Ab initio crystal structure prediction-I. Rigid molecules

A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum.     

Conformation of BEDT-TTF molecules in the crystal

Based on comparison of low-temperature x-ray diffraction data for BEDT-TTF salts and quantum chemical MNDO calculations, we have shown that the most energetically favorable conformation of the BEDT-TTF molecule is not realized in the crystal. A local energy minimum 0.035 eV above the ground state corresponds to the conformation detected in the crystal. The x-ray diffraction data and the MNDO results suggest weak participation of the heteroatoms of the six-membered rings in the conjugation with the -system of the TTF-fragment in the BEDT-TTF and BEDO-TTF molecules.Institute of Chemical Physics at Chernogolovka, Russian Academy of Sciences, Chernogolovka 142432. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 890–894, April, 1992.     

Water and the relationship to the crystal structure stability of azithromycin

Journal of Thermal Analysis and Calorimetry - This study investigated the solid-state physical stabilities of azithromycin dihydrate (AZM-DH), thermally prepared anhydrate and hemihydrate...     

Synthesis of the tricyclic core structure of vindoline

An efficient synthesis of the core tricyclic structure (18) of vindoline has been achieved using the strategy, which features an intramolecular 1,3-dipolar cycloaddition of the azido dienone (12) to give aziridine (13) with complete region- and stereocontrol.     

The crystal structure of octakispentoxy-phthalocyaninatocopper with pyridines axially substituted: the molecules stacked with J-aggregates

For coordination with two pyridines at the axis, the ring skeleton of octakispentoxyphthalo- cyaninatocopper maintains planar conformation, different from the structure of octakisbutoxy- phthalocyaninatocopper reported previously. The structure shows all molecules stacked along the b axis to form a one-dimensional molecular chain; neighboring molecules in the chain are arranged as J-aggregates, consistent with its crystal diffuse reflectance spectroscopy (DRS) having a red shift compared with its electronic absorption spectroscopy in pyridine.     

Inequivalent molecules in a two-dimensional crystal

Physisorbed monolayers formed at solution-solid interfaces are two-dimensional crystals sharing many structural characteristics, such as packing motifs and reactivity, with their three-dimensional counterparts. Study of these monolayers with scanning tunneling microscopy (STM) offers a promising tool for exploring crystallization phenomena. Although the analogy between the structures of two-dimensional and three-dimensional crystals is becoming clearer with the imaging of increasing numbers of molecules with STM, the occurrence of inequivalent molecules in a unit cell has been limited to three-dimensional crystals. We report that the monolayer of 1,3-dinonadecanoyl benzene formed at the solution-HOPG interface possesses a unit cell with 1.5 inequivalent molecules (Z' = 1.5) demonstrating that, as in the case of three-dimensional crystals, simple molecules can give rise to inequivalent packing in the solid state.     

Enantiospecific synthesis of the tricyclic core structure of lippifolianes

An enantiospecific synthesis of the [6.6.3]-tricyclic carbon framework, 2,6,6,9-tetra-methyltricyclo[5.4.0.0^2,4]undecane, present in the sesquiterpenes lippifolianes and the diterpenes cyclosclareol, metasequoic acids and parguerols, starting from the readily available monoterpene (R)-carvone, is described.     

Dielectric and elastic properties of fluorine-containing tricyclic isothiocyanate liquid crystal

The dielectric and elastic properties of liquid crystals (LCs) generally depend on the molecule structure, such as polar group and carbon chain length. For further investigation of the influence of molecular structure on the dielectric and elastic properties of fluorine-containing tricyclic isothiocyanate LC, the experimental temperature was controlled at 25°C by precision hot stage, and a precision LCR meter was used to measure the capacitance of six LC cells under the voltage from 0.1 to 20 V at 1 kHz. An LC cell capacitance model and a dual-cell model were adopted to obtain the dielectric anisotropy, and the capacitance–voltage curves of six LC materials were plotted. The threshold voltage of Fréedericksz transition was analysed, and a finite difference iterative method was used to attain specific values of three elastic constants. The influence of molecular structure on the dielectric and elastic constants was finally analysed. Experimental results showed that the introduction of meta-difluoro group would increase the dielectric anisotropy and reduce the threshold voltage of LC. As the length of the alkyl carbon chain increased, the dielectric anisotropy would have an odd–even alternation effect, which would lead to changes in the elastic constants of LC.     

Molecular shape of liquid crystal molecules

It is shown that vibrational spectroscopy can provide information on the molecular structure of complex systems such as liquid crystals. Methods are mentioned and data are reported for dodecyl-cyano-biphenyl and for a thermotropic liquid crystal aromatic polyester.     

Synthesis and structure of tricyclic quinazoline alkaloid oxalates

Oxalates of the alkaloids deoxyvasicinone, 2,3-tetra-, and their seven-membered analog 2,3-pentamethylen-3,4-dihydroquinazol-4-one and the complex of 2,3-pentamethylen-3,4-dihydroquinazol-4-one hydrochloride with oxalic acid were synthesized. It was found that 2:1, 2:1, and 1:1 alkaloid:oxalic acid complexes, respectively, were formed. The last complex had 2,3-pentamethylen-3,4-dihydroquinazol-4-one, oxalic acid, and HCl in a 2:1:2 ratio, respectively. X-ray crystal structures of single crystals were performed. The oxalate of 2,3-pentamethylen-3,4-dihydroquinazol-4-one and its hydrochloride formed salts with a protonated N1 atom and involvement of only one hydroxyl. The other alkaloids formed a complex with oxalic acid through N1…H-O H-bonds involving both acid hydroxyls. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 152–156, March–April, 2007.     

