1
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Amadei A, Aschi M. On the Statistical Regime, Coherence versus Incoherence and Ergodicity of Quantum Vibrational Trajectories in Soft Condensed Molecular Systems. Chemphyschem 2024; 25:e202300969. [PMID: 38516958 DOI: 10.1002/cphc.202300969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Indexed: 03/23/2024]
Abstract
A theoretical-computational procedure, recently proposed for modelling Vibrational Energy Relaxation (VER) processes of a molecule (Quantum Center, QC) embedded in a complex atomic-molecular system, is extended and applied for analyzing in detail the features of the QC density matrix (DM) temporal evolution. The results, obtained using aqueous azide ion as a case study, show the total lack of coherence in the DM, when the system is prepared to be initially in a pure vibrational eigenstate. This finding is fully in line with the statistical interpretation of the process typically adopted also in the experimental studies where the relaxation processes are all described within the typical schemes of chemical kinetics. Consistently, when the initial vibrational state corresponds to an eigenstate mixture, although initially coherent, the DM relaxes to a fully incoherent condition with a mean lifetime related to the one of the diagonal elements relaxation. These specific DM features turn out to be essentially governed by the thermal equilibrium condition of the atomic-molecular classical coordinates which drive the ensemble of the quantum-trajectories toward the observed statistical regime. Finally, from the analysis of a single long timescale quantum vibrational trajectory it also clearly emerges its ergodic behaviour.
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Affiliation(s)
- Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133, Roma, Italy
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università dell'Aquila, Via Vetoio s.n.c., 67100, L'Aquila, Italy
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2
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Stemo G, Nishiuchi J, Bhakta H, Mao H, Wiesehan G, Xiong W, Katsuki H. Ultrafast Spectroscopy under Vibrational Strong Coupling in Diphenylphosphoryl Azide. J Phys Chem A 2024; 128:1817-1824. [PMID: 38437187 PMCID: PMC10945483 DOI: 10.1021/acs.jpca.3c07847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024]
Abstract
Strong coupling of cavity photons and molecular vibrations creates vibrational polaritons that have been shown to modify chemical reactivity and alter material properties. While ultrafast spectroscopy of vibrational polaritons has been performed intensively in metal complexes, ultrafast dynamics in vibrationally strongly coupled organic molecules remain unexplored. Here, we report ultrafast pump-probe measurement and two-dimensional infrared spectroscopy in diphenylphosphoryl azide under vibrational strong coupling. Early time oscillatory structures indicate coherent energy exchange between the two polariton modes, which decays in ∼2 ps. We observe a large transient absorptive feature around the lower polariton, which can be explained by the overlapped excited-state absorption and derivative-shaped structures around the lower and upper polaritons. The latter feature is explained by the Rabi splitting contraction, which is ascribed to a reduced population in the ground state. These results reassure the previously reported spectroscopic theory to describe nonlinear spectroscopy of vibrational polaritons. We have also noticed the influence of the complicated layer structure of the cavity mirrors. The penetration of the electric field distribution into the layered structure of the dielectric-mirror cavities can significantly affect the Rabi splitting and the decay time constant of polaritonic systems.
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Affiliation(s)
- Garrek Stemo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Joel Nishiuchi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Harsh Bhakta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Haochuan Mao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Garret Wiesehan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Wei Xiong
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Hiroyuki Katsuki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
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3
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Islam MM, Nawagamuwage SU, Parshin IV, Richard MC, Burin AL, Rubtsov IV. Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy. J Am Chem Soc 2023; 145:26363-26373. [PMID: 37982703 DOI: 10.1021/jacs.3c10178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an azido moiety and a cyano or carboxylic acid moiety, connected by an alkyl chain of different lengths, was synthesized. FTIR data and molecular dynamics calculations indicated that the test compounds in a bilayer are oriented so that the cyano or carboxylic acid moiety is located in the lipid head-group region, while the azido group stays inside the bilayer at the depth determined by its alkyl chain length. We found that the asymmetric stretching mode of the azido group (νN3) can serve as a reporter of the membrane interior dynamics. FTIR and two-dimensional infrared (2DIR) studies were performed at different temperatures, ranging from 22 to 45 °C, covering the Lβ-Lα phase transition temperature of dipalmitoylphosphatidylcholine (∼41 °C). The width of the νN3 peak was found to be very sensitive to the phase transition and to the temperature in general. We introduced an order parameter, SN3, which characterizes restrictions to motion inside the bilayer. 2DIR spectra of νN3 showed different extents of inhomogeneity at different depths in the bilayer, with the smallest inhomogeneity in the middle of the leaflet. The spectral diffusion dynamics of the N3 peak was found to be dependent on the depth of the N3 group location in the bilayer. The obtained results enhance our understanding of the bilayer dynamics and can be extended to investigate membranes with more complex compositions.
