Pair Radial Distribution Functions Research Articles

The hydration of sucrose

The structural and dynamical features of the hydration of sucrose have been derived from a 500 ps molecular dynamics simulation with explicit water molecules. In order to obtain the degree and structure of the solvation of the sucrose solute, radial atomic pair distribution functions have been calculated between selected solute atoms and the water molecules. The analysis provides a molecular hydration number of 37.6 water molecules in the first hydration shell. If the ‘hydration criterion’ is restricted to include oxygen-oxygen distances less than 2.8 Å, an average hydration number of 7 is obtained, which is close to that derived experimentally from viscosity and apparent molar volume. This indicates that the firmly hydrogen bonded water molecules have more impact on the macroscopic properties than the shielding effect formed by the first hydration shell. Both the radial and orientational hydration of acetal and hydroxyl oxygens have been fully characterized. The analysis reveals significant differences between the glycosidic oxygen and the ring oxygen atoms. It also shows that the water structure around the three secondary hydroxyl groups of the pyranosyl moiety is more structured than around the rest of the molecule. This indicates a more perfect hydration of this relatively rigid part of sucrose. The residence times for polar water molecules around the sucrose solute were also characterized. Whereas typical values are in the order of 1 to 2 ps, some extremely long residence times of about 30 ps may occur in the vicinity of the O-3 hydroxyl group of the fructofuranosyl moiety. Extension of the analysis to significant bridging water molecules points towards the existence of two cases (O-2g … Ow … O-3f and O-2g … Ow … O-1f) being populated more than 41% and 66% of the time. In comparison, the direct interresidue hydrogen bond O-2g … O-1f is populated less than 4% of the time. The bridging water between O-2g and O-3f is found in the crystalline complex between sucrose and a lentil lectin. In an aqueous environment the ability of sucrose to establish these water-mediated hydrogen bonds between its two moieties may be relevant in explaining the oversaturation range which prevails before nucleation occurs. It may also have significant implications as far as the sweet-taste elicitation mechanism is concerned.

Neutron diffraction results from some nitrate melts

Results of atomic structure of some molten nitrate systems are discussed. Particular attention is focused on the local co-ordination around the nitrate ions, as determined by the neutron diffraction isotopic substitution technique (NDIS) at the partial pair radial distribution function level. It is shown that the progressive increase in cation size has no effect on the structure of the nitrate ion. However, a trend is observed in the near-neighbour correlations of the cation-anion terms of the three alkali metal nitrates which indicate that the near-neighbour distances scale with the cation size ( r Li + < r Na + < r Rb + ). ammonium ion is often reported to be similar in ionic size to Rb +. A comparison of the cross-terms in their nitrate melts reveals that the effective size of ND 4 + ion in the melt is somewhat larger than the reported value. It is also found that the presence of Ca 2+ brings a significant difference into the ND 4 +-NO 3 − co-ordination. A comparison between experimental and molecular dynamic simulation results shows that refinements in model potentials are required to reproduce experimental details.

Molecular Dynamics Study of the Structure and Dynamics of the Hydration Shell of Alkaline and Alkaline-Earth Metal Cations

Molecular dynamics simulations of hydrated alkaline and alkaline-earth metal cations at room temperature (T = 300 K) were carried out using the CHARMM22 force field. Dynamic and static properties of systems containing one ion and 123 or 525 water molecules were investigated by analysis of trajectories of 1 ns duration and compared to experimental and theoretical results. In addition, the size and the direction of the elementary motions of both the ions and the water molecules were investigated on the scale of the integration time step of 1 fs. Comparison between systems of different size revealed that for the larger system the diffusion coefficient and the number of hydrogen bonds were increased. Radial pair distribution functions and coordination numbers are in good agreement with X-ray and neutron scattering data. The diffusion coefficient D of bulk TIP3P water in a system with 528 water molecules was by one-fourth higher than the experimental value. Minor differences of approximately 10% between experi...

Local-field distribution in systems with dipolar interparticle interaction.

It is shown that the interaction (local) field distribution in disordered systems with dipolar interparticle interaction transforms from the Lorentzian to the Gaussian when the particle volume concentration is increased. To evaluate correctly the local-field dispersion ${\mathit{h}}^{2}$ in systems with randomly oriented dipoles it is sufficient to take into account the nonmonotonic behavior of the particle radial pair distribution function. For aligned dipoles angular correlations of particle positions in the first coordination sphere play a dominant role, strongly decreasing h${\mathrm{\ifmmode\bar\else\textasciimacron\fi{}}}^{2}$. \textcopyright{} 1996 The American Physical Society.

