Driving Force for Hydrophobic Interaction at Different Length Scales

We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called "bonded") and those that do not (called "free"). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is significantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.

The potential of mean force between two large parallel hydrophobic oblate ellipsoidal plates in liquid water is determined by molecular dynamics. Each ellipsoid displaces approximately 40 water molecules and has major and minor axes of 3.1 and 9.3 A, respectively, has a surface area of 650 A*, and interacts repulsively with the solvent water molecules. The potential of mean force is calculated from thermodynamic perturbation theory for a series of decreasing plate separations, using constant-pressure molecular dynamics. As the plates are moved together, they are first separated by three water layers and then by two, but for shorter distances, a dewetting transition occurs, and one water layer is never observed despite the fact that one can fit. As the plates are brought together, there is a corresponding weak oscillation in the potential of mean force corresponding to the removal of each water layer until the dewetting transition takes place, and for closer separations, the surrounding water molecules induce a constant average attractive force of 25 (kJ/mol)/A between the plates. This hydrophobic attraction is largely entropic in character, and the potential of mean force is found to be proportional to the area of the water-vacuum surface in this dewetting regime. The constant of proportionality is found to be smaller than the gas-liquid surface tension of the water model used. There is a very strong short-range driving force toward contact pairing. 1.

Layers of graphene oxide (GO) are found to be good for the permeation of water but not for helium (Science, 2012, 335(6067), 442-444) suggesting that the GO layers are dynamic in the formation of a permeation route depending on the environment they are in (i.e., water or helium). To probe the microscopic origin of this observation we calculate the potential of mean force (PMF) of GO sheets (with oxidized and reduced parts), with the inter-planar distance as a reaction coordinate in helium and water. Our PMF calculation shows that the equilibrium interlayer distance between the oxidized part of the GO sheets in helium is at 4.8 Å leaving no space for helium permeation. In contrast, the PMF of the oxidized part of the GO in water shows two minima, one at 4.8 Å and another at 6.8 Å, corresponding to no water and a water filled region, thus giving rise to a permeation path. The increased electrostatic interaction between water with the oxidized part of the sheet helps the sheet open up and pushes water inside. Based on the entropy calculations for water trapped between graphene sheets and oxidized graphene sheets at different inter-sheet spacings, we also show the thermodynamics of filling.

We investigate the thermodynamics of the binding of a poly(amidoamine) dendrimer to an uncharged graphene sheet as a function of the pH level using umbrella sampling simulations and a mean-field theory for generations three and four. We find that the dendrimer strongly binds to the graphene sheet ( (100) kcal/mol) from our potential of mean force (PMF) calculations. In specific, we find that the dendrimer binds the most at neutral pH (∼7) and the least at low pH (∼4). We explain this nonmonotonic nature of the dendrimer's adsorption by studying the interactions contributing to the PMF, i.e., the dendrimer-graphene, dendrimer-water, and dendrimer-ion interactions. We also corroborate our PMF calculations with molecular mechanics generalized Born surface area analysis and free energies obtained from a mean-field theory of Flory-Huggins-Debye-Hückel type [ Muthukumar , M. , J. Chem. Phys. 2010 , 132 , 084901 ], including electrostatic interactions. We find that the van der Waals interactions between the dendrimer and the graphene alone cannot capture the accurate trends in the binding free energies (BEs) as a function of pH. The solvent and the counterions present in the system are also found to have a major influence on these trends. We demonstrate that the dendrimer-graphene and dendrimer-water interactions become favorable, whereas the dendrimer-ion interaction becomes unfavorable, as the dendrimer binds to graphene. These opposing effects lead to the observed nonmonotonicity in the BE trends. Our theoretical model also reproduces these trends in the subinteractions contributing to the PMF. To the best of our knowledge, this is a novel attempt where an equivalence between theory and simulations is made in the context of the dendrimer's adsorption.

Functionalization of graphene sheets by the diazonium chemistry during electrochemical exfoliation of graphite

Development of porosity during the combustion of coals and cokes

Free energy barriers associated with the transfer of an excess proton in water and related to the potentials of mean force in proton transfer episodes have been computed in a wide range of thermodynamic states, from low-density amorphous ices to high-temperature liquids under the critical point for unconstrained and constrained systems. The latter were represented by set-ups placed inside hydrophobic graphene slabs at the nanometric scale allocating a few water layers, namely one or two in the narrowest case. Water–proton and carbon–proton forces were modelled with a Multi-State Empirical Valence Bond method. As a general trend, a competition between the effects of confinement and temperature is observed on the local hydrogen-bonded structures around the lone proton and, consequently, on the mean force exerted by its environment on the water molecule carrying the proton. Free energy barriers estimated from the computed potentials of mean force tend to rise with the combined effect of increasing temperatures and the packing effect due to a larger extent of hydrophobic confinement. The main reason observed for such enhancement of the free energy barriers was the breaking of the second coordination shell around the lone proton.

