Site Radial Distribution Functions Research Articles

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids.

We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid-water molar ratios. It was shown that there is a non-negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse-grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles.

Molecular Dynamics Simulation for the Binary Mixtures of High Pressure Carbon Dioxide and Ionic Liquids

Molecular dynamics simulation with an all-atom force field has been carried out on the two binary systems of [bmim][PF6]-CO2 and [bmim][NO3]-CO2 to study the transport properties, volume expansion and microstructures. It was found that addition of CO2 in the liquid phase can greatly decrease the viscosity of ionic liquids (ILs) and increase their diffusion coefficient obviously. Furthermore, the volume expansion of ionic liquids was found to increase with the increase of the mole fraction of CO2 in the liquid phase but less than 35% for the two simulated systems, which had a significant difference with CO2 expanded organic solvents. The main reason was that there were some void spaces inter and intra the molecules of ionic liquids. Finally, site to site radial distribution functions and corresponding number integrals were investigated and it was found that the change of microstructures of ILs by addition CO2 had a great influence on the properties of ILs.

Effects of methanol on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution

The effect of methanol on the hydrogen bonding structure and dynamics in aqueous solution of N-methylacetamide (NMA) is investigated by classical molecular dynamics simulations. The modifications of structure and interaction between water and NMA in presence of methanol are calculated by different site–site radial distribution functions and average interaction energies between these species in the solution. It is observed that the methyl–methyl interaction between NMA and methanol prefers even at lower methanol concentration. The slower translational and rotational dynamics of NMA is observed in water–methanol mixtures as it is found for both water and methanol in the mixtures. The lifetime and structural-relaxation time of NMA–water and NMA–methanol hydrogen bonds show a strong increase with addition of methanol in the solution, whereas the change is not linearly dependent on concentration. It is also found that the lifetime of water–water and water–methanol hydrogen bond increases with increasing methanol concentration in the solution.

Computer simulation as a tool for the interpretation of total scattering data from glasses and liquids

Ever since the pioneering work by McGreevy and Pusztai [Mol. Simul. 1 (1988), pp. 359–367] in developing the reverse Monte Carlo (RMC) technique, computer simulation has become a widely used tool for the interpretation of total scattering data from liquid, glassy and crystalline materials. A variant on this approach, empirical potential structure refinement (EPSR), was introduced in 1996 for the study of molecular materials. Both approaches perform routine Monte Carlo simulations of the systems under study but derive their structural information partly from the assumed knowledge of the system in question (such as density, limits on atomic overlap, likely forces between atoms and molecular structure) and partly from radiation total scattering data, which contain weighted sums of the relevant site–site radial distribution functions (rdfs) via the corresponding partial structure factors. The latter information is carried in the form of a fit factor (RMC) or empirical potential (EPSR) which is included in the Hamiltonian used to assess whether individual atom or molecule moves should be accepted or rejected. The present account illustrates the use of EPSR to investigate two well-known liquids, water and dimethylsulphoxide. In the former case, it is possible, at least in principle, to recover the set of three site–site partial structure factors directly from the available scattering data. In the latter case, this is not possible, even in principle, because there are insufficient isotope or X-ray contrasts available to recover the full set of 10 partial structure factors needed to define the structure of the liquid. Although the information content of the data-sets for each liquid is different, EPSR is able to distinguish the intermolecular force field between models in both cases, and thus produce a set of site–site rdfs which are both consistent with the scattering data and derived from a non-overlapping 3D distribution of molecules.

Pronounced Microheterogeneity in a Sorbitol–Water Mixture Observed through Variable Temperature Neutron Scattering

