Generation of structures of molecular crystals with two molecules related by a twofold axis or a plane of symmetry in a primitive unit cell

Within the method of discrete modeling of packings, an algorithm of generation of possible structures of molecular crystals with two molecules of known shape in the primitive unit cell, related by a twofold (screw or rotary) axis or a plane of mirror or glide reflection symmetry, is proposed. The algorithm is based on the approximation of molecules by polycubes (geometric figures composed of identical cubes) and calculation of all possible periodic packings of these polycubes with a specified packing factor. On the basis of this algorithm, a software package for personal computers is developed. Examples of approval of this package for several crystal structures, identified previously by X-ray diffraction analysis, are reported.     

Morphogenesis of crystal structures in the discrete modeling of packings

Within the framework of the discrete modeling of molecular packings, a metric approach to the investigation of the mechanisms of crystal formation is proposed. This method is based on the construction of a combination of polyhedra in a space in which the space division into polyhedra (or the periodic packing of polyhedra) is specified by the multistage addition to the initial “seeding” polyhedron set of this division (packing) of the adjacent polyhedra. Crystal growth is modeled using the constructions of bounding boxes in the division of the plane into polyominoes and the three-dimensional space, into polycubes. The formation of phenomenological polygons (polyhedra) in the growth of periodic structures is revealed and theoretically grounded.     

Generation of molecular Bravais structures by the method of discrete modeling of packings

An algorithm for the generation of possible crystal structures consisting of molecules with the known shapes in the symmetry classes with one translationally independent molecule (the so-called molecular Bravais structures) has been proposed within the framework of the method of discrete modeling of packings in molecular structures. The algorithm was used to write a special complex of computer programs. Some examples of testing this complex on molecules with the structures determined earlier by the methods of X-ray diffraction analysis are also considered.     

Coordination sequences and coordination waves in matter

A possible way of partitioning a space into polycubes (n-dimensional modifications of Golomb polyominoes, which are generally nonconvex) is used as a basic model of ordered matter structure. It is suggested that layer-by-layer growth of a structure, occurring along the geodetics of the digraph of a net defined by the local rules of bonding of polycubes, justifies the phenomenological laws of shaping (self-similarity during the growth, independence of the polyhedron shape on the “seed,” the symmetry of the growth polyhedron, etc.). Specific results of the analysis of number sequences of the increase in coordination circles for planar periodic partitions of model and real crystal structures, as well as the preliminary results of investigation of standing coordination topological waves, revealed for the first time in computer experiments, are reported.     

Prediction of molecular crystal structures using a genetic algorithm: Validation by GenMol™ on energetic compounds

This work deals with the problem of finding for a given industrial target the molecule conformation leading to the most efficient crystal polymorph and/or designing unknown crystal packing of new molecules. The originality of the method relies first on constraining the domain of the most probable crystals, before converging towards the predicted packing by a double genetic-refining optimization algorithm. Validation of this approach is discussed on the case study of 46 energetic crystal compounds, using the semi Ab Initio and Molecular Mechanics code GenMol™. This validation shows that all observed structures are retrieved in any circumstances with a relatively high number of good rankings.     

Generation of crystal structures of heteromolecular compounds by the method of discrete modeling of packings

Within the method of discrete modeling of packings, an algorithm of generation of possible crystal structures of heteromolecular compounds containing two or three molecules in the primitive unit cell, one of which has an arbitrary shape and the other (two others) has a shape close to spherical, is proposed. On the basis of this algorithm, a software package for personal computers is developed. This package has been approved for a number of compounds, investigated previously by X-ray diffraction analysis. The results of generation of structures of five compounds—four organic salts (with one or two spherical anions) and one solvate—are represented.     

