51
|
Berthoumieux H, Maggs AC. Fluctuation-induced forces governed by the dielectric properties of water-A contribution to the hydrophobic interaction. J Chem Phys 2015; 143:104501. [PMID: 26374044 DOI: 10.1063/1.4928509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The hydrophobic interaction between objects immersed in water is typically attractive and adds to the well-known van der Waals interaction. The former supposedly dominates the latter on nanometric distances and could be of major importance in the assembly of biologic objects. Here, we show that the fluctuation-induced attraction between two objects immersed in a correlated dielectric medium which models water is the sum of a van der Waals term and a short-range contribution that can be identified as part of the hydrophobic interaction. In this framework, we calculate analytically the fluid correlation function and the fluctuation-induced interaction between small and extended inclusions embedded in water and we characterize the hydrophobic terms.
Collapse
Affiliation(s)
- H Berthoumieux
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 7600, LPTMC, F-75005 Paris, France
| | - A C Maggs
- Laboratoire PCT, Gulliver CNRS-ESPCI UMR 7083, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| |
Collapse
|
52
|
Cao S, Sheong FK, Huang X. Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules. J Chem Phys 2015; 143:054110. [DOI: 10.1063/1.4928051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Siqin Cao
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fu Kit Sheong
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuhui Huang
- The HKUST Shenzhen Research Institute, Shenzhen, China
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Division of Biomedical Engineering, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| |
Collapse
|
53
|
MacDermaid CM, DeVane RH, Klein ML, Fiorin G. Dehydration of multilamellar fatty acid membranes: towards a computational model of the stratum corneum. J Chem Phys 2015; 141:22D526. [PMID: 25494797 DOI: 10.1063/1.4902363] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The level of hydration controls the cohesion between apposed lamellae of saturated free fatty acids found in the lipid matrix of stratum corneum, the outermost layer of mammalian skin. This multilamellar lipid matrix is highly impermeable to water and ions, so that the local hydration shell of its fatty acids may not always be in equilibrium with the acidity and relative humidity, which significantly change over a course of days during skin growth. The homeostasis of the stratum corneum at each moment of its growth likely requires a balance between two factors, which affect in opposite ways the diffusion of hydrophilic species through the stratum corneum: (i) an increase in water order as the lipid lamellae come in closer contact, and (ii) a decrease in water order as the fraction of charged fatty acids is lowered by pH. Herein molecular dynamics simulations are employed to estimate the impact of both effects on water molecules confined between lamellae of fatty acids. Under conditions where membrane undulations are energetically favorable, the charged fatty acids are able to sequester cations around points of contact between lamellae that are fully dehydrated, while essentially maintaining a multilamellar structure for the entire system. This observation suggests that the undulations of the fatty acid lamellae control the diffusion of hydrophilic species through the water phase by altering the positional and rotational order of water molecules in the embedded/occluded "droplets."
Collapse
Affiliation(s)
- Christopher M MacDermaid
- Institute for Computational Molecular Science, SERC Building (035-07), Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122, USA
| | - Russell H DeVane
- Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069, USA
| | - Michael L Klein
- Institute for Computational Molecular Science, SERC Building (035-07), Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122, USA
| | - Giacomo Fiorin
- Institute for Computational Molecular Science, SERC Building (035-07), Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122, USA
| |
Collapse
|
54
|
Remsing RC, Xi E, Vembanur S, Sharma S, Debenedetti PG, Garde S, Patel AJ. Pathways to dewetting in hydrophobic confinement. Proc Natl Acad Sci U S A 2015; 112:8181-6. [PMID: 26100866 PMCID: PMC4500207 DOI: 10.1073/pnas.1503302112] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Liquid water can become metastable with respect to its vapor in hydrophobic confinement. The resulting dewetting transitions are often impeded by large kinetic barriers. According to macroscopic theory, such barriers arise from the free energy required to nucleate a critical vapor tube that spans the region between two hydrophobic surfaces--tubes with smaller radii collapse, whereas larger ones grow to dry the entire confined region. Using extensive molecular simulations of water between two nanoscopic hydrophobic surfaces, in conjunction with advanced sampling techniques, here we show that for intersurface separations that thermodynamically favor dewetting, the barrier to dewetting does not correspond to the formation of a (classical) critical vapor tube. Instead, it corresponds to an abrupt transition from an isolated cavity adjacent to one of the confining surfaces to a gap-spanning vapor tube that is already larger than the critical vapor tube anticipated by macroscopic theory. Correspondingly, the barrier to dewetting is also smaller than the classical expectation. We show that the peculiar nature of water density fluctuations adjacent to extended hydrophobic surfaces--namely, the enhanced likelihood of observing low-density fluctuations relative to Gaussian statistics--facilitates this nonclassical behavior. By stabilizing isolated cavities relative to vapor tubes, enhanced water density fluctuations thus stabilize novel pathways, which circumvent the classical barriers and offer diminished resistance to dewetting. Our results thus suggest a key role for fluctuations in speeding up the kinetics of numerous phenomena ranging from Cassie-Wenzel transitions on superhydrophobic surfaces, to hydrophobically driven biomolecular folding and assembly.
