Parallelism in quantum chemistry: Hydrogen bond study in DNA base pairs as an example

Abstract

We present results on the energetics of the hydrogen bridges for the Guanine-Cytosine pair obtained in a DNA fragment consisting of three stacked base pairs in the B-DNA conformation. The wave function computations on the 87 atom system are all-electron ab initio SCF-MO computations obtained with a basis set of 1032 primitive gaussian functions contracted to 315. Even if the results are only preliminary, one can tentatively advance conclusions relative to the molecular field effect of stacked base-pairs on the potential energy surface for a hydrogen bond. These computations have been performed with a modified version of our molecular program, which uses an IBM 4341 host and six to ten attached array processors (FPS-164) in parallel. The strategy to convert the program from sequential to parallel is briefly outlined and comparisons with our parallel system are made with a present-day "vector" super-computer. From these studies, we conclude that if one adopts the "parallel" approach presented and tested here, much larger chemical systems than previously are now amenable to all-electron ab initio computations.

A Polymerase Tautomeric Model for Radiation Induced Bystander Effects: A Model for Untargeted Base Substitution Mutagenesis during Error Prone and SOS Replication of Double Stranded DNA Containing Thymine and Adenine in Rare Tautomeric Forms

“…There exist several models of semi open metastable states [118,119]. In my opinion, the model developed by Hovorun [119] is well-grounded; it explains a number of phenomena and is confirmed by experimental data. It is rather probable that the process of tautomeric state change goes in two stages.…”

“…Metastable states developing with incomplete opening of the pair and with partial conservation of H-bonds and with the amine group free from H-bond are called semi open metastable states [118]. There exist several models of semi open metastable states [118,119]. In my opinion, the model developed by Hovorun [119] is well-grounded; it explains a number of phenomena and is confirmed by experimental data.…”

“…It is rather probable that the process of tautomeric state change goes in two stages. At the first stage, the metastable semi open DNA states predicted in Ref [119] are formed. At the second stage, the formed rare metastable tautomeric states transform into the stable ones.…”

“…In a canonical DNA molecule, conformational fluctuations of different DNA sites result in different metastable states [118,119]. The exposure of bases from a double spiral to the solution is known as "opening" or "melting" of Watson and Crick's pairs.…”

“…At the second stage, the formed rare metastable tautomeric states transform into the stable ones. Allowance the predicted [119] a metastable state leading to that rare tautomeric forms of thymine T* 4 and T* 5 and rare tautomeric forms of adenine А* 4 and А* 5 ( Figure 2) [82,83] can be formed. Double-stranded DNA contains the guanine-cytosine and adenine-thymine base pairs.…”