The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.     

Stability of Ca-montmorillonite hydrates: a computer simulation study

Classic simulations are used to study interlayer structure, swelling curves, and stability of Ca-montmorillonite hydrates. For this purpose, NP(zz)T and muP(zz)T ensembles are sampled for ground level and given burial conditions. For ground level conditions, a double layer hydrate having 15.0 A of basal spacing is the predominant state for relative vapor pressures (p/p0) ranging 0.6-1.0. A triple hydrate counting on 17.9 A of interlaminar distance was also found stable for p/p0 = 1.0. For low vapor pressures, the system may produce a less hydrated but still double layer state with 13.5 A or even a single layer hydrate with 12.2 A of interlaminar distance. This depends on the established initial conditions. On the other hand, the effect of burial conditions is two sided. It was found that it enhances dehydration for all vapor pressures except for saturation, where swelling is promoted.     

Structure of star-burst dendrimers: a comparison between small angle x-ray scattering and computer simulation results

We investigated the generation dependent shape and internal structure of star-burst dendrimers under good solvent conditions using small angle x-ray scattering and molecular modeling. Measurements have been performed on poly(amidoamine) dendrimers with generations ranging from g=0 up to g=8 at low concentrations in methanol. We described the static form factor P(q) by a model taking into account the compact, globular shape as well as the loose, polymeric character of dendrimers. Monomer distributions within dendrimers are of special interest for potential applications and have been characterized by the pair correlation function gamma(r), as well as by the monomer and end-group density profile, rho(r) and rho(e)(r), respectively. Monomer density profiles and gamma(r) can be derived from P(q) by modeling and via a model independent approach using the inverse Fourier transformation algorithm first introduced by Glatter. Experimental results are compared with computer simulations performed for single dendrimers of various generations using the cooperative motion algorithm. The simulation gives direct access to gamma(r) and rho(r), allows an independent determination of P(q), and yields in addition to the scattering experiment information about the distribution of the end groups. Excellent qualitative agreement between experiment and simulation has been found.     

Hydrogen bonding in liquid alcohols: a computer simulation study

A series of molecular dynamics simulations has been performed to investigate hydrogen bonding in liquid alcohols. The systems considered have been methanol, ethanol, ethylene glycol and glycerol at 298 K. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed. The results are compared with those corresponding to liquid water.     

A conformational study of bafilomycin A1 by x-ray crystallography and nmr techniques

We report the structure determination of bafilomycin A₁ by X-ray crystallography and a reassignment of the ¹H and ¹³C NMR spectra. By the measurement of ¹³C NT₁ and n.O.e. values the solution conformation was shown to be indistinguishable from that in the crystal.     

Anesthetic molecules embedded in a lipid membrane: a computer simulation study

The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations. Furthermore, to address the problem of pressure reversal, the effect of pressure on the anesthetic containing membranes is also investigated. In order to ensure sufficient equilibration and adequate sampling, the simulations performed have been at least an order of magnitude longer than the studies reported previously in the literature on general anesthetics. The results obtained can help in resolving several long-standing contradictions concerning the effect of anesthetics, some of which were the consequence of too short simulation time used in several previous studies. More importantly, a number of seeming contradictions are found to originate from the fact that different anesthetic molecules affect the membrane structure differently in several respects. In particular, halothane, being able to weakly hydrogen bound to the ester group of the lipid tails, is found to behave in a markedly different way than the other three molecules considered. Besides, we also found that two changes, namely lateral expansion of the membrane and increasing local disorder in the lipid tails next to the anesthetic molecules, are clearly induced by all four anesthetic molecules tested here in the same way, and both of these effects are reverted by the increase in pressure.     

Adhesive transitions in Newton black films: a computer simulation study

We report molecular dynamics simulations of Newton black films (NBFs), ultra thin films of aqueous solutions stabilized with two monolayers of ionic surfactants, sodium dodecyl sulfate. We show that at low water content conditions and areas per surfactant corresponding to experimental estimates in NBFs, homogeneous films undergo an adhesion "transition," which results in a very thin adhesive film coexisting with a thicker film. We identify the adhesive film with the equilibrium structure of the Newton black film. We provide here a direct microscopic view of the formation of these important structures, which have been observed in experimental studies of emulsions and foams. We also report a detailed investigation of the structural properties and interfacial fluctuation spectrum of the adhesive film. Our analysis relies on the definition of an "intrinsic surface," which is used to remove the averaging effect that the capillary waves have on the film properties.     

