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Dhurua S, Maity S, Maity B, Jana M. Comparative Bindings of Glycosaminoglycans with CXCL8 Monomer and Dimer: Insights from Conformational Dynamics and Kinetics of Hydrogen Bonds. J Phys Chem B 2024; 128:10348-10362. [PMID: 39405497 DOI: 10.1021/acs.jpcb.4c03670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
GAGs bind to both the monomeric and dimeric forms of CXCL8, helping to form a concentration gradient of the chemokine that facilitates the recruitment of neutrophils to an injury site and supports other biological functions. In this study, atomistic molecular dynamics simulations were conducted to investigate the binding behavior of two hexameric GAGs sulfated at two different positions, chondroitin sulfate (CS) and heparan sulfate (HS), with the monomer (SIL8) and dimer (DIL8) forms of the CXCL8 protein. The results support that the conformational diversity of CS and HS appeared to be more when binding with monomer SIL8 than dimer DIL8. CS gained more configurational entropy from glycosidic linkage flexibility when bound to SIL8 than DIL8, with a higher energy barrier, whereas HS exhibited a lower energy barrier for configurational entropy when bound to SIL8 and DIL8. The monomer SIL8 exhibited more favorable and preferential binding with GAGs compared to DIL8. Formation of hydrogen bonds with the basic amino acids of SIL8 and GAG was more rigid and required higher activation energy to break than the other identified hydrogen bondings. Water molecules involved in hydrogen bonding with GAGs, excluding those with basic amino acids of DIL8, showed longer lifetimes and slower relaxation compared to SIL8. This suggests that water-mediated interactions also favor binding of DIL8 with GAGs. Despite having more basic amino acids, DIL8 did not display stronger binding than SIL8, indicating the significant role of basic residues in stabilizing the GAG-protein interactions in the monomers. The reason could be that the greater number of nonbasic amino acids in dimeric CXCL8 stabilizes the complex by forming water-mediated hydrogen bonds, reducing the conformational preferences for binding with GAGs. In contrast, the monomeric form of CXCL8 exhibits a higher conformational preference for protein-GAG interactions.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India
| | - Sankar Maity
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India
| | - Bilash Maity
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, India
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2
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Vibrational couplings and energy transfer pathways of water's bending mode. Nat Commun 2020; 11:5977. [PMID: 33239630 PMCID: PMC7688972 DOI: 10.1038/s41467-020-19759-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Coupling between vibrational modes is essential for energy transfer and dissipation in condensed matter. For water, different O-H stretch modes are known to be very strongly coupled both within and between water molecules, leading to ultrafast dissipation and delocalization of vibrational energy. In contrast, the information on the vibrational coupling of the H-O-H bending mode of water is lacking, even though the bending mode is an essential intermediate for the energy relaxation pathway from the stretch mode to the heat bath. By combining static and femtosecond infrared, Raman, and hyper-Raman spectroscopies for isotopically diluted water with ab initio molecular dynamics simulations, we find the vibrational coupling of the bending mode differs significantly from the stretch mode: the intramode intermolecular coupling of the bending mode is very weak, in stark contrast to the stretch mode. Our results elucidate the vibrational energy transfer pathways of water. Specifically, the librational motion is essential for the vibrational energy relaxation and orientational dynamics of H-O-H bending mode. Vibrational energy transfer in water involves intermolecular coupling of O-H stretching modes, but much less is known about the role of the bending modes. Here the authors, combining static and femtosecond infrared, Raman, and hyper-Raman spectroscopy and ab initio molecular dynamics simulations, provide insight into the energy dynamics of the bend vibrations.
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Seki T, Chiang KY, Yu CC, Yu X, Okuno M, Hunger J, Nagata Y, Bonn M. The Bending Mode of Water: A Powerful Probe for Hydrogen Bond Structure of Aqueous Systems. J Phys Chem Lett 2020; 11:8459-8469. [PMID: 32931284 PMCID: PMC7584361 DOI: 10.1021/acs.jpclett.0c01259] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/15/2020] [Indexed: 05/16/2023]
Abstract
Insights into the microscopic structure and dynamics of the water's hydrogen-bonded network are crucial to understand the role of water in biology, atmospheric and geochemical processes, and chemical reactions in aqueous systems. Vibrational spectroscopy of water has provided many such insights, in particular using the O-H stretch mode. In this Perspective, we summarize our recent studies that have revealed that the H-O-H bending mode can be an equally powerful reporter for the microscopic structure of water and provides more direct access to the hydrogen-bonded network than the conventionally studied O-H stretch mode. We discuss the fundamental vibrational properties of the water bending mode, such as the intermolecular vibrational coupling, and its effects on the spectral lineshapes and vibrational dynamics. Several examples of static and ultrafast bending mode spectroscopy illustrate how the water bending mode provides an excellent window on the microscopic structure of both bulk and interfacial water.
