101
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Nihonyanagi S, Ishiyama T, Lee TK, Yamaguchi S, Bonn M, Morita A, Tahara T. Unified molecular view of the air/water interface based on experimental and theoretical χ(2) spectra of an isotopically diluted water surface. J Am Chem Soc 2011; 133:16875-80. [PMID: 21899354 DOI: 10.1021/ja2053754] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The energetically unfavorable termination of the hydrogen-bonded network of water molecules at the air/water interface causes molecular rearrangement to minimize the free energy. The long-standing question is how water minimizes the surface free energy. The combination of advanced, surface-specific nonlinear spectroscopy and theoretical simulation provides new insights. The complex χ((2)) spectra of isotopically diluted water surfaces obtained by heterodyne-detected sum frequency generation spectroscopy and molecular dynamics simulation show excellent agreement, assuring the validity of the microscopic picture given in the simulation. The present study indicates that there is no ice-like structure at the surface--in other words, there is no increase of tetrahedrally coordinated structure compared to the bulk--but that there are water pairs interacting with a strong hydrogen bond at the outermost surface. Intuitively, this can be considered a consequence of the lack of a hydrogen bond toward the upper gas phase, enhancing the lateral interaction at the boundary. This study also confirms that the major source of the isotope effect on the water χ((2)) spectra is the intramolecular anharmonic coupling, i.e., Fermi resonance.
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Affiliation(s)
- Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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102
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Mecinović J, Snyder PW, Mirica KA, Bai S, Mack ET, Kwant RL, Moustakas DT, Heroux A, Whitesides GM. Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase. J Am Chem Soc 2011; 133:14017-26. [PMID: 21790183 PMCID: PMC3171206 DOI: 10.1021/ja2045293] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H(2)NSO(2)C(6)H(4)-CONHCH(2)(CX(2))(n)CX(3), n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).
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Affiliation(s)
- Jasmin Mecinović
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Phillip W. Snyder
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Katherine A. Mirica
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Serena Bai
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Eric T. Mack
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Richard L. Kwant
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Demetri T. Moustakas
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Annie Heroux
- National Synchrotron Light Source, Brookhaven National Laboratory, 725 Brookhaven Avenue, Upton, NY 11973-5000
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
- Wyss Institute for Biologically Inspired Engineering, 725 Brookhaven Avenue, Upton, NY 11973-5000
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103
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Remarkable patterns of surface water ordering around polarized buckminsterfullerene. Proc Natl Acad Sci U S A 2011; 108:14455-60. [PMID: 21844369 DOI: 10.1073/pnas.1110626108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate description of water structure affects simulation of protein folding, substrate binding, macromolecular recognition, and complex formation. We study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere, by molecular dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3), derived from quantum mechanical data at the MP2/aug-cc-pVTZ(-hp) level augmented by CCSD(T). QMPFF3 calculation of the hydrophobic effect is compared to that obtained with empirical force fields. Using a novel and highly sensitive method, we see polarization increases ordered water structure so that the imprint of the hydrophobic surface atoms on the surrounding waters is stronger and extends to long-range. We see less water order for empirical force fields. The greater order seen with QMPFF3 will affect biological processes through a stronger hydrophobic effect.
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104
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Gibb BC. Supramolecular Assembly and Binding in Aqueous Solution: Useful Tips Regarding the Hofmeister and Hydrophobic Effects. Isr J Chem 2011. [DOI: 10.1002/ijch.201100058] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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105
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106
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Nau WM, Florea M, Assaf KI. Deep Inside Cucurbiturils: Physical Properties and Volumes of their Inner Cavity Determine the Hydrophobic Driving Force for Host-Guest Complexation. Isr J Chem 2011. [DOI: 10.1002/ijch.201100044] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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107
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Tamam L, Pontoni D, Sapir Z, Yefet S, Sloutskin E, Ocko BM, Reichert H, Deutsch M. Modification of deeply buried hydrophobic interfaces by ionic surfactants. Proc Natl Acad Sci U S A 2011; 108:5522-5. [PMID: 21422287 PMCID: PMC3078380 DOI: 10.1073/pnas.1014100108] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobicity, the spontaneous segregation of oil and water, can be modified by surfactants. The way this modification occurs is studied at the oil-water interface for a range of alkanes and two ionic surfactants. A liquid interfacial monolayer, consisting of a mixture of alkane molecules and surfactant tails, is found. Upon cooling, it freezes at T(s), well above the alkane's bulk freezing temperature, T(b). The monolayer's phase diagram, derived by surface tensiometry, is accounted for by a mixtures-based theory. The monolayer's structure is measured by high-energy X-ray reflectivity above and below T(s). A solid-solid transition in the frozen monolayer, occurring approximately 3 °C below T(s), is discovered and tentatively suggested to be a rotator-to-crystal transition.
