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NBO 2008 (Jan-Dec) - 910 references Compiled by Emily Wixson; Updated by Ariel Neff 4/16/13 Adalsteinsson, H.; Debusschere, B. J.; Long, K. R.; Najm, H. N. Components for atomistic-to-continuum multiscale modeling of flow in micro- and nanofluidic systems Scientific Programming, (16): 297-313 2008. Adcock, W.; Trout, N. A. Diastereofacial selectivity in some 4-substituted (X) 2-adamantyl derivatives: electronic versus steric effects Journal of Physical Organic Chemistry, (21): 68-72 2008. Agapito, F.; Nunes, P. A.; Costa Cabral, B. J.; Borges dos Santos, R. A.; Martinho Simoes, J. A. Energetic differences between the five- and six-membered ring hydrocarbons: Strain energies in the parent and radical molecules Journal of Organic Chemistry, (73): 6213-6223 2008. Aguilar-Castro, L.; Tlahuextl, M.; Mendoza-Huizar, L. H.; Tapia-Benavides, A. R.; Tlahuext, H. Hydrogen bond studies in substituted N-(2-hydroxyphenyl)-2-[(4- methylbenzenesulfonyl)amino]acetamides Arkivoc: 210-226 2008. Alajarin, M.; Cabrera, J.; Pastor, A.; Sanchez-Andrada, P.; Bautista, D. Polar hetero-Diels-alder reactions of 4-alkenylthiazoles with 1,2,4-triazoline-3,5-diones: An experimental and computational study Journal of Organic Chemistry, (73): 963-973 2008. Albertin, G.; Antoniutti, S.; Baldan, D.; Castro, J.; Garcia-Fontan, S. Preparation of benzyl azide complexes of iridium(III) Inorganic Chemistry, (47): 742-748 2008. Alcoba, D. R.; Ona, O. Determination of energies and electronic densities of functional groups according to partitionings in the physical space Journal of Physical Chemistry A, (112): 10023-10028 2008. Alia, J. D.; Vlaisavljevich, B. Prediction of molecular properties including symmetry from quantum-based molecular structural formulas, VIF Journal of Physical Chemistry A, (112): 9784-9795 2008. Alizadeh, M. H.; Eshtiagh-Hosseini, H.; Mirzaei, M.; Salimi, A. R.; Razavi, H. Synthesis, X-ray crystallography characterization, vibrational spectroscopy, and DFT theoretical studies of a new organic-inorganic hybrid material Structural Chemistry, (19): 155-164 2008. Alkorta, I.; Blanco, F.; Eiguero, J. Molecular complexes of pentazolo[1,2-a]pentazole, N-8 Journal of Physical Chemistry A, (112): 1817-1822 2008. Alkorta, I.; Blanco, F.; Elguero, J. pi-systems as simultaneous hydride and hydrogen bond acceptors Journal of Physical Chemistry A, (112): 6753-6759 2008. Alkorta, I.; Blanco, F.; Solimannejad, M.; Elguero, J. Competition of Hydrogen Bonds and Halogen Bonds in Complexes of Hypohalous Acids with Nitrogenated Bases Journal of Physical Chemistry A, (112): 10856-10863 2008. Alkorta, I.; Elguero, J.; Grabowski, S. J. How to determine whether intramolecular H center dot center dot center dot H interactions can be classified as dihydrogen bonds Journal of Physical Chemistry A, (112): 2721-2727 2008. Alkorta, I.; Elguero, J.; Solimannejad, M. Dihydrogen bond cooperativity in (HCCBeH)(n) clusters Journal of Chemical Physics, (129) 2008. Alkorta, M.; Blanco, F.; Solimannejad, M.; Eiguero, J. Competition of Hydrogen Bonds and Halogen Bonds in Complexes of Hypohalous Acids with Nitrogenated Bases Journal of Physical