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.     

Synthesis of aromatic liquid crystals with asymmetric diester based on rod-like multi-ring system by two-step esterification method

A novel method of two-step esterifications was developed to synthesize compounds with asymmetric double ester groups. By using this method, six rod-like double ester compounds were prepared with p-hydroxy benzaldehyde, p-hydroxy benzoic acid bicyclohexyl carboxylic acid, cyclohexyl benzoic acid and biphenyl carboxylic acid substituted by n-propyl and n-pentyl as main reactants. The structures and properties of target compounds were confirmed by IR, MS, ¹H NMR, elemental analysis, differential scanning calorimetry (DSC) and hot stage polarizing optical microscope (HS-POM). Typical yields of the target molecules were more than 70%. All the molecules have mesophases with the textures of nematic type, indicating a rod-like molecule with a longer rigid skeleton can keep its mesophases. There was no clearing point observed for any of the derivatives before they decomposed so that the temperature ranges of the mesophases could not be determined. The energy differences between frontier molecular orbitals (HOMO-LUMO) (E_g) of the compounds were calculated by cyclic voltammetry (CV). The terminal ring system has an obvious influence on the energy levels and the energy gaps (E_g).     

Study of structural order in porphyrin-fullerene dyad ZnDHD6ee monolayers by electron diffraction and atomic force microscopy

The structure of porphyrin-fullerene dyad ZnDHD6ee monolayers formed on the surface of aqueous subphase in a Langmuir trough and transferred onto solid substrates has been studied. The data obtained are interpreted using simulation of the structure of isolated molecules and their packing in monolayer and modeling of diffraction patterns from molecular aggregates having different sizes and degrees of order. Experiments on the formation of condensed ZnDHD6ee monolayers are described. The structure of these monolayers on a water surface is analyzed using π-A isotherms. The structure of the monolayers transferred onto solid substrates is investigated by electron diffraction and atomic force microscopy. The unit-cell parameters of two-dimensional domains, which are characteristic of molecular packing in monolayers and deposited films, are determined. Domains are found to be organized into a texture (the molecular axes are oriented by the [001] direction perpendicular to the substrate). The monolayers contain a limited number of small 3D domains.     

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.     

Molecular beam epitaxy of GaSb/AlxGa1 − xSb quantum well structures

Molecular beam epitaxy (MBE) is used to grow GaSb/Al_xGa_{1 − x}Sb quantum well (QW) structures on GaSb(001) substrates using both Sb₂ and Sb₄ molecules. While the optoelectronic properties of thick GaSb epitaxial layers are significantly affected by the type of molecule used, no influence is noted on the QW photoluminescence properties. It is shown that MBE allows a very precise and reproducible control of the QW structure parameters such as QW widths for which monolayer precision is obtained. Through the variation of the QW associated PL energy as a function of the growth temperature, the occurrence of a surface segregation-like phenomenon is evidenced. However, this effect is rather weak so that a good estimation of the valence band offset through the PL energy variation with the QW width can be made. Moreover, the QW width for which the Γ-L crossover occurs is very precisely determined.     

Solution structures of human immunoglobulins IgG and IgM and rheumatoid factor IgM-RF

The low-resolution structures of human immunoglobulins M (IgM) and G (IgG) and the rheumatoid factor (IgM-RF) in solution were determined from synchrotron-radiation small-angle X-ray scattering by the method of dummy atom modeling (bead models). The structural models of IgM determined on the assumption that the molecule has a fivefold symmetry axis are in good agreement with the atomic structure of this protein proposed earlier. The molecular structure of the rheumatoid factor IgM-RF reconstructed by dummy atom modeling differs from the model of the IgM molecule: the F(ab)2 regions in the IgM-RF pentamer are asymmetric. This result confirms the earlier assumption that these regions in IgM-RF are different both structurally and biochemically. The typical shape of the IgG molecule in solution was demonstrated to be closer to the Y type, with the maximum size being larger than the size of the known crystallographic models.     

Crystal structure of 4-[benzylideneamino]-3-thiophen-2-yl-methyl-4,5-dihydro-1H-[1,2,4]triazole-5-one

The crystal structure of the title compound C₁₄H₁₂N₄OS was determined by the X-ray diffraction method. The compound crystallizes in the triclinic space group $P\bar 1$ with Z = 2. The molecule is not planar: the dihedral angle between the triazole and thiophene rings is 73.98(2)°, and that between the triazole and benzene rings is 4.05(2)°. The thiophene ring is disordered over two positions, which are approximately parallel and oppositely oriented. The major component refined to a site-occupancy factor of 0.573(3). An intramolecular C-H...O hydrogen bond generates an S(6) ring motif. In the crystal, molecules are linked together by two pairs of N-H...O interactions (to the same O atom as acceptor), forming inversion dimers. The crystal packing is also stabilized by π-π interactions [centroid-centroid distance is 3.978 Å].     