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Affiliation(s)
- Takakazu Seki
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kuo-Yang Chiang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Chun-Chieh Yu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Xiaoqing Yu
- 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, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Johannes Hunger
- 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
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Priyadarshini A, Biswas A, Chakraborty D, Mallik BS. Structural and Thermophysical Anomalies of Liquid Water: A Tale of Molecules in the Instantaneous Low- and High-Density Regions. J Phys Chem B 2020; 124:1071-1081. [DOI: 10.1021/acs.jpcb.9b11596] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adyasa Priyadarshini
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
| | - Aritri Biswas
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
| | - Debashree Chakraborty
- Department of Chemistry, National Institute of Technology Karnataka, Surathkal, 575025 Mangalore, Karnataka, India
| | - Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi-502285 Sangareddy, Telangana, India
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5
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Lentz J, Garofalini SH. Role of the hydrogen bond lifetimes and rotations at the water/amorphous silica interface on proton transport. Phys Chem Chem Phys 2019; 21:12265-12278. [PMID: 31139793 DOI: 10.1039/c9cp01994d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a highly robust and reactive all-atom potential, molecular dynamics computer simulations have been used to provide detailed analysis of the behavior of water and protons at a large-scale amorphous silica surface that offers the heterogeneity of surface sites and water/silica interactions. Structural data of the H-O distances as a function of distance from the glass surface showed variation in hydrogen bond (H-bond) lengths to second and third nearest oxygen neighbors that play an important role in H-bond lifetimes, rotations, and proton transfer, especially at the glass surface. The higher density and inherently closer average spacing between oxygens in the glass surface (2.6 Å) in comparison to that in water (2.8 Å) create a significantly different environment for H-bond lifetimes and proton transfers. Continuous H-bond lifetime autocorrelation functions for water H-bonded to the surface are considerably shorter than those of bulk water, whereas the intermittent lifetime autocorrelation functions are longer. Such results affect proton transfers that are over an order of magnitude higher at the surface than farther from the surface or in bulk water. However, most of these transfers are rattling events between the participating oxygens, one of which is the newly formed H3O+ ion adjacent to the interface. Such a H3O+ ion has an extremely low barrier to proton transfer back to the surface site in comparison to a H3O+ ion in bulk water. Nonetheless, the simulations showed that rotation of the H3O+ ion away from the initial transfer site allowed for structural diffusion of an excess proton away from the surface. Proton conduction from such rotations could be enhanced by external forces.
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Affiliation(s)
- Jesse Lentz
- Interfacial Molecular Science Laboratory, Department of Materials Science and Engineering, Rutgers University, USA.
| | - Stephen H Garofalini
- Interfacial Molecular Science Laboratory, Department of Materials Science and Engineering, Rutgers University, USA.
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6
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Piskulich ZA, Thompson WH. The activation energy for water reorientation differs between IR pump-probe and NMR measurements. J Chem Phys 2018; 149:164504. [DOI: 10.1063/1.5050203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zeke A. Piskulich
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66047, USA
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
- Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, Kansas 66047, USA
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7
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Gordon BP, Moore FG, Scatena LF, Valley NA, Wren SN, Richmond GL. Model Behavior: Characterization of Hydroxyacetone at the Air-Water Interface Using Experimental and Computational Vibrational Sum Frequency Spectroscopy. J Phys Chem A 2018; 122:3837-3849. [PMID: 29608301 DOI: 10.1021/acs.jpca.8b01193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Small atmospheric aldehydes and ketones are known to play a significant role in the formation of secondary organic aerosols (SOA). However, many of them are difficult to experimentally isolate, as they tend to form hydration and oligomer species. Hydroxyacetone (HA) is unusual in this class as it contributes to SOA while existing predominantly in its unhydrated monomeric form. This allows HA to serve as a valuable model system for similar secondary organic carbonyls. In this paper the surface behavior of HA at the air-water interface has been investigated using vibrational sum frequency (VSF) spectroscopy and Wilhelmy plate surface tensiometry in combination with computational molecular dynamics simulations and density functional theory calculations. The experimental results demonstrate that HA has a high degree of surface activity and is ordered at the interface. Furthermore, oriented water is observed at the interface, even at high HA concentrations. Spectral features also reveal the presence of both cis and trans HA conformers at the interface, in differing orientations. Molecular dynamics results indicate conformer dependent shifts in HA orientation between the subsurface (∼5 Å deep) and surface. Together, these results provide a picture of a highly dynamic, but statistically ordered, interface composed of multiple HA conformers with solvated water. These results have implications for HA's behavior in aqueous particles, which may affect its role in the atmosphere and SOA formation.