Molecular structures and crystal packings of 2-styrylquinoxaline derivatives

The crystal and molecular structures of 2-styrylquinoxaline derivatives with different substituents in the styryl fragment are determined. The degree of planarity of the molecules studied varies in a very wide range, from 1.7° to 33.5°. In the ethylene fragment, the double bond is essentially localized. The bicycle-pedal disordering of the ethylene fragment is found in the crystals of the methoxy and oxyacetyl derivatives of 2-styrylquinoxaline. None of the packings contains packing motifs favorable for the photocycloaddition (PCA) reaction with single crystal retention. The crystal packings of these compounds and that of 2-(4-methylstyryl)quinoxaline are characterized by a stacking motif of the head-to-head type, which eliminates the possibility of PCA taking place with single crystal retention but is suitable for this reaction in polycrystalline films. The crystal packing of 2-(3,4-dimethoxystyryl)quinoxaline does not contain elements with stacking interactions.     

An X – Ray Study of the p-n-Alkoxycinnamic Acids. Part III.1

The effect upon molecular packing of increasing chain length in a homologous series of mesogens has been examined in the case of the p-n-alkoxycinnamic acids by determination of the crystal structures of the four nematogenic acids having two, four, six, and eight carbon atoms in the alkyl chain. The chains have the all-trans extended conformation, and the molecules exist in the crystal as planar hydrogen-bonded dimers. The dimers are arranged in end-to end fashion in parallel rows. Similar side-to-side packing of pairs of dimmers is found in each crystal structure giving a good fit between adjacent aromatic cores, but the amplitudes of thermal vibration of the chain carbon atoms increase markedly with increasing chain length, indicating a low packing efficiency for these moieties.     

Molecular and crystal structures of 1-methyl-2-Oxo-3-acetoxy-4-hydroxy-4-(Phenyl)piperidine, 1-ethyl-2-oxo-3,4-dihydroxy-4-(Pyridyl)piperidine, and 1-benzyl-2-oxo-3,4-dihydroxy-4-(Pyridyl)piperidine and the role of hydrogen bonds in molecular packing in crystals

The molecular and crystal structures of 1-methyl-2-oxo-3-acetoxy-4-hydroxy-4-(phenyl)hydropyridine, 1-ethyl-2-oxo-3,4-dihydroxy-4-(pyridyl)piperidine, and 1-benzyl-2-oxo-3,4-dihydroxy-4-(pyridyl)piperidine are determined by X-ray diffraction analysis. These three hydroxy derivatives of hydropyridine are the convenient model compounds in studies of the influence of intramolecular and intermolecular hydrogen bonds on the conformation and packing of molecules in crystals. The molecules of hydroxy derivatives possess a considerable conformational flexibility and can form an extended network of intramolecular and intermolecular hydrogen bonds. It is shown that these compounds more often than others form noncentrosymmetric and polysystem crystals. The role of the molecular association and the type of hydrogen-bonded associates (syntons) in crystal packing are discussed.     

Structures of Complex Crystals of Alkylammonium Salts with Aromatic Molecules

Abstract

The complex crystal structures of dodecyltrimethylammonium chloride (DTAC) with catechol and hydroquinone were analysed by an X-ray diffraction method. Both complexes have isomorphous layered structures. The guest molecules locate between the interdigitated host molecules. Crystal structures are stabilized by mainly hydrogen bonds including water molecules. A cross-section balance between hydrophilic and hydrophobic parts is important for an energetically stable packing. DTAC can form the crystalline complexes with catechol and hydroquinone by both crystallizing from the solution and mixing host and guest powders in a mortar. In addition, DTAC can also make a complex with resorcinol. Powder diffraction pattern indicates that this complex has similar layered structure with complexes of DTAC / catechol and DTAC / hydroquinone. However, it is unstable in atmospheric condition.     

