Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.     

Polarity,anisotropy of polarizability,and steric structure of two tetrahalonorcaranes

Conclusions On the basis of the dipole moments and Kerr constants of trans-3,4,7,7-tetrabromobicyclo[4,1,0]heptane and trans-3,4-dibromo-7,7-dichlorobicyclo[4,1,0]heptane, it was established that the most stable conformation is an anti-boat with a two-faced angle between the planes 2-3-4-5 and 5-6-1-2 of 200–215°.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 10, pp. 2231–2234, October, 1973.     

Impact of anisotropy on the structure and dynamics of ionic liquids: a computational study of 1-butyl-3-methyl-imidazolium trifluoroacetate

The complex ionic network of 1-butyl-3-methyl-imidazolium trifluoroacetate was simulated by means of the molecular dynamics methods over a time period of 100 ns. The influence of the anisotropy of the shape and charge distribution of both the cations and the anions on the local (molecular) and global (collective) structure and dynamics is analyzed. The distance-dependent g coefficients of the orientational probability function g(r,Omega) were found to be an excellent way to interpret local structure. Thereby, the combination and interrelation of individual g coefficients elucidate the mutual orientation. Dynamics at the molecular level is characterized by the time correlation function of the center-of-mass corrected molecular dipole moment mucm. Upon uniting the set of molecular dipoles to a single collective rotational dipole moment, MD, dynamics on a global level is studied. Decomposing into subsets of cations and anions respective self terms as well as the prominent cross term can be extracted. This decomposition also enables a detailed peak assignment in dielectric spectra.     

Molecular polarizability and the three-dimensional structure of substituted trinitromethanes

A method is suggested for estimating the assymmetry of molecules based on analysing their polarizability ellipsoids. This method is applied to fluoro-, chloro- and bromo- trinitromethanes and to 1,1,1-trinitroethane. The effective angles of rotation of nitro groups have been determined.     

Molecular reorientation dynamics and microscopic friction in liquids

Molecular rotation reorientation times are investigated using time resolved fluorescence depolarization studies of three solutes of similar size and shape (nile red, neutral nile blue and cationic nile blue) dissolved in alcohol and alkane solvents as well as an extensive compilation of previous results for neautral and charged solutes dissolved in non-polar, polar and associated solvents. A universal correlation is foung between reorientation time, solvent viscosity, and solute volume for solutes dissolved in alkanes, while strongly interacting solutes experience relatively enhanced friction, and non-polar solutes dissolved in alcohols experience reduced friction. The results are compared and contrasted with slip and stick hydrodynamic predictions, and used to develop empirical correlations, which can be used to predict molecular reorientation times with an uncetainty on the order of a factor of two in virtually any solute-solvent system.     

Molecular structure of azachalcogenenes with aromatic substituents

The molecular structure of acyclic and cyclic azachalcogenenes with aromatic substituents is analyzed and compared with related compounds using the data of XRD, NMR, and quantum chemical calculations. Translated fromZhurnal Strukturnoi Khimii, Vol. 38, No. 5, pp. 988–1006, September-October, 1997.     

Molecular relaxation dynamics of self-assembled monolayers

Dielectric relaxation spectroscopy is used to quantify molecular motion in alkylsilane SAMs coated on porous glass over a broad temperature range, -30 to -150 degrees C. Systematic measurements using SAMs with variable coating densities allow us to determine the effect of monolayer disorder on molecular mobility in thin molecular films. A relaxation process with an activation energy of approximately 25 kJ/mol is found to dominate dynamics of SAM-chain segments near the substrate. By introducing polar CN groups at the ends of the chain, we show that the relaxation process in the monolayer canopy can be isolated and studied. This approach can be generalized to other substituent polar groups to probe localized relaxation dynamics in surface-grafted monolayer films.     

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modeling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Lagrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g., CCl₄, alkanes, etc.) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.     

