1
|
Perets EA, Konstantinovsky D, Santiago T, Videla PE, Tremblay M, Velarde L, Batista VS, Hammes-Schiffer S, Yan ECY. Beyond the "spine of hydration": Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures. J Chem Phys 2024; 161:095104. [PMID: 39230381 DOI: 10.1063/5.0220479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration.
Collapse
Affiliation(s)
- Ethan A Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Ty Santiago
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Pablo E Videla
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Matthew Tremblay
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Luis Velarde
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| |
Collapse
|
2
|
Gabriel JP, Horstmann R, Tress M. Local and global expansivity in water. J Chem Phys 2024; 160:234502. [PMID: 38884401 DOI: 10.1063/5.0203924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
The supra-molecular structure of a liquid is strongly connected to its dynamics, which in turn control macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential to understand the thermal evolution of the dynamics ranging from the liquid to the glass. Here, we combine infrared spectroscopy (IR) measurements of the hydrogen (H) bond stretching vibration of water with molecular dynamics simulations and employ a quantitative analysis to extract the inter-molecular H-bond length in a wide temperature range of the liquid. The extracted expansivity of this H-bond differs strongly from that of the average nearest neighbor distance of oxygen atoms obtained through a common conversion of mass density. However, both properties can be connected through a simple model based on a random loose packing of spheres with a variable coordination number, which demonstrates the relevance of supra-molecular arrangement. Furthermore, the exclusion of the expansivity of the inter-molecular H-bonds reveals that the most compact molecular arrangement is formed in the range of ∼316-331K (i.e., above the density maximum) close to the temperature of several pressure-related anomalies, which indicates a characteristic point in the supra-molecular arrangement. These results confirm our earlier approach to deduce inter-molecular H-bond lengths via IR in polyalcohols [Gabriel et al. J. Chem. Phys. 154, 024503 (2021)] quantitatively and open a new alley to investigate the role of inter-molecular expansion as a precursor of molecular fluctuations on a bond-specific level.
Collapse
Affiliation(s)
- Jan Philipp Gabriel
- Institute of Materials Physics in Space, German Aerospace Center, 51170 Köln, Germany
| | - Robin Horstmann
- Institute for Condensed Matter Physics, Technical University Darmstadt, 64289 Darmstadt, Germany
| | - Martin Tress
- Peter Debye Institute for Soft Matter Research, Leipzig University, 04103 Leipzig, Germany
| |
Collapse
|
3
|
Sung W, Inoue KI, Nihonyanagi S, Tahara T. Unified picture of vibrational relaxation of OH stretch at the air/water interface. Nat Commun 2024; 15:1258. [PMID: 38341439 DOI: 10.1038/s41467-024-45388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The elucidation of the energy dissipation process is crucial for understanding various phenomena occurring in nature. Yet, the vibrational relaxation and its timescale at the water interface, where the hydrogen-bonding network is truncated, are not well understood and are still under debate. In the present study, we focus on the OH stretch of interfacial water at the air/water interface and investigate its vibrational relaxation by femtosecond time-resolved, heterodyne-detected vibrational sum-frequency generation (TR-HD-VSFG) spectroscopy. The temporal change of the vibrationally excited hydrogen-bonded (HB) OH stretch band (ν=1→2 transition) is measured, enabling us to determine reliable vibrational relaxation (T1) time. The T1 times obtained with direct excitations of HB OH stretch are 0.2-0.4 ps, which are similar to the T1 time in bulk water and do not noticeably change with the excitation frequency. It suggests that vibrational relaxation of the interfacial HB OH proceeds predominantly with the intramolecular relaxation mechanism as in the case of bulk water. The delayed rise and following decay of the excited-state HB OH band are observed with excitation of free OH stretch, indicating conversion from excited free OH to excited HB OH (~0.9 ps) followed by relaxation to low-frequency vibrations (~0.3 ps). This study provides a complete set of the T1 time of the interfacial OH stretch and presents a unified picture of its vibrational relaxation at the air/water interface.
Collapse
Affiliation(s)
- Woongmo Sung
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Ken-Ichi Inoue
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| |
Collapse
|
4
|
Inoue K, Litman Y, Wilkins DM, Nagata Y, Okuno M. Is Unified Understanding of Vibrational Coupling of Water Possible? Hyper-Raman Measurement and Machine Learning Spectra. J Phys Chem Lett 2023; 14:3063-3068. [PMID: 36947156 DOI: 10.1021/acs.jpclett.3c00398] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The impact of the vibrational coupling of the OH stretch mode on the spectra differs significantly between IR and Raman spectra of water. Unified understanding of the vibrational couplings is not yet achieved. By using a different class of vibrational spectroscopy, hyper-Raman (HR) spectroscopy, together with machine-learning-assisted HR spectra calculation, we examine the impact of the vibrational couplings of water through the comparison of isotopically diluted H2O and pure H2O. We found that the isotopic dilution reduces the HR bandwidths, but the impact of the vibrational coupling is smaller than in the IR and parallel-polarized Raman. Machine learning HR spectra indicate that the intermolecular coupling plays a major role in broadening the bandwidth, while the intramolecular coupling is negligibly small, which is consistent with the IR and Raman spectra. Our result clearly demonstrates a limited impact of the intramolecular vibration, independent of the selection rules of vibrational spectroscopies.
