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Bai Y, He J, Gao Y, Zhang M, Zhou D, Tang Y, Liu J, Bian H, Fang Y. Dynamics of Formamide-Water Mixtures Investigated by Linear and Nonlinear Infrared Spectroscopy. J Phys Chem B 2024. [PMID: 38417258 DOI: 10.1021/acs.jpcb.3c07850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Formamide (FA) exhibits complete miscibility with water, offering a simplified model for exploring the solvation dynamics of peptide linkages in biophysical processes. Its liquid state demonstrates a three-dimensional hydrogen bonding network akin to water, reflecting solvent-like behavior. Analyzing the microscopic structure and dynamics of FA-water mixtures is expected to provide crucial insights into hydrogen bonding dynamics─a key aspect of various biophysical phenomena. This study is focused on the dynamics of FA-water mixtures using linear and femtosecond infrared spectroscopies. By using the intrinsic OD stretch and extrinsic probe SCN-, the local vibrational behaviors across various FA-water compositions were systematically investigated. The vibrational relaxation of OD stretch revealed a negligible impact of FA addition on the vibrational lifetime of water molecules, underscoring the mixture's water-like behavior. However, the reorientational dynamics of OD stretch slowed with increasing FA mole fraction (XFA), plateauing beyond XFA > 0.5. This suggests a correlation between OD's reorientational time and the strength of the hydrogen bond network, likely tied to the solution's changing dielectric constant. Conversely, the vibrational relaxation dynamics of SCN- was strongly correlated with XFA, highlighting a competition between water and FA molecules in solvating SCN-. Moreover, a linear relationship between rising viscosity and the prolonged correlation time of SCN-'s slow dynamics indicates that the solution's macroscopic viscosity is dictated by the extended structures formed between FA and water molecules. The relation between the reorientation dynamics of the SCN- and the macroscopic viscosity in aqueous FA-water mixture solutions was analyzed by using the Stokes-Einstein-Debye equations. The direct viscosity-diffusion coupling is observed, which can be attributed to the homogeneous dynamics feature in FA-water mixture solutions. The inclusion of these intrinsic and extrinsic probes not only enhances the comprehensiveness of our analysis but also provides valuable insights into various aspects of the dynamics within the FA-water system. This investigation sheds light on the fundamental dynamics of FA-water mixtures, emphasizing their molecular-level homogeneity in this binary mixture solution.
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Affiliation(s)
- Yimin Bai
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jiman He
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yuting Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Miaomiao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yun Tang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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2
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Lineshape analysis of concentrated perchlorate anion aqueous solution with coherence exchange model incorporating multiple bath modes. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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3
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Lineshape analysis of perchlorate anions on manganese(III) porphyrin and observing nanoscopic water environments. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Perticaroli S, Comez L, Sassi P, Morresi A, Fioretto D, Paolantoni M. Water-like Behavior of Formamide: Jump Reorientation Probed by Extended Depolarized Light Scattering. J Phys Chem Lett 2018; 9:120-125. [PMID: 29243934 DOI: 10.1021/acs.jpclett.7b02943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water is a strong self-associated liquid with peculiar properties that crucially depend on H-bonding. As regards its molecular dynamics, only recently has water reorientation been successfully described based on a jump mechanism, which is responsible for the overall H-bonding exchange. Here, using high-resolution broad-band depolarized light scattering, we have investigated the reorientational dynamics of formamide (FA) as a function of concentration from the neat liquid to diluted aqueous solutions. Our main findings indicate that in the diluted regime the water rearrangement can trigger the motion of FA solute molecules, which are forced to reorient at the same rate as water. This highlights an exceptional behavior of FA, which perfectly substitutes water within its network. Besides other fundamental implications connected with the relevance of FA, its water-like behavior provides rare experimental evidence of a solute whose dynamics is completely slaved to the solvent.
