p‐Phenylenediamine and its dihydrate: two‐dimensional isomorphism and mechanism of the dehydration process,and N—H...N and N—H...π interactions

p‐Phenylenediamine can be obtained as the dihydrate, C₆H₈N₂·2H₂O, (I), and in its anhydrous form, C₆H₈N₂, (II). The asymmetric unit of (I) contains one half of the p‐phenylenediamine molecule lying about an inversion centre and two halves of water molecules, one lying on a mirror plane and the other lying across a mirror plane. In (II), the asymmetric unit consists of one molecule in a general position and two half molecules located around inversion centres. In both structures, the p‐phenylenediamine molecules are arranged in layers stabilized by N—H...π interactions. The diamine layers in (I) are isostructural with half of the layers in (II). On dehydration, crystals of (I) transform to (II). Comparison of their crystal structures suggests the most plausible mechanism of the transformation process which requires, in addition to translational motion of the diamine molecules, in‐plane rotation of every fourth p‐phenylenediamine molecule by ca 60°. A search of the Cambridge Structural Database shows that the formation of hydrates by aromatic amines should be considered exceptional.     

Crystal Structure and Theoretical Calculation of 1,4-Bis-(1-ferrocenesulfonyl-2-benzimidazolyl) Butane

A N,N′‐bisferrocenesulfonyl bisbenzimidazole compound 1,4‐bis(1‐ferrocenesulfonyl‐2‐benzimidazolyl) butane was prepared. Its crystal structure was determined. The crystal belongs to triclinic with space group P‐1 and a=0.87241(13) nm, b=0.97553(15) nm, c=1.4120(2) nm, and α=83.041(2) °, β=72.454(2)°, γ=69.732(2)°, the unit cell volume V=1.0746(3) nm³, the molecule number in one unit cell Z=1, the absorption coefficient μ=1.191 mm^?1, the calculated density D_c=1.584 g/cm³. The theoretical investigation of the compound as a structure unit was fully optimized by B3LYP/6‐31G method in Gaussian 03 package, and the most stable structure of the compound in theory was obtained. The two results were compared. The optimized structure was in accordance with the crystal structure in the main, suggesting that the molecular geometry optimization of the structures was reliable and the calculation method used was reliable. The distribution of atomic charges and the energy, and composition of frontier molecular orbits were analyzed. Thermal analysis indicated that it is stable before melting.     

Computer modelling studies of 18-crown-6 with urea and thiourea

Abstract

Computer modelling studies have been carried out on the interaction of 18-crown-6 with a variety of guest molecules, including urea, thiourea and substituted ureas. The five known crystal structures of these host/guest systems were used as models. We were interested to establish whether the arrangement of guest molecules around a host molecule in the crystal was indicative of the lowest energy configuration for a host/guest fragment or was a consequence of packing effects. Two models were therefore considered for each structure and the structures minimised via molecular mechanics. In the first mode, the structure consisted of one unit cell and periodic boundary conditions were used in the calculation. Coulombic effects were calculated using the Ewald summation. In the second model, the structure consisted of an 18-crown-6 molecule surrounded by two hydrogen-bonded guest molecules. Both models were minimised using the CERIUS package using the DreidingII forcefield.

The crystal structure minimisations reproduced the structures very well with an average change in cell volume of 3.6% and a mean r.m.s. positional deviation of 0.20 Å. The fits for the fragment models were significantly larger for all structures (mean 0.30 Å) but even so it can be concluded that the arrangement in the crystal gave a good indication of the lowest energy configuration of the host/guest in vacuo.     

X-Ray Diffraction Study of 2-Aminopropenenitrile at 97 K

2-Aminopropenenitrile crystallizes in the space group P2₁2₁2₁ with two molecules in the asymmetric unit. Both molecules show appreciable pyramidalization at the amino group. The crystal structure is built from approximately centrosymmetric dimers stabilized by hydrogen bonding between the amino group of each molecule and the nitrile group of its partner. The dimers are linked into chains by further hydrogen bonds in which the amino group of one molecule acts as donor, the amino group of the other as acceptor. The two types of molecule thus play different roles in the crystal structure. Electron density difference maps for the two independent molecules show characteristic bonding density features. The molecular structure as obtained by the low-temperature X-ray analysis is closely similar to that derived from ab initio molecular orbital calculations and leads to rotational constants close to those obtained from a microwave spectroscopic study.     

