Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media

Reversible geminate recombination of hydrogen-bonded water molecule pair

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t(-3/2) asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

Fast in silico protein folding by introduction of alternating hydrogen bond potentials

We accelerate protein folding in all-atom molecular dynamics simulations by introducing alternating hydrogen bond potentials as a supplement to the force field. The alternating hydrogen bond potentials result in accelerated hydrogen bond reordering, which leads to rapid formation of secondary structure elements. The method does not require knowledge of the native state but generates the potentials based on the development of the tertiary structure in the simulation. In protein folding, the formation of secondary structure elements, especially alpha-helix and beta-sheet, is very important, and we show that our method can fold both efficiently and with great speed.

Strength in numbers: probing and understanding intermolecular bonding with chemical force microscopy

Scanning probe microscopy (SPM) provided researchers with a simple, intuitive, and versatile tool for probing intermolecular interactions using SPM probes functionalized with distinct chemical species. Chemical force microscopy (CFM) was developed as a way to probe and map these interactions in a rational and systematic way. But does the rupture strength of a bond measured in these experiments provide the definitive and useful information about the interaction? The answer to this question is closely linked to understanding the fundamental physics of bond rupture under an external loading force. Even a simple model shows that bond rupture can proceed in a variety of different regimes. I discuss the approaches for extracting quantitative information about the interaction from these experiments and show that even though the measured rupture force is almost never unique for a given bond, force spectroscopy measurements can still determine the essential interaction parameters.

1-Alkanols and membranes: a story of attraction

Although 1-alkanols have long been known to act as penetration enhancers and anesthetics, the mode of operation is not yet understood. In this study, long-time molecular dynamics simulations have been performed to investigate the effect of 1-alkanols of various carbon chain lengths onto the structure and dynamics of dimyristoylphosphatidylcholine bilayers. The simulations were complemented by microcalorimetry, continuous bleaching and film balance experiments. In the simulations, all investigated 1-alkanols assembled inside the lipid bilayer within tens of nanoseconds. Their hydroxyl groups bound preferentially to the lipid carbonyl group and the hydrocarbon chains stretched into the hydrophobic core of the bilayer. Both molecular dynamics simulations and experiments showed that all 1-alkanols drastically affected the bilayer properties. Insertion of long-chain 1-alkanols decreased the area per lipid while increasing the thickness of the bilayer and the order of the lipids. The bilayer elasticity was reduced and the diffusive motion of the lipids within the bilayer plane was suppressed. On the other hand, integration of ethanol into the bilayer enlarged the area per lipid. The bilayer became softer and lipid diffusion was enhanced.

Solvent-exposed backbone loosens the hydration shell of soluble folded proteins

The hydration shell of a soluble folded protein is not uniform: its tightness, marked by the mobility of interfacial water, is site dependent and modulates the propensity for protein associations. We found that the most pronounced interfacial dehydration propensity for representative folds is promoted by solvent-exposed intramolecular hydrogen bonds that are incompletely shielded from water attack. These bonds are poorly wrapped by surrounding nonpolar groups from the side chains and their dehydration is energetically favored.

Distributions of H-Bonding Aggregates in tert-Butyl Alcohol: The Pure Liquid and Its Alkane Mixtures

A vibrational analysis using FTIR and Raman spectroscopies was carried out on pure liquid t-butyl alcohol (TBA) in the range of temperatures 15 < or = t < or = 70 degrees C. The whole range of molar fractions for TBA in 2,2'dimethylbutane (2,2'DMB) was also explored and compared with the t dependence of pure alcohol properties. Temperature and composition dependence of vibrational spectra were reproduced by simultaneous fitting of IR and Raman OH-stretching band contours by using harmonic frequencies and intensities derived from ab initio calculations for the various hydrogen-bonded structures. Adopting this fitting procedure, size and shape distributions of H-bonding aggregates have been derived, thus giving a quantitative description of balancing factors between hydrophilic and hydrophobic interactions in this liquid system.