Brownian Dynamics Simulations of Polyalanine in Salt Solutions

The distribution and dynamics of the mobile monovalent ion atmosphere around polyalanine in aqueous solution at various ionic strengths have been simulated by the Brownian dynamics method. Initial simulations of pure sodium chloride solutions were performed to examine the influence of the choice of nonbonded cutoff distance on simulation results. Simulations were then performed to study how different conformations of polyalanine affect the distribution and dynamics of the mobile monovalent ion atmosphere. We found that it was necessary to use a nonbonded cutoff >30 A in order to get reliable results for the ion pair radial distribution functions, the ionic polarizabilities, and the auto time-correlation functions of the collective dipole moments of the sodium chloride solutions. We also found that α-helical polyalanines preferentially bound sodium ions at 0.1 M sodium chloride concentration. The preferential binding of sodium ions was still noticeable but less pronounced when the polyalanines were in the ...

The structure of molecular dynamics simulated oxide glasses viewed through Voronoi polyhedra tesselation

The concept of generalized coordination polyhedra, following from the Voronoi tesselation, is compared with the commonly used coordination scheme based on partial pair radial distribution functions (PP RDF). Molecular dynamics simulated calcium aluminosilicate glasses were investigated. The results obtained for the Al and Si coordination through smoothed Voronoi and direct polyhedra agree well with those based on the cut-off radius determined from the respective partial pair radial distribution function. In the case of Ca2+ central cation, the situation is more complex. The strong compositional dependence of the Ca2+ cation clustering round the oxygen anions has been extracted from the distribution of generalized coordination polyhedra.

The structure of MD simulated cryolite melt

Molecular dynamics (MD) simulations have been performed for molten cryolite (Na3AlF6), employing Born-Mayer-type pair potential functions. The structure of the simulated liquid is characterized by the partial pair radial distribution functions and also by the distribution of Voronoi and direct polyhedra. The results obtained are compared with those obtained from the Monte Carlo (MC) calculations of Qiu and Xie and with X-ray crystal data. The MD results agree well with the equilibrium crystal structure, while significant differences between the MD and MC simulations are attributed to various sources. Both the MD and MC simulated melt structures do not confirm Gilbert's dissociation scheme for the hexafluoroaluminate anion.

A quantitative method to study co-adhesion of microorganisms in a parallel plate flow chamber. II: Analysis of the kinetics of co-adhesion

Recently (J. Microbiological Methods 20, 289–305, 1994), it was suggested that dental plaque formation involved both interspecies binding between planktonic microorganisms (‘coaggregation’) as well as between planktonic and sessile microorganisms (‘co-adhesion’) and that co-adhesion could be measured by analyzing the spatial arrangements of co-adhering microorganisms in a stationary end point state. Limited information is available, however, on the kinetics of coaggregation and co-adhesion. The aim of this work was to develop a quantitative method to study the kinetics of co-adhesion and to determine the effects of mass transport conditions, like shear and concentration, on the kinetics of co-adhesion. The kinetics of co-adhesion of the coaggregating and non-coaggregating streptococci ( S. oralis J22 and S. sanguis PK1889) to glass with adhering A. naeslundii T14V-J1 cells, have been studied in a parallel plate flow chamber using real time image analysis. Initial local deposition rates in the vicinity of the Actinomyces were similar as observed on other regions over the substratum surface (‘non-local deposition rates’) for the non-co-adhering pair, but were up to 19 times higher for the co-adhering pair. Thus, whereas we have previously shown that co-adhesion in a stationary end point state can be quantified by radial pair distribution functions, this paper demonstrates that the tendency of coaggregating strains to co-adhere is also reflected in the kinetics of co-adhesion. Local deposition rates increased with increasing streptococcal concentration for the coaggregating pair. However, if it is attempted to increase the local deposition rate by increasing the shear, it was found that local deposition rates decreased, most likely because the interaction time between the adhering actinomyces and the flowing streptococci becomes too short. The high deposition rates for the coaggregating pair could not be explained on the basis of convective-diffusional mass transport towards the substratum, but required accounting for collisions between adhering actinomyces and streptococci flowing parallel to the surface.