Twinning in 5‐fluorosalicylic acid: description of a new polymorph

The crystal structure of 5‐fluorosalicylic acid is known from the literature [Choudhury & Guru Row (2004). Acta Cryst. E 60 , o1595–o1597] as crystallizing in the monoclinic crystal system with space‐group setting P2₁/n and with one molecule in the asymmetric unit (polymorph I). We describe here a new polymorph which is again monoclinic but with different unit‐cell parameters (polymorph II). Polymorph II has two molecules in the asymmetric unit. Its structure was modelled as a twin, with a pseudo‐orthorhombic C‐centred twin cell.     

The synthesis and crystal structure of heteronuclear complex of lanthanide with sulfo-salicylic acid [Na3YLa2(C7H3SO6)4.26H2O]n

The titled complex has been synthesized by the reaction of sodium sulfo-salicylate with lanthanum and yttrium perchlorate. The crystal structure has been determined by single crystal X-ray diffractometry. The crystal is monoclinic with space group C2/c. The unit cell parameters are as follows: a=16.289(8), b=18.323(8), c=22.044(8) A, β=106.34(2)°, V=6314(6) A3, Z=4 and Dc=1.764 g/cm3. The structure was solved by direct method. The least-square refinement based on 3776 observed reflections [F > 6σ(F)] converged to a final R=8.6% and F(000) is 3548. Yttrium ion with eight-coordinate is located in central of the molecule, the two lanthanum ions with ten-coordinate are located at the two sides of yttrium ion. There are two positions for Na in the molecule, one is in the C2 axis with six coordinate, the other one is in a general position with five-coordinate.     

Cocrystal of cis‐ and trans‐N‐phenylformamide

N‐Phenylformamide, C₇H₇NO, crystallizes with two molecules in the asymmetric unit which have different conformations of the formylamino group, one being cis and the other trans. This is the first example of an arylformamide crystal containing both conformational isomers and it may thus be considered a cocrystal of the two conformers. The two molecules in the unit cell are linked through N—H...O hydrogen bonding to two other molecules, thereby forming hydrogen‐bonded tetramers within the crystal structure.     

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.     

Crystal structure and hydrogen bonding in the hydrated cocrystalline salt tryptaminium–3,5‐dinitrobenzoate–quinoline–water (3/3/2/2)

The study of ternary systems is interesting because it introduces the concept of molecular preference/competition into the system where one molecule may be displaced because the association between the other two is significantly stronger. Current definitions of a tertiary system indicate that solvent molecules are excluded from the molecule count of the system and some of the latest definitions state that any molecule that is not a solid in the parent form at room temperature should also be excluded from the molecule count. In the structure of the quinoline adduct hydrate of tryptaminium 3,5‐dinitrobenzoate, 3C₁₀H₁₃N₂⁺·3C₇H₃N₂O₆⁻·2C₉H₇N·2H₂O, the asymmetric unit comprises multiple cation and anion species which are conformationally similar among each type set. In the crystal, a one‐dimensional hydrogen‐bonded supramolecular structure is generated through extensive intra‐ and inter‐unit aminium N—H…O and N—H…N, and water O—H…O hydrogen bonds. Within the central‐core hydrogen‐bonding associations, conjoined cyclic R₄⁴(10), R₅³(10) and R₄⁴(12) motifs are generated. The unit is expanded into a one‐dimensional column‐like polymer extending along [010]. Present also in the crystal packing of the structure are a total of 19 π–π interactions involving both cation, anion and quinoline species [ring‐centroid separation range = 3.395 (3)–3.797 (3) Å], as well as a number of weak C—H…O hydrogen‐bonding associations. The presence of the two water molecules in the crystal structure is considered to be the principal causative factor in the low symmetry of the asymmetric unit.     