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Affiliation(s)
- Lilach Tamam
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 52900, Israel
| | - Diego Pontoni
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
| | - Zvi Sapir
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 52900, Israel
| | - Shai Yefet
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 52900, Israel
| | - Eli Sloutskin
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 52900, Israel
| | - Benjamin M. Ocko
- Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, NY 11973; and
| | - Harald Reichert
- European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble, France
- Max-Planck-Institut für Metallforschung, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
| | - Moshe Deutsch
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-llan University, Ramat-Gan 52900, Israel
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108
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Kathmann SM, Kuo IFW, Mundy CJ, Schenter GK. Understanding the Surface Potential of Water. J Phys Chem B 2011; 115:4369-77. [DOI: 10.1021/jp1116036] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shawn M. Kathmann
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - I-Feng William Kuo
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Christopher J. Mundy
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Gregory K. Schenter
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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109
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Zhang H, Singer SJ. Analysis of the subcritical carbon dioxide-water interface. J Phys Chem A 2011; 115:6285-96. [PMID: 21438534 DOI: 10.1021/jp200190k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We follow the evolution of the H(2)O/CO(2) interface at 300 K from the low pressure limit to near-critical pressures in molecular dynamics simulations using the SPC water and EPM2 carbon dioxide models. The intrinsic structure of the interface is elucidated by accumulating density profiles relative to the fluctuating capillary wave surface. Our main finding is that a carbon dioxide film of increasing density and thickness grows in two stages at the interface while the structure of the water surface barely changes. At low density, the entire film density profile grows linearly with the bulk CO(2) density. This regime continues up to a bulk CO(2) density of roughly 0.00095 Å(-3). At pressures above this point, we observe a distinct second peak in the CO(2) density, along with a tail of excess density that decays exponentially with distance from the interface. The decay length of the exponential tail diverges with increasing CO(2) pressure according to an inverse power law decay. Over the entire range of pressures, the CO(2) film had no detectable effect on the orientational order of the water surface. As expected, when the film of excess CO(2) at the interface grows, we find that the surface tension drops with increasing pressure. This is in qualitative accord with existing measurements, although the rate at which the surface tension falls with increasing pressure according to the SPC and EPM2 models is too small, indicating that the surface excess of CO(2) is underestimated by these models.
