1
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Whaley-Mayda L, Guha A, Tokmakoff A. Multimode vibrational dynamics and orientational effects in fluorescence-encoded infrared spectroscopy. I. Response function theory. J Chem Phys 2023; 159:194201. [PMID: 37966137 DOI: 10.1063/5.0171939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023] Open
Abstract
Fluorescence-encoded infrared (FEIR) spectroscopy is an emerging technique for performing vibrational spectroscopy in solution with detection sensitivity down to single molecules. FEIR experiments use ultrashort pulses to excite a fluorescent molecule's vibrational and electronic transitions in a sequential, time-resolved manner, and are therefore sensitive to intervening vibrational dynamics on the ground state, vibronic coupling, and the relative orientation of vibrational and electronic transition dipole moments. This series of papers presents a theoretical treatment of FEIR spectroscopy that describes these phenomena and examines their manifestation in experimental data. This first paper develops a nonlinear response function description of Fourier-transform FEIR experiments for a two-level electronic system coupled to multiple vibrations, which is then applied to interpret experimental measurements in the second paper [L. Whaley-Mayda et al., J. Chem. Phys. 159, 194202 (2023)]. Vibrational coherence between pairs of modes produce oscillatory features that interfere with the vibrations' population response in a manner dependent on the relative signs of their respective Franck-Condon wavefunction overlaps, leading to time-dependent distortions in FEIR spectra. The orientational response of population and coherence contributions are analyzed and the ability of polarization-dependent experiments to extract relative transition dipole angles is discussed. Overall, this work presents a framework for understanding the full spectroscopic information content of FEIR measurements to aid data interpretation and inform optimal experimental design.
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Affiliation(s)
- Lukas Whaley-Mayda
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Abhirup Guha
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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2
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van Hengel CDN, van Adrichem KE, Jansen TLC. Simulation of two-dimensional infrared Raman spectroscopy with application to proteins. J Chem Phys 2023; 158:064106. [PMID: 36792507 DOI: 10.1063/5.0138958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.
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Affiliation(s)
- Carleen D N van Hengel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kim E van Adrichem
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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3
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Relative molecular orientations in organic optoelectronic films probed via polarization-selected UV/IR mixed frequency ultrafast spectroscopy. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2111260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Vazquez de Vasquez MG, Carter-Fenk KA, McCaslin LM, Beasley EE, Clark JB, Allen HC. Hydration and Hydrogen Bond Order of Octadecanoic Acid and Octadecanol Films on Water at 21 and 1 °C. J Phys Chem A 2021; 125:10065-10078. [PMID: 34761931 DOI: 10.1021/acs.jpca.1c06101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The temperature-dependent hydration structure of long-chain fatty acids and alcohols at air-water interfaces has great significance in the fundamental interactions underlying ice nucleation in the atmosphere. We present an integrated theoretical and experimental study of the temperature-dependent vibrational structure and electric field character of the immediate hydration shells of fatty alcohol and acid headgroups. We use a combination of surface-sensitive infrared reflection-absorption spectroscopy (IRRAS), surface potentiometry, and ab initio molecular dynamics simulations to elucidate detailed molecular structures of the octadecanoic acid and octadecanol (stearic acid and stearyl alcohol) headgroup hydration shells at room temperature and near freezing. In experiments, the alcohol at high surface concentration exhibits the largest surface potential; yet we observe a strengthening of the hydrogen-bonding for the solvating water molecules near freezing for both the alcohol and the fatty acid IRRAS experiments. Results reveal that the hydration shells for both compounds screen their polar headgroup dipole moments reducing the surface potential at low surface coverages; at higher surface coverage, the polar headgroups become dehydrated, which reduces the screening, correlating to higher observed surface potential values. Lowering the temperature promotes tighter chain packing and an increase in surface potential. IRRAS reveals that the intra- and intermolecular vibrational coupling mechanisms are highly sensitive to changes in temperature. We find that intramolecular coupling dominates the vibrational relaxation pathways for interfacial water determined by comparing the H2O and the HOD spectra. Using ab initio molecular dynamics (AIMD) calculations on cluster systems of propanol + 6H2O and propionic acid + 10H2O, a spectral decomposition scheme was used to correlate the OH stretching motion with the IRRAS spectral features, revealing the effects of intra- and intermolecular coupling on the spectra. Spectra calculated with AIMD reproduce the red shift and increase in intensity observed in experimental spectra corresponding to the OH stretching region of the first solvation shell. These findings suggest that intra- and intermolecular vibrational couplings strongly impact the OH stretching region at fatty acid and fatty alcohol water interfaces. Overall, results are consistent with ice templating behavior for both the fatty acid and the alcohol, yet the surface potential signature is strongest for the fatty alcohol. These findings develop a better understanding of the complex surface potential and spectral signatures involved in ice templating.