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Affiliation(s)
- S Perticaroli
- Shull Wollan Center, a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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5
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Torii H. Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide. Phys Chem Chem Phys 2018; 20:3029-3039. [DOI: 10.1039/c7cp02644g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular charge fluxes induced by hydrogen-bond length modulations occurring upon molecular librations lead to intensity enhancement of the far-infrared spectrum.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry
- Faculty of Education, and Department of Optoelectronics and Nanostructure Science
- Graduate School of Science and Technology
- Shizuoka University
- Shizuoka 422-8529
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6
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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Marroux HJB, Orr-Ewing AJ. Distinguishing Population and Coherence Transfer Pathways in a Metal Dicarbonyl Complex Using Pulse-Shaped Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2016; 120:4125-30. [DOI: 10.1021/acs.jpcb.6b02979] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Hamm P, Zewail AH, Fleming GR. A tribute to Robin Hochstrasser. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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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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Anna JM, Baiz CR, Ross MR, McCanne R, Kubarych KJ. Ultrafast equilibrium and non-equilibrium chemical reaction dynamics probed with multidimensional infrared spectroscopy. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.716610] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
This Perspective is focused on amide groups of peptides interacting with water. The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes. Here we describe why nonlinear IR is emerging as the method of choice to examine the fast components of the water dynamics near peptides and how isotopically edited peptide links can be used to probe the local water at a residue level in proteins. This type of research necessarily involves an intimate mix of theory and experiment. The description of the results is underpinned by relatively well established quantum-statistical theories that describe the important manifestations of peptide vibrational frequency fluctuations.
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Affiliation(s)
- Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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Keating CS, McClure BA, Rack JJ, Rubtsov IV. Sulfoxide stretching mode as a structural reporter via dual-frequency two-dimensional infrared spectroscopy. J Chem Phys 2011; 133:144513. [PMID: 20950023 DOI: 10.1063/1.3482708] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The S=O stretching mode in sulfoxides, having a frequency in the 950-1150 cm(-1) range, is tested as a structural label via dual-frequency two-dimensional infrared (2DIR) spectroscopy. The properties of this structural reporter are studied in several compounds, including (4,4(')-dimethyl-2,2(')-bipyridyl)(o-methylsulfinylbenzoate) ruthenium II, [Ru(dmb)(2)(BzSO)](+), (RuBzSO), octylsulfinylpropionic acid (OSPA), and o- and p-methylsulfinyl-benzoic acid (oMSBA and pMSBA). The mode assignment in the fingerprint region for these compounds is made using a combination of density functional theory calculations and 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies. The SO stretching mode frequency and IR intensity demonstrate substantial sensitivity to the molecular structure. Multiple cross peaks of the C=O and S=O stretching modes with modes in the fingerprint region (930-1450 cm(-1)) were recorded. The 2DIR and RA 2DIR spectra focusing at interactions of a high-frequency mode of a ligand with the modes in the fingerprint region provide a spectral fingerprint of a compound and help mode assignment in the often congested fingerprint region. The cross-peak amplitudes in oMSBA, pMSBA, and OSPA were compared with the theoretical predictions based on the computed values for the off-diagonal anharmonicities and a reasonable match is found. The SO stretching mode provides means for assigning other modes in the fingerprint region and constitutes a promising structural reporter for the 2DIR and RA 2DIR spectroscopy measurements.