Collapse
Affiliation(s)
- Richard C Remsing
- Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Erte Xi
- Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Srivathsan Vembanur
- Howard P. Isermann Department of Chemical & Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Sumit Sharma
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Pablo G Debenedetti
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Shekhar Garde
- Howard P. Isermann Department of Chemical & Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Amish J Patel
- Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104;
| |
Collapse
|
55
|
Hande VR, Chakrabarty S. Structural Order of Water Molecules around Hydrophobic Solutes: Length-Scale Dependence and Solute–Solvent Coupling. J Phys Chem B 2015; 119:11346-57. [DOI: 10.1021/acs.jpcb.5b03449] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vrushali R. Hande
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune-411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune-411008, India
| |
Collapse
|
56
|
Weiß RG, Heyden M, Dzubiella J. Curvature dependence of hydrophobic hydration dynamics. PHYSICAL REVIEW LETTERS 2015; 114:187802. [PMID: 26001018 DOI: 10.1103/physrevlett.114.187802] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 06/04/2023]
Abstract
We investigate the solute curvature dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both the lateral and perpendicular diffusivity, as well as for H-bond kinetics of water in the first hydration shell, we find a nonmonotonic solute-size dependence, exhibiting extrema close to the well-known structural crossover length scale for hydrophobic hydration. Additionally, we find an apparent anomalous diffusion for water moving parallel to the surface of small solutes, which, however, can be explained by topology effects. Our findings regarding the intimate connection between solute curvature and water dynamics has implications for our understanding of hydration dynamics at heterogeneous biomolecular surfaces.
Collapse
Affiliation(s)
- R Gregor Weiß
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstrasse 15, D-12489 Berlin, Germany
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
| | - Matthias Heyden
- Max-Planck-Insitut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstrasse 15, D-12489 Berlin, Germany
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, D-14109 Berlin, Germany
| |
Collapse
|
57
|
Remsing RC, Patel AJ. Water density fluctuations relevant to hydrophobic hydration are unaltered by attractions. J Chem Phys 2015; 142:024502. [DOI: 10.1063/1.4905009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Richard C. Remsing
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Amish J. Patel
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
58
|
Peter EK, Agarwal M, Kim B, Pivkin IV, Shea JE. How water layers on graphene affect folding and adsorption of TrpZip2. J Chem Phys 2014; 141:22D511. [DOI: 10.1063/1.4896984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Mrigya Agarwal
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - BongKeun Kim
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| | - Igor V. Pivkin
- Insitute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and Department of Physics, University of California Santa Barbara, California 93106, USA
| |
Collapse
|
59
|
Wu E, Garde S. Lengthscale-Dependent Solvation and Density Fluctuations in n-Octane. J Phys Chem B 2014; 119:9287-94. [DOI: 10.1021/jp509912v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eugene Wu
- Howard P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Shekhar Garde
- Howard P. Isermann Department
of Chemical and Biological Engineering and Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| |
Collapse
|
60
|
Varma S, Botlani M, Leighty RE. Discerning intersecting fusion-activation pathways in the Nipah virus using machine learning. Proteins 2014; 82:3241-54. [DOI: 10.1002/prot.24541] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/10/2014] [Accepted: 02/14/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sameer Varma
- Department of Cell Biology; Microbiology and Molecular Biology, University of South Florida; Tampa Florida 33620
| | - Mohsen Botlani
- Department of Cell Biology; Microbiology and Molecular Biology, University of South Florida; Tampa Florida 33620
| | - Ralph E. Leighty
- Department of Cell Biology; Microbiology and Molecular Biology, University of South Florida; Tampa Florida 33620
| |
Collapse
|
61
|
Ou SC, Patel S. Electrostatic contribution from solvent in modulating single-walled carbon nanotube association. J Chem Phys 2014; 141:114906. [PMID: 25240371 PMCID: PMC4187323 DOI: 10.1063/1.4892566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/28/2014] [Indexed: 11/14/2022] Open
Abstract
We perform all-atom molecular dynamics simulations to compute the potential of mean force (PMF) between two (10,10) single-walled carbon nanotubes solvated in pure nonpolarizable SPC/E and polarizable TIP4P-FQ water, at various temperatures. In general, the reversible work required to bring two nanotubes from a dissociated state (free energy reference) to contact state (free energy minimum) is more favorable and less temperature-dependent in TIP4P-FQ than in SPC/E water models. In contrast, molecular properties and behavior of water such as the spatially-resolved water number density (intertube, intratube, or outer regions), for TIP4P-FQ are more sensitive to temperature than SPC/E. Decomposition of the solvent-induced PMF into different spatial regions suggests that TIP4P-FQ has stronger temperature dependence; the opposing destabilizing/stabilizing contributions from intertube water and more distal water balance each other and suppress the temperature dependence of total association free energy. Further investigation of hydrogen bonding network in intertube water reveals that TIP4P-FQ retains fewer hydrogen bonds than SPC/E, which correlates with the lower water number density in this region. This reduction of hydrogen bonds affects the intertube water dipoles. As the intertube volume decreases, TIP4P-FQ dipole moment approaches the gas phase value; the distribution of dipole magnitude also becomes narrower due to less average polarization/perturbation from other water molecules. Our results imply that the reduction of water under confinement may seem trivial, but underlying effects to structure and free energetics are non-negligible.
