Determination of structure and properties of molecular crystals from first principles.

Science.gov (United States)

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be

Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

OpenAIRE

Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

1981-01-01

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

Science.gov (United States)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

Crystal structures and Hirshfeld surface analyses of bis-[N,N-bis-(2-meth-oxy-eth-yl)di-thio-carbamato-κ2S,S']di-n-butyl-tin(IV) and [N-(2-meth-oxy-eth-yl)-N-methyl-dithio-carbamato-κ2S,S']tri-phenyl-tin(IV).

Science.gov (United States)

Mohamad, Rapidah; Awang, Normah; Kamaludin, Nurul Farahana; Jotani, Mukesh M; Tiekink, Edward R T

2018-03-01

The crystal and mol-ecular structures of the two title organotin di-thio-carbamate compounds, [Sn(C 4 H 9 ) 2 (C 7 H 14 NO 2 S 2 ) 2 ], (I), and [Sn(C 6 H 5 ) 3 (C 5 H 10 NOS 2 )], (II), are described. Both structures feature asymmetrically bound di-thio-carbamate ligands leading to a skew-trapezoidal bipyramidal geometry for the metal atom in (I) and a distorted tetra-hedral geometry in (II). The complete mol-ecule of (I) is generated by a crystallographic twofold axis (Sn site symmetry 2). In the crystal of (I), mol-ecules self-assemble into a supra-molecular array parallel to (10-1) via methyl-ene-C-H⋯O(meth-oxy) inter-actions. In the crystal of (II), supra-molecular dimers are formed via pairs of weak phenyl-C-H⋯π(phen-yl) contacts. In each of (I) and (II), the specified assemblies connect into a three-dimensional architecture without directional inter-actions between them. Hirshfeld surface analyses confirm the importance of H⋯H contacts in the mol-ecular packing of each of (I) and (II), and in the case of (I), highlight the importance of short meth-oxy-H⋯H(but-yl) contacts between layers.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

Science.gov (United States)

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

SUPRA SOFT SEPARATION AXIOMS AND SUPRA IRRESOLUTENESS BASED ON SUPRA B-SOFT SETS

OpenAIRE

Abd El-latif, Alaa Mohamed; Hosny, Rodyna Ahmed

2016-01-01

This paper introduces supra soft b-separation axioms based on the supra b-open soft sets which are more general than supra open soft sets. We investigate the relationships between these supra soft separation axioms. Furthermore, with the help of examples it is established that the converse does not hold. We show that, a supra soft topological space (X; t;E) is supra soft b-T1-space, if xE is supra b-closed soft set in for each x 2 X. Also, we prove that xE is supra b-closed soft set for each ...

Molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine

International Nuclear Information System (INIS)

Kuleshova, L.N.; Khrustalev, V.N.; Struchkov, Yu.T.; Soldatenkov, A.T.; Bekro, I.A.; Mamyrbekova, Zh.A.; Soldatova, S.A.

1996-01-01

The molecular and crystal structure of 3,4-dihydroxy-2-oxo-1-methyl-4-phenylpiperidine was determined. The crystal is orthorhombic: sp. gr. Pca21; a=15.764, b=5.635, and c=25.536 A; and Z=8. The structure was solved by direct methods; R1=0.051, for 2643 unique refections. Symmetry-independent molecules are related by a pseudocenter of symmetry. The piperidine cycle has an asymmetric half-chair conformation. The orientation of substituents is determined. In the crystal, intermolecular OH...O hydrogen bonds link the molecules into chains parallel to the Y-axis

Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

Science.gov (United States)

Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

2012-06-01

The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

Monolayer atomic crystal molecular superlattices

Science.gov (United States)

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

2018-03-01

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Formation of the molecular crystal structure during the vacuum sublimation of paracetamol

Science.gov (United States)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.; Bordei, N. S.

2015-04-01

The results from structural and thermal studies on the formation of molecular crystals during the vacuum sublimation of paracetamol from its vapor phase are given. It is established that the vapor-crystal phase transition proceeds in a complicated way as the superposition of two phase transitions: a first-order phase transition with a change in density, and a second-order phase transition with a change in ordering. It is shown that the latter is a smeared phase transition that proceeds with the formation of a pretransitional phase that is irreversibly dissipated during phase transformation, leading to the formation of crystals of the rhombic syngony. Data from differential scanning calorimetry and X-ray diffraction analysis are presented along with microphotographs.

Crystal structure of 4-meth-oxy-N-(piperidine-1-carbono-thio-yl)benzamide.

Science.gov (United States)

Suhud, Khairi; Hasbullah, Siti Aishah; Ahmad, Musa; Heng, Lee Yook; Kassim, Mohammad B

2017-10-01

In the title compound, C 14 H 18 N 2 O 2 S, the piperidine ring has a chair conformation. Its mean plane is twisted with respect to the 4-meth-oxy-benzoyl ring, with a dihedral angle of 63.0 (3)°. The central N-C(=S)-N(H)-C(=O) bridge is twisted with an N-C-N-C torsion angle of 74.8 (6)°. In the crystal, mol-ecules are linked by N-H⋯O and C-H⋯O hydrogen bonds, forming chains along the c -axis direction. Adjacent chains are linked by C-H⋯π inter-actions, forming layers parallel to the ac plane. The layers are linked by offset π-π inter-actions [inter-centroid distance = 3.927 (3) Å], forming a supra-molecular three-dimensional structure.

Amphiphilic building blocks for self-assembly: from amphiphiles to supra-amphiphiles.

Science.gov (United States)

Wang, Chao; Wang, Zhiqiang; Zhang, Xi

2012-04-17

The process of self-assembly spontaneously creates well-defined structures from various chemical building blocks. Self-assembly can include different levels of complexity: it can be as simple as the dimerization of two small building blocks driven by hydrogen bonding or as complicated as a cell membrane, a remarkable supramolecular architecture created by a bilayer of phospholipids embedded with functional proteins. The study of self-assembly in simple systems provides a fundamental understanding of the driving forces and cooperativity behind these processes. Once the rules are understood, these guidelines can facilitate the research of highly complex self-assembly processes. Among the various components for self-assembly, an amphiphilic molecule, which contains both hydrophilic and hydrophobic parts, forms one of the most powerful building blocks. When amphiphiles are dispersed in water, the hydrophilic component of the amphiphile preferentially interacts with the aqueous phase while the hydrophobic portion tends to reside in the air or in the nonpolar solvent. Therefore, the amphiphiles aggregate to form different molecular assemblies based on the repelling and coordinating forces between the hydrophilic and hydrophobic parts of the component molecules and the surrounding medium. In contrast to conventional amphiphiles, supra-amphiphiles are constructed on the basis of noncovalent interactions or dynamic covalent bonds. In supra-amphiphiles, the functional groups can be attached to the amphiphiles by noncovalent synthesis, greatly speeding their construction. The building blocks for supra-amphiphiles can be either small organic molecules or polymers. Advances in the development of supra-amphiphiles will not only enrich the family of conventional amphiphiles that are based on covalent bonds but will also provide a new kind of building block for the preparation of complex self-assemblies. When polymers are used to construct supra-amphiphiles, the resulting

A two-dimensional Zn coordination polymer with a three-dimensional supra-molecular architecture.

Science.gov (United States)

Liu, Fuhong; Ding, Yan; Li, Qiuyu; Zhang, Liping

2017-10-01

The title compound, poly[bis-{μ 2 -4,4'-bis-[(1,2,4-triazol-1-yl)meth-yl]biphenyl-κ 2 N 4 : N 4' }bis-(nitrato-κ O )zinc(II)], [Zn(NO 3 ) 2 (C 18 H 16 N 6 ) 2 ] n , is a two-dimensional zinc coordination polymer constructed from 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The Zn II cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligands, forming a distorted octa-hedral {ZnN 4 O 2 } coordination geometry. The linear 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligand links two Zn II cations, generating two-dimensional layers parallel to the crystallographic (132) plane. The parallel layers are connected by C-H⋯O, C-H⋯N, C-H⋯π and π-π stacking inter-actions, resulting in a three-dimensional supra-molecular architecture.

[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

Science.gov (United States)

Abaturov, L V; Nosova, N G

2013-01-01

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the

Chirality and helicity of poly-benzyl-L-glutamate in liquid crystals and a wave structure that mimics collagen helicity in crimp

Directory of Open Access Journals (Sweden)

Vidal Benedicto de Campos

2001-01-01

Full Text Available Ideal biocompatible polymers must show a mimetic superstructure with biological supra-organization. Collagen-rich structures like tendons and ligaments are materials with various levels of order, from molecules to bundles of fibers, which affect their biomechanical properties and cellular interactions. Poly-benzyl-L-glutamate (PBLG displaying helicity was used here to test the development of wave-like structures as those occurring in collagen fibers. Birefringence of PBLG under various crystallization conditions was studied with a lambda/4 compensator according to Sénarmont. Qualitative observations were plainly sufficient to conclude that the PBLG fibrils were supra-organized helically as a chiral object. During crystallization stretched PBLG formed a helical superstructure with characteristic striation resembling waves (crimp. Supported by optical anisotropy findings, a twisted grain boundary liquid crystal type is proposed as a transition phase in the formation of the PBLG chiral object. A similarity with the wavy organization (crimp of collagen bundles is proposed.

On Supra-Additive and Supra-Multiplicative Maps

OpenAIRE

Jin Xi Chen; Zi Li Chen

2013-01-01

Let A and B be ordered algebras over ℝ, where A has a generating positive cone and B satisfies the property that b2>0 if 0≠b∈B. We give some conditions for a map T:A→B which is supra-additive and supra-multiplicative for all positive and negative elements to be linear and multiplicative; that is, T is a homomorphism of algebras. Our results generalize some known results on supra-additive and supra-multiplicative maps between spaces of real functions.

Plasma upflows and microwave emission in hot supra-arcade structure associated with AN M1.6 limb flare

International Nuclear Information System (INIS)

Kim, S.; Shibasaki, K.; Bain, H.-M.; Cho, K.-S.

2014-01-01

We have investigated a supra-arcade structure associated with an M1.6 flare, which occurred on the south-east limb on 2010 November 4. It is observed in EUV with the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory, microwaves at 17 and 34 GHz with the Nobeyama Radioheliograph (NoRH), and soft X-rays of 8-20 keV with RHESSI. Interestingly, we found exceptional properties of the supra-arcade thermal plasma from the AIA 131 Å and the NoRH: (1) plasma upflows along large coronal loops and (2) enhancing microwave emission. RHESSI detected two soft X-ray sources, a broad one in the middle of the supra-arcade structure and a bright one just above the flare-arcade. We estimated the number density and thermal energy for these two source regions during the decay phase of the flare. In the supra-arcade source, we found that there were increases of the thermal energy and the density at the early and last stages, respectively. On the contrary, the density and thermal energy of the source on the top of the flare-arcade decreases throughout. The observed upflows imply that there is continuous energy supply into the supra-arcade structure from below during the decay phase of the flare. It is hard to explain by the standard flare model in which the energy release site is located high in the corona. Thus, we suggest that a potential candidate of the energy source for the hot supra-arcade structure is the flare-arcade, which has exhibited a predominant emission throughout.

Asymmetric and symmetric bolaform supra-amphiphiles: formation of imine bond influenced by aggregation.

Science.gov (United States)

Wang, Guangtong; Wu, Guanglu; Wang, Zhiqiang; Zhang, Xi

2014-02-18

A series of bolaform supra-amphilphiles with different symmetries were fabricated through dynamic benzoic imine bond formation. The pH dependence of imine formations of these supra-amphiphiles were characterazied. We found that the extent of the imine formation of these supra-amphiphies were different. The supra-amphiphiles with a poorer symmetry always exhibited a lower imine formation at a given pH. Therefore, the varied extent of imine bond formation indicate the different aggregations of these supra-amphilphiles, which are controlled by the molecular symmetry of the supra-amphiphiles.

Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

NARCIS (Netherlands)

Giovannetti, G.; Brocks, G.; van den Brink, J.

2008-01-01

We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

Changes of synovial fluid protein concentrations in supra-patellar bursitis patients after the injection of different molecular weights of hyaluronic acid.

Science.gov (United States)

Chen, Carl P C; Hsu, Chih Chin; Pei, Yu-Cheng; Chen, Ruo Li; Zhou, Shaobo; Shen, Hsuan-Chen; Lin, Shih-Cherng; Tsai, Wen Chung

2014-04-01

Knee pain is commonly seen in orthopedic and rehabilitation outpatient clinical settings, and in the aging population. Bursitis of the knee joint, especially when the volume of the synovial fluid is large enough, can compress and distend the nearby soft tissues, causing pain in the knee joint. Out of all the bursae surrounding the knee joint, supra-patellar bursitis is most often associated with knee pain. Treatment strategies in managing supra-patellar bursitis include the aspiration of joint synovial fluid and then followed by steroid injection into the bursa. When supra-patellar bursitis is caused by degenerative disorders, the concept of viscosupplementation treatment may be effective by injecting hyaluronic acid into the bursa. However, the rheology or the changes in the concentrations of proteins (biomarkers) that are related to the development of bursitis in the synovial fluid is virtually unexplored. Therefore, this study aimed to identify the concentration changes in the synovial fluid total protein amount and individual proteins associated with supra-patellar bursitis using the Bradford protein assay and western immunoglobulin methods. A total of 20 patients were divided into two groups with 10 patients in each group. One group received the high molecular weight hyaluronic acid product of Synvisc Hylan G-F 20 and the other group received the low molecular weight hyaluronic acid product of Hya-Joint Synovial Fluid Supplement once per week injection into the bursa for a total of 3 weeks. Significant decreases in the synovial fluid total protein concentrations were observed after the second dosage of high molecular weight hyaluronic acid injections. Apolipoprotein A-I, interleukin 1 beta, alpha 1 antitrypsin, and matrix metalloproteinase 1 proteins revealed a trend of decreasing western immunoblotting band densities after hyaluronic acid injections. The decreases in apolipoprotein A-I and interleukin 1 beta protein band densities were significant in the high

Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

Molecular mechanisms of crystal growth

International Nuclear Information System (INIS)

Pina, C. M.

2000-01-01

In this paper I present an example of the research that the Mineral Surface Group of the Munster University is conducting in the field of Crystal Growth. Atomic Force Microscopy (Am) in situ observations of different barite (BaSO4) faces growing from aqueous solutions, in combination with computer simulations of the surface attachment of growth units allows us to test crystal growth models. Our results demonstrate the strong structural control that a crystal can exert on its own growth, revealing also the limitation of the classical crystal growth theories (two dimensional nucleation and spiral growth models) in providing a complete explanation for the growth behaviour at a molecular scale. (Author) 6 refs

Dielectric relaxation spectra of liquid crystals in relation to molecular structure

International Nuclear Information System (INIS)

Wrobel, S.

1986-07-01

The dielectric spectra obtained for some members of two homologous series, i.e. for di-alkoxyazoxybenzenes and penthyl-alkoxythiobenzoates, are discussed qualitatively on the basis of the Nordio-Rigatti-Segre diffusion model. It is additionally assumed that the molecular reorientations take place about the principal axes of the inertia tensor. The distribution of correlation times, which is strongly temperature dependent in the vicinity of the clearing point, is interpreted as being caused by fluctuations of the principal axes frame which are due to conformation changes inside the end chains. The Bauer equation is used to describe both principal molecular reorientations, i.e. the reorientations about the long and short axis, observed in liquid crystalline structure by means of dielectric relaxation methods. The energies and entropies of activation have been computed for both principal reorientations. The differences between the high frequency limit of the dielectric permittivity and the refractive index squared of liquid crystals are explained in terms of two librational motions of the molecules observed by other experimental techniques, viz. far infra-red, Raman and inelastic neutron scattering spectroscopies, and found in this work on the basis of dielectrically measured energy barriers. It has been shown qualitatively that intramolecular libratory motions greatly effect the high frequency dielectric spectrum. Finally, molecular motions in liquid crystals are divided into two types: coherent and incoherent. 127 refs., 56 figs., 17 tabs. (author)

Structure of fault stackings of molecular layers X-M-X in CdI2 polytypic crystals

International Nuclear Information System (INIS)

Palosz, B.; Przedmojski, J.

1984-01-01

The arrangements of molecular layers I-Cd-I, which may be regarded as 'faulted' for CdI 2 polytypic crystals, are analyzed. Tentative classification of faults into those which are intermediate structure between the basic polytypes 2H and 4H and faults occurring between different blocks of pure structure 4 H is proposed. The connection between some growth parameters and the structure of faults in CdI 2 crystals grown from solutions is discussed. It is shown that the geometrical classification of stacking faults used for layered inorganic crystals is not appropriate for the description of the faults existing in polytypic crystals of MX 2 type. The effect of weak external electric and magnetic fields on the polytypic structure of CdI 2 is analyzed. The experiments performed for several hundred of polytypes of CdI 2 showed that the external fields may, in some conditions, affect the organization of the polytypic structure of crystals very strongly. In particular, it was found that the external fields may change the period of polytype cells and that the relative number of hexagonal and rhombohedral polytypes differ very strongly for crystals grown in the absence and in the presence of external electric and magnetic fields. (author)

Characterization of molecular associations involving L-ornithine and α-ketoglutaric acid: crystal structure of L-ornithinium α-ketoglutarate.

Science.gov (United States)

Allouchi, H; Céolin, R; Berthon, L; Tombret, F; Rietveld, I B

2014-07-01

The crystal structure of L-ornithinium α-ketoglutarate (C5H13N2O2, C5H5O5) has been solved by direct methods using single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group P21, unit cell parameters a=15.4326(3), b=5.2015(1), c=16.2067(3) Å and β=91.986(1)°, containing two independent pairs of molecular ions in the asymmetric unit. An extensive hydrogen-bond network and electrostatic charges due to proton transfer provide an important part of the cohesive energy of the crystal. The conformational versatility of L-ornithine and α-ketoglutaric acid is illustrated by the present results and crystal structures available from the Cambridge Structural Database. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURES ...

African Journals Online (AJOL)

B. S. Chandravanshi

ABSTRACT. Reaction of [VO(acac)2] (acac = acetylacetonate) with ... Single crystal X-ray structural studies indicate that the hydrazone ligands coordinate to ..... Molecular structure of complex (1) at 30% probability displacement. Figure 4.

Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

Science.gov (United States)

Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

1981-08-04

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

Charge-Transfer Supra-Amphiphiles Built by Water-Soluble Tetrathiafulvalenes and Viologen-Containing Amphiphiles: Supramolecular Nanoassemblies with Modifiable Dimensions.

Science.gov (United States)

Lv, Zhong-Peng; Chen, Bin; Wang, Hai-Ying; Wu, Yue; Zuo, Jing-Lin

2015-08-05

In this study, multidimensional nanoassemblies with various morphologies such as nanosheets, nanorods, and nanofibers are developed via charge-transfer interaction and supra-amphiphile self-assembling in aqueous phase. The charge-transfer interactions between tetrathiafulvalene derivatives (TTFs) and methyl viologen derivatives (MVs) have been confirmed by the characteristic charger-transfer absorption. (1) H NMR and electrospray ionizsation mass spectrometry (ESI-MS) analyses also indicate supra-amphiphiles are formed by the combination of TTFs and MVs head group through charge-transfer interaction and Coulombic force. X-ray single crystal structural studies, transmission electron microscopy (TEM), and scanning electron microscopy (SEM) reveal that both linkage pattern of TTFs in hydrophilic part and alkane chain structure in hydrophobic part have significant influence on nanoassemblies morphology and microstructure. Moreover, gold nanoparticles (AuNPs) are introduced in the above supramolecular nanoassemblies to construct a supra-amphiphile-driven organic-AuNPs assembly system. AuNPs could be assembled into 1D-3D structures by adding different amount of MVs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

African Journals Online (AJOL)

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Reaction of [MoO2(acac)2] (where acac = acetylacetonate) with N'-(2-hydroxy-4- ... Single crystal X-ray structural studies indicate that the hydrazone ligand coordinates .... Molecular structure of the complex at 30% probability displacement.

What makes a crystal structure report valid?

NARCIS (Netherlands)

Spek, Anthony L.|info:eu-repo/dai/nl/156517566

2018-01-01

Single crystal X-ray crystallography has developed into a unique, highly automated and accessible tool to obtain detailed information on molecular structures. Proper archival makes that referees, readers and users of the results of reported crystal structures no longer need to depend solely on the

Hole Mobility of Molecular β-Copper Phthalocyanine Crystal

International Nuclear Information System (INIS)

Pengmanayol, S.; Osotchan, T.; Suewattana, M.; Ingadapa, N.; Girdpun, J.

2011-01-01

A Monte Carlo approach is used to estimate hole mobilities in molecular β-copper phthalocyanine (CuPc) crystal for different applied electric field directions. Due to the crystal symmetry, the twelve neighboring molecules in the three-dimensional crystal are selected in the hopping rate calculation. Density functional theory is employed to derive the molecular interaction between the central and neighboring molecules for various applied electric fields. The derived molecular hopping rate is applied to 80 × 80 × 80 lattice sites under periodic boundary conditions. In order to achieve accurate statistics, each calculation includes 6561 particles with more than 10000 hopping steps under an applied electric field of 0.5–3.5 MV/cm. The results indicate that the molecular hopping strongly depends on the molecular orientation and neighboring sites related to the applied electric field direction. The estimated carrier mobility can be described by the percentage occupation in each neighboring site and the obtained hole mobility value is in the same range of the measured values of single crystal CuPc. The calculated mobility for applied electric field along the c crystal axis exhibits the highest values while the mobility along the b axis has the smallest value. (condensed matter: structure, mechanical and thermal properties)

Electrical properties of molecular crystals; Proprietes electriques des cristaux moleculaires

Energy Technology Data Exchange (ETDEWEB)

Barraud, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-07-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [French] Cette etude bibliographique resume les proprietes electriques des cristaux moleculaires: structure des cristaux moleculaires, mecanismes de transport et d'excitation des porteurs de charge et differences avec les semiconducteurs mineraux. Les principaux resultats sur la conductibilite electrique des cristaux moleculaires les plus etudies y sont exposes, ainsi que les proprietes optiques et photoelectriques de ces cristaux. Enfin les differents types de mesures electriques utilisees sont passees en revue ainsi que les limites de chaque methode. (auteur)

Electrical properties of molecular crystals; Proprietes electriques des cristaux moleculaires

Energy Technology Data Exchange (ETDEWEB)

Barraud, A. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-07-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [French] Cette etude bibliographique resume les proprietes electriques des cristaux moleculaires: structure des cristaux moleculaires, mecanismes de transport et d'excitation des porteurs de charge et differences avec les semiconducteurs mineraux. Les principaux resultats sur la conductibilite electrique des cristaux moleculaires les plus etudies y sont exposes, ainsi que les proprietes optiques et photoelectriques de ces cristaux. Enfin les differents types de mesures electriques utilisees sont passees en revue ainsi que les limites de chaque methode. (auteur)

Crystal and molecular simulation of high-performance polymers.

Science.gov (United States)

Colquhoun, H M; Williams, D J

2000-03-01

Single-crystal X-ray analyses of oligomeric models for high-performance aromatic polymers, interfaced to computer-based molecular modeling and diffraction simulation, have enabled the determination of a range of previously unknown polymer crystal structures from X-ray powder data. Materials which have been successfully analyzed using this approach include aromatic polyesters, polyetherketones, polythioetherketones, polyphenylenes, and polycarboranes. Pure macrocyclic homologues of noncrystalline polyethersulfones afford high-quality single crystals-even at very large ring sizes-and have provided the first examples of a "protein crystallographic" approach to the structures of conventionally amorphous synthetic polymers.

Crystal structure of 4-meth­oxy-N-(piperidine-1-carbono­thio­yl)benzamide

Science.gov (United States)

Suhud, Khairi; Hasbullah, Siti Aishah; Ahmad, Musa; Heng, Lee Yook

2017-01-01

In the title compound, C14H18N2O2S, the piperidine ring has a chair conformation. Its mean plane is twisted with respect to the 4-meth­oxy­benzoyl ring, with a dihedral angle of 63.0 (3)°. The central N—C(=S)—N(H)—C(=O) bridge is twisted with an N—C—N—C torsion angle of 74.8 (6)°. In the crystal, mol­ecules are linked by N—H⋯O and C—H⋯O hydrogen bonds, forming chains along the c-axis direction. Adjacent chains are linked by C—H⋯π inter­actions, forming layers parallel to the ac plane. The layers are linked by offset π–π inter­actions [inter­centroid distance = 3.927 (3) Å], forming a supra­molecular three-dimensional structure. PMID:29250374

Study of plasma-wall interactions in Tore-supra; Etude des phenomenes d'interaction plasma/paroi dans Tore Supra

Energy Technology Data Exchange (ETDEWEB)

Ruggieri, R

2000-01-01

In tokamaks the interaction between wall and plasma generates impurities that affect the thermonuclear fusion. This thesis is divided into 2 parts. The first part describes the physico-chemical processes that are involved in chemical erosion, the second part deals with the study of the wear of Tore-supra's walls due to chemical erosion. Chapter 1 presents the wall-plasma interaction and reviews the different processes between plasma and carbon that occur in Tore-supra. Chapter 2 considers the various crystallographic and electronic structures of the carbon that interferes with Tore-supra plasma, the evolution of these structures during irradiation and their temperature dependence are studied. Chapter 3 presents a crystallo-chemical study of graphite samples that have undergone different surface treatments: ionic bombardment, annealing and air exposure. This experimental study has been performed by using energy-loss spectroscopy. It is shown that air exposure modifies the crystallo-chemical structure of surfaces, so it is necessary to prevent air from contaminating wall samples from Tore-supra. Chapter 4 presents a parametric study of chemical erosion rate of plasma facing components (LPM) of Tore-supra. A relation such as Y{sub cd4}{alpha}{gamma}{sup -0.1} gives a good agreement for chemical erosion rate between measurements and the numerical values of the simulation. (A.C.)

Molecular-crystal approach to accounting of correlation corrections in the chemical bond theory in crystals: electronic structure of Ti2O3 crystal

International Nuclear Information System (INIS)

Ehvarestov, R.A.; Panin, A.I.

2000-01-01

The problem on the possibility of partial accounting for the electron correlation effects within the frames of the Hartree-Fock unlimited method (HF). The local characteristic of the electron structure of the molecular systems for the case of the multi-determinant wave functions, configurational interaction methods and multiconfigurational self-consistent field (MCSCF) are determined. The molecular-crystalline approach is applied to studies on the electron correlation effects in the Ti 2 O 3 crystal. It is shown on the basis of the [Ti 2 O 9 ] 12- cluster electron structure calculation, that the Hartree-Fock unlimited method accounts in a number of cases for an essential part of statistical correlation effects. The energy values and local characteristics of the [Ti 2 O 9 ] 12- cluster, calculated through the HF and MCSCF methods, are presented [ru

Supra-annular structure assessment for self-expanding transcatheter heart valve size selection in patients with bicuspid aortic valve.

Science.gov (United States)

Liu, Xianbao; He, Yuxin; Zhu, Qifeng; Gao, Feng; He, Wei; Yu, Lei; Zhou, Qijing; Kong, Minjian; Wang, Jian'an

2018-04-01

To explore assessment of supra-annular structure for self-expanding transcatheter heart valve (THV) size selection in patients with bicuspid aortic stenosis (AS). Annulus-based device selection from CT measurement is the standard sizing strategy for tricuspid aortic valve before transcatheter aortic valve replacement (TAVR). Because of supra-annular deformity, device selection for bicuspid AS has not been systemically studied. Twelve patients with bicuspid AS who underwent TAVR with self-expanding THVs were included in this study. To assess supra-annular structure, sequential balloon aortic valvuloplasty was performed in every 2 mm increments until waist sign occurred with less than mild regurgitation. Procedural results and 30 day follow-up outcomes were analyzed. Seven patients (58.3%) with 18 mm; three patients (25%) with sequential 18 mm, 20 mm; and only two patients (16.7%) with sequential 18 mm, 20 mm, and 22 mm balloon sizing were performed, respectively. According to the results of supra-annular assessment, a smaller device size (91.7%) was selected in all but one patient compared with annulus based sizing strategy, and the outcomes were satisfactory with 100% procedural success. No mortality and 1 minor stroke were observed at 30 d follow-up. The percentage of NYHA III/IV decreased from 83.3% (9/12) to 16.7% (2/12). No new permanent pacemaker implantation and no moderate or severe paravalvular leakage were found. A supra-annular structure based sizing strategy is feasible for TAVR in patients with bicuspid AS. © 2018 The Authors Catheterization and Cardiovascular Interventions Published by Wiley Periodicals, Inc.

Preparation and crystal and molecular structure of mer-trichlorotris(dimethylphenylphosphine)technetium(III)

Energy Technology Data Exchange (ETDEWEB)

Bandoli, G; Clemente, D A; Mazzi, U [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi

1976-01-01

The crystal and molecular structure of the title compound has been determined from single-crystal X-ray diffractometer data by Fourier methods and refined by anisotropic block-diagonal least-squares to R 0.054 for 4 065 independent observed reflections. Crystals are monoclinic, space group P2/sub 1//n, with cell parameters a = 10.935(9), b = 39.191(11), c = 13.738(7) A, ..beta.. = 107.33(7)/sup 0/, and Z = 8. The two crystallographically independent molecules are stereochemically equivalent (there is only a small difference in the orientation of a benzene ring) and the metal atom has a somewhat distorted octahedral co-ordination, with two pairs of like ligands mutually trans. Technetium-ligand bond distances are: Tc-Cl(trans to P) 2.46(1), Tc-Cl(trans to Cl) both 2.33(1), Tc-P(trans to Cl) 2.42(1) and Tc-P(trans to P) both 2.47(1) A. The noticeable trans-influence of the phosphine ligands on Tc-Cl bonds is discussed.

Ab initio study of structural and mechanical property of solid molecular hydrogens

Science.gov (United States)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

INFERRING THE MAGNETOHYDRODYNAMIC STRUCTURE OF SOLAR FLARE SUPRA-ARCADE PLASMAS FROM A DATA-ASSIMILATED FIELD TRANSPORT MODEL

Energy Technology Data Exchange (ETDEWEB)

Scott, Roger B.; McKenzie, David E.; Longcope, Dana W. [Montana State University, P.O. Box 173840, Bozeman, MT 59717-3840 (United States)

2016-03-01

Supra-arcade fans are highly dynamic structures that form in the region above post-reconnection flare arcades. In these features the plasma density and temperature evolve on the scale of a few seconds, despite the much slower dynamics of the underlying arcade. Further, the motion of supra-arcade plasma plumes appears to be inconsistent with the low-beta conditions that are often assumed to exist in the solar corona. In order to understand the nature of these highly debated structures, it is, therefore, important to investigate the interplay of the magnetic field with the plasma. Here we present a technique for inferring the underlying magnetohydrodynamic processes that might lead to the types of motions seen in supra-arcade structures. Taking as a case study the 2011 October 22 event, we begin with extreme-ultraviolet observations and develop a time-dependent velocity field that is consistent with both continuity and local correlation tracking. We then assimilate this velocity field into a simplified magnetohydrodynamic simulation, which deals simultaneously with regions of high and low signal-to-noise ratio, thereby allowing the magnetic field to evolve self-consistently with the fluid. Ultimately, we extract the missing contributions from the momentum equation in order to estimate the relative strength of the various forcing terms. In this way we are able to make estimates of the plasma beta, as well as predict the spectral character and total power of Alfvén waves radiated from the supra-arcade region.

Crystal structure of di?methyl?ammonium hydrogen oxalate hemi(oxalic acid)

OpenAIRE

Diallo, Waly; Gueye, Ndongo; Crochet, Aur?lien; Plasseraud, Laurent; Cattey, H?l?ne

2015-01-01

Single crystals of the title salt, Me2NH2 +?HC2O4 ??0.5H2C2O4, were isolated as a side product from the reaction involving Me2NH, H2C2O4 and Sn(n-Bu)3Cl in a 1:2 ratio in methanol or by the reaction of the (Me2NH2)2C2O4 salt and Sn(CH3)3Cl in a 2:1 ratio in ethanol. The asymmetric unit comprises a di?methyl?ammonium cation (Me2NH2 +), an hydrogenoxalate anion (HC2O4 ?), and half a mol?ecule of oxalic acid (H2C2O4) situated about an inversion center. From a supra?molecular point of view, the t...

Molecular toxicity of cerium oxide nanoparticles to the freshwater alga Chlamydomonas reinhardtii is associated with supra-environmental exposure concentrations

Science.gov (United States)

Taylor, Nadine S.; Merrifield, Ruth; Williams, Tim D.; Chipman, J. Kevin; Lead, Jamie R.; Viant, Mark R.

2016-01-01

Abstract Ceria nanoparticles (NPs) are widely used as fuel catalysts and consequently are likely to enter the environment. Their potential impacts on. biota at environmentally relevant concentrations, including uptake and toxicity, remain to be elucidated and quantitative data on which to assess risk are sparse. Therefore, a definitive assessment of the molecular and phenotypic effects of ceria NPs was undertaken, using well-characterised mono-dispersed NPs as their toxicity is likely to be higher, enabling a conservative hazard assessment. Unbiased transcriptomics and metabolomics approaches were used to investigate the potential toxicity of tightly constrained 4–5 nm ceria NPs to the unicellular green alga, Chlamydomonas reinhardtii, a sentinel freshwater species. A wide range of exposure concentrations were investigated from predicted environmental levels, to support hazard assessment, to supra-environmental levels to provide insight into molecular toxicity pathways. Ceria NPs were internalised into intracellular vesicles within C. reinhardtii, yet caused no significant effect on algal growth at any exposure concentration. Molecular perturbations were only detected at supra-environmental ceria NP-concentrations, primarily down-regulation of photosynthesis and carbon fixation with associated effects on energy metabolism. For acute exposures to small mono-dispersed particles, it can be concluded there should be little concern regarding their dispersal into the environment for this trophic level. PMID:25740379

Intuitionistic supra fuzzy topological spaces

International Nuclear Information System (INIS)

Abbas, S.E.

2004-01-01

In this paper, We introduce an intuitionistic supra fuzzy closure space and investigate the relationship between intuitionistic supra fuzzy topological spaces and intuitionistic supra fuzzy closure spaces. Moreover, we can obtain intuitionistic supra fuzzy topological space induced by an intuitionistic fuzzy bitopological space. We study the relationship between intuitionistic supra fuzzy closure space and the intuitionistic supra fuzzy topological space induced by an intuitionistic fuzzy bitopological space

Two modifications of Y2Piv6(HPiv)6 crystals: synthesis and structures

International Nuclear Information System (INIS)

Kiseleva, E.A.; Troyanov, S.I.; Korenev, Yu.M.

2006-01-01

Crystal structure of solvate of yttrium pivalate YPiv 3 ·3HPiv is studied. Existing of two polymorphous modifications of the compound is detected. It is shown that α- and β-modifications of yttrium pivalate solvate have molecular crystal structures and are built of Y 2 Piv 6 (HPiv) 6 dimers. Difference of these two modifications is in package of dimer molecules and in center-symmetricity of dimers in α-modification structure. Molecular and crystal structure, crystal lattice parameters are determined [ru

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2014-01-01

The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method. In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom

Molecular morphology and crystallization in the quantum limit

DEFF Research Database (Denmark)

Bohr, Jakob

2002-01-01

The effects of phonons on crystallization and crystal morphology are investigated. It is shown that the commensuration of the lattice vibrations with the lattice will favor certain crystal morphologies. Vibrational effects can also be important for the molecular structure of chain molecules...... protein are estimated to differ by several electron volts. For a biomolecule, such energy is significant and may contribute to cold denaturing as seen for proteins. This is consistent with the empirical observation that cold denaturation is exothermic and hot denaturation endothermic....

Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy.

Science.gov (United States)

Ban, David; Sabo, T Michael; Griesinger, Christian; Lee, Donghan

2013-09-26

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-tc window (defined as τ(c) supra-τ(c) supra-τ(c) window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τ(c) scale by up to a factor of two (motion up to 25 μs). From the data obtained with these techniques and methodology, the importance of the supra-τ(c) scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τ(c) scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.

Novel technique and simple approach for supra-alar region and supra-alar crease correction by supra-alar cinching.

Science.gov (United States)

Selvaraj, Loganathan

2016-01-01

This technical report describes a simple and innovative surgical technique for supra-alar sidewall region constriction and supra-alar crease attenuation by cinching technique through intraoral approach.

Novel technique and simple approach for supra-alar region and supra-alar crease correction by supra-alar cinching

OpenAIRE

Selvaraj, Loganathan

2016-01-01

This technical report describes a simple and innovative surgical technique for supra-alar sidewall region constriction and supra-alar crease attenuation by cinching technique through intraoral approach.

Dipole plasma in molecular crystals

International Nuclear Information System (INIS)

Kotel'nikov, Yu.E.; Kochelaev, B.I.

1976-01-01

Collective oscillations in a system of electric dipoles of molecular crystals are investigated. It has been proved in the exciton approximation that in an elementary cell of a molecular crystal with one molecule there may exist energy fluctuations of the ''dipole'' plasma, analogous to plasma oscillations in the charged Fermi liquid

Structural templating in a nonplanar phthalocyanine using single crystal copper iodide

OpenAIRE

Rochford, L. A. (Luke A.); Ramadan, Alexandra J.; Keeble, Dean S.; Ryan, Mary P.; Heutz, Sandrine; Jones, T. S. (Tim S.)