Disorder in ice polymorphs: A Monte Carlo simulation study

Two water molecules connected by hydrogen bond in hexagonal ice can have four possible configurations. These configurations are distinguished by the relative orientation of the two molecules and termed for obvious reasons as c-cis, h-cis, c-trans, and h-trans. The occurrence of symmetry permitted dimer orientations is a characteristic feature of each ice polymorph. In the proton-ordered structures the occurrence of orientations is strictly determined, while in the proton-disordered structures it can vary within certain limits. We performed Monte Carlo simulations using the so-called TIP5P-EW, TIP4P-EW and TIP4P-2005 interaction models to study this isomerism for the polymorphs of ice. We found that the variation of energy with the frequency of different dimer orientations in the proton-disordered phases is large enough to influence the results of phase stability studies. Knowing the distributions of dimer orientations of the ice IX-ice III ordered-disordered polymorph pairs, we could estimate the internal energy of ice IX using dimer energies assigned to certain orientations in the disordered phase of ice III. In agreement with experimental evidences at low temperatures the TIP4P-EW and TIP4P-2005 potentials predicted lower energy for ice VIII than for ice VII.     

Disclinations and ovals in the Smectic B and E phases

Near to the clearing temperature the formation of the texture of a B phase was investigated. The growth of the B phase is beginning with germs, in shape similar to 2π-disclinations whic some tenths of a degree below the clearing temperature dissociate to a system of two π-disclinations. At further lowering the temperature, the latter change to the ovals which contain a set of wedge like material with plane smectic layers. By a competition of surface free energy and elastic free energy the sequence of textures can be explained theoretically.     

Heterogeneous Nucleation of Hen‐Egg‐White Lysozyme — Molecular Approach

The heterogeneous nucleation of hen‐egg‐white lysozyme (HEWL) crystals has been repeatedly investigated using a double‐(thermal)‐pulse technique, thus detaching nucleation from growth stage. n(t) dependencies of the nucleus number n, on templates of poly‐L‐lysine, vs time, t were plotted and the steady‐state nucleation rates I were determined. They were compared with the results obtained earlier for surfaces rendered hydrophobic (by means of hexamethyl‐disilazane) as well as for bare glass surfaces. In the present paper we determine the number of HEWL molecules in the (heterogeneously formed) critical nucleus. It turned out that it is build of 3 (to 4) HEWL molecules on glass substrate and 8 molecules for both hexamethyl‐disilazane and poly‐L‐lysine templates. The energy Ak required for heterogeneous formation of a critical nucleus on poly‐L‐lysine has been calculated, on the basis of the steady‐state nucleation rates I. Intermolecular binding energy in the HEWL crystal lattice has been estimated again (approximately 10‐9 erg/molecule). This time the basis was the adhesion of HEWL crystals to poly‐L‐lysine substrate.     

Conductance Mechanism in a Linear Non-Conjugated Trimethylsilyl-Acetylene Molecule: Tunneling Through Localized States

The conductance properties of 1,3-(trimethylsilyl)-1-tridecene-6,12-diyne, a non-conjugated trimethylsil-acetylene molecule have been investigated both experimentally and theoretically. Based on scanning tunnelling spectroscopy experiments, a discussion on the mechanisms controlling the charge transfer through this linear molecule is carried out. A specific property of the studied molecule is that it contains localized molecular orbitals. The shifts of the MOs energy levels caused by the applied voltage as well as a distant superexchange coupling between the respective localized MOs are shown to become determining in the formation of a nonlinear hole current through the molecule.     

The Crystal and Molecular Structure of an Antidepressant Drug (Isocarboxazid)

The crystal arid molecular structure of 5-methyl-3-isoxazole carboxylic acid 2-benzylhydrazine (isocarboxazid, C₁₂H₁₃N₃O₂), an antidepressant drug, has been determined by X-ray diffraction method and IR analysis. The compound crystallizes in the monoclinic space group P2₁/c, with a = 6.376(1), b = 14.131(1), c = 13.256(1) Å, β = 99.75(1)°. The structure has been solved by using SIR program and refined to R = 0.048. The benzene and isoxazoles rings are not coplanar and have a dihedral angle of 167.7(5)° between their respective planes. Some of the bond lengths and angles found in the molecule are distorted due to π-electron delocalization and strain. The infrared spectrum of isocarboxazid has been also reported and assignments have been suggested for some characteristic bands. These assignments were confirmed by X-ray analysis.     

Li吸附对石墨烯、BC5、C5N电学性质影响的第一性原理研究

基于密度泛函理论(DFT)的第一性原理方法,对Li在本征石墨烯和BC5,C5N表面最稳定位置的吸附进行了结构优化,计算了本征石墨烯及BC5,C5N吸附Li前后的能带结构,态密度,电荷转移,差分电荷密度和结合能.计算结果表明,B掺杂浓度为16.67;(原子分数)时可显著提高石墨烯的Li吸附能,N掺杂浓度为16.67;(原子分数)时减弱了石墨烯的Li吸附能.吸附Li 后的graphene-Li、BC5-Li 和C5N-Li 体系均显示出金属性,巨Li 与石墨烯、BC5和C5N体系间存在离子键和共价键的混合.     

