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Vinogradov I, Feng Y, Kumar SKK, Guo C, Udagawa NS, Ge NH. Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy. J Chem Phys 2021; 155:035102. [PMID: 34293882 DOI: 10.1063/5.0054428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.
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Affiliation(s)
- Ilya Vinogradov
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Yuan Feng
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - S K Karthick Kumar
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Chenxu Guo
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Nina Saki Udagawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
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2
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Chen X, Fulfer KD, Woodard KT, Kuroda DG. Structure and Dynamics of the Lithium-Ion Solvation Shell in Ureas. J Phys Chem B 2019; 123:9889-9898. [DOI: 10.1021/acs.jpcb.9b07623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kristen D. Fulfer
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Chemistry Program, Centre College, Danville, Kentucky 40422, United States
| | - Kaylee T. Woodard
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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3
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Leger JD, Varner C, Rubtsov IV. Multi-mode heterodyned 5th-order infrared spectroscopy. J Chem Phys 2016; 145:154201. [DOI: 10.1063/1.4963815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joel D. Leger
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Clyde Varner
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Igor V. Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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4
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Cui Y, Fulfer KD, Ma J, Weldeghiorghis TK, Kuroda DG. Solvation dynamics of an ionic probe in choline chloride-based deep eutectic solvents. Phys Chem Chem Phys 2016; 18:31471-31479. [DOI: 10.1039/c6cp06318g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Study of the solvation dynamics of an ionic probe in different choline-based deep eutectic solvents shows that the process is controlled by the motions of the choline ions within the pseudo lattice formed by the solvent.
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Affiliation(s)
- Y. Cui
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | - K. D. Fulfer
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | - J. Ma
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
| | | | - D. G. Kuroda
- Department of Chemistry
- Louisiana State University
- Baton Rouge
- USA
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5
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Rubtsova NI, Rubtsov IV. Vibrational energy transport in molecules studied by relaxation-assisted two-dimensional infrared spectroscopy. Annu Rev Phys Chem 2015; 66:717-38. [PMID: 25747112 DOI: 10.1146/annurev-physchem-040214-121337] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review presents an overview of the relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy method for measuring structures and energy transport dynamics in molecules. The method strongly enhances the range of accessible distances compared to traditional 2DIR and offers new structural reporters, such as the energy transport time, cross-peak amplification factors, and connectivity patterns. The use of the method for assigning vibrational modes with various levels of delocalization is illustrated. RA 2DIR relies on vibrational energy transport in molecules; as such, the transport mechanism can be conveniently studied by the method. Applications to identify diffusive and ballistic energy transport are demonstrated.
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Affiliation(s)
- Natalia I Rubtsova
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118;
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Leger JD, Nyby CM, Varner C, Tang J, Rubtsova NI, Yue Y, Kireev VV, Burtsev VD, Qasim LN, Rubtsov GI, Rubtsov IV. Fully automated dual-frequency three-pulse-echo 2DIR spectrometer accessing spectral range from 800 to 4000 wavenumbers. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:083109. [PMID: 25173248 DOI: 10.1063/1.4892480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel dual-frequency two-dimensional infrared instrument is designed and built that permits three-pulse heterodyned echo measurements of any cross-peak within a spectral range from 800 to 4000 cm(-1) to be performed in a fully automated fashion. The superior sensitivity of the instrument is achieved by a combination of spectral interferometry, phase cycling, and closed-loop phase stabilization accurate to ~70 as. The anharmonicity of smaller than 10(-4) cm(-1) was recorded for strong carbonyl stretching modes using 800 laser shot accumulations. The novel design of the phase stabilization scheme permits tuning polarizations of the mid-infrared (m-IR) pulses, thus supporting measurements of the angles between vibrational transition dipoles. The automatic frequency tuning is achieved by implementing beam direction stabilization schemes for each m-IR beam, providing better than 50 μrad beam stability, and novel scheme for setting the phase-matching geometry for the m-IR beams at the sample. The errors in the cross-peak amplitudes associated with imperfect phase matching conditions and alignment are found to be at the level of 20%. The instrument can be used by non-specialists in ultrafast spectroscopy.
