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Wu Y, Zhu Z, Yang J, Wang J, Ji T, Zhu H, Peng W, Chen M, Zhao H. Insights into the terahertz response of L-glutamic acid and its receptor. Analyst 2024. [PMID: 39037577 DOI: 10.1039/d4an00697f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
L-Glutamic acid (L-Glu) is a basic unit of proteins and also serves as an important neurotransmitter in the central nervous system. Its structural properties are critical for biological functions and selective receptor recognition. Although this molecule has been extensively studied, the low frequency vibrational behavior that is closely related to conformational changes and the intermolecular interactions between L-Glu and its receptors are still unclear. In this study, we acquired the fingerprint spectrum of L-Glu by using air plasma terahertz (THz) time-domain spectroscopy in the 0.5-18 THz range. The low frequency vibrational characteristics of L-Glu were investigated through density functional theory (DFT) calculations. The THz responses of the ligand binding domain of the NMDAR-L-Glu complex were studied by the ONIOM method, with a focus on discussing the normal modes and interactions of ligand L-Glu and water molecules. The results illustrate that THz spectroscopy exhibits a sensitive response to the influence of L-Glu on the structure of the NMDAR. The water molecules in proteins have various strong vibration modes in the THz band, showing specificity, diversity and complexity of vibrational behavior. There is potential for influencing and regulating the structural stability of the NMDAR-L-Glu complex through water molecules.
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Affiliation(s)
- Yu Wu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongjie Zhu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Jinrong Yang
- East China Normal University, Shanghai 200241, China
| | - Jie Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Te Ji
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Huachun Zhu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Weiwei Peng
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Min Chen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Hongwei Zhao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.
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2
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Li Y, Xu L, Ouyang J, Lei J, Hu J, Xing X, Chen P, Li J, Zhong C, Yang B, Li H. Harmonic and anharmonic studies on THz spectra of two vanillin polymorphs. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123869. [PMID: 38198992 DOI: 10.1016/j.saa.2024.123869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/05/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Polymorphism commonly exists in organic molecular crystals. The fingerprint features in low-frequency vibrational range are important information reflecting different intermolecular interactions of polymorphs. Interpreting these features is very helpful to understand vibrational property of polymorphs and reveal the thermodynamic stability. In this work, the low-frequency vibrations of form I and II of vanillin are investigated using terahertz time-domain spectroscopy. Static DFT calculation and ab initio molecular dynamics (AIMD) are employed to interpret their low-frequency vibrations of both forms in harmonic and anharmonic ways, respectively. Their low-frequency vibration characteristics in harmonic calculations are discussed, and anharmonic mode couplings between OH bond stretch and the stretching and bending motion of hydrogen bonds are uncovered. Moreover, the thermodynamic energies including electronic potential energy and vibrational/kinetic energy arising from nuclear motions are calculated. The result reveals that the stability order of the two forms is mainly dependent on their electric potential energy difference.
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Affiliation(s)
- Yin Li
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
| | - Li Xu
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Jinbo Ouyang
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China.
| | - Jiangtao Lei
- Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Jun Hu
- School of Mechatronics & Vehicle Engineering, East China Jiaotong University, Nanchang, Jiangxi 330013, China
| | - Xiaohong Xing
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Peng Chen
- School of Chemistry, Biology and Materials Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Jiaqing Li
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Changqing Zhong
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Bo Yang
- School of Physics and Materials Science, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Heng Li
- Fujian Provincial Key Laboratory of Semiconductors and Applications, Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Department of Physics, Xiamen University, Xiamen 361005, China; Jiujiang Research Institute, Xiamen University, Jiujiang 332000, China
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3
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Du W, Gao F, Cui P, Yu Z, Tong W, Wang J, Ren Z, Song C, Xu J, Ma H, Dang L, Zhang D, Lu Q, Jiang J, Wang J, Pi L, Sheng Z, Lu Q. Twisting, untwisting, and retwisting of elastic Co-based nanohelices. Nat Commun 2023; 14:4426. [PMID: 37481654 PMCID: PMC10363140 DOI: 10.1038/s41467-023-40001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/07/2023] [Indexed: 07/24/2023] Open
Abstract
The reversible transformation of a nanohelix is one of the most exquisite and important phenomena in nature. However, nanomaterials usually fail to twist into helical crystals. Considering the irreversibility of the previously studied twisting forces, the reverse process (untwisting) is more difficult to achieve, let alone the retwisting of the untwisted crystalline nanohelices. Herein, we report a new reciprocal effect between molecular geometry and crystal structure which triggers a twisting-untwisting-retwisting cycle for tri-cobalt salicylate hydroxide hexahydrate. The twisting force stems from competition between the condensation reaction and stacking process, different from the previously reported twisting mechanisms. The resulting distinct nanohelices give rise to unusual structure elasticity, as reflected in the reversible change of crystal lattice parameters and the mutual transformation between the nanowires and nanohelices. This study proposes a fresh concept for designing reversible processes and brings a new perspective in crystallography.
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Affiliation(s)
- Wei Du
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 211816, Nanjing, P. R. China
| | - Feng Gao
- Department of Materials Science and Engineering, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, College of Engineering and Applied Science, Nanjing University, 210023, Nanjing, P. R. China.
| | - Peng Cui
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China
| | - Zhiwu Yu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Wei Tong
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Jihao Wang
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Zhuang Ren
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Chuang Song
- Department of Materials Science and Engineering, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, College of Engineering and Applied Science, Nanjing University, 210023, Nanjing, P. R. China
| | - Jiaying Xu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Haifeng Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Liyun Dang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Di Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China
| | - Qingyou Lu
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China.
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China.
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China.
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China.
| | - Li Pi
- Hefei National Laboratory for Physical Sciences at Microscale and Anhui Laboratory of Advanced Photon Science and Technology, University of Science and Technology of China, 230026, Hefei, AnHui, P. R. China
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Zhigao Sheng
- Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory and High Magnetic Field Laboratory of Anhui Province, HFIPS, Chinese Academy of Sciences, 230031, Hefei, Anhui, P. R. China
| | - Qingyi Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing National Laboratory of Microstructures, Nanjing University, 210023, Nanjing, P. R. China.
