The Effects of Split Valence Basis Sets on Muon Hyperfine Interaction in Guanine Nucleobase and Nucleotide Structures

Abstract

The DFT cluster method was employed to investigate the electronic structures and muonium hyperfine interactions in guanine nucleobase and nucleotide using three different basis sets. The total energy and Fermi contact values were calculated for muon trapped at carbon '8'. The three basis sets, 6-31G, 6-311G and 6-311G(d,p), were used in tandem with the B3LYP functional. There are significant quantitative differences in the calculated total energy. 6-311G(d,p) produced the lowest total energy as compared to the other basis sets. The lowering of the total energy is due to the increase in the number of basis functions to describe the atomic orbitals, which is consistent with the postulate on basis set completeness. The 6-31G basis set produced the muon Fermi contact value that is the closest to the experimental value. The calculated Fermi contact values for the nucleobase and nucleotide are significantly lowered in going from the double-zeta to the triple-zeta basis set by 5% and 4% respectively. The lowering of the Fermi contact value can be attributed to the extension of the triple-zeta basis set in describing the valence atomic orbitals. The presence of the sugar phosphate group in the nucleotide instead of the methyl group tends to lower the Fermi contact value. Thus, the sugar phosphate group should be taken into consideration when designing a calculation model.

Density Functional Theory Studies of the Electronic Structure and Muon Hyperfine Interaction in [Au25(SR)18]0 and [Au25(SeR)18]0 Nanoclusters

“…In Figure a, the S1/Se1 atom is indicated as S central, while the S2/Se2 is shown as S terminal. As is customary in muon site calculation, hydrogen with the mass of muonium was used to mimic muonium. ,− After a positive muon was introduced into the host systems, we performed another geometry optimization that allowed the muon and several host atoms in its vicinity to move. This condition is to allow those atoms to relax into new positions and to stabilize the muon stopping sites.…”

First Principles Theory Of Hyperfine Interactions In Guanine Nucleobase

“…In this investigation, the eight muoniated systems were optimized such that the muonium and all atoms in the guanine nucleobase were allowed to relax. The Cluster Method was employed and the Hartree-Fock procedure (Sulaiman et al, 1994) at 6-311G(d,p) level (Zaharim et al, 2019) was applied to optimize the structure of the muoniated system. 6-311G(d,p) basis set describes the core atomic orbital by using one basis function (Zaharim et al, 2019).…”

Basis Set Effects in Density Functional Theory Calculation of Muoniated Cytosine Nucleobase

“…DFT has been considered as a good alternative to post Hartree-Fock methods for the calculation of Fermi contact coupling constant (FCCC) [8,9]. The efficiency of DFT calculation strongly relies on the reasonable choice of functional and basis set [10,11]. In this study, we investigate the effect of basis sets on the electronic structure of muoniated cytosine nucleobase and the associated HFCC.…”