Structure of an unusual cage dimer diol

The title compound arises from an unexpected rearrangement and oxidation. The molecules contain a center of symmetry and are held together by hydrogen bonds. The relatively strain-free molecules are closely packed with a density of 1.441 g cm^–3. The compound crystallizes in space group P-1 with cell dimensions a = 8.999(3), b = 9.142(2), c = 8.625(3) Å, = 95.47(3), = 105.06(3), and = 83.08(2)° There are two independent molecules per cell with each sitting on a center of symmetry.     

Synthesis and structure of new systems containing pyramidalized double bonds

Syn- andanti-isomers of substituted tetracyclo[6.2.2.2^3.6.1^2.7]tetradeca-2(7)-ene have been synthesized. In thesyn-isomers steric interactions between cyclopropane hydrogen atoms lead to a pyramidalization of the C(sp²) atoms of the central double bond. The parameters from three crystal structures are compared with geometry optimized structures using PCWIN, MM3, and MOPAC. Plots of X-ray distances versus theoretically optimized distances give correlation coefficients between 0.91 and 0.97. Analysis of the discrepancies suggest modifications in some molecular mechanics parameters are needed to model the solid state structures.     

Synthesis of an unusual, cage-functionalized molecular cleft

The synthesis and X-ray crystal structure of a novel, cage-functionalized bis(-diketone), 4, is described. A molecular cleft is formed by two parallel planar aromatic diketone units bridged by a polycarbocyclic cage. Crystal data: T = 100(1) K, monoclinic, C2/c, a = 35.6383(2), b = 11.8110(1), c = 15.6319(2) Å, = 110.7745(2)°, V = 6152.04(9) ų, Z = 12, R = 0.0691. Compound 4 is of potential interest as a new type of host molecule for the study of host–guest interactions in solution.     

Conformational polymorphism in thiophenyl substituted quinones and the disappearing NMR spectrum

The stepwise addition of thiophenol to benzoquinone gives thiophenylbenzoquinone (1b), 2,5-and 2,6-di-(thiophenyl)benzoquinone (2,3),2,3,6-tri(thiophenyl)benzoquinone (4) and 2,3,5,6-tetra(thiophenyl)benzoquinone. (5). Compounds1–4 can be crystallized, and the¹³C NMR spectra are readily interpreted. Compound5 could not be crystallized easily, and the NMR showed more than twice as many lines as the number of carbon atoms. Slow evaporation in an NMR tube produced three distinct crystals. X-ray analysis of two crystals (5a and5c) showed the compounds to be conformational polymorphs. Direct synthesis of5 from tetrachlorobenzoquinone and thiophenol yielded only conformer5a, and the¹³C NMR spectrum showed only the 6 lines expected for four equivalent phenyl substituents on benzoquinone. Subjecting5a to a variety of solvents, reagents and temperatures did not regenerate the original¹³C NMR spectrum. The crystal structures, conformations, and polymorphs are discussed.     

Statistical characterization of the pore space of random systems of hard spheres

An improved statistical characterization of disordered structures such as metallic glasses, random porous media, or granular matter is presented. Suitable structure models follow the idea of dense random packed spheres, where the spheres represent atoms and particles in the case of metallic glasses and porous or granular matter, respectively. The geometry of the empty space between the atoms or particles is described by means of the already otherwise successful concept of so-called contact distributions. Their exact mathematical forms are unknown for hard sphere systems. Knowledge on these is obtained by means of Monte Carlo simulations of the structure models. The numerical results are approximated by simple and general mathematical expressions, with parameters that can be easily determined. These may serve as additional tools for the structural characterization of disordered matter, including systems of partly penetrable spheres.     

Diamagnetic Anisotropy Measurements of Nematic Liquid Crystals

Electro-optic effect of liquid crystals in the presence of a magnetic field was investigated. Two independent techniques: magnetic field dependent threshold voltage and magnetic field-assisted relaxation time, were used to evaluate the diamagnetic anisotropy for three nematic liquid crystals: BDH-E7, RO-TN-103 and ZLI-1132. Correlation between the diamagnetic anisotropy and the molecular structures was obtained. This information is particularly important for synthesizing liquid crystal components with desired diamagnetic anisotropy.     

