Testing Semiempirical Quantum Mechanical Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules

The Journal of Physical Chemistry. a
V M Miriyala, Jan Rezác

Abstract

Semiempirical quantum mechanical (QM) methods with corrections for noncovalent interactions provide a favorable combination of accuracy and computational efficiency that makes them a useful tool for a study of large molecular systems. It was, however, noted that the accuracy of these methods deteriorates at intermolecular distances shorter than equilibrium. In this work, we explore this issue systematically using a newly developed data set of benchmark interaction energies named R160×6. This data set maps repulsive contacts in organic molecules, and it consists of 160 model complexes for which six points along the dissociation curve are provided. Testing a wide range of semiempirical QM methods against the CCSD(T)/CBS benchmark revealed that most methods, and all the dispersion-corrected ones, underestimate the repulsion systematically. The worst cases are usually hydrogen-hydrogen contacts. The best results were obtained with PM6-D3H4 and DFTB3-D3H4, as these methods already contain a correction for the H-H repulsion, but the errors are still about twice as large as in equilibrium geometries.

References

May 13, 2006·Journal of Computational Chemistry·Gerd B RochaJames J P Stewart
Jun 15, 2007·The Journal of Physical Chemistry. a·B AradiTh Frauenheim
Aug 13, 2011·Journal of Chemical Theory and Computation·Jan RezáčPavel Hobza
Dec 4, 2012·Journal of Chemical Theory and Computation·Michael GausMarcus Elstner
Dec 3, 2014·European Journal of Medicinal Chemistry·Barbora VorlováMartin Lepšík
Jul 4, 2015·Physical Chemistry Chemical Physics : PCCP·Jan ŘezáčPavel Hobza
Jan 8, 2013·Journal of Chemical Theory and Computation·Michael GausMarcus Elstner
Jan 10, 2012·Journal of Chemical Theory and Computation·Jan Řezáč, Pavel Hobza
Jan 12, 2010·Journal of Chemical Theory and Computation·Martin KorthPavel Hobza
Feb 4, 2016·Journal of Computational Chemistry·Jan Řezáč
Feb 19, 2016·Journal of Chemical Theory and Computation·Maximilian KubillusMarcus Elstner
Jan 4, 2017·Journal of Chemical Information and Modeling·Adam PecinaPavel Hobza
Jan 18, 2017·Journal of Computational Chemistry·Vijay Madhav Miriyala, Jan Řezáč
Sep 28, 2017·Journal of Chemical Theory and Computation·Jan Řezáč

❮ Previous
Next ❯

Citations

Nov 18, 2018·Journal of Molecular Modeling·Maximilian KriebelTimothy Clark
May 13, 2019·Journal of Molecular Modeling·Maximilian KriebelTimothy Clark
Feb 17, 2021·The Journal of Chemical Physics·Stefan GrimmeJan-Michael Mewes
Feb 24, 2021·Journal of Chemical Theory and Computation·Kristian KřížJan Řezáč

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.