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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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Streu K, Hunsberger S, Patel J, Wan X, Daly CA. Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch. J Chem Phys 2024; 160:074106. [PMID: 38364010 DOI: 10.1063/5.0185580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024] Open
Abstract
The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.
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Affiliation(s)
- Kristina Streu
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Sara Hunsberger
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Jeanette Patel
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Xiang Wan
- Department of Mathematics and Statistics, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, Illinois 60660, USA
| | - Clyde A Daly
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
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3
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Sepulveda-Montaño LX, Galindo JF, Kuroda DG. Infrared Spectroscopy of Liquid Solutions as a Benchmarking Tool of Semiempirical QM Methods: The Case of GFN2-xTB. J Phys Chem B 2023; 127:7955-7963. [PMID: 37676972 DOI: 10.1021/acs.jpcb.3c03174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The accurate description of large molecular systems has triggered the development of new computational methods. Due to the computational cost of modeling large systems, the methods usually require a trade-off between accuracy and speed. Therefore, benchmarking to test the accuracy and precision of the method is an important step in their development. The typical gold standard for evaluating these methods is isolated molecules, because of the low computational cost. However, the advent of high-performance computing has made it possible to benchmark computational methods using observables from more complex systems such as liquid solutions. To this end, infrared spectroscopy provides a suitable set of observables (i.e., vibrational transitions) for liquid systems. Here, IR spectroscopy observables are used to benchmark the predictions of the newly developed GFN2-xTB semiempirical method. Three different IR probes (i.e., N-methylacetamide, benzonitrile, and semiheavy water) in solution are selected for this purpose. The work presented here shows that GFN2-xTB predicts central frequencies with errors of less than 10% in all probes. In addition, the method captures detailed properties of the molecular environment such as weak interactions. Finally, the GFN2-xTB correctly assesses the vibrational solvatochromism for N-methylacetamide and semiheavy water but does not have the accuracy needed to properly describe benzonitrile. Overall, the results indicate not only that GFN2-xTB can be used to predict the central frequencies and their dependence on the molecular environment with reasonable accuracy but also that IR spectroscopy data of liquid solutions provide a suitable set of observables for the benchmarking of computational methods.
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Affiliation(s)
| | - Johan Fabian Galindo
- Department of Chemistry, Universidad Nacional de Colombia sede Bogotá, 111321 Bogotá, Colombia
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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4
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Solvation structure and dynamics of a small ion in an organic electrolyte. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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5
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Multi-fluorous-included Counter Anions-based Ionic Copolymers: Synthesis and Enhanced Hydrophobic Adsorption Films on Copper Surface for Super Protection. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2276-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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6
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Afandiyeva M, Kadam AA, Wu X, Brennessel WW, Kennedy CR. Synthesis, Structure, and Hydroboration Reactivity of Anionic Nickel(0) Complexes Supported by Bidentate NHC-Pyridone Ligands. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Medina Afandiyeva
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Abhishek A. Kadam
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Xijue Wu
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - William W. Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - C. Rose Kennedy
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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7
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Ghosh S, Srivastava AK, Sharma M, Pal S. Chiral Diuranyl(VI) Complexes and Their Catecholase Activities: Experimental and Theoretical Insights. ChemistrySelect 2022. [DOI: 10.1002/slct.202200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sabari Ghosh
- School of Chemistry University of Hyderabad Hyderabad 500046 India
| | | | - Manju Sharma
- School of Chemistry University of Hyderabad Hyderabad 500046 India
| | - Samudranil Pal
- School of Chemistry University of Hyderabad Hyderabad 500046 India
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8
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Cong F, Cheng J, Cho HG, Huang T, Wang X, Andrews L. M←NCCH 3, M-η 2-(NC)-CH 3, and CN-M-CH 3 Prepared by Reactions of Ce, Sm, Eu, and Lu Atoms with Acetonitrile: Matrix Infrared Spectra and Theoretical Calculations. Inorg Chem 2021; 60:17649-17656. [PMID: 34747602 DOI: 10.1021/acs.inorgchem.1c02232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reactions of laser-ablated Ce, Sm, Eu, and Lu atoms with acetonitrile were studied by matrix infrared spectra in a neon matrix, and M←NCCH3, M-η2-(NC)-CH3, and CN-M-CH3 were identified with isotopic substitution and quantum chemical calculations. The major product is the insertion complex (CN-M-CH3), while the end-on and side-on complexes (M←NCCH3 and M-η2-(NC)-CH3) are also trapped in the matrix. The CCN antisymmetric stretching mode for Ce-η2-(NC)-CH3 was observed at 1536.9 cm-1, which is much lower than the same modes observed for other lanthanides. NBO analysis reveals that Ce exhibits a remarkable 4f-orbital contribution in bonding to N and to C, reconfirming an active 4f-orbital contribution of cerium in bonding in the side-on complex, while the 4f contributions of Sm and Eu to the M-N and M-C bonds are much lower and the 4f orbital of Lu is not involved in bonding.
