1
|
Kaiser S, Yue Z, Peng Y, Nguyen TD, Chen S, Teng D, Voth GA. Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package. J Phys Chem B 2024; 128:4959-4974. [PMID: 38742764 PMCID: PMC11129700 DOI: 10.1021/acs.jpcb.4c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system's bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.
Collapse
Affiliation(s)
- Scott Kaiser
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Zhi Yue
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Yuxing Peng
- NVIDIA
Corporation, Santa
Clara, California 95051, United States
| | - Trung Dac Nguyen
- Research
Computing Center, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sijia Chen
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Da Teng
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
2
|
de la Puente M, Gomez A, Laage D. Neural Network-Based Sum-Frequency Generation Spectra of Pure and Acidified Water Interfaces with Air. J Phys Chem Lett 2024; 15:3096-3102. [PMID: 38470065 DOI: 10.1021/acs.jpclett.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The affinity of hydronium ions (H3O+) for the air-water interface is a crucial question in environmental chemistry. While sum-frequency generation (SFG) spectroscopy has been instrumental in indicating the preference of H3O+ for the interface, key questions persist regarding the molecular origin of the SFG spectral changes in acidified water. Here we combine nanosecond long neural network (NN) reactive simulations of pure and acidified water slabs with NN predictions of molecular dipoles and polarizabilities to calculate SFG spectra of long reactive trajectories including proton transfer events. Our simulations show that H3O+ ions cause two distinct changes in phase-resolved SFG spectra: first, a low-frequency tail due to the vibrations of H3O+ and its first hydration shell, analogous to the bulk proton continuum, and second, an enhanced hydrogen-bonded band due to the ion-induced static field polarizing molecules in deeper layers. Our calculations confirm that changes in the SFG spectra of acidic solutions are caused by hydronium ions preferentially residing at the interface.
Collapse
Affiliation(s)
- Miguel de la Puente
- PASTEUR, Department of Chemistry, École Normale Supérieur, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Axel Gomez
- PASTEUR, Department of Chemistry, École Normale Supérieur, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieur, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| |
Collapse
|
3
|
Rashid MAM, Rahman M, Acter T, Uddin N. Identifying the acidic or basic behavior of surface water: a QM/MM-MD study. Phys Chem Chem Phys 2023; 25:31194-31205. [PMID: 37955174 DOI: 10.1039/d3cp02080k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Controversies on the water surface were theoretically addressed with the help of large scale quantum mechanical molecular dynamics (QMMD) simulations on water surface model systems with and without excess hydroniums and hydroxides. It was revealed that the thermodynamic surface structures of these ions strongly depend on their location and dipole orientation. Fast hydronium diffusion by proton transfer establishes a wider kinetic depth distribution (∼6 Å) than that predicted by its thermodynamic affinity for the water surface, while slow hydroxide is shallowly trapped below the outermost molecular layer (3-4 Å). In addition, the anisotropic orientation of surface water dipole can generate a substantial magnitude of surface potential, which extends to a depth of a few molecular layers. With these distinctively different surface properties of two ions and water molecules, the seemingly contradictory observations of acidic and negatively charged water surfaces may be successfully explained. That is, the negative surface charge of neutral water mostly stems from intrinsic water properties such as water dipole orientation and electron density spillage at the surface, rather than surface OH- ions. The enhanced acidity of the water surface can be attributed in large part to the kinetic depth profile of ion density in addition to static thermodynamic origin. Furthermore, the different depth profiles of the two ions may differently affect the surface-sensitive spectroscopic observations.
Collapse
Affiliation(s)
- Md Al Mamunur Rashid
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Mofizur Rahman
- Research and Development Center, Berger Paints Bangladesh Limited, Berger House, Dhaka-1230, Bangladesh
| | - Thamina Acter
- Department of Mathematical and Physical Sciences, East West University, Aftabnagar, Dhaka-1212, Bangladesh
| | - Nizam Uddin
- Department of Nutrition and Food Engineering, Daffodil International University, Birulia, Dhaka-1216, Bangladesh.
| |
Collapse
|
4
|
David R, Kumar R. Reactive events at the graphene oxide-water interface. Chem Commun (Camb) 2021; 57:11697-11700. [PMID: 34676846 DOI: 10.1039/d1cc04589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Graphene oxide exhibits interesting reactive events at its interface with water, with water as an active participant. The reactive events are influenced by the level of oxidation of the graphene oxide sheet. The fully oxidized sheet tends to make the interfacial water media acidic leaving the sheet negatively charged, whereas the reduced sheet can form comparatively long lived carbocations as well as split water forming two alcohol groups on the sheet.