Specific features of the crystal packing that enable styryl dyes of the pyridine series to undergo the solid-phase [2 + 2] photocycloaddition including the process with single crystal retention

The crystal packing of a number of styryl dyes of the pyridine series is analyzed. The structures of three dyes and three [2 + 2] photocycloaddition (PCA) products, 1,2,3,4-tetrasubstituted cyclobutanes, obtained in single crystals are determined by X-ray diffraction. Stacks of planar organic cations are characteristic of styryl dye packings. The proceeding of the PCA reaction as a single crystal-to-single crystal transformation in the syn head-to-head stacks is in principle impossible. The syn head-to-tail stacking packings are favorable for the PCA reactions resulting in the centrosymmetric rctt isomers of cyclobutane. The stacking packings, in which molecules are related by the twofold axes (the anti arrangement of molecules), are also favorable for PCA in single crystals. In this case, the products are the rtct isomers of cyclobutane. The presence of the I^? counterions in a packing is a factor impeding the PCA reaction, because the secondary I…H-C bonds increase the rigidity of the crystal lattice. The conditions necessary for proceeding the PCA reactions in styryl dyes as single crystal-to-single crystal processes are as follows: (1) the stacks split into pairs of organic cations (dimers) with the d distances within 4.2 Å in a dimer and d exceeding 4.2 Å between the dimers; and (2) the dimers are surrounded by flexible shells consisting of anions, solvate molecules, or flexible moieties of the organic cations themselves.     

Principle of modular crystal structure

The principle of modular crystal structure has been formulated and the possibility of choosing a module of a specified structure type for its subsequent modular design is discussed. The modular characteristics of some structure types based on cubic close packing (fundamental and basic modules and the module that can be used to obtain a certain variety of modular structures related to the initial parent type) are described. Possible ways to obtain such a module and the algorithm for choosing it are considered. A comparative analysis of the theoretically derived module with the modules of experimentally determined modular structures is performed by the example of spinelloids (materials with spinel-like structure).     

An Investigation of the Dynamic Structures of Ferrocene,Ruthenocene and Dibenzenechromium in the Solid State and in Solution

Pulse nuclear magnetic resonance measurements have been used to determine the activation enthalpies for the reorientation of the organic rings in ferrocene, ruthenocene and dibenzenechromium. The contribution from non-bonded interactions to the total potential for reorientation of the rings has been calculated and is compared to the experimental activation enthalpies. The results indicate that there is no contribution to the potential from the non-bonded interactions between the two rings on a single molecule and that the observed potential barrier is due to a combination of crystal packing forces and bonding forces within the molecule.

The crystal structure of ferrocene is thought to be disordered above 135[ddot]K, and a model is proposed for the order-disorder transition in the solid state. On this basis, dynamic models are proposed for the structures of the three metallocenes in solution.     

A method for automated determination of the crystal structures from X-ray powder diffraction data

An algorithm is proposed for determining the crystal structure of compounds. In the framework of this algorithm, X-ray powder diffraction patterns are compared using a new similarity index. Unlike the indices traditionally employed in X-ray powder diffraction analysis, the new similarity index can be applied even in the case of overlapping peaks and large differences in unit cell parameters. The capabilities of the proposed procedure are demonstrated by solving the crystal structures of a number of organic pigments (PY111, PR181, Me-PR170).     

Packing analysis of racket-like molecules: C6H5MX (M=metal,X=Cl,Br, I). Crystal structure determination of microcrystalline C6H5HgCl by XRD

Relationships between molecular shape and its crystal packing are studied. The XRD crystal structure of macrocrystals and microcrystals of C₆H₅HgX, and their VDW packing analysis, suggest two isoenergetic packing models for racket-like molecules. One of them favoring the crystal growth, and the other more frequent forming microcrystalline aggregates.     

Polymorphism of dianilinegossypol

Polymorphs of dianilinegossypol are obtained by selecting the precipitation medium and the crystallization temperature. Four dianilinegossypol polymorphs are found. Two solvate forms and three polymorphic modifications of dianilinegossypol are prepared from an acetone solution by varying the crystallization temperature from room temperature to 6°C. The crystal structures of the P1, P2, and P4 polymorphs are determined. The P1 and P2 polymorphs are characterized by the same hydrogen-bond system, but their crystal structures differ in the mode of packing of layers formed by dimers of dianilinegossypol molecules. In the P4 polymorph, homochiral hydrogen-bonded dianilinegossypol molecules form trimers. This mode of H-agglomeraton of dianilinegossypol molecules is characteristic only of the P4 polymorph.     

