1
|
Sakpal S, Chakrabarty S, Reddy KD, Deshmukh SH, Biswas R, Bagchi S, Ghosh A. Perturbation of Fermi Resonance on Hydrogen-Bonded > C═O: 2D IR Studies of Small Ester Probes. J Phys Chem B 2024. [PMID: 38686937 DOI: 10.1021/acs.jpcb.3c06698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
We utilized linear and 2D infrared spectroscopy to analyze the carbonyl stretching modes of small esters in different solvents. Particularly noteworthy were the distinct carbonyl spectral line shapes in aqueous solutions, prompting our investigation of the underlying factors responsible for these differences. Through our experimental and theoretical calculations, we identified the presence of the hydrogen-bond-induced Fermi resonance as the primary contributor to the varied line shapes of small esters in aqueous solutions. Furthermore, our findings revealed that the skeletal deformation mode plays a crucial role in the Fermi resonance for all small esters. Specifically, the first overtone band of the skeletal deformation mode intensifies when hydrogen bonds form with the carbonyl group of esters, whereas such coupling is rare in aprotic organic solvents. These spectral insights carry significant implications for the utilization of esters as infrared probes in both biological and chemical systems.
Collapse
Affiliation(s)
- Sushil Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suranjana Chakrabarty
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Kambham Devendra Reddy
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati, Andhra Pradesh, India 517619
| | - Samadhan H Deshmukh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rajib Biswas
- Department of Chemistry, Indian Institute of Technology Tirupati, Tirupati, Andhra Pradesh, India 517619
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anup Ghosh
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
- Department of Chemical Science, Bose Institute, Kolkata 700091, India
| |
Collapse
|
2
|
Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
| |
Collapse
|
3
|
Weaver JB, Kozuch J, Kirsh JM, Boxer SG. Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments. J Am Chem Soc 2022; 144:7562-7567. [PMID: 35467853 PMCID: PMC10082610 DOI: 10.1021/jacs.2c00675] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C≡N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.
Collapse
Affiliation(s)
- Jared Bryce Weaver
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Jacek Kozuch
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Jacob M Kirsh
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| |
Collapse
|
4
|
Kwon HJ, Gwak S, Park JY, Cho M, Han H. TfNN 15N: A γ- 15N-Labeled Diazo-Transfer Reagent for the Synthesis of β- 15N-Labeled Azides. ACS OMEGA 2022; 7:293-298. [PMID: 35036700 PMCID: PMC8757338 DOI: 10.1021/acsomega.1c04679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Azides are infrared (IR) probes that are important for structure and dynamics studies of proteins. However, they often display complex IR spectra owing to Fermi resonances and multiple conformers. Isotopic substitution of azides weakens the Fermi resonance, allowing more accurate IR spectral analysis. Site-specifically 15N-labeled aromatic azides, but not aliphatic azides, are synthesized through nitrosation. Both 15N-labeled aromatic and aliphatic azides are synthesized through nucleophilic substitution or diazo-transfer reaction but as an isotopomeric mixture. We present the synthesis of TfNN15N, a γ-15N-labeled diazo-transfer reagent, and its use to prepare β-15N-labeled aliphatic as well as aromatic azides.
Collapse
Affiliation(s)
- Hyeok-Jun Kwon
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Sungduk Gwak
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Jun Young Park
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hogyu Han
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| |
Collapse
|
5
|
Geometrical, electrical, and energetic parameters of hetero-disubstituted cumulenes and polyynes in the presence and absence of the external electric field. Struct Chem 2021. [DOI: 10.1007/s11224-021-01858-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
AbstractCumulenes and polyynes have the potential to be applied as linear, sp-hybridized, one-dimensional all-carbon nanowires in molecular electronics and optoelectronics. The delocalization and conductivity descriptors of the two π-conjugated systems, heterodisubstituted with the NO2, CN, NH2, and OH groups, were studied using the B3LYP, B3LYP/D3, CAM-B3LYP, and ωB97XD DFT functionals, combined with the aug-cc-pVTZ basis set. Three independent types of molecular descriptors, based on geometry (the HOMA index), electrical properties (trace of the polarizability tensor), and energetic (the HOMO-LUMO energy gap) were shown to be mutually correlated and provided concordant indication that communication through the cumulene chain was considerably better than through the polyyne one. The communication can be tuned by using substituents of significantly different π-electron donor-acceptor properties as well as by the external electric field directed along the carbon chain.
