Empirical Potential Structure Refinement Simulations Research Articles

Microscopic Structure of Liquid Nitric Oxide.

The microscopic structure of nitric oxide is investigated using neutron scattering experiments. The measurements are performed at various temperatures between 120 and 144 K and at pressures between 1.1 and 9 bar. Using the technique of empirical potential structure refinement (EPSR), our results show that the dimer is the main form, around 80%, of nitric oxide in the liquid phase at 120 K, but the degree of dissociation to monomers increases with increasing temperature. The reported degree of dissociation of dimers, and its trend with increasing temperature, is consistent with earlier measurements and studies. It is also shown that nonplanar dimers are not inconsistent with the diffraction data and that the possibility of nitric oxide molecules forming longer oligomers, consisting of bonded nitrogen atoms along the backbone, cannot be ruled out in the liquid. A molecular dynamics simulation is used to compare the present EPSR simulations with an earlier proposed intermolecular potential for the liquid.

Linking excess order to co-solvent aggregation in solvent mixtures

Small amphiphilic molecules dissolved in alcohol–water mixtures have been seen to have a tendency to aggregate. Here we present a thorough neutron diffraction experiment, aided by H/D isotopic substitution and empirical potential structure refinement simulations of four mixtures of tert-butyl alcohol (x=0.03 molar) in methanol and water (x=0.27, 0.54, 0.73, 1.0 molar). The tert-butyl alcohol is found to segregate in the methanol rich regions at all concentrations; at x=0.27 the mixture is found to be a bi-percolating mixture, with water forming one interconnected cluster, and methanol and tert-butyl alcohol (apolar–apolar) forming another. At the same x=0.27 concentration, tert-butyl alcohol molecules become closer each other at this concentration, forming more dimers than at the other concentrations, and even trimers. Results are discussed in terms of the ability of water molecules to form flexible tetrahedral networks.

Is water one liquid or two?

The idea that water is a mixture of two distinct states is analyzed in some detail. It is shown that the known compressibility of water is in fact sufficiently small that for a volume of water of size 1 nm3, the density fluctuations are of order 4% of the average density. This is much smaller than the ≈25% density fluctuations that would be required for significant regions of high and low density water to occur on this volume scale. It is also pointed out that the density fluctuations in water are, if anything, smaller than those that occur in other common liquids which do not have the anomalous properties of water. It is shown that if the distribution of density fluctuations is unimodal, the system is in the one-phase region, and if bimodal, it is in the two-phase region. None of the liquid or amorphous phases of water explored in this work give any sign of being in the two-phase region. Existing neutron and X-ray scattering data on water in the amorphous phases, and in the stable liquid phases as a function pressure and temperature, are subject to a new set of empirical potential structure refinement simulations. These simulations are interrogated for their configurational entropy, using a spherical harmonic reconstruction of the full orientational pair correlation function. It is shown that the excess pair entropy derived from this function, plus the known perfect gas contributions, give a reasonable account of the total entropy of water, within the likely errors. This estimated entropy follows the expected declining trend with decreasing temperature. Evidence that higher density water will have higher entropy than lower density water emerges, in accordance with what is expected from the negative thermal expansion coefficient of water at low temperatures. However, this entropy increase is not large and goes through a maximum before declining at yet higher densities and pressures, in a manner reminiscent of what has been previously observed in the diffusion coefficient as a function of pressure. There is no evidence that ambient water can be regarded as patches of high density, high entropy and low density, low entropy liquid, as some have claimed, since high density water has a similar entropy to low density water. There is some evidence that the distinction between these two states will become more pronounced as the temperature is lowered. Extensive discussion of the use of order parameters to describe water structure is given, and it is pointed out that these indices generally cannot be used to infer two-state behavior.