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4
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Hou S, Liu Q, Deng H, He J, Zhao W, Wu Z, Zhang Q, Shang L. Identification and low-frequency vibrational analysis of three free anthraquinones via terahertz spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 293:122439. [PMID: 36773425 DOI: 10.1016/j.saa.2023.122439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
In this study, terahertz time-domain spectroscopy (THz-TDS) was used to obtain the terahertz absorption spectra of three free anthraquinones (Chrysophanol, Emodin, Physcion) in the frequency range of 0.2-4.3 THz. The results show that terahertz spectroscopy is an effective detecting such compounds. Meanwhile, the theoretical spectrum using density functional theory calculations agrees well with the experimental spectrum. A modal decoupling method was used to identify each low-frequency vibrational mode and determine the average contribution of different atoms and groups. Modal decoupling provides a better understanding of molecules' mixed vibrational modes and enables quantifying the atoms' vibrational contributions. Results show that the substituent group facilitates the transition between the fundamental vibrational modes; subsequently, the substituent group shifts the vibrational centre of gravity of the three molecules and affects the vibrational contribution of hydrogen bonds. Furthermore, insignificant Emodin absorption is related to the nearly symmetrical structure formed by the substituents. The feasibility of terahertz analysis of differential molecular structures has also been confirmed.
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Affiliation(s)
- Senlin Hou
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Quancheng Liu
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Hu Deng
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China; Tianfu Institute of Research and Innovation, Southwest University of Science and Technology, ChengDu 610299, China
| | - Jun He
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Wei Zhao
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Zhixiang Wu
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Qi Zhang
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang, China
| | - Liping Shang
- School of Information Engineering, Southwest University of Science and Technology, Mianyang 621010, China; Tianfu Institute of Research and Innovation, Southwest University of Science and Technology, ChengDu 610299, China.
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5
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Yang B, Li Y, Lei J, Cai M, Hu Z, Shen Y, Deng X. Dehydration kinetics and mechanism of the stable isonicotinamide hydrate revealed by terahertz spectroscopy and DFT calculation. Int J Pharm 2023; 638:122893. [PMID: 36990167 DOI: 10.1016/j.ijpharm.2023.122893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/13/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023]
Abstract
The dehydration behavior of pharmaceutical hydrates has a great influence on its physiochemical properties such as stability, dissolution rate and bioavailability. However, how the intermolecular interactions vary during dehydration process remains elusive. In this work, we employed terahertz time-domain spectroscopy (THz-TDS) to probe the low-frequency vibrations and the dehydration process of isonicotinamide hydrate I (INA-H I). Theoretical solid-state DFT calculation was conducted to reveal its mechanism. Vibrational modes which are responsible for the THz absorption peaks were decomposed for better understanding the characters of these low-frequency modes. The result suggests translational motion is the dominant component for water molecules in THz region. Evolution of the THz spectrum of INA-H I during dehydration provides direct evidence of the variations of crystal structure. Based on the THz measurements, a two-step kinetics mode including first-rate reaction and three-dimensional nuclei growth is proposed. And we nure that the low-frequency vibrations of water molecules are the origin of dehydration process of hydrate.
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6
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Choi WJ, Lee SH, Park BC, Kotov NA. Terahertz Circular Dichroism Spectroscopy of Molecular Assemblies and Nanostructures. J Am Chem Soc 2022; 144:22789-22804. [DOI: 10.1021/jacs.2c04817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Won Jin Choi
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sang Hyun Lee
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bum Chul Park
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas A. Kotov
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Rogers FJM, Radhanpura K, Horvat J, Farrant D. On the use of a volume constraint to account for thermal expansion effects on the low-frequency vibrations of molecular crystals. Phys Chem Chem Phys 2022; 24:10408-10419. [PMID: 35441620 DOI: 10.1039/d1cp05718a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A volume-constraint method is presented as a means to capture the influence of thermal expansion on the low-frequency vibrations in molecular crystals. In particular, the room-temperature terahertz absorption spectra of L-tartaric acid, α-lactose monohydrate, and α-para-aminobenzoic acid (PABA) have been simulated using dispersion-corrected, solid-state density functional theory (DFT-D). By comparing the normal modes obtained with a unit cell optimised without constraints to those obtained with a unit cell optimised while constrained to keep its experimental volume, wholesale improvements to the resultant spectrum is achieved when using the constrained geometry by inhibiting cell contraction. These improvements are demonstrated over a range of popular density functionals and basis sets up to triple-zeta complexity. A correlation method is then presented as a means to quantitatively compare the vibrational pattern of normal modes obtained from both unit cells. This analysis reveals that thermal expansion can effect the character and relative frequency of normal modes, with the choice of geometry ultimately affecting the assignment of the experimental absorptions. The sensibility of using the experimental volume as an approximation is then discussed, where it is speculated that large basis sets or hybrid functionals are necessary to ensure that the thermal expansion effect is not overestimated. The low-frequency absorption spectrum of PABA is then fully characterised using the PBE-D3BJ/6-311G(2d,2p) method.
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Affiliation(s)
- Fergus J M Rogers
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Krunal Radhanpura
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, NSW 2070, Australia
| | - Joseph Horvat
- School of Physics and Institute for Superconducting and Electronic Materials, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - David Farrant
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, NSW 2070, Australia
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8
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Zhu Z, Bian Y, Zhang X, Zeng R, Yang B. Examination of proline, hydroxyproline and pyroglutamic acid with different polar groups by terahertz spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120539. [PMID: 34742154 DOI: 10.1016/j.saa.2021.120539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/08/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Hydroxyproline (HYP) and pyroglutamic acid (PGA), as amino acid derivatives, are highly similar in structure to proline (Pro). However, their low-frequency vibrations show significant differences in the range of 0.25-2.6 THz. Therefore, this study investigated the reasons for the differences combined with terahertz time domain spectroscopy (THz-TDS) and density functional theory (DFT). The results show that HYP and PGA have stronger absorption of terahertz waves due to the existence of polar substituents. Furthermore, the absorption peaks of HYP and PGA are significant red shifted and blue shifted, respectively. We believe that this is caused by the change in the strength of intermolecular hydrogen bonds. Our findings demonstrate that dipole and hydrogen bond effects play a significant role in low-frequency vibrations.
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Affiliation(s)
- Zhenqi Zhu
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Yujing Bian
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xun Zhang
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Ruonan Zeng
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Bin Yang
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China; Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
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9
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Abstract
Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.
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10
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Li Y, Sun Y, Li Q, Lei J, Yang B, Shen Y, Cai Y, Deng X. Study of temperature-dependent terahertz spectra of isonicotinamide in the form I using the quasi-harmonic approximation. Chemphyschem 2022; 23:e202100849. [PMID: 35098625 DOI: 10.1002/cphc.202100849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/20/2022] [Indexed: 11/08/2022]
Abstract
Anharmonicity of molecular vibrational motions is closely associated with the thermal property of crystals. However, the origin of anharmonicity is still not fully understood. Low-frequency vibrations, which are usually defined in the terahertz (THz) range, show excellent sensitivity to anharmonicity. In this work, anharmonicity of isonicotinamide in the form I was investigated by using temperature-dependent terahertz time-domain spectroscopy and quasi-harmonic approximation (QHA) approach at PBE-D3 and PBE-MBD levels. Both DFT calculations suggest the variation of p-p stacking conformation dominates in the thermal expansion of unit cell. The frequency shifts of the modes in THz range obtained by QHA approach are found to be qualitatively consistent with the observation, demonstrating QHA approach is a useful tool for the interpretation of frequency shifts of modes induced by temperature.