Collapse
|
6
|
Park Y, Shin S, Kang H. Recent Progress in the Manipulation of Molecules with DC Electric Fields. Acc Chem Res 2021; 54:323-331. [PMID: 33377765 DOI: 10.1021/acs.accounts.0c00609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and reactivity of a molecule in the condensed phase are governed by its intermolecular interactions with the surrounding environment. The multipole expansion of each molecule in the condensed phase indicates that the intermolecular interactions are essentially electrostatic (e.g., ion-dipole, dipole-dipole, dipole-quadrupole, dipole-induced dipole). The electrostatic field is a fundamental language of intermolecular communications. Therefore, understanding the influence of the electrostatic field on a molecule, that is, the mechanisms by which an electrostatic field manipulates a molecule, from the perspective of molecular structure, energy states, and dynamics is indispensable for illustrating and, by extension, controlling the chemistry in molecular systems.In this Account, we describe the recent progress made in manipulation of molecular processes using an external DC electrostatic field. An electrostatic field with unprecedentedly high strength (≤4 × 108 V/m) was applied in a controlled manner across a molecular film sample using the ice film nanocapacitor method. This field strength is comparable in magnitude to that of weak intermolecular interactions such as van der Waals interactions in the condensed phases. The samples were prepared using a thin film growing technique in vacuum to obtain the desired chemically tailored molecular systems. The examples of prepared systems included small molecules and molecular clusters isolated in cryogenic Ar matrices, frozen molecular films in amorphous or crystalline phase, and interfaces of multilayered molecular films. The response of the molecules to the external field was monitored by reflection-absorption infrared spectroscopy. This approach allowed us to investigate a variety of molecular systems with various intermolecular strength and environments under the influence of strong electrostatic fields. The range of observed molecular behaviors includes the manipulation of molecular orientation, intramolecular dynamics, and proton transfer reactions as an example of stereodynamic control of chemical reactivity. These observations improve our understanding of molecular behaviors in strong electric fields and broaden our perspective on electrostatic manipulation of molecules. This information is also relevant to a variety of research topics in physical and biological sciences where electric fields play a role in molecular and biological functions.
Collapse
Affiliation(s)
- Youngwook Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul 08826, South Korea
| | - Sunghwan Shin
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul 08826, South Korea
| | - Heon Kang
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul 08826, South Korea
| |
Collapse
|
7
|
Zhang S, Sun L, Ju H, Bao Z, Zeng XA, Lin S. Research advances and application of pulsed electric field on proteins and peptides in food. Food Res Int 2021; 139:109914. [DOI: 10.1016/j.foodres.2020.109914] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/14/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
|
8
|
Park JY, Kwon HJ, Mondal S, Han H, Kwak K, Cho M. Two-dimensional IR spectroscopy reveals a hidden Fermi resonance band in the azido stretch spectrum of β-azidoalanine. Phys Chem Chem Phys 2020; 22:19223-19229. [PMID: 32812969 DOI: 10.1039/d0cp02693j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Azido stretch modes in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local electrostatic environments. The vibrational bands of azide probes are often accompanied by complex line shapes with shoulder peaks, which may arise either from incomplete background subtraction, Fermi resonance, or multiple conformers. The isotope substitution in the infrared probe has thus been introduced to remove Fermi resonances without causing a significant perturbation to the structure. Here, we synthesized and labeled the mid-N atoms of aliphatic azide derivatives with 15N to study the effects of isotope labelling on their vibrational properties. The FT-IR spectra of the aliphatic azide with asymmetric lineshape became a single symmetric band upon isotope substitution, which might be an indication of the removal of the hidden Fermi resonance from the system. We also noticed that the 2D-IR spectrum of unlabeled aliphatic azide has cross-peaks, even though it is not apparently identifiable. The 1D slice spectra obtained from the 2D-IR spectra reveal the existence of a hidden Fermi resonance peak. Furthermore, we show that this weak Fermi resonance does not produce discernible oscillatory beating patterns in the IR pump-probe spectrum, which has been used as evidence of the Fermi resonance. Therefore, we confirm that isotope labelling combined with 2D-IR spectroscopy is the most efficient and incisive way to identify the origin of small shoulder peaks in the linear and nonlinear vibrational spectra of various IR probe molecules.
Collapse
Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| |
Collapse
|
9
|
Devereux SJ, Poynton FE, Baptista FR, Gunnlaugsson T, Cardin CJ, Sazanovich IV, Towrie M, Kelly JM, Quinn SJ. Caught in the Loop: Binding of the [Ru(phen) 2 (dppz)] 2+ Light-Switch Compound to Quadruplex DNA in Solution Informed by Time-Resolved Infrared Spectroscopy. Chemistry 2020; 26:17103-17109. [PMID: 32725823 DOI: 10.1002/chem.202002165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/05/2023]
Abstract
Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)2 (dppz)]2+ "light-switch" complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K+ and Na+ containing solutions. TRIR permits the simultaneous monitoring both of the "dark" and "bright" states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na+ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.
Collapse
Affiliation(s)
| | - Fergus E Poynton
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland.,Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, 2, Ireland
| | | | - Thorfinnur Gunnlaugsson
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland.,Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, 2, Ireland
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | | | - Michael Towrie
- Rutherford Appleton Laboratory, STFC, Harwell Campus, OX11 0FA, UK
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Dublin, 4, Ireland
| |
Collapse
|
10
|
Park JY, Mondal S, Kwon HJ, Sahu PK, Han H, Kwak K, Cho M. Effect of isotope substitution on the Fermi resonance and vibrational lifetime of unnatural amino acids modified with IR probe: A 2D-IR and pump-probe study of 4-azido-L-phenyl alanine. J Chem Phys 2020; 153:164309. [DOI: 10.1063/5.0025289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Prabhat Kumar Sahu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, 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), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| |
Collapse
|
11
|
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: 160] [Impact Index Per Article: 40.0] [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.
