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Allen JL, Sanders TJ, Horvat J, Lewis RA, Rule KC. Determination of Vibrational Modes of l-Alanine Single Crystals by a Combination of Terahertz Spectroscopy Measurements and Density Functional Calculations. PHYSICAL REVIEW LETTERS 2023; 130:226901. [PMID: 37327443 DOI: 10.1103/physrevlett.130.226901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Density-functional theory may be used to predict both the frequency and the dipole moment of the fundamental oscillations of molecular crystals. Suitably polarized photons at those frequencies excite such oscillations. Thus, in principle, terahertz spectroscopy may confirm the calculated fundamental modes of amino acids. However, reports to date have multiple shortcomings: (a) material of uncertain purity and morphology and diluted in a binder material is employed; (b) consequently, vibrations along all crystal axes are excited simultaneously; (c) data are restricted to room temperature, where resonances are broad and the background dominant; and (d) comparison with theory has been unsatisfactory (in part because the theory assumes zero temperature). Here, we overcome all four obstacles, in reporting detailed low-temperature polarized THz spectra of single-crystal l-alanine, assigning vibrational modes using density-functional theory, and comparing the calculated dipole moment vector direction to the electric field polarization of the measured spectra. Our direct and detailed comparison of theory with experiment corrects previous mode assignments for l-alanine, and reveals unreported modes, previously obscured by closely spaced spectral absorptions. The fundamental modes are thereby determined.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J Horvat
- 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
| | - K C Rule
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
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Sanders TJ, Allen JL, Plathe R, Appadoo D, Horvat J, Lewis RA. Terahertz tyrosine modes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121970. [PMID: 36302282 DOI: 10.1016/j.saa.2022.121970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
We have measured the terahertz spectrum of pure l-tyrosine at nineteen temperatures in the range 6K to 300K using a synchrotron as the source of radiation. By fitting the temperature dependence of the observed modes with a Bose-Einstein model, we determine unequivocal low-frequency modes of l-tyrosine at absolute zero temperature occur at 1.02 ± 0.01, 1.61 ± 0.01, 1.97 ± 0.01, and 2.19 ± 0.01THz. This determination is consistent with the more reliable of the earlier measurements. We conclude that many of the recently reported features in the terahertz spectrum of l-tyrosine are experimental artefacts.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia.
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R Plathe
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - D Appadoo
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
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Sanders TJ, Allen JL, Horvat J, Lewis RA. High-quality, temperature-dependent terahertz spectroscopy of single crystalline L-alanine: Experiment and density-functional theory. J Chem Phys 2021; 154:244311. [PMID: 34241345 DOI: 10.1063/5.0054063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
For the first time, the terahertz transmittance spectra of l-alanine have been measured using a single crystal. Measurements were obtained over a large temperature range (12-300 K) and revealed 18 absorptions between 20 and 250 cm-1. These modes were sharp and symmetric, a feature of single crystals and low temperatures. The spectra were directly compared to those of a powdered pellet sample. Raman spectroscopy and x-ray diffraction were used to confirm the sample's structure and purity. With increasing temperature, all modes exhibit spectral redshift, well described by a Bose-Einstein model, indicating the phonon origin of the absorptions. The exceptions are the 91 and 128 cm-1 modes. The former blueshifts. The latter initially blueshifts but transitions to redshifting. Both behaviors are anomalous. Density-functional theory modeling helped assign all the observed modes.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J Horvat
- 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
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Sanders TJ, Allen JL, Plathe R, Horvat J, Lewis RA. The 3, 5, 6, and 7 THz resonances of α-glycine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119544. [PMID: 33631628 DOI: 10.1016/j.saa.2021.119544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Using an optically thin single crystal sample, mounted in a cryostat permitting cooling to 6 K, and a synchrotron as a bright light source, exceptionally well defined absorption spectra of well-characterised α-glycine have been obtained in the spectral range 2.5-7.5 THz (approximately 80-240 cm-1). Four separate resonances have been observed, respectively at 93, 152, 188, and 223 cm-1 at the lowest temperature. Each reduces in frequency (redshifts) as temperature increases. The origin of this observed behaviour is attributed to a phonon-mediated anharmonicity in the crystal potential.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia.
