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Puro RL, Gray TP, Kapfunde TA, Richter-Addo GB, Raschke MB. Vibrational Coupling Infrared Nanocrystallography. NANO LETTERS 2024; 24:1909-1915. [PMID: 38315708 DOI: 10.1021/acs.nanolett.3c03958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Coupling between molecular vibrations leads to collective vibrational states with spectral features sensitive to local molecular order. This provides spectroscopic access to the low-frequency intermolecular energy landscape. In its nanospectroscopic implementation, this technique of vibrational coupling nanocrystallography (VCNC) offers information on molecular disorder and domain formation with nanometer spatial resolution. However, deriving local molecular order relies on prior knowledge of the transition dipole magnitude and crystal structure of the underlying ordered phase. Here we develop a quantitative model for VCNC by relating nano-FTIR collective vibrational spectra to the molecular crystal structure from X-ray crystallography. We experimentally validate our approach at the example of a metal organic porphyrin complex with a carbonyl ligand as the probe vibration. This framework establishes VCNC as a powerful tool for measuring low-energy molecular interactions, wave function delocalization, nanoscale disorder, and domain formation in a wide range of molecular systems.
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Affiliation(s)
- Richard L Puro
- Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Thomas P Gray
- Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Tsitsi A Kapfunde
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - George B Richter-Addo
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Markus B Raschke
- Department of Physics and JILA, University of Colorado, Boulder, Colorado 80309, United States
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2
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Zhao R, Shirley JC, Lee E, Grofe A, Li H, Baiz CR, Gao J. Origin of thiocyanate spectral shifts in water and organic solvents. J Chem Phys 2022; 156:104106. [PMID: 35291777 PMCID: PMC8923707 DOI: 10.1063/5.0082969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.
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Affiliation(s)
- Ruoqi Zhao
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Joseph C Shirley
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Euihyun Lee
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Adam Grofe
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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Abstract
Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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4
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Joodaki F, Martin LM, Greenfield ML. Computational Study of Helical and Helix-Hinge-Helix Conformations of an Anti-Microbial Peptide in Solution by Molecular Dynamics and Vibrational Analysis. J Phys Chem B 2021; 125:703-721. [PMID: 33464100 DOI: 10.1021/acs.jpcb.0c07988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many classical antimicrobial peptides adopt an amphipathic helical structure at a water-membrane interface. Prior studies led to the hypothesis that a hinge near the middle of a helical peptide plays an important role in facilitating peptide-membrane interactions. Here, dynamics and vibrations of a designed hybrid antimicrobial peptide LM7-2 in solution were simulated to investigate its hinge formation. Molecular dynamics simulation results on the basis of the CHARMM36 force field showed that the α-helix LM7-2 bent around two or three residues near the middle of the peptide, stayed in a helix-hinge-helix conformation for a short period of time, and then returned to a helical conformation. High-resolution computational vibrational techniques were applied on the LM7-2 system when it has α-helical and helix-hinge-helix conformations to understand how this structural change affects its inherent vibrations. These studies concentrated on the calculation of frequencies that correspond to backbone amide bands I, II, and III: vibrational modes that are sensitive to changes in the secondary structure of peptides and proteins. To that end, Fourier transforms were applied to thermal fluctuations in C-N-H angles, C-N bond lengths, and C═O bond lengths of each amide group. In addition, instantaneous all-atom normal mode analysis was applied to monitor and detect the characteristic amide bands of each amide group within LM7-2 during the MD simulation. Computational vibrational results indicate that shapes and frequencies of amide bands II and especially III were altered only for amide groups near the hinge. These methods provide high-resolution vibrational information that can complement spectroscopic vibrational studies. They assist in interpreting spectra of similar systems and suggest a marker for the presence of the helix-hinge-helix motif. Moreover, radial distribution functions indicated an increase in the probability of hydrogen bonding between water and a hydrogen atom connected to nitrogen (HN) in such a hinge. The probability of intramolecular hydrogen bond formation between HN and an amide group oxygen atom within LM7-2 was lower around the hinge. No correlation has been found between the presence of a hinge and hydrogen bonds between amide group oxygen atoms and the hydrogen atoms of water molecules. This result suggests a mechanism for hinge formation wherein hydrogen bonds to oxygen atoms of water replace intramolecular hydrogen bonds as the peptide backbone folds.