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Affiliation(s)
- Hui Zhang
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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110
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Uehara K, Mizuno N. Heterolytic Dissociation of Water Demonstrated by Crystal-to-Crystal Core Interconversion from (μ-Oxo)divanadium to Bis(μ-hydroxo)divanadium Substituted Polyoxometalates. J Am Chem Soc 2011; 133:1622-5. [DOI: 10.1021/ja108245g] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazuhiro Uehara
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Noritaka Mizuno
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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111
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Muscatello J, Römer F, Sala J, Bresme F. Water under temperature gradients: polarization effects and microscopic mechanisms of heat transfer. Phys Chem Chem Phys 2011; 13:19970-8. [DOI: 10.1039/c1cp21895f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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112
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Laughrey Z, Gibb BC. Water-soluble, self-assembling container molecules: an update. Chem Soc Rev 2011; 40:363-86. [DOI: 10.1039/c0cs00030b] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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113
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Abramczyk H, Brozek-Pluska B, Surmacki J, Jablonska-Gajewicz J, Kordek R. Hydrogen bonds of interfacial water in human breast cancer tissue compared to lipid and DNA interfaces. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/jbpc.2011.22020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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114
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Le L, Molinero V. Nanophase segregation in supercooled aqueous solutions and their glasses driven by the polyamorphism of water. J Phys Chem A 2010; 115:5900-7. [PMID: 21166394 DOI: 10.1021/jp1102065] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We use large-scale molecular dynamics simulations to investigate the phase transformation of aqueous solutions of electrolytes cooled at the critical rate to avoid the crystallization of ice. Homogeneous liquid solutions with up to 20% moles of ions demix on cooling producing nanophase segregated glasses with characteristic dimensions of phase segregation of about 5 nm. The immiscibility is driven by the transformation of water to form a four-coordinated low-density liquid (LDL) as it crosses the liquid-liquid transformation temperature T(LL) of the solution. The ions cannot be incorporated into the tetrahedral LDL network and are expelled to form a solute-rich water nanophase. The simulations quantitatively reproduce the relative amounts of low and high-density liquid water as a function of solute content in LiCl glasses [Suzuki and Mishima, Phys. Rev. Lett. 2000, 85, 1322-1325] and provide direct evidence of segregation in aqueous glasses and their dimensions of phase segregation.
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Affiliation(s)
- Ly Le
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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115
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Ye M, Zhang Y, Li H, Xie M, Hu J. Supramolecular Structures of Amyloid-Related Peptides in an Ambient Water Nanofilm. J Phys Chem B 2010; 114:15759-65. [PMID: 21077660 DOI: 10.1021/jp105501x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ming Ye
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
| | - Muyun Xie
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
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116
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Choudhury N. Orientational dynamics of water trapped between two nanoscopic hydrophobic solutes: A molecular dynamics simulation study. J Chem Phys 2010; 133:154515. [DOI: 10.1063/1.3499850] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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117
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Lin B, Pettitt BM. Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water. J Comput Chem 2010; 32:878-85. [PMID: 20941733 DOI: 10.1002/jcc.21668] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 08/02/2010] [Accepted: 08/12/2010] [Indexed: 11/10/2022]
Abstract
Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLS-AA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirms that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.
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Affiliation(s)
- Bin Lin
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, USA
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118
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Burakowski A, Gliński J. Hydration of Amino Acids from Ultrasonic Measurements. J Phys Chem B 2010; 114:12157-61. [DOI: 10.1021/jp105255b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Burakowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jacek Gliński
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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119
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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.
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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
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120
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Lopes A, Schmidt Am Busch M, Simonson T. Computational design of protein-ligand binding: modifying the specificity of asparaginyl-tRNA synthetase. J Comput Chem 2010; 31:1273-86. [PMID: 19862811 DOI: 10.1002/jcc.21414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A method for computational design of protein-ligand interactions is implemented and tested on the asparaginyl- and aspartyl-tRNA synthetase enzymes (AsnRS, AspRS). The substrate specificity of these enzymes is crucial for the accurate translation of the genetic code. The method relies on a molecular mechanics energy function and a simple, continuum electrostatic, implicit solvent model. As test calculations, we first compute AspRS-substrate binding free energy changes due to nine point mutations, for which experimental data are available; we also perform large-scale redesign of the entire active site of each enzyme (40 amino acids) and compare to experimental sequences. We then apply the method to engineer an increased binding of aspartyl-adenylate (AspAMP) into AsnRS. Mutants are obtained using several directed evolution protocols, where four or five amino acid positions in the active site are randomized. Promising mutants are subjected to molecular dynamics simulations; Poisson-Boltzmann calculations provide an estimate of the corresponding, AspAMP, binding free energy changes, relative to the native AsnRS. Several of the mutants are predicted to have an inverted binding specificity, preferring to bind AspAMP rather than the natural substrate, AsnAMP. The computed binding affinities are significantly weaker than the native, AsnRS:AsnAMP affinity, and in most cases, the active site structure is significantly changed, compared to the native complex. This almost certainly precludes catalytic activity. One of the designed sequences has a higher affinity and more native-like structure and may represent a valid candidate for Asp activity.