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Affiliation(s)
- Maria G Vazquez de Vasquez
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Kimberly A Carter-Fenk
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Laura M McCaslin
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, United States
| | - Emma E Beasley
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jessica B Clark
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Heather C Allen
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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5
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Abstract
Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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6
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Ghosh R, Mora AK, Nath S. Disentangling Time Scales of Vibrational Cooling, Solvation, and Hydrogen Bond Reorganization Dynamics Using Ultrafast Transient Infrared Spectroscopy of Formylperylene. J Phys Chem B 2019; 123:4408-4414. [DOI: 10.1021/acs.jpcb.9b01920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajib Ghosh
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Aruna K. Mora
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Sukhendu Nath
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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7
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Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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8
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Yadav VK, Chandra A. Dynamics of vibrational frequency fluctuations in deuterated liquid ammonia: roles of fluctuating hydrogen bonds and free ND modes. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1475739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Vivek Kumar Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur, India
- Department of Theoretical and Computational Molecular Science, Institute of Molecular Science , Okazaki, Japan
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9
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Yamada SA, Thompson WH, Fayer MD. Water-anion hydrogen bonding dynamics: Ultrafast IR experiments and simulations. J Chem Phys 2017. [DOI: 10.1063/1.4984766] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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10
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Kundu A, Verma PK, Ha JH, Cho M. Studying Water Hydrogen-Bonding Network near the Lipid Multibilayer with Multiple IR Probes. J Phys Chem A 2017; 121:1435-1441. [DOI: 10.1021/acs.jpca.6b12152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Achintya Kundu
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jeong-Hyon Ha
- Space-Time
Resolved Molecular Imaging Research Team, Korea Basic Science Institute (KBSI), Seoul 136-075, Republic of Korea
| | - Minhaeng Cho
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
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11
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Kwon Y, Lee J, Park S. Effect of ion–ligand binding on ion pairing dynamics studied by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2017; 19:10889-10897. [DOI: 10.1039/c6cp08852j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-specific ion pairing dynamics between M+ (M = Ag or Cu) and SCN− in N,N-dimethylthioformamide (DMTF) are studied by probing the nitrile (CN) stretching vibration.
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Affiliation(s)
- YoungAh Kwon
- Department of Chemistry
- Korea University
- Seoul
- Korea
| | - Junho Lee
- Department of Chemistry
- Korea University
- Seoul
- Korea
| | - Sungnam Park
- Department of Chemistry
- Korea University
- Seoul
- Korea
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12
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Giammanco CH, Kramer PL, Wong DB, Fayer MD. Water Dynamics in 1-Alkyl-3-methylimidazolium Tetrafluoroborate Ionic Liquids. J Phys Chem B 2016; 120:11523-11538. [DOI: 10.1021/acs.jpcb.6b08410] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Patrick L. Kramer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Daryl B. Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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13
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Okuda M, Ohta K, Tominaga K. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies. J Chem Phys 2016. [DOI: 10.1063/1.4962344] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Masaki Okuda
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Kaoru Ohta
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
- Moleuclar Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
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14
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Lee C, Son H, Park S. Effect of Hydrogen Bonds on the Vibrational Relaxation and Orientational Relaxation Dynamics of HN3 and N3(-) in Solutions. J Phys Chem B 2016; 120:9723-31. [PMID: 27537433 DOI: 10.1021/acs.jpcb.6b06239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen bonds (H-bonds) play an important role in determining the structures and dynamics of molecular systems. In this work, we investigated the effect of H-bonds on the vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in methanol (CH3OH) and N,N-dimethyl sulfoxide (DMSO) using polarization-controlled infrared pump-probe spectroscopy and quantum chemical calculations. Our detailed analysis of experimental and computational results reveals that both vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in CH3OH and DMSO are substantially dependent on the strength of the H-bonds between the probing solute and its surrounding solvent. Especially in the case of N3(-) in CH3OH, the vibrational population relaxation of N3(-) is found to occur by a direct intermolecular vibrational energy transfer to CH3OH due to large vibrational coupling strength. The orientational relaxation dynamics of HN3 and N3(-), which are well fit by a biexponential function, are analyzed by the wobbling-in-a-cone model and extended Debye-Stokes-Einstein equation. Depending on the intermolecular interactions, the slow overall orientational relaxation occurs under slip, stick, and superstick boundary conditions. For HN3 and N3(-) in CH3OH and DMSO, the vibrational population relaxation becomes faster but the orientational relaxation becomes slower as the H-bond strength is increased. Our current results imply that H-bonds have significant effects on the vibrational population relaxation and orientational relaxation dynamics of a small solute whose size is comparable to the size of the solvent.
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Affiliation(s)
- Chiho Lee
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Hyewon Son
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Sungnam Park
- Department of Chemistry, Korea University , Seoul 136-701, Korea
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15
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Kundu A, Kwak K, Cho M. Water Structure at the Lipid Multibilayer Surface: Anionic Versus Cationic Head Group Effects. J Phys Chem B 2016; 120:5002-7. [PMID: 27171689 DOI: 10.1021/acs.jpcb.6b02340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane water interface is a potential reaction site for many biochemical reactions. Therefore, a molecular level understanding of water structure and dynamics that strongly depend on the chemical structure of lipid is prerequisite for elucidating the role of water in biological reactions on membrane surface. Recently, we carried out femtosecond infrared pump-probe studies of water structure and dynamics at multibilayer surfaces of zwitterionic phosphatidylcholine-analogue lipid ( J. Phys. Chem. Lett. 2016 , 7 , 741 ). Here, to further elucidate the anionic and cationic headgroup effects on water, we study vibrational dynamics of water on lipid multibilayers formed by anionic phospho-glycerol lipid molecules as well as by cationic choline-derivatized lipid molecules. We observed two significantly different vibrational lifetime components (very fast 0.5 ps and slow 1.9 ps) of the OD stretch mode of HOD molecules at the negatively charged phospho-lipid multibilayer whereas only one vibrational lifetime component (1.6 ps) was observed at the positively charged choline-derivatized lipid multibilayer. From the detailed analyses about the vibrational energy and rotational relaxations of HOD molecules in lipid multibilayers composed of anionic lipid with phosphate and cationic lipid without phosphate, the role of phosphate group in structuring water molecules at phospholipid membrane interface is revealed.