2015-01-01

Solution-grown copper iodide crystals are used as substrates for the templated growth of the nonplanar vanadyl phthalocyanine using organic molecular beam deposition. Structural characterization reveals a single molecular orientation produced by the (111) Miller plane of the copper iodide crystals. These fundamental measurements show the importance of morphology and structure in templating interactions for organic electronics applications.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2010-01-01

The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

International Nuclear Information System (INIS)

Kaynar, Nihal Kan; Tanak, Hasan; Şahin, Songul; Dege, Necmi; Ağar, Erbil; Yavuz, Metin

2016-01-01

The crystal structure of the title compound, C_1_4H_1_2N_2O_3, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

Energy Technology Data Exchange (ETDEWEB)

Kaynar, Nihal Kan, E-mail: nihal-kan84@windowslive.com [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey); Tanak, Hasan [Amasya University, Department of Physics, Faculty of Arts and Sciences (Turkey); Şahin, Songul [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Dege, Necmi [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey); Ağar, Erbil [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Yavuz, Metin [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey)

2016-03-15

The crystal structure of the title compound, C{sub 14}H{sub 12}N{sub 2}O{sub 3}, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction II: Nonplanar Molecules.

Science.gov (United States)

Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

2017-11-14

The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment (XDM) dispersion model for crystal structure prediction. In this article, we study the relatively large, nonplanar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre. Four of the seven experimental structures are predicted as the energy minimum, and thermal effects are demonstrated to have a large impact on the ranking of at least another compound. As in the first part of this series, delocalization error affects the results for a single crystal (compound X), in this case by detrimentally overstabilizing the π-conjugated conformation of the monomer. Overall, B86bPBE-XDM correctly predicts 16 of the 21 compounds in the five blind tests, a result similar to the one obtained using the best CSP method available to date (dispersion-corrected PW91 by Neumann et al.). Perhaps more importantly, the systems for which B86bPBE-XDM fails to predict the experimental structure as the energy minimum are mostly the same as with Neumann's method, which suggests that similar difficulties (absence of vibrational free energy corrections, delocalization error,...) are not limited to B86bPBE-XDM but affect GGA-based DFT-methods in general. Our work confirms B86bPBE-XDM as an excellent option for crystal energy ranking in CSP and offers a guide to identify crystals (organic salts, conjugated flexible systems) where difficulties may appear.

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

Science.gov (United States)

Marchewka, M. K.; Pietraszko, A.

2008-02-01

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

Crystal and Molecular Structure of Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II Complex

Directory of Open Access Journals (Sweden)

Hakan Arslan

2011-01-01

Full Text Available Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II complex has been synthesized and characterized by elemental analysis and FT-IR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, with a = 13.046(2 Å, b = 13.135(2 Å, c = 13.179(2 Å, α= 67.083(4°, β= 67.968(4°, γ = 84.756(4° and Dcalc =1.330 g/cm3 for Z = 2. The crystal structure confirms that the complex is a mononuclear copper(II complex and the 2,2-diphenyl-N-(di-n-propyl-carbamothioylacetamide ligand is a bidentate chelating ligand, coordinating to the copper atom through the thiocarbonyl and carbonyl groups. This coordination has a slightly distorted square-planar geometry (O1-Cu1-O2: 86.48(11°, O1-Cu1-S1: 93.85(9°, O2-Cu1-S2: 94.20(9° and S1-Cu1-S2: 91.21(4°. The title molecule shows a cis-arrangement and C–O, C–S and C–N bond lengths of the complex suggest considerable electronic delocalization in the chelate rings.

Crystal and molecular structure of 2-thiouridine

Energy Technology Data Exchange (ETDEWEB)

Hawkinson, S W

1977-01-01

The ''minor'' nucleoside 2-thiouridine, C/sub 9/H/sub 12/O/sub 5/N/sub 2/S, crystallizes in a monoclinic cell, space group P2/sub 1/ with a = 5.049 (2), b = 7.526 (2), c = 14.050 (3) A, ..beta.. = 90.17 (2)/sup 0/, and d = 1.619 g cm/sup -3/ (for Z = 2) at 22 +- 2/sup 0/C. The structure was derived from 1334 unique intensities measured with an Oak Ridge computer-controlled diffractometer to a limit of sin theta/lambda = 0.65 A/sup -1/ with Nb-filtered Mo K..cap alpha.. radiation. Atomic parameters were obtained by a combination of Patterson and Fourier techniques and refined by full-matrix least squares to a final R(F) value of 0.023 for all data. The bond lengths and angles in the molecule agree well with those of other thiopyrimidines (C(2) - S = 1.677 A). The conformation of the sugar ring relative to the base is anti with a torsion angle chi(O(1')--C(1') ..-->.. N(1)--C(6)) of 17/sup 0/. The sugar exists in the 3'-endo conformation. The O(5')--C(5') bond is gauche to C(4) - O(1') and trans to C(4')--C(3') (torsion angles of 74 and -169/sup 0/ respectively). The molecules are linked together in the crystal by hydrogen bonds in an intricate network which is identical to that inferred by Kojic-Prodic, Liminga, Sljukic and Ruzic-Toros (Acta Cryst. (1974), B30, 1550-1555) for the crystal structure of 5,6-dihydro-2-thiouridine. 2 figures; 6 tables.

Crystal structure of an organic–inorganic supra­molecular salt based on a 4,4′-methyl­enebis(3,5-dimethyl-1H-pyrazol-2-ium) cation and a β-octa­molybdate anion

Science.gov (United States)

Amarante, Tatiana R.; Gonçalves, Isabel S.; Almeida Paz, Filipe A.

2016-01-01

The asymmetric unit of the title compound, bis­[4,4′-methyl­enebis(3,5-dimethyl-1H-pyrazol-2-ium)] β-octa­molybdate, (C11H18N4)2[Mo8O26] or (H4mbdpz)2[Mo8O26], is composed of an H4mbdpz2+ cation and half of the β-octa­molybdate anion which is completed by inversion symmetry. The organic mol­ecular units are engaged in a series of N—H⋯O hydrogen bonds with neighbouring anions, with N⋯O distances and N—H⋯O angles in the ranges 2.730 (2)–2.941 (2) Å and 122–166°, respectively. These inter­actions lead to the formation of a supra­molecular two-dimensional network parallel to the (010) plane. PMID:26958369

On Bitopological Supra B-Open Sets

OpenAIRE

M.Lellis Thivagar; B.Meera Devi

2012-01-01

In this paper, we introduce and investigate a new class of sets and maps be- tween bitopological spaces called supra(1,2) b-open, and supra (1,2) b-continuous maps, respectively. Furthermore, we introduce the concepts of supra(1,2) locally-closed, supra(1,2) locally b-closed sets. We also introduce supra(1,2) extremely disconnected. Finally, additional properties of these sets are investigated.

Structural, vibrational and theoretical studies of anilinium trichloroacetate: New hydrogen bonded molecular crystal with nonlinear optical properties

Science.gov (United States)

Tanak, H.; Pawlus, K.; Marchewka, M. K.; Pietraszko, A.

2014-01-01

In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm-1 and 3600-80 cm-1 regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be deff = 0.70 deff (KDP).

Tore Supra

International Nuclear Information System (INIS)

Supra, E.T.

1989-01-01

Tore Supra is a tokamak implemented on the site of CEN Cadarache by the EURATOM-CEA Association. The machine technology integrates all problems related to the fabrication and the operation of large cyrogenic superconducting coils and of the associated cryogenic system. Tore Supra will provide a significant experience to prepare the next generation of machines for controlled design. Tore Supra has been designed to implement a lage physics program that takes advantage of the capability of operation with plasma pulses in excess of 30 seconds. Operation started in April, with a toroidal field of 2 teslas. Discharges of 500 kA with a 3 second current flat top were obtained after a few days. Machine parameters will be raised to their nominal values ( B -- 4.5 Teslas and Ip -- 1.7 MA) during summer

Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

Science.gov (United States)

Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

2004-10-01

Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

Crystal structure of enolase from Drosophila melanogaster.

Science.gov (United States)

Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

2017-04-01

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

On Neutrosophic Semi-Supra Open Set and Neutrosophic Semi-Supra Continuous Functions

OpenAIRE

R. Dhavaseelan; M. Parimala; S. Jafari; F. Smarandache

2017-01-01

In this paper, we introduce and investigate a new class of sets and functions between topological space called neutrosophic semi-supra open set and neutrosophic semi-supra open continuous functions respectively.

Modeling of ultrafast THz interactions in molecular crystals

DEFF Research Database (Denmark)

Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

2014-01-01

In this paper we present a numerical study of terahertz pulses interacting with crystals of cesium iodide. We model the molecular dynamics of the cesium iodide crystals with the Density Functional Theory software CASTEP, where ultrafast terahertz pulses are implemented to the CASTEP software...... to interact with molecular crystals. We investigate the molecular dynamics of cesium iodide crystals when interacting with realistic terahertz pulses of field strengths from 0 to 50 MV/cm. We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

Crystal structures of seven molecular salts derived from benzylamine and organic acidic components

Science.gov (United States)

Wen, Xianhong; Jin, Xiunan; Lv, Chengcai; Jin, Shouwen; Zheng, Xiuqing; Liu, Bin; Wang, Daqi; Guo, Ming; Xu, Weiqiang

2017-07-01

Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids gave a total of seven molecular salts with the compositions: (benzylamine): (p-toluenesulfonic acid) (1) [(HL)+ · (tsa-)], (benzylamine): (o-nitrobenzoic acid) (2) [(HL+) · (onba)-], (benzylamine): (3,4-methylenedioxybenzoic acid) (3) [(HL+) · (mdba-)], (benzylamine): (mandelic acid) (4) [(HL+) · (mda-)], (benzylamine): (5-bromosalicylic acid)2(5) [(HL+) · (bsac-) · (Hbsac)], (benzylamine): (m-phthalic acid) (6) [(HL+) · (Hmpta-)], and (benzylamine)2: (trimesic acid) (7) [(HL+)2 · (Htma2-)]. The seven salts have been characterised by X-ray diffraction technique, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the seven investigated crystals the NH2 groups in the benzylamine moieties are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond formation between the ammonium and the deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 4-7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CHsbnd π/CH2sbnd π, Osbnd O, and Osbnd Cπ associations contribute to the stabilization and expansion of the total high-dimensional (2D-3D) framework structures. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R42(8), R43(10) and R44(12), usually observed in organic solids of organic acids with amine, were again shown to be involved in constructing most of these hydrogen bonding networks.

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

Energy Technology Data Exchange (ETDEWEB)

Linko, R. V., E-mail: rlinko@mail.ru [Peoples' Friendship University of Russia (Russian Federation); Sokol, V. I. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

2013-05-15

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

International Nuclear Information System (INIS)

Linko, R. V.; Sokol, V. I.; Polyanskaya, N. A.; Ryabov, M. A.; Strashnov, P. V.; Davydov, V. V.; Sergienko, V. S.

2013-01-01

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL 2 ] · CHCl 3 (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL 2 are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

Molecular and crystal structure of the antibiotic enniatin B, a secondary microbial metabolite

International Nuclear Information System (INIS)

Zhukhlistova, N.E.; Tishchenko, G.N.; Tolstykh, I.V.; Zenkova, V.A.

1999-01-01

Single crystals of the secondary microbial metabolite C 33 H 57 N 3 O 9 ·1(2/3)H 2 O with the known molecular weight were studied by the method of X-ray diffraction analysis, where a=b=15.102(3) A, c=14.548(3) A, sp. gr.R3, R=0.057. In the course of the structure determination, it was established that the substance is a natural antibiotic, namely, enniatin B. The conformation of its molecule is similar to that of the known synthetic antibiotic. The main difference between the natural and synthesized forms reduces to the different numbers of water molecules and their arrangement in the cavity of the antibiotic molecule

An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

International Nuclear Information System (INIS)

Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

2016-01-01

An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

Science.gov (United States)

Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

2016-04-01

Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions.

Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

Science.gov (United States)

Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

2016-06-01

The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

Crystal structure of [(2R,3R,4S)-3,4-bis(acet-yloxy)-5-iodo-3,4-di-hydro-2H-pyran-2-yl]methyl acetate.

Science.gov (United States)

Zukerman-Schpector, Julio; Caracelli, Ignez; Stefani, Hélio A; Shamim, Anwar; Tiekink, Edward R T

2015-01-01

In the title compound, C12H15IO7, the 3,4-di-hydro-2H-pyran ring is in a distorted half-boat conformation with the atom bearing the acet-yloxy group adjacent to the C atom bearing the methyl-acetate group lying 0.633 (6) Å above the plane of the remaining ring atoms (r.m.s. deviation = 0.0907 Å). In the crystal, mol-ecules are linked into a supra-molecular chain along the a axis through two C-H⋯O inter-actions to the same acceptor carbonyl O atom; these chains pack with no specific inter-molecular inter-actions between them.

Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form

Directory of Open Access Journals (Sweden)

Boguslaw Stec

2007-10-01

Full Text Available We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCOfrom the red algae Galdieria Sulphuraria. The protein crystallized in two different crystalforms, the I422 crystal form being obtained from high salt and the P21 crystal form beingobtained from lower concentration of salt and PEG. We report here the crystallization,preliminary stages of structure determination and the detection of the structural phasetransition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzymebelongs to the hexadecameric class (L8S8 with an approximate molecular weight 0.6MDa.The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a singlehexadecamer per asymmetric unit. The preservation of diffraction power in a phasetransition for such a large macromolecule is rare.

Measuring Dynamic and Kinetic Information in the Previously Inaccessible Supra-tc Window of Nanoseconds to Microseconds by Solution NMR Spectroscopy

Directory of Open Access Journals (Sweden)

Donghan Lee

2013-09-01

Full Text Available Nuclear Magnetic Resonance (NMR spectroscopy is a powerful tool that has enabled experimentalists to characterize molecular dynamics and kinetics spanning a wide range of time-scales from picoseconds to days. This review focuses on addressing the previously inaccessible supra-τc window (defined as τc < supra-τc < 40 μs; in which τc is the overall tumbling time of a molecule from the perspective of local inter-nuclear vector dynamics extracted from residual dipolar couplings (RDCs and from the perspective of conformational exchange captured by relaxation dispersion measurements (RD. The goal of the first section is to present a detailed analysis of how to extract protein dynamics encoded in RDCs and how to relate this information to protein functionality within the previously inaccessible supra-τc window. In the second section, the current state of the art for RD is analyzed, as well as the considerable progress toward pushing the sensitivity of RD further into the supra-τc scale by up to a factor of two (motion up to 25 ms. From the data obtained with these techniques and methodology, the importance of the supra-τ c scale for protein function and molecular recognition is becoming increasingly clearer as the connection between motion on the supra-τc scale and protein functionality from the experimental side is further strengthened with results from molecular dynamics simulations.

On Some Maps in Supra Topological Ordered Spaces

OpenAIRE

Al-shami, Tareq Mohammed

2018-01-01

In [6] the notion of supra semi open sets was presented and some of its properties were discussed. In this study, we introduce and investigate four main concepts namely supra continuous (supra open, supra closed, supra homeomorphism) maps via supra topological ordered spaces. Our findings in this work generalize some previous results in ([1], [13]). Many examples are considered to show the concepts introduced and main results obtained herein.

Studies on growth, crystal structure and characterization of novel organic nicotinium trifluoroacetate single crystals

Energy Technology Data Exchange (ETDEWEB)

Dhanaraj, P.V. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Rajesh, N.P., E-mail: rajeshnp@hotmail.com [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Sundar, J. Kalyana; Natarajan, S. [Department of Physics, Madurai Kamaraj University, Madurai 625 021 (India); Vinitha, G. [Department of Physics, Crescent Engineering College, Chennai 600 048 (India)

2011-09-15

Highlights: {yields} Good quality crystals of nicotinium trifluoroacetate in monoclinic system were grown for first time. {yields} Nicotinium trifluoroacetate crystal exhibits third order nonlinear optical properties. {yields} The optical spectrum of nicotinium trifluoroacetate crystal reveals the wide transmission in the entire range with cutoff wavelength at 286 nm. {yields} Nicotinium trifluoroacetate is a low dielectric constant material. - Abstract: An organic material, nicotinium trifluoroacetate (NTF) was synthesized and single crystals in monoclinic system were grown from aqueous solution for the first time. Its solubility and metastable zone width were estimated. The crystal structure of NTF was analyzed to reveal the molecular arrangements and the formation of hydrogen bonds in the crystal. High-resolution X-ray diffraction rocking curve measurements were performed to analyze the structural perfection of the grown crystals. Functional groups in NTF were identified by Fourier transform infrared spectral analysis. Thermal behaviour and stability of NTF were studied by thermogravimetric and differential thermal analysis and differential scanning calorimetry. Mechanical and dielectric properties of NTF crystals were analyzed. Optical studies reveal that NTF crystals are transparent in the wavelength range 286-1100 nm. The third order nonlinear optical parameters of NTF were derived by the Z-scan technique.

Balancing sub- and supra-salt strain in salt-influenced rifts: Implications for extension estimates

Science.gov (United States)

Coleman, Alexander J.; Jackson, Christopher A.-L.; Duffy, Oliver B.

2017-09-01

The structural style of salt-influenced rifts may differ from those formed in predominantly brittle crust. Salt can decouple sub- and supra-salt strain, causing sub-salt faults to be geometrically decoupled from, but kinematically coupled to and responsible for, supra-salt forced folding. Salt-influenced rifts thus contain more folds than their brittle counterparts, an observation often ignored in extension estimates. Fundamental to determining whether sub- and supra-salt structures are kinematically coherent, and the relative contributions of thin- (i.e. gravity-driven) and thick-skinned (i.e. whole-plate stretching) deformation to accommodating rift-related strain, is our ability to measure extension at both structural levels. We here use published physical models of salt-influenced extension to show that line-length estimates yield more accurate values of sub- and supra-salt extension compared to fault-heave, before applying these methods to seismic data from the Halten Terrace, offshore Norway. We show that, given the abundance of ductile deformation in salt-influenced rifts, significant amounts of extension may be ignored, leading to the erroneous interpretations of thin-skinned, gravity-gliding. If a system is kinematically coherent, supra-salt structures can help predict the occurrence and kinematics of sub-salt faults that may be poorly imaged and otherwise poorly constrained.

Crystal and molecular structure of neodymium (3) p-aminobenzoaate

International Nuclear Information System (INIS)

Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

1981-01-01

X-ray structural study (lambda MoKsub(α), automatic diffractometer, the method of heavy atom, anisotropic specification) of neodymium (3) n-aminobenzoate has been carried out. The crystals are monoclinic: a=9.882 (5), b=22.810 (12), c=9.851 (8)A, β=100.02 (5)deg, v=2186.59 A 3 , Z=4, sp. gr. P2 1 /n, R=0.046. The crystal structure of Nd(OOCC 6 H 4 NH 2 ) 3 xH 2 O consists of dimer-periodic layers alternating along the b axis. Surrounding of Nd atom in the chain is formed with four oxygen atoms of four carboxyl groups of bidentate-bridge and one carboxyl bidentate-cyclic ligands, one water molecule and N atom of ligand aminogroup from the neigbouring chain. The atom simultaneously bonds the neighbouring chains into continuous layer. The mean distances Nd-O, and Nd-N are equal to 2.45 and 2.74 A. An attempt to determine hydrogen atom coordinates has failed [ru

The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix

Science.gov (United States)

Landis, W. J.

1995-01-01

High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.

Spatially resolved analysis of short-range structure perturbations in a plastically bent molecular crystal

Science.gov (United States)

Panda, Manas K.; Ghosh, Soumyajit; Yasuda, Nobuhiro; Moriwaki, Taro; Mukherjee, Goutam Dev; Reddy, C. Malla; Naumov, Panče

2015-01-01

The exceptional mechanical flexibility observed with certain organic crystals defies the common perception of single crystals as brittle objects. Here, we describe the morphostructural consequences of plastic deformation in crystals of hexachlorobenzene that can be bent mechanically at multiple locations to 360° with retention of macroscopic integrity. This extraordinary plasticity proceeds by segregation of the bent section into flexible layers that slide on top of each other, thereby generating domains with slightly different lattice orientations. Microscopic, spectroscopic and diffraction analyses of the bent crystal showed that the preservation of crystal integrity when stress is applied on the (001) face requires sliding of layers by breaking and re-formation of halogen-halogen interactions. Application of stress on the (100) face, in the direction where π···π interactions dominate the packing, leads to immediate crystal disintegration. Within a broader perspective, this study highlights the yet unrecognized extraordinary malleability of molecular crystals with strongly anisotropic supramolecular interactions.

Tore Supra: technical description

International Nuclear Information System (INIS)

1985-08-01

This report is aimed, after a brief recall of physics and technologic perspectives of Tore Supra, at giving a detailed description of the basic machine; details of each component are defined. Volume 1 is specifically concerned with the general aspects of Tore Supra and the toroidal field system [fr

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

Science.gov (United States)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

Slow neutron scattering in molecular crystals. 5-4

International Nuclear Information System (INIS)

Inoue, Kazuhiko

1976-01-01

The utilization of incoherent inelastic neutron scattering (INS) as a probe for molecular crystals is reviewed. In particular, some typical examples of the measurement of incoherent inelastic neutron scattering spectra (INSS) in molecular crystals are presented in the first section of this report. The results of measurement are shown for theta-xylene, benzene, polypropylene oxide, deuteride, and formic acid. The second section presents an equation for the incoherent scattering cross section of a crystal by dividing the molecular motion into the outer and inner modes. Phonon expansion is also used for the easy understanding of the relation between the INSS and the dynamic characteristics of molecular crystals. In the third section, the measured results are analyzed on the basis of the theory presented in the previous section. And the difference between the van der Waals bond and the hydrogen bond is shortly discussed. (Aoki, K.)

The crystal structure of the phosphatidylinositol 4-kinase IIalpha

Czech Academy of Sciences Publication Activity Database

Bäumlová, Adriana; Chalupská, Dominika; Rozycki, B.; Jovic, M.; Wisniewski, E.; Klíma, Martin; Dubánková, Anna; Kloer, D. P.; Nencka, Radim; Balla, T.; Bouřa, Evžen

2015-01-01

Roč. 22, č. 1 (2015), s. 5 ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /13./. 19.03.2015-21.03.2015, Nové Hrady] EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : PI4K IIalpha * crystal structure Subject RIV: CE - Biochemistry

X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

DEFF Research Database (Denmark)

Yennawar, Hemant; Møller, Magda; Gillilan, Richard

2011-01-01

The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer...

Crystal and molecular structure of dichlorodioxobis (triphenylphosphine oxide)uranium(VI)

Energy Technology Data Exchange (ETDEWEB)

Bombieri, G; Forsellini, E [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi; Day, J P; Azeez, W I

1978-01-01

The crystal structure of (UO/sub 2/Cl/sub 2/(PPh/sub 3/O)/sub 2/) has been determined from three-dimensional X-ray diffraction data. Crystals are triclinic, space group P1, with a = 10.0101(6), b = 10.2589(9), c = 9.2347(8) A, ..cap alpha.. = 110.093(6). ..beta.. = 92.129(6), and ..gamma.. = 78.384(6), and Z = 1. The structure has been solved by the heavy-atom method from counter data, and refined by least squares to a final R of 0.054. The coordination polyhedron around uranium is a distorted octahedron, with a linear uranyl group (U-O 1.764A) perpendicular to a plane in which the two chloride and two oxide ions trans to each other occupy the corners of a rectangle (U-O 2.300; U-Cl 2.645 A).

Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

Science.gov (United States)

Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

2016-02-01

In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

Neutron diffraction investigation of the crystal and molecular structure of the anisotropic superconductor Hg3AsF6

International Nuclear Information System (INIS)

Schultz, A.J.; Williams, J.M.; Miro, N.D.; MacDiarmid, A.G.; Heeger, A.J.

1978-01-01

The crystal and molecular structure of Hg 3 AsF 6 has been investigated by single-crystal neutron diffraction. This metallic compound crystallizes in the body-centered tetragonal space group I4 1 /amd with cell dimensions of a = 7.549 (5) A and c = 12.390 (9) A. The crystal structure consists of two orthogonal and nonintersecting linear chains of Hg/sup 0.33+/ cations passing through a lattice of octahedral AsF 6 - anions. The intrachain Hg--Hg distance of 2.64 (2) A is derived from planes of diffuse scattering normal to a* and b*. Since the a and b axis lattice constants are not simple multiples of the Hg--Hg intrachain distance, the mercury chains are incommensurate with the tetragonal lattice; hence we have the apparent formula Hg 2 . 86 AsF 6 . These results are in essential agreement with a previously reported x-ray diffraction study. However, from the neutron diffraction data, we have established that the Hg chains are not strictly one-dimensional. The maximum room-temperature deviation from the chain axis is 0.07 (1) A with neighboring chains distorted away from each other. The closest interchain Hg--Hg contact is 3.24 (2) A. Furthermore, analytical data consistently indicate a stoichiometric empirical formula of Hg 3 AsF 6 . These results together with precise density measurements imply that the incommensurate structure is stabilized by anion vacancies, such that there are four formula weights of Hg 2 . 86 (AsF 6 ) 0 . 953 per unit cell. 4 tables, 2 figures

Crystal structure of (2R-1-[(methylsulfonyloxy]propan-2-aminium chloride: a chiral molecular salt

Directory of Open Access Journals (Sweden)

H. R. Rajegowda

2015-10-01

Full Text Available In the title chiral molecular salt, C4H12NO3S+·Cl−, the cation is protonated at the N atom, producing [RNH3]+, where R is CH3SO2OCH2C(HCH3. The N atom in the cation is sp3-hybridized. In the crystal, cations and anions are connected by strong N—H...Cl hydrogen bonds to generate edge-shared 12-membered rings of the form {...Cl...HNH}3. This pattern of hydrogen bonding gives rise to zigzag supramolecular layers in the ab plane. The layers are connected into a three-dimensional architecture by C—H...O hydrogen bonds. The structure was refined as an inversion twin.

Crystal and molecular structures of 3-amino-4-hydroxy benzenesulfonamide and its hydrochloride: Quantum-chemical study of their tautomerism

Energy Technology Data Exchange (ETDEWEB)

Kovalchukova, O. V., E-mail: okovalchukova@mail.ru; Strashnova, S. B.; Romashkina, E. P.; Strashnov, P. V.; Zaitsev, B. E. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

2013-03-15

3-amino-4-hydroxy benzenesulfonamide and its hydrochloride have been isolated in the crystalline state. Their crystal and molecular structures are determined by X-ray diffraction. The equilibrium between neutral tautomeric forms of the 3-amino-4-hydroxy benzenesulfonamide molecule is studied within the approximation of density functional theory (B3LYP/aug-cc-pVDZ). The constants of acid-base equilibrium of 3-amino-4-hydroxy benzenesulfonamide are deter-mined using spectrophotometry.

short communication synthesis and crystal structure of a polymeric

African Journals Online (AJOL)

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A new polymeric zinc(II) complex, [ZnL2(PDA)]n, has been prepared by the reaction of zinc sulfate ... complex has been characterized by single-crystal X-ray diffraction. .... Molecular structure of the complex at 30% probability displacement.

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

International Nuclear Information System (INIS)

Jagadeesan, G.; Malathy, P.; Gunasekaran, K.; Harikrishna Etti, S.; Aravindhan, S.

2014-01-01

The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3 1 21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit

Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

Energy Technology Data Exchange (ETDEWEB)

Jagadeesan, G. [Presidency College, Chennai 600 005 (India); Malathy, P.; Gunasekaran, K. [University of Madras, Chennai 600 025 (India); Harikrishna Etti, S. [GKM College of Engineering and Technology, Kamaraj Salai, Chennai 600 063 (India); Aravindhan, S., E-mail: aravindhanpresidency@gmail.com [Presidency College, Chennai 600 005 (India)

2014-10-25

The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

Revolving supramolecular chiral structures powered by light in nanomotor-doped liquid crystals

Science.gov (United States)

Orlova, Tetiana; Lancia, Federico; Loussert, Charles; Iamsaard, Supitchaya; Katsonis, Nathalie; Brasselet, Etienne

2018-04-01

Molecular machines operated by light have been recently shown to be able to produce oriented motion at the molecular scale1,2 as well as do macroscopic work when embedded in supramolecular structures3-5. However, any supramolecular movement irremediably ceases as soon as the concentration of the interconverting molecular motors or switches reaches a photo-stationary state6,7. To circumvent this limitation, researchers have typically relied on establishing oscillating illumination conditions—either by modulating the source intensity8,9 or by using bespoke illumination arrangements10-13. In contrast, here we report a supramolecular system in which the emergence of oscillating patterns is encoded at the molecular level. Our system comprises chiral liquid crystal structures that revolve continuously when illuminated, under the action of embedded light-driven molecular motors. The rotation at the supramolecular level is sustained by the diffusion of the motors away from a localized illumination area. Above a critical irradiation power, we observe a spontaneous symmetry breaking that dictates the directionality of the supramolecular rotation. The interplay between the twist of the supramolecular structure and the diffusion14 of the chiral molecular motors creates continuous, regular and unidirectional rotation of the liquid crystal structure under non-equilibrium conditions.

Routine phasing of coiled-coil protein crystal structures with AMPLE

Directory of Open Access Journals (Sweden)

Jens M. H. Thomas

2015-03-01

Full Text Available Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

Energy Technology Data Exchange (ETDEWEB)

Cornaby, Sterling [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Szebenyi, Doletha M. E. [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Smilgies, Detlef-M. [CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States); Schuller, David J.; Gillilan, Richard; Hao, Quan [MacCHESS (Macromolecular Diffraction Facilities at CHESS), Cornell University, Ithaca, New York (United States); Bilderback, Donald H., E-mail: dhb2@cornell.edu [School of Applied and Engineering Physics, Cornell University, Ithaca, New York (United States); CHESS (Cornell High Energy Synchrotron Source), Cornell University, Ithaca, New York (United States)

2010-01-01

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

International Nuclear Information System (INIS)

Cornaby, Sterling; Szebenyi, Doletha M. E.; Smilgies, Detlef-M.; Schuller, David J.; Gillilan, Richard; Hao, Quan; Bilderback, Donald H.

2010-01-01

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used

Stochastic field line structures appearing in field line tracing calculations for a helical magnetic limiter on TORE SUPRA

International Nuclear Information System (INIS)

Fuchs, G.; Steffen, B.; Blenski, T.; Grosman, A.; Samain, A.

1985-05-01

The influence on the structure of the magnetic field of a tokamak produced by small helical currents flowing near the plasma in TORE SUPRA was investigated numerically by drawing Poincare plots. The current in the helical conductors, the pitch of the windings, the rotational transform and the plasma pressure have been varied. The topology of the magnetic field line structure is discussed in some detail and simple examples are given for illustration. (orig.)

First principles investigation of the structure of a bacteriochlorophyll crystal

Energy Technology Data Exchange (ETDEWEB)

Marchi, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)]|[Centre d`Etudes Saclay, Gif-sur-Yvette (France); Hutter, J.; Parrinello, M. [Max-Planck-Institut fuer Festkoerperforschung, Stuttgart (Germany)

1996-08-21

In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

supraHex: An R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map☆

Science.gov (United States)

Fang, Hai; Gough, Julian

2014-01-01

Biologists are increasingly confronted with the challenge of quickly understanding genome-wide biological data, which usually involve a large number of genomic coordinates (e.g. genes) but a much smaller number of samples. To meet the need for data of this shape, we present an open-source package called ‘supraHex’ for training, analysing and visualising omics data. This package devises a supra-hexagonal map to self-organise the input data, offers scalable functionalities for post-analysing the map, and more importantly, allows for overlaying additional data for multilayer omics data comparisons. Via applying to DNA replication timing data of mouse embryogenesis, we demonstrate that supraHex is capable of simultaneously carrying out gene clustering and sample correlation, providing intuitive visualisation at each step of the analysis. By overlaying CpG and expression data onto the trained replication-timing map, we also show that supraHex is able to intuitively capture an inherent relationship between late replication, low CpG density promoters and low expression levels. As part of the Bioconductor project, supraHex makes accessible to a wide community in a simple way, what would otherwise be a complex framework for the ultrafast understanding of any tabular omics data, both scientifically and artistically. This package can run on Windows, Mac and Linux, and is freely available together with many tutorials on featuring real examples at http://supfam.org/supraHex. PMID:24309102

A mononuclear zinc(II) complex with piroxicam: Crystal structure, DNA- and BSA-binding studies; in vitro cell cytotoxicity and molecular modeling of oxicam complexes

Science.gov (United States)

Jannesari, Zahra; Hadadzadeh, Hassan; Amirghofran, Zahra; Simpson, Jim; Khayamian, Taghi; Maleki, Batool

2015-02-01

A new mononuclear Zn(II) complex, trans-[Zn(Pir)2(DMSO)2], where Pir- is 4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (piroxicam), has been synthesized and characterized. The crystal structure of the complex was obtained by the single crystal X-ray diffraction technique. The interaction of the complex with DNA and BSA was investigated. The complex interacts with FS-DNA by two binding modes, viz., electrostatic and groove binding (major and minor). The microenvironment and the secondary structure of BSA are changed in the presence of the complex. The anticancer effects of the seven complexes of oxicam family were also determined on the human K562 cell lines and the results showed reasonable cytotoxicities. The interactions of the oxicam complexes with BSA and DNA were modeled by molecular docking and molecular dynamic simulation methods.

Preparation and crystal and molecular structure of tris(diethyldithiocarbamato)dimethylphenylphosphinetechnetium(III)

International Nuclear Information System (INIS)

Batsanov, A.S.; Struchkov, Yu.T.; Lorenz, B.; Wahren, M.

1984-01-01

The title compound Tc(S 2 CNEt 2 ) 3 (Me 2 PhP) I has been prepared by the reaction of TcCl 3 (Me 2 PhP) 3 with NaS 2 CNEt 2 . The crystal structure of I has been determined by single-crystal X-ray diffraction methods at room temperature. Crystals are rhombic, space group P2 1 2 1 2 1 , with a = 8.708(1), b = 12.012(1), c = 29.626(3) A and Z = 4. The compound consists of discrete I molecules. The technetium atom has a seven-coordinated environment which is best described as a distorted pentagonal bipyramid. The Tc-P distance (2.330(3) A) is remarkably short compared with other technetium complexes with mono-dentate phosphine ligands. (author)

Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

Science.gov (United States)

Teschke, Omar; Soares, David Mendez

2016-03-29

Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

Site specific mineral composition and microstructure of human supra-gingival dental calculus.

Science.gov (United States)

Hayashizaki, Junko; Ban, Seiji; Nakagaki, Haruo; Okumura, Akihiko; Yoshii, Saori; Robinson, Colin

2008-02-01

Dental calculus has been implicated in the aetiology of several periodontal conditions. Its prevention and removal are therefore desirable clinical goals. While it is known that calculus is very variable in chemical composition, crystallinity and crystallite size little is known about site specific variability within a dentition and between individuals. With this in mind, a study was undertaken to investigate the comparative site specific nature and composition of human dental supra-gingival dental calculus obtained from 66 male patients visiting for their dental check-up using fluorescent X-ray spectroscopy, X-ray diffractometry and Fourier transform infrared spectroscopy. The supra-gingival dental calculus formed on the lingual surfaces of lower anterior teeth and the buccal surfaces of upper molar teeth were classified into four types based on calcium phosphate phases present. There was significant difference in composition of the crystal phase types between lower and upper teeth (pdental calculus on anterior or molar teeth of all samples. The degree of crystallinity of dental calculus formed on the upper molar teeth was higher than that formed on the lower anterior teeth (pdental calculus formed on the lower anterior teeth were higher than on upper molar teeth (pdental supra-gingival dental calculus is related to its location in the mouth.

Crystal and molecular structure of new fullerides (Ph4P)2C60Hal (Hal = Br, I) and (Ph4As)2C60Cl

International Nuclear Information System (INIS)

Gritsenko, V.V.; D'yachenko, O.A.; Shilov, G.V.; Spitsyn, N.G.; Yagubskij, E h.B.

1997-01-01

New stable on air fullerides (Ph 4 P) 2 C 60 Hal (Hal = Br, I) and (Ph 4 As) 2 C 60 Cl were synthesized and their crystal structure were determined. On the basis of their relative crystallochemical analysis fullerides obtained were shown to be isostructural. They are described by general formula (Ph 4 X) 2 C 60 Hal (X = H, As; Hal = Cl, Br, I) and crystallized in triclinic system. Anions C 60 - and Hal - occupy the centre-symmetrical positions, cations (PH 4 P) + and (Ph 4 As) + occupy the general positions. The main parameters of molecular structure are presented

An Amylase-Responsive Bolaform Supra-Amphiphile.

Science.gov (United States)

Kang, Yuetong; Cai, Zhengguo; Tang, Xiaoyan; Liu, Kai; Wang, Guangtong; Zhang, Xi

2016-02-01

An amylase-responsive bolaform supra-amphiphile was constructed by the complexation between β-cyclodextrin and a bolaform covalent amphiphile on the basis of host-guest interaction. The bolaform covalent amphiphile could self-assemble in solution, forming sheet-like aggregates and displaying weak fluorescence because of aggregation-induced quenching. The addition of β-cyclodextrin led to the formation of the bolaform supra-amphiphile, prohibiting the aggregation of the bolaform covalent amphiphile and accompanying with the significant recovery of fluorescence. Upon the addition of α-amylase, with the degradation β-cyclodextrin, the fluorescence of the supra-amphiphile would quench gradually and significantly, and the quenching rate linearly correlated to the concentration of α-amylase. This study enriches the field of supra-amphiphiles on the basis of noncovalent interactions, and moreover, it may provide a facile way to estimate the activity of α-amylase.