Collapse
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
| |
Collapse
|
12
|
Cracchiolo OM, Geremia DK, Corcelli SA, Serrano AL. Hydrogen Bond Exchange and Ca2+ Binding of Aqueous N-Methylacetamide Revealed by 2DIR Spectroscopy. J Phys Chem B 2020; 124:6947-6954. [DOI: 10.1021/acs.jpcb.0c02444] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Olivia M. Cracchiolo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Danielle K. Geremia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Arnaldo L. Serrano
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
13
|
Verma N, Tao Y, Zou W, Chen X, Chen X, Freindorf M, Kraka E. A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory. SENSORS 2020; 20:s20082358. [PMID: 32326248 PMCID: PMC7219233 DOI: 10.3390/s20082358] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.
Collapse
Affiliation(s)
- Niraj Verma
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
| | - Yunwen Tao
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, Xi’an 710127, China;
| | - Xia Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China;
| | - Xin Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China;
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (N.V.); (Y.T.); (M.F.)
- Correspondence:
| |
Collapse
|
14
|
|
15
|
Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
Collapse
Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| |
Collapse
|
16
|
Saggu M, Fried SD, Boxer SG. Local and Global Electric Field Asymmetry in Photosynthetic Reaction Centers. J Phys Chem B 2019; 123:1527-1536. [PMID: 30668130 DOI: 10.1021/acs.jpcb.8b11458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of unidirectional electron transfer in photosynthetic reaction centers (RCs) has been widely discussed. Despite the high level of structural similarity between the two branches of pigments that participate in the initial electron transfer steps of photosynthesis, electron transfer only occurs along one branch. One possible explanation for this functional asymmetry is the differences in the electrostatic environment between the active and the inactive branches arising from the charges and dipoles of the organized protein structure. We present an analysis of electric fields in the RC of the purple bacterium Rhodobacter sphaeroides using the intrinsic carbonyl groups of the pigments as vibrational reporters whose vibrational frequency shifts can be converted into electric fields based on the vibrational Stark effect and also provide Stark effect data for plant pigments that can be used in future studies. The carbonyl stretches of the isolated pigments show pronounced Stark effects. We use these data, solvatochromism, molecular dynamics simulations, and data in the literature from IR and Raman spectra to evaluate differences in fields at symmetry-related positions, in particular at the 9-keto and 2-acetyl positions of the pigments involved in primary charge separation.
Collapse
Affiliation(s)
- Miguel Saggu
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| | - Stephen D Fried
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| |
Collapse
|
17
|
Grafton AB, Cheatum CM. Two-dimensional infrared study of the C D and C O stretching vibrations in strongly hydrogen-bonded complexes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
18
|
Slocum JD, Webb LJ. Measuring Electric Fields in Biological Matter Using the Vibrational Stark Effect of Nitrile Probes. Annu Rev Phys Chem 2018; 69:253-271. [DOI: 10.1146/annurev-physchem-052516-045011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua D. Slocum
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA
| | - Lauren J. Webb
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA
| |
Collapse
|
19
|
Yang W, Tu Z, Wang H, Zhang L, Gao Y, Li X, Tian M. Immunogenic and structural properties of ovalbumin treated by pulsed electric fields. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2017.1396479] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Wenhua Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Zongcai Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Hui Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Lu Zhang
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Yuanyuan Gao
- Weibao Food Biology Co., LLC, Gaoan, Jiangxi, China
| | - Xue Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Ming Tian
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| |
Collapse
|
20
|
Bhat ZF, Morton JD, Mason SL, Bekhit AEDA. Current and future prospects for the use of pulsed electric field in the meat industry. Crit Rev Food Sci Nutr 2018; 59:1660-1674. [PMID: 29393666 DOI: 10.1080/10408398.2018.1425825] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Pulsed electric field (PEF) is a novel non-thermal technology that has recently attracted the attention of meat scientists and technologists due to its ability to modify membrane structure and enhance mass transfer. Several studies have confirmed the potential of pulsed electric field for improving meat tenderness in both pre-rigor and post-rigor muscles during aging. However, there is a high degree of variability between studies and the underlying mechanisms are not clearly understood. While some studies have suggested physical disruption as the main cause of PEF induced tenderness, enzymatic nature of the tenderization seems to be the most plausible mechanism. Several studies have suggested the potential of PEF to mediate the tenderization process due to its membrane altering properties causing early release of calcium ions and early activation of the calpain proteases. However, experimental research is yet to confirm this postulation. Recent studies have also reported increased post-mortem proteolysis in PEF treated muscles during aging. PEF has also been reported to accelerate curing, enhance drying and reduce the numbers of both pathogens and spoilage organisms in meat, although that demands intense processing conditions. While tenderization, meat safety and accelerated curing appears to be the areas where PEF could provide attractive options in meat processing, further research is required before the application of PEF becomes a commercial reality in the meat industry. It needs to deal with carcasses which vary biochemically and in composition (muscle, fat, and bones). This review critically evaluates the published reports on the topic with the aim of reaching a clear understanding of the possible applications of PEF in the meat sector in addition to providing some insight on critical issues that need to be addressed for the technology to be a practical option for the meat industry.
Collapse
Affiliation(s)
- Zuhaib F Bhat
- a Lincoln University Faculty of Agriculture and Life Sciences, Wine Food and Molecular Biosciences , Lincoln , New Zealand
| | - James D Morton
- a Lincoln University Faculty of Agriculture and Life Sciences, Wine Food and Molecular Biosciences , Lincoln , New Zealand
| | - Susan L Mason
- a Lincoln University Faculty of Agriculture and Life Sciences, Wine Food and Molecular Biosciences , Lincoln , New Zealand
| | | |
Collapse
|
21
|
Abstract
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.