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Affiliation(s)
- Fei Cong
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Juanjuan Cheng
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Han-Gook Cho
- Department of Chemistry, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012 South Korea
| | - Tengfei Huang
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Xuefeng Wang
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Lester Andrews
- Department of Chemistry, University of Virginia, P.O. Box 400319, Charlottesville, Virginia 22904-4319, United States
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9
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Schröder C, Haugg PA, Baumann A, Schmidt MC, Smyczek J, Schauermann S. Competing Reaction Pathways in Heterogeneously Catalyzed Hydrogenation of Allyl Cyanide: The Chemical Nature of Surface Species. Chemistry 2021; 27:17240-17254. [PMID: 34608688 PMCID: PMC9297874 DOI: 10.1002/chem.202103238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Indexed: 11/11/2022]
Abstract
We present a mechanistic study on the formation of an active ligand layer over Pd(111), turning the catalytic surface highly active and selective in partial hydrogenation of an α,β-unsaturated aldehyde acrolein. Specifically, we investigate the chemical composition of a ligand layer consisting of allyl cyanide deposited on Pd(111) and its dynamic changes under the hydrogenation conditions. On pristine surface, allyl cyanide largely retains its chemical structure and forms a layer of molecular species with the CN bond oriented nearly parallel to the underlying metal. In the presence of hydrogen, the chemical composition of allyl cyanide strongly changes. At 100 K, allyl cyanide transforms to unsaturated imine species, containing the C=C and C=N double bonds. At increasing temperatures, these species undergo two competing reaction pathways. First, the C=C bond become hydrogenated and the stable N-butylimine species are produced. In the competing pathway, the unsaturated imine reacts with hydrogen to fully hydrogenate the imine group and produce butylamine. The latter species are unstable under the hydrogenation reaction conditions and desorb from the surface, while the N-butylimine adsorbates formed in the first reaction pathway remain adsorbed and act as an active ligand layer in selective hydrogenation of acrolein.
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Affiliation(s)
- Carsten Schröder
- Institute of Physical ChemistryChristian-Albrechts-University KielMax-Eyth-Str. 224118KielGermany
| | - Philipp A. Haugg
- Institute of Physical ChemistryChristian-Albrechts-University KielMax-Eyth-Str. 224118KielGermany
| | - Ann‐Katrin Baumann
- Institute of Physical ChemistryChristian-Albrechts-University KielMax-Eyth-Str. 224118KielGermany
| | - Marvin C. Schmidt
- Institute of Physical ChemistryChristian-Albrechts-University KielMax-Eyth-Str. 224118KielGermany
| | - Jan Smyczek
- Institute of Physical ChemistryChristian-Albrechts-University KielMax-Eyth-Str. 224118KielGermany
| | - Swetlana Schauermann
- Institute of Physical ChemistryChristian-Albrechts-University KielMax-Eyth-Str. 224118KielGermany
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10
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Maitra A, Sarkar S, Leitner DM, Dawlaty JM. Electric Fields Influence Intramolecular Vibrational Energy Relaxation and Line Widths. J Phys Chem Lett 2021; 12:7818-7825. [PMID: 34378946 DOI: 10.1021/acs.jpclett.1c02238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Intramolecular vibrational energy relaxation (IVR) is fundamentally important to chemical dynamics. We show that externally applied electric fields affect IVR and vibrational line widths by changing the anharmonic couplings and frequency detunings between modes. We demonstrate this effect in benzonitrile for which prior experimental results show a decrease in vibrational line width as a function of applied electric field. We identify three major channels for IVR that depend on electric field. In the dominant channel, the electric field affects the frequency detuning, while in the other two channels, variation of anharmonic couplings as a function of field is the underlying mechanism. Consistent with experimental results, we show that the combination of all channels gives rise to reduced line widths with increasing electric field in benzonitrile. Our results are relevant for controlling IVR with external or internal fields and for gaining a more complete interpretation of line widths of vibrational Stark probes.
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Affiliation(s)
- Anwesha Maitra
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0001, United States
| | - Sohini Sarkar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0001, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada Reno, Reno, Nevada 89519, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0001, United States
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11
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Johnson CA, Parker AW, Donaldson PM, Garrett-Roe S. An ultrafast vibrational study of dynamical heterogeneity in the protic ionic liquid ethyl-ammonium nitrate. I. Room temperature dynamics. J Chem Phys 2021; 154:134502. [PMID: 33832238 DOI: 10.1063/5.0044822] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using ultrafast two-dimensional infrared spectroscopy (2D-IR), a vibrational probe (thiocyanate, SCN-) was used to investigate the hydrogen bonding network of the protic ionic liquid ethyl-ammonium nitrate (EAN) in comparison to H2O. The 2D-IR experiments were performed in both parallel (⟨ZZZZ⟩) and perpendicular (⟨ZZXX⟩) polarizations at room temperature. In EAN, the non-Gaussian lineshape in the FTIR spectrum of SCN- suggests two sub-ensembles. Vibrational relaxation rates extracted from the 2D-IR spectra provide evidence of the dynamical differences between the two sub-ensembles. We support the interpretation of two sub-ensembles with response function simulations of two overlapping bands with different vibrational relaxation rates and, otherwise, similar dynamics. The measured rates for spectral diffusion depend on polarization, indicating reorientation-induced spectral diffusion (RISD). A model of restricted molecular rotation (wobbling in a cone) fully describes the observed spectral diffusion in EAN. In H2O, both RISD and structural spectral diffusion contribute with similar timescales. This complete characterization of the dynamics at room temperature provides the basis for the temperature-dependent measurements in Paper II of this series.