Inorganic bromine in organic molecular crystals: Database survey and four case studies

Science.gov (United States)

Nemec, Vinko; Lisac, Katarina; Stilinović, Vladimir; Cinčić, Dominik

2017-01-01

We present a Cambridge Structural Database and experimental study of multicomponent molecular crystals containing bromine. The CSD study covers supramolecular behaviour of bromide and tribromide anions as well as halogen bonded dibromine molecules in crystal structures of organic salts and cocrystals, and a study of the geometries and complexities in polybromide anion systems. In addition, we present four case studies of organic structures with bromide, tribromide and polybromide anions as well as the neutral dibromine molecule. These include the first observed crystal with diprotonated phenazine, a double salt of phenazinium bromide and tribromide, a cocrystal of 4-methoxypyridine with the neutral dibromine molecule as a halogen bond donor, as well as bis(4-methoxypyridine)bromonium polybromide. Structural features of the four case studies are in the most part consistent with the statistically prevalent behaviour indicated by the CSD study for given bromine species, although they do exhibit some unorthodox structural features and in that indicate possible supramolecular causes for aberrations from the statistically most abundant (and presumably most favourable) geometries.

DGR, GGR; molecular dynamical codes for simulating radiation damages in diamond and graphite crystals

International Nuclear Information System (INIS)

Taji, Yukichi

1984-06-01

Development has been made of molecular dynamical codes DGR and GGR to simulate radiation damages yielded in the diamond and graphite structure crystals, respectively. Though the usual molecular dynamical codes deal only with the central forces as the mutual interactions between atoms, the present codes can take account of noncentral forces to represent the effect of the covalent bonds characteristic of diamond or graphite crystals. It is shown that lattice defects yielded in these crystals are stable by themselves in the present method without any supports of virtual surface forces set on the crystallite surfaces. By this effect the behavior of lattice defects has become possible to be simulated in a more realistic manner. Some examples of the simulation with these codes are shown. (author)

Simulation and understanding of atomic and molecular quantum crystals

Science.gov (United States)

Cazorla, Claudio; Boronat, Jordi

2017-07-01

Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

Supra-ballistic phonons

International Nuclear Information System (INIS)

Russell, F.M.

1989-05-01

Energetic particles moving with a solid, either from nuclear reactions or externally injected, deposit energy by inelastic scattering processes which eventually appears as thermal energy. If the transfer of energy occurs in a crystalline solid then it is possible to couple some of the energy directly to the nuclei forming the lattice by generating phonons. In this paper the transfer of energy from a compound excited nucleus to the lattice is examined by introducing a virtual particle Π. It is shown that by including a Π in the nuclear reaction a substantial amount of energy can be coupled directly to the lattice. In the lattice this particle behaves as a spatially localized phonon of high energy, the so-called supra-ballistic phonon. By multiple inelastic scattering the supra-ballistic phonon eventually thermalizes. Because both the virtual particle Π and the equivalent supra-ballistic phonon have no charge or spin and can only exist within a lattice it is difficult to detect other than by its decay into thermal phonons. The possibility of a Π removing excess energy from a compound nucleus formed by the cold fusion of deuterium is examined. (Author)

Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

Science.gov (United States)

Marchewka, M. K.; Drozd, M.; Janczak, J.

2011-08-01

The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

Control of liquid crystal molecular orientation using ultrasound vibration

Energy Technology Data Exchange (ETDEWEB)

Taniguchi, Satoki [Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Wave Electronics Research Center, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Koyama, Daisuke; Matsukawa, Mami [Wave Electronics Research Center, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Shimizu, Yuki; Emoto, Akira [Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321 (Japan); Nakamura, Kentaro [Precision and Intelligence Laboratory, Tokyo Institute of Technology, 4259-R2-26, Nagatsuta-cho, Midori-ku, Yokohama 226-8503 (Japan)

2016-03-07

We propose a technique to control the orientation of nematic liquid crystals using ultrasound and investigate the optical characteristics of the oriented samples. An ultrasonic liquid crystal cell with a thickness of 5–25 μm and two ultrasonic lead zirconate titanate transducers was fabricated. By exciting the ultrasonic transducers, the flexural vibration modes were generated on the cell. An acoustic radiation force to the liquid crystal layer was generated, changing the molecular orientation and thus the light transmission. By modulating the ultrasonic driving frequency and voltage, the spatial distribution of the molecular orientation of the liquid crystals could be controlled. The distribution of the transmitted light intensity depends on the thickness of the liquid crystal layer because the acoustic field in the liquid crystal layer is changed by the orientational film.

Crystal structure, conformational analysis, and molecular dynamics of tetra-0-methyl-(+)-catechin

Science.gov (United States)

Frank R. Fronczek; Richard W. Hemingway; G. Wayne McGraw; Jan P. Steynberg; Carin A. Helfer; Wayne L. Mattice

1993-01-01

The structure of tetra-O-methyl-(+)-catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1, a=4.8125(2) Ǻ, b=12.9148(8) Ǻ, c=13.8862(11) Ǻ, α=86.962(6)°, β=89.120(5)°, γ=...

Molecular nucleation mechanisms and control strategies for crystal polymorph selection

Science.gov (United States)

van Driessche, Alexander E. S.; van Gerven, Nani; Bomans, Paul H. H.; Joosten, Rick R. M.; Friedrich, Heiner; Gil-Carton, David; Sommerdijk, Nico A. J. M.; Sleutel, Mike

2018-04-01

The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer’s disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures (‘polymorphs’) of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

Science.gov (United States)

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Multi-structure docking analysis of BACE1 crystal structures and non-peptidic ligands.

Science.gov (United States)

Haghighijoo, Zahra; Hemmateenejad, Bahram; Edraki, Najmeh; Miri, Ramin; Emami, Saeed

2017-09-01

In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis. It was found that using one crystal structure for docking did not result in high accuracy for predicting activity of the BACE1 inhibitors. Instead, using of the multi-structural docking scores, post-processed by chemometrics methods arrived to highly accurate predictive models. In this regards, the PDB accession codes of 4B70, 4DVF and 2WEZ could discriminate between active and inactive compounds, with higher accuracy. Clustering of the BACE1 structures based on principal component analysis of the crystallographic structures the revealed that the discriminant structures are in the center of the clusters. Thus, these structures can be selected as predominant crystal structures for docking studies of non-peptidic BACE1 inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

A computer-aided molecular design framework for crystallization solvent design

DEFF Research Database (Denmark)

Karunanithi, Arunprakash T.; Achenie, Luke E.K.; Gani, Rafiqul

2006-01-01

One of the key decisions in designing solution crystallization processes is the selection of solvents. In this paper, we present a computer-aided molecular design (CAMD) framework for the design and selection of solvents and/or anti-solvents for solution crystallization. The CAMD problem is formu......One of the key decisions in designing solution crystallization processes is the selection of solvents. In this paper, we present a computer-aided molecular design (CAMD) framework for the design and selection of solvents and/or anti-solvents for solution crystallization. The CAMD problem...... solvent molecules. Solvent design and selection for two types of solution crystallization processes namely cooling crystallization and drowning out crystallization are presented. In the first case study, the design of single compound solvent for crystallization of ibuprofen, which is an important...

Molecular crystals of 2-amino-1,3,4-thiadiazole with inorganic oxyacids – crystal engineering, phase transformations and NLO properties

Czech Academy of Sciences Publication Activity Database

Matulková, Irena; Cihelka, J.; Pojarová, Michaela; Fejfarová, Karla; Dušek, Michal; Císařová, I.; Vaněk, Přemysl; Kroupa, Jan; Němec, P.; Tesařová, N.; Němec, I.

2014-01-01

Roč. 16, č. 9 (2014), s. 1763-1776 ISSN 1466-8033 Grant - others:AVČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : molecular crystals * inorganic salts * structure determination * second harmonic generation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.034, year: 2014

Grain boundary barrier modification due to coupling effect of crystal polar field and water molecular dipole in ZnO-based structures

International Nuclear Information System (INIS)

Ji, Xu; Zhu, Yuan; Chen, Mingming; Su, Longxing; Chen, Anqi; Zhao, Chengchun; Gui, Xuchun; Xiang, Rong; Huang, Feng; Tang, Zikang

2014-01-01

Surface water molecules induced grain boundaries (GBs) barrier modification was investigated in ZnO and ZnMgO/ZnO films. Tunable electronic transport properties of the samples by water were characterized via a field effect transistor (FET) device structure. The FETs fabricated from polar C-plane ZnO and ZnMgO/ZnO films that have lots of GBs exhibited obvious double Schottky-like current-voltage property, whereas that fabricated from nonpolar M-plane samples with GBs and ZnO bulk single-crystal had no obvious conduction modulation effects. Physically, these hallmark properties are supposed to be caused by the electrostatical coupling effect of crystal polar field and molecular dipole on GBs barrier.

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

International Nuclear Information System (INIS)

Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Tools for systematic comparisons of NMR and crystal structures developed by the JCSG were applied to two proteins with known functions: the T. maritima anti-σ factor antagonist TM1081 and the mouse γ-glutamylamine cyclotransferase A2LD1 (gi:13879369). In an attempt to exploit the complementarity of crystal and NMR data, the combined use of the two structure-determination techniques was explored for the initial steps in the challenge of searching proteins of unknown functions for putative active sites. The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the

Synthesis and Crystal Structure of 1-Chloro-2-methyl-4-nitrobenzene

Directory of Open Access Journals (Sweden)

Jim Simpson

2012-03-01

Full Text Available The title compound (3 was prepared from 4-chloroaniline in good yield on successive oxidation and methylation and its crystal and molecular structure is reported. The compound crystallizes in the monoclinic space group P 21/n with unit cell dimensions a = 13.5698(8, b = 3.7195 (3, c = 13.5967 (8 Å, ß = 91.703(3 °, V = 685.96 (10 Å3. The molecule is essentially planar with a dihedral angle of 6.2(3 ° between the nitro group and the phenyl ring. The crystal structure is stabilised by π...π contacts between adjacent benzene rings together with C–H...O hydrogen bonds and close Cl...O contacts.

Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca.

Science.gov (United States)

Singh, D D; Saikrishnan, K; Kumar, Prashant; Dauter, Z; Sekar, K; Surolia, A; Vijayan, M

2004-11-01

The banana lectin from Musa paradisiaca, MW 29.4 kDa, has been isolated, purified and crystallized. The trigonal crystals contain one dimeric molecule in the asymmetric unit. The structure has been solved using molecular replacement to a resolution of 3 A. The structure of the subunit is similar to that of jacalin-like lectins.

Synthesis and crystal structure analysis of uranyl triple acetates

Energy Technology Data Exchange (ETDEWEB)

Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Serezhkina, Larisa B.; Serezhkin, Victor N. [Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Alekseev, Evgeny V., E-mail: e.alekseev@fz-juelich.de [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)

2016-12-15

Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.

3.2.1. Synthesis, crystal and molecular structure of catena-(bis(µ1-oxalic acid)-µ3-hydrogen oxalate-di-aqua-sodium(I)).

OpenAIRE

Olga Kovalchukova*, Sergey Aldoshin, Andrey Utenyshev, Konstantin Bogenko, Valeriy Tkachev

2015-01-01

The crystal and molecular structure of catena-(bis(µ- oxalic acid)-µ-hydrogen oxalate-di-aqua-sodium(I)) was detected by X-Ray analysis. The compound crystallizes in the triclinic space group P-1, with a(Å) 6.2378(12); b(Å) 7,1115(14); c(Å) 10.489(2); α(°) 94.65(3); β(°) 100.12(3); γ(°) 97.78(3). The sodium cation in the title compound is eight coordinated and forms a square antiprism. It is surrounded by two molecules of oxalic acid, one hydrogen oxalate anion and one water molecule. Both ox...

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

Energy Technology Data Exchange (ETDEWEB)

Goto, Kaname [Department of Electronics, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yamashita, Kenichi, E-mail: yamasita@kit.ac.jp [Faculty of Electrical Engineering and Electronics, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Yanagi, Hisao [Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); Yamao, Takeshi; Hotta, Shu [Faculty of Materials Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan)

2016-08-08

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

Science.gov (United States)

Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

2016-08-01

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ˜100 meV even in the "half-vertical cavity surface emitting lasing" microcavity structure.

Strong exciton-photon coupling in organic single crystal microcavity with high molecular orientation

International Nuclear Information System (INIS)

Goto, Kaname; Yamashita, Kenichi; Yanagi, Hisao; Yamao, Takeshi; Hotta, Shu

2016-01-01

Strong exciton-photon coupling has been observed in a highly oriented organic single crystal microcavity. This microcavity consists of a thiophene/phenylene co-oligomer (TPCO) single crystal laminated on a high-reflection distributed Bragg reflector. In the TPCO crystal, molecular transition dipole was strongly polarized along a certain horizontal directions with respect to the main crystal plane. This dipole polarization causes significantly large anisotropies in the exciton transition and optical constants. Especially the anisotropic exciton transition was found to provide the strong enhancement in the coupling with the cavity mode, which was demonstrated by a Rabi splitting energy as large as ∼100 meV even in the “half-vertical cavity surface emitting lasing” microcavity structure.

Superradiance from crystals of molecular nanomagnets.

Science.gov (United States)

Chudnovsky, E M; Garanin, D A

2002-10-07

We show that crystals of molecular nanomagnets can exhibit giant magnetic relaxation due to the Dicke superradiance of electromagnetic waves. Rigorous theory is presented that combines superradiance with the Landau-Zener effect.

Synthesis, crystal structure, physicochemical properties of hydrogen bonded supramolecular assembly of N,N-diethylanilinium-3, 5-dinitrosalicylate crystal

Science.gov (United States)

Rajkumar, M.; Chandramohan, A.

2017-12-01

An organic salt, N,N-diethylanilinium 3,5-dinitrosalicylate was synthesized and single crystals grown by employing the slow solvent evaporation solution growth technique in methanol-acetone (1:1) mixture. The electronic transitions of the salt crystal were studied by UV-Visible spectrum. The optical transmittance window and lower wavelength cut-off of grown crystal have been identified by UV-Vis-NIR studies. The FT-IR spectrum was recorded to confirm the presence of various functional groups in the grown crystal. 1H and 13C NMR spectrum were recorded to establish the molecular structure of the title crystal. Single crystal X-ray diffraction data indicated that the crystal belongs to monoclinic crystal system with P21/n space group. The thermal stability of the crystal was established by TG/DTA studies. The mechanical properties of the grown crystal were studied by Vickers' microhardness technique. The dielectric studies indicated that the dielectric constant and dielectric loss decrease exponentially with frequency at different temperatures.

The 1.1 Å resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank.

Science.gov (United States)

Keegan, Ronan; Waterman, David G; Hopper, David J; Coates, Leighton; Taylor, Graham; Guo, Jingxu; Coker, Alun R; Erskine, Peter T; Wood, Steve P; Cooper, Jonathan B

2016-08-01

During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement using MOLREP in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate-binding protein from Stenotrophomonas maltophilia (UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of the S. maltophilia protein has been refined to an R factor of 10.15% and an Rfree of 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate

Ripple losses during ICRF heating in Tore Supra

International Nuclear Information System (INIS)

Basiuk, V.; Eriksson, L.-G.; Bergeaud, V.; Chantant, M.; Martin, G.; Nguyen, F.; Reichle, R.; Vallet, J.C.; Delpeche, L.; Surle, F.

2004-01-01

The toroidal field coils in Tore Supra are supra-conducting, and their number is restricted to 18. As a result, the ripple is fairly large, about 7% at the plasma boundary. Tore Supra has consequently been equipped with dedicated ripple loss diagnostics, which has allowed ripple loss studies. This paper reports on the measurements made with these diagnostics and provides an analysis of the experimental results, comparing them with theoretical expectations whenever possible. Furthermore, the main heating source accelerating ions in Tore Supra is ion cyclotron resonance range of frequency (ICRF) heating, and the paper provides new information on the ripple losses of ICRF accelerated ions. (author)

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

Science.gov (United States)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Effects of spin orbital coupling on atomic and electronic structures in Al2Cu and Al2Au crystal and liquid phases via ab initio molecular dynamics simulations

International Nuclear Information System (INIS)

Wang, Y.; Lu, Y.H.; Wang, X.D.; Cao, Q.P.; Zhang, D.X.; Jiang, J.Z.

2014-01-01

Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al 2 Cu and Al 2 Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al 2 Cu and Al 2 Au

Synthesis, crystal growth and characterization of bioactive material: 2- Amino-1H-benzimidazolium pyridine-3-carboxylate single crystal- a proton transfer molecular complex

Science.gov (United States)

Fathima, K. Saiadali; Kavitha, P.; Anitha, K.

2017-09-01

The 1:1 molecular adducts 2- Amino-1H-benzimidazolium pyridine-3-carboxylate (2ABPC) was synthesized and grown as single crystal where 2-aminobenzimidazole (ABI) acts as a donor and nicotinic acid (NA) acts as an acceptor. The presence of proton and carbon were predicted using 1H and 13C NMR spectral analysis. The molecular structure of the crystal was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R = 0.038 for 2469 reflections. The vibrational modes of functional group have been studied using FTIR and Raman spectroscopic analysis. The UV-Vis spectrum exhibited a visible band at 246 nm for 2ABPC due to the nicotinate anion of the molecule. Further, the antimicrobial activity of 2ABPC complex against B. subtilis, klebsiella pneumonia, Pseudomonas eruginos and E. coli pathogens was investigated. Minimum Inhibitory Concentration (MIC) for this crystal was obtained using UV spectrometer against MRSA pathogen. It was found that the benzimidazole with aminogroup at position 2 increases the general antimicrobial activities of 2ABPC crystal.

Crystal and molecular structure of tetrathiocyanato tetrakis (triphenylphosphine oxide)uranium(IV)

Energy Technology Data Exchange (ETDEWEB)

Bombieri, G; De Paoli, G; Forsellini, E [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi; Brown, D

1979-01-01

The crystal structure of the title compound has been determined from three dimensional X-ray diffraction data. The space group and lattice parameters are given. The asymmetric unit comprises two independent U(NCS)/sub 4/(tppo)/sub 4/ molecules in each of which the coordination polyhedron around the uranium atom is close to square antiprismatic.

Production, purification, crystallization and structure determination of H-1 Parvovirus

International Nuclear Information System (INIS)

Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

2012-01-01

The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

Science.gov (United States)

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Long pulse operation on Tore Supra

International Nuclear Information System (INIS)

Monier-Garbet, P.

2004-01-01

This document gathers a series of transparencies dedicated to the long pulse operation on Tore-Supra. The structure of the document is described as follows: the first part is an introduction recalling fusion basis and presenting the different physical and technological phenomenon time scales. The second part is dedicated to the production of long pulses through non-inductive drive and some experimental scenarios illustrate it. The final part is devoted to physics issues like particle retention

Theory of piezoelectricity, electrostriction, and pyroelectricity in molecular crystals.

Science.gov (United States)

Munn, R W

2010-03-14

A microscopic theory is presented for piezoelectricity, electrostriction, and pyroelectricity in molecular crystals. The required coefficients are derived by combining a theoretical treatment of the dependence of molecular dipole moments on molecular displacement and a generalized elastic theory for internal strain.

Edge plasma diagnostics on Tore Supra tokamak

International Nuclear Information System (INIS)

Fujita, Junji

1991-01-01

From 1988 to 1991, the international scientific research 'Diagnosis of peripheral plasma in Tore Supra tokamak' was carried out as a three-year plan receiving the support of the scientific research expense of the Ministry of Education. This is to apply the method of measuring electron density distribution by neutral lithium beam probe spectroscopy to the measurement of the electron density distribution in the peripheral plasma in Tore Supra Tokamak in France. Among many tokamaks in operation doing respective characteristics researches, the Tore Supra generates the toroidal magnetic field by using superconducting coils, and aims at the long time discharge for 30 sec. for the time being, and for 300 sec. in future. In the plasma generators for long time discharge like this, the technology of particle control is a large problem. For this purpose, a divertor was added to the Tore Supra. In order to advance the research on particle control, it is necessary to examine the behavior of plasma in the peripheral part in detail. The measurement of peripheral plasma in tokamaks, beam probe spectroscopy, the Tore Supra tokamak, the progress of the joint research, the problems in the joint research and the perspective of hereafter are reported. (K.I.)

Crystal water as the mol-ecular glue for obtaining different co-crystal ratios: the case of gallic acid tris-caffeine hexa-hydrate.

Science.gov (United States)

Vella-Zarb, L; Baisch, U

2018-04-01

The crystal structure of the hexa-hydrate co-crystal of gallic acid and caffeine, C 7 H 6 O 5 ·3C 8 H 10 N 4 O 2 ·6H 2 O or GAL3CAF·6H 2 O , is a remarkable example of the importance of hydrate water acting as structural glue to facilitate the crystallization of two components of different stoichiometries and thus to compensate an imbalance of hydrogen-bond donors and acceptors. The water mol-ecules provide the additional hydrogen bonds required to form a crystalline solid. Whereas the majority of hydrogen bonds forming the inter-molecular network between gallic acid and caffeine are formed by crystal water, only one direct classical hydrogen bond between two mol-ecules is formed between the carb-oxy-lic oxygen of gallic acid and the carbonyl oxygen of caffeine with d ( D ⋯ A ) = 2.672 (2) Å. All other hydrogen bonds either involve crystal water or utilize protonated carbon atoms as donors.

Cochlear neuropathy and the coding of supra-threshold sound.

Science.gov (United States)

Bharadwaj, Hari M; Verhulst, Sarah; Shaheen, Luke; Liberman, M Charles; Shinn-Cunningham, Barbara G

2014-01-01

Many listeners with hearing thresholds within the clinically normal range nonetheless complain of difficulty hearing in everyday settings and understanding speech in noise. Converging evidence from human and animal studies points to one potential source of such difficulties: differences in the fidelity with which supra-threshold sound is encoded in the early portions of the auditory pathway. Measures of auditory subcortical steady-state responses (SSSRs) in humans and animals support the idea that the temporal precision of the early auditory representation can be poor even when hearing thresholds are normal. In humans with normal hearing thresholds (NHTs), paradigms that require listeners to make use of the detailed spectro-temporal structure of supra-threshold sound, such as selective attention and discrimination of frequency modulation (FM), reveal individual differences that correlate with subcortical temporal coding precision. Animal studies show that noise exposure and aging can cause a loss of a large percentage of auditory nerve fibers (ANFs) without any significant change in measured audiograms. Here, we argue that cochlear neuropathy may reduce encoding precision of supra-threshold sound, and that this manifests both behaviorally and in SSSRs in humans. Furthermore, recent studies suggest that noise-induced neuropathy may be selective for higher-threshold, lower-spontaneous-rate nerve fibers. Based on our hypothesis, we suggest some approaches that may yield particularly sensitive, objective measures of supra-threshold coding deficits that arise due to neuropathy. Finally, we comment on the potential clinical significance of these ideas and identify areas for future investigation.

Cochlear Neuropathy and the Coding of Supra-threshold Sound

Directory of Open Access Journals (Sweden)

Hari M Bharadwaj

2014-02-01

Full Text Available Many listeners with hearing thresholds within the clinically normal range nonetheless complain of difficulty hearing in everyday settings and understanding speech in noise. Converging evidence from human and animal studies points to one potential source of such difficulties: differences in the fidelity with which supra-threshold sound is encoded in the early portions of the auditory pathway. Measures of auditory subcortical steady-state responses in humans and animals support the idea that the temporal precision of the early auditory representation can be poor even when hearing thresholds are normal. In humans with normal hearing thresholds, behavioral ability in paradigms that require listeners to make use of the detailed spectro-temporal structure of supra-threshold sound, such as selective attention and discrimination of frequency modulation, correlate with subcortical temporal coding precision. Animal studies show that noise exposure and aging can cause a loss of a large percentage of auditory nerve fibers without any significant change in measured audiograms. Here, we argue that cochlear neuropathy may reduce encoding precision of supra-threshold sound, and that this manifests both behaviorally and in subcortical steady-state responses in humans. Furthermore, recent studies suggest that noise-induced neuropathy may be selective for higher-threshold, lower-spontaneous-rate nerve fibers. Based on our hypothesis, we suggest some approaches that may yield particularly sensitive, objective measures of supra-threshold coding deficits that arise due to neuropathy. Finally, we comment on the potential clinical significance of these ideas and identify areas for future investigation.

Activation/Inhibition of mast cells by supra-optimal antigen concentrations.

Science.gov (United States)

Huber, Michael

2013-01-22

Mast cells (MCs) are tissue resident cells of hemopoietic origin and are critically involved in allergic diseases. MCs bind IgE by means of their high-affinity receptor for IgE (FcεRI). The FcεRI belongs to a family of multi-chain immune recognition receptors and is activated by cross-linking in response to multivalent antigens (Ags)/allergens. Activation of the FcεRI results in immediate release of preformed granular substances (e.g. histamine, heparin, and proteases), generation of arachidonic acid metabolites, and production of pro-inflammatory cytokines. The FcεRI shows a remarkable, bell-shaped dose-response behavior with weak induction of effector responses at both low and high (so-called supra-optimal) Ag concentrations. This is significantly different from many other receptors, which reach a plateau phase in response to high ligand concentrations. To explain this unusual dose-response behavior of the FcεRI, scientists in the past have drawn parallels to so-called precipitin curves resulting from titration of Ag against a fixed concentration of antibody (Ab) in solution (a.k.a. Heidelberger curves). Thus, for high, supra-optimal Ag concentrations one could assume that every IgE-bound FcεRI formed a monovalent complex with "its own Ag", thus resulting in marginal induction of effector functions due to absence of receptor cross-linking. However, this was never proven to be the case. More recently, careful studies of FcεRI activation and signaling events in MCs in response to supra-optimal Ag concentrations have suggested a molecular explanation for the descending part of this bell-shaped curve. It is obvious now that extensive FcεRI/IgE/Ag clusters are formed and inhibitory molecules and signalosomes are engaged in response to supra-optimal cross-linking (amongst them the Src family kinase Lyn and the inositol-5'-phosphatase SHIP1) and they actively down-regulate MC effector responses. Thus, the analysis of MC signaling triggered by supra

Plasticity induced phase transformation in molecular crystals

OpenAIRE

Koslowski, Marisol

2014-01-01

Solid state amorphization (SSA) can be achieved in crystalline materials including metal alloys, intermetallics, semiconductors, minerals and molecular crystals. Even though the mechanisms may differ in different materials, the crystalline to amorphous transformation occurs when the crystal reaches a metastable state in which its free energy is higher than that of the amorphous phase. SSA is observed in metal alloys because of interdiffusion of the crystalline elements during mechanical milli...

Disruption mitigation on Tore Supra

International Nuclear Information System (INIS)

Martin, G.; Sourd, F.; Saint-Laurent, F.; Bucalossi, J.; Eriksson, L.G.

2004-01-01

During disruptions, the plasma energy is lost on the first wall within 1 ms, forces up to hundred tons are applied to the structures and kA of electrons are accelerated up to 50 MeV (runaway electrons). Already sources of concern in present day tokamaks, extrapolation to ITER shows the necessity of mitigation procedures, to avoid serious damages to in-vessel components. Massive gas injection was proposed, and encouraging tests have been done on Textor and DIII-D. Similar experiments where performed on Tore Supra, with the goal to validate their effect on runaway electrons, observed during the majority of disruptions. 0.1 mole of helium was injected within 5 ms in ohmic plasmas, up to 1.2 MA, either stable, or in a pre-disruptive phase (argon puffing). Beneficial effects where obtained: reduction of the current fall rate and eddy currents, total disappearance of runaway electrons and easy recovery for the next pulse, without noticeable helium pollution of following plasmas. Analysis of the 4 ms period between injection and disruption indicates that to reach these goals, one need to inject enough helium to keep it only partially ionised. It corresponds to 0.1 g for Tore Supra, and extrapolate to hundreds of grams for ITER. (authors)

Disruption mitigation on Tore Supra

International Nuclear Information System (INIS)

Martin, G.; Sourd, F.; Saint-Laurent, F.; Bucalossi, J.; Eriksson, L.G.

2005-01-01

During disruptions, the plasma energy is lost on the first wall within 1 ms, forces up to hundred tons are applied to the structures and kA of electrons are accelerated up to 50 MeV (runaway electrons). Already sources of concern in present day tokamaks, extrapolation to ITER shows the necessity of mitigation procedures, to avoid serious damages to in-vessel components. Massive gas injection was proposed, and encouraging tests have been done on Textor and DIII-D. Similar experiments where performed on Tore Supra, with the goal to validate their effect on runaway electrons, observed during the majority of disruptions. 0.1 mole of helium was injected within 5 ms in ohmic plasmas, up to 1.2 MA, either stable, or in a pre-disruptive phase (argon puffing). Beneficial effects where obtained: reduction of the current fall rate and eddy currents, total disappearance of runaway electrons and easy recovery for the next pulse, without noticeable helium pollution of following plasmas. Analysis of the 4 ms period between injection and disruption indicates that to reach these goals, one need to inject enough helium to keep it only partially ionised. It correspond to 0.1 g for Tore Supra, and extrapolate to hundred's of grams for ITER. (author)

Crystal and electronic structure study of AgAu and AgCu bimetallic alloy thin films by X-ray techniques

Energy Technology Data Exchange (ETDEWEB)

Ozkendir, O. Murat, E-mail: ozkendir@gmail.com [Mersin University, Faculty of Technology, Energy Systems Engineering, Tarsus (Turkey); Mersin University, Institute of Natural Science, Department of Nanotechnology and Advanced Materials, Mersin (Turkey); Cengiz, E. [Karadeniz Technical University, Faculty of Science, Department of Physics, Trabzon (Turkey); Yalaz, E. [Mersin University, Institute of Natural Science, Department of Nanotechnology and Advanced Materials, Mersin (Turkey); Söğüt, Ö.; Ayas, D.H. [Kahramanmaraş Sütçü İmam Üniversitesi, Faculty of Science and Letters, Department of Physics, Kahramanmaraş (Turkey); Thammajak, B. Nirawat [Synchrotron Light Research Institute (Public Organisation), 111 University Avenue, T. Suranaree, A. Muang, Nakhon Ratchasima 30000 (Thailand)

2016-05-15

Highlights: • Crystal and electronic properties of bimetallic AgCu and AgAu alloy thin films were studied. • Both AgCu and AgAu bimetallic samples were determined to have cubic crystal geometry. • Strong influence of Cu and Au atoms on the electronic structure of the Ag atoms were determined. - Abstract: Crystal and electronic structure properties of bimetallic AgAu and AgCu alloy thin films were investigated by X-ray spectroscopic techniques. The aim of this study is to probe the influence of Au or Cu atoms on the electronic behaviors of Ag ions in bimetallic alloy materials that yields different crystal properties. To identify the mechanisms causing crystal phase transitions, study were supported by the collected EXAFS (Extended X-ray Absorption Fine Structure) data. Crystal structures of both Cu and Au doped bimetallic Ag samples were determined mainly in cubic geometry with “Fm3m” space group. Through the Ag–Au and Ag–Cu molecular interactions during bimetallic alloy formations, highly overlapped electronic levels that supports large molecular band formations were observed with different ionization states. Besides, traces of the d–d interactions in Au rich samples were determined as the main interplay in the broad molecular bond formations. The exact atomic locations and types in the samples were determined by EXAFS studies and supported by the performed calculations with FEFF scientific code.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

Energy Technology Data Exchange (ETDEWEB)

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan [Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

DEFF Research Database (Denmark)

van de Streek, Jacco; Neumann, Marcus A

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published...

NMR structure of the protein NP-247299.1: comparison with the crystal structure

International Nuclear Information System (INIS)

Jaudzems, Kristaps; Geralt, Michael; Serrano, Pedro; Mohanty, Biswaranjan; Horst, Reto; Pedrini, Bill; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution. The NMR structure of the protein NP-247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves

Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

Science.gov (United States)

Karthigha, S.; Krishnamoorthi, C.

2018-03-01

An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

Solvent-shared pairs of densely charged ions induce intense but short-range supra-additive slowdown of water rotation.

Science.gov (United States)

Vila Verde, Ana; Santer, Mark; Lipowsky, Reinhard

2016-01-21

The question "Can ions exert supra-additive effects on water dynamics?" has had several opposing answers from both simulation and experiment. We address this ongoing controversy by investigating water reorientation in aqueous solutions of two salts with large (magnesium sulfate) and small (cesium chloride) effects on water dynamics using molecular dynamics simulations and classical, polarizable models. The salt models are reparameterized to reproduce properties of both dilute and concentrated solutions. We demonstrate that water rotation in concentrated MgSO4 solutions is unexpectedly slow, in agreement with experiment, and that the slowdown is supra-additive: the observed slowdown is larger than that predicted by assuming that the resultant of the extra forces induced by the ions on the rotating water molecules tilts the free energy landscape associated with water rotation. Supra-additive slow down is very intense but short-range, and is strongly ion-specific: in contrast to the long-range picture initially proposed based on experiment, we find that intense supra-additivity is limited to water molecules directly bridging two ions in solvent-shared ion pair configuration; in contrast to a non-ion-specific origin to supra-additive effects proposed from simulations, we find that the magnitude of supra-additive slowdown strongly depends on the identity of the cations and anions. Supra-additive slowdown of water dynamics requires long-lived solvent-shared ion pairs; long-lived ion pairs should be typical for salts of multivalent ions. We discuss the origin of the apparent disagreement between the various studies on this topic and show that the short-range cooperative slowdown scenario proposed here resolves the existing controversy.

Studying the Impact of Modified Saccharides on the Molecular Dynamics and Crystallization Tendencies of Model API Nifedipine.

Science.gov (United States)

Kaminska, E; Tarnacka, M; Wlodarczyk, P; Jurkiewicz, K; Kolodziejczyk, K; Dulski, M; Haznar-Garbacz, D; Hawelek, L; Kaminski, K; Wlodarczyk, A; Paluch, M

2015-08-03

Molecular dynamics of pure nifedipine and its solid dispersions with modified carbohydrates as well as the crystallization kinetics of active pharmaceutical ingredient (API) above and below the glass transition temperature were studied in detail by means of broadband dielectric spectroscopy (BDS), differential scanning calorimetry (DSC), and X-ray diffraction method. It was found that the activation barrier of crystallization increases in molecular dispersions composed of acetylated disaccharides, whereas it slightly decreases in those consisting of modified monocarbohydrates for the experiments carried out above the glass transition temperature. As shown by molecular dynamics simulations it can be related to the strength, character, and structure of intermolecular interactions between API and saccharides, which vary dependently on the excipient. Long-term physical stability studies showed that, in solid dispersions consisting of acetylated maltose and acetylated sucrose, the crystallization of nifedipine is dramatically slowed down, although it is still observable for a low concentration of excipients. With increasing content of modified carbohydrates, the crystallization of API becomes completely suppressed. This is most likely due to additional barriers relating to the intermolecular interactions and diffusion of nifedipine that must be overcome to trigger the crystallization process.

Crystal structure of bis-[(phenyl-methanamine-κN)(phthalocyaninato-κ(4) N)zinc] phenyl-methan-amine tris-olvate.

Science.gov (United States)

Shamsudin, Norzianah; Tan, Ai Ling; Wimmer, Franz L; Young, David J; Tiekink, Edward R T

2015-09-01

The asymmetric unit of the title compound, 2[Zn(C32H16N8)(C7H9N)]·3C7H9N, comprises two independent complex mol-ecules and three benzyl-amine solvent mol-ecules. Each complex mol-ecule features a penta-coordinated Zn(2+) ion within a square-pyramidal geometry, whereby the N5 donor set is defined by four atoms of the phthalocyaninate dianion (PC) and an N-bound benzyl-amine mol-ecule; it is the relative orientations of the latter that differentiate between the independent complex mol-ecules. The uncoordinated benzyl-amine mol-ecules display different conformations in the structure, with syn-Car-Car-Cm-N (ar = aromatic, m = methyl-ene) torsion angles spanning the range -28.7 (10) to 35.1 (14)°. In the crystal, N-H⋯N and N-H⋯π inter-actions lead to supra-molecular layers in the ab plane. The layers have a zigzag topology, have the coordinating and non-coordinating benzyl-amine mol-ecules directed to the inside, and present the essentially flat PC resides to the outside. This arrangement enables adjacent layers to associate via π-π inter-actions [inter-centroid distance between pyrrolyl and fused-benzene rings = 3.593 (2) Å] so that a three-dimensional architecture is formed.

Understanding and control of nucleation, growth, habit, dissolution and structure of two- and three-dimensional crystals using 'Tailor-made' auxiliaries

International Nuclear Information System (INIS)

Weissbuch, I.; Popovitz-Biro, R.; Lahav, M.; Leiserowitz, L.

1995-01-01

Tailor-made auxiliaries for the control of nucleation and growth of molecular crystals may be classified into two broad categories: inhibitors and promoters. Tailor-made inhibitors of crystal growth can be used for a variety of purposes, which include morphological engineering and etching, reduction of crystal symmetry, assignment of absolute structure of chiral molecules and polar crystals, elucidation of the effect of solvent on crystal growth, and crystallization of a desired polymorph. As for crystal growth promoters, monolayers of amphiphilic molecules on water have been used to induce the growth of a variety of three-dimensional crystals at the monolayer-solution interface by means of structural match, molecular complementarity or electrostatic interaction. A particular focus is made on the induced nucleation of ice by monolayers of water-insoluble aliphatic alcohols. The two-dimensional crystalline structures of such monolayers have been studied by grazing incidence X-ray diffraction. It has become possible to monitor, by this method, the growth, dissolution and structure of self-aggregated crystalline monolayers, and indeed multilayers, affected by the interaction of solvent molecules in the aqueous subphase with the amphiphilic headgroups, and by the use of tailor-made amphiphilic additives. (orig.)