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Affiliation(s)
- Faramarz Joodaki
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Lenore M Martin
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Michael L Greenfield
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
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Biswas S, Mallik BS. Solvent-mediated dynamics and stretching profile of amide modes: QM/MM simulations of N-methylacetamide in ionic and various molecular liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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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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7
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Kovács A, Neyts EC, Cornet I, Wijnants M, Billen P. Modeling the Physicochemical Properties of Natural Deep Eutectic Solvents. CHEMSUSCHEM 2020; 13:3789-3804. [PMID: 32378359 DOI: 10.1002/cssc.202000286] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/04/2020] [Indexed: 05/08/2023]
Abstract
Natural deep eutectic solvents (NADES) are mixtures of naturally derived compounds with a significantly decreased melting point owing to specific interactions among the constituents. NADES have benign properties (low volatility, flammability, toxicity, cost) and tailorable physicochemical properties (by altering the type and molar ratio of constituents); hence, they are often considered to be a green alternative to common organic solvents. Modeling the relation between their composition and properties is crucial though, both for understanding and predicting their behavior. Several efforts have been made to this end. This Review aims at structuring the present knowledge as an outline for future research. First, the key properties of NADES are reviewed and related to their structure on the basis of the available experimental data. Second, available modeling methods applicable to NADES are reviewed. At the molecular level, DFT and molecular dynamics allow density differences and vibrational spectra to be interpreted, and interaction energies to be computed. Additionally, properties at the level of the bulk medium can be explained and predicted by semi-empirical methods based on ab initio methods (COSMO-RS) and equation of state models (PC-SAFT). Finally, methods based on large datasets are discussed: models based on group-contribution methods and machine learning. A combination of bulk-medium and dataset modeling allows qualitative prediction and interpretation of phase equilibria properties on the one hand, and quantitative prediction of melting point, density, viscosity, surface tension, and refractive index on the other. Multiscale modeling, combining molecular and macroscale methods, is expected to strongly enhance the predictability of NADES properties and their interaction with solutes, and thus yield truly tailorable solvents to accommodate (bio)chemical reactions.
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Affiliation(s)
- Attila Kovács
- Department of Chemistry/Biochemistry, iPRACS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Erik C Neyts
- Department of Chemistry, PLASMANT Research Group, NANOLab Center of Excellence, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Iris Cornet
- Department of Chemistry/Biochemistry, BioWAVE Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Marc Wijnants
- Department of Chemistry/Biochemistry, BioWAVE Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Pieter Billen
- Department of Chemistry/Biochemistry, iPRACS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
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8
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Kwac K, Cho M. Machine learning approach for describing vibrational solvatochromism. J Chem Phys 2020; 152:174101. [DOI: 10.1063/5.0005591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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9
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Muller EA, Gray TP, Zhou Z, Cheng X, Khatib O, Bechtel HA, Raschke MB. Vibrational exciton nanoimaging of phases and domains in porphyrin nanocrystals. Proc Natl Acad Sci U S A 2020; 117:7030-7037. [PMID: 32170023 PMCID: PMC7132254 DOI: 10.1073/pnas.1914172117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Much of the electronic transport, photophysical, or biological functions of molecular materials emerge from intermolecular interactions and associated nanoscale structure and morphology. However, competing phases, defects, and disorder give rise to confinement and many-body localization of the associated wavefunction, disturbing the performance of the material. Here, we employ vibrational excitons as a sensitive local probe of intermolecular coupling in hyperspectral infrared scattering scanning near-field optical microscopy (IR s-SNOM) with complementary small-angle X-ray scattering to map multiscale structure from molecular coupling to long-range order. In the model organic electronic material octaethyl porphyrin ruthenium(II) carbonyl (RuOEP), we observe the evolution of competing ordered and disordered phases, in nucleation, growth, and ripening of porphyrin nanocrystals. From measurement of vibrational exciton delocalization, we identify coexistence of ordered and disordered phases in RuOEP that extend down to the molecular scale. Even when reaching a high degree of macroscopic crystallinity, identify significant local disorder with correlation lengths of only a few nanometers. This minimally invasive approach of vibrational exciton nanospectroscopy and -imaging is generally applicable to provide the molecular-level insight into photoresponse and energy transport in organic photovoltaics, electronics, or proteins.
