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Kobayashi T, Ikeda T, Nakayama A. Long-range proton and hydroxide ion transfer dynamics at the water/CeO 2 interface in the nanosecond regime: reactive molecular dynamics simulations and kinetic analysis. Chem Sci 2024; 15:6816-6832. [PMID: 38725504 PMCID: PMC11077578 DOI: 10.1039/d4sc01422g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/02/2024] [Indexed: 05/12/2024] Open
Abstract
The structural properties, dynamical behaviors, and ion transport phenomena at the interface between water and cerium oxide are investigated by reactive molecular dynamics (MD) simulations employing neural network potentials (NNPs). The NNPs are trained to reproduce density functional theory (DFT) results, and DFT-based MD (DFT-MD) simulations with enhanced sampling techniques and refinement schemes are employed to efficiently and systematically acquire training data that include diverse hydrogen-bonding configurations caused by proton hopping events. The water interfaces with two low-index surfaces of (111) and (110) are explored with these NNPs, and the structure and long-range proton and hydroxide ion transfer dynamics are examined with unprecedented system sizes and long simulation times. Various types of proton hopping events at the interface are categorized and analyzed in detail. Furthermore, in order to decipher the proton and hydroxide ion transport phenomena along the surface, a counting analysis based on the semi-Markov process is formulated and applied to the MD trajectories to obtain reaction rates by considering the transport as stochastic jump processes. Through this model, the coupling between hopping events, vibrational motions, and hydrogen bond networks at the interface are quantitatively examined, and the high activity and ion transport phenomena at the water/CeO2 interface are unequivocally revealed in the nanosecond regime.
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Affiliation(s)
- Taro Kobayashi
- Department of Chemical System Engineering, The University of Tokyo Tokyo 113-8656 Japan
| | - Tatsushi Ikeda
- Department of Chemical System Engineering, The University of Tokyo Tokyo 113-8656 Japan
| | - Akira Nakayama
- Department of Chemical System Engineering, The University of Tokyo Tokyo 113-8656 Japan
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2
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Frezza E, Laage D, Duboué-Dijon E. Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences. J Phys Chem Lett 2024; 15:4351-4358. [PMID: 38619551 DOI: 10.1021/acs.jpclett.4c00629] [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: 04/16/2024]
Abstract
Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.
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Affiliation(s)
- Elisa Frezza
- Université Paris Cité, CNRS, CiTCoM, Paris 75006, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Elise Duboué-Dijon
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris 75005, France
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3
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Zhou Y, Ouyang Y, Zhang Y, Li Q, Wang J. Machine Learning Assisted Simulations of Electrochemical Interfaces: Recent Progress and Challenges. J Phys Chem Lett 2023; 14:2308-2316. [PMID: 36847421 DOI: 10.1021/acs.jpclett.2c03288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The electrochemical interface, where the adsorption of reactants and electrocatalytic reactions take place, has long been a focus of attention. Some of the important processes on it tend to possess relatively slow kinetic characteristics, which are usually beyond the scope of ab initio molecular dynamics. The newly emerging technique, machine learning methods, provides an alternative approach to achieve thousands of atoms and nanosecond time scale while ensuring precision and efficiency. In this Perspective, we summarize in detail the recent progress and achievements made by the introduction of machine learning to simulate electrochemical interfaces, and focus on the limitations of current machine learning models, such as accurate descriptions of long-range electrostatic interactions and the kinetics of the electrochemical reactions occurring at the interface. Finally, we further point out the future directions for machine learning to expand in the field of electrochemical interfaces.
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Affiliation(s)
- Yipeng Zhou
- School of Physics, Southeast University, Nanjing 211189, China
| | - Yixin Ouyang
- School of Physics, Southeast University, Nanjing 211189, China
| | - Yehui Zhang
- School of Physics, Southeast University, Nanjing 211189, China
| | - Qiang Li
- School of Physics, Southeast University, Nanjing 211189, China
| | - Jinlan Wang
- School of Physics, Southeast University, Nanjing 211189, China
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4
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Kurapothula PJ, Shepherd S, Wilkins DM. Competing Nuclear Quantum Effects and Hydrogen-Bond Jumps in Hydrated Kaolinite. J Phys Chem Lett 2023; 14:1542-1547. [PMID: 36745462 PMCID: PMC9940297 DOI: 10.1021/acs.jpclett.2c03896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Recent work has shown that the dynamics of hydrogen bonds in pure clays are affected by nuclear quantum fluctuations, with different effects for the hydrogen bonds holding different layers of the clay together and for those within the same layer. At the clay-water interface there is an even wider range of types of hydrogen bond, suggesting that the quantum effects may be yet more varied. We apply classical and thermostated ring polymer molecular dynamics simulations to show that nuclear quantum effects accelerate hydrogen-bond dynamics to varying degrees. By interpreting the results in terms of the extended jump model of hydrogen-bond switching, we can understand the origins of these effects in terms of changes in the quantum kinetic energy of hydrogen atoms during an exchange. We also show that the extended jump mechanism is applicable not only to the hydrogen bonds involving water, but also those internal to the clay.