Supra-National Organisations and Conflict Resolution during the ...

African Journals Online (AJOL)

Supra-National Organisations and Conflict Resolution during the Nigeria Civil War: ... or part of the non-state actors that impinge on the international environment. ... the importance or roles of Supra-national organisations in conflict resolution ...

Crystal structure and magnetic susceptibility of UOSe single crystals

International Nuclear Information System (INIS)

Kaczorowski, D.; Muenster Univ.; Poettgen, R.; Jeitschko, W.; Gajek, Z.; Zygmunt, A.

1993-01-01

The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T N =100±2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author)

Crystal structure and magnetic susceptibility of UOSe single crystals

Energy Technology Data Exchange (ETDEWEB)

Kaczorowski, D. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Poettgen, R.; Jeitschko, W. (Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Gajek, Z.; Zygmunt, A. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research)

1993-01-01

The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T[sub N]=100[+-]2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author).

H-shaped supra-amphiphiles based on a dynamic covalent bond.

Science.gov (United States)

Wang, Guangtong; Wang, Chao; Wang, Zhiqiang; Zhang, Xi

2012-10-16

The imine bond, a kind of dynamic covalent bond, is used to bind two bolaform amphiphiles together with spacers, yielding H-shaped supra-amphiphiles. Micellar aggregates formed by the self-assembly of the H-shaped supra-amphiphiles are observed. When pH is tuned down from basic to slightly acidic, the benzoic imine bond can be hydrolyzed, leading to the dissociation of H-shaped supra-amphiphiles. Moreover, H-shaped supra-amphiphiles have a lower critical micelle concentration than their building blocks, which is very helpful in enhancing the stability of the benzoic imine bond being hydrolyzed by acid. The surface tension isotherms of the H-shaped supra-amphiphiles with different spacers indicate their twisty conformation at a gas-water interface. The study of H-shaped supra-amphiphiles can enrich the family of amphiphiles, and moreover, the pH-responsiveness may make them apply to controlled or targetable drug delivery in a biological environment.

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda).

Science.gov (United States)

Seng, Hoi-Ling; Ong, Han-Kiat Alan; Rahman, Raja Noor Zaliha Raja Abd; Yamin, Bohari M; Tiekink, Edward R T; Tan, Kong Wai; Maah, Mohd Jamil; Caracelli, Ignez; Ng, Chew Hee

2008-11-01

The binding selectivity of the M(phen)(edda) (M=Cu, Co, Ni, Zn; phen=1,10-phenanthroline, edda=ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(II) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N(4)O(2) octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling.

3.2.1. Synthesis, crystal and molecular structure of catena-(bis(µ1-oxalic acid-µ3-hydrogen oxalate-di-aqua-sodium(I.

Directory of Open Access Journals (Sweden)

Olga Kovalchukova*, Sergey Aldoshin, Andrey Utenyshev, Konstantin Bogenko, Valeriy Tkachev

2015-07-01

Full Text Available The crystal and molecular structure of catena-(bis(µ- oxalic acid-µ-hydrogen oxalate-di-aqua-sodium(I was detected by X-Ray analysis. The compound crystallizes in the triclinic space group P-1, with a(Å 6.2378(12; b(Å 7,1115(14; c(Å 10.489(2; α(° 94.65(3; β(° 100.12(3; γ(° 97.78(3. The sodium cation in the title compound is eight coordinated and forms a square antiprism. It is surrounded by two molecules of oxalic acid, one hydrogen oxalate anion and one water molecule. Both oxalic acid and hydrogen oxalate anion act as polydentate bridging ligands. Centrosymmetric sodium cations are bounded by hydrogen oxalate anions through a system of H bonds involving the molecules of oxalic acid. In the lattice, the 3D structure stabilized by H bonds is formed.

Crystal and molecular structure of adduct of 6-benzylaminopurine and 5-sulfosalicylic acid

Energy Technology Data Exchange (ETDEWEB)

Xia Min, E-mail: xiamin@hytc.edu.cn; Ma Kuirong [Huaiyin Normal University, Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, School of Chemistry and Chemical Engineering (China)

2010-12-15

The crystal structure of adduct of 6-benzylaminopurine and 5-sulfosalicylic acid C{sub 19}H{sub 25}N{sub 5}O{sub 10}S 1 is studied using single-crystal diffraction (R = 0.0482 for 2852 reflections with I > 2{sigma}(I)). The asymmetric unit of 1 contains one 6-benzylaminopurine molecule and one 5-sulfosalicylic acid molecule, as well as four lattice water molecules. Hydrogen bonds, formed by 6-benzylaminopurine and 5-sulfosalicylic acid, link the two molecules into one-dimensional chain (omitting four water molecules), further joined to two-dimensional layer network. Short ring-interactions with intra-chain {pi}-{pi} stacking are observed. The data of IR spectroscopy confirm the formation of the two-dimensional supramolecular layer structure. At last, a 3D supramolecular network constructs via hydrogen bonds.

Crystal structure, growth and nonlinear optical studies of isonicotinamide p-nitrophenol: A new organic crystal for optical limiting applications

Science.gov (United States)

Vijayalakshmi, A.; Vidyavathy, B.; Vinitha, G.

2016-08-01

Isonicotinamide p-nitrophenol (ICPNP), a new organic material, was synthesized using methanol solvent. Single crystals of ICPNP were grown using a slow evaporation solution growth technique. Crystal structure of ICPNP is elucidated by single crystal X-ray diffraction analysis. It belongs to monoclinic crystal system with space group of P21/c. It forms two dimensional networks by O-H…O, N-H…O and C-H…O hydrogen bonds. The molecular structure of ICPNP was further confirmed by Fourier transform infrared (FTIR) spectral analysis. The optical transmittance range and the lower cut-off wavelength (421 nm) with the optical band gap (2.90 eV) of the ICPNP crystal were determined by UV-vis-NIR spectral study. Thermal behavior of ICPNP was studied by thermo gravimetric and differential thermal analyses (TG/DTA). The relative dielectric permittivity was calculated for various temperature ranges. Laser damage threshold of ICPNP crystal was found to be 1.9 GW/cm2 using an Nd:YAG laser. A Z-scan technique was employed to measure the nonlinear absorption coefficient, nonlinear refractive index and nonlinear optical susceptibility. Optical limiting behavior of ICPNP was observed at 35 mW input power.

Local structural ordering in surface-confined liquid crystals

Science.gov (United States)

Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

2017-06-01

The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Taylor, R.D.

1989-01-01

The Moessbauer effect in 129 I in conjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPAa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P ∼20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P > 20 GPa, HP2 is the only phase up to P = 34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. 11 refs., 3 figs

High pressure 129I Moessbauer studies of GeI4 molecular crystals

International Nuclear Information System (INIS)

Pasternak, M.P.; Los Alamos National Lab.; Taylor, R.D.

1990-01-01

The Moessbauer effect in 129 I in cunjunction with Diamond-Anvil-Cell high pressure techniques was applied to investigate the high pressure phase(s) of the molecular crystal GeI 4 . The 129 I Quadrupole Interaction was the main probe for characterizing the intermolecular structural transformation with pressure. With increasing pressure, at about 15 GPa, the onset of a partial molecular-association phase (HP1) is first observed. In HP1 two out of the four iodines strongly overlap to form linear chains of GeI 4 . The HP1 phase coexists with the low pressure (LP) molecular phase, but its population increases with increasing pressure. At P≅20 GPa a second high pressure phase (HP2) is identified where all four iodines strongly overlap to form a three dimensional, fully molecular-associated structure. With increasing pressure and at P>20 GPa, HP2 is the only phase up to P=34 GPa, the highest pressure used. A significant hysteresis of the relative abundances with pressure is observed. The isomer shift of the HP2 and HP1 structures is considerably larger than that of the LP one. (orig.)

Pressure-induced organic topological nodal-line semimetal in the three-dimensional molecular crystal Pd (dddt) 2

Science.gov (United States)

Liu, Zhao; Wang, Haidi; Wang, Z. F.; Yang, Jinlong; Liu, Feng

2018-04-01

The nodal-line semimetal represents a class of topological materials characterized with highest band degeneracy. It is usually found in inorganic materials of high crystal symmetry or a minimum symmetry of inversion aided with accidental band degeneracy [Phys. Rev. Lett. 118, 176402 (2017), 10.1103/PhysRevLett.118.176402]. Based on first-principles band structure, Wannier charge center, and topological surface state calculations, here we predict a pressure-induced topological nodal-line semimetal in the absence of spin-orbit coupling (SOC) in the synthesized single-component 3D molecular crystal Pd (dddt) 2 . We show a Γ -centered single nodal line undulating within a narrow energy window across the Fermi level. This intriguing nodal line is generated by pressure-induced accidental band degeneracy, without protection from any crystal symmetry. When SOC is included, the fourfold degenerated nodal line is gapped and Pd (dddt) 2 becomes a strong 3D topological metal with an Z2 index of (1;000). However, the tiny SOC gap makes it still possible to detect the nodal-line properties experimentally. Our findings afford an attractive route for designing and realizing topological states in 3D molecular crystals, as they are weakly bonded through van der Waals forces with a low crystal symmetry so that their electronic structures can be easily tuned by pressure.

Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

Science.gov (United States)

2014-01-01

We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5–22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10–25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function. PMID:24392845

Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

Science.gov (United States)

Ramya, L; Ramakrishnan, Vigneshwar

2016-07-01

Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal and molecular structure of three molybdenum (6) dioxocomplexes with heterocyclic hydrazones

International Nuclear Information System (INIS)

Ilyukhin, A.B.; Sergienko, V.S.

1994-01-01

The X-ray diffraction investigation into three Mo(6) dioxocomplexes with heterocyclic hydrazones has been made. In all compounds the Mo atom has a deformed octahedral coordination by two O atoms of cis-dioxogroups, N atoms (azomethane), N (heterocyclie), O (phenol) of tridentate organic ligand. Sixth position in Mo coordination octahedron is due to O atom of methanol solvated molecule in the 1,3 structures or N atom of γ-picoline molecule in the 2 structure. The packing of structural units in the crystals of the 1-3 compounds is under consideration. 12 refs., 5 figs., 3 tabs

Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

KAUST Repository

Stevens, Loah A.; Goetz, Katelyn P.; Fonari, Alexandr; Shu, Ying; Williamson, Rachel M.; Bredas, Jean-Luc; Coropceanu, Veaceslav P.; Jurchescu, Oana D.; Collis, Gavin E.

2015-01-01

We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

KAUST Repository

Stevens, Loah A.

2015-01-13

We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

Measurements of earplug attenuation under supra-aural and circumaural headphones.

Science.gov (United States)

Tufts, Jennifer B; Palmer, Jillian V; Marshall, Lynne

2012-10-01

Supra-aural audiometric headphones are generally not recommended for use in measuring the attenuation of earplugs, because contact between the headphone and pinna and/or earplug could alter the attenuation obtained, and because of concerns of non-comparability between modes of excitation from supra-aural headphones and the sound-field procedure required by the standardized method. In this study, we compared measurements of earplug attenuation obtained under Telephonics TDH-50P supra-aural headphones with measurements obtained under circumaural headphones designed expressly for such testing. The attenuation of three types of earplugs (foam, premolded quadruple-flange, and custom-molded) was measured in a repeated-measures design. The study sample comprised 42 normal-hearing adults (21 females, 21 males). With the foam earplugs, nearly all of the attenuation measurements under the supra-aural headphones fell within 10 dB of the measurements under the circumaural headphones. With the flange and custom earplugs, approximately 10% of individuals obtained spuriously high attenuation under the supra-aural headphones. We conclude that standard supra-aural audiometric headphones are suitable for measuring the attenuation provided by foam earplugs. However, supra-aural headphones should not be used to measure the attenuation of flange or custom-molded earplugs. The potential exists for substantial over-estimation of attenuation, especially of custom plugs.

Tetra-, Penta- and Hexa-Coordinated Transition Metal Complexes Constructed from Coumarin-Containing N2O2 Ligand

Directory of Open Access Journals (Sweden)

Lei Gao

2018-02-01

Full Text Available Three newly designed complexes, [Cu(L]·CHCl3 (1, [Co(L(MeOH]·CHCl3 (2 and [{Ni(L(MeOH(PhCOO}2Ni] (3 a coumarin-containing Salamo-type chelating ligand (H2L have been synthesized and characterized by elemental analyses, IR and UV-VIS spectra, and X-ray crystallography. Complex 1 includes one Cu(II atom, one completely deprotonated (L2− unit and one crystalling chloroform molecule, the Cu(II atom shows a square-planar geometry. Complex 2 includes one Co(II atom, one completely deprotonated (L2− unit, one coordinated methanol molecule and one crystalling chloroform molecule. The Co(II atom is a distorted trigonal-bipyramidal geometry. While complex 3 includes three Ni(II atoms, two completely deprotonated (L2− units, two benzoates and two coordinated methanol molecules. The complexes 1 and 2 are both possess three-dimensional supra-molecular structures by abundant noncovalent interactions. But, complex 3 formed a two-dimensional supra-molecular structure by intra-molecular hydrogen bonds. In addition, the antimicrobial and fluorescence properties of H2L and its complexes 1, 2 and 3 were also investigated.

Quantum simulation and quantum information processing with molecular dipolar crystals

International Nuclear Information System (INIS)

Ortner, M.

2011-01-01

In this thesis interactions between dipolar crystals and neutral atoms or separated molecules have been investigated. They were motivated to realize new kinds of lattice models in mixtures of atoms and polar molecules where an MDC functions as an underlying periodic lattice structure for the second species. Such models bring out the peculiar features of MDC's, that include a controllable, potentially sub-optical wavelength periodicity and strong particle phonon interactions. Only stable collisional configurations have been investigated, excluding chemical reactions between the substituents, and crystal distortions beyond the scope of perturbation theory. The system was treated in the polaron picture where particles of the second species are dressed by surrounding crystal phonons. To describe the competition between coherent and incoherent dynamics of the polarons, a master equation in the Brownian motion limit was used with phonons treated as a thermal heat bath. It was shown analytically that in a wide range of realistic parameters the corrections to the coherent time evolution are small, and that the dynamics of the dressed particles can be described by an effective extended Hubbard model with controllable system parameters. The last chapter of this thesis contains a proposal for QIP with cold polar molecules that, in contrast to previous works, uses an MDC as a quantum register. It was motivated by the unique features of dipolar molecules and to exploit the peculiar physical conditions in dipolar crystals. In this proposal the molecular dipole moments were tailored by non-local fields to include a small, switchable, state-dependent dipole moment in addition to the large internal state independent moment that stabilizes the crystal. It was shown analytically that a controllable, non-trivial phonon-mediated interaction can be generated that exceeds non-trivial, direct dipole-dipole couplings. The addressability problem due to high crystal densities was overcome by

Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

Energy Technology Data Exchange (ETDEWEB)

Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

1994-12-31

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

International Nuclear Information System (INIS)

Wei Gu; Garcia, A.E.; Schoenborn, B.P.

1994-01-01

Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies

Duration Adaptation Occurs Across the Sub- and Supra-Second Systems.

Science.gov (United States)

Shima, Shuhei; Murai, Yuki; Hashimoto, Yuki; Yotsumoto, Yuko

2016-01-01

After repetitive exposure to a stimulus of relatively short duration, a subsequent stimulus of long duration is perceived as being even longer, and after repetitive exposure to a stimulus of relatively long duration, a subsequent stimulus of short duration is perceived as being even shorter. This phenomenon is called duration adaptation, and has been reported only for sub-second durations. We examined whether duration adaptation also occurs for supra-second durations (Experiment 1) and whether duration adaptation occurs across sub- and supra-second durations (Experiment 2). Duration adaptation occurred not only for sub-second durations, but also for supra-second durations and across sub- and supra-second durations. These results suggest that duration adaptation involves an interval-independent system or two functionally related systems that are associated with both the sub- and supra-second durations.

Molecular rotation-vibration dynamics of low-symmetric hydrate crystal in the terahertz region.

Science.gov (United States)

Fu, Xiaojian; Wu, Hongya; Xi, Xiaoqing; Zhou, Ji

2014-01-16

The rotational and vibrational dynamics of molecules in copper sulfate pentahydrate crystal are investigated with terahertz dielectric spectra. It is shown that the relaxation-like dielectric dispersion in the low frequency region is related to the reorientation of water molecules under the driving of terahertz electric field, whereas the resonant dispersion can be ascribed to lattice vibration. It is also found that, due to the hydrogen-bond effect, the vibrational mode at about 1.83 THz along [-111] direction softens with decreasing temperature, that is, the crystal expands in this direction when cooled. On the contrary, the mode hardens in the direction perpendicular to [-111] during the cooling process. This contributes to the further understanding of the molecular structure and bonding features of hydrate crystals.

Tore Supra. Basic design Tokamak system

International Nuclear Information System (INIS)

Aymar, R.; Bareyt, B.; Bon Mardion, G.

1980-10-01

This document describes the basic design for the main components of the Tokamak system of Tora Supra. As such, it focuses on the engineering problems, and refers to last year report on Tora Supra (EUR-CEA-1021) for objectives and experimental programme of the apparatus on one hand, and for qualifying tests of the main technical solutions on the other hand. Superconducting toroidal field coil system, vacuum vessels and radiation shields, poloidal field system and cryogenic system are described

Fast imaging system on Tore Supra

International Nuclear Information System (INIS)

Geraud, A.; Salasca, S.; Verger, J. M.; Alarcon, T.; Agarici, G.; Bremond, S.; Chenevois, J. P.; Geynet, M.; Migozzi, J. B.; Reux, C.

2009-01-01

A new endoscope aiming at transferring the image of a poloidal section of the Tore Supra plasma to a fast camera able to record frames at a speed up to 4800 frames per second at full resolution, or much faster for a limited number of pixel, has been installed on Tore Supra. First movies showing the light emission associated to fast phenomena such as plasma start up, disruptions or gas and pellet injections have been produced.

Band structure and optical properties of diglycine nitrate crystal

International Nuclear Information System (INIS)

Andriyevsky, Bohdan; Ciepluch-Trojanek, Wioleta; Romanyuk, Mykola; Patryn, Aleksy; Jaskolski, Marcin

2005-01-01

Experimental and theoretical investigations of the electron energy characteristics and optical spectra for diglycine nitrate crystal (DGN) (NH 2 CH 2 COOH) 2 .HNO 3 , in the paraelectric phase (T=295K) are presented. Spectral dispersion of light reflection R(E) have been measured in the range of 3-22eV and the optical functions n(E) and k(E) have been calculated using Kramers-Kronig relations. First principal calculations of the electron energy characteristic and optical spectra of DGN crystal have been performed in the frame of density functional theory using CASTEP code (CAmbridge Serial Total Energy Package). Optical transitions forming the low-energy edge of fundamental absorption are associated with the nitrate groups NO 3 . Peculiarities of the band structure and DOS projected onto glycine and NO 3 groups confirm the molecular character of DGN crystal

Molecular dynamics simulations of liquid crystals at interfaces

International Nuclear Information System (INIS)

Shield, Mark

2002-01-01

Molecular dynamics simulations of an atomistic model of 4-n-octyl-4'-cyanobiphenyl (8CB) were performed for thin films of 8CB on solid substrates (a pseudopotential representation of the molecular topography of the (100) crystal surface of polyethylene (PE), a highly ordered atomistic model of a pseudo-crystalline PE surface and an atomistic model of a partially orientated film of PE), free standing thin films of 8CB and 8CB droplets in a hexagonal pit. The systems showed strong homeotropic anchoring at the free volume interface and planar anchoring at the solid interface whose strength was dependent upon the surface present. The free volume interface also demonstrated weak signs of smectic wetting of the bulk. Simulations of thin free standing films of liquid crystals showed the ordered nature of the liquid crystals at the two free volume interfaces can be adopted by the region of liquid crystal molecules between the homeotropic layer at each interface only if there is a certain number of liquid crystal molecules present. The perpendicular anchoring imposed by the free volume interface and the solid interface for the thin films on the solid substrates resulted in some evidence for the liquid crystal director undergoing a continual rotation at low temperatures and a definite discontinuous change at higher temperatures. The liquid crystal alignment imparted by these substrates was found to depend upon the topography of the surface and not the direction of the polymer chains in the substrate. The liquid crystal was found to order via an epitaxy-like mechanism. The perpendicular anchoring results in a drop in the order - disorder transition temperature for the molecules in the region between the homeotropic layer at the free volume interface and the planar layers at the solid interface. An increase in the size of this region does not alter the transition temperature. The shape of the liquid crystal molecules is dependent upon the degree of order and thus the nematic

Solid-melt interface structure and growth of Cu alloy single crystals

International Nuclear Information System (INIS)

Tomimitsu, Hiroshi; Kamada, Kohji.

1983-01-01

Crystal-melt interface behavior during the growth of Cu-base solid solutions by the Bridgman method is discussed on the basis of experimental evidence obtained by neutron diffraction topography. Advantages of neutron diffraction topography for the characterization of large single crystals, such as dealt with in this paper, are emphasized. Evidence was odserved of extremely regular crystal growth along directions, irrespective of the macroscopic growth direction. This contrasts with the previously believed (110) normal growth which is a conclusion of growth theory based on molecular kinetics at the solid-melt interface. In consequence, we believe that the kinetics at the interface is a minor factor in the meltgrowth of metal single crystals. Revised melt-growth theory should include both the growth and the formation of the regular structure as evidenced by neutron diffraction topography. (author)

Eddy current calculations for the tore supra tokamak

International Nuclear Information System (INIS)

Blum, J.; Dupas, L.; Leloup, C.; Thooris, B.

1983-01-01

This paper deals with the calculation of the eddy currents in the structures of a Tokamak, which can be assimilated to thin conductors, so that the three-dimensional problem can be reduced mathematically to a two-dimensional one, the variables being two orthogonal coordinates of the considered surface. A variational formulation of the problem in terms of the electric vector potential is then given and a finite element method has been used, which enables to treat the complicated geometry of the toroidal field magnet, the mechanical structures and the vacuum vessels of Tore Supra

Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

Science.gov (United States)

Hendriks, Frank C; Schmidt, Joel E; Rombouts, Jeroen A; Lammertsma, Koop; Bruijnincx, Pieter C A; Weckhuysen, Bert M

2017-05-05

A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Supra-auricular versus Sinusectomy Approaches for Preauricular Sinuses.

Science.gov (United States)

El-Anwar, Mohammad Waheed; ElAassar, Ahmed Shaker

2016-10-01

Introduction  Several surgical techniques and modifications have been described to reduce the high recurrence rate after excision of preauricular sinus. Objectives  The aim of this study is to review the literature regarding surgical approaches for preauricular sinus. Data Synthesis  We performed searches in the LILACS, MEDLINE, SciELO, PubMed databases and Cochrane Library in September, 2015, and the key words used in the search were "preauricular sinus," "sinusectomy," "supra-auricular approach," "methylene blue," and/or "recurrence." We revised the results of 17 studies, including 1270 preauricular sinuses that were surgically excised by sinusectomy in 937 ears and by supra-auricular approach in 333 ears. Recurrence with supra-auricular was 4 (1.3%) while sinusectomy was 76 (8.1%) with significant difference ( p  Supra-auricular approach had significantly less recurrence rate than tract sinusectomy approaches. Thus, it could be regularly chosen as the standard procedure for preauricular sinus excision. As such, it would be helpful for surgeons to be familiar with this approach.

Molecular dynamics of liquid crystals

Science.gov (United States)

Sarman, Sten

1997-02-01

We derive Green-Kubo relations for the viscosities of a nematic liquid crystal. The derivation is based on the application of a Gaussian constraint algorithm that makes the director angular velocity of a liquid crystal a constant of motion. Setting this velocity equal to zero means that a director-based coordinate system becomes an inertial frame and that the constraint torques do not do any work on the system. The system consequently remains in equilibrium. However, one generates a different equilibrium ensemble. The great advantage of this ensemble is that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals, whereas they are complicated rational functions in the conventional canonical ensemble. This facilitates the numerical evaluation of the viscosities by molecular dynamics simulations.

A novel option for reducing free light chains in myeloma kidney: supra-hemodiafiltration with endogenous reinfusion (HFR).

Science.gov (United States)

Pasquali, Sonia; Iannuzzella, Francesco; Corradini, Mattia; Mattei, Silvia; Bovino, Achiropita; Stefani, Alfredo; Palladino, Giuseppe; Caiazzo, Marialuisa

2015-04-01

In myeloma cast nephropathy, fast reduction of serum free light chain (FLC) levels correlates with renal recovery. Recently, extracorporeal treatments using filters with a high-molecular weight cut-off have been successfully used for FLC removal. However, using these new filters, high cost and elevated albumin leakage are common drawbacks. We studied a new and cheaper therapeutic approach with adsorbent resins to evaluate its efficacy. We treated four patients, affected by dialysis-dependent acute kidney injury (AKI) due to biopsy proven de novo FLC myeloma cast nephropathy. Each patient underwent bortezomib chemotherapy and extracorporeal treatment with the supra-hemodiafiltration with endogenous reinfusion (HFR) technique (Supra-HFR, Bellco Mirandola, Modena, Italy). Supra-HFR is a kind of hemodiafiltration that utilizes separated convection, diffusion and adsorption. The sorbent cartridge has a high affinity for FLC (both κ and λ) but is able to re-infuse albumin, avoiding the need for albumin perfusions. Supra HFR treatments (4 h each) were carried out for eight consecutive days and then every other day. All patients showed a significant reduction of serum FLC, whereas serum albumin concentration remained unchanged. Renal function recovered in three out of four patients. FLC removal with adsorbent resins represents an effective therapeutic strategy that does not require replacement with albumin .

Snake studies on Tore Supra

International Nuclear Information System (INIS)

Cristofani, P.; Desgranges, C.; Garbet, X.; Geraud, A.; Gil, C.; Hoang, G.T.; Joffrin, E.; Pecquet, A.L.

1995-01-01

Snakes have been achieved after pellet injection in Tore Supra during ohmic as well as ICRH discharges as it has already been observed in other machines. On Tore Supra, high speed H 2 pellets were injected into D 2 plasmas under the specified experimental conditions, the matter is deposited in the centre and snakes are produced in 50% of the cases, but they are created on a second much more internal q=1 surface leading probably to a non monotonic current profile. The properties of the snake, induced current modification and the important role of the bootstrap current in the snake formation are described. (K.A.) 5 refs.; 7 figs

Crystal structure of bile salt hydrolase from Lactobacillus salivarius.

Science.gov (United States)

Xu, Fuzhou; Guo, Fangfang; Hu, Xiao Jian; Lin, Jun

2016-05-01

Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of BSH function, which has hampered the development of BSH-based strategies for improving human and animal health. As an initial step towards the structure-function analysis of BSH, C-terminally His-tagged BSH from Lactobacillus salivarius NRRL B-30514 was crystallized in this study. The 1.90 Å resolution crystal structure of L. salivarius BSH was determined by molecular replacement using the structure of Clostridium perfringens BSH as a starting model. It revealed this BSH to be a member of the N-terminal nucleophile hydrolase superfamily. Crystals of apo BSH belonged to space group P21212, with unit-cell parameters a = 90.79, b = 87.35, c = 86.76 Å (PDB entry 5hke). Two BSH molecules packed perfectly as a dimer in one asymmetric unit. Comparative structural analysis of L. salivarius BSH also identified potential residues that contribute to catalysis and substrate specificity.

Effects of spin orbital coupling on atomic and electronic structures in Al{sub 2}Cu and Al{sub 2}Au crystal and liquid phases via ab initio molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Wang, Y. [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Lu, Y.H., E-mail: luyh@zju.edu.cn [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Wang, X.D.; Cao, Q.P. [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Zhang, D.X. [State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310027 (China); Jiang, J.Z., E-mail: jiangjz@zju.edu.cn [International Center for New-Structured Materials (ICNSM), Laboratory of New-Structured Materials, State Key Laboratory of Silicon Materials, and Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China)

2014-11-15

Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al{sub 2}Cu and Al{sub 2}Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al{sub 2}Cu and Al{sub 2}Au.

Runaway electrons dynamics and confinement in Tore-Supra

International Nuclear Information System (INIS)

Chatelier, M.; Geraud, A.; Joyer, P.; Martin, G.; Rax, J.M.

1989-01-01

The lack of energy of runaway electrons, confined in Tore Supra tokamak, is studied. Ohmic discharges, obtained with helium gas, exhibit a small amount of runaway electrons on both hard X-ray monitors and neutron sensors. The observations show an important lack of energy for runaway electrons confined in Tore Supra. It is assumed to be dued to a small pitch-angle scattering (a few degrees), and many candidates for this are compared: the strongest known one collisions seems not to be enough by an order of magnitude. Density and magnetic scans on Tore Supra are needed to discriminate between enhanced collisional scattering processes and purely magnetic phenomena

Crystal and molecular structure of dysprosium (3) n-aminobenzoate

International Nuclear Information System (INIS)

Khiyalov, M.S.; Amiraslanov, I.R.; Mamedov, Kh.S.; Movsumov, Eh.M.

1981-01-01

The X ray diffraction investigation of the Dy(NH 2 C 6 H 4 COO) 3 x3H 2 O complex is carried out. Triclinic crystals have lattice parameters α=11.095(15), b=9.099(17), c=12.780 (15)A, α=108.051(12), β=89.072(10); γ=104.954(12) 0 , space group P anti 1, Z=2. The structure consists of dimer molecules. The third water molecule in the formula is an outer spherical one. The average lengths of Dy-O and Dy-OH 2 are 2.39 and 2.40 A respectively, the average value of Dy-O in bridge carboxylates (2.26A) is remarkably shorter. Hydrogen bonds between amine ligand ends, carboxylic groups oxygen and water molecules bind complex molecules into the three-dimensional frame [ru

Direct Photolithography on Molecular Crystals for High Performance Organic Optoelectronic Devices.

Science.gov (United States)

Yao, Yifan; Zhang, Lei; Leydecker, Tim; Samorì, Paolo

2018-05-23

Organic crystals are generated via the bottom-up self-assembly of molecular building blocks which are held together through weak noncovalent interactions. Although they revealed extraordinary charge transport characteristics, their labile nature represents a major drawback toward their integration in optoelectronic devices when the use of sophisticated patterning techniques is required. Here we have devised a radically new method to enable the use of photolithography directly on molecular crystals, with a spatial resolution below 300 nm, thereby allowing the precise wiring up of multiple crystals on demand. Two archetypal organic crystals, i.e., p-type 2,7-diphenyl[1]benzothieno[3,2- b][1]benzothiophene (Dph-BTBT) nanoflakes and n-type N, N'-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) nanowires, have been exploited as active materials to realize high-performance top-contact organic field-effect transistors (OFETs), inverter and p-n heterojunction photovoltaic devices supported on plastic substrate. The compatibility of our direct photolithography technique with organic molecular crystals is key for exploiting the full potential of organic electronics for sophisticated large-area devices and logic circuitries, thus paving the way toward novel applications in plastic (opto)electronics.

Two Organic Cation Salts Containing Tetra(isothiocyanatecobaltate(II: Synthesis, Crystal Structures, Spectroscopic, Optical and Magnetic Properties

Directory of Open Access Journals (Sweden)

Zheng Zhang

2017-03-01

Full Text Available Single crystals of two hybrid organic-inorganic molecular solids, benzyl pyridinium tetra(isothiocyanatecobalt ([BzPy]2[Co(NCS4] (1 and benzyl quinolinium tetra(isothiocyanatecobalt ([BzQl]2[Co(NCS4] (2, were grown using a slow evaporation growth technique at room temperature and their IR, UV-Vis, X-ray crystal structures, luminescence, and magnetism were reported. The crystal structural analysis revealed that two molecular solids crystallize in the monoclinic space group P21/c of 1 and P21/n of 2. The cations form a dimer through weak C–H···π/π···π interactions in 1 and 2, and the adjacent cation (containing N(6 atom in 2 forms a columnar structure through π···π weak interactions between the quinoline and benzene rings, while the anions in 1 form a layer structure via short S···Co interactions. The anions (A and cations (C are arranged alternatively into a column in the sequence of ···A–CC–A–CC–A··· for 1, while the two anions and cationic dimer in 2 form an alliance by the C–H···π, C–H···S and C–H···N hydrogen bonds. A weak S···π interaction was found in 1 and 2. The two molecular solids show a broad fluorescence emission around 400 nm in the solid state at room temperature, and weak antiferromagnetic coupling behavior when the temperature is lowered.

Amine free crystal structure: The crystal structure of d(CGCGCG)2 and methylamine complex crystal

International Nuclear Information System (INIS)

Ohishi, Hirofumi; Tsukamoto, Koji; Hiyama, Yoichi; Maezaki, Naoyoshi; Tanaka, Tetsuaki; Ishida, Toshimasa

2006-01-01

We succeeded in the crystallization of d(CGCGCG) 2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2F o - F c map was much clear and easily traced. It is First time monoamine co-crystallizes with d(CGCGCG) 2 . However, methylamine was not found from the complex crystal of d(CGCGCG) 2 and methylamine. Five Mg ions were found around d(CGCGCG) 2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg 2+ . DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG) 2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this

Topological Characterization of Carbon Graphite and Crystal Cubic Carbon Structures.

Science.gov (United States)

Siddiqui, Wei Gao Muhammad Kamran; Naeem, Muhammad; Rehman, Najma Abdul

2017-09-07

Graph theory is used for modeling, designing, analysis and understanding chemical structures or chemical networks and their properties. The molecular graph is a graph consisting of atoms called vertices and the chemical bond between atoms called edges. In this article, we study the chemical graphs of carbon graphite and crystal structure of cubic carbon. Moreover, we compute and give closed formulas of degree based additive topological indices, namely hyper-Zagreb index, first multiple and second multiple Zagreb indices, and first and second Zagreb polynomials.

Microscopic Rate Constants of Crystal Growth from Molecular Dynamic Simulations Combined with Metadynamics

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Dániel Kozma

2012-01-01

Full Text Available Atomistic simulation of crystal growth can be decomposed into two steps: the determination of the microscopic rate constants and a mesoscopic kinetic Monte Carlo simulation. We proposed a method to determine kinetic rate constants of crystal growth. We performed classical molecular dynamics on the equilibrium liquid/crystal interface of argon. Metadynamics was used to explore the free energy surface of crystal growth. A crystalline atom was selected at the interface, and it was displaced to the liquid phase by adding repulsive Gaussian potentials. The activation free energy of this process was calculated as the maximal potential energy density of the Gaussian potentials. We calculated the rate constants at different interfacial structures using the transition state theory. In order to mimic real crystallization, we applied a temperature difference in the calculations of the two opposite rate constants, and they were applied in kinetic Monte Carlo simulation. The novelty of our technique is that it can be used for slow crystallization processes, while the simple following of trajectories can be applied only for fast reactions. Our method is a possibility for determination of elementary rate constants of crystal growth that seems to be necessary for the long-time goal of computer-aided crystal design.

Crystallization and preliminary characterization of three different crystal forms of human saposin C heterologously expressed in Pichia pastoris

International Nuclear Information System (INIS)

Schultz-Heienbrok, Robert; Remmel, Natascha; Klingenstein, R.; Rossocha, Maksim; Sandhoff, Konrad; Saenger, Wolfram; Maier, Timm

2006-01-01

Three different crystal forms were obtained of human saposin C. The structures could not be determined by molecular replacement using known solution structures of the protein as search models, supporting the notion of a highly flexible protein. The amphiphilic saposin proteins (A, B, C and D) act at the lipid–water interface in lysosomes, mediating the hydrolysis of membrane building blocks by water-soluble exohydrolases. Human saposin C activates glucocerebrosidase and β-galactosylceramidase. The protein has been expressed in Pichia pastoris, purified and crystallized in three different crystal forms, diffracting to a maximum resolution of 2.5 Å. Hexagonal crystals grew from 2-propanol-containing solution and contain a single molecule in the asymmetric unit according to the Matthews coefficient. Orthorhombic and tetragonal crystals were both obtained with pentaerythritol ethoxylate and are predicted to contain two molecules in the asymmetric unit. Attempts to determine the respective crystal structures by molecular replacement using either the known NMR structure of human saposin C or a related crystal structure as search models have so far failed. The failure of the molecular-replacement method is attributed to conformational changes of the protein, which are known to be required for its biological activity. Crystal structures of human saposin C therefore might be the key to mapping out the conformational trajectory of saposin-like proteins

Photonic Crystal Laser-Driven Accelerator Structures

International Nuclear Information System (INIS)

Cowan, B

2004-01-01

The authors discuss simulated photonic crystal structure designs for laser-driven particle acceleration. They focus on three-dimensional planar structures based on the so-called ''woodpile'' lattice, demonstrating guiding of a speed-of-light accelerating mode by a defect in the photonic crystal lattice. They introduce a candidate geometry and discuss the properties of the accelerating mode. They also discuss the linear beam dynamics in the structure present a novelmethod for focusing the beam. In addition they describe ongoing investigations of photonic crystal fiber-based structures

Crystal structure of hemoglobin from the maned wolf (Chrysocyon brachyurus) using synchrotron radiation.