Collapse
Affiliation(s)
- Stephen D Fried
- Proteins and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305;
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Völler JS, Biava H, Hildebrandt P, Budisa N. An expanded genetic code for probing the role of electrostatics in enzyme catalysis by vibrational Stark spectroscopy. Biochim Biophys Acta Gen Subj 2017; 1861:3053-3059. [PMID: 28229928 DOI: 10.1016/j.bbagen.2017.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND To find experimental validation for electrostatic interactions essential for catalytic reactions represents a challenge due to practical limitations in assessing electric fields within protein structures. SCOPE OF REVIEW This review examines the applications of non-canonical amino acids (ncAAs) as genetically encoded probes for studying the role of electrostatic interactions in enzyme catalysis. MAJOR CONCLUSIONS ncAAs constitute sensitive spectroscopic probes to detect local electric fields by exploiting the vibrational Stark effect (VSE) and thus have the potential to map the protein electrostatics. GENERAL SIGNIFICANCE Mapping the electrostatics in proteins will improve our understanding of natural catalytic processes and, in beyond, will be helpful for biocatalyst engineering. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
Collapse
Affiliation(s)
- Jan-Stefan Völler
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany.
| | - Hernan Biava
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany; Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, D-10623 Berlin, Germany.
| |
Collapse
|
24
|
Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
25
|
Schneider SH, Boxer SG. Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site. J Phys Chem B 2016; 120:9672-84. [PMID: 27541577 DOI: 10.1021/acs.jpcb.6b08133] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.
Collapse
Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| |
Collapse
|
26
|
Poynton FE, Hall JP, Keane PM, Schwarz C, Sazanovich IV, Towrie M, Gunnlaugsson T, Cardin CJ, Cardin DJ, Quinn SJ, Long C, Kelly JM. Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen) 2(dppz)] 2+ light-switch compound in solution and when bound to DNA. Chem Sci 2016; 7:3075-3084. [PMID: 29997799 PMCID: PMC6005197 DOI: 10.1039/c5sc04514b] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/26/2016] [Indexed: 02/01/2023] Open
Abstract
The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this "light-switch" effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280-1450 cm-1, which characterise both the emissive "bright" and the non-emissive "dark" excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the "dark" excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the "bright" state are observed for both Λ- and Δ-enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the Λ-enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.
Collapse
Affiliation(s)
- Fergus E Poynton
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
- Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland
| | - James P Hall
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0QX , UK
| | - Páraic M Keane
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
| | - Christine Schwarz
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
| | - Igor V Sazanovich
- Central Laser Facility , Research Complex at Harwell , STFC Rutherford Appleton Laboratory , Oxfordshire OX11 0QX , UK
| | - Michael Towrie
- Central Laser Facility , Research Complex at Harwell , STFC Rutherford Appleton Laboratory , Oxfordshire OX11 0QX , UK
| | - Thorfinnur Gunnlaugsson
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
- Trinity Biomedical Sciences Institute (TBSI) , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland
| | | | - David J Cardin
- Department of Chemistry , University of Reading , Reading RG6 6AD , UK
| | - Susan J Quinn
- School of Chemistry , University College Dublin , Dublin 4 , Ireland
| | - Conor Long
- The School of Chemical Sciences , Dublin City University , Dublin 9 , Ireland .
| | - John M Kelly
- School of Chemistry , Trinity College Dublin , The University of Dublin , Dublin 2 , Ireland .
| |
Collapse
|
27
|
Sevinc PC, Dhital B, Govind Rao V, Wang Y, Lu HP. Probing Electric Field Effect on Covalent Interactions at a Molecule–Semiconductor Interface. J Am Chem Soc 2016; 138:1536-42. [PMID: 26735967 DOI: 10.1021/jacs.5b10253] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Papatya C. Sevinc
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Bharat Dhital
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Vishal Govind Rao
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Yuanmin Wang
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Department of Chemistry and
Center for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| |
Collapse
|
28
|
Sun J, Tian S, Cai X, Xiong D, Verma SK, Zhang Q, Chen W, Zhu M, Zhao X. Low-temperature solution synthesis of a ZnO nanorod array with a mesoporous surface mediated by cadmium ions. CrystEngComm 2016. [DOI: 10.1039/c6ce01989g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
29
|
Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy. Nat Chem 2015; 7:961-7. [PMID: 26587711 DOI: 10.1038/nchem.2369] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/04/2015] [Indexed: 12/19/2022]
Abstract
To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.
Collapse
|
30
|
List NH, Beerepoot MTP, Olsen JMH, Gao B, Ruud K, Jensen HJA, Kongsted J. Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone. J Chem Phys 2015; 142:034119. [PMID: 25612701 DOI: 10.1063/1.4905909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn-Sham density functional theory. As the first application of the implementation, we consider the internal vibrational Stark effect of the C=O group of acetophenone in different solvents and derive its vibrational linear Stark tuning rate using harmonic frequencies calculated from analytical gradients and computed local electric fields. Comparisons to PE calculations employing an enlarged quantum region as well as to a non-polarizable embedding scheme show that the inclusion of mutual polarization between acetophenone and water is essential in order to capture the structural modifications and the associated frequency shifts observed in water. For more apolar solvents, a proper description of dispersion and exchange-repulsion becomes increasingly important, and the quality of the optimized structures relies to a larger extent on the quality of the Lennard-Jones parameters.
