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Buhrke D, Lahav Y, Rao A, Ruf J, Schapiro I, Hamm P. Transient 2D IR Spectroscopy and Multiscale Simulations Reveal Vibrational Couplings in the Cyanobacteriochrome Slr1393-g3. J Am Chem Soc 2023. [PMID: 37450891 DOI: 10.1021/jacs.3c00896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.
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Affiliation(s)
- David Buhrke
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
- Institute of Biology, Humboldt University Berlin, 10115 Berlin, Germany
| | - Yigal Lahav
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
- MIGAL - Galilee Research Institute, 1101602 Kiryat Shmona, Israel
| | - Aditya Rao
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Peter Hamm
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
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2
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Pios S, Domcke W. Ab Initio Electronic Structure Study of the Photoinduced Reduction of Carbon Dioxide with the Heptazinyl Radical. J Phys Chem A 2022; 126:2778-2787. [PMID: 35476421 DOI: 10.1021/acs.jpca.2c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photocatalytic conversion of carbon dioxide to liquid fuels with electrons taken from water with solar photons is one of the grand goals of renewable energy research. Polymeric carbon nitrides recently emerged as metal-free materials with promising functionalities for hydrogen evolution from water as well as the activation of carbon dioxide. Molecular heptazine (Hz), the building block of polymeric carbon nitrides, is one the strongest known organic photo-oxidants and has been shown to be able to photo-oxidize water with near-visible light, resulting in reduced (hydrogenated) heptazine (HzH) and OH radicals. In the present work, we explored with ab initio computational methods whether the HzH chromophore is able to reduce carbon dioxide to the hydroxy-formyl (HOCO) radical in hydrogen-bonded HzH-CO2 complexes by the absorption of a photon. In remarkable contrast to the high barrier for carbon dioxide activation in the electronic ground state, the excited-state proton-coupled electron transfer (PCET) reaction is nearly barrierless, but requires the diabatic passage of three conical intersections. The possibility of barrierless carbon dioxide activation by excited-state PCET has so far not been taken into consideration in the interpretation of photocatalytic carbon dioxide reduction on carbon nitride materials.
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Affiliation(s)
- Sebastian Pios
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
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3
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Tikhonov DS. A simplistic computational procedure for tunneling splittings caused by proton transfer. Struct Chem 2021. [DOI: 10.1007/s11224-021-01845-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractIn this manuscript, we present an approach for computing tunneling splittings for large amplitude motions. The core of the approach is a solution of an effective one-dimensional Schrödinger equation with an effective mass and an effective potential energy surface composed of electronic and harmonic zero-point vibrational energies of small amplitude motions in the molecule. The method has been shown to work in cases of three model motions: nitrogen inversion in ammonia, single proton transfer in malonaldehyde, and double proton transfer in the formic acid dimer. In the current work, we also investigate the performance of different DFT and post-Hartree–Fock methods for prediction of the proton transfer tunneling splittings, quality of the effective Schrödinger equation parameters upon the isotopic substitution, and possibility of a complete basis set (CBS) extrapolation for the resulting tunneling splittings.
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Domcke W, Sobolewski AL, Schlenker CW. Photooxidation of water with heptazine-based molecular photocatalysts: Insights from spectroscopy and computational chemistry. J Chem Phys 2020; 153:100902. [PMID: 32933269 DOI: 10.1063/5.0019984] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a conspectus of recent joint spectroscopic and computational studies that provided novel insight into the photochemistry of hydrogen-bonded complexes of the heptazine (Hz) chromophore with hydroxylic substrate molecules (water and phenol). It was found that a functionalized derivative of Hz, tri-anisole-heptazine (TAHz), can photooxidize water and phenol in a homogeneous photochemical reaction. This allows the exploration of the basic mechanisms of the proton-coupled electron-transfer (PCET) process involved in the water photooxidation reaction in well-defined complexes of chemically tunable molecular chromophores with chemically tunable substrate molecules. The unique properties of the excited electronic states of the Hz molecule and derivatives thereof are highlighted. The potential energy landscape relevant for the PCET reaction has been characterized by judicious computational studies. These data provided the basis for the demonstration of rational laser control of PCET reactions in TAHz-phenol complexes by pump-push-probe spectroscopy, which sheds light on the branching mechanisms occurring by the interaction of nonreactive locally excited states of the chromophore with reactive intermolecular charge-transfer states. Extrapolating from these results, we propose a general scenario that unravels the complex photoinduced water-splitting reaction into simple sequential light-driven one-electron redox reactions followed by simple dark radical-radical recombination reactions.
