Molecular Correlation Functions Research Articles

Molecular correlation function integrals for condensed systems with solid-liquid-liquid equilibria

Fluctuation Solution Theory (FST) is an exact statistical mechanical formulation for solution thermodynamic properties and their derivatives via integrals of direct correlation functions (DCFI) and total correlation functions (TCFI). This work tabulates DCFIs and TCFIs for a series of strongly nonideal systems involving condensed-phase equilibria (LLE, SLE and SLLE) over wide ranges of temperature, pressure, and composition. The values obtained can be used for FST modeling of such systems as well as to test the accuracy of other models such as equations of state.

Molecular dynamics simulation on vegetable oil modified model asphalt

Vegetable oil is a common waste in the food and hospitality industries. It has been proposed as a modifier for asphalt to improve its performance on road pavement. In order to understand the functional mechanism of vegetable oil modifying the properties of model asphalt mixture, investigating the chemical composition, microstructure and property relationship of vegetable oil modified asphalt mixture in a wide temperature range is important. To understand the mechanism with molecular details, molecular dynamics (MD) simulations have been conducted on major fatty acid components in waste vegetable oil (WVO) (including linoleic acid, oleic acid, palmitic acid) and their mixture with model asphalt at different temperatures. One model WVO ternary mixture was built based on the literature data of the chemical composition of three kinds of fatty acids. Major properties such as density, diffusion coefficient, radial distribution function, thermal conductivity, molecular correlation functions, and viscosity were calculated. It was found that oleic acid, linoleic acid and palmitic acid have similar densities, diffusion activation energies, diffusion coefficient prefactors, and thermal conductivities from the room temperature to the hot-mix asphalt temperature. The bulk viscosities of fatty acids predicted using Green-Kubo method are similar as well, and are close to available literature data. All three kinds of fatty acids and their mixture can mix well with components in model asphalt mixture at different temperatures, and can help components in asphalt to mix more homogeneously. The zero-shear-rate viscosities of fatty acids modified asphalts at 443 K, 400 K, and 358 K were calculated running non-equilibrium MD simulations, while the viscosity at the room temperature was predicted using the Debye-Stoke-Einstein equation based on the correlation function and relaxation time calculation. Based on result in this project, implementing vegetable oil improves the density of model asphalt mixture and the mixing of components in asphalt. It does not change the viscosity of asphalt significantly at high temperature but decreases the viscosity at low temperature. The thermal conductivities of pure fatty acids, model vegetable oil ternary mixture, and model vegetable oil modified asphalt mixtures are very similar and show negligible dependence on temperature. The findings in this project suggest the functional mechanism of vegetable oil on asphalt that implementing vegetable oil can improve the performance of asphalt by facilitating the mixing of components in asphalt mixture and reorientation relaxation of asphalt at low temperatures but not at high temperatures, thus reducing the viscosity of mixture at low temperatures while having negligible effect at high temperatures.

Non-empirical calculations of rotovibrational band wings: Carbon dioxide–rare gas mixtures

We consider spectral characteristics of rotational perturbation for CO2-Rg collisions (Rg = Ar, Xe) using molecular torques time correlation function and three-dimensional classical trajectories without several conventionally used simplifications. The results are applied to the band wing calculation. The calculated wing profiles depend on the potential energy surface and agree well with the experimental data. The relative contributions of collision-induced absorption and the role of dimer absorption are discussed.

Vibrational response and motion of carbon monoxide on Cu(100) driven by femtosecond laser pulses: Molecular dynamics with electronic friction

Carbon monoxide on copper surfaces continues to be a fascinating, rich microlab for many questions evolving in surface science. Recently, hot-electron mediated, femtosecond-laser pulse induced dynamics of CO molecules on Cu(100) were the focus of experiments [Inoue et al., Phys. Rev. Lett. 117, 186101 (2016)] and theory [Novko et al., Phys. Rev. Lett. 122, 016806 (2019)], unraveling details of the vibrational nonequilibrium dynamics on ultrashort (subpicoseconds) timescales. In the present work, full-dimensional time-resolved hot-electron driven dynamics are studied by molecular dynamics with electronic friction (MDEF). Dissipation is included by a friction term in a Langevin equation which describes the coupling of molecular degrees of freedom to electron-hole pairs in the copper surface, calculated from gradient-corrected density functional theory (DFT) via a local density friction approximation (LDFA). Relaxation due to surface phonons is included by a generalized Langevin oscillator model. The hot-electron induced excitation is described via a time-dependent electronic temperature, the latter derived from an improved two-temperature model. Our parameter-free simulations on a precomputed potential energy surface allow for excellent statistics, and the observed trends are confirmed by on-the-fly ab initio molecular dynamics with electronic friction (AIMDEF) calculations. By computing time-resolved frequency maps for selected molecular vibrations, instantaneous frequencies, probability distributions, and correlation functions, we gain microscopic insight into hot-electron driven dynamics and we can relate the time evolution of vibrational internal CO stretch-mode frequencies to measured data, notably an observed redshift. Quantitatively, the latter is found to be larger in MDEF than in experiment and possible reasons are discussed for this observation. In our model, in addition we observe the excitation and time evolution of large-amplitude low-frequency modes, lateral CO surface diffusion, and molecular desorption. Effects of surface atom motion and of the laser fluence are also discussed.

