Affiliation:
1. College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
2. College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
Abstract
Water molecules were easy to combine with organic molecules and embed into the lattice of solid molecules to form a hydrate. Compared with anhydrous compounds, a hydrate has completely different physical and chemical properties. In this paper, terahertz (THz) spectra of five nucleosides in the solid and liquid phases were studied experimentally by Fourier-transform infrared spectroscopy (FTIR) in the frequency of 0.5–9 THz. In addition, the lattice energy, geometric structure, and vibration spectrum of the molecular crystal of the nucleosides were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). Furthermore, different nucleoside molecular morphology (monomer, polymer, and crystal), solvent (implicit and explicit water), and temperature/theoretical model effect on the THz spectra were mainly investigated. It was found that in the low-frequency band, the vibrational modes were generally originated from the collective vibration of all molecules involved (more than 99% of them were vibration; only less than 1% of them were rotation and translation), which can reflect the molecular structure and spatial distribution of different substances. The Gibbs free energy of thymidine monomer, dimer, tetramer, and crystal was studied. It was found that the cell-stacking energy had the greatest influence on the spectrum, indicating that only the crystal structure constrained by the periodic boundary conditions could well describe the experimental results. In addition, hydrophobic forces dominated the formation of new chemical bonds and strong inter-molecular interactions; the free water had little contribution to the THz spectrum of nucleosides, while crystalline water had a great influence on the spectrum.
Funder
National Natural Science Foundation of China
Jiangsu Postdoctoral Research Foundation
Jiangsu University Student Innovation and Entrepreneurship Training Plan
the Key Research and Development plan of Jiangsu Province
Jiangsu Modern Agricultural Machinery Equipment and Technology Demonstration and Promotion Project
the Nanjing Modern Agricultural Machinery Equipment and Technological Innovation Demonstration Projects
Subject
Chemistry (miscellaneous),Analytical Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Molecular Medicine,Drug Discovery,Pharmaceutical Science