-spin states. The energy gap between the A1g and Eg states is insignificant (∼0.1 eV) and varies in the order L = Py < L = THF < L = Im. The results and their trend are consistent with 19F 4 NMR studies which show partial population of the Eg state in CoTPPF28(THF)2 and CoTPPF28(Py)2 and a complete conversion to the high spin state in CoTPPF28(1-MeIm)2. Upon coordination by two very strong-field axial CO ligands, CoTPPF28(CO)2 becomes low spin, as in unligated CoTPPFx. The influence of the peripheral substituents and axial ligands on the ionization potentials, electron affinities, and CoTPPFx−(L)2 binding strength was also investigated in detail.

Y Y Y Y X Y X Y β Y Y α Y N Y X X N M N X X Y N Y Y Y Y Y X X Y Y Y Y

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Ab Initio Theory and on-the-fly Dynamics: the Photochemistry of the C=C Bond and Excited-State Proton Transfer

Hans Lischka

Institute for Theoretical Chemistry. University of Vienna, Währingerstrasse 17 1090 Vienna, Austria

The theoretical treatment of the photodynamics of molecular systems is a very challenging task. One of the biggest problems is the computation of excited-state surfaces since the required wave functions have a complicated multireference structure and conical intersection will occur at which the fundament of Quantum Chemistry, the Born-Oppenheimer, is breaking down. The performance of dynamics calculations on such surfaces is also not straightforward. Quantum dynamics calculations are limited to a few internal degrees of freedom and usually require the pre-computation of the energy surfaces. Therefore, as an alternative, classical on-the-fly surface- hopping dynamics calculations can be performed. The on-the-fly strategy implies that only those points on the energy surfaces need to be considered, which are actually accessed during the dynamics. No pre-computation is required and all internal degrees of freedom are taken into account. However, it is necessary to keep in mind that the classical approach will not be able to reproduce all features of a quantum mechanical dynamics. In the present contribution the possibilities of combining analytic gradient/nonadiabatic coupling-vector facilities with surface-hopping dynamics will be presented for two classes of compounds. In the first one the photodynamical properties of ethylene and a selected set of molecules containing polar C=C bonds (silaethylene, fluorethylene and formiminium cation) will be treated. In these investigations the progress in terms of analytic multireference configuration interaction (MR-CI) gradients and nonadiabatic couplings based on the COLUMBUS program + system will be used. The formiminium cation CH2NH2 is the smallest example of a protonated Schiff base (PSB) and is the starting point of ongoing investigations (see below) on larger PSBs in connection with retinal models. In the calculations on ethylene we concentrated our investigations on the description of the topology of the intersection seam [1] and its consequences on mechanistic aspects of the dynamics [2]. The following figure shows the intersection seam characterized in terms of the hydrogen migration angle θ and the pyramidalization angle β.

The S0/S1 crossing seam for ethylene

8 )

) 7

V V e

e θ

( (

y y g

g β

r r

e e

n

n 6

E E

5 100 Twisted 50 4 s) H-migration 0 ee 40 gr 60 de -50 ( 80 β Pyramidalized θ ( 100 deg -100 ree 120 Ethylidene s) Ethylidene 102 Conference on Current Trends in Computational Chemistry 2005

As can be seen from the figure, the seam extends over a wide range of structures starting from a hydrogen-migration region up to ethylidene structures. The surface-hopping dynamics has been performed in this case by means of a combined FOMO/AM1 approach [3] where the AM1 parameters have been fitted to our MR-CI data. For more details see Ref. 4. An overview of the relative importance of different regions of the seam is given in the following figure: τ ~ 100-140 fs

Ethylidene MXS ~7.6 eV 11% 23%

60%

Pyram. MXS H-migration

Torsion + Pyramid.

Potential curves for rigid torsion are displayed for the polar π-bond systems investigated here.

2 π∗ + C2H4 CH2NH2 10 ππ∗10

ππ∗ σπ∗

π2 π2 0 0 03060900306090 Rigid torsion (degrees) Rigid torsion (degrees) π∗2 C2H3F 10 π∗2 CSiH4 ππ∗ 10

ππ∗

π2 0 π2 0 3060900 Rigid torsion (degrees) 0 306090 Rigid torsion (degrees)

In the ethylene case there is an energy gap of about 2 eV between S0 and S1. Quite complicated pyramidalization/hydrogen motions are necessary in order to drive the molecular system into the S0/S1intersection region. This fact is responsible for the relatively large life time of around 150 fs [4]. In case of the remaining three systems, the situation seems to be simpler since the torsion leads directly to an intersection between S0 and S1. However, surface hopping calculations on + CH2NH2 and CH2SiH2 showed a number of unexpected features. + Energy surfaces for CH2NH2

14

12

10

) ) V

V 8

e e

( (

y y g

g 6

r r

e e

n n E E 4

2 1.6 ) Å 0 1.5 ( h tc e 90 1.4 tr 75 S 60 1.3 N 45 C 30 T 1.2 orsio 15 n (°) 0

+ The S0, S1 and S2 energy surfaces for CH2NH2 are displayed above in terms of the CN torsion and the CN distance [5]. After vertical excitation to S2 (ππ*), the molecules experiences a Conference on Current Trends in Computational Chemistry 2005 103

force along the CN bond and, after passing through the intersection with S1, keeps this momentum and does not show tendencies for torsion. On the contrary, excitation to S1 (σπ*) leads to a torsional motion and to the expected intersection with S0. In case of SiH2CH2, a bi- pyramidalization pathway to intersection with S0 was found to be an important alternative to torsion around the CSi bond [6]. About 30% of the trajectories followed the bi-pyramidalization pathway. Both examples demonstrate the importance of dynamics investigations even for a qualitative analysis of photochemical reaction mechanisms. By using static reaction path methods important features of the photodynamical behavior of molecular systems could easily be missed. The possibilities of extending our present approaches to larger molecular systems, in particular to protonated Schiff bases, will be discussed also. One of the most challenging tasks is the inclusion of environmental effects, which play a crucial role for the photodynamics of retinal. Based on the work of Sugihara et al. [7], a simple model for the Glu113 residue has been developed using formiate interacting with four water molecules (Fm4W–):

MR-CISD, RI-CC2 and TDDFT calculations have been performed mainly with the aim to compute structural changes along the PSB chain on electronic excitation and interaction with the Fm4W– complex. In the next steps QM/MM approaches based on MRCI and also lower level methods will be developed for the simulation of the photochemical cis-trans isomerization of protonated Schiff bases in a protein environment as compared to solution. HBQ HBT O O 1 H 1 1 1 1 H 1 2 2 N N 3 3

S 2-(2’-Hydroxyphenyl)benzothiazole 10-hydroxybenzoquinoline In the second class of examples excited-state proton transfer for 2-(2’- hydroxyphenyl)benzothiazole and 10-hydroxybenzoquinoline were investigated using the TDDFT methodology. In this case nonadiabatic coupling terms are not available, but interesting conclusions can be drawn already from the dynamics on one excited-state energy surface. The coupling of low-frequency modes with the proton-transfer motion had been shown by de Vivie- Riedle et al. [8]. The following figure displays the temporal behavior of selected bond distances. Full lines show the average values and broken lines indicate standard deviations. The NO bond distance shows a systematic decrease first, in line with the findings of de Vivie-Riedle et al. [8]. After the proton transfer it increases again. The CO frequency shows an increase demonstrating gain of partial double-bond character.

104 Conference on Current Trends in Computational Chemistry 2005

HBT S1-state dynamics: 35 trajectories, TD-DFT(B3LYP)/SV(P)

2.7

1.8

1.6 OH 2.6

1.4 NO

1.2 NH

NO Distance(Å) 2.5

1.0 Proton-transfer Distances Distances (Å) (Å) -1 1355 cm-1 1505 cm 0.8 2.4 0 20406080100 0 20406080100 1.36 Time (fs) Time (fs)

1.34

1.32 H O 1.30 CO C N 1.28 CO Distance Distance (Å) (Å) 1.26

1.24 1457 cm-1 1712 cm-1 1.22 0 20406080100 Time (fs)

Collaborations: Vienna: Mario Barbatti, Adélia Aquino, Daniel Tunega, Matthias Ruckenbauer, Gunther Zechmann, Daniela Raab Pisa: Maurizio Persico, Giovanni Granucci Berlin/Prague: V. Bonačić-Koutecký, J. Pittner Munich: R. de Vivie-Riedle, E. Riedle

Funding: Austrian Research Fund (FWF), Brazilian National Council for Scientific and Technological Development (CNPq), COST

References: [1] M. Barbatti, J. Paier and H. Lischka, J. Chem. Phys., 121, 11614 (2004) [2] M. Barbatti, M. Ruckenbauer and H. Lischka, J. Chem. Phys., 122 (2005) 174307-1-9 [3] G. Granucci, M. Persico and A. Toniolo, J. Chem. Phys. 114, 10608 (2001) [4] M. Barbatti, G. Granucci, M. Persico and H. Lischka, Chem. Phys. Lett., 401 276 (2005) [5] M. Barbatti, A. J. A. Aquino and H. Lischka, Mol. Phys., in press [6] Gunther Zechmann, Mario Barbatti, Hans Lischka, Jiří Pittner, and Vlasta Bonačić- Koutecký, Chem. Phys. Lett., submitted for publication [7] M. Sugihara, V. Buss, P. Entel and J. Hafner , J. Phys. Chem. B 108, 3673 (2004) [8] R. De Vivie-Riedle, V. De Waele, L. Kurtz and E. Riedle, J. Phys. Chem. A 107, 10591 (2003) Conference on Current Trends in Computational Chemistry 2005 105

Relationship between Structural Stability and Cage – Core Interaction for Sc3@C82 and Sc2@C84

Dan Liu and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Jackson State University, Jackson, MS 39217

Metallofullerenes have been attracting a high level of continuous interest due to their relevance for the fundamentals of cluster science as well as their potential nanotechnological applications. Specifically, various Sc-encapsulated fullerenes have been fabricated in the laboratory, such as Sc@C82 [1] Sc3@C82 [1,2] and Sc2@C84 [3], as well as NSc3@C68 [4] and NSc3@C78 [5]. On the basis of quantum calculations and orbital interaction analysis, we have clarified the cage-core interaction mechanisms, taking NSc3@C68 and NSc3@C78 as examples, where NSc3 turns out to be a six-valence-electron metal-like species [6]. The underlying process is described as a cooperation of electron transfer from the enclosed cluster to the surrounding cage and orbital hybridization, i.e. electron backdonation. In the project presented here, we explore the conditions for the experimentally established stability of fullerenes containing pure Scn units with n = 2 and 3, such as Sc3@C82 and Sc2@C84. Markedly different structures, corresponding to deviating charge states of the core clusters, are found for these two composites. 3+ In Sc3@C82, a Sc3 trication was identified by both experimental and computational studies. In Sc2@C84, in contrast, where Sc2 is realized as a free ion, a charge state of +6 was proposed by 4+ experimentalists for the Sc2 subsystem, while a Sc2 dimer emerges from quantum chemical calculations. The in-depth understanding of the relation between the electronic cage – core interaction and the cluster geometry and stability is expected to be helpful in designing novel nanostructures and predicting their properties.

References.

[1] Shinohara, H.; Sato, H; Ohkohchi, M.; Ando, Y.; Kodama, T.; Shida,. T.; Kato, T.; Saito,.Y. Nature, 1992, 357, 92. [2] Yannoni, C.S.; Hoinkis, M.; de Vries, M.S.; Bethune, D.S.; Salem, J.R.; Crowder, M.S., Johnson, R. D. Science, 1992, 256,1191. [3] Beyers, R.; Kiang, C.H.; Jphnson, R.D.; Salem, J.R.; de Vires, M.S.; Yannoni, C.S., Bethune, D.S., Dorn, H.C.; Burbank, P; Harich, K.; Stevenson, S., Nature, 1994, 370, 196. [4] Stevenson, S.; Fowler, P.W.; Heine, T.; Ducham, J.C.; Rice, G.; Glass, T.; Harich, K.; Hadju, F.; Bible, R.; Dorn, H.C. Nature, 2000, 408, 427. [5] Olmstead, M.M.; de Bettencourt-Dias, A.; Duchamp, J.C.; Stevenson, S.; Marciu, D.; Dorn, H.C.; Balch, A.L. Angew. Chem. Int. Ed, 2001, 40, 1223. [6] S. S. Park, D. Liu, F. Hagelberg, J. Phys. Chem. A, in press

106 Conference on Current Trends in Computational Chemistry 2005

Comparison of Reaction Pathways of Acetylcholine and Sarin in the Acetylcholinesterase Adduct

Christa Loar and E. Johnson

Department of Chemistry, Florida A&M University Room 219 Jones Hall, Tallahassee, FL 32307

Sarin, an organophosphate nerve agent, acts on acetylcholinesterase (AChE) by binding to its active site, serin residue. The serine moiety is inhibited from binding and degrading acetylcholine causing the accumulation of high concentrations of acetylcholine in the nerve endings of the body. The objective of this work is to reveal possible mechanisms involving the inhibition of sarin by comparing the different pathways of acetylcholine and AChE against sarin and AChE. Using PM3 semiempirical quantum chemistry method in Gaussian 98, acylation of AChE with acetylcholine (ACh) and hydrolysis reaction of the AChE-Ach adduct, phosphonylation of AChE with sarin, and hydrolysis of AChE-sarin adduct were explored. A transition state was first determined, followed by reaction pathways. Rates of reactions and energy barriers were calculated for the 4 reactions above. Reaction pathways, reaction barrier heights, and rates of reaction will be presented at the conference.

Conference on Current Trends in Computational Chemistry 2005 107

Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Silicon

Brandon Magers, Harley McAlexander, Crystal B. Coghlan, and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

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, disilacyclopropane, silacyclobutane, 1,2-disilacyclobutane, 1,3- disilacyclobutane, and trisilacyclobutane. 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. Cross-sections of the electron density in the plane of the ring for each of the three- membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems. Results indicate that silicon reduces the conventional strain energy of cyclobutane, most likely because the Baeyer strain is reduced since the silicon can more easily accommodate a small bond angle. However, silicon substitution increases the conventional strain energy in cyclopropane by destroying the stabilizing factor of sigma delocalization. Finally, the conventional strain energy for cyclotrisilane is computed to determine if the stability returns when the three-membered ring is again a homocycle and for cyclotetrasilane to see if additional substitution of silicon for carbon continues to reduce the strain energy in the four-membered system. Electron-density plots show that only in cyclopropane is the electron density thoroughly delocalized in the sigma bonds of the ring. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618). 108 Conference on Current Trends in Computational Chemistry 2005

Modulation and De Novo Design of Protein-Protein Interactions

Stephen L. Mayo

California Institute of Technology, HHMI/Caltech 114-96 1200 E. California Blvd., Pasadena, CA 91125-9600

All major cellular processes depend on the precise, highly specific self-assembly of proteins into functional units. Understanding and controlling the physical/chemical parameters that drive protein association is a major goal of protein biochemistry. To date, much progress has been made in this area by analyzing the large body of data collected on naturally occurring protein- protein interfaces. The field of protein design is uniquely positioned to complement these efforts with an inverse approach. That is, instead of analyzing and/or predicting the structures of native complexes, we can explore the physical chemistry of self-assembly through the modulation of naturally occurring protein-protein interfaces and through the de novo design of self-assembling protein complexes. The ability to direct a designed protein to bind to a target protein in a site- specific manner has potential therapeutic as well as other technological applications. Here we report recent progress in modulating the binding specificity of calmodulin (a naturally occurring protein involved in regulating the activity of a large number of proteins via calcium mediated binding interactions) and in designing de novo protein-protein homo- and hetero-dimers from naturally occurring monomeric proteins. A highly interdisciplinary approach will be described that includes large-scale computation, experimentally determined binding affinities, and NMR and X-ray crystallographic structure analysis. Conference on Current Trends in Computational Chemistry 2005 109

Conventional Strain Energy in Boracyclobutane and Diboracyclobutane

Harley McAlexander, Brandon Magers, Crystal B. Coghlan, and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

The conventional strain energies for boracyclobutane, 1,2-diboracyclobutane, and 1,3- diboracyclobutane 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. 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). Results are compared to the conventional strain energies of cyclobutane and heterocycles involving oxygen and nitrogen to determine what effect boron substitution has on the conventional strain energy of cyclobutane. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).

110 Conference on Current Trends in Computational Chemistry 2005

Ab Initio Studies of Boron Carbonyl Molecules

James L. Meeks

Department of Physics, P.O. Box 7380, West Kentucky Community and Technical College, Paducah, KY 42002-7380

The optimized molecular energies and geometries of the novel boronated carbonyl molecules, H4B2CO, H5B3C2O2, and H6B4C2O2, molecules were computed. These computations used ab initio (HF/6-31G**) and DFT (with the B3LYP hybrid functional) of Gaussian 2003.

The changes of the molecular energies, bond distances and angles of the carbonyl boron molecules are compared. Analyses, by ab initio calculations, of similar urea carbonyl systems are reported. Geometry optimizations and minimum energies for the different boron carbonyl molecular systems using the different basis sets of Gaussian 2003 will be discussed. The optimized (B3LYP/6-31G, 6-31G **, and 6-311++G**) geometrical structures of the boron carbonyl molecules are presented.

Conference on Current Trends in Computational Chemistry 2005 111

Theoretical Study of Adsorption of Sarin and Soman on Tetrahedral Edge Clay Surfaces

A. Michalkovaa, J. Martinezb, O. A. Zhikolc, L. Gorba, J. Leszczynskia

a 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 b Departamento de Quimica Fisica, Facultad de Quimica, QTC, Pontificia Universidad Catolica de Chile, Santiago, Chile c Institute for Scintillation Materials, National Academy of Sciences of Ukraine, 60 Lenina ave., 61001 Kharkov, Ukraine

Sarin (GB – isopropyl methylphosphonofluoridate (C4H10FO2P)) and Soman (GD - 3,3- dimethyl-2-butyl methylphosphonoflouridate (C7H16FO2P)) are substances belonging to the group of chemical weapons. They have an extreme volatility (22,000 mg/m3 for Sarin and 3,900 mg/m3 for Soman at 20 Celsius degrees) at ambient temperature. That makes them extremely dangerous. GB and GD exist in several stereoisomers and conformers. Clay minerals (layered aluminosilicates that consist of a continuous sheet of corner sharing tetrahedra bound to parallel sheets of edge sharing metal octahedra) are one part of soil. Due to their high surface areas, clay minerals are often used as adsorbents and catalysts. Mastering the fundamental nature of adsorption of organic compounds on clay minerals will help in developing precise descriptions of processes such as subsurface transport of natural and contaminate species. Basal surfaces of clay minerals are characterized exclusively by charge-satisfied and extremely stable siloxane bonds. The edge surfaces are characterized by broken bonds and a well-known tendency to form inner-sphere complexes with protons and other cations. In order to extend our study of the adsorption of nerve agents on clay minerals, the research of the adsorption of GB and GD on tetrahedral edge clay surfaces has been carried out. The purpose of this theoretical study is to bring more insight to the usefulness of clay minerals as adsorbents. It could lead to a finding of the optimum way how these compounds can be used for the decomposition of nerve agents. The adsorption of GB and GD on the tetrahedral edge surfaces of clay minerals has been studied at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory using the Gaussian98 program package. The studied systems were fully optimized. We have studied the structure and interactions of GB and GD with the mineral fragment. We have calculated the interactions energies corrected by the basis set superposition error (BSSE). The adsorption mechanism of Sarin and Soman on differently terminated tetrahedral fragments of clay minerals containing the Si4+, and Al3+ central cations was investigated. The charge of the mineral fragment affects the most significantly the intermolecular interactions of the studied systems. In the neutral complexes Sarin and Soman interact with the mineral fragments due to the formation of C-H…O, and O-H…O hydrogen bonds. The charged mineral clusters interact more strongly with Sarin and Soman than electroneutral clusters. The chemical bond is formed between the phosphorus atom of Sarin and Soman and the -2 charged clusters containing the Al3+ central cation and -1 charged complex containing the Si4+ central cation. Sarin and Soman interact mostly in the same way with the same terminated mineral fragments containing different central cations. However, the interaction energies of the complexes with the Al3+ central cation are larger than these values of the Si4+ complexes. The interaction energies of all studied systems corrected by the basis set superposition error were found to be negative. However, only strongly interacting complexes are stable according to the Gibbs free energy 112 Conference on Current Trends in Computational Chemistry 2005

values. It is caused by a large entropy contribution. The formation of hydrogen bonds leads to the changes of geometrical parameters of Sarin and Soman.

a) b)

1- Figure 1. The optimized structure of GB in the GB-[Al(OH)4] (a) and in the GB-Si(OH)4 (b) systems obtained at the MP2/6-31G(d) level of theory.

Conference on Current Trends in Computational Chemistry 2005 113

What is Halogen Bonding?

Jane S. Murray, Pat Lane, Monica C. Concha, Tim Clark and Peter Politzer

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

Halogen bonding (XB) is a type of noncovalent interaction between a halogen atom X in one molecule and a negative site in another. X can be chlorine, bromine or iodine. The strength of the interaction increases in the order Cl < Br < I. In this poster we present an explanation for the occurrence of halogen bonding in terms of a region of positive electrostatic potential that is present on the outermost portions of some covalently-bonded halogen atoms. The existence and magnitude of this positive region, which we call the σ-hole, depends upon the relative electron- attracting powers of X and the remainder of its molecule, as well as the degree of sp hybridization of the s unshared electrons of X. These factors together account for the failure of fluorine to halogen bond. We present and discuss some computed XB interaction energies and also discuss the importance of halogen bonding in crystal engineering and in biological systems and processes, including, in particular, anesthesia.

