Investigation of selected structural parameters in Fe 95Si 5 amorphous alloy during crystallization process

NASA Astrophysics Data System (ADS)

Fronczyk, Adam

2007-04-01

In this study, we report on a crystallization behavior of the Fe 95Si 5 metallic glasses using a differential scanning cabrimetry (DSC), and X-ray diffraction. The paper presents the results of experimental investigation of Fe 95Si 5 amorphous alloy, subjected to the crystallizing process by the isothermal annealing. The objective of the experiment was to determine changes in the structural parameters during crystallization process of the examined alloy. Crystalline diameter and the lattice constant of the crystallizing phase were used as parameters to evaluate structural changes in material.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Experimental and theoretical study of pure and doped crystals: Gd2O2S, Gd2O2S:Eu3+ and Gd2O2S:Tb3+

NASA Astrophysics Data System (ADS)

Wang, Fei; Chen, Xiumin; Liu, Dachun; Yang, Bin; Dai, Yongnian

2012-08-01

Quantum chemistry and experimental method were used to study on pure and doped Gd2O2S crystals in this paper. The band structure and DOS diagrams of pure and doped Gd2O2S crystals which calculated by using DFT (Density Functional Theory) method were illustrated to explain the luminescent properties of impurities in crystals. The calculations of the crystal structure were finished by using the program of CASTEP (Cambridge Sequential Total Energy Package). The samples showed the characteristic emissions of Tb3+ ions with 5D4-7FJ transitions and Eu3+ ions with 5D0-7FJ transitions which emit pure green luminescence and red luminescence respectively. The experimental excitation spectra of Tb3+ and Eu3+ doped Gd2O2S are in agreement of the DOS diagrams over the explored energy range, which has allowed a better understanding of different luminescence mechanisms of Tb3+ and Eu3+ in Gd2O2S crystals.

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

NASA Astrophysics Data System (ADS)

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.

TaRh2B2 and NbRh2B2: Superconductors with a chiral noncentrosymmetric crystal structure.

PubMed

Carnicom, Elizabeth M; Xie, Weiwei; Klimczuk, Tomasz; Lin, Jingjing; Górnicka, Karolina; Sobczak, Zuzanna; Ong, Nai Phuan; Cava, Robert J

2018-05-01

It is a fundamental truth in solid compounds that the physical properties follow the symmetry of the crystal structure. Nowhere is the effect of symmetry more pronounced than in the electronic and magnetic properties of materials-even the projection of the bulk crystal symmetry onto different crystal faces is known to have a substantial impact on the surface electronic states. The effect of bulk crystal symmetry on the properties of superconductors is widely appreciated, although its study presents substantial challenges. The effect of a lack of a center of symmetry in a crystal structure, for example, has long been understood to necessitate that the wave function of the collective electron state that gives rise to superconductivity has to be more complex than usual. However, few nonhypothetical materials, if any, have actually been proven to display exotic superconducting properties as a result. We introduce two new superconductors that in addition to having noncentrosymmetric crystal structures also have chiral crystal structures. Because the wave function of electrons in solids is particularly sensitive to the host material's symmetry, crystal structure chirality is expected to have a substantial effect on their superconducting wave functions. Our two experimentally obtained chiral noncentrosymmetric superconducting materials have transition temperatures to superconductivity that are easily experimentally accessible, and our basic property characterization suggests that their superconducting properties may be unusual. We propose that their study may allow for a more in-depth understanding of how chirality influences the properties of superconductors and devices that incorporate them.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Calligraphic Poling for WGM Resonators

NASA Technical Reports Server (NTRS)

Mohageg, Makan; Strekalov, Dmitry; Savchenkov, Anatoliy; Matsko, Andrey; Ilchenko, Vladimir; Maleki, Lute

2007-01-01

By engineering the geometry of a nonlinear optical crystal, the effective efficiency of all nonlinear optical oscillations can be increased dramatically. Specifically, sphere and disk shaped crystal resonators have been used to demonstrate nonlinear optical oscillations at sub-milliwatt input power when cs light propagates in a Whispering Gallery Mode (WGM) of such a resonant cavity. in terms of both device production and experimentation in quantum optics, some nonlinear optical effects with naturally high efficiency can occult the desired nonlinear scattering process. the structure to the crystal resonator. In this paper, I will discuss a new method for generating poling structures in ferroelectric crystal resonators called calligraphic poling. The details of the poling apparatus, experimental results and speculation on future applications will be discussed.

Luminescence spectra of a cholesteric photonic crystal

NASA Astrophysics Data System (ADS)

Dolganov, P. V.

2017-05-01

The transmission and luminescence spectra of a cholesteric photonic crystal doped with an organic dye are measured. The density of photon states is calculated using the material parameters obtained from the comparison of the experimental and theoretical spectra. The shape of the luminescence spectra is modified with respect to the density of photon states owing to the difference in the structure of the normal modes of the photonic crystal near the short-wavelength and long-wavelength edges of the photonic quasi-band gap upon the "pushing" of the photon states from the gap and to the nonvanishing orientation ordering of the luminescent molecules. The luminescence spectrum calculated taking into account the chiral structure of the photonic crystal agrees with the experimental spectrum.

Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

2010-05-01

Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

Control of morphology and crystal purity of InP nanowires by variation of phosphine flux during selective area MOMBE

NASA Astrophysics Data System (ADS)

Kelrich, A.; Dubrovskii, V. G.; Calahorra, Y.; Cohen, S.; Ritter, D.

2015-02-01

We present experimental results showing how the growth rate, morphology and crystal structure of Au-catalyzed InP nanowires (NWs) fabricated by selective area metal organic molecular beam epitaxy can be tuned by the growth parameters: temperature and phosphine flux. The InP NWs with 20-65 nm diameters are grown at temperatures of 420 and 480 °C with the PH3 flow varying from 1 to 9 sccm. The NW tapering is suppressed at a higher temperature, while pure wurtzite crystal structure is preferred at higher phosphine flows. Therefore, by combining high temperature and high phosphine flux, we are able to fabricate non-tapered and stacking fault-free InP NWs with the quality that other methods rarely achieve. We also develop a model for NW growth and crystal structure which explains fairly well the observed experimental tendencies.

Hydrostatic Compression of 2,4,6,8,10,12 hexanitrohexaaza isowurtzitane (CL20) Co Crystals

DTIC Science & Technology

2016-12-01

crystal with analyses of the unit cell volume, band structure , elastic coefficients, and optical absorption Approved for public release...studied and for each system the high pressure (to 50 GPa) unit cell parameters, bulk modulus, and estimates of the shock, particle, and sound ...List of Figures Fig. 1 Experimental unit cell structures of ε-CL20 and co-crystals. For each structure , the CL20 molecules are red and the guest

Combinatorial and High Throughput Discovery of High Temperature Piezoelectric Ceramics

DTIC Science & Technology

2011-10-10

the known candidate piezoelectric ferroelectric perovskites. Unlike most computational studies on crystal chemistry, where the starting point is some...studies on crystal chemistry, where the starting point is some form of electronic structure calculation, we use a data driven approach to initiate our...experimental measurements reported in the literature. Given that our models are based solely on crystal and electronic structure data and did not

Coupling of free space sub-terahertz waves into dielectric slabs using PC waveguides.

PubMed

Ghattan, Z; Hasek, T; Shahabadi, M; Koch, M

2008-04-28

The paper presents theoretical and experimental results on photonic crystal structures which work under the self-collimation condition to couple free space waves into dielectric slabs in the sub-terahertz range. Using a standard machining process, two-dimensional photonic crystal structures consisting of a square array of air holes in the dielectric medium are fabricated. One of the structures has two adjacent parallel line-defects that improve the coupling efficiency. This leads to a combination of self-collimation and directional emission of electromagnetic waves. The experimental results are in good agreement with those of the Finite- Element-Method calculations. Experimentally we achieve a coupling efficiency of 63%.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

DOE PAGES

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; ...

2016-04-12

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. Furthermore, this observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn 3N 4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

NASA Astrophysics Data System (ADS)

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; Christensen, Steven T.; Diercks, David; Schwartz, Craig P.; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S.; Tumas, William; Perkins, John D.; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M.; Zakutayev, Andriy

2016-04-01

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures.

PubMed

Caskey, Christopher M; Holder, Aaron; Shulda, Sarah; Christensen, Steven T; Diercks, David; Schwartz, Craig P; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S; Tumas, William; Perkins, John D; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M; Zakutayev, Andriy

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caskey, Christopher M.; Colorado School of Mines, Golden, Colorado 80401; Larix Chemical Science, Golden, Colorado 80401

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Electronic and crystal structure of NiTi martensite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanati, M.; Albers, R.C.; Pinski, F.J.

1998-11-01

All of the first-principles electronic-structure calculations for the martensitic structure of NiTi have used the experimental atomic parameters reported by Michal and Sinclair [Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. {bold B37}, 1803 (1981)]. We have used first-principles, full-potential, linear muffin-tin orbital calculations to examine the total energy of all the experimental martensitic structures reported in the literature. We find that another crystal structure, that of Kudoh {ital et al.} [Acta Metall. Mater. {bold 33}, 2049 (1985)], has the lowest total energy at zero temperature. Ground-state and formation energies were calculated for all of the experimental structures. Total andmore » local densities of states were calculated and compared with each other for the structures of both Kudoh {ital et al.} and Michal and Sinclair thinsp {copyright} {ital 1998} {ital The American Physical Society}« less

Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures.

PubMed

Tasolamprou, Anna C; Zhang, Lei; Kafesaki, Maria; Koschny, Thomas; Soukoulis, Costas M

2015-06-01

We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. The angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

Frequency splitter based on the directional emission from surface modes in dielectric photonic crystal structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tasolamprou, Anna C.; Zhang, Lei; Kafesaki, Maria

2015-05-19

We demonstrate the numerical design and the experimental validation of frequency dependent directional emission from a dielectric photonic crystal structure. The wave propagates through a photonic crystal line-defect waveguide, while a surface layer at the termination of the photonic crystal enables the excitation of surface modes and a subsequent grating layer transforms the surface energy into outgoing propagating waves of the form of a directional beam. Furthermore, the angle of the beam is controlled by the frequency and the structure operates as a frequency splitter in the intermediate and far field region.

A first principles prediction of the crystal structure of C6Br2ClFH2

NASA Astrophysics Data System (ADS)

Misquitta, Alston J.; Welch, Gareth W. A.; Stone, Anthony J.; Price, Sarah L.

2008-04-01

We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-fluorobenzene molecule from first principles using SAPT(DFT) interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of CBrClFH and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.

Multiphysical simulation analysis of the dislocation structure in germanium single crystals

NASA Astrophysics Data System (ADS)

Podkopaev, O. I.; Artemyev, V. V.; Smirnov, A. D.; Mamedov, V. M.; Sid'ko, A. P.; Kalaev, V. V.; Kravtsova, E. D.; Shimanskii, A. F.

2016-09-01

To grow high-quality germanium crystals is one of the most important problems of growth industry. The dislocation density is an important parameter of the quality of single crystals. The dislocation densities in germanium crystals 100 mm in diameter, which have various shapes of the side surface and are grown by the Czochralski technique, are experimentally measured. The crystal growth is numerically simulated using heat-transfer and hydrodynamics models and the Alexander-Haasen dislocation model in terms of the CGSim software package. A comparison of the experimental and calculated dislocation densities shows that the dislocation model can be applied to study lattice defects in germanium crystals and to improve their quality.

Stochastic generation of complex crystal structures combining group and graph theory with application to carbon

NASA Astrophysics Data System (ADS)

Shi, Xizhi; He, Chaoyu; Pickard, Chris J.; Tang, Chao; Zhong, Jianxin

2018-01-01

A method is introduced to stochastically generate crystal structures with defined structural characteristics. Reasonable quotient graphs for symmetric crystals are constructed using a random strategy combined with space group and graph theory. Our algorithm enables the search for large-size and complex crystal structures with a specified connectivity, such as threefold sp2 carbons, fourfold sp3 carbons, as well as mixed sp2-sp3 carbons. To demonstrate the method, we randomly construct initial structures adhering to space groups from 75 to 230 and a range of lattice constants, and we identify 281 new sp3 carbon crystals. First-principles optimization of these structures show that most of them are dynamically and mechanically stable and are energetically comparable to those previously proposed. Some of the new structures can be considered as candidates to explain the experimental cold compression of graphite.

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data† †Electronic supplementary information (ESI) available: Results of similarity analysis between the 11 structures of lowest energy obtained in the AIRSS calculations and the reported structures of form III and form IV of m-ABA; unit cell parameters and volumes for all structures considered; comparison of 2θ values derived from the unit cell parameters of different structural models representing form III of m-ABA; Le Bail fitting of the experimental powder XRD pattern of form IV of m-ABA recorded at 70 K using, as the initial structural model, the reported crystal structure following geometry optimization; table of calculated (GIPAW) absolute isotropic NMR shieldings; simulated powder XRD data for the considered structures after precise geometry optimization; experimental 1H MAS NMR spectra of forms III and IV. (pdf) The calculated and experimental data for this study are provided as a supporting dataset from WRAP, the Warwick Research Archive Portal at http://wrap.warwick.ac.uk/91884. See DOI: 10.1039/c7cp04186a

PubMed Central

Zilka, Miri; Dudenko, Dmytro V.; Hughes, Colan E.; Williams, P. Andrew; Sturniolo, Simone; Franks, W. Trent; Pickard, Chris J.

2017-01-01

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated. PMID:28944393

Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

PubMed Central

Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

2015-01-01

Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

Weyl points and Fermi arcs in a chiral phononic crystal

NASA Astrophysics Data System (ADS)

Li, Feng; Huang, Xueqin; Lu, Jiuyang; Ma, Jiahong; Liu, Zhengyou

2018-01-01

Topological semimetals are materials whose band structure contains touching points that are topologically nontrivial and can host quasiparticle excitations that behave as Dirac or Weyl fermions. These so-called Weyl points not only exist in electronic systems, but can also be found in artificial periodic structures with classical waves, such as electromagnetic waves in photonic crystals and acoustic waves in phononic crystals. Due to the lack of spin and a difficulty in breaking time-reversal symmetry for sound, however, topological acoustic materials cannot be achieved in the same way as electronic or optical systems. And despite many theoretical predictions, experimentally realizing Weyl points in phononic crystals remains challenging. Here, we experimentally realize Weyl points in a chiral phononic crystal system, and demonstrate surface states associated with the Weyl points that are topological in nature, and can host modes that propagate only in one direction. As with their photonic counterparts, chiral phononic crystals bring topological physics to the macroscopic scale.

Two distinct crystallization processes in supercooled liquid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tane, Masakazu, E-mail: mtane@sanken.osaka-u.ac.jp; Kimizuka, Hajime; Ichitsubo, Tetsu

2016-05-21

Using molecular dynamics simulations we show that two distinct crystallization processes, depending on the temperature at which crystallization occurs, appear in a supercooled liquid. As a model for glass-forming materials, an Al{sub 2}O{sub 3} model system, in which both the glass transition and crystallization from the supercooled liquid can be well reproduced, is employed. Simulations in the framework of an isothermal-isobaric ensemble indicate that the calculated time-temperature-transformation curve for the crystallization to γ(defect spinel)-Al{sub 2}O{sub 3} exhibited a typical nose shape, as experimentally observed in various glass materials. During annealing above the nose temperature, the structure of the supercooled liquidmore » does not change before the crystallization, because of the high atomic mobility (material transport). Thus, the crystallization is governed by the abrupt crystal nucleation, which results in the formation of a stable crystal structure. In contrast, during annealing below the nose temperature, the structure of the supercooled liquid gradually changes before the crystallization, and the formed crystal structure is less stable than that formed above the nose temperature, because of the restricted material transport.« less

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy.

PubMed

Zhang, Hang; Xu, Qingyan

2017-10-27

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter ( d w ), the spiral pitch ( h b ) and the spiral diameter ( h s ), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure.

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy

PubMed Central

Zhang, Hang; Xu, Qingyan

2017-01-01

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter (dw), the spiral pitch (hb) and the spiral diameter (hs), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure. PMID:29077067

Amorphous photonic crystals with only short-range order.

PubMed

Shi, Lei; Zhang, Yafeng; Dong, Biqin; Zhan, Tianrong; Liu, Xiaohan; Zi, Jian

2013-10-04

Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-Pressure Structural Response of an Insensitive Energetic Crystal: Dihydroxylammonium 5,5'-Bistetrazole-1,1'-diolate (TKX-50)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi-Gang

2017-03-06

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. The present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

High-pressure structural response of an insensitive energetic crystal: Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2017-02-28

The structural response of a novel, insensitive energetic crystal—dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50)—was examined under high pressure. Using synchrotron single-crystal X-ray diffraction measurements, details of molecular, intermolecular, and crystal changes were determined to ~10 GPa to understand its structural stability. The experimental results showed that TKX-50 exhibits highly anisotropic compression and significantly lower volume compressibility than currently known energetic crystals. These results are found to be in general agreement with our previous predictions from the DFT calculations. Additionally, the experimental data revealed anomalous compression—an expansion of the unit cell along the a axis (negative linear compressibility, NLC) upon compression to ~3 GPa.more » The structural analyses demonstrated that this unusual effect, the first such observation in an energetic crystal, is a consequence of the highly anisotropic response of 3D motifs, comprised of two parallel anions [(C 2N 8O 2) 2–] linked with two cations [(NH 3OH) +] through four strong hydrogen bonds. Finally, the present results demonstrate that the structural stability of TKX-50 is controlled by the strong and highly anisotropic intermolecular interactions, and these may contribute to its shock insensitivity.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajian, Hodjat, E-mail: hodjat.hajian@bilkent.edu.tr; Ozbay, Ekmel; Department of Physics, Bilkent University, 06800 Ankara

Certain types of photonic crystals with Dirac cones at the Γ point of their band structure have a zero effective index of refraction at Dirac cone frequency. Here, by an appropriate design of the photonic structure, we obtain a strong coupling between modes around the Dirac cone frequency of an all-dielectric zero-index photonic crystal and the guided ones supported by a photonic crystal waveguide. Consequently, we experimentally demonstrate that the presence of the zero-index photonic crystal at the inner side of the photonic crystal waveguide leads to an enhancement in the transmission of some of the guided waves passing throughmore » this hybrid system. Moreover, those electromagnetic waves extracted from the structure with enhanced transmission exhibit high directional beaming due to the presence of the zero-index photonic crystal at the outer side of the photonic crystal waveguide.« less

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

PubMed

Lemieux, M Joanne

2007-01-01

The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

Dipicolinate salt of imidazole: Discovering its structure and properties using different experimental methodologies and quantum chemical investigations

NASA Astrophysics Data System (ADS)

Thirumurugan, R.; Anitha, K.