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Affiliation(s)
- Md Muhaiminul Islam
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - Igor V Parshin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Margaret C Richard
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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4
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Amadei A, Aschi M. Theoretical-Computational Modelling of the Vibrational Relaxation of Small Inorganic Species in Condensed Phase. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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5
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Abstract
The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN3) in lysozyme are characterized. It is found that AlaN3 is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ2 range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ0 ∼ 0 ps-1) or to a remaining, static contribution of ∼0.5 ps-1 (corresponding to 2.5 cm-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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6
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Patel K, Bittner ER. Mixed Quantum Classical Simulations of Charge-Transfer Dynamics in a Model Light-Harvesting Complex. II. Transient Vibrational Analysis. J Phys Chem B 2020; 124:2158-2167. [PMID: 32118439 DOI: 10.1021/acs.jpcb.0c00203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We perform dynamics simulations of donor-bridge-acceptor triads following photoexcitation and correlate nuclear motions with the charge-transfer event using the short-time Fourier transform technique. Broadly, the porphyrin bridges undergo higher energy vibrations, whereas the fullerene acceptors undergo low energy modes. Aryl side groups exhibit torsional motions relative to the porphyrin. Aryl linkers between the bridge and acceptor are restricted from such motions and therefore express ring distortion modes. Finally, we find an amide linker mode that is directionally sensitive to electron motion. This work supports the notion of vibrationally coupled ultrafast charge transfer found in both experimental and theoretical studies and lays a foundational method for identifying key vibrational modes for parametrizing future theoretical models.
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Affiliation(s)
- Kush Patel
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Eric R Bittner
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States.,Department of Physics, Durham University, South Road, Durham DH1 3LE, United Kingdom
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7
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Salehi SM, Koner D, Meuwly M. Vibrational Spectroscopy of N 3- in the Gas and Condensed Phase. J Phys Chem B 2019; 123:3282-3290. [PMID: 30830786 DOI: 10.1021/acs.jpcb.8b11430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Azido-derivatized amino acids are potentially useful, positionally resolved spectroscopic probes for studying the structural dynamics of proteins and macromolecules in solution. To this end, a computational model for the vibrational modes of N3- based on accurate electronic structure calculations and a reproducing kernel Hilbert space representation of the potential energy surface for the internal degrees of freedom is developed. Fully dimensional quantum bound state calculations yield the antisymmetric stretch vibration at 1974 cm-1 compared with 1986 cm-1 from experiment. This mode shifts by 64 cm-1 (from the frequency distribution) and 74 cm-1 (from the IR line shape) to the blue, respectively, compared with 61 cm-1 from experiment for N3- in water. The decay time of the frequency fluctuation correlation function is 1.1 ps, which is in good agreement with experiment (1.2-1.3 ps) and the full width at half maximum of the asymmetric stretch in solution is 18.5 cm-1 compared with 25.2 cm-1 from experiment. A computationally more efficient analysis based on instantaneous normal modes is shown to provide comparable, albeit somewhat less quantitative results compared to solving the three-dimensional Schrödinger equation for the fundamental vibrations.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - Debasish Koner
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - Markus Meuwly
- Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
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8
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Roy VP, Kubarych KJ. Interfacial Hydration Dynamics in Cationic Micelles Using 2D-IR and NMR. J Phys Chem B 2017; 121:9621-9630. [DOI: 10.1021/acs.jpcb.7b08225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ved Prakash Roy
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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9
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Jin GY, Kim YS. Phase-Resolved Heterodyne-Detected Transient Grating Enhances the Capabilities of 2D IR Echo Spectroscopy. J Phys Chem A 2017; 121:1007-1011. [DOI: 10.1021/acs.jpca.6b12713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Korea
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Korea
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10
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Modified relaxation dynamics and coherent energy exchange in coupled vibration-cavity polaritons. Nat Commun 2016; 7:13504. [PMID: 27874010 PMCID: PMC5121416 DOI: 10.1038/ncomms13504] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/10/2016] [Indexed: 11/08/2022] Open
Abstract
Coupling vibrational transitions to resonant optical modes creates vibrational polaritons shifted from the uncoupled molecular resonances and provides a convenient way to modify the energetics of molecular vibrations. This approach is a viable method to explore controlling chemical reactivity. In this work, we report pump–probe infrared spectroscopy of the cavity-coupled C–O stretching band of W(CO)6 and the direct measurement of the lifetime of a vibration-cavity polariton. The upper polariton relaxes 10 times more quickly than the uncoupled vibrational mode. Tuning the polariton energy changes the polariton transient spectra and relaxation times. We also observe quantum beats, so-called vacuum Rabi oscillations, between the upper and lower vibration-cavity polaritons. In addition to establishing that coupling to an optical cavity modifies the energy-transfer dynamics of the coupled molecules, this work points out the possibility of systematic and predictive modification of the excited-state kinetics of vibration-cavity polariton systems. Vibration-cavity polaritons are mixed states produced by strong coupling between a vibrational mode and an optical cavity. Here, the authors show that these polaritons can coherently exchange energy and exhibit drastically altered transient spectra and dynamics compared to uncoupled vibrations.