114 Conference on Current Trends in Computational Chemistry 2005

Chemistry of Hydrated Cations: I. Ab Initio and QTAIM + Calculations on [Li(H2O)n] , n=1,2,3

Jamshid Najafpour, Abdolreza Sadjadi

Department of Chemistry, Faculty of science, Islamic Azad University Shahr-e-Rey Branch, Tehran, P.O. Box: 18735/334, IRAN

Aqueous solutions of cations are the subject of broad investigations in both experimental and theoretical chemistry, [1-3] among them the cations of group IA serve as a large portions of works in theoretical chemistry because of their vital role in biological systems [4-13]. From the + time of clementi’s paper [14] till now lots of reports have been published on [Li(H2O)n] PES to investigate the geometries, hydration energies, coordination number around cation as well as bonding nature in these clusters. The goal of this work is to look at the results of ab initio calculations on cited ion-molecules in the light of fundamental quantum theory of Atoms in Molecules [15-18]. It will be interesting to investigate the chemistry of hydrated cations with the physical theory which governs the classical approaches. RHF(SCVS)/UGBS [19,20] level of calculations were used to both satisfying the virial condition (which will reduces lots of integration errors in AIM) and obtaining the near HF limit geometries.The choice of method is reasonable because of negligible effects of electronic- correlation energy on geometries of these small clusters [6]. Ab initio results from GAMESS6-4 + program [21,22] for [Li(H2O)] were gathered in table 1.Gradient vector field and contour map of ρ(r) function of this ion-molecule from MORPHY99 package [23-28] is depicted in Figure 1. Total energy, derived from AIM calculations is -83.35419 a.u., in excellent agreement with ab initio energy.

q = 0.9669 q = 0.6672

E= -7.2908134 E = -0.31971658

q = 0.6672 q = -1.3010

E = -0.31971582 E = -75.423946

+ Figure 1. Gradient Vector Field and Contour Map of ρ(r) function of [Li(H2O)] at RHF(SCVS)/UGBS. BCP: Bond Critical Point, BP: Bond Path, IAS:Interatomic Surface. Atomic Charges and energies in (a.u.) are given next to each atomic basin.

Conference on Current Trends in Computational Chemistry 2005 115

+ Table 1. Ab initio results for [Li(H2O)] local minimum, at RHF(SCVS)/UGBS

E(a.u) R(Li---O) (Ǻ) R(O---H) (Ǻ) HOH V/T

-83.3541025902 1.817 0.946 107.8˚ 2.0000000077

References

1. Glendening, E. D., Feller, D., J.Phys.Chem., 100 (1996) 4790. 2. Ugalde , J. M ., et al., J. Am. Chem. Soc., 122 ( 2000) 114. 3. Merrill, G. N., Webb, S. P., Bivin, D. B., J. Phys. Chem A., 107 (2003) 386. 4. Del Bene, J. E., et al., J. Phys. Chem., 87 (1983) 73. 5. Bauschlicher, C. W., J. Chem. Phys., 95 (1991) 5142. 6. Feller, D., et al., J. Chem. Phys., 100 (1994) 4981. 7. Woon, D. E., Dunning Jr, T. H., J. Am. Chem. Soc., 117 ( 1995) 1090. 8. Glendening , E. D., J. Am. Chem. Soc., 118 ( 1996) 2473. 9. Del Bene, J. E., J. Phys. Chem., 100 (1996) 6284. 10. Saneyouand, Y. H., et al., J. Phys. Chem. B., 101 (1997) 5018. 11. Sawunyama , P., Baily, G. W., J. Phys. Chem. A., 105 (2001) 9717. 12. Lyubartsev, A. P., et al., J. Chem. Phys., 114 (2001) 3120. 13. Tarakeshwar, P., et al., J. Phys. Chem. A., 108 (2004) 2949. 14. Clementi, E., Popkie, H., J. Chem. Phys., 57 (1972) 1077. 15. Bader, R. F. W. Atoms in Molecules, Clarendon, Oxford, 1990. 16. Bader, R. F. W. Acc. Chem. Res., 8 (1975) 34. 17. Bader, R. F. W., Chem. Rev., 91 (1991) 893. 18. Bader, R. F. W., Guzman, F., Coord. Chem. Rev., 249 (2005) 633. 19. Bader, R. F. W., Guzman, F., Chem. Phys. Lett., 379 (2003) 183. 20. Jorge, P. E., Neto, A. C., J. Molec. Struc (TheoChem), 589-590 (2002) 359. 21. Granovsky, A. A. http://classic.chem.msu.su/gran/gamess/index.html 22. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S. J., Windus, T. L., Dupuis, M., Montgomery, J. A., J. Comput. Chem., 14 (1993) 1347. 23. "MORPHY99, a topological analysis program written by PLA Popelier with a contribution from RGA Bone (UMIST, Engl, EU)" . 24. Popelier, P. L. A., Comp. Phys. Comm., 93 (1996) 212. 25. Popelier, P. L. A., Theor. Chim. Acta., 87 (1994) 465. 26. Popelier, P. L. A., Mol. Phys., 87 (1996) 169. 27. Popelier, P. L. A., Comp. Phys. Comm., 108 (1998) 180. 28. Popelier, P. L. A. Can. J. Chem., 74 (1996) 829. 116 Conference on Current Trends in Computational Chemistry 2005

Theoretical Studies of AZT and AZT Analogues

Edmund Moses N. Ndip

Chemistry Department, School of Science, Hampton University, Hampton, VA 23668

SARs often relate biological activity to structural characteristics of conformers of active molecules. Most of the literature on AZT (a nucleoside reverse transcriptase inhibitor – NRTI) has focused on improving potency and safety based on conformational analysis. Chirality, it is known is an important aspect of drug design. There are various examples in the literature for which configurational differences result in differences in biological activity. The examples of dopamine, adrenalin, thalidomide, and AZT are well known. This study is an attempt to develop a predictive methodology for including configurational analysis in the design process. The variation in molecular, electronic and structural parameters of AZT and some AZT analogues (FLT - Fluorothymidine, ddI - Didanosine, ddC - Zalcitabine) will be examined on the basis of configurational changes ((+) and (-))at the semi empirical (AM1, PM3) and ab initio (MO MP2) / DFT (B3LYP) levels of theory.

AZT FLT

ddI ddC

Conference on Current Trends in Computational Chemistry 2005 117

Understanding Binding of Phosphates to Sevelamar Hydrochloride through Molecular Dynamics and Thermodynamic Modeling

R. Parkera, J. Edwardsa, D. Fishera, A. A. Odukaleb, C. Batichb, and E. Rossb

aFlorida Agricultural and Mechanical University bUniversity of Florida

Sevelamar hydrochloride is a crosslinked poly(allylamine hydrochloride) that binds phosphates by ionic interactions between protonated amide groups along the polymer backbone. Sevelamar hydrochloride is used with Renagel® to reduce the level of phosphates in the body. High phosphate levels results in end-state renal disease (ERSD). Other methods used to reduce phosphate levels involve the use of calcium and aluminum salts. This results in a build up of aluminum and calcium in the body, another deleterious health effect. Current simulation shows that the interaction between Sevelamar Hydrochloride and Phosphates can be modeled in terms of predicted volume which is consistent with experimental observations (see figure below).

Size of Monomer Unit (Angstrom Cubed)

1000 923 733 800

600

400

200

0 No Phosphates 4 Phosphates

Figure 1: 25% swelling observed due to uptake of Phosphate ions

Using molecular mechanics and thermodynamic modeling, further simulation of the binding mechanism will be performed. The coupled analyses will be used to predict the required structure and activity for molecular systems for optimal phosphate uptake. 118 Conference on Current Trends in Computational Chemistry 2005

New Strategies for Large Scale Atomistic Modeling

Michele Parrinello

Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland.

Computer simulation methods based on empirical potentials or on the ab-initio approach have made invaluable contributions to our understanding of complex chemical and biochemical processes. However in spite of great progress in hardware, computer simulations often fall short of what is needed for a realistic description of the systems of interest, for instance in nanoscience or biochemistry. In this talk we shall present our new ideas on how to extend the length and time scale of the simulation. We shall also underline that these methods are designed so as to optimally exploit the new massively parallel computer architectures.

Conference on Current Trends in Computational Chemistry 2005 119

Theoretical Studies on the Conformational and Electrostatic Properties of Tabun to Probe its Cholinesterase Inhibition Characteristics

Yuliya Paukku, Devashis Majumdar, Andrea Michalkova, and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry , Jackson State University, Jackson, MS 39217, USA

Conformational studies have been carried out at the density functional (DFT) and Moller- Plessett second order perturbation (MP2) level of theories on the nerve agent tabun (Ethyl N,N- dimethylphosphoramidocyanidate). This molecule, like other commmon nerve agents (e.g., soman and sarin), is acetylcholinesterase (ACHE) inhibitor. The mechanism of the toxic action of these organophosphorus nerve agents has been interpreted as the blockage of hydrolysis of the neurotransmitter molecule, acetylcholine (ACH), through competetive binding with the active part of the cholinesterase enzyme. Since ACH adapts a specific conformation while binding with the active ACHE site, it could be imagined that the nerve gases would adapt similar conformation during the competetive binding process. The conformational studies on tabun is extremely important to understand its’ ACHE inhibition in this context. The presence of the N(CH3)2 group in tabun would make its binding nature with ACHE quite different with respect to its other nerve agent analogs viz., sarin and soman and the conformational properties of tabun is also quite interesting in that respect. Different enatiomers of tabun has been taken into account during the conformational analyses and the aqueous solvation of this molecule has been studied at the DFT level using polarized continuum model with the conductor like reaction filed approach. The results show that tabun has more conformational fexibility in aqueous medium than in the gas phase and the transition barrier to different low energy conformers decreases due to solvation. The electrostatic properties of the different conformers have studied through generation of molecular electrostatic potential surfaces and have been compared with those of ACH.

120 Conference on Current Trends in Computational Chemistry 2005

Theoretical Study of the Adsorption of Tabun on Calcium Oxide

Y. Paukku, A. Michalkova, D. Majumdar, and J. Leszczynski

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

Tabun (GA), O-ethyl N,N-dimethylphosphoramidocyanidate (CHNO2P) is very strong organophosphate compound. It belongs to the group of powerful nerve agents. Nerve agents act by blocking nerve impulses, causing convulsions and heart and respiratory failure. They are among the most toxic compounds produced. Metal oxides have been shown to mediate the mineralization of chemical weapon agent simulants by oxygen and peroxide. Basic oxides are known as suitable catalyst support materials and adsorbents. In recent years, MgO- and CaO-like materials have received increased attention as potential adsorbents for the decomposition of chemical warfare agents. This work is devoted to the study of the adsorption of Tabun on calcium oxide. It is part of more complex work attempting to understand the interaction of nerve gas with metal oxides that could lead to development of the method for destruction of hazardous substances. The adsorption of Tabun on the small representative cluster models of calcium oxide is investigated at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. The geometry of Tabun was fully optimized while the geometry of the oxide fragment was kept frozen.

Figure 1. The optimized structure of Tabun adsorbed on the surface of non-hydroxylated CaO fragment obtained at the B3LYP/6-31G(d) level of theory.

The structure of Tabun adsorbed on small non-hydroxylated and hydroxylated calcium oxide fragments was found (for example see Figure 1). Tabun interacts with the non-hydroxylated CaO surface in such a way that one P-Oa chemical bond is formed between the phosphorus atom of GA and the oxygen atom of the CaO fragment. Interactions of Tabun with partially and completely hydroxylated CaO fragments are weaker than with non-hydroxylated ones. Conference on Current Trends in Computational Chemistry 2005 121

Interaction energy of the CaO-GA complex containing the non-hydroxylated fragment (-30.2 kcal/mol) was found relatively large because of the formation of a strong chemical bond. Partially and completely hydroxylated CaO fragments because of steric reasons interact less strongly with Tabun. Changes of geometrical parameters and atomic charges of Tabun and the CaO fragment caused by the adsorption were found. The largest changes were found for the atoms of Tabun and atoms of the CaO surface involved in the formation of the intermolecular interactions. 122 Conference on Current Trends in Computational Chemistry 2005

Structure – Hepatotropic Activity Relationship Study of Sesquiterpene Lactones: A QSAR Analysis

Yuliya Paukku, Bakhtiyor Rasulev and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J.R.Lynch St., 39217-0510, Jackson, MS, USA

Sesquiterpenoids, the largest class of terpenoids, are a widespread group of substances occurring in various plant organisms. Sesquiterpene lactones are natural products, which show very interesting biological activities, such as antibiotic, antitumoral, antileukemic, cytotoxic, hepatoprotective, antihelmintic, anti-inflammatory and etc. Various medical products have been developed and keep on developing on basis of sesquiterpene lactones. The hepatotropic activity data for these compounds have been obtained by the pharmacologists and then have been used for our structure-activity relationship studies. This study has been carried out using Quantitative Structure-Activity Relationship analysis (QSAR) for 22 sesquiterpene lactones to correlate and predict the hepatotropic activity. QSAR analysis was held using such methods as Genetic algorithm for variables selection among generated and calculated descriptors and multiple linear regression analysis (MLRA). Quantum- chemical calculations have been carried out at semi-empirical AM1 method for geometry optimization and density functional (DFT) at B3LYP/ 6-311G(d,p) level of theory for electronic properties calculations in a single point mode.

Obtained mathematical models consist of one to three descriptors calculated from characteristics of the molecular structures using DRAGON software and quantum-chemical methods. Among obtained descriptors a good correlation has been shown by certain topological descriptors and quantum-chemical descriptor - dipole moment μ. These models are expected to be useful for screening of sesquiterpene lactones with hepatotropic activity.

Conference on Current Trends in Computational Chemistry 2005 123

Conformational Study of HCO2C(CF3)2OH by Dynamic NMR Spectroscopy and Computational Methods

Diwakar M. Pawar, Eric A. Noe

Department of Chemistry, Jackson State University, Jackson, MS, 39217 - 0510

The E - Z conformational equilibrium for the adduct of formic acid and hexafluoroacetone, HCO2C(CF3)2OH (1) was studied by dynamic NMR spectroscopy . The carbon -13 spectrum of a dilute solution of 1 in 1:3 CD2Cl2 / (CH3)2O solvent mixture showed two peaks of nearly equal intensities at -151.6 oC for the carbonyl carbons, with the minor isomer ( 48 %) absorbing downfield of the major ( 52 %). The coalescence temperature was -143.2 oC. The 1H NMR spectrum at -153.8 oC also showed two signals for the formyl protons (δ 9.01 and 8.20) and the hydroxyl protons (δ 9.91 and 9.86). Ab initio calculations and determination of the rotational barriers by total line shape analysis are in progress. This work was supported by NIH - SCORE Grant No. S06GM008047.

124 Conference on Current Trends in Computational Chemistry 2005

Quantum-Chemical and NMR Spectral Investigation of Products of Amidoacids of Norbornene Row Oxidation

T. Petrova a,b, S.Okovytyy a,b, Tarabara I.N.b, Palchikov V.A.b, Kasyan L.I.b, J.Leszczynski a

aDepartment of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University 1400 J.R. Lynch Street, Jackson, MS 39217-0510, USA bDepartment of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk 49625, Ukraine

Amidoacids of norbornene row are well known as polyfunctional compounds with strained double bond and substances with high biological activity [1]. In oxidation reaction of substituted amodoacid either epoxidic derivatives or heterocyclic products formation can take place. We have investigated a composition and structure of products of oxidation of various amidoacids of norbornene (I) by peroxiformic acid by NMR 1H-spectral analysis method (compounds II, III). In addition, the quantum-chemical calculations (PBE1PBE/6-311G**) of optimal geometry and relative energies of possible amidolactons (II) and salts of amidoacids (III) with pyridine or thiazole fragments have been carried out.

HO HO HCO H, 0-(-5) 0C O 3 + C (HCO H) O C COO- H NR+ OH 2 O 3 C C O C O NHR O NHR O I II a,b III a,b N N R = (a) , (b) S

Since 1H NMR spectra for products of reaction have been measured for the mixture of compounds (II, III), a comparison of the calculated parameters of NMR spectra with experimental data is the only way to reliable assign NMR signals to the corresponding 1H nuclei. We have calculated values of 1H chemical shifts and spin-spin coupling constants for the compounds (II, III) at GIAO-PBE1PBE level using EPR-II basis set for carbon, hydrogen, oxygen and nitrogen atoms and cc-pVTZ basis set for sulfur atom. Additionally chemical shifts of 1H nuclei have been calculated at CSGT-PBE1PBE/6-311++G** level of theory. The results of our calculations allowed to solve a problem of the signal assignments in the mixture of products of oxidation reaction.

[1] Moench S.I., Pagani G., Graecialanza G et al. // Farmaco. Ed.sci. – 1970. –Vol. 25, № 3. – P.203-225.

Conference on Current Trends in Computational Chemistry 2005 125

Microscopic Theory of Fluorescent Resonance Energy Transfer for Molecules Adsorbed at Noble-Metal Nanoparticles

V. N. Pustovit and T. V. Shahbazyan

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

Fluorescence spectroscopy is a widely used research tool in biochemistry and molecular biology. Fluorescence has also become the dominant method enabling the revolution in medical diagnostics, DNA sequencing, and genomics. In this forward-looking paper we describe a new opportunity in fluorescence, radiative decay engineering: the fluorescence by molecule modified and enhanced by the resonance energy transfer between molecule and noble-metal nanoparticles. The main mechanism of resonance energy transfer (RET) has electromagnetic (EM) origin and is due to quenching or energy transfer of the strong surface plasmon (SP) of local field near the metal surface and fluorophore [1] (see also [2] for review of RET mechanisms). Although a classical RET mechanism is size-independent, finite-size effects in small nanoparticles and quantum corrections due to the discreteness of the electron spectrum may significantly modify a local field enhancement in small nanoparticles. Here we describe a novel finite-size quantum- mechanical mechanism that leads to a relative increase of RET in molecule – metallic nanoparticle system. 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 [3]. Specifically, we performed calculations of the total decay rate of molecule-nanoparticle system and its radiative and nonradiative contributions with account of finite-size effects in small nanoparticle. 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 fluorophore molecule located in a close proximity to the metal surface. This result in an additional enhancement of the RET. 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] Lakowicz, J.R “Principles of Fluorescence Spectroscopy”, 2nd ed., Kluwer Academic/Plenum, New York. .(1999) [2] David L. Andrews and Andrey A Demidov, “Resonance Energy Transfer”, Wiley, (1999) [3] A. Liebsch, Phys. Rev. 48, 11317 (1993). 126 Conference on Current Trends in Computational Chemistry 2005

RNA Kink-turns as Flexible Molecular Hinges of the Ribosomal “LEGO”. The Role of Aecond A-minor Motif and Nominally Unpaired Bases

Filip Razga,1,2 Jaroslav Koca,2 Neocles B.Leontis3 and Jiri Sponer1,2*

1Institute of Biophysics,Academy of Sciences of the Czech Republic Kralovopolska 135, 61265 Brno, Czech Republic 2National Centre for Biomolecular Research, Kotlarska 2, 61137 Brno, Czech Republic 3Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403 4Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing “V”-shaped structures. Explicit-solvent Molecular Dynamics (MD) simulations were carried out for selected K-turns from 23S rRNA (Kt-38, Kt-42 and Kt-58) and for K-turn of human U4 snRNA (Kt-U4). The MD simulations reveal hinge-like K-turn motions on the nanosecond time-scale and thus indicate that K-turns are dynamically flexible, and capable of regulating significant inter-segmental motions. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. The presence of K-turns at key functional sites in the ribosome suggests that they confer flexibility to RNA protuberances that regulate the traversal of tRNAs from one binding site to another across the interface between the small and large subunit during protein synthesis cycle. Specifically, Kt-42 is suggested to allow the large scale motions of the factor binding domain (seen in Cryo-EM) in all three kingdoms while Kt-38 (when present) may be essential for the dynamics of the A-finger regulating the access of tRNA from A-site to P-site. Thus, while the whole ribosomal assembly superficially resembles a sophisticated LEGO toy, the K-turns are well poised to act as major recurrent elbow-like dynamical ribosomal building blocks.

References F. Razga, N. Spackova, K. Reblova, J. Koca, N. B. Leontis, and J. Sponer: Ribosomal RNA kink-turn motif - A flexible molecular hinge. J. Biomol. Struct. Dyn. 22, 183-194 (2004). F. Razga, J. Koca, J. Sponer, and N. B. Leontis: Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases. Biophys. J. 88, 3466-3485 (2005).

Conference on Current Trends in Computational Chemistry 2005 127

The Effect of Multiple Substituents in π-π Interactions: Sandwich and T-shaped Configurations

Ashley L. Ringer, Mutasem O. Sinnokrot, Ryan P. Lively, and C. David Sherrill

Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, 30332-0400

Non-covalent π–π interactions play an important role in a variety of chemical and biochemical processes. Substituents alter these interactions and could therefore be used to tune their affects. Sandwich and T-shaped configurations of substituted benzene dimers are studied by second-order perturbation theory to characterize the substituent effect. Symmetric substitution patterns for the monomers were chosen to represent mono, di, tri, and hexasubstituted configurations, as shown in Figure 1. Remarkably, multiple substituents have an additive effect on the binding energy of sandwich dimers (leftmost two dimers of Figure 2), except when substituents are aligned on top of each other (as in the third dimer of Figure 2). T-shaped configurations are more complex, but a simple model (shown in Figure 3) that accounts for electrostatic and dispersion interactions, plus direct contacts between substituents on one ring and hydrogens on the other, provides a good match to quantum mechanical results. Increased understanding of the action of substituents on the strength of π–π interactions will aid in the design of drugs or supermolecular systems which utilize these interactions.

X X X X X X

X X

X X X X

Figure 1. Symmetric substitution patterns for substituted dimers; X = H, OH, CH3, F, CN, NH2

Y X H H

Xn X X Y Y X

Xn

Mixed Aligned Anti-aligned Sandwich Sandwich Sandwich Sandwich T-shaped X T-shaped(a)

Figure 2. Dimer configurations for sandwich and T-shaped configurations 128 Conference on Current Trends in Computational Chemistry 2005

ΔΔE = aΣσm + bΔα + dδ,

where Σσm is the sum of the Hammett parameters for all substituents, Δα is the change in the experimentally determined scalar molecular polarizibiltity (in 10-24 cm3) and δ is a parameter to account for direct substituent-hydrogen interactions.

1.2 1 0.8 0.6 0.4 0.2 0 -1 -0.8 -0.6 -0.4 -0.2-0.2 0 0.2 0.4 0.6 0.8 1 -0.4 R2 = 0.83 -0.6 -0.8

Figure 3. Multi-linear model predicting ΔΔE (interaction energy relative to benzene dimer).

