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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
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Insights into the adsorption mechanism and dynamic behavior of tetracycline antibiotics on reduced graphene oxide (RGO) and graphene oxide (GO) materials
TL;DR: In this paper, the authors used density functional theory (DFT) and molecular dynamics simulations to analyze the adsorption mechanism and dynamic behavior of three tetracycline molecules.
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Operational Strategies and Comprehensive Evaluation of Menthol Based Deep Eutectic Solvent for the Extraction of Lower Alcohols from Aqueous Media
TL;DR: In this article, the authors explored the extraction of alcohols namely ethanol, 1-propanol, and 1-butanol from the aqueous phase using two novel hydrophobic DES at 303.15 K and 1 atm.
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Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: application to hole transfer in DNA.
T. Kubar,Marcus Elstner +1 more
TL;DR: A coarse-grained tight-binding method based on density functional theory (DFT) for the simulation of charge transfer in complex materials, which allows to follow the dynamics of excess charge along nanosecond MD trajectories, still accounting for the important impact of structural fluctuations and solvent effects.
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Molecular Dynamics Simulation of Benzenethiolate and Benzyl Mercaptide on Au(111)
TL;DR: In this article, the authors report the results of theoretical studies on the self-assembled monolayers of benzenethiolate (BT) and benzyl mercaptide (BZM) on a Au(111) surface.
Journal ArticleDOI
Empirical Conversion of pKa Values between Different Solvents and Interpretation of the Parameters: Application to Water, Acetonitrile, Dimethyl Sulfoxide, and Methanol
TL;DR: The method can be formulated with a single additive parameter, and that the extra multiplicative parameter used in other works is not required, and the method’s usefulness and performance on pKa conversions involving water and organic solvents acetonitrile, dimethyl sulfoxide, and methanol are demonstrated.
References
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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.