Intermolecular Force Field Research Articles

Improved intermolecular force field for crystalline hydrocarbons containing four- or three-coordinated carbon

A new intermolecular force field of the (exp-6-1) type was derived from observed hydrocarbon crystal structures selected from a comprehensive set of 134 molecules with 5–16 carbon atoms, and eight observed heats of sublimation. Carbon atoms with four bonds, C(4), and those with three bonds, C(3), were assigned separate parameters. Wavefunctions were calculated for each molecule and the molecular electric potential was modelled with net atomic charges. Methylene bisector or ring center site charges were added as necessary to fit the molecular electric potential. Each crystal structure was relaxed by energy minimization; for 101 of the structures the force field predicted changes in unit cell edge lengths less than 3%. The remaining 33 crystal structures, while otherwise meeting data quality criteria, showed predicted unit cell edge length changes greater than 3% and were not included in the training set.

Intermolecular vibrations of water molecules in the crystalline hydrates of MCl2·2H2O (M=Cu, Fe, Mn, Ba, Co)

Force constants of the water molecules in the crystal hydrates MCl2·2H2O (M=Cu, Fe, Mn, Ba, Co) were analyzed using IR and Raman spectral data. The water intermolecular force constants and wavenumbers for the rock and translation vibrations were calculated using the relationship between changes in the intramolecular force field and the intermolecular force field appearing in the transition from the free state to the condensed phase of water molecules. The spectra of the crystalline hydrates in the low-wavenumber region were interpreted. A correlation between the intermolecular force constants and the Ow—Cl interatomic distance was observed. © 1998 John Wiley & Sons, Ltd.

High-resolution zero-kinetic-energy pulsed field ionization photoelectron spectra of the Na(H2O) complex

Measured single-photon zero-kinetic-energy pulsed field ionization (ZEKE-PFI) photoelectron spectra of the sodium–water complex are presented and compared with the results of rotationally resolved ab initio calculations. The very nonatomiclike behavior of the photoionization of this Na(H2O) complex is essential in accounting for several significant features in these spectra. Agreement between the calculated and measured photoelectron spectra is encouraging. Furthermore, these results suggest that combined experimental and theoretical studies of ZEKE-PFI spectra can be very useful in elucidating the molecular structure and intermolecular force fields of small clusters.

Effects of Molecular Electric Potential and Anisotropic Atomic Repulsion in the Dichlorine Dimer and Crystalline Chlorine

Molecular packing analysis of crystalline dichlorine (Cl2) shows that the crystal structure is compatible with an isotropic intermolecular force field that includes polar flattening of the exchange repulsion energy and a five-center distributed monopole representation of the molecular electric potential. Polar flattening largely accounts for the short intermolecular contacts in the crystal, and the molecular electric potential is critical in determining the molecular orientation and space group. Neither an atom-centered model for repulsion nor a molecular quadrupole model for the electric potential is adequate to describe the force field of this molecule.

Molecular docking to ensembles of protein structures

Until recently, applications of molecular docking assumed that the macromolecular receptor exists in a single, rigid conformation. However, structural studies involving different ligands bound to the same target biomolecule frequently reveal modest but significant conformational changes in the target. In this paper, two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures. One method combines the information into an “energy-weighted average” of the interaction energy between a ligand and each receptor structure. The other method performs the averaging on a structural level, producing a “geometry-weighted average” of the inter-molecular force field score used in DOCK 3.5. Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. The use of composite grids, when conformationally different protein structures are available, yields an improvement in computational speed for database searches in proportion to the number of structures.

Vibronic intensities in centrosymmetric coordination compounds of the rare earths Part II. A vibronic crystal field-closure-ligand polarisation model and applications to the PrCl 3−6 and UBr 2−6 complex ions in octahedral symmetry