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Affiliation(s)
- Joel D Leger
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Clara M Nyby
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Clyde Varner
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Jianan Tang
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Natalia I Rubtsova
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Yuankai Yue
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Victor V Kireev
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | | | - Layla N Qasim
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Grigory I Rubtsov
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312, Russian Federation
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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7
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Chuntonov L, Ma J. Quantum process tomography quantifies coherence transfer dynamics in vibrational exciton. J Phys Chem B 2013; 117:13631-8. [PMID: 24079417 DOI: 10.1021/jp4075493] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quantum coherence has been a subject of great interest in many scientific disciplines. However, detailed characterization of the quantum coherence in molecular systems, especially its transfer and relaxation mechanisms, still remains a major challenge. The difficulties arise in part because the spectroscopic signatures of the coherence transfer are typically overwhelmed by other excitation-relaxation processes. We use quantum process tomography (QPT) via two-dimensional infrared spectroscopy to quantify the rate of the elusive coherence transfer between two vibrational exciton states. QPT retrieves the dynamics of the dissipative quantum system directly from the experimental observables. It thus serves as an experimental alternative to theoretical models of the system-bath interaction and can be used to validate these theories. Our results for coupled carbonyl groups of a diketone molecule in chloroform, used as a benchmark system, reveal the nonsecular nature of the interaction between the exciton and the Markovian bath and open the door for the systematic studies of the dissipative quantum systems dynamics in detail.
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Affiliation(s)
- Lev Chuntonov
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania , Philadelphia, PA 19104, United States
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Kuroda DG, Abdo M, Chuntonov L, Smith AB, Hochstrasser RM. Vibrational dynamics of a non-degenerate ultrafast rotor: the (C12,C13)-oxalate ion. J Chem Phys 2013; 139:164514. [PMID: 24182056 PMCID: PMC3829914 DOI: 10.1063/1.4826137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/04/2013] [Indexed: 12/17/2022] Open
Abstract
Molecular ions undergoing ultrafast conformational changes on the same time scale of water motions are of significant importance in condensed phase dynamics. However, the characterization of systems with fast molecular motions has proven to be both experimentally and theoretically challenging. Here, we report the vibrational dynamics of the non-degenerate (C12,C13)-oxalate anion, an ultrafast rotor, in aqueous solution. The infrared absorption spectrum of the (C12,C13)-oxalate ion in solution reveals two vibrational transitions separated by approximately 40 cm(-1) in the 1500-1600 cm(-1) region. These two transitions are assigned to vibrational modes mainly localized in each of the carboxylate asymmetric stretch of the ion. Two-dimensional infrared spectra reveal the presence and growth of cross-peaks between these two transitions which are indicative of coupling and population transfer, respectively. A characteristic time of sub-picosecond cross-peaks growth is observed. Ultrafast pump-probe anisotropy studies reveal essentially the same characteristic time for the dipole reorientation. All the experimental data are well modeled in terms of a system undergoing ultrafast population transfer between localized states. Comparison of the experimental observations with simulations reveal a reasonable agreement, although a mechanism including only the fluctuations of the coupling caused by the changes in the dihedral angle of the rotor, is not sufficient to explain the observed ultrafast population transfer.
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Affiliation(s)
- Daniel G Kuroda
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Maekawa H, Sul S, Ge NH. Vibrational correlation between conjugated carbonyl and diazo modes studied by single- and dual-frequency two-dimensional infrared spectroscopy. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Chuntonov L, Kuroda DG, Ghosh A, Ma J, Hochstrasser RM. Quantum Beats and Coherence Decay in Degenerate States Split by Solvation. J Phys Chem Lett 2013; 4:1866-1871. [PMID: 23956817 PMCID: PMC3743118 DOI: 10.1021/jz400826a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Coherent dynamics of degenerate quantum states symmetry-broken on the femtosecond timescale is found to exhibit the phenomenon of quantum beats. Frequency-resolved and polarization-selective heterodyned transient grating spectroscopy enabled us to retrieve the oscillation pattern characteristic of the beating in systems undergoing ultrafast dynamical processes. This methodology applies to the general phenomena of coherence dynamics which is important in any ultrafast multidimensional spectroscopy. A particular application to the vibrational spectroscopy of coherence in the degenerate normal modes of the tricyanomethanide anion solvated in water is explored in this study. The relaxation of the cross-polarization transient grating anisotropy is shown to reflect the loss of the vibrational coherence, which is caused by ultrafast dynamics of the water solvation shell.
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Affiliation(s)
- Lev Chuntonov
- Corresponding author, , phone: 215-898-8247, fax: 215-898-0590
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Han C, Zhao J, Yang F, Wang J. Structural Dynamics of N-Propionyl-d-glucosamine Probed by Infrared Spectroscopies and Ab Initio Computations. J Phys Chem A 2013; 117:6105-15. [DOI: 10.1021/jp400096a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chen Han
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
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