Collapse
Affiliation(s)
- Kazuki Inoue
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Yair Litman
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David M Wilkins
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Masanari Okuno
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| |
Collapse
|
5
|
Honegger P, Steinhauser O, Schröder C. Collective Spectroscopy of Solvation Phenomena: Conflicts, Challenges, and Opportunities. J Phys Chem Lett 2023; 14:609-618. [PMID: 36634000 DOI: 10.1021/acs.jpclett.2c03574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Different spectroscopy types reveal different aspects of molecular processes in soft matter. In particular, collective observables can provide insights into intermolecular correlations invisible to the more popular single-particle methods. In this perspective we feature the dielectric relaxation spectroscopy (DRS) with an emphasis on the proper interpretation of this complex observable aided by computational spectroscopy. While we focus on the history and recent advances of DRS in the fields of biomolecular hydration and nanoconfinement, the discussion transcends this particular field and provides a guide for how collective spectroscopy types supported by computational decomposition can be employed to further our understanding of soft matter phenomena.
Collapse
Affiliation(s)
- Philipp Honegger
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, BostonMassachusetts02115, United States
| | - Othmar Steinhauser
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
| | - Christian Schröder
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
| |
Collapse
|
6
|
Hu Q, Zhao H, Ouyang S, Liang Y, Yang H, Zhu X. The water structure around chloride ion investigated from D2O ↔ H2O substitution effect. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
7
|
Role of the electrostatic interactions in the changes in the CN stretching frequency of benzonitrile interacting with hydrogen-bond donating molecules. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119714] [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]
|
8
|
Lee E, Baiz CR. How cryoprotectants work: hydrogen-bonding in low-temperature vitrified solutions. Chem Sci 2022; 13:9980-9984. [PMID: 36128234 PMCID: PMC9430440 DOI: 10.1039/d2sc03188d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) increases cell and tissue viability at low temperatures and is commonly used as a cryoprotectant for cryogenic storage of biological materials. DMSO disorders the water hydrogen-bond networks and inhibits ice-crystal growth, though the specific DMSO interactions with water are difficult to characterize. In this study, we use a combination of Fourier Transform infrared spectroscopy (FTIR), molecular dynamics simulations, and vibrational frequency maps to characterize the temperature-dependent hydrogen bonding interactions of DMSO with water from 30 °C to -80 °C. Specifically, broad peaks in O-D stretch vibrational spectra of DMSO and deuterated water (HDO) cosolvent systems show that the hydrogen bond networks become increasingly disrupted compared to pure water. Simulations demonstrated that these disrupted hydrogen bond networks remain largely localized to the first hydration shell of DMSO, which explains the high DMSO concentrations needed to prevent ice crystal formation in cryopreservation applications.
Collapse
Affiliation(s)
- Euihyun Lee
- Department of Chemistry, The University of Texas at Austin Austin TX 78712 USA
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin Austin TX 78712 USA
| |
Collapse
|
9
|
Kwac K, Freedman H, Cho M. Machine Learning Approach for Describing Water OH Stretch Vibrations. J Chem Theory Comput 2021; 17:6353-6365. [PMID: 34498885 DOI: 10.1021/acs.jctc.1c00540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A machine learning approach employing neural networks is developed to calculate the vibrational frequency shifts and transition dipole moments of the symmetric and antisymmetric OH stretch vibrations of a water molecule surrounded by water molecules. We employed the atom-centered symmetry functions (ACSFs), polynomial functions, and Gaussian-type orbital-based density vectors as descriptor functions and compared their performances in predicting vibrational frequency shifts using the trained neural networks. The ACSFs perform best in modeling the frequency shifts of the OH stretch vibration of water among the types of descriptor functions considered in this paper. However, the differences in performance among these three descriptors are not significant. We also tried a feature selection method called CUR matrix decomposition to assess the importance and leverage of the individual functions in the set of selected descriptor functions. We found that a significant number of those functions included in the set of descriptor functions give redundant information in describing the configuration of the water system. We here show that the predicted vibrational frequency shifts by trained neural networks successfully describe the solvent-solute interaction-induced fluctuations of OH stretch frequencies.
Collapse
Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Holly Freedman
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, 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
| |
Collapse
|
10
|
Surface, textural and catalytic properties of pyridinium hydrogen sulfate ionic liquid heterogenized on activated carbon carrier. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117192] [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]
|
11
|
Hanson MD, Readnour JA, Hassanali AA, Corcelli SA. Coupled Local-Mode Approach for the Calculation of Vibrational Spectra: Application to Protonated Water Clusters. J Phys Chem Lett 2021; 12:9226-9232. [PMID: 34529914 DOI: 10.1021/acs.jpclett.1c02254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Spectroscopic studies of protonated water clusters (PWCs) have yielded enormous insights into the fundamental nature of the hydrated proton. Here, we introduce a new coupled local-mode (CLM) approach to calculate PWC OH stretch vibrational spectra. The CLM method combines a sampling of representative configurations from density functional theory (DFT)-based ab initio molecular dynamics (AIMD) simulations with DFT calculations of local-mode vibrational frequencies and couplings. Calculations of inhomogeneous OH stretch vibrational spectra for H+(H2O)4 and H+(H2O)21 agree well with experiment and higher-level calculations, and decompositions of the calculated spectra in terms of the coupled modes aids in the interpretation of the spectra. This observation is consistent with the idea that capturing anharmonicity and coupling is as important to accuracy as the underlying level of electronic structure theory. The CLM calculations can easily discern the configuration that dominates the experimental measurement for H+(H2O)5, which can adopt several low-energy conformations.