Collapse
Affiliation(s)
- Rolf David
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA. .,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris 75005, France
| | - Revati Kumar
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA.
| |
Collapse
|
5
|
Stoppelman JP, McDaniel JG. Proton Transport in [BMIM+][BF4–]/Water Mixtures Near the Percolation Threshold. J Phys Chem B 2020; 124:5957-5970. [DOI: 10.1021/acs.jpcb.0c02487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- John P. Stoppelman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia30332-0400, United States
| | - Jesse G. McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia30332-0400, United States
| |
Collapse
|
6
|
Li Z, Li C, Wang Z, Voth GA. What Coordinate Best Describes the Affinity of the Hydrated Excess Proton for the Air-Water Interface? J Phys Chem B 2020; 124:5039-5046. [PMID: 32426982 DOI: 10.1021/acs.jpcb.0c03288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations and free energy sampling are employed in this work to investigate the surface affinity of the hydrated excess proton with two definitions of the interface: The Gibbs dividing interface (GDI) and the Willard-Chandler interface (WCI). Both the multistate empirical valence bond (MS-EVB) reactive molecular dynamics method and the density functional theory-based ab initio molecular dynamics (AIMD) were used to describe the hydrated excess proton species, including "vehicular" (standard diffusion) transport and (Grotthuss) proton hopping transport and associated structures of the hydrated excess proton net positive charge defect. The excess proton is found to exhibit a similar trend and quantitative free energy behavior in terms of its surface affinity as a function of the GDI or WCI. Importantly, the definitions of the two interfaces in terms of the excess proton charge defect are highly correlated and far from independent of one another, thus undermining the argument that one interface is superior to the other when describing the proton interface affinity. Moreover, the hydrated excess proton and its solvation shell significantly influence the location and local curvature of the WCI, making it difficult to disentangle the interfacial thermodynamics of the excess proton from the influence of that species on the instantaneous surface curvature.
Collapse
Affiliation(s)
- Zhefu Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute of Biophysics Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute of Biophysics Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Zhi Wang
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute of Biophysics Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute of Biophysics Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
7
|
Charge transfer as a ubiquitous mechanism in determining the negative charge at hydrophobic interfaces. Nat Commun 2020; 11:901. [PMID: 32060273 PMCID: PMC7021814 DOI: 10.1038/s41467-020-14659-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/22/2020] [Indexed: 01/17/2023] Open
Abstract
The origin of the apparent negative charge at hydrophobic–water interfaces has fueled debates in the physical chemistry community for decades. The most common interpretation given to explain this observation is that negatively charged hydroxide ions (OH–) bind strongly to the interfaces. Using first principles calculations of extended air–water and oil–water interfaces, we unravel a mechanism that does not require the presence of OH–. Small amounts of charge transfer along hydrogen bonds and asymmetries in the hydrogen bond network due to topological defects can lead to the accumulation of negative surface charge at both interfaces. For water near oil, some spillage of electron density into the oil phase is also observed. The computed surface charge densities at both interfaces is approximately \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$-0.015\ {\rm{e}}/{{\rm{nm}}}^{2}$$\end{document}−0.015e∕nm2 in agreement with electrophoretic experiments. We also show, using an energy decomposition analysis, that the electronic origin of this phenomena is rooted in a collective polarization/charge transfer effect. The accumulation of negative charge at hydrophobic–water interfaces has been a source of debate for a long time. Here the authors use ab initio calculations to show that the charge accumulation at air–water and oil–water interfaces is caused by subtle charge transfer processes.