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11
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12
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Karmakar A, Chandra A. Ab initio molecular dynamics studies of hydrogen bonded structure, molecular motion, and frequency fluctuations of water in the vicinity of azide ions. J Chem Phys 2015; 142:164505. [DOI: 10.1063/1.4918579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Anwesa Karmakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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13
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Lee C, Nam D, Park S. Vibrational probing of the hydrogen-bond structure and dynamics of water in aqueous NaPF6 solutions. NEW J CHEM 2015. [DOI: 10.1039/c5nj00160a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The H-bond structures and dynamics of water in bulk and ionic hydration shells in aqueous NaPF6 solutions were measured at different NaPF6 concentrations.
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Affiliation(s)
- Chiho Lee
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
| | - Dayoung Nam
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
| | - Sungnam Park
- Department of Chemistry
- Korea University
- Seoul 136-701
- Korea
- Multidimensional Spectroscopy Laboratory
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14
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Czurlok D, von Domaros M, Thomas M, Gleim J, Lindner J, Kirchner B, Vöhringer P. Femtosecond 2DIR spectroscopy of the nitrile stretching vibration of thiocyanate anions in liquid-to-supercritical heavy water. Spectral diffusion and libration-induced hydrogen-bond dynamics. Phys Chem Chem Phys 2015; 17:29776-85. [DOI: 10.1039/c5cp05237h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Femtosecond two-dimensional infrared (2DIR) spectroscopy was carried out to study the dynamics of vibrational spectral diffusion of the nitrile stretching vibration of thiocyanate.
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Affiliation(s)
- Denis Czurlok
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Michael von Domaros
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Martin Thomas
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Jeannine Gleim
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Jörg Lindner
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Barbara Kirchner
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
| | - Peter Vöhringer
- Institut für Physikalische und Theoretische Chemie
- Rheinische Friedrich-Wilhelms-Universität
- 53115 Bonn
- Germany
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15
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Czurlok D, Gleim J, Lindner J, Vöhringer P. Vibrational Energy Relaxation of Thiocyanate Ions in Liquid-to-Supercritical Light and Heavy Water. A Fermi's Golden Rule Analysis. J Phys Chem Lett 2014; 5:3373-3379. [PMID: 26278447 DOI: 10.1021/jz501710c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The vibrational relaxation dynamics following an ultrafast nitrile stretching (ν3) excitation of thiocyanate anions dissolved in light and heavy water have been studied over a wide temperature and density range corresponding to the aqueous liquid up to the supercritical phase. In both solvents, the relaxation of the ν3 = 1 state of the anion leads to a direct recovery of the vibrational ground state and involves the resonant transfer of the excess vibrational energy onto the solvent. In light water, the energy-accepting states are provided by the bending-librational combination band (νb + νL), while in heavy water, the relaxation is thermally assisted by virtual acceptor states derived from the stretching-librational/restricted translational hot band (νS - νL,T). The relaxation rate is found to strictly obey Fermi's Golden Rule when the density of resonant solvent states is estimated from the linear infrared spectra of the solute and the pure solvents.