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13
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Perchlorate anion on manganese(III) porphyrin as an ATR-IR probe for nanoscopic water environments. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.12.029] [Citation(s) in RCA: 5] [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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Paarmann A, Lima M, Chelli R, Volkov VV, Righini R, Miller RJD. Excitonic effects in two-dimensional vibrational spectra of liquid formamide. Phys Chem Chem Phys 2011; 13:11351-8. [PMID: 21573300 DOI: 10.1039/c0cp02961k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Nydegger MW, Rock W, Cheatum CM. 2D IR Spectroscopy of the C–D stretching vibration of the deuterated formic acid dimer. Phys Chem Chem Phys 2011; 13:6098-104. [DOI: 10.1039/c0cp01087a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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16
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Ha JH, Lee KK, Park KH, Choi JH, Jeon SJ, Cho M. Integrated and dispersed photon echo studies of nitrile stretching vibration of 4-cyanophenol in methanol. J Chem Phys 2009; 130:204509. [PMID: 19485459 DOI: 10.1063/1.3140402] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
By means of integrated and dispersed IR photon echo measurement methods, the vibrational dynamics of C-N stretch modes in 4-cyanophenol and 4-cyanophenoxide in methanol is investigated. The vibrational frequency-frequency correlation function (FFCF) is retrieved from the integrated photon echo signals by assuming that the FFCF is described by two exponential functions with about 400 fs and a few picosecond components. The excited state lifetimes of the C-N stretch modes of neutral and anionic 4-cyanophenols are 1.45 and 0.91 ps, respectively, and the overtone anharmonic frequency shifts are 25 and 28 cm(-1). At short waiting times, a notable underdamped oscillation, which is attributed to a low-frequency intramolecular vibration coupled to the CN stretch, in the integrated and dispersed vibrational echo as well as transient grating signals was observed. The spectral bandwidths of IR absorption and dispersed vibrational echo spectra of the 4-cyanophenoxide are significantly larger than those of its neutral form, indicating that the strong interaction between phenoxide and methanol causes large frequency fluctuation and rapid population relaxation. The resonance effects in a paradisubstituted aromatic compound would be of interest in understanding the conjugation effects and their influences on chemical reactivity of various aromatic compounds in organic solvents.
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Affiliation(s)
- Jeong-Hyon Ha
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Republic of Korea
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Kim YS, Hochstrasser RM. Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics. J Phys Chem B 2009; 113:8231-51. [PMID: 19351162 PMCID: PMC2845308 DOI: 10.1021/jp8113978] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.
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Affiliation(s)
- Yung Sam Kim
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323, U.S.A
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323, U.S.A
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18
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Lima M, Chelli R, Volkov VV, Righini R. Two-dimensional infrared spectroscopy of a structured liquid: Neat formamide. J Chem Phys 2009; 130:204518. [DOI: 10.1063/1.3139002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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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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20
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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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21
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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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22
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Fournier F, Gardner EM, Guo R, Donaldson PM, Barter LM, Palmer DJ, Barnett CJ, Willison KR, Gould IR, Klug DR. Optical fingerprinting of peptides using two-dimensional infrared spectroscopy: Proof of principle. Anal Biochem 2008; 374:358-65. [DOI: 10.1016/j.ab.2007.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 10/29/2007] [Accepted: 11/01/2007] [Indexed: 11/30/2022]
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23
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Vibrational population relaxation of hydrogen-bonded phenol complexes in solution: Investigation by ultrafast infrared pump–probe spectroscopy. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.07.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Lavoine JP. Effects of permanent dipole moments in transient four-wave mixing experiments. J Chem Phys 2007; 127:094107. [PMID: 17824732 DOI: 10.1063/1.2753472] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A two-pulse degenerate four-wave mixing experiment is analyzed in the case where the medium under investigation can be modeled by two-level systems having unequal permanent dipole moments. By modeling the light pulses by double exponentials [exp(-Gamma/t/)], we give an analytical expression of the third-order nonlinear polarization of the medium. We apply this result to simulate the measured signal in such experiment. We show that in the case of a two-photon transition, a signal can be detected if the pump pulse interacts with the medium before the probe pulse contrary to what is observed for excitations in the resonance region. An attempt to explain this behavior is made and the detected signal is analyzed in terms of pure coherent processes. This effect appears as a signature of the presence of permanent dipole moments. To test this property on a more realistic system, we then have considered a one-dimensional frequency-selected infrared degenerate four-wave mixing experiment on a molecular anharmonic vibrational mode modeled by a Morse potential and coupled to a dissipative bath of harmonic oscillators. We show that the two-photon transitions allowed by the presence of permanent dipole moments enable to analyze the multilevel system dynamics as if they were the one of a two-level system. Our results can also be extended to the case of inhomogeneous broadening and are of interest to study the infrared photon-echo response of anharmonic vibrational modes.
