1
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Becker MR, Loche P, Netz RR. Electrokinetic, electrochemical, and electrostatic surface potentials of the pristine water liquid-vapor interface. J Chem Phys 2022; 157:240902. [PMID: 36586978 DOI: 10.1063/5.0127869] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Although conceptually simple, the air-water interface displays rich behavior and is subject to intense experimental and theoretical investigations. Different definitions of the electrostatic surface potential as well as different calculation methods, each relevant for distinct experimental scenarios, lead to widely varying potential magnitudes and sometimes even different signs. Based on quantum-chemical density-functional-theory molecular dynamics (DFT-MD) simulations, different surface potentials are evaluated and compared to force-field (FF) MD simulations. As well explained in the literature, the laterally averaged electrostatic surface potential, accessible to electron holography, is dominated by the trace of the water molecular quadrupole moment, and using DFT-MD amounts to +4.35 V inside the water phase, very different from results obtained with FF water models which yield negative values of the order of -0.4 to -0.6 V. Thus, when predicting potentials within water molecules, as relevant for photoelectron spectroscopy and non-linear interface-specific spectroscopy, DFT simulations should be used. The electrochemical surface potential, relevant for ion transfer reactions and ion surface adsorption, is much smaller, less than 200 mV in magnitude, and depends specifically on the ion radius. Charge transfer between interfacial water molecules leads to a sizable surface potential as well. However, when probing electrokinetics by explicitly applying a lateral electric field in DFT-MD simulations, the electrokinetic ζ-potential turns out to be negligible, in agreement with predictions using continuous hydrodynamic models. Thus, interfacial polarization charges from intermolecular charge transfer do not lead to significant electrokinetic mobility at the pristine vapor-liquid water interface, even assuming these transfer charges are mobile in an external electric field.
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Affiliation(s)
| | - Philip Loche
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
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2
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Hao H, Ruiz Pestana L, Qian J, Liu M, Xu Q, Head‐Gordon T. Chemical transformations and transport phenomena at interfaces. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Luis Ruiz Pestana
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Jin Qian
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Meili Liu
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Qiang Xu
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
- Department of Bioengineering and Chemical and Biomolecular Engineering University of California Berkeley California USA
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3
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Hao H, Leven I, Head-Gordon T. Can electric fields drive chemistry for an aqueous microdroplet? Nat Commun 2022; 13:280. [PMID: 35022410 PMCID: PMC8755715 DOI: 10.1038/s41467-021-27941-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022] Open
Abstract
Reaction rates of common organic reactions have been reported to increase by one to six orders of magnitude in aqueous microdroplets compared to bulk solution, but the reasons for the rate acceleration are poorly understood. Using a coarse-grained electron model that describes structural organization and electron densities for water droplets without the expense of ab initio methods, we investigate the electric field distributions at the air-water interface to understand the origin of surface reactivity. We find that electric field alignments along free O-H bonds at the surface are ~16 MV/cm larger on average than that found for O-H bonds in the interior of the water droplet. Furthermore, electric field distributions can be an order of magnitude larger than the average due to non-linear coupling of intramolecular solvent polarization with intermolecular solvent modes which may contribute to even greater surface reactivity for weakening or breaking chemical bonds at the droplet surface.
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Affiliation(s)
- Hongxia Hao
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA, 94720, USA
- Departments of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Itai Leven
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA, 94720, USA
- Departments of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA.
- Pitzer Center for Theoretical Chemistry, University of California, Berkeley, CA, 94720, USA.