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Affiliation(s)
- Clinton A Johnson
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Anthony W Parker
- Central Laser Facility, STFC, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, STFC, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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12
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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: 173] [Impact Index Per Article: 43.3] [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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13
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Guchhait B, Tibbetts CA, Tracy KM, Luther BM, Krummel AT. Ultrafast vibrational dynamics of a trigonal planar anionic probe in ionic liquids (ILs): A two-dimensional infrared (2DIR) spectroscopic investigation. J Chem Phys 2020; 152:164501. [PMID: 32357764 DOI: 10.1063/1.5141751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A major impediment limiting the widespread application of ionic liquids (ILs) is their high shear viscosity. Incorporation of a tricyanomethanide (TCM-) anion in ILs leads to low shear viscosity and improvement of several characteristics suitable for large scale applications. However, properties including interactions of TCM- with the local environment and dynamics of TCM- have not been thoroughly investigated. Herein, we have studied the ultrafast dynamics of TCM- in several imidazolium ILs using linear IR and two-dimensional infrared spectroscopy techniques. The spectral diffusion dynamics of the CN stretching modes of TCM- in all ILs exhibit a nonexponential behavior with a short time component of ∼2 ps and a long time component spanning ∼9 ps to 14 ps. The TCM- vibrational probe reports a significantly faster relaxation of ILs compared to those observed previously using linear vibrational probes, such as thiocyanate and selenocyanate. Our results indicate a rapid relaxation of the local ion-cage structure embedding the vibrational probe in the ILs. The faster relaxation suggests that the lifetime of the local ion-cage structure decreases in the presence of TCM- in the ILs. Linear IR spectroscopic results show that the hydrogen-bonding interaction between TCM- and imidazolium cations in ILs is much weaker. Shorter ion-cage lifetimes together with weaker hydrogen-bonding interactions account for the low shear viscosity of TCM- based ILs compared to commonly used ILs. In addition, this study demonstrates that TCM- can be used as a potential vibrational reporter to study the structure and dynamics of ILs and other molecular systems.
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Affiliation(s)
- Biswajit Guchhait
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Clara A Tibbetts
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kathryn M Tracy
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Bradley M Luther
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Amber T Krummel
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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14
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Goldsmith Z, Secor M, Hammes-Schiffer S. Inhomogeneity of Interfacial Electric Fields at Vibrational Probes on Electrode Surfaces. ACS CENTRAL SCIENCE 2020; 6:304-311. [PMID: 32123749 PMCID: PMC7047426 DOI: 10.1021/acscentsci.9b01297] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 05/06/2023]
Abstract
Electric fields control chemical reactivity in a wide range of systems, including enzymes and electrochemical interfaces. Characterizing the electric fields at electrode-solution interfaces is critical for understanding heterogeneous catalysis and associated energy conversion processes. To address this challenge, recent experiments have probed the response of the nitrile stretching frequency of 4-mercaptobenzonitrile (4-MBN) attached to a gold electrode to changes in the solvent and applied electrode potential. Herein, this system is modeled with periodic density functional theory using a multilayer dielectric continuum treatment of the solvent and at constant applied potentials. The impact of the solvent dielectric constant and the applied electrode potential on the nitrile stretching frequency computed with a grid-based method is in qualitative agreement with the experimental data. In addition, the interfacial electrostatic potentials and electric fields as a function of applied potential were calculated directly with density functional theory. Substantial spatial inhomogeneity of the interfacial electric fields was observed, including oscillations in the region of the molecular probe attached to the electrode. These simulations highlight the microscopic inhomogeneity of the electric fields and the role of molecular polarizability at electrode-solution interfaces, thereby demonstrating the limitations of mean-field models and providing insights relevant to the interpretation of vibrational Stark effect experiments.
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15
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Yalcin D, Christofferson AJ, Drummond CJ, Greaves TL. Solvation properties of protic ionic liquid–molecular solvent mixtures. Phys Chem Chem Phys 2020; 22:10995-11011. [DOI: 10.1039/d0cp00201a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this study, we have investigated the solvation properties of binary mixtures of PILs with molecular solvents. The selected binary solvent systems are the PILs ethylammonium nitrate (EAN) and propylammonium nitrate (PAN) combined with either water, methanol, acetonitrile or DMSO.