Graphene sheets, one-atom-thick layers of carbon atoms, are receiving enormous scientific attention because of extraordinary electronic and mechanical properties. These intrinsic properties will lead to innovative nanocomposite materials that could be used to produce novel transistors and thermally conductive polymeric materials. Such applications are currently hindered by the difficulty of producing large quantities of individual graphene sheets and by the propensity of these nanoparticles to agglomerate when dispersed in aqueous and/or organic matrixes. We report here molecular dynamics simulations for pristine and functionalized graphene nanosheets of 54 and 96 carbon atoms each dispersed in liquid organic linear alkanes (oils) at room conditions. For the first time, our results show that, although pristine graphene sheets agglomerate in the oils considered, graphene sheets functionalized at their edges with short branched alkanes yield stable dispersions. We characterized the simulated systems by computing radial distribution functions between the graphene sheets centers of mass, pair potentials of mean force between the graphene sheets in solution, and site-site radial distribution functions. The latter were used to determine the preferential orientation between approaching graphene sheets and the packing of the organic oils on the graphene sheets. Our results are useful not only for designing practical recipes for stabilizing graphene sheets in organic systems, but also for comparing the molecular mechanisms responsible for the graphene sheets aggregation to those that stabilize graphene sheets-containing dispersions, and for controlling the coupling between organic oils and graphene sheets used as fillers. In particular, we demonstrated that excluded-volume effects, generated by the branched architecture of the functional groups grafted on the graphene sheets, are responsible for the stabilization of small graphene sheets in the organic systems considered here.

The state of intracellular water has been a matter of controversy for a long time for two reasons. First, experiments have often given conflicting results. Second, hitherto, there have been no plausible grounds for assuming that intracellular water should be significantly different from bulk water. A collective behavior of water molecules is suggested here as a thermodynamically inevitable mechanism for generation of appreciable zones of abnormal water. At a highly charged surface, water molecules move together, generating a zone of water perhaps 6 nm thick, which is weakly hydrogen bonded, fluid, and reactive and selectively accumulates small cations, multivalent anions, and hydrophobic solutes. At a hydrophobic surface, molecules move apart and local water becomes strongly bonded, inert, and viscous and accumulates large cations, univalent anions, and compatible solutes. Proteins and many other biopolymers have patchy surfaces which therefore induce, by the two mechanisms described, patchy interfacial water structures, which extended appreciable distances from the surface. The reason for many conflicting experimental results now becomes apparent. Average values of properties of water measured in gels, cells, or solutions of proteins are often not very different from the same properties of normal water, giving no indication that they are averages of extreme values. To detect the operation of this phenomenon, it is necessary to probe selectively a single abnormal population. Examples of such experiments are given. It is shown that this collective behavior of water molecules amounts to a considerable biological force, which can be equivalent to a pressure of 1,000 atm (1.013 x 10(5) kPa). It is suggested that cells selectively accumulate K+ ions and compatible solutes to avoid extremes of water structure in their aqueous compartments, but that cation pumps and other enzymes exploit the different solvent properties and reactivities of water to perform work of transport or synthesis.

Liposomal formulation of curcumin is an important therapeutic agent for the treatment of various cancers. Despite extensive studies on the biological effects of this formulation in cancer treatment, much remains unknown about curcumin–liposome interactions. Understanding how different lipid bilayers respond to curcumin molecule may help us to design more effective liposomal curcumin. Here, we used molecular dynamics simulation method to investigate the behavior of curcumin in two lipid bilayers commonly used in preparation of liposomal curcumin, namely dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylglycerol (DMPG). First, the free energy barriers for translocation of one curcumin molecule from water to the lipid bilayer were determined by using the potential of mean force (PMF). The computed free energy profile exhibits a global minimum at the solvent–headgroup interface (LH region) for both lipid membranes. We also evaluated the free energy difference between the equilibrium position of curcumin in the lipid bilayer and bulk water as the excess chemical potential. Our results show that curcumin has the higher affinity in DMPG compared to DPPC lipid bilayer (−8.39 vs. −1.69 kBT) and this is related to more hydrogen bond possibility for curcumin in DMPG lipid membrane. Next, using an unconstrained molecular dynamic simulation with curcumin initially positioned at the center of lipid bilayer, we studied various properties of each lipid bilayer system in the presence of curcumin molecule that was in full agreement with PMF and experimental data. The results of these simulation studies suggest that membrane composition could have a large effect on interaction of curcumin–lipid bilayer.