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5
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Bubon T, Zdorevskyi O, Perepelytsya S. Molecular dynamics study of collective water vibrations in a DNA hydration shell. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:69-79. [PMID: 36920489 DOI: 10.1007/s00249-023-01638-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 03/16/2023]
Abstract
The structure of DNA double helix is stabilized by water molecules and metal counterions that form the ion-hydration shell around the macromolecule. Understanding the role of the ion-hydration shell in the physical mechanisms of the biological functioning of DNA requires detailed studies of its structure and dynamics at the atomistic level. In the present work, the study of collective vibrations of water molecules around the DNA double helix was performed within the framework of classical all-atom molecular dynamics methods. Calculating the vibrational density of states, the vibrations of water molecules in the low-frequency spectra ranged from [Formula: see text]30 to [Formula: see text]300 [Formula: see text] were analyzed for the case of different regions of the DNA double helix (minor groove, major groove, and phosphate groups). The analysis revealed significant differences in the collective vibrations behavior of water molecules in the DNA hydration shell, compared to the vibrations of bulk water. All low-frequency modes of the DNA ion-hydration shell are shifted by about 15-20 [Formula: see text] towards higher frequencies, which is more significant for water molecules in the minor groove region of the double helix. The interactions of water molecules with the atoms of the macromolecule induce intensity decrease of the mode of hydrogen-bond symmetrical stretching near 150 [Formula: see text], leading to the disappearance of this mode in the DNA spectra. The obtained results can provide an interpretation of the experimental data for DNA low-frequency spectra and may be important for the understanding of the processes of indirect protein-nucleic recognition.
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Affiliation(s)
- Tetiana Bubon
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14b, Metrolohichna Str., Kyiv, 03143, Ukraine.
- Condensed Matter and Statistical Physics, Abdus Salam International Centre for Theoretical Physics, Strada Costiera, 11, Trieste, 34151, Italy.
| | - Oleksii Zdorevskyi
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, Helsinki, 00014, Finland
| | - Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14b, Metrolohichna Str., Kyiv, 03143, Ukraine
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6
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Abstract
In this work, efficient methods are proposed for the calculation, from molecular dynamics trajectories, of residence times (RTs) and related quantities. One of these was designed to obtain RT distributions, from which mean residence times (MRTs), residual time distributions, and mean residual times can be computed. This method does not require the assumptions and approximations made by the most commonly used methods. Its link to the most popular method in the literature is identified. It is shown how the much faster new method can be used as a replacement for the latter and the advantages of doing so. Also, a prescription for estimating the uncertainty in the MRTs obtained though the proposed method is provided. Another even faster method for the calculation of the MRTs, their uncertainties, and the mean residual times is also proposed. It yields exactly the same results as the first one but does not allow to obtain the mentioned distributions. Another very popular method, based on autocorrelation functions, for computing MRTs is analyzed in terms of its assumptions and approximations. An alternative, also based on autocorrelation functions, which is faster and requires fewer assumptions is presented. A prescription for the calculation of the uncertainty of the MRTs obtained with the latter method is also provided. In the literature, there are a few methods to discard short transient escapes. Here, an algorithm is suggested that is much faster than the most used one and allows a more integral treatment of the process. Also, it is more widely applicable because it is a preprocessing step that can be used in conjunction with any of the proposed methods mentioned above. The main disadvantage of these two approaches to discard brief escapes is that the maximum duration allowed for an escape to be considered transient appears as a parameter to be determined for the particular system under study. As an alternative, a parameter-free method of a similar character is also proposed to estimate the mean residence time of particles that reached a constant probability of leaving the region of interest.
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Affiliation(s)
- Hernán R Sánchez
- Instituto de Física de Líquidos y Sistemas Biológicos, UNLP-CONICET, La Plata1900, Argentina
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7
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Pluhařová E, Stirnemann G, Laage D. On water reorientation dynamics in cation hydration shells. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Benjamin I. Structure, Thermodynamics, and Dynamics of Thiocyanate Ion Adsorption and Transfer across the Water/Toluene Interface. J Phys Chem B 2022; 126:5706-5714. [PMID: 35861680 DOI: 10.1021/acs.jpcb.2c03956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are used to examine in detail the structure, thermodynamics, and dynamics involve in the adsorption and transfer of the thiocyanate ion (SCN-) across the water/toluene interface. Free energy, hydration structure, and several dynamical properties as a function of the ion location along the interface normal are calculated and contrasted with recent experiments. The free energy profile exhibits a local minimum near the interface corresponding to adsorption free energy relative to bulk water of -6 kJ/mol, in reasonable agreement with experiments. The simulations provide insight into the water surface fluctuations that are coupled to the ion transfer, demonstrating formation of water finger-like structures assisting the transfer process.
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Affiliation(s)
- Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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9
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Schienbein P, Blumberger J. Nanosecond solvation dynamics of the hematite/liquid water interface at hybrid DFT accuracy using committee neural network potentials. Phys Chem Chem Phys 2022; 24:15365-15375. [PMID: 35703465 DOI: 10.1039/d2cp01708c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal oxide/water interfaces play an important role in biology, catalysis, energy storage and photocatalytic water splitting. The atomistic structure at these interfaces is often difficult to characterize by experimental techniques, whilst results from ab initio molecular dynamics simulations tend to be uncertain due to the limited length and time scales accessible. In this work, we train a committee neural network potential to simulate the hematite/water interface at the hybrid DFT level of theory to reach the nanosecond timescale and systems containing more than 3000 atoms. The NNP enables us to converge dynamical properties, not possible with brute-force ab initio molecular dynamics. Our simulations uncover a rich solvation dynamics at the hematite/water interface spanning three different time scales: picosecond H-bond dynamics between surface hydroxyls and the first water layer, in-plane/out-of-plane tilt motion of surface hydroxyls on the 10 ps time scale, and diffusion of water molecules from the oxide surface characterized by a mean residence lifetime of about 60 ps. Calculation of vibrational spectra confirm that H-bonds between surface hydroxyls and first layer water molecules are stronger than H-bonds in bulk water. Our study showcases how state of the art machine learning approaches can routinely be utilized to explore the structural dynamics at transition metal oxide interfaces with complex electronic structure. It foreshadows that c-NNPs are a promising tool to tackle the sampling problem in ab initio electrochemistry with explicit solvent molecules.