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Affiliation(s)
- Dilek Yalcin
- School of Science
- College of Science
- Engineering and Health
- RMIT University
- Melbourne
| | | | - Calum J. Drummond
- School of Science
- College of Science
- Engineering and Health
- RMIT University
- Melbourne
| | - Tamar L. Greaves
- School of Science
- College of Science
- Engineering and Health
- RMIT University
- Melbourne
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16
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Chatterjee S, Ghosh D, Haldar T, Deb P, Sakpal SS, Deshmukh SH, Kashid SM, Bagchi S. Hydrocarbon Chain-Length Dependence of Solvation Dynamics in Alcohol-Based Deep Eutectic Solvents: A Two-Dimensional Infrared Spectroscopic Investigation. J Phys Chem B 2019; 123:9355-9363. [DOI: 10.1021/acs.jpcb.9b08954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Deborin Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sushil S. Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Samadhan H. Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Somnath M. Kashid
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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17
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Beć KB, Karczmit D, Kwaśniewicz M, Ozaki Y, Czarnecki MA. Overtones of νC≡N Vibration as a Probe of Structure of Liquid CH3CN, CD3CN, and CCl3CN: Combined Infrared, Near-Infrared, and Raman Spectroscopic Studies with Anharmonic Density Functional Theory Calculations. J Phys Chem A 2019; 123:4431-4442. [DOI: 10.1021/acs.jpca.9b02170] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krzysztof Bernard Beć
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Daniel Karczmit
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Michał Kwaśniewicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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18
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Cao X, Gong N, Zhao H, Li Z, Sun C, Men Z. Raman spectroscopic study of nonlinear modulation on Fermi resonance of acetonitrile by hydrogen-bonding network. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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20
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Brinzer T, Daly CA, Allison C, Garrett-Roe S, Corcelli SA. Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: III. Dynamics and Spectroscopy. J Phys Chem B 2018; 122:8931-8942. [PMID: 30160958 DOI: 10.1021/acs.jpcb.8b05659] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, interest in carbon capture and sequestration has led to numerous investigations of the ability of ionic liquids to act as recyclable CO2-sorbent materials. Herein, we investigate the structure and dynamics of a model physisorbing ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([C4C1Im][PF6]), from the perspective of CO2 using two-dimensional (2D) IR spectroscopy and molecular dynamics simulations. A direct comparison of experimentally measured and calculated 2D IR line shapes confirms the validity of the simulations and spectroscopic calculations. Taken together, the simulations and experiments reveal new insights into the interactions of a CO2 solute with the surrounding ionic liquid and how these interactions manifest in the 2D IR spectra. In particular, higher CO2 asymmetric stretch vibrational frequencies are associated with softer, less populated solvent cages and lower frequencies are associated with tighter, more highly populated solvent cages. The CO2 interacts most strongly with the anions, and these interactions persist for more than 1 ns. The second strongest interactions are with the imidazolium cation ring that last 100 ps, and the weakest interactions are with the cation butyl tail that persist for 10 ps. The principal contributors to spectral diffusion of the CO2 asymmetric stretch vibrational frequency due to the dynamical evolution of the solvent are through Lennard-Jones interactions at short times and electrostatics at long times.
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Affiliation(s)
- 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
| | - Clyde A Daly
- Department of Chemistry and Biochemistry , University of Notre Dame , 251 Nieuwland Science Hall , Notre Dame , Indiana 46656 , United States
| | - Cecelia Allison
- Department of Chemistry and Biochemistry , University of Notre Dame , 251 Nieuwland Science Hall , Notre Dame , Indiana 46656 , 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
| | - 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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21
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Liu H, Morris C, Lantz R, Kent TW, Elbassal EA, Wojcikiewicz EP, Du D. Residue‐Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Haiyang Liu
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Clifford Morris
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Richard Lantz
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Thomas W. Kent
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Esmail A. Elbassal
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Ewa P. Wojcikiewicz
- Department of Biomedical ScienceFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
| | - Deguo Du
- Department of Chemistry and BiochemistryFlorida Atlantic University 777 Glades Road Boca Raton FL 33431 USA
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22
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Chalyavi F, Gilmartin PH, Schmitz AJ, Fennie MW, Tucker MJ. Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure. Angew Chem Int Ed Engl 2018; 57:7528-7532. [PMID: 29710418 PMCID: PMC6002807 DOI: 10.1002/anie.201803849] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Indexed: 12/20/2022]
Abstract
A concise synthesis of protected 5-cyano-l-tryptophan (Trp5CN ) has been developed for 2D IR spectroscopic investigations within either peptides or proteins. To assess the potential of differently substituted cyano-tryptophans, several model cyano-indole systems were characterized using IR spectroscopy. Upon assessment of their spectroscopic properties, Trp5CN was integrated into a model peptide sequence, Trp5CN -Gly-Phe4CN , to elucidate its structure. This peptide demonstrates the capability of this probe to capture structural information by 2D IR spectroscopy. The 2D IR spectrum of the peptide in water was simulated to reveal a unique spectral signature resulting from the presence of dipolar coupling. The coupling strength between cyano labels was determined to be 1.4 cm-1 by matching the slopes along the max contour for the simulated and experimental spectrum. Using transition dipole coupling, a distance between the two probes of 13 Å was calculated.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Philip H Gilmartin
- Department of Chemistry, University of Scranton, 204 Monroe Ave., Scranton, PA, 18510, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Michael W Fennie
- Department of Chemistry, University of Scranton, 204 Monroe Ave., Scranton, PA, 18510, USA
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
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23
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Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Liu H, Morris C, Lantz R, Kent TW, Elbassal EA, Wojcikiewicz EP, Du D. Residue-Specific Dynamics and Local Environmental Changes in Aβ40 Oligomer and Fibril Formation. Angew Chem Int Ed Engl 2018; 57:8017-8021. [PMID: 29750857 DOI: 10.1002/anie.201802490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/12/2022]
Abstract
Elucidating local dynamics of protein aggregation is crucial for understanding the mechanistic details of protein amyloidogenesis. Herein, we studied the residue-specific dynamics and local environmental changes of Aβ40 along the course of aggregation by using para-cyanophenylalanine (PheCN ) as a fluorescent and vibrational probe. Our results show that the PheCN residues introduced at various positions all exhibited an immediate decay of fluorescence intensity, indicating a relatively synergistic process in early oligomer formation. The fast decreases in the fluorescence intensities of residues 19 and 20 in the central hydrophobic core region and residue 10 in the N-terminal region suggest that they play crucial roles in the formation of the oligomeric core. The PheCN 4 residue exhibits a remarkably slower decrease in fluorescence intensity, implicating its dynamic conformational characteristics in oligomer and fibril formation. Our results also suggest that the N-terminal residues in fibrils are surrounded by a relatively hydrophobic local environment, as opposed to being solvated.