Structures of two sterically crowded molecular propeller systems

The crystal structures of two molecular propellers are described. Enol phosphate 1 is triclinic P 1¯ with a = 10.1110(4), b = 12.0647(6), c = 14.2112(7) Å; = 96.421(3), = 98.633(3), = 108.594(2)° and Z = 2. Enol phosphinate 2 is monoclinic P2₁/n with a = 13.527(3), b = 11.980(2), c = 17.326(3) Å, = 98.616(9),° and Z = 4. Data from dynamic NMR investigations are in agreement with the size of the aryl torsion angles in the two enol propellers.     

Comparison of the crystal structure and molecular models of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide (CMPO)

The crystal structure of N,N-diisobutyl-2-(octylphenylphosphinyl)acetamide, or CMPO was recently determined. The compound crystallizes in the space group P2₁/c witha=13.446(6),b=22.280(7),c=17.217(7) Å, =92.07(4)°, andD _calc=1.05 g/cm³ forZ=8 @20°C). Molecular mechanics, molecular dynamics, and MNDO calculations were also performed on CMPO utilizing the SYBYL¹ suite of programs. The results from these calculations are compared to the crystal structure and to similar calculations performed on CMPO using ALCHEMY^2,3. In general, the results from the calculations agree fairly well with the parameters from the crystal structure.     

Crystal and molecular structure of augustamine

The crystal and molecular structure of augustamine (1), C₁₇H₁₉NO₄ an amaryllidaceae alkaloid of the tazettine group has been determined by direct methods from single crystal x-ray diffractometer data and refined by full-matrix least squares. The alkaloid (1) crystallizes in the space group P2₁2₁2₁, with cell parameters: a = 7.833(8) b = 11.08(2) å, c = 16.69(6) Å, Z = 4, D_c = 1.381 g/cm^–3, R = 7.6% for 1115 observed reflections. The molecule, having a hexacyclic ring system, is very rigid with the ring B in a chair conformation. Molecular mechanics calculations have been made using MM3(2000) force field.     

Hydrogen Adsorption of Alkali Metal Complexes of Polycyclic Aromatic Hydrocarbon and Graphite,and Their Solid State Properties

The hydrogen adsorption in alkali metal complexes of graphite and triphenylene has been investigated by means of ESR and electrical resistivity under hydrogen atmosphere. In the first stage graphite compound C₈Rb, hydrogen molecules are dissociated into atoms which are stabilized in graphite gaps. C⁸K has a two stage hydrogen adsorption process: dissociation and charge transfer. For C₈Cs, the catalytic activity for hydrogen comes from the surface. The second stage compounds C₂₄M (M=K, Rb, and Cs) show weaker activities for hydrogen than the first stage ones. Triphenylene-potassium complex has a two stage process for hydrogen adsorption.     

A Theoretical Study of Molecular Ordering of Some Smectic Liquid Crystals

Abstract

A theoretical investigation of molecular ordering of smectic C liquuid crystals C₈H₁₇O-C₆H₄-C₆H ₄-COO-C₆H₄-OC₈H₁₇ { A }, C₉H₁₉O-C₆H₄-COO- C₆H₄-COO-C₆H₄-NO₂ { B } and its binary mixtures { A+B } has been carried out by the method based on the Rayleigth-Schrodinger perturbation theory. The mutual arrangement of two molecules corresponding to the minimum of the total interaction energy between them U_pair has been established. The curves of the dependence of U_pair and its various contributions on displacement of molecules from each other along the molecular long X-axis and angle θ between molecules' long axes has been also computed in the minimum point vicinity. The obtained results make it possible to determine the peculiarities of the structural organization of molecules, as well as to construct a model of the structure of A and B compounds in different phases taking into account the most probable packing of molecules.     

Crystal Structure of 6, 6' ‐ Dihydroxy ‐ 2, 2' ‐ biphenyl ‐ 19 ‐ crown ‐ 5 ; Comparison of Some Structural Features among Related Ligands and Compounds

It has been determined the crystal structure of 6,6'‐dihydroxy‐2,2'‐biphenyl‐19‐crown‐5, C₂₂H₂₈O₇ (1a). Likewise, it has been set up a comparison between the results and some features of this structure obtained by molecular mechanics calculations. Due the presence of a hydrogen bond, the crown oxygens have not a geometrical disposition to lead its electronic pairs into the cavity and therefore the system complexation constant decreases, compared to some related ligands and compounds.     