Packing considerations of 10‐oxa‐9‐boraphenanthrene derivatives

The crystal structures of three products of the reaction of 2‐phenylphenol and BCl₃ have been determined. The structures show intriguing packing patterns and an interesting case of pseudosymmetry. In addition, one of the two polymorphs has a primitive monoclinic crystal system, but it is twinned and emulates an orthorhombic C‐centred structure. Tris(biphenyl‐2‐yl) borate, C₃₆H₂₇BO₃, ( III ), crystallizes with only one molecule in the asymmetric unit. The dihedral angles between the planes of the aromatic rings in the biphenyl moieties are 50.47 (13), 44.95 (13) and 42.60 (13)°. The boron centre is in a trigonal planar coordination with two of the biphenyl residues on one side of the BO₃ plane and the remaining biphenyl residue on the other side. One polymorph of 10‐oxa‐9‐boraphenanthren‐9‐ol, C₁₂H₉BO₂, ( V a ), crystallizes with two almost identical molecules (r.m.s. deviation of all non‐H atoms = 0.039 Å) in the asymmetric unit. All non‐H atoms lie in a common plane (r.m.s. deviation = 0.015 Å for both molecules in the asymmetric unit). The two molecules in the asymmetric unit are connected into dimers via O—H...O hydrogen bonds. A second polymorph of 10‐oxa‐9‐boraphenanthren‐9‐ol, ( V b ), crystallizes as a pseudo‐merohedral twin with two almost identical molecules (r.m.s. deviation of all non‐H atoms = 0.035 Å) in the asymmetric unit. All non‐H atoms lie in a common plane (r.m.s. deviation = 0.012 Å for molecule 1 and 0.014 Å for molecule A). Each of the two molecules in the asymmetric unit is connected into a centrosymmetric dimer via O—H...O hydrogen bonds. The main difference between the two polymorphic structures is that in ( V a ) the two molecules in the asymmetric unit are hydrogen bonded to each other, whereas in ( V b ), each molecule in the asymmetric unit forms a hydrogen‐bonded dimer with its centrosymmetric equivalent. 9‐[(Biphenyl‐2‐yl)oxy]‐10‐oxa‐9‐boraphenanthrene, C₂₄H₁₇BO₂, ( VI ), crystallizes with four molecules in the asymmetric unit. The main differences between them are the dihedral angles between the ring planes. Apart from the biphenyl moiety, all non‐H atoms lie in a common plane (r.m.s. deviations = 0.026, 0.0231, 0.019 and 0.033 Å for molecules 1, A, B and C, respectively). This structure shows pseudosymmetry; molecules 1 and A, as well as molecules B and C, are related by a pseudo‐translation of about in the direction of the b axis. Molecules 1 and B, as well as molecules A and C, are related by a pseudo‐inversion centre at ,,. Neither between molecules 1 and C nor between molecules A and B can pseudosymmetry be found.     

Synthesis,crystal structures,spectral FT‐IR,NMR and UV–Vis investigations and Hirshfeld surface analysis of two new 2‐hydroxyethyl‐substituted N‐heterocyclic carbene precursors

This study discusses the synthesis of two new 2‐hydroxyethyl substituted N‐heterocyclic carbene (NHC) precursors. The NHC precursors were prepared from 1‐(alkyl/aryl)benzimidazole and alkyl halides. They were characterized using ¹H NMR, ¹³C NMR, FT‐IR, UV–Vis spectroscopy, and elemental analysis techniques. Molecular and crystal structures of 1 and 2 were determined using the single‐crystal X‐ray diffraction method. Crystal structure of the compounds features NHC precursors and chloride anions. Additionally in 2 , the asymmetric unit has a water molecule, which forms a tetrameric chloride‐hydrate assembly with the chloride anion. The chloride anions play an important role in the stabilization of crystal structures to form a two‐dimensional supramolecular architecture. The 3D Hirshfeld surface and the associated 2D fingerprint plots were also drawn to gain insights into the behavior of the interactions in the compounds.     