Collapse
|
8
|
Villa AM, Doglia SM, De Gioia L, Bertini L, Natalello A. Anomalous Intrinsic Fluorescence of HCl and NaOH Aqueous Solutions. J Phys Chem Lett 2019; 10:7230-7236. [PMID: 31689111 DOI: 10.1021/acs.jpclett.9b02163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The unique properties of liquid water mainly arise from its hydrogen bond network. The geometry and dynamics of this network play a key role in shaping the characteristics of soft matter, from simple solutions to biosystems. Here we report an anomalous intrinsic fluorescence of HCl and NaOH aqueous solutions at room temperature that shows important differences in the excitation and emission bands between the two solutes. From ab initio time-dependent density functional theory modeling we propose that fluorescence emission could originate from hydrated ion species contained in transient cavities of the bulk solvent. These cavities, which are characterized by a stiff surface, could provide an environment that, upon trapping the excited state, suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway.
Collapse
Affiliation(s)
- Anna Maria Villa
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| |
Collapse
|
9
|
Lindberg GE. Structure and diffusion of molten alkali carbonate salts at the liquid-vacuum interface. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The liquid-vacuum interface of molten alkali carbonate salts is studied with molecular dynamics simulations. Three salts comprised of LixNayKzCO3 near their respective eutectic concentrations are considered to understand the distribution of ions relative to a liquid-vacuum interface and their diffusivity. These simulations show that each of the cations accumulate at the interface preferentially compared to carbonate. The cation ordering is found to inversely correspond to cation radius, with K being the most likely occupant at the surface, followed by Na, Li, and then the anion. Similar to other studies, the carbonate is found to diffuse more slowly than the cations, but we do observe small differences in diffusion between compositions that present opportunities to optimize ion transport. These results hold consequences for our understanding of ion behavior in molten carbonate salts and the performance of devices employ these electrolytes.
Collapse
Affiliation(s)
- Gerrick E. Lindberg
- Department of Applied Physics and Materials Science, Department of Chemistry and Biochemistry, Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, AZ, United States of America
| |
Collapse
|
10
|
Spectroscopic BIL-SFG Invariance Hides the Chaotropic Effect of Protons at the Air-Water Interface. ATMOSPHERE 2018. [DOI: 10.3390/atmos9100396] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The knowledge of the water structure at the interface with the air in acidic pH conditions is of utmost importance for chemistry in the atmosphere. We shed light on the acidic air-water (AW) interfacial structure by DFT-MD simulations of the interface containing one hydronium ion coupled with theoretical SFG (Sum Frequency Generation) spectroscopy. The interpretation of SFG spectra at charged interfaces requires a deconvolution of the signal into BIL (Binding Interfacial Layer) and DL (Diffuse Layer) SFG contributions, which is achieved here, and hence reveals that even though H 3 O + has a chaotropic effect on the BIL water structure (by weakening the 2D-HBond-Network observed at the neat air-water interface) it has no direct probing in SFG spectroscopy. The changes observed experimentally in the SFG of the acidic AW interface from the SFG at the neat AW are shown here to be solely due to the DL-SFG contribution to the spectroscopy. Such BIL-SFG and DL-SFG deconvolution rationalizes the experimental SFG data in the literature, while the hydronium chaotropic effect on the water 2D-HBond-Network in the BIL can be put in perspective of the decrease in surface tension at acidic AW interfaces.
Collapse
|
11
|
Cox SJ, Geissler PL. Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations. J Chem Phys 2018; 148:222823. [DOI: 10.1063/1.5020563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Stephen J. Cox
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Phillip L. Geissler
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
12
|
Li W, Pak CY, Tse YLS. Free energy study of H2O, N2O5, SO2, and O3 gas sorption by water droplets/slabs. J Chem Phys 2018; 148:164706. [DOI: 10.1063/1.5022389] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wentao Li
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Chi Yuen Pak
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Ying-Lung Steve Tse
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| |
Collapse
|
13
|
Li X, Batchelor-McAuley C, Laborda E, Compton RG. Aqueous Voltammetry in the Near Absence of Electrolyte. Chemistry 2017; 23:15222-15226. [PMID: 28876501 DOI: 10.1002/chem.201703525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 11/09/2022]
Abstract
In order to minimize the incidence of the CO2 hydrolysis and conduct aqueous electrochemistry in the virtual absence of electrolyte, a novel methodology is developed to achieve the near minimum conductivity (≈60 nS cm-1 ) for an aqueous solution through in situ deionization with ion exchange resin beads. Aqueous electrochemistry studying the oxidations of platinum, ferrocenemethanol, and hydrogen (H2 ) were conducted in the near complete absence of trace ionic species at a platinum microelectrode (d=10 μm). Both surface and solution phase electrochemical reactions were clearly observed, indicating that under these conditions there is a sufficiently compressed double layer for an interfacial electron transfer to be driven and the iR effects are significantly smaller than theoretically expected.