Synthesis and Characterization of [(1-benzylpyrazole) [<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-bis(2-aminoethyl)-1,2-ethanediamine]copper(II)] Diperchlorate,a Structure with a Sterically Strained,Distorted-Trigonal-Bipyramidal Cation

Abstract  The synthesis, characterization, and molecular structure of the title compound, [(1-benzylpyrazole)[N,N-bis(2-aminoethyl)-1,2-ethanediamine]copper(II)] diperchlorate, [(nbp)(tren)Cu(II)](ClO₄)₂, 2  · 2ClO₄, is reported. The salt crystallized in the monoclinic space group P2₁/n with a = 10.1453(5) ?, b = 17.5250(8) ?, c = 13.6021(6) ?, β = 100.737(19)° and V = 2376.06(19) ?³ with Z = 4. The structure contains copper(II) (nbp)(tren) cations, each with a distorted-trigonal-bipyramidal CuN₅ coordination geometry, separated by perchlorate anions. The cations exhibit steric strain associated primarily with close contacts between the methylene protons of the nbp ligand and one of the amine groups of the tren ligand. The strain has a noticeable effect on the coordination geometry and certain physical properties of the complex. Graphical Abstract  In the title structure, steric strain in the (nbp)(tren)Cu(II) cations, associated with close contacts between protons of the nbp ligand and two of the amine groups of the tren ligand (dashed lines in the figure below) affects certain physical properties of the cation and is consistent with an anomalously long Cu(II)–N(pyrazole) distance (Cu–N41) and an unusually large axial–equatorial angle, N41–Cu–N12.      

The structure of 11,12-bis[spiro(cyclopropyl)]-1,4,4a,5,8,8a,9a,10a-octahydro-1,4∶5,8-dimethano-9,10-anthraquinone

In the solid state the 21 Diels-Alder adduct between spiro[4.2]hepta-1,3-diene and p-benzoquinone has a planar cyclohexadione ring with a center of symmetry. Both planar and boat conformations have been observed in similar systems, and the relative stability of the two conformers is of interest. The adduct in the gas phase should contain a mirror plane perpendicular to the cyclohexadione ring; however, a data set collected on a crystal in a capillary resulted in a structure where some bond lengths related by this mirror plane differed by more than 4 in the solid state. Molecular mechanics, MOPAC, and the Cambridge Structural Data Base were used to investigate the factors influencing the conformation of the cyclohexadione ring and the asymmetry across the noncrystallographic mirror plane. The energy differences between the planar and nonplanar ring system is small, and the conformation is determined by crystal packing. No reason for the bond length asymmetry could be found, and a recollection of data on a crystal exposed to the environment led to a structure with statistically equivalent bond lengths.     

Theoretical stress calculations in polar,semipolar and nonpolar AlGaN/GaN heterostructures of different compositions

The new comprehensive model of the process for matching epitaxial layers to substrates, in dependence of theirs crystallographic orientation, was developed to allow a theoretical prediction of the strain and stress in thin AlGaN epitaxial layers with different composition grown on GaN template. The elements of the continuous anisotropic materials strength theory was applied to develop the model. It was observed that in AlGaN/GaN heterostructures the stress was greater than the upper limit of acceptable tensile stress even for a small Al content and also that the stress could greatly vary, in a value and a direction, depending on substrate crystallographic orientation and an Al content in AlGaN layer. The obtained results theoretically explained the commonly observed technological problems occurring during the growth of AlGaN layers even with a small Al content.     

Structure of a ring enlarged product from the base induced rearrangement of dibromomethylenebenzonorbornene

The base-catalyzed rearrangement reactions of 2-bromomethylenebenzonorbornene8 and 2,2-dibromomethylenebenzonorbornene9 were studied. Reaction of8 with potassiumtert-butoxide in THF gave only the enol ether11 whose formation is rationalized via a carbene-cycloalkyne mechanism. However, treatment of9 with phenyllithium in THF at –40°C gave the ringenlarged dibromide13 whose structure is reported herein. The ring-enlarged product13 is rationalized in terms of carbanionic rearrangement. Quantum mechanical calculations are consistent with these observations.     