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Affiliation(s)
- Haiyang Liu
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Clifford Morris
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Richard Lantz
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Thomas W Kent
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Esmail A Elbassal
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Ewa P Wojcikiewicz
- Department of Biomedical Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
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25
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Dalton SR, Vienneau AR, Burstein SR, Xu RJ, Linse S, Londergan CH. Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein-Binding Interfaces Without Perturbation. Biochemistry 2018; 57:3702-3712. [PMID: 29787228 PMCID: PMC6034165 DOI: 10.1021/acs.biochem.8b00283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
To investigate the
cyanylated cysteine vibrational probe group’s
ability to report on binding-induced changes along a protein–protein
interface, the probe group was incorporated at several sites in a
peptide of the calmodulin (CaM)-binding domain of skeletal muscle
myosin light chain kinase. Isothermal titration calorimetry was used
to determine the binding thermodynamics between calmodulin and each
peptide. For all probe positions, the binding affinity was nearly
identical to that of the unlabeled peptide. The CN stretching infrared
band was collected for each peptide free in solution and bound to
calmodulin. Binding-induced shifts in the IR spectral frequencies
were correlated with estimated solvent accessibility based on molecular
dynamics simulations. This work generally suggests (1) that site-specific
incorporation of this vibrational probe group does not cause major
perturbations to its local structural environment and (2) that this
small probe group might be used quite broadly to map dynamic protein-binding
interfaces. However, site-specific perturbations due to artificial
labeling groups can be somewhat unpredictable and should be evaluated
on a site-by-site basis through complementary measurements. A fully
quantitative, simulation-based interpretation of the rich probe IR
spectra is still needed but appears to be possible given recent advances
in simulation techniques.
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Affiliation(s)
- Shannon R Dalton
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Alice R Vienneau
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Shana R Burstein
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Rosalind J Xu
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Sara Linse
- Department of Chemistry and Biochemistry , Lund University , Kemicentrum, Box 118 , 221 00 Lund , Sweden
| | - Casey H Londergan
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
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26
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Xu RJ, Blasiak B, Cho M, Layfield JP, Londergan CH. A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes. J Phys Chem Lett 2018; 9:2560-2567. [PMID: 29697984 DOI: 10.1021/acs.jpclett.8b00969] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.
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Affiliation(s)
- Rosalind J Xu
- Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States
| | - Bartosz Blasiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Joshua P Layfield
- Department of Chemistry , St. Thomas University , Minneapolis , Minnesota , United States
| | - Casey H Londergan
- Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States
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27
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Mondal P, Meuwly M. Vibrational Stark spectroscopy for assessing ligand-binding strengths in a protein. Phys Chem Chem Phys 2018; 19:16131-16143. [PMID: 28604854 DOI: 10.1039/c7cp01892d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nitrile groups are potentially useful spectroscopic probes in the infrared to characterize the binding and dynamics of ligands in proteins. This opens the possibility of locating and determining the binding mode of suitably labelled ligands in proteins based on optical spectroscopy, without the need for determining an X-ray structure. However, relating structure and spectroscopy requires means to accurately compute infrared spectra. This is investigated for benzonitrile (PhCN) in water, wild type (WT) and two lysozyme mutants in solution. The force field is validated by comparing with experimental data for benzonitrile in water which is the basis for computing the Stark shift and time scale for spectral diffusion of PhCN in WT and the L99A and L99G mutants of T4 lysozyme. The 1-d spectra for PhCN in WT and the two mutant proteins differ in their maximum absorption by up to 4 cm-1, which reflects the modified electrostatic environments in the three proteins. It is also tested whether extending from 1-d to 2-d infrared spectroscopy provides further discrimination in the ligand-binding modes. First, for PhCN in solution the frequency fluctuation correlation function (FFCF) decays to zero at short times whereas in the protein a pronounced static inhomogeneous component is found. Secondly, the decay time of the FFCF for the mutant to which PhCN binds most strongly has the longest decay time. It is demonstrated explicitly that the ligand-binding free energy with respect to the three protein variants correlates with the Stark shift. This makes 1-d infrared spectroscopy together with computations a valuable tool for characterizing binding modes and potentially binding locations in proteins.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056-Basel, Switzerland.