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Affiliation(s)
- Anne Lopes
- Laboratoire de Biochimie, Department of Biology, UMR CNRS 7654, Ecole Polytechnique, 91128 Palaiseau, France
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121
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Anand G, Jamadagni SN, Garde S, Belfort G. Self-assembly of TMAO at hydrophobic interfaces and its effect on protein adsorption: insights from experiments and simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9695-9702. [PMID: 20334401 DOI: 10.1021/la100363m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We offer a novel process to render hydrophobic surfaces resistant to relatively small proteins during adsorption. This was accomplished by self-assembly of a well-known natural osmolyte, trimethylamine oxide (TMAO), a small amphiphilic molecule, on a hydrophobic alkanethiol surface. Measurements of lysozyme (LYS) adsorption on several homogeneous substrates formed from functionalized alkanethiol self-assembled monolayers (SAMs) in the presence and absence of TMAO, and direct interaction energy between the protein and functionalized surfaces, demonstrate the protein-resistant properties of a noncovalently adsorbed self-assembled TMAO layer. Molecular dynamics simulations clearly show that TMAO molecules concentrate near the CH(3)-SAM surface and are preferentially excluded from LYS. Interestingly, TMAO molecules adsorb strongly on a hydrophobic CH(3)-SAM surface, but a trade-off between hydrogen bonding with water, and hydrophobic interactions with the underlying substrate results in a nonintuitive orientation of TMAO molecules at the interface. Additionally, hydrophobic interactions, usually responsible for nonspecific adsorption of proteins, are weakly affected by TMAO. In addition to TMAO, other osmolytes (sucrose, taurine, and betaine) and a larger homologue of TMAO (N,N-dimethylheptylamine-N-oxide) were tested for protein resistance and only N,N-dimethylheptylamine-N-oxide exhibited resistance similar to TMAO. The principle of osmolyte exclusion from the protein backbone is responsible for the protein-resistant property of the surface. We speculate that this novel process of surface modification may have wide applications due to its simplicity, low cost, regenerability, and flexibility.
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Affiliation(s)
- Gaurav Anand
- The Howard P. Isermann Department of Chemical Biological Engineering, and The Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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122
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Chiessi E, Lonardi A, Paradossi G. Toward Modeling Thermoresponsive Polymer Networks: A Molecular Dynamics Simulation Study of N-Isopropyl Acrylamide Co-oligomers. J Phys Chem B 2010; 114:8301-12. [DOI: 10.1021/jp912209z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ester Chiessi
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133 Rome, Italy
| | - Alice Lonardi
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133 Rome, Italy
| | - Gaio Paradossi
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133 Rome, Italy
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123
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Vorobyov I, Allen TW. The electrostatics of solvent and membrane interfaces and the role of electronic polarizability. J Chem Phys 2010. [DOI: 10.1063/1.3402125] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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124
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Jacobson LC, Molinero V. A Methane−Water Model for Coarse-Grained Simulations of Solutions and Clathrate Hydrates. J Phys Chem B 2010; 114:7302-11. [DOI: 10.1021/jp1013576] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Liam C. Jacobson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
| | - Valeria Molinero
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
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125
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Zavitsas A. The Nature of Aqueous Solutions: Insights into Multiple Facets of Chemistry and Biochemistry from Freezing-Point Depressions. Chemistry 2010; 16:5942-60. [DOI: 10.1002/chem.200903063] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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126
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Matsumoto S, Iwamoto H, Mizutani T. Water Accessibility to the Binding Cleft as a Major Switching Factor from Entropy-Driven to Enthalpy-Driven Binding of an Alkyl Group by Synthetic Receptors. Chem Asian J 2010; 5:1163-70. [DOI: 10.1002/asia.200900679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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127
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Nguyen PT, Nguyen AV. Drainage, rupture, and lifetime of deionized water films: effect of dissolved gases? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:3356-3363. [PMID: 19947613 DOI: 10.1021/la9031333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Gas bubbles coalesce in deionized (DI) water because the water (foam) films between the bubbles are not stable. The so-called hydrophobic attraction has been suggested as the cause of the film instability and the bubble coalescence. In this work, microinterferometry experiments show that foam films of ultrapure DI water can last up to 10 s and the contact time between the two gas bubble surfaces at close proximity (approximately 1 microm separation distance) significantly influences the film drainage, rupture, and lifetime. Specifically, when the two bubbles were first brought into contact, the films instantly ruptured at 0.5 microm thickness. However, the film drainage rate and rupture thickness sharply decreased and the film lifetime steeply increased with increasing contact time up to 10 min, but then they leveled off. The constant thickness of film rupture was around 35 nm. Possible contamination was vigorously investigated and ruled out. It is argued that migration of gases inherently dissolved in water might cause the transient behavior of the water films at the short contact time. The film drainage rate and instability at the long contact time were analyzed employing Eriksson et al.'s phenomenological theory of long-range hydrophobic attraction (Eriksson, J. C.; Ljunggren, S.; Claesson, P. M., J. Chem. Soc., Faraday Trans. 2 1989, 85, 163-176) and the hypothesis of water molecular structure modified by dissolved gases, and the extended Stefan-Reynolds theory by incorporating the mobility of the air-DI-water interfaces.