Chemistry A, (112): 10856-10863 2008. Alkorta, M.; Elguero, J.; Grabowski, S. J. How to determine whether intramolecular H center dot center dot center dot H interactions can be classified as dihydrogen bonds Journal of Physical Chemistry A, (112): 2721-2727 2008. Altamura, M.; Dapporto, P.; Guidi, A.; Harmat, N. J. S.; Jierry, L.; Libralesso, E.; Paoli, P.; Rossi, P. Investigation on the flexibility of chiral tricyclic derivatives New Journal of Chemistry, (32): 1617-1627 2008. Anane, H.; El Houssame, S.; El Guerraze, A.; Guermoune, A.; Boutalib, A.; Jarid, A.; Nebot-Gil, I.; Tomas, F. A G2(MP2) theoretical study of substituent effects on H3BNHnCl3-n (n=3-0) donor-acceptor complexes Central European Journal of Chemistry, (6): 400-403 2008. Andruniow, T.; Jaworska, M.; Lodowski, P.; Zgierski, M. Z.; Dreos, R.; Randaccio, L.; Kozlowski, P. M. Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of methylcobalamin Journal of Chemical Physics, (129) 2008. Anizelli, P. R.; Vilcachagua, J. D.; Cunha Neto, A.; Tormena, C. F. Stereoelectronic interaction and their effects on conformational preference for 2-substituted methylenecyclohexane: An experimental and theoretical investigation Journal of Physical Chemistry A, (112): 8785-8789 2008. Antonczak, S. Electronic description of four flavonoids revisited by DFT method Journal of Molecular Structure-Theochem, (856): 38-45 2008. Aragoni, M. C.; Arca, M.; Devillanova, F. A.; Hursthouse, M. B.; Huth, S. L.; Isaia, F.; Lippolis, V.; Mancini, A.; Verani, G. Reactions of Halogens/Interhalogens with polypyridyl substrates: The case of 2,4,6-tris(2- pyridyl)-1,3,5-triazine European Journal of Inorganic Chemistry: 3921-3928 2008. Aragoni, M. C.; Arca, M.; Devillanova, F. A.; Isaia, F.; Lippolis, V. Polyiodides and polytellurides: Analogies and differences Phosphorus Sulfur and Silicon and the Related Elements, (183): 1036-1045 2008. Arciniegas, M.; Pena, J.; Manero, J. M.; Paniagua, J. C.; Gil, F. J. Quantum parameters for guiding the design of Ti alloys with shape memory and/or low elastic modulus Philosophical Magazine, (88): 2529-2548 2008. Aronica, C.; Chumakov, Y.; Jeanneau, E.; Luneau, D.; Neugebauer, P.; Barra, A. L.; Gillon, B.; Goujon, A.; Cousson, A.; Tercero, J.; Ruiz, E. Structure, Magnetic Properties, Polarized Neutron Diffraction, and Theoretical Study of a Copper(II) Cubane Chemistry-a European Journal, (14): 9540-9548 2008. Auer, B. M.; Skinner, J. L. Vibrational sum-frequency spectroscopy of the liquid/vapor interface for dilute HOD in D2O Journal of Chemical Physics, (129) 2008. Autschbach, J.; Zheng, S. H. Analyzing Pt chemical shifts calculated from relativistic density functional theory using localized orbitals: The role of Pt 5d lone pairs Magnetic Resonance in Chemistry, (46): S45-S55 2008. Autschbacha, J. Analyzing NMR shielding tensors calculated with two-component relativistic methods using spin- free localized molecular orbitals Journal of Chemical Physics, (128) 2008. Ayotte, P.; Plessis, S.; Marchand, P. Trapping proton transfer intermediates in the disordered hydrogen-bonded network of cryogenic hydrofluoric acid solutions Physical Chemistry Chemical Physics, (10): 4785-4792 