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28
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Garrett-Roe S. Reorientation-induced spectral diffusion of non-isotropic orientation distributions. J Chem Phys 2017; 147:144504. [DOI: 10.1063/1.4993864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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29
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Yamada SA, Thompson WH, Fayer MD. Water-anion hydrogen bonding dynamics: Ultrafast IR experiments and simulations. J Chem Phys 2017. [DOI: 10.1063/1.4984766] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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30
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Yuan R, Yan C, Nishida J, Fayer MD. Dynamics in a Water Interfacial Boundary Layer Investigated with IR Polarization-Selective Pump–Probe Experiments. J Phys Chem B 2017; 121:4530-4537. [DOI: 10.1021/acs.jpcb.7b01028] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rongfeng Yuan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chang Yan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jun Nishida
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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31
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Berquist EJ, Daly CA, Brinzer T, Bullard KK, Campbell ZM, Corcelli SA, Garrett-Roe S, Lambrecht DS. Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: I. Ab Initio Calculations. J Phys Chem B 2016; 121:208-220. [DOI: 10.1021/acs.jpcb.6b09489] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric J. Berquist
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh Quantum Institute, Pittsburgh, Pennsylvania 15260, United States
| | - Clyde A. Daly
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Thomas Brinzer
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh Quantum Institute, Pittsburgh, Pennsylvania 15260, United States
| | - Krista K. Bullard
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh Quantum Institute, Pittsburgh, Pennsylvania 15260, United States
| | - Zachary M. Campbell
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh Quantum Institute, Pittsburgh, Pennsylvania 15260, United States
| | - Steven A. Corcelli
- Department
of Chemistry and Biochemistry, University of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Sean Garrett-Roe
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh Quantum Institute, 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, Pittsburgh, Pennsylvania 15260, United States
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32
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Deb P, Haldar T, Kashid SM, Banerjee S, Chakrabarty S, Bagchi S. Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. J Phys Chem B 2016; 120:4034-46. [DOI: 10.1021/acs.jpcb.6b02732] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Subhrashis Banerjee
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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33
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Yuan R, Yan C, Tamimi A, Fayer MD. Molecular Anion Hydrogen Bonding Dynamics in Aqueous Solution. J Phys Chem B 2015; 119:13407-15. [DOI: 10.1021/acs.jpcb.5b08168] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rongfeng Yuan
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chang Yan
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Amr Tamimi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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34
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Brinzer T, Berquist EJ, Ren Z, Dutta S, Johnson CA, Krisher CS, Lambrecht DS, Garrett-Roe S. Ultrafast vibrational spectroscopy (2D-IR) of CO2 in ionic liquids: Carbon capture from carbon dioxide's point of view. J Chem Phys 2015; 142:212425. [PMID: 26049445 DOI: 10.1063/1.4917467] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The CO2ν3 asymmetric stretching mode is established as a vibrational chromophore for ultrafast two-dimensional infrared (2D-IR) spectroscopic studies of local structure and dynamics in ionic liquids, which are of interest for carbon capture applications. CO2 is dissolved in a series of 1-butyl-3-methylimidazolium-based ionic liquids ([C4C1im][X], where [X](-) is the anion from the series hexafluorophosphate (PF6 (-)), tetrafluoroborate (BF4 (-)), bis-(trifluoromethyl)sulfonylimide (Tf2N(-)), triflate (TfO(-)), trifluoroacetate (TFA(-)), dicyanamide (DCA(-)), and thiocyanate (SCN(-))). In the ionic liquids studied, the ν3 center frequency is sensitive to the local solvation environment and reports on the timescales for local structural relaxation. Density functional theory calculations predict charge transfer from the anion to the CO2 and from CO2 to the cation. The charge transfer drives geometrical distortion of CO2, which in turn changes the ν3 frequency. The observed structural relaxation timescales vary by up to an order of magnitude between ionic liquids. Shoulders in the 2D-IR spectra arise from anharmonic coupling of the ν2 and ν3 normal modes of CO2. Thermal fluctuations in the ν2 population stochastically modulate the ν3 frequency and generate dynamic cross-peaks. These timescales are attributed to the breakup of ion cages that create a well-defined local environment for CO2. The results suggest that the picosecond dynamics of CO2 are gated by local diffusion of anions and cations.
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Affiliation(s)
- Thomas Brinzer
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Eric J Berquist
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Zhe Ren
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Samrat Dutta
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Clinton A Johnson
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Cullen S Krisher
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Daniel S Lambrecht
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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35
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Abstract
Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
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36
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Liu H, Lantz R, Cosme P, Rivera N, Andino C, Gonzalez WG, Terentis AC, Wojcikiewicz EP, Oyola R, Miksovska J, Du D. Site-specific dynamics of amyloid formation and fibrillar configuration of Aβ1–23 using an unnatural amino acid. Chem Commun (Camb) 2015; 51:7000-3. [DOI: 10.1039/c5cc00149h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Distinct local dynamics of Aβ1–23 amyloid formation are characterized using an unnatural amino acid p-cyanophenylalanine as a spectroscopic probe.
