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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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AMBER Empirical Potential Describes the Geometry and Energy of Noncovalent Halogen Interactions Better than Advanced Semiempirical Quantum Mechanical Method PM6-DH2X
TL;DR: The current study employs the positive extra-point (PEP) approach for halogen bonding, in which the σ-hole on the halogen atom is represented by an extra point of charge, and yields much better results than the PM6-DH2X method.
Journal ArticleDOI
The application of quantum mechanics in structure-based drug design.
Daniel Mucs,Richard A. Bryce +1 more
TL;DR: Although computation of binding energies remains a challenging and evolving area, current QM methods can underpin improved docking approaches and offer detailed insights into ligand strain and into the nature and relative strengths of complex active site interactions.
Journal ArticleDOI
One-electron reduction potential for oxygen- and sulfur-centered organic radicals in protic and aprotic solvents.
TL;DR: One-electron redox potentials of redox-active organic molecules for a spectrum of eight different functional groups in protic (water) and aprotic (acetonitrile, N,N-dimethylacetamide) solvents are estimated.
Journal ArticleDOI
Toward an Understanding of Zeolite Y as a Cracking Catalyst with the Use of Periodic Charge Equilibration
TL;DR: In this article, the role of the zeolite Y lattice in cracking catalysis was investigated and a local dipole was found to induce a change in the partial charge distribution of a cracking hydride transfer transition state model (C4H9+ plus n-octane).
Journal ArticleDOI
Deconstructing the catalytic efficiency of peroxiredoxin-5 peroxidatic cysteine.
Stephanie Portillo-Ledesma,Florencia Sardi,Bruno Manta,María Victoria Tourn,André Clippe,Bernard Knoops,Beatriz Alvarez,E. Laura Coitiño,Gerardo Ferrer-Sueta +8 more
TL;DR: QM/MM results with WT PRDX5 showed that hydrogen bonds in the active site are the cornerstone of two effects that make catalysis possible: the enhancement of thiolate nucleophilicity upon substrate ingress and the stabilization of the transition state.
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.