Atom-atom Potential Method Research Articles

Calculation of the microstructure of Langmuir-Blodgett films derived from stilbazolium salts

The atom-atom potential method was used to calculate the microstructure of Langmuir-Blodgett films derived from stilbazolium salts and previously obtained experimental results were analyzed. The structure, in which the positively charged stilbazolium heads are arranged perpendicularly to the plane of the film with bromide ions between them, was found to be the most stable. The hydrocarbon tails in this packing may be displaced relative to each other such that the total thickness of the bilayer is reduced. The calculated thickness of the bilayer (48 A) is in accord with the experimental value (49 A). The calculated surface area of the films per molecule is 1.5 times greater than the experimental value. We propose that partial creep of the molecules relative to each other occurs upon film formation on the water surface.

Atom-atom potential calculations on Langmuir-Blodgett films: Structure of stearate films

The atom-atom potential method is used to determine the microstructure of the Langmuir-Blodgett stearate monolayer and Y-type bilayer. It is shown that the two-dimensional crystalline lattice of stearate films has no hexagonal symmetry; however, the deviation from the hexagonal structure is small. The packing of the molecules is determined by the electrostatic interaction as well as by the hydrocarbon tail size. The structural parameters of monolayer and bilayer are similar, but the bilayer lattice is more rigid.

Computer simulation of an edge dislocation in anthracene crystals

The equilibrium configuration for the core of a (010)(001) edge dislocation in an anthracene crystal has been calculated using the atom-atom potential method. A boundary condition has been examined in which molecular rotations were taken into account together with translational displacements on the basis of anisotropic elasticity. The dislocation had a spread-out shear misfit, and the width of the Burgers vector density at half peak height reached 6.2 times the magnitude of the Burgers vector.

Investigation of pretransition phenomena in organic crystals by vibrational spectroscopy

Some examples illustrate the efficiency of the investigation of reorientational molecular motion and order-disorder phenomena in organic crystals near their points of phase transition and melting by the temperature dependence of low-frequency vibrational spectra combined with simultaneous calculations of the lattice dynamics by the atom-atom potential method.

Calculation of the formation and migration energies for a vacancy in anthracene crystals

The formation energy of a molecular vacancy in a crystal of anthracene was calculated using the atom-atom potential method. this energy was found to be 93% of the packing energy of a regular lattice. The relaxation of molecules surrounding the vacancy was very small and anisotropic. The migration of an anthracene molecule from one site to another vacant site was also studied in two directions. The calculated value of the self-diffusion energy for the (010) jump was 125% of the regular lattice energy, whereas that for the (001) jump was 138%.

Computer simulation of the adsorption and diffusion of benzene in silicalite, theta-1, and a new zeolite, EU-1

The diffusion of benzene in three zeolites, silicalite, theta-1, and EU-1, is studied using the method of atom-atom potentials. Activation energies of diffusion for benzene were predicted to be about 25 kJ/mol in the silicalite straight channel and 3 kJ/mol in theta-1. Two modes of diffusion are suggested for benzene in EU-1: (a) solely along the straight channel with an activation energy of 22 kJ/mol and (b) diffusion along the straight channel into the side pocket with an activation energy of 28 kJ/mol. Limitations of the minimization routine employed are discussed.

C-H ... O hydrogen bonding in solutions of methylated nucleic acid base analogs as revealed by NMR.