Water as a lubricant for graphite: a computer simulation study

The phase state and shear behavior of water confined between parallel graphite sheets are studied using the grand canonical Monte Carlo technique and TIP4P model for water. In describing the water-graphite interaction, two orientation-dependent potentials are tried. Both potentials are fitted to many-body polarizable model predictions for the binding energy and the equilibrium conformation of the water-graphite complex [K. Karapetian and K. D. Jordan in Water in Confining Geometries, edited by V. Buch and J. P. Devlin (Springer, Berlin, 2003), pp. 139-150]. Based on the simulation results, the property of water to serve as a lubricant between the rubbing surfaces of graphitic particles is associated, first, with the capillary condensation of water occurring in graphitic pores of monolayer width and, second, with the fact that the water monolayer compressed between graphite particles retains a liquidlike structure and offers only slight resistance to shear.     

Evaluation of small-angle x-ray scattering data of a Raney-type Ni catalyst with computer simulation

A reverse Monte Carlo-type simulation method was developed for the evaluation of anomalous small-angle x-ray scattering data of a Raney-type Ni catalyst. Based on other experimental data the catalytic Ni particles were modeled as small crystalline cylinders dispersed in the matrix. The average size of the Ni particles and their pair-correlation function were determined. Despite the unknown density of the catalyst, it is shown that each particle has about 2 neighbors in the first neighboring shell independent of the modeling density, and the position of the first peak of the pair-correlation function does not depend on the modeling density. A method was elaborated to get reasonable performance of the Reverse Monte Carlo-type simulation. The scattered intensity was calculated on the basis of probe scattering atoms put inside the cylinders. The effects of the omission of the real number of the atoms, the unknown density, the lack of normalization and the uncertainties in the cross sections were unified in two constants that were determined during the simulation. The method can be used for nanoparticles with other shape, where analytic form factors are complicated, and it may be powerful in the investigation of the usually neglected or simplified inter-particle structure of these systems.     

Arrest of fluid demixing by nanoparticles: a computer simulation study

We use lattice Boltzmann simulations to investigate the formation of arrested structures upon demixing of a binary solvent containing neutrally wetting colloidal particles. Previous simulations for symmetric fluid quenches pointed to the formation of "bijels": bicontinuous interfacially jammed emulsion gels. These should be created when a glassy monolayer of particles forms at the fluid-fluid interface, arresting further demixing and rigidifying the structure. Experimental work has broadly confirmed this scenario, but it shows that bijels can also be formed in volumetrically asymmetric quenches. Here, we present new simulation results for such quenches, compare these to the symmetric case, and find a crossover to an arrested droplet phase at strong asymmetry. We then make extensive new analyses of the postarrest dynamics in our simulated bijel and droplet structures, on time scales comparable to the Brownian time for colloid motion. Our results suggest that, on these intermediate time scales, the effective activation barrier to ejection of particles from the fluid-fluid interface is smaller by at least 2 orders of magnitude than the corresponding barrier for an isolated particle on a flat interface.     

Helix formation in linear achiral dendronized polymers: a computer simulation study

We present a molecular simulation study of the structure of linear dendronized polymers. We use excluded volume interactions in the context of a generic coarse grained molecular model whose geometrical parameters are tuned to represent a poly(paraphenylene) backbone with benzyl ether, Frechet-type dendrons. We apply Monte Carlo sampling in order to investigate the formation of packing-induced chiral structures along the polymer backbone of these chemically achiral systems. We find that helical structures can be formed, usually with defects consisting of domains with reversed helical handedness. Clear signs of helical arrangements of the dendrons begin to appear for dendritic generation g=4, while for g=5 these arrangements dominate and perfect helices can be observed as equilibrium structures obtained from certain types of starting configurations.     

Properties of star-branched and linear chains in confined space: a computer simulation study

We studied the properties of simple models of linear and star-branched polymer chains confined in a slit. The polymer chains were built of united atoms and were restricted to a simple cubic lattice. Two macromolecular architectures of the chain linear and star-branched with three branches (of equal length) were studied. The excluded volume was the only potential introduced into the model and thus, the system was athermal. The chains were put between two parallel and impenetrable surfaces. Monte Carlo simulations with a sampling algorithm based on chain’s local changes of conformation were carried out. The differences and similarities in the global size and the structure and of linear and star-branched chains were shown and discussed.     

Chiolite,a case study for combining NMR crystallography,diffraction and structural simulation

Chiolite has been selected as a test case for developing a general approach to solve inorganic structures from powders by combining NMR, modeling, and X-ray diffraction. The different steps of the strategy are successfully performed, building the candidate integrant units using NMR, simulating candidate crystal structures using the computational AASBU method, and checking the consistency of the candidate structures against the diffraction data analyzed with FOX computer program.     

Free volume properties of a linear soft polymer: a computer simulation study

Molecular dynamics simulation of a linear soft polymer has been performed and the free volume properties of the system have been analyzed in detail in terms of the Voronoi polyhedra of the monomers. It is found that there are only small density fluctuations present in the system. The local environment of the monomers is found to be rather spherical, even in comparison with liquids of atoms or small molecules. The monomers are found to be, on average, eight coordinated by their nearest geometric neighbors, including intra-chain and inter-chain ones. The packing of the monomers is found to be rather compact, in a configuration of 1900 monomers there are, on average, only three voids large enough to incorporate a spherical particle as large as a monomer, indicating that the density of the large vacancies in the system is considerably, i.e., by a few orders of magnitude lower than in molecular liquids corresponding to roughly the same reduced densities.     

Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study

The phase behaviour of achiral banana-shaped molecules was studied by computer simulation. The banana-shaped molecules were described by model intermolecular interactions based on the Gay-Berne potential. The characteristic molecular structure was considered by joining two calamitic Gay-Berne particles through a bond to form a biaxial molecule of point symmetry group C 2v with a suitable bending angle. The dependence on temperature of systems of N =1024 rigid banana-shaped molecules with bending angle ϕ=140° has been studied by means of Monte Carlo simulations in the isobaric-isothermal ensemble ( NpT ). On cooling an isotropic system, two phase transitions characterized by phase transition enthalpy, entropy and relative volume change have been observed. For the first time by computer simulation of a many-particle system of banana-shaped molecules, at low temperature an untilted smectic phase showing a global phase biaxiality and a spontaneous local polarization in the layers, i.e. a local polar arrangement of the steric dipoles, with an antiferroelectric-like superstructure could be proven, a phase structure which recently has been discovered experimentally. Additionally, at intermediate temperature a nematic-like phase has been proved, whereas close to the transition to the smectic phase hints of a spontaneous achiral symmetry breaking have been determined. Here, in the absence of a layered structure a helical superstructure has been formed. All phases have been characterized by visual representations of selected configurations, scalar and pseudoscalar correlation functions, and order parameters.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

On the Debye-Waller factor of hexagonal ice: a computer simulation study

We investigate by molecular dynamics (MD) simulations the temperature dependence of the Debye-Waller (DW) factor of hexagonal ice with 25 different proton-disordered configurations. Each initial configuration is composed of 288 water molecules with no net dipole moment. The intermolecular interaction of water is described by TIP4P potential. Each production run of the simulation is 15 ns or longer. We observe a change in slope of the DW factor around 200 K, which cannot be explained within the framework of either classical or quantum harmonic approximation. Configurations generated by MD simulations are subjected to the steepest descent energy minimization. Analysis of the local energy minimum structures reveals that water molecules above 200 K jump to other lattice sites via some local energy minimum structures which contain some water molecules sitting on the locations other than the lattice sites. As time evolves, these defect molecules move back and forth to the lattice sites yielding defect-free structures. Those motions are responsible for the unusual increase in the DW factor at high temperatures. In making a transition from an energy-minimum structure to another one, a small number of water molecules are involved in a highly cooperative fashion. The larger DW factor at higher temperature arises from jump-like motions of water molecules among these locally stable configurations which may or may not be a family of the proton-disordered ice forms satisfying the "ice rule".     

Dynamics in a room-temperature ionic liquid: a computer simulation study of 1,3-dimethylimidazolium chloride

The transport properties and solvation dynamics of model 1,3-dialkylimidazolium chloride melt at 425 K is studied using molecular-dynamics simulations. Long trajectories of a large system have been generated and quantities such as the self-diffusion coefficient of ions, shear viscosity, and ionic conductivity have been calculated. Interestingly, the diffusion of the heavier cation is found to be faster than the anion, in agreement with experiment. The interaction model is found to predict a higher viscosity and lower electrical conductivity compared to experimental estimates. Analysis of the latter calculations points to correlated ion motions in this melt. The solvation time correlation function for dipolar and ionic probes studied using equilibrium simulations exhibits three time components, which include an ultrafast (subpicosecond) part as well as one with a time constant of around 150 ps. The ultrafast solvent relaxation is ascribed to the rattling of anions in their cage, while the slow component could be related to the reorientation of the cations as well as to ion diffusion.     

Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO.

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.     

A critical assessment of capillary condensation and evaporation equations: a computer simulation study

Nonaqueous reverse micelles of brij surfactants are prepared in benzene and ethylammonium nitrate (EAN). The effect of polar head group bulk on reverse micellar size was studied with brij-52, brij-56 and brij-58 whereas the effect of polarity of hydrocarbon chain was investigated taking brij-52 and brij-93 with varying W(s) (W(s)=[EAN]/[surfactant]). Dynamic light scattering (DLS) has been employed to reveal the size and shape of the reverse micelles. Micropolarities of these reverse micelles were investigated by visible spectroscopy using methylene blue (MB) and methyl orange (MO) as molecular optical probes. It has been revealed from the experimental results that with increase in polar head group size reverse micellar size increases. Moreover, it is also observed that with increasing polarity of the hydrocarbon chain the average size of the reverse micelles decreases. It can be concluded that polar head group size and polarity of hydrocarbon chain play important roles in determining reverse micellar size of the brij surfactants apart from the W(s) ratio, nature of the solvent medium, and concentration of the surfactants.