Collapse
Affiliation(s)
- Matthew D Hanson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Janel A Readnour
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ali A Hassanali
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera, 11 I - 34151 Trieste, Italy
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
12
|
Zhang X, Chen X, Kuroda DG. Computing the frequency fluctuation dynamics of highly coupled vibrational transitions using neural networks. J Chem Phys 2021; 154:164514. [PMID: 33940799 DOI: 10.1063/5.0044911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The description of frequency fluctuations for highly coupled vibrational transitions has been a challenging problem in physical chemistry. In particular, the complexity of their vibrational Hamiltonian does not allow us to directly derive the time evolution of vibrational frequencies for these systems. In this paper, we present a new approach to this problem by exploiting the artificial neural network to describe the vibrational frequencies without relying on the deconstruction of the vibrational Hamiltonian. To this end, we first explored the use of the methodology to predict the frequency fluctuations of the amide I mode of N-methylacetamide in water. The results show good performance compared with the previous experimental and theoretical results. In the second part, the neural network approach is used to investigate the frequency fluctuations of the highly coupled carbonyl stretch modes for the organic carbonates in the solvation shell of the lithium ion. In this case, the frequency fluctuation predicted by the neural networks shows a good agreement with the experimental results, which suggests that this model can be used to describe the dynamics of the frequency in highly coupled transitions.
Collapse
Affiliation(s)
- Xiaoliu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| |
Collapse
|
13
|
Torii H, Ukawa R. Role of Intermolecular Charge Fluxes in the Hydrogen-Bond-Induced Frequency Shifts of the OH Stretching Mode of Water. J Phys Chem B 2021; 125:1468-1475. [PMID: 33506673 DOI: 10.1021/acs.jpcb.0c11461] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relation between the vibrational properties and the electrostatic situations of the vibrating functional group is useful to predict vibrational spectroscopic features based on, for example, classical molecular dynamics of liquids or biomolecular systems, but to pursue its generality or the extent of applicability, it is required to understand the mechanisms giving rise to it. Here such an analysis is carried out for the OH stretching mode of water. By examining the correlations among various (structural, vibrational, and electrostatic) properties and by analyzing the spatial characteristics of the behavior of electrons occurring upon the vibration, it is shown that the dependence of the vibrational frequency and the dipole derivative of the OH stretching mode on the electric field is not of purely electrostatic origin, and the delocalized electronic motions occurring with this mode, called intermolecular charge fluxes, related to both the dipole first and second derivatives play important roles.
Collapse
Affiliation(s)
- Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Ryota Ukawa
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| |
Collapse
|
14
|
From Infrared Spectra to Macroscopic Mechanical Properties of sH Gas Hydrates through Atomistic Calculations. Molecules 2020; 25:molecules25235568. [PMID: 33260942 PMCID: PMC7729739 DOI: 10.3390/molecules25235568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/31/2020] [Accepted: 11/23/2020] [Indexed: 11/17/2022] Open
Abstract
The vibrational characteristics of gas hydrates are key identifying molecular features of their structure and chemical composition. Density functional theory (DFT)-based IR spectra are one of the efficient tools that can be used to distinguish the vibrational signatures of gas hydrates. In this work, ab initio DFT-based IR technique is applied to analyze the vibrational and mechanical features of structure-H (sH) gas hydrate. IR spectra of different sH hydrates are obtained at 0 K at equilibrium and under applied pressure. Information about the main vibrational modes of sH hydrates and the factors that affect them such as guest type and pressure are revealed. The obtained IR spectra of sH gas hydrates agree with experimental/computational literature values. Hydrogen bond’s vibrational frequencies are used to determine the hydrate’s Young’s modulus which confirms the role of these bonds in defining sH hydrate’s elasticity. Vibrational frequencies depend on pressure and hydrate’s O···O interatomic distance. OH vibrational frequency shifts are related to the OH covalent bond length and present an indication of sH hydrate’s hydrogen bond strength. This work presents a new route to determine mechanical properties for sH hydrate based on IR spectra and contributes to the relatively small database of gas hydrates’ physical and vibrational properties.
Collapse
|
15
|
|
16
|
Mason TG, Seeger ZL, Nguyen ALP, Fujita K, Izgorodina EI. Predicting Entropic Effects of Water Mixing with Ionic Liquids Containing Anions of Strong Hydrogen Bonding Ability: Role of the Cation. J Phys Chem B 2020; 124:9182-9194. [PMID: 33007160 DOI: 10.1021/acs.jpcb.0c07732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionic liquids (ILs) such as choline dihydrogen phosphate exhibit an extraordinary solubilizing ability for proteins such as cytochrome C when mixed with 20 wt % water. Most widely used imidazolium-based ionic liquids coupled with dihydrogen phosphate do not exhibit the same solubilizing properties, suggesting that a multifunctional cation such as choline might play a key role in enhancing these properties of ionic liquid mixtures with water. In this theoretical work, we compare intermolecular interactions between the water molecule and ionic liquid ions in two ion-paired clusters of choline- and 1-butyl-3-methyl-imidazolium-based ionic liquids coupled with acetate, dihydrogen phosphate, and mesylate. Gibbs free energy (GFE) of solvation of water in these ionic liquids was calculated. Incorporation of a water molecule into ionic liquid clusters was accompanied by negative GFEs of solvation in both types of cations. These results were in good agreement with previously reported experimental GFEs of solvation of water in ILs. Compared to imidazolium-based clusters, strong interionic interactions of choline ionic liquids resulted in more negative GFEs due to their smaller deformation upon the addition of a water molecule, with dihydrogen phosphate and mesylate predicting the lowest GFEs of -30.1 and -43.5 kJ/mol-1, respectively. Lower GFEs of solvation of water in choline-based clusters were also accompanied with smaller entropic penalties, suggesting that water easily incorporates itself into the existing ionic network. Analysis of the intramolecular bonds within the water molecule showed that the choline hydroxyl group donates electron density to the neighboring water molecule, leading to additional polarization. The predicted infrared spectra of clusters of ionic liquids with water showed a pronounced red shift due to strongly polarized O-H bonds, in excellent agreement with the experimentally measured infrared spectra of ionic liquid mixtures with water. Increased polarization of water in choline-based ionic liquids undoubtedly creates more effective solvents for stabilizing biological molecules such as proteins.
