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Földes D, Kováts É, Bortel G, Kamarás K, Tarczay G, Jakab E, Pekker S. Preparation and characterization of a new chiral metal-organic framework with spiranes. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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Mazzeo G, Santoro E, Abbate S, Zonta C, Fabris F, Longhi G. Testing the vibrational exciton and the local mode models on the instructive cases of dicarvone, dipinocarvone, and dimenthol vibrational circular dichroism spectra. Chirality 2020; 32:907-921. [DOI: 10.1002/chir.23232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/11/2020] [Accepted: 04/06/2020] [Indexed: 01/30/2023]
Affiliation(s)
- Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità di Brescia Brescia Italy
| | - Ernesto Santoro
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità di Brescia Brescia Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità di Brescia Brescia Italy
- Research Unit of BresciaIstituto Nazionale di Ottica (INO), CNR Brescia Italy
| | - Cristiano Zonta
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padova Padova Italy
| | - Fabrizio Fabris
- Dipartimento di Scienze Molecolari e NanosistemiUniversità Ca' Foscari Venezia Mestre Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità di Brescia Brescia Italy
- Research Unit of BresciaIstituto Nazionale di Ottica (INO), CNR Brescia Italy
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4
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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5
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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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Campi LB, Lopes FC, Soares LES, de Queiroz AM, de Oliveira HF, Saquy PC, de Sousa-Neto MD. Effect of radiotherapy on the chemical composition of root dentin. Head Neck 2018; 41:162-169. [PMID: 30552849 DOI: 10.1002/hed.25493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/23/2018] [Accepted: 07/06/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The radiotherapy can directly affect the bond strength of the adhesive materials, interfering in the prognosis of restorative treatments, which may be caused by chemical changes in dentin structure. METHODS Twenty inferior homologues premolars were distributed in 2 groups (in vitro study) (n = 10): nonirradiated and irradiated. The specimens were submitted to the analysis of phosphate (ν1 PO4 3- ;ν2 PO4 3- ;ν4 PO4 3- ), carbonate (ν3 CO3 2- ), amide I, CH2 , amide III, and amide I/III ratio by confocal Raman spectroscopy. Data were submitted to statistical analysis (T test, P < .05). RESULTS In intracanal dentin, the irradiated group had lower ν4 PO4 3- values (1.23 ± 0.06) compared to nonirradiated group (1.40 ± 0.18) (P < .05), with no difference for ν1 PO4 3- and ν2 PO4 3 peaks (P > .05). The irradiated (1.56 ± 0.06) had lower carbonate, amide III (1.05 ± 0.19), and amide I/III ratio values (0.19 ± 0.06) compared to nonirradiated group (1.42 ± 0.10, 1.28 ± 0.24, and 0.31 ± 0.10, respectively) (P < .05). For medium dentin irradiated group (1.30 ± 0.12) had lower phosphate values compared to nonirradiated group (1.48 ± 0.22) (P < .05). In cementum, there was no statistical difference between the groups. CONCLUSION The radiotherapy was able to cause changes in ν4 PO4 3- , carbonate, and amide III peaks of root dentin.
