منابع مشابه
Accurate treatment of nonbonded interactions within systematic molecular fragmentation
The accuracy of the systematic fragment approach to the estimation of molecular electronic energies is enhanced by a significantly improved treatment of nonbonded interactions between molecular fragments. Distributed electrostatic interactions, pairwise dispersion interactions, and many-body induction are evaluated from ab initio calculations of small molecular fragments. The accuracy of the co...
متن کاملVerification of protein structures: patterns of nonbonded atomic interactions.
A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interaction is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distr...
متن کاملExtending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions
Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded t...
متن کاملDesign of density functionals that are broadly accurate for thermochemistry, thermochemical kinetics, and nonbonded interactions.
This paper develops two new hybrid meta exchange-correlation functionals for thermochemistry, thermochemical kinetics, and nonbonded interactions. The new functionals are called PW6B95 (6-parameter functional based on Perdew-Wang-91 exchange and Becke-95 correlation) and PWB6K (6-parameter functional for kinetics based on Perdew-Wang-91 exchange and Becke-95 correlation). The resulting methods ...
متن کاملBenchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory.
We present four benchmark databases of binding energies for nonbonded complexes. Four types of nonbonded interactions are considered: hydrogen bonding, charge transfer, dipole interactions, and weak interactions. We tested 44 DFT methods and 1 WFT method against the new databases; one of the DFT methods (PBE1KCIS) is new, and all of the other methods are from the literature. Among the tested m...
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ژورنال
عنوان ژورنال: ACS Omega
سال: 2021
ISSN: 2470-1343,2470-1343
DOI: 10.1021/acsomega.1c01356