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Affiliation(s)
- Eric A Muller
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309;
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309
- JILA, University of Colorado Boulder, Boulder, CO 80309
| | - Thomas P Gray
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309
- JILA, University of Colorado Boulder, Boulder, CO 80309
| | - Zhou Zhou
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xinbin Cheng
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
| | - Omar Khatib
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309
- JILA, University of Colorado Boulder, Boulder, CO 80309
- Advanced Light Source Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720
| | - Hans A Bechtel
- Advanced Light Source Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720
| | - Markus B Raschke
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309;
- Department of Chemistry, University of Colorado Boulder, Boulder, CO 80309
- JILA, University of Colorado Boulder, Boulder, CO 80309
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10
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Biswas S, Mallik BS. Aqueous hydroxyl group as the vibrational probe to access the hydrophobicity of amide derivatives. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Cai K, Liu J, Liu Y, Chen F, Yan G, Lin H. Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117681. [PMID: 31685425 DOI: 10.1016/j.saa.2019.117681] [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: 08/15/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ37-42 and N3-Aβ37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ37-42 and N3-Aβ37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China.
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China
| | - Ya'nan Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China
| | - Feng Chen
- Fujian Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde, 352100, PR China
| | - Guiyang Yan
- Fujian Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde, 352100, PR China
| | - Huiqiu Lin
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China
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12
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Ram Lamichhane T, Prasad Lamichhane H. Structural changes in thyroid hormone receptor-beta by T3 binding and L330S mutational interactions. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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13
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Abstract
Dimethyl sulfoxide (DMSO) water mixtures have been widely studied due to their unique concentration-dependent bulk properties. Here, we present an empirical spectroscopic map for the sulfinyl (S=O) stretching mode. The model can be used to interpret infrared (IR) absorption and ultrafast two-dimensional infrared (2D IR) spectra and quantify hydrogen bond populations and lifetimes by directly connecting spectroscopic measurements with structures and dynamics from molecular dynamics simulations. The electrostatic map is directly parameterized against experimental absorption spectra in the S=O stretching region (980-1100 cm-1) of dilute DMSO in water. A comparison of center peak frequencies shows that the map performs well across the entire DMSO concentration range, accurately reproducing the ∼10 cm-1 red-shift per hydrogen bond observed in the experiments. We further benchmark the map by comparing experimental and simulated 2D IR spectra generated by direct numerical integration of the Schrödinger equation. We expect that this empirical frequency map will provide a quantitative platform for investigating intermolecular interactions, microscopic heterogeneity, and ultrafast dynamics in complex liquid mixtures containing DMSO.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, USA
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14
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Kwac K, Cho M. Differential evolution algorithm approach for describing vibrational solvatochromism. J Chem Phys 2019; 151:134112. [PMID: 31594319 DOI: 10.1063/1.5120777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We model the solvation-induced vibrational frequency shifts of the amide I and amide II modes of N-methylacetamide in water and the nitrile stretch mode of acetonitrile in water by expressing the frequency shift as a polynomial function expanded by the inverse power of interatomic distances. The coefficients of the polynomial are optimized to minimize the deviation between the predicted frequency shifts and those calculated with quantum chemistry methods. Here, we show that a differential evolution algorithm combined with singular value decomposition is useful to find the optimum set of coefficients of polynomial terms. The differential evolution optimization shows that only a few terms in the polynomial are dominant in the contribution to the vibrational frequency shifts. We anticipate that the present work paves the way for further developing different genetic algorithms and machine learning schemes for their applications to vibrational spectroscopic studies.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
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15
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Cai K, Zheng X, Liu J, Du F, Yan G, Zhuang D, Yan S. Mapping the amide-I vibrations of model dipeptides with secondary structure sensitivity and amino acid residue specificity, and its application to amyloid β-peptide in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:391-400. [PMID: 31059891 DOI: 10.1016/j.saa.2019.04.070] [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: 04/14/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Vibrational spectroscopy has been known as particularly well-suited for deciphering the polypeptide's structure. To decode structural information encoded in IR spectra, we developed amide-I frequency maps on the basis of model dipeptides to correlate the amide-I frequency of interest to the combination of the calculated secondary structure dependent amide-I frequency by using DFT method and the electrostatic potentials that projected onto the amide unit from the micro-environment within molecular mechanics force field. The constructed maps were applied to model dipeptides and amyloid β-peptide fragment (Aβ25-35). The dipeptide specified map (DS map) and the hybrid map (HYB map) predicted amide-I bands of Aβ25-35 in solution satisfactorily reproduce experimental observation, and indicate the preference of forming β-sheet and random coil structure for Aβ25-35 in D2O just as the results of cluster analysis suggested. These maps with secondary structural sensitivity and amino acid residue specificity open up a way for the interpretation of amide-I vibrations and show their potentials in the understanding of molecular structure of polypeptides in solution.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China; Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China.