- Departments of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Departments of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Departments of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
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4
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Herbert JM, Paul SK. Interaction Energy Analysis of Monovalent Inorganic Anions in Bulk Water Versus Air/Water Interface. Molecules 2021; 26:6719. [PMID: 34771133 PMCID: PMC8588468 DOI: 10.3390/molecules26216719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Soft anions exhibit surface activity at the air/water interface that can be probed using surface-sensitive vibrational spectroscopy, but the structural implications of this surface activity remain a matter of debate. Here, we examine the nature of anion-water interactions at the air/water interface using a combination of molecular dynamics simulations and quantum-mechanical energy decomposition analysis based on symmetry-adapted perturbation theory. Results are presented for a set of monovalent anions, including Cl-, Br-, I-, CN-, OCN-, SCN-, NO2-, NO3-, and ClOn- (n=1,2,3,4), several of which are archetypal examples of surface-active species. In all cases, we find that average anion-water interaction energies are systematically larger in bulk water although the difference (with respect to the same quantity computed in the interfacial environment) is well within the magnitude of the instantaneous fluctuations. Specifically for the surface-active species Br-(aq), I-(aq), ClO4-(aq), and SCN-(aq), and also for ClO-(aq), the charge-transfer (CT) energy is found to be larger at the interface than it is in bulk water, by an amount that is greater than the standard deviation of the fluctuations. The Cl-(aq) ion has a slightly larger CT energy at the interface, but NO3-(aq) does not; these two species are borderline cases where consensus is lacking regarding their surface activity. However, CT stabilization amounts to <20% of the total induction energy for each of the ions considered here, and CT-free polarization energies are systematically larger in bulk water in all cases. As such, the role of these effects in the surface activity of soft anions remains unclear. This analysis complements our recent work suggesting that the short-range solvation structure around these ions is scarcely different at the air/water interface from what it is in bulk water. Together, these observations suggest that changes in first-shell hydration structure around soft anions cannot explain observed surface activities.
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Affiliation(s)
- John M. Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, USA;
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5
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Han B, Isborn CM, Shi L. Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models. J Chem Theory Comput 2021; 17:889-901. [PMID: 33405925 DOI: 10.1021/acs.jctc.0c01102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.
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Affiliation(s)
- Bowen Han
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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6
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Carpenter AP, Altman RM, Tran E, Richmond GL. How Low Can You Go? Molecular Details of Low-Charge Nanoemulsion Surfaces. J Phys Chem B 2020; 124:4234-4245. [DOI: 10.1021/acs.jpcb.0c03293] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrew P. Carpenter
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Rebecca M. Altman
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Emma Tran
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Geraldine L. Richmond
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
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7
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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}
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\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.
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8
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Schröder C, Lyons A, Rick SW. Polarizable MD simulations of ionic liquids: How does additional charge transfer change the dynamics? Phys Chem Chem Phys 2020; 22:467-477. [DOI: 10.1039/c9cp05478b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new model for treating charge transfer in ionic liquids is developed and applied to 1-ethyl-3-methylimidazolium tetrafluoroborate. The model allows for us to examine the roles of charge transfer, polarizability, and charge scaling effects on the dynamics of ionic liquids.
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Affiliation(s)
- Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Alex Lyons
- University of New Orleans
- Department of Chemistry
- New Orleans
- USA
| | - Steven W. Rick
- University of New Orleans
- Department of Chemistry
- New Orleans
- USA
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9
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Cai X, Cui X, Zu L, Zhang Y, Gao X, Lian H, Liu Y, Wang X. Ultra High Electrical Performance of Nano Nickel Oxide and Polyaniline Composite Materials. Polymers (Basel) 2017; 9:E288. [PMID: 30970970 PMCID: PMC6432493 DOI: 10.3390/polym9070288] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 01/27/2023] Open
Abstract
The cooperative effects between the PANI (polyaniline)/nano-NiO (nano nickel oxide) composite electrode material and redox electrolytes (potassium iodide, KI) for supercapacitor applications was firstly discussed in this article, providing a novel method to prepare nano-NiO by using β-cyelodextrin (β-CD) as the template agent. The experimental results revealed that the composite electrode processed a high specific capacitance (2122.75 F·g-1 at 0.1 A·g-1 in 0.05 M KI electrolyte solution), superior energy density (64.05 Wh·kg-1 at 0.2 A·g-1 in the two-electrode system) and excellent cycle performance (86% capacitance retention after 1000 cycles at 1.5 A·g-1). All those ultra-high electrical performances owe to the KI active material in the electrolyte and the PANI coated nano-NiO structure.