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Affiliation(s)
- Haiyang Liu
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Richard Lantz
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Patrick Cosme
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | - Nelson Rivera
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Carlos Andino
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Walter G. Gonzalez
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Andrew C. Terentis
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
| | | | - Rolando Oyola
- Department of Chemistry
- University of Puerto Rico-Humacao
- Humacao
- Puerto Rico
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry
- Florida International University
- Miami
- USA
| | - Deguo Du
- Department of Chemistry and Biochemistry
- Florida Atlantic University
- Boca Raton
- USA
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37
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Min A, Ahn A, Moon CJ, Lee JH, Choi MY, Kim SK. Conformational structures of 3-cyanoindole-(H 2 O) n ( n = 0–2) by UV–UV hole-burning and IR-dip spectroscopy. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.09.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Marr JM, Gezelter JD. Nitrile Vibrations as Reporters of Field-Induced Phase Transitions in 4-Cyano-4′-pentylbiphenyl (5CB). J Phys Chem B 2014; 118:8441-8. [DOI: 10.1021/jp503235s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James M. Marr
- Department of Chemistry and
Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - J. Daniel Gezelter
- Department of Chemistry and
Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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39
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Liu CT, Layfield JP, Stewart RJ, French JB, Hanoian P, Asbury JB, Hammes-Schiffer S, Benkovic SJ. Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase. J Am Chem Soc 2014; 136:10349-60. [PMID: 24977791 PMCID: PMC4183630 DOI: 10.1021/ja5038947] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Electrostatic interactions play an
important role in enzyme catalysis
by guiding ligand binding and facilitating chemical reactions. These
electrostatic interactions are modulated by conformational changes
occurring over the catalytic cycle. Herein, the changes in active
site electrostatic microenvironments are examined for all enzyme complexes
along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation
of thiocyanate probes at two site-specific locations in the active
site. The electrostatics and degree of hydration of the microenvironments
surrounding the probes are investigated with spectroscopic techniques
and mixed quantum mechanical/molecular mechanical (QM/MM) calculations.
Changes in the electrostatic microenvironments along the catalytic
environment lead to different nitrile (CN) vibrational stretching
frequencies and 13C NMR chemical shifts. These environmental
changes arise from protein conformational rearrangements during catalysis.
The QM/MM calculations reproduce the experimentally measured vibrational
frequency shifts of the thiocyanate probes across the catalyzed hydride
transfer step, which spans the closed and occluded conformations of
the enzyme. Analysis of the molecular dynamics trajectories provides
insight into the conformational changes occurring between these two
states and the resulting changes in classical electrostatics and specific
hydrogen-bonding interactions. The electric fields along the CN axes
of the probes are decomposed into contributions from specific residues,
ligands, and solvent molecules that make up the microenvironments
around the probes. Moreover, calculation of the electric field along
the hydride donor–acceptor axis, along with decomposition of
this field into specific contributions, indicates that the cofactor
and substrate, as well as the enzyme, impose a substantial electric
field that facilitates hydride transfer. Overall, experimental and
theoretical data provide evidence for significant electrostatic changes
in the active site microenvironments due to conformational motion
occurring over the catalytic cycle of ecDHFR.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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40
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Błasiak B, Lee H, Cho M. Vibrational solvatochromism: towards systematic approach to modeling solvation phenomena. J Chem Phys 2014; 139:044111. [PMID: 23901964 DOI: 10.1063/1.4816041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational solvatochromic frequency shift of IR probe is an effect of interaction between local electric field and IR probe in condensed phases. Despite prolonged efforts to develop empirical maps for vibrational frequency shifts and transition dipoles of IR probes, a systematic approach to ab initio calculation of vibrational solvatochromic charges and multipoles has not been developed. Here, we report on density functional theory (DFT) calculations of N-methylacetamide (NMA) frequency shifts using implicit and coarse-grained models. The solvatochromic infrared spectral shifts are estimated based on the distributed multipole analysis of electronic densities calculated for gas-phase equilibrium structure of NMA. Thus obtained distributed solvatochromic multipole parameters are used to calculate the amide I vibrational frequency shifts of NMA in water clusters that mimic the instantaneous configurations of the liquid water. Our results indicate that the spectral shifts are primarily electrostatic in nature and can be quantitatively reproduced using the proposed model with semi-quantitative accuracy when compared to the corresponding DFT results.
