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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.Abstract:
We present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactionsread more
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On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds
TL;DR: Three methods of ESH construction are introduced and it is shown how various schemes depend on the selection of the ESH parameters and to what extent the energies and geometries are reliable.
Journal ArticleDOI
Accuracy of free energies of hydration using CM1 and CM3 atomic charges.
Marina Udier-Blagovi,Patricia I. Morales de Tirado,Shoshannah A. Pearlman,William L. Jorgensen +3 more
TL;DR: Absolute free energies of hydration (ΔGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers.
Journal ArticleDOI
Interaction of carboranes with biomolecules: formation of dihydrogen bonds.
TL;DR: The dominant interaction between carborane and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms, which can be used to explain the specificity of inhibition of HIV protease by carboranes.
Journal ArticleDOI
Interaction of pyrimethamine, cycloguanil, WR99210 and their analogues with Plasmodium falciparum dihydrofolate reductase: structural basis of antifolate resistance.
Giulio Rastelli,Worachart Sirawaraporn,Pornthep Sompornpisut,Tirayut Vilaivan,Sumalee Kamchonwongpaisan,Rachel Quarrell,Gordon Lowe,Yodhathai Thebtaranonth,Yongyuth Yuthavong +8 more
TL;DR: The nature of the interactions between Plasmodium falciparum dihydrofolate reductase and antimalarial antifolates including some of their analogues was investigated by molecular modeling in conjunction with the determination of the inhibition constants.
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Absorption of CO2 in the ionic liquid 1-n-hexyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([hmim][FEP]): a molecular view by computer simulations.
TL;DR: A united-atom force field for the [FEP] anion is developed and the continuous fractional component Monte Carlo (CFC MC) method is used to predict CO2 absorption isotherms in 1-n-hexyl-3-methylimidazolium ([hmim]) [F EP] at 298.2 and 323.2 K and pressures up to 20.0 bar.
References
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The MIDAS display system
TL;DR: At the core of MIDAS is a hierarchical database system, designed specifically for macromolecules, that is both compact in its storage requirements and fast in its data access.