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Affiliation(s)
- Xiaomin Cai
- College of Material Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
- State Key Laboratory of Organic⁻Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiuguo Cui
- College of Material Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
| | - Lei Zu
- College of Material Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
- State Key Laboratory of Organic⁻Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
| | - You Zhang
- College of Material Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
- State Key Laboratory of Organic⁻Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xing Gao
- College of Material Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
- State Key Laboratory of Organic⁻Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Huiqin Lian
- Beijing Key Laboratory of Specialty Elastomer Composite Materials, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
| | - Yang Liu
- College of Material Science and Engineering, Beijing Institute of Petrochemical Technology, Beijing 102617, China.
| | - Xiaodong Wang
- State Key Laboratory of Organic⁻Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, China.
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10
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Giberti F, Hassanali AA. The excess proton at the air-water interface: The role of instantaneous liquid interfaces. J Chem Phys 2017; 146:244703. [DOI: 10.1063/1.4986082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Federico Giberti
- Institute for Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, USA
| | - Ali A. Hassanali
- Condensed Matter and Statistical Physics, The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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11
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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: 294] [Impact Index Per Article: 36.8] [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.
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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
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12
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Rick SW. A polarizable, charge transfer model of water using the drude oscillator. J Comput Chem 2016; 37:2060-6. [DOI: 10.1002/jcc.24426] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 04/14/2016] [Accepted: 05/17/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Steven W. Rick
- Department of ChemistryUniversity of New OrleansNew Orleans70148 Los Angeles
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13
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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
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14
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Soniat M, Hartman L, Rick SW. Charge Transfer Models of Zinc and Magnesium in Water. J Chem Theory Comput 2015; 11:1658-67. [DOI: 10.1021/ct501173n] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Marielle Soniat
- Department
of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Lisa Hartman
- Benjamin Franklin High School, New Orleans, Louisiana 70122, United States
| | - Steven W. Rick
- Department
of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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15
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Samson JS, Scheu R, Smolentsev N, Rick SW, Roke S. Sum frequency spectroscopy of the hydrophobic nanodroplet/water interface: Absence of hydroxyl ion and dangling OH bond signatures. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.09.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
Conspectus Quantum mechanics (QM) has revolutionized our understanding of the structure and reactivity of small molecular systems. Given the tremendous impact of QM in this research area, it is attractive to believe that this could also be brought into the biological realm where systems of a few thousand atoms and beyond are routine. Applying QM methods to biological problems brings an improved representation to these systems by the direct inclusion of inherently QM effects such as polarization and charge transfer. Because of the improved representation, novel insights can be gleaned from the application of QM tools to biomacromolecules in aqueous solution. To achieve this goal, the computational bottlenecks of QM methods had to be addressed. In semiempirical theory, matrix diagonalization is rate limiting, while in density functional theory or Hartree-Fock theory electron repulsion integral computation is rate-limiting. In this Account, we primarily focus on semiempirical models where the divide and conquer (D&C) approach linearizes the matrix diagonalization step with respect to the system size. Through the D&C approach, a number of applications to biological problems became tractable. Herein, we provide examples of QM studies on biological systems that focus on protein solvation as viewed by QM, QM enabled structure-based drug design, and NMR and X-ray biological structure refinement using QM derived restraints. Through the examples chosen, we show the power of QM to provide novel insights into biological systems, while also impacting practical applications such as structure refinement. While these methods can be more expensive than classical approaches, they make up for this deficiency by the more realistic modeling of the electronic nature of biological systems and in their ability to be broadly applied. Of the tools and applications discussed in this Account, X-ray structure refinement using QM models is now generally available to the community in the refinement package Phenix. While the power of this approach is manifest, challenges still remain. In particular, QM models are generally applied to static structures, so ways in which to include sampling is an ongoing challenge. Car-Parrinello or Born-Oppenheimer molecular dynamics approaches address the short time scale sampling issue, but how to effectively use QM to study phenomenon covering longer time scales will be the focus of future research. Finally, how to accurately and efficiently include electron correlation effects to facilitate the modeling of, for example, dispersive interactions, is also a major hurdle that a broad range of groups are addressing The use of QM models in biology is in its infancy, leading to the expectation that the most significant use of these tools to address biological problems will be seen in the coming years. It is hoped that while this Account summarizes where we have been, it will also help set the stage for future research directions at the interface of quantum mechanics and biology.