Collapse
Affiliation(s)
- Shu-Ching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| |
Collapse
|
62
|
Abstract
The stability of liquids under solvophobic confinement can tip in favor of the vapor phase, nucleating a liquid-to-vapor phase transition that induces attractive forces between confining surfaces. In the case of water adjacent to hydrophobic surfaces, experimental and theoretical evidence support confinement-mediated evaporation stabilization of biomolecular and colloidal assemblies. The macroscopic thermodynamic theory of cavitation under confinement establishes the connection between the size of the confining surfaces, interfacial free energies, and bulk solvent pressure with the critical evaporation separation and interfacial forces. While molecular simulations have confirmed the broad theoretical trends, a quantitative comparison based on independent measurements of the interfacial free energies and liquid-vapor coexistence properties has, to the best of our knowledge, not yet been performed. To overcome the challenges of simulating a large number of systems to validate scaling predictions for a three-dimensional fluid, we simulate both the forces and liquid-vapor coexistence properties of a two-dimensional Lennard-Jones fluid confined between solvophobic plates over a range of plate sizes and reservoir pressures. Our simulations quantitatively agree with theoretical predictions for solvent-mediated forces and critical evaporation separations once the length dependence of the solvation free energy of an individual confining plate is taken into account. The effective solid-liquid line tension length dependence results from molecular scale correlations for solvating microscopic plates and asymptotically decays to the macroscopic value for plates longer than 150 solvent diameters. The success of the macroscopic thermodynamic theory at describing two-dimensional liquids suggests application to surfactant monolayers to experimentally confirm confinement-mediated cavitation.
Collapse
Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA.
| |
Collapse
|
63
|
|
64
|
Deshmukh SA, Kamath G, Sankaranarayanan SKRS. Comparison of the interfacial dynamics of water sandwiched between static and free-standing fully flexible graphene sheets. SOFT MATTER 2014; 10:4067-4083. [PMID: 24845025 DOI: 10.1039/c3sm53044b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Classical molecular dynamics simulations are used to present a detailed atomistic picture of the instantaneous local structures of water and the structural evolution of stationary and dynamically evolving graphene-water interfaces. The confinement effects are strongly coupled to the nature of the interface, which eventually governs its nanoscopic structural arrangements and interface dynamics. We show that the structure, transport properties, and vibrational densities of states of proximal water molecules are strongly correlated with the nature of the graphene-water interface. We identify and correlate features in vibrational spectra with characteristic structural features observed at the atomic scale for the confined water molecules near a stationary and dynamically evolving hydrophobic surface such as graphene. Our simulations indicate that the local orientation, ordering, and solvation dynamics of interfacial water molecules are a strong function of the graphene slit-width, which is controlled by the nature of the interface (fully flexible vs. static). A monotonic decrease in local ordering with increasing slit-width was observed for the static graphene-water interface, whereas a non-monotonic variation was seen for its fully flexible counterpart. The simulation results offer useful insights into the effect of interfacial dynamics in defining the structure and transport properties at graphene-aqueous media interfaces. Finally these simulations provide a molecular level interpretation of the differential confinement effects arising from the dynamically evolving graphene-water interface.
Collapse
Affiliation(s)
- Sanket A Deshmukh
- Argonne National Laboratory, Center for Nanoscale Materials, 9700 S. Cass Avenue, Argonne, IL 60439-4806, USA.
| | | | | |
Collapse
|
65
|
Vaikuntanathan S, Geissler PL. Putting water on a lattice: the importance of long wavelength density fluctuations in theories of hydrophobic and interfacial phenomena. PHYSICAL REVIEW LETTERS 2014; 112:020603. [PMID: 24483999 DOI: 10.1103/physrevlett.112.020603] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Indexed: 06/03/2023]
Abstract
The physics of air-water interfaces plays a central role in modern theories of the hydrophobic effect. Implementing these theories, however, has been hampered by the difficulty of addressing fluctuations in the shape of such soft interfaces. We show that this challenge is a fundamental consequence of mapping long wavelength density variations onto discrete degrees of freedom. Drawing from studies of surface roughness in lattice models, we account for the resulting nonlinearities simply but accurately. Simulations show that this approach captures complex solvation behaviors quantitatively.
Collapse
Affiliation(s)
| | - Phillip L Geissler
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA and Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
66
|
Fu CF, Tian SX. Different aggregation dynamics of benzene–water mixtures. Phys Chem Chem Phys 2014; 16:21957-63. [DOI: 10.1039/c4cp01537a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The differences between the molecular aggregations in benzene–water mixtures are identified using all-atom molecular dynamics simulations.
Collapse
Affiliation(s)
- Cen-Feng Fu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics
- University of Science and Technology of China
- Hefei, China
| | - Shan Xi Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics
- University of Science and Technology of China
- Hefei, China
| |
Collapse
|
67
|
Zhao Y, Kwan YY, Che J, Li B, McCammon JA. Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. J Chem Phys 2013; 139:024111. [PMID: 23862933 DOI: 10.1063/1.4812839] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A phase-field variational implicit-solvent approach is developed for the solvation of charged molecules. The starting point of such an approach is the representation of a solute-solvent interface by a phase field that takes one value in the solute region and another in the solvent region, with a smooth transition from one to the other on a small transition layer. The minimization of an effective free-energy functional of all possible phase fields determines the equilibrium conformations and free energies of an underlying molecular system. All the surface energy, the solute-solvent van der Waals interaction, and the electrostatic interaction are coupled together self-consistently through a phase field. The surface energy results from the minimization of a double-well potential and the gradient of a field. The electrostatic interaction is described by the Coulomb-field approximation. Accurate and efficient methods are designed and implemented to numerically relax an underlying charged molecular system. Applications to single ions, a two-plate system, and a two-domain protein reveal that the new theory and methods can capture capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics simulations. Comparisons of the phase-field and the original sharp-interface variational approaches are discussed.
