51
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Yin P, Pradeep CP, Zhang B, Li FY, Lydon C, Rosnes MH, Li D, Bitterlich E, Xu L, Cronin L, Liu T. Controllable self-assembly of organic-inorganic amphiphiles containing Dawson polyoxometalate clusters. Chemistry 2012; 18:8157-62. [PMID: 22618885 DOI: 10.1002/chem.201200362] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 11/06/2022]
Abstract
An organic-inorganic molecular hybrid containing the Dawson polyoxometalate, ((C(4)H(9))(4)N)(5)H[P(2)V(3)W(15)O(59)(OCH(2))(3)CNHCOC(15)H(31)], was synthesized and its surfactant-like amphiphilic properties, represented by the formation of bilayer vesicles, were studied in polar solvents. The vesicle size decreases with both decreasing hybrid concentration and with increasing polarity of the solvent, independently. The self-assembly behavior of this hybrid can be controlled by introducing different counterions into the acetonitrile solutions. The addition of ZnCl(2) and NaI can cause a gradual decrease and increase of vesicular sizes, respectively. Tetraalkylammonium bromide is found to disassemble the vesicle assemblies. Moreover, the original counterions of the hybrid can be replaced with protons, resulting in pH-dependent formation of vesicles in aqueous solutions. The hybrid surfactant can further form micro-needle structures in aqueous solutions upon addition of Ca(2+) ions.
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Affiliation(s)
- Panchao Yin
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
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52
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Magazù S, Migliardo F, Benedetto A. Reply to “Comment on 'Puzzle of the Protein Dynamical Transition'”. J Phys Chem B 2012. [DOI: 10.1021/jp300926f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Salvatore Magazù
- Department of Physics, University of Messina, Viale Ferdinando Stagno D’Alcontres n° 31, P.O. Box
55, 98166 S. Agata, Messina, Italy
| | - Federica Migliardo
- Department of Physics, University of Messina, Viale Ferdinando Stagno D’Alcontres n° 31, P.O. Box
55, 98166 S. Agata, Messina, Italy
| | - Antonio Benedetto
- Department of Physics, University of Messina, Viale Ferdinando Stagno D’Alcontres n° 31, P.O. Box
55, 98166 S. Agata, Messina, Italy
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53
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Role of methyl groups in dynamics and evolution of biomolecules. J Biol Phys 2012; 38:497-505. [PMID: 23729910 DOI: 10.1007/s10867-012-9268-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/19/2012] [Indexed: 10/28/2022] Open
Abstract
Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules.Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9268-6) contains supplementary material, which is available to authorized users.
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54
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Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering. J Phys Chem B 2012; 116:5028-36. [PMID: 22471396 DOI: 10.1021/jp2102868] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The derivation of mean-square displacements from elastic incoherent neutron scattering (EINS) of proteins is examined, with the aid of experiments on camphor-bound cytochrome P450cam and complementary molecular dynamics simulations. It is shown that a q(4) correction to the elastic incoherent structure factor (where q is the scattering vector) can be simply used to reliably estimate from the experiment both the average mean-square atomic displacement, <Δr(2)> of the nonexchanged hydrogen atoms in the protein and its variance, σ(2). The molecular dynamics simulation results are in broad agreement with the experimentally derived <Δr(2)> and σ(2) derived from EINS on instruments at two different energy resolutions, corresponding to dynamics on the ∼100 ps and ∼1 ns time scales. Significant dynamical heterogeneity is found to arise from methyl-group rotations. The easy-to-apply q(4) correction extends the information extracted from elastic incoherent neutron scattering experiments and should be of wide applicability.
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Affiliation(s)
- Zheng Yi
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics , P.O. Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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55
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Mamontov E, O'Neill H, Zhang Q, Wang W, Wesolowski DJ. Common features in the microscopic dynamics of hydration water on organic and inorganic surfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:064104. [PMID: 22277314 DOI: 10.1088/0953-8984/24/6/064104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The microscopic dynamics of hydration water exhibits some universal features that do not depend on the nature of the hydrated surface. We show that the hydration level dependence of the dynamic transition in the mean squared atomic displacements measured by means of elastic neutron scattering is qualitatively similar for hydration water in inorganic and organic hosts. The difference is that the former are 'rigid', whereas the dynamics of the latter can be enhanced by the motions of the hydration water. The overall hydration level appears to be the main parameter governing the magnitude of the mean squared atomic displacements in the hydration water, irrespective of the details of the hydrated host.