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Affiliation(s)
- Brittany P Gordon
- Department of Chemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403 , United States
| | - Frederick G Moore
- Department of Physics , Whitman College , Walla Walla , Washington 99362 , United States
| | - Lawrence F Scatena
- Department of Chemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403 , United States
| | - Nicholas A Valley
- Department of Chemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403 , United States.,Department of Science and Mathematics , California Northstate University College of Health Sciences , Rancho Cordova , California 95670 , United States
| | - Sumi N Wren
- Department of Chemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403 , United States.,Department of Air Quality Process Research , Environment and Climate Change Canada (ECCC) , Toronto , Ontario M3H 5T4 , Canada
| | - Geraldine L Richmond
- Department of Chemistry , University of Oregon , 1253 University of Oregon , Eugene , Oregon 97403 , United States
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8
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Karmakar A, Chandra A. Water under Supercritical Conditions: Hydrogen Bonds, Polarity, and Vibrational Frequency Fluctuations from Ab Initio Simulations with a Dispersion Corrected Density Functional. ACS OMEGA 2018; 3:3453-3462. [PMID: 31458597 PMCID: PMC6641502 DOI: 10.1021/acsomega.7b02036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/09/2018] [Indexed: 05/27/2023]
Abstract
We have studied the effects of dispersion interactions on the dynamics of vibrational frequency fluctuations, hydrogen bonds, and free OD modes in supercritical heavy water at three different densities by means of ab initio molecular dynamics simulations. The vibrational spectral diffusion, as described by the frequency fluctuations, is studied through calculations of frequency time correlation of stretch modes of deuterated water, and its relations to the dynamics of hydrogen bonds and free OD modes are described. In addition, some of the other dynamical, structural, and electronic properties such as diffusion, rotational relaxation, radial distribution functions, hydrogen bond and coordination numbers, and dipole moments are also investigated from the perspectives of their variation with inclusion of dispersion interactions at varying density of the solvent. Although some changes in the structural properties are found on inclusion of dispersion corrections, no significant difference in the fluctuation dynamics of OD stretching frequencies and also in other dynamical quantities of supercritical water are found because of dispersion effects. The dynamics of water molecules under supercritical conditions is very fast compared to the corresponding dynamics under ambient conditions. The large thermal effects at such a high temperature seem to take over any relatively minor changes that might be introduced by weak dispersion interaction.
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9
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Cyran JD, Backus EHG, Nagata Y, Bonn M. Structure from Dynamics: Vibrational Dynamics of Interfacial Water as a Probe of Aqueous Heterogeneity. J Phys Chem B 2018; 122:3667-3679. [PMID: 29490138 PMCID: PMC5900549 DOI: 10.1021/acs.jpcb.7b10574] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The structural heterogeneity of water
at various interfaces can be revealed by time-resolved sum-frequency
generation spectroscopy. The vibrational dynamics of the O–H
stretch vibration of interfacial water can reflect structural variations.
Specifically, the vibrational lifetime is typically found to increase
with increasing frequency of the O–H stretch vibration, which
can report on the hydrogen-bonding heterogeneity of water. We compare
and contrast vibrational dynamics of water in contact with various
surfaces, including vapor, biomolecules, and solid interfaces. The
results reveal that variations in the vibrational lifetime with vibrational
frequency are very typical, and can frequently be accounted for by
the bulk-like heterogeneous response of interfacial water. Specific
interfaces exist, however, for which the behavior is less straightforward.
These insights into the heterogeneity of interfacial water thus obtained
contribute to a better understanding of complex phenomena taking place
at aqueous interfaces, such as photocatalytic reactions and protein
folding.
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Affiliation(s)
- Jenée D Cyran
- 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
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10
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Srivastava A, Debnath A. Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations. J Chem Phys 2018. [DOI: 10.1063/1.5011803] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
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11
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Lentz J, Garofalini SH. Structural aspects of the topological model of the hydrogen bond in water on auto-dissociation via proton transfer. Phys Chem Chem Phys 2018; 20:16414-16427. [DOI: 10.1039/c8cp02592d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different H-bond structures of donor and acceptor water molecules significantly affect structure, H-bond lifetimes, and autodissociation via proton transfer.
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Affiliation(s)
- Jesse Lentz
- Department of Materials Science and Engineering
- Rutgers University
- Piscataway
- USA
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12
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McWilliams LE, Valley NA, Vincent NM, Richmond GL. Interfacial Insights into a Carbon Capture System: CO2 Uptake to an Aqueous Monoethanolamine Surface. J Phys Chem A 2017; 121:7956-7967. [DOI: 10.1021/acs.jpca.7b07742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura E. McWilliams
- Department
of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Nicholas A. Valley
- California Northstate University College of Health Sciences, Rancho Cordova, California 95670, United States
| | - Nina M. Vincent
- Department
of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
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13
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Dettori R, Ceriotti M, Hunger J, Melis C, Colombo L, Donadio D. Simulating Energy Relaxation in Pump–Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids. J Chem Theory Comput 2017; 13:1284-1292. [DOI: 10.1021/acs.jctc.6b01108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Riccardo Dettori
- Dipartimento
di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Claudio Melis
- Dipartimento
di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Luciano Colombo
- Dipartimento
di Fisica, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Davide Donadio
- Department
of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
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14
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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
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15
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Śmiechowski M. Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4and NaPF6. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1157219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Mukherjee B. Microscopic origin of temporal heterogeneities in translational dynamics of liquid water. J Chem Phys 2015; 143:054503. [PMID: 26254657 DOI: 10.1063/1.4927709] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Liquid water is known to reorient via a combination of large angular jumps (due to exchange of hydrogen bonding (H-bond) partners) and diffusive orientations. Translation of the molecule undergoing the orientational jump and its initial and final H-bond acceptors plays a key role in the microscopic reorientation process. Here, we partition the translational dynamics into those occurring during intervals when rotating water molecules (and their initial and final H-bonding partners) undergo orientational jump and those arising when molecules wait between consecutive orientational jumps. These intervals are chosen in such a way that none of the four possible H-bonds involving the chosen water molecule undergo an exchange process within its duration. Translational dynamics is analysed in terms of the distribution of particle displacements, van Hove functions, and its moments. We observe that the translational dynamics, calculated from molecular dynamics simulations of liquid water, is fastest during the orientational jumps and slowest during periods of waiting. The translational dynamics during all temporal intervals shows an intermediate behaviour. This is the microscopic origin of temporal dynamic heterogeneity in liquid water, which is mild at 300 K and systematically increases with supercooling. Study of such partitioned dynamics in supercooled water shows increased disparity in dynamics occurring in the two different types of intervals. Nature of the distribution of particle displacements in supercooled water is investigated and it reveals signatures non-Gaussian behaviour.