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R Plathe
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
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Allen JL, Sanders TJ, Horvat J, Lewis RA. Anharmonicity-driven redshift and broadening of sharp terahertz features of α-glycine single crystal from 20 K to 300 K: Theory and experiment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118635. [PMID: 32858447 DOI: 10.1016/j.saa.2020.118635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
For the first time, large single crystals of the simplest amino acid, glycine, have been used to determine the temperature dependence of its terahertz spectrum. High-quality spectra with very sharp absorption features are observed at cryogenic temperatures. The α-glycine structure and the purity of the crystals were verified via Raman spectroscopy and X-ray diffraction. Spectral redshift with increasing temperature was observed for all absorption bands in the terahertz region (10-250 cm-1, or 1-8 THz) over the temperature range of 20-300 K. X-ray diffraction revealed expansion in all planes of the crystal lattice over the same temperature range. A Bose-Einstein distribution was used to model the frequency position shift of the two lowest-energy fundamental modes at 50 cm-1 and 69 cm-1. On this basis, we attribute the observed redshift and broadening with increasing temperature to the anharmonic potential associated with the phonon bath.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - T J Sanders
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia
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Yang X, Zhang L, Liang Y, Wang Y, Shen Y, Xing Q, Qi W, Wang P, Liu X, Yang M, Su R, He M, He Z. Self-Assembled Bio-Organometallic Nanocatalysts for Highly Enantioselective Direct Aldol Reactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13735-13742. [PMID: 33175547 DOI: 10.1021/acs.langmuir.0c01485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Supramolecular nanocatalysts were designed for asymmetric reactions through the self-assembly process of a bio-organometallic molecule, ferrocene-l-prolinamide (Fc-CO-NH-P). Fc-CO-NH-P could self-assemble into versatile nanostructures in water, including nanospheres, nanosheets, nanoflowers, and pieces. In particular, the self-assembled nanoflowers exhibited a superior specific surface area, high stability, and delicate three-dimensional (3D) chiral catalytic active sites. The nanoflowers could serve as heterogeneous catalysts with an excellent catalytic performance toward direct aldol reactions in aqueous solution, achieving both high yield (>99%) and stereoselectivity (anti/syn = 97:3, ee% >99%). This study proposed a significant strategy to fabricate supramolecular chiral catalysts, serving as a favorable template for designing new asymmetric catalysts.
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Affiliation(s)
- Xuejiao Yang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Liwei Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yaoyu Liang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Qiguo Xing
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Pengfei Wang
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 30072, P. R. China
| | - Xiao Liu
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Mengyao Yang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Mingxia He
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 30072, P. R. China
| | - Zhimin He
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
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Zhang F, Wang HW, Tominaga K, Hayashi M, Sasaki T. Terahertz Fingerprints of Short-Range Correlations of Disordered Atoms in Diflunisal. J Phys Chem A 2019; 123:4555-4564. [PMID: 31038953 DOI: 10.1021/acs.jpca.9b00580] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work proposes a terahertz (THz) spectroscopy approach to the investigation of one of the outstanding problems in crystallography-the structure analysis of a crystal with disorder. Form I of diflunisal, in which the two ortho sites on one phenyl ring of diflunisal show occupational disorder, was used for an illustration. THz radiation interacts with the collective vibrations of correlated disorder, thus providing a promising tool to examine the symmetry of short-range correlations of disordered atoms. Through a thorough examination of the selection rule of THz vibrations in which the disordered atoms are involved to different extents, we deduced that only four short-range correlation possibilities of disorder exist and all of them display unambiguous fingerprint peaks in the 50-170 cm-1 frequency region. We finally proposed an alternating packing model in which the correlation lengths of disorder are on the nanometer scale.
