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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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Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields
TL;DR: The transferability of the force parameters to β‐D‐glucose‐6‐sulfate and isopropyl sulfate appears to be better than to isoprostyl sulfamate, and the frequencies compared favorably with the AMBER and CHARMm calculated frequencies.
Journal ArticleDOI
Homology modeling of rat and human cytochrome P450 2D (CYP2D) isoforms and computational rationalization of experimental ligand-binding specificities.
Jennifer Venhorst,Antonius Ter Laak,Jan N. M. Commandeur,Yoshihiko Funae,Toyoko Hiroi,Nico P. E. Vermeulen +5 more
TL;DR: New insights are provided into differences in the active site topology of the investigated CYP2D isoforms and MD studies on the binding mode of sparteine, quinidine, and quinine concurred well with experimentally determined IC(50) values and metabolic profiles.
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Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides
Kalju Kahn,Thomas C. Bruice +1 more
TL;DR: The parameters for the OPLS–AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides and it is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.
Journal ArticleDOI
Fast electron correlation methods for molecular clusters without basis set superposition errors.
TL;DR: Two critical extensions to the fast, accurate, and easy-to-implement binary or ternary interaction method for weakly interacting molecular clusters have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine-water clusters with an excellent initial performance assessment result.
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Aggregation effects on the optical emission of 1,1,2,3,4,5-hexaphenylsilole (HPS): a QM/MM study.
TL;DR: The photophysical property for 1,1,2,3,4,5-hexaphenylsilole (HPS) is investigated through combined quantum mechanical and molecular mechanical simulations and the calculated solid-phase absorption and emission optical spectra of HPS are found to be in agreement with the experiment.
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.