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Wang F, Lin H, Tong J, Tai J, Wu J, Yao Y, Liu Y. Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example. Molecules 2023; 28:molecules28041528. [PMID: 36838517 PMCID: PMC9965851 DOI: 10.3390/molecules28041528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
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.
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Affiliation(s)
- Fang Wang
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Haifeng Lin
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
| | - Jiawen Tong
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Junbin Tai
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Jiaen Wu
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Yaru Yao
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
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Wang F, Nan Z, Sun X, Liu C, Zhuang Y, Zan J, Dai C, Liu Y. Characterization of degradation behaviors of PLA biodegradable plastics by infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121376. [PMID: 35660145 DOI: 10.1016/j.saa.2022.121376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
In this paper, the degradation behavior of two kinds of polylactic acid (PLA) biodegradable material products (pure PLA cup cover and modified PLA straw) was studied. It was found that under the composting environment specified in the International Standard, in the first 35 days, the degradation rate of the straw (with 50%-60% poly butylenes succinate (PBS)) was faster than that of the pure PLA cup cover, but in the later stage, the PLA cup cover exceeded the straw and disintegrated preferentially, and both could be degraded in about 70 days. After further analyzing the far-infrared (FIR, can also be called THz) and mid infrared (MIR) spectra of cup cover and straw, we observed that the material structure had not changed until disintegration, only the ester bond was hydrolyzed, the polymers became oligomers, which could be reflected in the change of the effective area of the characteristic peak at 7.15 THz (cup cover, labeled 1921) and 6.99 THz (straw, labeled 4386) in the THz spectrum. With the degradation, the effective area decreased continuously. Due to the strong absorption of the material in MIR band, most characteristic peaks were flattened and lost analytical value. The bivariate correlation of degradation time, biodegradation rate, total carbon dioxide release and the effective area of the characteristic peak at 7.15 THz (1921) and 6.99 THz (4386) in THz spectrum was analyzed by SPSS software. We discovered that the degradation time was significantly positively correlated with biodegradation rate and carbon dioxide release at the level of 0.01 and negatively correlated with the effective area of characteristic peak at the level of 0.05. The biodegradation rate was significantly negatively correlated with the effective area of characteristic peak at the level of 0.01. Taking the degradation time as the independent variable and the biodegradation rate, carbon dioxide release and effective area of characteristic peak as the dependent variables, we got that the THz spectrum could be used to describe the degradation behavior of PLA products as long as appropriate coefficient correction was made. In this way, we could separate from the laboratory environment, study the impact of environmental diversification on material degradation performance, and reduce the cost of material degradation performance identification. Using density functional theory (DFT), reduced density gradient (RDG) method and visualization software, the changes of weak interaction position and intensity in the molecule during the polymerization of lactic acid into PLA were further analyzed. We found that the vibration of ester bond corresponded to the characteristic peak with weak intensity in the spectrum, and the peak with large intensity mainly originated from the out-of-plane swing of O-H bond in the molecule.
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Affiliation(s)
- Fang Wang
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, People's Republic of China; College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Zhu Nan
- Nanjing Institute of Product Quality Inspection, Nanjing 210019, People's Republic of China
| | - Xiaolin Sun
- School of Aeronautical Engineering, Nanjing Vocational University of Industry Technology, Nanjing 210046, People's Republic of China
| | - Chang Liu
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, People's Republic of China
| | - Yan Zhuang
- Nanjing Institute of Product Quality Inspection, Nanjing 210019, People's Republic of China
| | - Jianan Zan
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Chunfa Dai
- CSIC Pacli (Nanjing) Technology Co., Ltd, Nanjing 210000, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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Xiang X, Bao Y, Zhang Y, Xu G, Zhao B, Guo X. Accurate assembly and direct characterization of DNA nanogels crosslinked by G-quadruplex, i-motif and duplex with surface-enhanced Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121161. [PMID: 35306309 DOI: 10.1016/j.saa.2022.121161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/22/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The direct characterization of DNA nanogels at the atomic level is desirable and of great significance, however, has been challenging because of structural complexity and the larger size of nanogels. Herein, we demonstrated a simple, sensitive and reliable SERS (Surface-enhanced Raman spectroscopy)-based approach towards direct monitoring microstructures, such as three types of nanogels crosslinked by DNA G-quadruplex, i-motif and GC duplex. The achievement is attributed to the detection of featured Raman bands corresponding to the formation of Watson-Crick and Hoogsteen hydrogen bonds as well as C·C+ base pairs. Importantly, this work reveals that the silver nanoparticles attaching on the surface of nanogels can form local 'hotspots' and produce high-quality of Raman spectra under the assistance of iodide, aluminum ions and dichloromethane, therefore, shows great potential for wide applications in accurate characterization of various DNA nanostructures.