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Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
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16
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Shinokita K, Cunha AV, Jansen TLC, Pshenichnikov MS. Hydrogen bond dynamics in bulk alcohols. J Chem Phys 2016; 142:212450. [PMID: 26049470 DOI: 10.1063/1.4921574] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics-quantum mechanical simulation have established many intriguing features of hydrogen bond dynamics in one of the fundamental solvents in nature, water. The next class of a hydrogen-bonded liquid--alcohols--has attracted much less attention. This is surprising given such important differences between water and alcohols as the imbalance between the number of hydrogen bonds, each molecule can accept (two) and donate (one) and the very presence of the hydrophobic group in alcohols. Here, we use polarization-resolved pump-probe and 2D infrared spectroscopy supported by extensive theoretical modeling to investigate hydrogen bond dynamics in methanol, ethanol, and isopropanol employing the OH stretching mode as a reporter. The sub-ps dynamics in alcohols are similar to those in water as they are determined by similar librational and hydrogen-bond stretch motions. However, lower density of hydrogen bond acceptors and donors in alcohols leads to the appearance of slow diffusion-controlled hydrogen bond exchange dynamics, which are essentially absent in water. We anticipate that the findings herein would have a potential impact on fundamental chemistry and biology as many processes in nature involve the interplay of hydrophobic and hydrophilic groups.
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Affiliation(s)
- Keisuke Shinokita
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maxim S Pshenichnikov
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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17
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Shi L, Skinner JL, Jansen TLC. Two-dimensional infrared spectroscopy of neat ice Ih. Phys Chem Chem Phys 2016; 18:3772-9. [PMID: 26765972 DOI: 10.1039/c5cp07264f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assignment of the distinct peaks observed in the OH stretch lineshape of ice Ih is controversial. Recent two-dimensional infrared spectroscopic measurements provided new data. The spectra are, however, challenging to interpret and here we provide simulations that help overcome experimental issues as thermal signals and finite pulse duration. We find good agreement with experiment and the difference between H2O and D2O ices is well accounted for. The overall dynamics is demonstrated to be faster than observed for the corresponding liquid water. We find that excitonic cross peaks exist between the dominant exciton peaks. This leads us to conclude that the cross peaks arise due to the formation of delocalized exciton states, which have essentially no directional correlation between their transition dipoles as opposed to what is commonly seen, for example, in isolated water, where the transition dipoles of the eigenstates are perpendicular to each other.
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Affiliation(s)
- Liang Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA 02139, USA
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18
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Ross MR, White AM, Yu F, King JT, Pecoraro VL, Kubarych KJ. Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site. J Am Chem Soc 2015; 137:10164-76. [PMID: 26247178 PMCID: PMC5250509 DOI: 10.1021/jacs.5b02840] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ultrafast dynamics of a de novo metalloenzyme active site is monitored using two-dimensional infrared spectroscopy. The homotrimer of parallel, coiled coil α-helices contains a His3-Cu(I) metal site where CO is bound and serves as a vibrational probe of the hydrophobic interior of the self-assembled complex. The ultrafast spectral dynamics of Cu-CO reveals unprecedented ultrafast (2 ps) nonequilibrium structural rearrangements launched by vibrational excitation of CO. This initial rapid phase is followed by much slower ∼40 ps vibrational relaxation typical of metal-CO vibrations in natural proteins. To identify the hidden coupled coordinate, small molecule analogues and the full peptide were studied by QM and QM/MM calculations, respectively. The calculations show that variation of the histidines' dihedral angles in coordinating Cu controls the coupling between the CO stretch and the Cu-C-O bending coordinates. Analysis of different optimized structures with significantly different electrostatic field magnitudes at the CO ligand site indicates that the origin of the stretch-bend coupling is not directly due to through-space electrostatics. Instead, the large, ∼3.6 D dipole moments of the histidine side chains effectively transduce the electrostatic environment to the local metal coordination orientation. The sensitivity of the first coordination sphere to the protein electrostatics and its role in altering the potential energy surface of the bound ligands suggests that long-range electrostatics can be leveraged to fine-tune function through enzyme design.
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Affiliation(s)
| | | | | | | | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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19
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Le Caër S, Klein G, Ortiz D, Lima M, Devineau S, Pin S, Brubach JB, Roy P, Pommeret S, Leibl W, Righini R, Renault JP. The effect of myoglobin crowding on the dynamics of water: an infrared study. Phys Chem Chem Phys 2015; 16:22841-52. [PMID: 25242637 DOI: 10.1039/c4cp03102d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solutions containing 8 and 32 wt% myoglobin are studied by means of infrared spectroscopy, as a function of temperature (290 K and lower temperatures), in the mid- and far-infrared spectral range. Moreover, ultrafast time-resolved infrared measurements are performed at ambient temperature in the O-D stretching region. The results evidence that the vibrational properties of water remain the same in these myoglobin solutions (anharmonicity, vibrational relaxation lifetime…) and in neat water. However, the collective properties of the water molecules are significantly affected by the presence of the protein: the orientational time increases, the solid-liquid transition is affected in the most concentrated solution and the dynamical transition of the protein is observed, from the point of view of water, even in the least concentrated solution, proving that the water and myoglobin dynamics are coupled.