Structure and Energetics of the Hydronium Hydration Shells

Proton solvation and proton mobility are both subjects of great interest in chemistry and biology. Here we have studied the hydration shells of H3O+ at temperatures ranging from 260 to 340 K using the multistate empirical valence-bond methodology (MS-EVB2). We have calculated the radial distribution functions for the protonium and its solvation shells. Furthermore, we have determined the Gibbs energy and the enthalpy for hydrogen bonds donated or accepted by the first two solvation shells, in comparison to bulk water. We find systematic bond-energy differences that appear to agree with a recent IR study on proton hydration. Implications of our results to various proton mobility mechanisms are discussed.

Protein Structures under Electrospray Conditions

During electrospray ionization (ESI), proteins are transferred from solution into vacuum, a process that influences the conformation of the protein. Exactly how much the conformation changes due to the dehydration process, and in what way, is difficult to determine experimentally. The aim of this study is therefore to monitor what happens to protein structures as the surrounding waters gradually evaporate, using computer simulations of the transition of proteins from water to vacuum. Five different proteins have been simulated with water shells of varying thickness, enabling us to mimic the entire dehydration process. We find that all protein structures are affected, at least to some extent, by the transfer but that the major features are preserved. A water shell with a thickness of roughly two molecules is enough to emulate bulk water and to largely maintain the solution phase structure. The conformations obtained in vacuum are quite similar and make up an ensemble which differs from the structure obtained by experimental means, and from the solution phase structure as found in simulations. Dehydration forces the protein to make more intramolecular hydrogen bonds, at the expense of exposing more hydrophobic area (to vacuum). Native hydrogen bonds usually persist in vacuum, yielding an easy route to refolding upon rehydration. The findings presented here are promising for future bio-imaging experiments with X-ray free electron lasers, and they strongly support the validity of mass spectrometry experiments for studies of intra- and intermolecular interactions.

Evaporation from water clusters containing singly charged ions

Molecular dynamics simulations were used to study the evaporation from water clusters containing either Cl(-), H(2)PO(4)(-), Na(+) or NH(4)(+) ions. The simulations ranged between 10 and 500 ns, and were performed in vacuum starting at 275 K. A number of different models were used including polarizable models. The clusters contain 216 or 512 molecules, 0, 4 or 8 of which were ions. The ions with hydrogen bonding properties do not affect evaporation, even though the phosphate ions have a pronounced ion-ion structure and tend to be inside the cluster whereas ammonium shows little ion-ion structure and has a distribution within the cluster similar to that of the water molecules. Since the individual ion-water interactions are much stronger in the case of Na(+)-water and Cl(-)-water clusters, evaporation is somewhat slower for clusters containing these ions. It seems therefore that the main determinant of the evaporation rate in ion-water clusters is the strength of the interaction. Fission of droplets that contain more ions than allowed according to the Rayleigh limit seems to occur more rapidly in clusters containing ammonium and sodium ions.

Molecular-dynamic studies of carbon-water-carbon composite nanotubes

We recently reported the discovery via molecular-dynamic simulations that single-walled carbon nanotubes (SWCNTs) with different diameters, lengths, and chiralities can coaxially self-assemble into multi-walled carbon nanotubes (MWCNTs) in water via the spontaneous insertion of smaller tubes into larger ones. Here, we extend that study to investigate the various water structures formed between two selected SWCNTs after such coaxial assembly. Depending on the tube geometry, typical water structures, besides the bulk phase, include a one-dimensional (1D) ordered water chain inside the smaller tube, a uniform or nonuniform water shell between the two tubes, and a "boundary layer" of water near the exterior wall of the larger tube. It was found that a concentric water shell consisting of up to three layers of water molecules can form between the two SWCNTs, which leads to a class of carbon-water-carbon composite nanotubes. Analysis of the potential energy of the SWCNT-water system indicated that the composite nanotubes are stabilized by both the tube-tube and tube-water van der Waals interactions. Geometrically confined between the two SWCNTs, water mono- and bilayers are found to be stable, highly condensed, and ordered, although the average number of hydrogen bonds per water molecule is reduced. In contrast, a water trilayer between the two CNTs can be easily disrupted by thermal fluctuations.

Temperature and structural changes of water clusters in vacuum due to evaporation

This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 micros of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 micros (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t-->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.

Protein folding kinetics and thermodynamics from atomistic simulations

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/- 0.4 micros, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.