1
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Eastwood J, Procacci B, Gurung S, Lynam JM, Hunt NT. Understanding the Vibrational Structure and Ultrafast Dynamics of the Metal Carbonyl Precatalyst [Mn(ppy)(CO) 4]. ACS PHYSICAL CHEMISTRY AU 2024; 4:536-545. [PMID: 39346610 PMCID: PMC11428260 DOI: 10.1021/acsphyschemau.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 10/01/2024]
Abstract
The solution phase structure, vibrational spectroscopy, and ultrafast relaxation dynamics of the precatalyst species [Mn(ppy)(CO)4] (1) in solution have been investigated using ultrafast two-dimensional infrared (2D-IR) spectroscopy. By comparing 2D-IR data with the results of anharmonic density functional theory (DFT) calculations, we establish an excellent agreement between measured and predicted inter-mode couplings of the carbonyl stretching vibrational modes of 1 that relates to the atomic displacements of axial and equatorial ligands in the modes and the nature of the molecular orbitals involved in M-CO bonding. Measurements of IR pump-probe spectra and 2D-IR spectra as a function of waiting time reveal the presence of ultrafast (few ps) intramolecular vibrational energy redistribution between carbonyl stretching modes prior to vibrational relaxation. The vibrational relaxation times of the CO-stretching modes of 1 are found to be relatively solvent-insensitive, suggestive of limited solvent-solute interactions in the ground electronic state. Overall, these data provide a detailed picture of the complex potential energy surface, bonding and vibrational dynamics of 1, establishing a fundamental basis for the next steps in understanding and modulating precatalyst behavior.
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Affiliation(s)
| | - Barbara Procacci
- Department
of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, U.K.
| | - Sabina Gurung
- Department
of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, U.K.
| | - Jason M. Lynam
- Department
of Chemistry, University of York, York YO10 5DD, U.K.
| | - Neil T. Hunt
- Department
of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, U.K.
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2
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Procacci B, Wrathall SLD, Farmer AL, Shaw DJ, Greetham GM, Parker AW, Rippers Y, Horch M, Lynam JM, Hunt NT. Understanding the [NiFe] Hydrogenase Active Site Environment through Ultrafast Infrared and 2D-IR Spectroscopy of the Subsite Analogue K[CpFe(CO)(CN) 2] in Polar and Protic Solvents. J Phys Chem B 2024; 128:1461-1472. [PMID: 38301127 PMCID: PMC10875664 DOI: 10.1021/acs.jpcb.3c07965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.
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Affiliation(s)
- Barbara Procacci
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Solomon L. D. Wrathall
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Amy L. Farmer
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Daniel J. Shaw
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Yvonne Rippers
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Marius Horch
- Department
of Physics, Ultrafast Dynamics in Catalysis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jason M. Lynam
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
| | - Neil T. Hunt
- Department
of Chemistry, York Biomedical Research Institute,
University of York, York YO10 5DD, U.K.
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3
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Abstract
The vibrational Stark effect in proteins yields line shifts indicative of strong internal electric fields up to a few volts per angstrom. These values are supported by numerical simulations of proteins. The simulations also show a significant breadth of field fluctuations translating to inhomogeneous broadening of vibrational lines. According to fluctuation-dissipation arguments, strong internal fields should lead to broad lines. Experimentally reported vibrational lines in proteins are, however, very narrow. This disconnect is explained here in terms of the insufficient (nonergodic) sampling of the protein's configurations on the lifetime of the vibrational probe. The slow component of the electric field fluctuations in proteins relaxes on the time scale of tens of nanoseconds and is dynamically frozen on the vibrational lifetime.