In this study, the structure of concentrated d-sorbitol-water mixtures is studied by wide- and small-angle neutron scattering (WANS and SANS) as a function of temperature. The mixtures are prepared using both deuterated and regular sorbitol and water at a molar fraction of sorbitol of 0.19 (equivalent to 70% by weight of regular sorbitol in water). Retention of an amorphous structure (i.e., absence of crystallinity) is confirmed for this system over the entire temperature range, 100-298 K. The glass transition temperature, Tg, is found from differential scanning calorimetry to be approximately 200 K. WANS data are analyzed using empirical potential structure refinement, to obtain the site-site radial distribution functions (RDFs) and coordination numbers. This analysis reveals the presence of nanoscaled water clusters surrounded by (and interacting with) sorbitol molecules. The water clusters appear more structured compared to bulk water and, especially at the lowest temperatures, resemble the structure of low-density amorphous ice (LDA). Upon cooling to 100 K the peaks in the water RDFs become markedly sharper, with increased coordination number, indicating enhanced local (nanometer-scale) ordering, with changes taking place both above and well below the Tg. On the mesoscopic (submicrometer) scale, although there are no changes between 298 and 213 K, cooling the sample to 100 K results in a significant increase in the SANS signal, which is indicative of pronounced inhomogeneities. This increase in the scattering is partly reversed during heating, although some hysteresis is observed. Furthermore, a power law analysis of the SANS data indicates the existence of domains with well-defined interfaces on the submicrometer length scale, probably as a result of the appearance and growth of microscopic voids in the glassy matrix. Because of the unusual combination of small and wide scattering data used here, the present results provide new physical insight into the structure of aqueous glasses over a broad temperature and length scale, leading to an improved understanding of the mechanisms of temperature- and water-induced (de)stabilization of various systems, including proteins, pharmaceuticals, and biological objects.

Thermodynamics and structure of the {water + methanol} system viewed from three simple additive pair-wise intermolecular potentials based on the rigid molecule approximation

The ability of three additive pair-wise intermolecular potentials to reproduce both thermodynamics and structure of the {methanol + water} system is analysed in detail using Metropolis Monte Carlo simulations. The three potentials were constructed using the OPLS model for methanol and for water, in each case, were used the TIP4P, TIP4P/2005, and TIP4P/ice, respectively. For all the potentials, the Lorentz–Berthelot combining rule was considered to calculate water–methanol cross interactions. A wide set of first- and second-order excess thermodynamic derivatives and the site–site radial distribution functions were chosen for the study. The properties were obtained at room conditions over the whole composition range and were critically compared with selected experimental data. It turns out that the simulation results of the different potentials show no qualitative differences in the radial distribution functions whereas that the excess thermodynamic properties usually decreases in the sense TIP4P > TIP4P/2005 > TIP4P/ice. The best agreement with the experiments has been found for the potential that uses the TIP4P/2005 model which demonstrates that using potentials based on phase diagram calculations significantly improve the results for this mixture. However, even in this case only partial success was found. As regards thermodynamics, it has been detected problems to describe the excess compressibility and the excess molar enthalpy. As regards structure, although it predicts clustering of methanol molecules via methyl groups after mixing, it was unable to reproduce the preservation of the pure water structure in the mixture, a well-established phenomenon observed by neutron scattering experiments.

Absorption of CO2 in the Ionic Liquid 1-n-Hexyl-3-methylimidazolium Tris(pentafluoroethyl)trifluorophosphate ([hmim][FEP]): A Molecular View by Computer Simulations

Using a computational screening methodology, we predicted (AIChE J. 2008, 54, 2717) that the anion tris(pentafluoroethyl)trifluorophosphate ([FEP]) should increase the solubility of CO2 in ionic liquids (ILs) relative to a wide range of conventional anions. This prediction was confirmed experimentally. In this work, we develop a united-atom force field for the [FEP] anion and use the continuous fractional component Monte Carlo (CFC MC) method to predict CO2 absorption isotherms in 1-n-hexyl-3-methylimidazolium ([hmim]) [FEP] at 298.2 and 323.2 K and pressures up to 20.0 bar. The simulated isotherms overestimate the solubility of CO2 by about 20% but capture the experimental trends quite well. Additional Monte Carlo (MC) and molecular dynamics (MD) simulations are performed to study the mechanisms of CO2 absorption in [hmim][FEP] and [hmim][PF6]. The site-site radial distribution functions (RDFs) show that CO2 is highly organized around the [PF6] anion due to its symmetry and smaller size, while less ordered distributions were found around [FEP] and [hmim]. However, more CO2 can be found in the first coordination shell of [FEP] compared with [PF6]. The structures of ILs, illustrated by P-P radial distribution functions, change very little upon the addition of as much as 50 mol % CO2. An energetic analysis shows that the van der Waals interactions between CO2 and ILs are generally larger than electrostatic interactions.