2018-03-01

A novel organic proton transfer complex of imidazolium dipicolinate (ID) has been synthesized and it was grown as single crystals using slow evaporation method. The molecular structure of synthesized compound and vibrational modes of its functional groups were confirmed by (1H and 13C) NMR, FTIR and FT-Raman spectroscopic studies, respectively. Single crystal X-ray diffraction (SCXRD) analysis confirmed the orthorhombic system with noncentrosymmetric (NCS), P212121, space group of grown ID crystal. UV-Vis-NIR spectral study confirmed its high optical transparency within the region of 285-1500 nm. Powder second harmonic generation (SHG) efficiency of ID crystal was confirmed and it was 6.8 times that of KDP crystal. TG-DTA and DSC analysis revealed the higher thermal stability of grown crystal as 249 °C. The dielectric response and mechanical behaviour of grown crystal were studied effectively. Density functional theory calculations were performed to probe the relationship between the structure and its properties including molecular optimization, Mulliken atomic charge distribution, frontier molecular orbital (FMOs) and molecular electrostatic potential map (MEP) analysis and first hyperpolarizability. All these experimental and computational results were discussed in this communication and it endorsed the ID compound as a potential NLO candidate could be employed in optoelectronics device applications in near future.

Reflectivity of 1D photonic crystals: A comparison of computational schemes with experimental results

NASA Astrophysics Data System (ADS)

Pérez-Huerta, J. S.; Ariza-Flores, D.; Castro-García, R.; Mochán, W. L.; Ortiz, G. P.; Agarwal, V.

2018-04-01

We report the reflectivity of one-dimensional finite and semi-infinite photonic crystals, computed through the coupling to Bloch modes (BM) and through a transfer matrix method (TMM), and their comparison to the experimental spectral line shapes of porous silicon (PS) multilayer structures. Both methods reproduce a forbidden photonic bandgap (PBG), but slowly-converging oscillations are observed in the TMM as the number of layers increases to infinity, while a smooth converged behavior is presented with BM. The experimental reflectivity spectra is in good agreement with the TMM results for multilayer structures with a small number of periods. However, for structures with large amount of periods, the measured spectral line shapes exhibit better agreement with the smooth behavior predicted by BM.

Structure, dynamics and bifurcations of discrete solitons in trapped ion crystals

NASA Astrophysics Data System (ADS)

Landa, H.; Reznik, B.; Brox, J.; Mielenz, M.; Schaetz, T.

2013-09-01

We study discrete solitons (kinks) accessible in the state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-three-dimensional configurations, both theoretically and experimentally. We first extend the theoretical understanding of different phenomena predicted and recently experimentally observed in the structure and dynamics of these topological excitations. Employing tools from topological degree theory, we analyze bifurcations of crystal configurations in dependence on the trapping parameters, and investigate the formation of kink configurations and the transformations of kinks between different structures. This allows us to accurately define and calculate the effective potential experienced by solitons within the Wigner crystal, and study how this (so-called Peierls-Nabarro) potential gets modified to a non-periodic globally trapping potential in certain parameter regimes. The kinks' rest mass (energy) and spectrum of modes are computed and the dynamics of linear and nonlinear kink oscillations are analyzed. We also present novel, experimentally observed, configurations of kinks incorporating a large-mass defect realized by an embedded molecular ion, and of pairs of interacting kinks stable for long times, offering the perspective for exploring and exploiting complex collective nonlinear excitations, controllable on the quantum level.

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Superprism effect in a metal-clad terahertz photonic crystal slab.

PubMed

Prasad, Tushar; Colvin, Vicki L; Jian, Zhongping; Mittleman, Daniel M

2007-03-15

We report an experimental demonstration of the superprism effect in a photonic crystal slab at terahertz frequencies. For a 10% frequency variation around 0.28 THz, the refraction angle at the output facet of a wedge-shaped photonic crystal varies by about 15 degrees. A comparison with the predictions of a band structure calculation demonstrates that a three-dimensional treatment, accurately modeling the finite slab thickness and the metallic boundary conditions, is required for even a qualitative agreement with the experimental observations.

Structural, spectroscopic and electronic properties of hydrogen-bonded water molecules in crystals. Ab initio calculations and experimental data of MC1 2· n(H,D) 2O, M = Sr or Ba

NASA Astrophysics Data System (ADS)

Möller, H.; Niu, J. E.; Lutz, H. D.; Schwarz, W. H. E.

1997-12-01

Structural, spectroscopic and electronic properties of (more or less deuterated) water molecules in the crystal fields of SrCl 2·2H 2O, SrCl 2·H 2O and BaCl 2·H 2O, previously investigated by experimental techniques, were calculated by ab initio SCF-MP methods. The H 2O molecules of each compound are asymmetrically surrounded by three adjacent chloride ions, one hydrogen atom being attached to a nearby Cl -, the other less perturbed hydrogen atom bridging the two less near Cl -. The diversity of structural and spectroscopic features found experimentally, for instance the trends from free H 2O to H 2O in BaCl 2·H 2OSrCl 2·H 2OSrCl 2·2H 2O, are well reproduced by the model calculations, which provide the correct assignment and physical interpretation. The differences between the compounds and the asymmetry of the hydrate water molecules can be rationalized with the help of crystal fields. The crystal environment expands the internuclear distances of H 2O by up to 3 pm. The change of vibrational frequencies can be explained qualitatively by only taking the coupling and anharmonicity of the free water molecule and its modified structure in the crystals into account. The infra-red intensities, however, are strongly influenced by the electronic polarization.

Crystal growth, electronic structure and optical properties of Sr2Mg(BO3)2

NASA Astrophysics Data System (ADS)

Lv, Xianshun; Wei, Lei; Wang, Xuping; Xu, Jianhua; Yu, Huajian; Hu, Yanyan; Zhang, Huadi; Zhang, Cong; Wang, Jiyang; Li, Qinggang

2018-02-01

Single crystals of Sr2Mg(BO3)2 (SMBO) were grown by Kyropoulos method. X-ray powder diffraction (XRD) analysis, transmission spectrum, thermal properties, band structure, density of states and charge distribution as well as Raman spectra of SMBO were described. The as-grown SMBO crystals show wide transparency range with UV cut-off below 180 nm. A direct band gap of 4.66 eV was obtained from the calculated electronic structure results. The calculated band structure and density of states results indicated the top valence band is determined by O 2p states whereas the low conduction band mainly consists of Sr 5s states. Twelve Raman peaks were observed in the experimental spectrum, fewer than the number predicted by the site group analysis. Raman peaks of SMBO were assigned combining first-principle calculation and site group analysis results. The strongest peak at 917 cm-1 in the experimental spectrum is assigned to symmetric stretching mode A1‧(ν1) of free BO3 units. SMBO is a potential Raman crystal which can be used in deep UV laser frequency conversion.

Elastic and viscoelastic effects in rubber/air acoustic band gap structures: A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Merheb, B.; Deymier, P. A.; Jain, M.; Aloshyna-Lesuffleur, M.; Mohanty, S.; Berker, A.; Greger, R. W.

2008-09-01

The transmission of acoustic waves through centimeter-scale elastic and viscoelastic two-dimensional silicone rubber/air phononic crystal structures is investigated theoretically and experimentally. We introduce a finite difference time domain method for two-dimensional elastic and viscoelastic composite structures. Elastic fluid-solid phononic crystals composed of a two-dimensional array of cylindrical air inclusions in a solid rubber matrix, as well as an array of rubber cylinders in an air matrix, are shown to behave similarly to fluid-fluid composite structures. These systems exhibit very wide band gaps in their transmission spectra that extend to frequencies in the audible range of the spectrum. This effect is associated with the very low value of the transverse speed of sound in rubber compared to that of the longitudinal polarization. The difference in transmission between elastic and viscoelastic rubber/air crystals results from attenuation of transmission over a very wide frequency range, leaving only narrow passing bands at very low frequencies. These phononic crystals demonstrate the practical design of elastic or viscoelastic solid rubber/air acoustic band gap sound barriers with small dimensions.

In-situ study on growth units of Ba2Mg(B3O6)2 crystal

NASA Astrophysics Data System (ADS)

Lv, X. S.; Sun, Y. L.; Tang, X. L.; Wan, S. M.; Zhang, Q. L.; You, J. L.; Yin, S. T.

2013-05-01

BMBO (Ba2Mg(B3O6)2 crystal) is an excellent birefringent crystal and a potential stimulated Raman scattering (SRS) crystal. In this paper, high temperature Raman spectroscopy was used to in-situ study the melt structure near a BMBO crystal-melt interface. [B3O6]3- groups were found in this region. The result reveals that both of BaO bonds and MgO bonds are the weak bonds in the BMBO crystal structure. During the melting process, the crystal structure broke into Ba2+ ions, Mg2+ ions and [B3O6]3- groups. Our experimental results confirmed that the well-developed faces of BMBO crystals are the (001), (101) and (012) faces. Based on attachment energy theory, the crystal growth habit was discussed. The (001) (101) and (012) crystal faces linked by the weak BaO bonds and MgO bonds have smaller attachment energies and slower growth rates, and thus present in the final morphology. The (012) crystal face has a multi-terrace structure, which suggests that BMBO crystal grows with a layer-by-layer mode.

Crystallization of Stretched Polyimides: A Structure-Property Study

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Dezern, James F.

2002-01-01

A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

On the Relationship of the Fractal Dimension of Structure with the State of Drying Drops of Crystallizing Solutions (Thermodynamic and Experimental Modeling)

NASA Astrophysics Data System (ADS)

Golovanova, O. A.; Chikanova, E. S.; Fedoseev, V. B.

2018-05-01

The processes occurring in aqueous salt solutions have been investigated based on thermodynamic and experimental modeling. The self-organization in a drying drop of dehydrated liquids is analyzed using the fractal theory, due to which the quantitative characteristics of the crystallization processes in a small volume are obtained.

The structure of small, vapor-deposited particles. II - Experimental study of particles with hexagonal profile

NASA Technical Reports Server (NTRS)

Yacaman, M. J.; Heinemann, K.; Yang, C. Y.; Poppa, H.

1979-01-01

'Multiply-twinned' gold particles with hexagonal bright field TEM profile were determined to be icosahedra composed of 20 identical and twin-related tetrahedral building units that do not have an fcc structure. The crystal structure of these slightly deformed tetrahedra is rhombohedral. Experimental evidence supporting this particle model was obtained by selected-zone dark field and weak beam dark field electron microscopy. In conjunction with the results of part I, it has been concluded that multiply-twinned gold particles of pentagonal or hexagonal profile that are found during the early stages of the vapor deposition growth process on alkali halide surfaces do not have an fcc crystal structure, which is in obvious contrast to the structure of bulk gold.

Experimental study on slow flexural waves around the defect modes in a phononic crystal beam using fiber Bragg gratings

NASA Astrophysics Data System (ADS)

Chuang, Kuo-Chih; Zhang, Zhi-Qiang; Wang, Hua-Xin

2016-12-01

This work experimentally studies influences of the point defect modes on the group velocity of flexural waves in a phononic crystal Timoshenko beam. Using the transfer matrix method with a supercell technique, the band structures and the group velocities around the defect modes are theoretically obtained. Particularly, to demonstrate the existence of the localized defect modes inside the band gaps, a high-sensitivity fiber Bragg grating sensing system is set up and the displacement transmittance is measured. Slow propagation of flexural waves via defect coupling in the phononic crystal beam is then experimentally demonstrated with Hanning windowed tone burst excitations.

Analysis of synthetic diamond single crystals by X-ray topography and double-crystal diffractometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prokhorov, I. A., E-mail: igor.prokhorov@mail.ru; Ralchenko, V. G.; Bolshakov, A. P.

2013-12-15

Structural features of diamond single crystals synthesized under high pressure and homoepitaxial films grown by chemical vapor deposition (CVD) have been analyzed by double-crystal X-ray diffractometry and topography. The conditions of a diffraction analysis of diamond crystals using Ge monochromators have been optimized. The main structural defects (dislocations, stacking faults, growth striations, second-phase inclusions, etc.) formed during crystal growth have been revealed. The nitrogen concentration in high-pressure/high-temperature (HPHT) diamond substrates is estimated based on X-ray diffraction data. The formation of dislocation bundles at the film-substrate interface in the epitaxial structures has been revealed by plane-wave topography; these dislocations are likelymore » due to the relaxation of elastic macroscopic stresses caused by the lattice mismatch between the substrate and film. The critical thicknesses of plastic relaxation onset in CVD diamond films are calculated. The experimental techniques for studying the real diamond structure in optimizing crystal-growth technology are proven to be highly efficient.« less

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

PubMed

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.

Peptide crystal simulations reveal hidden dynamics

PubMed Central

Janowski, Pawel A.; Cerutti, David S.; Holton, James; Case, David A.

2013-01-01

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in the X-ray diffraction data. We present here 9.6 microseconds of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to within 0.28 Å backbone and 0.42 Å all-atom rmsd; a model refined against the average simulation density agrees with the experimental structure to within 0.20 Å backbone and 0.33 Å all-atom rmsd. The R-factor between the experimental structure factors and those derived from this unrestrained simulation is 23% to 1.0 Å resolution. The B-factors for most heavy atoms agree well with experiment (Pearson correlation of 0.90), but B-factors obtained by refinement against the average simulation density underestimate the coordinate fluctuations in the underlying simulation where the simulation samples alternate conformations. A dynamic flow of water molecules through channels within the crystal lattice is observed, yet the average water density is in remarkable agreement with experiment. A minor population of unit cells is characterized by reduced water content, 310 helical propensity and a gauche(−) side-chain rotamer for one of the valine residues. Careful examination of the experimental data suggests that transitions of the helices are a simulation artifact, although there is indeed evidence for alternate valine conformers and variable water content. This study highlights the potential for crystal simulations to detect dynamics and heterogeneity in experimental diffraction data, as well as to validate computational chemistry methods. PMID:23631449

Functional materials discovery using energy-structure-function maps

NASA Astrophysics Data System (ADS)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

2017-03-01

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Functional materials discovery using energy-structure-function maps.

PubMed

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Optical, Fluorescence with quantum analysis of hydrazine (1, 3- Dinitro Phenyl) by DFT and Ab initio approach

NASA Astrophysics Data System (ADS)

Cecily Mary Glory, D.; Sambathkumar, K.; Madivanane, R.; Velmurugan, G.; Gayathri, R.; Nithiyanantham, S.; Venkatachalapathy, M.; Rajkamal, N.

2018-07-01

Experimental and computational study of molecular structure, vibrational and UV-spectral analysis of Hydrazine (1, 3- Dinitrophenyl) (HDP) derivatives. The crystal was grown by slow cooling method and the crystalline perfection of single crystals was evaluated by high resolution X-ray diffractometry (HRXRD) using a multicrystal X-ray diffractometer. Fluorescence, FT-IR and FT-Raman spectra of HDP crystal were recorded. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) followed by scaled quantum force field methodology (SQMFF). NMR studies have confirmed respectively the crystal structure and functional groups of the grown crystal. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) result complements the experimental findings. The calculated MESP, UV, HOMO-LUMO energies show that charge transfer done within the molecule. And various thermodynamic parameters are studied. Fukui determines the local reactive site of electrophilic, nucleophilic, descriptor.

A model of insulin fibrils derived from the x-ray crystal structure of a monomeric insulin (despentapeptide insulin).

PubMed

Brange, J; Dodson, G G; Edwards, D J; Holden, P H; Whittingham, J L

1997-04-01

The crystal structure of despentapeptide insulin, a monomeric insulin, has been refined at 1.3 A spacing and subsequently used to predict and model the organization in the insulin fibril. The model makes use of the contacts in the densely packed despentapeptide insulin crystal, and takes into account other experimental evidence, including binding studies with Congo red. The dimensions of this model fibril correspond well with those measured experimentally, and the monomer-monomer contacts within the fibril are in accordance with the known physical chemistry of insulin fibrils. Using this model, it may be possible to predict mutations in insulin that might alleviate problems associated with fibril formation during insulin therapy.

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids

PubMed Central

2013-01-01

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1H and 13C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1H and 13C chemical shifts for directly bonded 13C–1H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure. PMID:24386493

Exploiting the Synergy of Powder X-ray Diffraction and Solid-State NMR Spectroscopy in Structure Determination of Organic Molecular Solids.

PubMed

Dudenko, Dmytro V; Williams, P Andrew; Hughes, Colan E; Antzutkin, Oleg N; Velaga, Sitaram P; Brown, Steven P; Harris, Kenneth D M

2013-06-13

We report a strategy for structure determination of organic materials in which complete solid-state nuclear magnetic resonance (NMR) spectral data is utilized within the context of structure determination from powder X-ray diffraction (XRD) data. Following determination of the crystal structure from powder XRD data, first-principles density functional theory-based techniques within the GIPAW approach are exploited to calculate the solid-state NMR data for the structure, followed by careful scrutiny of the agreement with experimental solid-state NMR data. The successful application of this approach is demonstrated by structure determination of the 1:1 cocrystal of indomethacin and nicotinamide. The 1 H and 13 C chemical shifts calculated for the crystal structure determined from the powder XRD data are in excellent agreement with those measured experimentally, notably including the two-dimensional correlation of 1 H and 13 C chemical shifts for directly bonded 13 C- 1 H moieties. The key feature of this combined approach is that the quality of the structure determined is assessed both against experimental powder XRD data and against experimental solid-state NMR data, thus providing a very robust validation of the veracity of the structure.

Crystal structure and habit of dirithromycin acetone solvate: A combined experimental and simulative study

NASA Astrophysics Data System (ADS)

Yi, Qinhua; Chen, Jianfeng; Le, Yuan; Wang, Jiexin; Xue, Chunyu; Zhao, Hong

2013-06-01

Dirithromycin (DIR) was crystallized from acetone solvent in the form of an acetone solvate. Its crystal structure belongs to monoclinic, space group P21, with the unit cell parameters a=14.688(3) Å, b=11.6120(12) Å, c=14.9129(12) Å, β=94.794(10)°, and Z=2. Results of X-ray diffraction (XRD) and thermogravimetry-differential scanning calorimetry (TG-DSC) indicated that the solvent molecules could enter the crystal lattice and thus the solvate is formed. The molecular dynamics (MD) simulation method was applied to study the solvent effect. It revealed that the relative growth rates of the main crystal habit faces changed a lot, which made the most morphologically important habit face shift from (001) face to (100) face due to polar groups or atoms exposure and hence a large solvent interaction. The prism habit predicted by a modified attachment energy (AE) model agreed well with the observed experimental morphology grown from the acetone solution. This prediction method may help for a solvent selection to improve the morphology in the drug crystallization process.

Why don't we find more polymorphs?

PubMed

Price, Sarah L

2013-08-01

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Solid iron-hydrogen alloys under high pressure by first principles

NASA Astrophysics Data System (ADS)

Umemoto, K.; Hirose, K.