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Affiliation(s)
- Phong T Nguyen
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
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128
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Choudhury N. Dynamics of water at the nanoscale hydrophobic confinement. J Chem Phys 2010; 132:064505. [DOI: 10.1063/1.3319504] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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129
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Shaytan AK, Ivanov VA, Shaitan KV, Khokhlov AR. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations. J Comput Chem 2010; 31:204-16. [DOI: 10.1002/jcc.21267] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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130
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Jalan A, Ashcraft RW, West RH, Green WH. Predicting solvation energies for kinetic modeling. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b811056p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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131
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Politi R, Harries D. Enthalpically driven peptide stabilization by protective osmolytes. Chem Commun (Camb) 2010; 46:6449-51. [DOI: 10.1039/c0cc01763a] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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132
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Mittal J, Hummer G. Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discuss 2010; 146:341-52; discussion 367-93, 395-401. [PMID: 21043431 PMCID: PMC3470880 DOI: 10.1039/b925913a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the effects of nanoscopic roughness on the interfacial free energy of water confined between solid surfaces. SPC/E water is simulated in confinement between two infinite planar surfaces that differ in their physical topology: one is smooth and the other one is physically rough on a sub-nanometre length scale. The two thermodynamic ensembles considered, with constant pressure either normal or parallel to the walls, correspond to different experimental conditions. We find that molecular-scale surface roughness significantly increases the solid-liquid interfacial free energy compared to the smooth surface. For our surfaces with a water-wall interaction energy minimum of -1.2 kcal mol(-1), we observe a transition from a hydrophilic surface to a hydrophobic surface at a roughness amplitude of about 3 angstroms and a wavelength of 11.6 angstroms, with the interfacial free energy changing sign from negative to positive. In agreement with previous studies of water near hydrophobic surfaces, we find an increase in the isothermal compressibility of water with increasing surface roughness. Interestingly, average measures of the water density and hydrogen-bond number do not contain distinct signatures of increased hydrophobicity. In contrast, a local analysis indicates transient dewetting of water in the valleys of the rough surface, together with a significant loss of hydrogen bonds, and a change in the dipole orientation toward the surface. These microscopic changes in the density, hydrogen bonding, and water orientation contribute to the large increase in the interfacial free energy, and the change from a hydrophilic to a hydrophobic character of the surface.