Orientation of liquid crystal molecules in polydimethylsiloxane micro-channels

The orientation of liquid crystal (LC) molecules confined in polydimethylsiloxane micro-channels, which are produced using mould-replica technique, with a rectangular cross section, is studied. The rod-like molecules of the LC adopt the vertical anchoring at every surface of the channels. The macroscopic alignment of the confined LC can be changed by altering the aspect ratio of the channels. The change in the macroscopic alignment of the LC is attributed directly to the restructuring of the proportion of the number of molecules anchored to the respective surfaces due to the changes in specific area of the bounding surface of the channels. Solutions for the elastic energy function obtained using conformal mapping method were used to predict director profile of the LC in the confinement.     

Predictability of the polymorphs of small organic compounds: crystal structure predictions of four benchmark blind test molecules

Predicting the crystal structure of an organic molecule from first principles has been a major challenge in physical chemistry. Recently, the application of Density Functional Theory including a dispersive energy correction (the DFT(d) method) has been shown to be a reliable method for predicting experimental structures based purely on their ranking according to lattice energy. Further validation results of the application of the DFT(d) method to four organic molecules are presented here. The compounds were targets (labelled molecule II, VI, VII and XI) in previous blind tests of crystal structure prediction, and their structures proved difficult to predict. However, this study shows that the DFT(d) approach is capable of predicting the solid state structures of these small molecules. For molecule VII, the most stable (rank 1) predicted crystal structure corresponds to the experimentally observed structure. For molecule VI, the rank 1, 2 and 3 predicted structures correspond to the three experimental polymorphs, forms I, III and II, respectively. For molecules II and XI, their rank 1 predicted structures are energetically more stable than those corresponding to the experimental crystal structures, and were not found amongst the structures submitted by the participants in the blind tests. The rank 1 structure of molecule II is predicted to exist under high pressure, whilst the rank 1 structure predicted for molecule XI has the same space group and hydrogen bonding pattern as observed in the crystal of 1-amino-1-methyl-cyclopropane, which is structurally related to molecule XI. The experimental crystal structure of molecule II corresponds to the rank 4 prediction, 0.8 kJ mol(-1) above the global minimum structure, and the experimental structure of molecule XI corresponds to the rank 2 prediction, 0.4 kJ mol(-1) above the global minimum.     

Novel sulphur-containing banana-shaped liquid crystal molecules

In this preliminary report we present the mesomorphic properties and electro-optic investigations of three new 'banana-shaped' mesogens. The materials are structurally similar to Niori's the original bent-core materials but possess alkylthio substituents in place of alkoxy substituents. Microscopic investigations revealed an unusual 'spiral-domain texture', similar to that observed in the 'B₇' phase of related materials. Further investigations support our earlier observations that the materials display antiferroelectric switching in this phase, in two of the new materials studied. The nature of this phase, in comparison with the 'switchable' (B₂) and 'chiral-domain' (B₄) phases of the original materials, is discussed.     

Novel sulphur-containing banana-shaped liquid crystal molecules

In this preliminary report we present the mesomorphic properties and electro-optic investigations of three new 'banana-shaped' mesogens. The materials are structurally similar to Niori's the original bent-core materials but possess alkylthio substituents in place of alkoxy substituents. Microscopic investigations revealed an unusual 'spiral-domain texture', similar to that observed in the 'B₇' phase of related materials. Further investigations support our earlier observations that the materials display antiferroelectric switching in this phase, in two of the new materials studied. The nature of this phase, in comparison with the 'switchable' (B₂) and 'chiral-domain' (B₄) phases of the original materials, is discussed.     

Modification of surface crystal formation on mother crystal by additive molecules

Additive molecules and excess reactant species (NaOH and NH4F) in NaF crystallization were used to control surface crystal formation on a mother crystal. When the surface integration was inhibited or bulk diffusion facilitated, more surface crystals were found on the mother crystal due to an increase in the interfacial supersaturation on the crystal. The inclusion of KCl as an additive and increases in the reactant concentration and agitation speed resulted in a higher population of surface crystals on the mother crystal, because surface integration was inhibited. However, surface crystal formation was suppressed by the polymer gelatin due to retardation of the bulk diffusion by the gelatin layer formed around the crystal. In addition, surface crystal formation significantly changed according to the feeding mode, and the excess species of NaOH originating from the NH4F feeding mode were more effective in facilitating surface crystal formation than the excess species of NH4F coming from the NaOH feeding mode due to the smaller ionic radii of NaOH than of NH4F.     

Conformational energy landscapes of liquid crystal molecules

The conformational energy landscape of the prototypical nematic liquid crystal 4-pentyl-4cyanobiphenyl (5CB) is studied using first principles computer modelling. It is found that the most favourable conformation occurs when the two constituent phenyl rings are inclined at an angle of 31 with respect to each other. Also, the orientation of the alkyl chain is found to have an important influence on the ring-ring torsional potential. We fit the energy surface of these coupled torsions to yield an accurate intramolecular potential for use in empirical modelling. To test the strength of the coupling between the alkyl tail and the phenyl rings and the cyano group, we also calculate potentials for the relative orientation of the phenyl rings in biphenyl and cyanobiphenyl (0CB). Our calculations are performed using density functional theory using pseudo-potentials and the generalized gradient approximation to exchange and correlation. The molecular electronic wavefunction is expanded in terms of a plane wave basis set. We compare our results with recent NMR and Gaussian-based quantum chemistry calculations where available.