2016-12-01

Hydrogen and iron are two of major constituents of the Earth and planetary interiors. The crystal structure of solid FeHx is one of the most fundamental information in order to understand properties of planetary cores. It is well known that FeH takes closed-packed structures: dhcp, hcp, and fcc. Recently, hydrogen-rich phases, FeH2 and FeH3, were experimentally synthesized [1]. Although a tetragonal structure of FeH2 was proposed, it could not explain experimental observations, energetic stability and compression curve. Here we propose a new crystal structure of FeH2. The symmetry of the new structure is completely identical to that in originally proposed one, but the hydrogen sublattice which cannot be directly determined by XRD experiments is different. It will be demonstrated by first principles that the new structure can be fully consistent with experimental observations. [1] C. M. Pépin, A. Dewaele, G. Geneste, P. Loubeyre, and M. Mezouar, Phys. Rev. Lett. 113, 265504 (2014).

Collection of X-ray diffraction data from macromolecular crystals

PubMed Central

Dauter, Zbigniew

2017-01-01

Diffraction data acquisition is the final experimental stage of the crystal structure analysis. All subsequent steps involve mainly computer calculations. Optimally measured and accurate data make the structure solution and refinement easier and lead to more faithful interpretation of the final models. Here, the important factors in data collection from macromolecular crystals are discussed and strategies appropriate for various applications, such as molecular replacement, anomalous phasing, atomic-resolution refinement etc., are presented. Criteria useful for judging the diffraction data quality are also discussed. PMID:28573573

Experimental demonstrations in audible frequency range of band gap tunability and negative refraction in two-dimensional sonic crystal.

PubMed

Pichard, Hélène; Richoux, Olivier; Groby, Jean-Philippe

2012-10-01

The propagation of audible acoustic waves in two-dimensional square lattice tunable sonic crystals (SC) made of square cross-section infinitely rigid rods embedded in air is investigated experimentally. The band structure is calculated with the plane wave expansion (PWE) method and compared with experimental measurements carried out on a finite extend structure of 200 cm width, 70 cm depth and 15 cm height. The structure is made of square inclusions of 5 cm side with a periodicity of L = 7.5 cm placed inbetween two rigid plates. The existence of tunable complete band gaps in the audible frequency range is demonstrated experimentally by rotating the scatterers around their vertical axis. Negative refraction is then analyzed by use of the anisotropy of the equi-frequency surface (EFS) in the first band and of a finite difference time domain (FDTD) method. Experimental results finally show negative refraction in the audible frequency range.

Spontaneously Flowing Crystal of Self-Propelled Particles

NASA Astrophysics Data System (ADS)

Briand, Guillaume; Schindler, Michael; Dauchot, Olivier

2018-05-01

We experimentally and numerically study the structure and dynamics of a monodisperse packing of spontaneously aligning self-propelled hard disks. The packings are such that their equilibrium counterparts form perfectly ordered hexagonal structures. Experimentally, we first form a perfect crystal in a hexagonal arena which respects the same crystalline symmetry. Frustration of the hexagonal order, obtained by removing a few particles, leads to the formation of a rapidly diffusing "droplet." Removing more particles, the whole system spontaneously forms a macroscopic sheared flow, while conserving an overall crystalline structure. This flowing crystalline structure, which we call a "rheocrystal," is made possible by the condensation of shear along localized stacking faults. Numerical simulations very well reproduce the experimental observations and allow us to explore the parameter space. They demonstrate that the rheocrystal is induced neither by frustration nor by noise. They further show that larger systems flow faster while still remaining ordered.

Optical spectra and band structure of Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals: experiment and theory.

PubMed

Reshak, A H; Parasyuk, O V; Fedorchuk, A O; Kamarudin, H; Auluck, S; Chyský, J

2013-12-05

Theoretical and experimental studies of the Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals are performed. These crystals possess a lot of intrinsic defects which are responsible for their optoelectronic features. The theoretical investigations were performed by means of DFT calculations using different exchange-correlation potentials. The experimental studies were carried out using the modulated VUV ellipsometry for dielectric constants and birefringence studies. The comparison of the structure obtained from X-ray with the theoretically optimized structure is presented. The crucial role of the intrinsic defect states is manifested in the choice of the exchange correlation potential used. The data may be applicable for a large number of the ternary chalcogenides which are sensitive to the presence of the local disordered states near the band edges.

The prediction of crystal structure by merging knowledge methods with first principles quantum mechanics

NASA Astrophysics Data System (ADS)

Ceder, Gerbrand

2007-03-01

The prediction of structure is a key problem in computational materials science that forms the platform on which rational materials design can be performed. Finding structure by traditional optimization methods on quantum mechanical energy models is not possible due to the complexity and high dimensionality of the coordinate space. An unusual, but efficient solution to this problem can be obtained by merging ideas from heuristic and ab initio methods: In the same way that scientist build empirical rules by observation of experimental trends, we have developed machine learning approaches that extract knowledge from a large set of experimental information and a database of over 15,000 first principles computations, and used these to rapidly direct accurate quantum mechanical techniques to the lowest energy crystal structure of a material. Knowledge is captured in a Bayesian probability network that relates the probability to find a particular crystal structure at a given composition to structure and energy information at other compositions. We show that this approach is highly efficient in finding the ground states of binary metallic alloys and can be easily generalized to more complex systems.

Lamb waves in phononic crystal slabs with square or rectangular symmetries

NASA Astrophysics Data System (ADS)

Brunet, Thomas; Vasseur, Jérôme; Bonello, Bernard; Djafari-Rouhani, Bahram; Hladky-Hennion, Anne-Christine

2008-08-01

We report on both numerical and experimental results showing the occurrence of band gaps for Lamb waves propagating in phononic crystal plates. The structures are made of centered rectangular and square arrays of holes drilled in a silicon plate. A supercell plane wave expansion method is used to calculate the band structures and to predict the position and the magnitude of the gaps. The band structures of phononic crystal slabs are then measured using a laser ultrasonic technique. Lamb waves in the megahertz range and with wave vectors ranging over more than the first two reduced Brillouin zones are investigated.

Compact 3D photonic crystals sensing platform with 45 degree angle polished fibers

NASA Astrophysics Data System (ADS)

Guo, Yuqing; Chen, Lu; Zhu, Jiali; Ni, Haibin; Xia, Wei; Wang, Ming

2017-07-01

Three dimensional photonic crystals are a kind of promising sensing materials in biology and chemistry. A compact structure, consists of planner colloidal crystals and 45 degree angle polished fiber, is proposed as a platform for accurate, fast, reliable three dimensional photonic crystals sensing in practice. This structure show advantages in compact size for integration and it is ease for large scale manufacture. Reflectivity of the 45 degree angle polished surface with and without a layer of Ag film are simulated by FDTD simulation. Refractive index sensing properties as well as mode distribution of this structure consists of both polystyrene opal and silica inverse opal film is investigated, and an experimental demonstration of silica inverse opal film is performed, which shows a sensitivity of 733 nm/RIU. Different kinds of three dimensional photonic crystals can also be applied in this structure for particular purpose.

Synthesis, spectral, structural prediction and computational studies of octylcarbazole ornamented 3-phenothiazinal

NASA Astrophysics Data System (ADS)

Karuppasamy, Ayyanar; Udhaya kumar, Chandran; Karthikeyan, Subramanian; Velayutham Pillai, Muthiah Pillai; Ramalingan, Chennan

2017-11-01

A novel conjugated octylcarbazole ornamented 3-phenothiazinal, 10-(9-octyl-9H-carbazol-3-yl)-10H-phenothiazine-3-carbaldehyde (OCPTC) was synthesized and fully characterized by 1H-NMR, 13C-NMR, elemental and single crystal XRD analyses. The optimized geometrical structure, vibrational frequencies and NMR have been computed with M06-2X method using 6-31+G(d,p) basis set. Total electronic energies and HOMO-LUMO energy gaps in gas phase are discussed. The geometrical parameters of the title compound obtained from single crystal XRD studies have been found in accord with the calculated (DFT) values. The experimental and theoretical FT-IR and NMR results of the title molecule have been investigated. The experimentally observed vibrational frequencies have been compared with the calculated ones, which are in good agreement with each other. Single crystal X-ray structural analysis of OCPTC, evidences the ''butterfly conformation'' of phenothiazine ring with nearly perpendicular orientation of the carbazole structural motif to the phenothiazine moiety.

Structural and mechanical features of the order-disorder transition in experimental hard-sphere packings

NASA Astrophysics Data System (ADS)

Hanifpour, M.; Francois, N.; Robins, V.; Kingston, A.; Vaez Allaei, S. M.; Saadatfar, M.

2015-06-01

Here we present an experimental and numerical investigation on the grain-scale geometrical and mechanical properties of partially crystallized structures made of macroscopic frictional grains. Crystallization is inevitable in arrangements of monosized hard spheres with packing densities exceeding Bernal's limiting density ϕBernal≈0.64 . We study packings of monosized hard spheres whose density spans over a wide range (0.59 <ϕ <0.72 ) . These experiments harness x-ray computed tomography, three-dimensional image analysis, and numerical simulations to access precisely the geometry and the 3D structure of internal forces within the sphere packings. We show that clear geometrical transitions coincide with modifications of the mechanical backbone of the packing both at the grain and global scale. Notably, two transitions are identified at ϕBernal≈0.64 and ϕc≈0.68 . These results provide insights on how geometrical and mechanical features at the grain scale conspire to yield partially crystallized structures that are mechanically stable.

REVIEW: Optics of globular photonic crystals

NASA Astrophysics Data System (ADS)

Gorelik, V. S.

2007-05-01

The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter ~200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported.

Experimental evidence for a chiral symmetry-breaking mechanism in aspartic acid: Lattice and sub-lattice matching

NASA Astrophysics Data System (ADS)

Teschke, Omar; Soares, David Mendez

2017-10-01

A mother crystal formed from a transient molecular structure of (D+L) aspartic acid in solution is reported. Hexagonal structures with a lattice constant of 1.04 nm were crystallized from a solution in which three aspartic acid species coexist: right- and left-handed enantiomorphs, denoted D-aspartic and L-aspartic, respectively, and transitory (D+L) aspartic acid specie. Atomic force microscopy images of the crystalline deposits reveal domains of the transitory (D+L) aspartic acid crystal forming the substrate deposit on silicon wafers, and on top of this hexagonal lattice only L-aspartic acid is observed to conform and crystallize. A preferential crystallization mechanism is then observed for (D+L) aspartic acid crystals that seed only L-aspartic deposits by the geometrical matching of their multiple hexagonal lattice structures with periodicities of 1.04 nm and 0.52 nm, respectively.

Predictions of Crystal Structures from First Principles

DTIC Science & Technology

2007-06-01

RDX crystal in hoped that the problem could be resolved by the molecular dynamics simulations . The fully ab initio development of density functional... Molecular Dynamics Simulations of RDX i.e., without any use of experimental results (except that Crystal the geometry of monomers was derived from X-ray...applied in molecular dynamics simulations of the RDX system, due to its size, is intractable by any high-level ab crystal. We performed isothermal

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

PubMed Central

2016-01-01

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results. PMID:27983843

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

PubMed

Hayatshahi, Hamed S; Roe, Daniel R; Galindo-Murillo, Rodrigo; Hall, Kathleen B; Cheatham, Thomas E

2017-01-26

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results.

Synthesis, Crystal Structure, and Magnetic Properties of the YbFeTi2O7 Compound

NASA Astrophysics Data System (ADS)

Drokina, T. V.; Petrakovskii, G. A.; Molokeev, M. S.; Velikanov, D. A.

2018-03-01

We report on the synthesis conductions and results of experimental investigations of the crystal structure and magnetic properties of a new magnetic compound YbFeTi2O7. According to the X-ray diffractometry data, the crystal structure of the investigated compound is described by the rhombic space group Pcnb with unit cell parameters of a = 9.8115(1) Å, b = 13.5106(2) Å, and c = 7.31302(9) Å and atomic disordering in the distribution of iron ions Fe3+ over five structural sites. The magnetic measurements in the lowtemperature region revealed a kink in the temperature dependence of the magnetic moment and its dependence on the sample magnetic prehistory. The experimental results obtained suggest that with a decrease in temperature the sample passes from the paramagnetic state to the spin-glass-like magnetic state characterized by a freezing temperature of T f = 4.5 K at the preferred antiferromagnetic exchange coupling in the sample spin system. The chemical pressure variation upon replacement of rare-earth ion R by Yb in the RFeTi2O7 system does not change the crystal lattice symmetry and magnetic state.

Designing functionality in perovskite thin films using ion implantation techniques: Assessment and insights from first-principles calculations

DOE PAGES

Sharma, Vinit K.; Herklotz, Andreas; Ward, Thomas Zac; ...

2017-09-11

Ion implantation has been widely used in the semiconductor industry for decades to selectively control electron/hole doping for device applications. Recently, experimental studies on ion implantation into more structurally and electronically complex materials have been undertaken in which defect generation has been used to control a variety of functional phenomena. Of particular interest, are recent findings demonstrating that low doses of low energy helium ions into single crystal films can be used to tailor the structural properties. These initial experimental studies have shown that crystal symmetry can be continuously controlled by applying increasingly large doses of He ions into amore » crystal. The observed changes in lattice structure were then observed to correlate with functional changes, such as metal-insulator transition temperature2 and optical bandgap3. In these preliminary experimental studies, changes to lattice expansion was proposed to be the direct result of chemical pressure originating predominantly from the implanted He applying chemical pressure at interstitial sites. However, the influence of possible secondary knock-on damage arising from the He atoms transferring energy to the lattice through nuclear-nuclear collision with the crystal lattice remains largely unaddressed. In this work, we focus on a SrRuO3 model system to provide a comprehensive examination of the impact of common defects on structural and electronic properties, obtain calculated defect formation energies, and define defect migration barriers. Our model indicates that, while interstitial He can modify the crystal properties, a dose significantly larger than those reported in experimental studies would be required. The true origin of the observed structural changes is likely the result of a combination of secondary defects created during He implantation. Of particular importance, we observe that different defect types can generate greatly varied local electronic structures and that the formation energies and migration energy barriers vary by defect type. Thus, we may have identified a new method of selectively inducing controlled defect complexes into single crystal materials. Development of this approach would have a broad impact on both our ability to probe specific defect contributions in fundamental studies and allow a new level of control over functional properties driven by specific defect complexes.« less

The microdopant effects of surfactant elements on structure-phase transitions during the rapid quenched crystallization of Fe-C-based melts

NASA Astrophysics Data System (ADS)

Polukhin, V. A.; Belyakova, R. M.; Rigmant, L. K.

2008-02-01

The nature of microdopant effects of surfactant Te and H2 reagents on structure-phase transitions in rapidly quenched and crystallized eutectic Fe-C-based melts were studied by experimental and computer methods. On the base of results of statistic-geometrical analysis the new information about the structure changes in multi-scaling systems -from meso- to nano-ones were obtained.

EPR investigation of gamma irradiated single crystal guaifenesin: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Tasdemir, Halil Ugur; Sayin, Ulku; Türkkan, Ercan; Ozmen, Ayhan

2016-04-01

Gamma irradiated single crystal of Guaifenesin (Glyceryl Guaiacolate), an important expectorant drug, were investigated with Electron Paramagnetic Resonance (EPR) spectroscopy between 123 and 333 K temperature at different orientations in the magnetic field. Considering the chemical structure and the experimental spectra of the gamma irradiated single crystal of guaifenesin sample, we assumed that alkoxy or alkyl-type paramagnetic species may be produced by irradiation. Depending on this assumption, eight possible alkoxy and alkyl-type radicals were modeled and EPR parameters of these modeled radicals were calculated using the B3LYP/6-311++G(d,p)-level of density functional theory (DFT). Theoretically calculated values of alkyl-type modeled radical(R3) are in good agreement with experimentally determined EPR parameters of single crystal. Furthermore, simulation spectra which are obtained by using the theoretical initial values are well matched with the experimental spectra. It was determined that a stable Cα •H2αCβHβCγH2γ (R3) alkyl radical was produced in the host crystal as a result of gamma irradiation.

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

DOE PAGES

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang; ...

2015-12-03

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

High-pressure crystal structures of an insensitive energetic crystal: 1,1-diamino-2,2-dinitroethene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreger, Zbigniew A.; Stash, Adam I.; Yu, Zhi -Gang

Understanding the insensitivity/stability of insensitive high explosive crystals requires detailed structural information at high pressures and high temperatures of interest. Synchrotron single crystal x-ray diffraction experiments were used to determine the high-pressure structures of 1,1-diamino-2,2-dinitroethene (FOX-7), a prototypical insensitive high explosive. The phase transition around 4.5 GPa was investigated and the structures were determined at 4.27 GPa (α’-phase) and 5.9 GPa (ε-phase). The α’-phase (monoclinic, P2 1/ n), structurally indistinguishable from the ambient α-phase, transforms to the new ε-phase (triclinic, P1). The most notable features of the ε-phase, compared to the α’-phase, are: formation of planar layers and flattening ofmore » molecules. Density functional theory (DFT-D2) calculations complemented the experimental results. Furthermore, the results presented here are important for understanding the molecular and crystalline attributes governing the high-pressure insensitivity/stability of insensitive high explosive crystals.« less

Optical Anisotropy of Photonic Crystals of Cubic Symmetry Induced by Multiple Diffraction of Light

NASA Astrophysics Data System (ADS)

Ukleev, T. A.; Shevchenko, N. N.; Iurasova, D. I.; Sel'kin, A. V.

2018-05-01

The optical spectra of Bragg reflection from opal-like photonic crystals under conditions of the resonant enhancement of the multiple diffraction of light have been studied experimentally and theoretically using the photonic crystal structures prepared of monodisperse polystyrene globules. It is shown that the reflection signal registered in mutually orthogonal configurations of the polarizer and analyzer is related to the intrinsic optical anisotropy of the crystals and is a specific manifestation of the multiple Bragg diffraction in three-dimensional photonic crystals.

Controllable light diffraction in woodpile photonic crystals filled with liquid crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, Chih-Hua; Zeng, Hao; Wiersma, Diederik S.

2015-01-12

An approach to switching between different patterns of light beams transmitted through the woodpile photonic crystals filled with liquid crystals is proposed. The phase transition between the nematic and isotropic liquid crystal states leads to an observable variation of the spatial pattern transmitted through the photonic structure. The transmission profiles in the nematic phase also show polarization sensibility due to refractive index dependence on the field polarization. The experimental results are consistent with a numerical calculation by Finite Difference Time Domain method.

