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.

Effects of monohydration on an adenine–thymine base pair

“…The ratio of ν opening mode in the quantum simulation is the same as in the classical simulation in this case. These tendencies, arising from nuclear quantum effect, have also been found in the study by Daido et al [13] using the path integral hybrid Monte Carlo simulation. The ratio of the three PCs in the classical simulation is in the order of the ν buckle , ν propeller and ν opening modes, which order is the same as the opposite order of the frequency of the vibrational normal modes.…”

“…These various PM6 derivatives could be reliable on the electronic structure calculations for hydrogen-bonded system. Daido et al [13] reported that PM6-DH+ method performed well for the electronic structure calculation in the molecular dynamics of a single adenine-thymine and guanine-cytosine pair. We found that PM6-DH+ method is a good candidate for our simulation.…”

“…Daido et al [13] have discussed the relative position of protons along the hydrogen bonds of the adenine-thymine base pair. We investigated the structures of these hydrogen bonds in detail to understand the adenine-thymine base pair as well.…”

“…Daido et al [12,13] studied the structure of Watson-Crick type isolated adenine-thymine and guanine-cytosine base pairs using the path integral hybrid Monte Carlo simulation. They found that the contributions of the nuclear quantum effect on hydrogen-bonded structures and the dynamics of the base pairs are significant, not only at low temperature, but also at temperature higher than room temperature.…”

“…Recently, various studies reported that both thermal and nuclear quantum effects are important to determine the hydrogen-bonded structures accurately [12][13][14][15][16][17][18][19][20][21][22]. Daido et al [12,13] studied the structure of Watson-Crick type isolated adenine-thymine and guanine-cytosine base pairs using the path integral hybrid Monte Carlo simulation.…”