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Affiliation(s)
- Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | | | - Cody W Schlenker
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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5
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Durlak P, Latajka Z. Investigations of the hydrogen bond in the crystals of tropolone and thiotropolone via car‐parrinello and path integral molecular dynamics. J Comput Chem 2018; 40:671-687. [DOI: 10.1002/jcc.25753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Durlak
- Faculty of ChemistryUniversity of Wrocław Wrocław 50‐383 Poland
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6
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Durlak P, Latajka Z. Car–Parrinello and Path Integral Molecular Dynamics Study of the Proton Transfer in the Intramolecular Hydrogen Bonds in the Ketohydrazone–Azoenol System. J Phys Chem B 2018; 122:7862-7873. [DOI: 10.1021/acs.jpcb.8b04883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Durlak
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Zdzisław Latajka
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
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7
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Lin C, Kumar M, Finney BA, Francisco JS. Intramolecular hydrogen bonding in malonaldehyde and its radical analogues. J Chem Phys 2017; 147:124309. [PMID: 28964036 DOI: 10.1063/1.4996563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MARS, and cis-MARA, both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MARA, in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MARS, in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ* orbital of acceptor O-H bond (n → σ*OH). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MARS.
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Affiliation(s)
- Chen Lin
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Manoj Kumar
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0321, USA
| | - Brian A Finney
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Joseph S Francisco
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
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8
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Changing pictures of molecular faces and depths of potential acting on an electron in molecule for intramolecular proton transfer reactions of formic acid and malonaldehyde. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.05.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Mizukami W, Habershon S, Tew DP. A compact and accurate semi-global potential energy surface for malonaldehyde from constrained least squares regression. J Chem Phys 2014; 141:144310. [DOI: 10.1063/1.4897486] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wataru Mizukami
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - David P. Tew
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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10
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Durlak P, Mierzwicki K, Latajka Z. Investigations of the Very Short Hydrogen Bond in the Crystal of Nitromalonamide via Car–Parrinello and Path Integral Molecular Dynamics. J Phys Chem B 2013; 117:5430-40. [DOI: 10.1021/jp312473b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Durlak
- Faculty
of Chemistry, University of Wrocław,
14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Krzysztof Mierzwicki
- Faculty
of Chemistry, University of Wrocław,
14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Zdzisław Latajka
- Faculty
of Chemistry, University of Wrocław,
14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
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11
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Affiliation(s)
- Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich , Zürich, Switzerland
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, Germany
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12
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Greve C, Preketes NK, Fidder H, Costard R, Koeppe B, Heisler IA, Mukamel S, Temps F, Nibbering ETJ, Elsaesser T. N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics. J Phys Chem A 2013; 117:594-606. [PMID: 23234439 DOI: 10.1021/jp310177e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.
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Affiliation(s)
- Christian Greve
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
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13
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Hamm P, Stock G. Vibrational conical intersections as a mechanism of ultrafast vibrational relaxation. PHYSICAL REVIEW LETTERS 2012; 109:173201. [PMID: 23215183 DOI: 10.1103/physrevlett.109.173201] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Indexed: 06/01/2023]
Abstract
Presenting true crossings of adiabatic potential energy surfaces, conical intersections are a paradigm of ultrafast and efficient electronic relaxation dynamics. The same mechanism is shown to apply also for vibrational conical intersections, which may occur when two high-frequency modes (such as OH stretch vibrations) are coupled to low-frequency modes (such as hydrogen bonding modes). By derivation of a model Hamiltonian and its parametrization for a concrete example, malonaldehyde, the conditions that such conical intersections occur are identified and the consequences for the vibrational dynamics and spectra are demonstrated.
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Affiliation(s)
- Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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14
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Greve C, Preketes NK, Costard R, Koeppe B, Fidder H, Nibbering ETJ, Temps F, Mukamel S, Elsaesser T. N-H stretching modes of adenosine monomer in solution studied by ultrafast nonlinear infrared spectroscopy and ab initio calculations. J Phys Chem A 2012; 116:7636-44. [PMID: 22724894 PMCID: PMC3441835 DOI: 10.1021/jp303864m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N-H stretching vibrations of adenine, one of the building blocks of DNA, are studied by combining infrared absorption and nonlinear two-dimensional infrared spectroscopy with ab initio calculations. We determine diagonal and off-diagonal anharmonicities of N-H stretching vibrations in chemically modified adenosine monomer dissolved in chloroform. For the single-quantum excitation manifold, the normal mode picture with symmetric and asymmetric NH(2) stretching vibrations is fully appropriate. For the two-quantum excitation manifold, however, the interplay between intermode coupling and frequency shifts due to a large diagonal anharmonicity leads to a situation where strong mixing does not occur. We compare our findings with previously reported values obtained on overtone spectroscopy of coupled hydrogen stretching oscillators.
