Abstract
Cytosine and cytosine monohydrate are representative biomolecules for investigating the effect of hydrogen bonds in deoxyribonucleic acid. To better understand intermolecular interactions, such as hydrogen bonds, between nucleobases it is necessary to identify the low-frequency vibrational modes associated with intermolecular interactions and crystalline structures. In this study, we investigated the characteristic low-frequency vibrational modes of cytosine and cytosine monohydrate using terahertz time-domain spectroscopy (THz-TDS). The crystal geometry was obtained by the powder X-ray diffraction technique. The optimized atomic positions and the normal modes in the terahertz region were calculated using density functional theory (DFT), which agreed well with the experimental results. We found that overall terahertz absorption peaks of cytosine and cytosine monohydrate consist of collective vibrations mixed with intermolecular and intramolecular vibrations in mode character analysis, and that the most intense peaks of both samples involve remarkable intermolecular translational vibration. These results indicate that THz-TDS combined with DFT calculations including mode character analysis can be an effective method for understanding how water molecules contribute to the characteristics of the low-frequency vibrational modes by intermolecular vibrations with hydrogen bonding in biological and biomedical applications.
Highlights
We present the THz spectra of C and cytosine monohydrate (C-MH) to indicate the characteristic influence of water on C and demonstrate that intermolecular vibrations significantly contribute to the THz absorption peaks
Based on our experimental and theoretical results, we show the low-frequency vibrational mode characteristics of C and C-MH, as well as how water molecules contribute to intermolecular vibrations
We separated the main vibrational modes into intermolecular and intramolecular vibrations following the method organized in ref. 50 using Cartesian coordinate atomic positions and displacement vectors
Summary
We present the THz spectra of C and C-MH to indicate the characteristic influence of water on C and demonstrate that intermolecular vibrations significantly contribute to the THz absorption peaks. The distinct characteristic peaks of C and C-MH were obtained in the absorption spectra at room temperature, using the THz-TDS system. The crystalline nature inducing the different THz spectra of the two molecules was distinguished by powder X-ray diffraction (PXRD) pattern analysis. The experimentally acquired THz spectra were compared to the calculation results of the normal modes, acquired using density functional theory (DFT). Each normal mode was decomposed into intermolecular and intramolecular vibrations using mode characteristic analysis. Based on our experimental and theoretical results, we show the low-frequency vibrational mode characteristics of C and C-MH, as well as how water molecules contribute to intermolecular vibrations
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