Formation and thermodynamic characteristics of C-H ... O hydrogen bonding of methylated uracils and caffeine have been studied by nmr along two lines. 1. The concentration and temperature dependencies of the PMR spectra of 1,3-dimethyluracil (m2 1,3Ura), 1,3-dimethylthymine (m2 1,3Thy), and 1,3,6-trimethyluracil (m3 1,3,6Ura) in chloroform at high concentrations of base analogs indicated the self-association of m2 1,3Ura and m2 1,3Thy via C(6)H ... O hydrogen bonding and the competitive formation of C-H ... O bonds between carbonyl oxygens and chloroform. The intermolecular interaction energy and the arrangement of molecules in the local minima of various m2 1,3Ura dimers were calculated by the method of atom-atom potentials. The deepest minimum for the m2 1,3Ura coplanar dimer corresponds to a C(6)-H ... O hydrogen-bond formation. 2. At low concentration of m2 1,3Ura and caffeine in CCl4, C(6)-H ... O bonding for m2 1,3Ura and C(8)-H ... O bonding for caffeine with oxygens of dimethyl sulfoxide (DMSO) and acetone were observed. The association constants of these complexes were obtained at different temperatures. The enthalpies delta H, of the m2 1,3Ura-DMSO, m2 1,3Ura-accetone, caffeine-DMSO, and caffeine-acetone complexes were -2 +/- 0.1 kcal/mol. The calculations showed that the deepest minimum of the caffeine-acetone coplanar complex corresponds to C(8)-H ... O bonding with energy of -3.5 kcal/mol and that of the m2 1,3Ura-acetone complexes corresponds to C(6)-H ... O bonding with energy of -3.4 kcal/mol. The approximate correction for the solvent effect provides good agreement of the experimental data with the calculations.

Computer Simulation of the Location of Para-Xylene in Silicalite

Abstract The method of atom-atom potentials has been applied to the localisation of para-xylene molecules within the channels and intersections of silicalite. Two minima were found at the intersection, with interaction energies of −82 and −80 kJmol−1 respectively. These two positions are in good agreement with the results of a recent, room temperature powder X-ray diffraction study. A third, slightly deeper minimum (interaction energy −85kJmol−1) was located in the straight channels but was not occupied in the X-ray diffraction study. This result has been explained by considering entropic effects.

Theoretical Calculations on Nonlinear Susceptibilities of Organic Crystals

ABSTRACTTheoretical calculations on nonlinear susceptibilities of organic crystals are made. Under the oriented gas model approximation, nonlinear susceptibility of a crystal can be calculated both from the molecular hyperpo1arizability and crystal structure data. Molecular hyperpolarizabilities are calculated by an ab initio molecular orbital (MO) method and the energy minimum crystal structures are obtained by an empirical atom-atom pairwise potential method. Finally the effect of intermolecul ar interactions on molecular hyperpolarizabilities, which is neglected in the above approximation, is investigated quantitatively by using a “super molecule” method of ab initio MO calculations.

Experimental and Theoretical Morphology of p-Nitro p'-Methyl Benzilidine Aniline, A Non-Linear Optic Material

Abstract The theoretical habit of the non-linear optic material p-Nitro p'-Methyl Benzilidine Aniline, is calculated using an atom-atom potential method. This habit is compared with the habit predicted by the method of Donnay and Harker, and with the experimental habit. Differences in the three habits are explained in terms of the molecular structure at the growing crystal surfaces.

The Atom-Atom Potential Method as an Aid in Determining Possible Pathways of Polymorphic Transformations in the Solid State

The Atom-Atom Potential Method as an Aid in Determining Possible Pathways of Polymorphic Transformations in the Solid State

The Atom-Atom Potential Method as an Aid in Determining Possible Pathways of Polymorphic Transformations in the Solid State

Abstract Using as hypothesis a second order transition and a pure cooperative mechanism, energy calculations were performed for the polymorphic transformation of Z,Z solid diacetamide into its E,Z form along a possible pathway. The low calculated barriers are in agreement with the ability of diacetamide to isomerize.

New Ligands: Poly(diphenylphosphorylmethyl)arenes

Abstract To find out the influence of structure factors on efficincy and selectivity of complexformation the oxides of aromatic tret. di-, tri- and tetraphosphines were synthesized. The molecules contain as conformationaly hard bridges between coordination centres (P[dbnd]O groups) - fragments of polymethylarenes (isomeric xylenes, mesythylene, durene, dimethylnafthalene, dibenzo-18-crown-6). These compounds were obtained by the Arbusov reaction of Ph2POEt with corresponding bromomethylarenes. Extraction and complexformation with transplutonium elements, europium, uranium, copper, cobalt were studied. It was found, that among investigated ligands the action selectivity is determined, mainly, by the mutual location of P[dbnd]O groups. A theoretical conformational analysis using the atom-atom potential function method was applied to the isolated ligands. To reveal conformers suitable for chelating the energy minimisation was carred out with the penalty function constraints keeping the P[dbnd]O…O[dbnd]P dist...