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Affiliation(s)
- Lívia Bueno Campi
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Fabiane Carneiro Lopes
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luís Eduardo Silva Soares
- Laboratory of Dentistry and Applied Materials (LDAM), Research and Development Institute (IP&D), Universidade do Vale do Paraíba, Univap, São José dos Campos, São Paulo, Brazil
| | - Alexandra Mussolino de Queiroz
- Department Children's Clinic, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Harley Francisco de Oliveira
- Medical Clinic Department, Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Paulo César Saquy
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Manoel Damião de Sousa-Neto
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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Lung PW, Tippavajhala VK, de Oliveira Mendes T, Téllez-Soto CA, Schuck DC, Brohem CA, Lorencini M, Martin AA. In vivo study of dermal collagen of striae distensae by confocal Raman spectroscopy. Lasers Med Sci 2018; 33:609-617. [PMID: 29308552 DOI: 10.1007/s10103-017-2431-3] [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: 10/04/2016] [Accepted: 12/26/2017] [Indexed: 11/29/2022]
Abstract
This research work mainly deals with studying qualitatively the changes in the dermal collagen of two forms of striae distensae (SD) namely striae rubrae (SR) and striae albae (SA) when compared to normal skin (NS) using confocal Raman spectroscopy. The methodology includes an in vivo human skin study for the comparison of confocal Raman spectra of dermis region of SR, SA, and NS by supervised multivariate analysis using partial least squares discriminant analysis (PLS-DA) to determine qualitatively the changes in dermal collagen. These groups are further analyzed for the extent of hydration of dermal collagen by studying the changes in the water content bound to it. PLS-DA score plot showed good separation of the confocal Raman spectra of dermis region into SR, SA, and NS data groups. Further analysis using loading plot and S-plot indicated the participation of various components of dermal collagen in the separation of these groups. Bound water content analysis showed that the extent of hydration of collagen is more in SD when compared to NS. Based on the results obtained, this study confirms the active involvement of dermal collagen in the formation of SD. It also emphasizes the need to study quantitatively the role of these various biochemical changes in the dermal collagen responsible for the variance between SR, SA, and NS.
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Affiliation(s)
- Pam Wen Lung
- Institute of Research and Development (IP&D), Universidade do Vale do Paraiba (UNIVAP), Av. Shishima Hifumi, 2911, Urbanova, São José dos Campos, SP, CEP: 12244-000, Brazil
| | - Vamshi Krishna Tippavajhala
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
| | - Thiago de Oliveira Mendes
- Biomedical Engineering Innovation Center, Biomedical Vibrational Spectroscopy Group, Universidade Brasil-UNBr, Rua Carolina Fonseca, 235-08230-030, Itaquera, Sao Paulo, Brazil
| | - Claudio A Téllez-Soto
- Biomedical Engineering Innovation Center, Biomedical Vibrational Spectroscopy Group, Universidade Brasil-UNBr, Rua Carolina Fonseca, 235-08230-030, Itaquera, Sao Paulo, Brazil
| | - Desirée Cigaran Schuck
- Grupo O Boticário, Av. Rui Barbosa, 4.110, Parque da Fonte, São José dos Pinhais, PR, CEP: 83050-010, Brazil
| | - Carla Abdo Brohem
- Grupo O Boticário, Av. Rui Barbosa, 4.110, Parque da Fonte, São José dos Pinhais, PR, CEP: 83050-010, Brazil
| | - Marcio Lorencini
- Grupo O Boticário, Av. Rui Barbosa, 4.110, Parque da Fonte, São José dos Pinhais, PR, CEP: 83050-010, Brazil
| | - Airton Abrahão Martin
- Biomedical Engineering Innovation Center, Biomedical Vibrational Spectroscopy Group, Universidade Brasil-UNBr, Rua Carolina Fonseca, 235-08230-030, Itaquera, Sao Paulo, Brazil. .,Departmento de Fisica, Universidade Federal do Piaui (UFPI), Campus Ministro Petronio Portella, Teresina, PI, CEP: 64049-550, Brazil.
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8
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Zimudzi TJ, Feldman KE, Sturnfield JF, Roy A, Hickner MA, Stafford CM. Quantifying Carboxylic Acid Concentration in Model Polyamide Desalination Membranes via Fourier Transform Infrared Spectroscopy. Macromolecules 2018; 51:10.1021/acs.macromol.8b01194. [PMID: 30983631 PMCID: PMC6459611 DOI: 10.1021/acs.macromol.8b01194] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carboxylic acid groups impart hydrophilicity and ionizable moieties to polyamide membranes for desalination, hence influencing water and ion transport through the material. Model polyamide films were synthesized via molecular layer-by-layer deposition on planar substrates to study the formation process of these materials and overcome the chemical and topological inhomogeneity inherent to conventional interfacially polymerized polyamide membranes. The carboxylic acid content in these model films was characterized using Fourier transform infrared (FTIR) spectroscopy by quantifying the C=O band at 1718 cm-1. The concentration of carboxylic acid groups decreased as the thickness of the membrane increased, suggestive of an increase in crosslink density as the polyamide network develops. For the thinnest molecular layer-by-layer (mLbL) samples, the carboxylic acid concentration for films on gold was 0.35 mmol g-1, whereas analogous films on silicon had an acid content of 0.56 mmol g-1, indicating a clear influence of the substrate on the initial network formation. As the thickness of the membrane increased, the influence of the substrate and initial layer growth became less significant as the carboxylic acid concentration on both substrates reached a value of 0.12 mmol g-1. We demonstrate that FTIR spectroscopy is a practical and accessible way to quantify the carboxylic acid content in these types of extremely thin polyamide membranes to help quantify network formation in these materials.