Path-integral Monte Carlo energy and structure of the quantum hard-sphere system using efficient propagators

Path-integral Monte Carlo simulations neglecting exchange and involving different propagators (crude, Barker’s, Jacucci-Omerti’s, and Cao-Berne’s) have been performed to study the quantum hard-sphere system at several state points ranging from the fluid to the solid phase (ρ*=0.7834; 0.1&amp;lt;λB*≤0.4). Energies, necklace radii of gyration and quantum pair radial distribution functions (instantaneous, linear response, self-correlation, and necklace center of mass) have been computed and compared where possible with available data. The results indicate remarkably great performances for the efficient propagators as compared with the crude choice. Even though by lowering the temperature the three efficient propagators lead to the formation of a solid phase, quantitative differences between them are significant just from that stage (λB*≥0.3).

Studies on commercial carbon black by radial distribution function and rietveld refinement

The x-ray scattering was measured using a Philips diffractometer, the step-scanning method, molybdenum and copper radiation and a graphite monochromator.The structural models of graphite- and diamond-type have been tested to describe the type of short-range order in three types of commercial carbon black (CARBEX-330, SAKAP-6, SAPEX-20). The Rietveld refinement was used to fit the experimental diffraction pattern of the carbon black to structural data of those crystalline models. Assuming that the "crystallite" size in the carbon black is comparable with the size of the unit cell of corresponding crystalline model, the line broadening in the Rietveld refinement was modelled. The DBWS-9006PC program was used for calculations of lattice constants and atom positions in unit cell. The best fit was obtained for the graphite-type model.The radial distribution analysis was made to compare the results with values of atomic distances obtained by the Rietveld method for the graphite-type model. After the background correction (Ib), effects of the polarization (P), the absorption (A), the fluorescence (IF) and the Compton correction (IC) we may describe the diffusion x-ray scattering [ID(k)] as:ID(k) = (Iexp − Ib − IF − Ic)PAThe calculating of radial distribution function (RDF) and pair distribution function P(r) for the carbon black were performed using a computer program on an IBM At computer. The radii of coordinate spheres for the carbon black were determined by the analysis of peak positions of the pair distribution function.

Comparison of the Structure of Liquid Amides as Determined by Diffraction Experiments and Molecular Dynamics Simulations

The intermodular structures of liquid formamide, N-methylformamide and N,N-dimethylformamide at room temperature are studied by means of NVE molecular dynamics computer simulations. Newly developed flexible models are used. X-ray and neutron weighted structure and total radial pair distribution functions are computed from the simulated site-site pair distribution functions. They are compared with experimental results. The agreement is usually satisfactory as far as heavy atom pairs are concerned while the lengths of the hydrogen bonds are found to be systematically too long in the simulations.

A quantitative method to study co-adhesion of microorganisms in a parallel plate flow chamber: basic principles of the analysis

Intermicrobial aggregation is described as one of the factors contributing to dental plaque formation. Intermicrobial aggregation is usually measured by mixing potential partners suspended in a liquid phase (‘coaggregation’). However, even if aggregation in the liquid phase occurs, adhesion of microorganisms to partners already adhering to a substratum surface may also occur (‘co-adhesion’). Coaggregation assays have been performed in order to measure coaggregation and to model co-adhesion, although it is not yet clear which the two prevails in vivo. Apart from being semi-quantitative (scores run from 0 to 4) it is questionable whether coaggregation assays really mimic co-adhesion. This study was designed to develop a method to quantitative assess co-adhesion of microbial pairs in order to gain a better understanding of the mechanisms governing co-adhesion. Co-adhesion of coaggregating and non-coaggregating partners ( S. oralis, S. sanguis and A. naeslundii) to glass has been studied in a parallel plate flow chamber using real time image analysis. The spatial arrangements of adhering bacteria were analyzed by radial pair distribution functions, revealing the relative density of adhering bacteria around adhering bacteria from the same (g 22(r)) or a partner strain (g 21(r)). Pair distribution functions g 21(r) of coaggregating pairs clearly reveal a preference of coaggregating streptococci ( S. oralis J22 and S. sanguis PK2951) to adhere around the actimomyces ( A. naeslundii PK213 or T14V-J1), which were used to coat the bare glass substratum. Besides, the distribution function g 21(r) showed differences in co-adhesion patterns for strains with the same coaggregation score. From the results presented in this paper it can be concluded that with a parallel plate flow chamber, co-adhesion can be quantified on a continuous scale under well controlled conditions, more closely resembling those occurring in vivo.