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Affiliation(s)
- Christian Greve
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2 A, D-12489 Berlin, Germany
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15
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Terranova ZL, Corcelli SA. Monitoring Intramolecular Proton Transfer with Two-Dimensional Infrared Spectroscopy: A Computational Prediction. J Phys Chem Lett 2012; 3:1842-1846. [PMID: 26291870 DOI: 10.1021/jz300714t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proton transfer processes are ubiquitous and play a vital role in a broad range of chemical and biochemical phenomena. The ability of two-dimensional infrared (2D IR) spectroscopy with a carbon-deuterium (C-D) reporter to monitor the kinetics of proton transfer in the model compound malonaldehyde was demonstrated computationally. One of the two carbonyl/enol carbon atoms in malonaldehyde was labeled with a C-D bond. The C-D stretch vibrational frequency provides ∼150 cm(-1) of sensitivity to the two tautomers of malonaldehyde. Mixed quantum mechanics/molecular mechanics simulations employing the self-consistent-charge density functional tight binding (SCC-DFTB) method were used to compute 2D IR line shapes for the C-D stretch of labeled malonaldehyde in aqueous solution. The 2D IR spectra reveal cross peaks from the chemical exchange of the proton. The kinetics for the growth of the cross-peaks (and the decay of the diagonal peaks) precisely match the proton transfer rate observed in the SCC-DFTB simulations.
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Affiliation(s)
- Z L Terranova
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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16
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Hanna G, Geva E. Computational study of the signature of hydrogen-bond strength on the infrared spectra of a hydrogen-bonded complex dissolved in a polar liquid. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Lüttschwager NOB, Wassermann TN, Coussan S, Suhm MA. Periodic bond breaking and making in the electronic ground state on a sub-picosecond timescale: OH bending spectroscopy of malonaldehyde in the frequency domain at low temperature. Phys Chem Chem Phys 2010; 12:8201-7. [DOI: 10.1039/c002345k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Baiz CR, McRobbie PL, Anna JM, Geva E, Kubarych KJ. Two-dimensional infrared spectroscopy of metal carbonyls. Acc Chem Res 2009; 42:1395-404. [PMID: 19453102 DOI: 10.1021/ar9000263] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Metal carbonyl complexes offer both rich chemistry and complex vibrational spectroscopy due to strong coupling among the carbonyl stretches. Using two-dimensional infrared (2DIR) spectroscopy, it is possible to resolve the underlying transitions between vibrational energy levels, determine the orientations and relative magnitude of the corresponding transition dipole moments, measure the coupling between modes due to the anharmonicity of the potential, and probe energy redistribution among the modes as well as energy relaxation to other degrees of freedom. Measurements on metal carbonyl complexes have played, and continue to play, a crucial role in facilitating the development of 2DIR spectroscopy. These compounds have provided powerful demonstrations of the unique ability of 2DIR spectroscopy to resolve vibrational structure and dynamics in multimode systems. In addition, invaluable new information has been obtained on metal-to-ligand charge transfer processes, solvent-solute interactions and fluxionality. Since transition metal complexes play important roles in catalysis and as dye sensitizers for semiconductor nanoparticle photocatalysis, detailed probes of equilibrium and phototriggered dynamics should aid our understanding of these key catalytic systems. The richness and level of detail provided by the 2DIR spectra of metal carbonyl complexes turn them into extremely useful model systems for testing the accuracy of ab initio quantum chemical calculations. Accurate modeling of the 2DIR spectra of solvated metal carbonyl complexes requires the development of new theoretical and computational tools beyond those employed in the standard analysis of one-dimensional IR spectra, and represents an ongoing challenge to currently available computational methodologies. These challenges are further compounded by the increasing interest in triggered 2DIR experiments that involve nonequilibrium vibrational dynamics on multiple electronic potential surfaces. In this Account, we review the various metal carbonyl complexes studied via 2DIR spectroscopy and outline the theoretical approaches used in order to model the spectra. The capabilities of 2DIR spectroscopy and its interplay with modern ab initio calculations are demonstrated in the context of the metal carbonyl complex Mn(2)(CO)(10) recently studied in our lab. Continued progress in experimental implementation and theoretical analysis will enable transient 2D spectroscopy to provide structurally sensitive details of complex, highly interacting nonequilibrium processes that are central to diverse chemical transformations.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | | | - Jessica M. Anna
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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19
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Baiz CR, McRobbie PL, Preketes NK, Kubarych KJ, Geva E. Two-Dimensional Infrared Spectroscopy of Dimanganese Decacarbonyl and Its Photoproducts: An Ab Initio Study. J Phys Chem A 2009; 113:9617-23. [DOI: 10.1021/jp9054654] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | | | | | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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20
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Hanna G, Geva E. Multidimensional Spectra via the Mixed Quantum-Classical Liouville Method: Signatures of Nonequilibrium Dynamics. J Phys Chem B 2009; 113:9278-88. [DOI: 10.1021/jp902797z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Hanna
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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21
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Petković M, Novak J, Došlić N. Shaping the infrared spectrum of the acetic acid dimer in the OH-stretching range: Multiple conformers and anharmonic coupling. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Paarmann A, Hayashi T, Mukamel S, Miller RJD. Nonlinear response of vibrational excitons: simulating the two-dimensional infrared spectrum of liquid water. J Chem Phys 2009; 130:204110. [PMID: 19485440 PMCID: PMC2719475 DOI: 10.1063/1.3139003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 04/28/2009] [Indexed: 11/15/2022] Open
Abstract
A simulation formalism for the nonlinear response of vibrational excitons is presented and applied to the OH stretching vibrations of neat liquid H(2)O. The method employs numerical integration of the Schrodinger equation and allows explicit treatment of fluctuating transition frequencies, vibrational couplings, dipole moments, and the anharmonicities of all these quantities, as well as nonadiabatic effects. The split operator technique greatly increases computational feasibility and performance. The electrostatic map for the OH stretching vibrations in liquid water employed in our previous study [A. Paarmann et al., J. Chem. Phys. 128, 191103 (2008)] is presented. The two-dimensional spectra are in close agreement with experiment. The fast 100 fs dynamics are primarily attributed to intramolecular mixing between states in the two-dimensional OH stretching potential. Small intermolecular couplings are sufficient to reproduce the experimental energy transfer time scales. Interference effects between Liouville pathways in excitonic systems and their impact on the analysis of the nonlinear response are discussed.