Collapse
Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Bin Gao
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense M, Odense DK-5230 Denmark
| |
Collapse
|
31
|
Takashima K, Furukawa Y. Vibrational Stark effect of 9-cyanoanthracene dispersed in a poly(methyl methacrylate) film. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
32
|
Fried SD, Boxer SG. Measuring electric fields and noncovalent interactions using the vibrational stark effect. Acc Chem Res 2015; 48:998-1006. [PMID: 25799082 DOI: 10.1021/ar500464j] [Citation(s) in RCA: 317] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past decade, we have developed a spectroscopic approach to measure electric fields inside matter with high spatial (<1 Å) and field (<1 MV/cm) resolution. The approach hinges on exploiting a physical phenomenon known as the vibrational Stark effect (VSE), which ultimately provides a direct mapping between observed vibrational frequencies and electric fields. Therefore, the frequency of a vibrational probe encodes information about the local electric field in the vicinity around the probe. The VSE method has enabled us to understand in great detail the underlying physical nature of several important biomolecular phenomena, such as drug-receptor selectivity in tyrosine kinases, catalysis by the enzyme ketosteroid isomerase, and unidirectional electron transfer in the photosynthetic reaction center. Beyond these specific examples, the VSE has provided a conceptual foundation for how to model intermolecular (noncovalent) interactions in a quantitative, consistent, and general manner. The starting point for research in this area is to choose (or design) a vibrational probe to interrogate the particular system of interest. Vibrational probes are sometimes intrinsic to the system in question, but we have also devised ways to build them into the system (extrinsic probes), often with minimal perturbation. With modern instruments, vibrational frequencies can increasingly be recorded with very high spatial, temporal, and frequency resolution, affording electric field maps correspondingly resolved in space, time, and field magnitude. In this Account, we set out to explain the VSE in broad strokes to make its relevance accessible to chemists of all specialties. Our intention is not to provide an encyclopedic review of published work but rather to motivate the underlying framework of the methodology and to describe how we make and interpret the measurements. Using certain vibrational probes, benchmarked against computer models, it is possible to use the VSE to measure absolute electric fields in arbitrary environments. The VSE approach provides an organizing framework for thinking generally about intermolecular interactions in a quantitative way and may serve as a useful conceptual tool for molecular design.
Collapse
Affiliation(s)
- Stephen D. Fried
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
| | - Steven G. Boxer
- Department
of Chemistry; Stanford University, Stanford, California 94305-5080, United States
| |
Collapse
|
33
|
Lasne J, Rosu-Finsen A, Cassidy A, McCoustra MRS, Field D. Spontaneous electric fields in solid carbon monoxide. Phys Chem Chem Phys 2015; 17:30177-87. [DOI: 10.1039/c5cp04536c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Reflection–absorption infrared spectroscopy (RAIRS) is shown to provide a means of observing the spontelectric phase of matter, the defining characteristic of which is the occurrence of a spontaneous and powerful static electric field within a film of material.
Collapse
Affiliation(s)
- Jérôme Lasne
- Institute of Chemical Sciences
- Heriot-Watt University
- Riccarton
- UK
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA)
| | | | - Andrew Cassidy
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | | | - David Field
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| |
Collapse
|
34
|
Lasne J, Rosu-Finsen A, Cassidy A, McCoustra MRS, Field D. Spontaneously electrical solids in a new light. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp03174e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Reflection–absorption infrared spectroscopy (RAIRS) of nitrous oxide (N2O) thin films is shown to provide an independent means of observing the spontelectric state; the first new structural phase of matter, with unique electrical properties, to have emerged in decades.
Collapse
Affiliation(s)
- Jérôme Lasne
- Institute of Chemical Sciences
- Heriot-Watt University
- Riccarton
- UK
| | | | - Andrew Cassidy
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | | | - David Field
- Department of Physics and Astronomy
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| |
Collapse
|
35
|
Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 DOI: 10.12688/f1000research.5836.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2014] [Indexed: 03/23/2024] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
Collapse
Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany ; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
36
|
Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 PMCID: PMC4304226 DOI: 10.12688/f1000research.5836.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/11/2014] [Indexed: 11/20/2022] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
Collapse
Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
37
|
|
38
|
Abstract
UNLABELLED In recent decades, Raman spectroscopy has entered the biological and medical fields. It enables nondestructive analysis of structural details at the molecular level and has been used to study viruses and their constituents. Here, we used Raman spectroscopy to study echovirus 1 (EV1), a small, nonenveloped human pathogen, in two different uncoating states induced by heat treatments. Raman signals of capsid proteins and RNA genome were observed from the intact virus, the uncoating intermediate, and disrupted virions. Transmission electron microscopy data revealed general structural changes between the studied particles. Compared to spectral characteristics of proteins in the intact virion, those of the proteins of the heat-treated particles indicated reduced α-helix content with respect to β-sheets and coil structures. Changes observed in tryptophan and tyrosine signals suggest an increasingly hydrophilic environment around these residues. RNA signals revealed a change in the environment of the genome and in its conformation. The ionized-carbonyl vibrations showed small changes between the intact virion and the uncoating intermediate, which points to cleavage of salt bridges in the protein structure during the uncoating process. In conclusion, our data reveal distinguishable Raman signatures of the intact, intermediate, and disrupted EV1 particles. These changes indicate structural, chemical, and solute-solvent alterations in the genome and in the capsid proteins and lay the essential groundwork for investigating the uncoating of EV1 and related viruses in real time. IMPORTANCE In order to combat virus infection, we need to know the details of virus uncoating. We present here the novel Raman signatures for opened and intact echovirus 1. This gives hope that the signatures may be used in the near future to evaluate the ambient conditions in endosomes leading to virus uncoating using, e.g., coherent anti-Stokes Raman spectroscopy (CARS) imaging. These studies will complement structural studies on virus uncoating. In addition, Raman/CARS imaging offers the possibility of making dynamic live measurements in vitro and in cells which are impossible to measure by, for example, cryo-electron tomography. Furthermore, as viral Raman spectra can be overwhelmed with various contaminants, our study is highly relevant in demonstrating the importance of sample preparation for Raman spectroscopy in the field of virology.