Conference on Current Trends in Computational Chemistry 2005 129

Adsorption of Thymine on the Surface of Dickite: An ab Initio Study

T. L. Robinson, A. Michalkova, L. Gorb, and 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

Genetic information is stored in DNA. The classical view of its structure reveals a double helix witch a linear order of four nucleotides. The nucleotides contain four bases: adenine, cytosine, guanine, and thymine. In this study, we have focused on the latter base, thymine. Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase which is known as an informational molecule. It is found in the nucleic acid DNA. In RNA thymine is replaced with uracil in most cases. Mineral surfaces have been suggested as providing substrates for support of the catalytic assembly of organic and biochemical molecules. Specifically, clay minerals and their charged aluminosilicate layered structure - envisioned as having the appropriate characteristics to harbor precursor organic molecules for the synthesis of important biomolecules. Clay minerals have played an indispensable role in the process of assembling complex structures such as biological polymers. This study examines interactions between DNA bases and clay mineral surfaces with an emphasis on the persistence and stability of DNA bases. In this framework, we studied the adsorption effects of the surface of clay minerals on the structure and interactions of thymine. This nucleic acid was adsorbed on the tetrahedral and octahedral surface of dickite (1:1 dioctahedral clay mineral of the kaolinite group). For this purpose the calculations of hydrated dickite-thymine and non-hydrated dickite-thymine complexes have been performed at the B3LYP/6-31G(d) level of theory. The thymine molecule was placed above the ring in several initial positions to investigate the most advantageous orientation. The geometry of the tetrahedral mineral part was kept frozen while thymine was optimized. The target molecule and six hydrogen atoms of the surface hydroxyls were allowed to relax in the case of the adsorption on the octahedral surface.

Figure 1. The optimized structure of thymine adsorbed on non-hydrated tetrahedral surface of dickite obtained at the B3LYP/6-31G(d) level of theory. 130 Conference on Current Trends in Computational Chemistry 2005

We have found the position and orientation of thymine on the hydrated and non-hydrated tetrahedral (see Figure 1) and octahedral surface of dickite. Thymine is mostly stabilized by the formation of hydrogen bonds with the non-hydrated surface of the mineral. In the case of the models containing the hydrated surface of dickite thymine forms the dipole-dipole interactions with this type of surface. Hydrogen bonds formed between the water molecule and the surface provide an additional stabilization of this molecule on the hydrated surface. The adsorption of thymine on the surface of dickite results in changes of the geometry and polarization of thymine. These effects are more significant in the case of the octahedral adsorption than for the tetrahedral adsorption.

Conference on Current Trends in Computational Chemistry 2005 131

The Accurate Calculations of Hyperfine Couplings with Density Functional Theory

David M. Close

Department of Physics, East Tennessee State University, Johnson City, TN, 37614

The aim of this presentation will be first to review what is known about the primary radiation induced defects (free radicals) in nucleic acid constituents from detailed EPR/ENDOR experiments1, then to explore the use of theoretical calculations to assist in making free radical assignments.2 The theoretical calculations include estimates of spin densities which can be compared with the experimental results. However the calculation of accurate hyperfine couplings is rather difficult. As reported by Tom Zeigler, nuclear magnetic shielding and chemical shifts are known to be sensitive to everything.3 The same can be said of hyperfine couplings. Two factors are involved in the calculations: the isotropic component (Aiso) and the anisotropic component (Txx , Tyy , Tzz ). One must have a good description of electron correlation and a well defined basis set in order to calculate accurate hyperfine couplings. This is not easy to do with molecules the size of the DNA bases. Even when the computational demands are met, the theoretical calculations may deviate more than 20% from the experimental results. Recently it has been shown that the calculation of anisotropic hyperfine couplings for hydrogens are often within 5-10% of the experimental values. The goal is to make comparisons of calculated and experimental isotropic and anisotropic hyperfine couplings a useful guide in identifying radiation induced free radicals. All of the calculations discussed here involve a single point calculation on the optimized structure using triple-zeta plus polarization functions (B3LYP/6-311G(2df,p)) in order to compute spin densities. However the detailed DFT calculations discussed here were performed on isolated molecules, whereas some of the experimental results reported involve free radical formation in the solid state, mainly in single crystals. Therefore the theoretical calculations are ignoring the electrostatic environment of the radicals discussed, in particular the intricate hydrogen bonding structure that the free radicals are imbedded in. This can be shown to lead to non-planar radicals that may or may not represent what is believed to be observed experi- mentally. The successes and failures of DFT to calculate spin densities and hyperfine couplings of more than twenty primary radiation induced radicals observed in the nucleobases are presented. Some unsolved problems and suggestions for future work will be discussed. Next the problem of free radical stability will be discussed. Since radiation scatters electrons from different molecular orbitals at random, one might expect to see a great variety of damaged products. Usually this is not the case. Theoretical calculations are useful here in ranking the energies of the various oxidation and reduction products. It is often possible there- fore to predict which products will be observed in a particular system. Bernhard has considered the stability of radicals in various crystalline environments.4 For example, after irradiation, 1-MethylCytosine (1-MeC) is known to have a very low radical yield, so it is argued that a large percentage of the initial radicals formed by the ionizing radiation must recombine. Looking at the hydrogen bonding network of 1-MeC one sees that the network does not favor long range proton displacements. Consequently there are no energetically favorable paths which would promote the separation of unpaired spin and charge, leaving the initial sites prone to recombination. On the other hand, in many of the systems considered here, there are 132 Conference on Current Trends in Computational Chemistry 2005

efficient pathways for returning ionization sites to their original charge states, thereby effectively inhibiting recombination. As a consequence, many of the radiation induced defects reported are not the primary radiations induced events, i.e. native cations or anions, but rather neutral products, (deprotonated cations or protonated anions) which are less susceptible to re- combination. These ideas have been brought together in a recent study of the co-crystalline complex of 1- MethylCytosine:5-FluoroUracil.5 Using model calculations it was shown how the hydrogen bonding network of the crystal is able to sustain a proton shuttle which leads to the selective formation of certain radicals. Calculation were able to predict that the site of reduction would be the cytosine base (yielding the N3 protonated cytosine anion), while the uracil base would be the site of oxidation (yielding the N1 deprotonated uracil cation). These are indeed the primary radiation induced species observed experimentally.

This work supported by PHS Grant RO1 CA36810-18 awarded by the National Cancer Institute, DHHS.

References 1) Radical Ions and Their Reactions in DNA Constituents. ESR/ENDOR Studies of Radiation Damage in the Solid-State. D.M. Close. Radiat. Res. 135, 1-15 (1993). 2) Model Calculations of Radiation Induced Damage in DNA Constituents Using Density Functional Theory, D. M. Close, Chapter 5 in Computational Chemistry, Review of Current Trends, Vol. 8, J. Leszczynski ed., World Scientific, New Jersey, p. 209-247 (2003). 3) NMR Shielding Calculations across the Periodic Table: Diamagnetic Uranium Compounds. 1. Methods and Issues, G. Schreckenbach, S.K. Wolff, and T. Ziegler, J. Phys. Chem. A, 104, 8244-8255 (2000). 4) The Influence of Packing on free Radical Yields in Crystalli8ne Nucleic Acids: The Pyrimidine Bases, W.A. Bernhard, J. Barnes, K.M. Mercer and N. Mroczka, Radiat. Res. 140, 199-214 (1994). 5) Experimental and Theoretical Investigation of the Mechanism of Radiation-Induced Radical Formation in Hydrogen Bonded Cocrystals of 1-Methylcytosine and 5-Fluorouracil, D.M. Close, L.A. Eriksson, E.O. Hole, E. Sagstuen, and W.H. Nelson, J. Phys. Chem. B, 104, 9343-9350 (2000).

Conference on Current Trends in Computational Chemistry 2005 133

Vibrational Dynamic (hyper)Polarizability of Push-Pull Organic Molecules: A Quantum Chemistry Study

Amar Saal and Ourida Ouamerali

Laboratoire de Physico-Chimie Théorique et Chimie Informatique, Faculty of Chemistry- USTHB, 16111 Algiers, Algeria

Compounds with fast nonlinear optical responses have created an immense interest due to their multiple applications for optical devices such as: electro-optics, integrated optics, telecommunication, and optical computer. Conjugated organic molecules with donor and/or acceptor groups present a particular interest for this technology. Quantum chemistry plays an important role in this context since it allows to predict molecular system structures with interesting nonlinear optical properties. Recently, we have calculated the static vibrational polarizability αv(0) and hyperpolarizability βv(0) of a set of push-pull π-conjugated molecules with two aromatic rings. The inter-ring linker’s effect and the strength of the D/A pair effect on the geometrical structure, the charge transfer and on αv(0) and βv(0) have been studied[1]. The purpose of this present investigation is to complete the previous work [1] by calculating αv(w) and βv(w) at different optical frequencies w of the considered molecules.

______[1] A. Saal and O. Ouamerali; Journal Computational Methods in Sciences and Engineering 4 (2004) 333-344.

134 Conference on Current Trends in Computational Chemistry 2005

Full Accuracy Local MP2

Svein Saeboa, and Peter Pulayb

aDepartment of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA bDepartment of Chemistry and Biochemistry, University of Arkansas, Faytetteville, AR 72701, USA

Recently, we have proposed a low-scaling method for full-accuracy second order Møller- Plesset (MP2) calculations. This method uses only natural sparsity, and thus yields results which are essentially numerically identical with the traditional canonical results. In contrast to other LMP2 schemes, this method avoids introducing a new model chemistry, and it is free from localization artifacts. Pair correlation can be classified as strong or weak. Physically, these two types are quite different. Strong pair correlation, which includes intrapair correlation, and correlation between neighboring localized orbitals that overlap significantly, is dominated by short-range interaction. Weak pair correlation is dispersion attraction between non-overlapping charge densities, and its magnitude is much smaller. In our first implementation, we used a fixed domain for a given occupied orbital, regardless of its pair partner, i.e. whether it was participating in a strong or weak correlation. As a result, most of the computational effort was spent in the LMP2 iterations involving weak pairs, in spite of their modest contribution to the correlation energy. A simple solution to accelerate these calculations would be to use reduced domains for the weak pairs. It is obvious that the large local basis sets used in our current program are not required for weak pairs. A more efficient solution is, however, to exploit the physical nature of weak correlation as dispersion energy between distant, nonoverlapping orbitals to reduce the size of the virtual space. We will describe the set of molecular orbitals, called dispersion orbitals, used to describe weak pairs, and we will demonstrate that a relatively small number of well-chosen MOs are sufficient to accurately describe weak pairs. Test calculations demonstrating accuracy and scaling of the method will be presented. Conference on Current Trends in Computational Chemistry 2005 135

Extrapolation Methods for Improving Convergence of Coulomb Integrals over Slater type Functions

Hassan Safouhi and Ahmed Bouferguene

Campus Saint-Jean, University of Alberta 8406, 91street. Edmoton (AB), Canada T6C 4G9

Multi-center two-electron Coulomb integrals over Slater type functions are required for any accurate molecular electronic structure calculations. These integrals, which are numerous, are to be evaluated rapidly to a high pre-determined accuracy. Slater type functions are expressed in terms of the so-called B functions, which are best suited to apply the Fourier transform method. The Fourier transform method allowed analytic expressions for these integrals to be developed. Unfortunately, the obtained analytic expressions turned out to be extremely difficult to evaluate accurately due to the presence of highly oscillatory spherical Bessel integrals. In previous work, we showed that the techniques based on nonlinear transformation and extrapolation methods led to highly efficient and rapid algorithms for the numerical evaluation of three- and four-center two-electron Coulomb and exchange integrals. The present work focuses on the use of the abovementioned techniques to develop a highly accurate algorithm for the numerical evaluation of the two-center two-electron Coulomb integrals over Slater type functions and over B functions. The numerical results obtained for the molecular integrals under consideration illustrate the efficiency of the algorithm described in the present work.

Introduction Multi-center two-electron Coulomb and exchange integrals over Slater type functions, which are the most difficult type of molecular integrals, are required for ab initio molecular structure calculations. They occur in many millions of terms, even for small molecules and require rapid and accurate evaluation. These integrals contribute to the total energy of the molecule which is required to a precision sufficient for small fractional changes to be evaluated reliably. In practice, the precision threshold for the total energy is of order 10−3 au (atomic unit) and therefore individual integrals must be accurate to 10−8 -10−10 au. The choice of a basis set for the expansion of atomic orbitals is of great importance in ab initio calculations. A good atomic orbital basis should decay exponentially for large distances [1] and should also satisfy Kato's conditions for analytical solutions of the appropriate Schrödinger equation [2]. Slater type functions (STFs) [3] satisfy the the above mathematical conditions. Unfortunately, the use of these functions as a basis set of atomic orbitals has been prevented by the fact that their multi-center integrals turned out to be extremely difficult to evaluate for polyatomic molecules. Various studies have focused on the use of B functions [4-6]. These B functions have remarkable mathematical properties applicable to multi-center integral problems [6-8] and their Fourier transform is of exceptional simplicity [9]. In the present contribution, we used STFs as a basis set of atomic orbitals. These STFs are expressed as finite linear combination in terms of B functions [5]. Thus, the molecular integrals over STFs can be expressed as finite linear combinations in terms of the molecular integrals over B functions. The advantage of this approach is the fact that the basis set of B functions are well adapted to the Fourier transformation method [10,11]. 136 Conference on Current Trends in Computational Chemistry 2005

The Fourier transformation method, which is one of the most successful approaches for the evaluation of multi-center integrals, allowed analytic expressions for the molecular Coulomb integrals over B functions to be developed [9-12] The obtained analytic expressions turned out to be extremely difficult to evaluate because of the presence of highly oscillatory semi-infinite integrals, involving spherical Bessel functions. As it is well known, the oscillatory integrals are beset with difficulties when the oscillatory part is a spherical Bessel function and not a simple trigonometric function. These semi-infinite integrals are the principal source of severe numerical and computation difficulties in the numerical evaluation of molecular integrals under consideration. In previous work, we demonstrate the efficiency of the nonlinear transformations D due to Levin and Sidi [13] and D due to Sidi [14,15], for improving convergence of oscillatory integrals for the numerical evaluation of the semi-infinite integrals occurring in the analytic expressions of overlap, three-center nuclear attraction, hybrid, three- four-center two-electron Coulomb and exchange integrals [16-22]. In the case of these most complicated molecular integrals, our approach produced remarkably good results. In this work, we showed that this approach can also be applied to the two-center two- electron Coulomb integrals over STFs and over B functions. Practical extrapolation techniques suited to particular needs of the two-center integrals are developed to further improve the efficiency of the nonlinear transformations. Even if these two-center integrals are in some sense very simple compared to the integrals mentioned above, one needs to develop a general algorithm based on nonlinear transformation techniques, for the numerical evaluation of all molecular integrals cited above. The numerical result section illustrate clearly that the extrapolation methods are also capable of producing highly accurate numerical results for the two-center Coulomb integrals. Extensive numerical results obtained for more complicated molecular integrals over linear and nonlinear systems can be found in [22-26].

Acknowledgments The first author, Hassan Safouhi, acknowledges the financial support of the Natural Sciences and Engineering Research Council of Canada (NSERC).

References 1. S. Agmon. Lectures on exponential decay of solutions of second-order elliptic equations: Bounds of eigenfunctions of N-body Schrödinger operators. Princeton University, Princeton, N.J., 1982. 2. T. Kato. On the eigenfunctions of many-particle systems in quantum mechanics. Commun. Pure Appl. Math., 10:151, 1957. 3. J. C. Slater. Phys. Rev., 42:33, 1932. 4. I. Shavitt. The Gaussian functions in calculation of statistical mechanics and quantum mechanics, Methods in Computational Physics.2. Quantum.Mechanics. edited by B. Alder, S. Fernbach, M. Rotenberg, Academic Press, New York, 1963. 5. E. Filter and E. O. Steinbor. Phys. Rev. A., 18:1, 1978. 6. E. O. Steinborn and E. Filter. Theor. Chim. Acta., 38:273, 1975. 7. E. J. Weniger and E. O. Steinborn. J. Math. Phys., 30:774, 1989. 8. E. J. Weniger and E. O. Steinborn. Phys. Rev. A., 28:2026, 1983. 9. E. J. Weniger and E. O. Steinborn. J. Chem. Phys., 78:6121, 1983. 10. H. P. Trivedi and E. O. Steinborn. Phys. Rev. A., 27:670, 1983. 11. J. Grotendorst and E. O. Steinborn. Phys. Rev. A., 38:3857, 1988. 12. E. J. Weniger, J. Grotendorst and E. O. Steinborn. Phys. Rev. A., 33:3688, 1986. 13. D. Levin and A. Sidi. Appl. Math. Comput., 9:175, 1981. Conference on Current Trends in Computational Chemistry 2005 137

14. A. Sidi. J. Inst. Maths. Applics., 26:1, 1980. 15. A. Sidi. J. Comp. Appl. Math., 78:125, 1997. 16. H. Safouhi and P. E. Hoggan. J. Math. Chem., 25:259, 1999. 17. H. Safouhi and P. E. Hoggan. J. Phys. A: Math. Gen., 32:6203, 1999. 18. H. Safouhi and P. E. Hoggan. J. Comp. Phys., 155:331, 1999. 19. H. Safouhi. J. Phys. A: Math. Gen., 34:881, 2001. 20. H. Safouhi and A. Bouferguene. Int. Elec. J. Mol. Design, in press, 4:413, 2005. 21. H. Safouhi. J. Mol. Mod., in press, 2005. 22. H. Safouhi. Int. J. Quantum Chem., 100:172, 2004. 23. L. Berlu, H. Safouhi and P. Hoggan. Int. J. Quantum Chem., 99:221, 2004. 24. L. Berlu and H. Safouhi. J. Phys. A: Math. Gen., 36:11791, 2003. 25. L. Berlu and H. Safouhi. J. Phys. A: Math. Gen., 36:11267, 2003. 26. L. Berlu and H. Safouhi. J. Phys. A: Math. Gen., 37:3393, 2004.

138 Conference on Current Trends in Computational Chemistry 2005

Mass Spectrometric and Theoretical Studies of the NaCl-SnCl2 Quasi-Binary System

Julia Saloni,a Szczepan Roszak,a,b and Jerzy Leszczynskia

a Computational Centre for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217, USA. b Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.

The quasi-binary NaCl-SnCl2 system has been studied over past few years because of its unique properties useful in metal-halide discharge lamps. Major role in experimental research plays mass spectrometry supplemented with Knudsen cell, where NaCl-SnCl2 is vaporized, ionized and variety of fragments are recorded. Based on fragments’ analysis thermodynamic data is established. However the experimental investigations do not provide sufficient data to enhance the efficiency of metal-halide lamps. We present theoretical studies on thermodynamical properties of NaCl-SnCl2 system along with the bond interactions analysis based on the interaction energy decomposition scheme. The structure and the bonding are obtained by applying advanced ab initio methods and they are verified by vibrational frequency calculations. Enthalpy and entropy changes of the dissociation, ion-exchange, and atomization reaction are determined based on mass spectrometric and theoretical data. The nature of bonding in molecules and cations is discussed by applying the Mulliken and Natural Bond Orbital electron population analysis approaches.

Figure 1. C3V and C2V isomers of the NaSnCl3 complex Conference on Current Trends in Computational Chemistry 2005 139

Nonlinear Optical Properties of Zwitterionic Merocyanine Aggregates: Role of Intermolecular Interaction and Solvent Polarity

Zuhail Sansudeen and Paresh Chandra Ray

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

We present a time-dependent quantum-chemical analysis on merocyanine aggregates to understand the insight of the intermolecular interactions and finding the relationship between structural and collective nonlinear optical properties. The first hyperpolarizabilities are evaluated for monomer and aggregates of a series of zwitterionic merocyanine dyes, whose synthesis and formation of H and J type aggregates in solvents are reported recently in literature (J. Am. Chem. Soc. 124, 9431, 2002). The molecular geometries are obtained via B3LYP/6-31G** (hybrid density-functional theory) optimization including PCM approach, while the dynamics NLO properties are calculated with the TD-DFT/SOS and ZINDO/CV method including solvent effects. It has been observed that the first hyperpolarizability changes tremendously as monomer undergo in aggregation and the magnitude of first hyperpolarizabilities are highly depends on the nature of aggregates. It is found that solvents play a remarkable role on the structure and first hyperpolarizabilities of merocyanine monomers and aggregates. Changing the solvent from low to high dielectric causes not only an increase in magnitude of β but also a change in sign, therefore passing through zero at intermediate dielectric. Importances of our results on the design of electro-optic materials have been discussed

140 Conference on Current Trends in Computational Chemistry 2005

Theoretical Studies of Dissociation of Perfluorohydroxylamine (F2NOF)

Hasan Sayin and Michael L. McKee*

Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849

A computational study is report of the potential energy surface containing trifluoroamine oxide (NF3O) and its less well-known isomer perfluorohydroxylamine (F2NOF). Stationary points were located with several types of DFT methods (B3LYP, BB1K, MPWB1K and KMLYP) using a 6-311+G(d) basis set and were found to be in good agreement with stationary points located at the CCSD/6-31+G(d) level. At the CCSD(T)/cc-pVTZ//B3LYP/6-311+G(d) level the enthalpy (298K) of c-F2NOF was 3.8 kcal/mol lower than t-F2NOF. Interestingly, the lowest-energy concerted activation barrier separating F2NOF and NF3O was 15.3 kcal/mol higher than the enthalpy of F2NO + F radicals. The most favorable process is the concerted loss of F2 which has an activation enthalpy of 13.8 kcal/mol (c-F2NOF → F2NO+F). Rate constants were calculated for the dissociation of F2NOF by using transition state theory and variational transition state theory. The intrinsic reaction coordinate (IRC) or minimum energy path is constructed starting from the saddle point and going downhill to both asymptotic reactant and product channels. The transition states for the fragmentation reaction, t-F2NOF → F2NO+F and the concerted reaction, c-F2NOF → FNO+F2, were characterized by significant spin-symmetry breaking. For that reaction, single-point calculations were carried out at the MCQDPT2(16e,11o)/6-311+G(d)//B3LYP/6-311+G(d) level (a sixteen-electron in eleven-orbital active space) for points along the IRC in both reaction paths in order to determine the rate constant.

