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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
Citations
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Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies.
Samuel Genheden,Ulf Ryde +1 more
TL;DR: The results indicate that both the truncation and neutralization of the proteins may slow the convergence and emphasize small differences in the calculations, e.g., differences between the four subunits in avidin.
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Polysulfonate suramin inhibits Zika virus infection.
TL;DR: The inhibitory effect of glycosaminoglycans and analogues against ZIKV infection, including highly sulfated heparin, dextran sulfate and suramin significantly inhibited ZikV infection in Vero cells, suggests that sulfonate groups are critical for viral inhibition.
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Applying Classical, Ab Initio, and Machine-Learning Molecular Dynamics Simulations to the Liquid Electrolyte for Rechargeable Batteries.
TL;DR: In this paper , the authors provide an overview of applying molecular dynamics simulations in the study of liquid electrolytes for rechargeable batteries, including probing bulk and interfacial structures, deriving macroscopic properties such as ionic conductivity and dielectric constant, and revealing the electrode-electrolyte interfacial reaction mechanisms.
Journal ArticleDOI
Metal–Organic Framework/Polymer Mixed-Matrix Membranes for H2/CO2 Separation: A Fully Atomistic Simulation Study
TL;DR: In this paper, a fully atomistic simulation study was performed on mixed-matrix membranes composed of polybenzimidazole (PBI) and zeolitic imidazolate framework-7 (ZIF-7).
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Theoretical study of the discrimination between O(2) and CO by myoglobin.
Emma Sigfridsson,Ulf Ryde +1 more
TL;DR: The results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.
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.