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Affiliation(s)
- Philipp Schienbein
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London, WC1E 6BT, UK.
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London, WC1E 6BT, UK.
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10
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Jon JS, Ri WK, Sin KR, Son YC, Jo KW, Pak JS, Kim SJ, Ri YJ, An YC. Derivation of the solvation effect-incorporated Poisson-Boltzmann equation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Cohen SR, Plazanet M, Rols S, Voneshen DJ, Fourkas JT, Coasne B. Structure and dynamics of acetonitrile: Molecular simulation and neutron scattering. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Das B, Chandra A. Ab Initio Molecular Dynamics Study of Aqueous Solutions of Magnesium and Calcium Nitrates: Hydration Shell Structure, Dynamics and Vibrational Echo Spectroscopy. J Phys Chem B 2022; 126:528-544. [PMID: 35001626 DOI: 10.1021/acs.jpcb.1c08545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio molecular dynamics simulations are performed to study the hydration shell structure, dynamics, and vibrational echo spectroscopy of aqueous Mg(NO3)2 and Ca(NO3)2 solutions. The hydration shell structure is probed through calculations of various ion-ion and ion-water radial and spatial distribution functions. On the dynamical side, calculations have been made for the hydrogen bond dynamics of hydration shells and also residence dynamics and lifetimes of water in different solvation environments. Subsequently, we looked at the dynamics of frequency fluctuations of OD modes of heavy water in different hydration environments. Specifically, the temporal decay of spectral observables of two-dimensional infrared (2DIR) spectroscopy, three pulse echo peak shift (3PEPS) measurements and also of time correlations of frequency fluctuations are calculated to investigate the dynamics of vibrational spectral diffusion of water in different hydration environments in these solutions. The OD stretch frequencies of water molecules in the vicinity of both divalent cations are found to be red-shifted and also fluctuating at a slower rate than other water molecules present in the solutions. The Mg2+ ions are found to be strongly hydrated which can be linked to their lower tendency to form contact ion-pairs and essentially no water exchange between the cationic hydration shells and bulk during the time scale of the current simulations. The stronger hydration of Mg2+ ions make their hydration shells structurally and dynamically more rigid and make the dynamics of hydrogen bonds and vibrational spectral diffusion, as revealed through spectral observables of 2DIR and 3PEPS slower than that for the Ca2+ ions. The structural and spectral dynamics of water molecules outside the cationic solvation shells in the Mg(NO3)2 solution are also found to be relatively slower than that of the Ca(NO3)2 solution and pure water which show the effects of stronger electric fields of Mg2+ ions extending beyond their first hydration shells. Also, water molecules in the hydration shells of the NO3- ions are found to relax at a slower rate in the Mg(NO3)2 solution which manifests the effect countercations have on anionic hydration shells for divalent metal nitrate solutions.
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Affiliation(s)
- Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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13
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Faux DA, Rahaman AA, McDonald PJ. Water as a Lévy Rotor. PHYSICAL REVIEW LETTERS 2021; 127:256001. [PMID: 35029422 DOI: 10.1103/physrevlett.127.256001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/24/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
A probability density function describing the angular evolution of a fixed-length atom-atom vector as a Lévy rotor is derived containing just two dynamical parameters: the Lévy parameter α and a rotational time constant τ. A Lévy parameter α<2 signals anomalous (non-Brownian) motion. Molecular dynamics simulation of water at 298 K validates the probability density function for the intramolecular ^{1}H─^{1}H dynamics. The rotational dynamics of water is found to be approximately Brownian at subpicosecond time intervals, becomes increasingly anomalous at longer time intervals due to hydrogen-bond breaking and reforming, before becoming indistinguishable from Brownian dynamics beyond about 25 ps. The Lévy rotor model is used to estimate the intramolecular contribution to the longitudinal nuclear-magnetic-resonance (NMR) relaxation rate R_{1,intra}. It is found that R_{1,intra} contributes 65%±7% to the overall relaxation rate of water at room temperature.
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Affiliation(s)
- David A Faux
- Department of Physics, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Arifah A Rahaman
- Department of Physics, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Peter J McDonald
- Department of Physics, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
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14
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Petersen J, Møller KB, Hynes JT, Rey R. Ultrafast Rotational and Translational Energy Relaxation in Neat Liquids. J Phys Chem B 2021; 125:12806-12819. [PMID: 34762424 DOI: 10.1021/acs.jpcb.1c08014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The excess energy flow pathways during rotational and translational relaxation induced by rotational or translational excitation of a single molecule of and within each of four different neat liquids (H2O, MeOH, CCl4, and CH4) are studied using classical molecular dynamics simulations and energy flux analysis. For all four liquids, the relaxation processes for both types of excitation are ultrafast, but the energy flow is significantly faster for the polar, hydrogen-bonded (H-bonded) liquids H2O and MeOH. Whereas the majority of the initial excess energy is transferred into hindered rotations (librations) for rotational excitation in the H-bonded liquids, an almost equal efficiency for transfer to translational and rotational motions is observed in the nonpolar, non-H-bonded liquids CCl4 and CH4. For translational excitation, transfer to translational motions dominates for all liquids. In general, the energy flows are quite local; i.e., more than 70% of the energy flows directly to the first solvent shell molecules, reaching almost 100% for CCl4 and CH4. Finally, the determined validity of linear response theory for these nonequilibrium relaxation processes is quite solvent-dependent, with the deviation from linear response most marked for rotational excitation and for the nonpolar liquids.