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Affiliation(s)
- Yin Li
- Nanchang University, Department of Physics, Nanchang, CHINA
| | - Yiwen Sun
- Shenzhen University, School of Biomedical Engineering, Shenzhen, CHINA
| | - Qiqi Li
- Shenzhen University, School of Biomedical Engineering, Shenzhen, CHINA
| | - Jiangtao Lei
- Nanchang University, Institute of Space Science and Technology, Nanchang, CHINA
| | - Bo Yang
- Nanchang University, Department of Materials and Chemicals, Nanchang, CHINA
| | - Yun Shen
- Nanchang University, Department of Physics, Nanchang, CHINA
| | - Yingxiang Cai
- Nanchang University, Department of Physics, Nanchang, CHINA
| | - Xiaohua Deng
- Nanchang University, department of physics, Xuefu Avenue 999, Nanchang City, Jiangxi Province, 330031, Nanchang, CHINA
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11
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Tayvah U, Spies JA, Neu J, Schmuttenmaer CA. Nelly: A User-Friendly and Open-Source Implementation of Tree-Based Complex Refractive Index Analysis for Terahertz Spectroscopy. Anal Chem 2021; 93:11243-11250. [PMID: 34355556 DOI: 10.1021/acs.analchem.1c02132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Terahertz (THz) spectroscopy is a powerful tool for unambiguously extracting complex-valued material properties (e.g., refractive index, conductivity, etc.) from a wide range of samples, with applications ranging from materials science to biology. However, extracting complex refractive indices from THz time-domain spectroscopy data can prove challenging, especially for multilayer samples. These challenges arise from the large number of transmission-reflection paths the THz pulse can take through the sample layers, leading to unwieldy strings of Fresnel coefficients. This issue has often been addressed using various approximations. However, these approximations are only applicable to specific classes of samples and can give erroneous results when misapplied. An alternative to this approach is to programmatically model all possible paths through the sample. The many paths through the sample layers can be modeled as a tree that branches at every point where the paths diverge, i.e., whenever the pulse can either be transmitted or reflected. This tree can then be used to generate expressions relating the unknown refractive index to the observed time domain data. Here, we provide a freely available open-source package implementing this method as both a MATLAB library and a corresponding graphical user interface, which can also be run without a MATLAB license (https://github.com/YaleTHz/nelly). We have tested this method for a range of samples and compared the results to commonly used approximations to demonstrate its accuracy and wide applicability. Our method consistently gives better agreement than common approximations.
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Affiliation(s)
- Uriel Tayvah
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 065111, United States
| | - Jacob A Spies
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 065111, United States
| | - Jens Neu
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 065111, United States.,Department of Molecular Biophysics and Biochemistry and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06511, United States
| | - Charles A Schmuttenmaer
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 065111, United States
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12
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Ben Uliel T, Farber EM, Aviv H, Stroek W, Farbinteanu M, Tischler YR, Eisenberg D. Combining polarized low-frequency Raman with XRD to identify directional structural motifs in a pyrolysis precursor. Chem Commun (Camb) 2021; 57:7015-7018. [PMID: 34165132 DOI: 10.1039/d1cc00420d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-range structures and dynamics are central to coordination chemistry, yet are hard to identify experimentally. By combining polarized low-frequency Raman spectroscopy with single crystal XRD to study barium nitrilotriacetate, a metal-organic coordination polymer and a useful pyrolysis precursor, we could assign Raman peaks experimentally to layer shear motions and perpendicular hydrogen bond vibrations. These directional long-range interactions further determined the preferred fracture directions during crystallization, establishing an important link between structural motifs in the precursor, and the porosity of the carbon it yields upon pyrolysis.
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Affiliation(s)
- Tal Ben Uliel
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| | - Eliyahu M Farber
- Schulich Faculty of Chemistry and the Grand Technion Energy Program (GTEP), Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Hagit Aviv
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| | - Wowa Stroek
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Marilena Farbinteanu
- Faculty of Chemistry, Inorganic Chemistry Department, University of Bucharest, Dumbrava Rosie 23, Bucharest 020462, Romania
| | - Yaakov R Tischler
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, 5290002, Israel.
| | - David Eisenberg
- Schulich Faculty of Chemistry and the Grand Technion Energy Program (GTEP), Technion-Israel Institute of Technology, Haifa 3200003, Israel.
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13
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Isogai M, Seshimo M, Houjou H. Optimizing a coarse-grained space for approximate normal-mode vibrations of molecular heterodimers. J Mol Model 2021; 27:140. [PMID: 33905009 DOI: 10.1007/s00894-021-04743-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/14/2021] [Indexed: 10/21/2022]
Abstract
We applied the method of coarse-graining the intermolecular vibrations to molecular heterodimers assembled by double hydrogen bonding. This method is based on principal component analysis, by which the original atomic displacement vectors are projected onto a lower-dimensional space spanned by a basis set of translations, librations, and intramolecular vibrations of the constituent molecules. Compared with homodimers, the following points are particularly noted: (1) alignment of the constituent molecules in a non-symmetric atomic arrangement of the whole system and (2) the scheme of reordering the bases to construct an optimal coarse-grained space. We tested three schemes for reordering the intramolecular vibration vectors to determine that the best one is equivalent to size reduction based on the singular value decomposition. The coarse-graining analysis affords three parameters, Φintra, Φinter, and Φapp, which are relevant to the mechanical nature of the molecular assembly. The Φintra values account for the internal stiffness of molecules, while the Φinter values are true stiffness constants of the intermolecular force and show a good correlation with the association energies of the dimers. The Φapp values are the apparent intermolecular stiffness smaller than Φinter, as a result of compensation for neglecting intramolecular vibrations. All these values are consistent with each other under the coupled oscillator model, showing that the present coarse-graining analysis is valid for heterodimers as well as homodimers.
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Affiliation(s)
- Makoto Isogai
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Masataka Seshimo
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hirohiko Houjou
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
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14
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Hutereau M, Banks PA, Slater B, Zeitler JA, Bond AD, Ruggiero MT. Resolving Anharmonic Lattice Dynamics in Molecular Crystals with X-Ray Diffraction and Terahertz Spectroscopy. PHYSICAL REVIEW LETTERS 2020; 125:103001. [PMID: 32955315 DOI: 10.1103/physrevlett.125.103001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/06/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Molecular crystals are increasingly being used for advanced applications, ranging from pharmaceutics to organic electronics, with their utility dictated by a combination of their three-dimensional structures and molecular dynamics-with anharmonicity in the low-frequency vibrations crucial to numerous bulk phenomena. Through the use of temperature-dependent x-ray diffraction and terahertz time-domain spectroscopy, the structures and dynamics of a pair of isomeric molecular crystals exhibiting nearly free rotation of a CF_{3} functional group at ambient conditions are fully characterized. Using a recently developed solid-state anharmonic vibrational correction, and applying it to a molecular crystal for the first time, the temperature-dependent spatial displacements of atoms along particular terahertz modes are obtained, and are found to be in excellent agreement with the experimental observations, including the assignment of a previously unexplained absorption feature in the low-frequency spectrum of one of the solids.