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Affiliation(s)
- Daniel R Martin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States
| | - Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States
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4
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Horch M, Schoknecht J, Wrathall SLD, Greetham GM, Lenz O, Hunt NT. Understanding the structure and dynamics of hydrogenases by ultrafast and two-dimensional infrared spectroscopy. Chem Sci 2019; 10:8981-8989. [PMID: 31762978 PMCID: PMC6857670 DOI: 10.1039/c9sc02851j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
Hydrogenases are valuable model enzymes for sustainable energy conversion approaches using H2, but rational utilization of these base-metal biocatalysts requires a detailed understanding of the structure and dynamics of their complex active sites. The intrinsic CO and CN- ligands of these metalloenzymes represent ideal chromophores for infrared (IR) spectroscopy, but structural and dynamic insight from conventional IR absorption experiments is limited. Here, we apply ultrafast and two-dimensional (2D) IR spectroscopic techniques, for the first time, to study hydrogenases in detail. Using an O2-tolerant [NiFe] hydrogenase as a model system, we demonstrate that IR pump-probe spectroscopy can explore catalytically relevant ligand bonding by accessing high-lying vibrational states. This ultrafast technique also shows that the protein matrix is influential in vibrational relaxation, which may be relevant for energy dissipation from the active site during fast reaction steps. Further insights into the relevance of the active site environment are provided by 2D-IR spectroscopy, which reveals equilibrium dynamics and structural constraints imposed on the H2-accepting intermediate of [NiFe] hydrogenases. Both techniques offer new strategies for uniquely identifying redox-structural states in complex catalytic mixtures via vibrational quantum beats and 2D-IR off-diagonal peaks. Together, these findings considerably expand the scope of IR spectroscopy in hydrogenase research, and new perspectives for the characterization of these enzymes and other (bio-)organometallic targets are presented.
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Affiliation(s)
- Marius Horch
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Janna Schoknecht
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Solomon L D Wrathall
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , Oxford , OX110PE , UK
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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5
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Eckert PA, Kubarych KJ. Solvent Quality Controls Macromolecular Structural Dynamics of a Dendrimeric Hydrogenase Model. J Phys Chem B 2018; 122:12154-12163. [PMID: 30427195 DOI: 10.1021/acs.jpcb.8b07259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report a spectroscopic investigation of the ultrafast dynamics of the second-generation poly(aryl ether) dendritic hydrogenase model using two-dimensional infrared (2D-IR) spectroscopy to probe the metal carbonyl vibrations of the dendrimer and a reference small molecule, [Fe(μ-S)(CO)3]2. We find that the structural dynamics of the dendrimer are reflected in a slow phase of the spectral diffusion, which is absent from [Fe(μ-S)(CO)3]2, and we relate the slow phase to the quality of the solvent for poly(aryl ether) dendrimers. We observe a solvent-dependent modulation of the initial phase of vibrational relaxation of the carbonyl groups, which we attribute to an inhibition of solvent assistance in the intramolecular vibrational redistribution process for the dendrimer. There is also a clear solvent dependence of the vibrational frequencies of both the dendrimer and [Fe(μ-S)(CO)3]2. Our data represent the first 2D-IR study of a dendritic complex and provide insight into the solvent dependence of molecular conformation in solution and the ultrafast dynamics of moderately sized, conformationally mobile compounds.
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Affiliation(s)
- Peter A Eckert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 49109 , United States
| | - Kevin J Kubarych
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 49109 , United States
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6
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Kiefer LM, Kubarych KJ. Two-dimensional infrared spectroscopy of coordination complexes: From solvent dynamics to photocatalysis. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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7
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Stromberg CJ, Heilweil EJ. Ultrafast Photodynamics of Cyano-Functionalized [FeFe] Hydrogenase Model Compounds. J Phys Chem A 2018; 122:4023-4030. [PMID: 29652502 PMCID: PMC6051340 DOI: 10.1021/acs.jpca.8b00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[FeFe] hydrogenases are efficient enzymes that produce hydrogen gas under mild conditions. Synthetic model compounds containing all CO or mixed CO/PMe3 ligands were previously studied by us and others with ultrafast ultraviolet or visible pump-infrared probe spectroscopy in an effort to better understand the function and interactions of the active site with light. Studies of anionic species containing cyano groups, which more closely match the biological active site, have been elusive. In this work, two model compounds dissolved in room-temperature acetonitrile solution were examined: [Fe2(μ-S2C3H6)(CO)4(CN)2]2- (1) and [Fe2(μ-S2C2H4)(CO)4(CN)2]2- (2). These species exhibit long-lived transient signals consistent with loss of one CO ligand with potential isomerization of newly formed ground electronic state photoproducts, as previously observed with all-CO and CO/PMe3-containing models. We find no evidence for fast (ca. 150 ps) relaxation seen in the all-CO and CO/PMe3 compounds because of the absence of the metal-to-metal charge transfer band in the cyano-functionalized models. These results indicate that incorporation of cyano ligands may significantly alter the electronic properties and photoproducts produced immediately after photoexcitation, which may influence the catalytic activity of model compounds when attached to photosensitizers.