A symmetry adapted formalism to evaluate the vibronic intensities induced by the ungerade vibrational modes in centrosymmetric coordination compounds of the rare earths is put forward and applied to several selected electronic transitions of the PrCl 3− 6 and UCl 2− 6 complex ions in octahedral symmetry. This current model is based upon a modified symmetry adapted version of the combined vibronic crystal field-closure-ligand polarisation approach. This model differs from that developed in Part I of this series, in that for the vibronic crystal field contribution to the total transition dipole moment, the closure procedure is employed rather than the utilisation of a truncated basis set for the central metal intermediate electronic states. A criterion is introduced to choose an appropriate set of phases for both the electronic and the vibrational coordinates so that to ensure the right sign for the interference term (which couples together both the vibronic crystal field and the vibronic ligand polarisation contributions to the total transition dipole moment). We have focused our attention on the modulation of the intermolecular force field and a version of a modified general valence force field has been adopted. The reasons for using this formalism rather than the superposition model (SM) are fully discussed in the text. Finally, it is shown that the agreement with experiment is satisfactory for most of the components of the transitions studied, despite the apparent simplicity of our model calculation. General master equations applicable to any f N electronic configurations are derived to show the utility and flexibility of this current formalism.

Molecular-Field-Enhanced Optical Kerr Effect in Absorbing Liquids

A large enhancement of the optical Kerr nonlinearity associated with light-induced molecular orientation is observed in a liquid of anisotropic organic molecules when it is doped with a small amount of dye. The effect is ascribed to a photoinduced intermolecular force field, whose orienting action adds to the direct optical field action. The experimental results are in agreement with a model based on such interpretation. The proposed mechanism is in principle very general, and should work in all absorbing liquids made of anisotropic molecules.

Ab initio molecular packing analysis

A method is presented which, given a molecular structure and an intermolecular force field, can predict observed polymorphic crystal structures and molecular clusters without any prior assumption of space symmetry.

Molecular Dynamics Investigation of the Lamellar Liquid-Crystal D-Phase in the Octylammonium Chloride/Water System

Abstract The two-component cationic surfactant system octylammonium chloride/water (20/80 mole percent) has been investigated by molecular dynamics simulations using an intermolecular force field taken from the literature. The multi-lamella bilayer structure is demonstrated to be stable over a nanosecond molecular dynamics trajectory and to possess physical characteristics in reasonable accord with available experimental data. The results are sufficiently encouraging that further studies of this system seem warranted.

Deformation in glassy polymers

On the basis of known nonlinearity of intermolecular force fields, we discuss the interpretation of PVT (pressure, volume, and temperature) behavior, pressure-temperature superposition for polymers, and the relationship between yield stress and tensile modulus. For PVT behavior of polymers, our theoretical results coincide with the experimental data, and their response to pressure is universal. The maximum theoretical yield strain, ϵy for glassy polymers is 1.08, and this value is beyond the elastic limit for glassy polymers. The previously established empirical relationship between yield stress, σy and tensile modulus, E: σy - 0.028 E, which again, is universal for glassy polymers, is predicted also by our phenomenological model. The theoretically predicted values of yield stress for glassy polymers range from 24 MPa to 84 MPa, coinciding with published experimental results. We discuss how the phenomenological model is helpful in the understanding of nonlinear viscoelasticity of glassy polymers © 1996 John Wiley & Sons, Inc.

Temperature dependence of Raman scattering in vapour-grown C60 crystals

The temperature dependence of the Raman spectra of vapour-grown C60 crystals is investigated with deep-red excitation. The excitation using a deep-red laser can avoid a photo-induced transformation of C60 crystals during the Raman measurement. It is found that discontinuous changes occur in the Raman spectra at the SC-FCC phase transition temperature (260 K). Most intramolecular vibrational modes broaden drastically as the temperature exceeds 260 K. Crystal-field splitting of the intramolecular vibrational modes is observed below 260 K. The broadening of the Raman bands would be caused by the increase in the inhomogeneity of intermolecular force fields in the FCC phase. This broadening corresponds to the increase in the orientational disorder of C60 molecules above the phase transition.

Intermolecular force field and approximate equilibrium structure of various complexes containing one or two rare gas atoms from microwave spectroscopic constants

Intermolecular force field and approximate equilibrium structure of various complexes containing one or two rare gas atoms from microwave spectroscopic constants

Intermolecular force field and approximate equilibrium structure of various complexes containing one or two rare gas atoms from microwave spectroscopic constants

Abstract The quartic centrifugal distortion constants of a class of van der Waals complexes containing one or two rare gas atoms have been used to determine a complete force field for the intermolecular vibrations. In such complexes with Cs or C2v symmetry the rare gas atom is attached above a symmetry plane or two rare gas atoms are arranged symmetrically to this plane. Small amplitude motions and an analytical form of an anharmonic interaction potential have been assumed for the centrifugal distortion analysis. Vibrational corrections have been applied to two of the planar moments of inertia for the estimation of a pseudoequilibrium structure. The influence of the intramolecular vibrations on the centrifugal distortion of these complexes has also been considered.