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Affiliation(s)
- Bartosz Błasiak
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
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41
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Ritchie AW, Webb LJ. Optimizing Electrostatic Field Calculations with the Adaptive Poisson–Boltzmann Solver to Predict Electric Fields at Protein–Protein Interfaces II: Explicit Near-Probe and Hydrogen-Bonding Water Molecules. J Phys Chem B 2014; 118:7692-702. [DOI: 10.1021/jp4092656] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrew W. Ritchie
- Department
of Chemistry,
Center for Nano- and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1
University Station, A5300, Austin, Texas 78712, 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, 1
University Station, A5300, Austin, Texas 78712, United States
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42
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Gonzalez JD, Levonyak NS, Schneider SC, Smith MJ, Cremeens ME. Using infrared spectroscopy of a nitrile labeled phenylalanine and tryptophan fluorescence to probe the α-MSH peptide’s side-chain interactions with a micelle model membrane. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.09.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Ritchie AW, Webb LJ. Optimizing Electrostatic Field Calculations with the Adaptive Poisson–Boltzmann Solver to Predict Electric Fields at Protein–Protein Interfaces. I. Sampling and Focusing. J Phys Chem B 2013; 117:11473-89. [DOI: 10.1021/jp404582w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Andrew W. Ritchie
- Department
of Chemistry,
Center for Nano- and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1
University Station, A5300, Austin, Texas 78712, 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, 1
University Station, A5300, Austin, Texas 78712, United States
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44
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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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45
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Wang X, He X, Zhang JZH. Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field. J Phys Chem A 2013; 117:6015-23. [PMID: 23517423 DOI: 10.1021/jp312063h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electric field inside a protein has a significant effect on the protein structure, function, and dynamics. Recent experimental developments have offered a direct approach to measure the electric field by utilizing a nitrile-containing inhibitor as a probe that can deliver a unique vibration to the specific site of interest in the protein. The observed frequency shift of the nitrile stretching vibration exhibits a linear dependence on the electric field at the nitrile site, thus providing a direct measurement of the relative electric field. In the present work, molecular dynamics simulations were carried out to compute the electric field shift in human aldose reductase (hALR2) using a polarized protein-specific charge (PPC) model derived from fragment-based quantum-chemistry calculations in implicit solvent. Calculated changes of electric field in the active site of hALR2 between the wild type and mutants were directly compared with measured vibrational frequency shifts (Stark shifts). Our study demonstrates that the Stark shifts calculated using the PPC model are in much better agreement with the experimental data than widely used nonpolarizable force fields, indicating that the electronic polarization effect is important for the accurate prediction of changes in the electric field inside proteins.
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Affiliation(s)
- Xianwei Wang
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
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46
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Photochemical activity of Titan’s low-altitude condensed haze. Nat Commun 2013; 4:1648. [DOI: 10.1038/ncomms2649] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 02/26/2013] [Indexed: 12/14/2022] Open
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47
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Zhang S, Zhang Y, Ma X, Lu L, He Y, Deng Y. Benzonitrile as a Probe of Local Environment in Ionic Liquids. J Phys Chem B 2013; 117:2764-72. [DOI: 10.1021/jp312251q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shiguo Zhang
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yan Zhang
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xiangyuan Ma
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Liujin Lu
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Yude He
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Youquan Deng
- Center for Green Chemistry and Catalysis, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
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48
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Lee H, Choi JH, Cho M. Vibrational solvatochromism and electrochromism. II. Multipole analysis. J Chem Phys 2013; 137:114307. [PMID: 22998262 DOI: 10.1063/1.4751477] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Small infrared probe molecules have been widely used to study local electrostatic environment in solutions and proteins. Using a variety of time- and frequency-resolved vibrational spectroscopic methods, one can accurately measure the solvation-induced vibrational frequency shifts and the timescales and amplitudes of frequency fluctuations of such IR probes. Since the corresponding frequency shifts are directly related to the local electric field and its spatial derivatives of the surrounding solvent molecules or amino acids in proteins, one can extract information on local electric field around an IR probe directly from the vibrational spectroscopic results. Here, we show that, carrying out a multipole analysis of the solvatochromic frequency shift, the solvatochromic dipole contribution to the frequency shift is not always the dominant factor. In the cases of the nitrile-, thiocyanato-, and azido-derivatized molecules, the solvatochromic quadrupole contributions to the corresponding stretch mode frequency shifts are particularly large and often comparable to the solvatochromic dipole contributions. Noting that the higher multipole moment-solvent electric field interactions are short range effects in comparison to the dipole interaction, the H-bonding interaction-induced vibrational frequency shift can be caused by such short-range multipole-field interaction effects. We anticipate that the present multipole analysis method specifically developed to describe the solvatochromic vibrational frequency shifts will be useful to understand the intermolecular interaction-induced vibrational property changes and to find out a relationship between vibrational solvatochromism and electrochromism of IR probes in condensed phases.
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Affiliation(s)
- Hochan Lee
- Department of Chemistry and Research Institute for Basic Sciences, Korea University, Seoul 136-713, South Korea
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49
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Layfield JP, Hammes-Schiffer S. Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding. J Am Chem Soc 2012; 135:717-25. [PMID: 23210919 DOI: 10.1021/ja3084384] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.
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Affiliation(s)
- Joshua P Layfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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50
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Pazos IM, Gai F. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability. J Phys Chem B 2012; 116:12473-8. [PMID: 22998405 PMCID: PMC3475735 DOI: 10.1021/jp307414s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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