The Scholl reaction was adopted to synthesize the very large polycyclic aromatic hydrocarbons (VLPAHs) hexabenzocoronene (HBC), quaterrylene and dicoronylene as well as their nonalternant isomers. These molecules can be considered subsections of a graphene sheet since the radial diameter of HBC is 13.5 Å and the length of both quaterrylene and dicoronylene is about 17.9 Å. Improved synthetic procedures of synthesis are presented, and the resulting VLPAHs were isolated and recognized from their characteristic electronic absorption spectra. The precursor PAHs used in the Scholl's synthesis where studied by differential scanning calorimetry (DSC), and the thermal behavior of the resulting VLPAHs was studied by thermogravimetric analysis and differential thermal analysis (TGA-DTA). The VLPAHs hexabenzocoronene (HBC), quaterrylene and dicoronylene show a trend to carbonization (growth of the laminar molecules into stacked and large graphene sheets) when heated slowly to high temperature in a nitrogen atmosphere.

The experimentally well-known convergence of solvation entropies and enthalpies of different small hydrophobic solutes at universal temperatures seems to indicate that hydrophobic solvation is dominated by universal water features and not so much by solute specifics. The reported convergence of the denaturing entropy of a group of different proteins at roughly the same temperature as hydrophobic solutes was consequently argued to indicate that the denaturing entropy of proteins is dominated by the hydrophobic effect and used to estimate the hydrophobic contribution to protein stability. However, this appealing picture was subsequently questioned since the initially claimed universal convergence of denaturing entropies holds only for a small subset of proteins; for a larger data collection no convergence is seen. We report extensive simulation results for the solvation of small spherical solutes in explicit water with varying solute-water potentials. We show that convergence of solvation properties for solutes of different radii exists but that the convergence temperatures depend sensitively on solute-water potential features such as stiffness of the repulsive part and attraction strength, not so much on the attraction range. Accordingly, convergence of solvation properties is only expected for solutes of a homologous series that differ in the number of one species of subunits (which attests to the additivity of solvation properties) or solutes that are characterized by similar solute-water interaction potentials. In contrast, for peptides that arguably consist of multiple groups with widely disperse interactions with water, it means that thermodynamic convergence at a universal temperature cannot be expected, in general, in agreement with experimental results.

Ligand-Protein Interaction Studied by Computer Simulation and Time-Resolved X-Ray Crystallography

Experimentally, it has been determined that at large scales graphene sheets grown on amorphous or liquid copper have less defects than graphene sheets grown on crystalline copper. No information has been obtained however for small-scale graphene flakes. Understanding defects in flakes is crucial as they serve as intermediates in large-scale graphene growth. Our goal in this work is to quantify defects in graphene flakes grown on different copper substrates. We performed a computational study using Density Functional Theory calculations on a copper-graphene system. A global minima search was performed using the Minima Hopping algorithm to find multiple graphene isomers that can appear on different substrates. As a model of copper substrate, we used a 112 copper atom cluster and as a model of graphene flake, we used 40 carbon atoms on top of the copper surface. The system was placed in vacuum to guarantee no interaction between images. The global minima search identified multiple graphene isomers on crystalline and amorphous substrates with dangling bonds and with all defects located on the edge. However, graphene on amorphous copper exhibits a higher frequency and greater variety of polygon defects than on crystalline copper. To estimate inner defects, a Stone-Wales defect was introduced, showing higher formation energy on amorphous surfaces than crystalline ones. These findings show that substrate type influences defect formation in graphene isomers. As a result, we propose that in the growth of graphene sheets the flakes on amorphous surfaces will have much lower inner defects (because of higher energy formation) while the edge defects will reconstruct more easily (having more available isomers and relaxation paths). The combination of both mechanisms could then be a contributing factor to the final formation of a more pristine graphene sheet in the amorphous surface.

The distribution of hydrophobic solutes, such as methane, enclosed in a nanosized water droplet contained in a reverse micelle of diameter 2.82 nm is investigated using Monte Carlo simulations. The effect of the hydrophobic solute's atomic diameter on the solute-solute potential of mean force is also studied. The study reveals that confinement has a strong influence on the solute's tendency to associate. The potential of mean force exhibits only a single minimum, indicating that the contact pair is the only stable configuration between solutes. The solvent-separated pair that is universally observed for small solutes in bulk water is conspicuously absent. This enhanced hydrophobic effect is attributed to the lack of sufficient water to completely hydrate and stabilize the solvent-separated configurations. The study is expected to be important in understanding the role of hydrophobic forces during protein folding and nucleation under confinement.