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Affiliation(s)
- A Paarmann
- Department of Physics and Institute for Optical Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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23
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Zhuang W, Hayashi T, Mukamel S. Kohärente mehrdimensionale Schwingungsspektroskopie von Biomolekülen: Konzepte, Simulationen und Herausforderungen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200802644] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Zhuang W, Hayashi T, Mukamel S. Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges. Angew Chem Int Ed Engl 2009; 48:3750-81. [PMID: 19415637 PMCID: PMC3526115 DOI: 10.1002/anie.200802644] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The response of complex molecules to sequences of femtosecond infrared pulses provides a unique window into their structure, dynamics, and fluctuating environments. Herein we survey the basic principles of modern two-dimensional infrared (2DIR) spectroscopy, which analogous to those of multidimensional NMR spectroscopy. The perturbative approach for computing the nonlinear optical response of coupled localized chromophores is introduced and applied to the amide backbone transitions of proteins, liquid water, membrane lipids, and amyloid fibrils. The signals are analyzed using classical molecular dynamics simulations combined with an effective fluctuating Hamiltonian for coupled localized anharmonic vibrations whose dependence on the local electrostatic environment is parameterized by an ab initio map. Several simulation methods, (cumulant expansion of Gaussian fluctuation, quasiparticle scattering, the stochastic Liouville equations, direct numerical propagation) are surveyed. Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen-bonding fluctuations, protein folding, and chemical-exchange processes are discussed.
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Affiliation(s)
- Wei Zhuang
- Department of Chemistry, University of California at Irvine, CA 92697-2025, USA
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25
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Hanna G, Geva E. Computational Study of the One and Two Dimensional Infrared Spectra of a Vibrational Mode Strongly Coupled to Its Environment: Beyond the Cumulant and Condon Approximations. J Phys Chem B 2008; 112:12991-3004. [DOI: 10.1021/jp804120v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Hanna
- Department of Chemistry and FOCUS center, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Eitan Geva
- Department of Chemistry and FOCUS center, University of Michigan, Ann Arbor, Michigan 48109-1055
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26
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Yamaguchi S, Banno M, Ohta K, Tominaga K, Hayashi T. Vibrational dynamics of benzoic acid in nonpolar solvents studied by subpicosecond infrared pump–probe spectroscopy. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Kikuta Y, Ishimoto T, Nagashima U. Geometrical and Kinetic Isotope Effects on R–H(D)···R Type Intramolecular Hydrogen Bonds (R = CH2, NH, and O) Using a Multi-Component Molecular Orbital Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.820] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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28
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Stare J, Panek J, Eckert J, Grdadolnik J, Mavri J, Hadži D. Proton Dynamics in the Strong Chelate Hydrogen Bond of Crystalline Picolinic Acid N-Oxide. A New Computational Approach and Infrared, Raman and INS Study. J Phys Chem A 2008; 112:1576-86. [DOI: 10.1021/jp077107u] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Jarosław Panek
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Juergen Eckert
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Jože Grdadolnik
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Janez Mavri
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Dušan Hadži
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
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29
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Matanović I, Doslić N, Kühn O. Ground and asymmetric CO-stretch excited state tunneling splittings in the formic acid dimer. J Chem Phys 2007; 127:014309. [PMID: 17627348 DOI: 10.1063/1.2748048] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
There has been some controversy concerning the assignment of measured tunneling splittings for the formic acid dimer in the vibrational ground state and the asymmetric CO-stretching excited state. The discussion is intimately related to the question whether the fundamental excitation of the CO-vibration promotes or hinders tunneling. Here we will address this issue on the basis of a five-dimensional reaction space Hamiltonian which includes three large amplitude coordinates as well as two harmonic modes whose linear superposition reproduces the asymmetric CO-vibrational mode. Within density functional theory using the B3LYP functional together with a 6-311++G(3df,3pd) basis set we obtain a ground state tunneling splitting which is about 2.4 larger than the one for the CO-stretching excited state.
