Literature DB >> 19882732

How dependent are molecular and atomic properties on the electronic structure method? Comparison of Hartree-Fock, DFT, and MP2 on a biologically relevant set of molecules.

Chérif F Matta1.   

Abstract

This article compares molecular properties and atomic properties defined by the quantum theory of atoms in molecules (QTAIM) obtained from three underlying levels of theory: MP2(full), density functional theory (DFT) (B3LYP), and Hartree-Fock (H-F). The same basis set (6-311++G(d,p)) has been used throughout the study. The calculations and comparisons were applied to a set of 30 small molecules representing common fragments of biological molecules. The molecular properties investigated are the energies and the electrostatic moments (up to and including the quadrupoles), and the atomic properties include electron populations (and atomic charge), atomic dipolar and quadrupolar polarizations, atomic volumes, and corrected and raw atomic energies. The Cartesian distance between dipole vectors and the Frobenius distance between the quadrupole tensors calculated at the three levels of theory provide a measure of their correlation (or lack thereof). With the exception of energies (atomic and molecular), it is found that both DFT and H-F are in excellent agreement with MP2, especially with regards to the electrostatic mutipoles up to the quadrupoles, but DFT and MP2 agree better in almost all studied properties (with the exception of molecular geometries). QTAIM properties whether obtained from H-F, DFT(B3LYP), or MP2 calculations when used in the construction of empirical correlations with experiment such as quantitative structure-activity-(or property)-relationships (QSAR/QSPR) are equivalent (because the properties calculated at the three levels are very highly correlated among themselves with r(2) typically >0.95, and therefore preserving trends). These results suggest that the massive volume of results that were published in the older literature at the H-F level is valid especially when used to study trends or in QSAR or QSPR studies, and, as long as our test set of molecules is representative, there is no pressing need to re-evaluate them at other levels of theory except when inadequate basis sets were used by today's standards. Extensive tabulation of molecular and atomic properties at the three theoretical levels is available in the Supporting Information, including optimized geometries, molecular energies, virial ratios, molecular electrostatic moments up to and including hexadecapoles, atomic populations, atomic volumes, atomic electrostatic moments up to and including the quadrupoles, and atomic energies. 2009 Wiley Periodicals, Inc.

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Year:  2010        PMID: 19882732     DOI: 10.1002/jcc.21417

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  13 in total

1.  The physico-chemical "anatomy" of the tautomerization through the DPT of the biologically important pairs of hypoxanthine with DNA bases: QM and QTAIM perspectives.

Authors:  Ol'ha O Brovarets'; Roman O Zhurakivsky; Dmytro M Hovorun
Journal:  J Mol Model       Date:  2013-01-05       Impact factor: 1.810

2.  Atomistic mechanisms of the tautomerization of the G·C base pairs through the proton transfer: quantum-chemical survey.

Authors:  Ol'ha O Brovarets'; Alona Muradova; Dmytro M Hovorun
Journal:  J Mol Model       Date:  2021-12-02       Impact factor: 1.810

3.  Accurate description of molecular dipole surface with charge flux implemented for molecular mechanics.

Authors:  Xudong Yang; Chengwen Liu; Brandon D Walker; Pengyu Ren
Journal:  J Chem Phys       Date:  2020-08-14       Impact factor: 3.488

4.  Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential.

Authors:  Chérif F Matta
Journal:  J Comput Chem       Date:  2014-04-29       Impact factor: 3.376

5.  DPT tautomerization of the long A∙A Watson-Crick base pair formed by the amino and imino tautomers of adenine: combined QM and QTAIM investigation.

Authors:  Ol'ha O Brovarets'; Roman O Zhurakivsky; Dmytro M Hovorun
Journal:  J Mol Model       Date:  2013-05-29       Impact factor: 1.810

6.  Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Dmytro M Hovorun
Journal:  Front Chem       Date:  2018-02-27       Impact factor: 5.221

7.  Novel pathway for mutagenic tautomerization of classical А∙Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Dmytro M Hovorun
Journal:  PLoS One       Date:  2018-06-27       Impact factor: 3.240

8.  Unexpected Routes of the Mutagenic Tautomerization of the T Nucleobase in the Classical A·T DNA Base Pairs: A QM/QTAIM Comprehensive View.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Andrii Dinets; Dmytro M Hovorun
Journal:  Front Chem       Date:  2018-11-27       Impact factor: 5.221

9.  Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Dmytro M Hovorun
Journal:  Sci Rep       Date:  2018-07-10       Impact factor: 4.379

10.  Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey.

Authors:  Ol'ha O Brovarets'; Timothy A Oliynyk; Dmytro M Hovorun
Journal:  Front Chem       Date:  2019-09-18       Impact factor: 5.221

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