| | - Xuan Zheng
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Guiyang Yan
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China
| | - Danling Zhuang
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Siyi Yan
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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16
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Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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17
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Baronio CM, Baldassarre M, Barth A. Insight into the internal structure of amyloid-β oligomers by isotope-edited Fourier transform infrared spectroscopy. Phys Chem Chem Phys 2019; 21:8587-8597. [DOI: 10.1039/c9cp00717b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isotope-edited infrared spectroscopy reveals the structural unit of amyloid-β oligomers.
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Affiliation(s)
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics
- Stockholm University
- Sweden
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18
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Anderson J, Lake PT, McCullagh M. Initial Aggregation and Ordering Mechanism of Diphenylalanine from Microsecond All-Atom Molecular Dynamics Simulations. J Phys Chem B 2018; 122:12331-12341. [PMID: 30511861 DOI: 10.1021/acs.jpcb.8b10335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-assembled diphenylalanine (FF) nanostructures have recently been demonstrated to be interesting materials for antibacterial and anticancer applications. These applications, among others, seek to take advantage of the high-order and resulting appealing physical properties of FF nanostructures by modifying the peptide in some way to achieve specific functionality. To rationally design modifications to the dipeptide that allow for this behavior, the driving forces of FF self-assembly must be understood. Molecular simulations have been utilized to assess these properties but have yielded conflicting conclusions due to inconsistencies in models chosen as well as the lack of quantitative analyses on the specific driving forces. Here, we present an all-atom explicit solvent molecular dynamics-based study on different length scales of FF aggregation. We utilize a free energy decomposition analysis as well as a dimer cluster analysis to identify the initial aggregation driving force to be FF intermolecular electrostatics, whereas solvent-mediated forces drive crystal growth. These data are consistent with the hypothesis that all hydrophobic dipeptides will have a similar initial aggregation mechanism until a critical aggregate size is reached, at which point crystallization occurs and subsequent crystal growth is dominated by solvent-mediated forces. We demonstrate that this proposed mechanism is testable by infrared spectroscopy focusing on the blueshift of the amide I peak as well as the ordering of the carboxylate peak.
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Affiliation(s)
- Jakob Anderson
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Peter T Lake
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
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19
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Hassan I, Donati L, Stensitzki T, Keller BG, Heyne K, Imhof P. The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Torii H. Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins. J Phys Chem B 2017; 122:154-164. [PMID: 29192780 DOI: 10.1021/acs.jpcb.7b10791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe2+ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, Faculty of Education and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University , 836 Ohya, Shizuoka 422-8529, Japan
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21
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Cai K, Zheng X, Du F. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:150-157. [PMID: 28448953 DOI: 10.1016/j.saa.2017.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/09/2017] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
Abstract
The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China.
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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22
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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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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24
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Cunha AV, Salamatova E, Bloem R, Roeters SJ, Woutersen S, Pshenichnikov MS, Jansen TLC. Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide. J Phys Chem Lett 2017; 8:2438-2444. [PMID: 28510458 PMCID: PMC5462486 DOI: 10.1021/acs.jpclett.7b00731] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
Intrinsically disordered proteins play an important role in biology, and unraveling their labile structure presents a vital challenge. However, the dynamical structure of such proteins thwarts their study by standard techniques such as X-ray diffraction and NMR spectroscopy. Here, we use a neat liquid composed of N-methylacetamide molecules as a model system to elucidate dynamical and structural properties similar to those one can expect to see in intrinsically disordered proteins. To examine the structural dynamics in the neat liquid, we combine molecular dynamics, response-function-based spectral simulations, and two-dimensional polarization-resolved infrared spectroscopy in the amide I (CO stretch) region. The two-dimensional spectra reveal a delicate interplay between hydrogen bonding and intermolecular vibrational coupling effects, observed through a fast anisotropy decay. The present study constitutes a general platform for understanding the structure and dynamics of highly disordered proteins.