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Affiliation(s)
- Tawanda J. Zimudzi
- Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kathleen E. Feldman
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - James F. Sturnfield
- Engineering and Process Sciences, Process Optimization, The Dow Chemical Company, Freeport, Texas 77541, USA
| | - Abhishek Roy
- Dow Water and Process Solutions, The Dow Chemical Company, Edina, Minnesota 55439, USA
| | - Michael A. Hickner
- Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher M. Stafford
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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9
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Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
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10
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Hahn S. Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results. J Chem Phys 2016; 145:164113. [PMID: 27802648 DOI: 10.1063/1.4965958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.
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Affiliation(s)
- Seungsoo Hahn
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu 156-756, Seoul, South Korea
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11
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Affiliation(s)
- Juan Zhao
- Beijing
National Laboratory
for Molecular Sciences; Laboratory of Molecular Reaction Dynamics,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory
for Molecular Sciences; Laboratory of Molecular Reaction Dynamics,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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12
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Góbi S, Magyarfalvi G, Tarczay G. VCD Robustness of the Amide-I and Amide-II Vibrational Modes of Small Peptide Models. Chirality 2015; 27:625-34. [DOI: 10.1002/chir.22475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/21/2015] [Accepted: 05/08/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Sándor Góbi
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
| | - György Tarczay
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
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13
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Carr JK, Zabuga AV, Roy S, Rizzo TR, Skinner JL. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations. J Chem Phys 2014; 140:224111. [PMID: 24929378 PMCID: PMC4187283 DOI: 10.1063/1.4882059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/26/2014] [Indexed: 02/04/2023] Open
Abstract
The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.
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Affiliation(s)
- J K Carr
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - A V Zabuga
- Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - S Roy
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - T R Rizzo
- Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - J L Skinner
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706, USA
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14
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Zeko T, Hannigan SF, Jacisin T, Guberman-Pfeffer MJ, Falcone ER, Guildford MJ, Szabo C, Cole KE, Placido J, Daly E, Kubasik MA. FT-IR Spectroscopy and Density Functional Theory Calculations of 13C Isotopologues of the Helical Peptide Z-Aib6-OtBu. J Phys Chem B 2013; 118:58-68. [DOI: 10.1021/jp408818g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Timothy Zeko
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Steven F. Hannigan
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Timothy Jacisin
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | | | - Eric R. Falcone
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Melissa J. Guildford
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Christopher Szabo
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Kathryn E. Cole
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Jessica Placido
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Erin Daly
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Matthew A. Kubasik
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
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15
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Jiang F, Han W, Wu YD. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development. Phys Chem Chem Phys 2013; 15:3413-28. [PMID: 23385383 DOI: 10.1039/c2cp43633g] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The local conformational (φ, ψ, χ) preferences of amino acid residues remain an active research area, which are important for the development of protein force fields. In this perspective article, we first summarize spectroscopic studies of alanine-based short peptides in aqueous solution. While most studies indicate a preference for the P(II) conformation in the unfolded state over α and β conformations, significant variations are also observed. A statistical analysis from various coil libraries of high-resolution protein structures is then summarized, which gives a more coherent view of the local conformational features. The φ, ψ, χ distributions of the 20 amino acids have been obtained from a protein coil library, considering both backbone and side-chain conformational preferences. The intrinsic side-chain χ(1) rotamer preference and χ(1)-dependent Ramachandran plot can be generally understood by combining the interaction of the side-chain Cγ/Oγ atom with two neighboring backbone peptide groups. Current all-atom force fields such as AMBER ff99sb-ILDN, ff03 and OPLS-AA/L do not reproduce these distributions well. A method has been developed by combining the φ, ψ plot of alanine with the influence of side-chain χ(1) rotamers to derive the local conformational features of various amino acids. It has been further applied to improve the OPLS-AA force field. The modified force field (OPLS-AA/C) reproduces experimental (3)J coupling constants for various short peptides quite well. It also better reproduces the temperature-dependence of the helix-coil transition for alanine-based peptides. The new force field can fold a series of peptides and proteins with various secondary structures to their experimental structures. MD simulations of several globular proteins using the improved force field give significantly less deviation (RMSD) to experimental structures. The results indicate that the local conformational features from coil libraries are valuable for the development of balanced protein force fields.