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Affiliation(s)
- I Matanović
- Department of Physical Chemistry, Rudjer Bosković Institute, 10000 Zagreb, Croatia
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30
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Hayashi T, Mukamel S. Vibrational-exciton couplings for the amide I, II, III, and A modes of peptides. J Phys Chem B 2007; 111:11032-46. [PMID: 17725341 DOI: 10.1021/jp070369b] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The couplings between all amide fundamentals and their overtones and combination vibrational states are calculated. Combined with the level energies reported previously (Hayashi, T.; Zhuang, W.; Mukamel, S. J. Phys. Chem. A 2005, 109, 9747), we obtain a complete effective vibrational Hamiltonian for the entire amide system. Couplings between neighboring peptide units are obtained using the anharmonic vibrational Hamiltonian of glycine dipeptide (GLDP) at the BPW91/6-31G(d,p) level. Electrostatic couplings between non-neighboring units are calculated by the fourth rank transition multipole coupling (TMC) expansion, including 1/R3 (dipole-dipole), 1/R4 (quadrupole-dipole), and 1/R5 (quadrupole-quadrupole and octapole-dipole) interactions. Exciton delocalization length and its variation with frequency in the various amide bands are calculated. The simulated infrared amide I and II absorptions and CD spectra of 24 residue alpha-helical motifs (SPE3) are in good agreement with experiment.
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Affiliation(s)
- Tomoyuki Hayashi
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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31
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Dreyer J. Unraveling the structure of hydrogen bond stretching mode infrared absorption bands: An anharmonic density functional theory study on 7-azaindole dimers. J Chem Phys 2007; 127:054309. [PMID: 17688342 DOI: 10.1063/1.2759213] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The structure of the linear infrared absorption spectrum of the N-H stretching mode in 7-azaindole dimers is analyzed by quartic anharmonic vibrational force field calculations based on density functional theory. It is demonstrated that a multiple Fermi resonance model including contributions from 12 fingerprint vibrational modes, most of them containing considerable contributions of N-H bending motions, combined with a single low-frequency mode satisfactorily explains the complex line shape of N-H stretching mode absorption band.
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Affiliation(s)
- Jens Dreyer
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2A, D-12489 Berlin, Germany.
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32
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Freitag MA, Pruden TL, Moody DR, Parker JT, Fallet M. On the Keto−Enol Tautomerization of Malonaldehyde: An Effective Fragment Potential Study. J Phys Chem A 2007; 111:1659-66. [PMID: 17298039 DOI: 10.1021/jp065979a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent studies have mapped the keto-enol tautomerization of malonaldehyde through a general transition structure that leads exclusively to the Z isomer of the enol. However, it will be shown that a competing general transition structure exists that leads to both the E and Z isomers of the enol at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels of theory. Both the RHF- and DFT-based effective fragment potential methods have been used to model solvation effects, and the results are compared with full ab initio calculations. It is found that two bridging water molecules with two discrete DFT-based effective fragment potential solvent waters at the MP2/6-31G(d,p) level of ab initio theory provides the most computationally effective model for solvent effects in this system. It is shown that the relative energies for this QM/MM model differ from the full MP2/6-31G(d,p) energies by an average absolute relative difference of 2.2 kcal mol-1 across the reaction path when the zero-point vibrational energy correction is included.
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Affiliation(s)
- Mark A Freitag
- Department of Chemistry, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA.
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33
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Viel A, Coutinho-Neto MD, Manthe U. The ground state tunneling splitting and the zero point energy of malonaldehyde: A quantum Monte Carlo determination. J Chem Phys 2007; 126:024308. [PMID: 17228955 DOI: 10.1063/1.2406074] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quantum dynamics calculations of the ground state tunneling splitting and of the zero point energy of malonaldehyde on the full dimensional potential energy surface proposed by Yagi et al. [J. Chem. Phys. 1154, 10647 (2001)] are reported. The exact diffusion Monte Carlo and the projection operator imaginary time spectral evolution methods are used to compute accurate benchmark results for this 21-dimensional ab initio potential energy surface. A tunneling splitting of 25.7+/-0.3 cm-1 is obtained, and the vibrational ground state energy is found to be 15 122+/-4 cm-1. Isotopic substitution of the tunneling hydrogen modifies the tunneling splitting down to 3.21+/-0.09 cm-1 and the vibrational ground state energy to 14 385+/-2 cm-1. The computed tunneling splittings are slightly higher than the experimental values as expected from the potential energy surface which slightly underestimates the barrier height, and they are slightly lower than the results from the instanton theory obtained using the same potential energy surface.