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Affiliation(s)
- Martin Hutereau
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Peter A Banks
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA
| | - Ben Slater
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - J Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Andrew D Bond
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael T Ruggiero
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA
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15
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Transformation of terahertz vibrational modes of cytosine under hydration. Sci Rep 2020; 10:10271. [PMID: 32581269 PMCID: PMC7314841 DOI: 10.1038/s41598-020-67179-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/01/2020] [Indexed: 11/08/2022] Open
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.
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16
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Spies JA, Hilibrand MJ, Neu J, Ostresh S, Swierk JR, Schmuttenmaer CA. Suspensions of Semiconducting Nanoparticles in Nafion for Transient Spectroscopy and Terahertz Photoconductivity Measurements. Anal Chem 2020; 92:4187-4192. [DOI: 10.1021/acs.analchem.9b05723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jacob A. Spies
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Miryl J. Hilibrand
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Jens Neu
- Department of Molecular Biophysics and Biochemistry and Microbial Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Sarah Ostresh
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - John R. Swierk
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
| | - Charles A. Schmuttenmaer
- Department of Chemistry and Energy Sciences Institute, Yale University, New Haven, Connecticut 06520, United States
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17
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Xu L, Li Y, Zhou Q, Deng X. A comparative study of the low-frequency vibrations of l-histidine molecule in different solid states. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 224:117468. [PMID: 31425861 DOI: 10.1016/j.saa.2019.117468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/04/2019] [Accepted: 08/11/2019] [Indexed: 06/10/2023]
Abstract
Low-frequency vibrations of l-histidine in a neat solid state and its monohydrochloride monohydrate are both investigated using THz spectroscopy and DFT calculations. The molecular motions in those modes are further quantitatively decomposed into a number of submotions and discussed in terms of their contributions to a mode. The results show significant differences in the averaged contribution percentage of intermolecular motions and the dihedral angle distortions of the imidazole ring between these two crystals. Those phenomena are interpreted from the viewpoint of their hydrogen-bond configurations.
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Affiliation(s)
- Li Xu
- Department of Chemical Engineering and Technology, School of Chemistry, Biology and Materials of Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Yin Li
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
| | - Qi Zhou
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Xiaohua Deng
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China; Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
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18
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Červinka C, Fulem M. Cohesive properties of the crystalline phases of twenty proteinogenic α-aminoacids from first-principles calculations. Phys Chem Chem Phys 2019; 21:18501-18515. [PMID: 31411212 DOI: 10.1039/c9cp03102b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cohesive properties (lattice and cohesive energy of the crystal and corresponding sublimation enthalpy) of the complete set of twenty enantiopure anhydrous proteinogenic amino acids are investigated using first-principles calculations. In contrast to neutral amino acid molecules in the vapor phase, all amino acids form crystals in their zwitterionic form. Therefore, reliable ab initio calculations of the proton transfer energy are an indispensable step of such calculations. Simplifying procedures, designed to rationalize the computational cost of the quasi-harmonic approximation, which proves too demanding if performed fully at the given quantum level of theory, are presented and tested. For this purpose, atomic multipoles (up to the quadrupoles) for the amoeba force field are parametrized for all amino acid zwitterions. While the calculated lattice energies of the amino acids range from 235-458 kJ mol-1 in absolute value, the proton transfer energies typically amount to 100-220 kJ mol-1, which translates to sublimation enthalpies ranging from 117-202 kJ mol-1, appreciably exceeding the sublimation enthalpy values common for nonionic molecular crystals. Critically assessed experimental data on sublimation enthalpies are used as a benchmark for comparison of the data calculated in this work. Cohesive properties of most amino acids calculated in this work, combining the PBE-D3(BJ)/PAW and CCSD(T)-F12/aug-cc-pVDZ levels of theory used for predictions of the lattice energies and of the proton transfer energies, respectively, exhibit a reasonable agreement with the experiment. At the same time, this work contains the first published data on cohesive properties for several enantiopure amino acids.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
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19
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Polarization Dependence of Low-Frequency Vibrations from Multiple Faces in an Organic Single Crystal. CRYSTALS 2019. [DOI: 10.3390/cryst9080425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent developments in optical filters have enabled the facile use of Raman spectroscopy for detection of low frequency (LF) vibrational modes. LF-Raman spectroscopy offers fast and sensitive characterization of LF vibrations, and enables the measurement of single microcrystals and detection of defects. It is useful for probing intermolecular interactions in crystals, which are lower in energy, such as hydrogen bonds, shear modes, and breathing modes. Crystal excitation from multiple faces allows learning the orientation of intermolecular interactions, as polarization dependence varies with the polarizability of the interactions along the planes. Elucidating the orientations of the intermolecular interactions in organic crystals is essential for guiding the reactions or adsorption to a specific crystal face. In this study, we investigated the dependence of the LF-Raman signal intensity on the orientation of an organic single microcrystal of L-alanine. Three incident beam directions provided the orientations of the intermolecular interactions by analyzing the corresponding LF-Raman spectra. The signal intensity correlated well with the proximity between the incident beam’s direction and the orientations of the intermolecular interactions. Excellent compatibility was found between the spectra and simulated orientations based on structural information.
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20
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Neu J, Stone EA, Spies JA, Storch G, Hatano AS, Mercado BQ, Miller SJ, Schmuttenmaer CA. Terahertz Spectroscopy of Tetrameric Peptides. J Phys Chem Lett 2019; 10:2624-2628. [PMID: 31039310 PMCID: PMC6936601 DOI: 10.1021/acs.jpclett.9b01091] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Determining the sequence and structure of peptides is crucial for understanding their structure-property relationships. Among many techniques, structures are typically elucidated using nuclear magnetic resonance spectroscopy and single crystal X-ray diffraction measurements. In this study, we present terahertz time-domain spectroscopy (THz-TDS) as a complementary, nondestructive technique that is sensitive to both the primary and secondary structures of tetrapeptides. Using only a few milligrams of peptide, THz-TDS spectra have been measured, some of which have been supported by density functional theory (DFT) calculations, to distinguish six tetrameric peptides with similar primary and secondary structures.
