Literature DB >> 26943241

Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications.

Jan Řezáč1, Pavel Hobza1,2.   

Abstract

Data sets of benchmark interaction energies in noncovalent complexes are an important tool for quantifying the accuracy of computational methods used in this field, as well as for the development of new computational approaches. This review is intended as a guide to conscious use of these data sets. We discuss their construction and accuracy, list the data sets available in the literature, and demonstrate their application to validation and parametrization of quantum-mechanical computational methods. In practical model systems, the benchmark interaction energies are usually obtained using composite CCSD(T)/CBS schemes. To use these results as a benchmark, their accuracy should be estimated first. We analyze the errors of this methodology with respect to both the approximations involved and the basis set size. We list the most prominent data sets covering various aspects of the field, from general ones to sets focusing on specific types of interactions or systems. The benchmark data are then used to validate more efficient computational approaches, including those based on explicitly correlated methods. Special attention is paid to the transition to large systems, where accurate benchmarking is difficult or impossible, and to the importance of nonequilibrium geometries in parametrization of more approximate methods.

Entities:  

Year:  2016        PMID: 26943241     DOI: 10.1021/acs.chemrev.5b00526

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  29 in total

Review 1.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

2.  Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.

Authors:  Antti Siiskonen; Arri Priimagi
Journal:  J Mol Model       Date:  2017-02-04       Impact factor: 1.810

3.  Co-operativity in non-covalent interactions in ternary complexes: a comprehensive electronic structure theory based investigation.

Authors:  Shyam Vinod Kumar Panneer; Mahesh Kumar Ravva; Brijesh Kumar Mishra; Venkatesan Subramanian; Narayanasami Sathyamurthy
Journal:  J Mol Model       Date:  2018-08-29       Impact factor: 1.810

4.  Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).

Authors:  Isha Singh; Myong-Jung Kim; Robert W Molt; Shuichi Hoshika; Steven A Benner; Millie M Georgiadis
Journal:  ACS Synth Biol       Date:  2017-08-15       Impact factor: 5.110

5.  Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry.

Authors:  James Luccarelli; Robert S Paton
Journal:  J Org Chem       Date:  2019-01-09       Impact factor: 4.354

6.  The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.

Authors:  Lori A Burns; John C Faver; Zheng Zheng; Michael S Marshall; Daniel G A Smith; Kenno Vanommeslaeghe; Alexander D MacKerell; Kenneth M Merz; C David Sherrill
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

Review 7.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

8.  Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy.

Authors:  Teobald Kupka; Aneta Buczek; Małgorzata A Broda; Adrianna Mnich; Tapas Kar
Journal:  J Mol Model       Date:  2019-09-12       Impact factor: 1.810

9.  Ultrafast energy transfer between π-stacked aromatic rings upon inner-valence ionization.

Authors:  Xueguang Ren; Jiaqi Zhou; Enliang Wang; Tao Yang; Zhongfeng Xu; Nicolas Sisourat; Thomas Pfeifer; Alexander Dorn
Journal:  Nat Chem       Date:  2021-12-20       Impact factor: 24.427

10.  Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks.

Authors:  Daniele Ongari; Davide Tiana; Samuel J Stoneburner; Laura Gagliardi; Berend Smit
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2017-06-27       Impact factor: 4.126

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