A MO-SCF study of hydroxyl binding and hydroxyl diffusion in pure and fluorine-containing hydroxyapatite

Hydroxyl diffusion and interhydroxyl binding in hydroxyapatite has been studied. LCGO -MO -SCF calculations have been carried out on groups of hydroxyl ions in a perfect and a vacancy-containing crystal. Electrostatic crystal effects were accounted for by including the crystal potential field in the SCF calculations. Nearest-neighbour interactions were calculated to first order. Effects exerted by fluorine impurities were considered for the vacancy-containing crystal. The calculations indicate that narrow bandwidths obtained in nmr experiments on biological hydroxyapatite may be caused by a hydroxyl displacement mechanism and that no interhydroxyl hydrogen bonds exist in hydroxyapatite. The suggestion that the caries-inhibiting properties of fluorine impurities in human dental enamel is caused by a diffusion-binding mechanism is supported by the results.     

Microsolvation effects on the optical properties of crystal violet

We present a joint experimental and theoretical study of the photoabsorption and photodissociation behavior of crystal violet, that is, the tris[p-(dimethylamino)phenyl]methyl cation. The photodissociation spectra of isolated and microsolvated crystal violet have been measured. A single band is observed for the bare cation. This is in good agreement with the calculated vibronic absorption spectrum based on time-dependent density functional theory calculations. The interaction of crystal violet with a single water molecule shifts and broadens the photodissociation spectrum, so that it approaches the spectrum obtained in solution. Theoretical calculations of the structure of the complex suggest that the shift in the absorption spectrum originates from a water molecule bonding with the central carbon atom of crystal violet.     

Theoretical characterization of titanyl phthalocyanine as a p-type organic semiconductor: short intermolecular pi-pi interactions yield large electronic couplings and hole transport bandwidths

The charge-transport properties of the triclinic phase II crystal of titanyl phthalocyanine (alpha-TiOPc) are explored within both a hopping and bandlike regime. Electronic coupling elements in convex- and concave-type dimers are calculated using density functional theory, and the relationship between molecular structure and crystal packing structure in model dimer configurations is considered. Hole transport bandwidths derived from crystal structure dimers are compared to those obtained from electronic band structure calculations; very good agreement between the two approaches is found. The calculations predict large hole bandwidths, on the order of 0.4 eV, and correspondingly very low hole reorganization energies.     

Random fluorinated copolymers of tetrafluoroethylene: a study of the inclusion/exclusion of defects from the crystal by conformational and packing energy calculations

A conformational analysis has been performed on the isolated chains of copolymers of tetrafluoroethylene with hexafluoropropene, chlorotrifluoroethylene or perfluoromethyl vinyl ether, in comparison with polytetrafluoroethylene. The lowest energy conformations in accordance with the chain repeating distance of polytetrafluoroethylene in the low temperature crystal phase have been used in packing energy calculations. The results of both conformational and packing energy calculations suggest that the  Cl group is easily tolerated in the crystal phase. The —CF₃ group could also be tolerated in the crystal phase but at the cost of conformational and crystal lattice deformations. On the contrary, it can be concluded that the —OCF₃ group is excluded from the crystal phase because its presence should require high energy values and wide deformations in the unit cell parameters.     

Ab initio study of (13)C(alpha) chemical shift anisotropy tensors in peptides

This study reports magnitudes and the orientation of the (13)C(alpha) chemical shift anisotropy (CSA) tensors of peptides obtained using quantum chemical calculations. The dependency of the CSA tensor parameters on the energy optimization of hydrogen atom positions and hydrogen bonding effects and the use of zwitterionic peptides in the calculations are examined. Our results indicate that the energy optimization of the hydrogen atom positions in crystal structures is necessary to obtain accurate CSA tensors. The inclusion of intermolecular effects such as hydrogen bonding in the calculations provided better agreement between the calculated and experimental values; however, the use of zwitterionic peptides in calculations, with or without the inclusion of hydrogen bonding, did not improve the results. In addition, our calculated values are in good agreement with tensor values obtained from solid-state NMR experiments on glycine-containing tripeptides. In the case of peptides containing an aromatic residue, calculations on an isolated peptide yielded more accurate isotropic shift values than the calculations on extended structures of the peptide. The calculations also suggested that the presence of an aromatic ring in the extended crystal peptide structure influences the magnitude of the delta(22) which the present level of ab initio calculations are unable to reproduce.     

Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques

Summary The conformational preferences of 12 molecular substructures in the crystalline state have been determined and compared with those predicted for relevant model compounds by ab initio molecular orbital calculations. Least-squares regression shows that there is a statistically significant correlation between the crystal-structure conformer distributions and the calculated potential-energy differences, even though the calculations relate to a gas-phase environment. Torsion angles associated with high strain energy (>1 kcal mol^-1) appear to be very unusual in crystal structures and, in general, high-energy conformers are underrepresented in crystal structures compared with a gas-phase, room-temperature Boltzmann distribution. It is concluded that crystal packing effects rarely have a strong systematic effect on molecular conformations. Therefore, the conformational distribution of a molecular substructure in a series of related crystal structures is likely to be a good guide to the corresponding gas-phase potential energy surface.     