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Affiliation(s)
- Ana V. Cunha
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Evgeniia Salamatova
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robbert Bloem
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Steven J. Roeters
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Maxim S. Pshenichnikov
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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25
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Błasiak B, Londergan CH, Webb LJ, Cho M. Vibrational Probes: From Small Molecule Solvatochromism Theory and Experiments to Applications in Complex Systems. Acc Chem Res 2017; 50:968-976. [PMID: 28345879 DOI: 10.1021/acs.accounts.7b00002] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies. To fully utilize IR probe functional groups for quantitative bioassays, a variety of biological and chemical techniques have been developed to site-specifically introduce vibrational probe groups into proteins and nucleic acids. These IR-probe-labeled biomolecules and chemically reactive systems are subject to linear and nonlinear vibrational spectroscopic investigations and provide information on the local electric field, conformational changes, site-site protein contacts, and/or function-defining features of biomolecules. A rapidly expanding library of data from such experiments requires an interpretive method with atom-level chemical accuracy. However, despite prolonged efforts to develop an all-encompassing theory for describing vibrational solvatochromism and electrochromism as well as dynamic fluctuations of instantaneous vibrational frequencies, purely empirical and highly approximate theoretical models have often been used to interpret experimental results. They are, in many cases, based on the simple assumption that the vibrational frequency of an IR reporter is solely dictated by electric potential or field distribution around the vibrational chromophore. Such simplified description of vibrational solvatochromism generally referred to as vibrational Stark effect theory has been considered to be quite appealing and, even in some cases, e.g., carbonyl stretch modes in amide, ester, ketone, and carbonate compounds or proteins, it works quantitatively well, which makes it highly useful in determining the strength of local electric field around the IR chromophore. However, noting that the vibrational frequency shift results from changes of solute-solvent intermolecular interaction potential along its normal coordinate, Pauli exclusion repulsion, polarization, charge transfer, and dispersion interactions, in addition to the electrostatic interaction between distributed charges of both vibrational chromophore and solvent molecules, are to be properly included in the theoretical description of vibrational solvatochromism. Since the electrostatic and nonelectrostatic intermolecular interaction components have distinctively different distance and orientation dependences, they affect the solvatochromic vibrational properties in a completely different manner. Over the past few years, we have developed a systematic approach to simulating vibrational solvatochromic data based on the effective fragment potential approach, one of the most accurate and rigorous theories on intermolecular interactions. We have further elucidated the interplay of local electric field with the general vibrational solvatochromism of small IR probes in either solvents or complicated biological systems, with emphasis on contributions from non-Coulombic intermolecular interactions to vibrational frequency shifts and fluctuations. With its rigorous foundation and close relation to quantitative interpretation of experimental data, this and related theoretical approaches and experiments will be of use in studying and quantifying the structure and dynamics of biomolecules with unprecedented time and spatial resolution when combined with time-resolved vibrational spectroscopy and chemically sensitive vibrational imaging techniques.
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Affiliation(s)
- Bartosz Błasiak
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Casey H. Londergan
- Department
of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Lauren J. Webb
- Department
of Chemistry, Center for Nano- and Molecular Science and Technology,
and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105
E. 24th Street, STOP A5300, Austin, Texas 78712, United States
| | - Minhaeng Cho
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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26
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Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B 2017; 121:2331-2338. [PMID: 28225620 DOI: 10.1021/acs.jpcb.7b00537] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D2O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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27
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Yadav VK, Klein ML. Probing the dynamics of N-methylacetamide in methanol via ab initio molecular dynamics. Phys Chem Chem Phys 2017; 19:12868-12875. [PMID: 28470307 DOI: 10.1039/c7cp00690j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-dimensional infrared (2D IR) spectroscopy of amide 1 vibrational bands provides a valuable probe of proteins as well as molecules such as N-methylacetamide (NMA), which present peptide-like H-bonding possibilities to a solvent.