Collapse
Affiliation(s)
- Thomas G Mason
- School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, VIC 3800, Australia
| | - Zoe L Seeger
- School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, VIC 3800, Australia
| | - Anh L P Nguyen
- School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, VIC 3800, Australia
| | - Kyoko Fujita
- Department of Pathophysiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Ekaterina I Izgorodina
- School of Chemistry, Monash University, 17 Rainforest Walk, Clayton, VIC 3800, Australia
| |
Collapse
|
17
|
Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
Collapse
Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
| |
Collapse
|
18
|
Yeadon DJ, Jacquemin J, Plechkova NV, Maréchal M, Seddon KR. Induced Protic Behaviour in Aprotonic Ionic Liquids by Anion Basicity for Efficient Carbon Dioxide Capture. Chemphyschem 2020; 21:1369-1374. [PMID: 32421223 DOI: 10.1002/cphc.202000320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/18/2020] [Indexed: 11/09/2022]
Abstract
The interactions between aprotonic tetrabutylphosphonium carboxylate ionic liquids (ILs), [P4 4 4 4 ][Cn COO] (n=1, 2 and 7), and water were investigated. The cation-anion interactions occur via the α-1 H on [P4 4 4 4 ]+ and the carboxylate headgroup of the anion. Upon addition, H2 O localises around the carboxylate headgroups, inducing an electron inductive effect towards the oxygens, leading to ion-pair separation. Studies with D2 O and [P4 4 4 4 ][Cn COO] revealed protic behaviour of the systems, with proton/deuterium exchange occurring at the α-1 H of the cation, promoted by the basicity of the anion, forming an intermediate ylide. The greater influence of van der Waals forces of the [P4 4 4 4 ][C7 COO] system allows for re-orientation of the ions through larger interdigitation. The protic behaviour of the neat ILs allows for CO2 to be chemically absorbed on the ylide intermediate, forming a phosphonium-carboxylate zwitterion, signifying proton exchange occurs even in the absence of H2 O. The absorption of CO2 in equimolar IL-H2 O mixtures forms a hydrogen carbonate, through a proposed reaction of the CO2 with an intermediate hydroxide, and carboxylic acid.
Collapse
Affiliation(s)
- Darius J Yeadon
- The QUILL Research Centre The School of Chemistry & Chemical Engineering, Queen's University of Belfast, Belfast, BT9 5AG, United Kingdom.,Laboratoire PCM2E, Université de Tours, Parc de Grandmont, 37200, Tours, France
| | - Johan Jacquemin
- The QUILL Research Centre The School of Chemistry & Chemical Engineering, Queen's University of Belfast, Belfast, BT9 5AG, United Kingdom.,Laboratoire PCM2E, Université de Tours, Parc de Grandmont, 37200, Tours, France.,Materials Science and Nano-engineering (MSN) Department, Mohammed VI Polytechnic University (UM6P), Lot 660 - Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Natalia V Plechkova
- The QUILL Research Centre The School of Chemistry & Chemical Engineering, Queen's University of Belfast, Belfast, BT9 5AG, United Kingdom
| | - Manuel Maréchal
- Univ. Grenoble Alpes, CNRS, CEA, IRIG-SyMMES, 38000, Grenoble, France
| | - Kenneth R Seddon
- The QUILL Research Centre The School of Chemistry & Chemical Engineering, Queen's University of Belfast, Belfast, BT9 5AG, United Kingdom
| |
Collapse
|
19
|
Yu Y, Shi L. Vibrational solvatochromism of the ester carbonyl vibration of PCBM in organic solutions. J Chem Phys 2019. [DOI: 10.1063/1.5111046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Yue Yu
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Liang Shi
- School of Natural Sciences, University of California, Merced, California 95343, USA
| |
Collapse
|
20
|
Kaliannan NK, Henao Aristizabal A, Wiebeler H, Zysk F, Ohto T, Nagata Y, Kühne TD. Impact of intermolecular vibrational coupling effects on the sum-frequency generation spectra of the water/air interface. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1620358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Naveen Kumar Kaliannan
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Andres Henao Aristizabal
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Hendrik Wiebeler
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Frederik Zysk
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
| | - Tatsuhiko Ohto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Yuki Nagata
- Max-Planck Institute for Polymer Research, Mainz, Germany
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Paderborn, Germany
- Paderborn Center for Parallel Computing and Institute for Lightweight Design, University of Paderborn, Paderborn, Germany
| |
Collapse
|
21
|
Vlasic TM, Servio PD, Rey AD. Infrared Spectra of Gas Hydrates from First-Principles. J Phys Chem B 2019; 123:936-947. [PMID: 30608166 DOI: 10.1021/acs.jpcb.8b10223] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The infrared spectra of sII gas hydrates have been computed using density functional theory for the first time, at equilibrium, and under pressure. It is also the first account of a full vibrational analysis (both guest and host vibrations) for gas hydrates with hydrocarbon guest molecules. Five hydrate structures were investigated: empty, propane, isobutane, ethane-methane, and propane-methane sII hydrates. The computed IR spectra are in good agreement with available experimental and theoretical results. The OH stretching frequencies were found to increase, while the H-bond stretching and H2O libration frequencies decreased with an increase in guest size and cage occupancy and with a decrease in pressure. The H2O bending vibrations are relatively independent of guest size, cage occupancy, pressure, temperature, and crystal structure. The guest vibrational modes, especially the bending modes, also have minimal pressure dependence. We have also provided more quantitative evidence that gas hydrate material properties are defined by their hydrogen bond properties, by linking H-bond strength to Young's modulus. The results and ensuing vibrational analysis presented in this paper are a valuable contribution to the ongoing efforts into developing more accurate gas hydrate identification and characterization methods in the laboratory, in industry/nature, and even in outer space.