Collapse
|
39
|
Elenewski JE, Hackett JC. Solvatochromism and the solvation structure of benzophenone. J Chem Phys 2014; 138:224308. [PMID: 23781796 DOI: 10.1063/1.4809529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many complex molecular phenomena, including macromolecular association, protein folding, and chemical reactivity, are determined by the nuances of their electrostatic landscapes. The measurement of such electrostatic effects is nonetheless difficult, and is typically accomplished by exploiting a spectroscopic probe within the system of interest, such as through the vibrational Stark effect. Raman spectroscopy and solvatochromism afford an alternative to this method, circumventing the limitations of infrared spectroscopy, providing a lower detection limit, and permitting measurement in a native chemical environment. To explore this possibility, the solvatochromism of the C=O and aromatic C-H stretching modes of benzophenone are investigated using Raman spectroscopy. In conjunction with density functional theory calculations, these observations are sufficient to determine the probe electrostatic environment as well as contributions from halogen and hydrogen bonding. Further analysis using a detailed Kubo-Anderson lineshape model permits the detailed assignment of distinct hydrogen bonding configurations for water in the benzophenone solvation shell. These observations reinforce the use of benzophenone as an effective electrostatic probe for complex chemical systems.
Collapse
Affiliation(s)
- Justin E Elenewski
- Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540, USA
| | | |
Collapse
|
40
|
Kalescky R, Kraka E, Cremer D. New approach to Tolman's electronic parameter based on local vibrational modes. Inorg Chem 2013; 53:478-95. [PMID: 24320732 DOI: 10.1021/ic4024663] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tolman's electronic parameter (TEP) derived from the A1-symmetrical CO stretching frequency of nickel-phosphine-tricarbonyl complexes, R3PNi(CO)3, is brought to a new, improved level by replacing normal with local vibrational frequencies. CO normal vibrational frequencies are always flawed by mode-mode coupling especially with metal-carbon stretching modes, which leads to coupling frequencies as large as 100 cm(-1) and can become even larger when the transition metal and the number of ligands is changed. Local TEP (LTEP) values, being based on local CO stretching force constants rather than normal mode frequencies, no longer suffer from mode coupling and mass effects. For 42 nickel complexes of the type LNi(CO)3, it is shown that LTEP values provide a different ordering of ligand electronic effects as previously suggested by TEP and CEP values. The general applicability of the LTEP concept is demonstrated.
Collapse
Affiliation(s)
- Robert Kalescky
- Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | | | | |
Collapse
|
41
|
Fried SD, Wang LP, Boxer SG, Ren P, Pande VS. Calculations of the electric fields in liquid solutions. J Phys Chem B 2013; 117:16236-48. [PMID: 24304155 DOI: 10.1021/jp410720y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electric field created by a condensed-phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution-phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe nonpolar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and to identify for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins.
Collapse
Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | | | | | | | | |
Collapse
|
42
|
Choi JH, Kwak KW, Cho M. Computational infrared and two-dimensional infrared photon echo spectroscopy of both wild-type and double mutant myoglobin-CO proteins. J Phys Chem B 2013; 117:15462-78. [PMID: 23869523 DOI: 10.1021/jp405210s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The CO stretching mode of both wild-type and double mutant ( T67R / S92D ) MbCO (carbonmonoxymyoglobin) proteins is an ideal infrared (IR) probe for studying the local electrostatic environment inside the myoglobin heme pocket. Recently, to elucidate the conformational switching dynamics between two distinguishable states, extensive IR absorption, IR pump-probe, and two-dimensional (2D) IR spectroscopic studies for various mutant MbCO's have been performed by the Fayer group. They showed that the 2D IR spectroscopy of the double mutant, which has a peroxidase enzyme activity, reveals a rapid chemical exchange between two distinct states, whereas that of the wild-type does not. Despite the fact that a few simulation studies on these systems were already performed and reported, such complicated experimental results have not been fully reproduced nor described in terms of conformational state-to-state transition processes. Here, we first develop a distributed vibrational solvatochromic charge model for describing the CO stretch frequency shift reflecting local electric potential changes. Then, by carrying out molecular dynamic simulations of the two MbCO's and examining their CO frequency trajectories, it becomes possible to identify a proper reaction coordinate consisting of His64 imidazole ring rotation and its distance to the CO ligand. From the 2D surfaces of the resulting potential of mean forces, the spectroscopically distinguished A1 and A3 states of the wild-type as well as two more substates of the double mutant are identified and their vibrational frequencies and distributions are separately examined. Our simulated IR absorption and 2D IR spectra of the two MbCO's are directly compared with the previous experimental results reported by the Fayer group. The chemical exchange rate constants extracted from the two-state kinetic analyses of the simulated 2D IR spectra are in excellent agreement with the experimental values. On the basis of the quantitative agreement between the simulated spectra and experimental ones, we further examine the conformational differences in the heme pockets of the two proteins and show that the double mutation, T67R / S92D , suppresses the A1 population, restricts the imidazole ring rotation, and increases hydrogen-bond strength between the imidazole Nε-H and the oxygen atom of the CO ligand. It is believed that such delicate change of distal His64 imidazole ring dynamics induced by the double mutation may be responsible for its enhanced peroxidase catalytic activity as compared to the wild-type myoglobin.