Science.gov (United States)

Fadel, Valmir; Canduri, Fernanda; Olivieri, Johnny R; Smarra, André L S; Colombo, Marcio F; Bonilla-Rodriguez, Gustavo O; de Azevedo, Walter F

2003-12-01

Crystal structure of hemoglobin isolated from the Brazilian maned wolf (Chrysocyon brachyurus) was determined using standard molecular replacement technique and refined using maximum-likelihood and simulated annealing protocols to 1.87A resolution. Structural and functional comparisons between hemoglobins from the Chrysocyon brachyurus and Homo sapiens are discussed, in order to provide further insights in the comparative biochemistry of vertebrate hemoglobins.

Regio-Regular Oligo and Poly(3-hexyl thiophene): Precise Structural Markers from the Vibrational Spectra of Oligomer Single Crystals.

KAUST Repository

Brambilla, Luigi

2014-10-14

© 2014 American Chemical Society. In this work, we report a comparative analysis of the infrared and Raman spectra of octa(3-hexylthiophene) (3HT)8, trideca(3-hexylthiophene) (3HT)13, and poly(3-hexylthiophene) P3HT recorded in various phases, namely, amorphous, semicrystalline, polycrystalline and single crystal. We have based our analysis on the spectra of the (3HT)8 single crystal (whose structure has been determined by selected area electron diffraction) taken as reference and on the results of DFT calculations and molecular vibrational dynamics. New and precise spectroscopic markers of the molecular structures show the existence of three phases, namely: hairy (phase 1), ordered (phase 2), and disordered/amorphous (phase 3). Conceptually, the identified markers can be used for the molecular structure analysis of other similar systems.

Crystal structure determination of Efavirenz

International Nuclear Information System (INIS)

Popeneciu, Horea; Dumitru, Ristoiu; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria

2015-01-01

Needle-shaped single crystals of the title compound, C 14 H 9 ClF 3 NO 2 , were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring

Refikite from Krásno, Czech Republic: a crystal- and molecular-structure study

Czech Academy of Sciences Publication Activity Database

Pažout, R.; Sejkora, J.; Maixner, J.; Dušek, Michal; Tvrdý, J.

2015-01-01

Roč. 79, č. 1 (2015), s. 59-70 ISSN 0026-461X Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : refikite * crystal structure * infrared spectroscopy * Raman spectroscopy * NMR * high-resolution mass spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.212, year: 2015

Growth, structure, Hirshfeld surface and spectroscopic properties of 2-amino-4-hydroxy-6-methylpyrimidinium-2,3-pyrazinedicorboxylate single crystal

Science.gov (United States)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Rodrigues, Vítor Hugo Nunes; Ahmad, Shabbir

2018-03-01

The present work is focused on the crystal structure, vibrational spectroscopy and DFT calculations of hydrogen bonded 2,3-pyrazinedicorboxylic acid and 2-amino-4-hydroxy-6-methylpyrimidine (PDCA-.AHMP+) crystal. The crystal structure has been determined using single crystal X-ray diffraction analysis which shows that the crystal belongs to monoclinic space group P21/n. The PDCA-.AHMP+ crystal has been characterized by FTIR, FT-Raman and FT-NMR spectroscopic techniques. The FTIR and FT-Raman spectra of the complex have unique spectroscopic feature as compared with those of the starting material to confirm salt formation. The theoretical vibrational studies have been performed to understand the modes of the vibrations of asymmetric unit of the complex by DFT methods. Hirschfeld surface and 2D fingerprint plots analyses were carried out to investigate the intermolecular interactions and its contribution in the building of PDCA-.AHMP+ crystal. The experimental and simulated 13C and 1H NMR studies have assisted in structural analysis of PDCA-.AHMP+ crystal. The electronic spectroscopic properties of the complex were explored by the experimental as well as theoretical electronic spectra simulated using TD-DFT/IEF-PCM method at B3LYP/6-311++G (d,p) level of theory. In addition, frontier molecular orbitals, molecular electrostatic potential map (MEP) and nonlinear optical (NLO) properties using DFT method have been also presented.

Crystal structure of Cryptosporidium parvum pyruvate kinase.

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William J Cook

Full Text Available Pyruvate kinase plays a critical role in cellular metabolism of glucose by serving as a major regulator of glycolysis. This tetrameric enzyme is allosterically regulated by different effector molecules, mainly phosphosugars. In response to binding of effector molecules and substrates, significant structural changes have been identified in various pyruvate kinase structures. Pyruvate kinase of Cryptosporidium parvum is exceptional among known enzymes of protozoan origin in that it exhibits no allosteric property in the presence of commonly known effector molecules. The crystal structure of pyruvate kinase from C. parvum has been solved by molecular replacement techniques and refined to 2.5 Å resolution. In the active site a glycerol molecule is located near the γ-phosphate site of ATP, and the protein structure displays a partially closed active site. However, unlike other structures where the active site is closed, the α6' helix in C. parvum pyruvate kinase unwinds and assumes an extended conformation. In the crystal structure a sulfate ion is found at a site that is occupied by a phosphate of the effector molecule in many pyruvate kinase structures. A new feature of the C. parvum pyruvate kinase structure is the presence of a disulfide bond cross-linking the two monomers in the asymmetric unit. The disulfide bond is formed between cysteine residue 26 in the short N-helix of one monomer with cysteine residue 312 in a long helix (residues 303-320 of the second monomer at the interface of these monomers. Both cysteine residues are unique to C. parvum, and the disulfide bond remained intact in a reduced environment. However, the significance of this bond, if any, remains unknown at this time.

Molecular Dynamics Study on Nucleation Behavior and Lamellar Mergence of Polyethylene Globule Crystallization

Science.gov (United States)

Yang, Xiaozhen; Wang, Simiao

2012-02-01

The site order parameter (SOP) has been adopted to analyze various order structure formation and distribution during the crystallization of a multi-chain polyethylene globule simulated by molecular dynamics. We found that the nucleation relies on crystallinity fluctuation with increase of amplitude, and the baby nucleus in the fluctuation suddenly appears with different shape and increasing size. In the growth stage, a number of lamellar mergence was observed and their selective behaviors were suggested to be related to the orientation difference between the merging lamellae. We obtained that SOP distribution of all atoms in the system during crystallization appears with two peaks: one for the amorphous phase and the other for the crystalline phase. Mesomorphic structures with medium orders locate between the two peaks as an order promotion pathway. Obtained data show that the medium order structure fluctuates at the growth front and does not always be available; the medium order structure existing at the front is not always good for developing. It is possibly caused by chain entanglement.

Measurements of scrape-off layer ion-to-electron temperature ratio in Tore Supra ohmic plasmas

Czech Academy of Sciences Publication Activity Database

Kočan, M.; Gunn, J. P.; Pascal, J.-Y.; Bonhomme, G.; Devynck, P.; Ďuran, Ivan; Gauthier, E.; Ghendrih, P.; Marandet, Y.; Pegourie, B.; Vallet, J.-C.

390-391, - (2009), s. 1074-1077 ISSN 0022-3115. [International Conference on Plasma-Surface Interactions in Controlled Fusion Devices/18th./. Toledo, 26.05.2008-30.05. 2008] Institutional research plan: CEZ:AV0Z20430508 Keywords : Ion temperature * Electron temperature * Edge plasma * Tore Supra Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.933, year: 2009

Overexpression, purification, crystallization and preliminary structural studies of p-coumaric acid decarboxylase from Lactobacillus plantarum

International Nuclear Information System (INIS)

Rodríguez, Héctor; Rivas, Blanca de las; Muñoz, Rosario; Mancheño, José M.

2007-01-01

The enzyme p-coumaric acid decarboxylase (PDC) from L. plantarum has been recombinantly expressed, purified and crystallized. The structure has been solved at 2.04 Å resolution by the molecular-replacement method. The substrate-inducible p-coumaric acid decarboxylase (PDC) from Lactobacillus plantarum has been overexpressed in Escherichia coli, purified and confirmed to possess decarboxylase activity. The recombinant His 6 -tagged enzyme was crystallized using the hanging-drop vapour-diffusion method from a solution containing 20%(w/v) PEG 4000, 12%(w/v) 2-propanol, 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.0 with 0.1 M barium chloride as an additive. Diffraction data were collected in-house to 2.04 Å resolution. Crystals belonged to the tetragonal space group P4 3 , with unit-cell parameters a = b = 43.15, c = 231.86 Å. The estimated Matthews coefficient was 2.36 Å 3 Da −1 , corresponding to 48% solvent content, which is consistent with the presence of two protein molecules in the asymmetric unit. The structure of PDC has been determined by the molecular-replacement method. Currently, the structure of PDC complexed with substrate analogues is in progress, with the aim of elucidating the structural basis of the catalytic mechanism

Overexpression, purification, crystallization and preliminary structural studies of p-coumaric acid decarboxylase from Lactobacillus plantarum

Energy Technology Data Exchange (ETDEWEB)

Rodríguez, Héctor; Rivas, Blanca de las; Muñoz, Rosario [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Mancheño, José M., E-mail: xjosemi@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain)

2007-04-01

The enzyme p-coumaric acid decarboxylase (PDC) from L. plantarum has been recombinantly expressed, purified and crystallized. The structure has been solved at 2.04 Å resolution by the molecular-replacement method. The substrate-inducible p-coumaric acid decarboxylase (PDC) from Lactobacillus plantarum has been overexpressed in Escherichia coli, purified and confirmed to possess decarboxylase activity. The recombinant His{sub 6}-tagged enzyme was crystallized using the hanging-drop vapour-diffusion method from a solution containing 20%(w/v) PEG 4000, 12%(w/v) 2-propanol, 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.0 with 0.1 M barium chloride as an additive. Diffraction data were collected in-house to 2.04 Å resolution. Crystals belonged to the tetragonal space group P4{sub 3}, with unit-cell parameters a = b = 43.15, c = 231.86 Å. The estimated Matthews coefficient was 2.36 Å{sup 3} Da{sup −1}, corresponding to 48% solvent content, which is consistent with the presence of two protein molecules in the asymmetric unit. The structure of PDC has been determined by the molecular-replacement method. Currently, the structure of PDC complexed with substrate analogues is in progress, with the aim of elucidating the structural basis of the catalytic mechanism.

Ciel, a new breath for Tore Supra

International Nuclear Information System (INIS)

Garin, P.

1998-01-01

In view of preparing next generation of tokamaks, a new goal has been given to Tore Supra, initially designed for 30 second operation. In order to fulfill this target, with the ultimate aim of injecting in the plasma 25 MW for 1000 s shots: all existing components (including the 6 ergodic divertor modules) present inside the inner vessel of Tore Supra will be removed by the end of 1999, they will be replaced in 2000 by a set of up to date technology components, designed to withstand an overall power of 25 MW for shots up to 1000 s constituting the so-called 'CIEL' project (French acronym for 'Composants Internes Et Limiteur'). It is planned to stop present Tore Supra's operation in autumn 1999, and start again with CIEL environment at the end of 2000. Full capacity (pumping and cooling) will be available in 2002. (author)

Remote experiment participation on Tore-Supra

International Nuclear Information System (INIS)

Theis, J.-M.; Larsen, J.-M.

2004-01-01

The DRFC has traditionally had a very large external collaboration involvement. In particular, 15% of the DRFC work is directed towards the JET programme. As a consequence substantial telecommunications facilities have been installed [F.E.D. 60/3 (2002) 449; F.E.D. 60/3 (2002) 459]. A specific station for remote communication has been set up in the Tore-Supra control room, closely coupled to a collaborating team at INRS Que., Canada. This paper describes our pilot experience with the Canadian participation, which gives details of the communication and data sharing tools used to fully work on Tore-Supra

X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

Energy Technology Data Exchange (ETDEWEB)

Yennawar, Hemant [Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802 (United States); Møller, Magda [Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); University of Copenhagen, DK-2100 Copenhagen (Denmark); Gillilan, Richard [Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); Yennawar, Neela, E-mail: nhy1@psu.edu [Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802 (United States)

2011-05-01

The X-ray crystal structure and a small-angle X-ray scattering solution structure of sheep liver sorbitol dehydrogenase have been determined. The details of the interactions that enable the tetramer scaffold to be the functional biological unit have been analyzed. The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.

Anisotropic frictional heating and defect generation in cyclotrimethylene-trinitramine molecular crystals

Science.gov (United States)

Rajak, Pankaj; Mishra, Ankit; Sheng, Chunyang; Tiwari, Subodh; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2018-05-01

Anisotropic frictional response and corresponding heating in cyclotrimethylene-trinitramine molecular crystals are studied using molecular dynamics simulations. The nature of damage and temperature rise due to frictional forces is monitored along different sliding directions on the primary slip plane, (010), and on non-slip planes, (100) and (001). Correlations between the friction coefficient, deformation, and frictional heating are established. We find that the friction coefficients on slip planes are smaller than those on non-slip planes. In response to sliding on a slip plane, the crystal deforms easily via dislocation generation and shows less heating. On non-slip planes, due to the inability of the crystal to deform via dislocation generation, a large damage zone is formed just below the contact area, accompanied by the change in the molecular ring conformation from chair to boat/half-boat. This in turn leads to a large temperature rise below the contact area.

Supra-amphiphiles: a new bridge between colloidal science and supramolecular chemistry.

Science.gov (United States)

Kang, Yuetong; Liu, Kai; Zhang, Xi

2014-06-03

In addition to conventional amphiphiles, an emerging research area is supra-amphiphiles, which are constructed on the basis of noncovalent interactions and dynamic covalent bonds. In this feature article, we have provided a general introduction to the concept, design principles, and topologies of supra-amphiphiles, starting from some rationally tailored building blocks. In addition, we highlight some progress in the functional assembly of supra-amphiphiles, such as responsive nanoscale carriers, antibacterial and antitumor agents, fluorescent-based chemical sensors, and enzyme mimics. The supra-amphiphile is a new bridge between colloidal science and supramolecular chemistry, and it is a field where we can make full use of our imaginative power.

Atypical initial presentation of Takayasu arteritis as isolated supra-valvular aortic stenosis.

Science.gov (United States)

Kim, Do Yeon; Kim, Hwan Wook

2016-01-19

Among the vascular involvements of Takayasu arteritis, a supra-valvular aortic stenosis has been reported very rarely. We report a case of surgically corrected, supra-valvular aortic stenosis caused by Takayasu arteritis. A 32-year-old female was diagnosed with supra-valvular aortic stenosis by transthoracic echocardiography for the evaluation of cardiac murmur with constitutional symptoms. Under the impression of non-familial sporadic type of supra-valvular aortic stenosis, surgical correction was performed. However, after 1 year from the operation, we could know the cause of her disease through the findings of computed tomographic aortography that Takayasu arteritis was suspected. Takayasu arteritis should be considered in adult female patients presenting supra-valvular aortic stenosis with constitutional symptoms, even if no typical features of vascular involvement.

Runaway electrons dynamics and confinement in TORE-SUPRA

International Nuclear Information System (INIS)

Chatelier, M.; Geraud, A.; Joyer, P.; Martin, G.; Rax, J.M.

1989-01-01

Ohmic discharges in TORE-SUPRA are sufficiently long (∼ 6 s) for runaway electrons (R.E.) to reach a steady energy state: their energy limit is determined by the balance between parallel electric field acceleration (20 MeV/V.s in TORE-SUPRA) and radiation losses due to the curvature of the trajectories. When R.E. energy is supposed to be only parallel, this provides estimate of order of 70 MeV (value usually called 'synchrotron limit') reached in less than 2 seconds. Experimental observations on TORE-SUPRA of photoneutron emission together with residual induced radioactivity in the first wall components tend to prove that the actual value is much lower than 70 MeV (i.e. 15-35 MeV). Earlier observations in ORMAK, PLT and TFR already showed R.E. energy a slightly less than expected from standard loop voltage acceleration calculations. Explanations given for this lack of energy (as skin-effect lowering the electric field during the ramp-up phase or balance between continuous creation and losses) seems not to hold on TORE-SUPRA and therefore another mechanism must be considered to explain the R.E. energy limitation. 4 refs., 2 figs

Crystal structure, Hirshfeld analysis and molecular docking with the vascular endothelial growth factor receptor-2 of (3Z-5-fluoro-3-(hydroxyiminoindolin-2-one

Directory of Open Access Journals (Sweden)

Bianca Barreto Martins

2017-07-01

Full Text Available The reaction between 5-fluoroisatin and hydroxylamine hydrochloride in acidic ethanol yields the title compound, C8H5FN2O2, whose molecular structure matches the asymmetric unit and is nearly planar with an r.m.s. deviation for the mean plane through all non-H atoms of 0.0363 Å. In the crystal, the molecules are linked by N—H...N, N—H...O and O—H...O hydrogen-bonding interactions into a two-dimensional network along the (100 plane, forming rings with R22(8 and R12(5 graph-set motifs. The crystal packing also features weak π–π interactions along the [100] direction [centroid-to-centroid distance 3.9860 (5 Å]. Additionally, the Hirshfeld surface analysis indicates that the major contributions for the crystal structure are the O...H (28.50% and H...F (16.40% interactions. An in silico evaluation of the title compound with the vascular endothelial growth factor receptor-2 (VEGFR-2 was carried out. The title compound and the selected biological target VEGFR-2 show the N—H...O(GLU94, (CYS96N—H...O(isatine and (PHE95N—H...O(isatine intermolecular interactions, which suggests a solid theoretical structure–activity relationship.

Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) ₂ extend the repertoire of crystal structures of Z-DNA

Energy Technology Data Exchange (ETDEWEB)

Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

2017-10-30

DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG)₂duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP2₁lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

Effect of polar surfaces on organic molecular crystals

Science.gov (United States)

Sharia, Onise; Tsyshevskiy, Roman; Kuklja, Maija; University of Maryland College Park Team

Polar oxide materials reveal intriguing opportunities in the field of electronics, superconductivity and nanotechnology. While behavior of polar surfaces has been widely studied on oxide materials and oxide-oxide interfaces, manifestations and properties of polar surfaces in molecular crystals are still poorly understood. Here we discover that the polar catastrophe phenomenon, known on oxides, also takes place in molecular materials as illustrated with an example of cyclotetramethylene tetranitramine (HMX) crystals. We show that the surface charge separation is a feasible compensation mechanism to counterbalance the macroscopic dipole moment and remove the electrostatic instability. We discuss the role of surface charge on degradation of polar surfaces, electrical conductivity, optical band-gap closure and surface metallization. Research is supported by the US ONR (Grants N00014-16-1-2069 and N00014-16-1-2346) and NSF. We used NERSC, XSEDE and MARCC computational resources.

Introduction to crystal growth and characterization

CERN Document Server

Benz, Klaus-Werner

2014-01-01

This new textbook provides for the first time a comprehensive treatment of the basics of contemporary crystallography and crystal growth in a single volume. The reader will be familiarized with the concepts for the description of morphological and structural symmetry of crystals. The architecture of crystal structures of selected inorganic and molecular crystals is illustrated. The main crystallographic databases as data sources of crystal structures are described. Nucleation processes, their kinetics and main growth mechanism will be introduced in fundamentals of crystal growth. Some phase d

Method of fabricating patterned crystal structures

KAUST Repository

Yu, Liyang

2016-12-15

A method of manufacturing a patterned crystal structure for includes depositing an amorphous material. The amorphous material is modified such that a first portion of the amorphous thin-film layer has a first height/volume and a second portion of the amorphous thin-film layer has a second height/volume greater than the first portion. The amorphous material is annealed to induce crystallization, wherein crystallization is induced in the second portion first due to the greater height/volume of the second portion relative to the first portion to form patterned crystal structures.

Self assembly of amphiphilic C60 fullerene derivatives into nanoscale supramolecular structures

Directory of Open Access Journals (Sweden)

Casscells S Ward

2007-08-01

Full Text Available Abstract Background The amphiphilic fullerene monomer (AF-1 consists of a "buckyball" cage to which a Newkome-like dendrimer unit and five lipophilic C12 chains positioned octahedrally to the dendrimer unit are attached. In this study, we report a novel fullerene-based liposome termed 'buckysome' that is water soluble and forms stable spherical nanometer sized vesicles. Cryogenic electron microscopy (Cryo-EM, transmission electron microscopy (TEM, and dynamic light scattering (DLS studies were used to characterize the different supra-molecular structures readily formed from the fullerene monomers under varying pH, aqueous solvents, and preparative conditions. Results Electron microscopy results indicate the formation of bilayer membranes with a width of ~6.5 nm, consistent with previously reported molecular dynamics simulations. Cryo-EM indicates the formation of large (400 nm diameter multilamellar, liposome-like vesicles and unilamellar vesicles in the size range of 50–150 nm diameter. In addition, complex networks of cylindrical, tube-like aggregates with varying lengths and packing densities were observed. Under controlled experimental conditions, high concentrations of spherical vesicles could be formed. In vitro results suggest that these supra-molecular structures impose little to no toxicity. Cytotoxicity of 10–200 μM buckysomes were assessed in various cell lines. Ongoing studies are aimed at understanding cellular internalization of these nanoparticle aggregates. Conclusion In this current study, we have designed a core platform based on a novel amphiphilic fullerene nanostructure, which readily assembles into supra-molecular structures. This delivery vector might provide promising features such as ease of preparation, long-term stability and controlled release.

Crystalline Hybrid Polyphenylene Macromolecules from Octaalkynylsilsesquioxanes, Crystal Structures, and a Potential Route to 3-D Graphenes

Energy Technology Data Exchange (ETDEWEB)

Roll, Mark F; Kampf, Jeffrey W.; Laine, Richard M

2011-05-10

We report here the Diels–Alder reaction of octa(diphenylacetylene)silsesquioxane [DPA₈OS] with tetraphenylcyclopentadienone or tetra(p-tolyl)cyclopentadienone to form octa(hexaphenylbenzene)octasilsesquioxane, (Ph₆C₆)₈OS, or octa(tetratolyldiphenylbenzene)octasilsesquioxane, (p-Tolyl₄Ph₂C₆)₈OS. Likewise, tetra(p-tolyl)cyclopentadienone reacts with octa(p-tolylethynylphenyl)OS to form octa(pentatolylphenylbenzene)octasilsesquioxane (p-Tolyl₅PhC₆)₈OS. These compounds, with molecular weights of 4685–5245 Da, were isolated and characterized using a variety of analytical methods. The crystal structure of DPA₈OS offers a 3 nm³ unit cell with Z = 1. The crystal structure of (Ph₆C₆)₈OS was determined to have a triclinic unit cell of 11 nm³ with Z = 1. The latter structure is believed to be the largest discrete molecular structure reported with 330 carbons. Efforts to dehydrogenatively cyclize (Scholl reaction) the hexaarylbenzene groups to form 3-D octgraphene compounds are described.

Inulin crystal initiation via a glucose-fructose cross-link of adjacent polymer chains: atomic force microscopy and static molecular modelling.

Science.gov (United States)

Cooper, Peter D; Rajapaksha, K Harinda; Barclay, Thomas G; Ginic-Markovic, Milena; Gerson, Andrea R; Petrovsky, Nikolai

2015-03-06

Semi-crystalline microparticles of inulin (MPI) have clinical utility as potent human vaccine adjuvants but their relevant surface structure and crystal assembly remain undefined. We show inulin crystal surfaces to resemble multi-layered, discoid radial spherulites resulting from very rapid formation of complex tertiary structures, implying directed crystal initiation. Physical and in silico molecular modelling of unit cells confirm steric feasibility of initiation by hydrogen-bonded cross-linking of terminal glucose to a fructose of another chain, mimicking bonding in sucrose crystals. A strong, chelate-like dual H-bond is proposed to compel the known antiparallel alignment of inulin chains. Such cross-linking would require one extra fructose per chain in the native inulin crystal, as observed. Completion of five H-bonded internal ring-domains would 'lock in' each new 6-fructose structural unit of each antiparallel helix pair to create a new isoform. All known properties of inulin isoforms follow readily from these concepts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Determination of the Temperature Dependence of Heat Capacity for Some Molecular Crystals of Nitro Compounds

Science.gov (United States)

Kovalev, Yu. M.; Kuropatenko, V. F.

2018-05-01

An analysis of the existing approximations used for describing the dependence of heat capacity at a constant volume on the temperature of a molecular crystal has been carried out. It is shown that the considered Debye and Einstein approximations do not enable one to adequately describe the dependence of heat capacity at a constant volume on the temperature of the molecular crystals of nitro compounds. This inference requires the development of special approximations that would describe both low-frequency and high-frequency parts of the vibrational spectra of molecular crystals. This work presents a universal dependence allowing one to describe the dependence of heat capacity at a constant volume on temperature for a number of molecular crystals of nitro compounds.

Molecular and crystal structures of the products of crystallization of (N'-furfurylidene)isonicotinoylhydrazide from aqueous solutions of hydrochloric and acetic acids

International Nuclear Information System (INIS)

Chuev, I.I.; Nikonova, L.A.; Atovmyan, E.G.; Utenyshev, A.N.; Aldoshin, S.M.

2001-01-01

Crystals of (N ' -furfurylidene)isonicotinoylhydrazide (I), which have been isolated from a water-methanol solution of hydrochloric acid (Ia) and an aqueous solution (∼50%) of acetic acid (Ib), are studied by X-ray diffraction. In Ia, the nitrogen atom of the pyridine ring is protonated. In the crystal, the intermolecular C=O···HN(Py) hydrogen bonds link the I · H + cations into chains which are bound through centrosymmetric NH···W···Cl - ···W ' ···H ' N ' bridges. In molecule Ib, no protonation occurs; however, its pyridine N atom is blocked by the hydroxyl H atom of a solvate molecule of acetic acid. Crystals Ib have a layered structure. The crystallization water molecule is involved in the formation of three intermolecular hydrogen bonds, namely, those with the H atom of the amide group and the carbonyl O atoms of molecule I and an acetic acid molecule of the neighboring layer

Molecular structure and vibrational spectroscopy of isoproturon

Science.gov (United States)

Vrielynck, L.; Dupuy, N.; Kister, J.; Nowogrocki, G.

2006-05-01

The crystal structure of isoproturon [ N-(4-isopropylphenyl)- N', N'-dimethylurea] has been determined: the compound crystallizes in the space group Pbca with unit cell parameters a=10.186(2) Å, b=11.030(2) Å, c=20.981(4) Å. The structure was solved and refined down to R1=0.0508 and ωR2=0.12470 for 3056 reflections. The crystalline molecular network of this pesticide is stabilized, as for many molecules of the same family, by π-π interactions but especially by a medium-strong N-H⋯C dbnd6 O intermolecular hydrogen bond (2.14 Å). The X-ray parameters were then compared with the results of DFT quantum chemical calculation computed with the GAUSSIAN 94 package. A tentative assignment of the ATR-FT-IR and Raman spectra was proposed supported by vibrational mode calculation and spectroscopic data on benzenic and urea derivatives available in the literature. The presence of a tight band around 3300 cm -1, which can be assigned to the NH bond stretching mode as well as the low frequency position of the amide I band at 1640 cm -1, sensitive to solvent polarity, confirms the existence of a quite strong intermolecular hydrogen bond between neighboring molecules in the crystal of isoproturon.

Towards high-power long-pulse operation on Tore Supra

International Nuclear Information System (INIS)

2000-01-01

The Tore Supra tokamak was given the main mission to investigate the route towards long pulse plasma discharges. This includes the problem of heat exhaust and particle control (via the development of high-performance plasma facing components), and in parallel the physics of fully non inductive discharges and its optimization with respect to the confinement. Tore Supra is thus equipped with a superconducting toroidal magnet (maximum magnetic field on axis 4.5T), a full set of actively cooled plasma facing components (PFC), and a heating and current drive capability based on high power RIF systems connected to actively cooled antennas. The encouraging results already obtained, as well as recent progress in PFC, allowed us to envisage a significant improvement in the heat exhaust capability of Tore Supra. The so-called CIEL-project consists in a complete upgrade of the inner chamber of Tore Supra, planned to be installed during the year 2000. The present paper deals with the experimental and modeling activity linked to the preparation of the long-pulse high-power discharges using the present Tore Supra equipment: heating and current drive scenarios, power coupling, confinement and transport studies, discharge control... An overview of the results obtained in that field is presented, as well as the progress required in the coming years, and the expected performance, for the CIEL phase, in terms of current drive and confinement. (author)

Structural studies on the actinide carboxylates. 4. The crystal and molecular structure of succinate dioxouranium(VI) monohydrate

Energy Technology Data Exchange (ETDEWEB)

Bombieri, G; Benetollo, F [Consiglio Nazionale delle Ricerche, Padua (Italy). Lab. di Chimica e Tecnologia dei Radioelementi; Del Pra, A; Rojas, R

1979-01-01

The structure of the title compound, UO/sub 2/(CH/sub 2/COO)/sub 2/.H/sub 2/O, has been determined from three-dimensional X-ray data. The crystals are orthorhombic, space group Pbcn with four formula units in a cell. The coordination geometry about the uranium atom is pentagonal bipyramidal. The uranyl ions are equatorially surrounded by one water oxygen and by four carboxylate oxygen atoms of different succinic ligands. Each ligand is shared by four uranyl units giving rise to a polymeric-like structure.

Capillary crystallization and molecular-replacement solution of haemoglobin II from the clam Lucina pectinata

International Nuclear Information System (INIS)

Gavira, José A.; Jesus, Walleska de; Camara-Artigas, Ana; López-Garriga, Juan; García-Ruiz, Juan M.

2006-01-01

The haemoglobin II from the clam L. pectinata has been crystallized using counter-diffusion in single capillary in the presence of agarose to improve crystal quality. Initial phases have been obtained by molecular replacement. Haemoglobin II is one of three haemoglobins present in the cytoplasm of the Lucina pectinata mollusc that inhabits the Caribbean coast. Using HBII purified from its natural source, crystallization screening was performed using the counter-diffusion method with capillaries of 0.2 mm inner diameter. Crystals of HbII suitable for data collection and structure determination were grown in the presence of agarose at 0.1%(w/v) in order to improve their quality. The crystals belong to the tetragonal space group P4 2 2 1 2, with unit-cell parameters a = b = 73.92, c = 152.35 Å, and diffracted X-rays to a resolution of better than 2.0 Å. The asymmetric unit is a homodimer with a corresponding Matthews coefficient (V M ) of 3.15 Å 3 Da −1 and a solvent content of 61% by volume

Solid-state dynamics and single-crystal to single-crystal structural transformations in octakis(3-chloropropyl)octasilsesquioxane and octavinyloctasilsesquioxane.

Science.gov (United States)

Kowalewska, A; Nowacka, M; Włodarska, M; Zgardzińska, B; Zaleski, R; Oszajca, M; Krajenta, J; Kaźmierski, S

2017-10-18

Reactive octahedral silsesquioxanes of rod-like [octakis(3-chloropropyl)octasilsesquioxane - T 8 (CH 2 CH 2 CH 2 Cl) 8 ] and spherical [octavinyloctasilsesquioxane - T 8 (CH[double bond, length as m-dash]CH 2 ) 8 ] structure can undergo reversible thermally induced phase transitions in the solid state. The phase behaviour has been studied with differential scanning calorimetry (DSC, including temperature modulated DSC), X-ray diffraction, dielectric relaxation spectroscopy (DRS), and nuclear magnetic resonance spectroscopy in the solid state (SS NMR), as well as positron annihilation lifetime spectroscopy (PALS) and polarized optical microscopy (POM). The mechanisms involving fitting the molecules into most symmetrical crystal lattices vary for species of different structure. Thermal energy can be used to expand the crystal lattice leading to thermochromism in the case of T 8 (CH[double bond, length as m-dash]CH 2 ) 8 or conversely to an unusual negative thermal expansion of crystals of T 8 (CH 2 CH 2 CH 2 Cl) 8 that results in their self-actuation. The complex behaviour is reflected in unusual changes in the capacitance and fractional free volume of the material. These phenomena can be used for molecular design of advanced well-defined hybrid materials capable of reversible thermally induced structural transformations. The findings present a new perspective for POSS-based flexible metal-organic frameworks (MOF) of cooperative structural transformability via entropy-based translational sub-net sliding.

Poloidal asymmetries of flows in the Tore Supra tokamak

Science.gov (United States)

Vermare, L.; Hennequin, P.; Gürcan, Ö. D.; Garbet, X.; Honoré, C.; Clairet, F.; Giacalone, J. C.; Morel, P.; Storelli, A.; Tore Supra Team

2018-02-01

Simultaneous measurements of binormal velocity of density fluctuations using two separate Doppler backscattering systems at the low field side and at the top of the plasma show significant poloidal asymmetry. The measurements are performed in the core region between the radii 0.7 Supra tokamak. A possible generation mechanism by the ballooned structure of the underlying turbulence, in the form of convective cells, is proposed for explaining the observation of these poloidally asymmetric mean flows.

Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus: Purification, Crystallization and Structure Determination

International Nuclear Information System (INIS)

Clemons, William M. Jr.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

2001-01-01

We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 (angstrom) resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 (angstrom) resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

Crystal structure of 3-{1′-[3,5-bis(trifluoromethylphenyl]ferrocenyl}-4-bromothiophene

Directory of Open Access Journals (Sweden)

Elisabeth A. Poppitz

2014-10-01

Full Text Available The molecular structure of the title compound, [Fe(C9H6BrS(C13H7F6], consists of a ferrocene backbone with a bis(trifluoromethylphenyl group at one cyclopentadienyl ring and a thiophene heterocycle at the other cyclopentadienyl ring. The latter is disordered over two sets of sites in a 0.6:0.4 ratio. In the crystal structure, intramolecular π–π interactions between the thienyl and the phenyl substituent [centroid–centroid distance 3.695 (4 Å] and additional weak T-shaped π–π interactions between the thienyl and the phenyl-substituted cyclopentadienyl ring [4.688 (6 Å] consolidate the crystal packing.

Scattering of atomic and molecular ions from single crystal surfaces of Cu, Ag and Fe

International Nuclear Information System (INIS)

Zoest, J.M. van.

1986-01-01

This thesis deals with analysis of crystal surfaces of Cu, Ag and Fe with Low Energy Ion scattering Spectroscopy (LEIS). Different atomic and molecular ions with fixed energies below 7 keV are scattered by a metal single crystal (with adsorbates). The energy and direction of the scattered particles are analysed for different selected charge states. In that way information can be obtained concerning the composition and atomic and electronic structure of the single crystal surface. Energy spectra contain information on the composition of the surface, while structural atomic information is obtained by direction measurements (photograms). In Ch.1 a description is given of the experimental equipment, in Ch.2 a characterization of the LEIS method. Ch.3 deals with the neutralization of keV-ions in surface scattering. Two different ways of data interpretation are presented. First a model is treated in which the observed directional dependence of neutralization action of the first atom layer of the surface is presented by a laterally varying thickness of the neutralizing layer. Secondly it is shown that the data can be reproduced by a more realistic, physical model based on atomic transition matrix elements. In Ch.4 the low energy hydrogen scattering is described. The study of the dissociation of H 2 + at an Ag surface r0230ted in a model based on electronic dissociation, initialized by electron capture into a repulsive (molecular) state. In Ch.5 finally the method is applied to the investigation of the surface structure of oxidized Fe. (Auth.)

Synthesis, crystal structure and magnetic characterization of a cyanide-bridged Mo-Ni nanosized molecular wheel

Energy Technology Data Exchange (ETDEWEB)

Zhang, Daopeng; Zhang, Hongyan; Wang, Ping [Shandong Univ. of Technology, College of Chemical Engineering, Zibo (China); Kong, Lingqian [Liaocheng Univ. (China). Dongchang College

2015-11-01

By using K{sub 4}[Mo(CN){sub 8}] and [Ni(L)(H{sub 2}O){sub 2}][ClO{sub 4}]{sub 2} as reagents (L = 2,12-dimethyl-3,7,11,17-tetraazabicyclo [11.3.1]heptadeca-1(17),13,15-triene), a new cyanide-bridged Mo-Ni complex containing the building blocks [Ni(H{sub 2}O)(L)]{sup 2+} and [Ni(L)]{sup 2+} bridged by [Mo(CN){sub 8}]{sup 4-} units has been obtained. The complex with the formula {[Ni(H_2O)(L)][Ni(L)][Mo(CN)_8]}{sub 6} . 36H{sub 2}O . 2CH{sub 3}OH (1) was characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction. The structure determination reveals an octadecanuclear cluster in the form of a 36-membered macrocycle, in which the largest intramolecular W..W and Ni..Ni distances are 16.5 and 14.4 Aa, respectively, indicating that complex 1 is a nanosized molecular wheel. Investigation of its magnetic properties has shown weak antiferromagnetic coupling between the adjacent Ni(II) ions bridged by the diamagnetic [Mo(CN){sub 8}]{sup 4-} ions.

Crystal Structure of an LSD-Bound Human Serotonin Receptor

Energy Technology Data Exchange (ETDEWEB)

Wacker, Daniel; Wang, Sheng; McCorvy, John D.; Betz, Robin M.; Venkatakrishnan, A.J.; Levit, Anat; Lansu, Katherine; Schools, Zachary L.; Che, Tao; Nichols, David E.; Shoichet, Brian K.; Dror, Ron O.; Roth, Bryan L. (UNCSM); (UNC); (Stanford); (Stanford-MED); (UCSF)

2017-01-01

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.

Crystal Structure of an LSD-Bound Human Serotonin Receptor.

