title: Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of base pairs.
abstract: The structure of Watson-Crick-type adenine-thymine and guanine-cytosine pairs has been studied by hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations with the use of semiempirical PM6-DH+ method in the gas phase. We elucidated the nuclear quantum effect and temperature dependency on the hydrogen-bonded moiety of base pairs. It was shown that the contribution of nuclear quantum effect on the hydrogen-bonded structure is significant not only at low temperature 150 K but also at temperature as high as 450 K. The relative position of hydrogen-bonded proton between two heavy atoms and the nuclear quantum nature of the proton are also shown. Furthermore, we have applied principal component analysis to HMC and PIHMC simulations to analyze the nuclear quantum effect on intermolecular motions. We found that the ratio of Buckle mode (lowest vibrational mode from normal mode analysis) decreases due to the nuclear quantum effect, whereas that of Propeller mode (second lowest vibrational mode) increases. In addition, nonplanar structures of base pairs were found to become stable due to the nuclear quantum effect from two-dimensional free energy landscape along Buckle and Propeller modes.
authors.affiliation: Quantum Chemistry Division, Graduate School of Science, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama, 236-0027, Japan.
authors.forename: Masashi
authors.initials: M
authors.lastname: Daido
authors.forename: Yukio
authors.initials: Y
authors.lastname: Kawashima
authors.forename: Masanori
authors.initials: M
authors.lastname: Tachikawa
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020029:Base Pairing; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011789:Quantum Theory; D013696:Temperature; D013941:Thymine / Q000737:chemistry*
chemical_list: D006147:Guanine; D000225:Adenine; D013941:Thymine
keywords: Watson-Crick-type base pair; hybrid Monte Carlo; nuclear quantum effect; path integral simulation; semiempirical PM6-DH+ method; temperature dependency