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Affiliation(s)
- Vivek K. Yadav
- ICMS
- Department of Chemistry
- Temple University
- Philadelphia
- USA
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28
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Daly CA, Berquist EJ, Brinzer T, Garrett-Roe S, Lambrecht DS, Corcelli SA. Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: II. Spectroscopic Map. J Phys Chem B 2016; 120:12633-12642. [DOI: 10.1021/acs.jpcb.6b09509] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clyde A. Daly
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
| | - Eric J. Berquist
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Thomas Brinzer
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Sean Garrett-Roe
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel S. Lambrecht
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Steven A. Corcelli
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
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29
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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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30
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Yagi K, Li PC, Shirota K, Kobayashi T, Sugita Y. A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer. Phys Chem Chem Phys 2016; 17:29113-23. [PMID: 26460816 DOI: 10.1039/c5cp04131g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infrared (IR) and Raman spectra of a sphingomyelin (SM) bilayer have been calculated for the amide I, II and A modes and the double-bonded CC stretching mode by a weight averaged approach, based on an all-atom molecular dynamics (MD) simulation and a vibrational structure calculation. Representative structures and statistical weights of SM clusters connected by hydrogen bonds (HBs) are observed in MD trajectories. After constructing smaller fragments from the SM clusters, the vibrational spectra of the target modes were calculated by normal mode analysis with a correction for anharmonicity, using density functional theory. The final IR and Raman spectra of a SM bilayer were obtained as the weight averages over all SM clusters. The calculated Raman spectrum is in excellent agreement with a recent measurement, providing a clear assignment of the peak in question observed at 1643 cm(-1) to the amide I modes of a SM bilayer. The analysis of the IR spectrum has also revealed that the amide bands are sensitive to the water content inside the membrane, since their band positions are strongly modulated by the HB between SM and water molecules. The present study suggests that the amide I band serves as a marker to identify the formation of SM clusters, and opens a new way to detect lipid rafts in the biological membrane.
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Affiliation(s)
- Kiyoshi Yagi
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Pai-Chi Li
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Koichiro Shirota
- RIKEN Lipid Biology Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshihide Kobayashi
- RIKEN Lipid Biology Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and INSERM, Villeurbanne, France
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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31
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Cunha AV, Bondarenko AS, Jansen TLC. Assessing Spectral Simulation Protocols for the Amide I Band of Proteins. J Chem Theory Comput 2016; 12:3982-92. [PMID: 27348022 DOI: 10.1021/acs.jctc.6b00420] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.
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Affiliation(s)
- Ana V Cunha
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Anna S Bondarenko
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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32
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Edington SC, Flanagan JC, Baiz CR. An Empirical IR Frequency Map for Ester C═O Stretching Vibrations. J Phys Chem A 2016; 120:3888-96. [DOI: 10.1021/acs.jpca.6b02887] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean C. Edington
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
| | - Jennifer C. Flanagan
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R. Baiz
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
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33
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Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annu Rev Phys Chem 2016; 67:359-86. [DOI: 10.1146/annurev-physchem-040215-112055] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Reppert
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
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34
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Bondarenko AS, Jansen TLC. Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins. J Chem Phys 2016; 142:212437. [PMID: 26049457 DOI: 10.1063/1.4919716] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.