MOLECULAR CLOSE-PACKING METHOD AND ITS APPLICATION TO CRYSTAL STRUCTURE DETERMINATION OF DESHEXAPEPTIDE (B25--B30) INSULIN

Based on the molecule-packing theory, we defined a molecule-packing function express-ing the compatibility of packing among the symmetry-related molecules in a unit cell. Acomputer program imitating the close-packing of molecules in the objective crystal latticeand giving the function value of each rotation and translation of the molecule in the unitcell was performed, and it therefore made the close-packing of molecules expressquantitatively. This method not only could judge a correct solution from several peaks ofthe rotation or translation function but it may also independently, quantitatively and quicklysolve some specific problems of rotation and translation. Using known structure of despenta-peptide (B26--B30) insulin as an example, the effectiveness of this method and its programwas inspected, and this method was successfully applied to solving the translation problem ofthe unknown structure of deshexapeptide (B25--B30) insulin. The molecular close-packingmethod proved by the results of R--search     

应用分子图形学、分子力学、量子化学及静电势研究农药分子结构与性能关系(XI)──抗植物病毒病药物──胡椒醛肟醚基-4-喹唑啉的结构特征

测定了标题化合物的晶体结构,它是由2个相似结构的化合物分子组成.晶体属单斜晶系,空间群为P2₁,晶胞参数:a=0.8431(3)nm,b=0.7297(1)nm,c=2.1880(7)nm,β=100.90(3)°,V=1.322(1)nm₃,Z=2.应用分子力学程序MMX及逐步旋转单键法探讨了它的构型和其它可能的优势构象.还应用MNDO方法计算了电荷分布及CNDO/2方法计算了静电势.结果表明,在该化合物中存在3个明显的负电区域,此结构与活性密切相关.     

A pentacyclic triterpene from Maytenus imbricata: structure elucidation by X-ray crystallography

A pentacyclic triterpene, 3β,30-dihydroxy-lup-20(29)-ene, was isolated from the powder extract of Maytenus imbricata. The structure and stereochemistry of the compound were established by spectroscopic techniques and unambiguously determined by single crystal X-ray crystallography. The crystal structure shows one molecule in the asymmetric unit. The crystal packing is stabilized by O–H···O intermolecular hydrogen bonds, which give rise to infinite helical chains along the c unit cell axis. The intra-molecular geometry was analyzed using MOGUL, a knowledge base of molecular geometry derived from the Cambridge Structural Database (CSD).     

Ab Initio Study of the Nonequivalence of Adsorption of D- and L-Peptides on Clay Mineral Surfaces

Ab initio geometry optimizations were performed of the structures of the L and D enantiomers of the model dipeptide, N-formyl alanine amide (L-Ala and D-Ala, respectively) adsorbed on the mineral surface in the interlayer space of the 2:1 clay, nontronite. Density functional procedures were used as implemented in the ab initio program CASTEP, in fully periodic calculations in which the properties of a model unit cell are determined by including the effects of its neighboring cells in an infinite crystal. Geometry optimization included the atomic positions of the mineral and the adsorbates within the unit cell, in addition to unit cell lengths and angles, achieving full optimization of the entire crystal system. In agreement with previous studies of the adsorption of organic compounds on clay mineral surfaces, in the most stable arrangement of L-Ala and D-Ala found here, the two molecules reside flat on the mineral basal plane, forming a parallel monolayer. The resulting L-Ala/mineral cocrystal is more stable, by 6 kcal/mol, than D-Ala. A characteristic structural difference exists for the enantiomers in that, in the optimized structure of L-Ala, the C()–C() bond is directed away from one of the mineral basal planes toward the dioctahedral cavity of the other, while the side group of D-Ala is parallel to the mineral basal plane and pointing to the nearest neighbor in an adjacent unit cell. As expected, the reverse results are obtained for the adsorption of L-Ala and D-Ala on a nontronite surface that is the enantiomer of the one used above. The geometry optimizations illustrate the structural compatibility of clay mineral lattices with peptide structures. That is, balance of adsorption energies and peptide interaction energies, and mineral lattice structure and periodicity allow for adsorption structures, which involve the entire backbone of a single peptide molecule and can, at the same time, immobilize the adsorbates in such a way that stabilizing intermolecular interactions occur across unit cell boundaries. Compatibility of the repeat distances on the clay surface with repeat distances of peptides should be an important property when clay minerals serve as templates for protein synthesis.     