Rheology of several hundred rigid bodies

A novel nonequilibrium molecular dynamics, originating in mesoscopic theory of suspensions, is introduced to investigate the behavior of model polymeric fluids consisting of several hundred ellipsoids of revolution (spheroids) that interact via the Gay-Berne potential. This dynamics is used to generate new microstructural, thermodynamic and rheological data. The microcanonical equtions of motion for the translational and angular momenta as well as for mass-centers and orientational unit vectors are derived from a Hamiltonian. These expresssions are then augmented by SLLOD-like and Gaussian thermostat terms added consistently to equations for both the rotational and translational degrees of freedom; the role of Gaussian thermostat is to maintain constant kinetic temperature of the assembly of spheroids. The thermodynamic results are calculated along one isotherm (nondimensional temperature T maintained at unity). Rheology is investigated for two state points (namely for particle number density p equal to 0.25, 0.4 and T set to 1), that lie well inside the isotropic phase if no external flow is applied. A state point is defined by the fluid's temperature T,. and the concentration of particles per unit volume p. As indicated by snapshots of molecular configurations, at the intermediate shear rates (nondimensional shear rate approximately 1–2), ellipsoids become aligned to the direction of flow and the stress tensor begins to be nonsymmetric. At even higher shear rates, this configuration breaks down leading to the formation of a transitory isotropic-type fluid, and then to the build-up of a highly ordered structure exhibiting global orientation of particles in the direction of the vorticity axis. For ϱ = 0.4, the first ( N 1 ) and the second ( N 2 ) normal stress differences are positive and negative respectively, but at low densities (ϱ = 0.25), n 1 becomes slightly negative. In addition to the stress tensor, we compute the conformation tensor, the order parameter and the components of the pair radial distribution function. At high shear rates the radial distribution functions become significantly anisotropic. Furthermore, we investigate the phenomenon of the stress overshoot at the inception of the simple shear flow from a molecular perspective, and study the evolution of the distribution of translational velocities as a function of the shear rate.

Theory and computer simulation of hard-sphere site models of ring molecules

A previous theory for hard-sphere site models of non-spherical molecules, the bonded hard sphere (BHS) theory, is reviewed and a generalization is proposed to extend the theory to ring-like molecules. New simulation data are presented for rigid ring molecules formed from three, four and five tangent hard spheres of equal size, and the results are compared with the predictions of the generalization. In all, four models are studied consisting of hard spheres at the corners of an equilateral triangle, a square, a regular tetrahedron, and a regular pentagon, respectively. Good agreement between the exact Monte Carlo data and the approximate theory is found. The two approximations made in the BHS theory and in its generalization are discussed, as is the extent of their validity. Theories of this type, based on the bonding of spheres into the desired molecules, require distribution functions for three or more spheres; the problem of estimating these functions given only the pair radial distribution function is ...

Structure of complex systems using electronic excitation transport: Theory, Monte Carlo simulations, and experiments on micelle solutions

Monte Carlo (MC) simulations and an analytical theory are presented to describe electronic excitation transport (EET) among static chromophores constrained to lie on the surfaces of spherical micelles. Both donor–trap (DT) and donor–donor (DD) EET are examined for two types of systems: probe molecules on the surfaces of isolated (low concentration) micelles, and probes on the surfaces of interacting (concentrated) micelles. The EET dynamics are described by the function, 〈G s(t)〉, the probability of finding the excitation on the originally excited chromophore. For the isolated micelle calculations, the excitation dynamics depend on the distribution of probes on a single hard sphere surface. For the interacting micelle calculations, the hard sphere structure is accounted for by using the radial pair distribution function, g(r). Both single micelle and many micelle DT calculations do not involve approximations. Consequently, the DT expressions agree exactly with the MC calculations. For the DD calculations, a first order cumulant approximation is used to obtain analytically tractable solutions to 〈G s(t)〉. Padé approximants of the cumulant solution, accurate over a broad range of chromophore number and Förster interaction strengths, are used to describe DD EET on isolated micelles. For DD EET in many micelle systems, the first order cumulant approach is shown to be a suitable method for intermicelle structural studies. Both the cumulant and MC calculations are simultaneously compared to time resolved flourescence depolarization measurements performed on octadecylrhodamine B(ODRB)/triton X-100/water systems made in previous investigations.

Determination of bond lengths, atomic mean-square relative displacements, and local thermal expansion by means of soft-x-ray photoabsorption.