Molecular Design of Stable Graphene Nanosheets Dispersions

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.

Time evolution of average rotation axis directions and mean rotation angles of pressurized liquid methyl iodide by molecular dynamics simulation

The rotational motion of liquid methyl iodide has been modelled by molecular dynamics simulations under input parameters optimized from literature values to yield the experimental enthalpy of vaporization and permanent dipole moment of the molecule. First, it is shown that results describing the correlation function of the tumbling motion of the molecules agree reasonably well with some corresponding findings from a spectroscopic Raman study. Second, the rotational motion involving the spinning component around the molecule's symmetry axis was simulated, an effect inaccessible by experiment. Third, and most relevant to the author's interests, a group-theoretical formalism was used that generates the time evolution of the average direction of the average rotation axis as well as the mean rotation angle around it. This approach allowed a more realistic understanding of the effects of density and temperature on molecular rotational motion, as well as a better quantification of the influence of short-time inertial decay, than the common approach of studying orientational correlation data along permanently molecule-fixed axis directions. Fourth, site–site radial distribution functions between neighbouring molecules were simulated, establishing a shielding effect that prevents a carbon atom from approaching any other site by their closest distance.

CO 2–water supercritical mixtures: Test of a potential model against neutron diffraction data

A neutron diffraction experiment on supercritical mixtures of water and CO 2 at two concentrations is presented. Data are analyzed within the EPSR framework and the water–water and water–CO 2 radial distribution functions are compared with those calculated by a Molecular Dynamics simulation performed by using the TIPS2 and EPM-M potential models for water and CO 2 respectively. It is found that the Molecular Dynamics simulation reproduces the overall shape of the site–site radial distribution functions, although missing a few subtle changes brought along when the CO 2 concentration is increased.

Water structure around trehalose

A diluted solution of trehalose in water has been investigated by means of neutron diffraction with isotopic H/D substitution of the water hydrogens. Data have been analyzed in terms of site–site radial distribution functions, via the EPSR simulation code. This is the first time that the capabilities of this data refinement method are tested against neutron diffraction data of a complex carbohydrate molecule. A small perturbation of water hydration shell and short hydrogen bonds between trehalose oxygens and water hydrogens has been evidenced.

Solvation by benzene: molecular dynamics simulation of orientational motion, translational diffusion, and site–site radial distributions of the solutes di- and trichloromethane (chloroform)

By a standard, proven molecular dynamics procedure we generated individual equilibrium systems of dichloromethane and trichloromethane (chloroform) in benzene, each at equimolar concentration, as well as those of the neat components. We analysed the orientational dynamics of the C–H bond direction of chloroform in benzene-solvated and neat chloroform by the tumbling motion of its l = 1 and l = 2 Legendre polynomial auto-correlations between 250 and 438 K at iso-density conditions specific to the solution and neat system, respectively. We find that solvent benzene exerts a hindering effect on the orientational motion of chloroform over its neat state under an activation energy of 3.8 kJ mol−1, although the density of the solution is less than that of the neat solute. The hindering effect diminishes with increasing kinetic energy to eventually disappear near the critical region. Probing benzene as solute within an equimolar solution with chloroform does not show a correspondingly increased hindering of the orientational motion of the (in-plane) axes of benzene. The short-time rotational regimes at ambient conditions were examined by simulating the auto-correlation functions of the three components of angular velocity, the results implying that the coherence in the correlation of the primary rotational variable is rather short-lived. The long-time translational–diffusional characteristics were examined by the mean-square distance of chloroform travelled during 100 ps, establishing that chloroform diffuses slightly faster in equimolar solution with benzene than in its neat state—most likely on account of more favourable free volume conditions in the solution. From various site–site radial distribution functions between solute and solvent species and from appropriate atom–atom distances between nearest-neighbour molecules, we found that chloroform aggregates, to a minimum, with two nearest-neighbour benzene shells in a three-member configuration. We conjecture that the hindering effect by benzene on the chloroform solute is caused by its temporary entrapment, on time scales of the order of 0.2 ps, in cages from momentary perpendicular and parallel configurations of nearest- and near-neighbour benzene molecules. We find no convincing evidence for the existence of a stable, symmetric-top 1:1 chloroform–benzene complex. Solute species dichloromethane in benzene exhibits similar, but less pronounced, solution dynamics.

