Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds

• Type: Article in International Scientific Journal
• Date: 2010

Authors

Antonio J M Ribeiro (Author) Other; Maria J Ramos (Author) FCUP; Pedro A Fernandes (Author) FCUP

Journal

Title: Journal of Chemical Theory and Computation

Vol. 6 No. 8

Pages: 2281-2292

ISSN: 1549-9618

Publisher: American Chemical Society

Indexing

ISI Web of Knowledge - 64 Citations

Scopus - 63 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-003-4DE

DOI: 10.1021/ct900649e

Abstract (EN): Phosphodiester bonds are an important chemical component of biological systems, and their hydrolysis and formation reactions are involved in major steps throughout metabolic pathways of all organisms In this work, we applied dimethylphosphate as a model for this kind of bonds and calculated the potential energy surface for its hydrolysis at the approximated CCSD(T)/CBS//B3LYP/6-311++G(2d,2p) level. By varying the nucleophile (water or hydroxide) and the medium (vacuum or aqueous implicit solvent) we obtained and described four reaction paths These structures were then used in a DFT functional benchmarking in which we tested a total of 52 functionals Furthermore, the performances of HF, MP2, MP3, MP4, and CCSD were also evaluated. This benchmarking showed that MPWB1K, MPW1B95, and PBE1PBE are the more accurate functionals to calculate the energies of dimethylphosphate hydrolysis as far as activation and reaction energies are concerned. If considering only the activation energies, MPWB1K, MPW1B95, and B1B95 give the lowest errors when comparing to CCSD(T) A basis set benchmarking on the same system shows that 6-311+G(2d,2p) is the best basis set concerning the relationship between computational time and accuracy We believe that our results will be of great help to further studies on related phosphodiester systems. This includes not only pure chemical problems but also biochemical studies in which DNA, RNA, and phospholipids are required to be depicted at a quantum level.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 12