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Affiliation(s)
- Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Gerhard Hummer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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133
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Kurhe DN, Dagade DH, Jadhav JP, Govindwar SP, Patil KJ. Studies of Enthalpy−Entropy Compensation, Partial Entropies, and Kirkwood−Buff Integrals for Aqueous Solutions of Glycine, l-Leucine, and Glycylglycine at 298.15 K. J Phys Chem B 2009; 113:16612-21. [DOI: 10.1021/jp9078585] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Deepti N. Kurhe
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Dilip H. Dagade
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Jyoti P. Jadhav
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Sanjay P. Govindwar
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
| | - Kesharsingh J. Patil
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India, Department of Chemistry, Shivaji University, Kolhapur 416004, India
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134
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Abstract
Abstract
We simulate the solubility and solvation free energy of methane dissolved in water at infinite dilution. Molecular dynamics simulations of TIP4P-Ew model water are carried out at ambient pressure conditions over a large temperature interval, ranging from 250 K to 370 K. Solvation free energies are determined using the Widom particle insertion method. The fitted temperature dependent data is used to calculate solvation enthalpies, entropies, as well as the heat capacity of solvation. In particular we study the effect of polarizability of methane on those thermodynamic parameters. Solute polarization leads to a lowering of the solvation free energy at 298 K to 8.3 kJ mol−1, almost exactly matching the experimental value. A close inspection of the enthalpic and entropic contributions, however, reveals that this coincidence is a consequence of a compensation of enthalpic and entropic contributions, each of them deviating even larger from their respective experimental values. Surprisingly, the solute polarizability is apparently affecting the solvation entropy more strongly than the solvation enthalpy, leading to an about 5 J K−1 mol−1 smaller (less negative) solvation entropy compared to the non-polarizable model. The solute-water radial distribution functions of the polarizable particle reveals significant modifications, favoring small distances, as well as structural changes, very similar to those caused by a temperature increase. This is suggesting that the reduced negative solvation entropy of a polarizable methane particle is related to a more disordered, "high-temperature"-like hydration shell.
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135
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Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations. Proc Natl Acad Sci U S A 2009; 106:15119-24. [PMID: 19706896 DOI: 10.1073/pnas.0902778106] [Citation(s) in RCA: 248] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobicity is often characterized macroscopically by the droplet contact angle. Molecular signatures of hydrophobicity have, however, remained elusive. Successful theories predict a drying transition leading to a vapor-like region near large hard-sphere solutes and interfaces. Adding attractions wets the interface with local density increasing with attractions. Here we present extensive molecular simulation studies of hydration of realistic surfaces with a wide range of chemistries from hydrophobic (-CF(3), -CH(3)) to hydrophilic (-OH, -CONH(2)). We show that the water density near weakly attractive hydrophobic surfaces (e.g., -CF(3)) can be bulk-like or larger, and provides a poor quantification of surface hydrophobicity. In contrast, the probability of cavity formation or the free energy of binding of hydrophobic solutes to interfaces correlates quantitatively with the macroscopic wetting properties and serves as an excellent signature of hydrophobicity. Specifically, the probability of cavity formation is enhanced in the vicinity of hydrophobic surfaces, and water-water correlations correspondingly display characteristics similar to those near a vapor-liquid interface. Hydrophilic surfaces suppress cavity formation and reduce the water-water correlation length. Our results suggest a potentially robust approach for characterizing hydrophobicity of more complex and heterogeneous surfaces of proteins and biomolecules, and other nanoscopic objects.
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136
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Jayasinghe M, Beck TL. Molecular Dynamics Simulations of the Structure and Thermodynamics of Carrier-Assisted Uranyl Ion Extraction. J Phys Chem B 2009; 113:11662-71. [DOI: 10.1021/jp903470n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manori Jayasinghe
- Department of Chemistry and Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221-0172
| | - Thomas L. Beck
- Department of Chemistry and Department of Physics, University of Cincinnati, Cincinnati, Ohio 45221-0172
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137
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Choudhury N. Molecular dynamics investigation of hydration of nanoscopic hydrophobic paraffin-like plates. J Chem Phys 2009; 131:014507. [DOI: 10.1063/1.3155186] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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138
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Abstract
Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
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Affiliation(s)
- Hans-Jörg Schneider
- Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken, Deutschland.