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Affiliation(s)
- Jens Neu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elizabeth A. Stone
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Jacob A. Spies
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Energy Sciences Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Golo Storch
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ayaka S. Hatano
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Charles A. Schmuttenmaer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Energy Sciences Institute, Yale University, West Haven, Connecticut 06516, United States
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21
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Li Y, Xu L, Zhou Q, Xiong G, Shen Y, Deng X. A comparative evaluation of the activities of thiol group and hydroxyl group in low-frequency vibrations using terahertz spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:246-251. [PMID: 30785044 DOI: 10.1016/j.saa.2019.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/30/2019] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Low-frequency vibrations of biomolecules govern many biological processes like allostery of proteins, binding interaction and solvation. Revealing how involved are different groups of molecules in low-frequency vibrations is of significance to understand the behaviors of biomolecules. To compare the activities of hydroxyl group and thiol group in low-frequency vibrations, we conducted THz measurements and DFT calculations of l‑serine and l‑cysteine. We performed quantitative analyses on their low-frequency vibrations to study their difference. Statistical analyses on the vibrational modes in our studied range suggest the thiol group shows a higher level of activity in low-frequency vibrations than hydroxyl group.
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Affiliation(s)
- Yin Li
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Li Xu
- Department of Chemical Engineering and Technology, School of Chemistry, Biology and Materials of Science, East China University of Technology, Guanglan Avenue 418, Nanchang City 330013, China
| | - Qi Zhou
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Guangyun Xiong
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Yun Shen
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Xiaohua Deng
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China; Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
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22
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Niessen KA, Xu M, George DK, Chen MC, Ferré-D'Amaré AR, Snell EH, Cody V, Pace J, Schmidt M, Markelz AG. Protein and RNA dynamical fingerprinting. Nat Commun 2019; 10:1026. [PMID: 30833555 PMCID: PMC6399446 DOI: 10.1038/s41467-019-08926-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/04/2019] [Indexed: 01/30/2023] Open
Abstract
Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology. The characterization of biomacromolecule structural vibrations has been impeded by a broad continuous vibrational density of states obscuring molecule specific vibrations. A terahertz microscopy system using polarization control produces signatures to dynamically fingerprint proteins and a RNA G-quadruplex.
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Affiliation(s)
| | - Mengyang Xu
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Deepu K George
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Michael C Chen
- National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Edward H Snell
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Vivian Cody
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - James Pace
- Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin, Milwaukee, WI, USA
| | - Andrea G Markelz
- Department of Physics, University at Buffalo, SUNY, Buffalo, NY, USA. .,Hauptman-Woodward Medical Research Institute & Department of Structural Biology, University at Buffalo, SUNY, Buffalo, NY, USA.
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23
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Impact of hydrogen bonding network configuration on intramolecular distortion in solid state: Studies on low-frequency vibrations of L-glutamic acid and L-glutamine. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Wei L, Yu L, Jiaoqi H, Guorong H, Yang Z, Weiling F. Application of terahertz spectroscopy in biomolecule detection. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.flm.2019.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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25
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Nemtsov I, Mastai Y, Tischler YR, Aviv H. Chiral Purity of Crystals Using Low-Frequency Raman Spectroscopy. Chemphyschem 2018; 19:3116-3121. [PMID: 30178918 DOI: 10.1002/cphc.201800739] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 11/09/2022]
Abstract
The pharmaceutical industry is in need of new techniques to identify the chirality of solids due to regulatory and safety concerns regarding the biological activity of enantiomers. In this study, we present for the first time the application of low-frequency Raman spectroscopy as a new and sensitive method for analyzing the chiral purity of crystals. Using this method, we were able to identify small amounts, as low as 1 % w/w, of an enantiomer in racemic crystals. To demonstrate the capabilities of the method, we used a model system based on chiral crystals of enantiopure, racemic crystals and their mixtures in various ratios. We found that the low-frequency Raman spectra of racemic and enantiopure crystals are significantly different, reflecting the different hydrogen bond networks. Moreover, a comparison of the sensitivity of enantiomeric excess in chiral crystals to that of circular dichroism and X-ray diffraction measurements showed that low-frequency Raman attains high sensitivity comparable to chiral optical methods used for solutions. Overall, our proposed approach of using Raman spectroscopy for determining enantiomeric excess in crystals is simple, fast, and offers a high degree of chiral sensitivity.
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Affiliation(s)
- Irena Nemtsov
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Yitzhak Mastai
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Yaakov R Tischler
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Hagit Aviv
- Department of Chemistry and Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan, 5290002, Israel
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26
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The effect of conformational freedom of side chain on low-frequency motions of amino acids in solid-state. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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27
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Isogai M, Houjou H. Indices to evaluate the reliability of coarse-grained representations of mixed inter/intramolecular vibrations. J Mol Model 2018; 24:221. [PMID: 30073513 DOI: 10.1007/s00894-018-3757-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/20/2018] [Indexed: 11/27/2022]
Abstract
We propose some methods for quantifying the reliability of coarse-grained representations of displacement vectors of normal mode vibrations. In the framework of our basic theory, the original displacement vectors are projected onto a lower-dimensional (i.e., a coarse-grained) space. Four types of functions denoted fidelity indices were introduced as measures of the similarity of the original to the restored displacement vectors. These indices were applied to several hydrogen-bonded homodimers, and the behavior of each index was examined. We found that a coarse-grained representation with high reliability resulted in the accurate restoration of properties such as eigenfrequency, modal mass, and modal stiffness.
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Affiliation(s)
- Makoto Isogai
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hirohiko Houjou
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
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28
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Neu J, Nikonow H, Schmuttenmaer CA. Terahertz Spectroscopy and Density Functional Theory Calculations of dl-Norleucine and dl-Methionine. J Phys Chem A 2018; 122:5978-5982. [DOI: 10.1021/acs.jpca.8b04978] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens Neu
- Yale University, Department of Chemistry, New Haven, Connecticut 06520, United States
| | - Heinrich Nikonow
- Yale University, Department of Chemistry, New Haven, Connecticut 06520, United States
| | - Charles A. Schmuttenmaer
- Yale University, Department of Chemistry, New Haven, Connecticut 06520, United States
- Yale University, Energy Science Institute (ESI), New Haven, Connecticut 06520, United States
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29
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Dai Z, Xu X, Gu Y, Li X, Wang F, Lian Y, Fan K, Cheng X, Chen Z, Sun M, Jiang Y, Yang C, Xu J. A terahertz study of taurine: Dispersion correction and mode couplings. J Chem Phys 2018; 146:124119. [PMID: 28388120 DOI: 10.1063/1.4978896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The low-frequency characteristics of polycrystalline taurine were studied experimentally by terahertz (THz) absorption spectroscopy and theoretically by ab initio density-functional simulations. Full optimizations with semi-empirical dispersion correction were performed in spectral computations and vibrational mode assignments. For comparison, partial optimizations with pure density functional theory were conducted in parallel. Results indicate that adding long-range dispersion correction to the standard DFT better reproduces the measured THz spectra than the popular partial optimizations. The main origins of the observed absorption features were also identified. Moreover, a coupled-oscillators model was proposed to explain the experimental observation of the unusual spectralblue-shift with the increase of temperature. Such coupled-oscillators model not only provides insights into the temperature dynamics of non-bonded interactions but also offers an opportunity to better understand the physical mechanisms behind the unusual THz spectral behaviors in taurine. Particularly, the simulation approach and novel coupled-oscillators model presented in this work are applicable to analyze the THz spectra of other molecular systems.
