In situ study of the state of lysozyme molecules at the very early stage of the crystallization process by small-angle X-ray scattering

The molecular state of hen egg white lysozyme in solution has been studied by small-angle X-ray scattering (SAXS) combined with molecular simulation. The addition of a precipitant is shown to change the state of the protein molecules in solution. The SAXS data were processed using the constructed models of different oligomers. Under the crystallization conditions, lysozyme is shown to be present in solution as monomers (96.0%), dimers (1.9%), and octamers (2.1%), whereas tetramers and hexamers are not found. The modeled structure of the octamer is not consistent with the commonly accepted unit cell containing eight lysozyme molecules. Meanwhile, the modeled octamers are well-fitted to the crystal structure and can serve as building blocks in the course of crystal growth.     

Icosahedral and dense random cluster packing in metallic glass structures

It has recently been shown that metallic glass structures can be idealized as inter-penetrating solute-centered atomic clusters that are packed with essentially periodic symmetry. The present work applies the same methodology to explore whether experimental observations can be matched by inter-connected solute-centered clusters that are organized in space via dense random cluster packing, Bergman icosahedral cluster packing or Mackay icosahedral cluster packing. Idealized partial pair distribution functions are developed where the symmetry of the solute positions in the structure is derived from the cluster-packing symmetry and the solute concentration, which establishes occupation of inter-cluster sites, especially β structural sites enclosed by an octahedron of solute-centered clusters. While each of the three models matches major features of the measured solute-solute partial pair distribution functions, the arrangement of clusters with Mackay icosahedral ordering provides the best fit. However, this model is not able to match an essential feature in solute-lean glasses and does not provide the same overall agreement as does periodic cluster packing for solute-rich glasses. Strong similarities between the structure factors in the Mackay icosahedral and periodic cluster-packing models, along with expected deviations from the idealized solute positions studied here, are likely to hinder an unambiguous distinction between these two models.     

Modeling and X-ray diffraction investigation of the crystal structure of 1,1-diphenyl-3-methyl-6,7-dimethoxy-1,3-dihydroisobenzofuran

The results of a priori generation and X-ray diffraction investigation of the crystal structure of 1,1-diphenyl-3-methyl-6,7-dimethoxy-1,3-dihydroisobenzofuran are reported. The generation is performed by the discrete modeling of molecular packings in a crystal for two possible conformers of the compound under investigation. Appropriate models that can serve as starting models for refining the crystal structure by the fullmatrix least-squares method using the X-ray diffraction data are chosen from a complete set of calculated structural models of the studied compound in accordance with specific criteria. The structure is solved for a starting model calculated by the discrete modeling method and refined according to the full-matrix least-squares procedure.     

Structure determination of polytypes (I)

Crystal structure determination of polytypes with diffraction methods can be divided into two steps. The first step is the structure determination of the building unit of the polytypic substance (in most cases layers). The second step is the determination of the stacking sequence of the corresponding building units. The stacking can be ordered as well as disordered. Various methods for solving these problems are described. The aim of this paper is to treate these methods from a uniform point of view.     

金刚石UV-Vis-MIR光谱常见特征综述

金刚石分类体系经过上百年发展已趋于成熟.以光谱为基础的分类依据是紫外可见近红外光谱(UV-Vis-NIR)和中红外光谱(MIR),主要涉及氮、硼杂质元素,所识别的有关晶格缺陷模型已得到较为合理的解释,但大量的晶格缺陷,包括跟氮有关的晶格缺陷研究尚不透彻,这将限制金刚石应用领域的开拓进程.本文汇集了金刚石紫外-可见光-红...     

Mathematical simulation and X-ray diffraction investigation of the crystal structure of 1-phenyl-1-<Emphasis Type="Italic">tert</Emphasis>-butyl-3-methyl-1,3-dihydroisobenzofuran

An algorithm for using a priori generation of crystal structures by the discrete modeling method for the interpretation of data obtained from single-crystal X-ray diffraction experiments is considered. The crystal structure of 1-phenyl-1-tert-butyl-3-methyl-1,3-dihydroisobenzofuran is mathematically simulated using the discrete modeling of molecular packings and studied by X-ray diffraction. The simulation is performed for two isomers of the initial chemical compound that are possible from the viewpoint of the mechanism of the chemical reaction used in the synthesis of this compound. Appropriate models that can serve as starting models for solving and refining the crystal structure with the use of X-ray diffraction data are chosen from a complete set of calculated structural models in accordance with specific criteria. The structure is solved using a starting model calculated using the discrete modeling method and refined by the full-matrix least-squares procedure.     

Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations

Peptide and protein self-assembly is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Sequence repeats from self-assembling proteins may provide useful elementary building blocks of peptide-based nanostructures. Sequences from the adenovirus fiber shaft self-assemble into amyloid-like fibrils outside their native context. In earlier simulations we studied the self-assembly of two shaft sequences, the octapeptide NSGAITIG and the hexapeptide GAITIG. Based on these simulations, cysteine residues were substituted at the first two positions of the octapeptide, yielding amyloid fibrils capable of binding to silver, gold and platinum nanoparticles. Here, we study by implicit-solvent replica-exchange simulations the self-assembly of a longer shaft sequence, the dodecapeptide LSFDNSGAITIG. The simulations provide insights on the molecular organization of the corresponding fibers. Individual molecules tend to adopt hairpin-like conformations in the observed intermolecular β-sheets, in line with the experimentally determined amyloid fiber diameters and the conformation of the peptide in the adenovirus fiber shaft. By analyzing the arrangement of individual peptides in the intermolecular sheets, we suggest possible structural models of the corresponding fibers and interpret their stability by energetic calculations.     

Molecular Organization of Porphyrin-Metal Complexes

Abstract

Tetraethyltetramethylporphyrin substituted at two facing meso positions by N-methylimidazolyl groupings and its metal complexes were prepared. The absorption spectra of Zn and Mg complexes showed a characteristic splitting of Soret band and red-shifts of Q-bands indicating the exciton interaction of porphyrins in a slipped cofacial arrangement, where each imidazolyl group in one metal porphyrin is coordinated to metals in the other porphyrin skeleton. Typical upfield shifts in the ¹H NMR spectra arising from such the stacking structure elucidated Zn and Mg complexes as a dimer and an oligomeric mixture, respectively. Bis(imidazolyl)substituted tetraethyltetramethyl-porphyrin was also prepared. It suggested the hydrogen bonded oligomer formation through imidazolyl-imidazolyl interactions in a columnar orientation.

Electric conductivities of films prepared from these compounds werecharacterized. In a same line with behaviors in solution, samples capable of π-stacking interaction with adjacent porphyrins via ligand-to-metal coordination or hydrogen bonding exhibited higher conductivities as well as lower activation energies for the thermal conduction. These behaviors are understood as due to the overlap of π-systems of one porphyrin with neighboring porphyrins.     

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.     

Orthorhombic Pbcn SnO2 nanowires for gas sensing applications

Pure monocrystalline orthorhombic SnO₂ nanowires decorated and non-decorated with cassiterite SnO₂ nanoclusters are analyzed and compared with pure monocrystalline cassiterite SnO₂. We corroborate the coexistence of both, cassiterite and orthorhombic phases, having a higher growth speed for the cassiterite one, in the obtained nanowires by the evaporation/condensation technique. For both phases, the building blocks are the [SnO₆]^8? octahedron which are forming chains of edge-sharing octahedral along the [0 0 1] direction for the cassiterite phase, while in the orthorhombic phase, chains run in a zigzag fashion and contains four octahedra on each unit of chain instead of two previously reported for orthorhombic material obtained at high pressure conditions as Pbcn SnO₂ orthorhombic structure. Results obtained reveal singular structural characteristics of these synthesized orthorhombic nanowires.     

Theoretical calculation of dense random packings of equal and non-equal sized hard spheres applications to amorphous metallic alloys

A model describing the structure of amorphous metallic alloys is proposed using a packing of non-equal-sized hard spheres. Models containing up to 1000 spheres were generated by computation. Hypotheses guiding the calculation are chosen in order to obtain a model as compact as possible and to take into account affinity between metal and metalloids: therefore two small spheres are not allowed to be in hard contact. This method of calculation is first tested by building up heaps of equal-sized spheres. Both the radial distribution function and the interference function are calculated for each model and the variations of these curves with the number of spheres are studied. In the case of two sizes of spheres heaps calculations are devoted to the study of the so-called ‘shoulder interference function’ which characterizes many amorphous alloys such as NiP, PdSi, etc. It is shown that the existence of such a shoulder depends on two parameters: the ratio of sphere diameters and the relative concentration of small and large spheres. These results are in good agreement with some recent experimental observations. This shoulder is well-marked when the diameter ratio reaches 10% and when the concentration in small spheres lies in the range 10–15%. In such a structure (e.g. amorphous NiP and PdSi alloys) it is observed that small spheres are always surrounded by nine large spheres such as P or Si atoms in crystalline Ni₃P or Pd₃Si. Large spheres, i.e. metallic atoms, form distorted icosahedra, the distortion of which varies from one to the other. The short-range order has a five-fold symmetry which is not compatible with any long-range order.     

Nonstoichiometry in oxides

Nonstoichiometry phenomena have been extensively studied in oxide systems. It is proposed that some models developed for oxides could be usefully extended for understanding nonstoichiometry in other systems.