Temperature-dependent extended x-ray-absorption fine-structure (EXAFS) measurements at the oxygen and fluorine K edges of CuO, ${\mathrm{Cu}}_{2}$O, ZnO, ${\mathrm{CaF}}_{2}$, and LiF have been performed. We present an EXAFS analysis of bulk samples in the soft-x-ray region of h\ensuremath{\nu}\ensuremath{\le}1500 eV determining the moments of the radial pair distribution function (RDF) of the oxygen and fluorine nearest-neighbor bonds by use of the conventional cumulant expansion method, i.e., coordination numbers, bond lengths, atomic mean-square, and mean-cubic relative displacements of the RDF. It is shown that high-quality K\ensuremath{\alpha}-fluorescence-yield measurements, analyzed in combination with theoretical standards, allow a determination of nearest-neighbor distances within 0.015 \AA{} and of coordination numbers with 10--20 % accuracy. Using quantum-mechanical models for the description of the atomic motions, the EXAFS Debye and Einstein temperatures, as well as the local thermal expansion of the bond under consideration, are obtained. In particular, these quantities for ${\mathrm{CaF}}_{2}$ are found to be in good agreement with those measured by other techniques. In contrast to the fluorides, no thermal expansion could be observed up to room temperature for the transition-metal oxides, which confirms a recent finding of enhanced anharmonicity in the low-Z adsorbate-surface interaction. A detailed compilation is given of the majority of EXAFS studies from the literature where moments of the RDF higher than the second one are reported. For these compounds the local thermal expansion is quantum mechanically calculated in contrast to previous calculations that were performed in the classical limit. Debye temperatures and the local thermal expansion measured by EXAFS and other techniques agree well for fcc metals. For binary compounds like alkali halides or superionic conductors a deviation up to 100% can be found.

Collective excitations in a potassium-rubidium melt

The partial and effective potentials of a potassium-rubidium melt is calculated at 50at% concentration of potassium, using a pseudopotential formalism. The effective pair-correlation function is obtained through the Fourier transform of the total structure factor. The longitudinal and transverse photon frequencies are computed from the effective pair potential and radial distribution function using the theory of Takeno and Goda. The eigenfrequency equations reproduce successfully the dispersion curves both for longitudinal and transverse photons. The longitudnal photon frequency curve shows characteristic oscillatory behaviour at short wave length limit while the transverse phonon frequency curve does not show any oscillation. After attaining a smooth maximum it becomes constant with increasing k value. However, in the long wavelength limit the dispersion relation for both types of excitations are found to be linear. Further it is observed that the position of the first minima in the longitudinal phonon dispersion curve coincides with the first maxima of the total structure factor curve as has been observed by Bhatia and Singh. From the dispersion curves, the elastic constants are evaluated and compared with those obtained from I 1 and I 2 integrals of Schofield. The results are in fair agreement with each other.

Preferential radiation damage of the oxygen sublattice in YBa2Cu3O7: A molecular-dynamics simulation.

We study the energetic ionic-displacement processes in orthorhombic YBa 2 Cu 3 O 7 by carrying out a molecular-dynamics simulation based on a pair potential mode. The model crystal contains 3328 atoms. In calculating the time evolution of the partial radial pair-distribution functions during the atomic-collision cascade, rue observed preferential radiation damage of the oxygen sublattice in YBa 2 Cu 3 O 7 . Detailed features of the preferential radiation damage in the lattice structure were revealed

Atom-based modeling of amorphous 1,4-cis-polybutadiene

The structure of amorphous 1,4-cis-polybutadiene is simulated with molecular mechanics and molecular dynamics subjected to periodic boundary conditions. All hydrogen atoms are explicitly taken into account. By means of the relaxation strategy which has been developed in this work, the low-energy states of relatively large systems can be reached within an acceptable computational time. With the five simulated structures, the distribution of bond angles, distribution of dihedral angles, and correlated distribution of pairs of neighbor dihedral angles, as well as cohesive energy, solubility parameter, and atom pair radial distribution functions, are evaluated and discussed

A quantum Monte Carlo study of liquid Lennard-Jones methane, path-integral and effective potentials

An intercomparative quantum study of liquid methane over a range of temperatures at zero experimental vapour pressure is presented. Interest is focused on the translational features. Classical, semi-classical (Wigner-Kirkwood (ħ2), Feynman-Hibbs) and path-integral Monte Carlo simulations have been performed. A basic one-centre Lennard-Jones potential has been used as the basic model to carry out computations. Energies, pressures and pair radial distribution functions are reported, and the reliability of the effective potentials is discussed. The results indicate, first, important quantum effects on the structure of this liquid and, second, that the Wigner-Kirkwood potential is a better semi-classical choice.