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Affiliation(s)
- Feng Zhang
- Molecular Photoscience Research Center , Kobe University , Nada, Kobe 657-0013 , 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 , Nada, Kobe 657-0013 , Japan
| | - Michitoshi Hayashi
- Center for Condensed Matter Sciences , National Taiwan University , 1 Roosevelt Rd., Sec. 4 , Taipei 10617 , Taiwan
| | - Tetsuo Sasaki
- Research Institute of Electronics , Shizuoka University , Hamamatsu , Shizuoka 432-8011 , Japan
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8
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Huang J, Liu J, Wang K, Yang Z, Liu X. Classification and identification of molecules through factor analysis method based on terahertz spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 198:198-203. [PMID: 29547821 DOI: 10.1016/j.saa.2018.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
By means of factor analysis approach, a method of molecule classification is built based on the measured terahertz absorption spectra of the molecules. A data matrix can be obtained by sampling the absorption spectra at different frequency points. The data matrix is then decomposed into the product of two matrices: a weight matrix and a characteristic matrix. By using the K-means clustering to deal with the weight matrix, these molecules can be classified. A group of samples (spirobenzopyran, indole, styrene derivatives and inorganic salts) has been prepared, and measured via a terahertz time-domain spectrometer. These samples are classified with 75% accuracy compared to that directly classified via their molecular formulas.
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Affiliation(s)
- Jianglou Huang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jinsong Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
| | - Kejia Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Zhengang Yang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongli Medical College, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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Zhou T, Wu Y, Cao J, Zou L, Yuan J, Yao Z, Xu G. Research on the Terahertz Absorption Spectra of Histidine Enantiomer (L) and its Racemic Compound (DL). APPLIED SPECTROSCOPY 2017; 71:194-202. [PMID: 27815434 DOI: 10.1177/0003702816669728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Terahertz time-domain spectroscopy (THz-TDS) is used to investigate the absorption spectra of polycrystalline L- and DL-histidine in the frequency range of 10-100 cm-1. The spectra exhibit distinct differences in peak frequencies between the enantiomer (L-histidine) and racemic compound (DL-histidine). The observed spectral differences are attributed to the intermolecular interactions. With the density function theory (DFT) method, the frequencies of vibrational modes of L-histidine and DL-histidine in the THz range are calculated and well assigned according to the measured spectra. The origin of the observed vibrational modes is found to be non-localized and of a collective (phonon-like) nature, which points to the lattice and skeleton vibrations mediated by the hydrogen bond. Furthermore, we propose and demonstrate a method for determining the composition ratio of histidine mixtures based on the THz absorption spectra.
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Affiliation(s)
- Tao Zhou
- 1 Key Laboratory of Terahertz Solid-State Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai, China
| | - Yidong Wu
- 1 Key Laboratory of Terahertz Solid-State Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai, China
| | - Juncheng Cao
- 1 Key Laboratory of Terahertz Solid-State Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai, China
| | | | - Jie Yuan
- 3 Department of Radiology, Hua shan Hospital, Fu dan University, Shanghai, China
| | - Zhenwei Yao
- 3 Department of Radiology, Hua shan Hospital, Fu dan University, Shanghai, China
| | - Gongjie Xu
- 4 Engineering Research Center of Optical Instrument and System, Ministry of Education and Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, China
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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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11
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Zhang M, Wei D, Tang M, Shi C, Cui HL, Du C. Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1059429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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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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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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14
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Chen T, Li Z, Mo W. Identification of biomolecules by terahertz spectroscopy and fuzzy pattern recognition. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 106:48-53. [PMID: 23357678 DOI: 10.1016/j.saa.2012.12.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 12/25/2012] [Accepted: 12/30/2012] [Indexed: 06/01/2023]
Abstract
An approach for automatic identification of terahertz (THz) spectra of biomolecules is proposed based on principal component analysis (PCA) and fuzzy pattern recognition in this paper, and THz transmittance spectra of some typical amino acid and saccharide biomolecular samples are investigated to prove its feasibility. Firstly, PCA is applied to reduce the dimensionality of the original spectrum data and extract features of the data. Secondly, instead of the original spectrum variables, the selected principal component scores matrix is fed into the model of fuzzy pattern recognition, where a principle of fuzzy closeness based optimization is employed to identify those samples. Results demonstrate that THz spectroscopy combined with PCA and fuzzy pattern recognition can be efficiently utilized for automatic identification of biomolecules. The proposed approach provides a new effective method in the detection and identification of biomolecules using THz spectroscopy.