Enhanced near-neighbour aggregation of dichloro- and trichloromethane in liquid methane solution from molecular dynamics simulation of radial site–site distribution functions: a simple predictor of solute–solvent compatibility

Molecular dynamics simulations have been performed for a range of equi-site and site–site radial distribution functions for the five-atom halomethane species dichloro-, trichloro-, and tetrachloromethane dissolved in the low-molecular weight hydrocarbons liquefied methane and cyclopropane, with the general aim of using this approach to predict good or bad solvent characteristics. It was found that methane solutions of dichloro- and trichloromethane showed an enhancement of near-neighbour occupancy, the methane solvent seemingly exhibiting a phobic, structure-promoting solvation behaviour towards the two solutes by increasing the number of nearest neighbours above the values that would result from a pure dilution effect caused by the solvent. It was verified that there were no significant regions of solid-like conformations nor remnants of imperfect average homogeneity within the system at the necessarily low temperature (183 K). On the other hand, simulated site–site radial functions with solvents tetrachloromethane and cyclopropane indicate normal solution characteristics towards solutes dichloro- and trichloromethane. The cause of the phobic solvation behaviour of solvent liquid methane towards di- and trichloromethane is not obvious, except that it seemingly involves the presence of hydrogen atoms on the solute species because the site–site centre-of-mass radial distribution functions of tetrachloromethane in liquid methane implied normal solution behaviour.

Monte Carlo simulations of CO2-expanded acetonitrile

The structure and phase-equilibrium properties of CO2-expanded acetonitrile (MeCN) were examined using Gibbs Ensemble Monte Carlo simulations. The results showed that the mole fraction of the CO2 in the binary system increased linearly with pressure and the predicted volume expansion of the liquid phase with pressure is nonlinear and in agreement with experiment. The site–site radial distribution functions (RDFs) were determined for this binary mixture, which show that the homomolecular CO2–CO2 and heteromolecular CO2–MeCN do not exhibit a significant dependence on CO2 mole fraction. The only major structural change that is seen to occur as the CO2 mole fraction is increased in the mixture is a decrease in the fraction of nearest neighbour MeCN molecules with parallel dipole orientations.

Impact of urea on water structure: a clue to its properties as a denaturant?

A new investigation of the structure of urea–water solutions at a mole ratio of 1 urea to 4 water molecules is described. Neutron diffraction is used in conjunction with isotope labelling on the water and urea hydrogen atoms and on the nitrogen atom of urea. The diffraction data are analysed using the empirical potential structure refinement procedure to yield a set of site–site radial distribution functions and spatial density functions that are consistent with the diffraction data. The results are discussed in relation to recent and past X-ray and neutron diffraction experiments and theoretical studies of this system. It is found that urea incorporates readily into water, forming pronounced hydrogen bonds with water at both the amine and carbonyl headgroups. In addition the urea also hydrogen bonds to itself, forming chains or clusters consisting of up to approximately 60 urea molecules in a cluster. There, is however, little or no evidence of urea segregating itself from water, in marked contrast to a recent study of the methanol–water system. This behaviour is discussed in the context of the great propensity of urea to effect protein denaturation.

Dynamic and structural behavior of different rigid nonpolarizable models of water

The local structure and the dynamical behavior of water have been analyzed in two different regimes (the dense isochore of 0.995 g/cm2 and the supercritical isotherm of 673 K) through four rigid nonpolarizable models of water. An important change in the slope of temperature dependence of the self-diffusion coefficient at ρ=0.995 has been observed at T≈450 K, showing two main regions that are related to a change on the activation energy of the process (originated for a change of the structure of the first solvation shell from a tetrahedral to dodecahedral arrangement). The local orientational structure of water has been analyzed through the use of tetrahedral order parameters q. A direct relation between q and D has been observed for all models showing some kind of master curve up to 450 K at the 0.995 g/cm3 isochore. The structure of the system at short and large radial distances has been analyzed through a decomposition of the site–site radial distribution functions in terms of spherical harmonics, and a three-dimensional picture of the total pair distribution function has been reconstructed from this set of spherical harmonic projections.