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Affiliation(s)
- Biswaroop Mukherjee
- Thematic Unit of Excellence-Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block JD, Sector-III, Salt Lake, Kolkata 700098, India
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17
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McWilliams LE, Valley NA, Wren SN, Richmond GL. A means to an interface: investigating monoethanolamine behavior at an aqueous surface. Phys Chem Chem Phys 2015. [PMID: 26220791 DOI: 10.1039/c5cp02931g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of amine scrubbers to trap carbon dioxide from flue gas streams is one of the most promising avenues for atmospheric carbon dioxide reduction. However, modifications are necessary to efficiently scale these scrubbers for use in fossil fuel plants. Current advances in tailoring amines for CO2 capture involve improvements of bulk kinetic and thermodynamic parameters, with little consideration to surface chemistry and behavior. Aqueous alkanolamine solutions, such as monoethanolamine (MEA), are currently highly favored sorbents in CO2 post-combustion capture. Although numerous studies have explored MEA-CO2 chemistry at the macroscopic scale, few have investigated the role of the interface in the gas adsorption process. Additionally, as these amines become more industrially ubiquitous, their presence on and the need to understand their behavior at atmospheric and environmental surfaces will increase. This study investigates the surface behavior of monoethanolamine at the vapor/water interface, with particular focus on MEA's surface orientation and footprint. Using vibrational sum frequency spectroscopy, surface tensiometry, and computational techniques, MEA is found to adopt a constrained gauche interfacial conformation with its methylene backbone oriented toward the vapor phase and its functional groups solvated in the bulk solution. Computational and experimental analysis agree well, giving a complete picture with vibrational mode assignments and surface orientation of MEA. These findings can assist in the tailoring of amine structures or to facilitate improvements in engineering design to exploit favorable surface chemistry, as well as to serve as a starting point toward understanding aqueous amine surface behavior relevant to environmental systems.
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18
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Wren SN, Gordon BP, Valley NA, McWilliams LE, Richmond GL. Hydration, Orientation, and Conformation of Methylglyoxal at the Air–Water Interface. J Phys Chem A 2015; 119:6391-403. [DOI: 10.1021/acs.jpca.5b03555] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sumi N. Wren
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Brittany P. Gordon
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Nicholas A. Valley
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Laura E. McWilliams
- Department of Chemistry, University of Oregon, Eugene, Oregon 97403, United States
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19
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Lin SR, Tang PH, Wu TM. Local structural effects on orientational relaxation of OH-bond in liquid water over short to intermediate timescales. J Chem Phys 2014; 141:214505. [PMID: 25481150 DOI: 10.1063/1.4902372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
By simulating the rigid simple point charge extended model at temperature T = 300 K, the orientational relaxation of the OH-bond in water was investigated over short to intermediate timescales, within which molecules undergo inertial rotation and libration and then enter the rotational diffusion regime. According to the second-cumulant approximation, the orientational time correlation function (TCF) of each axis that is parallel or perpendicular to an OH-bond is related to an effective rotational density of states (DOS), which is determined using the power spectra of angular velocity autocorrelation functions (AVAFs) of the other two axes. In addition, the AVAF power spectrum of an axis was approximated as the rotational stable instantaneous normal mode (INM) spectrum of the axis. As described in a previous study [S. L. Chang, T. M. Wu, and C. Y. Mou, J. Chem. Phys. 121, 3605 (2004)], simulated molecules were classified into subensembles, according to either the local structures or the H-bond configurations of the molecules. For global molecules and the classified subensembles, the simulation results for the first- and second-rank orientational TCFs were compared with the second-cumulant predictions obtained using the effective rotational DOSs and the rotational stable-INM spectra. On short timescales, the OH-bond in water behaves similar to an inertial rotor and its anisotropy is lower than that of a water molecule. For molecules with three or more H-bonds, the OH-bond orientational TCFs are characterized by a recurrence, which is an indication for libration of the OH-bond. The recurrence can generally be described by the second-cumulant prediction obtained using the rotational stable-INM spectra; however, the orientational TCFs after the recurrence switch to a behavior similar to that predicted using the AVAF power spectra. By contrast, the OH-bond orientational TCFs of molecules initially connected with one or two H-bonds decay monotonically or exhibit a weak recurrence, indicating rapid relaxation into the rotational diffusion regime after the initial Gaussian decay. In addition to accurately describing the Gaussian decay, the second-cumulant predictions formulated using the rotational stable-INM spectra and the AVAF power spectra serve as the upper and lower limits, respectively, for the OH-bond orientational TCFs of these molecules after the Gaussian decay.