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Affiliation(s)
- Kenneth M Merz
- Department of Chemistry and the Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing Michigan 48824-1322, United States
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17
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Yao Y, Kanai Y, Berkowitz ML. Role of Charge Transfer in Water Diffusivity in Aqueous Ionic Solutions. J Phys Chem Lett 2014; 5:2711-2716. [PMID: 26277968 DOI: 10.1021/jz501238v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We performed molecular dynamics simulations on four types of systems containing ion and solvating water. Two systems contained a cation (Na(+) or K(+)), and two other systems an anion (Cl(-) or I(-)). Classical molecular dynamics simulations were performed using three different force fields: a fixed charge force field, a polarizable force field that includes explicit polarization, and also a recently developed force field that includes polarization and charge transfer. These simulations were then compared to first-principles molecular dynamics simulations. While the first-principles simulations showed that the anions accelerated water translational diffusion, the cations slowed it down. In simulations with the classical force fields, only the force field that incorporates explicit charge transfer reproduced this ion-specific behavior. Additional simulations performed to understand the effect of charge transfer demonstrated that two competitive factors determine the behavior of water translational diffusion: the ions diminished charge accelerates water, while the net charge acquired by water either accelerates or slows down its dynamics. Our results show that charge transfer plays a crucial role in governing the water dynamics in aqueous ionic solutions.
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Affiliation(s)
- Yi Yao
- †Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- †Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- ‡Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Max L Berkowitz
- †Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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18
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Soniat M, Rick SW. Charge transfer effects of ions at the liquid water/vapor interface. J Chem Phys 2014; 140:184703. [DOI: 10.1063/1.4874256] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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19
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Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys 2013; 139:184103. [PMID: 24320250 PMCID: PMC3838431 DOI: 10.1063/1.4826261] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/30/2013] [Indexed: 01/12/2023] Open
Abstract
The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.
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Affiliation(s)
- Gabriel J Rocklin
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA
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Ou S, Cui D, Patel S. Liquid-vapor interfacial properties of aqueous solutions of guanidinium and methyl guanidinium chloride: influence of molecular orientation on interface fluctuations. J Phys Chem B 2013; 117:11719-31. [PMID: 23937431 DOI: 10.1021/jp405862p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The guanidinium cation (C(NH2)3(+)) is a highly stable cation in aqueous solution due to its efficient solvation by water molecules and resonance stabilization of the charge. Its salts increase the solubility of nonpolar molecules ("salting-in") and decrease the ordering of water. It is one of the strongest denaturants used in biophysical studies of protein folding. We investigate the behavior of guanidinium and its derivative, methyl guanidinium (an amino acid analogue) at the air-water surface, using atomistic molecular dynamics (MD) simulations and calculation of potentials of mean force. Methyl guanidinium cation is less excluded from the air-water surface than guanidinium cation, but both cations show orientational dependence of surface affinity. Parallel orientations of the guanidinium ring (relative to the Gibbs dividing surface) show pronounced free energy minima in the interfacial region, while ring orientations perpendicular to the GDS exhibit no discernible surface stability. Calculations of surface fluctuations demonstrate that, near the air-water surface, the parallel-oriented cations generate significantly greater interfacial fluctuations compared to other orientations, which induces more long-ranged perturbations and solvent density redistribution. Our results suggest a strong correlation with induced interfacial fluctuations and ion surface stability. These results have implications for interpreting molecular-level, mechanistic action of this osmolyte's interaction with hydrophobic interfaces as they impact protein denaturation (solubilization).