Conference on Current Trends in Computational Chemistry 2005 141

Theoretical Study on the Regioselectivity of the Cycloaddition Reaction between Cyclopentadiene and Methyleneketene

Yinghong Sheng and Jerzy Leszczynski

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

Three possible reaction schemes for the cycloaddition reaction between methyleneketene and cyclopentadiene were studied by DFT (density functional theory) and ab initio calculations. All these cycloaddition reaction are exothermic, concerted but asynchronous processes. The computed activation energies indicate that norbornene product yielded from 1,2-addition of methyelenketene with cyclopentadiene (reaction (1)) is the primary product. The performance of various computational methodologies, MP2, MP4 and CCSD(T), in conjunction with a wide array of basis sets, 6-31G(d), 6-311+G(d,p), aug-cc-pvDz in obtaining reliable activation and reaction energies of the reactions under investigation has been critically analyzed.

142 Conference on Current Trends in Computational Chemistry 2005

Energy Landscapes from π-Stacking to Bond-Breaking

C. David Sherrill

Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry, Georgia Institute of Technology

Weak interactions, such as the noncovalent interactions governing drug binding and the structures of organic crystals, are very challenging to understand. Experimentally, these interactions are often seen in complex environments, where it can be difficult to pick out only the interaction of interest. Theoretically, they feature shallow potential energy surfaces and require very accurate quantum-mechanical modeling for reliable results. Definitive theoretical investigations of π-π, alkyl-π, and sulfur-π interactions which elucidate the strength, geometrical preferences, and fundamental nature of these prototype biomolecular interactions will be presented. In particular, it is shown that the current paradigm for understanding π-π interactions, which emphasizes electrostatic interactions, fails qualitatively. Better models developed on the basis of high-quality quantum mechanical benchmarks will aid in rational design of drugs and supramolecular architectures. Complementary challenges for intermediate bonding regimes (e.g., lithium clusters) and strong bonding (reactions breaking covalent bonds) will also be briefly discussed.

Conference on Current Trends in Computational Chemistry 2005 143

Quantum Chemical Investigation of the Excited State Proton Transfer in Guanine

M.K. Shukla and Jerzy Leszczynski

Computational Centre for Molecular Structure and Interactions Department of Chemistry Jackson State University Jackson, MS 39217

Guanine is one of the most important building-blocks of nucleic acid. It has the maximum number of minor tautomers in different environments and is the most reactive site for oxidative damages. Therefore, it is not surprising that guanine has been subject of numerous experimental and theoretical investigations. Both experimental and theoretical methods have predicted the existence of several tautomers in the gas phase and in aqueous media. Recently, several high levels of spectroscopic investigations were performed on guanine and its derivatives in the supersonic jet expansion to unravel the structural and dynamical properties of the molecule. The existence of up to four tautomers of guanine has been detected in the supersonic beam experiments. Theoretically, the ground state barrier height corresponding to the keto-enol tautomerization of the guanine is predicted to be very high. The presence of a water molecule in the proton transfer reaction path is found to reduce the barrier height of proton transfer very significantly. The barrier height of the proton transfer in the excited state of guanine has not yet been investigated. This type of study is very significant, since in some model systems the proton transfer in excited state is predicted to proceed through significantly low barrier or even barrier less. In this work, we report the results of theoretical study of excited state keto-enol tautomerization barrier height of guanine in the isolated and hydrated form.

O6 Figure. Atomic numbering schemes in guanine (keto-N9H). The keto-N7H, enol- N9H and enol-N7H tautomers of guanine can C6 H1 N7 be obtained by moving H9 hydrogen to N7 C5 N1 site, H1 hydrogen to the O6 site and H1 C8 hydrogen to the O6 site of the keto-N7H tautomer, respectively. H21 H8 C2 C4 N9 N2 N3

H22 H9

Ground and transition state geometries were optimized at the B3LYP/6-311++G(d,p) level using the 6-311++G(d,p) basis set. Geometries of molecules in the excited state and that of geometries of transition states in the excited state were optimized at the CIS level using the 6- 311G(d,p) basis set. The vertical singlet electronic transition energies of different tautomers were computed using the TD-DFT method employing the B3LYP functional and the 6-311++G(d,p) basis set using the DFT optimized ground state geometries. In order to compute adiabatic transition energies, the vertical transition energy calculation were also performed at the TD- B3LYP/6-311++G(d,p) level using the excited state optimized geometries. The effect of aqueous solution on the ground and excited state energies were considered using the polarizable continuum (PCM) model. All calculations were performed using the Gaussian 03 suite of programs. The molecular orbitals were visualized using the Molekel program. 144 Conference on Current Trends in Computational Chemistry 2005

The TD-B3LYP computed transition energies were found to be generally in good agreement with the experimental data. The ground state proton transfer reaction is characterized by a very high barrier. The inclusion of the bulk aqueous solvation using the continuum model does not decrease the barrier height. However, the inclusion of a water molecule in the proton transfer reaction path significantly decreases the barrier height. Generally, in the lowest singlet ππ* excited state the proton transfer barrier height was found to be increased. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form. The ground state geometries of guanine tautomers including those of the transition states were found planar, except the amino group which was pyramidal. The geometries of the keto tautomers in the lowest singlet ππ* state were found to be significantly nonplanar, especially around the C6N1C2N3 part of the ring. The amino group non-planarity was increased for the keto-N9H tautomer and decreased for the keto-N7H tautomer in the excited state. The structural nonplanarity was found to be largest for the keto-N9H tautomer. The geometries of enol tautomers were predicted planar including amino group in the excited state. The structural deformation in the TS-N9H transition state in the excited state was predicted to be different than keto-N9H tautomer, while that for the TS-N7H transition state was predicted to be similar to the structural deformation of the keto-N7H tautomer, but to a lesser extent. Geometries of the hydrated transition states in the ground and lowest singlet ππ* excited states were found to be + zwitterionic form in which water molecule in the form of hydronium cation (H3O ) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH-) and the guanine is in the cationic form.

Acknowledgement Authors are thankful to financial supports from 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. Authors are also thankful to the Mississippi Center for Supercomputing Research (MCSR) for the generous computational facility.

Conference on Current Trends in Computational Chemistry 2005 145

Probing the Physico-Chemical and Structural Requirements among 3-Anilino-4-arylmaleimides for GSK-3α Inhibitory Activity Enhancement through 2D and 3D QSAR Investigations

Prasanna Sivaprakasam,1 Pankaj R. Daga,1 Aihua Xie,1 Robert J. Doerksen*1,2

1Department of Medicinal Chemistry and 2Research Institute for Pharmaceutical Sciences University of Mississippi, MS, 38677-1848, USA

Reported herein is our exploration of the binding forces and physico-chemical (hydrophobic, electronic and steric) requirements among reported 3-anilino-4-arylmaleimides for glycogen synthase kinase-3α (GSK-3α) inhibition. The lack of any reported 3D structure impedes structure-based drug design for this novel target, which has been implicated in type-II diabetes and in neurodegenerative conditions such as Alzheimer’s disease. 2D-QSAR investigations based on the Fujita-Ban and Hansch methods on 3-anilino- and 3- N-methyl anilino-4-arylmaleimides revealed electronic and steric interactions at the 4-phenyl ring and hydrophobic interactions at the 3-anilino ring to be crucial for GSK-3α inhibition. Optimization of the 4-phenyl ring of these compounds using Hansch-type QSAR analysis showed electron withdrawing ortho-substituents as imperative for GSK-3α inhibition. The negative Esortho term indicates that bulky ortho-substituents at the 4-phenyl ring are conducive to GSK-3α inhibitory activity. Fujita-Ban type analysis with 64 3-anilino- derivatives revealed that certain substitutions like 2-Cl, 2-OCH3 and 3-NO2, 4-Cl, 4-OCH3, 2-NO2, 3-OCH3 or 4-NO2 around the 4-phenyl ring are favorable for GSK-3α inhibition. Substituents like 3-Cl, 4-OH, 5- Cl, 3-COOH, 4-Cl, or 4-SCH3 at the 3-anilino ring are positively and 3-OH is negatively correlated with GSK-3α inhibitory activity. Hydrogen bonding interactions between the acceptor

146 Conference on Current Trends in Computational Chemistry 2005

groups like nitro or methoxy at 4-phenyl ring of these congeners and the complementary donor groups of amino acids in the active site of GSK-3α were identified. This finding is further corroborated by the contribution of the topological polar surface area (TPSA) of whole molecules. A combined analysis of 67 compounds with 3-anilino- and 3-N-methylanilino- derivatives showed that 3-N-methylation is not favorable for GSK-3α inhibition. Optimization of the 3-anilino and 3-N-methylanilino rings showed hydrophobic meta- substituents are crucial for enhancement of GSK-3α inhibitory activity. 3D-QSAR studies based on comparative molecular field analysis (CoMFA) on 56 compounds including indoline derivatives (which were not included in the 2D-QSAR analysis) resulted in a highly predictive model with conventional, non-validated r2 = 0.921, F = 94.67, SEE = 0.122 with 6 components, cross-validated r2 = 0.737 and a r2pred = 0.715 against an external test set of 18 compounds. CoMFA electrostatic and steric plots around the most active compound are shown below. Results discussed herein could be used in designing more potent analogs to target the GSK-3α protein which in turn may prove to be an efficient way to treat Alzheimer’s disease and diabetes.

Conference on Current Trends in Computational Chemistry 2005 147

Quantitative Structure-Activity Relationships of Anti-Inflammatory Agents: A Study of a Series of Sesquiterpene Lactone Austricine Derivatives Using Descriptors Derived From 3D Structures

Talibah Smith1, Bakhtiyor Rasulev1,2, Jerzy Leszczynski1

1) Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J.R.Lynch St., 39217-0510, Jackson, MS, USA 2) Institute of the Chemistry of Plant Substances, Academy of Sciences, Uzbekistan Kh.Abdullaev St. 77, Tashkent, 700170, Uzbekistan

Sesquiterpene lactones have been applied in Eastern folk medicine owing to a wide spectrum of their therapeutic actions including anti-tumoral, anti-viral, anti-inflammatory etc. A QSAR between the 3D structures and anti-inflammatory activity has been performed for a series of 18 sesquiterpene lactones. GA-MLRA (Genetic Algorithm combined with Multiple Linear Regression Analysis) techniques were applied for the generation of QSAR models. A number of molecular descriptors were obtained from the density functional theory (DFT) B3LYP/6-31(d, p) level optimized geometries (quantum-chemical descriptors). This study shows that the compounds' activity correlates reasonably well with the selected descriptors encoding the chemical structures. A number of QSAR models with additive and quantum-chemical descriptors have been obtained and discussed in terms of their relativity to the mode of anti-inflammatory action exhibited by sesquiterpene lactones.

Austricine Leucomisine

148 Conference on Current Trends in Computational Chemistry 2005

A DFT Study of the Singlet Oxygen Activation by Unique Transition-Metal Ion Structures in Fe(2+)/ZSM-5 and Zn(2+)/ZSM-5 Zeolites: Formation of the Sigma-Complex between Activated Oxygen and Benzene

Vitaly 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

The participation of singlet oxygen in the oxidation of hydrocarbons on heterogeneous catalysts was discussed previously [1]. However, these results are inadequately reproducible, and 1 until the present time there is no direct evidence of the participation of thermally generated ΔgO2 in oxidation reactions, although the possibility of the direct thermal excitation of oxygen to a singlet state was considered by Turro [2]. Previously [3], a sensitive chemiluminescence technique for the determination of extremely low concentrations of singlet oxygen in a gas phase was developed. This technique allowed us to perform continuous measurements of equilibrium 1 ΔgO2 concentrations in air at relatively low temperatures and to examine non-equilibrium 1 thermal desorption of ΔgO2 from zeolites. Recently, the first direct evidence of the non- 1 equilibrium thermal production of ΔgO2 on zeollite samples (ZSM-5 exchanged with alkaline and alkalin-earth cations) was obtained by chemiluminescence technique [4]. We present herein a density functional study of the interaction of molecular oxygen with Fe(2+) (3d6), and Zn(2+) (3d10), 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). We use Becke’s hybrid three parameter nonlocal exchange functional (B3) combined with the dynamical correlation functional of Lee, Yang and Parr (LYP) at the level B3LYP/6- 31G(d, p). Iron-containing clusters were calculated with four unpaired electrons. For zinc clusters spin-restricted calculation were performed. Natural bond orbital (NBO) population analysis were carried out on the optimized structures to determine the occupancies (number of electrons assigned to orbitals in each atom) and charges of atoms in the adsorption complexes. The DFT calculations were done by using the Gaussian 03 program. The applied methodology allows us accurately determine structural properties and binding energies, especially when the bonding with oxygen is involved. The oxygen adsorption on the Zn(2+) site is notable weaker 1 than on Fe(2+) site, hence ΔgO2 is activated to a lesser extent on the former site. This correlates with the finding (Fig. 1) that the O-O/Fe bond length is much longer than O-O/Zn bond length. The activated oxygen molecule on Fe(2+) (3d6) ZSM-5, and Zn(2+) (3d10) ZSM-5, as a one-electron acceptor, binds strongly to the benzene molecule, resulting in formation of sigma-complex (Fig. 2). Due to the electron withdrawing effect, electron transfer from the benzene molecule occurs and inducing subsequent stronger binding of the molecular oxygen to benzene. This results in the case of Fe/Zn-ZSM-5 in new oxide species, superoxo-like O2 subunit (=C(H)-O-O-Fe/Zn-ZSM-5). The changes in the geometrical parameters, charge distribution and dipole moment along the reaction coordinate are discussed. Some relationships between the amount of transferred electron density and the changes in geometrical parameters and energies are given. Theoretical results obtained employing DFT method provide a Conference on Current Trends in Computational Chemistry 2005 149

mechanism of benzene oxidation based on electronic effects responsible for selective reactivity of singlet oxygen adsorbed on Fe(2+)/Zn(2+)-ZSM-5.

1. M. Che and A. J. Tench., Adv. Catal., 1983, 32, 1. 2. N. Turro, Tetrahedron, 1985, 41, 2089. 3. A. N. Romanov, Yu.N. Rufov, Zh. Fiz. Khim., 1998, 72, 2094. 4. A. N. Romanov, Y. N. Rufov, and V.N. Korchack, Mendeleev Commun. 2000, 117.

a)

b) 1 Fig. 1. The exited state geometries of ΔgO2 molecule adsorbed on Fe(2+)- 10T, (a), (R(OO)=1.316 A), and Zn(2+)-10T, (b), (R(OO)=1.292 A), clusters from main channel of ZSM- 5 150 Conference on Current Trends in Computational Chemistry 2005

a)

b) Fig. 2. Optimized structures of sigma-complex between benzene and activated oxygen molecule on Fe(2+)-5T, (a), and Zn(2+)-5T, (b) clusters from main channel of ZSM-5. Conference on Current Trends in Computational Chemistry 2005 151

A DFT Study of the Ethane Activation by Unique Metal Ion Structures in O=Ga-O-Ga=O oxide and O=Ga(1+)/ZSM-5 Zeolites: Formation of the Ethene and Ethanol

Vitaly Solkan

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

Gallium-exchanged zeolites allow higher dehydrogenation activities [1-2]. Nevertheless, high reaction temperatures are still needed because of the endothermic nature of dehydrogenation reactions [3]. Moreover, conversion of alkanes leads to the formation of aromatics when the reaction is catalyzed by gallium-exchanged zeolite [2,4]. The commercial Cyclar process uses this class of catalyst [5]. Although proton-exchanged zeolites also shows some catalytic activity in dehydrogenation reactions [6], the activity is rather low due to the high barriers associated with the generation of carbonium ions. The details of the reaction mechanisms and the nature of the gallium active sites in these reactions are not precisely known [7-8]. However, the structure of gallium in the zeolitic precursors is understood to a better extent. Gallium is present as Ga(III). The gallium cation in tetrahedral position is connected to two hydrogen atoms and interacts with two oxygen atoms of an AlO4 tetrahedron. During alkanes dehydrogenation, the structure of the catalytic site becomes more complex. The first reason for this is that high temperature is required to perform the reaction, which blurred significantly a clear identification of reaction intermediates and lead to reconstructions of the catalytic active site [9]. Frash and Van Santen have performed a quantum chemical study of the dehydrogenation of ethane by gallium-exchanged zeolite [7]. For this purpose, they used as model of the gallium-exchanged zeolite catalyst a small molecular fragment within the framework of the cluster approach. Various structural alternatives of the active site were compared and the complete catalytic cycle for dehydrogenation was investigated. The limiting step in dehydrogenation of ethane catalyzed by a gallium-exchanged zeolite cluster model corresponds to a transition state structure that leads to the formation of ethene from ethyl chemisorbed to GaH-Z, where Z is the zeolite cluster. One notices that the energy barrier of the rate-limiting step in this reaction pathway is particularly high. The physical and chemical state of the active gallium species in metal-exchanged H-ZSM-5 zeolites has not, as yet, been unequivocally established. The ultimate state of the metal may vary depending upon conditions within which the catalyst works. In reducing atmosphere it could be a reduced Ga(1+) ion or a hydride moiety, while in the oxidizing atmosphere an oxidized GaO(1+) ion. The coordination of the GaO(1+) unit to the zeolite frame-work has been verified by DFT optimization of its position with respect to framework oxygens. Among the possible models of mono-, di-, and tricoordinated GaO, doubly coordinated bridging geometry, where the gallium takes planar position between two framework plus one extra framework oxygens, appeared to be the most stable structure [10]. In this study, we will use density functional theory to check the viability of some structures (O=Ga-O-Ga=O oxide and 3T-Ga=O cluster), which contain the GaO(1+) unit as potential active sites in dehydrogenation and oxidation of ethane. In fact, to our knowledge, until now no theoretical work has been devoted to the reactivity of oxide O=Ga-O-Ga=O with alkanes. Through this theoretical study, we hope to obtain a detailed understanding of the reactivity of ethane toward the Ga=O double bond of O=Ga-O-Ga=O oxide and 3T-Ga=O cluster. We have located the transition states (Fig. 1-2), precursor complexes and product complexes of all the reactions shown in Schemes 1-4 at the B3LYP/6-31G(d,p) level of theory. 152 Conference on Current Trends in Computational Chemistry 2005

CH3CH3 + O=Ga-O-Ga=O → CH2CH2 + O=Ga-O-GaH-OH (1)

CH3CH3 + 3T--Ga=O → CH2CH2 + 3T--GaH-OH (2)

CH3CH3 + O=Ga-O-Ga=O → CH3CH2 OH + O=Ga-O-Ga (3)

CH3CH3 + 3T--Ga=O → CH3CH2 OH + 3T—Ga (4)

The enthalpy changes and activation barriers for these reactions are presented in Table 1. The calculated enthalpy changes for the transfer of an oxygen atom from the O=Ga-O--Ga=O oxide is nearly 2 kcal/mol larger than the enthalpy changes for the corresponding transfer of an oxygen atom from the 3T-Ga=O cluster. The oxygen transfer in former case has a lower activation barrier than the corresponding oxygen transfer in latter case. We also note in Table 1 ≠ that the B3LYP/6-31G(d, p) calculated ΔG value for dehydrogenation reactions on the O=Ga- ≠ O--Ga=O oxide are somewhat closer to the ΔG value for dehydrogenation reactions on the 3T-Ga=O cluster. The major conclusions that can be drawn from this work are as follows: a) the oxygen-transfer reaction channel is expected to be exothermic for large alkanes and this reaction channel proceed with high rate ; b) the dehydrogenation reactions proceed with medium activation barriers ; c) the present results indicate the existance of a competition between the oxygen-transfer reaction (oxidation of ethane) and the dehydrogenation of ethane on O=Ga-O-Ga=O oxide and 3T-Ga=O cluster.

Acknowledgment. This work was supported by RFBR (project 05-03-33103a)

Table 1. Relative energies (kcal/mol) at DFT/B3LYP/6-31G(d, p) level for the process: precursor complex –> transition state –> product complex. ≠ ≠ Reactions ΔH ΔG ΔH δG 1 -19.63 -19.42 +29.26 +33.11 2 -21.35 -23.44 +27.74 +31.95 3 -35.62 -33.80 +24.71 +25.10 4 -33.64 -28.47 +28.69 +32.86

1. R. Fricke, H. Kooslick, G. Lischke, M. Richter, Chem. Rev. 100 (2000) 2303. 6. S. Senger, L. Radom, J. Am. Chem. Soc. 122 (2000) 2613. 2. G. D. Mériaudeau, C. Naccache, J. Mol. Catal. 59 (1990) L31. 3. G. D. Meitzner, E. Iglesia, J.E. Baumgartner, E.S. Huang, J. Catal. 140 (1993) 209. 4. M. Saito, S. Watanabe, I. Takahara, M. Inaba, K. Murata, Catal. Lett. 89 (2003) 213. 5. E. E. Davis, A.J. Kolombos, Australian Patent 509 285 (1979) to BP. 7. M.V. Frash, R.A. van Santen, J. Phys. Chem. A 104 (2000) 2468. 8. M. S. Pereira, M. A. C. Nascimento, Theor. Chem. Acc. 110 (2003) 441. 9. Y. H. Hu, E. Ruckenstein, Acc. Chem. Res. 36 (2003) 791. 10. E. Broclawik et al., J. Chem. Phys. 103 (1995) 2102. Conference on Current Trends in Computational Chemistry 2005 153

a) b) Fig. 1. B3LYP/6-31G(d,p) optimized geometries of the transition states for ethane dehydrogenation .

a) b) Fig. 2. B3LYP/6-31G(d,p) optimized geometries of the transition states for ethane oxidation. . 154 Conference on Current Trends in Computational Chemistry 2005

A DFT Study of the NO Activation by Unique Transition-Metal Ion Structures in Co(1+)/ZSM-5 and Ni(1+)/ZSM-5 Zeolites

Vitaly Solkan and Jerzy Leszczynski

N. D. Zelinsky 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

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 [1-5] 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+). Although Co(1+) is not a typical oxidation state of cobalt, it is stabilised in carbonyl complexes. Cyanides are also expected to form stable complexes with Co(1+). The latter species are often believed to be SCR reaction intermediates, in particular with Co–ZSM-5. The electronic properties of TM-ions vary, depending on the coordination environment. Therefore, the TM ability to bind NO can strongly depend on the TM- cation sitting site. FTIR studies of the interaction of these sites with NO probe molecules are common in the literature. The shift in N=O 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 NO molecule 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 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. All the calculations were performed using nonlocal hybrid density functional theory (B3LYP functional). The Gaussian 03 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 NO molecule; the 3-21G(d) or CEP-31G basis sets for O, Si, Al, Co and Ni atoms; the 3-21G basis set for hydrogen atoms. The calculated bond lengths, Mulliken charges, and vibrational frequencies of adsorbed NO molecules on 10T-cluster are presented in Table 1. An analysis of the electronic structure of (O=N)2Co(1+)-10T and (O=N)2Ni(1+)-10T clusters shows that the adsorbed NO molecules has an anion character. Both Figs. 1 and 2, display the final geometry as obtained in this work. It can be seen that the N=O bond of adsorbed NO molecules is consistently at least 0.06 A longer than the N=O bond for free molecule. This difference leads to a significant change in the calculated vibrational frequencies   A comparison of calculated vibrational frequencies for free NO and NO molecules adsorbed on TM(1+)-10T-clusters indicates the strong perturbation of adsorbed NO. The computational results reported above demonstrate that the TM-ion activation of NO molecule results in a weakening of the N=O bonds and hence can facilitate the dissociation of NO molecule along a possible “deoxygenation path” at elevated temperatures. From a chemical standpoint, it would be of interest to determine the enthalpy change for oxygen-transfer reactions for NO molecules Conference on Current Trends in Computational Chemistry 2005 155

bound at the Co(1+) and Ni(1+) site in ZSM-5. In this work, we investigated theoretically the oxygen transfer reactions from NO molecules adsorbed on TM(1+)-10T-clusters to methane that involves breaking of one of the CH bonds and formation of an OH bond: (O=N)2Co(1+)-10T + 2CH4 → N2 Co(1+)-10T +2CH3OH (1) (O=N)2Ni(1+)-10T + 2CH4 → N2 Ni(1+)-10T +2CH3OH (2) The calculations show that these reactions (see Scheme 1,2) are very thermodynamically favorable ΔE(1)=-54,3 kcal/mol and ΔE(2)=-68,2 kcal/mol. Thus, the present calculations suggest that oxygen-transfer from adsorbed NO molecules to methane might occur on the Co(1+) and Ni(1+) site in ZSM-5. There have been many investigations devoted to the selective catalytic reduction of NO catalyzed by CuZSM-5 and CoZSM-5. However, the present investigation has clarified another facet of this important reaction, namely why the Co catalyst is selective toward the formation N2 when CH4 is the reductant in comparison with the Cu catalyst.

