Density Functional Theory Study of Muon Hyperfine Interactions in 12mer Single-Strand Adenine, Cytosine, and Thymine Oligomers

• Published in: Journal of the Physical Society of Japan
• Main Author: Zaharim W.N.; Sulaiman S.; Bakar S.N.A.; Ismail N.E.; Jamaludin A.; Rozlan A.F.; Sin A.L.; Watanabe I.
• Format: Article
• Language: English
• Published: Physical Society of Japan 2022
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85152728893&doi=10.7566%2fJPSJ.91.094301&partnerID=40&md5=2f2580c80c17dd9e28725b3bf6b36311

Density Functional Theory method at B3LYP=6-31G level of theory was successfully applied to study the geometry and electronic structures of 12mer single-strand adenine, cytosine, and thymine oligomers. The observed high-resolution transmission electron microscopy images show similar oligomers’ dimensions to the calculated ones. Geometry optimization procedure was performed to examine possible muonium trapping sites in the oligomers and to determine the associated muon hyperfine interactions. Based on the total energy of the muoniated oligomers, the possible Mu sites are: C8 and C2 in adenine; N3, C5, and C6 in cytosine; and C6, C5, and O4 in thymine. Broad but non-overlapping polarization dips in the ALC-μSR spectrum are expected to be observed for adenine and thymine oligomers. In contrast, for cytosine oligomer, the calculated ALC-μSR applied fields suggested that there is one polarization dip due to N3, and the polarization dips that are attributed to C5 and C6 Mu sites will overlap. © 2022 The Physical Society of Japan.