Science.gov (United States)

Wacker, Daniel; Wang, Sheng; McCorvy, John D; Betz, Robin M; Venkatakrishnan, A J; Levit, Anat; Lansu, Katherine; Schools, Zachary L; Che, Tao; Nichols, David E; Shoichet, Brian K; Dror, Ron O; Roth, Bryan L

2017-01-26

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT 2B . The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT 2B R and 5-HT 2A R-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

Crystal structure of cyclic tris(ferrocene-1,1′-diyl

Directory of Open Access Journals (Sweden)

Ruslan Shekurov

2014-09-01

Full Text Available The molecular structure of the trinuclear title compound, [Fe3(C10H83] {systematic name: tris[μ-(η5:η5-1,1′-bicyclopentadienyl]triiron(II}, consists of three ferrocene subunits (each with an eclipsed conformation that are condensed via C—C bonds of the fulvalene moieties into a cyclic trimer. The angles between the planes of the cyclopentadienyl (Cp rings within the three fulvalene moieties are 76.1 (3, 80.9 (3 and 81.7 (3°. In the crystal, C—H...π interactions between neighbouring molecules lead to the cohesion of the structure.

Quantum dynamics of crystals of molecular magnets inside microwave resonators

Energy Technology Data Exchange (ETDEWEB)

Amigo, R.; Tejada, J.; Chudnovsky, E.M.; Hernandez, J.M.; Garcia-Santiago, A. E-mail: antonio@ubxlab.comtoni@ubxlab.com

2004-05-01

It is shown that crystals of molecular nanomagnets exhibit enhanced magnetic relaxation when placed inside a resonant cavity. Strong dependence of the magnetization curve on the geometry of the cavity has been observed, providing evidence of the coherent microwave radiation by the crystals. These observations open the possibility of building a nanomagnetic microwave laser pumped by the magnetic field.

Quantum dynamics of crystals of molecular magnets inside microwave resonators

International Nuclear Information System (INIS)

Amigo, R.; Tejada, J.; Chudnovsky, E.M.; Hernandez, J.M.; Garcia-Santiago, A.

2004-01-01

It is shown that crystals of molecular nanomagnets exhibit enhanced magnetic relaxation when placed inside a resonant cavity. Strong dependence of the magnetization curve on the geometry of the cavity has been observed, providing evidence of the coherent microwave radiation by the crystals. These observations open the possibility of building a nanomagnetic microwave laser pumped by the magnetic field

The crystal structure and twinning of neodymium gallium perovskite single crystals

International Nuclear Information System (INIS)

Ubizskii, S.B.; Vasylechko, L.O.; Savytskii, D.I.; Matkovskii, A.O.; Syvorotka, I.M.

1994-01-01

By means of X-ray structure analysis, the crystal structure of neodymium gallium perovskite (NGP) single crystals (NdGaO 3 ) being used as a substrate for HTSC film epitaxy has been refined and the position of atoms has been determined. The possibility of YBa 2 Cu 3 O 7-x film epitaxy on the plane (110) of NGP crystal as well as its advantages and pitfalls are analysed from structural data. The twinning types in the NGP crystal were established. The twinning structure of NGP substrates is found to be stable up to a temperature of 1173 K, as differentiated from the LaGaO 3 and LaAlO 3 substrates. It is intimated that the twinning in the NGP substrates oriented as (001) can result in creation of 90 degrees twin bonds in a film, and in the case of (110)-oriented plates it is possible to ignore the twinning presence in substrate completely. (author)

Crystal Structure of Mammalian Cysteine dioxygenase: A Novel Mononuclear Iron Center for Cysteine Thiol Oxidation

Energy Technology Data Exchange (ETDEWEB)

Simmons,C.; Liu, Q.; Huang, Q.; Hao, Q.; Begley, T.; Karplus, P.; Stipanuk, M.

2006-01-01

Cysteine dioxygenase is a mononuclear iron-dependent enzyme responsible for the oxidation of cysteine with molecular oxygen to form cysteinesulfinate. This reaction commits cysteine to either catabolism to sulfate and pyruvate or to the taurine biosynthetic pathway. Cysteine dioxygenase is a member of the cupin superfamily of proteins. The crystal structure of recombinant rat cysteine dioxygenase has been determined to 1.5 Angstroms resolution, and these results confirm the canonical cupin {beta}-sandwich fold and the rare cysteinyl-tyrosine intramolecular crosslink (between Cys93 and Tyr157) seen in the recently reported murine cysteine dioxygenase structure. In contrast to the catalytically inactive mononuclear Ni(II) metallocenter present in the murine structure, crystallization of a catalytically competent preparation of rat cysteine dioxygenase revealed a novel tetrahedrally coordinated mononuclear iron center involving three histidines (His86, His88, and His140) and a water molecule. Attempts to acquire a structure with bound ligand using either co-crystallization or soaks with cysteine revealed the formation of a mixed disulfide involving Cys164 near the active site, which may explain previously observed substrate inhibition. This work provides a framework for understanding the molecular mechanisms involved in thiol dioxygenation and sets the stage for exploring the chemistry of both the novel mononuclear iron center and the catalytic role of the cysteinyl-tyrosine linkage.

Nuclear fusion TORE SUPRA, a new stage

International Nuclear Information System (INIS)

Gregoire, M.; Laurent, L.

1995-01-01

Since almost forty years, the scientists try and neutralize in a pacific aim thermonuclear fusion energy and therefore they use the magnetic confinement of hot plasmas.In France, since 1960 the achieved studies permitted in 1988 to bring into service the TORE SUPRA TOKAMAK, which used, for the first time a superconducting magnet to generate the confinement magnetic field. TORE SUPRA, which didn't still explore its maximal potentialities, will be one of the apparatuses which will be used as basis of the international project ITER development. 5 figs

Structures and physicochemical properties of molecular aggregates of lipids

International Nuclear Information System (INIS)

Iwahashi, Makio

2005-01-01

Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

New developments on Tore Supra data acquisition units

International Nuclear Information System (INIS)

Leroux, F.; Caulier, G.; Ducobu, L.; Goniche, M.; Antar, G.

2012-01-01

The Tore Supra data acquisition system (DAS) was designed in the early eighties and has considerably evolved since then. Three generations of data acquisition units still coexist. As cost and maintenance of different operating systems is expensive, it was decided to explore an alternative solution based on an open source operating system (OS) with a disk-less system for the fourth generation. In 2010, Linux distributions for VME bus and PCI bus systems have been evaluated and compared to Lynx OS TM real time OS. The results obtained allowed to choose a version of Linux for VME and PC platform for DAS on Tore Supra. In 2011, the Tore Supra DAS dedicated software was ported on a Linux disk-less PCI platform. The new generation was successfully tested during real plasma experiments on one diagnostic, called DCEDRE. (authors)

Introduction to crystal structure determination methods using x-ray diffraction: application to some rare earth complexes

International Nuclear Information System (INIS)

Oliveira, M.A. de.

1986-01-01

This work is composed by a theoretical introduction studying crystal concept, interaction between X-ray and crystal medium, and methods for determining small molecular structures applied in solution of crystal structures of praseodymium, neodymium and europium complexes with perrhenate and trans - 1,4 - dithiane - 1,4 - dioxide, (TDTD), which general formula is [ Ln (H sub(2) O) sub(4) (η-TDTD) (η'Re O sub(4)) (μ-η sup(2)-TDTD)] sub(n) (Re O sub(4)) sub(2n). nTDTD, where, Ln = Eu, Pr, Nd and methyl-2,6-anhydrous-3-azido-4-0-benzoyl-3-deoxy-α-D-iodo pyranoside. The structure of C sub(14) H sub(15) N sub(3) O sub(5) organic complex was determined using direct methods. (M.C.K.)

The acquisition system for Tore Supra 1000 s discharges

International Nuclear Information System (INIS)

Guillerminet, B.; How, J.

2000-01-01

Long duration discharges are planned for Tore Supra in the near future. A study has been made to detect and correct all the possible limitations of the data acquisition system. Results and analysis of a few 1000 s 'dry-run' test pulses are presented in this paper as well as the solutions foreseen for Tore Supra

Alignment structures in ferroelectric liquid crystals

Energy Technology Data Exchange (ETDEWEB)

Islam, N.U

1998-07-01

Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S{sub C} phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes

Alignment structures in ferroelectric liquid crystals

International Nuclear Information System (INIS)

Islam, N.U.

1998-01-01

Although for many years liquid crystals were of purely scientific interest, they have now become ubiquitous in everyday life. The use of the nematic liquid crystal phase in flat panel display applications has been the main factor in this popularity. However, with the advent of the SuperTwist Nematic (STN) device, the limits to which this phase could be exploited for display applications was perhaps reached. With the discovery by Clark et al. of the Surface Stabilised Ferroelectric Liquid Crystal (SSFLC) configuration, the possibility arose of using chiral smectic liquid crystals to create large area, passively addressed, fast switching, flat panel displays. Unfortunately, the structures that form within smectic liquid crystals, and the dynamics of the switching within these, are still not fully understood. In this thesis we address the former of these, making a detailed the study of the structures that form within tilted smectic liquid crystal devices. We present here the first complete theoretical and experimental study of various different ferroelectric liquid crystal materials, where we employed theoretical models based on a simple set of assumptions to understand the behaviour of a set of increasingly complex experimental systems. We started with the simplest of these, Freely Suspended Smectic Films (FSSFs) and then worked with progressively more realistic systems in the form of homeotropically, and later, homogeneously aligned liquid crystal cells. The equilibrium structures that form get particularly complex in the last case, taking the form of tilted and chevron layering structures. In each of these cases, the predictions of the modelling are compared with our experimental results. Further, we present here the first model of the chevron cusp that seeks to include the effects of biaxiality in the S C phase. We also present a model that seeks to analyse the stability of the chevron layering structure and its relationship with tilted layers. This includes an

Synthesis and IR spectral study of MoO2Cl2 molecular complex with acetoacetanilides. Crystal structure of MoO2Cl2 complex with acetoacet-2-toluidine

International Nuclear Information System (INIS)

Abramenko, V.L.; Sergienko, V.S.; Churakov, A.V.

2000-01-01

Certain MoO 2 Cl 2 complexes with acetoacetanilide derivatives were synthesized, two IR spectral study being performed. Crystal and molecular structure of MoO 2 Cl 2 complex with acetoacet-2-toluidine (HL) was determined using X-ray diffraction analysis. The crystals are monoclinic, a = 7.621 (7), b = 9.498 (3), c = 19.980 (9) A, β = 95.16 (7), Z = 4, sp.gr. P2 1 /n. Coordination polyhedron of Mo atom is a distorted octahedron with two O oxoatoms in cis-position, two Cl atom in mutual trans-position and two O(HL) atoms in trans-positions in reference to O(oxo) [ru

Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein.

Science.gov (United States)

Tanaka, Yoshiki; Iwaki, Shigehiro; Tsukazaki, Tomoya

2017-09-05

The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins. Here, we describe the crystal structure of a MATE protein from the plant Camelina sativa at 2.9 Å resolution. Two sets of six transmembrane α helices, assembled pseudo-symmetrically, possess a negatively charged internal pocket with an outward-facing shape. The crystal structure provides insight into the diversity of plant MATE proteins and their substrate recognition and transport through the membrane. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis, growth, structural, optical and thermal properties of a new organic salt crystal: 3-nitroanilinium trichloroacetate

Science.gov (United States)

Selvakumar, E.; Chandramohan, A.; Anandha Babu, G.; Ramasamy, P.

2014-09-01

A new organic non-linear optical salt 3-nitroanilinium trichloroacetate has been synthesized and single crystals grown by slow solvent evaporation solution growth technique at room temperature using methanol as the solvent. The 1H and 13C Nuclear magnetic resonance spectra were recorded to establish the molecular structure of the title salt. The crystal structure of the title crystal has been determined by single crystal X-ray diffraction analysis and it belongs to monoclinic crystal system with non-centrosymmetric space group P21. Fourier transform infrared spectral study has been carried out to confirm the presence of various functional groups. The optical transmittance spectrum was recorded in the range 200-2500 nm, to find the optical transmittance window and lower cut off wavelength. The thermo gravimetric and differential thermal analyses were carried out to establish the thermal stability of the title crystal. The second harmonic generation in the title crystal was confirmed by the modified Kurtz-Perry powder test employing the Nd: YAG laser as the source for infrared radiation.

FT-IR, FT-Raman, and DFT computational studies of melaminium nitrate molecular-ionic crystal

Science.gov (United States)

Tanak, Hasan; Marchewka, Mariusz K.

2013-02-01

The experimental and theoretical vibrational spectra of melaminium nitrate were studied. The Raman and infrared (FT-IR) spectra of the melaminium nitrate and its deuterated analogue were recorded in the solid phase. Molecular geometry and vibrational frequency values of melaminium nitrate in the electronic ground state were calculated using the density functional method (B3LYP) with the 6-31++G(d,p) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequency values show good agreement with experimental values. The NBO analysis reveals that the N-H···O and N-H···N intermolecular interactions significantly influence crystal packing in this molecule.

The crystal structures of three pyrazine-2,5-dicarboxamides: three-dimensional supramolecular structures

Directory of Open Access Journals (Sweden)

Dilovan S. Cati

2017-05-01

Full Text Available The complete molecules of the title compounds, N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (I, 3,6-dimethyl-N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C20H20N6O2 (II, and N2,N5-bis(pyridin-4-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (III, are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each molecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7° in (I, 75.83 (8° in (II and by 82.71 (6° in (III. In the crystal of (I, molecules are linked by N—H...N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (II, molecules are also linked by N—H...N hydrogen bonds, forming layers lying parallel to the (10-1 plane. As in (I, the layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (III, molecules are again linked by N—H...N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π–π interactions [intercentroid distance = 3.739 (1 Å]. The sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. Compound (I crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008, 11, 1–4]. The molecular structures of the two polymorphs are compared.

Real chimney technique for total debranching of supra-aortic trunks.

Science.gov (United States)

Kato, Masaaki; Kagaya, Hideo; Kubo, Yoji; Banno, Hiroshi; Ohkubo, Nobukazu

2015-02-01

Side-clamping of the ascending aorta is an indispensable technique for proximal anastomosis in total debranching of supra-aortic trunks and in endovascular aneurysm repair for arch aneurysm. However, this procedure may lead to the dislodging of multiple plaques and to clamp injury of the ascending aorta. We developed a clampless technique to achieve proximal anastomosis between the ascending aorta and an artificial graft used for total debranching of supra-aortic trunks. We applied this method in six patients with arch aneurysm and a plaque-rich ascending aorta and were able to achieve total debranching of the supra-aortic trunks in all of the patients without side-clamping the ascending aorta and no procedurally related complications. This clampless anastomosis technique ("real chimney technique") in the ascending aorta is a valuable option for total debranching of supra-aortic trunks in the hybrid repair of arch aneurysms. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Can the nuclear symmetry potential at supra-saturation densities be negative?

International Nuclear Information System (INIS)

Yong Gaochan

2010-01-01

In the framework of an isospin-dependent Boltzmann-Uehling-Uhlenbeck (IBUU) transport model, for the central 197 Au+ 197 Au reaction at an incident beam energy of 400 MeV/nucleon, the effect of nuclear symmetry potential at supra-saturation densities on the preequilibrium clusters emission is studied. It is found that for the positive symmetry potential at supra-saturation densities the neutron-to-proton ratio of lighter clusters with mass number A≤3[(n/p) A≤3 ] is larger than that of the heavier clusters with mass number A>3[(n/p) A>3 ], whereas for the negative symmetry potential at supra-saturation densities the (n/p) A≤3 is smaller than the (n/p) A>3 . This may be considered as a probe of the negative symmetry potential at supra-saturation densities.

The synthesis, characterization, crystal structure and theoretical calculations of a new meso-BOBIPY substituted phthalonitrile

International Nuclear Information System (INIS)

Sen, Pinar; Yildiz, S. Zeki; Atalay, Yusuf; Dege, Necmi; Demirtas, Günes

2014-01-01

A novel 4-(2-meso-BOBIPY-phenoxy)phthalonitrile (6) derivative has been synthesized starting from BF 3 –OEt 2 complex and 4-(2-meso-dipyrromethene-phenoxy)phthalonitrile (5) which was prepared by the oxidation of 4-(2-meso-dipyrromethane-phenoxy)phthalonitrile (4). The final product exhibit noticeable spectroscopic properties which were examined by its absorption and fluorescence emission spectra. The original compounds prepared in the reaction pathway were characterized by the combination of FT-IR, 1 H and 13 C NMR, UV–vis, MS and HRMS spectral data. The final product (6) was obtained as single crystal which crystallized in the triclinic space group P-1 with a=7.9411 (6) Å, b=9.0150 (6) Å, c=14.419 (1) Å, α=74.917 (5)°, β=86.824 (6)°, γ=84.109 (5)° and Z=2. The crystal structure has intermolecular C–H···F–B and C–H···N interactions. These interactions construct bifurcated hydrogen bonds in the crystal structure. In this study, It has been calculated; molecular structure, vibrational frequencies, 1 H and 13 C NMR chemical shifts and HOMO and LUMO energies of the title compound by using B3LYP method with 6–311++G(dp) basis set, and the electronic spectral characterization was investigated for the target product, as well. - Highlights: • A novel 4-(2-meso-BOBIPY-phenoxy)phthalonitrile derivative has been synthesized. • The title product exhibit noticeable spectroscopic properties which were examined by its absorption and fluorescence emission spectra. • The final product (6) was obtained as single crystal which crystallized in the triclinic space group. • Molecular structure, vibrational frequencies, 1 H and 13 C NMR chemical shifts and HOMO and LUMO energies of the title compound were calculated theoretically. • The electronic spectral characterization was investigated, as well. • The title compound is also open to prepare further BODIPY substituted oligomeric molecules via on it

Water leak localization and recovery in Tore Supra

International Nuclear Information System (INIS)

Martinez, A.; Samaille, F.; Chantant, M.; Hatchressian, J.C.

2007-01-01

For almost 20 years at Tore Supra, plasma facing components (PFCs) are actively cooled by a pressurized water primary loop. Tore Supra can be considered as ITER relevant on this particular aspect. During plasma operation, it happened, that unexpected localized power deposits damaged a PFC leading to more or less large water leaks in the vacuum vessel. The improvement of the procedure to localize the leaky circuits, the investigation of technical solutions for minimizing the amount of water from steam condensation in the vacuum vessel and the optimisation of the quality of the draining and the drying of Tore Supra cooling loop circuits are the result of the experience gained during several years by the analysis of the water leak from plasma facing components (PFCs) and their consequences. Different new specific systems designed and installed during this year to fulfil these objectives are described in this paper

Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

Science.gov (United States)

Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

2018-04-01

The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

Tore Supra: technical description

International Nuclear Information System (INIS)

1985-08-01

Cryogenic system of Tore Supra is described with its principal functions and operation modes. Data control and acquisition with on line data processing is presented. Radiation dose and induced radioactivity evaluation is studied. Cooling system is detailed together with characteristics of facilities and circuits to cool. Then machine assembly and buildings are presented [fr

Crystallization, X-ray diffraction analysis and SIRAS/molecular-replacenent phasing of three crystal forms of Anabaena sensory rhodopsin transducer

International Nuclear Information System (INIS)

Vogeley, Lutz; Luecke, Hartmut

2006-01-01

Crystals of Anabaena sensory rhodopsin transducer, the transducer for the cyanobacterial photosensor Anabaena sensory rhodopsin, obtained in the space groups P4, C2 and P2 1 2 1 2 1 diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for these crystal forms were obtained by SIRAS phasing using an iodide quick-soak derivative (P4) and molecular replacement (C2 and P2 1 2 1 2 1 ). Anabaena sensory rhodopsin transducer (ASRT) is a 14.7 kDa soluble signaling protein associated with the membrane-embedded light receptor Anabaena sensory rhodopsin (ASR) from Anabaena sp., a freshwater cyanobacterium. Crystals of ASRT were obtained in three different space groups, P4, C2 and P2 1 2 1 2 1 , which diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for one of these crystal forms (P4) were obtained by SIRAS phasing using an iodide quick-soak derivative and a partial model was built. Phases for the remaining crystal forms were obtained by molecular replacement using the partial model from the P4 crystal form

Crystal and molecular structure of 6,9-bis(trimethylamine)-nido-decarborane(12) B10H12[N(CH3)3]2

International Nuclear Information System (INIS)

Polyanskaya, T.M.; Volkov, V.V.

1989-01-01

The spatial structure of 6.9-bis(trimethylamine)-nido-decarborane (12) is established on the basis of X-ray diffraction analysis. Crystals are rhombic, a = 12.619, b = 11.804, c = 11.058A, Z=4, sp. gr. P na 2 1 . The structure is of molecular type. Main geometrical parameters of the molecule are: symmetry - C1, interatomic distances - B-B 1.66-1.90, B-N 1.61, N-C 1.50 A, angles - BBB 55.0-66.5, CNC 108, BBN 119.5 deg. The (B 10 H 12 ) cluster size between B(6) and B(9) is 3.30 A. Increase approximately by 0.1 A of lengths of external bonds B-B in comparison with internal ones and tightening approximately by 3 deg of valent angles BBB at external atoms of boron also in comparison with internal ones are observed

Strong dielectric liquid crystal polymer (Part 3)

Energy Technology Data Exchange (ETDEWEB)

Kurata, Hideaki; Shibasaki, Akira

1988-11-01

Influence of change of molecular parameters on liquid crystal condition is studied to get the correlation between molecular structure of liquid crystal and phase structure or visco-elastic properties. Eight kinds of biphenyl type liquid crystals with polyacrilate main chain and triphenyl type liquid crystals were used as samples. Followings were found by a ploarizing microscope and X-ray diffraction: Phases are transferred from isotropic phase S/sub A/ phase S/sup *//sub C/ phase S/sub 1/ phase to solid on temperature desending sequence. Degree of polymerization changes only these transfer point but spacer length affects not only transfer points and layer distance but also liquid crystal structure itself. Visco-elasticity of isotropic phase shows Newtonian viscosity and is affected by the main chain length. Macroscopic and microscopic structures influence on viscoelasticity in S/sub A/ phase and S/sup *//sub C/ phase. Two rapid rises of viscoelasticity are found in low molecular weight liquid crystal when S/sub A/ transfer and S/sub A/ to S/sup *//sub C/ transfer occur by temperature desending from the isotropic phase. Viscoelastic behavior is contributed by the properties of domain itself and interaction between domains, and the interaction is changed by polymerization. 6 references, 13 figures, 1 table.

Crystallization, X-ray diffraction analysis and preliminary structure determination of the polygalacturonase PehA from Agrobacterium vitis

International Nuclear Information System (INIS)

Vordtriede, Paul B.; Yoder, Marilyn D.

2008-01-01

The acidic polygalacturonase PehA from A. vitis has been crystallized. A molecular-replacement solution indicated a right-handed parallel β-helix fold. Polygalacturonases are pectate-degrading enzymes that belong to glycoside hydrolase family 28 and hydrolyze the α-1,4 glycosidic bond between neighboring galacturonasyl residues of the homogalacturonan substrate. The acidic polygalacturonase PehA from Agrobacterium vitis was overexpressed in Escherichia coli, where it accumulated in the periplasmic fraction. It was purified to homogeneity via a two-step chromatography procedure and crystallized using the hanging-drop vapour-diffusion technique. PehA crystals belonged to space group P2 1 , with unit-cell parameters a = 52.387, b = 62.738, c = 149.165 Å, β = 89.98°. Crystals diffracted to 1.59 Å resolution and contained two molecules per asymmetric unit. An initial structure determination by molecular replacement indicated a right-handed parallel β-helix fold

Crystal structure of inactive form of Rab3B

International Nuclear Information System (INIS)

Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

2012-01-01

Highlights: ► This is the first structural information of human Rab3B. ► To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. ► The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 Å resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

Study of molecular movements in some organic crystals by NMR

International Nuclear Information System (INIS)

Alexandre, M.

1971-01-01

After a discussion on molecular crystals (generalities, movements within molecular solids, study of movements, complexes by charge transfer) and some specific ones (molecular complexes of trinitrobenzene or TNB), this research thesis reports the use of nuclear magnetic resonance (NMR) to study molecular movements: generalities on broadband NMR, spin relaxation and strong field network, observation of the absorption signal and measurement of the second moment. The last part reports and discusses experimental results obtained on TNB-naphthalene, on TNB-azulene, on TNB-benzothiophene, and on TNB-indole

Crystal structure of 2,5-di-methyl-anilinium salicylate.

Science.gov (United States)

Mani, A; Kumar, P Praveen; Chakkaravarthi, G

2015-09-01

The title mol-ecular salt, C8H12N(+)·C7H5O3 (-) arose from the proton-transfer reaction between 2,5-xylidine and salicylic acid. In the anion, the dihedral angle between the planes of the aromatic ring and the -CO2 (-) group is 11.08 (8)°; this near planarity is consolidated by an intra-molecular O-H⋯O hydrogen bond. In the crystal, the components are connected by N-H⋯O hydrogen bonds, with all three O atoms in the anion acting as acceptors; the result is a [100] chain. The structure also features weak C-H⋯O bonds and aromatic π-π stacking [centroid-to-centroid distance = 3.7416 (10) Å] inter-actions, which lead to a three-dimensional network.

ERP signs of categorical and supra-categorical processing of visual information.

Science.gov (United States)

Zani, Alberto; Marsili, Giulia; Senerchia, Annapaola; Orlandi, Andrea; Citron, Francesca M M; Rizzi, Ezia; Proverbio, Alice M

2015-01-01

The aim of the present study was to investigate to what extent shared and distinct brain mechanisms are possibly subserving the processing of visual supra-categorical and categorical knowledge as observed with event-related potentials of the brain. Access time to these knowledge types was also investigated. Picture pairs of animals, objects, and mixed types were presented. Participants were asked to decide whether each pair contained pictures belonging to the same category (either animals or man-made objects) or to different categories by pressing one of two buttons. Response accuracy and reaction times (RTs) were also recorded. Both ERPs and RTs were grand-averaged separately for the same-different supra-categories and the animal-object categories. Behavioral performance was faster for more endomorphic pairs, i.e., animals vs. objects and same vs. different category pairs. For ERPs, a modulation of the earliest C1 and subsequent P1 responses to the same vs. different supra-category pairs, but not to the animal vs. object category pairs, was found. This finding supports the view that early afferent processing in the striate cortex can be boosted as a by-product of attention allocated to the processing of shapes and basic features that are mismatched, but not to their semantic quintessence, during same-different supra-categorical judgment. Most importantly, the fact that this processing accrual occurred independent of a traditional experimental condition requiring selective attention to a stimulus source out of the various sources addressed makes it conceivable that this processing accrual may arise from the attentional demand deriving from the alternate focusing of visual attention within and across stimulus categorical pairs' basic structural features. Additional posterior ERP reflections of the brain more prominently processing animal category and same-category pairs were observed at the N1 and N2 levels, respectively, as well as at a late positive complex level

Molecular Recognition in the Colloidal World.

Science.gov (United States)

Elacqua, Elizabeth; Zheng, Xiaolong; Shillingford, Cicely; Liu, Mingzhu; Weck, Marcus

2017-11-21

) and can engage in tunable high-fidelity interactions. Examples include metal coordination and host-guest interactions as well as hydrogen bonding and DNA hybridization. On the colloidal scale, these interactions can be used to drive the reversible formation of open structures. Key to the design is the ability to covalently conjugate supramolecular motifs onto the particle surface and/or noncovalently associate with small molecules that can mediate and direct assembly. Efforts exploiting the binding strength inherent to DNA hybridization for the preparation of reversible open-packed structures are then detailed. We describe strategies that led to the introduction of dual-responsive DNA-mediated orthogonal assembly as well as colloidal clusters that afford distinct DNA-ligated close-packed lattices. Further focus is placed on two essential and related efforts: the engineering of complex superstructures that undergo phase transitions and colloidal crystals featuring a high density of functional anchors that aid in crystallization. The design principles discussed in this Account highlight the synergy stemming from coupling well-established noncovalent interactions common on the molecular and polymeric length scales with colloidal platforms to engineer reconfigurable functional architectures by design. Directional strategies and methods such as those illustrated herein feature molecular control and dynamic assembly that afford both open-packed 1D and 2D lattices and are amenable to 3D colloidal frameworks. Multiple methods to direct colloidal assembly have been reported, yet few are capable of crystallizing 2D and 3D architectures of interest for optical data storage, electronics, and photonics. Indeed, early implications are that [supra]molecular control over colloidal assembly can fabricate rationally structured designer materials from simple fundamental building blocks.

Lattice dynamics of a crystal with a molecular impurity

International Nuclear Information System (INIS)

Sahoo, D.; Venkataraman, G.

1975-01-01

The dynamics of a crystal containing a molecular impurity is discussed with allowance for the effects of internal vibrations of the molecule. Cartesian coordinates are used to describe internal vibrations, angular oscillations and centre of mass translations of the impurity, and the displacement of atoms of the host lattice. Next the Hamiltonian is set up and the equations of motion derived. In this process, use is made of Dirac brackets when dealing with vibrational coordinates (of the molecule) which have redundancy and constraints. A method of solution of the normal modes of the system is indicated by using the defect space matrixpartitioning technique. The special case of a rigid molecular impurity is then discussed along with the relevance of the present formalism in the interpretation of a recent neutron scattering experiment. It is also shown how the results of crystal-field approximation model and those of the molecular model approximation are obtained as further special cases of the present formalism. A comparison of the present work with those of others has been made. (author)

Controlled thermonuclear reactions and Tora Supra program

International Nuclear Information System (INIS)

1988-01-01

The research programs for the nuclear energy production by means of thermonuclear fusion are shown. TORA SUPRA, Joint European Torus, Next European Torus and those developed at the Atomic Energy Center are described. The controlled fusion necessary conditions, the energy and confinement balance, and the research of a better tokamak configuration are discussed. A description of TORA SUPRA, the ways of achieving the project and the expected delays are shown. The Controlled Fusion Research Department functions, concerning these programs, are described. The importance of international cooperation and the perspectives about the use of controlled fusion are underlined [fr

Pellet injection requirements for TORE SUPRA

International Nuclear Information System (INIS)

Lafferranderie, J.

1986-01-01

The main parameters of TORE SUPRA are outlined and pellet injection requirements to meet plasma density goals are discussed. Topics considered include plasma buildup, plasma refueling and penetration depth

Particles pumping in Tore Supra

International Nuclear Information System (INIS)

Bonnel, P.; Chappuis, P.; Lipa, M.

1989-01-01

TORE SUPRA and its peripheral equipments are provided with routine clean high vacuum by turbomolecular pumping. During plasma discharges large quantity of very hot gases activating at plasma edge and plasma density in scrape off layer has to be controlled before they strike violently solid wall provoking increase in impurities content and make density up to disruptive level. A Magnetic Ergodic Divertor made of six winding structures - MED - six Vertical Pumped Limiters - VPL - and one Horizontal Pumped Limiter - HPL - are set in the vacuum chamber in order to cope with plasma-wall interactions and neutral gas recycling. Each apparatus is equipped at front side with thermal shield respectively made of polycristallin and pyrolitic graphite bolted on stainless steel support for MED and HPL whereas for VPL it is made of CFC Aerolor 05 brazed on hardened copper. The total heat removal capacity of these plasma facing components is 12 MW. Design of particles collection openings and ducts conductance allow 10% of capture efficiency, that means for TORE SUPRA a flux of 3 x 10 21 particles/second has to be sorbed by water cooled titanium getter pumps, settled at rear side. All those facilities were put into plasma operation at the beginning of 1989 for a short time. Preliminary observations go along with theoretical predictions, that actions in scrappe-off layer may provoke effects in bulk plasma. Very first results drawn out, show that particle collection and heat removal were effective by MED, VPL and HPL and that plasma behaviour was not disturbed by their presence and actions but instead tendency to improvement was observed

Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

Science.gov (United States)

Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

2018-04-03

The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrilenucleation difficulty is a function of the strength of solvent-solute interaction, with emphasis on the interaction with specific H-bonding polar sites of importance in the crystal structure. A clear exception from this rule is the most difficult nucleation in toluene despite the weakest solvent-solute interactions. However molecular dynamics modelling predicts that tolbutamide assumes an intramolecularly H-bonded conformation in toluene, substantially different from and more stable than the conformation in the crystal structure, and thus presenting an additional barrier to nucleation. This explains why nucleation in toluene is the most difficult and why the relatively higher propensity for aggregation of tolbutamide molecules in toluene solution, as observed with FTIR spectroscopy, does not translate into easier nucleation. Thus, our combined experimental and molecular modelling study suggests that the solvent can influence on the nucleation not only via differences in the desolvation but also through the influence on molecular conformation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal and molecular structure of the membrane-active antibiotic enniatin C

International Nuclear Information System (INIS)

Tishchenko, G.N.; Zhukhlistova, N.E.

2000-01-01

The crystal structure of the cyclic hexadepsipeptide antibiotic enniatin C c[-(L-MeLeu-D-Hyi) 3 -], C 34 H 59 N 3 O 9 , was established by X-ray structure analysis (sp. gr. P2 1 , a = 20.205(5) A, b = 8.702(2) A, c 25.587(6) A, γ = 97.0(5) deg., V = 4465.3(18) A 3 , Z = 4, R = 0.089 for 3601 reflections with I > 2σ(I)). The unit cell contains two independent molecules of enniatin C, one ethanol molecule disordered over two positions, and approximately two water molecules occupying four positions and forming hydrogen bonds with each other. The independent antibiotic molecules adopt virtually identical conformations similar to those observed in the structures of enniatin B and its Na,Ni-complex. These conformations are characterized by alternating upward and downward orientations of the carbonyl groups and pseudoequatorial orientations of side radicals. The Leu residues have stretched conformations. The N-methylamide groups of the independent antibiotic molecules face each other, whereas the molecules are displaced by approximately 8.4 A with respect to each other along the mean planes of the rings

Crystallization, preliminary X-ray diffraction and structure solution of MosA, a dihydrodipicolinate synthase from Sinorhizobium meliloti L5-30

International Nuclear Information System (INIS)

Leduc, Yvonne A.; Phenix, Christopher P.; Puttick, Jennifer; Nienaber, Kurt; Palmer, David R. J.; Delbaere, Louis T. J.

2005-01-01

MosA from S. meliloti L5-30 has been crystallized in solution with pyruvate and the 2.3 Å resolution structure has been solved by molecular replacement using E. coli dihydrodipicolinate synthase as the model. The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Å resolution using synchrotron radiation and belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Å

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

International Nuclear Information System (INIS)

Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

2013-01-01

A new approach is presented that allows the efficient localization and orientation of heavy-atom cluster compounds used in experimental phasing by a molecular replacement procedure. This permits the calculation of meaningful phases up to the highest resolution of the diffraction data. Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome

NONLINEAR OPTICAL MOLECULAR CRYSTAL BASED ON 2,6-DIAMINOPYRIDINE: SYNTHESIS AND CHARACTERIZATION

Directory of Open Access Journals (Sweden)

I. M. Pavlovetc

2014-05-01

Full Text Available The paper deals with investigation of a new nonlinear optical material based on nonlinear optical chromophore (4-Nitrophenol and aminopyridine (2,6-Diaminopyridine. Calculation results are presented for molecular packing in the crystalline compound, based on the given components. According to these results the finite material must have a noncentrosymmetric lattice, which determines the presence of the second order nonlinear optical response. Investigations carried out in this work confirm these calculations. Results of experiments are given describing the co-crystallization of these components and the following re-crystallization of the obtained material. In order to get a monocrystal form, the optimal conditions for the synthesis of molecular crystals based on these components are determined. Sufficiently large homogeneous crystals are obtained, that gave the possibility to record their spectra in the visible and near infrared parts of the spectrum, to determine their nonlinear optical properties and the level of homogeneity. Their optical (optical transmission and optical laser damage threshold and nonlinear optical properties are presented. For observation and measurement of the nonlinear optical properties an installation was built which implements the comparative method for measurements of nonlinear optical properties. A potassium titanyl oxide phosphate crystal was used as a sample for comparison. Results are given for the conversion efficiency of the primary laser radiation in the second optical harmonic relative to the signal obtained on the potassium titanyl oxide phosphate crystal. Obtained results show that the molecular co-crystal based on 2,6-Diaminopyridine is a promising nonlinear optical material for generating the second optical harmonic on the Nd: YAG laser (532 nm.

Overexpression, purification, crystallization and preliminary structural studies of catabolic ornithine transcarbamylase from Lactobacillus hilgardii

Energy Technology Data Exchange (ETDEWEB)

Rivas, Blanca de las; Rodríguez, Héctor [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Angulo, Iván [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Muñoz, Rosario [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Mancheño, José M., E-mail: xjosemi@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain)

2007-07-01

The catabolic ornithine transcarbamylase (cOTC) from L. hilgardii has been overexpressed in E. coli, purified and crystallized under two different experimental conditions. The structure has been solved by the molecular-replacement method using the atomic coordinates of catabolic ornithine transcarbamylase from P. aeruginosa as the search model. The catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) from the lactic acid bacteria Lactobacillus hilgardii is a key protein involved in the degradation of arginine during malolactic fermentation. cOTC containing an N-terminal His{sub 6} tag has been overexpressed in Escherichia coli, purified and crystallized under two different experimental conditions using the hanging-drop vapour-diffusion method. Crystals obtained from a solution containing 8%(w/v) PEG 4000, 75 mM sodium acetate pH 4.6 belong to the trigonal space group P321 and have unit-cell parameters a = b = 157.04, c = 79.28 Å. Conversely, crystals grown in 20%(v/v) 2-methyl-2,4-pentanediol, 7.5%(w/v) PEG 4000, 100 mM HEPES pH 7.8 belong to the monoclinic space group C2 and have unit-cell parameters a = 80.06, b = 148.90, c = 91.67 Å, β = 100.25°. Diffraction data were collected in-house to 3.00 and 2.91 Å resolution for trigonal and monoclinic crystals, respectively. The estimated Matthews coefficient for the crystal forms were 2.36 and 2.24 Å{sup 3} Da{sup −1}, respectively, corresponding to 48% and 45% solvent content. In both cases, the results are consistent with the presence of three protein subunits in the asymmetric unit. The structure of cOTC has been determined by the molecular-replacement method using the atomic coordinates of cOTC from Pseudomonas aeruginosa (PDB code) as the search model.