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Affiliation(s)
- S Le Caër
- Institut Rayonnement Matière de Saclay, LIDyL et Service Interdisciplinaire sur les Systèmes Moléculaires et les Matériaux, UMR 3299, CNRS/CEA, Groupe Physico-Chimie sous Rayonnement, Bâtiment 546, F-91191 Gif-sur-Yvette Cedex, France.
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20
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Description of cross-peaks induced by intermolecular vibrational energy transfer in two-dimensional infrared spectroscopy. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Chen H, Bian H, Li J, Wen X, Zhang Q, Zhuang W, Zheng J. Vibrational Energy Transfer: An Angstrom Molecular Ruler in Studies of Ion Pairing and Clustering in Aqueous Solutions. J Phys Chem B 2015; 119:4333-49. [DOI: 10.1021/jp512320a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hailong Chen
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
| | - Hongtao Bian
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
| | - Jiebo Li
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
| | - Xiewen Wen
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
| | - Qiang Zhang
- Institute of Chemistry,
Chemical Engineering and Food Safety, Bohai University, Jinzhou 121000, People’s Republic of China
| | - 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
| | - Junrong Zheng
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States
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22
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Giammanco CH, Kramer PL, Fayer MD. Dynamics of Dihydrogen Bonding in Aqueous Solutions of Sodium Borohydride. J Phys Chem B 2015; 119:3546-59. [DOI: 10.1021/jp512426y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chiara H. Giammanco
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Patrick L. Kramer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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23
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Mazur K, Bonn M, Hunger J. Hydrogen bond dynamics in primary alcohols: a femtosecond infrared study. J Phys Chem B 2015; 119:1558-66. [PMID: 25531023 DOI: 10.1021/jp509816q] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-bonded liquids are excellent solvents, in part due to the highly dynamic character of the directional interaction associated with the hydrogen bond. Here we study the vibrational and reorientational dynamics of deuterated hydroxyl groups in various primary alcohols using polarization-resolved femtosecond infrared spectroscopy. We show that the relaxation of the OD stretch vibration is similar for ethanol and its higher homologues (∼0.9 ps), while it is appreciably faster for methanol (∼0.75 ps). The fast relaxation for methanol is attributed to strong coupling of the OD stretch vibration to the overtone of the CH3 rocking mode. Subsequent to excited state relaxation, the dissipation of the excess energy leads to structural relaxation of the alcohol liquid structure. We show that this relaxation of the H-bonded network depends on the alkyl chain length. We find that the anisotropy of the excitation decays by both thermal diffusion from excited OD groups to nonexcited molecules and reorientational motion. The reorientation is described well by a model employing two relaxation times that increase linearly with increasing alcohol size. The short reorientation time is assigned to the partial reorientation of molecules within the alcohol cluster, while the long reorientation times can be attributed to breaking and reforming of hydrogen bonds.
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Affiliation(s)
- Kamila Mazur
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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24
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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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25
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Kwon Y, Park S. Complexation dynamics of CH3SCN and Li+ in acetonitrile studied by two-dimensional infrared spectroscopy. Phys Chem Chem Phys 2015; 17:24193-200. [DOI: 10.1039/c5cp02833g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chemical exchange 2DIR study of ion–molecule complexation dynamics in electrolyte solutions.
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Affiliation(s)
- YoungAh Kwon
- 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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26
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Panman MR, Shaw DJ, Ensing B, Woutersen S. Local orientational order in liquids revealed by resonant vibrational energy transfer. PHYSICAL REVIEW LETTERS 2014; 113:207801. [PMID: 25432055 DOI: 10.1103/physrevlett.113.207801] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Indexed: 06/04/2023]
Abstract
We demonstrate that local orientational ordering in a liquid can be observed in the decay of the vibrational anisotropy caused by resonant transfer of vibrational excitations between its constituent molecules. We show that the functional form of this decay is determined by the (distribution of) angles between the vibrating bonds of the molecules between which energy transfer occurs, and that the initial drop in the decay reflects the average angle between nearest neighbors. We use this effect to observe the difference in local orientational ordering in the two hydrogen-bonded liquids ethanol and N-methylacetamide.