Protein Partial Molar Volumes in Multicomponent Solutions from the Perspective of Inverse Kirkwood-Buff Theory.

Inverse Kirkwood-Buff (KB) solution theory can be used to relate macroscopic quantities with molecular scale interactions and correlation functions, in the form of KB integrals. Protein partial specific volumes ([Formula: see text]) from high-precision density measurements can be used to quantify solvent-solute and solute-solute KB integrals. Currently, general expressions for [Formula: see text] as a function of cosolute concentration (c3) have been provided for only binary and ternary solutions. We derive a general multicomponent expression for [Formula: see text] in terms of the relevant KB integrals for the case of low (infinite dilution) protein concentration but arbitrary cosolute concentrations. To test the utility of treating a quaternary system with a pseudoternary approximation, α-Chymotrypsinogen (aCgn) solutions with a series of solutes (NaCl, sucrose, and trehalose) were compared as a function of solute concentration with and without buffer present. Comparison between those ternary and quaternary solutions shows equivalent results within experimental uncertainty and suggests the pseudoternary approximation may be reasonable. In the case of aCgn, doing so also revealed that the preferential interactions can depend on pH. Analysis of steric contributions also provides an example that illustrates how KB integrals allow one to interpret [Formula: see text] in terms of contributions from molecular volume, excluded volume, and hydration/solvation effects.

Long-range orientation correlation in dipolar liquids probed by hyper-Rayleigh scattering.

Hyper-Rayleigh scattering (HRS) is sensitive to long-range molecular orientation correlation in isotropic liquids composed of dipolar molecules. The correlation functions that appear in the calculation of HRS mediated by the vector part of the first hyperpolarizability β are the same as the correlation functions for the homogeneous isotropic random vector fields that appear in the description of fluid turbulence. Recent experiments measuring the angle and polarization dependence of HRS from water find a dominant transverse mode contribution with amplitude independent of the scattering wavevector, and this observation of transverse mode HRS strongly constrains the form of the orientation correlation function. Analysis of these HRS results for water determines that the long-range molecular orientation correlation function varies as r(-3±ε) with |ε| < 0.03 on spatial scales up to 2000 nm.

Coherent (photon) vs incoherent (current) detection of multidimensional optical signals from single molecules in open junctions.

The nonlinear optical response of a current-carrying single molecule coupled to two metal leads and driven by a sequence of impulsive optical pulses with controllable phases and time delays is calculated. Coherent (stimulated, heterodyne) detection of photons and incoherent detection of the optically induced current are compared. Using a diagrammatic Liouville space superoperator formalism, the signals are recast in terms of molecular correlation functions which are then expanded in the many-body molecular states. Two dimensional signals in benzene-1,4-dithiol molecule show cross peaks involving charged states. The correlation between optical and charge current signal is also observed.

Frequency-domain stimulated and spontaneous light emission signals at molecular junctions.

Using a diagrammatic superoperator formalism we calculate optical signals at molecular junctions where a single molecule is coupled to two metal leads which are held at different chemical potentials. The molecule starts in a nonequilibrium steady state whereby it continuously exchanges electrons with the leads with a constant electron flux. Expressions for frequency domain optical signals measured in response to continuous laser fields are derived by expanding the molecular correlation functions in terms of its many-body states. The nonunitary evolution of molecular states is described by the quantum master equation.

Simulations of solid-liquid friction at ice-Ih/water interfaces

We have investigated the structural and dynamic properties of the basal and prismatic facets of the ice Ih/water interface when the solid phase is drawn through the liquid (i.e., sheared relative to the fluid phase). To impose the shear, we utilized a velocity-shearing and scaling approach to reverse non-equilibrium molecular dynamics. This method can create simultaneous temperature and velocity gradients and allow the measurement of transport properties at interfaces. The interfacial width was found to be independent of the relative velocity of the ice and liquid layers over a wide range of shear rates. Decays of molecular orientational time correlation functions gave similar estimates for the width of the interfaces, although the short- and longer-time decay components behave differently closer to the interface. Although both facets of ice are in "stick" boundary conditions in liquid water, the solid-liquid friction coefficients were found to be significantly different for the basal and prismatic facets of ice.