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Affiliation(s)
- Anna S Bondarenko
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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35
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Hanson-Heine MWD, Husseini FS, Hirst JD, Besley NA. Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes. J Chem Theory Comput 2016; 12:1905-18. [DOI: 10.1021/acs.jctc.5b01198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fouad S. Husseini
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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36
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Cai K, Du F, Zheng X, Liu J, Zheng R, Zhao J, Wang J. General Applicable Frequency Map for the Amide-I Mode in β-Peptides. J Phys Chem B 2016; 120:1069-79. [PMID: 26824578 DOI: 10.1021/acs.jpcb.5b11643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this work, a general applicable amide-I vibrational frequency map (GA map) for β-peptides in a number of common solvents was constructed, based on a peptide derivative, N-ethylpropionamide (NEPA). The map utilizes force fields at the ab initio computational level to accurately describe molecular structure and solute-solvent interactions, and also force fields at the molecular mechanics level to take into account long-range solute-solvent interactions. The results indicate that the GA map works reasonably for mapping the vibrational frequencies of the amide-I local-modes for β-peptides, holding promises for understanding the complicated infrared spectra of the amide-I mode in β-polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Renhui Zheng
- Beijing National Laboratory for Molecular Sciences, Structural Chemistry of Unstable and Stable Species Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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37
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Martinez AV, Małolepsza E, Rivera E, Lu Q, Straub JE. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles. J Chem Phys 2015; 141:22D530. [PMID: 25494801 DOI: 10.1063/1.4902550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.
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Affiliation(s)
| | - Edyta Małolepsza
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Eva Rivera
- Department of Chemistry and Biochemistry, Queens College, City University of New York (CUNY), Flushing, New York 11791, USA
| | - Qing Lu
- Division of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, USA
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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38
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Martinez AV, Małolepsza E, Domínguez L, Lu Q, Straub JE. Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles. J Phys Chem B 2015; 119:9084-90. [PMID: 25337983 PMCID: PMC4516319 DOI: 10.1021/jp508813n] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/20/2014] [Indexed: 11/28/2022]
Abstract
The propensity of peptides to form α-helices has been intensely studied using theory, computation, and experiment. Important model peptides for the study of the coil-to-helix transition have been alanine-lysine (AKA) peptides in which the lysine residues are placed on opposite sides of the helix avoiding charge repulsion while enhancing solubility. In this study, the effects of capped versus zwitterionic peptide termini on the secondary structure of alanine-rich peptides in reverse micelles are explored. The reverse micelles are found to undergo substantial shape fluctuations, a property observed in previous studies of AOT reverse micelles in the absence of solvated peptide. The peptides are observed to interact with water, as well as the AOT surfactant, including interactions between the nonpolar residues and the aliphatic surfactant tails. Computation of IR spectra for the amide I band of the peptide allows for direct comparison with experimental spectra. The results demonstrate that capped AKA2 peptides form more stable α helices than zwitterionic AKA2 peptides in reverse micelles. The rotational anisotropy decay of water is found to be distinctly different in the presence or absence of peptide within the reverse micelle, suggesting that the introduction of peptide significantly alters the number of free waters within the reverse micelle nanopool. However, neither the nature of the peptide termini (capped or charged) nor the degree of peptide helicity is found to significantly alter the balance of interactions between the peptides and the environment. Observed changes in the degree of helicity in AKA2 peptides in bulk solution and in reverse micelle environments result from changes in peptide confinement and hydration as well as direct nonpolar and polar interactions with the water-surfactant interface.
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Affiliation(s)
- Anna Victoria Martinez
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Edyta Małolepsza
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Domínguez
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qing Lu
- Division
of Materials Science and Engineering, Boston
University, 15 Saint
Mary’s Street, Brookline, Massachusetts 02446, United States
| | - John E. Straub
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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39
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Cai K, Du F, Liu J, Su T. Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:701-710. [PMID: 25260065 DOI: 10.1016/j.saa.2014.08.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/05/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Tingting Su
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
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40
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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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41
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Jansen TLC. Linear absorption and two-dimensional infrared spectra of N-methylacetamide in chloroform revisited: polarizability and multipole effects. J Phys Chem B 2014; 118:8162-9. [PMID: 24666193 DOI: 10.1021/jp5012445] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of solvent polarizability and multipole effects on the amide I vibrational spectra of a peptide unit is investigated. Four molecular dynamics force fields of increasing complexity for the solvent are used to model both the linear absorption and two-dimensional infrared spectra. It is observed that, at least in chloroform solution, the predicted solvent shift is considerably improved when accounting for the polarizabiltiy and multipole effects. The latter are typically connected with halogen bonding. Significant deviations are still observed for more sensitive line shape parameters such as the spectral width and line skewness. However, the findings demonstrate that previously observed deviations have an origin in the force field treatment rather than in the electrostatic mapping procedure frequently employed to simulate linear absorption and two-dimensional infrared spectroscopy.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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