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Affiliation(s)
- Jakob Petersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs. Lyngby, Denmark
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs. Lyngby, Denmark
| | - James T Hynes
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Rossend Rey
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
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15
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Shepherd S, Lan J, Wilkins DM, Kapil V. Efficient Quantum Vibrational Spectroscopy of Water with High-Order Path Integrals: From Bulk to Interfaces. J Phys Chem Lett 2021; 12:9108-9114. [PMID: 34523941 DOI: 10.1021/acs.jpclett.1c02574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Vibrational spectroscopy is key in probing the interplay between the structure and dynamics of aqueous systems. To map different regions of experimental spectra to the microscopic structure of a system, it is important to combine them with first-principles atomistic simulations that incorporate the quantum nature of nuclei. Here we show that the large cost of calculating the quantum vibrational spectra of aqueous systems can be dramatically reduced compared with standard path integral methods by using approximate quantum dynamics based on high-order path integrals. Together with state-of-the-art machine-learned electronic properties, our approach gives an excellent description not only of the infrared and Raman spectra of bulk water but also of the 2D correlation and the more challenging sum-frequency generation spectra of the water-air interface. This paves the way for understanding complex interfaces such as water encapsulated between or in contact with hydrophobic and hydrophilic materials through robust and inexpensive surface-sensitive and multidimensional spectra with first-principles accuracy.
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Affiliation(s)
- Sam Shepherd
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Jinggang Lan
- Department of Chemistry, University of Zürich, Zürich 8057, Switzerland
| | - David M Wilkins
- Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, United Kingdom
| | - Venkat Kapil
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW,United Kingdom
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16
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Gudla H, Shao Y, Phunnarungsi S, Brandell D, Zhang C. Importance of the Ion-Pair Lifetime in Polymer Electrolytes. J Phys Chem Lett 2021; 12:8460-8464. [PMID: 34449227 PMCID: PMC8436209 DOI: 10.1021/acs.jpclett.1c02474] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Ion pairing is commonly considered as a culprit for the reduced ionic conductivity in polymer electrolyte systems. However, this simple thermodynamic picture should not be taken literally, as ion pairing is a dynamical phenomenon. Here we construct model poly(ethylene oxide)-bis(trifluoromethane)sulfonimide lithium salt systems with different degrees of ion pairing by tuning the solvent polarity and examine the relation between the cation-anion distinct conductivity σ+-d and the lifetime of ion pairs τ+- using molecular dynamics simulations. It is found that there exist two distinct regimes where σ+-d scales with 1/τ+- and τ+-, respectively, and the latter is a signature of longer-lived ion pairs that contribute negatively to the total ionic conductivity. This suggests that ion pairs are kinetically different depending on the solvent polarity, which renders the ion-pair lifetime highly important when discussing its effect on ion transport in polymer electrolyte systems.
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Affiliation(s)
- Harish Gudla
- Department of Chemistry-Ångström
Laboratory, Uppsala University, Lägerhyddsvägen 1, Box 538, 75121 Uppsala, Sweden
| | - Yunqi Shao
- Department of Chemistry-Ångström
Laboratory, Uppsala University, Lägerhyddsvägen 1, Box 538, 75121 Uppsala, Sweden
| | - Supho Phunnarungsi
- Department of Chemistry-Ångström
Laboratory, Uppsala University, Lägerhyddsvägen 1, Box 538, 75121 Uppsala, Sweden
| | - Daniel Brandell
- Department of Chemistry-Ångström
Laboratory, Uppsala University, Lägerhyddsvägen 1, Box 538, 75121 Uppsala, Sweden
| | - Chao Zhang
- Department of Chemistry-Ångström
Laboratory, Uppsala University, Lägerhyddsvägen 1, Box 538, 75121 Uppsala, Sweden
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17
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Kumar N, Servis MJ, Clark AE. Uranyl Speciation in the Presence of Specific Ion Gradients at the Electrolyte/Organic Interface. SOLVENT EXTRACTION AND ION EXCHANGE 2021. [DOI: 10.1080/07366299.2021.1954323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Nitesh Kumar
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Michael J. Servis
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Aurora E. Clark
- Department of Chemistry, Washington State University, Pullman, Washington, USA
- Pacific Northwest National Laboratory, Richland, Washington, USA
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18
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Fan C, Liu Y, Sebbah T, Cao X. A Theoretical Study on Terpene-Based Natural Deep Eutectic Solvent: Relationship between Viscosity and Hydrogen-Bonding Interactions. GLOBAL CHALLENGES (HOBOKEN, NJ) 2021; 5:2000103. [PMID: 33728054 PMCID: PMC7933815 DOI: 10.1002/gch2.202000103] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/10/2020] [Indexed: 05/24/2023]
Abstract
The aim of this work is to shed light on the origins of unique properties by studying the relationship between viscosity and hydrogen-bonding interactions of terpene-based natural deep eutectic solvents (NADES). Five systems including camphor/formic acid, menthol/acetic acid, menthol/β-citronellol, menthol/lactic acid, and thymol/β-citronellol are prepared (molar ratio 1:1). Their structures and nature of the associated hydrogen bonds are investigated through multiple methods and theories. The viscosity of NADES is consistent with the product of hydrogen-bond number and lifetime. Through visualization of non-covalent interactions, terpene-acid-based NADES with single sites show the lowest viscosity among the studied systems because of weak and unstable hydrogen bonding. Inversely, multi-site terpene-acid-based NADES possess relatively high viscosity. Owing to the stability of hydrogen bonds in the network, the terpene-terpene-based system is in the middle level of viscosity. In-depth analysis of these hydrogen bonds shows that they can be classified as "weak to medium" and are mainly derived from electrostatic interactions. Moreover, there is an obvious connection between viscosity and hydrogen-bonding strength (integrated core-valence bifurcation index) in the networks. The discovery of intrinsic rules between viscosity and hydrogen-bonding interactions is beneficial for the design of novel low-viscosity NADES in the future.