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Affiliation(s)
- Alexandra Viel
- Theoretische Chemie, TU München, Lichtenbergstrasse 4, D-85747 Garching, Germany.
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34
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Kozich V, Dreyer J, Ashihara S, Werncke W, Elsaesser T. Mode-selective O-H stretching relaxation in a hydrogen bond studied by ultrafast vibrational spectroscopy. J Chem Phys 2007; 125:074504. [PMID: 16942348 DOI: 10.1063/1.2219111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The ultrafast relaxation of the excited O-H stretching vibration is studied by ultrafast infrared-pump/infrared-probe and infrared-pump/Raman-probe spectroscopy. We demonstrate a 200 fs lifetime of the hydrogen-bonded O-H stretching mode in 2-(2'-hydroxy-5'-methyl-phenyl)benzotriazole (TINUVIN P). O-H stretching relaxation occurs through a few major channels that all involve combination and overtone bands of modes with considerable in-plane O-H bending character. In particular, the mode, which contains the largest O-H bending contribution, plays a prominent role for primary processes of intramolecular vibrational energy redistribution. Theoretical calculations of vibrational energy transfer rates based on a Fermi golden rule approach account for the experimental findings.
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Affiliation(s)
- Valeri Kozich
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2A, D-12489 Berlin, Germany
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35
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Coussan S, Ferro Y, Trivella A, Rajzmann M, Roubin P, Wieczorek R, Manca C, Piecuch P, Kowalski K, Włoch M, Kucharski SA, Musiał M. Experimental and Theoretical UV Characterizations of Acetylacetone and Its Isomers. J Phys Chem A 2006; 110:3920-6. [PMID: 16539413 DOI: 10.1021/jp056834r] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cryogenic matrix isolation experiments have allowed the measurement of the UV absorption spectra of the high-energy non-chelated isomers of acetylacetone, these isomers being produced by UV irradiation of the stable chelated form. Their identification has been done by coupling selective UV-induced isomerization, infrared spectroscopy, and harmonic vibrational frequency calculations using density functional theory. The relative energies of the chelated and non-chelated forms of acetylacetone in the S0 state have been obtained using density functional theory and coupled-cluster methods. For each isomer of acetylacetone, we have calculated the UV transition energies and dipole oscillator strengths using the excited-state coupled-cluster methods, including EOMCCSD (equation-of-motion coupled-cluster method with singles and doubles) and CR-EOMCCSD(T) (the completely renormalized EOMCC approach with singles, doubles, and non-iterative triples). For dipole-allowed transition energies, there is a very good agreement between experiment and theory. In particular, the CR-EOMCCSD(T) approach explains the blue shift in the electronic spectrum due to the formation of the non-chelated species after the UV irradiation of the chelated form of acetylacetone. Both experiment and CR-EOMCCSD(T) theory identify two among the seven non-chelated forms to be characterized by red-shifted UV transitions relative to the remaining five non-chelated isomers.
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Affiliation(s)
- S Coussan
- Laboratoire Physique des Interactions Ioniques et Moléculaires, UMR 6633, Université de Provence-CNRS, Centre St-Jérôme, 13397 Marseille Cedex 20, France.
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36
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Nagata Y, Tanimura Y. Two-dimensional Raman spectra of atomic solids and liquids. J Chem Phys 2006; 124:024508. [PMID: 16422612 DOI: 10.1063/1.2131053] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We calculate third- and fifth-order Raman spectra of simple atoms interacting through a soft-core potential by means of molecular-dynamics (MD) simulations. The total polarizability of molecules is treated by the dipole-induced dipole model. Two- and three-body correlation functions of the polarizability at various temperatures are evaluated from equilibrium MD simulations based on a stability matrix formulation. To analyze the processes involved in the spectroscopic measurements, we divide the fifth-order response functions into symmetric and antisymmetric integrated response functions; the symmetric one is written as a simple three-body correlation function, while the antisymmetric one depends on a stability matrix. This analysis leads to a better understanding of the time scales and molecular motions that govern the two-dimensional (2D) signal. The 2D Raman spectra show novel differences between the solid and liquid phases, which are associated with the decay rates of coherent motions. On the other hand, these differences are not observed in the linear Raman spectra.
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Affiliation(s)
- Yuki Nagata
- Department of Chemistry, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan.
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37
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Hermann JC, Ridder L, Höltje HD, Mulholland AJ. Molecular mechanisms of antibiotic resistance: QM/MM modelling of deacylation in a class A beta-lactamase. Org Biomol Chem 2005; 4:206-10. [PMID: 16391762 DOI: 10.1039/b512969a] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modelling of the first step of the deacylation reaction of benzylpenicillin in the E. coli TEM1 beta-lactamase (with B3LYP/6-31G + (d)//AM1-CHARMM22 quantum mechanics/molecular mechanics methods) shows that a mechanism in which Glu166 acts as the base to deprotonate a conserved water molecule is both energetically and structurally consistent with experimental data; the results may assist the design of new antibiotics and beta-lactamase inhibitors.
