Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures

Goerigk, L; Collyer, CA; Reimers, JR

Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures

Goerigk, L Collyer, CA Reimers, JR

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Publication Type:: Journal Article
Citation:: Journal of Physical Chemistry B, 2014, 118 (50), pp. 14612 - 14626
Issue Date:: 2014-12-18

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Field	Value	Language
dc.contributor.author	Goerigk, L	en_US
dc.contributor.author	Collyer, CA	en_US
dc.contributor.author	Reimers, JR https://orcid.org/0000-0001-5157-7422	en_US
dc.date.issued	2014-12-18	en_US
dc.identifier.citation	Journal of Physical Chemistry B, 2014, 118 (50), pp. 14612 - 14626	en_US
dc.identifier.issn	1520-6106	en_US
dc.identifier.uri	http://hdl.handle.net/10453/35817
dc.description.abstract	© 2014 American Chemical Society. We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G∗ approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications. (Chemical Presented).	en_US
dc.relation.ispartof	Journal of Physical Chemistry B	en_US
dc.relation.isbasedon	10.1021/jp510148h	en_US
dc.subject.mesh	Muramidase	en_US
dc.subject.mesh	Proteins	en_US
dc.subject.mesh	Crystallography, X-Ray	en_US
dc.subject.mesh	Protein Conformation	en_US
dc.subject.mesh	Quantum Theory	en_US
dc.subject.mesh	Models, Molecular	en_US
dc.title	Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures	en_US
dc.type	Journal Article
utslib.citation.volume	50	en_US
utslib.citation.volume	118	en_US
utslib.for	0306 Physical Chemistry (incl. Structural)	en_US
utslib.for	02 Physical Sciences	en_US
utslib.for	03 Chemical Sciences	en_US
utslib.for	09 Engineering	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
utslib.copyright.status	closed_access
pubs.issue	50	en_US
pubs.publication-status	Published	en_US
pubs.volume	118	en_US

Abstract:

© 2014 American Chemical Society. We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G∗ approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications. (Chemical Presented).

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http://hdl.handle.net/10453/35817