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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
Citations
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Allosteric transcriptional regulation via changes in the overall topology of the core promoter
Steven J. Philips,Mónica A. Canalizo-Hernández,Ilyas Yildirim,George C. Schatz,Alfonso Mondragón,Thomas V. O'Halloran +5 more
TL;DR: It is shown here how the prokaryotic regulatory protein CueR both represses and activates transcription by differentially modulating local DNA structure within the promoter by dramatically changing the shape of promotor DNA.
Journal ArticleDOI
Insight into NSAID-induced membrane alterations, pathogenesis and therapeutics: characterization of interaction of NSAIDs with phosphatidylcholine.
Lenard M. Lichtenberger,Yong Zhou,Vasanthi Jayaraman,Janice R. Doyen,Roger G. O'Neil,Elizabeth J. Dial,David E. Volk,David G. Gorenstein,Mohan Babu Boggara,Ramanan Krishnamoorti +9 more
TL;DR: It is proposed that the pH-dependent partition of these potent anti-inflammatory drugs into the phospholipid bilayer, and possibly extracellular mono/multilayers present on the luminal interface of the mucus gel layer, may result in profound changes in the hydrophobicity, fluidity, permeability, biomechanical properties and stability of these membranes and barriers.
Journal ArticleDOI
Elucidating the structure of the magnesium aluminum chloride complex electrolyte for magnesium-ion batteries
Pieremanuele Canepa,Pieremanuele Canepa,Saivenkataraman Jayaraman,Lei Cheng,Nav Nidhi Rajput,William D. Richards,Gopalakrishnan Sai Gautam,Gopalakrishnan Sai Gautam,Larry A. Curtiss,Kristin A. Persson,Gerbrand Ceder,Gerbrand Ceder +11 more
TL;DR: In this article, a rigorous analysis of the magnesium aluminum chloride complex (MACC) in tetrahydrofuran (THF), one of the few electrolytes that can reversibly plate and strip Mg, is presented.
Journal ArticleDOI
Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa.
TL;DR: This first application of GIST to protein–ligand modeling, for the case of Coagulation Factor Xa, shows that ligand scoring functions based on GIST perform at least as well as scoring functionsbased on a hydration-site approach (HSA), when applied to exactly the same simulation data.
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Potential energy functions
TL;DR: Improvements in methodology for determining parameters--particularly, in the systematic use of computational data obtained from quantum chemical calculations--and enhancements in functional form are leading to better potential energy functions for molecules in general and in improving the treatment of metal-ligand interactions in systems of biomolecular interest.
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.