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Affiliation(s)
- S R Lin
- Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan
| | - Ping-Han Tang
- Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan
| | - Ten-Ming Wu
- Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan
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20
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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
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21
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Nam D, Lee C, Park S. Temperature-dependent dynamics of water in aqueous NaPF6 solution. Phys Chem Chem Phys 2014; 16:21747-54. [DOI: 10.1039/c4cp02823f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
H-bond structure and dynamics of water in aqueous NaPF6 solution.
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Affiliation(s)
- Dayoung Nam
- Department of Chemistry
- Korea University
- Seoul 136-713, Korea
| | - Chiho Lee
- Department of Chemistry
- Korea University
- Seoul 136-713, Korea
| | - Sungnam Park
- Department of Chemistry
- Korea University
- Seoul 136-713, Korea
- Multidimensional Spectroscopy Laboratory
- Korea Basic Science Institute
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22
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Olschewski M, Knop S, Lindner J, Vöhringer P. From Single Hydrogen Bonds to Extended Hydrogen-Bond Wires: Low-Dimensional Model Systems for Vibrational Spectroscopy of Associated Liquids. Angew Chem Int Ed Engl 2013; 52:9634-54. [DOI: 10.1002/anie.201210009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 11/06/2022]
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Olschewski M, Knop S, Lindner J, Vöhringer P. Von einzelnen H-Brücken zu ausgedehnten H-verbrückten Drähten: niederdimensionale Modellsysteme für die Schwingungsspektroskopie vernetzter Flüssigkeiten. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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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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25
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Pitman MC, van Duin ACT. Dynamics of Confined Reactive Water in Smectite Clay–Zeolite Composites. J Am Chem Soc 2012; 134:3042-53. [DOI: 10.1021/ja208894m] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Michael C. Pitman
- Soft Matter Theory and Simulations
Group, Computational Biology Center, IBM Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Adri C. T. van Duin
- Department of Mechanical and
Nuclear Engineering, Pennsylvania State University, 136 Research East Building, University Park, Pennsylvania 16802,
United States
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26
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Paesani F. Hydrogen bond dynamics in heavy water studied with quantum dynamical simulations. Phys Chem Chem Phys 2011; 13:19865-75. [PMID: 21892511 DOI: 10.1039/c1cp21863h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The structure and dynamics of the hydrogen-bond network in heavy water (D(2)O) is studied as a function of the temperature using quantum dynamical simulations. Our approach combines an ab initio-based representation of the water interactions with an explicit quantum treatment of the molecular motion. A direct connection between the calculated linear and nonlinear vibrational spectra and the underlying molecular dynamics is made, which provides new insights into the rearrangement of the hydrogen-bond network in heavy water. A comparison with previous calculations on liquid H(2)O suggests that tunneling does not effectively contribute to the dynamics of the water hydrogen-bond network above the melting point. However, the effects of nuclear quantization are not negligible at all temperatures and become increasingly important near the melting point, which is in agreement with recent experimental analysis of the structural properties of liquid water as well as of the proton momentum distribution in supercooled water.
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Affiliation(s)
- Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA 92093, USA.
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27
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Laage D, Stirnemann G, Sterpone F, Rey R, Hynes JT. Reorientation and Allied Dynamics in Water and Aqueous Solutions. Annu Rev Phys Chem 2011; 62:395-416. [DOI: 10.1146/annurev.physchem.012809.103503] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Rossend Rey
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Barcelona 08034, Spain;
| | - James T. Hynes
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215;
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28
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Timmer RLA, Tielrooij KJ, Bakker HJ. Vibrational Förster transfer to hydrated protons. J Chem Phys 2010; 132:194504. [PMID: 20499976 DOI: 10.1063/1.3432616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have studied the influence of excess protons on the vibrational energy relaxation of the O-H and O-D stretching modes in water using femtosecond pump-probe spectroscopy. Without excess protons, we observe exponential decays with time constants of 1.7 and 4.3 ps for the bulk and anion bound O-D stretch vibrations. The addition of protons introduces a new energy relaxation pathway, which leads to an increasingly nonexponential decay of the O-D stretch vibration. This new pathway is attributed to a distance-dependent long range dipole-dipole (Forster) interaction between the O-D stretching vibration and modes associated with dissolved protons. The high efficiency of hydrated protons as receptors of vibrational energy follows from the very large absorption cross section and broad bandwidth of protons in water. For a proton concentration of 1M we find that Forster energy transfer occurs over an average distance of 4.5 A, which corresponds to a separation of about two water molecules.
