Transformation of terahertz vibrational modes of cytosine under hydration

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.

Quantum Chemical and Spectroscopic Study on Hydrogen Bonds in Hairpin DNA

“…From such correspondence, each absorption measured experimentally in the THz range is assigned as listed in Table III together with that of guanine mentioned above and thymine reported in our previous paper [16]. Note that the THz absorption peaks of cytosine almost agree with other studies [27]. To obtain a calculation result closer to measurement one, a larger number of cytosine seems to be needed as a calculation model.…”

A study of plant growth regulators detection based on terahertz time-domain spectroscopy and density functional theory

“…Vibrations of molecules in the THz frequency region mainly stem from the deformation vibration, bending vibration, and distortion produced by collective vibrational modes. 25,31 Different vibrations lead to variation in the position of peaks.…”

Machine Learning Techniques for THz Imaging and Time-Domain Spectroscopy

“…In recent years, numerous THz applications have been developed in biomedical and engineering fields [1][2][3][4][5][6][7]. In particular, they can be used for disease diagnosis in biological samples [8][9][10][11][12][13][14][15][16][17][18][19][20], characteristic analysis of biological samples [21][22][23][24][25][26] and biomolecules [27][28][29][30][31][32][33], non-destructive detection of artifacts and objects in samples [34][35][36][37][38][39][40][41], identification of hidden materials and their properties [42][43][44][45], estimation of the components in a mixture [46][47][48]…”