Collapse
Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry, Korea University , Seoul 136-713, Korea
| | | | | |
Collapse
|
43
|
Fried SD, Bagchi S, Boxer SG. Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes. J Am Chem Soc 2013; 135:11181-92. [PMID: 23808481 DOI: 10.1021/ja403917z] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Vibrational probes can provide a direct readout of the local electrostatic field in complex molecular environments, such as protein binding sites and enzyme active sites. This information provides an experimental method to explore the underlying physical causes of important biomolecular processes such as binding and catalysis. However, specific chemical interactions such as hydrogen bonds can have complicated effects on vibrational probes and confound simple electrostatic interpretations of their frequency shifts. We employ vibrational Stark spectroscopy along with infrared spectroscopy of carbonyl probes in different solvent environments and in ribonuclease S to understand the sensitivity of carbonyl frequencies to electrostatic fields, including those due to hydrogen bonds. Additionally, we carried out molecular dynamics simulations to calculate ensemble-averaged electric fields in solvents and in ribonuclease S and found excellent correlation between calculated fields and vibrational frequencies. These data enabled the construction of a robust field-frequency calibration curve for the C═O vibration. The present results suggest that carbonyl probes are capable of quantitatively assessing the electrostatics of hydrogen bonding, making them promising for future study of protein function.
Collapse
Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, USA
| | | | | |
Collapse
|
44
|
Brookes JF, Slenkamp KM, Lynch MS, Khalil M. Effect of solvent polarity on the vibrational dephasing dynamics of the nitrosyl stretch in an Fe(II) complex revealed by 2D IR spectroscopy. J Phys Chem A 2013; 117:6234-43. [PMID: 23480848 DOI: 10.1021/jp4005345] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational dephasing dynamics of the nitrosyl stretching vibration (ν(NO)) in sodium nitroprusside (SNP, Na2[Fe(CN)5NO]·2H2O) are investigated using two-dimensional infrared (2D IR) spectroscopy. The ν(NO) in SNP acts as a model system for the nitrosyl ligand found in metalloproteins which play an important role in the transportation and detection of nitric oxide (NO) in biological systems. We perform a 2D IR line shape study of the ν(NO) in the following solvents: water, deuterium oxide, methanol, ethanol, ethylene glycol, formamide, and dimethyl sulfoxide. The frequency of the ν(NO) exhibits a large vibrational solvatochromic shift of 52 cm(-1), ranging from 1884 cm(-1) in dimethyl sulfoxide to 1936 cm(-1) in water. The vibrational anharmonicity of the ν(NO) varies from 21 to 28 cm(-1) in the solvents used in this study. The frequency-frequency correlation functions (FFCFs) of the ν(NO) in SNP in each of the seven solvents are obtained by fitting the experimentally obtained 2D IR spectra using nonlinear response theory. The fits to the 2D IR line shape reveal that the spectral diffusion time scale of the ν(NO) in SNP varies from 0.8 to 4 ps and is negatively correlated with the empirical solvent polarity scales. We compare our results with the experimentally determined FFCFs of other charged vibrational probes in polar solvents and in the active sites of heme proteins. Our results suggest that the vibrational dephasing dynamics of the ν(NO) in SNP reflect the fluctuations of the nonhomogeneous electric field created by the polar solvents around the nitrosyl and cyanide ligands. The solute solvent interactions occurring at the trans-CN ligand are sensed through the π-back-bonding network along the Fe-NO bond in SNP.
Collapse
Affiliation(s)
- Jennifer F Brookes
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | | | | | | |
Collapse
|
45
|
Enchev V, Monev V, Markova N, Rogozherov M, Angelova S, Spassova M. A model system with intramolecular hydrogen bonding: Effect of external electric field on the tautomeric conversion and electronic structures. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
Spiro TG, Soldatova AV, Balakrishnan G. CO, NO and O 2 as Vibrational Probes of Heme Protein Interactions. Coord Chem Rev 2013; 257:511-527. [PMID: 23471138 PMCID: PMC3587108 DOI: 10.1016/j.ccr.2012.05.008] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The gaseous XO molecules (X = C, N or O) bind to the heme prosthetic group of heme proteins, and thereby activate or inhibit key biological processes. These events depend on interactions of the surrounding protein with the FeXO adduct, interactions that can be monitored via the frequencies of the Fe-X and X-O bond stretching modes, νFeX and νXO. The frequencies can be determined by vibrational spectroscopy, especially resonance Raman spectroscopy. Backbonding, the donation of Fe dπ electrons to the XO π* orbitals, is a major bonding feature in all the FeXO adducts. Variations in backbonding produce negative νFeX/νXO correlations, which can be used to gauge electrostatic and H-bonding effects in the protein binding pocket. Backbonding correlations have been established for all the FeXO adducts, using porphyrins with electron donating and withdrawing substituents. However the adducts differ in their response to variations in the nature of the axial ligand, and to specific distal interactions. These variations provide differing vantages for evaluating the nature of protein-heme interactions. We review experimental studies that explore these variations, and DFT computational studies that illuminate the underlying physical mechanisms.