Collapse
Affiliation(s)
- Xiuting Li
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, Oxford University, Oxford, OX1 3QZ, UK
| | | | - Eduardo Laborda
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30100, Murcia, Spain
| | - Richard G Compton
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, Oxford University, Oxford, OX1 3QZ, UK
| |
Collapse
|
14
|
Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
15
|
Mechanism of ion adsorption to aqueous interfaces: Graphene/water vs. air/water. Proc Natl Acad Sci U S A 2017; 114:13369-13373. [PMID: 28827359 DOI: 10.1073/pnas.1702760114] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The adsorption of ions to aqueous interfaces is a phenomenon that profoundly influences vital processes in many areas of science, including biology, atmospheric chemistry, electrical energy storage, and water process engineering. Although classical electrostatics theory predicts that ions are repelled from water/hydrophobe (e.g., air/water) interfaces, both computer simulations and experiments have shown that chaotropic ions actually exhibit enhanced concentrations at the air/water interface. Although mechanistic pictures have been developed to explain this counterintuitive observation, their general applicability, particularly in the presence of material substrates, remains unclear. Here we investigate ion adsorption to the model interface formed by water and graphene. Deep UV second harmonic generation measurements of the SCN- ion, a prototypical chaotrope, determined a free energy of adsorption within error of that for air/water. Unlike for the air/water interface, wherein repartitioning of the solvent energy drives ion adsorption, our computer simulations reveal that direct ion/graphene interactions dominate the favorable enthalpy change. Moreover, the graphene sheets dampen capillary waves such that rotational anisotropy of the solute, if present, is the dominant entropy contribution, in contrast to the air/water interface.
Collapse
|
16
|
Ben-Amotz D. Interfacial solvation thermodynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:414013. [PMID: 27545849 DOI: 10.1088/0953-8984/28/41/414013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Previous studies have reached conflicting conclusions regarding the interplay of cavity formation, polarizability, desolvation, and surface capillary waves in driving the interfacial adsorptions of ions and molecules at air-water interfaces. Here we revisit these questions by combining exact potential distribution results with linear response theory and other physically motivated approximations. The results highlight both exact and approximate compensation relations pertaining to direct (solute-solvent) and indirect (solvent-solvent) contributions to adsorption thermodynamics, of relevance to solvation at air-water interfaces, as well as a broader class of processes linked to the mean force potential between ions, molecules, nanoparticles, proteins, and biological assemblies.
Collapse
Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
17
|
Bera MK, Antonio MR. Aggregation of Heteropolyanions Implicates the Presence of Zundel Ions Near Air-Water Interfaces. ChemistrySelect 2016. [DOI: 10.1002/slct.201600441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mrinal K. Bera
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 United States
- DUBBLE-CRG; ESRF-The European Synchrotron Radiation Facility CS40220; 38043 Grenoble Cedex 9 France
| | - Mark R. Antonio
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 United States
| |
Collapse
|
18
|
Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
Collapse
Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
| |
Collapse
|
19
|
Bai C, Herzfeld J. Surface Propensities of the Self-Ions of Water. ACS CENTRAL SCIENCE 2016; 2:225-31. [PMID: 27163053 PMCID: PMC4850511 DOI: 10.1021/acscentsci.6b00013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Indexed: 05/15/2023]
Abstract
The surface charge of water, which is important in a wide range of chemical, biological, material, and environmental contexts, has been a subject of lengthy and heated debate. Recently, it has been shown that the highly efficient LEWIS force field, in which semiclassical, independently mobile valence electron pairs capture the amphiproticity, polarizability and H-bonding of water, provides an excellent description of the solvation and dynamics of hydroxide and hydronium in bulk water. Here we turn our attention to slabs, cylinders, and droplets. In extended simulations with 1000 molecules, we find that hydroxide consistently prefers the surface, hydronium consistently avoids the surface, and the two together form an electrical double layer until neutralization occurs. The behavior of hydroxide can largely be accounted for by the observation that hydroxide moving to the surface loses fewer hydrogen bonds than are gained by the water molecule that it displaces from the surface. At the same time, since the orientation of the hydroxide increases the ratio of dangling hydrogens to dangling lone pairs, the proton activity of the exposed surface may be increased, rather than decreased. Hydroxide also moves more rapidly in the surface than in the bulk, likely because the proton donating propensity of neighboring water molecules is focused on the one hydrogen that is not dangling from the surface.