2008. Azam, K. A.; Bennett, D. W. Double carbon-hydrogen activation of 2-vinylpyridine: Synthesis of tri- and pentanuclear clusters containing the mu-NC5H4CH=C ligand Organometallics, (27): 5163-5166 2008. Azizoglu, A.; Balci, M.; Mieusset, J. L.; Brinker, U. H. Substituent Effects on the Ring-Opening Mechanism of Lithium Bromocyclopropylidenoids to Allenes Journal of Organic Chemistry, (73): 8182-8188 2008. Bach, R. D.; Dmitrenko, O.; Thorpe, C. Mechanism of thiolate-disulfide interchange reactions in biochemistry Journal of Organic Chemistry, (73): 12-21 2008. Bachmann, C.; Frapper, G. Cl/F-exchange reaction in COCl2/SbF5 system: A theoretical investigation Chemical Physics Letters, (457): 292-297 2008. Balcells, D.; Nova, A.; Clot, E.; Gnanamgari, D.; Crabtree, R. H.; Eisenstein, O. Mechanism of homogeneous iridium-catalyzed alkylation of amines with alcohols from a DFT study Organometallics, (27): 2529-2535 2008. Balcells, D.; Raynaud, C.; Crabtree, R. H.; Eisenstein, O. A Rational Basis for the Axial Ligand Effect in C-H Oxidation by [MnO(porphyrin)(X)](+) (X = H2O, OH-, O2-) from a DFT Study Inorganic Chemistry, (47): 10090-10099 2008. Balta, B.; Ozturk, C.; Aviyente, V.; Vincent, M. A.; Hillier, I. H. Claisen rearrangement of aliphatic allyl vinyl ethers in the presence of copper(II) bisoxazoline Journal of Organic Chemistry, (73): 4800-4809 2008. Baric, D.; Maksic, Z. B. The Baeyer strain is strongly affected by the nucleus-electron attraction - a comment on the Letter of G. Hohlneicher and L. Packschies [Tetrahedron Lett. 2007, 48, 6429-6433] Tetrahedron Letters, (49): 1428-1431 2008. Barnett, C. B.; Naidoo, K. J. Stereoelectronic and Solvation Effects Determine Hydroxymethyl Conformational Preferences in Monosaccharides Journal of Physical Chemistry B, (112): 15450-15459 2008. Barone, C. R.; Cini, R.; Clot, E.; Eisenstein, O.; Maresca, L.; Natile, G.; Tamasi, G. A NMR, X-ray, and DFT combined study on the regio-chemistry of nucleophilic addition to platinum(II) coordinated terminal olefins Journal of Organometallic Chemistry, (693): 2819-2827 2008. Barros, N.; Eisenstein, O.; Maron, L.; Tilley, T. D. DFT investigation of the catalytic hydromethylation of olefins by scandocenes. 2. Influence of the ansa ligand on propene and isobutene hydromethylation Organometallics, (27): 2252-2257 2008. Baumann, W.; Schulz, A.; Villinger, A. A Blue Homoleptic Bismuth-Nitrogen Cation Angewandte Chemie-International Edition, (47): 9530-9532 2008. Beckmann, J.; Finke, P.; Heitz, S.; Hesse, M. Aryltellurenyl cation [RTe(CR '(2))]+ stabilized by an N-heterocyclic carbene European Journal of Inorganic Chemistry: 1921-1925 2008. Bei, Y.-L.; Zhu, C.-F. Dynamical and thermodynamic studies on the isomerization reaction of cis-halogeno silylene to halogeno silyl(silylene) Acta Chimica Sinica, (66): 810-816 2008. Bei, Y.-L.; Zhu, C.-F.; Liu, Q.-Y.; Qi, G.-B. Addition reaction of pentacoordinated silicon compounds by R3SiX with NR3' Acta Physico-Chimica Sinica, (24): 217-222 2008. Ben Said, R.; Tangour, B.; Barthelat, J.-C. Quantum chemical investigations of intramolecular isomerization in RuH2(CO)(2)(PMe3)(2) Journal of Molecular Structure-Theochem, (857): 115-122 2008.