Overexpression, purification, crystallization and preliminary structural studies of catabolic ornithine transcarbamylase from Lactobacillus hilgardii

International Nuclear Information System (INIS)

Rivas, Blanca de las; Rodríguez, Héctor; Angulo, Iván; Muñoz, Rosario; Mancheño, José M.

2007-01-01

The catabolic ornithine transcarbamylase (cOTC) from L. hilgardii has been overexpressed in E. coli, purified and crystallized under two different experimental conditions. The structure has been solved by the molecular-replacement method using the atomic coordinates of catabolic ornithine transcarbamylase from P. aeruginosa as the search model. The catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) from the lactic acid bacteria Lactobacillus hilgardii is a key protein involved in the degradation of arginine during malolactic fermentation. cOTC containing an N-terminal His 6 tag has been overexpressed in Escherichia coli, purified and crystallized under two different experimental conditions using the hanging-drop vapour-diffusion method. Crystals obtained from a solution containing 8%(w/v) PEG 4000, 75 mM sodium acetate pH 4.6 belong to the trigonal space group P321 and have unit-cell parameters a = b = 157.04, c = 79.28 Å. Conversely, crystals grown in 20%(v/v) 2-methyl-2,4-pentanediol, 7.5%(w/v) PEG 4000, 100 mM HEPES pH 7.8 belong to the monoclinic space group C2 and have unit-cell parameters a = 80.06, b = 148.90, c = 91.67 Å, β = 100.25°. Diffraction data were collected in-house to 3.00 and 2.91 Å resolution for trigonal and monoclinic crystals, respectively. The estimated Matthews coefficient for the crystal forms were 2.36 and 2.24 Å 3 Da −1 , respectively, corresponding to 48% and 45% solvent content. In both cases, the results are consistent with the presence of three protein subunits in the asymmetric unit. The structure of cOTC has been determined by the molecular-replacement method using the atomic coordinates of cOTC from Pseudomonas aeruginosa (PDB code) as the search model

Molecular type channeling of relativistic electrons in crystals

International Nuclear Information System (INIS)

Vyatkin, E.G.; Filimonov, Yu.M.; Taratin, A.M.; Vorobiev, S.A.

1983-01-01

Channeling of relativistic electrons in direction in a diamond crystal and the channeling radiation spectra are investigated using computer simulation by the binary collision model and using the model of a continuum potential of the atomic rows. In a computer experiment the atomic- and molecular-type states of channeled elcetrons are revealed, and the orientational dependence of the electron trapping probability in these states is obtained. The peculiarities revealed of the angular distributions and radiation spectra of electrons in the molecular-type states allow to discover these states in the experiment. (author)

Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

Science.gov (United States)

Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

2006-05-19

Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

Crystallization of carbohydrate oxidase from Microdochium nivale

International Nuclear Information System (INIS)

Dušková, Jarmila; Dohnálek, Jan; Skálová, Tereza; Østergaard, Lars Henrik; Fuglsang, Claus Crone; Kolenko, Petr; Štěpánková, Andrea; Hašek, Jindřich

2009-01-01

Industrially used carbohydrate oxidase was successfully crystallized in several forms, diffraction data suitable for structural analysis were collected. Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 Å resolution, with unit-cell parameters a = b = 55.7, c = 610.4 Å and apparent space group P6 2 22. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 Å, β = 95.7°. Data sets were collected to a resolution of 2.4 Å. The structure was solved by the molecular-replacement method. Model refinement is currently in progress

SUPRA - Enhanced upset recovery simulation

NARCIS (Netherlands)

Groen, E.; Ledegang, W.; Field, J.; Smaili, H.; Roza, M.; Fucke, L.; Nooij, S.; Goman, M.; Mayrhofer, M.; Zaichik, L.E.; Grigoryev, M.; Biryukov, V.

2012-01-01

The SUPRA research project - Simulation of Upset Recovery in Aviation - has been funded by the European Union 7th Framework Program to enhance the flight simulation envelope for upset recovery simulation. Within the project an extended aerodynamic model, capturing the key aerodynamics during and

Particle control studies on Tore Supra

International Nuclear Information System (INIS)

Mioduszewski, P.

1987-01-01

The report consists of viewgraphs. The goal of the particle control program at Tore Supra is to study plasma performance with strong pellet fueling and corresponding particle exhaust in a limiter tokamak

Crystal structure of di­methyl­ammonium hydrogen oxalate hemi(oxalic acid)

Science.gov (United States)

Diallo, Waly; Gueye, Ndongo; Crochet, Aurélien; Plasseraud, Laurent; Cattey, Hélène

2015-01-01

Single crystals of the title salt, Me2NH2 +·HC2O4 −·0.5H2C2O4, were isolated as a side product from the reaction involving Me2NH, H2C2O4 and Sn(n-Bu)3Cl in a 1:2 ratio in methanol or by the reaction of the (Me2NH2)2C2O4 salt and Sn(CH3)3Cl in a 2:1 ratio in ethanol. The asymmetric unit comprises a di­methyl­ammonium cation (Me2NH2 +), an hydrogenoxalate anion (HC2O4 −), and half a mol­ecule of oxalic acid (H2C2O4) situated about an inversion center. From a supra­molecular point of view, the three components inter­act together via hydrogen bonding. The Me2NH2 + cations and the HC2O4 − anions are in close proximity through bifurcated N—H⋯(O,O) hydrogen bonds, while the HC2O4 − anions are organized into infinite chains via O—H⋯O hydrogen bonds, propagating along the a-axis direction. In addition, the oxalic acid (H2C2O4) mol­ecules play the role of connectors between these chains. Both the carbonyl and hydroxyl groups of each diacid are involved in four inter­molecular inter­actions with two Me2NH2 + and two HC2O4 − ions of four distinct polymeric chains, via two N—H⋯O and two O—H⋯O hydrogen bonds, respectively. The resulting mol­ecular assembly can be viewed as a two-dimensional bilayer-like arrangement lying parallel to (010), and reinforced by a C—H⋯O hydrogen bond. PMID:25995858

Efficient green luminescence of terbium oxalate crystals: A case study with Judd-Ofelt theory and single crystal structure analysis and the effect of dehydration on luminescence

Science.gov (United States)

Alexander, Dinu; Joy, Monu; Thomas, Kukku; Sisira, S.; Biju, P. R.; Unnikrishnan, N. V.; Sudarsanakumar, C.; Ittyachen, M. A.; Joseph, Cyriac

2018-06-01

Design and synthesis of Lanthanide based metal organic framework is a frontier area of research owing to their structural diversity enabling specific applications. The luminescence properties of rare earths, tuned by the structural features of Ln-MOFs are investigated extensively. Rare earth oxalates which can be synthesized in a facile method, ensuring the structural features of MOFs with excellent photoluminescence characteristics deserves much attention. This work is the first time report on the single crystal structure and Judd-Ofelt (JO) theoretical analysis - their correlation with the intense and sharp green luminescence of Terbium oxalate crystals. The intense green luminescence observed for Terbium oxalate crystals for a wide range of excitation from DUV to visible region despite the luminescence limiting factors are discussed. The absence of concentration quenching and lifting up of forbidden nature of f-f transitions, allowing direct excitation of Terbium ions is analysed with the help of JO theory and single crystal structure analysis. The JO analysis predicted the asymmetry of Terbium sites, allowing the electric dipole transitions and from the JO intensity parameters, promising spectroscopic parameters - emission cross section, branching ratio, gain band width and gain coefficient of the material were calculated. The single crystal structure analysis revealed the asymmetry of Tb sites and structure of Terbium oxalate is formed by the hydrogen bonded stacking of overlapped six Terbium membered rings connected by the oxalate ligands. The molecularly thick layers thus formed on the crystal surface are imaged by the atomic force microscopy. The presence of water channels in the structure and the effect of lattice water molecules on the luminescence intensity are also investigated.

Characterisation of Supra- and Infratentorial ICP Profiles.

Science.gov (United States)

Moyse, Emmanuel; Ros, Maxime; Marhar, Fouad; Swider, Pascal; Schmidt, Eric Albert

2016-01-01

In pathophysiology and clinical practice, the intracranial pressure (ICP) profiles in the supratentorial and infratentorial compartments are unclear. We know that the pressure within the skull is unevenly distributed, with demonstrated ICP gradients. We recorded and characterised the supra- and infratentorial ICP patterns to understand what drives the transtentorial ICP gradient.A 70-year-old man was operated on for acute cerebellar infarction. One supratentorial probe and one cerebellar probe were implanted. Both signals were recorded concurrently and analysed off-line. We calculated mean ICP, ICP pulse amplitude, respiratory waves, slow waves and the RAP index of supra- and infratentorial ICP signals. Then, we measured transtentorial difference and performed correlation analysis for every index.Supratentorial ICP mean was 8.5 mmHg lower than infratentorial ICP, but the difference lessens for higher values. Both signals across the tentorium showed close correlation. Supra- and infratentorial pulse amplitude, respiratory waves and slow waves also showed a high degree of correlation. The compensatory reserve (RAP) showed good correlation. In this case report, we demonstrate that the mean value of ICP is higher in the posterior fossa, with a strong correlation across the tentorium. All other ICP-derived parameters display a symmetrical profile.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of chlorite dismutase: a detoxifying enzyme producing molecular oxygen

Energy Technology Data Exchange (ETDEWEB)

Geus, Daniël C. de, E-mail: d.de.geus@chem.leidenuniv.nl; Thomassen, Ellen A. J.; Feltz, Clarisse L. van der; Abrahams, Jan Pieter [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands)

2008-08-01

Preliminary X-ray data collection and analysis for crystals of chlorite dismutase, a haem-based enzyme that very effectively reduces chlorite to chloride while producing molecular oxygen, is reported to 2.1 Å resolution. Chlorite dismutase, a homotetrameric haem-based protein, is one of the key enzymes of (per)chlorate-reducing bacteria. It is highly active (< 2 kU mg{sup −1}) in reducing the toxic compound chlorite to the innocuous chloride anion and molecular oxygen. Chlorite itself is produced as the intermediate product of (per)chlorate reduction. The chlorite dismutase gene in Azospira oryzae strain GR-1 employing degenerate primers has been identified and the active enzyme was subsequently overexpressed in Escherichia coli. Chlorite dismutase was purified, proven to be active and crystallized using sitting drops with PEG 2000 MME, KSCN and ammonium sulfate as precipitants. The crystals belonged to space group P2{sub 1}2{sub 1}2 and were most likely to contain six subunits in the asymmetric unit. The refined unit-cell parameters were a = 164.46, b = 169.34, c = 60.79 Å. The crystals diffracted X-rays to 2.1 Å resolution on a synchrotron-radiation source and a three-wavelength MAD data set has been collected. Determination of the chlorite dismutase structure will provide insights into the active site of the enzyme, for which no structures are currently available.

Crystallization in nano-confinement seeded by a nanocrystal—A molecular dynamics study

KAUST Repository

Pan, Heng; Grigoropoulos, Costas

2014-01-01

Seeded crystallization and solidification in nanoscale confinement volumes have become an important and complex topic. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation, and seed size as explained by classical two-sphere model and Gibbs-Thomson effect. © 2014 AIP Publishing LLC.

Crystallization in nano-confinement seeded by a nanocrystal—A molecular dynamics study

KAUST Repository

Pan, Heng

2014-03-14

Seeded crystallization and solidification in nanoscale confinement volumes have become an important and complex topic. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation, and seed size as explained by classical two-sphere model and Gibbs-Thomson effect. © 2014 AIP Publishing LLC.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

Crystal structure of inactive form of Rab3B

Energy Technology Data Exchange (ETDEWEB)

Zhang, Wei [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Shen, Yang [Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, Canada M5G 1L7 (Canada); Jiao, Ronghong [Department of Function Inspection, Hebei Provincial People' s Hospital, Shijiazhuang 050051 (China); Liu, Yanli; Deng, Lingfu [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China); Qi, Chao, E-mail: qichao@mail.ccnu.edu.cn [Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079 (China)

2012-02-24

Highlights: Black-Right-Pointing-Pointer This is the first structural information of human Rab3B. Black-Right-Pointing-Pointer To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. Black-Right-Pointing-Pointer The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 A resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

Structural elucidation and physicochemical properties of an organic NLO crystal: 4-Nitrotoluene-2-sulphonic acid dihydrate

Science.gov (United States)

Sangeetha, K.; Guru Prasad, L.; Mathammal, R.

2018-03-01

4-nitrotoluene-2-sulphonic acid dihydrate single crystals have been developed using slow evaporation technique in methanol. Lattice parameters of the NTSAD crystal have been calculated and it confirms the grown material. The intermolecular interactions are studied from the 3D Hirshfeld surface analysis and 2D fingerprint plots. The NMR spectral analysis has been carried out to confirm the molecular structure of the grown material. Optical properties have been obtained from UV-VIS spectral analysis and photoluminescence studies. Frequency conversion property of the NTSAD crystal was investigated with the aid of Kurtz and Perry method.

Optically induced structural phase transitions in ion Coulomb crystals

DEFF Research Database (Denmark)

Horak, Peter; Dantan, Aurelien Romain; Drewsen, Michael

2012-01-01

We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures, such as b......We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures...

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

International Nuclear Information System (INIS)

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing; Qiu, Bingsheng; Rao, Zihe; Gao, George F.; Tien, Po

2005-01-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in the mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion

Crystal Structure of a Lipid G Protein-Coupled Receptor

Energy Technology Data Exchange (ETDEWEB)

Hanson, Michael A; Roth, Christopher B; Jo, Euijung; Griffith, Mark T; Scott, Fiona L; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M; Schuerer, Stephan C; Sanna, M Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C [Scripps; (Receptos)

2012-03-01

The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P₁-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P₁, resulting in the modulation of immune and stromal cell responses.

Escherichia coli MltA : MAD phasing and refinement of a tetartohedrally twinned protein crystal structure (vol D61, pg 613, 2005)

NARCIS (Netherlands)

Barends, Thomas R.M.; Jong, René M. de; Straaten, Karin E. van; Thunnissen, Andy-Mark W.H.; Dijkstra, Bauke W.

Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15 Å resolution. When phasing with molecular replacement using the native structure failed, selenium MAD was used to obtain initial phases. However, after MAD phasing the crystals were found

Crystal structure from one-electron theory

DEFF Research Database (Denmark)

Skriver, H. L.

1985-01-01

The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...

Studying Microstructure in Molecular Crystals With Nanoindentation

DEFF Research Database (Denmark)

Mishra, Manish Kumar; Desiraju, Gautam R; Ramamurty, Upadrasta

2014-01-01

Intergrowth polymorphism refers to the existence of distinct structural domains within a single crystal of a compound. The phenomenon is exhibited by form II of the active pharmaceutical ingredient felodipine, and the associated microstructure is a significant feature of the compound's structural...

Crystal Structure, Conformational Analysis, and Charge Density Distribution for Eng-Epifisetinidol: An Explanation for Regiospecific Aromatic Substitution of 5-Deoxyflavan

Science.gov (United States)

Fred L. Tobiason; Frank R. Fronczek; Jan P. Steynberg; Elizabeth C. Steynberg; Richard W. Hemingway; Wayne L. Mattice

1993-01-01

Molecular modeling and molecular orbital analyses of ent-epifisetinidol gave &ood predictions of the approximate "reverse half-chair" conformation found for the crystal structure. MNDO and AM1 analyses of HOMO electron densities provided an explanation for the stereospecific electrophilic aromatic substitution at C(6) in 5-deoxy-flavans...

Understanding molecular structure from molecular mechanics.

Science.gov (United States)

Allinger, Norman L

2011-04-01

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

International Nuclear Information System (INIS)

Wang, J.; Gutierre, M.S.

2010-01-01

This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

Nanoscale heterostructures with molecular-scale single-crystal metal wires.

Science.gov (United States)

Kundu, Paromita; Halder, Aditi; Viswanath, B; Kundu, Dipan; Ramanath, Ganpati; Ravishankar, N

2010-01-13

Creating nanoscale heterostructures with molecular-scale (synthesis of nanoscale heterostructures with single-crystal molecular-scale Au nanowires attached to different nanostructure substrates. Our method involves the formation of Au nanoparticle seeds by the reduction of rocksalt AuCl nanocubes heterogeneously nucleated on the substrates and subsequent nanowire growth by oriented attachment of Au nanoparticles from the solution phase. Nanoscale heterostructures fabricated by such site-specific nucleation and growth are attractive for many applications including nanoelectronic device wiring, catalysis, and sensing.

Tore-Supra: a Tokamak with superconducting toroidal field coils

International Nuclear Information System (INIS)

Turck, B.

1987-07-01

Tore Supra is a tokamak under construction on the site of Cen Cadarache by the Euratom-CEA Association. The machine technology integrates all problems related to the fabrication and the operation of large superconducting coils and of the associated cryogenic system. Tore Supra will provide a significant experience to prepare the next generation of machines for plasma physics and controlled fusion. Tore Supra is specially designed to implement a large physics program. The superconducting coils make possible the study of plasma confinement in long pulses (more than 60s), the impurities and the stability, and the efficiency of additional heating sources (neutral particle beams and radio frequency heating). The opportunity is taken to recall the particular features and requirements of the superconducting coils of the large future tokamaks in order to point out the problems that have to be faced by any new material (superconducting or not)

Crystal structure refinement with SHELXL

Energy Technology Data Exchange (ETDEWEB)

Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

2015-01-01

New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

Heat loads on Tore Supra ICRF Launchers Plasma Facing Components

International Nuclear Information System (INIS)

Bremond, S.; Colas, L.; Beaumont, B.; Chantant, M.; Goniche, M.; Mitteau, R.

2005-01-01

Understanding the heat loads on Ion Cyclotron Range of Frequency (ICRF) launchers plasma-facing components is a crucial task both for operating present tokamaks and for designing ITER ICRF launchers as these loads may limit the RF power coupling capability. Tore Supra facility is particularly well suited to take this issue. Parametric studies have been performed which enables to get an overall detailed picture of the different heat loads on several areas, pointing to different mechanisms at the origin of the heat power fluxes. It is found that the most critical items for Tore-Supra operation are localized heat loads on the Faraday screen top left corner and vertical edges. Warming up close to maximum temperature limit originally set for protection of the plasma-facing components is found of high power pulses, but no erosion was observed after detailed inspection of the launcher in Tore-Supra vessel. Yet, the associated heat loads could be limiting for Tore-Supra operation in the future, and some dedicated work is under progress to improve the understanding of these power fluxes, pointing out the importance of getting a better knowledge of particle flows in the scrape of layer

Two-dimensional photonic crystal accelerator structures

Directory of Open Access Journals (Sweden)

Benjamin M. Cowan

2003-10-01

Full Text Available Photonic crystals provide a method of confining a synchronous speed-of-light mode in an all-dielectric structure, likely a necessary feature in any optical accelerator. We explore computationally a class of photonic crystal structures with translational symmetry in a direction transverse to the electron beam. We demonstrate synchronous waveguide modes and discuss relevant parameters of such modes. We then explore how accelerator parameters vary as the geometry of the structure is changed and consider trade-offs inherent in the design of an accelerator of this type.

Supra Arcade Downflows with XRT Informed by Dipolarization Fronts with THEMIS

Science.gov (United States)

Kobelski, Adam; Savage, Sabrina L.; Malaspina, David M.

2016-01-01

Magnetic reconnection can rapidly reconfigure the magnetic field of the corona, accelerating plasma through the site of reconnection. Ambiguities due to the nature of remote sensing have complicated the interpretation of observations of the inflowing and outflowing plasma in reconnecting regions. In particular, the interpretation of sunward moving density depletions above flare arcades (known as Supra Arcade Downflows - SADs) is still debated. Hinode/XRT has provided a wealth of observations for SADs and helped inform our current understanding of these structures. SADs have been interpreted as wakes behind newly reconnected and outflowing loops (Supra Arcade Downflowing Loops - SADLs). Models have shown the plausibility of this interpretation, though this interpretation has not yet been fully accepted. We present here observations of newly reconnected outflowing loops observed via in situ instruments in the magnetosphere. These observations, provided by five THEMIS spacecraft, show that around retracting loops (dipolarization fronts in this context) similar dynamic temperature and density structures are found as seen in SADs. We compare data from multiple SADs and dipolarization fronts to show that the observational signatures implied in the corona can be directly observed in similar plasma regimes in the magnetosphere, strongly favoring the interpretation of SADs as wakes behind retracting loops.

Maximizing prosthetic valve size with the Top Hat supra-annular aortic valve

DEFF Research Database (Denmark)

Aagaard, Jan; Geha, Alexander S.

2007-01-01

BACKGROUND AND AIM OF THE STUDY: The CarboMedics Top Hat supra-annular aortic valve allows a one-size (and often two-size) increase over the standard intra-annular valve. This advantage should minimize the risk of patient-prosthesis mismatch, where the effective prosthetic valve orifice area....... This study evaluates the authors' clinical experience with Top Hat supra-annular aortic valve size selection, and the technical aspects of implantation. METHODS: Between January 1999 and October 2005, a total of 251 consecutive patients underwent 252 aortic valve replacements with Top Hat supra...... required unplanned coronary bypass, and 30-day mortality was 2.0% (5/251), indicating a good safety profile for the valves implanted in this series. CONCLUSION: The general distribution of implant sizes in the US indicates that cardiac surgeons may be under-sizing the Top Hat supra-annular aortic valve...

An Exploration of Heating Mechanisms in a Supra-arcade Plasma Sheet Formed after a Coronal Mass Ejection

Energy Technology Data Exchange (ETDEWEB)

Reeves, Katharine K. [Harvard-Smithsonian Center for Astrophysics, 60 Garden St. MS 58, Cambridge, MA 02138 (United States); Freed, Michael S.; McKenzie, David E. [Montana State University, Bozeman, MT 59717 (United States); Savage, Sabrina L., E-mail: kreeves@cfa.harvard.edu [NASA Marshall Space Flight Center, Huntsville, AL 35812 (United States)

2017-02-10

We perform a detailed analysis of the thermal structure of the region above the post-eruption arcade for a flare that occurred on 2011 October 22. During this event, a sheet of hot plasma is visible above the flare loops in the 131 Å bandpass of the Atmospheric Imaging Assembly (AIA) on the Solar Dynamics Observatory . Supra-arcade downflows (SADs) are observed traveling sunward through the post-eruption plasma sheet. We calculate differential emission measures using the AIA data and derive an emission measure weighted average temperature in the supra-arcade region. In areas where many SADs occur, the temperature of the supra-arcade plasma tends to increase, while in areas where no SADs are observed, the temperature tends to decrease. We calculate the plane-of-sky velocities in the supra-arcade plasma and use them to determine the potential heating due to adiabatic compression and viscous heating. Of the 13 SADs studied, 10 have noticeable signatures in both the adiabatic and the viscous terms. The adiabatic heating due to compression of plasma in front of the SADs is on the order of 0.1–0.2 MK/s, which is similar in magnitude to the estimated conductive cooling rate. This result supports the notion that SADs contribute locally to the heating of plasma in the supra-arcade region. We also find that in the region without SADs, the plasma cools at a rate that is slower than the estimated conductive cooling, indicating that additional heating mechanisms may act globally to keep the plasma temperature high.

An Exploration of Heating Mechanisms in a Supra-arcade Plasma Sheet Formed after a Coronal Mass Ejection

International Nuclear Information System (INIS)

Reeves, Katharine K.; Freed, Michael S.; McKenzie, David E.; Savage, Sabrina L.

2017-01-01

We perform a detailed analysis of the thermal structure of the region above the post-eruption arcade for a flare that occurred on 2011 October 22. During this event, a sheet of hot plasma is visible above the flare loops in the 131 Å bandpass of the Atmospheric Imaging Assembly (AIA) on the Solar Dynamics Observatory . Supra-arcade downflows (SADs) are observed traveling sunward through the post-eruption plasma sheet. We calculate differential emission measures using the AIA data and derive an emission measure weighted average temperature in the supra-arcade region. In areas where many SADs occur, the temperature of the supra-arcade plasma tends to increase, while in areas where no SADs are observed, the temperature tends to decrease. We calculate the plane-of-sky velocities in the supra-arcade plasma and use them to determine the potential heating due to adiabatic compression and viscous heating. Of the 13 SADs studied, 10 have noticeable signatures in both the adiabatic and the viscous terms. The adiabatic heating due to compression of plasma in front of the SADs is on the order of 0.1–0.2 MK/s, which is similar in magnitude to the estimated conductive cooling rate. This result supports the notion that SADs contribute locally to the heating of plasma in the supra-arcade region. We also find that in the region without SADs, the plasma cools at a rate that is slower than the estimated conductive cooling, indicating that additional heating mechanisms may act globally to keep the plasma temperature high.

Comparison of NMR and crystal structures for the proteins TM1112 and TM1367

International Nuclear Information System (INIS)

Mohanty, Biswaranjan; Serrano, Pedro; Pedrini, Bill; Jaudzems, Kristaps; Geralt, Michael; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

NMR structures of the proteins TM1112 and TM1367 solved by the JCSG in solution at 298 K could be superimposed with the corresponding crystal structures at 100 K with r.m.s.d. values of <1.0 Å for the backbone heavy atoms. For both proteins the structural differences between multiple molecules in the asymmetric unit of the crystals correlated with structural variations within the bundles of conformers used to represent the NMR solution structures. A recently introduced JCSG NMR structure-determination protocol, which makes use of the software package UNIO for extensive automation, was further evaluated by comparison of the TM1112 structure obtained using these automated methods with another NMR structure that was independently solved in another PSI center, where a largely interactive approach was applied. The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper-limit distance constraints derived from the molecular models that represent the results of structure

Contributions of different degrees of freedom to thermal transport in the C60 molecular crystal

Science.gov (United States)

Kumar, Sushant; Shao, Cheng; Lu, Simon; McGaughey, Alan J. H.

2018-03-01

Three models of the C60 molecular crystal are studied using molecular dynamics simulations to resolve the roles played by intermolecular and intramolecular degrees of freedom (DOF) in its structural, mechanical, and thermal properties at temperatures between 35 and 400 K. In the full DOF model, all DOF are active. In the rigid body model, the intramolecular DOF are frozen, such that only center of mass (COM) translations and molecular rotations/librations are active. In the point mass model, the molecule is replaced by a point mass, such that only COM translations are active. The zero-pressure lattice constants and bulk moduli predicted from the three models fall within ranges of 0.15 and 20%. The thermal conductivity of the point mass model is the largest across the temperature range, showing a crystal-like temperature dependence (i.e., it decreases with increasing temperature) due to the presence of phonon modes associated with the COM translations. The rigid body model thermal conductivity is the smallest and follows two distinct regimes. It is crystal-like at low temperatures and becomes temperature invariant at high temperatures. The latter is typical of the behavior of an amorphous material. By calculating the rotational diffusion coefficient, the transition between the two regimes is found to occur at the temperature where the molecules begin to rotate freely. Above this temperature, phonons related to COM translations are scattered by the rotational DOF. The full DOF model thermal conductivity is larger than that of the rigid body model, indicating that intramolecular DOF contribute to thermal transport.

Crystal and molecular structures of sixteen charge-assisted hydrogen bond-mediated diisopropylammonium salts from different carboxylic acids

Science.gov (United States)

Lin, Zhihao; Hu, Kaikai; Jin, Shouwen; Ding, Aihua; Wang, Yining; Dong, Lingfeng; Gao, Xingjun; Wang, Daqi

2017-10-01

salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the sixteen investigated crystals the NH groups in the diisopropylamine are protonated when the carboxylic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond formation between the ammonium and the deprotonated COOH groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 6, 8, 9, 10, 12, 13, 14, 15, and 16. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O/CH3sbnd O, CH-π/CH3-π, CH3-Cπ, N-π, and π-π associations contribute to the stabilization and expansion of the total structures. For the coexistence of the various weak interactions these structures adopted homo or hetero supramolecular synthons or both.

Post-magmatic structural evolution of the Troodos Ophiolite Pillow Lavas revealed by microthermometry within vein precipitates, with application to Alpine-Mediterranean supra-subduction zone settings

Science.gov (United States)

Kurz, W.; Quandt, D.; Micheuz, P.; Krenn, K.

2017-12-01

The Troodos ophiolite, Cyprus, is one of the best preserved ophiolites. Based on geochemical data a supra-subduction zone (SSZ) setting was proposed. Microtextures and fluid inclusions of veins and vesicles within the Pillow Lavas record the post-magmatic structural and geochemical evolution of this SSZ beginning at 75 Ma. Three different vein types from the Upper and Lower Pillow Lavas are distinguished and imply vein precipitation under a dominant extensional regime: (1) syntaxial calcite-, quartz- and zeolite-bearing veins are interpreted as mineralized extension fractures that were pervaded by seawater. This advective fluid flow in an open system changed later into a closed system characterized by geochemical self-organization. (2) Blocky and (3) antitaxial fibrous calcite veins are associated with brecciation due to hydrofracturing and diffusion-crystallization processes, respectively. Based on aqueous fluid inclusion chemistry with seawater salinities in all studied vein types, representative fluid inclusion isochores crossed with calculated litho- and hydrostatic pressure conditions yield mineral precipitation temperatures between 180 and 210 °C, for veins and vesicles hosted in the Upper and Lower Pillow Lavas. This points to a heat source for the circulating seawater and implies that vein and vesicle minerals precipitated shortly after pillow lava crystallization under dominant isobaric cooling conditions. Compared to previous suggestions derived from secondary mineralization a less steep geothermal gradient of 200 °C from the Sheeted Dyke Complex to the Pillow Lavas of the Troodos SSZ is proposed. Further fossil and recent SSZ like the Mirdita ophiolite, Albania, the South-Anatolian ophiolites, Turkey, and the Izu-Bonin fore arc, respectively, reveal similar volcanic sequences. Vein samples recovered during International Ocean Discovery Program expedition 351 and 352 in the Izu-Bonin back and fore arc, respectively, indicate also seawater infiltration

Molecular Weight and Crystallization Temperature Effects on Poly(ethylene terephthalate (PET Homopolymers, an Isothermal Crystallization Analysis

Directory of Open Access Journals (Sweden)

Leonardo A. Baldenegro-Perez

2014-02-01

Full Text Available The isothermal crystallization of poly(ethylene terephthalate (PET homopolymers with different molecular weight was studied in a wide temperature range (140–230 °C using different experimental techniques. Three different morphological regions, labeled r1, r2 and r3, were distinguished as a function of crystallization temperature (Tc. In r1 (low Tc crystallized samples were characterized by a low crystalline degree with a small spherulite texture containing thin crystals. In r2 (intermediate Tc samples showed medium size spherulites composed of two distinct crystalline families (thin and thick crystals. In this temperature range, the crystallization exhibited a maximum value and it was associated with a high content of secondary crystals. In r3 (high Tc, samples presented considerable amorphous zones and regions consisting of oversized spherulites containing only thick crystals. Time-resolved wide-angle X-ray diffraction measurements, using synchrotron radiation, indicated a rapid evolution of the crystalline degree within the second region, in contrast with the quite slow evolution observed in the third region. On the other hand, by small-angle X-ray scattering (SAXS and time-resolved SAXS experiment, it was found that the long period (L as well as the lamellar thickness (lc increase as a function of Tc, corroborating the formation of the thickest crystals in the third region. From all these observations, a morphological model was proposed for each region.

Molecular dynamics studies of the ion beam induced crystallization in silicon

International Nuclear Information System (INIS)

Marques, L.A.; Caturla, M.J.; Huang, H.

1995-01-01

We have studied the ion bombardment induced amorphous-to-crystal transition in silicon using molecular dynamics techniques. The growth of small crystal seeds embedded in the amorphous phase has been monitored for several temperatures in order to get information on the effect of the thermal temperature increase introduced by the incoming ion. The role of ion-induced defects on the growth has been also studied

Structural transitions in crystals of native aspartate carbamoyltransferase

International Nuclear Information System (INIS)

Gouaux, J.E.; Lipscomb, W.N.

1989-01-01

Screened precession x-ray photographs of crystals of native aspartate carbamoyltransferase ligated with L-aspartate and phosphate reveal the presence of a crystal unit-cell dimension that is intermediate between the T (tense) and R (relaxed) states. Characterizing the intermediate (I) crystal is a c-axis unit-cell dimension of 149 angstrom, halfway between the c-axis length of the T (c = 142 angstrom) and R (c = 156 angstrom) states, in the space group P321. Preservation of the P321 space group indicates that the intermediate crystal form retains a threefold axis of symmetry, and therefore the enzyme has at minimum a threefold axis; however, it is not known whether the molecular twofold axis is conserved. The I crystals are formed by soaking T-state crystals with L-aspartate and phosphate. By raising the concentration of L-aspartate the authors can further transform the I crystals, without fragmentation, to a form that has the same unit-cell dimensions as R-state crystals grown in the presence of N-(phosphonoacetyl)-L-aspartate

Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline–3-hydroxy-4-methoxybenzaldehyde

International Nuclear Information System (INIS)

Sharma, K.P.; Reddi, R.S.B.; Bhattacharya, S.; Rai, R.N.

2012-01-01

The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV–Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied. - Graphical abstarct: Exploiting phase diagram study and solvent free synthesis a novel compound was synthesized and its single crystal growth, atomic packing, energy band gap and refractive index were studied. Highlights: ► Novel organic complex was synthesized using Green or solvent free synthesis. ► Phase diagram study provided the information to identify the worthy composition of novel complex. ► The single crystal of the sufficient size was grown from the ethanol solution. ► Crystal analysis suggested that the covalent bond is formed between the two parent compounds. ► The transmittance of the crystal was found to be 70% and it was transparent from 412 to 850 nm.

Photonics of liquid-crystal structures: A review

Energy Technology Data Exchange (ETDEWEB)

Palto, S. P., E-mail: palto@online.ru; Blinov, L M; Barnik, M I; Lazarev, V V; Umanskii, B A; Shtykov, N M [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2011-07-15

The original results of studies of the electro-optical and laser effects which have been performed at the Laboratory of Liquid Crystals of the Institute of Crystallography, Russian Academy of Sciences, over the last few years are reviewed. Cholesteric liquid crystals as vivid representatives of photonic structures and their behavior in an electric field are considered in detail. The formation of higher harmonics in the periodic distribution of the director field in a helical liquid crystal structure and, correspondingly, the new (anharmonic) mode of electro-optical effects are discussed. Another group of studies is devoted to bistable light switching by an electric field in chiral nematics. Polarization diffraction gratings controlled by an electric field are also considered. The results of studies devoted to microlasers on various photonic structures with cholesteric and nematic liquid crystals are considered in detail. Particular attention is given to the new regime: leaky-mode lasing. Designs of liquid crystal light amplifiers and their polarization, field, and spectral characteristics are considered in the last section.

Crystal structure of 2,5-dimethylanilinium salicylate

Directory of Open Access Journals (Sweden)

A. Mani

2015-09-01

Full Text Available The title molecular salt, C8H12N+·C7H5O3− arose from the proton-transfer reaction between 2,5-xylidine and salicylic acid. In the anion, the dihedral angle between the planes of the aromatic ring and the –CO2− group is 11.08 (8°; this near planarity is consolidated by an intramolecular O—H...O hydrogen bond. In the crystal, the components are connected by N—H...O hydrogen bonds, with all three O atoms in the anion acting as acceptors; the result is a [100] chain. The structure also features weak C—H...O bonds and aromatic π–π stacking [centroid-to-centroid distance = 3.7416 (10 Å] interactions, which lead to a three-dimensional network.

Regional Themes and Global Means in Supra-National Higher Education Policy

Science.gov (United States)

Watson, Pam

2009-01-01

The supra-national level has become increasingly important in educational policy formulation. This paper describes and compares two settings in which growth in these supra-national policies is evident--in Europe and in Africa. Key themes arising in policy documents in each context are examined. A distinction is drawn in analysis between themes…

Steady state operation and control experiments on Tore Supra

International Nuclear Information System (INIS)

Saint-Laurent, F.

2000-01-01

The main programme of the Tore Supra tokamak is to investigate the route towards long pulse plasma discharges. Tore Supra is thus equipped with a superconducting toroidal magnet, a full set of actively cooled plasma facing components, and a heating and current drive capability based on high power RF systems connected to actively cooled antennas. After pioneering investigations using the LHCD system alone (2 min and zero loop voltage discharges), recent efforts have concentrated on finding scenarios to couple the two RF heating systems in order to perform high power, long duration discharges. To this aim, 6.5 MW, 25 s as well as 4 MW, 60 s discharges have been successfully achieved. At these high power levels, the plasma-wall interaction becomes a critical issue, and recycling fluxes must be controlled to maintain density and to avoid plasma contamination. All these results contributed to the validation of the upgrade of the Tore Supra first wall components (CIEL project) scheduled for 2000. (author)

Supra-molecular networks for CO2 capture

Science.gov (United States)

Sadowski, Jerzy; Kestell, John

Utilizing capabilities of low-energy electron microscopy (LEEM) for non-destructive interrogation of the real-time molecular self-assembly, we have investigated supramolecular systems based on carboxylic acid-metal complexes, such as trimesic and mellitic acid, doped with transition metals. Such 2D networks can act as host systems for transition-metal phthalocyanines (MPc; M = Fe, Ti, Sc). The electrostatic interactions of CO2 molecules with transition metal ions can be tuned by controlling the type of TM ion and the size of the pore in the host network. We further applied infrared reflection-absorption spectroscopy (IRRAS) to determine of the molecular orientation of the functional groups and the whole molecule in the 2D monolayers of carboxylic acid. The kinetics and mechanism of the CO2 adsorption/desorption on the 2D molecular network, with and without the TM ion doping, have been also investigated. This research used resources of the Center for Functional Nanomaterials, which is the U.S. DOE Office of Science User Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.

