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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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Asymmetric Synthesis of 2,3-Dihydro-2-arylquinazolin-4-ones: Methodology and Application to a Potent Fluorescent Tubulin Inhibitor with Anticancer Activity
Gary M. Chinigo,Mikell Paige,Scott Grindrod,Ernest Hamel,Sivanesan Dakshanamurthy,Maksymilian Chruszcz,Wladek Minor,Milton L. Brown +7 more
TL;DR: A synthetic route that allows access to either enantiomer of a variety of DHQZ derivatives is disclosed and the utility of this chemistry is illustrated with the asymmetric preparation and biological evaluation of a new chiral fluorescent tubulin binding agent with extremely potent antiproliferative properties against human cancer cells.
Journal ArticleDOI
Thermal and Transport Properties of Six Ionic Liquids: An Experimental and Molecular Dynamics Study
TL;DR: In this article, experimental measurements and molecular dynamics simulations are used to determine the density, heat capacity, self-diffusivity, shear viscosity, and thermal conductivity of six ionic liquids over a range of temperatures.
Journal ArticleDOI
Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Alan P. Graves,Devleena M. Shivakumar,S.E. Boyce,Matthew P. Jacobson,David A. Case,Brian K. Shoichet +5 more
TL;DR: This work re-ranked docking hit lists in three small buried sites in molecular mechanics-generalized Born surface area techniques, and rescoring not only rescued docking false positives, but also introduced several new false positives into the top-ranking molecules.
Journal ArticleDOI
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data.
TL;DR: This work introduces ForceBalance, a method and free software package for systematic force field optimization with the ability to parametrize a wide variety of functional forms using flexible combinations of reference data.
Journal ArticleDOI
A molecular dynamics investigation of the structural and dynamic properties of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide
Hongjun Liu,Edward J. Maginn +1 more
TL;DR: The results suggest that the dynamical behavior of this and related ionic liquids is extremely complex and consists of many different modes with widely varying timescales, making the prediction of dynamical trends extremely difficult.
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.