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Affiliation(s)
- Denis Czurlok
- Lehrstuhl für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Jeannine Gleim
- Lehrstuhl für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Jörg Lindner
- Lehrstuhl für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
| | - Peter Vöhringer
- Lehrstuhl für Molekulare Physikalische Chemie, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität, Wegelerstraße 12, 53115 Bonn, Germany
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16
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Shattuck JT, Schneck JR, Chieffo LR, Erramilli S, Ziegler LD. Dispersed Three-Pulse Infrared Photon Echoes of Nitrous Oxide in Water and Octanol. J Phys Chem B 2013; 117:15774-85. [DOI: 10.1021/jp4065533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J. T. Shattuck
- Department
of Chemistry and the Photonics Center, Boston University, 590 Commonwealth
Avenue, Boston, Massachusetts 02215, United States
| | - J. R. Schneck
- Department
of Chemistry and the Photonics Center, Boston University, 590 Commonwealth
Avenue, Boston, Massachusetts 02215, United States
| | - L. R. Chieffo
- Department
of Chemistry and the Photonics Center, Boston University, 590 Commonwealth
Avenue, Boston, Massachusetts 02215, United States
| | - S. Erramilli
- Department
of Physics and Department of Biomedical Engineering and the Photonics
Center, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - L. D. Ziegler
- Department
of Chemistry and the Photonics Center, Boston University, 590 Commonwealth
Avenue, Boston, Massachusetts 02215, United States
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17
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Compton R, Gerardi HK, Weidinger D, Brown DJ, Dressick WJ, Heilweil EJ, Owrutsky JC. Spectra and relaxation dynamics of the pseudohalide (PS) vibrational bands for Ru(bpy)2(PS)2 complexes, PS=CN, NCS and N3. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Guchhait B, Biswas R, Ghorai PK. Solute and Solvent Dynamics in Confined Equal-Sized Aqueous Environments of Charged and Neutral Reverse Micelles: A Combined Dynamic Fluorescence and All-Atom Molecular Dynamics Simulation Study. J Phys Chem B 2013; 117:3345-61. [DOI: 10.1021/jp310285k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Biswajit Guchhait
- Department
of Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt
Lake, Kolkata 700098, India
| | - Ranjit Biswas
- Department
of Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt
Lake, Kolkata 700098, India
| | - Pradip K. Ghorai
- Indian Institute of Science Education and Research, Kolkata, Mohanpur Campus, Nadia 741252,
India
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19
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Bian H, Li J, Zhang Q, Chen H, Zhuang W, Gao YQ, Zheng J. Ion Segregation in Aqueous Solutions. J Phys Chem B 2012. [DOI: 10.1021/jp310153n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Hongtao Bian
- Department
of Chemistry, Rice University, Houston,
Texas 77005, United States
| | - Jiebo Li
- Department
of Chemistry, Rice University, Houston,
Texas 77005, United States
| | - Qiang Zhang
- State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning,
People’s Republic of China
| | - Hailong Chen
- Department
of Chemistry, Rice University, Houston,
Texas 77005, United States
| | - Wei Zhuang
- State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning,
People’s Republic of China
| | - Yi Qin Gao
- College of Chemistry and Molecular
Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Junrong Zheng
- Department
of Chemistry, Rice University, Houston,
Texas 77005, United States
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20
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van der Loop TH, Panman MR, Lotze S, Zhang J, Vad T, Bakker HJ, Sager WFC, Woutersen S. Structure and dynamics of water in nonionic reverse micelles: A combined time-resolved infrared and small angle x-ray scattering study. J Chem Phys 2012; 137:044503. [DOI: 10.1063/1.4736562] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Correa NM, Silber JJ, Riter RE, Levinger NE. Nonaqueous Polar Solvents in Reverse Micelle Systems. Chem Rev 2012; 112:4569-602. [DOI: 10.1021/cr200254q] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Mariano Correa
- Departamento de Química, Universidad Nacional de Río Cuarto, Agencia
Postal #3, C.P. X5804BYA Río Cuarto, Argentina
| | - Juana J. Silber
- Departamento de Química, Universidad Nacional de Río Cuarto, Agencia
Postal #3, C.P. X5804BYA Río Cuarto, Argentina
| | - Ruth E. Riter
- Department of Chemistry, Agnes Scott College, Decatur, Georgia 30030-3770, United
States
| | - Nancy E. Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
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22
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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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23
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Ohta K, Tayama J, Tominaga K. Ultrafast vibrational dynamics of SCN− and N3− in polar solvents studied by nonlinear infrared spectroscopy. Phys Chem Chem Phys 2012; 14:10455-65. [DOI: 10.1039/c2cp40244k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Thielges MC, Axup JY, Wong D, Lee HS, Chung JK, Schultz PG, Fayer MD. Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand. J Phys Chem B 2011; 115:11294-304. [PMID: 21823631 PMCID: PMC3261801 DOI: 10.1021/jp206986v] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein.