Intermolecular force field and approximate equilibrium structure of various complexes containing one or two rare gas atoms from microwave spectroscopic constants

Intermolecular force field and approximate equilibrium structure of various complexes containing one or two rare gas atoms from microwave spectroscopic constants

A density functional/molecular dynamics study of the structure of liquid nitromethane

A molecular dynamics simulation of liquid nitromethane has been carried out, in which a density functional (DF) procedure was used to compute the properties needed to establish the intermolecular force field. The latter was subsequently updated by further DF calculations. The first and second shells of neighbors are found to be at radii of about 6 Å and 11 Å from a given nitromethane molecule. OH partial pair correlation functions are determined, and indicate the presence of C–H...O hydrogen bonding.

Bending force constants for weakly bound dimers AB (A = symmetric top, B = linear molecule) from centrifugal distortion in rotational spectra

The contribution of the harmonic intermolecular bending force field to the quartic centrifugal distortion constants of weakly bound dimers AB (where A is a symmetric-top molecule and B is a linear molecule) has been examined. Approximate formulae are derived that relate the force constant and the vibrational wavenumber for the oscillation of the A subunit to the combination 2 D J + D JK of distortion constants. These formulae are applied to 35 dimers, and a generalisation is made.

Lattice dynamics of semirigid molecules

A new approach to the lattice dynamics calculations for the crystals built up from semirigid molecules is presented. The rigid body approximation often used in the calculation of the lattice dynamics of molecular solid is extended to the molecules built from several rigid subunits (polyphenyles, etc.). The intermolecular force field is calculated from the atom–atom potential function. The intramolecular force field describing the dynamics of the rigid subunits within the molecule is calculated in the frame of the central force field model (CFF), i.e., assuming only the stretching coordinates between certain bonded and nonbonded atoms within the molecule. The parameters (force constants) are fitted in order to reproduce the observed low vibrational frequencies of the free molecule. The method is applied to the lattice dynamics of biphenyl, 2,2′-bipyridine and s-trans-bicyclopropyl. The possibility of the application of the present method in the calculation of Raman and coherent inelastic neutron scattering intensities is discussed.

Investigation of an Evaporating Extended Meniscus Based on the Augmented Young–Laplace Equation

The microscopic details of fluid flow and heat transfer near the contact line of an evaporating extended meniscus of heptane formed between a horizontal substrate and a “washer” were studied at low heat fluxes. The film profile in the contact line region was measured using ellipsometry and microcomputer-enhanced video microscopy, which demonstrated the details of the transition between a nonevaporating superheated flat thin film and an evaporating curved film. Using the augmented Young-Laplace equation, the interfacial properties of the system were initially evaluated in situ and then used to describe the transport processes. New analytical procedures demonstrated the importance of two dimensionless parameters. Both fluid flow and evaporation depend on the intermolecular force field, which is a function of the film profile. The thickness and curvature profiles agreed with the predictions based on interfacial transport phenomena models. The heat flux distribution and the pressure field were obtained. Since there are significant resistances to heat transfer in this small system due to interfacial forces, viscous stresses, and thermal conduction, the “ideal constant heat flux” cannot be attained. The description of the pressure field gives the details of the coupling between the disjoining and capillary pressures.

Induced dipole moments and intermolecular force fields of rare gas-carbon dioxide complexes studied by Fourier-transform microwave spectroscopy

Pure rotational spectra and their Stark effects of X-CO 2 type complexes (X:Ne, Kr, and Xe) have been studied by pulsed-nozzle Fourier-transform microwave spectroscopy. Structures, intermolecular force fields, and electric dipole moments in the ground state have been determined, which have been discussed in connection with the previously reported results of Ar-CO 2 and Hg-CO 2

Intermolecular interaction of antimony trichloride in the crystal of the bimolecular Menshutkin complex with diphenylamine

The relationship between the change in the constants of intra- and intermolecular force fields of the molecules at the gas-crystal transition is discussed. Raman spectra of the crystal of bimolecular complex (C 6 H 5 ) 2 NH.2SbCl 3 at 293 and 77 K are obtained. Theoretical group and normal coordinate analysis of vibrations in the complex are performed.