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Affiliation(s)
- Christopher J. Stromberg
- Department of Chemistry and Physics, Hood College, 401 Rosemont Avenue, Frederick, Maryland 21701-8524, United States
| | - Edwin J. Heilweil
- Engineering Physics Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899-8443 United States
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8
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Ge A, Rudshteyn B, Zhu J, Maurer RJ, Batista VS, Lian T. Electron-Hole-Pair-Induced Vibrational Energy Relaxation of Rhenium Catalysts on Gold Surfaces. J Phys Chem Lett 2018; 9:406-412. [PMID: 29227669 DOI: 10.1021/acs.jpclett.7b02885] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A combination of time-resolved vibrational spectroscopy and density functional theory techniques have been applied to study the vibrational energy relaxation dynamics of the Re(4,4'-dicyano-2,2'-bipyridine)(CO)3Cl (Re(CO)3Cl) catalyst for CO2 to CO conversion bound to gold surfaces. The kinetics of vibrational relaxation exhibits a biexponential decay including an ultrafast initial relaxation and complete recovery of the ground vibrational state. Ab initio molecular dynamics simulations and time-dependent perturbation theory reveal the former to be due to vibrational population exchange between CO stretching modes and the latter to be a combination of intramolecular vibrational relaxation (IVR) and electron-hole pair (EHP)-induced energy transfer into the gold substrate. EHP-induced energy transfer from the Re(CO)3Cl adsorbate into the gold surface occurs on the same time scale as IVR of Re(CO)3Cl in aprotic solvents. Therefore, it is expected to be particularly relevant to understanding the reduced catalytic activity of the homogeneous catalyst when anchored to a metal surface.
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Affiliation(s)
- Aimin Ge
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Benjamin Rudshteyn
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
- Yale Energy Sciences Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Jingyi Zhu
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - Reinhard J Maurer
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Victor S Batista
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
- Yale Energy Sciences Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Tianquan Lian
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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9
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Eckert PA, Kubarych KJ. Dynamic Flexibility of Hydrogenase Active Site Models Studied with 2D-IR Spectroscopy. J Phys Chem A 2017; 121:608-615. [PMID: 28032999 DOI: 10.1021/acs.jpca.6b11962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hydrogenase enzymes enable organisms to use H2 as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)3]2 and μ-edt-[Fe(CO)3]2 (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy. Since solvent fluctuations in nonpolar alkanes do not lead to substantial electrostatic modulations in a solute's vibrational mode frequencies, we attribute the spectral diffusion dynamics to intramolecular flexibility. The intramolecular origin is supported by the absence of any measurable solvent viscosity dependence, indicating that the frequency fluctuations are not coupled to the solvent motional dynamics. Quantum chemical calculations reveal a pronounced coupling between the low-frequency torsional rotation of the carbonyl ligands and the terminal CO stretching vibrations. The flexibility of the CO ligands has been proposed to play a central role in the catalytic reaction mechanism, and our results highlight that the CO ligands are highly flexible on a picosecond time scale.
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Affiliation(s)
- Peter A Eckert
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States
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10
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Fritzsch R, Brady O, Adair E, Wright JA, Pickett CJ, Hunt NT. Encapsulating Subsite Analogues of the [FeFe]-Hydrogenases in Micelles Enables Direct Water Interactions. J Phys Chem Lett 2016; 7:2838-2843. [PMID: 27396585 DOI: 10.1021/acs.jpclett.6b01338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Encapsulation of subsite analogues of the [FeFe]-hydrogenase enzymes in supramolecular structures has been shown to dramatically increase their catalytic ability, but the molecular basis for this enhancement remains unclear. We report the results of experiments employing infrared absorption, ultrafast infrared pump-probe, and 2D-IR spectroscopy to investigate the molecular environment of Fe2(pdt)(CO)6 (pdt: propanedithiolate) [1] encapsulated in the dispersed alkane phase of a heptane-dodecyltrimethylammonium bromide-water microemulsion. It is demonstrated that 1 is partitioned between two molecular environments, one that closely resembles bulk heptane solution and a second that features direct hydrogen-bonding interactions with water molecules that penetrate the surfactant shell. Our results demonstrate that the extent of water access to the normally water-insoluble subsite analogue 1 can be tuned with micelle size, while IR spectroscopy provides a straightforward tool that can be used to measure and fine-tune the chemical environment of catalyst species in self-assembled structures.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Owen Brady