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Affiliation(s)
- Chen Fan
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business UniversityNo. 11 Fucheng RoadBeijing100048China
| | - Yang Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business UniversityNo. 11 Fucheng RoadBeijing100048China
| | - Tarik Sebbah
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business UniversityNo. 11 Fucheng RoadBeijing100048China
| | - Xueli Cao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business UniversityNo. 11 Fucheng RoadBeijing100048China
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19
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Ashraf H, Cao B, Kalhor P, Yu ZW. Identification and properties of ion-pairs in the aqueous solutions of LiI and NaI by FTIR and quantum chemical calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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An isolated water droplet in the aqueous solution of a supramolecular tetrahedral cage. Proc Natl Acad Sci U S A 2020; 117:32954-32961. [PMID: 33318176 PMCID: PMC7777103 DOI: 10.1073/pnas.2012545117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Water under nanoconfinement at ambient conditions has exhibited low-dimensional ice formation and liquid-solid phase transitions, but with structural and dynamical signatures that map onto known regions of water's phase diagram. Using terahertz (THz) absorption spectroscopy and ab initio molecular dynamics, we have investigated the ambient water confined in a supramolecular tetrahedral assembly, and determined that a dynamically distinct network of 9 ± 1 water molecules is present within the nanocavity of the host. The low-frequency absorption spectrum and theoretical analysis of the water in the Ga4L6 12- host demonstrate that the structure and dynamics of the encapsulated droplet is distinct from any known phase of water. A further inference is that the release of the highly unusual encapsulated water droplet creates a strong thermodynamic driver for the high-affinity binding of guests in aqueous solution for the Ga4L6 12- supramolecular construct.
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21
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Benjamin I. Molecular Dynamics Studies on the Effect of Surface Roughness and Surface Tension on the Thermodynamics and Dynamics of Hydronium Ion Transfer Across the Liquid/Liquid Interface. J Phys Chem B 2020; 124:8711-8718. [PMID: 32902279 DOI: 10.1021/acs.jpcb.0c06304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Molecular dynamics simulations are used to examine the effect of surface roughness and surface tension on the transfer of the classical hydronium ion (H3O+) across the water/1,2-dichloroethane interface. Free energy of transfer, hydration structure, and dynamics as a function of the ion location along the interface normal are calculated with six different values of a control parameter whose variation modifies the surface tension without impacting the bulk properties of the two solvents. Transfer of the classical hydronium ion across the water/1,2-dichloroethan interface involves the cotransfer of three hydration shell water molecules, independent of the surface tension. However, as the interaction between the two liquids weakens, a rise in interfacial tension and decrease in intrinsic water fingering and capillary fluctuations result in fewer water molecules cotransported with the ion in the second shell and a reduction in the length of the finger that the ion is attached to, consistent with the reduced size of the second hydration shell. First shell water residence time and lateral ion diffusion constants vary with the surface tension in a way that is consistent with the abovementioned structural insight.
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Affiliation(s)
- Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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22
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Das B, Mondal S, Chandra A. Two-Dimensional Infrared Spectroscopy of Aqueous Solutions of Metal Nitrates: Slowdown of Spectral Diffusion in the Presence of Divalent Cations. J Phys Chem B 2020; 124:7391-7404. [PMID: 32790404 DOI: 10.1021/acs.jpcb.0c03471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrogen-bonded network of water can be affected both structurally and dynamically by the presence of ions. In the present study, we have considered three aqueous solutions of metal nitrates to investigate the effects of divalent cations (Mg2+ and Ca2+), compared to that of monovalent Na+ ions, on hydrogen-bond fluctuations and vibrational spectral diffusion through calculations of linear and two-dimensional infrared spectra of these solutions at room temperature. We have employed the methods of molecular dynamics simulations using effective polarizable models of ions combined with quantum mechanical calculations of transition variables and statistical mechanical calculations of spectral response functions of vibrational spectroscopy. Divalent cations are found to have much stronger and longer-ranged effects on the structure and dynamics of the hydrogen-bonded network than that induced by the monovalent sodium ions. The blue shifts in the calculated linear spectra are found to follow the Hofmeister trend for the cations. The 2D-IR spectral lineshape and intensity corresponding to three-pulse echo peak shift (3PEPS) experiments are calculated. The timescales of these nonlinear spectral responses and also frequency-time correlations show significant slowing down of spectral diffusion for solutions containing divalent Mg2+ and Ca2+ ions compared to the corresponding dynamics of the solution containing Na+ ions. Unlike NaNO3 solution, the relaxation of frequency and dipole orientational fluctuations of anion-bound water in Mg(NO3)2 and Ca(NO3)2 solutions are found to be somewhat slower than bulk water, which can be attributed to the presence of divalent cations whose effects go beyond their first solvation shells. This is also seen in the dynamics of bulk water in these solutions which is found to be notably slower for the solutions containing divalent cations than that in the NaNO3 solution. Unlike Mg2+ and Ca2+ ions, no specific cationic effect is observed for the Na+ ions.