Collapse
Affiliation(s)
- Thomas M Vlasic
- Department of Chemical Engineering , McGill University , Montréal , QC , H3A 0C5 , Canada
| | - Phillip D Servio
- Department of Chemical Engineering , McGill University , Montréal , QC , H3A 0C5 , Canada
| | - Alejandro D Rey
- Department of Chemical Engineering , McGill University , Montréal , QC , H3A 0C5 , Canada
| |
Collapse
|
22
|
Hu Q, Zhao H, Ouyang S. Interpreting the Raman OH/OD stretch band of ice from isotopic substitution and phase transition effects. Phys Chem Chem Phys 2018; 20:28600-28605. [PMID: 30406247 DOI: 10.1039/c8cp06281a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the OD/OH stretch band (ODSB/OHSB) features for the Raman spectra of ice remains a challenge. This study measures the ODSB/OHSB for isotopically substituted D2O/H2O (with volume ratio VD2O/VH2O of 1/0, 4/1, 1/1, 1/4 and 0/1) ice Ih, and compares them with those for liquid water and ices in various phases. The data show that istopic substitution (IS) narrows the ODSB/OHSB of ice from both the low-frequency and the high-frequency side to the middle of the OD/OH stretch regions, but in contrast, IS enhances the high-frequency part of the ODSB/OHSB for liquid water. The ODSB/OHSB features of ice and their dependences on IS and phase transition can be understood basically from the concept that ice has diverse HB configurations that depend on the ice lattice form and the proton (dis)order and essentially determine the intermolecular vibrational couplings in ice. Combined with a Gaussian fitting analysis, more details for the HB configurations in ice are revealed: tetrahedral HB profiles, which are responsible for the main peak, are dominant and non-tetrahedral ones, which bring about the high-frequency shoulders, are also important. On IS, the proportion of tetrahedral HB profiles sees a dramatic decrease.
Collapse
Affiliation(s)
- Qingcheng Hu
- Key Laboratory of Integrated Exploitation of Bayan Obo Multi-Metal Resources, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | | | | |
Collapse
|
23
|
Carpenter WB, Fournier JA, Biswas R, Voth GA, Tokmakoff A. Delocalization and stretch-bend mixing of the HOH bend in liquid water. J Chem Phys 2018; 147:084503. [PMID: 28863511 DOI: 10.1063/1.4987153] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Liquid water's rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H2O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H2O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm-1 to beyond 1900 cm-1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm-1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest dynamical time scale is 80 fs for the polarization anisotropy decay, providing evidence for the delocalized or excitonic character of the bend. Normal mode analysis conducted on water clusters extracted from molecular dynamics simulations corroborate significant stretch-bend mixing and indicate delocalization of δHOH on 2-7 water molecules.
Collapse
Affiliation(s)
- William B Carpenter
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Fournier
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rajib Biswas
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Gregory A Voth
- 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
| |
Collapse
|
24
|
Sanders SE, Vanselous H, Petersen PB. Water at surfaces with tunable surface chemistries. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:113001. [PMID: 29393860 DOI: 10.1088/1361-648x/aaacb5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Aqueous interfaces are ubiquitous in natural environments, spanning atmospheric, geological, oceanographic, and biological systems, as well as in technical applications, such as fuel cells and membrane filtration. Where liquid water terminates at a surface, an interfacial region is formed, which exhibits distinct properties from the bulk aqueous phase. The unique properties of water are governed by the hydrogen-bonded network. The chemical and physical properties of the surface dictate the boundary conditions of the bulk hydrogen-bonded network and thus the interfacial properties of the water and any molecules in that region. Understanding the properties of interfacial water requires systematically characterizing the structure and dynamics of interfacial water as a function of the surface chemistry. In this review, we focus on the use of experimental surface-specific spectroscopic methods to understand the properties of interfacial water as a function of surface chemistry. Investigations of the air-water interface, as well as efforts in tuning the properties of the air-water interface by adding solutes or surfactants, are briefly discussed. Buried aqueous interfaces can be accessed with careful selection of spectroscopic technique and sample configuration, further expanding the range of chemical environments that can be probed, including solid inorganic materials, polymers, and water immiscible liquids. Solid substrates can be finely tuned by functionalization with self-assembled monolayers, polymers, or biomolecules. These variables provide a platform for systematically tuning the chemical nature of the interface and examining the resulting water structure. Finally, time-resolved methods to probe the dynamics of interfacial water are briefly summarized before discussing the current status and future directions in studying the structure and dynamics of interfacial water.
Collapse
Affiliation(s)
- Stephanie E Sanders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States of America
| | | | | |
Collapse
|
25
|
Grechko M, Hasegawa T, D'Angelo F, Ito H, Turchinovich D, Nagata Y, Bonn M. Coupling between intra- and intermolecular motions in liquid water revealed by two-dimensional terahertz-infrared-visible spectroscopy. Nat Commun 2018; 9:885. [PMID: 29491413 PMCID: PMC5830436 DOI: 10.1038/s41467-018-03303-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
The interaction between intramolecular and intermolecular degrees of freedom in liquid water underlies fundamental chemical and physical phenomena such as energy dissipation and proton transfer. Yet, it has been challenging to elucidate the coupling between these different types of modes. Here, we report on the direct observation and quantification of the coupling between intermolecular and intramolecular coordinates using two-dimensional, ultra-broadband, terahertz-infrared-visible (2D TIRV) spectroscopy and molecular dynamics calculations. Our study reveals strong coupling of the O-H stretch vibration, independent of the degree of delocalization of this high-frequency mode, to low-frequency intermolecular motions over a wide frequency range from 50 to 250 cm-1, corresponding to both the intermolecular hydrogen bond bending (≈ 60 cm-1) and stretching (≈ 180 cm-1) modes. Our results provide mechanistic insights into the coupling of the O-H stretch vibration to collective, delocalized intermolecular modes.