Collapse
Affiliation(s)
- Yanxiang Zhao
- Department of Mathematics, University of California, San Diego, 9500 Gilman Drive, Mail code: 0112, La Jolla, California 92093-0112, USA.
| | | | | | | | | |
Collapse
|
68
|
McHedlov-Petrossyan NO. Fullerenes in liquid media: an unsettling intrusion into the solution chemistry. Chem Rev 2013; 113:5149-93. [PMID: 23614509 DOI: 10.1021/cr3005026] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
69
|
Oleinikova A, Brovchenko I. Thermodynamic Properties of Hydration Water around Solutes: Effect of Solute Size and Water–Solute Interaction. J Phys Chem B 2012; 116:14650-9. [DOI: 10.1021/jp306781y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A. Oleinikova
- Physical Chemistry, Dortmund University of Technology, Otto-Hahn-Str. 6, Dortmund, D-44227,
Germany
| | - I. Brovchenko
- Physical Chemistry, Dortmund University of Technology, Otto-Hahn-Str. 6, Dortmund, D-44227,
Germany
| |
Collapse
|
70
|
Activated drying in hydrophobic nanopores and the line tension of water. Proc Natl Acad Sci U S A 2012; 109:19557-62. [PMID: 23144219 DOI: 10.1073/pnas.1207658109] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We study the slow dynamics of water evaporation out of hydrophobic cavities by using model porous silica materials grafted with octylsilanes. The cylindrical pores are monodisperse, with a radius in the range of 1-2 nm. Liquid water penetrates in the nanopores at high pressure and empties the pores when the pressure is lowered. The drying pressure exhibits a logarithmic growth as a function of the driving rate over more than three decades, showing the thermally activated nucleation of vapor bubbles. We find that the slow dynamics and the critical volume of the vapor nucleus are quantitatively described by the classical theory of capillarity without adjustable parameter. However, classical capillarity utterly overestimates the critical bubble energy. We discuss the possible influence of surface heterogeneities, long-range interactions, and high-curvature effects, and we show that a classical theory can describe vapor nucleation provided that a negative line tension is taken into account. The drying pressure then provides a determination of this line tension with much higher precision than currently available methods. We find consistent values of the order of -30 pN in a variety of hydrophobic materials.
Collapse
|
71
|
Baron R, Setny P, Paesani F. Water Structure, Dynamics, and Spectral Signatures: Changes Upon Model Cavity–Ligand Recognition. J Phys Chem B 2012; 116:13774-80. [DOI: 10.1021/jp309373q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Riccardo Baron
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Center for Theoretical Biological
Physics, University of California, San Diego, La Jolla, California 92093, United States
| | - Piotr Setny
- Physics Department T38, Technical University Munich, James Franck Str. 1, 85748
Garching, Germany
| | - Francesco Paesani
- Department of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
72
|
Godec A, Merzel F. Physical origin underlying the entropy loss upon hydrophobic hydration. J Am Chem Soc 2012; 134:17574-81. [PMID: 23003674 DOI: 10.1021/ja306464u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the molecular scale HE has an entropic origin. It is believed that hydrophobic particles induce order in the surrounding water by reducing the volume of configuration space available for hydrogen bonding. Here we show with computer simulation results that this traditional picture, based on average structural features of hydration water, configurational properties of single water molecules, and up to pairwise correlations, is not correct. Analyzing collective fluctuations in water clusters we are able to provide a fundamentally new picture of HE based on pronounced many-body correlations affecting the switching of hydrogen bonds (HBs) between molecules. These correlations emerge as a nonlocal compensation of reduced fluctuations of local electrostatic fields in the presence of an apolar solute. We propose an alternative view which may also be formulated as a maximization principle: The electrostatic noise acting on water molecules is maximized under the constraint that each water molecule on average maintains as many HBs as possible. In the presence of the solute the maximized electrostatic noise is a result of nonlocal fluctuations in the labile HB network giving rise to strong correlations among at least up to four water molecules.