Many aspects of nonstoichiometry are closely connected with order-disorder phenomena. The broad field of nonstoichiometric compounds extends from variable composition phases with randomly distributed point defects (entropy controlled systems) to sets of discrete intermediate sompounds, each corresponding with a fully ordered state resulting from assimilation or annihilation of defects (enthalpy controlled systems). Between these two extreme cases, one finds intermediate situations such as clusters with a short range order, shear structures with possibly swinging shear planes, coherent intergrowths and infinitly adaptive structures in which any composition, even irrational, corresponds with an unique ordered structure.     

Generation mechanism of CuAu-I type ordered structures in InGaAs crystals grown on (110) InP substrates by molecular beam epitaxy

The generation mechanism for CuAu-I type ordered structures in InGaAs grown on (110) InP substrates by molecular beam epitaxy is discussed. On the basis of previous work together with considerations of the atomic arrangement of the ordered structure and surface reconstruction on the (110) plane, we propose four possible models for the ordering. Through precise evaluation of these models, two models are selected as the most probable ones: these involve formation of the ordered structures on surfaces dominated by two monolayer steps. This model have been experimentally proven by the analyses of electron diffraction patterns from different crystals grown on different growth surfaces.     

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.     

Recent developments in the understanding of the structure and properties of grain boundaries in metals

The basic physical problems of the geometric models and structural models of grain boundaries based on computer simulations are considered. By comparing the approximations made in these models with the general solution of the problem based on the theory of metallic cohesion, we are led to conclude that

• i geometric grain boundary models (coincidence models) may be used to derive certain geometric features of a boundary (e.g. the boundary periodicity). However, due to the fact that interatomic forces are neglected, it seems not possible to deduce the actual atomic structure and properties of grain boundaries on the basis of these models.
• ii Dislocation models of grain boundaries seem to be of physical significance only for low energy boundaries. In all other boundaries, misfit dislocation are theoretically and experimentally found to be delocalized in the sense that their core is smeared out in the plane of the boundary.
• iii Structural boundary models deduced by computing the minimum energy atomic configuration using pairwise interatomic potential functions seem to represent a reasonable approximation of the actual atomic structure.
• iv The experimental and theoretical evidence presented indicates that grain boundary properties can, in general, not be derived from computer models, as these properties depend partially on electronic effects.
• v Further developments of the physical understanding of grain boundaries seems to require the incorporation of electronic effects in the theory of interfaces.

     

Polymorphism and design of noncentrosymmetric crystals of 4-hydroxybenzaldehyde-4-nitrophenylhydrazone and N′-(2-phenyl-1H-indole-3-aldehyde)-4-nitrophenylhydrazone

The products of crystallization of 4-hydroxybenzaldehyde-4-nitrophenylhydrazone (I) and N′-(2-phenyl-1H-indole-3-aldehyde)-4-nitrophenylhydrazone (II) from different solvents are studied by X-ray diffraction with the aim of examining the polymorphism of hydrazone derivatives. The structural features of the crystals prepared are analyzed. It is shown that, in the case when molecules of organic compounds with a high molecular hyperpolarizability are capable of forming stable acentric supramolecular associates in the crystal, knowledge of their polymorphism offers strong possibilities for designing the noncentrosymmetric crystal structure necessary for a manifestation of the nonlinear optical activity.     

Short-range and medium-range order in amorphous barium germanate

Amorphous barium germanate of composition BaGe_2.55O_6.10 was prepared by ultra-rapid quenching using a double-roller melt-spinning device. The short-range and medium-range order was investigated by high-energy synchrotron X-ray diffraction, resonant scattering at the Ba K-absorption edge and by electron diffraction. There are indications that 6-fold coordinated germanium exists in the structure of the present amorphous alkaline earth germanate, i.e. both GeO₄ tetrahedra and GeO₆ octahedra are supposed to be basic building units. The ratio of 6-fold coordinated Ge to 4-fold coordinated Ge is approximately 1:3. A structure model is proposed which favours the existence of barium chains and/or barium layers, similar to the structure of barium silicate glasses.     

Liquid Crystal ordering of DNA Dickerson Dodecamer duplexes with different 5’- Phosphate terminations

Abstract

The onset of liquid crystal (LC) phases in concentrated aqueous solutions of DNA oligomers crucially depends on the end-to-end interaction between the DNA duplexes, which can be provided by the aromatic stacking of the terminal base-pairs or by the pairing of complementary dangling-ends. Here we investigated the LC behavior of three blunt-end 12-base-long DNA duplexes synthesized with hydroxyl, phosphate and triphosphate 5’-termini. We experimentally characterized the concentration-temperature phase diagrams and we quantitatively estimated the end-to-end stacking free energy, by comparing the empirical data with the predictions of coarse-grained linear aggregation models.

The preservation of LC ordering, even in presence of the bulky and highly charged triphosphate group, indicates that attractive stacking interactions are still present and capable of induce linear aggregation of the DNA duplexes. This finding strengthens the potential role of chromonic like self-assembly for the prebiotic formation of linear polymeric nucleic acids.