Collapse
Affiliation(s)
- Maksim Grechko
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany.
| | - Taisuke Hasegawa
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Francesco D'Angelo
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Hironobu Ito
- Department of Chemistry, Faculty of Education, Shizuoka University, 836 Ohya, 422-8529, Shizuoka, Japan
| | - Dmitry Turchinovich
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
- Fakultät für Physik, Universität Duisburg-Essen, Lotharstr. 1, 47057, Duisburg, Germany
| | - Yuki Nagata
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany
| |
Collapse
|
26
|
Affiliation(s)
- Xinzijian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| |
Collapse
|
27
|
Reddy SK, Moberg DR, Straight SC, Paesani F. Temperature-dependent vibrational spectra and structure of liquid water from classical and quantum simulations with the MB-pol potential energy function. J Chem Phys 2017; 147:244504. [DOI: 10.1063/1.5006480] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Sandeep K. Reddy
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Daniel R. Moberg
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Shelby C. Straight
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, Materials Science and Engineering, and San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
28
|
Jeon K, Yang M. Dimension of discrete variable representation for mixed quantum/classical computation of three lowest vibrational states of OH stretching in liquid water. J Chem Phys 2017; 146:054107. [PMID: 28178837 DOI: 10.1063/1.4974934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three low-lying vibrational states of molecular systems are responsible for the signals of linear and third-order nonlinear vibrational spectroscopies. Theoretical studies based on mixed quantum/classical calculations provide a powerful way to analyze those experiments. A statistically meaningful result can be obtained from the calculations by solving the vibrational Schrödinger equation over many numbers of molecular configurations. The discrete variable representation (DVR) method is a useful technique to calculate vibrational eigenstates subject to an arbitrary anharmonic potential surface. Considering the large number of molecular configurations over which the DVR calculations are repeated, the calculations are desired to be optimized in balance between the cost and accuracy. We determine a dimension of the DVR method which appears to be optimum for the calculations of the three states of molecular vibrations with anharmonic strengths often found in realistic molecular systems. We apply the numerical technique to calculate the local OH stretching frequencies of liquid water, which are well known to be widely distributed due to the inhomogeneity in molecular configuration, and found that the frequencies of the 0-1 and 1-2 transitions are highly correlated. An empirical relation between the two frequencies is suggested and compared with the experimental data of nonlinear IR spectroscopies.
Collapse
Affiliation(s)
- Kiyoung Jeon
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, South Korea
| | - Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, South Korea
| |
Collapse
|
29
|
Zhou R, Wu F, Zhou X, Wang H, Zheng X. The structural configurations of Ethylene Trithiocarbonate in the binary mixture (SCS 2 CH 2 CH 2 +CHCl 3 ) investigated by polarized Raman: Experimental and quantum chemical results. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.09.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Hu Q, Zhao H, Ouyang S. Understanding water structure from Raman spectra of isotopic substitution H2O/D2O up to 573 K. Phys Chem Chem Phys 2017; 19:21540-21547. [DOI: 10.1039/c7cp02065a] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The OH/OD stretch band features on Raman spectra of isotopic substitution H2O/D2O at temperatures up to 573 K are correlated with a multi-structure model that water has five dominant hydrogen bonding configurations: tetrahedral, deformed tetrahedral, single donor, single hydrogen bonded water and free water.
Collapse
Affiliation(s)
- Qingcheng Hu
- Key Laboratory of Integrated Exploitation of Bayan Obo Multi-Metal Resources
- Inner Mongolia University of Science and Technology
- Baotou 014010
- China
| | - Haiwen Zhao
- Key Laboratory of Integrated Exploitation of Bayan Obo Multi-Metal Resources
- Inner Mongolia University of Science and Technology
- Baotou 014010
- China
| | - Shunli Ouyang
- Key Laboratory of Integrated Exploitation of Bayan Obo Multi-Metal Resources
- Inner Mongolia University of Science and Technology
- Baotou 014010
- China
| |
Collapse
|
31
|
Schaefer J, Backus EHG, Nagata Y, Bonn M. Both Inter- and Intramolecular Coupling of O-H Groups Determine the Vibrational Response of the Water/Air Interface. J Phys Chem Lett 2016; 7:4591-4595. [PMID: 27797213 DOI: 10.1021/acs.jpclett.6b02513] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Vibrational coupling is relevant not only for dissipation of excess energy after chemical reactions but also for elucidating molecular structure and dynamics. It is particularly important for O-H stretch vibrational spectra of water, for which it is known that in bulk both intra- and intermolecular coupling alter the intensity and line shape of the spectra. In contrast with bulk, the unified picture of the inter/intra-molecular coupling of O-H groups at the water-air interface has been lacking. Here, combining sum-frequency generation experiments and simulation for isotopically diluted water and alcohols, we unveil effects of inter- and intramolecular coupling on the vibrational spectra of interfacial water. Our results show that both inter- and intramolecular coupling contribute to the O-H stretch vibrational response of the neat H2O surface, with intramolecular coupling generating a double-peak feature, while the intermolecular coupling induces a significant red shift in the O-H stretch response.