Optimization of the geometry of the diphenylamine molecule by semiempirical quantum chemical methods

Available data on experimental study of the geometry of the diphenylamine molecule (I) in solution and in the crystal are fragmentary and not always reliable. Previously, they did a conformational analysis of molecule I using the atom-atom potential method. In order to refine the geometric parameters found for molecule I, optimization of its geometry is provided in the paper using the CNDO/2, INDO, MINDO/3 methods with the use of programs for the BESM-6 computer which are part of the VIKING program set. The angles of rotation for the phenyl rings relative to the CNC plane, the bond angles C/sub 2/N/sub 7/C/sub 8/ and C/sub 2/N/sub 7/H/sub 19/, and also the dihedral angle H/sub 19/N/sub 7/C/sub 8/C/sub 9/ were subjected to optimization. For any set of values for the indicated parameters, the bond angle C/sub 8/N/sub 7/H/sub 19/ is determined unambiguously. The results of the calculations are evidence that the MINDO/3 method is not suitable for optimization of the geometry for molecules of the indicated series; in particular, it leads to much too high a value for the CNC angles (135.9/sup 0/). The CNDO/2 method reproduces well the real value of the CNC angle (124.1/sup 0/) and confirms the known pyrimidalmore » character of the nitrogen atom, the sum of the bond angles of which proved to be equal to 353.6/sup 0/. The calculation in the INDO approximation successfully gives the basic characteristics of the molecular geometry of (I); according to this approximation, the CNC angle is equal to 123.2/sup 0/, the CNH angles are equal to 118.0 and 118.8/sup 0/, the sum of the angles for the nitrogen atom is 360.0/sup 0/.« less

Search of the mutual packing of the macromolecules of aromatic polyamidoimides by the atom-atom potential method

Search of the mutual packing of the macromolecules of aromatic polyamidoimides by the atom-atom potential method

Theoretical analysis of hydrogen bonds in carbohydrate crystals

The rotational states of hydroxyl groups and the structure of hydrogen bonds in crystals of α- d-glucopyranose, β- d-glucopyranose, α- d-galactopyranose, β- d-galactopyranose, methyl α- d-altropyranoside, and methyl β- d-galactopyranoside are predicted by using the atom-atom potential method. Good agreement is observed between theoretical and neutron-diffraction data on the geometry of the hydrogen bond.

Structure of cyclolinear organosiloxanes

The method of X-ray structural analysis has been used to determine the structure of a number of oligomers of cyclolinear organopolysilsesquioxanes. The geometric parameters of the characteristic (support) fragments of these molecules have been compared and the deformational possibilities of these fragments evaluated by conformational calculations using the atom-atom potential method.

Phonon dispersion curves and elastic properties of polyoxymethylene single crystals

By growing large single crystals of fully deuterated polyoxymethylene (CD 2O) n , it has been possible to observe phonons for a number of different branches of the phonon dispersion curves using coherent neutron inelastic scattering. Using a hexagonal approximation for this crystal, four of the five independent stiffness constants at 300K have been determined as C 11 = 1.30 × 10 11; C 12 = 6.32 × 10 10; C 33 = 1.64 × 10 12; C 44 = 2.64 × 10 10 dyne cm −2 from the acoustic slopes. The hexagonal approximation is valid to within 10% and this is discussed. The inherent disorder and large size of the unit cell along the c axis (17.35 Å) have restricted modelling of the lattice dynamics by methods such as the atom-atom potential method, and made phonon measurements impracticable in some regions of the momentum transfer-energy transfer space.

A study of the three-dimensional structure of the molecule of the extracting agent lix 65N by the atom-atom potentials method

A study of the three-dimensional structure of the molecule of the extracting agent lix 65N by the atom-atom potentials method

The conformation of 2?-deoxythymidine-3?, 5?-cyclopyrophosphate by1H and31P NMR and atom-atom potential methods

The conformation of 2?-deoxythymidine-3?, 5?-cyclopyrophosphate by1H and31P NMR and atom-atom potential methods