Experimental determination of the site–site radial distribution functions of supercooled ultrapure bulk water

Neutron diffraction data on three isotopically substituted samples of liquid water in the supercooled regime are presented. Supercooling of ultrapure water has been achieved by means of a polytetrafluoroethylene coating on a standard vanadium sample container. Supercooling water to T=267 K, with density ρ=100.2 atoms/nm3, at ambient pressure gives a shift of the first peak of the three partial structure factors toward lower wave numbers, while the second peak of the oxygen–oxygen partial structure factor moves outwards compared to ambient water. The present data in Q space are compatible with previous x-ray experiments performed on supercooled water. Moreover the partial radial distribution functions obtained here for the first time for the bulk liquid at this thermodynamic state compare well with previous experiments performed at higher pressure.

Structure of tert-Butyl Alcohol−Water Mixtures Studied by the RISM Theory

We calculated the site−site radial distribution functions for binary mixtures of tert-butyl alcohol (TBA) and water over the whole range of TBA molar fraction. The description uses the reference interaction site model (RISM) integral equation theory in the dielectrically consistent approach of Perkyns and Pettitt (DRISM), and the closure approximation of Kovalenko and Hirata (KH) providing appropriate description for association of polar molecular species of density ranging from gas to liquid. We employed the extended simple point charge (SPC/E) model for water, and the optimized potential for liquid simulations (OPLS) force field for TBA. The partial radial distribution functions obtained for the TBA−water mixture are in qualitative agreement with those available from neutron diffraction experiments and molecular dynamics simulations. It is found that hydrogen bonds between all species are enhanced with rise of the TBA concentration. The tetrahedral-like network of hydrogen bonding in dilute TBA aqueous solution gradually turns into the zigzag-like structure for a high TBA concentration. In dilute aqueous solution, TBA molecules cluster by the hydrophobic methyl groups, whereas their hydroxyl groups are incorporated into the water hydrogen-bonding cage surrounding the TBA aggregate. In concentrated TBA, water as well as TBA molecules associate into the zigzag-like hydrogen-bonding chains. The present work shows that the RISM/KH theory is able to qualitatively predict the association structure of alcohol−water liquid mixtures.

Hydration structures of the squarate dianion C 4O 42−. A combined molecular dynamics simulation and quantum ab initio study

Molecular dynamics (MD) simulations are used to determine the structure of the first solvation shell around a single monocyclic oxocarbon dianion C 4O 4 2− in aqueous solution. The simulations were carried out using a fixed-geometry model for the oxocarbon with excess partial charges equally distributed over the oxygen atoms and the well-known SPC/E model for water. Quantum ab initio calculations for an isolated oxocarbon at different levels of approximation indicate that the such a description of the squarate dianion should be fairly accurate for the study of solvation structures. Analysis of a complete set of solute–solvent site–site radial distribution functions and hydrogen (H)-bonding distributions obtained from the MD simulations, indicates a well-defined first solvation shell consisting of approximately 18 water molecules. About 12 of these molecules are tightly H-bonded to the oxocarbon (an average of 3 molecules per oxygen atom) forming a highly symmetric solute–solvent complex, while the remaining six water molecules are more loosely distributed above and below the oxocarbon plane. The structure of a cluster consisting of a dianion and 12 water molecules was then examined through ab initio calculations at the Hartree–Fock 6-31G(d,p) level. The optimized ab initio structure of the cluster is in excellent agreement with the MD results.

Realization of Three-Dimensional Solvation-Structures from the Site–Site Radial Distribution Functions in Liquids

Abstract We propose a new procedure to realize a three-dimensional (3D) solvation structure around a solute molecule from a set of radial distribution functions (RDF), or distance information. The method consists of the minimization of a penalty function defined as the mean-square difference of the solute–solvent interatomic distances obtained from trial 3D configurations and from target RDFs. The hydration structures around several different solute molecules are visualized to demonstrate the method. The solvation structures realized with the present method correspond to the most plausible solvation structure (MPSS), which looks like a “snap shot” of the molecular dynamics trajectory. However, the MPSS is essentially different from the “snap shot,” since it represents an average configuration, and is therefore an observable quantity. The present procedure was originally developed for analyses of the RDF results obtained from the reference interaction site model (RISM), but can be applied straightforwardly to RDFs from other sources, such as molecular simulations and scattering experiments.