Die Molekül- und Kristallstruktur des N-Methyl-piperidinium-acet-para-brom-anilid-jodid

N-Methyl-piperidinium-acet-para-bromo-anilide-iodide crystallizes in the triclinic space group P 1 with two formula units C₁₄H₂₀N₂OBrJ and two H₂O molecules in the unit cell. The lattice constants are a = 8.950 Å, b = 14.721 Å, c = 7.440 Å, α = 80.19°, β = 112.57° and γ = 106.82°. The molecular structure of the compound was determined by the X-ray structure analysis and the interaction between the molecules in the crystal was investigated. Especially the influence of the water in the crystal on the form of the molecule was analysed.     

Ordering of the Water Molecule in the Crystal Structure of 2-[3-Methyl-4-(2,2,2-Trifluoroethoxy)-2-Pyridinyl]Methylthio-<Emphasis Type="Italic">1H</Emphasis>-Benzimidazole Hydrate (Lansoprazole Sulphide Hydrate)

Abstract  

Lansoprazole sulphide (2-[3-methyl-4-(2,2,2-trifluoroethoxy)-2-pyridinyl]methylthio-1H-benzimidazole) hydrate crystallizes in the triclinic space group P-1 with two molecules in the asymmetric part of the unit cell. The molecules are almost identical, the normal probability plots show that the differences between them are of statistical nature. The crystal structure is determined mainly by the O–H···N and N–H···O hydrogen bonds; and both symmetry independent molecules create the hydrogen-bonded structures on their own. The common motif is the C₂²(6) chain of molecules along x (A) or y (B), but the interactions between the chains are different: chains of molecules A are joined by O–H···N(pyridine) hydrogen bonds while those of molecules B– by relatively strong O–H···S hydrogen bonds. Additionally, in both cases there are also C–H···S, C–H···π and π–π interactions between the neighbouring molecules. The different intermolecular interactions might be connected with the observed disorder of water molecules in the B-chains. At room temperature the s.o.f.’s of two alternative positions refined at 0.760(17) and 0.240(17). The less-occupied water molecule does not take part in the O–H···S hydrogen bonding. When temperature decreases the importance of this interaction grows, the occupancy of less occupied position becomes smaller and finally, around 150 K the structure becomes fully ordered.     

Pyrene分子(小片石墨晶体)的电子传导特性

利用量子理论中基于Green函数的tight-binding方法,对pyrene分子的电子传导和电子流分布进行了理论研究。在考虑到界面耦合和Hopping积分的情况下,得出了电子透射谱和流分布的模拟结果。结果显示透射与电子的能量紧密相关;谱的振荡特征是能级量子化的结果;流分布有着特定的方向,并且在每一个原子点上符合Kirchhoff量子流守恒定律。另外还发现了桥接pyrene分子的正负能开关特性。     

Crystal and molecular structures of three ketoximes: (E)-O-hexanoyl phenyl 2-pyridyl ketone oxime (C18H20N2O2), (E)-O-octanoyl phenyl 2-pyridyl ketone oxime (C20H24N2O2), (E)-O-myristoyl phenyl 2-pyridyl ketone oxime (C26H38N2O2)

The crystal structures of the three title compounds have been determined by the X-ray structure analysis. The molecule of (E)-O-hexanoyl phenyl 2-pyridyl ketone oxime1 has an anti form at the N-O-C-C ester linkage, while the molecules of (E)-O-octanoyl phenyl 2-pyridyl ketone oxime2 and (E)-O-myristoyl phenyl 2-pyridyl ketone oxime 3 each have a syn form. Compounds2 and3 are crystallized in isomorphic bilayer structures, in which alkyl chains are packed in an antiparallel arrangement.     

PM3 semiempirical study and its comparison with X-ray crystal structure of 4-[2-Methyl-4-(4-methoxyphenylazo)] phenoxyphtalonitrile

  The molecular and crystal structures of the title compound, C₂₂H₁₆N₄O₂, were determined by single crystal X-ray diffraction technique. The title compound crystallizes in monoclinic space group P1 2 ₁ /n1, with a=12.7811(9) ?, b=8.2002(4) ?, c=17.8772(14) ?, Z=4, D _calc=1.3112(1) g/cm³, μ (Mo-K_α)=0.087 mm⁻¹. The structure was solved by direct methods and refined to a final R=0.056 for 1891 reflections with I > 2σ (I). The asymmetric unit in the crystal structure contains only one neutral molecule. The positions of nitrogen atoms in the azo groups were disordered. There is no classic hydrogen bond in the crystal structure. The molecules in the crystal structure are stacked by π–π stacking and one edge-to-face interactions. In order to determine conformational flexibility and crystal packing effects on the molecules, molecular energy profile of the title compound was obtained with respect to the selected torsion angle, which is varied from −180° to +180° in every 10° via PM3 semi-empirical method.     

Computer simulation of the structure of small tungsten oxide clusters

The structure of tungsten oxide clusters was simulated by constructing a random 3D grid either disregarding or taking into account the energy of Coulomb interaction between cluster particles and an attached ion. The obtained clusters are subjected to relaxation by the molecular dynamics method. It is shown that the relaxation of clusters modeled with or without using periodic boundary conditions leads to the formation of different atomic structures.