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Affiliation(s)
- M R Panman
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - D J Shaw
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - B Ensing
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S Woutersen
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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27
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Alberding BG, Lear BJ. Concentration-dependent dynamics of hydrogen bonding between acetonitrile and methanol as determined by 1D vibrational spectroscopy. J Phys Chem A 2014; 118:4363-71. [PMID: 24911870 DOI: 10.1021/jp4110147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solutions of acetonitrile (MeCN) in methanol (MeOH) at various concentrations have been investigated by variable temperature Raman spectroscopy. In the ν(CN) region of the spectrum, the variable temperature spectra at each concentration show two overlapping bands from hydrogen bound and free MeCN. These two species undergo dynamic exchange that gives rise to increasing coalescence of the two bands with increasing temperature. By simulation of the band shape, the rate of exchange was determined at each temperature. Arrhenius plots yielded values for the activation energy, Ea, and the natural log of the pre-exponential factor, ln[A/s(-1)], for the hydrogen bond formation/cleavage. Both of these dynamic parameters were found to depend on the relative amounts of MeCN and MeOH in the solutions. In particular, two different concentration regimes of dynamic hydrogen bonding were observed. First, at low MeCN concentration, the dynamics are largely independent of changes in MeCN concentration. Second, at higher MeCN concentration (above ∼0.2 MeCN mole fraction) the dynamics are strongly dependent on further increases of MeCN content. Over the range of MeCN mole fractions that we studied (0.03-0.5), the ln[A/s(-1)] changes from 32.5 ± 0.1 to 30.1 ± 0.2 and Ea changes from 3.73 ± 0.08 to 2.7 ± 0.1 kcal/mol. We suggest the observed changes in dynamics arise from changes in the local solvent microstructure that occur above a critical mole fraction of MeCN.
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Affiliation(s)
- Brian G Alberding
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16801, United States
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28
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Šoltésová M, Benda L, Peksa M, Czernek J, Lang J. Determination of size of molecular clusters of ethanol by means of NMR diffusometry and hydrodynamic calculations. J Phys Chem B 2014; 118:6864-74. [PMID: 24853047 DOI: 10.1021/jp501648x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The microscopic structure of ethanol in the liquid state is characterized as a dynamic equilibrium of hydrogen-bonded clusters of different sizes and topologies. We have developed a novel method for determination of the average size of the clusters that combines the measurement of diffusion coefficient by means of NMR diffusometry technique and hydrodynamic simulations. The approach includes the use of HydroNMR [J. Garcı̀a de la Torre, M. L. Huertas, and B. Carrasco, J. Magn. Reson. 147, 2000, 138] for small molecules, which is attained here by the calibration procedure using a dilute solution of tetramethylsilane. It is thus possible to correlate the experimentally determined diffusion coefficient of ethanol with calculated diffusion coefficients of the modeled clusters of different sizes. We found that average size of the clusters in 0.16 M solution of ethanol in n-hexane corresponds to the monomer above 300 K and to the pentamer/hexamer below 240 K. The clusters in the case of 0.44 M solution are generally slightly larger, from the average size corresponding to the dimer at 320 K and the hexamer at 210 K.
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Affiliation(s)
- Mária Šoltésová
- Department of Low Temperature Physics, Faculty of Mathematics and Physics, Charles University in Prague , V Holešovičkách 2, CZ-18000 Prague 8, Czech Republic
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29
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Sokolowsky KP, Fayer MD. Dynamics in the isotropic phase of nematogens using 2D IR vibrational echo measurements on natural-abundance 13CN and extended lifetime probes. J Phys Chem B 2013; 117:15060-71. [PMID: 24156524 DOI: 10.1021/jp4071955] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The long time scale orientational relaxation of nematogens in the isotropic phase is associated with the randomization of pseudonematic domains, which have a correlation length that grows as the isotropic-to-nematic phase transition temperature is approached from above. Here we begin to address the fast dynamics of the nematogen molecules within the domains using two-dimensional infrared (2D IR) vibrational echo experiments. The problems of performing ultrafast IR experiments in pure liquids are discussed, and solutions are presented. In addition, the issue of short vibrational lifetimes, which limit the ability of 2D IR experiments to examine dynamics over a wide range of times, is addressed. The experiments were performed on the nematogen 4-cyano-4'-pentylbiphenyl (5CB), with the CN stretch initially used as the vibrational probe. Although the CN stretch has a small transition dipole, because the sample is a pure liquid it is necessary to use an exceedingly thin sample to perform the experiments. The small sample volume leads to massive heating effects that distort the results. In addition, the high concentration in the pure liquid can result in vibrational excitation transfer that interferes with the measurements of structural dynamics, and the CN vibrational lifetime is very short (3.6 ps). These problems were overcome by performing the experiments on the natural-abundance (13)CN stretch (5(13)CB), which greatly reduced the absorbance, eliminating the heating problems; also, this stretch has a longer lifetime (7.9 ps). Experiments were also performed on benzonitrile, which showed that the heating problems associated with pure liquids are not unique to 5CB. Again, the problems were eliminated by conducting measurements on the (13)CN stretch, which has an even longer lifetime (20.2 ps) compared with the (12)CN stretch (5.6 ps). Finally, to extend the range of the dynamical measurements, 4-pentyl-4'-thiocyanobiphenyl (5SCB) was synthesized and studied as a dilute solute in 5CB. The CN stretch of 5SCB has a vibrational lifetime of 103 ps, which permits dynamical measurements to 200 ps, revealing the full range of fast structural dynamics in the isotropic phase of 5CB. It is shown that the 5SCB probe reports essentially the same dynamics as 5(13)CB on the short time scale that is observable with the 5(13)CB vibrational probe.