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Affiliation(s)
- R L A Timmer
- FOM-institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
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Affiliation(s)
- R. L. A. Timmer
- FOM-institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
| | - H. J. Bakker
- FOM-institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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30
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Yamamoto S, Ghosh A, Nienhuys HK, Bonn M. Ultrafast inter- and intramolecular vibrational energy transfer between molecules at interfaces studied by time- and polarization-resolved SFG spectroscopy. Phys Chem Chem Phys 2010; 12:12909-18. [DOI: 10.1039/c0cp00538j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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31
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Fayer MD, Levinger NE. Analysis of water in confined geometries and at interfaces. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:89-107. [PMID: 20636035 DOI: 10.1146/annurev-anchem-070109-103410] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The properties of water depend on its extended hydrogen bond network and the continual picosecond-time scale structural evolution of the network. Water molecules in confined environments with pools a few nanometers in diameter or at interfaces undergo hydrogen bond structural dynamics that differ drastically from the dynamics they undergo in bulk water. Orientational motions of water require hydrogen bond network rearrangement. Therefore, observations of orientational relaxation in nanoscopic water systems provide information about the influence of confinement and interfaces on hydrogen bond dynamics. Ultrafast infrared polarization- and wavelength-selective pump-probe experiments can measure the orientational relaxation of water and distinguish water at an interface from water removed from an interface. These experiments can be applied to water in reverse micelles (spherical nanopools). The results provide quantitative determination of the dynamics of water as a function of the size and nature of the confining structure.
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Affiliation(s)
- Michael D Fayer
- Department of Chemistry, Stanford University, California 94305, USA.
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32
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Bakker HJ, Skinner JL. Vibrational Spectroscopy as a Probe of Structure and Dynamics in Liquid Water. Chem Rev 2009; 110:1498-517. [DOI: 10.1021/cr9001879] [Citation(s) in RCA: 586] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- H. J. Bakker
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands, and Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - J. L. Skinner
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands, and Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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33
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Paesani F, Xantheas SS, Voth GA. Infrared Spectroscopy and Hydrogen-Bond Dynamics of Liquid Water from Centroid Molecular Dynamics with an Ab Initio-Based Force Field. J Phys Chem B 2009; 113:13118-30. [DOI: 10.1021/jp907648y] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesco Paesani
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112-0850, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352
| | - Sotiris S. Xantheas
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112-0850, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112-0850, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352
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34
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Paesani F, Voth GA. The properties of water: insights from quantum simulations. J Phys Chem B 2009; 113:5702-19. [PMID: 19385690 DOI: 10.1021/jp810590c] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The properties of water play a central role in many phenomena of relevance to different areas of science, including physics, chemistry, biology, geology, and climate research. Although well studied for decades, the behavior of water under different conditions and in different environments still remains mysterious and often surprising. In this article, various efforts aimed at providing a comprehensive representation of the water properties at a molecular level through computer modeling and simulation will be described. In particular, the unique role played by the hydrogen-bond network will be examined, first in liquid water, then in the solvation of model biological compounds, and finally in ice, especially highlighting the important effects related to the quantization of the nuclear motion.
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Affiliation(s)
- Francesco Paesani
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East Room 2020, Salt Lake City, Utah 84112-0850, USA
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35
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Mallik BS, Chandra A. Vibrational Spectral Diffusion in Supercritical D2O from First Principles: An Interplay between the Dynamics of Hydrogen Bonds, Dangling OD Groups, and Inertial Rotation. J Phys Chem A 2008; 112:13518-27. [DOI: 10.1021/jp808089q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bhabani S. Mallik
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology, Kanpur, India 208016
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36
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Skinner JL, Auer BM, Lin YS. Vibrational Line Shapes, Spectral Diffusion, and Hydrogen Bonding in Liquid Water. ADVANCES IN CHEMICAL PHYSICS 2008. [DOI: 10.1002/9780470475935.ch2] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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37
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Bakker HJ, Rezus YLA, Timmer RLA. Molecular Reorientation of Liquid Water Studied with Femtosecond Midinfrared Spectroscopy. J Phys Chem A 2008; 112:11523-34. [DOI: 10.1021/jp8012943] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- H. J. Bakker
- FOM Institute AMOLF, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
| | - Y. L. A. Rezus
- FOM Institute AMOLF, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
| | - R. L. A. Timmer
- FOM Institute AMOLF, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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38
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Affiliation(s)
- Damien Laage
- Chemistry Department, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, CNRS UMR Pasteur, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - James T. Hynes
- Chemistry Department, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, CNRS UMR Pasteur, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
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39
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An ab initio molecular dynamics study of the frequency dependence of rotational motion in liquid water. J Mol Liq 2008. [DOI: 10.1016/j.molliq.2008.04.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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40
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Moilanen DE, Fenn EE, Lin YS, Skinner JL, Bagchi B, Fayer MD. Water inertial reorientation: hydrogen bond strength and the angular potential. Proc Natl Acad Sci U S A 2008; 105:5295-300. [PMID: 18381817 PMCID: PMC2291089 DOI: 10.1073/pnas.0801554105] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Indexed: 11/18/2022] Open
Abstract
The short-time orientational relaxation of water is studied by ultrafast infrared pump-probe spectroscopy of the hydroxyl stretching mode (OD of dilute HOD in H(2)O). The anisotropy decay displays a sharp drop at very short times caused by inertial orientational motion, followed by a much slower decay that fully randomizes the orientation. Investigation of temperatures from 1 degrees C to 65 degrees C shows that the amplitude of the inertial component (extent of inertial angular displacement) depends strongly on the stretching frequency of the OD oscillator at higher temperatures, although the slow component is frequency-independent. The inertial component becomes frequency-independent at low temperatures. At high temperatures there is a correlation between the amplitude of the inertial decay and the strength of the O-D O hydrogen bond, but at low temperatures the correlation disappears, showing that a single hydrogen bond (OD O) is no longer a significant determinant of the inertial angular motion. It is suggested that the loss of correlation at lower temperatures is caused by the increased importance of collective effects of the extended hydrogen bonding network. By using a new harmonic cone model, the experimentally measured amplitudes of the inertial decays yield estimates of the characteristic frequencies of the intermolecular angular potential for various strengths of hydrogen bonds. The frequencies are in the range of approximately 400 cm(-1). A comparison with recent molecular dynamics simulations employing the simple point charge-extended water model at room temperature shows that the simulations qualitatively reflect the correlation between the inertial decay and the OD stretching frequency.