ER-BOC calculations of crystal bulk properties from smallest-cluster models

Ab initio calculation of bulk properties of crystals with a high accuracy, which is a long-time goal of solid chemistry and physics, is still difficult and expensive because a large cluster is required as a crystal structure model. This article proposes a model based on density functional theory (DFT) quantum chemistry calculations and the assumption that the bond order of a given atom with its nearest atoms in a compound is conserved over the entire range from its diatomic molecules to clusters and further to crystals. This entire range bond order conservation (ER-BOC) provides an effective way to correlate bulk properties of crystals with those of the corresponding molecules and small clusters. By combining this ER-BOC principle with hybrid DFT quantum chemistry calculations, accurate predictions of the bulk bond lengths of a crystal can be made using calculations on small clusters.     

Insights into the Crystallisation Process from Anhydrous,Hydrated and Solvated Crystal Forms of Diatrizoic Acid

Diatrizoic acid (DTA), a clinically used X‐ray contrast agent, crystallises in two hydrated, three anhydrous and nine solvated solid forms, all of which have been characterised by X‐ray crystallography. Single‐crystal neutron structures of DTA dihydrate and monosodium DTA tetrahydrate have been determined. All of the solid‐state structures have been analysed using partial atomic charges and hardness algorithm (PACHA) calculations. Even though in general all DTA crystal forms reveal similar intermolecular interactions, the overall crystal packing differs considerably from form to form. The water of the dihydrate is encapsulated between a pair of host molecules, which calculations reveal to be an extraordinarily stable motif. DTA presents functionalities that enable hydrogen and halogen bonding, and whilst an extended hydrogen‐bonding network is realised in all crystal forms, halogen bonding is not present in the hydrated crystal forms. This is due to the formation of a hydrogen‐bonding network based on individual enclosed water squares, which is not amenable to the concomitant formation of halogen bonds. The main interaction in the solvates involves the carboxylic acid, which corroborates the hypothesis that this strong interaction is the last one to be broken during the crystal desolvation and nucleation process.     

Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Lattice dynamics and interaction potentials in molecular crystals

This paper, based essentially on the work done in recent years in our laboratory, presents a critical analysis of harmonic and anharmonic calculations of crystal vibrations in the determination of intermolecular potentials. The main purpose is to show that the dynamical properties are specifically sensitive to different terms of the potential and thus that information extracted from vibrational spectra of crystals is of the greatest importance for the theory of intermolecular forces. The most important conclusion is that these calculations point to the development of anisotropic short-range potentials and orient future researches towards the more complex and elaborate anharmonic treatment of crystal vibrations.     

Refinement of linear polymer crystal structures determined from electron diffraction data

The reliability of linear polymer structures determined by using electron diffraction data is investigated. The results of n-beam dynamical calculations and kinematic calculations which take account of crystal bending are compared with experimental structure factors for five published structures. In specific cases, both dynamical scattering and crystal bending effects are found to be important. Finally, guidelines are given for obtaining electron diffraction data which are optimal for structure solution.     

Application of molecular mechanics to refine and understand the crystal structure of polythiophene and its oligomers

A molecular mechanics computational procedure, previously used for the refinement and the analysis of several crystalline polymers, was applied to investigate the crystal structures of the tetramer (T4) and hexamer (T6) of thiophene, as well as the crystal structure of polythiophene (PT). Simultaneous minimization of intra- and intermolecular energies of the T4 and T6 structures, obtained by Rietveld analysis of powder X-ray diffraction profiles, leads to molecular conformations showing smaller deviations from the ring co-planarity than the original models. For both oligomers the calculations confirm that the molecular centre of inversion is not a crystallographic centre of symmetry, as also revealed by X-ray diffraction of the T6 single crystal. This surprising effect appears to arise from intermolecular interactions between the terminal residues, hence is not relevant with respect to the PT polymer structure. The small energy cost for constraining the molecules at the crystallographic centre of symmetry is in agreement with experimental findings that reveal the existence of polymorphs for both T4 and T6. The calculations on the T6 single crystal were used to upgrade the MM2-like force field, which was then used to determine the minimum-energy model of the monoclinic crystal structure of polythiophene.     

Theory of radiationless transitions in a crystalline host material

Consistent calculations of the rate constant of radiationless electron transition are reported for a diatomic molecule in a crystal at zero temperature. The transition between electronic states occurs due to nonadiabaticity. Relaxation of the vibrational energy is stimulated by the interaction of the molecule with the crystal. The calculations have been carried out under the assumption that perturbation theory with respect to the nonadiabaticity operator is applicable. The vibrational interaction of the molecule with the environment is assumed not to be small. The electronic terms of the molecule are approximated by Morse potentials.     