Collapse
Affiliation(s)
- Thomas G. Spiro
- Department of Chemistry, University of Washington Box 351700, Seattle, Washington 98195
| | | | - Gurusamy Balakrishnan
- Department of Chemistry, University of Washington Box 351700, Seattle, Washington 98195
| |
Collapse
|
47
|
Nishida J, Shigeto S, Yabumoto S, Hamaguchi HO. Anharmonic coupling of the CH-stretch and CH-bend vibrations of chloroform as studied by near-infrared electroabsorption spectroscopy. J Chem Phys 2012; 137:234501. [DOI: 10.1063/1.4770264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
48
|
Saggu M, Levinson NM, Boxer SG. Experimental quantification of electrostatics in X-H···π hydrogen bonds. J Am Chem Soc 2012; 134:18986-97. [PMID: 23098379 PMCID: PMC3511793 DOI: 10.1021/ja305575t] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen-bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs quantum mechanical effects. In principle, the vibrational Stark effect, the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and nonelectrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to an electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc.2011, 133, 17414-17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H < N-H < S-H. The observed effects are consistent with differences in atomic polarizabilities of the X-H groups. Nonetheless, we find that the X-H stretching vibrations of the model compounds indole and thiophenol report quantitatively on the electric fields they experience when complexed with aromatic hydrogen-bond acceptors. These measurements can be used to estimate the electrostatic binding energies of the interactions, which are found to agree closely with the results of energy calculations. Taken together, these results highlight that with careful calibration vibrational probes can provide direct measurements of the electrostatic components of hydrogen bonds.
Collapse
Affiliation(s)
- Miguel Saggu
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012, USA
| | | | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012, USA
| |
Collapse
|
49
|
Nienhaus K, Zosel F, Nienhaus GU. Ligand binding to heme proteins: a comparison of cytochrome c variants with globins. J Phys Chem B 2012; 116:12180-8. [PMID: 22978708 DOI: 10.1021/jp306775n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have studied the binding of carbon monoxide (CO) in mutants of Cyt c having its methionine at position 80 replaced by alanine, aspartate, and arginine, so that the sixth coordination is available for ligand binding. We have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy to examine interactions of the heme-bound and photolyzed CO (and also nitric oxide, NO) in the small heme pocket created by the mutations. By using FTIR temperature derivative spectroscopy (TDS) and nanosecond flash photolysis, the enthalpy barrier distributions for CO rebinding were determined. In flash photolysis experiments, the majority of ligands rebind to the heme iron on picosecond time scales so that only the high-barrier tail of the distributions is visible on the nanosecond scale. By continuous wave excitation prior to TDS characterization of the barriers, however, each Cyt c molecule is photoexcited multiple times and complete photodissociation can be achieved, which likely arises from a rotation of the CO within the heme pocket so that the oxygen faces the heme iron. Apparently, reorientation prior to rebinding constitutes an additional and significant contribution to the rebinding barrier. Our experiments reveal that the compact, rigid structure of Cyt c offers no alternative binding sites for photodissociated ligands in the protein matrix. A comparison of ligand binding in these Cyt c mutants and hemoglobins underscores the importance of internal ligand docking sites and ligand migration routes for conveying a ligand binding function to heme proteins.
Collapse
Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
| | | | | |
Collapse
|
50
|
Dalosto SD, Vanderkooi JM, Sharp KA. Vibrational Stark Effects on Carbonyl, Nitrile, and Nitrosyl Compounds Including Heme Ligands, CO, CN, and NO, Studied with Density Functional Theory. J Phys Chem B 2012; 108:6450-7. [PMID: 18950134 DOI: 10.1021/jp0310697] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Changes in the matrix electric field in a protein, due for example to mutations or structural fluctuations, can be correlated with changes in the vibrational transition frequencies of suitable chromophores measured by IR spectroscopy through the Stark tuning rate. To make this correlation, the Stark tuning rate must be known from experiment or theory. In this paper, density functional theory at the B3LYP/TZV level of theory is used to compute the Stark tuning rate of adducts of heme porphyrin, namely, -CO, -CN, and -NO+ compounds. The results are compared with the corresponding vibrational frequencies-field dependencies from vibrational Stark spectroscopy of heme-proteins. The zero-field computed Stark tuning rate of 1.3 cm-1/MV/cm for heme-CO is in agreement with experiment, where typically the rate is 2.4/f cm-1/MV/cm for myoglobin, where f is a local field correction between 1.1 and 1.4. Several small nitrile, carbonyl, and dinitrile molecules were studied to rationalize the findings for the heme-adducted models. Here, the higher B3LYP/6-311++G(2d,2p) level of theory could be used so the agreement with recent experimental results is even better than for heme-adducted groups.
Collapse
Affiliation(s)
- Sergio D Dalosto
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | | | | |
Collapse
|