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Affiliation(s)
- J P Lavoine
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 ULP-CNRS, Groupe d'Optique Nonlinéaire et d'Optoélectronique, 23, rue du Loess, B.P. 43, 67034 Strasbourg Cedex 2, France.
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Hochstrasser RM. Two-dimensional spectroscopy at infrared and optical frequencies. Proc Natl Acad Sci U S A 2007; 104:14190-6. [PMID: 17664429 PMCID: PMC1964834 DOI: 10.1073/pnas.0704079104] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Indexed: 11/18/2022] Open
Abstract
This Perspective on multidimensional spectroscopy in the optical and infrared spectral regions focuses on the principles and the scientific and technical challenges facing these new fields. The methods hold great promise for advances in the visualization of time-dependent structural changes in complex systems ranging from liquids to biological assemblies, new materials, and fundamental physical processes. The papers in this special feature on multidimensional spectroscopy in chemistry, physics, and biology are typical of many recent advances.
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Affiliation(s)
- Robin M Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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27
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Kumar K, Sinks LE, Wang J, Kim YS, Hochstrasser RM. Coupling between C–D and CO motions using dual-frequency 2D IR photon echo spectroscopy. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.10.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Berg ER, Freeman SA, Green DD, Ulness DJ. Effects of Hydrogen Bonding on the Ring Stretching Modes of Pyridine. J Phys Chem A 2006; 110:13434-46. [PMID: 17165869 DOI: 10.1021/jp0655367] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of hydrogen bonding on the ring stretching modes (both ring breathing and triangle) of pyridine are experimentally investigated using noisy light based coherent Raman scattering spectroscopy. Three systems, pyridine/formamide, pyridine/water, and pyridine/acetic acid, provide varying degrees of strength for the diluent-pyridine hydrogen bond complex. Formamide forms a relatively weaker hydrogen bond, while acetic acid essentially fully transfers a proton to pyridine. Both dilution studies and temperature studies are performed on the three systems. Together, these provide a broad context in which a very simple model for the electronic behavior of pyridine is formulated. This model is based on a molecular orbital picture and electrostatic arguments, and it well explains the observed experimental results. Additionally, a new mechanism for the line broadening of the ring breathing mode for the pyridine-water hydrogen bonded complex is proposed.
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Affiliation(s)
- Erik R Berg
- Department of Chemistry, Concordia College, Moorhead, Minnesota 56562, USA
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Reckien W, Kirchner B, Peyerimhoff SD. Frequency Analysis of Amide-Linked Rotaxane Mimetics. J Phys Chem A 2006; 110:12963-70. [PMID: 17125313 DOI: 10.1021/jp065327m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A vibrational analysis of 2-fold hydrogen bonds between an isophthalic amide donor and different acceptors is presented. These systems can be considered as mimetics for the hydrogen-binding situation of numerous supramolecular compounds such as rotaxanes, catenanes, knotanes, and anion receptors. We calculated pronounced red-shifts up to 65 cm(-1) for the stretching modes of the acceptor carbonyl as well as for the donor NH2 groups, whereas we observe a blue shift for the NH2 bending modes and an additional weak hydrogen bond between the acceptor and the middle C-H group of the donor. The red and blue shifts observed for different modes in various complexes have been correlated with the binding energy of the complexes, independently. In comparison with comparable single hydrogen bonds, we find for the 2-fold hydrogen bonds smaller red shifts for the N-H stretch modes of the donor but larger red shifts for the C=O stretch mode of the acceptor. Furthermore, our results indicate that the pronounced blue shift of the C-H stretch mode is basically caused by the fact that the acceptor is fixed directly above this group due to the 2-fold hydrogen bond.
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Affiliation(s)
- Werner Reckien
- Theoretische Chemie, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
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