Experimental study on the Neapolitan Yellow Tuff: Salt weathering and consolidation

NASA Astrophysics Data System (ADS)

La Russa, Mauro Francesco; Ruffolo, Silvestro Antonio; Alvarez de Buergo, Monica; Ricca, Michela; Belfiore, Cristina Maria; Pezzino, Antonino; Mirocle Crisci, Gino

2016-04-01

Salt crystallization is one of the major weathering agents in porous building materials due to the crystallization pressure exerted by salt crystals growing in confined pores. The consolidation of such degraded stone materials is a crucial issue in the field of Cultural Heritage restoration. This contribution deals with laboratory experimentation carried out on the Neapolitan Tuff, a pyroclastic rock largely used in the Campanian architecture. Several specimens, collected from a historical quarry nearby the city of Naples, were treated with two different consolidating products: a suspension of nanosilica in water (Syton X30®) and ethyl silicate (Estel 1000®) dispersed in organic solvent (TEOS). Then, in order to assess the effectiveness of consolidation treatments, both treated and untreated samples underwent accelerated degradation through salt crystallization tests. A multi-analytical approach, including mercury intrusion porosimetry, peeling tests and point load test, was employed to evaluate the correlation between the salt crystallization and the micro-structural features of the examined tuff specimens. In addition, the calculation of the crystallization pressures was also performed in order to make a correlation between the porous structure of the tuff and its susceptivity to salt crystallization. Obtained results show that both the tested products increase the resistance of tuff to salt crystallization, although inducing an increase of crystallization pressure. Ethyl silicate, however, shows a better behaviour in terms of superficial cohesion, even after several degradation cycles.

PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection.

PubMed

Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

2014-01-01

X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed 'PredPPCrys' using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor.org/PredPPCrys.

Electronic structure of ytterbium-implanted GaN at ambient and high pressure: experimental and crystal field studies.

PubMed

Kaminska, A; Ma, C-G; Brik, M G; Kozanecki, A; Boćkowski, M; Alves, E; Suchocki, A

2012-03-07

The results of high-pressure low-temperature optical measurements in a diamond-anvil cell of bulk gallium nitride crystals implanted with ytterbium are reported in combination with crystal field calculations of the Yb(3+) energy levels. Crystal field analysis of splitting of the (2)F(7/2) and (2)F(5/2) states has been performed, with the aim of assigning all features of the experimental luminescence spectra. A thorough analysis of the pressure behavior of the Yb(3+) luminescence lines in GaN allowed the determination of the ambient-pressure positions and pressure dependence of the Yb(3+) energy levels in the trigonal crystal field as well as the pressure-induced changes of the spin-orbit coupling coefficient.

Synthesis, spectroscopic, crystal structure, biological activities and theoretical studies of 2-[(2E)-2-(2-chloro-6-fluorobenzylidene)hydrazinyl]pyridine

NASA Astrophysics Data System (ADS)

Dilek Özçelik, Nefise; Tunç, Tuncay; Çatak Çelik, Raziye; Erzengin, Mahmut; Özışık, Hacı

2017-05-01

We report in this paper the synthesis, spectroscopic, crystal structure, biological activities and theoretical results of the title compound. The crystal structure was defined by the X-ray diffraction (XRD) method. In addition, this newly synthesized hydrazone derivative was also subjected to its possible antioxidant activity with free radical scavenging ability of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals using butylated hydroxytoluene (BHT) as standard antioxidant. The structural calculations were performed by the density functional theory using the B3LYP method with 6-311++G(2d,2p) basis set. The calculated values were compared with experimental results.

Crystal growth and electronic structure of low-temperature phase SrMgF{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atuchin, Victor V.; Functional Electronics Laboratory, Tomsk State University, Tomsk 634050; Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, Novosibirsk 630090

2016-04-15

Using the vertical Bridgman method, the single crystal of low temperature phase SrMgF{sub 4} is obtained. The crystal is in a very good optical quality with the size of 10×7×5 mm{sup 3}. Detailed photoemission spectra of the element core levels are determined by a monochromatic AlKa (1486.6 eV) X-ray source. Moreover, the first-principles calculations are performed to investigate the electronic structure of SrMgF{sub 4}. A good agreement between experimental and calculated results is achieved. It is demonstrated that almost all the electronic orbitals are strongly localized and the hybridization with the others is very small, but the Mg–F bonds covalencymore » is relatively stronger than that of Sr–F bonds. - Graphical abstract: Large size of low-temperature phase SrMgF{sub 4} crystal was obtained (right) and its electronic structure was investigated by X-ray photoelectron spectroscopy and first-principles calculation (left). - Highlights: • Large size single crystal of low-temperature phase SrMgF{sub 4} is obtained. • Electronic structure of SrMgF{sub 4} is measured by X-ray photoelectron spectroscopy. • Partial densities of states are determined by first-principles calculation. • Good agreement between experimental and calculated results is achieved. • Strong ionic characteristics of chemical bonds are exhibited in SrMgF{sub 4}.« less

Photonic crystals possessing multiple Weyl points and the experimental observation of robust surface states

PubMed Central

Chen, Wen-Jie; Xiao, Meng; Chan, C. T.

2016-01-01

Weyl points, as monopoles of Berry curvature in momentum space, have captured much attention recently in various branches of physics. Realizing topological materials that exhibit such nodal points is challenging and indeed, Weyl points have been found experimentally in transition metal arsenide and phosphide and gyroid photonic crystal whose structure is complex. If realizing even the simplest type of single Weyl nodes with a topological charge of 1 is difficult, then making a real crystal carrying higher topological charges may seem more challenging. Here we design, and fabricate using planar fabrication technology, a photonic crystal possessing single Weyl points (including type-II nodes) and multiple Weyl points with topological charges of 2 and 3. We characterize this photonic crystal and find nontrivial 2D bulk band gaps for a fixed kz and the associated surface modes. The robustness of these surface states against kz-preserving scattering is experimentally observed for the first time. PMID:27703140

The young person's guide to the PDB.

PubMed

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.

The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more thanmore » the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.« less

In situ determination of crystal structure and chemistry of minerals at Earth's deep lower mantle conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Hongsheng; Zhang, Li

Recent advances in experimental techniques and data processing allow in situ determination of mineral crystal structure and chemistry up to Mbar pressures in a laser-heated diamond anvil cell (DAC), providing the fundamental information of the mineralogical constitution of our Earth's interior. This work highlights several recent breakthroughs in the field of high-pressure mineral crystallography, including the stability of bridgmanite, the single-crystal structure studies of post-perovskite and H-phase as well as the identification of hydrous minerals and iron oxides in the deep lower mantle. The future development of high-pressure crystallography is also discussed.

Anhydrous crystals of DNA bases are wide gap semiconductors.

PubMed

Maia, F F; Freire, V N; Caetano, E W S; Azevedo, D L; Sales, F A M; Albuquerque, E L

2011-05-07

We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

How large B-factors can be in protein crystal structures.

PubMed

Carugo, Oliviero

2018-02-23

Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.

Formation mechanism of self-assembled polarization-dependent periodic nanostructures in β-Ga2O3

NASA Astrophysics Data System (ADS)

Nakanishi, Y.; Shimotsuma, Y.; Sakakura, M.; Shimizu, M.; Miura, K.

2018-02-01

We have successfully observed self-assembled periodic nanostructures inside Si single crystal and GaP crystal, by the femtosecond double-pulse irradiation. These results experimentally indicate that the self-assembly of the periodic nanostructures inside semiconductors triggered by ultrashort pulses irradiation are possibly associated with a direct or an indirect band gap. More recently we have also empirically classified the photoinduced bulk nanogratings into the following three types: (1) structural deficiency, (2) compressed structure, (3) partial crystallization. We have still a big question about what material properties are involved in the bulk nanograting structure formation. In this study, to expand the selectivity of the material for bulk nanograting formation, we have employed β-Ga2O3 crystals (indirect bandgap Eg 4.8 eV) as a sample for femtosecond laser irradiation. The nanograting structure inside β-Ga2O3 crystal was aligned perpendicular to the laser polarization direction. Such phenomenon is similar to the nanograting in SiO2 glass (Eg 9 eV). Moreover, to clarify the band structure, we have also investigate the photoinduced structure in Sn doped β-Ga2O3 crystals, which exhibit direct bandgap according to the first principle calculation.

Transverse magnetic field impact on waveguide modes of photonic crystals.

PubMed

Sylgacheva, Daria; Khokhlov, Nikolai; Kalish, Andrey; Dagesyan, Sarkis; Prokopov, Anatoly; Shaposhnikov, Alexandr; Berzhansky, Vladimir; Nur-E-Alam, Mohammad; Vasiliev, Mikhail; Alameh, Kamal; Belotelov, Vladimir

2016-08-15

This Letter presents a theoretical and experimental study of waveguide modes of one-dimensional magneto-photonic crystals magnetized in the in-plane direction. It is shown that the propagation constants of the TM waveguide modes are sensitive to the transverse magnetization and the spectrum of the transverse magneto-optical Kerr effect has resonant features at mode excitation frequencies. Two types of structures are considered: a non-magnetic photonic crystal with an additional magnetic layer on top and a magneto-photonic crystal with a magnetic layer within each period. We found that the magneto-optical non-reciprocity effect is greater in the first case: it has a magnitude of δ∼10^-4, while the second structure type demonstrates δ∼10^-5 only, due to the higher asymmetry of the claddings of the magnetic layer. Experimental observations show resonant features in the optical and magneto-optical Kerr effect spectra. The measured dispersion properties are in good agreement with the theoretical predictions. An amplitude of light intensity modulation of up to 2.5% was observed for waveguide mode excitation within the magnetic top layer of the non-magnetic photonic crystal structure. The presented theoretical approach may be utilized for the design of magneto-optical sensors and modulators requiring pre-determined spectral features.

Selenium Derivatization of Nucleic Acids for Crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang,J.; Sheng, J.; Carrasco, N.

2007-01-01

The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 {angstrom} resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 {angstrom}). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 {angstrom} resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native andmore » Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.« less

Growth of a New Ternary BON Crystal on Si(100) by Plasma-Assisted MOCVD and Study on the Effects of Fed Gas and Growth Temperature

NASA Astrophysics Data System (ADS)

Chen, G. C.; Lee, S.-B.; Boo, J.-H.

A new ternary BOxNy crystal was grown on Si(100) substrate at 500°C by low-frequency (100 kHz) radio-frequency (rf) derived plasma-assisted MOCVD with an organoborate precursor. The as-grown deposits were characterized by SEM, TED, XPS, XRD, AFM and FT-IR. The experimental results showed that BOxNy crystal was apt to be formed at N-rich atmosphere and high temperature. The decrease of hydrogen flux in fed gases was of benefit to form BON crystal structure. The crystal structure of BOxNy was as similar to that of H3BO3 in this study.

Supramolecular features of 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino]-2,3-dihydroquinazolin-4(1H)-ones: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Mandal, Arkalekha; Patel, Bhisma K.

2018-03-01

The molecular structures of two isomeric 2-(chlorophenyl)-3-[(chlorobenzylidene)-amino] substituted 2,3-dihydroquinazolin-4(1H)-ones have been determined via single crystal XRD. Both isomers contain chloro substitutions on each of the phenyl rings and as a result a broad spectrum of halogen mediated weak interactions are viable in their crystal structures. The crystal packing of these compounds is stabilized by strong N-H⋯O hydrogen bond and various weak, non-classical hydrogen bonds acting synergistically. Both the molecules contain a chiral center and the weak interactions observed in them are either chiral self-discriminatory or chiral self-recognizing in nature. The weak interactions and spectral features of the compounds have been studied through experimental as well as computational methods including DFT, MEP, NBO and Hiresfeld surface analyses. In addition, the effect of different weak interactions to dictate either chiral self-recognition or self-discrimination in crystal packing has been elucidated.

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

PubMed

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.

Structure and crystallization of SiO2 and B2O3 doped lithium disilicate glasses from theory and experiment.

PubMed

Erlebach, Andreas; Thieme, Katrin; Sierka, Marek; Rüssel, Christian

2017-09-27

Solid solutions of SiO 2 and B 2 O 3 in Li 2 O·2SiO 2 are synthesized and characterized for the first time. Their structure and crystallization mechanisms are investigated employing a combination of simulations at the density functional theory level and experiments on the crystallization of SiO 2 and B 2 O 3 doped lithium disilicate glasses. The remarkable agreement of calculated and experimentally determined cell parameters reveals the preferential, kinetically controlled incorporation of [SiO 4 ] and [BO 4 ] at the Li + lattice sites of the Li 2 O·2SiO 2 crystal structure. While the addition of SiO 2 increases the glass viscosity resulting in lower crystal growth velocities, glasses containing B 2 O 3 show a reduction of both viscosities and crystal growth velocities. These observations could be rationalized by a change of the chemical composition of the glass matrix surrounding the precipitated crystal phase during the course of crystallization, which leads to a deceleration of the attachment of building units required for further crystal growth at the liquid-crystal interface.

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

PubMed Central

Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

2009-01-01

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

Ab initio crystal structure prediction of magnesium (poly)sulfides and calculation of their NMR parameters.

PubMed

Mali, Gregor

2017-03-01

Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS 2 , exhibiting a modified rocksalt structure, in which S 2- anions were replaced by S 2 2- dianions. Magnesium polysulfides with even larger fractions of sulfur were not predicted to be stable. For the lowest-energy structures, 25 Mg quadrupolar coupling constants and chemical shift parameters were calculated using the density functional theory approach. The calculated NMR parameters could be well rationalized by the symmetries of the local magnesium environments, by the coordination of magnesium cations and by the nature of the surrounding anions. In the future, these parameters could serve as a reference for the experimentally determined 25 Mg NMR parameters of magnesium sulfide species.

Experimental study of broadband unidirectional splitting in photonic crystal gratings with broken structural symmetry

NASA Astrophysics Data System (ADS)

Colak, Evrim; Serebryannikov, Andriy E.; Ozgur Cakmak, A.; Ozbay, Ekmel

2013-04-01

It is experimentally demonstrated that the combination of diode and splitter functions can be realized in one broadband reciprocal device. The suggested performance is based on the dielectric photonic crystal grating whose structural symmetry is broken owing to non-deep corrugations placed at one of the two interfaces. The study has been performed at a normally incident beam-type illumination obtained from a microwave horn antenna. The two unidirectionally transmitted, deflected beams can show large magnitude and high contrast, while the angular distance between their maxima is 90° and larger. The dual-band unidirectional splitting is possible when using TM and TE polarizations.

Achieving omnidirectional photonic band gap in sputter deposited TiO{sub 2}/SiO{sub 2} one dimensional photonic crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jena, S., E-mail: shuvendujena9@gmail.com; Tokas, R. B.; Sarkar, P.

2015-06-24

The multilayer structure of TiO{sub 2}/SiO{sub 2} (11 layers) as one dimensional photonic crystal (1D PC) has been designed and then fabricated by using asymmetric bipolar pulse DC magnetron sputtering technique for omnidirectional photonic band gap. The experimentally measured photonic band gap (PBG) in the visible region is well matched with the theoretically calculated band structure (ω vs. k) diagram. The experimentally measured omnidirectional reflection band of 44 nm over the incident angle range of 0°-70° is found almost matching within the theoretically calculated band.

Shaping Crystal-Crystal Phase Transitions

NASA Astrophysics Data System (ADS)

Du, Xiyu; van Anders, Greg; Dshemuchadse, Julia; Glotzer, Sharon

Previous computational and experimental studies have shown self-assembled structure depends strongly on building block shape. New synthesis techniques have led to building blocks with reconfigurable shape and it has been demonstrated that building block reconfiguration can induce bulk structural reconfiguration. However, we do not understand systematically how this transition happens as a function of building block shape. Using a recently developed ``digital alchemy'' framework, we study the thermodynamics of shape-driven crystal-crystal transitions. We find examples of shape-driven bulk reconfiguration that are accompanied by first-order phase transitions, and bulk reconfiguration that occurs without any thermodynamic phase transition. Our results suggest that for well-chosen shapes and structures, there exist facile means of bulk reconfiguration, and that shape-driven bulk reconfiguration provides a viable mechanism for developing functional materials.

Combinatorial selection of molecular conformations and supramolecular synthons in quercetin cocrystal landscapes: a route to ternary solids

PubMed Central

Dubey, Ritesh; Desiraju, Gautam R.

2015-01-01

The crystallization of 28 binary and ternary cocrystals of quercetin with dibasic coformers is analyzed in terms of a combinatorial selection from a solution of preferred molecular conformations and supramolecular synthons. The crystal structures are characterized by distinctive O—H⋯N and O—H⋯O based synthons and are classified as nonporous, porous and helical. Variability in molecular conformation and synthon structure led to an increase in the energetic and structural space around the crystallization event. This space is the crystal structure landscape of the compound and is explored by fine-tuning the experimental conditions of crystallization. In the landscape context, we develop a strategy for the isolation of ternary cocrystals with the use of auxiliary template molecules to reduce the molecular and supramolecular ‘confusion’ that is inherent in a molecule like quercetin. The absence of concomitant polymorphism in this study highlights the selectivity in conformation and synthon choice from the virtual combinatorial library in solution. PMID:26175900

Mono- and polynucleation, atomistic growth, and crystal phase of III-V nanowires under varying group V flow

NASA Astrophysics Data System (ADS)

Dubrovskii, V. G.

2015-05-01

We present a refined model for the vapor-liquid-solid growth and crystal structure of Au-catalyzed III-V nanowires, which revisits several assumptions used so far and is capable of describing the transition from mononuclear to polynuclear regime and ultimately to regular atomistic growth. We construct the crystal phase diagrams and calculate the wurtzite percentages, elongation rates, critical sizes, and polynucleation thresholds of Au-catalyzed GaAs nanowires depending on the As flow. We find a non-monotonic dependence of the crystal phase on the group V flow, with the zincblende structure being preferred at low and high group V flows and the wurtzite structure forming at intermediate group V flows. This correlates with most of the available experimental data. Finally, we discuss the atomistic growth picture which yields zincblende crystal structure and should be very advantageous for fabrication of ternary III-V nanowires with well-controlled composition and heterointerfaces.

Structural study of piracetam polymorphs and cocrystals: crystallography redetermination and quantum mechanics calculations.

PubMed

Tilborg, Anaëlle; Jacquemin, Denis; Norberg, Bernadette; Perpète, Eric; Michaux, Catherine; Wouters, Johan

2011-12-01

Pharmaceutical compounds are mostly developed as solid dosage forms containing a single-crystal form. It means that the selection of a particular crystal state for a given molecule is an important step for further clinical outlooks. In this context, piracetam, a pharmaceutical molecule known since the sixties for its nootropic properties, is considered in the present work. This molecule is analyzed using several experimental and theoretical approaches. First, the conformational space of the molecule has been systematically explored by performing a quantum mechanics scan of the two most relevant dihedral angles of the lateral chain. The predicted stable conformations have been compared to all the reported experimental geometries retrieved from the Cambridge Structural Database (CSD) covering polymorphs and cocrystals structures. In parallel, different batches of powders have been recrystallized. Under specific conditions, single crystals of polymorph (III) of piracetam have been obtained, an outcome confirmed by crystallographic analysis. © 2011 International Union of Crystallography. Printed in Singapore – all rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jiusheng; van den Bedem, Henry; Brunger, Axel T.