Collapse
Affiliation(s)
- Aljaž Godec
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | | |
Collapse
|
73
|
Muntean SA, Gerasimov RA, Lyulin AV. Dynamics of Water Near Oxidized Polystyrene Films. MACROMOL THEOR SIMUL 2012. [DOI: 10.1002/mats.201200025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
74
|
Bandyopadhyay D, Choudhury N. Characterizing hydrophobicity at the nanoscale: A molecular dynamics simulation study. J Chem Phys 2012; 136:224505. [DOI: 10.1063/1.4725185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
|
75
|
Giovambattista N, Rossky P, Debenedetti P. Computational Studies of Pressure, Temperature, and Surface Effects on the Structure and Thermodynamics of Confined Water. Annu Rev Phys Chem 2012; 63:179-200. [DOI: 10.1146/annurev-physchem-032811-112007] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N. Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210;
| | - P.J. Rossky
- Institute for Computational Engineering and Sciences, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712;
| | - P.G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544-5263;
| |
Collapse
|
76
|
|
77
|
Patel AJ, Varilly P, Jamadagni SN, Hagan MF, Chandler D, Garde S. Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function. J Phys Chem B 2012; 116:2498-503. [PMID: 22235927 DOI: 10.1021/jp2107523] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Water near extended hydrophobic surfaces is like that at a liquid-vapor interface, where fluctuations in water density are substantially enhanced compared to those in bulk water. Here we use molecular simulations with specialized sampling techniques to show that water density fluctuations are similarly enhanced, even near hydrophobic surfaces of complex biomolecules, situating them at the edge of a dewetting transition. Consequently, water near these surfaces is sensitive to subtle changes in surface conformation, topology, and chemistry, any of which can tip the balance toward or away from the wet state and thus significantly alter biomolecular interactions and function. Our work also resolves the long-standing puzzle of why some biological surfaces dewet and other seemingly similar surfaces do not.
Collapse
Affiliation(s)
- Amish J Patel
- Howard P. Isermann Department of Chemical & Biological Engineering, and Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | | | | | | | | | |
Collapse
|
78
|
Prakash P, Sayyed-Ahmad A, Gorfe AA. The role of conserved waters in conformational transitions of Q61H K-ras. PLoS Comput Biol 2012; 8:e1002394. [PMID: 22359497 PMCID: PMC3280954 DOI: 10.1371/journal.pcbi.1002394] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/04/2012] [Indexed: 12/30/2022] Open
Abstract
To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 µs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the Cα atoms of G60 at switch 2 and G10 at the P-loop and the N-Cα-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition. K-ras belongs to the Ras family of G-proteins that regulate cell proliferation and development. To execute its function, K-ras adopts different conformational states when it is active and inactive. In addition to these two states, it samples many transient intermediate conformations as it makes the transition from one state to the other. Mutations that affect the population of these states can cause cancer or developmental disorder. Using simulation approaches, here we show that a number of water molecules buried within the structure of an oncogenic K-ras protein modulate the distribution of its conformational states. Moreover, a detailed analysis based on two novel structural parameters revealed the existence of long-range water-mediated interactions that facilitate a dynamic coupling between the two lobes of the protein. These findings pave the way for a dynamics-guided strategy to inhibit abnormal Ras signaling.
Collapse
Affiliation(s)
- Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Abdallah Sayyed-Ahmad
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Center for Membrane Biology, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
79
|
Morrone JA, Li J, Berne BJ. Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes. J Phys Chem B 2011; 116:378-89. [DOI: 10.1021/jp209568n] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Morrone
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Jingyuan Li
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - B. J. Berne
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| |
Collapse
|
80
|
Rotenberg B, Patel AJ, Chandler D. Molecular explanation for why talc surfaces can be both hydrophilic and hydrophobic. J Am Chem Soc 2011; 133:20521-7. [PMID: 22035164 PMCID: PMC3249429 DOI: 10.1021/ja208687a] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While individual water molecules adsorb strongly on a talc surface (hydrophilic behavior), a droplet of water beads up on the same surface (hydrophobic behavior). To rationalize this dichotomy, we investigated the influence of the microscopic structure of the surface and the strength of adhesive (surface-water) interactions on surface hydrophobicity. We have shown that at low relative humidity, the competition between adhesion and the favorable entropy of being in the vapor phase determines the surface coverage. However, at saturation, it is the competition between adhesion and cohesion (water-water interactions) that determines the surface hydrophobicity. The adhesive interactions in talc are strong enough to overcome the unfavorable entropy, and water adsorbs strongly on talc surfaces. However, they are too weak to overcome the cohesive interactions, and water thus beads up on talc surfaces. Surprisingly, even talc-like surfaces that are highly adhesive do not fully wet at saturation. Instead, a water droplet forms on top of a strongly adsorbed monolayer of water. Our results imply that the interior of hydrophobic zeolites suspended in water may contain adsorbed water molecules at pressures much lower than the intrusion pressure.
Collapse
Affiliation(s)
- Benjamin Rotenberg
- Laboratoire PECSA, UMR 7195, CNRS et UPMC-Paris 6, 4 pl. Jussieu, F-75005 Paris, France.
| | | | | |
Collapse
|
81
|
Extended surfaces modulate hydrophobic interactions of neighboring solutes. Proc Natl Acad Sci U S A 2011; 108:17678-83. [PMID: 21987795 DOI: 10.1073/pnas.1110703108] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interfaces are a most common motif in complex systems. To understand how the presence of interfaces affects hydrophobic phenomena, we use molecular simulations and theory to study hydration of solutes at interfaces. The solutes range in size from subnanometer to a few nanometers. The interfaces are self-assembled monolayers with a range of chemistries, from hydrophilic to hydrophobic. We show that the driving force for assembly in the vicinity of a hydrophobic surface is weaker than that in bulk water and decreases with increasing temperature, in contrast to that in the bulk. We explain these distinct features in terms of an interplay between interfacial fluctuations and excluded volume effects--the physics encoded in Lum-Chandler-Weeks theory [Lum K, Chandler D, Weeks JD (1999) J Phys Chem B 103:4570-4577]. Our results suggest a catalytic role for hydrophobic interfaces in the unfolding of proteins, for example, in the interior of chaperonins and in amyloid formation.