Major progress on tore supra toward steady state operation of tokamaks

International Nuclear Information System (INIS)

Saoutic, Y.

2003-01-01

During winter 2000-2001, a major upgrade of the internal components of Tore Supra has been completed that increased the heat extraction capability to 25 MW in steady state. Operating Tore Supra in this new configuration has produced a wealth of new results. The highlights of the 2002 long duration discharges campaign are: 4 minutes 25 seconds long discharges with an integrated energy of 0.75 GJ, which is three time higher than the old Tore Supra world record; recharge of the primary transformer by Lower Hybrid Current Drive (LHCD) for about 1 minute; 4 minutes long LHCD pulses; 1 minute long Ion Cyclotron Resonant Heating (ICRH) pulse (0.11 GJ of ICRH injected energy). Beyond the quantitative step, significant qualitative progress in the steady state nature of the discharge has been accomplished: contrary to the situation in the old Tore Supra configuration, the plasma density is perfectly controlled by active pumping over the overall shot duration. The duration of Tore Supra discharges is sufficient to allow the complete diffusion of the resistive current. Surprising new physics is revealed in such discharges when approaching zero loop voltage. Slow central electron temperature oscillations have been observed in a variety of situations. Such oscillations are not likely to be linked to any MHD instabilities and probably results from an interplay between current profile shape, LHCD power deposition and transport. Analysis of the temperature gradient in the core region shows a very interesting behaviour and the normalised temperature gradient length is compared to the critical thresholds. Finally, the performance of heating and current drive systems and the observations made of the interior of Tore Supra after the long duration discharges campaign are reported. (author)

Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.

Science.gov (United States)

Dahms, Sven O; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E

2013-02-01

Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.

Crystal Structures of Murine Carnitine Acetyltransferase in Ternary Complexes with Its Substrates

Energy Technology Data Exchange (ETDEWEB)

Hsiao,Y.; Jogl, G.; Tong, L.

2006-01-01

Carnitine acyltransferases catalyze the reversible exchange of acyl groups between coenzyme A (CoA) and carnitine. They have important roles in many cellular processes, especially the oxidation of long-chain fatty acids in the mitochondria for energy production, and are attractive targets for drug discovery against diabetes and obesity. To help define in molecular detail the catalytic mechanism of these enzymes, we report here the high resolution crystal structure of wild-type murine carnitine acetyltransferase (CrAT) in a ternary complex with its substrates acetyl-CoA and carnitine, and the structure of the S554A/M564G double mutant in a ternary complex with the substrates CoA and hexanoylcarnitine. Detailed analyses suggest that these structures may be good mimics for the Michaelis complexes for the forward and reverse reactions of the enzyme, representing the first time that such complexes of CrAT have been studied in molecular detail. The structural information provides significant new insights into the catalytic mechanism of CrAT and possibly carnitine acyltransferases in general.

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

Energy Technology Data Exchange (ETDEWEB)

Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de [MPI for Medical Research, Heidelberg (Germany); Brosi, Richard W. W. [Freie Universitat Berlin, Berlin (Germany); Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten [MPI for Medical Research, Heidelberg (Germany); Seidel, Ralf [MPI for Molecular Physiology, Dortmund (Germany); Shoeman, Robert L.; Zimmermann, Sabine [MPI for Medical Research, Heidelberg (Germany); Bittl, Robert [Freie Universitat Berlin, Berlin (Germany); Schlichting, Ilme; Reinstein, Jochen [MPI for Medical Research, Heidelberg (Germany)

2013-08-01

The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

Crystal structure of a human single domain antibody dimer formed through V(H-V(H non-covalent interactions.

Directory of Open Access Journals (Sweden)

Toya Nath Baral

Full Text Available Single-domain antibodies (sdAbs derived from human V(H are considered to be less soluble and prone to aggregate which makes it difficult to determine the crystal structures. In this study, we isolated and characterized two anti-human epidermal growth factor receptor-2 (HER2 sdAbs, Gr3 and Gr6, from a synthetic human V(H phage display library. Size exclusion chromatography and surface plasmon resonance analyses demonstrated that Gr3 is a monomer, but that Gr6 is a strict dimer. To understand this different molecular behavior, we solved the crystal structure of Gr6 to 1.6 Å resolution. The crystal structure revealed that the homodimer assembly of Gr6 closely mimics the V(H-V(L heterodimer of immunoglobulin variable domains and the dimerization interface is dominated by hydrophobic interactions.

Supra-thermal charged particle energies in a low pressure radio-frequency electrical discharge in air

International Nuclear Information System (INIS)

Littlefield, R.G.

1976-01-01

Velocity spectra of supra-thermal electrons escaping from a low-pressure radio-frequency discharge in air have been measured by a time-of-flight method of original design. In addition, the energy spectra of the supra-thermal electrons and positive ions escaping from the rf discharge have been measured by a retarding potential method. Various parameters affecting the energy of the supra-thermal charged particles are experimentally investigated. A model accounting for the supra-thermal charged particle energies is developed and is shown to be consistent with experimental observations

Comparison of multiple crystal structures with NMR data for engrailed homeodomain

Energy Technology Data Exchange (ETDEWEB)

Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

2008-03-15

Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

Epitaxial Growth of an Organic p-n Heterojunction: C60 on Single-Crystal Pentacene.

Science.gov (United States)

Nakayama, Yasuo; Mizuno, Yuta; Hosokai, Takuya; Koganezawa, Tomoyuki; Tsuruta, Ryohei; Hinderhofer, Alexander; Gerlach, Alexander; Broch, Katharina; Belova, Valentina; Frank, Heiko; Yamamoto, Masayuki; Niederhausen, Jens; Glowatzki, Hendrik; Rabe, Jürgen P; Koch, Norbert; Ishii, Hisao; Schreiber, Frank; Ueno, Nobuo

2016-06-01

Designing molecular p-n heterojunction structures, i.e., electron donor-acceptor contacts, is one of the central challenges for further development of organic electronic devices. In the present study, a well-defined p-n heterojunction of two representative molecular semiconductors, pentacene and C60, formed on the single-crystal surface of pentacene is precisely investigated in terms of its growth behavior and crystallographic structure. C60 assembles into a (111)-oriented face-centered-cubic crystal structure with a specific epitaxial orientation on the (001) surface of the pentacene single crystal. The present experimental findings provide molecular scale insights into the formation mechanisms of the organic p-n heterojunction through an accurate structural analysis of the single-crystalline molecular contact.

Crystal structures of the ligand-binding region of uPARAP

DEFF Research Database (Denmark)

Yuan, Cai; Jürgensen, Henrik J; Engelholm, Lars H

2016-01-01

The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix...... remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH 7.4 in Ca(2+)-bound and Ca(2+)-free forms. The first domain....... These LLRs undergo a Ca(2+)-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformation of uPARAP. Our results provide a molecular mechanism to support the structural flexibility of uPARAP, and shed light on the structural flexibility of other...

Crystal structure and thin film morphology of BBL ladder polymer

Energy Technology Data Exchange (ETDEWEB)

Song, H H [Department of Macromolecular Science, Han Nam University, Taejon (Korea, Republic of); Fratini, A V [Department of Chemistry, University of Dayton, Dayton, OH (United States); Chabinyc, M [Department of Chemistry, University of Dayton, Dayton, OH (United States); Price, G E [University of Dayton Research, Dayton, OH (United States); Agrawal, A K [Systran Corporation, Dayton, OH (United States); Wang, C S [University of Dayton Research, Dayton, OH (United States); Burkette, J [University of Dayton Research, Dayton, OH (United States); Dudis, D S [Materials Directorate, Wright Laboratory, Wright-Patterson Air Force Base, OH (United States); Arnold, F E [Materials Directorate, Wright Laboratory, Wright-Patterson Air Force Base, OH (United States)

1995-03-01

Crystal structure and morphology of poly[7-oxo-7H-benz(d,e)imidazo(4`,5`:5,6)-benzimidazo(2,1-a)isoquinoline-3,4:10,11-tetrayl-10-carbonyl] (BBL) ladder-like polymer were studied. The polymer forms a two-dimensional lattice of nematic liquid crystalline structure. An orthorhombic unit cell with cell parameters of a=7.87 b=3.37 c=11.97A was determined from the fiber diffraction pattern. In thin films, the rigid chains spontaneously form a layered structure across the film thickness, but in a very unusual manner, i.e. the very large molecular plane is standing perpendicularly to the film surface plane. The results are identical to our recent results of poly(p-phenylene benzobisthiazole) (PBT) film [7]. The polymer, however, lost its anisotropic order upon extrusion into a film and resulted in a fiber-like structure. (orig.)

Crystal structure of 2-pentyloxybenzamide

Directory of Open Access Journals (Sweden)

Bernhard Bugenhagen

2014-10-01

Full Text Available In the title molecule, C12H17NO2, the amide NH2 group is oriented toward the pentyloxy substituent and an intramolecular N—H...O hydrogen bond is formed with the pentyloxy O atom. The benzene ring forms dihedral angles of 2.93 (2 and 5.60 (2° with the amide group and the pentyloxy group mean planes, respectively. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with their molecular planes parallel, but at an offset of 0.45 (1 Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121 and the other in a column approximately parallel to (1-21. The two planes form a dihedral angle of 85.31 (2°, and are linked via C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional framework structure.

Steady-State Operation in Tore Supra

Science.gov (United States)

Hoang, G. T.; Tore Supra, Equipe

1999-11-01

The Tore Supra superconducting tokamak is devoted to steady-state operation. The CIEL (French acronym for internal component and limiter) project( LIPA, M., et al., Proc. of the 17th IEEE/NPSS Symp. on Fus. Engineering, San Diego, USA, 1997.) consists of a complete upgrade of the inner chamber of Tore Supra, planned to be installed during the year 2000. This project will allow physics scenarios with up to 24 MW of radio frequency heating and current drive (typically 8 - 10 MW of ICRF, 10 - 12 MW of LHCD and 2 MW of ECRF) in stationary plasmas up to 1000 s, with active particle control. This paper presents an overview of the experiments planned to explore the properties, such as the confinement and MHD stability, of various heating and current drive scenarios for long duration discharges. The expected performance for the CIEL phase is also reported.

Edge density profile measurements by X-mode reflectometry on Tore Supra

International Nuclear Information System (INIS)

Clairet, F.; Bottereau, C.; Chareau, J.M.; Paume, M.; Sabot, R.

2000-10-01

A broadband reflectometer operating in the frequency range 50-75 GHz has been developed on Tore Supra to measure electron density profiles at the edge. The system uses extraordinary mode polarization and performs routine measurements in 20 μs with a heterodyne detection to ensure a high dynamic range sensitivity. It allows separate phase and amplitude information of the signal. The density profiles are fully automatically calculated from the raw phase. The initialization is done with an automatic detection of the first cut-off from the amplitude of the reflected signal with accuracy up to ±0.5 cm. The profiles are now part of the public database of Tore Supra (TS) and can provide details of density structures better than the centimeter range. High reliability of the measurements for various plasma conditions make this diagnostic an ideal tool to study specific edge plasma physics with given examples on detached plasma behaviour and RF antenna-plasma coupling processes. It also is shown how the presence of suprathermal electrons may perturb the measurements. (authors)

Nanoparticles in liquid crystals, and liquid crystals in nanoparticles

Science.gov (United States)

de Pablo, Juan

2015-03-01

Liquid crystals are remarkably sensitive to interfacial interactions. Small perturbations at a liquid crystal interface, for example, can be propagated over relatively long length scales, thereby providing the basis for a wide range of applications that rely on amplification of molecular events into macroscopic observables. Our recent research efforts have focused on the reverse phenomenon; that is, we have sought to manipulate the interfacial assembly of nanoparticles or the organization of surface active molecules by controlling the structure of a liquid crystal. This presentation will consist of a review of the basic principles that are responsible for liquid crystal-mediated interactions, followed by demonstrations of those principles in the context of two types of systems. In the first, a liquid crystal is used to direct the assembly of nanoparticles; through a combination of molecular and continuum models, it is found that minute changes in interfacial energy and particle size lead to liquid-crystal induced attractions that can span multiple orders of magnitude. Theoretical predictions are confirmed by experimental observations, which also suggest that LC-mediated assembly provides an effective means for fabrication of plasmonic devices. In the second type of system, the structure of a liquid crystal is controlled by confinement in submicron droplets. The morphology of the liquid crystal in a drop depends on a delicate balance between bulk and interfacial contributions to the free energy; that balance can be easily perturbed by adsorption of analytes or nanoparticles at the interface, thereby providing the basis for development of hierarchical assembly of responsive, anisotropic materials. Theoretical predictions also indicate that the three-dimensional order of a liquid crystal can be projected onto a two-dimensional interface, and give rise to novel nanostructures that are not found in simple isotropic fluids.

CRYSTAL-STRUCTURE OF DEOXYGENATED LIMULUS-POLYPHEMUS SUBUNIT-II HEMOCYANIN AT 2.18-ANGSTROM RESOLUTION - CLUES FOR A MECHANISM FOR ALLOSTERIC REGULATION

NARCIS (Netherlands)

HAZES, B; MAGNUS, KA; BONAVENTURA, C; BONAVENTURA, J; DAUTER, Z; KALK, KH; HOL, WGJ

The crystal structure of Limulus polyphemus subunit type II hemocyanin in the deoxygenated state has been determined to a resolution of 2.18 angstrom. Phase information for this first structure of a cheliceratan hemocyanin was obtained by molecular replacement using the crustacean hemocyanin

Structural analysis of CYP2C9 and CYP2C5 and an evaluation of commonly used molecular modeling techniques

DEFF Research Database (Denmark)

Afzelius, Lovisa; Raubacher, Florian; Karlén, Anders

2004-01-01

, newly built homology models, and repeated molecular dynamics simulations. The CPCA was based on molecular interaction fields focused on the active site regions of the proteins and include detailed amino acid analysis. The comparison of the CYP2C9 and CYP2C5 crystal structures revealed differences...... improved the similarity to the crystal target in some cases and could be recommended even though it requires a careful manual alignment process. The application of molecular dynamics simulations to highly flexible proteins such as cytochromes P450 is also explored and the information is extracted...... in the flexible regions such as the B-C and F-G loop and the N and C termini. Cross homology models of CYP2C9 and CYP2C5, using their respective crystal structures as templates, indicated that such models were more similar to their templates than to their target proteins. Inclusion of multiple templates slightly...

Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger.

Science.gov (United States)

Suyama, Yousuke; Muraki, Norifumi; Kusunoki, Masami; Miyake, Hideo

2017-10-01

Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the C α atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.

Liquid Crystals in Decorative and Visual Arts

Science.gov (United States)

Makow, David

The following sections are included: * INTRODUCTION * PIGMENT AND STRUCTURAL COLOURS AND THEIR RELEVANCE TO LIQUID CRYSTALS * LIQUID CRYSTAL MATERIALS AND TECHNIQUES FOR DECORATIVE AND VISUAL ARTS * Free cholesteric liquid crystals (FCLC's) * Encapsulated liquid crystals (ECLC's) * Nonsteroid Chiral nematics * Polymers with liquid crystalline properties (PLCs) * COLOUR PROPERTIES OF CHOLESTERIC LIQUID CRYSTALS (CLC's) * Molecular structure and the mechanism of colour production * Dependence of perceived colours on the angle of illumination and viewing * Dependence of perceived colours on temperature * Additive colour properties * Methods of doubling the peak reflectance of cholesteric liquid crystals * Colour gamut * Colours of superimposed and pigmented coatings * Colours in transmission * ACKNOWLEDGEMENTS * REFERENCES

Single crystal EPR study at 95 GHz of a large Fe based molecular nanomagnet: toward the structuring of magnetic nanoparticle properties.

Science.gov (United States)

Castelli, L; Fittipaldi, M; Powell, A K; Gatteschi, D; Sorace, L

2011-08-28

A W-band single-crystal EPR study has been performed on a molecular cluster comprising 19 iron(III) ions bridged by oxo- hydroxide ions, Fe(19), in order to investigate magnetic nanosystems with a behavior in between the one of Magnetic NanoParticles (MNP) and that of Single Molecule Magnets (SMM). The Fe(19) has a disk-like shape: a planar Fe(7) core with a brucite (Mg(OH)(2)) structure enclosed in a "shell" of 12 Fe(III) ions. EPR and magnetic measurements revealed an S = 35/2 ground state with an S = 33/2 excited state lying ∼ 8 K above. The presence of other low-lying excited states was also envisaged. Rhombic Zero Field Splitting (ZFS) tensors were determined, the easy axes lying in the Fe(19) plane for both the multiplets. At particular temperatures and orientations, a partially resolved fine structure could be observed which could not be distinguished in powder spectra, due to orientation disorder. The similarities of the EPR behavior of Fe(19) and MNP, together with the accuracy of single crystal analysis, helped to shed light on spectral features observed in MNP spectra, that is a sharp line at g = 2 and a low intensity transition at g = 4. Moreover, a theoretical analysis has been used to estimate the contribution to the total magnetic anisotropy of core and surface; this latter is crucial in determining the easy axis-type anisotropy, alike that of MNP surface. This journal is © The Royal Society of Chemistry 2011

Structure analysis on synthetic emerald crystals

Science.gov (United States)

Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

2013-05-01

Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

Crystal Structure of Escherichia coli L-Arabinose Isomerase (ECAI), The Putative Target of Biological Tagatose Production

Energy Technology Data Exchange (ETDEWEB)

Manjasetty,B.; Chance, M.

2006-01-01

Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 Angstroms resolution. The subunit structure of ECAI is organized into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.

Crystal structures of two solvates of (18-crown-6potassium acetate

Directory of Open Access Journals (Sweden)

Phil Liebing

2016-12-01

Full Text Available The crystal and molecular strutures of two solvated forms of [K(18c6]OAc (18c6 = 18-crown-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane and OAc = acetate were determined by single-crystal X-ray diffraction, namely (acetato-κ2O,O′(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium dihydrate, [K(CH3COO(C12H24O6]·2H2O (1 and (acetato-κ2O,O′aqua(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium acetic acid monosolvate [K(CH3COO(C12H24O6(H2O]·CH3COOH (2. In both compounds, the acetate anion is bonded to the potassium ion in a chelating fashion and the metal atom is consequently slightly displaced from the O6 plane of the crown ether. In the crystals, O—H...O hydrogen bonds lead to a polymeric ladder structure in the dihydrate 1, while the acetic acid hydrate 2 features inversion dimers.

Analysis of phase transitions and crystal structures of novel benzothiophene derivatives

Science.gov (United States)

Zhang, Shuo

Although single crystal X-ray diffraction remains the most important technique for analyzing periodically ordered structures at atomic resolution, single crystal X-ray diffraction of organic macromolecules is challenged by difficulty in growing single crystals of desired size and quality. Electron crystallography of organic macromolecules, on the other hand, is limited by image resolution due to radiation damage and highly dependent on high-resolution instrumentation. Novel alkylated benzothiophene derivatives synthesized previously can be readily fabricated into semiconductor devices for various applications (photodetectors, explosive sensors, field-effect transistors, light-emitting diodes, etc.) via solution process. The object of this research is to identify phase transitions of organic macromolecules of this kind via differential scanning calorimetry and temperature-resolved wide angle X-ray diffraction, and to determine their lattice parameters and space groups by reconstruction of their reciprocal space via transmission electron microscopy/selected area electron diffraction followed by refinement with X-ray diffraction, supplemented by polarized light microscopy. Computer simulation was performed to rationalize the molecular packing schemes, so as to understand the origin of their electronic performance from crystallographic perspective.

Structural studies of crystals of organic and organoelement compounds using modern quantum chemical calculations within the framework of the density functional theory

International Nuclear Information System (INIS)

Korlyukov, Alexander A; Antipin, Mikhail Yu

2012-01-01

The review generalizes the results of structural studies of crystals of organic and organometallic compounds by modern quantum chemical calculations within the framework of the density functional theory reported in the last decade. Features of the software for such calculations are discussed. Examples of the use of quantum chemical calculations for the studies of the electronic structure, spectroscopic and other physicochemical properties of molecular crystals are presented. The bibliography includes 223 references.

Synthesis, crystal growth, structural and physicochemical studies of novel binary organic complex: 4-chloroaniline-3-hydroxy-4-methoxybenzaldehyde

Energy Technology Data Exchange (ETDEWEB)

Sharma, K.P.; Reddi, R.S.B.; Bhattacharya, S. [Department of Chemistry, Centre of Advance Study, Banaras Hindu University, Varanasi-221005 (India); Rai, R.N., E-mail: rn_rai@yahoo.co.in [Department of Chemistry, Centre of Advance Study, Banaras Hindu University, Varanasi-221005 (India)

2012-06-15

The solid-state reaction, which is solvent free and green synthesis, has been adopted to explore the novel compound. The phase diagram of 4-chloroaniline (CA) and 3-hydroxy-4-methoxybenzaldehyde (HMB) system shows the formation of a novel 1:1 molecular complex, and two eutectics on either sides of complex. Thermochemical studies of complex and eutectics have been carried out for various properties such as heat of fusion, entropy of fusion, Jackson's parameters, interfacial energy and excess thermodynamic functions. The formation of molecular complex was also studied by IR, NMR, elemental analysis and UV-Vis absorption spectra. The single crystal of molecular complex was grown and its XRD study confirms the formation of complex and identifies the crystal structure and atomic packing of crystal of complex. Transmission spectra of grown crystal of the complex show 70% transmittance efficiency with cut off wavelength 412 nm. The band gap and refractive index of the crystal of complex have also been studied. - Graphical abstarct: Exploiting phase diagram study and solvent free synthesis a novel compound was synthesized and its single crystal growth, atomic packing, energy band gap and refractive index were studied. Highlights: Black-Right-Pointing-Pointer Novel organic complex was synthesized using Green or solvent free synthesis. Black-Right-Pointing-Pointer Phase diagram study provided the information to identify the worthy composition of novel complex. Black-Right-Pointing-Pointer The single crystal of the sufficient size was grown from the ethanol solution. Black-Right-Pointing-Pointer Crystal analysis suggested that the covalent bond is formed between the two parent compounds. Black-Right-Pointing-Pointer The transmittance of the crystal was found to be 70% and it was transparent from 412 to 850 nm.

Crystal structures of Schiff base derivatives of 1-(3,4,5-trimethoxybenzylidene)thiosemicarbazide and (E)-N′-(3-nitrobenzylidene)isonicotinohydrazide

Energy Technology Data Exchange (ETDEWEB)

Dileep, C. S., E-mail: dileep.mmp.phy@gmail.com; Sridhar, M. A. [Department of Studies in Physics, Manasagangotri, University of Mysore, Mysore-570006 (India); Mallesh, L. [Department of Chemistry, JSS College of Arts, Commerce and Science, Ooty Road, Mysore-570025 (India)

2014-04-24

The crystal structures of 1-(3,4,5-trimethoxybenzylidene)thiosemicarbazide (1) and N′-(3-nitrobenzylidene) isonicotinohydrazide (2) have been determined by single-crystal X-ray diffraction. In compound 1, the position of C8, O1, O2, O3 atoms are in a distorted trigonal planar geometry. The mean plane of 3,4,5-trimethoxybenzylidene ring forms a dihedral angle of 5.39(14)° with the mean plane of thiosemicarbazide group. In the structure, the molecular packing is stabilized by intermolecular N–H with diaresisN, O–H with diaresisS and intramolecular C–H with diaresisO hydrogen bonds. In compound 2, the position of C8 atom and N1 atom are in a distorted trigonal planar geometry. The mean plane of phenyl ring forms a dihedral angle of 8.09° with that of the pyridine ring. In the structure, the molecular packing is stabilized by intermolecular N–H with diaresisN and intramolecular C–H with diaresisO hydrogen bonds.

Lower hybrid current drive in Tore Supra and JET

International Nuclear Information System (INIS)

Moreau, D.; Gormezano, C.

1991-01-01

Recent Lower Hybrid Current Drive (LHCD) experiments in TORE SUPRA and JET are reported. Large multijunction launchers have allowed the coupling of 5MW to the plasma for several seconds with a maximum of 3.8 kW/cm 2 . Measurements of the scattering matrices of the antennae show good agreement with theory. The current drive efficiency in TORE SUPRA is about 0.2 x 10 20 Am -2 /W with LH power alone and reaches 0.4 x 10 20 Am -2 /W in JET thanks to a high volume-averaged electron temperature (1.9 keV) and also to a synergy between Lower Hybrid and Fast Magnetosonic Waves. At n e = 1.5 x 10 19 m -3 in TORE SUPRA, sawteeth are suppressed and m = 1MHD oscillations the frequency of which clearly depends on the amount of LH power are observed on soft X-rays, and also on non-thermal ECE. In Jet ICRH produced sawtooth free periods are extended by the application of LHCD and current profile broadening has been clearly observed consistent with off-axis fast electron populations. LH power modulation experiments performed in TORE SUPRA at n e = 4 x 10 19 m -3 show a delayed central electron heating despite the off-axis creation of suprathermal electrons, thus ruling out the possibility of a direct heating through central wave absorption. A possible explanation in terms of anomalous fast electron transport and classical slowing down would yield a diffusion coefficient of the order of 10 m 2 /s for the fast electrons. Finally, successful pellet fuelling of a partially LH driven plasma was obtained in TORE SUPRA, 28 successive pellets allowing the density to rise to n e = 4 x 10 19 m -3 . This could be achieved by switching the LH power off for 90 ms before each pellet injection, i.e. without modifying significantly the current density profile

Lower hybrid current drive in Tore Supra and jet

International Nuclear Information System (INIS)

Moreau, D.; Gormezano, C.

1991-07-01

Recent Lower Hybrid Current Drive (LHCD) experiments in TORE SUPRA and JET are reported. Large multijunction launchers have allowed the coupling of 5 MW to the plasma for several seconds with a maximum of 3.8 kW/cm 2 . Measurements of the scattering matrices of the antennae show good agreement with theory. The current drive efficiency in TORE SUPRA is about 0.2 x 10 20 Am -2 /W with LH power alone and reaches 0.4 x 10 20 Am -2 /W in JET thanks to a high volume-averaged electron temperature (1.9 keV) and also to a synergy between Lower Hybrid and Fast Magnetosonic Waves. At average n e = 1.5 x 10 19 m -3 in TORE SUPRA, sawteeth are suppressed and m = 1 MHD oscillations the frequency of which clearly depends on the amount of LH power are observed on soft X-rays, and also on non-thermal ECE. In JET ICRH produced sawtooth-free periods are extended by the application of LHCD (2.9 s. with 4 MW ICRH) and current profile broadening has been clearly observed consistent with off-axis fast electron populations. LH power modulation experiments performed in TORE SUPRA at average n e = 4 x 10 19 m -3 show a delayed central electron heating despite the off-axis creation of suprathermal electrons, thus ruling out the possibility of a direct heating through central wave absorption. A possible explanation in terms of anomalous fast electron transport and classical slowing down would yield a diffusion coefficient of the order of 10 m 2 /s for the fast electrons. Other interpretations such as an anomalous heat pinch or a central confinement enhancement cannot be excluded. Finally, successful pellet fuelling of a partially LH driven plasma was obtained in TORE SUPRA, 28 successive pellets allowing the density to rise to average n e = 4 x 10 19 m -3 . This could be achieved by switching the LH power off for 90 ms before each pellet injection, i.e. without modifying significantly the current density profile

NMR and molecular dynamics of small solutes in liquid crystals

International Nuclear Information System (INIS)

Luyten, P.R.

1984-01-01

NMR relaxation measurements, using a wide variety of modern pulse techniques, can yield valuable information about molecular motions. In this thesis the applicability of theories developed to describe spin relaxation phenomena in partially ordered media is studied for small solutes in liquid crystals. 1 H, 2 H, 13 C and 14 N relaxation measurements are interpreted by means of a model, in which fast anisotropic re-orientational motion in an orienting potential combined with contributions from cooperative fluctuations in the surrounding liquid crystal molecules, induce the observed frequency dependent relaxation behavior. (orig.)

Replica sizing strategy for aortic valve replacement improves haemodynamic outcome of the epic supra valve.

Science.gov (United States)

Gonzalez-Lopez, David; Faerber, Gloria; Diab, Mahmoud; Amorim, Paulo; Zeynalov, Natig; Doenst, Torsten

2017-10-01

Current sizing strategies suggest valve selection based on annulus diameter despite supra-annular placement of biological prostheses potentially allowing placement of a larger size. We assessed the frequency of selecting a larger prosthesis if prosthesis size was selected using a replica (upsizing) and evaluated its impact on haemodynamics. We analysed all discharge echocardiograms between June 2012 and June 2014, where a replica sizer was used for isolated aortic valve replacement (Epic Supra: 266 patients, Trifecta: 49 patients). Upsizing was possible in 71% of the Epic Supra valves (by 1 size: 168, by 2 sizes: 20) and in 59% of the Trifectas (by 1 size: 26, by 2 sizes: 3). Patients for whom upsizing was possible had the lowest pressure gradients within their annulus size groups. The difference was significant in annulus diameters of 21-22 or 25-26 mm (Epic Supra) and 23-24 mm (Trifecta). Trifecta gradients were the lowest. However, the ability to upsize the Epic Supra by 2 sizes eliminated the differences between Epic Supra and Trifecta. Upsizing did not cause intraoperative complications. Using replica sizers for aortic prosthesis size selection allows the implantation of bigger prostheses than recommended in most cases and reduces postoperative gradients, specifically for Epic Supra. © The Author 2017. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Synthesis, spectra, and the crystal structure of α-(3,3-dimethyl-3,4-dihydroisoquinolyl-1)-hydroxyiminoacetamide

International Nuclear Information System (INIS)

Sokol, V.I.; Davydov, V.V.; Kartashova, I.V.; Zaitsev, B.E.; Shklyaev, Yu.V.; Ryabov, M.A.; Sergienko, V.S.

1996-01-01

α-(3,3-Dimethyl-3,4-dihydroisoquinolyl-1)-hydroxyiminoacetamide (I) was synthesized, and its x-ray structure analysis was performed (Enraf-Nonius CAD-4 diffractometer; MoKα radiation; graphite monochromator; θ/2θ scan; 2θmax=56 deg. ; 2496 reflections with I≥2σ(I); and R=0.038). Crystals of I are monoclinic; a=11.67(1), b=8.365(3), and c=15.22(2) A; β=107.7(1) deg.; V=1415.2(2) A 3; ρ(calc)=1.236 g/cm3; Z=4; and sp. gr. P21/n. I crystallizes as a monohydrate, and its formula is C13H15N3O2·H2O. In a crystal, I exists in a azomethineoxime tautomeric form. The planes of amideoxime and dihydroisoquinoline moieties are nearly orthogonal to each other. According to IR and electronic spectra, when passing from crystal to solution the conformation of I changes only slightly. An effect of water molecules on the molecular structure of I is discussed

Structural Transitions in Cholesteric Liquid Crystal Droplets

Energy Technology Data Exchange (ETDEWEB)

Zhou, Ye; Bukusoglu, Emre; Martínez-González, José A.; Rahimi, Mohammad; Roberts, Tyler F.; Zhang, Rui; Wang, Xiaoguang; Abbott, Nicholas L.; de Pablo, Juan J.

2016-07-26

Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates.

The effect of temperature and pressure on the crystal structure of piperidine.

Science.gov (United States)

Budd, Laura E; Ibberson, Richard M; Marshall, William G; Parsons, Simon

2015-01-01

The response of molecular crystal structures to changes in externally applied conditions such as temperature and pressure are the result of a complex balance between strong intramolecular bonding, medium strength intermolecular interactions such as hydrogen bonds, and weaker intermolecular van der Waals contacts. At high pressure the additional thermodynamic requirement to fill space efficiently becomes increasingly important. The crystal structure of piperidine-d11 has been determined at 2 K and at room temperature at pressures between 0.22 and 1.09 GPa. Unit cell dimensions have been determined between 2 and 255 K, and at pressures up to 2.77 GPa at room temperature. All measurements were made using neutron powder diffraction. The crystal structure features chains of molecules formed by NH…N H-bonds with van der Waals interactions between the chains. Although the H-bonds are the strongest intermolecular contacts, the majority of the sublimation enthalpy may be ascribed to weaker but more numerous van der Waals interactions. Analysis of the thermal expansion data in the light of phonon frequencies determined in periodic DFT calculations indicates that the expansion at very low temperature is governed by external lattice modes, but above 100 K the influence of intramolecular ring-flexing modes also becomes significant. The principal directions of thermal expansion are determined by the sensitivity of different van der Waals interactions to changes in distance. The principal values of the strain developed on application of pressure are similarly oriented to those determined in the variable-temperature study, but more isotropic because of the need to minimise volume by filling interstitial voids at elevated pressure. Graphical AbstractThough H-bonds are important interactions in the crystal structure of piperidine, the response to externally-applied conditions are determined by van der Waals interactions.

Models of protein–ligand crystal structures: trust, but verify

Science.gov (United States)

Deller, Marc C.

2015-01-01

X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

Models of protein-ligand crystal structures: trust, but verify.

Science.gov (United States)

Deller, Marc C; Rupp, Bernhard

2015-09-01

X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

A step towards controlled fusion reactors: Tore Supra tokamak with superconducting magnets

International Nuclear Information System (INIS)

Turck, B.

1988-01-01

Tore Supra technology has to solve all the problems related to the development and the installaion of superconducting coils and associated cryogenic devices. Tore Supra will allow to get a significative experience to prepare next machines. Specifications and needs of tokamaks concerning the superconducting coils of future machines are recalled [fr

The Crystal Structures of Two Novel Cadmium-Picolinic Acid ...

African Journals Online (AJOL)

The crystal structures of two novel cadmium-picolinic acid complexes grown in aqueous solutions at selected pH values are reported. The structures are compared to expected solution species under the same conditions. The crystal structure of complex 1 exhibits a seven coordinate structure which contains a protonated ...

Synthesis and properties of large crystal of aluminum-deficient ultrasil molecular sieve materials

International Nuclear Information System (INIS)

Durrani, J.; Akhtar, J.; Chughtai, N.A.; Arif, M.; Saeed, K.; Ahmed, M.; Siddique, M.

2003-01-01

Large crystals of aluminum-deficient and silica rich molecular sieve materials such as Silicalite-I, Silicalite-II ZSM11-B and ZSM11-Fe have been synthesized hydro thermally from the aqueous silicate gel of (R/sub 2/O -SiO/sub 2/- B/sub 2/O/sub 3/ -Fe/sub 2/O/ sub 3/ -H/sub 2/O) using PTFE-lined stainless digestion bomb. The term R is a alkyl group. The synthesized materials were identified for crystallinity, thermal stability, phase, crystal structure, morphology and unit cell dimensions using thermogravimetry (TG/DTA), differential scanning calorimetric(DSC), X-ray diffraction (XRD), scanning electron microscopy (SEM) and other analytical techniques. All product materials were found to be white crystalline and crysto-graphically pure. Surface area and particle size distribution of materials were also ascertained. /sup 57/Fe Mossbauer spectroscopic studies on as-synthesized and calcined samples have confirmed the uniform dispersion of Fe/sup 3+/ ions in the tetrahedral framework of ZSM11-Fe material. (author)

Band structures in fractal grading porous phononic crystals

Science.gov (United States)

Wang, Kai; Liu, Ying; Liang, Tianshu; Wang, Bin

2018-05-01

In this paper, a new grading porous structure is introduced based on a Sierpinski triangle routine, and wave propagation in this fractal grading porous phononic crystal is investigated. The influences of fractal hierarchy and porosity on the band structures in fractal graidng porous phononic crystals are clarified. Vibration modes of unit cell at absolute band gap edges are given to manifest formation mechanism of absolute band gaps. The results show that absolute band gaps are easy to form in fractal structures comparatively to the normal ones with the same porosity. Structures with higher fractal hierarchies benefit multiple wider absolute band gaps. This work provides useful guidance in design of fractal porous phononic crystals.

Construction of crystal structure prototype database: methods and applications.

Science.gov (United States)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Construction of crystal structure prototype database: methods and applications

International Nuclear Information System (INIS)

Su, Chuanxun; Lv, Jian; Wang, Hui; Wang, Yanchao; Ma, Yanming; Li, Quan; Zhang, Lijun

2017-01-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery. (paper)

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis

Czech Academy of Sciences Publication Activity Database

Dostál, Jiří; Pecina, Adam; Hrušková-Heidingsfeldová, Olga; Marečková, L.; Pichová, Iva; Řezáčová, Pavlína; Lepšík, Martin; Brynda, Jiří

2015-01-01

Roč. 71, č. 12 (2015), s. 2494-2504 ISSN 1399-0047 R&D Projects: GA ČR(CZ) GA14-23022S Institutional support: RVO:61388963 ; RVO:68378050 Keywords : aspartic protease * Candida parapsilosis * Sapp2p * crystal structure * ultrahigh resolution * interaction energy * quantum mechanics Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 2.674, year: 2014

Molecular reorientation of dye doped nematic liquid crystals in the laser illumination

International Nuclear Information System (INIS)