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Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jun Y. Axup
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Daryl Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 121-742, Korea
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter G. Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Olschewski M, Knop S, Lindner J, Vöhringer P. Vibrational relaxation of azide ions in liquid-to-supercritical water. J Chem Phys 2011; 134:214504. [DOI: 10.1063/1.3598108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Houchins C, Weidinger D, Owrutsky JC. Vibrational Spectroscopy and Dynamics of the Hydrazoic and Isothiocyanic Acids in Water and Methanol. J Phys Chem A 2010; 114:6569-74. [DOI: 10.1021/jp102397b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Cassidy Houchins
- Chemistry Division, Code 6111, U.S. Naval Research Laboratory, Washington, D.C. 20375-5342
| | - Daniel Weidinger
- Chemistry Division, Code 6111, U.S. Naval Research Laboratory, Washington, D.C. 20375-5342
| | - Jeffrey C. Owrutsky
- Chemistry Division, Code 6111, U.S. Naval Research Laboratory, Washington, D.C. 20375-5342
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Abstract
Recent advances in ultrafast laser technology have spurred investigations of microheterogeneous solutions. In particular, researchers have explored details of reverse micelles (RMs), which present isolated droplets of polar solvent sequestered from a continuous nonpolar phase by a surfactant layer. This review explores recent studies utilizing a variety of ultrafast laser techniques to uncover details about structure and dynamics in various RMs. Using ultrafast vibrational spectroscopy, researchers have probed hydrogen-bond dynamics and vibrational energy relaxation in RMs. These studies have developed our understanding of reverse micellar structure, identifying varying water environments in the RMs. In a plethora of experiments employing probe molecules, researchers have explored the confined environment presented by RMs and their impact on a range of chemical reactions. These studies have shown that confinement, rather than the specific interactions with surfactants, is an important factor determining the impact of the reverse micellar environment on the chemistry.
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Affiliation(s)
- Nancy E Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA.
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Morales CM, Thompson WH. Simulations of Infrared Spectra of Nanoconfined Liquids: Acetonitrile Confined in Nanoscale, Hydrophilic Silica Pores. J Phys Chem A 2008; 113:1922-33. [DOI: 10.1021/jp8072969] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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Choi JH, Oh KI, Cho M. Azido-derivatized compounds as IR probes of local electrostatic environment: Theoretical studies. J Chem Phys 2008; 129:174512. [DOI: 10.1063/1.3001915] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Owrutsky JC, Pomfret MB, Barton DJ, Kidwell DA. Fourier transform infrared spectroscopy of azide and cyanate ion pairs in AOT reverse micelles. J Chem Phys 2008; 129:024513. [DOI: 10.1063/1.2952522] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Mitchell-Koch KR, Thompson WH. Infrared spectra of a model phenol-amine proton transfer complex in nanoconfined CH3Cl. J Phys Chem B 2008; 112:7448-59. [PMID: 18517239 DOI: 10.1021/jp076714e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The vibrational spectra of a model phenol-amine proton transfer complex dissolved in CH3Cl solvent confined in a 12 A radius spherical hydrophobic cavity were calculated using mixed quantum-classical molecular dynamics simulations. The reaction free energy of the proton transfer complex was varied in order to explore the contributions to the vibrational absorption band from product and reactant species. The vibrational spectra of the model proton transfer complex resulted in motionally narrowed spectral linewidths with two distinct peaks for products and reactants in cases where the system undergoes chemical exchange. It was found that the n=1 and n=2 vibrational excited states combine to form diabatic states such that the spectra have contributions from both n=0 --> n=1 and n=0 --> n=2 transitions. A strong relationship between the instantaneous vibrational frequency and a collective solvent coordinate was found that assists in understanding the origin of the spectral features.