Collapse
|
82
|
|
83
|
Force field measurements within the exclusion zone of water. J Biol Phys 2011; 38:113-20. [PMID: 23277674 DOI: 10.1007/s10867-011-9237-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022] Open
Abstract
Water molecules play critical roles in many biological functions, such as protein dynamics, enzymatic activities, and cellular responses. Previous nuclear magnetic resonance and neutron scattering studies have shown that water molecules bind to specific sites on surfaces and form localized clusters. However, most current experimental techniques cannot measure dynamic behaviors of ordered water molecules on cell-size (10 μm) scale. Recently, the long-distance effect of structured water has been demonstrated by Pollack and his colleagues. Namely, there is a structured water layer near the hydrophilic surface that can exclude solutes (Zheng et al, Adv Colloid Interface Sci 127:19-27, 2006; Pollack 2006, Adv Colloid Interface Sci 103:173-196, 2003). The repelling forces of water clusters inside this exclusion region are investigated in this study. With a laser tweezers system, we found the existence of an unexpected force fields inside the solute-free exclusion zone near a Nafion surface. Our results suggest that the water clusters could transduce mechanical signals on the micrometer range within the exclusion zone. This unexpected inhomogeneous force field near the hydrophilic surface would provide a new insight into cellular activities, leading to a potential new physical chemistry mechanism for cell biology.
Collapse
|
84
|
|
85
|
Muntean SA, Kemper M, van IJzendoorn LJ, Lyulin AV. Roughness and ordering at the interface of oxidized polystyrene and water. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:8678-8686. [PMID: 21699178 DOI: 10.1021/la200203s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
For the first time, atomistically detailed molecular dynamics calculations revealed molecular ordering of the water-oxidized atactic polystyrene (aPS) interface. Both ordering of the water molecules and the phenyl rings occur. In addition, the natural roughness of the surface has been simulated and compared to experimental values. The composition of the simulated aPS films is based on spin-coated aPS films that have been oxidized and characterized experimentally. The aPS surfaces are oxidized with ultraviolet-ozone radiation and have been characterized by XPS, AFM, and water contact angle measurements. XPS measurements show that the oxygen content in the sample increases rapidly with exposure and reaches saturation near 24 at. % of oxygen. The molecular dynamics simulations show smoothening of an hydrophobic aPS surface upon transition from vacuum to water. The smoothening decreases with increasing hydrophilicity. The calculations reveal ordering of oxidized phenyl rings for aPS surfaces in water. The order increases with increasing hydrophilicity. Additionally, we investigated the water structure near the aPS-water interface as a function of the surface hydrophilicity. With increasing hydrophilicity, the density of water at the aPS-water interface increases. The water density profile is steeper in the presence of hydrophobic aPS. The water shows an ordered layer near both the hydrophobic and hydrophilic surfaces; the position of this layer shifts toward the interface with increasing hydrophilicity.
Collapse
Affiliation(s)
- Stela Andrea Muntean
- Theory of Polymers and Soft Matter (TPS), Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | | | | | | |
Collapse
|
86
|
Vila Verde A, Campen RK. Disaccharide Topology Induces Slowdown in Local Water Dynamics. J Phys Chem B 2011; 115:7069-84. [DOI: 10.1021/jp112178c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ana Vila Verde
- FOM Institute AMOLF, 104 Science Park, 1098 XG Amsterdam, The Netherlands
- Centro de Física, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R. Kramer Campen
- FOM Institute AMOLF, 104 Science Park, 1098 XG Amsterdam, The Netherlands
| |
Collapse
|
87
|
Ashbaugh HS, Truskett TM. Putting the squeeze on cavities in liquids: Quantifying pressure effects on solvation using simulations and scaled-particle theory. J Chem Phys 2011; 134:014507. [PMID: 21219007 DOI: 10.1063/1.3510522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Extensive molecular simulations of the Lennard-Jones fluid are performed to examine the response of the excess chemical potential of cavitylike solutes to applied pressure. Solutes as large as ten times the solvent diameter are considered. The simulations are analyzed using the revised scaled-particle theory developed by Ashbaugh and Pratt to evaluate the thermodynamics of cavity solvation and curvature dependent interfacial properties well into the compressed liquid portion of the solvent phase diagram. The revised theory provides a quantitatively accurate description of the solvent-solute contact correlation function for all solutes and state points considered. The main structural effect of increasing pressure is to push the solvent molecules up against the solute surfaces, counteracting the dewetting that is observed at lower pressures along the solvent saturation curve. Decomposing the excess chemical potential of cavities into volume and surface-area contributions shows that pressure differentially affects the interfacial free energies of molecular versus macroscopic solutes. The interfacial free energy of surfaces of molecular dimension monotonically decreases with applied pressure, while that of surfaces larger than a small cluster of solvent molecules exhibit a maximum with increasing pressure, which may play a role in pressure-induced disaggregation of molecular assemblies. Moreover, since the pressure dependence of the interfacial free energy is thermodynamically linked to the excess adsorption of solvent on the solute surface, the former is potentially a measurable macroscopic indicator of microscopic wetting∕dewetting phenomena, implicated in hydrophobic interactions between macroscopic hydrophobic particles. Finally, some inferences about pressure-dependent solvation processes in water are made by using the revised theory to analyze previously published simulation data.
