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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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Molecular dynamics generation of nonarbitrary membrane models reveals lipid orientational correlations.
Yuji Takaoka,Marta Pasenkiewicz-Gierula,Marta Pasenkiewicz-Gierula,Hiroh Miyagawa,Kunihiro Kitamura,Yoshiyasu Tamura,Akihiro Kusumi +6 more
TL;DR: This report generated a computer model of the liquid-crystalline L-alpha-dimyristoylphosphatidylcholine bilayer, starting from a configuration based on a crystal structure (rather than from an arbitrary structure), which shows the presence of significant orientational correlations between neighboring alkyl chains and between shoulder vectors of neighboring DMPCs.
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Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.
TL;DR: The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computationally and shows that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from theOxirane than for the thiolate obtaining from the thiiranes.
Journal ArticleDOI
Pyrazolo[3,4-c]pyridazines as novel and selective inhibitors of cyclin-dependent kinases.
Miguel F. Braña,Mónica Cacho,M. Luisa García,Elena P. Mayoral,Berta López,Beatriz de Pascual-Teresa,Ana Ramos,Nuria Acero,F. Llinares,Dolores Muñoz-Mingarro,Olivier Lozach,Laurent Meijer +11 more
TL;DR: Monofuryl 1o has been synthesized and is one of the most active compounds against CDK1 of this series and has been rationalized on the basis of the proposed binding mode for compound 1a.
Journal ArticleDOI
Robustness in the fitting of molecular mechanics parameters
TL;DR: A novel restraining strategy is presented that overcomes robustness issues in the LLS fitting of bonded parameters while minimally impacting the fitted values of well‐behaved parameters.
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.