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Affiliation(s)
- Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Guantong Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China.
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Bao Y, Zhang X, Xiang X, Zhang Y, Zhao B, Guo X. Revealing the effect of intramolecular interactions on DNA SERS detection: SERS capability for structural analysis. Phys Chem Chem Phys 2022; 24:10311-10317. [PMID: 35437563 DOI: 10.1039/d1cp05607g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Intramolecular interactions are key factors for constructing the secondary conformations of biomolecules and they are also vital for biomolecular functions. Their effect on the surface-enhanced Raman spectroscopy (SERS) spectra is also important for reliable label-free detection. The current work focuses on three GCGC-quadruplexes as model molecules for SERS studies, which contain both the G-quartet and the GCGC-quartet. Their spectra are compared with the ones of the G-quadruplex and the duplex. The present work presents the specific effect of intramolecular interactions, including various Watson-Crick and Hoogsteen hydrogen bonds as well as base stacking, on the SERS signals of closely-related secondary conformations. The overall results indicated a significant influence on the direct label-free detection of DNA molecules and the SERS capability for secondary structural analysis.
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Affiliation(s)
- Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Xiaonong Zhang
- Key Laboratory of Polymer Ecomaterials Jilin Biomedical Polymers Engineering Laboratory Changchun Institute of Applied Chemistry Chinese Academy of Sciences, Changchun 130022, P. R. China.
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China.
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China. .,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, P. R. China
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Wang F, Sun X, Zan J, Li M, Liu Y, Chen J. Terahertz spectra and weak intermolecular interactions of nucleosides or nucleoside drugs. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120344. [PMID: 34481145 DOI: 10.1016/j.saa.2021.120344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/18/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
In this paper, terahertz (THz) spectra of four DNA nucleosides (Adenosine, Thymidine, Cytidine and Guanosine) and two nucleoside derivatives (Ribavirin and Entecavir, first time reported) in the solid phase were studied experimentally by Fourier Transform Infrared Spectroscopy (FTIR) in the frequency of 1-10 THz. The lattice energy, geometric structure, vibration spectrum of them were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF) and the density functional theory (DFT). The intra- and inter-molecular weak interactions corresponding to the vibrational modes of the crystal, polymer and monomer were obtained, with the help of the potential energy distribution (PED) and reduced density gradient (RDG) methods. It was found that the sum of electronic and thermal free energies increased from the monomer to polymer, and from the polymer to crystal. For example, the inter-molecular interaction energy from the monomer to dimer of adenosine increased 6.969 kcal/mol, and that from the dimer to crystal (the periodic boundary conditions were considered) increased 666.792 kcal/mol. Therefore, only the crystal structure constrained the periodic boundary conditions could well describe the experimental results, although the former scholars chose the monomer or polymer as the initial configuration due to the limitation of computing resources and methods. In THz band, the vibrational modes were generally originated from the collective vibration (more than 99% of them were vibration, only less than 1% of them were rotation and translation) of all molecules involved, which could reflect the molecular structure and spatial distribution of different substances. In order to accurately identify the spectra, we studied the location, type and contribution of all weak interactions, and found that the strong characteristic peaks corresponding to the strong hydrogen bonds came from inter-molecular, while the weak hydrogen bonds mainly originated from intra- and inter-molecular, the out-of-plane bending made the largest contribution, accounting for more than 90%. Furthermore, taking guanine, guanosine and two guanosine derivatives (Ribavirin and Entecavir) as examples, the differences of weak interaction among them caused by different molecular configuration, arrangement and substituent position were studied, and the fundamental reason of THz spectrum change was found. This research can lay a foundation for crystal engineering, supramolecular chemistry, molecular recognition and self-assembly, protein-ligand interaction, etc.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, People's Republic of China