Molecular dynamics simulations of the structure and transport properties of tetra-butylphosphonium amino acid ionic liquids

Systematic molecular dynamics simulations are used to study the structure, dynamics and transport properties of the ionic liquids composed of the tetra-butylphosphonium ([TBP](+), or [P(C(4)H(9))(4)](+)) cation with six amino acid ([AA](-)) anions. The structural features of these ionic liquids were characterized by calculating the partial site-site radial distribution functions, g(r), and computing the dihedral angle distribution of n-butyl side chains in the [TBP](+) cations. The dynamics of the ionic liquids are described by studying the velocity autocorrelation function (VACF) and the mean-square displacement (MSD) for the centers of mass of the ions at different temperatures. The ionic diffusion coefficients and the electrical conductivities were evaluated from both the Einstein and Green-Kubo methods. The cross-correlation terms in the electric-current autocorrelation functions, which are an indication of the ion pair correlations, are investigated. The cationic transference numbers were also estimated to study the contributions of the anions and cations to the transport of charge in these ionic liquids. We determined the role of the amino acid anion structures on the dynamical behavior and the transport coefficients of this family of ionic liquids. In general, the MSD and self-diffusion coefficients of the relatively heavier non-planar [TBP](+) cations are smaller than those of the lighter amino acid anions. Introducing polar functional groups (acid or amide) in the side chain of [AA](-) decreases the diffusion coefficient and electrical conductivity of AAILs. The major factors for determining the magnitude of the transport coefficients are the chemical functionality and the length of the alkyl side chain of the [AA](-) anion of these [TBP][AA] ionic liquids.     

Solvent structural relaxation dynamics in dipolar solvation studied by resonant pump polarizability response spectroscopy

Resonant pump polarizability response spectroscopy (RP-PORS) was used to study the isotropic and anisotropic solvent structural relaxation in solvation. RP-PORS is the optical heterodyne detected transient grating (OHD-TG) spectroscopy with an additional resonant pump pulse. A resonant pump excites the solute-solvent system and the subsequent relaxation of the solute-solvent system is monitored by the OHD-TG spectroscopy. This experimental method allows measuring the dispersive and absorptive parts of the signal as well as fully controlling the beam polarizations of incident pulses and signal. The experimental details of RP-PORS were described. By performing RP-PORS with Coumarin 153(C153) in CH(3)CN and CHCl(3), we have successfully measured the isotropic and anisotropic solvation polarizability spectra following electronic excitation of C153. The isotropic solvation polarizability responses result from the isotropic solvent structural relaxation of the solvent around the solute whereas the anisotropic solvation polarizability responses come from the anisotropic translational relaxation and orientational relaxation. The solvation polarizability responses were found to be solvent-specific. The intramolecular vibrations of CHCl(3) were also found to be coupled to the electronic excitation of C153.     

Molecular dynamics averaging of Xe chemical shifts in liquids

The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.     

Molecular mobility and the structure of polar liquids

Self-diffusion coefficients of different classes of polar solvents are measured by the proton spin echo method in the temperature range of 288–318 K. In the same temperature range viscosities and dielectric relaxation times of the liquids under study are measured or taken from the literature and the activation energies of self-diffusion processes, viscous flow, and dielectric relaxation are calculated. The results obtained are compared with the literature data on structural relaxation times in the studied solvents and the conclusion is drawn about the role of the spatial hydrogen bond network in the mobility of molecules forming this network.     

Molecular kerr relaxation theory for nondipolar liquids in reorienting pulse fields

The time variations of the difference in refractive index in optical birefringence are calculated for a liquid composed of nondipolar anisotropically polarizable molecules acted on by reorienting pulse fields. The molecular dynamics is based on Sack's equation, taking into account small inertial effects (a modification of the Smoluchowski rotational diffusion equation). The time variations in birefringence are analyzed for rectangular and cosine pulse shapes on the basis of Sack's equation and are plotted for a gaussian pulse on the basis of Smoluchowski's equation. Measurements are proposed of the birefringence component with frequency 4ω related to the square of the electric anisotropy reorientation parameter of the molecules.     

Structural relaxation in complex liquids: non-Markovian dynamics in a bistable potential

The time correlation function C(t) identical with of the distance fluctuations of a particle moving in a bistable potential under the action of fractional Gaussian noise (fGn) is calculated from a Smoluchowski-type equation derived from a generalized Langevin equation (GLE). The time derivative of this function, dC(t)dt, is compared with data from optical Kerr effect measurements of liquid crystal dynamics in the vicinity of the isotropic-to-nematic transition, which are related to the time derivative of an orientational correlation function. A number of characteristic features of the experimental decay curves, including short and intermediate time power law behavior and long time exponential relaxation, are qualitatively reproduced by the analytical calculations, even though the latter do not explicitly treat orientational degrees of freedom. The GLE formalism with fGn was, in fact, originally proposed as a model of protein conformational fluctuations, so the present results suggest that it may also serve more generally as a model of structural relaxation in complex condensed phase media.