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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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TLDR
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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Theoretical Study of Base-Catalyzed Amide Hydrolysis: Gas- and Aqueous-Phase Hydrolysis of Formamide
Dirk Bakowies,Peter A. Kollman +1 more
TL;DR: In this article, a three-step procedure has been applied which comprises the determination of a gas-phase reaction path by high-level ab initio calculations, the calibration of empirical solute−solvent potentials, and classical Monte Carlo simulations of the solute immersed in a bath of solvent molecules.
Journal ArticleDOI
Gaussian induced dipole polarization model.
TL;DR: A new induced dipole polarization model based on interacting Gaussian charge densities is presented and it will be shown that the Gaussian polarization model performs slightly better than the Thole model in terms of fitting to molecular polarizability tensors.
Journal ArticleDOI
A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases
María-Natalia Lisa,Antonela Rocio Palacios,Mahesh Aitha,Mariano M. González,Diego M. Moreno,Michael W. Crowder,Robert A. Bonomo,James Spencer,David L. Tierney,Leticia I. Llarrull,Alejandro J. Vila +10 more
TL;DR: It is shown that different MβLs share the same reaction mechanism, suggesting new strategies for drug design and open avenues for rationally designed inhibitors of all M βLs, notwithstanding the profound differences between these enzymes’ active site structure, β-lactam specificity and metal content.
Journal ArticleDOI
Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches
Dirk Bakowies,Walter Thiel +1 more
TL;DR: In this article, a semi-empirical treatment of electrostatic potentials and partial charges is presented, which is the basic components needed for the evaluation of the electrostatic interaction energies in combined quantum mechanical and molecular mechanical approaches.
Journal ArticleDOI
Overview of the SAMPL6 host–guest binding affinity prediction challenge
Andrea Rizzi,Steven Murkli,John N. McNeill,Wei Yao,Matthew R. Sullivan,Michael K. Gilson,Michael W. Chiu,Lyle Isaacs,Bruce C. Gibb,David L. Mobley,John D. Chodera +10 more
TL;DR: An overview of the SAMPL6 host–guest binding affinity prediction challenge, which featured three supramolecular hosts and an overall improvement in the correlation obtained by the affinity predictions for OA and TEMOA systems, but a surprising lack of improvement regarding root mean square error over the past several challenge rounds.
References
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Journal ArticleDOI
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.