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Affiliation(s)
- E Mamontov
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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56
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Lipps F, Levy S, Markelz AG. Hydration and temperature interdependence of protein picosecond dynamics. Phys Chem Chem Phys 2012; 14:6375-81. [DOI: 10.1039/c2cp23760a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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57
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Mamontov E, Chu XQ. Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions. Phys Chem Chem Phys 2012; 14:11573-88. [DOI: 10.1039/c2cp41443k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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58
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Schmidtke P, Luque FJ, Murray JB, Barril X. Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design. J Am Chem Soc 2011; 133:18903-10. [DOI: 10.1021/ja207494u] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Schmidtke
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - James B. Murray
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom
| | - Xavier Barril
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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59
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Roh JH, Tyagi M, Briber RM, Woodson SA, Sokolov AP. The Dynamics of Unfolded versus Folded tRNA: The Role of Electrostatic Interactions. J Am Chem Soc 2011; 133:16406-9. [DOI: 10.1021/ja207667u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Joon Ho Roh
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, United States
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, United States
| | - Madhu Tyagi
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, United States
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, United States
| | - R. M. Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, United States
| | - Sarah A. Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States
| | - Alexei P. Sokolov
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, United States
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60
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Vural D, Glyde HR. Vibrational dynamics of hydrogen in proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:031922. [PMID: 21517538 DOI: 10.1103/physreve.83.031922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 11/01/2010] [Indexed: 05/30/2023]
Abstract
Biological macromolecules expand with increasing temperature and this dynamic expansion is associated with the onset of function. The expansion is typically characterized by the mean square vibrational displacement (MSD), <u²> of specific constituents such as hydrogen within the macromolecules. The <u²> increases with increasing temperature and the slope of <u²> versus temperature can increase significantly at a temperature T{D} identified as a dynamical transition. We illustrate that the observed expansion and change in slope of <u²> with temperature at T{D} can be reproduced within a simple model of the vibration, an atom in an anharmonic potential, V(u). Given V(u), only the temperature is varied in the model. A simple Gaussian potential or a potential containing a hard wall is particularly effective is reproducing the observed change in the slope of <u²> with temperature around T{D}.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
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61
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Solvent effect on librational dynamics of spin-labelled haemoglobin by ED- and CW-EPR. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:273-9. [DOI: 10.1007/s00249-010-0644-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 10/08/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
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62
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Khodadadi S, Roh JH, Kisliuk A, Mamontov E, Tyagi M, Woodson SA, Briber RM, Sokolov AP. Dynamics of biological macromolecules: not a simple slaving by hydration water. Biophys J 2010; 98:1321-6. [PMID: 20371332 DOI: 10.1016/j.bpj.2009.12.4284] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/24/2009] [Accepted: 12/04/2009] [Indexed: 11/29/2022] Open
Abstract
We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account.
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Affiliation(s)
- S Khodadadi
- Department of Polymer Science, University of Akron, Akron, Ohio, USA
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63
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Kilburn D, Roh JH, Guo L, Briber RM, Woodson SA. Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc 2010; 132:8690-6. [PMID: 20521820 DOI: 10.1021/ja101500g] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crowder molecules in solution alter the equilibrium between folded and unfolded states of biological macromolecules. It is therefore critical to account for the influence of these other molecules when describing the folding of RNA inside the cell. Small angle X-ray scattering experiments are reported on a 64 kDa bacterial group I ribozyme in the presence of polyethylene-glycol 1000 (PEG-1000), a molecular crowder with an average molecular weight of 1000 Da. In agreement with expected excluded volume effects, PEG favors more compact RNA structures. First, the transition from the unfolded to the folded (more compact) state occurs at lower MgCl(2) concentrations in PEG. Second, the radius of gyration of the unfolded RNA decreases from 76 to 64 A as the PEG concentration increases from 0 to 20% wt/vol. Changes to water and ion activities were measured experimentally, and theoretical models were used to evaluate the excluded volume. We conclude that the dominant influence of the PEG crowder on the folding process is the excluded volume effect.