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Affiliation(s)
- Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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16
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Roeters SJ, van Dijk CN, Torres-Knoop A, Backus EHG, Campen RK, Bonn M, Woutersen S. Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment. J Phys Chem A 2013; 117:6311-22. [DOI: 10.1021/jp401159r] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- S. J. Roeters
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - C. N. van Dijk
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - A. Torres-Knoop
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - E. H. G. Backus
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - R. K. Campen
- Department of Physical
Chemistry, Fritz Haber Institute, Faradayweg
4-6, 14195 Berlin,
Germany
| | - M. Bonn
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - S. Woutersen
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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17
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Choi JH, Cho M. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants. J Chem Phys 2013; 138:174108. [DOI: 10.1063/1.4802991] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Woys AM, Almeida AM, Wang L, Chiu CC, McGovern M, de Pablo JJ, Skinner JL, Gellman SH, Zanni MT. Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra. J Am Chem Soc 2012; 134:19118-28. [PMID: 23113791 DOI: 10.1021/ja3074962] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel β-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of β-sheet containing proteins and protein assemblies, such as amyloid fibers.
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Affiliation(s)
- Ann Marie Woys
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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19
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Buchanan EG, James WH, Choi SH, Guo L, Gellman SH, Müller CW, Zwier TS. Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling. J Chem Phys 2012; 137:094301. [DOI: 10.1063/1.4747507] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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20
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Tosato MG, Alves RS, dos Santos EA, Raniero L, Menezes PF, Belletti KM, Praes CEO, Martin AA. Raman Spectroscopic Investigation of the Effects of Cosmetic Formulations on the Constituents and Properties of Human Skin. Photomed Laser Surg 2012; 30:85-91. [DOI: 10.1089/pho.2011.3059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maira G. Tosato
- Laboratory of Biomedical Vibrational Spectroscopy, Institute of Research and Development (IP&D), University of the Vale do Paraíba, São José dos Campos, Brazil
| | - Rani S. Alves
- Laboratory of Biomedical Vibrational Spectroscopy, Institute of Research and Development (IP&D), University of the Vale do Paraíba, São José dos Campos, Brazil
| | - Edson A.P. dos Santos
- Laboratory of Biomedical Vibrational Spectroscopy, Institute of Research and Development (IP&D), University of the Vale do Paraíba, São José dos Campos, Brazil
| | - Leandro Raniero
- Laboratory of Biomedical Vibrational Spectroscopy, Institute of Research and Development (IP&D), University of the Vale do Paraíba, São José dos Campos, Brazil
| | | | | | | | - Airton A. Martin
- Laboratory of Biomedical Vibrational Spectroscopy, Institute of Research and Development (IP&D), University of the Vale do Paraíba, São José dos Campos, Brazil
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21
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Choi JH, Cho M. Polarization-Angle-Scanning Two-Dimensional Spectroscopy: Application to Dipeptide Structure Determination. J Phys Chem A 2010; 115:3766-77. [DOI: 10.1021/jp106458j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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22
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Maekawa H, Ballano G, Toniolo C, Ge NH. Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains. J Phys Chem B 2010; 115:5168-82. [DOI: 10.1021/jp105527n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, California, 92697-2025
| | - Gema Ballano
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California, 92697-2025
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23
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Maekawa H, Ge NH. Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra. J Phys Chem B 2010; 114:1434-46. [DOI: 10.1021/jp908695g] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025
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