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+-CaM, but no assignment of these features has been made. In addition, Ca 2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+-CaM. Density-modified electron-density mapsmore » enabled the accurate assignment of Ca 2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.« less

Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.

PubMed Central

Hummer, G; García, A E; Soumpasis, D M

1995-01-01

A computationally efficient method to describe the organization of water around solvated biomolecules is presented. It is based on a statistical mechanical expression for the water-density distribution in terms of particle correlation functions. The method is applied to analyze the hydration of small nucleic acid molecules in the crystal environment, for which high-resolution x-ray crystal structures have been reported. Results for RNA [r(ApU).r(ApU)] and DNA [d(CpG).d(CpG) in Z form and with parallel strand orientation] and for DNA-drug complexes [d(CpG).d(CpG) with the drug proflavine intercalated] are described. A detailed comparison of theoretical and experimental data shows positional agreement for the experimentally observed water sites. The presented method can be used for refinement of the water structure in x-ray crystallography, hydration analysis of nuclear magnetic resonance structures, and theoretical modeling of biological macromolecules such as molecular docking studies. The speed of the computations allows hydration analyses of molecules of almost arbitrary size (tRNA, protein-nucleic acid complexes, etc.) in the crystal environment and in aqueous solution. Images FIGURE 1 FIGURE 2 FIGURE 5 FIGURE 6 FIGURE 9 FIGURE 12 FIGURE 13 PMID:7542034

A combined experimental and in silico characterization to highlight additional structural features and properties of a potentially new drug

NASA Astrophysics Data System (ADS)

Bastos, Isadora T. S.; Costa, Fanny N.; Silva, Tiago F.; Barreiro, Eliezer J.; Lima, Lídia M.; Braz, Delson; Lombardo, Giuseppe M.; Punzo, Francesco; Ferreira, Fabio F.; Barroso, Regina C.

2017-10-01

LASSBio-1755 is a new cycloalkyl-N-acylhydrazone parent compound designed for the development of derivatives with antinociceptive and anti-inflammatory activities. Although single crystal X-ray diffraction has been considered as the golden standard in structure determination, we successfully used X-ray powder diffraction data in the structural determination of new synthesized compounds, in order to overcome the bottle-neck due to the difficulties experienced in harvesting good quality single crystals of the compounds. We therefore unequivocally assigned the relative configuration (E) to the imine double bond and a s-cis conformation of the amide function of the N-acylhydrazone compound. These features are confirmed by a computational analysis performed on the basis of molecular dynamics calculations, which are extended not only to the structural characteristics but also to the analysis of the anisotropic atomic displacement parameters, a further information - missed in a typical powder diffraction analysis. The so inferred data were used to perform additional cycles of refinement and eventually generate a new cif file with additional physical information. Furthermore, crystal morphology prediction was performed, which is in agreement with the experimental images acquired by scanning electron microscopy, thus providing useful information on possible alternative paths for better crystallization strategies.

Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Gunasekaran, S.; Anbalagan, G.

Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.

Photonic crystal fiber sensing characteristics research based on alcohol asymmetry filling

NASA Astrophysics Data System (ADS)

Shi, Fu-quan; Luo, Yan; Li, Hai-tao; Peng, Bao-jin

2018-02-01

A new type of Sagnac fiber temperature sensor based on alcohol asymmetric filling photonic crystal fiber is proposed. First, the corrosion of photonic crystal fiber and the treatment of air hole collapse are carried out. Then, the asymmetric structure of photonic crystal fiber is filled with alcohol, and then the structure is connected to the Sagnac interference ring. When the temperature changes, the thermal expansion effect of filling alcohol will lead to the change of birefringence of photonic crystal fiber, so that the interference spectrum of the sensor will drift along with the change of temperature. The experimental results show that the interference red shift will occur with the increase of temperature, and the temperature sensitivity is 0.1864nm/ °C. The sensor has high sensitivity to temperature. At the same time, the structure has the advantages of high stability, anti electromagnetic interference and easy to build. It provides a new method for obtaining birefringence in ordinary photonic crystal fibers.

Spiro-OMeTAD single crystals: Remarkably enhanced charge-carrier transport via mesoscale ordering

PubMed Central

Shi, Dong; Qin, Xiang; Li, Yuan; He, Yao; Zhong, Cheng; Pan, Jun; Dong, Huanli; Xu, Wei; Li, Tao; Hu, Wenping; Brédas, Jean-Luc; Bakr, Osman M.

2016-01-01

We report the crystal structure and hole-transport mechanism in spiro-OMeTAD [2,2′,7,7′-tetrakis(N,N-di-p-methoxyphenyl-amine)9,9′-spirobifluorene], the dominant hole-transporting material in perovskite and solid-state dye-sensitized solar cells. Despite spiro-OMeTAD’s paramount role in such devices, its crystal structure was unknown because of highly disordered solution-processed films; the hole-transport pathways remained ill-defined and the charge carrier mobilities were low, posing a major bottleneck for advancing cell efficiencies. We devised an antisolvent crystallization strategy to grow single crystals of spiro-OMeTAD, which allowed us to experimentally elucidate its molecular packing and transport properties. Electronic structure calculations enabled us to map spiro-OMeTAD’s intermolecular charge-hopping pathways. Promisingly, single-crystal mobilities were found to exceed their thin-film counterparts by three orders of magnitude. Our findings underscore mesoscale ordering as a key strategy to achieving breakthroughs in hole-transport material engineering of solar cells. PMID:27152342

Protein crystal growth in space

NASA Technical Reports Server (NTRS)

Bugg, C. E.; Clifford, D. W.

1987-01-01

The advantages of protein crystallization in space, and the applications of protein crystallography to drug design, protein engineering, and the design of synthetic vaccines are examined. The steps involved in using protein crystallography to determine the three-dimensional structure of a protein are discussed. The growth chamber design and the hand-held apparatus developed for protein crystal growth by vapor diffusion techniques (hanging-drop method) are described; the experimental data from the four Shuttle missions are utilized to develop hardware for protein crystal growth in space and to evaluate the effects of gravity on protein crystal growth.

Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

NASA Astrophysics Data System (ADS)

Moreira, Rafael Y. O.; Brasil, Davi S. B.; Alves, Cláudio N.; Guilhon, Giselle M. S. P.; Santos, Lourivaldo S.; Arruda, Mara S. P.; Müller, Adolfo H.; Barbosa, Patrícia S.; Abreu, Alcicley S.; Silva, Edilene O.; Rumjanek, Victor M.; Souza, Jaime, Jr.; da Silva, Albérico B. F.; Santos, Regina H. De A.

Julocrotine, N-(2,6-dioxo-1-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data.0

Four-port coupled channel-guide device based on 2D photonic crystal structure

NASA Astrophysics Data System (ADS)

Camargo, Edilson A.; Chong, Harold M. H.; De La Rue, Richard M.

2004-12-01

We have fabricated and measured a four-port coupled channel-waveguide device using W1 channel waveguides oriented along ΓK directions in a two-dimensional (2D) hole-based planar photonic crystal (PhC) based on silicon-on-insulator (SOI) waveguide material, at operation wavelengths around 1550 nm. 2D FDTD simulations and experimental results are shown and compared. The structure has been designed using a mode conversion approach, combined with coupled-mode concepts. The overall length of the photonic crystal structure is typically about 39 μm and the structure has been fabricated using a combination of direct-write electron-beam lithography (EBL) and dry-etch processing. Devices were measured using a tunable laser with end-fire coupling into the planar structure.

Effects of surface stability on the morphological transformation of metals and metal oxides as investigated by first-principles calculations.

PubMed

Andrés, Juan; Gracia, Lourdes; Gouveia, Amanda Fernandes; Ferrer, Mateus Meneghetti; Longo, Elson

2015-10-09

Morphology is a key property of materials. Owing to their precise structure and morphology, crystals and nanocrystals provide excellent model systems for joint experimental and theoretical investigations into surface-related properties. Faceted polyhedral crystals and nanocrystals expose well-defined crystallographic planes depending on the synthesis method, which allow for thoughtful investigations into structure-reactivity relationships under practical conditions. This feature article introduces recent work, based on the combined use of experimental findings and first-principles calculations, to provide deeper knowledge of the electronic, structural, and energetic properties controlling the morphology and the transformation mechanisms of different metals and metal oxides: Ag, anatase TiO2, BaZrO3, and α-Ag2WO4. According to the Wulff theorem, the equilibrium shapes of these systems are obtained from the values of their respective surface energies. These investigations are useful to gain further understanding of how to achieve morphological control of complex three-dimensional crystals by tuning the ratio of the surface energy values of the different facets. This strategy allows the prediction of possible morphologies for a crystal and/or nanocrystal by controlling the relative values of surface energies.

Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4YbI 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yuntao; Chakoumakos, Bryan C.; Shi, Hongliang

A self-activated Cs 4YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of more » $$\\bar{R}$$3 c. By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.« less

Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4YbI 6

DOE PAGES

Wu, Yuntao; Chakoumakos, Bryan C.; Shi, Hongliang; ...

2018-05-14

A self-activated Cs 4YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of more » $$\\bar{R}$$3 c. By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.« less

A framework for multi-scale simulation of crystal growth in the presence of polymers.

PubMed

Mandal, Taraknath; Huang, Wenjun; Mecca, Jodi M; Getchell, Ashley; Porter, William W; Larson, Ronald G

2017-03-01

We present a multi-scale simulation method for modeling crystal growth in the presence of polymer excipients. The method includes a coarse-grained (CG) model for small molecules of known crystal structure whose force field is obtained using structural properties from atomistic simulations. This CG model is capable of stabilizing the molecular crystal structure and capturing the crystal growth from the melt for a wide range of small organic molecules, as demonstrated by application of our method to the molecules isoniazid, urea, sulfamethoxazole, prilocaine, oxcarbazepine, and phenytoin. This CG model can also be used to study the effect of additives, such as polymers, on the inhibition of crystal growth by polymers, as exemplified by our simulation of suppression of the rate of crystal growth of phenytoin, an active pharmaceutical ingredient (API), by a cellulose excipient, functionalized with acetate (Ac), hydroxy-propyl (Hp) and succinate (Su) groups. We show that the efficacy of the cellulosic polymers in slowing crystal growth of small molecules strongly depends on the functional group substitution on the cellulose backbone, with the acetate substituent group slowing crystal growth more than does the deprotonated succinate group, which we confirm by experimental drug supersaturation studies.

Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eliziario Nunes, Sayonara; Department of Materials Engineering, Federal University of São Carlos, 13565-905 São Carlos, SP; Wang, Chun-Hai

2015-02-15

We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu;more » A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.« less

Energetic band structure of Zn3P2 crystals

NASA Astrophysics Data System (ADS)

Stamov, I. G.; Syrbu, N. N.; Dorogan, A. V.

2013-01-01

Optical functions n, k, ε1, ε2 and d2ε2/dE2 have been determined from experimental reflection spectra in the region of 1-10 eV. The revealed electronic transitions are localized in the Brillouin zone. The magnitude of valence band splitting caused by the spin-orbital interaction ΔSO is lower than the splitting caused by the crystal field ΔCR in the center of Brillouin zone and L and X points. The switching effects are investigated in Zn3P2 crystals. The characteristics of experimental samples with electric switching, adjustable resistors, and time relays based on Zn3P2 are presented.

Optical properties of B12P2 crystals: Ab initio calculation and EELS

NASA Astrophysics Data System (ADS)

Reshetniak, V. V.; Mavrin, B. N.; Medvedev, V. V.; Perezhogin, I. A.; Kulnitskiy, B. A.

2018-05-01

We report an experimental and theoretical investigation of the electronic structure and optical properties of B12P2 crystals in the energy range up to 60 eV. Experimental studies are performed by the method of electron energy loss spectroscopy, and theoretical studies are carried out using density functional theory and the GW approximation. The calculated dependence of the energy loss function is in agreement with the experiment. Based on the results of the calculations, we determine the optical properties of B12P2 crystals and investigate their anisotropy. The dispersion and density of electronic states are calculated and analyzed.

The young person’s guide to the PDB*

PubMed Central

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2017-01-01

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120,000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview. PMID:28132477

Structure-property relationship of 3-(4-substituted benzyl)-1,3-diazaspiro[4.4]nonane-2,4-diones as new potentional anticonvulsant agents. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Lazić, Anita M.; Božić, Bojan Đ.; Vitnik, Vesna D.; Vitnik, Željko J.; Rogan, Jelena R.; Radovanović, Lidija D.; Valentić, Nataša V.; Ušćumlić, Gordana S.

2017-01-01

The structure-property relationship of newly synthesized 3-(4-substituted benzyl)-1,3-diazaspiro [4.4]nonane-2,4-diones was studied by experimental and calculated methods. The prepared compounds were characterized by UV-Vis, FT-IR, 1H NMR and 13C NMR spectroscopy and elemental analysis. The crystal structure was elucidated by single-crystal X-ray diffraction. The 3-benzyl-1,3-diazaspiro[4.4]nonane-2,4-dione crystallizes in triclinic P-1 space group, with two crystallographically independent molecules in the asymmetric unit. Cyclopentane ring adopts an envelope conformation. A three-dimensional crystal packing is governed by hydrogen N-H⋯O bonds, numerous C-H⋯O/N and C-H … π interactions between neighboring molecules. Density functional theory (DFT) calculations with B3LYP and M06-2X methods using 6-311++G(d,p) basis set were performed to provide structural and spectroscopic information. Comparisons between experimental and calculated UV-Vis spectral properties suggest that the monomeric form of the investigated spirohydantoins is dominant in all used solvents. The effects of substituents on the absorption spectra of spirohydantoins are interpreted by correlation of absorption frequencies with Hammett equation. The lipophilicities of the investigated molecules were estimated by calculation of their log P values. Some of the spirohydantoins synthesized in this work, exhibit the lipophilicities comparable to the standard medicine anticonvulsant drug Phenytoin. The results obtained in this investigation afford guidelines for the preparation of new derivatives of spirohydantoin as potential anticonvulsant agents and for better understanding the structure-activity relationship.

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Negative refraction angular characterization in one-dimensional photonic crystals.

PubMed

Lugo, Jesus Eduardo; Doti, Rafael; Faubert, Jocelyn

2011-04-06

Photonic crystals are artificial structures that have periodic dielectric components with different refractive indices. Under certain conditions, they abnormally refract the light, a phenomenon called negative refraction. Here we experimentally characterize negative refraction in a one dimensional photonic crystal structure; near the low frequency edge of the fourth photonic bandgap. We compare the experimental results with current theory and a theory based on the group velocity developed here. We also analytically derived the negative refraction correctness condition that gives the angular region where negative refraction occurs. By using standard photonic techniques we experimentally determined the relationship between incidence and negative refraction angles and found the negative refraction range by applying the correctness condition. In order to compare both theories with experimental results an output refraction correction was utilized. The correction uses Snell's law and an effective refractive index based on two effective dielectric constants. We found good agreement between experiment and both theories in the negative refraction zone. Since both theories and the experimental observations agreed well in the negative refraction region, we can use both negative refraction theories plus the output correction to predict negative refraction angles. This can be very useful from a practical point of view for space filtering applications such as a photonic demultiplexer or for sensing applications.

Negative Refraction Angular Characterization in One-Dimensional Photonic Crystals

PubMed Central

Lugo, Jesus Eduardo; Doti, Rafael; Faubert, Jocelyn

2011-01-01

Background Photonic crystals are artificial structures that have periodic dielectric components with different refractive indices. Under certain conditions, they abnormally refract the light, a phenomenon called negative refraction. Here we experimentally characterize negative refraction in a one dimensional photonic crystal structure; near the low frequency edge of the fourth photonic bandgap. We compare the experimental results with current theory and a theory based on the group velocity developed here. We also analytically derived the negative refraction correctness condition that gives the angular region where negative refraction occurs. Methodology/Principal Findings By using standard photonic techniques we experimentally determined the relationship between incidence and negative refraction angles and found the negative refraction range by applying the correctness condition. In order to compare both theories with experimental results an output refraction correction was utilized. The correction uses Snell's law and an effective refractive index based on two effective dielectric constants. We found good agreement between experiment and both theories in the negative refraction zone. Conclusions/Significance Since both theories and the experimental observations agreed well in the negative refraction region, we can use both negative refraction theories plus the output correction to predict negative refraction angles. This can be very useful from a practical point of view for space filtering applications such as a photonic demultiplexer or for sensing applications. PMID:21494332

Crystal growth, structure and morphology of hydrocortisone methanol solvate

NASA Astrophysics Data System (ADS)

Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

2004-04-01

Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

Atomistic polarizable force field for molecular dynamics simulations of azide anion containing ionic liquids and crystals.

NASA Astrophysics Data System (ADS)

Starovoytov, Oleg; Hooper, Justin; Borodin, Oleg; Smith, Grant

2010-03-01

Atomistic polarizable force field has been developed for a number of azide anion containing ionic liquids and crystals. Hybrid Molecular Dynamics/Monte Carlo (MD/MC) simulations were performed on methylguanazinium azide and 1-(2-butynyl)-3-methyl-imidazolium azide crystals, while 1-butyl-2,3-dimethylimidazolium azide and 1-amino-3-methyl-1,2,3-triazolium azide ionic liquids were investigated using MD simulations. Crystal cell parameters and crystal structures of 1-(2-butynyl)-3-methyl-imidazolium azide were found in good agreement with X-ray experimental data. Density and ion transport of 1-butyl-2,3-dimethylimidazolium azide predicted from MD simulations were in good agreement with experiments. Details of the ionic liquid structure and relaxation mechanism will be discussed.

Electrostatics at the nanoscale.

PubMed

Walker, David A; Kowalczyk, Bartlomiej; de la Cruz, Monica Olvera; Grzybowski, Bartosz A

2011-04-01

Electrostatic forces are amongst the most versatile interactions to mediate the assembly of nanostructured materials. Depending on experimental conditions, these forces can be long- or short-ranged, can be either attractive or repulsive, and their directionality can be controlled by the shapes of the charged nano-objects. This Review is intended to serve as a primer for experimentalists curious about the fundamentals of nanoscale electrostatics and for theorists wishing to learn about recent experimental advances in the field. Accordingly, the first portion introduces the theoretical models of electrostatic double layers and derives electrostatic interaction potentials applicable to particles of different sizes and/or shapes and under different experimental conditions. This discussion is followed by the review of the key experimental systems in which electrostatic interactions are operative. Examples include electroactive and "switchable" nanoparticles, mixtures of charged nanoparticles, nanoparticle chains, sheets, coatings, crystals, and crystals-within-crystals. Applications of these and other structures in chemical sensing and amplification are also illustrated.