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139
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Li H, Zhang F, Zhang Y, Ye M, Zhou B, Tang YZ, Yang HJ, Xie MY, Chen SF, He JH, Fang HP, Hu J. Peptide Diffusion and Self-Assembly in Ambient Water Nanofilm on Mica Surface. J Phys Chem B 2009; 113:8795-9. [DOI: 10.1021/jp903446g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Feng Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Yi Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Ming Ye
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Bo Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Yu-Zhao Tang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Hai-Jun Yang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Mu-Yun Xie
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Sheng-Fu Chen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Hai-Ping Fang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
| | - Jun Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Bio-X Life Sciences Research Center, College of Life Science and Biotechnology, Shanghai JiaoTong University, Shanghai 200240, China, Institute of Pharmaceutical Engineering, College of Materials Science and Chemical Engineering, Zhejiang University, Zhejiang 310027, China, and Shanghai Center for Systems Biomedicine, Shanghai 200240, China
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140
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Molinero V, Moore EB. Water modeled as an intermediate element between carbon and silicon. J Phys Chem B 2009; 113:4008-16. [PMID: 18956896 DOI: 10.1021/jp805227c] [Citation(s) in RCA: 579] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water and silicon are chemically dissimilar substances with common physical properties. Their liquids display a temperature of maximum density, increased diffusivity on compression, and they form tetrahedral crystals and tetrahedral amorphous phases. The common feature to water, silicon, and carbon is the formation of tetrahedrally coordinated units. We exploit these similarities to develop a coarse-grained model of water (mW) that is essentially an atom with tetrahedrality intermediate between carbon and silicon. mW mimics the hydrogen-bonded structure of water through the introduction of a nonbond angular dependent term that encourages tetrahedral configurations. The model departs from the prevailing paradigm in water modeling: the use of long-ranged forces (electrostatics) to produce short-ranged (hydrogen-bonded) structure. mW has only short-range interactions yet it reproduces the energetics, density and structure of liquid water, and its anomalies and phase transitions with comparable or better accuracy than the most popular atomistic models of water, at less than 1% of the computational cost. We conclude that it is not the nature of the interactions but the connectivity of the molecules that determines the structural and thermodynamic behavior of water. The speedup in computing time provided by mW makes it particularly useful for the study of slow processes in deeply supercooled water, the mechanism of ice nucleation, wetting-drying transitions, and as a realistic water model for coarse-grained simulations of biomolecules and complex materials.
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Affiliation(s)
- Valeria Molinero
- Department of Chemistry, University of Utah, Salt Lake City, 84112, USA.
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141
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142
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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143
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Yang G, Xu Y. Probing chiral solute-water hydrogen bonding networks by chirality transfer effects: A vibrational circular dichroism study of glycidol in water. J Chem Phys 2009; 130:164506. [DOI: 10.1063/1.3116582] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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144
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Yoshida Y, Miyamoto R, Nishioka T, Hashimoto H, Kinoshita I. “Compressed” Icelike Structures between Molecular Films Comparable with Ice Phase III. CHEM LETT 2009. [DOI: 10.1246/cl.2009.366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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145
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146
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147
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Alfonso I, Bolte M, Bru M, Burguete MI, Luis SV. Crystal structures of the HCl salts of pseudopeptidic macrocycles display “knobs into holes” hydrophobic interactions between aliphatic side chains. CrystEngComm 2009. [DOI: 10.1039/b821772f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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148
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Kleiner CM, Horst L, Würtele C, Wende R, Schreiner PR. Isolation of the key intermediates in the catalyst-free conversion of oxiranes to thiiranes in water at ambient temperature. Org Biomol Chem 2009; 7:1397-403. [DOI: 10.1039/b820232j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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149
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Jamadagni SN, Godawat R, Dordick JS, Garde S. How Interfaces Affect Hydrophobically Driven Polymer Folding. J Phys Chem B 2008; 113:4093-101. [DOI: 10.1021/jp806528m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sumanth N. Jamadagni
- The Howard P. Isermann Department of Chemical & Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Rahul Godawat
- The Howard P. Isermann Department of Chemical & Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jonathan S. Dordick
- The Howard P. Isermann Department of Chemical & Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Shekhar Garde
- The Howard P. Isermann Department of Chemical & Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
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150
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Kathmann SM, Kuo IFW, Mundy CJ. Electronic Effects on the Surface Potential at the Vapor−Liquid Interface of Water. J Am Chem Soc 2008; 130:16556-61. [DOI: 10.1021/ja802851w] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shawn M. Kathmann
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - I-Feng William Kuo
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Christopher J. Mundy
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550
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