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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Ou S, Hu Y, Patel S, Wan H. Spherical monovalent ions at aqueous liquid-vapor interfaces: interfacial stability and induced interface fluctuations. J Phys Chem B 2013; 117:11732-42. [PMID: 24032752 DOI: 10.1021/jp406001b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ion-specific interfacial behaviors of monovalent halides impact processes such as protein denaturation, interfacial stability, and surface tension modulation, and as such, their molecular and thermodynamic underpinnings garner much attention. We use molecular dynamics simulations of monovalent anions in water to explore effects on distant interfaces. We observe long-ranged ion-induced perturbations of the aqueous environment, as suggested by experiment and theory. Surface stable ions, characterized as such by minima in potentials of mean force computed using umbrella sampling MD simulations, induce larger interfacial fluctuations compared to nonsurface active species, conferring more entropy approaching the interface. Smaller anions and cations show no interfacial potential of mean force minima. The difference is traced to hydration shell properties of the anions, and the coupling of these shells with distant solvent. The effects correlate with the positions of the anions in the Hofmeister series (acknowledging variations in force field ability to recapitulate essential underlying physics), suggesting how differences in induced, nonlocal perturbations of interfaces may be related to different specific-ion effects in dilute biophysical and nanomaterial systems.
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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Cummings OT, Wick CD. Interfacial behavior of simple inorganic salts at the air-water interface investigated with a polarizable model with electrostatic damping. J Chem Phys 2013; 139:064708. [DOI: 10.1063/1.4817775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ou S, Patel S. Temperature dependence and energetics of single ions at the aqueous liquid-vapor interface. J Phys Chem B 2013; 117:6512-23. [PMID: 23537166 DOI: 10.1021/jp401243m] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate temperature-dependence of free energetics with two single halide anions, I(-) and Cl(-), crossing the aqueous liquid-vapor interface through molecular dynamics simulations. The result shows that I(-) has a modest surface stability of 0.5 kcal/mol at 300 K and the stability decreases as the temperature increases, indicating the surface adsorption process for the anion is entropically disfavored. In contrast, Cl(-) shows no such surface state at all temperatures. Decomposition of free energetics reveals that water-water interactions provide a favorable enthalpic contribution, while the desolvation of ion induces an increase in free energy. Calculations of surface fluctuations demonstrate that I(-) generates significantly greater interfacial fluctuations compared to Cl(-). The fluctuation is attributed to the malleability of the solvation shells, which allows for more long-ranged perturbations and solvent density redistribution induced by I(-) as the anion approaches the liquid-vapor interface. The increase in temperature of the solvent enhances the inherent thermally excited fluctuations and consequently reduces the relative contribution from anion to surface fluctuations, which is consistent with the decrease in surface stability of I(-). Our results indicate a strong correlation with induced interfacial fluctuations and anion surface stability; moreover, resulting temperature dependent behavior of induced fluctuations suggests the possibility of a critical level of induced fluctuations associated with surface stability.
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Affiliation(s)
- Shuching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Abstract
Simulations are carried out for the ice/vapor and ice/liquid interfaces using models for water which include intermolecular charge transfer, as well as polarizability. The models transfer a small amount of charge for each hydrogen bond formed, as indicated from electronic structure calculations, from the molecule that accepts the hydrogen bond to the molecule that donates the hydrogen bond. Depending on distance from the interface, molecules can, on average, have more of one type (donor or acceptor) than the other. The asymmetric local environment leads to net charge transfer at the interface, with layers of molecules with small net charges. Molecules at the ice side of the interface tend to be positively charged, while molecules at the vapor or liquid side tend to be negatively charged.
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Affiliation(s)
- Alexis J Lee
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
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