1. S. K. Park, Y. K. Park, S. E. Park and L. Kevan, Phys. Chem. Chem. Phys., 2000, 2, 5500. 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. 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.

Table 1. The calculated vibrational frequencies ν(NO) (in cm-1), bond lengths R(NO) (in A) and Mulliken charges q (in au) at B3LYP/6-31G(d, p) level for free and adsorbed NO molecules on TM(+1)-10T-cluster.

ON(gas) (ON)2Co(1+)ZSM-5 (ON)2Ni(1+)ZSM-5 ν(NO)=1995 1482 1471 ν(NO) 1563 1554 R(NO)=1.1582 1.2169 1.22513 R(NO) 1.2187 1.2257 q(N) +0.0718 +0.1347 q(O) -0.2824 -0.3040 q(N) +0.0544 +0.0993 q(O) -0.3067 -0.3157 q(Co)) +0.6965 q(Ni) +0.6183

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a)

b) Fig. 1. DFT/B3LYP optimized geometries of two NO molecules (a) and dinitrogen molecule (b) adsorbed on the Co(1+)-10T cluster.

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Fig. 2. DFT/B3LYP optimized geometries of two NO molecules adsorbed on the Ni(1+)-10T cluster. 158 Conference on Current Trends in Computational Chemistry 2005

A DFT Study of the Transition Metal Clusters Co4, Rh4, Pd4, and Pt4 in ZSM-5 Zeolite. Does Exist Transition Metal-Proton Adducts in High-Silica Zeolite ZSM-5?

Vitaly Solkan

N. D. Zelinsky Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr. 47, Russian Federation

Metal/zeolite catalysts offer challenging perspectives for catalysis. The catalytic characteristics of metal/zeolite catalysts can be manipulated by exploiting the chemistry, which drives metal ions in small cages or stabilizes them with appropriate ligands in large cages. In numerous catalysts at least one of the zeolite-supported elements is completely reduced to the zerovalent state. As a result, small clusters or even isolated atoms of the transition metal are formed. Coproducts of such reduction are protons, which act as strong acid site. The material thus exposes two types of catalytically active centers: transition metal atoms and protons. In 1973 Dalla Betta and Boudart reported an unusually high hydrogenation activity of small Pt particles in zeolite Y. They ascribed this to an electron transfer from the Pt clusters to the zeolite. Later studies with zeolite-supported Pt, Pd, and Rh showed that the electron deficiency is related to the proton concentration of the zeolite. The results suggest that transition metal clusters in zeolites interact with zeolite protons and form metal-proton adducts [1,2]. The resulting partial positive charge and its dependence on the proton concentration have been detected by X- photoelectron spectroscopy (XPS) [3]. Since protons in metal-proton adducts are bridging between metal atoms and oxygen ions of the zeolite wall, they also act as chemical anchors [4]. We present herein a density functional study of the interaction of H-form of ZSM-5 with different embedded clusters which contain four metal atoms (M4) namely: Co4, Rh4, Pd4, and Pt4. The Bronsted sites in ZSM-5 are represented by a variety of model clusters, including 5T- ring, 6T-ring, and 20T-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 20T-cluster is picked out from the main channel of the ZSM-5 zeolite (see Fig. 1). 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 the H atoms. All the calculations were performed using nonlocal hybrid density functional theory (B3LYP functional). The Gaussian-03 program package was used in this study. For practical purpose, we employed a larger basis set CEP-31G only for the metal cluster, the 3-21G(d) basis set for Si, Al atoms, and the 3-21G basis set for oxygen and hydrogen atoms. We report in detail the calculated results for M4-20T-clusters. The geometry optimization of the studied M4-20T-clusters has been performed only for active site including M4- moiety. In order to correctly predict the energy for proton transfer between a zeolite and a M4 cluster our cluster calculations have shown that a combined geometry optimization of the zeolite and embedded M4 is essential in order to obtain a proper balancing of the energy cost of charge separation and that inclusion of the energy gained by zwitter-ionic interaction. The NBO charges on the M4 cluster were calculated for the structures obtained by optimization calculations. One important result of our calculation is that during structure optimization the bridged proton which compensates the negative charge of an AlO4(-) tetrahedron in a zeolite framework moves to M4 embedded cluster (see Fig. 2-5). In accordance with DFT calculations this proton is bound to M4 embedded cluster in 20T-cluster. A comparison of calculated NBO charges for Co4, Rh4, Pd4, and Pt4 clusters embedded in large 20T-cluster indicates that the negative charge transfer occurs from zeolite framework to protonated M4 embedded cluster (the Conference on Current Trends in Computational Chemistry 2005 159

values of this transfer, decrease the summary positive charge on M4 from +1 to 0.59-0.65 au). One should note that such barrier-less proton transfer from zeolitic Bronsted sites to the embedded Co4, Rh4, Pd4, and Pt4 clusters has never been previously reported for ZSM-5 zeolite. The intriguing question we have been attempting to address in our research is the following: does exist transition metal-proton adduct in high-silica zeolite ZSM-5. Our modeling calculations at DFT/b3LYP level show clearly that transition metal-proton adduct in high-silica zeolite ZSM-5 are stable and bearing the high positive charge.

1. L. L. Sheu, H. Knozinger, and W. M. H. Sachtler, J. Am. Chem. Soc., 111, (1989), 8125 2. Z. Zhang, T. T. Wong, and W. M. H. Sachtler, J. Catal. 128, (1991), 13. 3. A. Yu. Stakheev and W. M. H. Sachtler, J. Chem. Soc. Faraday Trans. 1. 87, (1991), 3703. 4. Z. Zhang, H. Chen, and W. M. H. Sachtler, J. Chem. Soc. Faraday Trans. 1. 87, (1991), 1413.

Figure 1. The started geometry for embedded Pd4 cluster in large 20T cluster from ZSM-5.

Figure 2. The optimized geometry for embedded Pd4 cluster in large 20T cluster from ZSM-5.

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Figure 3. The optimized geometry for embedded Rh4 cluster in large 20T cluster from ZSM-5.

Figure 4. The optimized geometry for embedded Pt4 cluster in large 20T cluster from ZSM-5.

Figure 5. The optimized geometry for embedded Co4 cluster in large 20T cluster from ZSM-5. Conference on Current Trends in Computational Chemistry 2005 161

Enthalpies of Formation of TNT Derivatives by Isodesmic Reactions

Amika Sood, Patricia Honea, and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

TNT (2,4,6-trinitrotoluene) is a well known and widely used explosive. In the current study, we focus on the computation of the standard enthalpy of formation of TNT and several similar aromatic compounds by isodesmic reactions. Isodesmic reactions are reactions in which the number of each type of bond is conserved. To achieve this conservation, the aromatic ring in each system is treated as a single entity in determining bond conservation in each of our model reactions. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and enthalpies are computed for all pertinent molecular systems using SCF theory and density functional theory (DFT). The DFT functional employed is Becke's three-parameter hybrid functional using the LYP correlation functional. Basis sets of at least triple-zeta quality on valence electrons are employed. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).

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Side-Chain Mobility and Binding Selectivity of Naphthylquinoline Derivatives: Correlation of Conformational Energetics with Thermodynamic Binding Energies

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

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

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. 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. 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).

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

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Figure 3: OZ121 – thiol linkage Figure 4: G106 – amide linkage

164 Conference on Current Trends in Computational Chemistry 2005

Structure, Dynamics and Molecular Interactions of Functional RNAs. Advanced Computational Studies

Jiri Sponer

Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic

The basic principles of base pairing in DNA and RNA are strikingly different. While the DNA duplexes are dominated by standard Watson-Crick (WC) base pairs, atomic-resolution structures of RNA revealed that the nominally unpaired loop regions of RNAs are in fact involved in highly versatile non-Watson-Crick base pairing patterns. In functional RNAs, less than 60% of bases form Watson-Crick base pairs. The non-WC interactions determine the evolution and folding of RNA architectures. They stabilize tertiary contacts between remote segments of the RNA macromolecules and specific (often recurrent) non-WC regions called RNA motifs. Non-WC interactions often utilize the H-bonding capability of the ribose 2’-OH hydroxyl group. This architectural versatility sets the macromolecule to fulfil highly specific fundamental bio-catalytic functions. In my talk, I will show that modern computational techniques such as explicit solvent molecular dynamics simulations and ab initio quantum chemistry can provide very useful information about complex RNA molecules. Special attention will be given to ribosomal RNA motifs, such as Kink-turns, involved in large scale motions in ribosome during the protein synthesis cycle. Limitations of the simulation techniques related to for example backbone parametrization, sampling, cation and anion description will be briefly discussed, with attention paid to AMBER. I will show that AMBER, despite its limitations, remains the best classical molecular modelling tool to treat wide range of nucleic acids, and, when properly utilised, can in unique way complement the experimental techniques.

References

K. Csaszar, N. Spackova, R. Stefl, J. Sponer, N. B. Leontis: Molecular dynamics of frameshifting pseudoknot from Beet Western Yellows Virus (BWYV): The role of non-Watson- Crick base pairing, ordered hydration, cation binding and base mutations on stability and unfolding. J. Mol. Biol. 313, 2001, 1073-1091 K. Reblova, N. Spackova, R. Stefl, K. Csaszar, J. Koca, N.B. Leontis and J. Sponer: Non- Watson-Crick base pairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA Loop E. Biophys. J. 84, 2003, 3564-3582. J. Sponer, A. Mokdad, J.E. Sponer, N. Spackova, J. Leszczynski, N.B. Leontis: Unique tertiary and neighbor interactions determine conservation patterns of cis Watson-Crick A/G base pairs. J. Mol. Biol. 330, 2003, 967-978. K. Reblova, N. Spackova, J. E. Sponer, J. Koca, J. Sponer: Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucl. Acid Res. 31, 2003, 6942-6952. K. Reblova, N. Spackova, J. Koca, N. B. Leontis, J. Sponer: Long-residency hydration, cation binding and dynamics of Loop E/Helix IV rRNA - L25 protein komplex. Biophys. J. 87, 2004, 3397-3412 Conference on Current Trends in Computational Chemistry 2005 165

J. Sponer, P. Jurecka, P. Hobza: Accurate interaction energies of hydrogen-bonded nucleic acid base paris. J. Am. Chem. Soc. 126, 2004, 10142-10151. P. Jurecka, J. Sponer, P. Hobza: Potential energy surface of the cytosine dimer: MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field J. Phys. Chem. B 108, 2004, 5466-5471. J. E. Sponer, N. Spackova, P. Kulhanek, J. Leszczynski, J. Sponer: Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family J. Phys. Chem. A 109, 2292-2301 (2005). J. E. Sponer, N. Spackova, P., J. Leszczynski, J. Sponer: Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs. J. Phys. Chem. B 109, 11399-11410 (2005) F. Razga, N. Spackova, K. Reblova, J. Koca, N. B. Leontis, and J. Sponer: Ribosomal RNA kink-turn motif - A flexible molecular hinge J. Biomol. Struct. Dyn. 22, 183-194 (2004). F. Razga, J. Koca, J. Sponer, and N. B. Leontis: Hinge-like motions in RNA kink-turns: The role of the second A-minor motif and nominally unpaired bases Biophys. J. 88, 3466-3485 (2005). M. V. Krasovska, J. Sefcikova, N. Spackova, J. Sponer and N G. Walter: Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations J. Mol. Biol. 351, 731-748 (2005).

166 Conference on Current Trends in Computational Chemistry 2005

Accurate Interaction Energies of Base Pairing and Base Stacking

Jiri Sponer1,2, Petr Jurecka2 and Pavel Hobza2

1 Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic 2 Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. We present new reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from –5 to –47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc- pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G** basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of non-polarizable Cornell et al. (AMBER) force field is confirmed. This indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions. Similar systematic calculations for base stacking are under way, all with inclusion of the key triple electron excitations. After two decades of ab initio research, the present numbers converged to provide close to ultimate predictions of intrinsic energetics of H-bonding and stacking of NA bases. The overall agreement with the preceding reference studies reported by us in the middle of nineties is rather satisfactory, no change of the nature of interactions is evidenced and only small corrections are expected due to future improvements of QM theory.

References

Sponer J, Jurecka P, Hobza P: Accurate interaction energies of hydrogen-bonded nucleic acid base paris. J. Am. Chem. Soc. 126, 2004, 10142-10151. Jurecka P, Sponer J, Hobza P: Potential energy surface of the cytosine dimer: MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field J. Phys. Chem. B 108, 2004, 5466-5471. Hobza P, Sponer J: Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem. Rev. 1999, 99, 3247-3276.

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Principles of RNA Base Pairing

Judit E. Sponer,1 Jerzy Leszczynski2 and Jiri Sponer1,3

1Institute 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 3Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic

Due to the presence of 2’-OH hydroxyl group of ribose, RNA molecules utilize an astonishing variability of base pairing patterns to build up their structures and perform the biological functions. Many of the key RNA base-pairing families have no counterparts in DNA. In this study, the cis-Watson-Crick/Sugar Edge (cis-WC/SE) and trans-Watson-Crick/Sugar Edge (trans-WC/SE) RNA base pair families have been characterized using quantum chemical and molecular mechanics calculations. These two families may form up to 32 unique base pairing patterns. Gas-phase optimized geometries from DFT calculations and RIMP2 interaction energies are reported for the 10 crystallographically identified trans-WC/SE and 13 cis-WC/SE base pairing patterns. Further, stable structures are predicted for all 9 remaining possible members of these families not seen in RNAs so far. Among these novel 9 base pairs, the computations substantially refine several structures suggested earlier based on simple isosteric considerations. Plausible structures are also predicted for pairs where no arrangements were suggested before. Thus our study brings a complete set of 32 cis and trans-WC/SE base pairing patterns. Their computed steric sizes (lengths) are in a sound correlation with the x-ray data. This confirms that isostericity of RNA base pairs, which is one of the key factors determining the RNA sequence conservation patterns, originates in properties of the isolated base pairs. In contrast to the cis-structures, the isosteric subgroups of the trans-WC/SE family vary not only in their H-bonding patterns and steric dimensions, but also in the intrinsic strength of the intermolecular interactions. The present quantum-chemical calculations for the first time analyze base pairs involving the ribose 2’-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. Statistical analysis of the interaction energy terms over all WC/SE base pairs reveals that distribution of the total interaction energy over the sugar-base and base-base contributions is controlled by the cis-trans isomerism. Good performance of the AMBER force field is noticed.

References J. E. Sponer, N. Spackova, P. Kulhanek, J. Leszczynski, J. Sponer, Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family J. Phys. Chem. A 109, 2292-2301 (2005). J. E. Sponer, N. Spackova, P., J. Leszczynski, J. Sponer, Principles of RNA base pairing: Structures and energies of the trans Watson-Crick/sugar edge base pairs. J. Phys. Chem. B 109, 11399-11410 (2005) J.E. Sponer, J. Leszczynski, V. Sychrovsky, J. Sponer: The Sugar Edge/Sugar Edge base pairs in RNA. Stabilities and structures from quantum chemical calculations. Journal of Physical Chemistry B in press. 168 Conference on Current Trends in Computational Chemistry 2005

Anharmonic Calculations of CH3-nClnSiF3 (n=0-3) Molecules

S.V.Syn’ko, G.M.Kuramshina, Yu.A.Pentin

Department of Physical Chemistry, Faculty of Chemistry Moscow State University (M.V.Lomonosov, Moscow 119992, Russia

In this study we present the results of experimental and theoretical investigations of vibrational spectra of four fluoro and fluorochlorosubstituted methylsilanes. The IR and Raman spectra of CH3SIF3 (CD3SIF3) (I), CH2ClSiF3 (II), CHCl2SiF3 (III) and CCl3SiF3 (IV) obtained in different aggregate states were compared to the results of ab initio and DFT quantum mechanical calculations. Ab initio calculations were made with Gaussian 03 (Revision С.2) package on HF and MP2 levels of theory with 6-31G* and 6-311++G** basis sets. DFT quantum mechanical calculations were carried out with B3LYP functional using four basis sets (6-31G*, 6-311++G**, aug-cc- pVDZ and aug-cc-pVTZ) and optimized geometries, harmonic force fields, frequencies of I-IV (for all investigated levels of theory) were obtained. Additionally, the calculations of anharmonic frequencies of I-IV (for B3LYP level) were carried out. The barriers to hindered rotation calculated for some investigated levels (in kJ/mol) are performed below.

HF MP2 B3LYP B3LYP B3LYP Exp. 6-31G* 6-31G* 6-31G* 6-311++G** aug-cc-pVDZ [1] I 4.33 4.31 4.95 4.55 4.54 5.81 II 6.00 6.06 5.34 7.06 6.48 III 8.23 8.37 6.15 9.69 8.44 IV 13.69 13.87 9.62 15.49 13.30

It is seen that the barrier is systematically increased by the increasing the number of chloro substituents. The theoretical harmonic force fields were transformed from Cartesian coordinates to the redundant system of internal coordinates and potential energy distributions were calculated with a help of SPECTRUM package [2]. Numerical results demonstrate the trends in optimized geometries of I-IV which are similar for considered earlier chloromethylsilanes [3]: increasing number of chlorine substituents in the methyl group leads to the elongation of C-Si bond and parallel slight shortening the C-Cl bond. Some bond angles are distinctly deviated from tetrahedral values. Analysis of theoretical data shows that the harmonic frequencies obtained for the modest basis sets require some corrections on comparison to observed data. All used basis sets cannot be considered as completely satisfied for the investigated compounds. Additional efforts are necessary for the finding the theoretical level that is enough for the adequate description of methylsilane derivatives containing the fluorine atoms. As preliminary point the B3LYP/aug-cc- pVDZ values can be directly compared to the empirical data and this level is chosen as basic for the assignments of I-IV spectra. Calculation of anharmonic vibrational spectra allowed us to carry out more thorough and detailed analysis of spectral data and assignment of not only fundamentals but also combination frequencies and overtones. Conference on Current Trends in Computational Chemistry 2005 169

The main peculiarity of the considered spectra related to the complicated behavior of the C- Si stretching. Both dynamical and kinetic factors should lead to the lowering the corresponding frequency in I-IV series but the corresponding theoretical frequencies have very mixed PED. The NBO analysis [4] has been performed for the minimum energy structures of I-IV using the B3LYP electron densities and the investigated basis sets.

Acknowledgement. Authors thank the RFBR grant No 05-03-32135 and the RFBR-OB’ grant No 05-07-96842 for partial financial support.

References

1. J.R. Durig, Li Y.S., C.C. Tong, J. Mol. Struct. 14(1972)255. 2. A.G. Yagola , I.V. Kochikov, G.M. Kuramshina, Yu.A. Inverse Problems of Vibrational Spectroscopy. VSP, Zeist, The Netherlands, 1999. 3. G.M. Kuramshina, Yu.A. Pentin, S.V. Syn’ko, Russian Journal of Pjysical Chemistry, 77(2004)469. 4. A.E.Reed, L.A.Curtiss, F.Weinhold, Chem. Rev. 88 (1988)899.

170 Conference on Current Trends in Computational Chemistry 2005

The Influence of the Microsolvation on the Proton Affinity of Ammonia

Jaroslaw J. Szymczaka,b, Jan Urbanc,a, Szczepan Roszaka,b, and Jerzy Leszczynskia

aComputational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, Jackson, MS 39217, USA bInstitute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland cDepartment of Biophysics and Chemical Physics, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynska Dolina F1, 84248 Bratislava, Slovakia

The gas-phase processes may be sensitive to the presence of solvent molecules even when the environment is constituted by noble gases. The proton attachment/detachment processes are interesting as precursors of reactions observed in nature and are especially important for the atmospheric chemistry. The formation of micro-clusters is a possible way to influence the ”core” processes. The variation of the proton affinity has been investigated from the nature of interaction point of view.