The Nucleation and Growth of Protein Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc

2004-01-01

Obtaining crystals of suitable size and high quality continues to be a major bottleneck in macromolecular crystallography. Currently, structural genomics efforts are achieving on average about a 10% success rate in going from purified protein to a deposited crystal structure. Growth of crystals in microgravity was proposed as a means of overcoming size and quality problems, which subsequently led to a major NASA effort in microgravity crystal growth, with the agency also funding research into understanding the process. Studies of the macromolecule crystal nucleation and growth process were carried out in a number of labs in an effort to understand what affected the resultant crystal quality on Earth, and how microgravity improved the process. Based upon experimental evidence, as well as simple starting assumptions, we have proposed that crystal nucleation occurs by a series of discrete self assembly steps, which 'set' the underlying crystal symmetry. This talk will review the model developed, and its origins, in our laboratory for how crystals nucleate and grow, and will then present, along with preliminary data, how we propose to use this model to improve the success rate for obtaining crystals from a given protein.

Experimental demonstration of a ferroelectric liquid crystal tunable filter for fast demodulation of FBG sensors

NASA Astrophysics Data System (ADS)

Mathews, Sunish; Semenova, Yuliya; Rajan, Ginu; Farrell, Gerald

2009-05-01

A discretely tunable Surface-Stabilized Ferroelectric Liquid Crystal based Lyot Filter, with tuning speeds in the order of microseconds, is demonstrated experimentally as a channel dropper for the demodulation of multiple Fibre Bragg Grating sensors. The 3-stage Lyot Filter designed and experimentally verified can be used together with the high-speed ratiometric wavelength measurement system employing a fibre bend loss edge filter. Such systems can be used for the demodulation of distributed Fibre Bragg Grating sensors employed in applications such as structural monitoring, industrial sensing and haptic telerobotic surgical systems.

Time crystals: a review

NASA Astrophysics Data System (ADS)

Sacha, Krzysztof; Zakrzewski, Jakub

2018-01-01

Time crystals are time-periodic self-organized structures postulated by Frank Wilczek in 2012. While the original concept was strongly criticized, it stimulated at the same time an intensive research leading to propositions and experimental verifications of discrete (or Floquet) time crystals—the structures that appear in the time domain due to spontaneous breaking of discrete time translation symmetry. The struggle to observe discrete time crystals is reviewed here together with propositions that generalize this concept introducing condensed matter like physics in the time domain. We shall also revisit the original Wilczek’s idea and review strategies aimed at spontaneous breaking of continuous time translation symmetry.

Extraordinary absorption of sound in porous lamella-crystals.

PubMed

Christensen, J; Romero-García, V; Picó, R; Cebrecos, A; de Abajo, F J García; Mortensen, N A; Willatzen, M; Sánchez-Morcillo, V J

2014-04-14

We present the design of a structured material supporting complete absorption of sound with a broadband response and functional for any direction of incident radiation. The structure which is fabricated out of porous lamellas is arranged into a low-density crystal and backed by a reflecting support. Experimental measurements show that strong all-angle sound absorption with almost zero reflectance takes place for a frequency range exceeding two octaves. We demonstrate that lowering the crystal filling fraction increases the wave interaction time and is responsible for the enhancement of intrinsic material dissipation, making the system more absorptive with less material.

Extraordinary absorption of sound in porous lamella-crystals

PubMed Central

Christensen, J.; Romero-García, V.; Picó, R.; Cebrecos, A.; de Abajo, F. J. García; Mortensen, N. A.; Willatzen, M.; Sánchez-Morcillo, V. J.

2014-01-01

We present the design of a structured material supporting complete absorption of sound with a broadband response and functional for any direction of incident radiation. The structure which is fabricated out of porous lamellas is arranged into a low-density crystal and backed by a reflecting support. Experimental measurements show that strong all-angle sound absorption with almost zero reflectance takes place for a frequency range exceeding two octaves. We demonstrate that lowering the crystal filling fraction increases the wave interaction time and is responsible for the enhancement of intrinsic material dissipation, making the system more absorptive with less material. PMID:24728322

Photonic crystals, amorphous materials, and quasicrystals

PubMed Central

Edagawa, Keiichi

2014-01-01

Photonic crystals consist of artificial periodic structures of dielectrics, which have attracted much attention because of their wide range of potential applications in the field of optics. We may also fabricate artificial amorphous or quasicrystalline structures of dielectrics, i.e. photonic amorphous materials or photonic quasicrystals. So far, both theoretical and experimental studies have been conducted to reveal the characteristic features of their optical properties, as compared with those of conventional photonic crystals. In this article, we review these studies and discuss various aspects of photonic amorphous materials and photonic quasicrystals, including photonic band gap formation, light propagation properties, and characteristic photonic states. PMID:27877676

Photonic crystals, amorphous materials, and quasicrystals.

PubMed

Edagawa, Keiichi

2014-06-01

Photonic crystals consist of artificial periodic structures of dielectrics, which have attracted much attention because of their wide range of potential applications in the field of optics. We may also fabricate artificial amorphous or quasicrystalline structures of dielectrics, i.e. photonic amorphous materials or photonic quasicrystals. So far, both theoretical and experimental studies have been conducted to reveal the characteristic features of their optical properties, as compared with those of conventional photonic crystals. In this article, we review these studies and discuss various aspects of photonic amorphous materials and photonic quasicrystals, including photonic band gap formation, light propagation properties, and characteristic photonic states.

Experimental demonstration of two-dimensional hybrid waveguide-integrated plasmonic crystals on silicon-on-insulator platform

NASA Astrophysics Data System (ADS)

Ren, Guanghui; Yudistira, Didit; Nguyen, Thach G.; Khodasevych, Iryna; Schoenhardt, Steffen; Berean, Kyle J.; Hamm, Joachim M.; Hess, Ortwin; Mitchell, Arnan

2017-07-01

Nanoscale plasmonic structures can offer unique functionality due to extreme sub-wavelength optical confinement, but the realization of complex plasmonic circuits is hampered by high propagation losses. Hybrid approaches can potentially overcome this limitation, but only few practical approaches based on either single or few element arrays of nanoantennas on dielectric nanowire have been experimentally demonstrated. In this paper, we demonstrate a two dimensional hybrid photonic plasmonic crystal interfaced with a standard silicon photonic platform. Off resonance, we observe low loss propagation through our structure, while on resonance we observe strong propagation suppression and intense concentration of light into a dense lattice of nanoscale hot-spots on the surface providing clear evidence of a hybrid photonic plasmonic crystal bandgap. This fully integrated approach is compatible with established silicon-on-insulator (SOI) fabrication techniques and constitutes a significant step toward harnessing plasmonic functionality within SOI photonic circuits.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

Hydrolytic degradation of N,N‧-ethylenedimaleimide: Crystal structures of key intermediates and proposed mechanisms

NASA Astrophysics Data System (ADS)

Tan, Xue-Jie; Cheng, Shuang-Shuang; Shi, Yan; Xing, Dian-Xiang; Liu, Yun; Li, Hui; Feng, Wen-Quan; Yang, Jian-Bo

2016-12-01

Maleimide groups are used extensively in bioconjugation reactions, but limited mechanistic studies are available regarding their hydrolysis reactions. In this paper, five single-crystal structures related with the reaction of four-step hydrolytic degradation of N,N‧-ethylenedimaleimide have been investigated. On the basis of experimental results, the reaction mechanisms without or with water catalysis are proposed, which could provide some enlightenment into the study of similar hydrolytic degradations.

Solubility prediction of naphthalene in carbon dioxide from crystal microstructure

NASA Astrophysics Data System (ADS)

Sang, Jiarong; Jin, Junsu; Mi, Jianguo

2018-03-01

Crystals dissolved in solvents are ubiquitous in both natural and artificial systems. Due to the complicated structures and asymmetric interactions between the crystal and solvent, it is difficult to interpret the dissolution mechanism and predict solubility using traditional theories and models. Here we use the classical density functional theory (DFT) to describe the crystal dissolution behavior. As an example, naphthalene dissolved in carbon dioxide (CO2) is considered within the DFT framework. The unit cell dimensions and microstructure of crystalline naphthalene are determined by minimizing the free-energy of the crystal. According to the microstructure, the solubilities of naphthalene in CO2 are predicted based on the equality of naphthalene's chemical potential in crystal and solution phases, and the interfacial structures and free-energies between different crystal planes and solution are determined to investigate the dissolution mechanism at the molecular level. The theoretical predictions are in general agreement with the available experimental data, implying that the present model is quantitatively reliable in describing crystal dissolution.

Multiple chiral topological states in liquid crystals from unstructured light beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loussert, Charles; Brasselet, Etienne, E-mail: e.brasselet@loma.u-bordeaux1.fr

2014-02-03

It is shown experimentally that unstructured light beams can generate a wealth of distinct metastable defect structures in thin films of chiral liquid crystals. Various kinds of individual chiral topological states are obtained as well as dimers and trimers, which correspond to the entanglement of several topological unit cells. Self-assembled nested assemblies of several metastable particle-like topological states can also be formed. Finally, we propose and experimentally demonstrate an opto-electrical approach to generate tailor-made architectures.

Center for Macromolecular Crystallography, University of Alabama in Birmingham

NASA Technical Reports Server (NTRS)

Navia, Manuel A.

1991-01-01

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

Mechanical Characterization of Partially Crystallized Sphere Packings

NASA Astrophysics Data System (ADS)

Hanifpour, M.; Francois, N.; Vaez Allaei, S. M.; Senden, T.; Saadatfar, M.

2014-10-01

We study grain-scale mechanical and geometrical features of partially crystallized packings of frictional spheres, produced experimentally by a vibrational protocol. By combining x-ray computed tomography, 3D image analysis, and discrete element method simulations, we have access to the 3D structure of internal forces. We investigate how the network of mechanical contacts and intergranular forces change when the packing structure evolves from amorphous to near perfect crystalline arrangements. We compare the behavior of the geometrical neighbors (quasicontracts) of a grain to the evolution of the mechanical contacts. The mechanical coordination number Zm is a key parameter characterizing the crystallization onset. The high fluctuation level of Zm and of the force distribution in highly crystallized packings reveals that a geometrically ordered structure still possesses a highly random mechanical backbone similar to that of amorphous packings.

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

NASA Astrophysics Data System (ADS)

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.

Effect of local structures on crystallization in deeply undercooled metallic glass-forming liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, S. Q.; Li, M. Z., E-mail: maozhili@ruc.edu.cn; Wu, Z. W.

2016-04-21

The crystallization mechanism in deeply undercooled ZrCu metallic glass-forming liquids was investigated via molecular dynamics simulations. It was found that the crystallization process is mainly controlled by the growth of crystal nuclei formed by the BCC-like atomic clusters, consistent with experimental speculations. The crystallization rate is found to relate to the number of growing crystal nuclei in the crystallization process. The crystallization rate in systems with more crystal nuclei is significantly hindered by the larger surface fractions of crystal nuclei and their different crystalline orientations. It is further revealed that in the crystallization in deeply undercooled regions, the BCC-like crystalmore » nuclei are formed from the inside of the precursors formed by the FCC-like atomic clusters, and growing at the expense of the precursors. Meanwhile, the precursors are expanding at the expense of the outside atomic clusters. This process is consistent with the so-called Ostwald step rule. The atomic structures of metallic glasses are found to have significant impact on the subsequent crystallization process. In the Zr{sub 85}Cu{sub 15} system, the stronger spatial correlation of Cu atoms could hinder the crystallization processes in deeply undercooled regions.« less

Predicting the structure of screw dislocations in nanoporous materials

NASA Astrophysics Data System (ADS)

Walker, Andrew M.; Slater, Ben; Gale, Julian D.; Wright, Kate

2004-10-01

Extended microscale crystal defects, including dislocations and stacking faults, can radically alter the properties of technologically important materials. Determining the atomic structure and the influence of defects on properties remains a major experimental and computational challenge. Using a newly developed simulation technique, the structure of the 1/2a <100> screw dislocation in nanoporous zeolite A has been modelled. The predicted channel structure has a spiral form that resembles a nanoscale corkscrew. Our findings suggest that the dislocation will enhance the transport of molecules from the surface to the interior of the crystal while retarding transport parallel to the surface. Crucially, the dislocation creates an activated, locally chiral environment that may have enantioselective applications. These predictions highlight the influence that microscale defects have on the properties of structurally complex materials, in addition to their pivotal role in crystal growth.

Atomic and electronic structure of exfoliated black phosphorus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok

2015-11-15

Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolutionmore » view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.« less

PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection

PubMed Central

Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

2014-01-01

X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed ‘PredPPCrys’ using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor.org/PredPPCrys. PMID:25148528

Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.

Design and optimization of production parameters for boric acid crystals with the crystallization process in an MSMPR crystallizer using FBRM® and PVM® technologies

NASA Astrophysics Data System (ADS)

Kutluay, Sinan; Şahin, Ömer; Ceyhan, A. Abdullah; İzgi, M. Sait

2017-06-01

In crystallization studies, newly developed technologies, such as Focused Beam Reflectance Measurement (FBRM) and Particle Vision and Measurement (PVM) are applied for determining on-line monitoring of a representation of the Chord Length Distribution (CLD) and observe the photographs of crystals respectively; moreover recently they are widely used. Properly installed, the FBRM ensures on-line determination of the CLD, which is statistically associated to the Crystal Size Distribution (CSD). In industrial crystallization, CSD and mean crystal size as well as external habit and internal structure are important characteristics for further use of the crystals. In this paper, the effect of residence time, stirring speed, feeding rate, supersaturation level and the polyelectrolytes such as anionic polyacrylamide (APAM) and non-ionic polyacrylamide (NPAM) on the CLD as well as the shape of boric acid crystals were investigated by using the FBRM G600 and the PVM V819 probes respectively in an MSMPR (Mixed Suspension Mixed Product Removal) crystallizer. The CSD and kinetic data were determined experimentally using continuous MSMPR crystallizer running at steady state. The population density of nuclei, the nucleation rate and the growth rate were determined from the experimental population balance distribution when the steady state was reached.

Phonons in two-dimensional soft colloidal crystals.

PubMed

Chen, Ke; Still, Tim; Schoenholz, Samuel; Aptowicz, Kevin B; Schindler, Michael; Maggs, A C; Liu, Andrea J; Yodh, A G

2013-08-01

The vibrational modes of pristine and polycrystalline monolayer colloidal crystals composed of thermosensitive microgel particles are measured using video microscopy and covariance matrix analysis. At low frequencies, the Debye relation for two-dimensional harmonic crystals is observed in both crystal types; at higher frequencies, evidence for van Hove singularities in the phonon density of states is significantly smeared out by experimental noise and measurement statistics. The effects of these errors are analyzed using numerical simulations. We introduce methods to correct for these limitations, which can be applied to disordered systems as well as crystalline ones, and we show that application of the error correction procedure to the experimental data leads to more pronounced van Hove singularities in the pristine crystal. Finally, quasilocalized low-frequency modes in polycrystalline two-dimensional colloidal crystals are identified and demonstrated to correlate with structural defects such as dislocations, suggesting that quasilocalized low-frequency phonon modes may be used to identify local regions vulnerable to rearrangements in crystalline as well as amorphous solids.

Space manufacturing in an automated crystal growth facility

NASA Technical Reports Server (NTRS)

Quinn, Alberta W.; Herrmann, Melody C.; Nelson, Pamela J.

1989-01-01

An account is given of a Space Station Freedom-based robotic laboratory system for crystal growth experiments; the robot must interface with both the experimental apparatus and such human input as may be required for control and display. The goal of the system is the simultaneous growth of several hundred protein crystals in microgravity. The robot possesses six degrees-of-freedom, allowing it to efficiently manipulate the cultured crystals as well as their respective growth cells; the crystals produced are expected to be of sufficiently high quality for complete structural determination on the basis of XRD.

Topological photonic crystal with equifrequency Weyl points

NASA Astrophysics Data System (ADS)

Wang, Luyang; Jian, Shao-Kai; Yao, Hong

2016-06-01

Weyl points in three-dimensional photonic crystals behave as monopoles of Berry flux in momentum space. Here, based on general symmetry analysis, we show that a minimal number of four symmetry-related (consequently equifrequency) Weyl points can be realized in time-reversal invariant photonic crystals. We further propose an experimentally feasible way to modify double-gyroid photonic crystals to realize four equifrequency Weyl points, which is explicitly confirmed by our first-principle photonic band-structure calculations. Remarkably, photonic crystals with equifrequency Weyl points are qualitatively advantageous in applications including angular selectivity, frequency selectivity, invisibility cloaking, and three-dimensional imaging.

Structural and electronic properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2005-05-01

The structural and electronic properties of four L-amino acids alanine, leucine, isoleucine, and valine have been investigated using density functional theory (DFT) and the generalized gradient approximation. Within the crystals, it is found that the constituent molecules adopt zwitterionic configurations, in agreement with experimental work. Lattice constants are found to be in good agreement with experimentally determined values, although certain discrepancies do exist due to the description of van der Waals interactions. We find that these materials possess wide DFT band gaps in the region of 5 eV, with electrons highly localized to the constituent molecules. It is found that the main mechanisms behind crystal formation are dipolar interactions and hydrogen bonding of a primarily electrostatic character, in agreement with current biochemical understanding of these systems. The electronic structure suggests that the amine and carboxy functional groups are dominant in determining band structure.

Structural studies of homoisoflavonoids: NMR spectroscopy, X-ray diffraction, and theoretical calculations

NASA Astrophysics Data System (ADS)

Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek

2010-08-01

In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.

Crystal structures of carbonates up to Mbar pressures determined by single crystal synchrotron radiation diffraction

NASA Astrophysics Data System (ADS)

Merlini, M.

