Coupling of solvent and solute dynamics—molecular dynamics simulations of aqueous urea solutions with different intramolecular potentials

Kallies, Bernd

doi:10.1039/b105836n

Cited by 49 publications

(67 citation statements)

References 48 publications

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“…10,22,27,28 Several urea force fields exist in the literature. [10][11][12][13][14][29][30][31] Computational studies have reproduced the salting out effect ͑decrease in solute solubility͒ of urea solutions on methane and the noble gases, 27,32,33 illustrating that cavity formation is thermodynamically more unfavorable in urea solutions, which is supported by simple models of the salting in and out effects of urea solutions, 34 and in agreement with the observed experimental data on surface tension increases. 35 However, a recent comparison of urea force fields has appeared which demonstrates that current urea models display significantly different degrees of urea aggregation, 15 even though diffraction studies clearly show that urea does not disrupt the hydrogen bonding network of water.…”

Section: Introductionsupporting

confidence: 76%

Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation

Weerasinghe¹,

Smith²

2003

The Journal of Chemical Physics

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A series of models for 8 M urea solutions was investigated using molecular dynamics simulations. The models differed only in their charge distributions and displayed various degrees of urea aggregation. The relationship between urea aggregation and the thermodynamics of the solution was established using Kirkwood-Buff theory. It was observed that high urea aggregation resulted in lower predicted values for the solution activity, and that Kirkwood-Buff theory provided a sensitive test for the properties of a particular force field. The free energy for formation of repulsive cavities in the different solutions was also investigated. The free energy was more unfavorable than in pure water, but independent of the extent of urea aggregation. However, the preferential exclusion of urea from the cavities was very sensitive to the degree of urea aggregation and varied by more than an order of magnitude in response to changes in the activity derivatives. A simple explanation for these observations is presented.

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Section: Introductionsupporting

confidence: 76%

Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation

Weerasinghe¹,

Smith²

2003

The Journal of Chemical Physics

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“…Water molecules lost from the bulk water hydration shell cannot be fully replaced by contacts with pore-lining side chains because of a lack of sufficient hydrogen bonding partners, resulting in an energetic penalty associated with urea dehydration. In addition, the simulations show that urea, which has a liquid state dipole moment of 6–8 D11, preferentially orients inside the channel during transport, with the amino groups pointing away from the central lipid plug (see Fig. 2), resulting in an energetic penalty associated with a reduction in entropy.…”

Section: Discussionmentioning

confidence: 95%

Mechanisms of molecular transport through the urea channel of Helicobacter pylori

et al. 2013

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Helicobacter pylori survival in acidic environments relies on cytoplasmic hydrolysis of gastric urea into ammonia and carbon dioxide, which buffer the pathogen’s periplasm. Urea uptake is greatly enhanced and regulated by HpUreI, a proton-gated inner membrane channel protein essential for gastric survival of H. pylori. The crystal structure of HpUreI describes a static snapshot of the channel with two constriction sites near the center of the bilayer that are too narrow to allow passage of urea or even water. Here we describe the urea transport mechanism at atomic resolution, revealed by unrestrained microsecond equilibrium molecular dynamics simulations of the hexameric channel assembly. Two consecutive constrictions open to allow conduction of urea, which is guided through the channel by interplay between conserved residues that determine proton rejection and solute selectivity. Remarkably, HpUreI conducts water at rates equivalent to aquaporins, which might be essential for efficient transport of urea at small concentration gradients.

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“…The fact that the majority of the water molecules are unaffected by the presence of urea, even at a concentration of 8 M, is surprising. At such a high concentration all water molecules are essentially part of the solvation shell of a urea molecule, which consists of five to seven water molecules, as is known from molecular dynamics simulations (11). Given the fact that this number is slightly higher than the average number of water molecules available per urea molecule (between four and five), some water molecules may even be part of two solvation shells.…”

Section: Discussionmentioning

confidence: 96%

“…The desire to understand these properties has triggered a great deal of research regarding the structure of aqueous solutions of urea (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). An important question that is encountered throughout the literature is to what extent the hydrogen-bond network of water is perturbed by the incorporation of a urea molecule, as one of the models explaining protein denaturation by urea is built on the assumption that urea strongly alters the hydrogen-bond structure of water (14).…”

mentioning

confidence: 99%

Effect of urea on the structural dynamics of water

Rezus

Bakker

2006

Proc. Natl. Acad. Sci. U.S.A.

184

281

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We use polarization-resolved mid-infrared pump-probe spectroscopy to study the effect of urea on the structure and dynamics of water. Surprisingly, we find that, even at high concentrations of urea (8 M), the orientational dynamics of most water molecules are the same as in pure liquid water, showing that urea has a negligible effect on the hydrogen-bond dynamics of these molecules. However, a small fraction of the water molecules (approximately one water molecule per urea molecule) turns out to be strongly immobilized by urea, displaying orientational dynamics that are more than six times slower than in bulk water. A likely explanation is that these water molecules are tightly associated with urea, forming specific urea-water complexes. We discuss these results in light of the protein denaturing ability of aqueous urea.hydrogen bonding ͉ infrared pump-probe spectroscopy ͉ orientational dynamics ͉ protein denaturation S olutions of urea in water display a number of interesting properties: hydrocarbons dissolve more readily in them than in pure water, and concentrated solutions can be used to denature proteins in a reversible way. The desire to understand these properties has triggered a great deal of research regarding the structure of aqueous solutions of urea (1-13). An important question that is encountered throughout the literature is to what extent the hydrogen-bond network of water is perturbed by the incorporation of a urea molecule, as one of the models explaining protein denaturation by urea is built on the assumption that urea strongly alters the hydrogen-bond structure of water (14). The urea-water system has been studied by using a variety of experimental and theoretical techniques, all of which shed light on a different aspect of the system. Linear infrared and Raman spectroscopies can provide structural information about the hydrogen-bond network, but they depend on simulations to unravel the effect of intermolecular interactions on spectral band shapes (15). Neutron diffraction experiments produce atom-atom radial distribution functions, and, as such, form more direct methods to obtain structural information (7). A different class of experimental techniques probes the hydrogen-bond network by observing the dynamics of water molecules. A stiffening of the network is revealed by the slowing down of the water dynamics, whereas faster dynamics are indicative of the weakening of the network. Among these methods are dielectric relaxation (5), NMR (6), and optical Kerr effect (OKE) spectroscopy (8). Dielectric relaxation and OKE provide dynamical information down to the picosecond time scale but probe the response of the solution as a whole, making it difficult to separate the water response from the urea response. NMR experiments selectively probe the dynamics of water, but determine a timeaveraged response, so that water molecules in the urea solvation shell cannot be distinguished from molecules in the bulk. As a result, it is not yet clear to what extent the hydrogen-bond structure of water is change...

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Coupling of solvent and solute dynamics—molecular dynamics simulations of aqueous urea solutions with different intramolecular potentials

Cited by 49 publications

References 48 publications

Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation

Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation

Mechanisms of molecular transport through the urea channel of Helicobacter pylori

Effect of urea on the structural dynamics of water

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