10 EX

5

0

EL

MP2 -5 E [kcal/mol] De

TOT -10

DEL -15 1234 n

Conference on Current Trends in Computational Chemistry 2005 171

Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Germanium

Lyssa Taylor, Crystal B. Coghlan, and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

The conventional strain energies for three- and four-membered heterocycles of carbon and germanium are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include germacyclopropane, digermacyclopropane, germacyclobutane, 1,2- digermacyclobutane, 1,3-digermacyclobutane, and trigermacyclobutane. 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). Cross-sections of the electron density in the plane of the ring for each of the three-membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems. Results are compared to those obtained for heterocycles of carbon and silicon to determine if germanium has the same effect on the conventional strain energy of cyclopropane and cyclobutane as silicon which reduces the conventional strain energy of cyclobutane, but increases the conventional strain energy in cyclopropane. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618). 172 Conference on Current Trends in Computational Chemistry 2005

The Excitation Spectra of Dibenzoborole Containing π-electron Systems: Controlling the Electronic Spectra by Changing the pπ – π* Conjugation

Kanchana S. Thanthiriwatte and Steven R. Gwaltney

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

We report time dependent density functional theory (TDDFT) calculations of the vertical excitation energy of three-coordinate 5H-Dibenzoborole (DBB) derivatives and four-coordinate 5-Fluoro-5H-dibenzoborole ion (FDBB) derivatives. These molecules show remarkable hypsochromic (blue) shifts in their fluorescence spectra and bathochromic (red) shifts in their absorption spectra when the bridging boron atoms change their coordination number from three to four. We constructed a series of derivatives of DBB and FDBB and studied how the energies of the electronic excitations change. The states with prominent oscillator strength in all of the DBB and FDBB derivatives show similar shifts of their excitation energies upon coordination. We calculate the three-coordinate DBB derivative 5-(2,4,6-triisopropylphenyl)-2,8-dimethoxy- 3,7-bis[p-(N,N-diphenylamino)phenyl]-5H-dibenzo[d,b]borole to have an intense absorption at 3.25 eV, which shifts in the four-coordinate FDBB derivative 5-fluro-5-(2,4,6- triisopropylphenyl)-2,8-dimethoxy-3,7-bis[p-(N,N-diphenylamino)phenyl]-5H- dibenzo[d,b]borole ion to 3.17 eV. The experimental absorption peaks are found 3.43 eV and 3.31 eV, respectively. In addition, we investigated and analyzed the nature of these electronic excitations using attachment/detachment density plots, with which we characterized the changes in electron density that arose from the excitations.

Conference on Current Trends in Computational Chemistry 2005 173

Aconitum and Delphinium sp. Alkaloids as Antagonist Modulators of Voltage-Gated Na+ Channels. AM1/DFT Electronic Structure Investigations and QSAR Studies

Malakhat A. Turabekova 1,2, Bakhtiyor F. Rasulev 2,3, and Mikhail G. Levkovich 2 and Jerzy Leszczynski 3

1 Chemistry Department, National University of Uzbekistan named after Mirzo Ulugbek, Vuzgorodok, Tashkent, 700174, Uzbekistan 2 Institute of Chemistry of Plant Substances, Kh. Abdullaev Str., 77, Tashkent, 700170, Uzbekistan 3 Computational Center for Molecular Structure and Interactions, Jackson State University, 1325 J.R.Lynch Street, P.O.Box 17910, Jackson, Mississippi, 39217-0510 USA

Early pharmacological studies of Aconitum and Delphinium sp. alkaloids suggested that these neurotoxins act at site 2 of voltage-gated Na+ channel and allosterically modulate its function. Remarkably, despite of similar molecular structure, these alkaloids can be divided into two distinct groups: the blockers and the openers of the sodium ion channels. It was also reported that three crucial functional residues must be present in a molecule for it to exhibit channel activation: hydroxyl group at C13, benzoylester group at C14 and acetyl group at C8 of the lycoctonine skeleton. Though these alkaloids have received a great deal of attention by medicinal chemists, the literature survey resulted in little evidence on them being investigated by means of molecular modeling technique. A series of 18 antagonist alkaloids (9 blockers and 9 openers) have been subject to AM1//DFT/B3LYP studies in order to trace structure-activity (structure- toxicity) relationship at electronic level. An examination of frontier orbitals obtained for ground and protonated forms of the compounds revealed that HOMOs and LUMOs were mainly represented by nitrogen atom and benzyl/benzoylester orbitals with –OH and –OCOCH3 contributions being less than 1%. This suggests that opening or blocking activities are not controlled by frontier orbitals and instead biological activity is attributed to allosteric interactions of the alkaloids with the receptor site, which is in a good agreement with experiments. Genetic Algorithm with Multiple Linear Regression Analysis (GA-MLRA) technique was also applied for the generation of two-descriptor QSAR models for the set of 65 blockers. Energy of LUMO has been identified as the best descriptor controlling the endpoint of interest. A number of other descriptors such as logP, nNH2, nHDon, nCO have been selected as complementary ones to LUMO and their role in activity alteration has also been discussed.

174 Conference on Current Trends in Computational Chemistry 2005

Electron Impact Ionization of Hydrocarbons and Amino Acids – A Theoretical Study

J. Urbana, P. Macha and M.Probstb

aDepartment of Nuclear Physics and Biophysics, Comenius University, Bratislava, Slovak Republic bInstitute of Ion Physics, University of Innsbruck, Innsbruck, Austria

It has been recognized that small hydrocarbons are constituents of the plasma edge in fusion reactors and therefore there exists a strong interest in reliable data for ionization potentials of small hydrocarbon molecules. The effect of the oxidative damage in proteins has also been a subject of many studies. The precise assignment of ionization energy for a given molecule represents the first step in the theoretical study of reactions connected with electron ionization of molecules. At present state of theory the ionization energies (vertical and adiabatic) can be calculated at high level of precision and give indices about the mechanism of the ionization reaction by electron impact. Our contribution presents the results obtained from the study of the reactions occurring at the electron impact ionization of ethane, propane and alanine molecules. Also the temperature effects on appearance energies have been studied. The results are based on the high level ab initio MO calculations of the possible molecular structures occurring in the fragmentation mechanisms. To obtain more reliable relative energies for the studied molecules, calculations of the Gaussian-3 (G3MP2) [1] and G3MP2B3 [2] were carried out. These methods are complex energy computations involving several pre-defined calculations on the specified molecular system. All calculations have been performed by using of the Gaussian 98 program [3].

[1] L.A. Curtiss, K. Raghavachari, P.C. Redfern, V. Rassolov and J.A. Pople. J. Chem. Phys. 109 (1998), p. 7764. [2] A.G. Baboul, L.A. Curtiss, P.C. Redfern and K. Raghavachari. J. Chem. Phys. 110 (1999), p. 7650. [3] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery, R.E. Stratmann, J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B.G. Johnson, W. Chen, M.W. Wong, J.L. Andres, M. Head-Gordon, E.S. Replogle, J.A. Pople, Gaussian98 (RevisionA.11), Gaussian, Inc., Pittsburgh, PA, 1998.

Conference on Current Trends in Computational Chemistry 2005 175

Endohedral Carbon in Single-Wall Carbon Nanotubes

R. K. Vadapalli and J. W. Mintmire

Computational Materials Physics, Department of Physics Oklahoma State University Stillwater OK 74078

The discovery of carbon nanotubes (CNT) by Ijima and co-workers [1] revolutionized the research in carbon nanomaterials because of their potential in the next generation electronic device applications [2]. It has been widely demonstrated that the physical properties of CNTs and their conducting properties in particular can be controlled by intercalation of alkali and other atoms [3,4]. Recent experiments by Zhao et al. [5] provided an experimental evidence for the formation of carbon nanowires (CNW), a new type of nanostructure. A CNW could be viewed as a long linear carbon chain inserted inside the interior of a multi-walled carbon nanotube (MWNT) whose innermost tube radius is 3.4 Å, corresponding to the experimental interlayer spacing of graphene. Zhao et al., [5] also conducted density functional simulations of the CNWs constructed by inserting a cumulenic (…=C=C=C=…) carbon chain inside an armchair (5,5) SWNT. Liu et al. [6] speculated that during the formation of a MWNT, carbon atoms trapped inside the innermost CNT may lead to the formation of a linear carbon chain. In the CNW conformation, the interaction between the constituents units – the encapsulated carbon chain and the external CNT – plays a vital role in their usefulness in device applications. Both hybridization [7] and charge transfer [8] are important chemical effects to consider in the overall electronic structure of the CNW composite system. The encapsulated carbons of the linear carbon chain interacts with its own neighbors as well as with the wrapping CNT. Chen et al. [9] reported computational studies involving increasing the carbon-carbon nearest-neighbor distance, L, in the carbon chain, and reported an enhancement of interaction between the constituent units of zigzag (8,0) CNW structures when L=4.26 Å. Their calculations also showed additional states near the Fermi level due to the inserted carbon chain inside the interior of zigzag (8,0) SWNT which they speculated could lead to a potential increase in conductivity, in conformity with similar speculations by Zhao et al. [5]. To investigate the question of how the interactions between CNT and internal chain change with variations in the linear chain bond length, we have carried out a set of simulations using (7,3) SWNTs.

The simulations were carried out using the first-principles, all-electron, self-consistent local- density-functional (LDF) approach. This method was originally developed to treat chain polymers [10] and especially tailored to take advantage of helical symmetry [11]. This method calculates the total energy and electronic structure using Gaussian-type orbitals with one- dimensional band structure approach. In this method one electron wave functions are constructed from linear combinations of nuclear centered products of Gaussians and real solid spherical harmonics. In the present LDF calculations, we adopted 7s3p Gaussian basis set for carbon. We used 64 evenly spaced points over the Brillouin zone in solving the self-consistent LDF equations. Supercells were constructed to encapsulate the carbon chain so that the inter-carbon distance could be varied in the interval [1.2,3.0] Å. Commensurate periodic boundary conditions were imposed in these calculations. Mulliken population analysis is used to estimate the total charge transfer between the CNW and interior carbon chain.

Our preliminary calculations show that the constituent units of (7,3) CNW interact through charge transfer and hybridization. Fig.1 shows the amount of charge transfer on to the interior 176 Conference on Current Trends in Computational Chemistry 2005

carbon chain from the wrapping CNT. Fig. 1 indicates that the charge transfer increases with increase in L, the carbon-carbon bond distance in the carbon chain, and has an apparent maximum at L ≈ 2.0 Å. The corresponding electronic band structures are shown in Fig. 2. Comparison of Figs. 2(a) and 2(b) shows that additional states near the Fermi energy in Fig. 2(b) are due to the intercalated carbon leading to potentially quasimetallic behavior of the (7,3) CNW. The band structures of (7,3) CNW could be viewed as an additive sum of the electronic band structures of its constituent units and could be modeled within the rigid-band description. The lower Fermi level of the CNW compared to that of the (7,3) SWNT appears to be caused in large part by the charge transfer of electrons from the SWNT to the internal chain.

Intercalated (7,3) SWNT

0.12

0.1

0.08

0.06

0.04

0.02 Charge Transfer (e/C)

0 1 1.5 2 2.5 3 L (A)

Figure 1: Electron charge transfer to the carbon chain from the wrapping (7,3) SWNT as a function of bond length change in the interior carbon chain.

Figure 2: Electronic band structures of (a) pristine (7,3) SWNT (b) (7,3) CNW (c) isolated carbon chain. Conference on Current Trends in Computational Chemistry 2005 177

References: [1] S. Iijima, Nature 354, 56 (1991); S. Iijima and T. Ichihashi, Nature 363, 603 (1993) [2] Ph. Avouris, Chem. Phys. 281, 429 (2002); B. Ni, S. B. Sinnott, P. T. Mikulski, and J. A. Harrison, Phys. Rev. Lett. 88, 205505 (2002) [3] X. Yang and J. Ni, Phys. Rev. B 71, 165438 (2005) [4] Y. Wang, J. Theo. Comp. Chem, 4. 657 (2005) [5] X. Zhao, Y. Ando, Y. Liu, M. jinno, T. Suzuki, Phys. Rev. Lett. 90, 187401 (2003) [6] Y. Liu, R. O. Jones, X. Zhao, and Y. Ando, Phys. Rev. B 68, 125413 (2003) [7] X. Blase, L. X. Benedict, E. L. Shirley, and S. L. Louie, Phys. Rev. Lett. 72, 1878 (1994) [8] A. Rubio, Y. Miyamoto, X. Blase, M. L. Chohen, and S. G. Louie, Phys. Rev. B 53, 4023 (1996) [9] J. Chen, L. Yang, H. Yang, and J. Dong, Phys. Lett. A 316, 101 (2003) [10] J. W. Mintmire and C. T. White, Phys. Rev. Lett. 50, 101 (1983) [11] J. W. Mintmire, in “Density Functional Methods in Chemistry”, Edited by J. K.Labanowski (Springer-Verlag, Berlin, 1990) p. 125

178 Conference on Current Trends in Computational Chemistry 2005

Computational Study of Phosphonylation Mechanisms between Sarin and Acetylcholinesterase

Jing Wang, Jiande Gu, and Jerzy Leszczynski*

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

Potential energy surfaces for the phosphonylation between sarin and acetylcholinesterase have been theoretically studied by B3LYP/6-311G(d,p) level of theory. The effect of aqueous solvation was accounted for via the polarizable continuum model (PCM) at the same level. The results show that the phosphonylation process is a two-step addition-elimination mechanism, with the first step (addition process) being the rate-determining step while the ensuing steps are very rapid by comparison. The mechanisms also reveals that the catalytic triad of acetylcholinesterase plays the similar catalytic role in this reaction (speed up the phosphonylation process) as it does in the acylation reaction of ACh and AChE.

[ Sarin_Ser + F- ]

[ Sarin + SerO- ]

53.5 36.3 F F

4.9 4.4 11.5 8.0

F F F

Conference on Current Trends in Computational Chemistry 2005 179

Coupled-Cluster Studies of Photoelectron Spectra of Transition- Metal Halide Anions †

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 several 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)). The specific species studied are FeX4 and MX3 (M = Mn, Fe, Co, Ni; X = Cl, Br). 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 assist in the interpretation of the photoelectron spectra. In order to accomplish these tasks, a theoretical approach must: (a) provide a good account of the electron correlation in both the anion and several electronic states of the neutral species; (b) include a sufficiently flexible basis set to describe the anion and the different states of neutral species; and (c) have the ability to describe more than electronic state of a given computational or full symmetry. Our – initial work on FeCl3 has recently been published (J. D. Watts and M. Dupuis, Mol. Phys. 103, 2223-2227 (2005)). This work was quite successful in accounting for the observed data. - Calculations were performed on the ground states of FeCl3 and FeCl3, as well as the lowest - quartet states of FeCl3 and several excited sextet states of FeCl3. For FeCl3 , energies of six bands in the photoelectron spectrum have been reported. Our calculated data closely correspond to all of the observed energies. In particular, our results strongly suggest that the experimentally observed “A band” can be attributed to detachment of one of the unpaired 3d electrons, a conclusion that is not in accord with a simplistic analysis based on orbital energies. One – technique employed in our work on FeCl3 /FeCl3 was to describe several electronic states of FeCl3 with a common set of molecular orbitals. The practical difficulties of obtaining variationally optimum orbitals for several states are thereby avoided. Using common molecular orbitals, which is akin to quasi-restricted Hartree-Fock coupled-cluster methodology, depends on the ability of the coupled-cluster exponential ansatz to incorporate sufficient orbital relaxation. - We are now employing the techniques that were successful for FeCl3 to other first-row transition-metal chloride and bromide anions and neutral species, and some of these results will be reported.

† This work is supported by the National Science Foundation (grant numbers HRD0318519 and NSF300423-190200-21000) and the National Institutes of Health (S06 GM08047).

180 Conference on Current Trends in Computational Chemistry 2005

Searching for Nanowire Candidates among Synthetic Nucleic Acids

Jack C. Wells and Miguel Fuentes-Cabrera

Nanomaterials Theory Institute, Center for Nanophase Materials Sciences, and Computational Materials Science Group, Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN

The synthesis of modified versions of DNA is an area that is receiving much attention. The reasons for this are varied, and they span from the investigation of whether alternative genetic system could exist, to therapeutic and biotechnological applications. Recently, we are investigating whether synthetic nucleic acids could be used in nanotechnological applications that require good conductivity. We have concentrated on three synthetic nucleic acids: metalated DNA (M-DNA), xDNA and yDNA, the last two also known as size-expanded DNAs. Our interest in M-DNA sprang from the possibility that this nucleic acid could have metals atoms in between base pair, in particular one metal per base pair. Our interest on the size-expanded DNAs sprang from the possibility that these nucleic acids could have stronger π-π stacking interactions than natural DNA. Both metals and stronger π-π interactions could lead to better conductivity. Unfortunately, there is a paucity of experimental structural information on M-DNA, xDNA and yDNA. So it is wise to begin these investigations at the fundamental level, i.e. at the level of isolated bases and base pairs. Here theoretical and computational results concerning structural and electronic properties of isolated bases, base pairs, and columns of bases, will be presented. Our overarching goal is to probe whether the new field of Synthetic Biology could be an alternative route for synthesizing biological nanowires.

Conference on Current Trends in Computational Chemistry 2005 181

Combining Computational and Experimental Techniques to Study Complex Interfacial Adsorption Phenomena

Andrzej Wierzbicki

Department of Chemistry University of South Alabama Mobile, Alabama 36688

During the recent years the appreciation of the importance of interfacial adsorption phenomena has greatly increased. From complex biomineral structures present in nearly all biological systems, to intricate single crystals grown for modern technology applications, the understanding of molecular mechanisms of crystal growth control has became critical for both fundamental science and industry. Ultimately, the nanotechnology of the future will require precise, molecular-level control of the interfacial growth phenomena. The rapid progress of experimental techniques has greatly increased our ability to study crystal growth at interfaces. At the same time, however, it has opened a vast array of questions related to the molecular-level mechanisms governing interfacial phenomena. Computational chemistry methods were employed to pursue the investigation of the molecular mechanisms of crystal growth control at interfaces. Due to great complexity of interfacial systems, computational methods had to be closely complemented by experiment to aid the molecular-level interfacial studies. We will discuss the application of combined computational and experimental techniques, which were successfully employed to study the interfacial crystal growth in several important biomineralization systems involving crystallization of: calcite, hydroxyapatite, calcium oxalate monohydrate, and calcium pyrophosphate dihydrate. A similar approach, which was employed to study subtle structure-function relationship in the molecular-level mechanism of interfacial adsorption of antifreeze proteins will be presented. Potential future developments in the studies of the interfacial adsorption phenomena will be also discussed.

182 Conference on Current Trends in Computational Chemistry 2005

Chemical Reaction Pathway for the Phosphonylation of Serine

Adrian Wilson1,2, Gregory Woodall1,3, Elijah Johnson1,3, and Jerzy Leszczynski2

1Army High Performance Computing Research Center, 1200 Washington Avenue South, Minneapolis, MN 55415 2 Computational Center for Molecular Structures and Interactions, Jackson State University, P.O. Box 17910, Jackson, MS 39217 3 Florida A&M University, Tallahassee, Florida 32307

Chemical warfare was introduced to a shocked world during the World War I, when the French fired tear gas riffle grenades in 1914.The production of Sarin and other nerve agent began in Germany in the late 1930s.The German military immediately saw the potential of this compound and began producing it in large quantities. In this study the reaction pathway Sarin with Serine in the active site of Acetylcholinesterase has been investigated. Determining the minimum energy as a function of the distance between the phosphorus atom of Sarin and the oxygen atom of the hydroxyl group of Serine has been performed. In our study we have obtained a reaction pathway for Serine and Sarin molecule using GAMESS package. We also calculated the reaction pathway using effective fragments potential. Our objective for this study was achieved successfully.

Conference on Current Trends in Computational Chemistry 2005 183

Equilibrium Geometries of Mixed Metal-Semiconductor Clusters from Global Optimization and Associated Electronic Properties

Jianhua Wu and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Jackson State University, Jackson, MS 39217

The structural properties of MemSi7-m (Me=Cu and Li) clusters are systematically studied by density functional theory (DFT) within a plane wave approach. The geometric and energetic properties of these clusters are obtained by the Simulated Annealing method within the Nosé thermostat scheme. The lowest energy isomer thus obtained is further investigated using the all- electron B3LYP/6-311+G(d,p) procedure. Silicon clusters with metal atom impurities exhibit a rich variety of geometric and electronic characteristics. A metal atom added to a Sin cluster exerts a stabilizing effect on the cluster. 1 Beck fabricated MeSin (Me=Cu, Cr, Mo, and W) clusters that were found to be more stable towards photofragmenataion than bare Sin clusters of similar size by using a laser vaporization technique. Recently, Hiura et al.2 produced metal-encapsulating Si cluster ions of the form + MeSin (Me=Hf, Ta, W, Re, Ir, etc., with n=9,11--14). These indicate that combining Sin cluster with metal atoms leads to an enhanced stability, strong size selectively, and a widening of the HOMO-LUMO gap. Stimulated by these experimental findings, numerous computational investigations were performed for metal-doped silicon clusters.3-7 Studies dealing with several metal atoms in conjunction with silicion clusters, however, are rare, experimental work on 8,9 CuxSiy systems being an exception . This contribution focuses on the geometric and energetic properties of MemSi7-m (Me=Cu and Li) clusters. We chose these systems, since Si7, Li7 , and Cu7 all stabilize in equilibrium structures which share D5h symmetry. Due to the presence of two atom types in MemSi7-m (Me=Cu and Li) systems, these composites exhibit a much higher number of possible structural realizations than the respective pure metal and semiconductor clusters, which necessitates use of a global optimization scheme. Simulated annealing proved to be a reliable method for obtaining global minima, although it met with some difficulties for clusters of larger size. The global optimization of the geometry has been performed using the Vienna ab initio Simulation Package (VASP)10,11, which is based on Density Functional Theory (DFT). For further examination of the structures obtained by Simulated Annealing, we also analyzed the lowest isomers at the B3LYP/6-311+G(d,p) level.