Water Participation in Catalysis: An Atomistic Approach to Solvent Effects in the Catalytic Isomerization of Allylic Alcohols

We study the intermediate of the reaction between a ruthenium complex and 1-propen-3-ol in water using an atomistic approach for gaining information about the conformation and dynamics of complex molecules in aqueous solution, which combines density-functional-theory-based ab initio molecular dynamics and neutron scattering data based on empirical potential structure refinement simulations. We apply our method to the study of the water-soluble η2-allylic complex [RuCp(exo-η2-CH2═CH–CH2–OH)(PTA)2]+ (2) (PTA = 1,3,5-triaza-7-phosphaadamantane), an important intermediate in the isomerization of 1-propen-3-ol into propanal catalyzed by {RuCp(H2O-κO)(PTA)2}+. We identify the factors responsible for the stabilization of a specific conformer of 2 in water solution and we examine the involvement of water molecules in the formation of this species. In particular, we show that long-lived (ca. 10 ps) bonded chains of water molecules play a crucial role in influencing the conformation and, potentially, the chemical r...

Empirical potential structure refinement of semi-crystalline polymer systems: polytetrafluoroethylene and polychlorotrifluoroethylene

Empirical potential structure refinement (EPSR) simulations are performed on total neutron scattering data from powder samples of polytetrafluoroethylene (PTFE) and polychlorotrifluoroethylene (PCTFE), both at 300 K. Starting from single strands of polymer consisting of between 30 and 60 monomers of tetrafluoroethylene and chlorotrifluoroethylene in each case, hexagonal simulation cells are constructed consisting of an array 25 (5×5) such strands placed on a hexagonal lattice. Allowed simulation moves are polymer translation moves along all three Cartesian axes, whole polymer rotations about the polymer axis, and individual atom moves within each polymer. For PTFE a number of Bragg peaks are visible in the scattering data and these are found to be consistent with a lattice spacing a(=b) = 5.69(1) Å with a dihedral angle along the (helical) chain of 166° which gives a repeat distance along the chain (c-axis) of ∼19.6 Å. The positions of the Bragg peaks are well reproduced by this model, although there is a mismatch in the amplitudes of some of the higher order reflections between simulation and data. For PCTFE there is only one visible Bragg peak (100) which is well reproduced by a hexagonal lattice of atactic parallel polymers with a spacing of a(=b) = 6.37(1) Å. In this case the absence of distinct reflections along the polymer c-axis makes characterization of the internal dihedral angle difficult, but a model with a dihedral angle of 166° was less successful at fitting the diffuse scattering than a model where this angle was set to 180°, giving a nearly straight trans (zig-zag) structure. For PCTFE little change in structure could be discerned when the material was heated to 550 K, apart from a slight increase in lattice spacing. In both cases there is substantial diffuse scattering between the Bragg peaks, and this is correctly replicated by the EPSR simulations.

Density profile of water confined in cylindrical pores in MCM-41 silica

Recently, water absorbed in the porous silica material MCM-41-S15 has been used to demonstrate an apparent fragile to strong dynamical crossover on cooling below ∼220 K, and also to claim that the density of confined water reaches a minimum at a temperature around 200 K. Both of these behaviours are purported to arise from the crossing of a Widom line above a conjectured liquid–liquid critical point in bulk water. Here it is shown that traditional estimates of the pore diameter in this porous silica material (of order 15 Å) are too small to allow the amount of water that is observed to be absorbed by these materials (around 0.5 g H2O/g substrate) to be absorbed only inside the pore. Either the additional water is absorbed on the surface of the silica particles and outside the pores, or else the pores are larger than the traditional estimates. In addition the low Q Bragg intensities from a sample of MCM-41-S15 porous silica under different dry and wet conditions and with different hydrogen isotopes are simulated using a simple model of the water and silica density profile across the pore. It is found the best agreement of these intensities with experimental data is shown by assuming the much larger pore diameter of 25 Å (radius 12.5 Å). Qualitative agreement is found between these simulated density profiles and those found in recent empirical potential structure refinement simulations of the same data, even though the latter data did not specifically include the Bragg peaks in the structure refinement. It is shown that the change in the (100) peak intensity on cooling from 300 to 210 K, which previously has been ascribed to a change in density of the confined water on cooling, can equally be ascribed to a change in density profile at constant average density. It is further pointed out that, independent of whether the pore diameter really is as large as 25 Å or whether a significant amount of water is absorbed outside the pore, the earlier reports of a dynamic crossover in supercooled confined water could in fact be a crystallization transition in the larger pore or surface water.