Collapse
Affiliation(s)
- Jan Schaefer
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Ellen H G Backus
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
32
|
De Marco L, Fournier JA, Thämer M, Carpenter W, Tokmakoff A. Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy. J Chem Phys 2016; 145:094501. [DOI: 10.1063/1.4961752] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - Joseph A. Fournier
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - Martin Thämer
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - William Carpenter
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
| |
Collapse
|
33
|
Lee H, Choi JH, Verma PK, Cho M. Computational Vibrational Spectroscopy of HDO in Osmolyte–Water Solutions. J Phys Chem A 2016; 120:5874-86. [DOI: 10.1021/acs.jpca.6b06305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
34
|
De Marco L, Carpenter W, Liu H, Biswas R, Bowman JM, Tokmakoff A. Differences in the Vibrational Dynamics of H(2)O and D(2)O: Observation of Symmetric and Antisymmetric Stretching Vibrations in Heavy Water. J Phys Chem Lett 2016; 7:1769-1774. [PMID: 27115316 DOI: 10.1021/acs.jpclett.6b00668] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Water's ability to donate and accept hydrogen bonds leads to unique and complex collective dynamical phenomena associated with its hydrogen-bond network. It is appreciated that the vibrations governing liquid water's molecular dynamics are delocalized, with nuclear motion evolving coherently over the span of several molecules. Using two-dimensional infrared spectroscopy, we have found that the nuclear motions of heavy water, D2O, are qualitatively different than those of H2O. The nonlinear spectrum of liquid D2O reveals distinct O-D stretching resonances, in contrast to H2O. Furthermore, our data indicates that condensed-phase O-D vibrations have a different character than those in the gas phase, which we understand in terms of weakly delocalized symmetric and antisymmetric stretching vibrations. This difference in molecular dynamics reflects the shift in the balance between intra- and intermolecular couplings upon deuteration, an effect which can be understood in terms of the anharmonicity of the nuclear potential energy surface.
Collapse
Affiliation(s)
- Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - William Carpenter
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Hanchao Liu
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Rajib Biswas
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University , 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
| |
Collapse
|
35
|
Perakis F, De Marco L, Shalit A, Tang F, Kann ZR, Kühne TD, Torre R, Bonn M, Nagata Y. Vibrational Spectroscopy and Dynamics of Water. Chem Rev 2016; 116:7590-607. [DOI: 10.1021/acs.chemrev.5b00640] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fivos Perakis
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Luigi De Marco
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Chemistry and James Franck Institute, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Andrey Shalit
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Fujie Tang
- International Center for Quantum Materials, Peking University, 5 Yiheyuan Road, Haidian, Beijing 100871, China
| | - Zachary R. Kann
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States,
| | - Thomas D. Kühne
- Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Renato Torre
- European Lab for Nonlinear Spectroscopy and Dipartimento di Fisica e Astronomia, Università di Firenze, Via Nello Carrara 1, Sesto Fiorentino (Firenze) I-50019, Italy
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
36
|
Yang M. Validity of Förster Theory for Vibrational Energy Transfer in Low-Dimensional Water. J Phys Chem B 2015; 119:15516-21. [DOI: 10.1021/acs.jpcb.5b10371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Korea
| |
Collapse
|
37
|
Liu H, Wang Y, Bowman JM. Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment. J Chem Phys 2015; 142:194502. [PMID: 26001464 DOI: 10.1063/1.4921045] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
Collapse
Affiliation(s)
- Hanchao Liu
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Yimin Wang
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| |
Collapse
|
38
|
Ni Y, Skinner JL. IR and SFG vibrational spectroscopy of the water bend in the bulk liquid and at the liquid-vapor interface, respectively. J Chem Phys 2015; 143:014502. [DOI: 10.1063/1.4923462] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yicun Ni
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| |
Collapse
|
39
|
Choi JH, Kim H, Kim S, Lim S, Chon B, Cho M. Ion aggregation in high salt solutions. III. Computational vibrational spectroscopy of HDO in aqueous salt solutions. J Chem Phys 2015; 142:204102. [DOI: 10.1063/1.4920972] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Seongheun Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Sohee Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Bonghwan Chon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| |
Collapse
|
40
|
Zhang C, Guidoni L, Kühne TD. Competing factors on the frequency separation between the OH stretching modes in water. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2014.09.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
41
|
Medders GR, Paesani F. Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics. J Chem Theory Comput 2015; 11:1145-54. [PMID: 26579763 DOI: 10.1021/ct501131j] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Vibrational spectroscopy is a powerful technique to probe the structure and dynamics of water. However, deriving an unambiguous molecular-level interpretation of the experimental spectral features remains a challenge due to the complexity of the underlying hydrogen-bonding network. In this contribution, we present an integrated theoretical and computational framework (named many-body molecular dynamics or MB-MD) that, by systematically removing uncertainties associated with existing approaches, enables a rigorous modeling of vibrational spectra of water from quantum dynamical simulations. Specifically, we extend approaches used to model the many-body expansion of interaction energies to develop many-body representations of the dipole moment and polarizability of water. The combination of these "first-principles" representations with centroid molecular dynamics simulations enables the simulation of infrared and Raman spectra of liquid water under ambient conditions that, without relying on any ad hoc parameters, are in good agreement with the corresponding experimental results. Importantly, since the many-body energy, dipole, and polarizability surfaces employed in the simulations are derived independently from accurate fits to correlated electronic structure data, MB-MD allows for a systematic analysis of the calculated spectra in terms of both electronic and dynamical contributions. The present analysis suggests that, while MB-MD correctly reproduces both the shifts and the shapes of the main spectroscopic features, an improved description of quantum dynamical effects possibly combined with a dissociable water potential may be necessary for a quantitative representation of the OH stretch band.
