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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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Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials
TL;DR: In this paper, a modification of the CHELP method for fitting atomic charges to electrostatic potentials is presented, and a well-defined, computationally efficient algorithm (CHELP-SVD) is presented for determining the rank of the least-squares matrix in potential-derived charge fitting schemes, selecting the appropriate subset of atoms to which charges can be assigned based on that rank estimate, and then refitting the selected set of charges.
Journal ArticleDOI
Small molecule inhibitors of ezrin inhibit the invasive phenotype of osteosarcoma cells.
Gülay Bulut,Sung-Hyeok Hong,Kevin Chen,Em M. Beauchamp,Said Rahim,Gw W. Kosturko,Eric Glasgow,Sivanesan Dakshanamurthy,Hyun-Shik Lee,I Daar,Ja A. Toretsky,Chand Khanna,Aykut Üren +12 more
TL;DR: Two small molecule inhibitors, NSC305787 and NSC668394, demonstrate a novel targeted therapy that directly inhibits ezrin protein as an approach to prevent tumor metastasis and cause a unique developmental defect consistent with reduced cell motility in zebrafish.
Journal ArticleDOI
Electrostatic phenomena in organic semiconductors: fundamentals and implications for photovoltaics
Gabriele D'Avino,Luca Muccioli,Frédéric Castet,Carl Poelking,Denis Andrienko,Z. G. Soos,Jérôme Cornil,David Beljonne +7 more
TL;DR: This review summarizes the current understanding of electrostatic phenomena in ordered and disordered organic semiconductors, outlines numerical schemes developed for quantitative evaluation of electro static and induction contributions to ionization potentials and electron affinities of organic molecules in a solid state, and illustrates two applications of these techniques: interpretation of photoelectron spectroscopy of thin films and energetics of heterointerfaces in organic solar cells.
Journal ArticleDOI
Estimation of Drug-Target Residence Times by tau-Random Acceleration Molecular Dynamics Simulations.
Daria B. Kokh,Marta Amaral,Joerg Bomke,Ulrich Grädler,Djordje Musil,Hans-Peter Buchstaller,Matthias K. Dreyer,Matthias Frech,Maryse Lowinski,François Vallée,Marc Bianciotto,Alexey Rak,Rebecca C. Wade,Rebecca C. Wade,Rebecca C. Wade +14 more
TL;DR: An efficient computational method for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanisms are presented, suggesting that τRAMD will be widely applicable as a computationally efficient aid to improving drug residence times during lead optimization.
Journal ArticleDOI
Simulations of room temperature ionic liquids: from polarizable to coarse-grained force fields.
Mathieu Salanne,Mathieu Salanne +1 more
TL;DR: The most widely used methods for room temperature ionic liquids (RTILs) are described together with their main achievements and limitations in this article, where the authors focus on classical molecular dynamics, in which the level of complexity of the simulation, and therefore the computational cost, mostly depends on the force field.
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.