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Affiliation(s)
- Tao Chen
- School of Mechano-Electronic Engineering, Xidian University, Xi'an, Shanxi 710071, China
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15
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Stehle CU, Abuillan W, Gompf B, Dressel M. Far-infrared spectroscopy on free-standing protein films under defined temperature and hydration control. J Chem Phys 2012; 136:075102. [DOI: 10.1063/1.3686886] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Zakaria HA, Fischer BM, Bradley AP, Jones I, Abbott D, Middelberg APJ, Falconer RJ. Low-frequency spectroscopic analysis of monomeric and fibrillar lysozyme. APPLIED SPECTROSCOPY 2011; 65:260-4. [PMID: 21352645 DOI: 10.1366/10-06162] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Terahertz time-domain spectroscopy (THz-TDS) and Fourier transform infrared (FT-IR) spectroscopy were used to generate far-infrared and low-frequency spectral measurements of monomeric lysozyme and lysozyme fibrils. The formation of lysozyme fibrils was verified by the Thioflavin T assay and transmission electron microscopy (TEM). It was evident in the FT-IR spectra that between 150 and 350 cm(-1) the two spectra diverge, with the lysozyme fibrils showing higher absorbance intensity than the monomeric form. The broad absorption phenomenon is likely due to light scattered from the fibrillar architecture of lysozyme fibrils as supported by simulation of Rayleigh light scattering. The lack of discrete phonon-like peaks suggest that far-infrared spectroscopy cannot detect vibrational modes between the highly ordered hydrogen-bonded beta-pleated sheets of the lysozyme subunit.
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Affiliation(s)
- Hidayatul A Zakaria
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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Ding T, Li R, Zeitler JA, Huber TL, Gladden LF, Middelberg APJ, Falconer RJ. Terahertz and far infrared spectroscopy of alanine-rich peptides having variable ellipticity. OPTICS EXPRESS 2010; 18:27431-44. [PMID: 21197019 DOI: 10.1364/oe.18.027431] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Terahertz spectra of four alanine-rich peptides with known secondary structures were studied by terahertz time domain spectroscopy (THz-TDS) and by Fourier transform infrared spectroscopy (FTIR) using a synchrotron light source and a liquid-helium cooled bolometer. At ambient temperatures the usable bandwidth was restricted to 0.2-1.5 THz by the absorbance of water. The existence of a solvation shell around the peptide in solution was observed and its size estimated to be between 11 and 17 Å. By cooling the peptide solution to 80 K in order to reduce the water absorbance the bandwidth was increased to 0.1-3.0 THz for both THz-TDS and FTIR. Spectra were consistent with monotonic absorbance of the peptide and the existence of a solid amorphous low density solvation shell.
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Affiliation(s)
- Tao Ding
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
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Trivella A, Gaillard T, Stote RH, Hellwig P. Far infrared spectra of solid state aliphatic amino acids in different protonation states. J Chem Phys 2010; 132:115105. [DOI: 10.1063/1.3356027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Li X, Globus T, Gelmont B, Salay LC, Bykhovski A. Terahertz absorption of DNA decamer duplex. J Phys Chem A 2009; 112:12090-6. [PMID: 18928269 DOI: 10.1021/jp806630w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10-25 cm(-1) using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.
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Affiliation(s)
- Xiaowei Li
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, Virginia 22904, USA
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Abstract
Low-frequency vibrational modes of biological molecules consist of intramolecular modes, which are dependent on the molecule as a whole, as well as intermolecular modes, which arise from hydrogen-bonding interactions and van der Waals forces. Vibrational modes thus contain important information about conformation dynamics of biological molecules, and can also be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time-domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult to distinguish. The technique of waveguide THz-TDS has been recently developed, resulting in sharper features. For this technique, an ordered polycrystalline film of the molecule is formed on a metal sample plate. This plate is incorporated into a metal parallel-plate waveguide and probed via waveguide THz-TDS. The planar order of the film reduces the inhomogeneous broadening, and cooling of the samples to 77K reduces the homogenous broadening. This combination results in the line-narrowing of THz vibrational modes, in some cases to an unprecedented degree. Here, this technique has been demonstrated with seven small biological molecules, thymine, deoxycytidine, adenosine, D-glucose, tryptophan, glycine, and L-alanine. The successful demonstration of this technique shows the possibilities and promise for future studies of internal vibrational modes of large biological molecules.
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