Time-resolved broadband Raman spectroscopies: A unified six-wave-mixing representation

Excited-state vibrational dynamics in molecules can be studied by an electronically off-resonant Raman process induced by a probe pulse with variable delay with respect to an actinic pulse. We establish the connection between several variants of the technique that involve either spontaneous or stimulated Raman detection and different pulse configurations. By using loop diagrams in the frequency domain, we show that all signals can be described as six wave mixing which depend on the same four point molecular correlation functions involving two transition dipoles and two polarizabilities and accompanied by a different gating. Simulations for the stochastic two-state-jump model illustrate the origin of the absorptive and dispersive features observed experimentally.

Tetrahedratic mesophases, chiral order, and helical domains induced by quadrupolar and octupolar interactions

We present an exhaustive account of phases and phase transitions that can be stabilized in the recently introduced generalized Lebwohl-Lasher model with quadrupolar and octupolar microscopic interactions [L. Longa, G. Pająk, and T. Wydro, Phys. Rev. E 79, 040701(R) (2009)]. A complete mean-field analysis of the model, along with Monte Carlo simulations allows us to identify four distinct classes of the phase diagrams with a number of multicritical points where, in addition to the standard uniaxial and biaxial nematic phases, the other nematic like phases are stabilized. These involve, among the others, tetrahedratic (T), nematic tetrahedratic (N(T)), and chiral nematic tetrahedratic (N(T)(*)) phases of global T(d), D(2d), and D(2) symmetry, respectively. Molecular order parameters and correlation functions in these phases are determined. We conclude with generalizations of the model that give a simple molecular interpretation of macroscopic regions with opposite optical activity (ambidextrous chirality), observed, e.g., in bent-core systems. An estimate of the helical pitch in the N(T)(*) phase is also given.

Centroid molecular dynamics: Comparison with exact results for model systems

The relation between the accuracy of centroid molecular dynamics correlation functions, and the geometry of the centroid potential is investigated. It is shown that, depending on the temperature, there exist several regimes, and in each of them certain features of the exact Kubo correlation functions are reproduced. The change of regimes is related to the emergence of barriers in the centroid potential. In order to clarify how the above described picture of regimes is modified in real systems when dissipation is important, a methodology is developed to test the accuracy of centroid correlation functions for the model of a particle coupled to a harmonic heat bath. A modification of the centroid molecular dynamics method to include the influence of the heat bath is introduced. Preliminary results of comparison of centroid molecular dynamics with the numerically exact results of filtered propagator functional method are presented.

Effects of concentration on structure, dielectric, and dynamic properties of aqueous NaCl solutions using a polarizable model

The study of NaCl solutions in water at finite concentration, explicitly including polarization in water molecules and ions, has been carried out by molecular dynamics simulations. A comparison of the RPOL polarizable model with the rigid SPC/E potential for water has been included. Structure obtained with the two models does not show significant differences, although some deviations in the NaNa radial distribution functions at all concentrations are observed. Dielectric properties such as total and molecular dipole moment correlation functions revealed decay times of the order of 10 ps, roughly independent of concentration. The analysis of electric conductivity by means of current-current correlation functions also included the calculation of cross terms corresponding to dipole moment-current correlations, which proved to be non-neglectable at short times and especially relevant at high concentrations (m=4 mol kg(-1)). Frequency dependent dielectric constants and conductivities have been computed and the role of cross correlations has been analyzed. In all cases both concentration and cross correlations have significant influence in the results.

Transient time correlation function calculation of the viscosity of a molecular fluid at low shear rates: a comparison of stress tensors

Shear viscosity of n-decane was computed using the molecular stress transient time correlation function (TTCF) formalism for the wide range of shear rates from 1.7 × 1010 s−1 to 2.13 × 104 s−1. In earlier work calculations were presented for the shear viscosity of n-decane using the atomic stress formalism of the TTCF method (G. Pan and C. McCabe, J. Chem. Phys. 125(19), 4527 (2006)) in which we were able to close the gap between the lowest shear rates accessible by direct nonequilibrium molecular dynamics (NEMD) simulations and the highest shear rates possible in experimental studies. Here it is shown that the application of the molecular stress approach within the TTCF formalism, as an alternative to the atomic stress method, significantly reduces the number of NEMD trajectories necessary to obtain the shear viscosity.