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38
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Hayashi T, Zhuang W, Mukamel S. Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA. J Phys Chem A 2005; 109:9747-59. [PMID: 16833288 DOI: 10.1021/jp052324l] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.
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Affiliation(s)
- Tomoyuki Hayashi
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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39
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Meyer * R, Ha TK. Rotational constants of malonaldehyde and isotopic species derived fromab initioresults. Mol Phys 2005. [DOI: 10.1080/00268970500126199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Giese K, Kühn O. The all-Cartesian reaction plane Hamiltonian: Formulation and application to the H-atom transfer in tropolone. J Chem Phys 2005; 123:054315. [PMID: 16108647 DOI: 10.1063/1.1978869] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work we present an all-Cartesian reaction surface approach, where the large amplitude coordinates span the so-called reaction plane, that is, the unique plane defined by the two minima and the saddle-point structure of an isomerization reaction. Orthogonal modes are treated within harmonic approximation which gives the total Hamiltonian an almost separable form that is suitable for multidimensional quantum dynamics calculations. The reaction plane Hamiltonian is constructed for the H-atom transfer in tropolone as an example for a system with an intramolecular O...H-O hydrogen bond. We find ground-state tunneling splittings of 3.5 and 0.16 cm(-1) for the normal and deuterated species, respectively. We calculated infrared-absorption spectra for a four-dimensional model focusing on the low-frequency region. Here, we identify a reaction mode which is closely connected to the tautomerization that is reflected in the increase of tunneling splitting to 18 cm(-1) upon excitation.
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Affiliation(s)
- Kai Giese
- Institut für Chemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany
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41
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Ishizaki A, Tanimura Y. Multidimensional vibrational spectroscopy for tunneling processes in a dissipative environment. J Chem Phys 2005; 123:014503. [PMID: 16035851 DOI: 10.1063/1.1906215] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Simulating tunneling processes as well as their observation are challenging problems for many areas. In this study, we consider a double-well potential system coupled to a heat bath with a linear-linear (LL) and square-linear (SL) system-bath interactions. The LL interaction leads to longitudinal (T1) and transversal (T2) homogeneous relaxations, whereas the SL interaction leads to the inhomogeneous dephasing (T2*) relaxation in the white noise limit with a rotating wave approximation. We discuss the dynamics of the double-well system under infrared (IR) laser excitations from a Gaussian-Markovian quantum Fokker-Planck equation approach, which was developed by generalizing Kubo's stochastic Liouville equation. Analytical expression of the Green function is obtained for a case of two-state-jump modulation by performing the Fourier-Laplace transformation. We then calculate a two-dimensional infrared signal, which is defined by the four-body correlation function of optical dipole, for various noise correlation time, system-bath coupling parameters, and temperatures. It is shown that the bath-induced vibrational excitation and relaxation dynamics between the tunneling splitting levels can be detected as the isolated off-diagonal peaks in the third-order two-dimensional infrared (2D-IR) spectroscopy for a specific phase matching condition. Furthermore, this spectroscopy also allows us to directly evaluate the rate constants for tunneling reactions, which relates to the coherence between the splitting levels; it can be regarded as a novel technique for measuring chemical reaction rates. We depict the change of reaction rates as a function of system-bath coupling strength and a temperature through the 2D-IR signal.
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Affiliation(s)
- Akihito Ishizaki
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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42
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Dreyer J. Hydrogen-bonded acetic acid dimers: Anharmonic coupling and linear infrared spectra studied with density-functional theory. J Chem Phys 2005; 122:184306. [PMID: 15918703 DOI: 10.1063/1.1891727] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Anharmonic vibrational force field calculations provide a quantitative understanding of the width and substructure of the linear IR-absorption spectrum of the O-H stretching mode in acetic acid dimers (CH3-COOH)2 and (CD3-COOH)2. Anharmonic coupling of the high-frequency upsilon(OH) mode to fingerprint and low-frequency modes is included resulting in 11- and 9-dimensional vibrational Hamiltonians. A sixth-order force field covering up to three-body interactions is used. Force constants are calculated by fitting one-dimensional potential-energy surfaces and a finite difference procedure applying density-functional theory [Becke 3 Lee-Yang-Parr 6-311+G(d,p)]. It is demonstrated that both anharmonic coupling to low-frequency modes as well as Fermi resonance coupling with fingerprint modes are important mechanisms explaining the line shape of the O-H stretching IR-absorption band in acetic acid dimers.