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Elaine Adair
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Joseph A Wright
- Energy Materials Laboratory, School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Christopher J Pickett
- Energy Materials Laboratory, School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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11
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Hunt NT, Wright JA, Pickett C. Detection of Transient Intermediates Generated from Subsite Analogues of [FeFe] Hydrogenases. Inorg Chem 2015; 55:399-410. [DOI: 10.1021/acs.inorgchem.5b02477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA, Glasgow G4 0NG, United Kingdom
| | - Joseph A. Wright
- Energy Materials Laboratory, School of
Chemistry, University of East Anglia (UEA), Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Christopher Pickett
- Energy Materials Laboratory, School of
Chemistry, University of East Anglia (UEA), Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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12
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Cazade PA, Tran H, Bereau T, Das AK, Kläsi F, Hamm P, Meuwly M. Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study. J Chem Phys 2015; 142:212415. [DOI: 10.1063/1.4916630] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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Delor M, Sazanovich IV, Towrie M, Spall SJ, Keane T, Blake AJ, Wilson C, Meijer AJHM, Weinstein JA. Dynamics of Ground and Excited State Vibrational Relaxation and Energy Transfer in Transition Metal Carbonyls. J Phys Chem B 2014; 118:11781-91. [DOI: 10.1021/jp506326u] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milan Delor
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Igor V. Sazanovich
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, STFC, Chilton, Oxfordshire, OX11 0QX, U.K
| | - Michael Towrie
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, STFC, Chilton, Oxfordshire, OX11 0QX, U.K
| | - Steven J. Spall
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Theo Keane
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | | | - Claire Wilson
- School
of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
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14
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Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase. Nat Chem 2013; 5:174-81. [PMID: 23422558 PMCID: PMC3607437 DOI: 10.1038/nchem.1559] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/17/2012] [Indexed: 12/26/2022]
Abstract
The anti-AIDS drug rilpivirine undergoes conformational changes to bind HIV-1 reverse transcriptase (RT), which is an essential enzyme for the replication of HIV. These changes allow it to retain potency against mutations that otherwise would render the enzyme resistant. Here we report that water molecules play an essential role in this binding process. Femtosecond experiments and theory expose the molecular level dynamics of rilpivirine bound to HIV-1 RT. Two nitrile substituents, one on each arm of the drug, are used as vibrational probes of the structural dynamics within the binding pocket. Two-dimensional vibrational echo spectroscopy reveals that one nitrile group is unexpectedly hydrogen-bonded to a mobile water molecule, not identified in previous X-ray structures. Ultrafast nitrile-water dynamics are confirmed by simulations. A higher (1.51 Å) resolution X-ray structure also reveals a water-drug interaction network. Maintenance of a crucial anchoring hydrogen bond may help retain the potency of rilpivirine against pocket mutations despite the structural variations they cause.
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15
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King JT, Ross MR, Kubarych KJ. Water-Assisted Vibrational Relaxation of a Metal Carbonyl Complex Studied with Ultrafast 2D-IR. J Phys Chem B 2012; 116:3754-9. [DOI: 10.1021/jp2125747] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John T. King
- Department
of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan
48109, United States
| | - Matthew R. Ross
- Department
of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan
48109, United States
| | - Kevin J. Kubarych
- Department
of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan
48109, United States
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16
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Kania R, Frederix PWJM, Wright JA, Ulijn RV, Pickett CJ, Hunt NT. Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation. J Chem Phys 2012; 136:044521. [DOI: 10.1063/1.3679387] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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King JT, Anna JM, Kubarych KJ. Solvent-hindered intramolecular vibrational redistribution. Phys Chem Chem Phys 2011; 13:5579-83. [PMID: 21359345 DOI: 10.1039/c0cp02138e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations of Mn(2)(CO)(10) in a series of linear alcohols reveal that the rate of intramolecular vibrational redistribution among the terminal carbonyl stretches is dictated by the average number of hydrogen bonds formed between the solute and solvent. The presence of hydrogen bonds was found to hinder vibrational redistribution between eigenstates, while leaving the overall T(1) relaxation rate unchanged.