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Affiliation(s)
- Duncan Kilburn
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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64
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Wood K, Tobias DJ, Kessler B, Gabel F, Oesterhelt D, Mulder FAA, Zaccai G, Weik M. The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling and molecular dynamics simulations. J Am Chem Soc 2010; 132:4990-1. [PMID: 20302295 DOI: 10.1021/ja910502g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is increasing interest in the contribution of methyl groups to the overall dynamics measured by neutron scattering experiments of proteins. In particular an inflection observed in atomic mean square displacements measured as a function of temperature on high resolution spectrometers (approximately 1 microeV) was explained by the onset of methyl group rotations. By specifically labeling a non-methyl-containing side-chain in a native protein system, the purple membrane, and performing neutron scattering measurements, we here provide direct experimental evidence that the observed inflection is indeed due to methyl group rotations. Molecular dynamics simulations reproduce the experimental data, and their analysis suggests that the apparent transition is due to methyl group rotation entering the finite instrumental resolution of the spectrometer. Methyl group correlation times measured by solid state NMR in the purple membrane, taken from previous work, support the interpretation.
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65
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Mamontov E, O'Neill H, Zhang Q. Mean-squared atomic displacements in hydrated lysozyme, native and denatured. J Biol Phys 2010; 36:291-7. [PMID: 21629590 DOI: 10.1007/s10867-009-9184-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 12/22/2009] [Indexed: 10/20/2022] Open
Abstract
We use elastic neutron scattering to demonstrate that a sharp increase in the mean-squared atomic displacements, commonly observed in hydrated proteins above 200 K and often referred to as the dynamical transition, is present in the hydrated state of both native and denatured lysozyme. A direct comparison of the native and denatured protein thus confirms that the presence of the transition in the mean-squared atomic displacements is not specific to biologically functional molecules.
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66
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Jasnin M, van Eijck L, Marek Koza M, Peters J, Laguri C, Lortat-Jacob H, Zaccai G. Dynamics of heparan sulfate explored by neutron scattering. Phys Chem Chem Phys 2010; 12:3360-2. [DOI: 10.1039/b923878f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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67
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Alexander RW, Eargle J, Luthey-Schulten Z. Experimental and computational determination of tRNA dynamics. FEBS Lett 2009; 584:376-86. [PMID: 19932098 DOI: 10.1016/j.febslet.2009.11.061] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 11/14/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
As the molecular representation of the genetic code, tRNA plays a central role in the translational machinery where it interacts with several proteins and other RNAs during the course of protein synthesis. These interactions exploit the dynamic flexibility of tRNA. In this minireview, we discuss the effects of modified bases, ions, and proteins on tRNA structure and dynamics and the challenges of observing its motions over the cycle of translation.
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Affiliation(s)
- Rebecca W Alexander
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109-7486, United States.
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68
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Abstract
Using a parallel single molecule magnetic tweezers assay we demonstrate homologous pairing of two double-stranded (ds) DNA molecules in the absence of proteins, divalent metal ions, crowding agents, or free DNA ends. Pairing is accurate and rapid under physiological conditions of temperature and monovalent salt, even at DNA molecule concentrations orders of magnitude below those found in vivo, and in the presence of a large excess of nonspecific competitor DNA. Crowding agents further increase the reaction rate. Pairing is readily detected between regions of homology of 5 kb or more. Detected pairs are stable against thermal forces and shear forces up to 10 pN. These results strongly suggest that direct recognition of homology between chemically intact B-DNA molecules should be possible in vivo. The robustness of the observed signal raises the possibility that pairing might even be the "default" option, limited to desired situations by specific features. Protein-independent homologous pairing of intact dsDNA has been predicted theoretically, but further studies are needed to determine whether existing theories fit sequence length, temperature, and salt dependencies described here.
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69
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Mamontov E, Vlcek L, Wesolowski DJ, Cummings PT, Rosenqvist J, Wang W, Cole DR, Anovitz LM, Gasparovic G. Suppression of the dynamic transition in surface water at low hydration levels: a study of water on rutile. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:051504. [PMID: 19518459 DOI: 10.1103/physreve.79.051504] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 03/06/2009] [Indexed: 05/15/2023]
Abstract
Our quasielastic neutron-scattering experiments and molecular-dynamics simulations probing surface water on rutile (TiO2) have demonstrated that a sufficiently high hydration level is a prerequisite for the temperature-dependent crossover in the nanosecond dynamics of hydration water. Below the monolayer coverage of mobile surface water, a weak temperature dependence of the relaxation times with no apparent crossover is observed. We associate the dynamic crossover with interlayer jumps of the mobile water molecules, which become possible only at a sufficiently high hydration level.
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Affiliation(s)
- Eugene Mamontov
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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