Ab initio and molecular dynamics studies of crystalline TNAD (trans-1,4,5,8-tetranitro-1,4,5,8-tetraazadecalin)

The structural and electronic properties of the energetic crystal TNAD (trans-1,4,5,8-tetranitro-1,4,5,8- tetraazadecalin) have been studied using plane-wave ab initio calculations based on the density function theory method with the ultrasoft pseudopotentials. It is found that the predicted crystal structure is in good agreement with experimental data and there are strong inter- and intramolecular interactions in bulk TNAD. Band structure calculations indicate that TNAD is an insulator with the band gap of ca. 3.3 eV. The hydrostatic compression effect on TNAD has been studied in the pressure range of 0-600 GPa. The results show that a pressure less than 10 GPa does not significantly change the geometric parameters, charge distributions, and electronic bands. When the pressure is over 10 GPa, increasing the pressure determines significant changes of the geometrical and electronic structures and large broadening of the electronic bands together with a sharp decrease of the band gap. Isothermal-isobaric molecular dynamics simulations at atmospheric pressure were further performed on the TNAD crystal in the temperature range 5-500 K. Average equilibrium lattice parameters and elastic properties as functions of temperature were determined. The thermal expansion coefficients calculated for the crystal indicate anisotropic behavior with the largest expansion along the b axis.     

Structural and electronic properties of La‐doped CaTiO3 crystal

There is experimental and computational evidence that some important properties such as electrical conductivity and ferroelectricity in the CaTiO₃ crystal change according to the dopant states. Using an INDO quantum‐chemical computational method modified for crystal calculations we explore the stability of the La‐doped CaTiO₃ crystal in both phases, cubic and orthorhombic. The calculations are carried out by means of the supercell model based on the LUC (large unit cell) approach as it is implemented into the CLUSTERD computer code. The equilibrium geometry for impurity is found together with the crystalline lattice distortions. Atomic displacements and relaxation energies are analyzed in a comparative manner for the two crystallographic phases. A new effect of electron transfer from the local one‐electron energy level within the band‐gap to the conduction band is observed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Formation of the background component of the analytical signal in the long-wavelength region of X-ray fluorescence spectrum

Components of X-ray background in the long-wavelength spectral region of a crystal diffraction X-ray fluorescence spectrometer were calculated. The calculations took into account the bremsstrahlung radiation of free electrons, diffuse scattering and fluorescence of the crystal analyzer, and high-order reflections of the scattered radiation of the fluorescent sample by the crystal analyzer. The results of calculations were compared with the intensities of background samples measured in the region of the NaK _α fluorescence line on an SRM-25 wave X-ray spectrometer. The experimental background intensities (response function) well correlate with those found by the regression equation with calculated factors. The importance of particular processes in the formation of X-ray background was assessed.     

A first-principles DFT study of UN bulk and (001) surface: comparative LCAO and PW calculations

LCAO and PW DFT calculations of the lattice constant, bulk modulus, cohesive energy, charge distribution, band structure, and DOS for UN single crystal are analyzed. It is demonstrated that a choice of the uranium atom relativistic effective core potentials considerably affects the band structure and magnetic structure at low temperatures. All calculations indicate mixed metallic-covalent chemical bonding in UN crystal with U5f states near the Fermi level. On the basis of the experience accumulated in UN bulk simulations, we compare the atomic and electronic structure as well as the formation energy for UN(001) surface calculated on slabs of different thickness using both DFT approaches.     

Synthesis, structural characterization and conformational aspects of nostoclide analogues

The synthesis and structural analysis of a set of nostoclide analogues with potential herbicide activity is described. The influence of intra- and intermolecular hydrogen bonding, as well as other interactions on the conformation and packing of the compounds is thoroughly described using DFT calculations and single crystal X-ray diffraction analyses. All lactones exhibited the Z configuration as confirmed by NOESY experiments and by single crystal X-ray diffraction measurements.     

Structure prediction, disorder and dynamics in a DMSO solvate of carbamazepine

We have applied crystal structure prediction methods to understand and predict the formation of a DMSO solvate of the anti-convulsant drug carbamazepine (CBZ), in which the DMSO molecules are disordered. Crystal structure prediction calculations on the 1:1 CBZ:DMSO solvate revealed the generation of two similar low energy structures which differ only in the orientation of the DMSO molecules. Analysis of crystal energy landscapes generated at 0 K suggests the possibility of solvent disorder. A combined computational and experimental study of the changes in the orientation of the DMSO within the crystal structure revealed that the nature of the disorder changes with temperature. At low temperature, the DMSO disorder is static whilst at high temperature the DMSO configurations can interconvert by a 180° rotation of the DMSO molecules within the lattice. This 180° rotation of the DMSO molecules drives a phase change from a high temperature dynamically disordered phase to a low temperature phase with static disorder. Crystallisation of a DMSO solvate of the related molecule epoxycarbamazepine resulted in a different degree of DMSO disorder in the crystal structure, despite the similarity of the carbamazepine and epoxycarbamazepine molecules. We believe consideration of disorder and its contribution to entropy and crystal free energies at temperature other than 0 K is fundamental for the accuracy of future energy rankings in crystal structure prediction calculations of similar solvated structures.     

A comparison of the photoelectron spectrum and crystal orbital calculations of polyethylene

The experimentally observed photoelectron spectrum of C₃₆H₇₄ is compared with theoretical calculations based on crystal orbital theory at vario