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Banno M, Ohta K, Tominaga K. Ultrafast Dynamics of the Carbonyl Stretching Vibration in Acetic Acid in Aqueous Solution Studied by Sub-Picosecond Infrared Spectroscopy. J Phys Chem A 2008; 112:4170-5. [DOI: 10.1021/jp076920m] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Motohiro Banno
- Molecular Photoscience Research Center, Kobe University, Graduate School of Science and Technology, Kobe University, and CREST/JST, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Molecular Photoscience Research Center, Kobe University, Graduate School of Science and Technology, Kobe University, and CREST/JST, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Graduate School of Science and Technology, Kobe University, and CREST/JST, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
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Affiliation(s)
- H. J. Bakker
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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Lin YS, Ramesh SG, Shorb JM, Sibert EL, Skinner JL. Vibrational Energy Relaxation of the Bend Fundamental of Dilute Water in Liquid Chloroform and d-Chloroform. J Phys Chem B 2007; 112:390-8. [DOI: 10.1021/jp075682s] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Y.-S. Lin
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - S. G. Ramesh
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - J. M. Shorb
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - E. L. Sibert
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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39
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Li S, Schmidt JR, Piryatinski A, Lawrence CP, Skinner JL. Vibrational spectral diffusion of azide in water. J Phys Chem B 2007; 110:18933-8. [PMID: 16986886 DOI: 10.1021/jp057568k] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Vibrational spectral diffusion denotes the time-dependent fluctuations of a solute's vibrational frequencies due to local environmental dynamics. Vibrational line shapes are weakly sensitive to spectral diffusion, whereas three-pulse vibrational echoes are much more sensitive. We report here on theoretical studies of spectral diffusion of the asymmetric stretch of the azide anion in heavy water. We run a classical molecular dynamics simulation of rigid azide in rigid water, and at every time step we calculate the azide's anharmonic asymmetric stretch frequency using an optimized quantum mechanics/molecular mechanics method developed earlier. This generates a frequency trajectory, which we use to calculate the absorption line shape and integrated three-pulse echo intensity. Our results for both the line width and the integrated echo intensity are in excellent agreement with experiment. Our calculated frequency time-correlation function is in excellent agreement with experiment for long times (greater than 250 fs) but differs considerably from experiment at short times; our theoretical correlation function has a very pronounced oscillation, presumably due to intermolecular azide-water hydrogen-bond stretching dynamics.
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Affiliation(s)
- Shuzhou Li
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Li S, Schmidt JR, Corcelli SA, Lawrence CP, Skinner JL. Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters. J Chem Phys 2007; 124:204110. [PMID: 16774322 DOI: 10.1063/1.2200690] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ultrafast vibrational spectroscopy experiments, together with molecular-level theoretical interpretation, can provide important information about the structure and dynamics of complex condensed phase systems, including liquids. The theoretical challenge is to calculate the instantaneous vibrational frequencies of a molecule in contact with a molecular environment, accurately and quickly, and to this end a number of different methods have been developed. In this paper we critically analyze these different methods by comparing their results to accurate benchmark calculations on azide/water clusters. We also propose an optimized quantum mechanics/molecular mechanics method, which for this problem is superior to the other methods.
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Affiliation(s)
- Shuzhou Li
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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41
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Morales CM, Thompson WH. Mixed Quantum-Classical Molecular Dynamics Analysis of the Molecular-Level Mechanisms of Vibrational Frequency Shifts. J Phys Chem A 2007; 111:5422-33. [PMID: 17580980 DOI: 10.1021/jp071656i] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A detailed analysis of the origins of vibrational frequency shifts of diatomic molecules (I2 and ICl) in a rare gas (Xe) liquid is presented. Specifically, vibrationally adiabatic mixed quantum-classical molecular dynamics simulations are used to obtain the instantaneous frequency shifts and correlate the shifts to solvent configurations. With this approach, important mechanistic questions are addressed, including the following: How many solvent atoms determine the frequency shift? What solvent atom configurations lead to blue shifts, and which lead to red shifts? What is the effect of solute asymmetry? The mechanistic analysis can be generally applied and should be useful in understanding what information is provided by infrared and Raman spectra about the environment of the probed vibrational mode.
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Abstract
Vibrational lifetimes of the asymmetric stretch fundamental of azide anion in normal and heavy water have been measured experimentally, with results in the range of a few picoseconds. This is an interesting problem for theoretical study because of the competition between intramolecular (relaxation to the other excited vibrational states of azide) and purely intermolecular (relaxation to azide's ground vibrational state) pathways. In addition it is important to understand the origin of the solvent isotope effect. Building on the seminal work of Morita and Kato [J. Chem. Phys. 109, 5511 (1998)], the authors develop a simple model based on a two-dimensional description of the azide stretching vibrations. A novel aspect of their theory is the use of an "on-the-fly" optimized quantum mechanical/molecular mechanical approach to calculate the system-bath coupling. Their theoretical lifetimes are in good agreement with experiment for azide in both normal and heavy water. They find that the predominant relaxation pathway is intramolecular. The solvent isotope effect arises from the different librational frequencies in normal and heavy water.