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Affiliation(s)
- Jens Dreyer
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2A, D-12489 Berlin, Germany.
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43
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Arasaki Y, Yamazaki K, Varella MTDN, Takatsuka K. Real-time observation of ground state proton transfer: a model study. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2004.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Matanović I, Doslić N. Infrared Spectroscopy of the Intramolecular Hydrogen Bond in Acethylacetone: A Computational Approach. J Phys Chem A 2005; 109:4185-94. [PMID: 16833744 DOI: 10.1021/jp044695s] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The intramolecular hydrogen bond in the enol-acethylacetone (ACAC) is investigated by performing reduced-dimensional quantum calculations. To analyze the shared proton vibrations, two sets of coordinates were employed: normal mode coordinates describing the motion in the vicinity of the most stable configuration, and internal coordinates accounting for the double minimum proton motion. It is proved that the extreme broadness of the OH-stretch band in ACAC is a consequence of the coexistence of two enol-ACAC structures: the global minimum and the transition state for rotation of the distal methyl group. Further, a ground-state tunneling splitting of 116 cm(-1) is found, and it is shown that the inclusion of the kinematic coupling is mandatory when treating large-amplitude proton motion. In the OH-stretch direction a splitting of 853 cm(-1) was predicted.
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Affiliation(s)
- I Matanović
- Department of Physical Chemistry, R. Bosković Institute, Bijenicka 54, 10000 Zagreb, Croatia
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45
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Hermann JC, Hensen C, Ridder L, Mulholland AJ, Höltje HD. Mechanisms of Antibiotic Resistance: QM/MM Modeling of the Acylation Reaction of a Class A β-Lactamase with Benzylpenicillin. J Am Chem Soc 2005; 127:4454-65. [PMID: 15783228 DOI: 10.1021/ja044210d] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms by which beta-lactamases destroy beta-lactam antibiotics is potentially vital in developing effective therapies to overcome bacterial antibiotic resistance. Class A beta-lactamases are the most important and common type of these enzymes. A key process in the reaction mechanism of class A beta-lactamases is the acylation of the active site serine by the antibiotic. We have modeled the complete mechanism of acylation with benzylpenicillin, using a combined quantum mechanical and molecular mechanical (QM/MM) method (B3LYP/6-31G+(d)//AM1-CHARMM22). All active site residues directly involved in the reaction, and the substrate, were treated at the QM level, with reaction energies calculated at the hybrid density functional (B3LYP/6-31+Gd) level. Structures and interactions with the protein were modeled by the AM1-CHARMM22 QM/MM approach. Alternative reaction coordinates and mechanisms have been tested by calculating a number of potential energy surfaces for each step of the acylation mechanism. The results support a mechanism in which Glu166 acts as the general base. Glu166 deprotonates an intervening conserved water molecule, which in turn activates Ser70 for nucleophilic attack on the antibiotic. This formation of the tetrahedral intermediate is calculated to have the highest barrier of the chemical steps in acylation. Subsequently, the acylenzyme is formed with Ser130 as the proton donor to the antibiotic thiazolidine ring, and Lys73 as a proton shuttle residue. The presented mechanism is both structurally and energetically consistent with experimental data. The QM/MM energy barrier (B3LYP/ 6-31G+(d)//AM1-CHARMM22) for the enzymatic reaction of 9 kcal mol(-1) is consistent with the experimental activation energy of about 12 kcal mol(-1). The effects of essential catalytic residues have been investigated by decomposition analysis. The results demonstrate the importance of the "oxyanion hole" in stabilizing the transition state and the tetrahedral intermediate. In addition, Asn132 and a number of charged residues in the active site have been identified as being central to the stabilizing effect of the enzyme. These results will be potentially useful in the development of stable beta-lactam antibiotics and for the design of new inhibitors.
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Affiliation(s)
- Johannes C Hermann
- Institut für Pharmazeutische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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46
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Hayashi T, la Cour Jansen T, Zhuang W, Mukamel S. Collective Solvent Coordinates for the Infrared Spectrum of HOD in D2O Based on an ab Initio Electrostatic Map. J Phys Chem A 2004; 109:64-82. [PMID: 16839090 DOI: 10.1021/jp046685x] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D(2)O solvent obtained from molecular dynamics simulations, we calculate the infrared absorption of the O-H stretch. The resulting solvent shift and infrared line shape for three force fields (TIP4P, SPC/E, and SW) are in good agreement with the experiment. A collective coordinate response for the solvent effect is constructed by identifying the main electrostatic field and gradient components contributing to the line shape. This allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations.
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Affiliation(s)
- Tomoyuki Hayashi
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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Hayashi T, Mukamel S. Infrared Signatures of Proton Transfer in Guanine·Cytosine and Adenine·Thymine Base Pairs: DFT Study. Isr J Chem 2004. [DOI: 10.1560/m6na-f16j-nvkn-llm9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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