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Affiliation(s)
- David E. Moilanen
- *Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Emily E. Fenn
- *Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Yu-Shan Lin
- Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - J. L. Skinner
- Department of Chemistry, University of Wisconsin, Madison, WI 53706
| | - B. Bagchi
- *Department of Chemistry, Stanford University, Stanford, CA 94305; and
| | - Michael D. Fayer
- *Department of Chemistry, Stanford University, Stanford, CA 94305; and
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41
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Affiliation(s)
- H. J. Bakker
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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42
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Piletic IR, Moilanen DE, Levinger NE, Fayer MD. What nonlinear-IR experiments can tell you about water that the IR spectrum cannot. J Am Chem Soc 2007; 128:10366-7. [PMID: 16895392 DOI: 10.1021/ja062549p] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Frequently, the IR spectrum of water is used to characterize the structure and strength of the associated hydrogen bond network. Here, we use nonlinear-IR spectroscopy to investigate the dynamics of four aqueous systems that have very similar absorption spectra. We address the question: to what extent can the dynamics of water vary in systems with very similar absorption spectra? The results illustrate that the vibrational lifetimes and orientational relaxation time scales vary dramatically between the four samples and do not correlate with the amount of water relative to surfactant or solute in solution. Nonlinear-IR spectroscopies are therefore important for providing detailed information necessary to understand hydrogen bonded systems.
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Affiliation(s)
- Ivan R Piletic
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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43
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Rezus YLA, Bakker HJ. On the orientational relaxation of HDO in liquid water. J Chem Phys 2007; 123:114502. [PMID: 16392568 DOI: 10.1063/1.2009729] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use femtosecond mid-infrared pump-probe spectroscopy to study the orientational relaxation of HDO molecules dissolved in H2O. In order to obtain a reliable anisotropy decay we model the effects of heating and correct for these effects. We have measured the reorientation time constant of the OD vibration from 2430 to 2600 cm(-1), and observe a value of 2.5 ps that shows no variation over this frequency interval. Our results are discussed in the context of previous experiments that have been performed on the complementary system of HDO dissolved in D2O.
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Affiliation(s)
- Y L A Rezus
- Stichting voor Fundamenteel Onderzoek der Materie Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands.
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44
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Timmer RLA, Bakker HJ. Water as a molecular hinge in amidelike structures. J Chem Phys 2007; 126:154507. [PMID: 17461647 DOI: 10.1063/1.2723092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The authors have studied the reorientational dynamics of isolated water molecules in a solution of N,N-dimethylacetamide (DMA). From linear spectra, the authors find that the water in this solution forms double hydrogen bond connections to the DMA molecules, resulting in the formation of DMA-water-DMA complexes. The authors use polarization-resolved mid-infrared pump-probe spectroscopy on the water in these complexes to measure the depolarization of three distinct transition dipole moments, each with a different directionality relative to the molecular frame (OH stretch in HDO, symmetric and asymmetric stretch normal modes in H(2)O). By combining these measurements, the authors find that the system exhibits bimodal rotational dynamics with two distinct time scales: a slow (7+/-1 ps) reorientation of the entire DMA-water complex and a fast (0.5+/-0.2 ps) "hinging" motion of the water molecule around the axis parallel to the connecting hydrogen bonds. Additionally, the authors observe an exchange of energy between the two normal modes of H(2)O at a time scale of 0.8+/-0.1 ps and find that the vibrational excitation decays through the symmetric stretch normal mode with a time constant of 0.8+/-0.2 ps.
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Affiliation(s)
- R L A Timmer
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
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45
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Kobryn AE, Yamaguchi T, Hirata F. Site-site memory equation approach in study of density/pressure dependence of translational diffusion coefficient and rotational relaxation time of polar molecular solutions: acetonitrile in water, methanol in water, and methanol in acetonitrile. J Chem Phys 2007; 122:184511. [PMID: 15918733 DOI: 10.1063/1.1884998] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present results of the theoretical study and numerical calculation of the dynamics of molecular liquids based on the combination of the memory equation formalism and the reference interaction site model (RISM). Memory equations for the site-site intermediate scattering functions are studied in the mode-coupling approximation for the first-order memory kernels, while equilibrium properties such as site-site static structure factors are deduced from RISM. The results include the temperature-density (pressure) dependence of translational diffusion coefficients D and orientational relaxation times tau for acetonitrile in water, methanol in water, and methanol in acetonitrile--all in the limit of infinite dilution. Calculations are performed over the range of temperatures and densities employing the extended simple point charge model for water and optimized site-site potentials for acetonitrile and methanol. The theory is able to reproduce qualitatively all main features of temperature and density dependences of D and tau observed in real and computer experiments. In particular, anomalous behavior, i.e, the increase in mobility with density, is observed for D and tau of methanol in water, while acetonitrile in water and methanol in acetonitrile do not show deviations from the ordinary behavior. The variety exhibited by the different solute-solvent systems in the density dependence of the mobility is interpreted in terms of the two competing origins of friction, which interplay with each other as density increases: the collisional and dielectric frictions which, respectively, increase and decrease with increasing density.
