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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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Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications
George A. Khoury,Jeffrey P. Thompson,James Smadbeck,Chris A. Kieslich,Christodoulos A. Floudas +4 more
TL;DR: This forcefield for post-translational modifications in condensed-phase simulations can be applied to a number of biologically relevant and timely applications including protein structure prediction, protein and peptide design, docking, and to study the effect of PTMs on folding and dynamics.
Journal ArticleDOI
Simulation Studies of Amide I IR Absorption and Two-Dimensional IR Spectra of β Hairpins in Liquid Water
TL;DR: It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 betahairpin are the same, which demonstrates that the present computational method is quantitatively reliable.
Journal ArticleDOI
Carbohydrate force fields
TL;DR: The history of carbohydrate force fields is reviewed, examining and comparing their challenges, forms, philosophies, and development strategies, and a survey of recent uses is presented, noting trends, strengths, deficiencies, and possible directions for future expansion.
Journal ArticleDOI
In Situ Poling and Imidization of Amorphous Piezoelectric Polyimides
TL;DR: An amorphous piezoelectric polyimide containing polar functional groups has been developed using a combination of experimental and molecular modeling for potential use in high temperature applications as mentioned in this paper.
Journal ArticleDOI
Enzymatic Processing of Uracil Glycol, a Major Oxidative Product of DNA Cytosine
TL;DR: During translesion DNA synthesis, Ug was bypassed more efficiently than Tg in all sequence contexts examined and the steady state kinetic parameters indicated that Ug was a better substrate for endo III and formamidopyrimidine DNA glycosylase than TG; for endonuclease VIII, however, Tg was a best substrate.
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.