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Affiliation(s)
- Zelin Dai
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Xiangdong Xu
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Yu Gu
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Xinrong Li
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Fu Wang
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Yuxiang Lian
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Kai Fan
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Xiaomeng Cheng
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Zhegeng Chen
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Minghui Sun
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Yadong Jiang
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
| | - Chun Yang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, People's Republic of China
| | - Jimmy Xu
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China (UESTC), Chengdu 610054, People's Republic of China
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30
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Li Y, Lukács A, Bordács S, Móczár J, Nyitrai M, Hebling J. The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:8-15. [PMID: 28972911 DOI: 10.1016/j.saa.2017.09.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/24/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted "vibrational character ID strips" proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.
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Affiliation(s)
- Yin Li
- MTA-PTE High-Field Terahertz Research Group, Ifjúság Street 6, Pécs H-7624, Hungary; Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - András Lukács
- Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - Sándor Bordács
- Department of Physics, Budapest University of Technology and Economics, Budafoki Street 8, Budapest H-1111, Hungary
| | - János Móczár
- Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - Miklós Nyitrai
- Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - János Hebling
- MTA-PTE High-Field Terahertz Research Group, Ifjúság Street 6, Pécs H-7624, Hungary; Department of Experimental Physics, University of Pécs, Ifjúság Street 6, H-7624 Pécs, Hungary.
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31
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Li Q, Zaczek AJ, Korter TM, Zeitler JA, Ruggiero MT. Methyl-rotation dynamics in metal–organic frameworks probed with terahertz spectroscopy. Chem Commun (Camb) 2018; 54:5776-5779. [DOI: 10.1039/c8cc02650e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In ZIF-8 and its cobalt analogue ZIF-67, the imidazolate methyl-groups, which point directly into the void space, have been shown to freely rotate – even down to cryogenic temperatures.
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Affiliation(s)
- Qi Li
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Adam J. Zaczek
- Department of Chemistry, Syracuse University
- 1-014 Center for Science and Technology
- Syracuse
- USA
| | - Timothy M. Korter
- Department of Chemistry, Syracuse University
- 1-014 Center for Science and Technology
- Syracuse
- USA
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
| | - Michael T. Ruggiero
- Department of Chemical Engineering and Biotechnology, University of Cambridge
- Philippa Fawcett Drive
- Cambridge
- UK
- Department of Chemistry
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32
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Neu J, Nemes CT, Regan KP, Williams MRC, Schmuttenmaer CA. Exploring the solid state phase transition in dl-norvaline with terahertz spectroscopy. Phys Chem Chem Phys 2018; 20:276-283. [DOI: 10.1039/c7cp05479c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Experimental and theoretical demonstration of the power of terahertz spectroscopy to provide novel insights into solid-state phase-transformations in organic materials.
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Affiliation(s)
- Jens Neu
- Department of Chemistry
- Yale University
- New Haven
- USA
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33
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Aviv H, Nemtsov I, Mastai Y, Tischler YR. Characterization of Crystal Chirality in Amino Acids Using Low-Frequency Raman Spectroscopy. J Phys Chem A 2017; 121:7882-7888. [DOI: 10.1021/acs.jpca.7b07033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hagit Aviv
- Department of Chemistry and
Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan 5290002, Israel
| | - Irena Nemtsov
- Department of Chemistry and
Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan 5290002, Israel
| | - Yitzhak Mastai
- Department of Chemistry and
Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan 5290002, Israel
| | - Yaakov R. Tischler
- Department of Chemistry and
Bar-Ilan Institute for Nanotechnology and Advanced Materials (BINA), Bar Ilan University, Ramat Gan 5290002, Israel
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34
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Niessen KA, Xu M, Paciaroni A, Orecchini A, Snell EH, Markelz AG. Moving in the Right Direction: Protein Vibrations Steering Function. Biophys J 2017; 112:933-942. [PMID: 28297652 DOI: 10.1016/j.bpj.2016.12.049] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/22/2016] [Accepted: 12/28/2016] [Indexed: 11/29/2022] Open
Abstract
Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.
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Affiliation(s)
- Katherine A Niessen
- Department of Physics, University at Buffalo, State University of New York, Buffalo, New York.
| | - Mengyang Xu
- Department of Physics, University at Buffalo, State University of New York, Buffalo, New York
| | | | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy; CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, New York
| | - Andrea G Markelz
- Department of Physics, University at Buffalo, State University of New York, Buffalo, New York; Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, New York.
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35
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Squires AD, Lewis RA, Zaczek AJ, Korter TM. Distinguishing Quinacridone Pigments via Terahertz Spectroscopy: Absorption Experiments and Solid-State Density Functional Theory Simulations. J Phys Chem A 2017; 121:3423-3429. [DOI: 10.1021/acs.jpca.7b01582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. D. Squires
- Institute
for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong New South Wales 2522, Australia
| | - R. A. Lewis
- Institute
for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong New South Wales 2522, Australia
| | - Adam J. Zaczek
- Department
of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, United States of America
| | - Timothy M. Korter
- Department
of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, United States of America
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36
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Zhang F, Wang HW, Tominaga K, Hayashi M, Hasunuma T, Kondo A. Application of THz Vibrational Spectroscopy to Molecular Characterization and the Theoretical Fundamentals: An Illustration Using Saccharide Molecules. Chem Asian J 2017; 12:324-331. [DOI: 10.1002/asia.201601419] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Feng Zhang
- Molecular Photoscience Research Center; Kobe University; Kobe 657-8501 Japan
| | - Houng-Wei Wang
- Center for Condensed Matter Sciences; National; Taiwan) University 1 Roosevelt Rd. Sec. 4 Taipei 10617 Taiwan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center; Kobe University; Kobe 657-8501 Japan
| | - Michitoshi Hayashi
- Center for Condensed Matter Sciences; National; Taiwan) University 1 Roosevelt Rd. Sec. 4 Taipei 10617 Taiwan
| | - Tomohisa Hasunuma
- Graduate School of Science; Technology and Innovation; Kobe University; Kobe 657-8501 Japan
| | - Akihiko Kondo
- Graduate School of Science; Technology and Innovation; Kobe University; Kobe 657-8501 Japan
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37
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Ruggiero MT, Zeitler JA, Erba A. Intermolecular anharmonicity in molecular crystals: interplay between experimental low-frequency dynamics and quantum quasi-harmonic simulations of solid purine. Chem Commun (Camb) 2017; 53:3781-3784. [DOI: 10.1039/c7cc00509a] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental spectroscopic and theoretical quasi-harmonic investigation of intermolecular anharmonicity in crystalline purine.