Single-Molecule Photoactivation and Localization of Signaling Complexes in T cells

In T cells, membrane receptor and ligand engagement initiates a signaling cascade. Ligand binding is relayed through specific membrane receptors, protein tyrosine kinases, and critical adaptors to regulate downstream activation of transcription factors, cytokine production and cell proliferation. The membrane segregation and relocalization of these signaling components display highly dynamic protein networks in response to distinct stimulations. However, the membrane-protein and protein-protein interactions involved in the formation of signaling complexes are still poorly understood. We are currently using a high-resolution imaging technique to visualize the early stage of signal transduction events at the single-molecule level with photoactivatable or photoconvertable fluorescent markers. The photoactivation and localization of T-cell signaling components allow measurements of molecular spatial and temporal correlation in response to different stimulations. With dual-color application, molecular correlation functions will enhance the understanding of the protein-protein interactions in signaling complexes.

On the nature of the high-frequency relaxation in a molecular glass former: A joint study of glycerol by field cycling NMR, dielectric spectroscopy, and light scattering

Fast field cycling (1)H NMR relaxometry is applied to determine the dispersion of spin-lattice relaxation time T(1)(omega) of the glass former glycerol in broad temperature (75-360 K) and frequency (10 kHz-30 MHz) ranges. The relaxation data are analyzed in terms of a susceptibility chi(")(omega) proportional, variantomegaT(1)(omega), related to the second rank (l=2) molecular orientational correlation function. Broadband dielectric spectroscopic results suggest the validity of frequency temperature superposition above the glass transition temperature T(g). This allows to combine NMR data of different temperatures into a single master curve chi(")(omegatau(alpha)) that extends over 15 decades in reduced frequency omegatau(alpha), where tau(alpha) is the structural alpha-relaxation time. This master curve is compared with the corresponding ones from dielectric spectroscopy (l=1) and depolarized light scattering (l=2). At omegatau(alpha)<1, NMR susceptibility is significantly different from both the dielectric and light scattering results. At omegatau(alpha)>1, there rather appears a difference between the susceptibilities of rank l=1 and l=2. Specifically, at omegatau(alpha)>>1, where the susceptibility is dominated by the so-called excess wing, the NMR and light scattering spectra (both l=2) rather coincide with each other and are about three times more intense than the dielectric (l=1) spectrum. This is explained by assuming that the high frequency dynamics correspond to only small-angle excursions. Below T(g), dielectric and NMR susceptibility compare well and exhibit an exponential temperature dependence.

Incomplete molecular chaos within dense-fluid shock waves

Large-scale molecular dynamics simulations of an M(s) = 4.3 shock in dense argon (rho = 532 kg m(3), T = 300 K) and an M(s) = 3.6 shock in dense nitrogen (rho = 371 kg m(3), T = 300 K) have been performed. The two-point molecular velocity correlation function is calculated within slices in plane with the shock wave. Long-range (approximately ten molecular radii) positive correlations (correlation coefficient 0.05) are observed for the shock-normal velocity component, the in-plane velocity component, and the rotation rates. No correlations are found upstream or downstream of the shock, indicating that this is a nonequilibrium effect. These correlations violate one of the assumptions underlying the Boltzmann equation.

Self-assembly of patchy particles into polymer chains: A parameter-free comparison between Wertheim theory and Monte Carlo simulation

The authors numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory. This comparison offers a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameters and liquid state correlation functions. The Wertheim theory has not been previously subjected to stringent tests against simulation data for ordering across the polymerization transition. The authors numerically determine many of the thermodynamic properties governing this basic form of self-assembly (energy per particle, order parameter or average fraction of particles in the associated state, average chain length, chain length distribution, average end-to-end distance of the chains, and the static structure factor) and find that predictions of the Wertheim theory accord remarkably well with the simulation results.

Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations.

The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated: In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range.

Collisional polarizability correlation functions: A step towards rotational-translational coupling

A theory of the spectral distribution of the molecular time correlation function of the collision induced polarizabilities active in the collision induced light scattering has been developed. Within the framework of this approach a new concept of the averaging procedure is proposed, which - unlike the usually applied assumptions of total separation of the angle dependent and the translational contributions - partially includes the coupling between the rotational and translational degrees of freedom due to anisotropic intermolecular interactions. Introduction of the rotational spectral functions, valid for different frequency ranges, in order to produce a numerically treatable method of deriving collisional spectral profiles is discussed. The final results of the theory are formulated in a fashion providing a solid base for numerical calculations capable of interpreting data obtained in various fields of physical, environmental and astrophysical sciences.