Collapse
Affiliation(s)
- Gregory R Medders
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92037, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92037, United States
| |
Collapse
|
42
|
Sun YY, Liu FS, Xu LH, Liu QJ, Ma XJ, Cai LC. Vibrational spectrum of condensed H 2O in hydrogen-bonding environment: an ab initiosimulation study. Mol Phys 2015. [DOI: 10.1080/00268976.2014.944237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
43
|
Sanchéz-Lozano M, Mandado M, Pérez-Juste I, Hermida-Ramón JM. Theoretical vibrational Raman and surface-enhanced Raman scattering spectra of water interacting with silver clusters. Chemphyschem 2014; 15:4067-76. [PMID: 25263101 DOI: 10.1002/cphc.201402454] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Indexed: 11/11/2022]
Abstract
In this study, we analyzed the Raman spectrum of a water molecule adsorbed on a cluster of 20 silver atoms, and the plasmonic electromagnetic effect of the silver surface was also considered to give a theoretical prediction of the surface-enhanced Raman scattering spectrum. The calculations were performed at the density functional theory (DFT) level by using both frozen and unfrozen silver clusters. Two different models were used to consider the plasmonic enhancement; one of them was a modified classical (dipole) model and the other was the coupled perturbed Hartree-Fock method with excitation frequencies obtained from time-dependent DFT calculations and with proper detuning of these frequencies. The importance of small geometrical distortions of the silver surface in the orientation of the adsorbed water was shown. Moreover, it was shown how the symmetry of the transition dipole moment and the symmetry of the vibrational modes influence the Raman intensities of the SERS spectrum.
Collapse
Affiliation(s)
- Marta Sanchéz-Lozano
- Departamento de Química Física, Facultade de Química, Universidade de Vigo, Campus Lagoas Marcosende s/n, 36310 Vigo (Spain)
| | | | | | | |
Collapse
|
44
|
Rossi M, Liu H, Paesani F, Bowman J, Ceriotti M. Communication: On the consistency of approximate quantum dynamics simulation methods for vibrational spectra in the condensed phase. J Chem Phys 2014; 141:181101. [DOI: 10.1063/1.4901214] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mariana Rossi
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Hanchao Liu
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0314, USA
| | - Joel Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
45
|
Ni Y, Skinner JL. Ultrafast pump-probe and 2DIR anisotropy and temperature-dependent dynamics of liquid water within the E3B model. J Chem Phys 2014; 141:024509. [DOI: 10.1063/1.4886427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yicun Ni
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| |
Collapse
|
46
|
Yang M. Effects of excluded volume and correlated molecular orientations on Förster resonance energy transfer in liquid water. J Chem Phys 2014; 140:144508. [PMID: 24735306 DOI: 10.1063/1.4870937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Förster theory for the survival probability of excited chromophores is generalized to include the effects of excluded volume and orientation correlation in the molecular distribution. An analytical expression for survival probability was derived and written in terms of a few simple elementary functions. Because of the excluded volume, the survival probability exhibits exponential decay at early times and stretched exponential decay at later times. Experimental schemes to determine the size of the molecular excluded volume are suggested. With the present generalization of theory, we analyzed vibrational resonance energy transfer kinetics in neat water. Excluded volume effects prove to be important and slow down the kinetics at early times. The majority of intermolecular resonance energy transfer was found to occur with exponential kinetics, as opposed to the stretched exponential behavior predicted by Förster theory. Quantum yields of intra-molecular vibrational relaxation, intra-, and intermolecular energy transfer were calculated to be 0.413, 0.167, and 0.420, respectively.
Collapse
Affiliation(s)
- Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea
| |
Collapse
|
47
|
Jeon J, Cho M. An Accurate Classical Simulation of a Two-Dimensional Vibrational Spectrum: OD Stretch Spectrum of a Hydrated HOD Molecule. J Phys Chem B 2014; 118:8148-61. [DOI: 10.1021/jp501182d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonggu Jeon
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| |
Collapse
|
48
|
Jung YS, Oh KI, Hwang GS, Cho M. Neighboring residue effects in terminally blocked dipeptides: implications for residual secondary structures in intrinsically unfolded/disordered proteins. Chirality 2014; 26:443-52. [PMID: 24453185 DOI: 10.1002/chir.22285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022]
Abstract
For nuclear magnetic resonance (NMR)-based protein structure determinations, the random coil chemical shifts are very important because the secondary and tertiary protein structure predictions become possible by examining deviations of measured chemical shifts from those reference chemical shift values. In addition, neighboring residue effects on chemical shifts and J-coupling constants are crucial in understanding the nature of conformational propensities exhibited by unfolded or intrinsically disordered proteins. We recently reported the 1D NMR results for a complete set of terminally blocked dipeptides (Oh KI, Jung YS, Hwang GS, Cho M. J Biomol NMR 2012;53:25-41), but the NMR resonance assignments were not possible so that the average chemical shifts and J-coupling constants were only considered. In the present work, to thoroughly investigate the neighboring residue effects and random coil chemical shifts we extend the previous studies with 2D NMR, and measured all the (3) J(HNHα) values and H(α) and H(N) chemical shifts of the same set of terminally blocked dipeptides that are free from structural effects like secondary structure, hydrogen-bond, long-range backbone, and side-chain interactions. In particular, the preceding and following residue effects on amino-acid backbone conformational propensities are revealed and directly compared with previous works on either short peptides or empirical chemical shift database.
Collapse
|