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Affiliation(s)
- Michael T. Ruggiero
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge
- UK
| | - J. Axel Zeitler
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge
- UK
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38
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Aschaffenburg DJ, Williams MRC, Schmuttenmaer CA. Terahertz spectroscopic polarimetry of generalized anisotropic media composed of Archimedean spiral arrays: Experiments and simulations. J Chem Phys 2016; 144:174705. [DOI: 10.1063/1.4947469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel J. Aschaffenburg
- Department of Chemistry, Yale University, 225 Prospect St., P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
| | - Michael R. C. Williams
- Department of Chemistry, Yale University, 225 Prospect St., P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
| | - Charles A. Schmuttenmaer
- Department of Chemistry, Yale University, 225 Prospect St., P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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39
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Zhang F, Wang HW, Tominaga K, Hayashi M. Mixing of intermolecular and intramolecular vibrations in optical phonon modes: terahertz spectroscopy and solid-state density functional theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1256] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Feng Zhang
- Molecular Photoscience Research Center; Kobe University; Kobe Japan
| | - Houng-Wei Wang
- Center for Condensed Matte Sciences; National Taiwan University; Taipei Taiwan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center; Kobe University; Kobe Japan
| | - Michitoshi Hayashi
- Center for Condensed Matte Sciences; National Taiwan University; Taipei Taiwan
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40
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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41
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Zhang F, Wang HW, Tominaga K, Hayashi M. Characteristics of Low-Frequency Molecular Phonon Modes Studied by THz Spectroscopy and Solid-State ab Initio Theory: Polymorphs I and III of Diflunisal. J Phys Chem B 2016; 120:1698-710. [PMID: 26808927 DOI: 10.1021/acs.jpcb.5b08798] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
THz absorption spectra of two polymorphs of diflunisal, form I and form III, exhibit distinct features due to the influence of packing conformations on the frequency distributions and IR activities of gamma point phonon modes within the 100 cm(-1) region. In order to understand the origins of these THz modes, we perform a detailed mode analysis. The result shows that although the spectral features are different, these low-frequency phonon modes of the two molecular polymorphs have similar vibrational characteristics in terms of harmonic couplings of intermolecular and intramolecular vibrations.
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Affiliation(s)
- Feng Zhang
- Molecular Photoscience Research Center, Kobe University , Kobe 657-8501, Japan
| | - Houng-Wei Wang
- Center for Condensed Matter Sciences, National Taiwan University , 1 Roosevelt Road Sec. 4, Taipei 10617, Taiwan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University , Kobe 657-8501, Japan
| | - Michitoshi Hayashi
- Center for Condensed Matter Sciences, National Taiwan University , 1 Roosevelt Road Sec. 4, Taipei 10617, Taiwan
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42
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ISOGAI M, HOUJOU H. Quantification of Inter/intramolecular Stiffness by Coarse-graining Intermolecular Vibrations of Homo/hetero-dimers. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Makoto ISOGAI
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hirohiko HOUJOU
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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43
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Seoudi RS, Dowd A, Smith BJ, Mechler A. Structural analysis of bioinspired nano materials with synchrotron far IR spectroscopy. Phys Chem Chem Phys 2016; 18:11467-73. [DOI: 10.1039/c6cp01355d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Synchrotron far-infrared spectroscopy was used in conjunction with density functional theory vibrational analysis to ascertain the core structure of self-assembled fibrous superstructures formed by unnatural β3-tripeptides.
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Affiliation(s)
- Rania S. Seoudi
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Annette Dowd
- School of Mathematical and Physical Sciences
- University of Technology Sydney
- Australia
| | - Brian J. Smith
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Adam Mechler
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
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44
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Silva AM, Costa SN, Sales FAM, Freire VN, Bezerra EM, Santos RP, Fulco UL, Albuquerque EL, Caetano EWS. Vibrational Spectroscopy and Phonon-Related Properties of the L-Aspartic Acid Anhydrous Monoclinic Crystal. J Phys Chem A 2015; 119:11791-803. [PMID: 26623495 DOI: 10.1021/acs.jpca.5b08784] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The infrared absorption and Raman scattering spectra of the monoclinic P21 l-aspartic acid anhydrous crystal were recorded and interpreted with the help of density functional theory (DFT) calculations. The effect of dispersive forces was taken into account, and the optimized unit cells allowed us to obtain the vibrational normal modes. The computed data exhibits good agreement with the measurements for low wavenumbers, allowing for a very good assignment of the infrared and Raman spectral features. The vibrational spectra of the two lowest energy conformers of the l-aspartic molecule were also evaluated using the hybrid B3LYP functional for the sake of comparison, showing that the molecular calculations give a limited description of the measured IR and Raman spectra of the l-aspartic acid crystal for wavenumbers below 1000 cm(-1). The results obtained reinforce the need to use solid-state calculations to describe the vibrational properties of molecular crystals instead of calculations for a single isolated molecule picture even for wavenumbers beyond the range usually associated with lattice modes (200 cm(-1) < ω < 1000 cm(-1)).