A Monte Carlo revisiting of N-methylformamide and acetone

The pure liquids N-methylformamide and acetone have been revisited via Monte Carlo simulations in the NTP ensemble at 1 atm and 25 °C. The molecules are all-atom rigid structures, and the intermolecular potential used is the classical 6-12 Lennard-Jones plus Coulomb. The theoretical g(r)s of both liquids were compared with those obtained from neutron diffraction and empirical potential structure refinement simulations. The results point to the existence of H-bonds driving the N-methylformamide structure, while in acetone the correlations are dipole moment oriented. The structure of the liquid N-methylformamide is mainly guided by a dimer whose molecules are arranged in such a way that the angle between their dipole moments is 73°, while liquid acetone is much less organized and the orientation of the molecules changes from an antiparallel dipolar correlation at short distances to more parallel alignments of the molecular dipole moments for larger distances.

Investigation on the structure of liquid N-methylformamide–dimethylsulfoxide mixtures

The structures of liquid mixtures of N-methylformamide (NMF) and dimethyl sulfoxide (DMSO) at two concentrations (80% and 50% NMF) are investigated using a combination of neutron diffraction augmented with isotopic substitution and empirical potential structure refinement simulations. The results indicate that the NMF and DMSO molecules are hydrogen-bonded to one another with a preference for NMF–DMSO hydrogen bonding, compared to the NMF–NMF ones. The liquid is orientationally structured as a consequence of these hydrogen bonds between molecules. NMF–DMSO dimers are very stable species in the bulk of the mixture. The structure of the dimers is such that the angle between the molecular dipole moments is around 60°. The NMF molecules are well solvated in DMSO with potential implications for peptides solvation in this solvent.

Determination of Fe3+ sites in a NaFeSi2O6 glass by neutron diffraction with isotopic substitution coupled with numerical simulation

Isotopic substitution in neutron diffraction combined with empirical potential structure refinement simulations has been employed to probe the sites occupied by Fe3+ and Fe2+ in a NaFeSi2O6 glass. This study reveals the presence of two populations of Fe3+ sites. 95% of Fe3+ is in tetrahedral sites (dFe3+–O=1.866±0.001Å), as the remainder ferric iron and ferrous iron (∼20% of total Fe) are five coordinated.

Tests of the empirical potential structure refinement method and a new method of application to neutron diffraction data on water

Empirical potential structure refinement (EPSR) is a method for developing a structural model of a liquid for which diffraction measurements are available. The EPSR technique involves refining a starting interatomic potential energy function in a way that produces the best possible agreement between the simulated and measured site-site partial structure factors. Here a series of test simulations are performed to establish how well the EPSR method can recover the interatomic potential for a single component fluid of Lennard-Jones particles, and for a binary fluid consisting of charged atoms interacting at short range by a Lennard-Jones potential. Special attention is given to the problem of developing an accurate interatomic potential for water using these procedures. An alternative method for perturbing the starting potential is used to obtain the best possible fit to the diffraction data. The resulting parametrization of the water potential is in contrast to many existing effective potentials for water, and indicates that water molecules in the liquid at ambient conditions are highly polarized, as has been suggested in recent ‘first-principles’ simulations of water. Three-body correlation functions and spatial density functions derived from the EPSR simulations show excellent agreement with those obtained with the model potential simulations. However, the potentials extracted by EPSR are found to depend on the constraints applied to the hardness of the core potential and the energy and pressure of the simulation, even when the fits to the data are equally good. It is concluded that performing EPSR on diffraction data can be used as a good test for interatomic potentials and to derive reliable many-body structures in the liquid state, but cannot on its own be used to derive a reliable set of site-site pair potentials for a particular system.