Literature DB >> 25527923

Appointing silver and bronze standards for noncovalent interactions: a comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches.

Lori A Burns1, Michael S Marshall1, C David Sherrill1.   

Abstract

A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracy and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.

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Year:  2014        PMID: 25527923     DOI: 10.1063/1.4903765

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  10 in total

1.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

Review 2.  Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Authors:  Anders S Christensen; Tomáš Kubař; Qiang Cui; Marcus Elstner
Journal:  Chem Rev       Date:  2016-04-13       Impact factor: 60.622

3.  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

4.  Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability.

Authors:  Robert M Parrish; Lori A Burns; Daniel G A Smith; Andrew C Simmonett; A Eugene DePrince; Edward G Hohenstein; Uğur Bozkaya; Alexander Yu Sokolov; Roberto Di Remigio; Ryan M Richard; Jérôme F Gonthier; Andrew M James; Harley R McAlexander; Ashutosh Kumar; Masaaki Saitow; Xiao Wang; Benjamin P Pritchard; Prakash Verma; Henry F Schaefer; Konrad Patkowski; Rollin A King; Edward F Valeev; Francesco A Evangelista; Justin M Turney; T Daniel Crawford; C David Sherrill
Journal:  J Chem Theory Comput       Date:  2017-06-06       Impact factor: 6.006

5.  On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations.

Authors:  Leonid Pereyaslavets; Igor Kurnikov; Ganesh Kamath; Oleg Butin; Alexey Illarionov; Igor Leontyev; Michael Olevanov; Michael Levitt; Roger D Kornberg; Boris Fain
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-20       Impact factor: 11.205

6.  A Quadratic Pair Atomic Resolution of the Identity Based SOS-AO-MP2 Algorithm Using Slater Type Orbitals.

Authors:  Arno Förster; Mirko Franchini; Erik van Lenthe; Lucas Visscher
Journal:  J Chem Theory Comput       Date:  2020-01-24       Impact factor: 6.006

7.  Physical Mechanisms of Intermolecular Interactions and Cross-Space Charge Transfer in Two-Photon BDBT-TCNB Co-Crystals.

Authors:  Chen Lu; Ning Li; Ying Jin; Ying Sun; Jingang Wang
Journal:  Nanomaterials (Basel)       Date:  2022-08-11       Impact factor: 5.719

8.  Overcoming the difficulties of predicting conformational polymorph energetics in molecular crystals via correlated wavefunction methods.

Authors:  Chandler Greenwell; Jessica L McKinley; Peiyu Zhang; Qun Zeng; Guangxu Sun; Bochen Li; Shuhao Wen; Gregory J O Beran
Journal:  Chem Sci       Date:  2020-01-14       Impact factor: 9.825

9.  Quantum chemical benchmark databases of gold-standard dimer interaction energies.

Authors:  Alexander G Donchev; Andrew G Taube; Elizabeth Decolvenaere; Cory Hargus; Robert T McGibbon; Ka-Hei Law; Brent A Gregersen; Je-Luen Li; Kim Palmo; Karthik Siva; Michael Bergdorf; John L Klepeis; David E Shaw
Journal:  Sci Data       Date:  2021-02-10       Impact factor: 6.444

10.  Accurate determination of solvation free energies of neutral organic compounds from first principles.

Authors:  Leonid Pereyaslavets; Ganesh Kamath; Boris Fain; Oleg Butin; Alexey Illarionov; Michael Olevanov; Igor Kurnikov; Serzhan Sakipov; Igor Leontyev; Ekaterina Voronina; Tyler Gannon; Grzegorz Nawrocki; Mikhail Darkhovskiy; Ilya Ivahnenko; Alexander Kostikov; Jessica Scaranto; Maria G Kurnikova; Suvo Banik; Henry Chan; Michael G Sternberg; Subramanian K R S Sankaranarayanan; Brad Crawford; Jeffrey Potoff; Michael Levitt; Roger D Kornberg
Journal:  Nat Commun       Date:  2022-01-20       Impact factor: 14.919

  10 in total

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