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Affiliation(s)
- Alexander E Kobryn
- Department of Theoretical Study, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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46
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Rezus YLA, Madsen D, Bakker HJ. Orientational dynamics of hydrogen-bonded phenol. J Chem Phys 2006; 121:10599-604. [PMID: 15549942 DOI: 10.1063/1.1809589] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use femtosecond mid-infrared pump-probe spectroscopy to study the effects of hydrogen bonding on the orientational dynamics of the OD-stretch vibration of phenol-d. We study two samples: phenol-d in chloroform and phenol-d in chloroform to which we added excess acetone. For phenol-d in chloroform, we observe rotational diffusion of the OD group around the CO bond, with a correlation time of 3.7 ps. For phenol-d hydrogen bonded to acetone, the reorientation time is strongly dependent on the probe frequency, varying from 3 ps on the blue side of the spectrum to more than 30 ps on the red side. (c) 2004 American Institute of Physics.
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Affiliation(s)
- Y L A Rezus
- FOM-institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
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47
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Chang SL, Wu TM, Mou CY. Instantaneous normal mode analysis of orientational motions in liquid water: local structural effects. J Chem Phys 2006; 121:3605-12. [PMID: 15303927 DOI: 10.1063/1.1772759] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have investigated the effects of local structures on the orientational motions in liquid water in terms of the instantaneous normal mode (INM) analysis. The local structures of a molecule in liquid water are characterized by two different kinds of index: the asphericity parameter of its Voronoi polyhedron and the numbers of the H bonds donated and accepted by the molecule. According to the two kinds of index, the molecules in the simulated water are classified into subensembles, for which the rotational contributions to the INM spectrum are calculated. Our results indicate that by increasing the asphericity, the rotational contribution has a shift toward the high-frequency end in the real spectrum and a decrease in the fraction of the imaginary modes. Furthermore, we find that this shift essentially relies on the number of the donated H bonds of a molecule, but has almost nothing to do with that of the accepted H bonds. The local structural effects resulting from the geometry of water molecule are also discussed.
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Affiliation(s)
- S L Chang
- Institute of Physics, National Chiao-Tung University, Hsin Chu 300, Taiwan
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Park J, Ha JH, Hochstrasser RM. Multidimensional infrared spectroscopy of the N-H bond motions in formamide. J Chem Phys 2006; 121:7281-92. [PMID: 15473797 DOI: 10.1063/1.1792612] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The heterodyned two-dimensional (2D) IR spectra and equilibrium dynamics of the N-H stretching motion of DCONHD in deuterated formamide, DCOND(2), were studied with 80 fs pulses at 3 microm. The time evolution of the heterodyned 2D IR spectra, pump-probe spectra, and photon echo peak shift demonstrate that interstate dynamics is occurring by relaxation of the original N-H excitation. The N-H vibrational frequency correlation function can be expressed as a sum of three exponentials with correlation times 0.24 ps, 0.8 ps, and 11 ps. The intermediate component is attributed to motions of the N-Hcdots, three dots, centeredO unit involving only slight angular variations of the N-H bond. The slow component is attributed to the structure breaking and making. The anisotropy decay confirmed that the significant angular N-H bond motion occurs on the 11 ps time scale. The fast component, which is the least well determined, might correspond to the modulation of the H-bond distance without angular motion. The correlation coefficient between the pumped and relaxed state distributions was +0.51, implying that the excited state phase memory is only slightly diminished by the relaxation of the N-H excitation. The relaxed modes are concluded to be local to the driven N-H mode.
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Affiliation(s)
- Jaehun Park
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Dokter AM, Woutersen S, Bakker HJ. Inhomogeneous dynamics in confined water nanodroplets. Proc Natl Acad Sci U S A 2006; 103:15355-8. [PMID: 17028175 PMCID: PMC1592463 DOI: 10.1073/pnas.0603239103] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Indexed: 11/18/2022] Open
Abstract
The effect of confinement on the dynamical properties of liquid water was studied by mid-infrared ultrafast pump-probe spectroscopy on HDO:D2O in reverse micelles. By preparing water-containing reverse micelles of different well defined sizes, we varied the degree of geometric confinement in water nanodroplets with radii ranging from 0.2 to 4.5 nm. We find that water molecules located near the interface confining the droplet exhibit slower vibrational energy relaxation and have a different spectral absorption than those located in the droplet core. As a result, we can measure the orientational dynamics of these different types of water with high selectivity. We observe that the water molecules in the core show similar orientational dynamics as bulk water and that the water layer solvating the interface is highly immobile.
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Affiliation(s)
- Adriaan M Dokter
- FOM-Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ, Amsterdam, The Netherlands.
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