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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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Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies.
Roberto Gaspari,C. Rechlin,Andreas Heine,Giovanni Bottegoni,Walter Rocchia,Daniel Schwarz,Jörg Bomke,Hans Dieter Gerber,Gerhard Klebe,Andrea Cavalli,Andrea Cavalli +10 more
TL;DR: The para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides are investigated, providing a complete reconstruction of their binding pathway to hCAII by means of large-scale molecular dynamics simulations, density functional calculations, surface plasmon resonance measurements, and X-ray crystallography experiments.
Journal ArticleDOI
Atomistic Insight into Orthoborate-Based Ionic Liquids: Force Field Development and Evaluation
Yong-Lei Wang,Faiz Ullah Shah,Sergei Glavatskih,Sergei Glavatskih,Oleg N. Antzutkin,Oleg N. Antzutkin,Aatto Laaksonen,Aatto Laaksonen +7 more
TL;DR: An all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids is developed based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters.
Journal ArticleDOI
OH-Stretching Red Shifts in Bulky Hydrogen-Bonded Alcohols: Jet Spectroscopy and Modeling
TL;DR: The available database for OH-stretching bands of jet-cooled aliphatic alcohol dimers is extended, using a heated pulsed nozzle coupled to an FTIR spectrometer, to simplify and parametrize the standard AMBER/parm99.dat force field for the prediction of hydrogen-bond-induced red shifts.
Journal ArticleDOI
Variational and perturbative formulations of quantum mechanical/molecular mechanical free energy with mean-field embedding and its analytical gradients.
TL;DR: In this article, a direct quantum mechanical/molecular mechanical (QM/MM) analog of such a mean-field theory is formulated based on variational and perturbative frameworks.
Journal ArticleDOI
A proactive role of water molecules in acceptor recognition by protein O-fucosyltransferase 2
Jessika Valero-González,Christina Leonhard-Melief,Erandi Lira-Navarrete,Gonzalo Jiménez-Osés,Gonzalo Jiménez-Osés,Gonzalo Jiménez-Osés,Cristina Hernández-Ruiz,María Carmen Pallarés,Inmaculada Yruela,Deepika Vasudevan,Anabel Lostao,Francisco Corzana,Hideyuki Takeuchi,Robert S. Haltiwanger,Ramon Hurtado-Guerrero +14 more
TL;DR: Crystallographic and mutagenesis data, together with atomic-level simulations, uncover a binding mechanism by which POFUT2 promiscuously recognizes the structural fingerprint of poorly homologous TSRs through a dynamic network of water-mediated interactions.
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.