Structural and energetic aspects of the differences between real and predicted polymorphs

In crystal structure prediction simulations based on lattice energy minimization, usually hundreds of structures within a reasonable range of lattice energy and density are found, whereas in practice, it is very rare to find more than a few polymorphs of the same compound. In the work presented here, this discrepancy is investigated from a structural and energetic point of view. 56 crystal structures of 26 polymorphic mono‐ and disubstituted aromatic compounds, extracted from the Cambridge Structural Database, have been analysed with respect to inter‐polymorphic structural similarity. For comparison, potential crystal packing arrangements of the substances have been predicted with molecular mechanics simulations using a generic force field. The predicted structures are analysed with respect to structural features and similarity, and with respect to the number of structures and their lattice energy. It is found that the real polymorphs studied in this work tend to be structurally quite dissimilar with regard to hydrogen bonding and spatial packing of structural motifs, while many of the predicted structures of a given compound are very similar to each other. The results suggest that structure and lattice energy alone cannot explain why so few polymorphs are found in practice compared to the very large numbers predicted in simulations. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Characterization of the Hexatic B and Crystal B phases by Optical Microscopy

Recent investigations concerning the structure of the B Phase have unearthed a variety of packing arrangements of the molecular layers for this semctic modification. Two general structures have been discovered; one in which the B Phase has three-dimensional crystalline order (crystal B), and one that is characterized by short-range in-plane positional ordering of the constituent molecules, and long-range bond orientational order, both within and between the layers (heatic B). In this present study n-hexyl 4′-n-pentyloxybiphenyl-4-carboxylated (650BC) has been synthesized and its smectic phases charaterized. Typically, this ester exhibits an A, B,E, phase sequence, with the B Phase being of the hexactic type. The Synthesis, microscopic textures, and miscibility studise ar reported here. The results show that while the two types of B phase appear co-miscibly by conventional optical mehtods, in fact X-ray diffraction studies show that a transition occurs between the two phases in certain binary mixtures. Thus, the hexactic B and crystal B modification are thermodynamically distint phasaes.     

X-ray diffraction study of p-(alkoxybenzylidene)-p′-toluidines: Crystal and molecular structure of C10H21O-C6H4-CH=N-C6H4-CH3

The crystal and molecular structure of p-(decaoxybenzylidene)-p′-toluidine C₁₀H₂₁O-C₆H₄-CH=N-C₆H₄-CH₃ is studied. The molecule is nearly planar. In the crystal packing, loose regions formed by aliphatic fragments of molecules alternate with pseudostacks of aromatic fragments of molecules that are related by the centers of symmetry. The stacks are built of dimers, in which molecules are linked by π-stacking interactions between benzene rings. There are no weak directional interactions between dimers in a stack. The presence of a single structure-forming element in the crystal, namely, the π-stacking interactions in the dimers, along with the similarity of the crystal packing to that of the C₈H₁₇O-homologue, which forms a nematic mesophase on melting, indicate that the crystals under study should exhibit nematic properties.     

Structural study of the molecular complex in crystals of brucine with pantolactone

We have determined an X-ray crystal structure, a = 12.482(1), b = 14.349(1), c = 14.342(1) Å, orthorhombic, P2₁2₁2₁ for a molecular complex of brucine with pantolactone. The crystal structure is composed of corrugated sheets of brucine molecules containing the guest pantolactone molecules. The conformational twist of the pyrrolidine ring in brucine may probably be important in projecting the amine N2 to provide a strong and specific binding site for a chiral complexation. The pseudo-equatorial orientation of the hydroxyl group of the pantolactone anchors itself for binding via hydrogen bonding. In the crystal packing, the pantolactone molecules form helices and the brucine molecules are attached to these helices by O=H···N hydrogen bonds.