References 1. S.M. Beck, J. Chem. Phys. 90, 6306 (1989). 2. H. Hiura, T. Miyazaki, and T. Kanayama, Phys. Rev. Lett. 86, 1733 (2001). 3. J.G. Han and Y.Y Shi, Chem. Phys. 266, 33 (2001). 4. J.G. Han, C. Xiao, and F. Hagelberg, Struct. Chem. 13, 173 (2002). 5. C. Xiao and F. Hagelberg, J Mol. Struct.: THEOCHEM 529, 241 (2000). 6. C. Xiao, F. Hagelbeg, and W. A. Lester, Jr., Phys. Rev. B 66, 075425 (2002). 7. V. Kumar and Y. kawazoe, Phys, Rev. Lett. 87, 045503 (2001). 8. J.J. Scherer, J.B. Paul, C.P. Collier, and R. J. Saykally, J. Chem. Phys., 102, 5190 (1995), 103, 113 (1995). 9. J.J. Scherer, J.B. Paul, C.P. Collier, A. O’Keefe, and R. J. Saykally, J. Chem. Phys., 103, 9187 (1995). 10. G. Kresse and J. Hafner, Phys. Rev. B 47, 558 (1993), B 49, 14251 (1994). 11. G. Kresse and J. Furthmuller, Comput. Mater. Sci. 6, 15 (1996). 184 Conference on Current Trends in Computational Chemistry 2005

CoMFA Studies of Antimalarial Compounds Based on 2,5-Diaminobenzophenone Scaffold

Aihua Xie,1 Prasanna Sivaprakasam,1 Robert J. Doerksen*1,2

1Department of Medicinal Chemistry and 2Research Institute for Pharmaceutical SciencesUniversity of Mississippi, MS, 38677-1848, USA

With annual death tolls in the millions, it is crucial to develop novel therapies against malaria. A series of recent papers by Wiesner et al.[1-6] reported a novel class of antimalarial agents derived from 2,5-diaminobenzophenone-based farnesyltransferase inhibitors with promising activity against multiresistant strains of P. falciparum. The 94 compounds include 4- propoxycinnamic acid derivatives and 4-nitrophenylfurylacryloyl derivatives. In this work, the quantitative structure-activity relationship of these compounds was investigated using comparative molecular fields analysis (CoMFA). A highly predictive CoMFA model was obtained. The CoMFA contour plots identified essential steric and electrostatic features for modification of lead compounds. They show that for the 2-arylacetylamino moiety, the steric factor plays a critical role in the antimalarial activity of these compounds. At the para position of the phenyl group, a bulky substituent will improve the antimalarial activity; while a bulky group at other positions of the phenyl group will decrease the activity. The substituents at the 5-amino group of the scaffold affect the antimalarial activity of those compounds mainly by their electrostatic property. A polar group with hydrogen bond acceptor properties at the para position of the terminal phenyl of the arylfurylacryloyl group also should benefit the antimalarial activity. The results of this study will be useful for designing more potent farnesyltransferase inhibitor analogs to target malaria.

References

(1) Wiesner, J.; Mitsch, A.; Wißner, P.; Jomaa, H.; Schlitzer, M. Structure-Activity Relationship of Novel Anti- Malarial Agents. Part 2: Cinnamic Acid Derivatives. Bioorg. Med. Chem. Lett. 2001, 11, 423-424. (2) Wiesner, J.; Kettler, K.; Jomaa, H.; Schlitzer, M. Structure-Activity Relationship of Novel Anti-Malarial Agents. Part 3: N-(4-Acylamino-3-benzoylphenyl)-4-propoxycinnamic Acid Amides Bioorg. Med. Chem. Lett. 2002, 12, 543-545. (3) Wiesner, J.; Mitsch, A.; Wißner, P.; Krämer, O.; Jomaa, H.; Schlitzer, M. Structure-Activity Relationship of Novel Anti-Malarial Agents. Part 4: N-(3-Benzoyl-4-tolylacetylaminophenyl)-3-(5-aryl-2-furyl)acrylic Acid Amides. Bioorg. Med. Chem. Lett. 2002, 12, 2681-2683. (4) Wiesner, J.; Kettler, K.; Sakowski, J.; Ortmann, R.; Jomaa, H.; Schlitzer, M. Structure-Activity Relationship of Novel Anti-Malarial Agents. Part 5: N-(4-acylamino-3-benzoylphenyl)-[5-(4-nitrophenyl)-2-furyl]acrylic Acid Amides. Bioorg. Med. Chem. Lett. 2003, 13, 361-363. (5) Wiesner, J.; Fucik, K.; Kettler, K.; Sakowski, J.; Ortmann, R.; Jomaa, H.; Schlitzer, M. Structure-Activity Relationship of Novel Anti-Malarial Agents. Part 6: N-(4-arylpropionylamino-3-benzoylphenyl)-[5-(4- nitrophenyl)-2-furyl]acrylic Acid Amides. Bioorg. Med. Chem. Lett. 2003, 13, 1539-1541. (6) Wiesner, J.; Mitsch, A.; Jomaa, H.; Schlitzer, M. Structure-Activity Relationship of Novel Anti-Malarial Agents. Part 7: N-(3-Benzoyl-4-tolylacetylaminophenyl)-3-(5-aryl-2-furyl)acrylic Acid Amides with Polar Moieties. Bioorg. Med. Chem. Lett. 2003, 13, 2159-2161.

Conference on Current Trends in Computational Chemistry 2005 185

Film Formation from Reactive Aqueous Solutions Containing Hydrophobic and Polar Groups: A Computer Simulation Model

Shihai Yang1, Sam Bateman, Adam Seyfarth, Erik Heidenreich2, Ras Pandey1, Marek Urban2

1Department of Physics and Astronomy 2Shelby F. Thames polymer science Research Center, School of Polymers and High Performance Materials The University of Southern Mississippi Hattiesburg, MS 39406

An improved computer simulation model is developed to determine processes leading to the film growth and morphological changes resulting from film formation. Such properties as surface roughness is correlated with the solution properties in aqueous (A) phase containing hydrophobic (H) and hydrophilic (P) components in a simple three dimensional lattice of size Lx*Ly*Lz on an absorbing substrate. These constituents represent water (H2O: A), polyisocyanate (R-N=C=O: H), and polyol (R’-OH: P). In addition to the main reactions between H and P components, the side reaction between H and A has been included. The number of reactive functional groups of each H, P and A particles is 3, 2 and 1, respectively, and hydrophobic components (H) react with aqueous (A) and polar (P) groups. Reactions between a hydrophobic (H) and an aqueous (A) component lead to a modified hydrophobic (R-NH2: H*) group which exhibits three functional groups, thus capable of further reactions with H*, H, P, and A. Following represents the reaction pathways,

Simulation data show a fast increase of the film thickness (h), followed by a relatively slow increase before reaching steady-state equilibrium (hs) in asymptotic time step limit. For the film interface width (W), a non-monotonic increase is observed before reaching steady-state equilibrium (Ws). Unlike the previous study with non-reactive aqueous component where a rapid decay in hs and Ws is followed by a slow increase on raising the temperature, a fast expansion of hs at low temperature with an exception at T=1 is followed by a slow expansion at high temperatures. A non-monotonic decay of Ws with temperature is also observed.

186 Conference on Current Trends in Computational Chemistry 2005

Fragmentation Dynamics of Organic Species Deposited on a Semiconductor Substrate

Jian-Ge Zhou and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Jackson State University Jackson, MS 39217

The interaction between semiconductor substrates, and especially silicon surfaces, and organic adsorbates has attracted much interest from the sides of both theory and experiment. This may be ascribed to the fundamental nature of this problem, involving finite and periodic systems of considerable complexity in contact with each other, as well as to numerous actual and potential applications of these composites in the areas of nanolithography, coating, or electronic and biosensing materials. In this contribution, we focus on the reaction of 1-propanol (C3H8O) with the Si(001)-(2 x 1) surface which was experimentally investigated by Auger electron spectroscopy and thermal desorption spectroscopy [1]. From this study, the 1-propanol molecule initially interacts with the Si surface through the formation of a ``dative bond", followed by O-H bond cleavage. From the work reported in [1], the O-H bond cleavage is a kinetically preferred process, but the O-C bond cleavage is thermodynamically favored. Using Density Functional Theory (DFT) within periodic boundary conditions, and more specifically a five layer slab model to represent the silicon surface, we identified various adsorption modes. Two types of mechanisms can be distinguished, namely physisorption and chemisorption. In the first case, the organic species remains essentially intact when being attached to the surface, in the second case, it undergoes a chemical reaction on the surface. We characterized two dominant chemisorption pathways, involving the cleavage of an O - H bond of propanol and that of an O - C bond. Performing band structure computations, we studied these configurations at different propanol coverage levels. With increasing coverage, the nature of the surface changes, that is, the graphite surface becomes more and more insulating. This conclusion is drawn from the trend of the Density-of-states (DOS) distributions at various coverage levels. Enhancing the density of propanol adsorbates on the surface, a very distinct widening of the energy gap for the combined system is observed. We included finite temperature effects by carrying out ab initio molecular dynamics calculations. Starting with a physisorbed configuration, we increased the temperature from 0 to 300 K and continued the simulation at this target temperature. O - H and a Si - H bond distances were recorded as functions of time. As room temperature is reached, the O - H bond of the organic adsorbate is ruptured, and the dissociated H atom attaches to a Si atom of the surface. The principal result of this study is that the loss of a H atom from 1-propanol on the Si(001) surface is kinetically favored and occurs almost spontaneously at room temperature, associated with the transition from a metastable physisorbed to a stable chemisorbed structure, which is in accord with experiment.

[1] L. Zhang, A. Carman, S. Casey, J. Phys. Chem. B107, 8424 (2003). Conference on Current Trends in Computational Chemistry 2005 187

Chemisorption of Alkanethiols on Au(111): Is It Dissociative or Nondissociative?

Jian-Ge Zhou and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Jackson State University Jackson, MS 39217

Much attention has recently been paid to the interaction between alkanethiol molecules and the Au(111) surface. This interest is related to the basic nature of this adsorption problem, as well as to numerous actual and potential applications of these composites in the areas of corrosion inhibition, lithography, lubrication, catalysis, molecular recognition and biosensing materials. In this contribution, we study the reaction of alkanethiol with the Au(111) surface which was experimentally proved to be nondissociative chemisorption [1]. Using Density Functional Theory (DFT) within periodic boundary conditions, and more specifically a four layer slab model to represent the gold surface, we identified various adsorption modes. On the basis of these studies, we propose nondissociative chemisorption as the prevailing interaction mechanism. Our results in conjunction with the measurements reported in [1] provide a conclusive solution of the long standing controversy concerning the dominant chemisorption mode, dissociative or nondissociative.

[1] I. Rzeznicka, J. Lee, P. Maksymovych, and J. Yates, Jr., J. Phys. Chem. B 109, 15992 (2005).

LLiisstt ooff

Conference on Current Trends in Computational Chemistry 2005 November 4-5, 2005 Jackson, Miss.

List of Participants Conference on Current Trends in Computational Chemistry 2005 191

Dmitriy Afanasiev Pierre Bonifassi Ukrainian State University 6 rue Saint Charles of Chemical Technology Residence Borromee NIL BAV, r. 206, 223 Le Mans, Sarthe72000 Dnepropetrovsk, 49005 Ukraine France Tel: +38(0562)929475 Tel: 001 33 16024082043 Email: [email protected] Email: [email protected]

Reeshemah Allen Ahmed Bouferguene Jackson State University University of Alberta Department of Chemistry 8406 - 91 Street, 1325 J.R. Lynch Street Edmonton, AlbertaT6C 4G9 P.O. Box 17910 Canada Jackson, MS 39217 U.S.A. Tel: 780 465 8719 Tel: 601 979-3979 Email: [email protected] Fax: 601 979-7823 Email: [email protected]

Oscar Arillo Flores Sylke Boyd Universidad Autónoma del Estado de University of Minnesota-Morris Morelos Morris, MN 56267 Av. Universidad 1001 U.S.A. Cuernavaca, Morelos 62209 Tel: 320-589-6315 Mexico Fax: 320-589-6371 Tel: 777 329 7997 Email: [email protected] Fax: 777 329 7998 Email: [email protected]

Chun-Li Bai Judge Brown II Chinese Academy of Science Jackson State University Institute of Chemistry Department of Chemistry Key Laboratory of Molecular Nanostructure 1325 J.R. Lynch Street and Nanotechnology P.O. Box 17910 Beijing, 10060 China Jackson, MS 39217 U.S.A. Tel: +86 10 62652120 Tel: (601) 954-8634 Email: [email protected] Email: [email protected]

Jon Baker Deborah Bryan Parallel Quantum Solutions Florida A&M University 2013 Green Acres Road Chemistry Department Suite A Jones Hall 219 Fayetteville, AR 72703 Tallahassee, FL 32307 U.S.A. U.S.A. Tel: (479) 521-5118 Tel: (850) 599-3672 Fax: (479) 521-5167 Email: [email protected] Email: [email protected]

Axel D. Becke Jaroslav Burda Queen's University Charles University in Prague Department of Chemistry Ke Karlovu 3 Chernoff Hall, Room 310 Prague, 12116 Kingston, OntarioK7L 3N6 Czech Republic Canada Tel: +420221911246 Tel: (613) 533-2634 Fax: +420221911249 Fax: (613) 533-6669 Email: [email protected] Email: [email protected]

Margarita Bernal-Uruchurtu Louis Carlacci Universidad Autónoma del Estado de AHPCRC / Network CS Inc Morelos 1425 Porter St Av. Universidad 1001 Frederick, MD 21702 Cuernavaca, Morelos 62209 U.S.A. Mexico Tel: 301-619-6732 Tel: 777 329 7997 Email: [email protected] Fax: 777 329 7998 Email: [email protected]

192 Conference on Current Trends in Computational Chemistry 2005 List of Participants

Marion Carroll LaTanya Dixon Xavier University of Louisiana Jackson State University Department of Chemistry Department of Chemistry 1 Drexel Drive 1325 J.R. Lynch Street New Orleans, LA 70125 P.O. Box 17910 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-981-3993 Tel: 601-979-3723 Email: [email protected] Fax: 601-979-6865 Email: [email protected]

Qianyi Cheng Helena Dodziuk Mississippi College Polish Academy of Sciences Dept. of Chemistry & Biochemistry Institute of Physical Chemistry Box 4036 Kasprzaka 44 Clinton, MS 39058 Warsaw, 01-224 U.S.A. Poland Tel: 601-925-3852 Tel: (48-22) 632-52-76 Fax: 601-925-3933 Fax: (48-22) 632-52-76 Email: [email protected] Email: [email protected]

Anthony Chuma Robert Doerksen University of Arkansas University of Mississippi Chemistry and Biochemistry Department of Medicinal Chemistry Fayetteville, AR 72701 421 Faser Hall U.S.A. University, MS 38677-1848 Tel: (479)575-5080 U.S.A. Email: [email protected] Tel: 6629155880 Fax: 6629155638 Email: [email protected]

David Close Floyd Fayton East Tennessee State University Howard University Physics Dept. Department of Chemistry Box 70652 525 College St. Johnson City, TN 37614 Washington, DC 20059 U.S.A. U.S.A. Tel: 423-439-5646 Tel: 202.806.6882 Fax: 423-439-6905 Fax: 202-806-6882 Email: [email protected] Email: [email protected]

Monica Concha James Fells Department of Chemistry University of Memphis University of New Orleans 213 Smith Chemistry Building New Orleans, LA 70148 Memphis, TN 38152-3550 New Orleans, LA 70148 U.S.A. U.S.A. Tel: 901-678-4425 Tel: 504-280-7216 Email: [email protected] Fax: 504-280-6860 Email: [email protected]

Sheritta Cooks Alan Ford Department of Chemistry Department of Chemistry and Armstrong Hall Room 102 Biochemistry Tuskegee University University of Arkansas Tuskegee, AL 36088 Fayetteville, AR 72701 U.S.A. U.S.A. Tel: (334)727-8237 Tel: (479) 575-5080 Fax: (334)727-8907 Email: [email protected] Email: [email protected]

Yuanqing Ding Jason Ford-Green National Center of Natural Products Jackson State University Research Department of Chemistry The University of Mississippi 1325 J.R. Lynch Street University, MS 38677 P.O. Box 17910 U.S.A. Jackson, MS 39217 U.S.A. Tel: 662-915-1027 Tel: 850-443-9233 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2005 193

Ryan Fortenberry Leonid Gorb Mississippi College US Army ERDC Dept. of Chemistry & Biochemistry 3532 Manor Drive, Suite 3 Box 4036 Viksburg, MS 39180 USA Clinton, MS 39058 Tel: 601-634-3863 U.S.A. Email: [email protected] Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Fillmore Freeman Matthew Gravelle Department of Chemistry University of Minnesota-Morris University of California, Irvine Morris, MN 56267 Irvine, CA 92697-2025 U.S.A. U.S.A. Tel: 320-589-6315 Tel: 949-824-6501 Fax: 320-589-6371 Fax: 949-824-2210 Email: [email protected] Email: [email protected]

Miguel Fuentes-Cabrera Helen Grebneva Oak Ridge National Laboratory Rose Luxemburg str. 84 Oak Ridge, TN 37831 Donetsk, 83114 U.S.A. Ukraine Tel: (865) 576-6277 Tel: +38 062 304 81 21 Fax: (865) 241-0381 Email: [email protected] Email: [email protected]

Al'ona Furmanchuk Jiande Gu Jackson State University Shanghai Institute of Materia Medica Department of Chemistry Chinese Academy of Sciences 1325 J.R. Lynch Street Shanghai , 201203 P.O. Box 17910 China Jackson, MS 39217 U.S.A. Tel: 86-21-50806720 Tel: 601-979-1134 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

Jiali Gao Frank Hagelberg University of Minnesota Jackson State University Department of Chemistry Department of Physics 207 Pleasant Street, SE 1325 J.R. Lynch Street Minneapolis, MN 55455-0431 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601 979 3633 Tel: 612-625-0769 Fax: 601 979 3630 Fax: 612-626-7541 Email: [email protected] Email: [email protected]

Xiaoxia Ge Mark G. Hardy Weill Medical College and Graduate School Associate Dean, College of Science, of Cornell University Engineering, and Technology 1300 York Ave. W-203 Jackson State University New York, NY 10021 Jackson, MS 39217 U.S.A. Tel: 601-979-3449 Tel: (646)691-5886 Email: [email protected] Email: [email protected]

Ainsley Gibson John Harkless Howard University Howard University Department of Chemistry 525 College St., NW 525 College Street NW Washington, DC 20059 Washington , DC 20059 U.S.A. U.S.A. Tel: 202-806-6899 Tel: (202) 806-6882 Fax: 202-806-5442 Fax: (202) 806-5442 Email: [email protected] Email: [email protected]

194 Conference on Current Trends in Computational Chemistry 2005 List of Participants

Frances Hill Shelley Huskey Network Computing Services, Inc/AHPCRC Copiah-Lincoln Community College 1200 Washington Ave S Department of Chemistry Minneapolis, MN 55415 P.O. Box 649 U.S.A. Wesson, MS 39191 Tel: 612-337-3569 U.S.A. Fax: 612-337-3483 Tel: 601-643-8375 Email: [email protected] Email: [email protected]

Glake Hill, Jr. Olexandr Isayev Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 Lynch St. 1325 J.R. Lynch Street Jackson, MS 39217 U.S.A. P.O. Box 17910 Phone: (601) 979-1699 Jackson, MS 39217 U.S.A. Fax: (601) 979-7823 Tel: 601-979-1134 E-mail: [email protected] Fax: 601-979-7823 Email: [email protected]

Shonda Allen Hill Harsh Jain Jackson State University Florida A&M University Department of Chemistry Tallahassee, FL 32307 1325 Lynch St. U.S.A. Jackson, MS 39217 U.S.A. Tel: 850-599-8195 Phone: (601) 979-3723 Email: [email protected] Fax: (601) 979-7823 E-mail: [email protected]

Tiffani Holmes Cynthia Jeffries Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street 1325 J.R. Lynch Street P.O. Box 17910 P.O. Box 17910 Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 228-623-0673 Tel: 601-979-3723 Fax: 601-979-7823 Fax: 601-979-6865 Email: [email protected] Email: [email protected]

Ming-Ju Huang Hyun Joo Jackson State University Auburn University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street 179 Chemistry Building P.O. Box 17910 Auburn, AL 36830 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601-979-3492 Tel: 334-524-9108 Fax: 601-979-3674 Email: [email protected] Email: [email protected]

Danielle Hudson Yana Kholod Department of Chemistry Dnipropetrovsk National University Armstrong Hall Room 102 Department of Chemistry Tuskegee University Nauchny St. 13 Tuskegee, AL 36088 Dnepropetrovsk, 49625 Ukraine U.S.A. Tel: +38(0562)463143 Tel: (334)727-8878 Email: [email protected] Fax: (334)727-8907 Email: [email protected]

Estelle Huff Wim Klopper University of Arkansas Universität Karlsruhe, Institut für Chemistry Building 101 Physikalische Chemie Fayetteville, AR 72701 Lehrstuhl for Theoretische Chemie U.S.A. Kaiserstrasse 12 Tel: 479-575-5080 Karlsruhe, 76128 Germany Email: [email protected] Tel: (0721) 608 7263 [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2005 195

Dmytro Kosenkov Christa Loar Jackson State University Florida A&M University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street Room 219 Jones Hall P.O. Box 17910 Tallahassee, FL 32307 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601-979-3981 Tel: 850-524-1432 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Gulnara Kuramshina Brandon Magers Department of Physical Chemistry, Faculty Mississippi College of Chemistry Dept. of Chemistry & Biochemistry Moscow State University Box 4036 Vorob'evy Gory Clinton, MS 39058 Moscow, 119992 Russia U.S.A. Tel: 7(095)939-2950 Tel: 601-925-3852 Fax: 7(095)932-7746 Fax: 61-925-3933 Email: [email protected] Email: [email protected]

Danuta Leszczynska David Magers FAMU-FSU College of Engineering Mississippi College Department of Civil Engineering Dept. of Chemistry & Biochemistry 2525 Pottsdamer Str. Box 4036 Tallahassee, FL 32310 U.S.A. Clinton, MS 39058 Tel: 904-487-6137 U.S.A. Fax: 904-487-6142 Tel: 601-925-3851 Email: [email protected] Fax: 61-925-3933 Email: [email protected]

Jerzy Leszczynski Devashis Majumdar Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street 1325 J.R. Lynch Street P.O. Box 17910 P.O. Box 17910 Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-979-3482 Tel: 601-979-7824 Fax: 601-979-7823 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Meng-Sheng Liao Massimo Malagoli Jackson State University Parallel Quantum Solutions Department of Chemistry 2013 Green Acres Road, Suite A 1325 J.R. Lynch Street Fayetteville, AR 72703 P.O. Box 17910 U.S.A. Jackson, MS 39217 U.S.A. Tel: (479) 521-5118 Tel: (601)979-3714 Fax: (479) 521-5167 Fax: (601)979-3674 Email: malagoli@pqs-chem.com Email: [email protected]