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Affiliation(s)
- John T King
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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18
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King JT, Baiz CR, Kubarych KJ. Solvent-dependent spectral diffusion in a hydrogen bonded "vibrational aggregate". J Phys Chem A 2011; 114:10590-604. [PMID: 20831231 DOI: 10.1021/jp106142u] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two-dimensional infrared spectroscopy (2DIR) is used to measure the viscosity-dependent spectral diffusion of a model vibrational probe, Mn(2)(CO)(10) (dimanganese decacarbonyl, DMDC), in a series of alcohols with time scales ranging from 2.67 ps in methanol to 5.33 ps in 1-hexanol. Alcohol-alkane solvent mixtures were found to produce indistinguishable linear IR spectra, while still demonstrating viscosity-dependent spectral diffusion. Using a vibrational exciton model to characterize the inhomogeneous energy landscape, several analogies emerge with multichromophoric electronic systems, such as J-aggregates and light-harvesting protein complexes. An excitonic, local vibrational mode Hamiltonian parametrized to reproduce the vibrational structure of DMDC serves as a starting point from which site energies (i.e., local carbonyl frequencies) are given Gaussian distributed disorder. The model gives excellent agreement with both the linear IR spectrum and the inhomogeneous widths extracted from 2DIR, indicating the system can be considered to be a "vibrational aggregate." This model naturally leads to exchange narrowing due to disorder-induced exciton localization, producing line widths consistent with our 1D and 2D measurements. Further, the diagonal disorder alone effectively reduces the molecular symmetry, leading to the appearance of Raman bands in the IR spectrum in accord with the measurements. Here, we show that the static inhomogeneity of the excitonic model with disorder successfully captures the essential details of the 1D spectrum while predicting the degree of IR activity of forbidden modes as well as the inhomogeneous widths and relative magnitudes of the transition moments.
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Affiliation(s)
- John T King
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
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19
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Kaziannis S, Wright JA, Candelaresi M, Kania R, Greetham GM, Parker AW, Pickett CJ, Hunt NT. The role of CN and CO ligands in the vibrational relaxation dynamics of model compounds of the [FeFe]-hydrogenase enzyme. Phys Chem Chem Phys 2011; 13:10295-305. [DOI: 10.1039/c1cp20589g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tayama J, Ishihara A, Banno M, Ohta K, Saito S, Tominaga K. Temperature dependence of vibrational frequency fluctuation of N(3) (-) in D(2)O. J Chem Phys 2010; 133:014505. [PMID: 20614974 DOI: 10.1063/1.3428672] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have studied the temperature dependence of the vibrational frequency fluctuation of the antisymmetric stretching mode of N(3) (-) in D(2)O by three-pulse infrared (IR) photon echo experiments. IR pump-probe measurements were also carried out to investigate the population relaxation and the orientational relaxation of the same band. It was found that the time-correlation function (TCF) of the frequency fluctuation of this mode is well described by a biexponential function with a quasistatic term. The faster decay component has a time constant of about 0.1 ps, and the slower component varies from 1.4 to 1.1 ps in the temperature range from 283 to 353 K. This result indicates that liquid dynamics related to the frequency fluctuation are not highly sensitive to temperature. We discuss the relationship between the temperature dependence of the vibrational frequency fluctuation and that of the molecular motion of the system to investigate the molecular origin of the frequency fluctuation of the solute. We compare the temperature dependence of the frequency fluctuation with that of other dynamics such as dielectric relaxation of water. In contrast to the Debye dielectric relaxation time of D(2)O, the two time constants of the TCF of the frequency fluctuation do not exhibit strong temperature dependence. We propose a simple theoretical model for the frequency fluctuation in solutions based on perturbation theory and the dipole-dipole interaction between the vibrational mode of the solute and the solvent molecules. This model suggests that the neighboring solvent molecules in the vicinity of the solute play an important role in the frequency fluctuation. We suggest that the picosecond component of the frequency fluctuation results from structural fluctuation of the hydrogen-bonding network in water.
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Affiliation(s)
- Jumpei Tayama
- Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
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Stewart AI, Wright JA, Greetham GM, Kaziannis S, Santabarbara S, Towrie M, Parker AW, Pickett CJ, Hunt NT. Determination of the Photolysis Products of [FeFe]Hydrogenase Enzyme Model Systems using Ultrafast Multidimensional Infrared Spectroscopy. Inorg Chem 2010; 49:9563-73. [DOI: 10.1021/ic101289s] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew I. Stewart
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, U.K
| | - Joseph A. Wright
- School of Chemical Sciences, University of East Anglia, Norwich, U.K
| | - Gregory M. Greetham
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot, Oxon, U.K
| | - Spiridon Kaziannis
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, U.K
| | - Stefano Santabarbara
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, U.K
| | - Michael Towrie
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot, Oxon, U.K
| | - Anthony W. Parker
- Central Laser Facility, STFC Rutherford Appleton Laboratory, Didcot, Oxon, U.K
| | | | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, U.K
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Kania R, Stewart AI, Clark IP, Greetham GM, Parker AW, Towrie M, Hunt NT. Investigating the vibrational dynamics of a 17e−metallocarbonyl intermediate using ultrafast two dimensional infrared spectroscopy. Phys Chem Chem Phys 2010; 12:1051-63. [DOI: 10.1039/b919194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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