Hydrophobic hydration of the hydrocarbon adamantane in amorphous ice

Hydrophobic molecules are by definition difficult to hydrate. Previous studies in the area of hydrophobic hydration have therefore often relied on using amphiphilic molecules where the hydrophilic part of a molecule enabled the solubility in liquid water. Here, we show that the hydrophobic adamantane (C10H16) molecule can be fully hydrated through vapour codeposition with water onto a cryogenic substrate at 80 K resulting in the matrix isolation of adamantane in amorphous ice. Using neutron diffraction in combination with the isotopic substitution method and the empirical potential structure refinement technique, we find that the first hydration shell of adamantane is well structured consisting of a hydrogen-bonded cage of 28 water molecules that is also found in cubic structure II clathrate hydrates. The four hexagonal faces of the 51264 cage are situated above the four methine (CH) groups of adamantane whereas the methylene (CH2) groups are positioned below the edges of two adjoining pentagonal faces. The oxygen atoms of the 28 water molecules can be categorised on the basis of symmetry equivalences as twelve A, twelve B and four C oxygens. The water molecules of the first hydration shell display orientations consistent with those expected for a clathrate-hydrate-type cage, but also unfavourable ones with respect to the hydrogen bonding between the water molecules. Annealing the samples at 140 K, which is just below the crystallisation temperature of the matrix, removes the unfavourable orientations and leads to a slight increase in the structural order of the first hydration shell. The very closest water molecules display a tendency for their dipole moments to point towards the adamantane which is attributed to steric effects. Other than this, no significant polarisation effects are observed which is consistent with weak interactions between adamantane and the amorphous ice matrix. FT-IR spectroscopy shows that the incorporation of adamantane into amorphous ice leads to a weakening of the hydrogen bonds. In summary, the matrix-isolation of the highly symmetric adamantane in amorphous ice provides an interesting test case for hydrophobic hydration. Studying the structure and spectroscopic properties of water at the interface with hydrophobic hydrocarbons is also relevant for astrophysical environments, such as comets or the interstellar medium, where amorphous ice and hydrocarbons have been shown to coexist in large quantities.

Protonation and orientation: a computational approach to cocaine diffusion through a model membrane

We study the diffusion of cocaine through a DMPC lipid bilayer as an example of a protonable, amphiphilic molecule passing a biological membrane. Using classical molecular dynamics simulations, the free...

Hydrophilic and hydrophobic interactions in concentrated aqueous imidazole solutions: a neutron diffraction and total X-ray scattering study

A study of 5 M aqueous imidazole solutions combining neutron and X-ray diffraction with EPSR simulations shows dominance of hydrogen-bonding between imidazole and water and negligible hydrogen-bonding between imidazole molecules.

On the microscopic origin of the cryoprotective effect in lysine solutions

Lysine cryoprotective properties are due to the tight bonding of the first hydration Shell to the amino acid. However this effect is only possible for concentration up to 5.4 water molecules per lysine.

On the hydration of DOPE in solution

The atomic-scale hydration structure around the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) headgroup in a chloroform/water solution has been investigated using neutron diffraction enhanced by isotopic substitution and NMR, coupled with empirical potential structure refinement and molecular dynamics simulations. The results obtained show the preferential binding sites for water molecules on the DOPE headgroups, with the most predominant interactions being with the ammonium and phosphate groups. Interestingly, the level of hydration, as well as the association of DOPE molecules, varies according to the simulation method used. The results here suggest the presence of a tight water network around these lipid headgroups that could affect the permeability of the membrane for lipid-mediated diffusion.

Hydrogen Bond Length as a Key To Understanding Sweetness

Neutron diffraction experiments have been performed to investigate and compare the structure of the hydration shell of three monosaccharides, namely, fructose, glucose, and mannose. It is found that despite their differences with respect to many thermodynamical quantities, bioprotective properties against environmental stresses, and taste, the influence of these monosaccharides on the bulk water solvent structure is virtually identical. Conversely, these sugars interact with the neighboring water molecules by forming H bonds of different length and strength. Interestingly, the sweetness of these monosaccharides, along with that of the disaccharide trehalose, is correlated with the length of these H bonds. This suggests that the small differences in stereochemistry between the different sugars determine a relevant change in polarity, which has a fundamental impact on the behavior of these molecules in vivo.

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin

Water is often found to mediate interactions between a ligand and a protein. It can play a significant role in orientating the ligand within a binding pocket and contribute to the free energy of binding. It would thus be extremely useful to be able to accurately predict the position and orientation of water molecules within a binding pocket. Recently, we developed the WaterDock protocol that was able to predict 97% of the water molecules in a test set. However, this approach generated false positives at a rate of over 20% in most cases and whilst this might be acceptable for some applications, in high throughput scenarios this is not desirable. Here we tackle this problem via the inclusion of knowledge regarding the solvation structure of ligand functional groups. We call this new protocol WaterDock2 and demonstrate that this protocol maintains a similar true positive rate to the original implementation but is capable of reducing the false-positive rate by over 50%. To improve the usability of the method, we have also developed a plugin for the popular graphics program PyMOL. The plugin also contains an implementation of the original WaterDock.

On the structure of prilocaine in aqueous and amphiphilic solutions

The solvation of prilocaine has been investigated in pure water and in amphiphilic solutions using a combination of neutron diffraction and simulations.

Structure-activity relationships in carbohydrates revealed by their hydration

One of the more intriguing aspects of carbohydrate chemistry is that despite having very similar molecular structures, sugars have very different properties. For instance, there is a sensible difference in sweet taste between glucose and trehalose, even though trehalose is a disaccharide that comprised two glucose units, suggesting a different ability of these two carbohydrates to bind to sweet receptors. Here we have looked at the hydration of specific sites and at the three-dimensional configuration of water molecules around three carbohydrates (glucose, cellobiose, and trehalose), combining neutron diffraction data with computer modelling. Results indicate that identical chemical groups can have radically different hydration patterns depending on their location on a given molecule. These differences can be linked with the specific activity of glucose, cellobiose, and trehalose as a sweet substance, as building block of cellulose fiber, and as a bioprotective agent, respectively. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editors: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.

Atomic scale insights into urea–peptide interactions in solution

Investigations on the β-turn forming peptide, GPG, suggest that urea denatures proteins by replacing water molecules and subsequently weakening the peptide bonds as a possible mechanism of protein denaturation by urea.

The solvation structure of alprazolam

Alprazolam is a benzodiazepine that is commonly prescribed for the treatment of anxiety and other related disorders.

Microstructures of negative and positive azeotropes

Azeotropes famously impose fundamental restrictions on distillation processes, yet their special thermodynamic properties make them highly desirable for a diverse range of industrial and technological applications. Using neutron diffraction, this study provides first insights into the microstructures of azeotropes.

On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility

The increase in solubility for indole in methanol water solutions relative to pure water is a result methanol −OH–π interactions. In addition, excess entropy calculations suggest that this process is enthalpically rather than entropically driven.