Cargando…

Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Wang, Fang, Lin, Haifeng, Tong, Jiawen, Tai, Junbin, Wu, Jiaen, Yao, Yaru, Liu, Yunfei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9965851/
https://www.ncbi.nlm.nih.gov/pubmed/36838517
http://dx.doi.org/10.3390/molecules28041528
_version_ 1784896868705107968
author Wang, Fang
Lin, Haifeng
Tong, Jiawen
Tai, Junbin
Wu, Jiaen
Yao, Yaru
Liu, Yunfei
author_facet Wang, Fang
Lin, Haifeng
Tong, Jiawen
Tai, Junbin
Wu, Jiaen
Yao, Yaru
Liu, Yunfei
author_sort Wang, Fang
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9965851
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-99658512023-02-26 Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example Wang, Fang Lin, Haifeng Tong, Jiawen Tai, Junbin Wu, Jiaen Yao, Yaru Liu, Yunfei Molecules Article 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. MDPI 2023-02-04 /pmc/articles/PMC9965851/ /pubmed/36838517 http://dx.doi.org/10.3390/molecules28041528 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wang, Fang
Lin, Haifeng
Tong, Jiawen
Tai, Junbin
Wu, Jiaen
Yao, Yaru
Liu, Yunfei
Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example
title Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example
title_full Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example
title_fullStr Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example
title_full_unstemmed Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example
title_short Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example
title_sort effects of morphology and solvent/temperature on thz spectra: take nucleosides as example
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9965851/
https://www.ncbi.nlm.nih.gov/pubmed/36838517
http://dx.doi.org/10.3390/molecules28041528
work_keys_str_mv AT wangfang effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample
AT linhaifeng effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample
AT tongjiawen effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample
AT taijunbin effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample
AT wujiaen effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample
AT yaoyaru effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample
AT liuyunfei effectsofmorphologyandsolventtemperatureonthzspectratakenucleosidesasexample