Monte Carlo studies on the structure of a dilute aqueous solution of methane

Swaminathan, S.; Harrison, S. W.; Beveridge, David L.

doi:10.1021/ja00486a020

Cited by 193 publications

(74 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The most abundant polygon formed, assuming a hydrogen-bonding energy of -4.0 kcal/mol, is the pentagon, followed closely by the hexagon (33). Monte Carlo simulations have predicted quasiclathrate structures with nonplanar water pentagons for methane in water (34).…”

Section: Discussionmentioning

confidence: 99%

Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

Teeter

1984

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

325

171

View full text Add to dashboard Cite

The water structure has been analyzed for a model of the protein crambin refined against 0.945-x-ray diffraction data. Crystals contain 32% solvent by volume, and 77% of the solvent molecules have been located-i.e., 2 ethanol molecules and 64 water molecules with 10-14 alternate positions. Many water oxygen atoms found form chains between polar groups on the surface of the protein. However, a cluster of pentagonal arrays made up of 16 water molecules sits at a hydrophobic, intermolecular cleft and forms a cap around the methyl group of leucine-18. Several waters in the cluster are hydrogen-bonded directly to the protein. Additional closed circular arrays, which include both protein atoms and other water oxygen atoms, form next to the central cluster. This water array stretches in the b lattice direction between groups of three ionic side chains.Water is the most abundant molecule in living systems and plays an important role in their structure and function. From crystal structures of proteins (1-3), the following picture of tightly bound internal and surface water molecules has emerged (4, 5). First, internal water is found singly (6), in clusters (7), or bound to metal ions (8, 9). It either may stabilize the protein structure by connecting charged or polar groups, or both, or may serve a catalytic function (10). Second, surface water links polar groups at the intra-and intermolecular protein surface; 2-3 times more water hydrogen bonds are made to main-chain -CO groups than to -NH groups (4, 5) in both crystal structures and simulations, reflecting in part the greater capacity of -CO to form hydrogen bonds. Many surface waters bind at turn regions (11). Here, fewer secondary-structure, backbone hydrogen bonds are formed, and the side chains are often hydrophilic (12). Little if any ordered surtace water has been reported at nonpolar side chains, perhaps because such water may be mobile as inferred from computer simulations (13). Finally, less ordered water (about 30% of that in the first shell) is seen in the second shell (14).Water-protein interactions may be important for protein folding (4). Klotz proposed that hydrophobic residues would organize surface water into five-membered ring arrays analogous to the water clathrate (cage) hydrate structures (15). However, protein crystal structures reveal that many hydrophobic groups fold instead into the protein interior away from water, as suggested by Kauzmann (16). Nevertheless, 40-50%o are found on the protein surface in contact with solvent. The folded structure may be a balance between removal of hydrophobic groups from water to form van der Waals attractive contacts and the penalty for burial of polar groups which might not be able to form hydrogen bonds. The arrangement of water at surface hydrophobic sites is not known. If five-membered ring structures were formed (15) and were not hydrogen-bonded to the protein, they might become disordered or vibrate strongly. Such waters would contribute little scattering to an x-ray experiment.Crystals of the h...

show abstract

Section: Discussionmentioning

confidence: 99%

Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

Teeter

1984

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

325

171

View full text Add to dashboard Cite

show abstract

“…51 Simulations and theory computed the average number of water molecules in the first hydration shell around methane solutes. Numbers varied between 14 and 22 water molecules depending on the model and theory used, 40,[52][53][54] while experiments measured hydration shells with 16, 19, or 20 water molecules. [55][56][57] From Table I, we can conclude that when solutes form the SSC state, i.e., ISC → SSC, on average two shell water molecules are transferred to the bulk.…”

Section: Potential Of Mean Forcementioning

confidence: 99%

Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

Dias

Hynninen

Ala-Nissilä

et al. 2011

The Journal of Chemical Physics

View full text Add to dashboard Cite

Articles you may be interested inThe hydrophobic effect in a simple isotropic water-like model: Monte Carlo study J. Chem. Phys. 140, 144904 (2014) We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

show abstract

“…7 exposes the inherent hydrophobicity of the siloxane surface even more directly through a MC snapshot of a methane molecule adsorbed in the interlayer region of the three-layer hydrate of Na-montmoril- lonite (H 2 O͞CH 4 ϭ 23). The well known 20-fold coordination cage induced by CH 4 in bulk water (41,42) was reproduced successfully by the CH 4 -O potential function used in the MC simulation (43). In the interlayer of a Na-montmorillonite hydrate, however, methane coordinates to eight clay mineral O and approximately a dozen water molecule O to form this cage in a highly distorted coordination structure.…”

mentioning

confidence: 90%

“…Studies of the effect of layer charge on the adsorption of both water and hydrocarbon molecules by smectites (36,38) indeed show that surface hydrophobicity increases as the layer charge decreases. Recent molecular dynamics simulations of ion solvation and mobility in aqueous solution (39,40) suggest that large cations like K ϩ tend to interact with water molecules not only through their positive charge but also through solvent cage formation, which is just what hydrocarbon molecules do (41)(42)(43). This hydrophobic tendency may be the basis for K ϩ associating directly with clay mineral O (Fig.…”

mentioning

confidence: 99%

Surface geochemistry of the clay minerals

Sposito

Skipper

Sutton

et al. 1999

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

685

438

View full text Add to dashboard Cite

Clay minerals are layer type aluminosilicates that figure in terrestrial biogeochemical cycles, in the buffering capacity of the oceans, and in the containment of toxic waste materials. They are also used as lubricants in petroleum extraction and as industrial catalysts for the synthesis of many organic compounds. These applications derive fundamentally from the colloidal size and permanent structural charge of clay mineral particles, which endow them with significant surface reactivity. Unraveling the surface geochemistry of hydrated clay minerals is an abiding, if difficult, topic in earth sciences research. Recent experimental and computational studies that take advantage of new methodologies and basic insights derived from the study of concentrated ionic solutions have begun to clarify the structure of electrical double layers formed on hydrated clay mineral surfaces, particularly those in the interlayer region of swelling 2:1 layer type clay minerals. One emerging trend is that the coordination of interlayer cations with water molecules and clay mineral surface oxygens is governed largely by cation size and charge, similarly to a concentrated ionic solution, but the location of structural charge within a clay layer and the existence of hydrophobic patches on its surface provide important modulations. The larger the interlayer cation, the greater the inf luence of clay mineral structure and hydrophobicity on the configurations of adsorbed water molecules. This picture extends readily to hydrophobic molecules adsorbed within an interlayer region, with important implications for clay-hydrocarbon interactions and the design of catalysts for organic synthesis.

show abstract

Monte Carlo studies on the structure of a dilute aqueous solution of methane

Cited by 193 publications

References 6 publications

Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

Surface geochemistry of the clay minerals

Contact Info

Product

Resources

About