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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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Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained
TL;DR: A mechanistic rationale on how natural cinchona alkaloids act as efficient bifunctional catalysts is proposed by using a broad range of computational methods, including classical molecular dynamics, a mixed quantum mechanical/molecular mechanics (QM/MM) approach, and correlated ab-initio calculations.
Journal ArticleDOI
Vitamin D Receptor Agonists Specifically Modulate the Volume of the Ligand-binding Pocket
TL;DR: Variations in the volume of agonists lead to adaptations in thevolume of the LBP and alternative contacts of anchoring OH-groups, confirmed by in vitro assays.
Journal ArticleDOI
Melt Crystallization for Paracetamol Polymorphism
Alexander G. Shtukenberg,Melissa Tan,Leslie Vogt-Maranto,Eric J. Chan,Wenqian Xu,Jingxiang Yang,Mark E. Tuckerman,Mark E. Tuckerman,Chunhua Hu,Bart Kahr +9 more
TL;DR: Trimorphic paracetamol, one of the most commonly used analgesic and antipyretic drugs, has been a model system for studying transformations among phases of molecular crystalline materials.
Journal ArticleDOI
Multi-Scale Approach to Non-Adiabatic Charge Transport in High-Mobility Organic Semiconductors.
TL;DR: A linear scaling QM/MM model for studying charge transport in high-mobility molecular semiconductors is presented and applied to an anthracene single crystal and a hexabenzocoronene derivative in its liquid crystalline phase.
Journal ArticleDOI
The impact of molecular dynamics sampling on the performance of virtual screening against GPCRs.
TL;DR: It is proposed here that MD simulation can capture protein conformations representing the key interacting points of the receptor but less biased toward one specific chemotype, useful for the identification of a "consensus" binding site with improved performance in virtual screening.
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.