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Affiliation(s)
- Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Subhadip Mondal
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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23
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Roy S, Wu L, Goverapet Srinivasan S, Stack AG, Navrotsky A, Bryantsev VS. Hydration structure and water exchange kinetics at xenotime-water interfaces: implications for rare earth minerals separation. Phys Chem Chem Phys 2020; 22:7719-7727. [PMID: 32215419 DOI: 10.1039/d0cp00087f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydration of surface ions gives rise to structural heterogeneity and variable exchange kinetics of water at complex mineral-water interfaces. Here, we employ ab initio molecular dynamics (AIMD) simulations and water adsorption calorimetry to examine the aqueous interfaces of xenotime, a phosphate mineral that contains predominantly Y3+ and heavy rare earth elements. Consistent with natural crystal morphology, xenotime is predicted to have a tetragonal prismatic shape, dominated by the {100} surface. Hydration of this surface induces multilayer interfacial water structures with distinct OH orientations, which agrees with recent crystal truncation rod measurements. The exchange kinetics between two adjacent water layers exhibits a wide range of underlying timescales (5-180 picoseconds), dictated by ion-water electrostatics. Adsorption of a bidentate hydroxamate ligand reveals that {100} xenotime surface can only accommodate monodentate coordination with water exchange kinetics strongly depending on specific ligand orientation, prompting us to reconsider traditional strategies for selective separation of rare-earth minerals.
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Affiliation(s)
- Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN 37830, USA.
| | - Lili Wu
- Peter A. Rock Thermochemistry Laboratory and NEAT ORU, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | | | - Andrew G Stack
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN 37830, USA.
| | - Alexandra Navrotsky
- Peter A. Rock Thermochemistry Laboratory and NEAT ORU, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Vyacheslav S Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN 37830, USA.
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24
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Galle Kankanamge SR, Kuroda DG. Molecular Structure, Chemical Exchange, and Conductivity Mechanism of High Concentration LiTFSI Electrolytes. J Phys Chem B 2020; 124:1965-1977. [PMID: 32069048 PMCID: PMC7307920 DOI: 10.1021/acs.jpcb.9b10795] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
High
concentration lithium electrolytes have been found to be good
candidates for high energy density and high voltage lithium batteries.
Recent studies have shown that limiting the free solvent molecules
in the electrolytes prevents the degradation of the battery electrodes.
However, the molecular level knowledge of the structure and dynamics
of such an electrolyte system is limited, especially for electrolytes
based on typical organic carbonates. In this article, the interactions
and motions involved in lithium bis(trifluoromethanesulfonyl)imide
in carbonyl-containing solvents are investigated using linear and
time-resolved vibrational spectroscopies and computational methods.
Our results suggest that the overall structure and the speciation
of the three high concentration electrolytes are similar. However,
the cyclic carbonate-based electrolyte presents an additional interaction
as a result of dimer formation. Time-resolved studies reveal similar
and fast dynamics for the structural motions of solvent molecules
in electrolytes composed of linear molecules, while the electrolyte
made of cyclic solvent molecules shows slower structural changes as
a result of the dimer formation. Additionally, a picosecond time scale
process is observed and assigned to the coordination and decoordination
of solvent molecules from a lithium-ion solvation shell. This process
of solvent exchange is found to be directly correlated to the making
and breaking of structures between the lithium-ion and the anion and,
consequently, to the conduction mechanism. Overall, our data show
that the molecular structure of the solvent does not significantly
affect the speciation and distribution of the lithium-ion solvation
shells. However, the presence of dimerization between solvent molecules
of two neighboring lithium-ions appears to produce a microscopic ordering
that it is manifested macroscopically in properties of the electrolyte,
such as its viscosity.
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Affiliation(s)
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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25
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Hüfner-Wulsdorf T, Klebe G. Role of Water Molecules in Protein–Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics. J Chem Inf Model 2020; 60:1818-1832. [DOI: 10.1021/acs.jcim.0c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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26
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Shao Y, Hellström M, Yllö A, Mindemark J, Hermansson K, Behler J, Zhang C. Temperature effects on the ionic conductivity in concentrated alkaline electrolyte solutions. Phys Chem Chem Phys 2020; 22:10426-10430. [PMID: 31895378 DOI: 10.1039/c9cp06479f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alkaline electrolyte solutions are important components in rechargeable batteries and alkaline fuel cells. As the ionic conductivity is thought to be a limiting factor in the performance of these devices, which are often operated at elevated temperatures, its temperature dependence is of significant interest. Here we use NaOH as a prototypical example of alkaline electrolytes, and for this system we have carried out reactive molecular dynamics simulations with an experimentally verified high-dimensional neural network potential derived from density-functional theory calculations. It is found that in concentrated NaOH solutions elevated temperatures enhance both the contributions of proton transfer to the ionic conductivity and deviations from the Nernst-Einstein relation. These findings are expected to be of practical relevance for electrochemical devices based on alkaline electrolyte solutions.
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Affiliation(s)
- Yunqi Shao
- Department of Chemistry -Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala, Sweden.
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27
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Tomaník L, Muchová E, Slavíček P. Solvation energies of ions with ensemble cluster-continuum approach. Phys Chem Chem Phys 2020; 22:22357-22368. [DOI: 10.1039/d0cp02768e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An alternative cluster-continuum approach for the calculation of solvation free energies of ions.