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Affiliation(s)
- Kathleen P Sokolowsky
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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30
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Sun Z, Zhang W, Ji M, Hartsock R, Gaffney KJ. Aqueous Mg2+ and Ca2+ ligand exchange mechanisms identified with 2DIR spectroscopy. J Phys Chem B 2013; 117:12268-75. [PMID: 24016251 DOI: 10.1021/jp407960x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological systems must discriminate between calcium and magnesium for these ions to perform their distinct biological functions, but the mechanism for distinguishing aqueous ions has yet to be determined. Ionic recognition depends upon the rate and mechanism by which ligands enter and leave the first solvation shell surrounding these cations. We present a time-resolved vibrational spectroscopy study of these ligand exchange dynamics in aqueous solution. The sensitivity of the CN-stretch frequency of NCS(-) to ion pair formation has been utilized to investigate the mechanism and dynamics of ligand exchange into and out of the first solvation shell of aqueous magnesium and calcium ions with multidimensional vibrational (2DIR) spectroscopy. We have determined that anion exchange follows a dissociative mechanism for Mg(2+) and an associative mechanism for Ca(2+).
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Affiliation(s)
- Zheng Sun
- PULSE Institute, SLAC National Accelerator Laboratory, Stanford University , Stanford, California 94305, United States
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31
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Sun Z, Zhang W, Ji M, Hartsock R, Gaffney KJ. Contact Ion Pair Formation between Hard Acids and Soft Bases in Aqueous Solutions Observed with 2DIR Spectroscopy. J Phys Chem B 2013; 117:15306-12. [DOI: 10.1021/jp4033854] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Zheng Sun
- PULSE Institute, SLAC National Accelerator
Laboratory, Stanford University, Stanford,
California 94305, United
States
| | - Wenkai Zhang
- PULSE Institute, SLAC National Accelerator
Laboratory, Stanford University, Stanford,
California 94305, United
States
| | - Minbiao Ji
- PULSE Institute, SLAC National Accelerator
Laboratory, Stanford University, Stanford,
California 94305, United
States
| | - Robert Hartsock
- PULSE Institute, SLAC National Accelerator
Laboratory, Stanford University, Stanford,
California 94305, United
States
| | - Kelly J. Gaffney
- PULSE Institute, SLAC National Accelerator
Laboratory, Stanford University, Stanford,
California 94305, United
States
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32
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Yadav VK, Chandra A. Dynamics of supercritical methanol of varying density from first principles simulations: Hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation. J Chem Phys 2013; 138:224501. [DOI: 10.1063/1.4808034] [Citation(s) in RCA: 12] [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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33
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Frequency dependence of the reorientational motion of OD bonds of deuterated methanol in liquid phase: A first principles molecular dynamics study. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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Kumar SKK, Tamimi A, Fayer MD. Dynamics in the interior of AOT lamellae investigated with two-dimensional infrared spectroscopy. J Am Chem Soc 2013; 135:5118-26. [PMID: 23465101 DOI: 10.1021/ja312676e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics inside the organic regions of aerosol-OT (AOT)/water mixtures in the lamellar mesophase, bicontinuous cubic (BC) phase, and in an analogous molecule without the charged sulfonate headgroup are investigated by observing spectral diffusion, orientational relaxation and population relaxation using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy and IR pump-probe experiments on the asymmetric CO stretch of a vibrational probe, tungsten hexacarbonyl (W(CO)6). The water layer thickness between the bilayer planes in the lamellar phase was varied. For comparison, the dynamics of W(CO)6 in the normal liquid bis(2-ethylhexyl) succinate (EHS), which is analogous to AOT but has no charged sulfonate headgroup, were also studied. The 2D IR experiments measure spectral diffusion, which results from the structural evolution of the system. Spectral diffusion is quantified by the frequency-frequency correlation function (FFCF). In addition to a homogeneous component, the FFCFs are biexponential decays with fast and slow time components of ∼12.5 and ∼150 ps in the lamellar phase. Both components of the FFCF are independent of the number of water molecules per headgroup for the lamellae, but they slow somewhat in the BC phase. The dynamics in the ordered phases are in sharp contrast to the dynamics in EHS, which displays fast and slow components of the FFCF of 5 and 80 ps, respectively. As the hydration level of AOT increases, vibrational lifetime decreases, suggesting some change in the local environment of W(CO)6 with water content.