2013-12-01

The recent improvements at synchrotron beamlines, currently allow single crystal diffraction experiments at extreme pressures and temperatures [1,2] on very small single crystal domains. We successfully applied such technique to determine the crystal structure adopted by carbonates at mantle pressures. The knowledge of carbon-bearing phases is in fact fundamental for any quantitative modelling of global carbon cycle. The major technical difficulty arises after first order transitions or decomposition reactions, since original crystal (apx. 10x10x5 μm3) is transformed in much smaller crystalline domains often with random orientation. The use of 3D reciprocal space visualization software and the improved resolution of new generation flat panel detectors, however, allow both identification and integration of each single crystal domain, with suitable accuracy for ab-initio structure solution, performed with direct and charge-flipping methods and successive structure refinements. The results obtained on carbonates, indicate two major crystal-chemistry trends established at high pressures. The CO32- units, planar and parallel in ambient pressure calcite and dolomite structures, becomes non parallel in calcite- and dolomite-II and III phases, allowing more flexibility in the structures with possibility to accommodate strain arising from different cation sizes (Ca and Mg in particular). Dolomite-III is therefore also observed to be thermodynamically stable at lower mantle pressures and temperatures, differently from dolomite, which undergoes decomposition into pure end-members in upper mantle. At higher pressure, towards Mbar (lowermost mantle and D'' region) in agreement with theoretical calculations [3,4] and other experimental results [5], carbon coordination transform into 4-fold CO4 units, with different polymerisation in the structure depending on carbonate composition. The second important crystal chemistry feature detected is related to Fe2+ in Fe-bearing magnesite, which spontaneously oxidises at HP/HT, forming Fe3+ carbonates, Fe3+ oxides and reduced carbon (diamonds). Single crystal diffraction approach allowed full structure determination of these phases, yielding to the discovery of few unpredicted structures, such as Mg2Fe2C4O13 and Fe13O19, which can be well reproduced in different experiments. Mg2Fe2C4O13 carbonate present truncated chain C4O13 groups, and Fe13O19 oxide, whose stoichiometry is intermediate between magnetite and hematite, is a one-layer structure, with features encountered in superconducting materials. The results fully support the ideas of unexpected complexities in the mineralogy of the lowermost mantle, and single crystal technique, once properly optimized in ad-hoc synchrotron beamlines, is fundamental for extracting accurate structural information, otherwise rarely accessible with other experimental techniques. References: [1] Merlini M., Hanfland M. (2013). Single crystal diffraction at Mbar conditions by synchrotron radiation. High Pressure Research, in press. [2] Dubrovinsky et al., (2010). High Pressure Research, 30, 620-633. [3] Arapan et al. (1997). Phys. Rev. Lett., 98, 268501. [4] Oganov et al. (2008) EPSL, 273, 38-47. [5] Boulard et al. (2011) PNAS, 108, 5184-5187.

Silicon chip integrated photonic sensors for biological and chemical sensing

NASA Astrophysics Data System (ADS)

Chakravarty, Swapnajit; Zou, Yi; Yan, Hai; Tang, Naimei; Chen, Ray T.

2016-03-01

We experimentally demonstrate applications of photonic crystal waveguide based devices for on-chip optical absorption spectroscopy for the detection of chemical warfare simulant, triethylphosphate as well as applications with photonic crystal microcavity devices in the detection of biomarkers for pancreatic cancer in patient serum and cadmium metal ions in heavy metal pollution sensing. At mid-infrared wavelengths, we experimentally demonstrate the higher sensitivity of photonic crystal based structures compared to other nanophotonic devices such as strip and slot waveguides with detection down to 10ppm triethylphosphate. We also detected 5ppb (parts per billion) of cadmium metal ions in water at near-infrared wavelengths using established techniques for the detection of specific probe-target biomarker conjugation chemistries.

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

NASA Technical Reports Server (NTRS)

Timofeeva, Tatiana V.; Nesterov, Vladimir N.; Antipin, Mikhail Yu.; Clark, Ronald D.; Sanghadasa, Mohan; Cardelino, Beatriz H.; Moore, Craig E.; Frazier, Donald O.

1999-01-01

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

Crysalis: an integrated server for computational analysis and design of protein crystallization.

PubMed

Wang, Huilin; Feng, Liubin; Zhang, Ziding; Webb, Geoffrey I; Lin, Donghai; Song, Jiangning

2016-02-24

The failure of multi-step experimental procedures to yield diffraction-quality crystals is a major bottleneck in protein structure determination. Accordingly, several bioinformatics methods have been successfully developed and employed to select crystallizable proteins. Unfortunately, the majority of existing in silico methods only allow the prediction of crystallization propensity, seldom enabling computational design of protein mutants that can be targeted for enhancing protein crystallizability. Here, we present Crysalis, an integrated crystallization analysis tool that builds on support-vector regression (SVR) models to facilitate computational protein crystallization prediction, analysis, and design. More specifically, the functionality of this new tool includes: (1) rapid selection of target crystallizable proteins at the proteome level, (2) identification of site non-optimality for protein crystallization and systematic analysis of all potential single-point mutations that might enhance protein crystallization propensity, and (3) annotation of target protein based on predicted structural properties. We applied the design mode of Crysalis to identify site non-optimality for protein crystallization on a proteome-scale, focusing on proteins currently classified as non-crystallizable. Our results revealed that site non-optimality is based on biases related to residues, predicted structures, physicochemical properties, and sequence loci, which provides in-depth understanding of the features influencing protein crystallization. Crysalis is freely available at http://nmrcen.xmu.edu.cn/crysalis/.

Crysalis: an integrated server for computational analysis and design of protein crystallization

PubMed Central

Wang, Huilin; Feng, Liubin; Zhang, Ziding; Webb, Geoffrey I.; Lin, Donghai; Song, Jiangning

2016-01-01

The failure of multi-step experimental procedures to yield diffraction-quality crystals is a major bottleneck in protein structure determination. Accordingly, several bioinformatics methods have been successfully developed and employed to select crystallizable proteins. Unfortunately, the majority of existing in silico methods only allow the prediction of crystallization propensity, seldom enabling computational design of protein mutants that can be targeted for enhancing protein crystallizability. Here, we present Crysalis, an integrated crystallization analysis tool that builds on support-vector regression (SVR) models to facilitate computational protein crystallization prediction, analysis, and design. More specifically, the functionality of this new tool includes: (1) rapid selection of target crystallizable proteins at the proteome level, (2) identification of site non-optimality for protein crystallization and systematic analysis of all potential single-point mutations that might enhance protein crystallization propensity, and (3) annotation of target protein based on predicted structural properties. We applied the design mode of Crysalis to identify site non-optimality for protein crystallization on a proteome-scale, focusing on proteins currently classified as non-crystallizable. Our results revealed that site non-optimality is based on biases related to residues, predicted structures, physicochemical properties, and sequence loci, which provides in-depth understanding of the features influencing protein crystallization. Crysalis is freely available at http://nmrcen.xmu.edu.cn/crysalis/. PMID:26906024

Electrochemical fabrication and optical properties of porous tin oxide films with structural colors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Hua; Shu, Shiwei; Lee, Chris

2014-10-21

Photonic crystals with porous features not only provide the capability to control light but also enable structural colors that are environmentally sensitive. Here, we report a novel kind of tin oxide-based photonic crystal featuring periodically arranged air pores fabricated by the periodic anodization of tin foil. The existence of a photonic band gap in the fabricated structure is verified by its vivid color, and its reflective spectra which are responsive to environmental stimuli. Furthermore, the sample colors (i.e., the photonic band gap positions) can be easily adjusted by manipulating the anodization parameters. The theoretical modeling results of these tin oxidemore » photonic crystals agree well with the reported experimental ones.« less

Experimental study of modification mechanism at a wear-resistant surfacing

NASA Astrophysics Data System (ADS)

Dema, R. R.; Amirov, R. N.; Kalugina, O. B.

2018-01-01

In the study, a simulation of the crystallization process was carried out for the deposition of the near-eutectic structure alloys with inoculants presence in order to reveal the regularities of the inoculant effect and parameters of the process mode simulating surfacing on the structure of the crystallization front and on the nucleation rate and kinetics of growth of equiaxed crystallites of primary phases occurring in the volume of the melt. The simulation technique of primary crystallization of alloys similar to eutectic alloys in the presence of modifiers is offered. The possibility of fully eutectic structure during surfacing of nominal hypereutectic alloys of type white cast irons in wide range of deviations from the nominal composition is revealed.

Intricate Li-Sn Disorder in Rare-Earth Metal-Lithium Stannides. Crystal Chemistry of RE3Li4- xSn4+ x (RE = La-Nd, Sm; x < 0.3) and Eu7Li8- xSn10+ x ( x ≈ 2.0).

PubMed

Suen, Nian-Tzu; Guo, Sheng-Ping; Hoos, James; Bobev, Svilen

2018-05-07

Reported are the syntheses, crystal structures, and electronic structures of six rare-earth metal-lithium stannides with the general formulas RE 3 Li 4- x Sn 4+ x (RE = La-Nd, Sm) and Eu 7 Li 8- x Sn 10+ x . These new ternary compounds have been synthesized by high-temperature reactions of the corresponding elements. Their crystal structures have been established using single-crystal X-ray diffraction methods. The RE 3 Li 4- x Sn 4+ x phases crystallize in the orthorhombic body-centered space group Immm (No. 71) with the Zr 3 Cu 4 Si 4 structure type (Pearson code oI22), and the Eu 7 Li 8- x Sn 10+ x phase crystallizes in the orthorhombic base-centered space group Cmmm (No. 65) with the Ce 7 Li 8 Ge 10 structure type (Pearson code oC50). Both structures can be consdered as part of the [RESn 2 ] n [RELi 2 Sn] m homologous series, wherein the structures are intergrowths of imaginary RESn 2 (AlB 2 -like structure type) and RELi 2 Sn (MgAl 2 Cu-like structure type) fragments. Close examination the structures indicates complex occupational Li-Sn disorder, apparently governed by the drive of the structure to achieve an optimal number of valence electrons. This conclusion based on experimental results is supported by detailed electronic structure calculations, carried out using the tight-binding linear muffin-tin orbital method.

Magnetic field role on the structure and optical response of photonic crystals based on ferrofluids containing Co{sub 0.25}Zn{sub 0.75}Fe{sub 2}O{sub 4} nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

López, J., E-mail: javier.lopez@correounivalle.edu.co; González, Luz E.; Quiñonez, M. F.

2014-05-21

Ferrofluids based on magnetic Co{sub 0.25}Zn{sub 0.75}Fe{sub 2}O{sub 4} ferrite nanoparticles were prepared by co-precipitation method from aqueous salt solutions of Co (II), ZnSO{sub 4}, and Fe (III) in an alkaline medium. Ferrofluids placed in an external magnetic field show properties that make them interesting as magneto-controllable soft photonic crystals. Morphological and structural characterizations of the samples were obtained from Scanning Electron Microscopy and Transmission Electron Microscopy studies. Magnetic properties were investigated with the aid of a vibrating sample magnetometer at room temperature. Herein, the Co{sub 0.25}Zn{sub 0.75}Fe{sub 2}O{sub 4} samples showed superparamagnetic behavior, according to hysteresis loop results. Takingmore » in mind that the Co-Zn ferrite hysteresis loop is very small, our magnetic nanoparticles can be considered soft magnetic material with interesting technological applications. In addition, by using the plane-wave expansion method, we studied the photonic band structure of 2D photonic crystals made of ferrofluids with the same nanoparticles. Previous experimental results show that a magnetic field applied perpendicular to the ferrofluid plane agglomerates the magnetic nanoparticles in parallel rods to form a hexagonal 2D photonic crystal. We calculated the photonic band structure of photonic crystals by means of the effective refractive index of the magnetic fluid, basing the study on the Maxwell-Garnett theory, finding that the photonic band structure does not present any band gaps under the action of applied magnetic field strengths used in our experimental conditions.« less

Features of the structural states of KNbO{sub 3} single crystals before and after fast-neutron irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stash, A. I., E-mail: astas@yandex.ru; Ivanov, S. A.; Stefanovich, S. Yu.

Neutron irradiation is a unique tool for forming new structural states of ferroelectrics, which cannot be obtained by conventional methods. The inf luence of the irradiation by two doses of fast neutrons (F = 1 × 10{sup 17} and 3 × 10{sup 17} cm{sup –2}) on the structure and properties of KNbO{sub 3} single crystals has been considered for the first time. The developed method for taking into account the experimental correction to the diffuse scattering has been used to analyze the structural changes occurring in KNbO{sub 3} samples at T = 295 K and their correlations with the behaviormore » of dielectric and nonlinear optical characteristics. The irradiation to the aforementioned doses retains the KNbO{sub 3} polar structure, shifting Т{sub Ð}¡ to lower temperatures and significantly affecting only the thermal parameters and microstructure of single crystals. Neutron irradiation with small atomic displacements provides a structure similar to the high-temperature modification of an unirradiated KNbO{sub 3} crystal.« less

Pass-Band Characteristics of an L-Shaped Waveguide in a Diamond Structure Photonic Crystal

NASA Astrophysics Data System (ADS)

Chen, Shibin; Ma, Jingcun; Yao, Yunshi; Liu, Xin; Lin, Ping

2018-06-01

The conduction characteristics of a L-shaped waveguide in a diamond structure photonic crystal is investigated in this paper. The waveguides were fabricated with titanium dioxide ceramic via 3-D printing and sintering. The effects of the position and size of line defects on the transmission characteristics are first simulated using a finite-difference time-domain method. The simulated results show that, when the length of the rectangular defect equals the lattice constant, multiple extended modes are generated. When the centers of the single unit cell of the diamond structure and the line defect waveguide coincide, higher transmission efficiency in the line defect can be achieved. In addition, the corner of the L-shaped waveguide was optimized to reduce reflection loss at the turning point using the arc transition of the large diameter. Our experimental results indicate that L-shaped waveguides with an optimized photonic band gap structure and high-K materials can produce a pass-band between 13.8 GHz and 14.4 GHz and increase transmission efficiency. The computed results agree with the experimental results. Our results may help the integration of microwave devices in the future and possibly enable new applications of photonic crystals.

X-ray diffraction, crystal structure, and spectral features of the optical susceptibilities of single crystals of the ternary borate oxide lead bismuth tetraoxide, PbBiBO4.

PubMed

Reshak, Ali Hussain; Kityk, I V; Auluck, S; Chen, Xuean

2009-05-14

The all-electron full-potential linearized augmented plane-wave method has been used for an ab initio theoretical study of the band structure, the spectral features of the optical susceptibilities, the density of states, and the electron charge density for PbBiBO4. Our calculations show that the valence-band maximum (VBM) and conduction-band minimum (CBM) are located at the center of the Brillouin zone, resulting in a direct energy gap of about 3.2 eV. We have synthesized the PbBiBO4 crystal by employing a conventional solid-state reaction method. The theoretical calculations in this work are based on the structure built from our measured atomic parameters. We should emphasize that the observed experimental X-ray diffraction (XRD) pattern is in good agreement with the theoretical one, confirming that our structural model is valid. Our calculated bond lengths show excellent agreement with the experimental data. This agreement is attributed to our use of full-potential calculations. The spectral features of the optical susceptibilities show a small positive uniaxial anisotropy.

Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations.

PubMed

Sangeetha, V; Govindarajan, M; Kanagathara, N; Marchewka, M K; Gunasekaran, S; Anbalagan, G

2014-05-05

Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted. Copyright © 2014 Elsevier B.V. All rights reserved.

New five coordinated supramolecular structured cadmium complex as precursor for CdO nanoparticles: Synthesis, crystal structure, theoretical and 3D Hirshfeld surface analyses

NASA Astrophysics Data System (ADS)

Ghanbari Niyaky, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

2017-03-01

In this paper, a combined experimental and theoretical study on a new CdLBr2 complex (L = N1-(2-bromobenzylidene)-N2-(2-((E)-(2-bromobenzylidene) amino)ethyl) ethane-1,2-diamine) synthesized via template method, is described. The crystal structure analysis of the complex indicates that, the Cd(II) ion is centered in a distorted square pyramidal space constructed by three iminic nitrogens of the ligand as well as two bromide anions. More analysis of crystal packing proposed a supramolecular structure stabilized by some non-covalent interactions such as Br⋯Br and Xsbnd H⋯Br (X = N and C) in solid state. Furthermore, 3D Hirshfeld surface analyses and DFT studies were applied for theoretical investigation of the complexes. Theoretical achievements were found in a good agreement with respect to the experimental data. To evaluate the nature of bonding and the strength of the intra and inter-molecular interactions a natural bond orbital (NBO) analysis on the complex structure was performed. Time dependent density functional theory (TD-DFT) was also applied to predict the electronic spectral data of the complex as compared with the experimental ones. CdLBr2 complex as nano-structure compound was also prepared under ultrasonic conditions and characterized by scanning electron microscopy (SEM) and X-ray powder diffraction (XRPD). Finally, it was found that the cadmium complex can be used as a suitable precursor for preparation of CdO nanoparticles via calcination process at 600 °C under air atmosphere.

Design and experimental evidence of a flat graded-index photonic crystal lens

NASA Astrophysics Data System (ADS)

Gaufillet, F.; Akmansoy, É.

2013-08-01

We report on the design and the experimental evidence of a flat graded index photonic crystal lens. The gradient has been designed so that the flat slab focuses a plane wave and so that it converts the wave issued from a point source into a plane wave. This graded-index photonic crystal lens operates as a convex lens. The gradient of index results from varying the filling factor of the photonic crystal in the direction perpendicular to that of the propagation of the electromagnetic field. The shape of the gradient of index has been designed by engineering the iso-frequency curves of the photonic crystal. As only a few layers were necessary and as graded photonic crystals may be fabricated by a variety of processes, this shows the ability of graded photonic crystals to efficiently apply for various photonic devices, from microwave range to the optical domain. 42.70.Qs Photonic bandgap materials, 78.67.Pt Optical properties of photonic structures, 41.20.Jb Electromagnetic wave propagation; radiowave propagation 84.40.Ba Antennas.

Luminescence of Mn4+ ions in CaTiO3 and MgTiO3 perovskites: Relationship of experimental spectroscopic data and crystal field calculations

NASA Astrophysics Data System (ADS)

Đorđević, Vesna; Brik, Mikhail G.; Srivastava, Alok M.; Medić, Mina; Vulić, Predrag; Glais, Estelle; Viana, Bruno; Dramićanin, Miroslav D.

2017-12-01

Herein, the synthesis, structural and crystal field analysis and optical spectroscopy of Mn4+ doped metal titanates ATiO3 (A = Ca, Mg) are presented. Materials of desired phase were prepared by molten salt assisted sol-gel method in the powder form. Crystallographic data of samples were obtained by refinement of X-ray diffraction measurements. From experimental excitation and emission spectra and structural data, crystal field parameters and energy levels of Mn4+ in CaTiO3 and MgTiO3 were calculated by the exchange charge model of crystal-field theory. It is found that crystalline field strength is lower (Dq = 1831 cm-1) in the rhombohedral Ilmenite MgTiO3 structure due to the relatively longer average Mn4+sbnd O2- bond distance (2.059 Å), and higher (Dq = 2017 cm-1) in orthorhombic CaTiO3 which possess shorter average Mn4+sbnd O2- bond distance (1.956 Å). Spectral positions of the Mn4+2Eg → 4A2g transition maxima is 709 nm in MgTiO3 and 717 nm in CaTiO3 respectively in good agreement with calculated values.

Axial vibration control of melt structure of sodium nitrate in crystal growth process

NASA Astrophysics Data System (ADS)

Sadovskiy, Andrey; Sukhanova, Ekaterina; Belov, Stanislav; Kostikov, Vladimir; Zykova, Marina; Artyushenko, Maxim; Zharikov, Evgeny; Avetissov, Igor

2015-05-01

The melt structure evolution under the action of the low-frequency axial vibration control (AVC) technique was studied in situ by Raman spectroscopy for several complex chemical compound melts: sodium nitrate, margarine acid, paraffin mixture (C17-C20). The measurements were conducted in the temperature range from the melting point up to 60 °C above. Comparison of crystallization heats for AVC activated and steady melts with melting heats of AVC-CZ and conventional CZ produced powders allowed to propose the energy diagram of NaNO3 states for activated and non-activated melts and crystals based on DTA, XRD, DSC and Raman experimental data.