Collapse
Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA.
| | | |
Collapse
|
88
|
Probing surface tension additivity on chemically heterogeneous surfaces by a molecular approach. Proc Natl Acad Sci U S A 2011; 108:6374-9. [PMID: 21460249 DOI: 10.1073/pnas.1014970108] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Surface free energy of a chemically heterogeneous surface is often treated as an approximately additive quantity through the Cassie equation [Cassie ABD (1948) Discuss Faraday Soc 3:11-16]. However, deviations from additivity are common, and molecular interpretations are still lacking. We use molecular simulations to measure the microscopic analogue of contact angle, Θ(c), of aqueous nanodrops on heterogeneous synthetic and natural surfaces as a function of surface composition. The synthetic surfaces are layers of graphene functionalized with prototypical nonpolar and polar head group: methyl, amino, and nitrile. We demonstrate positive as well as negative deviations from the linear additivity. We show the deviations reflect the uneven exposure of mixture components to the solvent and the linear relation is recovered if fractions of solvent-accessible surface are used as the measure of composition. As the spatial variations in polarity become of larger amplitude, the linear relation can no longer be obtained. Protein surfaces represent such natural patterned surfaces, also characterized by larger patches and roughness. Our calculations reveal strong deviations from linear additivity on a prototypical surface comprising surface fragments of melittin dimer. The deviations reflect the disproportionately strong influence of isolated polar patches, preferential wetting, and changes in the position of the liquid interface above hydrophobic patches. Because solvent-induced contribution to the free energy of surface association grows as cos Θ(c), deviations of cos Θ(c) from the linear relation directly reflect nonadditive adhesive energies of biosurfaces.
Collapse
|
89
|
Tielrooij KJ, Hunger J, Buchner R, Bonn M, Bakker HJ. Influence of concentration and temperature on the dynamics of water in the hydrophobic hydration shell of tetramethylurea. J Am Chem Soc 2011; 132:15671-8. [PMID: 20949942 DOI: 10.1021/ja106273w] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the influence of the amphipilic compound tetramethylurea (TMU) on the dynamical properties of water, using dielectric relaxation spectroscopy in the regime between 0.2 GHz and 2 THz. This technique is capable of resolving different water species, their relative fractions, and their corresponding reorientation dynamics. We find that the reorientation dynamics of water molecules in the hydration shell of the hydrophobic groups of TMU is between 3 (at low concentrations) and 10 (at higher concentrations) times slower than the dynamics of bulk water. The data indicate that the effect of hydrophobic groups on water is strong but relatively short-ranged. With increasing temperature, the fraction of water contained in the hydrophobic hydration shell decreases, which implies that the overall effect of hydrophobic groups on water becomes smaller.
Collapse
|
90
|
Kasson PM, Lindahl E, Pande VS. Water Ordering at Membrane Interfaces Controls Fusion Dynamics. J Am Chem Soc 2011; 133:3812-5. [DOI: 10.1021/ja200310d] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter M. Kasson
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Erik Lindahl
- Department of Theoretical Physics, Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
91
|
Varilly P, Patel AJ, Chandler D. An improved coarse-grained model of solvation and the hydrophobic effect. J Chem Phys 2011; 134:074109. [PMID: 21341830 PMCID: PMC3077811 DOI: 10.1063/1.3532939] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/09/2010] [Indexed: 11/14/2022] Open
Abstract
We present a coarse-grained lattice model of solvation thermodynamics and the hydrophobic effect that implements the ideas of Lum-Chandler-Weeks theory [J. Phys. Chem. B 134, 4570 (1999)] and improves upon previous lattice models based on it. Through comparison with molecular simulation, we show that our model captures the length-scale and curvature dependence of solvation free energies with near-quantitative accuracy and 2-3 orders of magnitude less computational effort, and further, correctly describes the large but rare solvent fluctuations that are involved in dewetting, vapor tube formation, and hydrophobic assembly. Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations.
Collapse
Affiliation(s)
- Patrick Varilly
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
| | | | | |
Collapse
|
92
|
Stumpe MC, Blinov N, Wishart D, Kovalenko A, Pande VS. Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation. J Phys Chem B 2010; 115:319-28. [PMID: 21174421 DOI: 10.1021/jp102587q] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water plays a unique role in all living organisms. Not only is it nature's ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules such as proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces such as the hydrophobic effect are relevant. Computational methods such as molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are, indeed, the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods: MD simulations and the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems.