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Affiliation(s)
- S K Karthick Kumar
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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35
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Son H, Kwon Y, Kim J, Park S. Rotational Dynamics of Metal Azide Ion Pairs in Dimethylsulfoxide Solutions. J Phys Chem B 2013; 117:2748-56. [DOI: 10.1021/jp312055f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hyewon Son
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - YoungAh Kwon
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Jinwoo Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Sungnam Park
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy
Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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36
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Giammanco CH, Wong DB, Fayer MD. Water Dynamics in Divalent and Monovalent Concentrated Salt Solutions. J Phys Chem B 2012; 116:13781-92. [DOI: 10.1021/jp3095402] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Daryl B. Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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37
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Chen H, Bian H, Li J, Wen X, Zheng J. Ultrafast multiple-mode multiple-dimensional vibrational spectroscopy. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.733116] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Yadav VK, Karmakar A, Choudhuri JR, Chandra A. A first principles molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in liquid methanol. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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39
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Rosenfeld DE, Fayer MD. Excitation transfer induced spectral diffusion and the influence of structural spectral diffusion. J Chem Phys 2012; 137:064109. [DOI: 10.1063/1.4742762] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Son H, Jin H, Choi SR, Jung HW, Park S. Infrared Probing of Equilibrium and Dynamics of Metal–Selenocyanate Ion Pairs in N,N-Dimethylformamide Solutions. J Phys Chem B 2012; 116:9152-9. [DOI: 10.1021/jp304595n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hyewon Son
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Haneul Jin
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Seung Ryul Choi
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Hyun Wook Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul
136-713, Korea
| | - Sungnam Park
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional
Spectroscopy
Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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41
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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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42
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Wong DB, Sokolowsky KP, El-Barghouthi MI, Fenn EE, Giammanco CH, Sturlaugson AL, Fayer MD. Water Dynamics in Water/DMSO Binary Mixtures. J Phys Chem B 2012; 116:5479-90. [DOI: 10.1021/jp301967e] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daryl B. Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | | | - Musa I. El-Barghouthi
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Emily E. Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Adam L. Sturlaugson
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
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43
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Abstract
Water is a critical component of many chemical processes, in fields as diverse as biology and geology. Water in chemical, biological, and other systems frequently occurs in very crowded situations: the confined water must interact with a variety of interfaces and molecular groups, often on a characteristic length scale of nanometers. Water's behavior in diverse environments is an important contributor to the functioning of chemical systems. In biology, water is found in cells, where it hydrates membranes and large biomolecules. In geology, interfacial water molecules can control ion adsorption and mineral dissolution. Embedded water molecules can change the structure of zeolites. In chemistry, water is an important polar solvent that is often in contact with interfaces, for example, in ion-exchange resin systems. Water is a very small molecule; its unusual properties for its size are attributable to the formation of extended hydrogen bond networks. A water molecule is similar in mass and volume to methane, but methane is a gas at room temperature, with melting and boiling points of 91 and 112 K, respectively. This is in contrast to water, with melting and boiling points of 273 and 373 K, respectively. The difference is that water forms up to four hydrogen bonds with approximately tetrahedral geometry. Water's hydrogen bond network is not static. Hydrogen bonds are constantly forming and breaking. In bulk water, the time scale for hydrogen bond randomization through concerted formation and dissociation of hydrogen bonds is approximately 2 ps. Water's rapid hydrogen bond rearrangement makes possible many of the processes that occur in water, such as protein folding and ion solvation. However, many processes involving water do not take place in pure bulk water, and water's hydrogen bond structural dynamics can be substantially influenced by the presence of, for example, interfaces, ions, and large molecules. In this Account, spectroscopic studies that have been used to explore the details of these influences are discussed. Because rearrangements of water molecules occur so quickly, ultrafast infrared experiments that probe water's hydroxyl stretching mode are useful in providing direct information about water dynamics on the appropriate time scales. Infrared polarization-selective pump-probe experiments and two-dimensional infrared (2D IR) vibrational echo experiments have been used to study the hydrogen bond dynamics of water. Water orientational relaxation, which requires hydrogen bond rearrangements, has been studied at spherical interfaces of ionic reverse micelles and compared with planar interfaces of lamellar structures composed of the same surfactants. Water orientational relaxation slows considerably at interfaces. It is found that the geometry of the interface is less important than the presence of the interface. The influence of ions is shown to slow hydrogen bond rearrangements. However, comparing an ionic interface to a neutral interface demonstrates that the chemical nature of the interface is less important than the presence of the interface. Finally, it is found that the dynamics of water at an organic interface is very similar to water molecules interacting with a large polyether.
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Affiliation(s)
- Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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44
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Fenn EE, Fayer MD. Extracting 2D IR frequency-frequency correlation functions from two component systems. J Chem Phys 2011; 135:074502. [PMID: 21861571 DOI: 10.1063/1.3625278] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The center line slope (CLS) method is often used to extract the frequency-frequency correlation function (FFCF) from 2D IR spectra to delineate dynamics and to identify homogeneous and inhomogeneous contributions to the absorption line shape of a system. While the CLS method is extremely efficient, quite accurate, and immune to many experimental artifacts, it has only been developed and properly applied to systems that have a single vibrational band, or to systems of two species that have spectrally resolved absorption bands. In many cases, the constituent spectra of multiple component systems overlap and cannot be distinguished from each other. This situation creates ambiguity when analyzing 2D IR spectra because dynamics for different species cannot be separated. Here a mathematical formulation is presented that extends the CLS method for a system consisting of two components (chemically distinct uncoupled oscillators). In a single component system, the CLS corresponds to the time-dependent portion of the normalized FFCF. This is not the case for a two component system, as a much more complicated expression arises. The CLS method yields a series of peak locations originating from slices taken through the 2D spectra. The slope through these peak locations yields the CLS value for the 2D spectra at a given T(w). We derive analytically that for two component systems, the peak location of the system can be decomposed into a weighted combination of the peak locations of the constituent spectra. The weighting depends upon the fractional contribution of each species at each wavelength and also on the vibrational lifetimes of both components. It is found that an unknown FFCF for one species can be determined as long as the peak locations (referred to as center line data) of one of the components are known, as well as the vibrational lifetimes, absorption spectra, and other spectral information for both components. This situation can arise when a second species is introduced into a well characterized single species system. An example is a system in which water exists in bulk form and also as water interacting with an interface. An algorithm is presented for back-calculating the unknown FFCF of the second component. The accuracy of the algorithm is tested with a variety of model cases in which all components are initially known. The algorithm successfully reproduces the FFCF for the second component within a reasonable degree of error.