Powder X‐ray studies of meso‐hexamethyl propylene amine oxime (meso‐HMPAO) in two different phases

Two different forms of meso‐3,3′‐[2,2‐dimethylpropane‐1,3‐diylbis(azanediyl)]dibutan‐2‐one dioxime, commonly called meso‐hexamethyl propylene amine oxime (HMPAO), C₁₃H₂₈N₄O₂, designated α and β, were isolated by fractional crystallization and their crystal structures were determined by powder X‐ray diffraction using the direct‐space method with the parallel tempering algorithm. The α form was first crystallized from acetonitrile solution, while the β form was obtained by recrystallization of the α phase from diethyl ether. The α form crystallizes in the triclinic system (space group P), with one molecule in the asymmetric unit, while the crystal of the β form is monoclinic (space group P2₁/n), with one molecule in the asymmetric unit. In both phases, the molecules have similar conformations and RS/EE geometric isomerism. The crystal packing of the two phases is dominated by intermolecular hydrogen‐bonding interactions between the two O—H oxime groups of an individual molecule and the amine N atoms of two different adjacent molecules, which lead to segregation of extended poly(meso‐HMPAO) one‐dimensional chains along the c direction. The structures of the two phases are primarily different due to the different orientations of the molecules in the chains.     

Two modes of O—H...O hydrogen bonding utilized in dimorphs of racemic 6‐O‐acryloyl‐2‐O‐benzoyl‐myo‐inositol 1,3,5‐orthoformate

The title compound, C₁₇H₁₆O₈, yields conformational dimorphs [forms (I) and (II)] at room temperature, separately or concomitantly, depending on the solvent of crystallization. The yield of crystals of form (I) is always much more than that of crystals of form (II). The molecule has one donor –OH group that can make intermolecular O—H...O hydrogen bonds with one of the two acceptor C=O groups, as well as with the hydroxyl O atom; interestingly, each of the options is utilized separately in the dimorphs. The crystal structure of form (I) contains one molecule in the asymmetric unit and is organized as a planar sheet of centrosymmetric dimers via O—H...O hydrogen bonds involving the OH group and the carbonyl O atom of the acryloyl group. In the crystal structure of form (II), which contains two independent molecules in the asymmetric unit, two different O—H...O hydrogen bonds, viz. hydroxyl–hydroxyl and hydroxyl–carbonyl (benzoyl), connect the molecules in a layered arrangement. Another notable feature is the transformation of form (II) to form (I) via melt crystallization upon heating to 411 K. The higher yield of form (I) during crystallization and the thermal transition of form (II) to form (I) suggest that the association in form (I) is more highly favoured than that in form (II), which is valuable in understanding the priorities of molecular aggregation during nucleation of various polymorphs.     

Molecular Structure of 5-Methylchrysene-7,8-dihydro-7,8-trans-(e,e)-diol

The crystal structure of the weak carcinogen 5-methylchrysene-7,8-dihydro-7,8-trans-(e,e)-diol is reported. This molecule contains a distorted bay region as a result of the presence of the 5-methyl group as found in 5-methylchrysene and 5,6- and 5, 12-dimethylchrysene. One torsion angle in this bay region is 20. The two hydroxyl groups of this molecule form hydrogen bonds throughout the crystal along theb direction. This is similar to the packing in other crystal structures of dihydrodiols of polycyclic aromatic hydrocarbons, each hydroxyl group both receiving and donating one hydrogen bond.