Collapse
Affiliation(s)
- Martin C Stumpe
- Department of Bioengineering, Stanford University, 318 Campus Drive West, Stanford, California 94305, USA
| | | | | | | | | |
Collapse
|
93
|
Santana-Blank L, Rodríguez-Santana E. The interaction of light with nanoscopic layers of water may be essential to the future of photobiomodulation. Photomed Laser Surg 2010; 28 Suppl 1:S173-4. [PMID: 20666576 DOI: 10.1089/pho.2009.2745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
94
|
Lambeth BP, Junghans C, Kremer K, Clementi C, Site LD. Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces. J Chem Phys 2010; 133:221101. [DOI: 10.1063/1.3522773] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
95
|
Acharya H, Vembanur S, Jamadagni SN, Garde S. Mapping hydrophobicity at the nanoscale: applications to heterogeneous surfaces and proteins. Faraday Discuss 2010; 146:353-65; discussion 367-93, 395-401. [PMID: 21043432 DOI: 10.1039/b927019a] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Approaches to quantify wetting at the macroscale do not translate to the nanoscale, highlighting the need for new methods for characterizing hydrophobicity at the small scale. We use extensive molecular simulations to study the hydration of homo and heterogeneous self-assembled monolayers (SAMs) and of protein surfaces. For homogeneous SAMs, new pressure-dependent analysis shows that water displays higher compressibility and enhanced density fluctuations near hydrophobic surfaces, which are gradually quenched with increasing hydrophilicity, consistent with our previous studies. Heterogeneous surfaces show an interesting context dependence--adding a single -OH group in a CH3 terminated SAM has a more dramatic effect on water in the vicinity compared to that of a single CH3 group in an -OH background. For mixed -CH3/-OH SAMs, this asymmetry leads to a non-linear dependence of hydrophobicity on the surface concentration. We also present preliminary results to map hydrophobicity of protein surfaces by monitoring local density fluctuations and binding of probe hydrophobic solutes. These molecular measures account for the behavior of protein's hydration water, and present a more refined picture of its hydrophobicity map. At least for one protein, hydrophobin-II, we show that the hydrophobicity map is different from that suggested by a commonly used hydropathy scale.
Collapse
Affiliation(s)
- Hari Acharya
- The Howard P. Isermann Department of Chemical & Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | | | | | |
Collapse
|
96
|
Eun C, Berkowitz ML. Fluctuations in Number of Water Molecules Confined between Nanoparticles. J Phys Chem B 2010; 114:13410-4. [DOI: 10.1021/jp1072654] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Changsun Eun
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Max L. Berkowitz
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
97
|
Abstract
We use explicit solvent molecular dynamics simulations to estimate free energy, enthalpy, and entropy changes along the cavity-ligand association coordinate for a set of seven model systems with varying physicochemical properties. Owing to the simplicity of the considered systems we can directly investigate the role of water thermodynamics in molecular recognition. A broad range of thermodynamic signatures is found in which water (rather than cavity or ligand) enthalpic or entropic contributions appear to drive cavity-ligand binding or rejection. The unprecedented, nanoscale picture of hydration thermodynamics can help the interpretation and design of protein-ligand binding experiments. Our study opens appealing perspectives to tackle the challenge of solvent entropy estimation in complex systems and for improving molecular simulation models.
Collapse
|
98
|
LeBard DN, Matyushov DV. Ferroelectric Hydration Shells around Proteins: Electrostatics of the Protein−Water Interface. J Phys Chem B 2010; 114:9246-58. [DOI: 10.1021/jp1006999] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- David N. LeBard
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, Arizona 85287-1604
| | - Dmitry V. Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, Arizona 85287-1604
| |
Collapse
|
99
|
Bauer BA, Patel S. Role of electrostatics in modulating hydrophobic interactions and barriers to hydrophobic assembly. J Phys Chem B 2010; 114:8107-17. [PMID: 20509706 PMCID: PMC2916683 DOI: 10.1021/jp101995d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic effects continue to be an active area of research due to implications for a wide range of physicochemical phenomena. Molecular dynamics simulations have been used extensively in the study of such effects using various water potential models, with few studies addressing the differences between models. In particular, studies considering the explicit treatment of water polarizability are underrepresented in the literature. We present results from molecular dynamics simulations that systematically compare the dependence of large-scale hydrophobic effects on the water model. We consider three common nonpolarizable models (SPC/E, TIP3P, and TIP4P) and two common polarizable models (TIP4P-FQ and SWM4-NDP). Results highlight the similarities and differences of the different water models in the vicinity of two large hydrophobic plates. In particular, profiles of average density, density fluctuations, orientation, and hydrogen bonding show only minor differences among the water models studied. However, the potential of mean force for the hydrophobe dimerization is significantly reduced in the polarizable water systems. TIP4P-FQ shows the deepest minimum of approximately -54(+/-3) kcal/mol compared to -40(+/-3), -40(+/-2), -42(+/-3), and -45(+/-5) kcal/mol for TIP4P, TIP3P, SPC/E, and SWM4-NDP (all relative to the dissociated state). We discuss the relationship between hydrophobic association and the strength of water-water interactions in the liquid phase. Results suggest that models treating polarizability (both implicitly and explicitly) influence a stronger driving force toward hydrophobic assembly. Implications of these results, as well as prospectives on future work, are discussed.
Collapse
Affiliation(s)
- Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| |
Collapse
|
100
|
Sumi T, Imazaki N, Sekino H. Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins. J Chem Phys 2010; 132:165101. [DOI: 10.1063/1.3394864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|