Collapse
|
20
|
Rane K, van der Vegt NFA. Understanding the influence of capillary waves on solvation at the liquid-vapor interface. J Chem Phys 2016; 144:114111. [DOI: 10.1063/1.4943781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kaustubh Rane
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische and Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
| |
Collapse
|
21
|
McDaniel JG, Yethiraj A. Importance of hydrophobic traps for proton diffusion in lyotropic liquid crystals. J Chem Phys 2016; 144:094705. [DOI: 10.1063/1.4943131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| |
Collapse
|
22
|
Tse YLS, Chen C, Lindberg GE, Kumar R, Voth GA. Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface. J Am Chem Soc 2015; 137:12610-6. [PMID: 26366480 DOI: 10.1021/jacs.5b07232] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Significant effort has been undertaken to better understand the molecular details governing the propensity of ions for the air-water interface. Facilitated by computationally efficient reactive molecular dynamics simulations, new and statistically conclusive molecular-scale results on the affinity of the hydrated excess proton and hydroxide anion for the air-water interface are presented. These simulations capture the dynamic bond breaking and formation processes (charge defect delocalization) that are important for correctly describing the solvation and transport of these complex species. The excess proton is found to be attracted to the interface, which is correlated with a favorable enthalpic contribution and consistent with reducing the disruption in the hydrogen bond network caused by the ion complex. However, a recent refinement of the underlying reactive potential energy function for the hydrated excess proton shows the interfacial attraction to be weaker, albeit nonzero, a result that is consistent with the experimental surface tension measurements. The influence of a weak hydrogen bond donated from water to the protonated oxygen, recently found to play an important role in excess hydrated proton transport in bulk water, is seen to also be important for this study. In contrast, the hydroxide ion is found to be repelled from the air-water interface. This repulsion is characterized by a reduction of the energetically favorable ion-water interactions, which creates an enthalpic penalty as the ion approaches the interface. Finally, we find that the fluctuation in the coordination number around water sheds new light on the observed entropic trends for both ions.
Collapse
Affiliation(s)
- Ying-Lung Steve Tse
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Chen Chen
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States.,College of Chemistry and Molecular Sciences, Hubei Key Lab of Electrochemical Power Sources, Wuhan University , Wuhan 430072, China
| | - Gerrick E Lindberg
- Department of Chemistry and Biochemistry, Northern Arizona University , Flagstaff, Arizona 86011, United States
| | - Revati Kumar
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States
| |
Collapse
|
23
|
Tahat A, Martí J. Proton transfer in liquid water confined inside graphene slabs. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032402. [PMID: 26465477 DOI: 10.1103/physreve.92.032402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 06/05/2023]
Abstract
The microscopic structure and dynamics of an excess proton in water constrained in narrow graphene slabs between 0.7 and 3.1 nm wide has been studied by means of a series of molecular dynamics simulations. Interaction of water and carbon with the proton species was modeled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of confinement on proton solvation structure and on its dynamical properties has been considered for varying densities. The system is organized in one interfacial and a bulk-like region, both of variable size. In the widest interplate separations, the lone proton shows a marked tendency to place itself in the bulk phase of the system, due to the repulsive interaction with the carbon atoms. However, as the system is compressed and the proton is forced to move to the vicinity of graphene walls it moves closer to the interface, producing a neat enhancement of the local structure. We found a marked slowdown of proton transfer when the separation of the two graphene plates is reduced. In the case of lowest distances between graphene plates (0.7 and 0.9 nm), only one or two water layers persist and the two-dimensional character of water structure becomes evident. By means of spectroscopical analysis, we observed the persistence of Zundel and Eigen structures in all cases, although at low interplate separations a signature frequency band around 2500 cm^{-1} suffers a blue shift and moves to characteristic values of asymmetric hydronium ion vibrations, indicating some unstability of the typical Zundel-Eigen moieties and their eventual conversion to a single hydronium species solvated by water.