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Affiliation(s)
- Shuzhou Li
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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43
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Sando GM, Dahl K, Owrutsky JC. Vibrational Spectroscopy and Dynamics of Azide Ion in Ionic Liquid and Dimethyl Sulfoxide Water Mixtures. J Phys Chem B 2007; 111:4901-9. [PMID: 17388412 DOI: 10.1021/jp067143d] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Steady-state and time-resolved infrared spectroscopy of the azide (N(3)-) anion has been used to characterize aqueous mixtures both with the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF(4)]) and with dimethyl sulfoxide (DMSO). In the DMSO-water mixtures, two anion vibrational bands are observed for low water mole fractions (0 > X(w) > 0.25), which indicates a heterogeneous ion solvation environment. The band at 2000 cm(-1) observed for neat DMSO does not shift but decreases in amplitude as the amount of water is increased. Another band appears at slightly higher frequency at low X(w) (=0.05). As the amount of water is increased, this band shifts to higher frequency and becomes stronger and is attributed to azide with an increasing degree of hydration. At intermediate and high X(w), a single band is observed that shifts almost linearly with water mole fraction toward the bulk water value. The heterogeneity is evident from the infrared pump-probe studies in which the decay times depend on probe frequency at low mole fraction. For the azide spectra in IL-water mixtures, a single azide band is observed for each mole fraction mixture. The azide band shifts almost linearly with mole fraction, indicating nearly ideal mixing behavior. As with the DMSO-water mixtures, the time-resolved IR decay times are probe-frequency-dependent at low mole fraction, again indicating heterogeneous solvation. In both the DMSO and IL mixtures with water, the relaxation times are slower than would be expected from ideal mixing, suggesting that vibrational relaxation of azide is more sensitive than its vibrational frequency to the solvent structure. The results are discussed in terms of preferential solvation and the degree to which the azide shift and vibrational relaxation depend on the degree of water association in the mixtures.
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Affiliation(s)
- Gerald M Sando
- U.S. Naval Research Laboratory, Washington, District of Columbia 20375-5342, USA
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Kwac K, Lee C, Jung Y, Han J, Kwak K, Zheng J, Fayer MD, Cho M. Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy. J Chem Phys 2006; 125:244508. [PMID: 17199356 DOI: 10.1063/1.2403132] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.
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Affiliation(s)
- Kijeong Kwac
- Department of Chemistry, Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea
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45
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Gulmen TS, Thompson WH. Testing a two-state model of nanoconfined liquids: conformational equilibrium of ethylene glycol in amorphous silica pores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:10919-23. [PMID: 17154565 DOI: 10.1021/la062285k] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Molecular dynamics simulations of the conformational equilibrium of ethylene glycol in roughly cylindrical nanoscale amorphous silica pores are presented and analyzed in the context of a two-state model of confined liquids. This model assumes that an observable property of a confined liquid can be decomposed into a weighted average arising from two subensembles with distinct physical attributes: molecules at the surface and molecules in the interior of the pore. It is further assumed that the molecules in the interior exhibit behavior that is indistinguishable from that of the bulk liquid. However, the present simulation results are not consistent with this two-state model. Neither the assumption of two distinct subensembles nor the assumption that the interior molecules possess bulk-like behavior is supported.
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Affiliation(s)
- Tolga S Gulmen
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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46
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Danielsson J, Meuwly M. Energetics and Dynamics in MbCN: CN--Vibrational Relaxation from Molecular Dynamics Simulations. J Phys Chem B 2006; 111:218-26. [PMID: 17201446 DOI: 10.1021/jp0662698] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide-heme complex is calculated. Two deep minima with a stabilization energy of approximately 50 kcal/mol corresponding to two different binding orientations (Fe-CN and Fe-NC) of the ligand are found. The Fe-CN conformation is favored over Fe-NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe-CN unit is developed that captures polarization and ligand-metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe-CN conformation with epsilon-protonation of His epsilon 64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.