Détermination des structures désordonnée et ordonnée métastable du nickelocéne Ni(C5H5)2. Interprétation de l'évolution structurale comparée à celle du ferrocéne

Les données de diffraction X de la phase désordonnée du nickelocéne ont été enregistrées à 295K sur un diffractométre 4 cercles. La structure cristalline est isomorph de celle du ferrocéne: maille monoclinique, gruoups spatial statistiqe P2₁/a. Z=2. Utilisnt une méthod d'affinement en blocs moléculaires rigides et des calculs d’ énegie rétudiés. La Structure par 1’ existence de 4 états moléculaires possibles (anant un anlge interne de 20 ± 2[ddot] au lieu de 11.5° ± 1° pour le ferrocéne) symétriques deux à deux, sur chaque site cristallographique et formée de 2 types de clusters. L'emplilement moléculir de la phase ordonnée métastable du nickelocéne à 5 K a été déterminépar minimisation de son énergie éticulair. Les résultats obtenus (monoclinique, Z=2, à 101 K, indiquent quel l'évolution des phases désordonnées du nickelocéne et P2₁/a, configuration molécularie D ₅ d), Une interpétation de cette évolution differente fondée sur des hypothéses relatives à la dynamique du déordre est proposée.     

Spectroscopic investigation of strain induced by compositional variation in bulk InxGa1–xAs crystal grown by MCZM method

Raman scattering (RS), photoluminescence (PL) and energy dispersive X‐ray (EDX) experiments have been carried out to investigate residual strain and hence to understand breakage issue in bulk In_x Ga_1–x As crystal grown by multi component zone melting (MCZM) method. It is found from a comparison that there is a large discrepancy among the RS, PL and EDX results due to the strain induced by compositional variation in the crystal. The strain induced changes in TO_GaAs and PL peak positions are found to be 4.04 cm^–1 and 0.097 eV, respectively, for the variation of composition from 0.06 to 0.29 from the seed‐end to the tail‐end of the crystal. By assuming a simple one‐dimensional strain distribution, the strain value corresponding to 4.04 cm^–1/ 0.097 eV can be obtained of the order of 10^–2, which is large enough for understanding the breakage issue in the crystal investigated here. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Self-assembly of apoferritin molecules into crystals: thermodynamics and kinetics of molecular level processes

Aside from the biological, biomedical and materials importance of ferritin and apoferritin, the self-assembly of these molecules into crystals is of interest because it is a suitable model for protein crystallization and aggregation that impact many fundamental and applied fields. We use the atomic force microscope in-situ, during the crystallization of apoferritin to visualize and quantify at the molecular level the processes responsible for crystal growth. We image the configuration of the incorporation sites, “kinks”, on the surface of a growing crystal. We show that the kinks are due to thermal fluctuations of the molecules at the crystal-solution interface. This allows evaluation of the free energy of the intermolecular bond φ = 3.0 k_BT = 7.3 kJ/mol. The crystallization free energy, extracted from the protein solubility, is − 42 kJ/mol. Thermodynamics analyses based on these two values suggest that the main component in the crystallization driving force is the entropy gain of the waters bound to the protein molecules in solution and released upon crystallization. Furthermore, we determine the characteristic frequency of attachment of individual molecules into the kinks at one set of conditions. We show that the macroscopic step growth velocity, scaled by the molecular size, equals the product of independently determined kink density and attachment frequency, i.e., these are the molecular-level parameters for crystallization. Finally, we show that although new crystal layers are generated by intrinsically stochastic surface nucleation, for crystals > 200 μm layer generation predominantly occurs at the crystal edges. Numerical simulations of the concentration fields in the solution allow us to assign this localization to higher interfacial concentration at the edges. As the steps propagate to cover the crystal face, step density waves, or bunches, develop and may lead to non-uniformity and lower quality and utility of the growing crystal.