Hans Lischka Ronald Mason University of Vienna President, Jackson State University Institute of Theoretical Chemistry 1400 Lynch St. Währingerstraße 17 Jackson, MS 39217-0280 USA Vienna, A-1090 Tel: 601.979.2323 Austria Fax: 601.979.2948 Tel: +43-1-4277-52757 E-mail: [email protected] Fax: +43-1-4277-9527 Email: [email protected]

Dan Liu Stephen L. Mayo Jackson State University California Institute of Technology Department of Chemistry HHMI/Caltech 114-96 1325 J.R. Lynch Street 1200 E. California Blvd. P.O. Box 17910 Pasadena, CA 91125-9600 Jackson, MS 39217 U.S.A. U.S.A. Tel: (601) 201-3484 Tel: (626) 395-6408 Email: [email protected] Fax: (626) 568-0934 Email: [email protected]

196 Conference on Current Trends in Computational Chemistry 2005 List of Participants

Harley McAlexander Edmund Moses Ndip Mississippi College Hampton University Dept. of Chemistry & Biochemistry East Queen & Tyler Streets Box 4036 Hampton, VA 23668 Clinton, MS 39058 U.S.A. U.S.A. Tel: (757) 727 5043 Tel: 601-925-3852 Fax: (757) 727 5604 Fax: 601-925-3933 Email: [email protected] Email: [email protected]

James L. Meeks Felix Okojie West Kentucky Comm & Tech College Vice President for Research Department of Physics and Strategic Initiatives PO BOX 7380 Jackson State University Paducah, KY 42002-7380 Jackson, MS 39217 USA U.S.A. Tel: 601-979-2931 Tel: 270 534 3137 Fax: 601-979-3664 Fax: 270 534 6291 Email: [email protected] Email: [email protected]

Andrea Michalkova Sergiy Okovytyy Jackson State University Dnipropetrovsk National University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street Nauchny St. 13 P.O. Box 17910 Dnepropetrovsk, 49625 Ukraine Jackson, MS 39217 U.S.A. Tel: +(38050)5919276 Tel: 601-979-1041 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

Abdul K. Mohamed Irma Orellana Dean, College of Science, Engineering & 1ra ave. Km 23.5 casa 75-C Guatemala Technology Guatemala, Guatemala502 Jackson State University Guatemala Jackson, MS 39217 USA Tel: (502) 66329133 Tel: 601-979-2153 Email: [email protected] Email: [email protected]

R.D. Morris Ourida Ouamerali Xavier University of Louisiana USTHB BP N°32 El Alia Department of Chemistry Bab Ezzouar 1 Drexel Drive Algiers, 16111 New Orleans, LA 70125 Algeria U.S.A. Tel: + 213 21 24 73 11 Tel: 601-979-2171 Fax: + 213 21 24 73 11 Email: [email protected] Email: [email protected]

Jane Murray Ras Pandey Department of Chemistry University of Southern Mississippi University of New Orleans Physics & Astr., Box 5046 New Orleans, LA 70148 Hattiesburg, MS 39406 U.S.A. U.S.A. Tel: 504-280-3250 Tel: 601 266 4485 Fax: 504-280-6860 Fax: 601 266 5149 Email: [email protected] Email: [email protected]

Jamshid Najafpour John. A Parmentola Khalig-e fars freeway Director for Research and Laboratory Shahr-e-rey, Tehran1645779711 Management, US Army Iran SAAL-TR, Suite 9000 Tel: +98-21-7255373 2511 Jefferson Davis Highway Fax: +98-21-2296122 Arlington, VA 22202-3911 U.S.A. Email: [email protected] Tel: (703) 601-1524 Fax: (703) 607-5989

List of Participants Conference on Current Trends in Computational Chemistry 2005 197

Michele Parrinello Morgan Ponder Swiss Federal Institute of Technology Samford University Zurich, Department of Chemistry and Department of Chemistry Applied Biosciences Birmingham, AL 35229-2236 USI-Campus, Via Giuseppe Buffi 13, LUI U.S.A. Lugano, CH-6900 Switzerland Tel: 205-726-2680 Tel: +41 91 913 88 01 Fax: 205-726-2479 Fax: +41 91 913 88 17 Email: [email protected] Email: [email protected]

Yuliya Paukku Rita Presley Jackson State University Associate Vice President for Research & Department of Chemistry Sponsored Programs 1325 J.R. Lynch Street Jackson State University P.O. Box 17910 Jackson, MS 39217 USA Jackson, MS 39217 U.S.A. Phone: 601.979.2457 Tel: (601) 979-7824 E-mail: [email protected] Fax: (601) 979-7823 Email: [email protected]

James Perkins Peter Pulay Director of Research, Industrial & University of Arkansas Community Relations Department of Chemistry and Jackson State University Biochemistry College of Science, Engineering & Phoenix Hall Technology (CSET) Fayetteville, AR 72701 U.S.A. Jackson, MS 39217 USA Tel: (479)-575-6612 Phone: 601-979- 2024 Fax: (479)-575-4049 E-mail: [email protected] Email: [email protected]

Gurusamy Perumal Bakhtiyor Rasulev SRNM College Jackson State University Sattur, 626203 Department of Chemistry India 1325 J.R. Lynch Street Tel: 04562260187 P.O. Box 17910 Email: [email protected] Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Tetyana Petrova Paresh Ray Dnipropetrovsk National University Jackson State University Department of Chemistry Department of Chemistry Nauchny St. 13 1325 J.R. Lynch Street Dnepropetrovsk, 49625 Ukraine P.O. Box 17910 Tel: +380 56 246-3143 Jackson, MS 39217 U.S.A. Email: [email protected] U.S.A. Tel: 601-979-3486 Fax: Email: [email protected] Yevgeniy Podolyan Melissa Reeves Jackson State University Department of Chemistry Department of Chemistry Armstrong Hall Room 102 1325 J.R. Lynch Street Tuskegee University P.O. Box 17910 Tuskegee, AL 36088 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601-979-4114 Tel: (334)727-8237 Fax: 601-979-7823 Fax: (334)727-8907 Email: [email protected] Email: [email protected]

Peter Politzer Ashley Ringer Department of Chemistry Georgia Institute of Technology University of New Orleans School of Chemistry and Biochemistry New Orleans, LA 70148 770 State Street U.S.A. Atlanta, GA 30332-0400 Tel: 504-280-6850 U.S.A. Fax: 504-280-6860 Tel: 404-385-1310 Email: [email protected] Fax: 404-894-7452 [email protected]

198 Conference on Current Trends in Computational Chemistry 2005 List of Participants

Carmen Robinson Julia Saloni Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street 1325 J.R. Lynch Street P.O. Box 17910 P.O. Box 17910 Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-979-3981 Tel: 601-979-3979 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

Teri Robinson Hasan Sayin Jackson State University Chemistry and Biochemistry Department of Chemistry 179 Chemistry BLDG 1325 J.R. Lynch Street Auburn Univeristy P.O. Box 17910 Auburn, AL 36830 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601-979-3981 Tel: 334 8446953 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Szczepan Roszak Yinghong Sheng Institute of Physical and Theoretical Jackson State University Chemistry Department of Chemistry Wroclaw University of Technology 1325 J.R. Lynch Street Wyb. Wyspianskiego 27 P.O. Box 17910 Wroclaw, 50370 Poland Jackson, MS 39217 U.S.A. Tel: 48 71 3466041 Tel: 6019791219 Fax: 48 71 3203364 Fax: 6019797823 Email: [email protected] Email: [email protected]

Manuel F. Ruiz-López C. David Sherrill Université Henri Poincaré Georgia Institute of Technology Domaine Scientifique, Boulevard des School of Chemistry and Biochemistry Aiguillettes, Nancy-I, BP 239 Atlanta, GA 30332-0400 UMR CNRS-UHP No. 7565, BP 239 U.S.A. Vandoeuvre-les-Nancy, 54506 France Tel: 404-894-4037 Tel: (+33) 83 68 43 72 Fax: 404-894-7452 Fax: (+33) 83 68 43 71 Email: [email protected] Email: [email protected]

Svein Saebo Manoj Shukla Department of Chemistry Jackson State University Mississippi State University Department of Chemistry Mississippi State, MS 39762 1325 J.R. Lynch Street U.S.A. P.O. Box 17910 Tel: 662-325-7813 Jackson, MS 39217 U.S.A. Fax: 662-325-1618 Tel: 601-979-1136 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

Hassan Safouhi Tomekia Simeon University of Alberta Jackson State University Campus Saint-Jean Department of Chemistry 8406, 91 Street 1325 J.R. Lynch Street Edmonton, T6C 4G9 P.O. Box 17910 Canada Jackson, MS 39217 U.S.A. Tel: + 1 (780) 485 8631 Tel: 601-918-3424 Fax: + 1 (780) 465 8760 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Zuhail Sainudeen Prasanna Sivaprakasam Jackson State University 417, Faser Hall, Department of Chemistry Department of Medicinal Chemistry, 1325 J.R. Lynch Street School of Pharmacy, University P.O. Box 17910 University of Mississippi Jackson, MS 39217 U.S.A. University, MS 38677 U.S.A. Tel: 601-940-3390 Tel: 662-915-1853 Email: [email protected] Fax: 662-915-5638 Email: [email protected]

List of Participants Conference on Current Trends in Computational Chemistry 2005 199

Talibah Smith Dinadayalane Tandabany Jackson State University Jackson State University Department of Chemistry Department of Chemistry 1325 J.R. Lynch Street 1325 J.R. Lynch Street P.O. Box 17910 P.O. Box 17910 Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-238-8134 Tel: 601-979-7824 Fax: 601-979-7823 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Vitaly Solkan Lyssa Taylor Leninskii pr-t 47 Mississippi College Moscow, 119991 Dept. of Chemistry & Biochemistry Russia Box 4036 Tel: 7(095)1356425 Clinton, MS 39058 Fax: 7(095)1355328 U.S.A. Email: [email protected] Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Amika Sood Tamara Taylor Mississippi College Jackson State University Dept. of Chemistry & Biochemistry Department of Chemistry Box 4036 1325 J.R. Lynch Street Clinton, MS 39058 P.O. Box 17910 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-925-3852 Tel: 601-454-0052 Fax: 601-925-3933 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Angela Sood Kanchana Thanthiriwatte Mississippi College Department of Chemistry, Dept. of Chemistry & Biochemistry Mississippi State University Box 4036 Box 9573 Clinton, MS 39058 Mississippi State, MS 30762 U.S.A. U.S.A. Tel: 601-925-3852 Tel: (662)-325-4633 Fax: 601-925-3933 Fax: (662)-325-1618 Email: [email protected] Email: [email protected]

Jiří Šponer Gregory Tschumper Academy of Sciences of the Czech Department of Chemistry and Republic, Institute of Biophysics Biochemistry Kralovopolska 135 University of Mississippi Brno, 612 65 Czech Republic University, MS 38677 Tel: 420 5412 12179 USA Fax: 420 5412 12179 Tel: (662) 915-7301 Email: [email protected] Fax: (662) 915-7300 Email: [email protected]

Jaroslaw Szymczak Mark Turner Jackson State University University of Arkansas Department of Chemistry Dept. of Chemistry and Biochemistry 1325 J.R. Lynch Street Fayetteville, AR 72701 P.O. Box 17910 U.S.A. Jackson, MS 39217 U.S.A. Tel: (479)525-5080 Tel: 601-979-1632 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

Genzo Tanaka Jan Urban Florida A&M University Mlynska dolina F1 205 Jones Hall Bratislava, 84248 Tallahassee, FL 32307 Slovak Republic U.S.A. Tel: 00421260295682 Tel: 850-599-3666 Fax: 00421265425882 Fax: 850-599-3953 Email: [email protected] Email: [email protected]

200 Conference on Current Trends in Computational Chemistry 2005 List of Participants

Jing Wang Zhijian Wu Jackson State University Institute for Materials Research Department of Chemistry Tohoku University 1325 J.R. Lynch Street Sendai, 980-8577 P.O. Box 17910 Japan Jackson, MS 39217 U.S.A. Tel: +81-22-215-2237 Tel: 601-979-1159 Email: [email protected] Fax: 601-979-7823 Email: [email protected]

John Watts Aihua Xie Jackson State University Faser Hall 417 Department of Chemistry Department of Medicinal Chemistry 1325 J.R. Lynch Street School of Pharmacy P.O. Box 17910 University, MS 38677 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601 979 3488 Tel: 662-915-1853 Fax: 601 979 3674 Fax: 662-915-5638 Email: [email protected] Email: [email protected]

Jack C. Wells Shihai Yang Oak Ridge National Laboratory The University of Southern Mississippi Computer Science and Mathematics Hattiesburg, MS 39406 Division U.S.A. Oak Ridge, TN 37831 Tel: 601-297-5459 U.S.A. Email: [email protected] Tel: 865-241-2853 Email: [email protected]

Robert W. Whalin Ilya Yanov Associate Dean, College of Science, Jackson State University Engineering & Technology Department of Chemistry Jackson State University 1325 J.R. Lynch Street Jackson, MS 39217 USA P.O. Box 17910 Tel: 601-979-4043 Jackson, MS 39217 U.S.A. Email: [email protected] Tel: (601)9794136 Fax: (601)9797823 Email: [email protected]

Andrzej Wierzbicki Hongtao Yu University of South Alabama Jackson State University Department of Chemistry Department of Chemistry Mobile, AL 36688 1325 Lynch St. U.S.A. Jackson, MS 39217 U.S.A. Tel: (251) 460-7436 Tel: (601)979-2174 Fax: (251) 460-7359 Fax: (601)979-3674 Email: [email protected] Email: [email protected]

Adrian Wilson Shuming Zhang Jackson State University Department of Chemistry and Department of Chemistry Biochemistry 1325 J.R. Lynch Street University of Arkansas P.O. Box 17910 Fayetteville, AR 72701 Jackson, MS 39217 U.S.A. U.S.A. Tel: 601-979-7824 Tel: 479-575-5080 Fax: 601-979-7823 Email: [email protected] Email: [email protected]

Jianhua Wu Jian-Ge Zhou Jackson State University Jackson State University Department of Physics Department of Physics 1325 J.R. Lynch Street 1325 J.R. Lynch Street Jackson, MS 39217 U.S.A. Jackson, MS 39217 U.S.A. Tel: 601-979-3640 Tel: 601-979-3640 Fax: 601-979-3630 Fax: 601-979-3630 Email: [email protected] Email: [email protected]

Author Index Conference on Current Trends in Computational Chemistry 2005 201

Author Index

Afanasyev, Dmitriy Y...... 19,50 Ge, Xiaoxia ...... 70 Agwaramgbo, Lovell ...... 21,22 Gibson, Ainsley A...... 57,72 Allen, Reeshemah N...... 23 Gill, Gurvinder ...... 73,74 Arillo-Flores, O. I...... 24 Gomarooni, Mahshid ...... 64 Baker, Jon ...... 27 Gonzalez, Jose ...... 72 Bateman, Sam ...... 28,185 Gorb, Leonid ...... 65,83,87,90,111,129 Batich, C...... 117 Gravelle, Matthew ...... 75 Becke, Axel D...... 29 Grebneva, H. A...... 78 Bernal-Uruchurtu, M. I...... 24,30 Gu, Jiande ...... 40,178 Bishop, G. Reid ...... 162 Gwaltney, Steven R...... 172 Bonifassi, P...... 32 Hagelberg, Frank ...... 105,183,186,187 Bouferguene, Ahmed ...... 35,135 Harb , W...... 30 Boyd, Sylke ...... 75 Harkless, John A.W...... 57,72 Brown, Judge ...... 38 Hättig, Christof ...... 89 Bryan, Deborah J...... 39 Heidenreich, Erik ...... 185 Burda, Jaroslav V...... 40 Hill, Glake ...... 21,22,52 Buynak, John ...... 70 Hobza, Pavel ...... 166 Carroll, Marion L...... 41 Holmes, April ...... 41 Cheng, Mu-Jeng ...... 44 Honea, Patricia ...... 161 Chu San-Yan ...... 44 Huang, Ming-Ju ...... 82,100 Chuma, Anthony ...... 45 Isayev, Olexandr ...... 65,83 Clark, Tim ...... 113 Janowski, Tomasz ...... 84 Cline,Tiffarah ...... 21 Johnson, Elijah ...... 182 Close, David M...... 46,131 Johnson, Erin R...... 29,106 Coghlan, Crystal B...... 107,109,171 Joo, Hyun ...... 86 Concha, Monica C...... 113 Jurecka, Petr ...... 166 Cooks, Sherrita M...... 47 Kasyan, L.I...... 124 Daga, Pankaj R...... 145 Kelly, Algernon ...... 41 Dinadayalane, T. C...... 48,50,68 Kholod, Yana ...... 87 Dixon, LaTanya ...... 52 Kirakosyan, Arman S...... 88 Dodziuk, Helena ...... 53 Klopper, Wim ...... 89 Doerksen, Robert J...... 145,184 Koca, Jaroslav ...... 126 Doskocz, Marek ...... 55 Kosenkov, Dmytro ...... 90 Edwards, Jesse ...... 39,117 Krasovska, Maryna V...... 91 Fayton, Floyd, Jr.,...... 57,72 Kukueva, V...... 92 Fells, James, I...... 58 Kuramshina, G.M...... 96,168 Fisher, D...... 117 Lee, Thuy ...... 41 Fliegl, Heike ...... 89 Leontis, Neocles B...... 126 Ford, Alan ...... 59 Leszczynski, Jerzy...... Ford, Endia ...... 41 21,23,32,40,48,50,52,55,60,65,68,83,87,90,111, Ford-Green, Jason ...... 60 119,120,122,124,129,138,141,143,147,148,154, Fortenberry, Ryan ...... 61 167,170,173,178,182 Fowler, Patrick W...... 27 Levkovich, Mikhail G...... 173 Fredrickson, Herbert ...... 87 Liao, Meng-Sheng ...... 100 Freeman , Fillmore...... 62,64 Lillington, Mark ...... 27 Fuentes-Cabrera, Miguel ...... 180 Lischka, Hans ...... 101 Furey, John ...... 87 Liu, Dan ...... 105 Furmanchuk, Al’ona ...... 65,83 Lively, Ryan P...... 127 Gancarz, Roman ...... 55 Loar, Christa ...... 106 Gao, Jiali ...... 67 Lovell, M. Jeanann ...... 162 Gayatri, G...... 68 Mach, P...... 174 202 Conference on Current Trends in Computational Chemistry 2005 Author Index

Magers, Brandon ...... 107,109 Sample, Shemika ...... 41 Magers, David H...... 61,107,109,161,162,100 Sansudeen, Zuhail ...... 139 Majumdar, Devashis ...... 55,60,119,120 Sastry, G. Narahari ...... 68 Martinez, J...... 111 Sayin , Hasan ...... 140 Matveev, V.K...... 96 Sefcikova, Jana ...... 91 Mayo, Stephen L...... 108 Seyfarth, Adam ...... 28,185 McAlexander, Harley ...... 107,109 Shahbazyan, Tigran V...... 88,125 McKee, Michael L...... 86,140 Sharapov, D.A...... 96 Meeks, James L...... 110 Sharapova, S.A...... 96 Metoyer, Toye ...... 41 Sheng, Yinghong ...... 141 Michalkova, A...... 111,119,120,129 Sherrill, C. David ...... 127,142 Mintmire, J. W...... 175 Shevlin, Philip B...... 86 Morris, R. D...... 41 Shishkin, Oleg ...... 65 Murray, Jane S...... 113 Shukla, M.K...... 23,143 Najafpour, Jamshid ...... 114 Sinnokrot, Mutasem O...... 127 Ndip, Edmund Moses N...... 116 Sivaprakasam, Prasanna ...... 145,184 Neiss, Christian ...... 89 Smith, Talibah ...... 147 Noe, Eric A ...... 73,74,123 Solkan, Vitaly ...... 148,151,154,158 Odukale, A. A...... 117 Soncini , Alessandro ...... 27 Okegbe, Tishina ...... 21 Sood, Amika ...... 161 Okovytyy, Sergiy ...... 87,124 Sood, Angela ...... 162 Ouamerali, Ourida ...... 133 Speaks, Chi-Cobi ...... 22 Palchikov, V.A...... 124 Sponer, Jiri ...... 91,126,164,166,167 Pandey, R.B...... 28,185 Sponer, Judit E...... 167 Parker, R...... 117 Sukhanov, Oleg ...... 65 Parrill, Abby L...... 58 Syn’ko, S.V...... 168 Parrinello, Michele ...... 118 Szymczak, Jaroslaw J...... 170 Pat Lane, ...... 113 Tarabara, I.N...... 124 Paukku, Y ...... 119,120,122 Taylor, Gordon J. P...... 72 Pawar, Diwakar M...... 73,123 Taylor, Lyssa ...... 171 Pentin, Yu.A...... 96,168 Tew, David P...... 89 Petrova, T...... 124 Thanthiriwatte, Kanchana S...... 172 Po, Henry N...... 62 Turabekova, Malakhat A...... 173 Podolyan, Yevgeniy ...... 90 Turner, Jo-Lyque ...... 52 Politzer, Peter ...... 113 Urban, J...... 174 Probst, M...... 174 Urban, Marek W...... 28,170,185 Prosyanik, Alexander V...... 19 Vadapalli, R. K...... 175 Pulay, Peter ...... 59,84,134 Walter, Nils G...... 91 Pustovit, V. N...... 125 Wang, Jing ...... 178 Qasim, Mohammad (Mo) ...... 87 Watts, John D...... 38,100,179 Rasulev, Bakhtiyor F...... 122,147,173 Wells, Jack C...... 180 Ray, Paresh Chandra ...... 32,139 Wierzbicki, Andrzej ...... 181 Razga, Filip ...... 126 Wilson, Adrian ...... 182 Reeves, Melissa S...... 47 Woodall, Gregory ...... 182 Ringer, Ashley L...... 127 Wu, Jianhua ...... 183 Robinson, T. L...... 129 Xie, Aihua ...... 145 Ross, E...... 117 Xie, Aihua ...... 184 Roszak, Szczepan ...... 55,138,170 Yang, Shihai ...... 185 Saal, Amar ...... 133 Zhikol, O. A...... 111 Sadjadi, Abdolreza ...... 114 Zhou, Jian-Ge ...... 186,187 Saebo, Svein ...... 134 Safouhi, Hassan ...... 35,135 Saloni, Julia ...... 138