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Affiliation(s)
- A M Silva
- Universidade Estadual do Piauí , 64260-000 Piripiri, Pi Brazil
| | - S N Costa
- Departamento de Física, Universidade Federal do Ceará, Centro de Ciências , Caixa Postal 6030, Campus do Pici, 60455-760 Fortaleza, CE Brazil
| | - F A M Sales
- Departamento de Física, Universidade Federal do Ceará, Centro de Ciências , Caixa Postal 6030, Campus do Pici, 60455-760 Fortaleza, CE Brazil
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, Centro de Ciências , Caixa Postal 6030, Campus do Pici, 60455-760 Fortaleza, CE Brazil
| | - E M Bezerra
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Ceará , Campus do Porangabuçu, 60430-270 Fortaleza, CE Brazil
| | - R P Santos
- Engenharia de Computação, Universidade Federal do Ceará , 62042-280 Sobral, CE Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte , 59072-970 Natal, RN Brazil
| | - E L Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte , 59072-970 Natal, RN Brazil
| | - E W S Caetano
- Instituto Federal de Educação, Ciência e Tecnologia do Ceará, 60040-531 Fortaleza, CE Brazil
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45
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Milot RL, Schmuttenmaer CA. Electron injection dynamics in high-potential porphyrin photoanodes. Acc Chem Res 2015; 48:1423-31. [PMID: 25938858 DOI: 10.1021/ar500363q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
There is a growing need to utilize carbon neutral energy sources, and it is well known that solar energy can easily satisfy all of humanity's requirements. In order to make solar energy a viable alternative to fossil fuels, the problem of intermittency must be solved. Batteries and supercapacitors are an area of active research, but they currently have relatively low energy-to-mass storage capacity. An alternative and very promising possibility is to store energy in chemical bonds, or make a solar fuel. The process of making solar fuel is not new, since photosynthesis has been occurring on earth for about 3 billion years. In order to produce any fuel, protons and electrons must be harvested from a species in its oxidized form. Photosynthesis uses the only viable source of electrons and protons on the scale needed for global energy demands: water. Because artificial photosynthesis is a lofty goal, water oxidation, which is a crucial step in the process, has been the initial focus. This Account provides an overview of how terahertz spectroscopy is used to study electron injection, highlights trends from previously published reports, and concludes with a future outlook. It begins by exploring similarities and differences between dye-sensitized solar cells (DSSCs) for producing electricity and a putative device for splitting water and producing a solar fuel. It then identifies two important problems encountered when adapting DSSC technology to water oxidation-improper energy matching between sensitizer energy levels with the potential for water oxidation and the instability of common anchoring groups in water-and discusses steps to address them. Emphasis is placed on electron injection from sensitizers to metal oxides because this process is the initial step in charge transport. Both the rate and efficiency of electron injection are analyzed on a sub-picosecond time scale using time-resolved terahertz spectroscopy (TRTS). Bio-inspired pentafluorophenyl porphyrins are promising sensitizers because their high reduction potentials are compatible with the energy requirements of water oxidation. TRTS of free-base and metalated pentafluorophenyl porphyrins reveal inefficient electron injection into TiO2 nanoparticles but more efficient electron injection into SnO2 nanoparticles. With SnO2, injection time scales depend strongly on the identity of the central substituent and are affected by competition with excited-state deactivation processes. Heavy or paramagnetic metal ions increase the electron injection time scale by roughly one order of magnitude relative to free-base or Zn(2+) porphyrins due to the possibility of electron injection from longer-lived, lower-lying triplet states. Furthermore, electron injection efficiency loosely correlates with DSSC performance. The carboxylate anchoring group is commonly used to bind DSSC sensitizers to metal oxide surfaces but typically is not stable under the aqueous and oxidative conditions required for water oxidation. Electron injection efficiency of several water-stable alternatives, including phosphonic acid, hydroxamic acid, acetylacetone, and boronic acid, were evaluated using TRTS, and hydroxamate was found to perform as well as the carboxylate. The next challenge is incorporating a water oxidation catalyst into the design. An early example, in which an Ir-based precatalyst is cosensitized with a fluorinated porphyrin, reveals decreased electron injection efficiency despite an increase in photocurrent. Future research will seek to better understand and address these difficulties.
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Affiliation(s)
- Rebecca L. Milot
- Department of Chemistry and
Energy Sciences Institute, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Charles A. Schmuttenmaer
- Department of Chemistry and
Energy Sciences Institute, Yale University, 225 Prospect Street, P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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46
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Gaillard T, Trivella A, Stote RH, Hellwig P. Far infrared spectra of solid state L-serine, L-threonine, L-cysteine, and L-methionine in different protonation states. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:301-307. [PMID: 26056980 DOI: 10.1016/j.saa.2015.05.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/08/2015] [Accepted: 05/10/2015] [Indexed: 06/04/2023]
Abstract
In this study, experimental far infrared measurements of L-serine, L-threonine, L-cysteine, and L-methionine are presented showing the spectra for the 1.0-13.0 pH range. In parallel, solid state DFT calculations were performed on the amino acid zwitterions in the crystalline form. We focused on the lowest frequency far infrared normal modes, which required the most precision and convergence of the calculations. Analysis of the computational results, which included the potential energy distribution of the vibrational modes, permitted a detailed and almost complete assignment of the experimental spectrum. In addition to characteristic signals of the two main acid-base couples, CO2H/CO2(-) and NH3(+)/NH2, specific side chain contributions for these amino acids, including CCO and CCS vibrational modes were analyzed. This study is in line with the growing application of FIR measurements to biomolecules.
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Affiliation(s)
- Thomas Gaillard
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
| | - Aurélien Trivella
- Laboratoire de bio électrochimie et spectroscopie, UMR7140, Chimie de la Matière complexe, Université de Strasbourg, CNRS, 1 rue Blaise Pascal, F-67070 Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964/Centre National de Recherche Scientifique (CNRS) UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, 67404 Illkirch CEDEX, France
| | - Petra Hellwig
- Laboratoire de bio électrochimie et spectroscopie, UMR7140, Chimie de la Matière complexe, Université de Strasbourg, CNRS, 1 rue Blaise Pascal, F-67070 Strasbourg, France.
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47
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Zhang F, Wang HW, Tominaga K, Hayashi M. Intramolecular vibrations in low-frequency normal modes of amino acids: L-alanine in the neat solid state. J Phys Chem A 2015; 119:3008-22. [PMID: 25723274 DOI: 10.1021/jp512164y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper presents a theoretical analysis of the low-frequency phonons of L-alanine by using the solid-state density functional theory at the Γ point. We are particularly interested in the intramolecular vibrations accessing low-frequency phonons via harmonic coupling with intermolecular vibrations. A new mode-analysis method is introduced to quantify the vibrational characteristics of such intramolecular vibrations. We find that the torsional motions of COO(-) are involved in low-frequency phonons, although COO(-) is conventionally assumed to undergo localized torsion. We also find the broad distributions of intramolecular vibrations relevant to important functional groups of amino acids, e.g., the COO(-) and NH3(+) torsions, in the low-frequency phonons. The latter finding is illustrated by the concept of frequency distribution of vibrations. These findings may lead to immediate implications in other amino acid systems.
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Affiliation(s)
- Feng Zhang
- †Molecular Photoscience Research Center, Kobe University, Kobe 657-8501, Japan
| | - Houng-Wei Wang
- ‡Center for Condensed Matter Sciences, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei 10617, Taiwan
| | - Keisuke Tominaga
- †Molecular Photoscience Research Center, Kobe University, Kobe 657-8501, Japan
| | - Michitoshi Hayashi
- ‡Center for Condensed Matter Sciences, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei 10617, Taiwan
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Zhang F, Hayashi M, Wang HW, Tominaga K, Kambara O, Nishizawa JI, Sasaki T. Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: Effect of dispersion force on the vibrational modes. J Chem Phys 2014; 140:174509. [DOI: 10.1063/1.4873421] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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49
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Delaney SP, Smith TM, Korter TM. Conformation versus cohesion in the relative stabilities of gabapentin polymorphs. RSC Adv 2014. [DOI: 10.1039/c3ra43887b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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