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Affiliation(s)
- Jonas Danielsson
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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Sando GM, Zhong Q, Owrutsky JC. Vibrational and rotational dynamics of cyanoferrates in solution. J Chem Phys 2006; 121:2158-68. [PMID: 15260770 DOI: 10.1063/1.1767072] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Ultrafast infrared spectroscopy has been used to measure vibrational energy relaxation (VER) and reorientation (Tr) times for the high frequency vibrational bands of potassium ferrocyanide and ferricyanide (CN stretches), and sodium nitroprusside (SNP, CN, and NO stretches) in water and several other solvents. Relatively short VER times (4-43 ps) are determined for the hexacyano species and for the NO band of SNP, but the CN band of SNP relaxes much more slowly (55-365 ps). The solvent dependence of the VER times is similar for all the solutes and resembles what has been previously observed for triatomic molecular ions [Li et al., J. Chem. Phys. 98, 5499 (1993)]. Anisotropy decay times are also measured from the polarization dependence of the transient absorptions. The Tr times determined for SNP are different for the different vibrational bands; for the nondegenerate NO mode of nitroprusside (SNP) they are much longer (>15 ps), correlate with solvent viscosity, and are attributed to overall molecular rotation. The short Tr (<10 ps) times for the CN band in SNP and for the hexacyanoferrates are due to dipole orientational relaxation in which the transition moment rapidly redistributes among the degenerate modes. There is no evidence of intramolecular vibrational relaxation (IVR) to other high frequency modes. VER times measured for hexacarbonyls and SNP in methanol are similar, which suggests that the generally faster VER for the latter is in part because they are soluble in more strongly interacting polar solvents. The results are compared to those for small ions and metal carbonyls and are discussed in terms of the importance of solute charge and symmetry on VER.
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Affiliation(s)
- Gerald M Sando
- Code 6111, US Naval Research Laboratory, Washington, DC 20375-5342, USA
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48
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Ohta K, Tominaga K. Vibrational population relaxation of thiocyanate ion in polar solvents studied by ultrafast infrared spectroscopy. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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49
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Lenchenkov V, She C, Lian T. Vibrational Relaxation of CN Stretch of Pseudo-Halide Anions (OCN-, SCN-, and SeCN-) in Polar Solvents. J Phys Chem B 2006; 110:19990-7. [PMID: 17020387 DOI: 10.1021/jp062326l] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The vibrational relaxation dynamics of pseudo-halide anions XCN- (X = O, S, Se) in polar solvents were studied to understand the effect of charge on solute-to-solvent intermolecular energy transfer (IET) and solvent assisted intramolecular vibrational relaxation (IVR) pathways. The T1 relaxation times of the CN stretch in these anions were measured by IR pump/IR probe spectroscopy, in which the 0-1 transition was excited, and the 0-1 and 1-2 transitions were monitored to follow the recovery of the ground state and decay of the excited state. For these anions in five solvents, H2O, D2O, CH3OH, CH3CN, and (CH3)2SO, relaxation rates followed the trend of OCN- > SCN- > SeCN-. For these anions and isotopes of SCN-, the relaxation rate was a factor of a few (2.5-10) higher in H2O than in D2O. To further probe the solvent isotope effect, the relaxation rates of S12C14N-, S13C14N-, and S12C15N- in deuterated methanols (CH3OH, CH3OD, CH3OH, CD3OD) were compared. Relaxation rate was found to be affected by the change of solvent vibrational band at the CN- stretching mode (CD3 symmetric stretch) and lower frequency regions, suggesting the presence of both direct IET and solvent assisted IVR relaxation pathways. The possible relaxation pathways and mechanisms for the observed trends in solute and solvent dependence were discussed.
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Affiliation(s)
- Victor Lenchenkov
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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50
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Abstract
Solvated electrons have been generated in reverse micelles (RMs) through photodetachment of ferrocyanide (Fe(CN)(6)(4-)) in sodium bis(2-ethylhexyl) sulfosuccinate (AOT) RMs. We have measured both bleach recovery of the parent ferrocyanide CN stretch in the infrared and the decay of the solvated electron absorption at 800 nm. The bleach recovery has been fit to a diffusion model for the geminate recombination process. The fit parameters suggest a narrowing of the spatial distribution of ejected electrons due to confinement in the RMs when compared to bulk water. The diffusion coefficient of the solvated electron does not appear to be significantly affected by RM confinement. The decay of the solvated electron absorption exhibits an additional decay component that is not observed in bulk water and is smaller for larger RMs. No corresponding additional component is seen in the parent ferrocyanide IR bleach recovery, which supports our interpretation that the confinement-induced new decay process in RMs is due to electrons reacting with AOT headgroups.
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Affiliation(s)
- Gerald M Sando
- Code 6111, US Naval Research Laboratory, Washington D.C. 20375-5342, USA
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