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Affiliation(s)
- Lukáš Tomaník
- Department of Physical Chemistry
- University of Chemistry and TechnologyTechnická 5
- 16628 Prague 6
- Czech Republic
| | - Eva Muchová
- Department of Physical Chemistry
- University of Chemistry and TechnologyTechnická 5
- 16628 Prague 6
- Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry
- University of Chemistry and TechnologyTechnická 5
- 16628 Prague 6
- Czech Republic
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28
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Benjamin I. Hydronium ion at the water/1,2-dichloroethane interface: Structure, thermodynamics, and dynamics of ion transfer. J Chem Phys 2019; 151:094701. [DOI: 10.1063/1.5116008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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29
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Siwaipram S, Bopp PA, Soetens JC, Schmid R, Bureekaew S. Development of a MOF-FF-compatible interaction model for liquid methanol and Cl− in methanol. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Roy S, Bryantsev VS. Finding Order in the Disordered Hydration Shell of Rapidly Exchanging Water Molecules around the Heaviest Alkali Cs+ and Fr+. J Phys Chem B 2018; 122:12067-12076. [DOI: 10.1021/acs.jpcb.8b08414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Santanu Roy
- Chemical Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Vyacheslav S. Bryantsev
- Chemical Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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31
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Hellström M, Ceriotti M, Behler J. Nuclear Quantum Effects in Sodium Hydroxide Solutions from Neural Network Molecular Dynamics Simulations. J Phys Chem B 2018; 122:10158-10171. [DOI: 10.1021/acs.jpcb.8b06433] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Matti Hellström
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jörg Behler
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
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32
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33
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Prakash A, Fu CD, Bonomi M, Pfaendtner J. Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics. J Chem Theory Comput 2018; 14:4985-4990. [DOI: 10.1021/acs.jctc.8b00448] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Arushi Prakash
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher D. Fu
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Massimiliano Bonomi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Senior Scientist, Pacific Northwest National Laboratory, Richland, Washington, United States
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34
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Nguyen M, Rick SW. The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions. J Chem Phys 2018; 148:222803. [PMID: 29907071 DOI: 10.1063/1.5012682] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.
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Affiliation(s)
- Mary Nguyen
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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35
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Qiu Y, Schwegler BR, Wang LP. Polarizable Molecular Simulations Reveal How Silicon-Containing Functional Groups Govern the Desalination Mechanism in Nanoporous Graphene. J Chem Theory Comput 2018; 14:4279-4290. [DOI: 10.1021/acs.jctc.8b00226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yudong Qiu
- Chemistry Department, The University of California, Davis, Davis, California 95616, United States
| | - Benedict R. Schwegler
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Lee-Ping Wang
- Chemistry Department, The University of California, Davis, Davis, California 95616, United States
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36
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Zhang Q, Pan Z, Zhang L, Zhang R, Chen Z, Jin T, Wu T, Chen X, Zhuang W. Ion effect on the dynamics of water hydrogen bonding network: A theoretical and computational spectroscopy point of view. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
- Department of ChemistryBohai UniversityJinzhouChina
| | - Zhijun Pan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Ruiting Zhang
- School of Physics and Optoelectronic EngineeringXidian UniversityXi'anChina
| | - Zhening Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Tianmin Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Xian Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
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37
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Weiss LB, Dahirel V, Marry V, Jardat M. Computation of the Hydrodynamic Radius of Charged Nanoparticles from Nonequilibrium Molecular Dynamics. J Phys Chem B 2018; 122:5940-5950. [DOI: 10.1021/acs.jpcb.8b01153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lisa B. Weiss
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
- Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Vincent Dahirel
- Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Virginie Marry
- Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, CNRS, F-75005 Paris, France
| | - Marie Jardat
- Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, Sorbonne Université, CNRS, F-75005 Paris, France
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38
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Hudait A, Odendahl N, Qiu Y, Paesani F, Molinero V. Ice-Nucleating and Antifreeze Proteins Recognize Ice through a Diversity of Anchored Clathrate and Ice-like Motifs. J Am Chem Soc 2018; 140:4905-4912. [PMID: 29564892 DOI: 10.1021/jacs.8b01246] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cold-adapted organisms produce antifreeze and ice-nucleating proteins to prevent and promote ice formation. The crystal structure of hyperactive bacterial antifreeze protein (AFP) MpAFP suggests that this protein binds ice through an anchored clathrate motif. It is not known whether other hyperactive AFPs and ice-nucleating proteins (INPs) use the same motif to recognize or nucleate ice. Here we use molecular simulations to elucidate the ice-binding motifs of hyperactive insect AFPs and a model INP of Pseudomonas syringae. We find that insect AFPs recognize ice through anchored clathrate motifs distinct from that of MpAFP. By performing simulations of ice nucleation by PsINP, we identify two distinct ice-binding sites on opposite sides of the β-helix. The ice-nucleating sequences identified in the simulations agree with those previously proposed for the closely related INP of Pseudomonas borealis based on the structure of the protein. The simulations indicate that these sites have comparable ice-nucleating efficiency, but distinct binding motifs, controlled by the amino acid sequence: one is an anchored clathrate and the other ice-like. We conclude that anchored clathrate and ice-like motifs can be equally effective for binding proteins to ice and promoting ice nucleation.
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Affiliation(s)
- Arpa Hudait
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Nathan Odendahl
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Yuqing Qiu
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Valeria Molinero
- Department of Chemistry , 315 South 1400 East , The University of Utah , Salt Lake City , Utah 84112-0580 , United States
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39
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Sharma B, Chandra A. Born-Oppenheimer Molecular Dynamics Simulations of a Bromate Ion in Water Reveal Its Dual Kosmotropic and Chaotropic Behavior. J Phys Chem B 2018; 122:2090-2101. [PMID: 29376361 DOI: 10.1021/acs.jpcb.7b09300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvation structure and dynamics of a bromate (BrO3-) ion in water are studied by means of Born-Oppenheimer molecular dynamics simulations at two different temperatures using the Becke-Lee-Yang-Parr functional with Grimme D3 dispersion corrections. The bromate ion possesses a pyramidal structure, and it has two types of solvation sites, namely, the bromine and oxygen atoms. We have looked at different radial and orientational distributions of water molecules around the bromate ion and also investigated their hydrogen bonding properties. The solvation structure of the bromate ion is also compared with that of the iodate (IO3-) ion, which is structurally rather similar to the bromate ion and was found to have some unusual solvation properties in water. It is found that the bromate ion follows a similar trend as that followed by the iodate ion as far as the solvation structure is concerned. However, the effect of the former on surrounding water is found to be much weaker than that of the latter. On the dynamical side, we have looked at diffusion, residence dynamics, and also the orientational and hydrogen bond relaxation of water molecules around the BrO3- ion and compared them with those of the bulk. Dynamical results are presented for both H2O and D2O around the BrO3- ion. Interpretation of the dynamical results in terms of structure-making (kosmotropic)/-breaking (chaotropic) properties of the BrO3- ion reveals that the bromine atom of this ion acts as a water structure breaker, whereas the three oxygens act as water structure makers. Thus, in spite of being a single ion, the bromate ion has dual characteristics and the experimentally observed kosmotropic ability of this ion is actually a trade-off between a chaotropic site (the bromine atom) and three kosmotropic sites (three oxygen atoms) that are present in the ion.