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    04/21/2011 Organometallics Study Meeting H.Mitsunuma 1. Crystal field theory (CFT) and ligand field theory (LFT) CFT: interaction between positively charged metal cation and negative charge on the non-bonding electrons of the ligand LFT: molecular orbital theory (back donation...etc) Octahedral (figure 9-1a) d-electrons closer to the ligands will have a higher energy than those further away which results in the d-orbitals splitting in energy. ligand field splitting parameter ( 0): energy between eg orbital and t2g orbital 1) high oxidation state 2) 3d<4d<5d 3) spectrochemical series I-< Br-< S2-< SCN-< Cl-< N -,F-< (H N) CO, OH-< ox, O2-< H O< NCS- <C H N, NH < H NCH CH NH < bpy, phen< NO - - - - 3 2 2 2 5 5 3 2 2 2 2 2 < CH3 ,C6H5 < CN <CO cf) pairing energy: energy cost of placing an electron into an already singly occupied orbital Low spin: If 0 is large, then the lower energy orbitals(t2g) are completely filled before population of the higher orbitals(eg) High spin: If 0 is small enough then it is easier to put electrons into the higher energy orbitals than it is to put two into the same low-energy orbital, because of the repulsion resulting from matching two electrons in the same orbital 3 n ex) (t2g) (eg) (n= 1,2) Tetrahedral (figure 9-1b), Square planar (figure 9-1c) LFT (figure 9-3, 9-4) - - Cl , Br : lower 0 (figure 9-4 a) CO: higher 0 (figure 9-4 b) 2. Ligand metal complex hapticity formal chargeelectron donation metal complex hapticity formal chargeelectron donation MR alkyl 1 -1 2 6-arene 6 0 6 MH hydride 1 -1 2 M MX H 1 -1 2 halogen 1 -1 2 M M -hydride M OR alkoxide 1 -1 2 X 1 -1 4 M M -halogen O R acyl 1 -1 2 O 1 -1 4 M R M M -alkoxide O 1-alkenyl 1 -1 2 C -carbonyl 1 0 2 M M M R2 C -alkylidene 1 -2 4 1-allyl 1 -1 2 M M M O C 3-carbonyl 1 0 2 M R acetylide 1 -1 2 MMM R R C 3-alkylidine 1 -3 6 M carbene 1 0 2 MMM R R M carbene 1 -2 4 R M carbyne 1 -3 6 M CO carbonyl 1 0 2 M 2-alkene 2 0 2 M 2-alkyne 2 0 2 M 3-allyl 3 -1 4 M 4-diene 4 0 4 5 -cyclo 5 -1 6 M pentadienyl 1 3.
  • The Application of Semiempirical Methods in Drug Design

    The Application of Semiempirical Methods in Drug Design

    THE APPLICATION OF SEMIEMPIRICAL METHODS IN DRUG DESIGN By MARTIN B. PETERS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2007 1 c 2007 Martin B. Peters 2 For Jane 3 ACKNOWLEDGMENTS Words cannot describe my Jane. She is everything I can could ask for. She has stood by me even when I left Ireland to pursue my dream of getting my PhD. Thank you honey for your love, support and the sacrifices you have made for us. I thank my mother for always giving me tremendous support and for her words of wisdom and encouragement. I would also like to thank my two brothers, Patrick and Francis, and my two sisters, Marian and Deirdre, for all their encouragement and support. Kennie thank you for giving me the opportunity to work with you; I have truly enjoyed the experience. I would like to express my gratitude to all Merz group members especially Kaushik, Andrew, Ken, Kevin, and Duane for their support and friendship. Also I would like to acknowledge the effort of Mike Weaver who helped by editing this dissertation. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS ................................. 4 LIST OF TABLES ..................................... 8 LIST OF FIGURES .................................... 11 LIST OF ABBREVIATIONS ............................... 15 ABSTRACT ........................................ 19 CHAPTER 1 INTRODUCTION .................................. 21 2 THEORY AND METHODS ............................. 25 2.1 Receptor-Ligand Binding Free Energy ..................... 28 2.2 Computational Drug Design .......................... 30 2.3 Molecular Mechanics .............................. 32 2.4 Quantum Mechanics .............................. 33 2.5 Ligand Based Drug Design ..........................