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Affiliation(s)
- Emily E Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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45
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Abstract
In many situations, form biology to geology, water occurs not as the pure bulk liquid but rather in nanoscopic environments, in contact with interfaces, interacting with ionic species, and interacting with large organic molecules. In such situations, water does not behave in the same manner as it does in the pure bulk liquid. Water dynamics are fundamental to many processes such as protein folding and proton transport. Such processes depend on the dynamics of water's hydrogen bonding network. Here, the results of ultrafast infrared experiments are described that shed light on the influences of nanoconfinement, interfaces, ions, and organic molecules on water hydrogen bond dynamics.
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Affiliation(s)
- Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California
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46
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Bian H, Chen H, Li J, Wen X, Zheng J. Nonresonant and Resonant Mode-Specific Intermolecular Vibrational Energy Transfers in Electrolyte Aqueous Solutions. J Phys Chem A 2011; 115:11657-64. [DOI: 10.1021/jp206937u] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hongtao Bian
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Hailong Chen
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jiebo Li
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Xiewen Wen
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Junrong Zheng
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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47
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Fenn EE, Wong DB, Giammanco CH, Fayer MD. Dynamics of Water at the Interface in Reverse Micelles: Measurements of Spectral Diffusion with Two-Dimensional Infrared Vibrational Echoes. J Phys Chem B 2011; 115:11658-70. [DOI: 10.1021/jp206903k] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emily E. Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Daryl B. Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chiara H. Giammanco
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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48
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Fenn EE, Wong DB, Fayer MD. Water dynamics in small reverse micelles in two solvents: two-dimensional infrared vibrational echoes with two-dimensional background subtraction. J Chem Phys 2011; 134:054512. [PMID: 21303143 DOI: 10.1063/1.3532542] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water dynamics as reflected by the spectral diffusion of the water hydroxyl stretch were measured in w(0) = 2 (1.7 nm diameter) Aerosol-OT (AOT)/water reverse micelles in carbon tetrachloride and in isooctane solvents using ultrafast 2D IR vibrational echo spectroscopy. Orientational relaxation and population relaxation are observed for w(0) = 2, 4, and 7.5 in both solvents using IR pump-probe measurements. It is found that the pump-probe observables are sensitive to w(0), but not to the solvent. However, initial analysis of the vibrational echo data from the water nanopool in the reverse micelles in the isooctane solvent seems to yield different dynamics than the CCl(4) system in spite of the fact that the spectra, vibrational lifetimes, and orientational relaxation are the same in the two systems. It is found that there are beat patterns in the interferograms with isooctane as the solvent. The beats are observed from a signal generated by the AOT/isooctane system even when there is no water in the system. A beat subtraction data processing procedure does a reasonable job of removing the distortions in the isooctane data, showing that the reverse micelle dynamics are the same within experimental error regardless of whether isooctane or carbon tetrachloride is used as the organic phase. Two time scales are observed in the vibrational echo data, ~1 and ~10 ps. The slower component contains a significant amount of the total inhomogeneous broadening. Physical arguments indicate that there is a much slower component of spectral diffusion that is too slow to observe within the experimental window, which is limited by the OD stretch vibrational lifetime.
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Affiliation(s)
- Emily E Fenn
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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49
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Max JJ, Chapados C. Isotope effects in liquid water by infrared spectroscopy. V. A sea of OH4ofC2vsymmetry. J Chem Phys 2011; 134:164502. [PMID: 21528968 DOI: 10.1063/1.3581035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jean-Joseph Max
- Département de chimie-biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec G9A 5H7, Canada.
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50
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Bian H, Wen X, Li J, Chen H, Han S, Sun X, Song J, Zhuang W, Zheng J. Ion clustering in aqueous solutions probed with vibrational energy transfer. Proc Natl Acad Sci U S A 2011; 108:4737-4742. [PMCID: PMC3064342 DOI: 10.1073/pnas.1019565108] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023] Open
Abstract
Despite prolonged scientific efforts to unravel the hydration structures of ions in water, many open questions remain, in particular concerning the existences and structures of ion clusters in 1∶1 strong electrolyte aqueous solutions. A combined ultrafast 2D IR and pump/probe study through vibrational energy transfers directly observes ion clustering in aqueous solutions of LiSCN, NaSCN, KSCN and CsSCN. In a near saturated KSCN aqueous solution (water/KSCN molar ratio = 2.4/1), 95% of the anions form ion clusters. Diluting the solution results in fewer, smaller, and tighter clusters. Cations have significant effects on cluster formation. A small cation results in smaller and fewer clusters. The vibrational energy transfer method holds promise for studying a wide variety of other fast short-range molecular interactions.
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Affiliation(s)
- Hongtao Bian
- Department of Chemistry, Rice University, Houston, TX 77005; and
| | - Xiewen Wen
- Department of Chemistry, Rice University, Houston, TX 77005; and
| | - Jiebo Li
- Department of Chemistry, Rice University, Houston, TX 77005; and
| | - Hailong Chen
- Department of Chemistry, Rice University, Houston, TX 77005; and
| | - Suzee Han
- Department of Chemistry, Rice University, Houston, TX 77005; and
| | - Xiuquan Sun
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Jian Song
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Junrong Zheng
- Department of Chemistry, Rice University, Houston, TX 77005; and
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