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Affiliation(s)
- Bikramjit Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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40
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Yadav S, Chandra A. Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts. J Chem Phys 2017; 147:244503. [DOI: 10.1063/1.4996273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sushma Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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41
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Houriez C, Vallet V, Réal F, Meot-Ner (Mautner) M, Masella M. Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts. J Chem Phys 2017; 147:161720. [DOI: 10.1063/1.4997996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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43
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Carof A, Salanne M, Charpentier T, Rotenberg B. Collective water dynamics in the first solvation shell drive the NMR relaxation of aqueous quadrupolar cations. J Chem Phys 2017; 145:124508. [PMID: 27782645 DOI: 10.1063/1.4963682] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using molecular simulations, we analyze the microscopic processes driving the Nuclear Magnetic Resonance (NMR) relaxation of quadrupolar cations in water. The fluctuations of the Electric Field Gradient (EFG) experienced by alkaline and magnesium cations, which determine the NMR relaxation time, are mainly due to the dynamics of water molecules in their solvation shell. The dynamics of the ion plays a less important role, with the exception of the short-time dynamics in the lighter Li+ case, for which rattling in the solvent cage results in oscillations of the EFG autocorrelation function (ACF). Several microscopic mechanisms that may a priori contribute to the decay of the EFG-ACF occur in fact over too long time scales: entrance/exit of individual water molecules into/from the solvation shell, rotation of a molecule around the ion, or reorientation of the molecule. In contrast, the fluctuations of the ion-water distance are clearly correlated to that of the EFG. Nevertheless, it is not sufficient to consider a single molecule due to the cancellations arising from the symmetry of the solvation shell. The decay of the EFG-ACF, hence NMR relaxation, is in fact governed by the collective symmetry-breaking fluctuations of water in the first solvation shell.
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Affiliation(s)
- Antoine Carof
- Sorbonne Universités, UPMC Universités Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
| | - Mathieu Salanne
- Sorbonne Universités, UPMC Universités Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
| | - Thibault Charpentier
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette cedex, France
| | - Benjamin Rotenberg
- Sorbonne Universités, UPMC Universités Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
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44
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Hellström M, Behler J. Proton-Transfer-Driven Water Exchange Mechanism in the Na+ Solvation Shell. J Phys Chem B 2017; 121:4184-4190. [DOI: 10.1021/acs.jpcb.7b01490] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matti Hellström
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jörg Behler
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
- Universität Göttingen, Institut für Physikalische
Chemie, Tammannstr. 6, 37077 Göttingen, Germany
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45
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Thaunay F, Ohanessian G, Clavaguéra C. Dynamics of ions in a water drop using the AMOEBA polarizable force field. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Volgin IV, Larin SV, Abad E, Lyulin SV. Molecular Dynamics Simulations of Fullerene Diffusion in Polymer Melts. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02050] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Igor V. Volgin
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 Saint Petersburg, Russia
| | - Sergey V. Larin
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 Saint Petersburg, Russia
| | - Enrique Abad
- Departamento
de Física Aplicada and Instituto de Computación Científica
Avanzada (ICCAEX), Centro Universitario de Mérida, Universidad de Extremadura, E-06800 Mérida, Spain
| | - Sergey V. Lyulin
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 Saint Petersburg, Russia
- Physical
Faculty, Saint-Petersburg University, Ulyanovskaya str. 1, 198504 Petrodvorets, Russia
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47
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Sessa F, Spezia R, D'Angelo P. Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex. J Chem Phys 2017; 144:204505. [PMID: 27250314 DOI: 10.1063/1.4951714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.
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Affiliation(s)
- Francesco Sessa
- Dipartimento di Chimica, Università di Roma "La Sapienza," P. le A. Moro 5, 00185 Roma, Italy
| | - Riccardo Spezia
- CNRS, UMR 8587, Laboratoire Analyse et Modelisation Pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Blvd. F. Mitterrand, 91025 Evry Cedex, France
| | - Paola D'Angelo
- Dipartimento di Chimica, Università di Roma "La Sapienza," P. le A. Moro 5, 00185 Roma, Italy
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48
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Gavrilov Y, Leuchter JD, Levy Y. On the coupling between the dynamics of protein and water. Phys Chem Chem Phys 2017; 19:8243-8257. [DOI: 10.1039/c6cp07669f] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Jessica D. Leuchter
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yaakov Levy
- Department of Structural Biology
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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49
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Giammanco CH, Kramer PL, Fayer MD. Ionic Liquid versus Li+ Aqueous Solutions: Water Dynamics near Bistriflimide Anions. J Phys Chem B 2016; 120:9997-10009. [DOI: 10.1021/acs.jpcb.6b07145] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chiara H. Giammanco
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Patrick L. Kramer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Michael D. Fayer
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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50
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Wang YL, Wang Y, Yi HB. High-Order Ca(II)–Chloro Complexes in Mixed CaCl2–LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations. J Phys Chem A 2016; 120:5635-48. [DOI: 10.1021/acs.jpca.6b01694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu-Lin Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Ying Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Hai-Bo Yi
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
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