Collapse
Affiliation(s)
- Amani Tahat
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, Building B5, Northern Campus UPC. Jordi Girona, 1-3, 08034 Barcelona, Catalonia, Spain
| | - Jordi Martí
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, Building B5, Northern Campus UPC. Jordi Girona, 1-3, 08034 Barcelona, Catalonia, Spain
| |
Collapse
|
24
|
Soniat M, Kumar R, Rick SW. Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water. J Chem Phys 2015; 143:044702. [DOI: 10.1063/1.4926831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marielle Soniat
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| | - Revati Kumar
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70808, USA
| | - Steven W. Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
| |
Collapse
|
25
|
Wang H, Agmon N. Protonated Water Dimer on Benzene: Standing Eigen or Crouching Zundel? J Phys Chem B 2015; 119:2658-67. [DOI: 10.1021/jp509004j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Huan Wang
- The Fritz Haber Research
Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Noam Agmon
- The Fritz Haber Research
Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
26
|
Tse YLS, Knight C, Voth GA. An analysis of hydrated proton diffusion in ab initio molecular dynamics. J Chem Phys 2015; 142:014104. [DOI: 10.1063/1.4905077] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ying-Lung Steve Tse
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637, USA
| | - Chris Knight
- Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Gregory A. Voth
- Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
27
|
Brorsen KR, Pruitt SR, Gordon MS. Surface Affinity of the Hydronium Ion: The Effective Fragment Potential and Umbrella Sampling. J Phys Chem B 2014; 118:14382-7. [DOI: 10.1021/jp506906w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kurt R. Brorsen
- Ames
Laboratory, US-DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Spencer R. Pruitt
- Ames
Laboratory, US-DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Argonne Leadership
Computing Facility, Argonne, Illinois 60439, United States
| | - Mark S. Gordon
- Ames
Laboratory, US-DOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| |
Collapse
|
28
|
Kumar R, Knight C, Wick CD, Chen B. Bringing Reactivity to the Aggregation-Volume-Bias Monte Carlo Based Simulation Framework: Water Nucleation Induced by a Reactive Proton. J Phys Chem B 2014; 119:9068-75. [DOI: 10.1021/jp508749x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Revati Kumar
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Center for Computation and Technology, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
| | - Chris Knight
- Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Collin D. Wick
- College
of Engineering and Science, Louisiana Tech University, Ruston, Louisiana 71272, United States
| | - Bin Chen
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
29
|
Pruitt SR, Bertoni C, Brorsen KR, Gordon MS. Efficient and accurate fragmentation methods. Acc Chem Res 2014; 47:2786-94. [PMID: 24810424 DOI: 10.1021/ar500097m] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method.
Collapse
Affiliation(s)
- Spencer R. Pruitt
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, United States
| | - Colleen Bertoni
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Kurt R. Brorsen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| |
Collapse
|
30
|
Baer MD, Kuo IFW, Tobias DJ, Mundy CJ. Toward a unified picture of the water self-ions at the air-water interface: a density functional theory perspective. J Phys Chem B 2014; 118:8364-72. [PMID: 24762096 DOI: 10.1021/jp501854h] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The propensities of the water self-ions, H3O(+) and OH(-), for the air-water interface have implications for interfacial acid-base chemistry. Despite numerous experimental and computational studies, no consensus has been reached on the question of whether or not H3O(+) and/or OH(-) prefer to be at the water surface or in the bulk. Here we report a molecular dynamics simulation study of the bulk vs interfacial behavior of H3O(+) and OH(-) that employs forces derived from density functional theory with a generalized gradient approximation exchange-correlation functional (specifically, BLYP) and empirical dispersion corrections. We computed the potential of mean force (PMF) for H3O(+) as a function of the position of the ion in the vicinity of an air-water interface. The PMF suggests that H3O(+) has equal propensity for the interface and the bulk. We compare the PMF for H3O(+) to our previously computed PMF for OH(-) adsorption, which contains a shallow minimum at the interface, and we explore how differences in solvation of each ion at the interface vs in the bulk are connected with interfacial propensity. We find that the solvation shell of H3O(+) is only slightly dependent on its position in the water slab, while OH(-) partially desolvates as it approaches the interface, and we examine how this difference in solvation behavior is manifested in the electronic structure and chemistry of the two ions.
Collapse
Affiliation(s)
- Marcel D Baer
- Physical Science Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | |
Collapse
|