| | - Xiaolin Sun
- School of Electronic and Information Engineering, Nanjing Vocational University of Industry Technology, Nanjing 210046, People's Republic of China
| | - Jianan Zan
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Mingshi Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Jingyi Chen
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, People's Republic of China
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Wang F, Jiang L, Song J, Huang L, Ju Y, Liu Y. Sub-THz spectroscopic characterization identification for pine wood nematode ribosomal DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 232:118152. [PMID: 32088532 DOI: 10.1016/j.saa.2020.118152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/02/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
This paper, we introduced Sub-terahertz (Sub-THz) technology to identify nematode DNA sequence. First, data mining technology and restriction enzyme digestion were used to cut out two corresponding sequences, each containing about 100 base pairs that could represent the characteristic fragments of Bursaphelenchus xylophilus (Bx) and Bursaphelenchus mucronatus (Bm) rDNA in internal transcribed spacer 1 (ITS1) region. Then, vibration spectra of the two enzyme-cut sequences were measured by Fourier transform infrared spectroscopy (FTIR). Meanwhile, the spectrum was analyzed by molecular dynamics method. It was found that the calculated and experimental spectra of the two enzyme-cut sequences were consistent, although the differences of the sequences could not be well reflected in the spectra. The vibration modes corresponding to diverse absorption peaks in the spectra were quite different, which were closely related to the internal bases sequencing. This can be used as an indicator for identifying Bx and Bm DNA. Moreover, the normal mode analysis (NMA) method was first adopted for spectral attribution analysis of DNA long sequences. Finally, the vibration spectra of shorter sequences predicted by second-order Markov chains and Monte Carlo method were studied. To some extent, the predicted short sequences can represent the complete sequence as the initial calculation structure.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, People's Republic of China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Jun Song
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Lin Huang
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunwei Ju
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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De La Pierre M, Pouchan C. Ab initio periodic modelling of the vibrational spectra of molecular crystals: the case of uracil. Theor Chem Acc 2018. [DOI: 10.1007/s00214-017-2191-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Jiang KM, Zhang JQ, Jin Y, Lin J. 1,3-Dipolar Cycloaddition of Imidazole Derivatives with Nitrile Oxide: Synthesis of Imidazo[1,2,4]oxadiazole Derivatives. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kun-Ming Jiang
- Key Laboratory of Medicinal Chemistry for Natural Resource (Yunnan University); Ministry of Education, School of Chemical Science and Technology; Yunnan University; Kunming 650091 P. R. China
| | - Jian-Qiang Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource (Yunnan University); Ministry of Education, School of Chemical Science and Technology; Yunnan University; Kunming 650091 P. R. China
- Department of Biology and Chemistry; Puer College; Puer 665000 Yunnan China
| | - Yi Jin
- Key Laboratory of Medicinal Chemistry for Natural Resource (Yunnan University); Ministry of Education, School of Chemical Science and Technology; Yunnan University; Kunming 650091 P. R. China
| | - Jun Lin
- Key Laboratory of Medicinal Chemistry for Natural Resource (Yunnan University); Ministry of Education, School of Chemical Science and Technology; Yunnan University; Kunming 650091 P. R. China
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