Monolithic phononic crystals with a surface acoustic band gap from surface phonon-polariton coupling.

PubMed

Yudistira, D; Boes, A; Djafari-Rouhani, B; Pennec, Y; Yeo, L Y; Mitchell, A; Friend, J R

2014-11-21

We theoretically and experimentally demonstrate the existence of complete surface acoustic wave band gaps in surface phonon-polariton phononic crystals, in a completely monolithic structure formed from a two-dimensional honeycomb array of hexagonal shape domain-inverted inclusions in single crystal piezoelectric Z-cut lithium niobate. The band gaps appear at a frequency of about twice the Bragg band gap at the center of the Brillouin zone, formed through phonon-polariton coupling. The structure is mechanically, electromagnetically, and topographically homogeneous, without any physical alteration of the surface, offering an ideal platform for many acoustic wave applications for photonics, phononics, and microfluidics.

Au133(SPh-tBu)52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the “nanostructure problem”. Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than inmore » the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.« less

Au 133 (SPh - t Bu) 52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au-133(SPh-tBu)(52), was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than inmore » the slightly larger Au-144(SCH2CH2Ph)(60). Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.« less

Au133(SPh-tBu)52 nanomolecules: X-ray crystallography, optical, electrochemical, and theoretical analysis.

PubMed

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy; Kumara, Chanaka; Jupally, Vijay Reddy; Fortunelli, Alessandro; Sementa, Luca; Barcaro, Giovanni; Zuo, Xiaobing; Noll, Bruce C

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than in the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.

New supramolecular cocrystal of 2-amino-5-chloropyridine with 3-methylbenzoic acids: Syntheses, structural characterization, Hirshfeld surfaces and quantum chemical investigations

NASA Astrophysics Data System (ADS)

Thanigaimani, Kaliyaperumal; Khalib, Nuridayanti Che; Temel, Ersin; Arshad, Suhana; Razak, Ibrahim Abdul

2015-11-01

2-amino-5-chloropyridine: 3-methylbenzoic acid [(2A5CP) (3MBA)] (I) cocrystal was synthesized and its single crystal was grown by slow evaporation technique. The structure of the grown crystal was elucidated by using single crystal X-ray diffraction technique. The cocrystal belongs to the monoclinic crystallographic system with space group P21/c, Z = 4, and a = 13.3155 (5) Å, b = 5.5980 (2) Å, c = 18.3787 (7) Å, β = 110.045 (2)°. The crystal structure is stabilized by Npyridine-H•••Odbnd C, Cdbnd O-H•••Npyridine and C-H⋯O type hydrogen bonding interactions. The presence of unionized -COOH functional group in the cocrystal was identified both by spectral methods and X-ray structural analysis. The experimental studies obtained by using the methods of single crystal X-ray analysis, powder X-ray diffraction (PXRD) analysis, FTIR, 1H NMR and 13C NMR spectroscopies confirmed the predicted cocrystal. The supramolecular assembly of the cocrystal was analyzed and discussed. The molecular geometry, vibrational frequencies of the compound in the ground state were calculated by using the density functional theory (DFT) method with 6-311++G (d,p) basis set and were compared with the experimental data. Additionally, HOMO-LUMO energy gap, natural bond orbital (NBO) analysis and nonlinear optical (NLO) properties of the compound were performed at B3LYP/6-311++G (d,p) level. Hirshfeld surfaces were used to confirm the existence of inter-molecular interactions in the compound.

Discrete Breathers in One-Dimensional Diatomic Granular Crystals

NASA Astrophysics Data System (ADS)

Boechler, N.; Theocharis, G.; Job, S.; Kevrekidis, P. G.; Porter, Mason A.; Daraio, C.

2010-06-01

We report the experimental observation of modulational instability and discrete breathers in a one-dimensional diatomic granular crystal composed of compressed elastic beads that interact via Hertzian contact. We first characterize their effective linear spectrum both theoretically and experimentally. We then illustrate theoretically and numerically the modulational instability of the lower edge of the optical band. This leads to the dynamical formation of long-lived breather structures, whose families of solutions we compute throughout the linear spectral gap. Finally, we experimentally observe the manifestation of the modulational instability and the resulting generation of localized breathing modes with quantitative characteristics that agree with our numerical results.

Structure of periodic crystals and quasicrystals in ultrathin films of Ba-Ti-O

DOE PAGES

Cockayne, Eric; Mihalkovič, Marek; Henley, Christopher L.

2016-01-07

Here, we model the remarkable thin-film Ba-Ti-O structures formed by heat treatment of an initial perovskite BaTiO 3 thin film on a Pt(111) surface. All structures contain a rumpled Ti-O network with all Ti threefold coordinated with O, and with Ba occupying the larger. mainly Ti 7O 7, pores. The quasicrystal structue is a simple decoration of three types of tiles: square, triangle and 30° rhombus, with edge lengths 6.85 Å, joined edge-to-edge in a quasicrystalline pattern; observed periodic crystals in ultrathin film Ba-Ti-O are built from these and other tiles. Simulated STM images reproduce the patterns seen experimentally, andmore » identify the bright protrusions as Ba atoms. The models are consistent with all experimental observations.« less

Can computed crystal energy landscapes help understand pharmaceutical solids?

PubMed Central

Price, Sarah L.; Braun, Doris E.; Reutzel-Edens, Susan M.

2017-01-01

Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape. PMID:27067116

Photonic Crystals on the Wing

DTIC Science & Technology

2009-04-30

The Green Hairstreak butterfly has ventrally scales consisting of 3D gyroid domains acting as photonic crystals, which can be easily...study on the structural coloration of the Green Hairstreak , Callophrys rubi. Extensive experimental measurements have been complemented with three...colorations, produced by purely dielectric materials are widely encountered [1-3]. Famous examples are the metallic- green buprestid and golden scarab

Optical Tamm states in one-dimensional magnetophotonic structures.

PubMed

Goto, T; Dorofeenko, A V; Merzlikin, A M; Baryshev, A V; Vinogradov, A P; Inoue, M; Lisyansky, A A; Granovsky, A B

2008-09-12

We demonstrate the existence of a spectrally narrow localized surface state, the so-called optical Tamm state, at the interface between one-dimensional magnetophotonic and nonmagnetic photonic crystals. The state is spectrally located inside the photonic band gaps of each of the photonic crystals comprising this magnetophotonic structure. This state is associated with a sharp transmission peak through the sample and is responsible for the substantial enhancement of the Faraday rotation for the corresponding wavelength. The experimental results are in excellent agreement with the theoretical predictions.

Cracking a chemical conundrum

NASA Astrophysics Data System (ADS)

Adams, James M.; Ivanov, Alexandre S.; Johnson, Mark R.; Stride, John A.

2004-07-01

An everyday laboratory chemical, hexamethylbenzene (HMB) has assumed an important role in the history of molecular structure and crystallography. It was one of the first organic crystal structures to be solved and provided direct experimental proof for the hypothesis of planarity in aromatic systems. Very soon after this, HMB was found to undergo a phase transition at 117K, resulting in crystal shattering. Since then, many attempts have been made to obtain the low-temperature structure, but none have succeeded until now. Making use of the unique properties of the neutron, we have performed powder diffraction measurements to obtain the low-temperature crystal structure and inelastic measurements to determine the dynamics of the system. These experiments have been augmented by the use of ab initio calculations and molecular modelling to obtain a complete picture of HMB in the solid state.

[Effect of annealing temperature on the crystallization and spectroscopic response of a small-molecule semiconductor doped in polymer film].

PubMed

Yin, Ming; Zhang, Xin-Ping; Liu, Hong-Mei

2012-11-01

The crystallization properties of the perylene (EPPTC) molecules doped in the solid film of the derivative of polyfluorene (F8BT) at different annealing temperatures, as well as the consequently induced spectroscopic response of the exciplex emission in the heterojunction structures, were studied in the present paper. Experimental results showed that the phase separation between the small and the polymer molecules in the blend film is enhanced with increasing the annealing temperature, which leads to the crystallization of the EPPTC molecules due to the strong pi-pi stacking. The size of the crystal phase increases with increasing the annealing temperature. However, this process weakens the mechanisms of the heterojunction configuration, thus, the total interfacial area between the small and the polymer molecules and the amount of exciplex are reduced significantly in the blend film. Meanwhile, the energy transfer from the polymer to the small molecules is also reduced. As a result, the emission from the exciplex becomes weaker with increasing the annealing temperature, whereas the stronger emission from the polymer molecules and from the crystal phase of the small molecules can be observed. These experimental results are very important for understanding and tailoring the organic heterojunction structures. Furthermore, this provides photophysics for improving the performance of photovoltaic or solar cell devices.

Modeling local structure using crystal field and spin Hamiltonian parameters: the tetragonal FeK3+-OI2- defect center in KTaO3 crystal

NASA Astrophysics Data System (ADS)

Gnutek, P.; Y Yang, Z.; Rudowicz, C.

2009-11-01

The local structure and the spin Hamiltonian (SH) parameters, including the zero-field-splitting (ZFS) parameters D and (a+2F/3), and the Zeeman g factors g_{\\parallel } and g_{\\perp } , are theoretically investigated for the FeK3+-OI2- center in KTaO3 crystal. The microscopic SH (MSH) parameters are modeled within the framework of the crystal field (CF) theory employing the CF analysis (CFA) package, which also incorporates the MSH modules. Our approach takes into account the spin-orbit interaction as well as the spin-spin and spin-other-orbit interactions omitted in previous studies. The superposition model (SPM) calculations are carried out to provide input CF parameters for the CFA/MSH package. The combined SPM-CFA/MSH approach is used to consider various structural models for the FeK3+-OI2- defect center in KTaO3. This modeling reveals that the off-center displacement of the Fe3+ ions, Δ1(Fe3+), combined with an inward relaxation of the nearest oxygen ligands, Δ2(O2-), and the existence of the interstitial oxygen OI2- give rise to a strong tetragonal crystal field. This finding may explain the large ZFS experimentally observed for the FeK3+-OI2- center in KTaO3. Matching the theoretical MSH predictions with the available structural data as well as electron magnetic resonance (EMR) and optical spectroscopy data enables predicting reasonable ranges of values of Δ1(Fe3+) and Δ2(O2-) as well as the possible location of OI2- ligands around Fe3+ ions in KTaO3. The defect structure model obtained using the SPM-CFA/MSH approach reproduces very well the ranges of the experimental SH parameters D, g_{\\parallel } and g_{\\perp } and importantly yields not only the correct magnitude of D but also the sign, unlike previous studies. More reliable predictions may be achieved when experimental data on (a+2F/3) and/or crystal field energy levels become available. Comparison of our results with those arising from alternative models existing in the literature indicates considerable advantages of our method and presumably higher reliability of our predictions.

Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

PubMed Central

Garcia-Garibay, Miguel A.

2005-01-01

Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the close-packed, self-assembled environment of crystalline solids. In this article, we outline some of the general guidelines for their design and apply them for the construction of molecular crystals with units intended to emulate macroscopic gyroscopes and compasses. Recent advances in the preparation, crystallization, and dynamic characterization of these interesting systems offer a foothold to the possibilities and help highlight some avenues for future experimentation. PMID:16046543

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.

Two-dimensional and three-dimensional evaluation of the deformation relief

NASA Astrophysics Data System (ADS)

Alfyorova, E. A.; Lychagin, D. V.

2017-12-01

This work presents the experimental results concerning the research of the morphology of the face-centered cubic single crystal surface after compression deformation. Our aim is to identify the method of forming a quasiperiodic profile of single crystals with different crystal geometrical orientation and quantitative description of deformation structures. A set of modern methods such as optical and confocal microscopy is applied to determine the morphology of surface parameters. The results show that octahedral slip is an integral part of the formation of the quasiperiodic profile surface starting with initial strain. The similarity of the formation process of the surface profile at different scale levels is given. The size of consistent deformation regions is found. This is 45 µm for slip lines ([001]-single crystal) and 30 µm for mesobands ([110]-single crystal). The possibility of using two- and three-dimensional roughness parameters to describe the deformation structures was shown.

High-throughput screening for thermoelectric sulphides by using crystal structure features as descriptors

NASA Astrophysics Data System (ADS)

Zhang, Ruizhi; Du, Baoli; Chen, Kan; Reece, Mike; Materials Research Insititute Team

With the increasing computational power and reliable databases, high-throughput screening is playing a more and more important role in the search of new thermoelectric materials. Rather than the well established density functional theory (DFT) calculation based methods, we propose an alternative approach to screen for new TE materials: using crystal structural features as 'descriptors'. We show that a non-distorted transition metal sulphide polyhedral network can be a good descriptor for high power factor according to crystal filed theory. By using Cu/S containing compounds as an example, 1600+ Cu/S containing entries in the Inorganic Crystal Structure Database (ICSD) were screened, and of those 84 phases are identified as promising thermoelectric materials. The screening results are validated by both electronic structure calculations and experimental results from the literature. We also fabricated some new compounds to test our screening results. Another advantage of using crystal structure features as descriptors is that we can easily establish structural relationships between the identified phases. Based on this, two material design approaches are discussed: 1) High-pressure synthesis of metastable phase; 2) In-situ 2-phase composites with coherent interface. This work was supported by a Marie Curie International Incoming Fellowship of the European Community Human Potential Program.

First-principles study on structure stabilities of α-S and Na-S battery systems

NASA Astrophysics Data System (ADS)

Momida, Hiroyoshi; Oguchi, Tamio

2014-03-01

To understand microscopic mechanisms of charge and discharge reactions in Na-S batteries, there has been increasing needs to study fundamental atomic and electronic structures of elemental S as well as that of Na-S phases. The most stable form of S is known to be an orthorhombic α-S crystal at ambient temperature and pressure, and α-S consists of puckered S8 rings which crystallize in space group Fddd . In this study, the crystal structure of α-S is examined by using first-principles calculations with and without the van der Waals interaction corrections of Grimme's method, and results clearly show that the van der Waals interactions between the S8 rings have crucial roles on cohesion of α-S. We also study structure stabilities of Na2S, NaS, NaS2, and Na2S5 phases with reported crystal structures. Using calculated total energies of the crystal structure models, we estimate discharge voltages assuming discharge reactions from 2Na+ xS -->Na2Sx, and discharge reactions in Na/S battery systems are discussed by comparing with experimental results. This work was partially supported by Elements Strategy Initiative for Catalysts and Batteries (ESICB) of Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan.

Site-discrimination by molecular imposters at dissymmetric molecular crystal surfaces

NASA Astrophysics Data System (ADS)

Poloni, Laura N.

The organization of atoms and molecules into crystalline forms is ubiquitous in nature and has been critical to the development of many technologies on which modern society relies. Classical crystal growth theory can describe atomic crystal growth, however, a description of molecular crystal growth is lacking. Molecular crystals are often characterized by anisotropic intermolecular interactions and dissymmetric crystal surfaces with anisotropic growth rates along different crystallographic directions. This thesis describes combination of experimental and computational techniques to relate crystal structure to surface structure and observed growth rates. Molecular imposters, also known as tailor-made impurities, can be used to control crystal growth for practical applications such as inhibition of pathological crystals, but can also be used to understand site specificity at crystal growth surfaces. The first part of this thesis builds on previous real-time in situ atomic force microscopy (AFM) observations of dislocation-actuated growth on the morphologically significant face of hexagonal L-cystine crystals, which aggregate in vivo to form kidney stones in patients suffering from cystinuria. The inhibitory effect of various L-cystine structural mimics (a.k.a. molecular imposters) was investigated through experimental and computational methods to identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal surface sites. The investigation of L-cystine crystal growth in the presence of molecular imposters through a combination of kinetic analysis using in situ AFM, morphology analysis and birefringence measurements of bulk crystals, and molecular modeling of imposter binding to energetically inequivalent surface sites revealed that different molecular imposters inhibited crystal growth by a Cabrera-Vermilyea pinning mechanism and that imposters bind to a single binding site on the dissymmetric {1000} L-cystine surfaces. Collectively, these findings identify the key structural factors responsible for molecular recognition between molecular imposters and L-cystine crystal step sites, thereby articulating a strategy for stone prevention based on molecular design. The second part of this thesis describes the crystal growth and inhibition of a P2X3 receptor antagonist, denoted as DAPSA, recently reported as a non-opioid treatment of chronic pain. The low solubility of this compound results in the formation of drug-induced renal calculi (a.k.a. xenostones). in situ AFM of the morphologically significant (011) DAPSA surface revealed dislocation-actuated growth spirals with an anisotropic morphology, behavior that can be attributed to the non-uniform rate of solute attachment to eight crystallographically unique steps of the spiral, a direct consequence of the dissymmetry of this crystal surface. Eighteen molecular imposters were selected from the screening library to systematically investigate the roles of imposter substitute position, size, and functionality on the step velocities along the eight unique crystallographic directions. A non-uniform reduction in step velocities was observed, signaling site discrimination of imposter binding that can be attributed to stereochemical recognition of the imposters at specific crystal sites. The anisotropy of growth inhibition observed in the presence of the various imposters is consistent with binding energies calculated for the thirty-two crystallographically unique kink sites on steps advancing along predominant growth directions. These results provide insight to the design of growth inhibitors for molecular crystalline solids with complex and dissymmetric surfaces, while also suggesting a strategy for formulations containing congeners that can prevent harmful crystal growth in human renal structures. The last two crystalline systems discussed in this thesis are two isomorphous crystal systems that are ideal for the study of impurity incorporation at dissymmetric surfaces because their morphology is dominated by dissymmetric {101} growth faces. Growth processes on the dissymmetric (101) surfaces of these crystalline systems were investigated using metadynamics simulations to determine the free energy of adsorption for solute and impurity attachment to different flat, stepped, and kinked (101) surface terminations. Results suggest that growth occurs via a non-Kossel crystal growth mechanism, and highlights the need for dissymmetric surface structures (i.e. steps and kinks) for a higher fidelity in the orientation of adsorbed molecules. Overall, the results presented in this thesis suggest that growth of molecular crystals, particularly at dissymmetric surfaces, is complex and requires the combination of several experimental and computational techniques to decipher the mechanisms responsible for growth phenomena. The use of molecular imposters to inhibit growth can be useful for the development of therapeutics for pathological crystals, but can also inform processes by which crystal growth occurs at complex surfaces as a result of their site selectivity.

The Crystal Structures of Potentially Tautomeric Compounds

NASA Astrophysics Data System (ADS)

Furmanova, Nina G.

1981-08-01

Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

Structural Characterization Studies on Semiconducting ZnSnN 2 Films using Synchrotron X-ray Diffraction

NASA Astrophysics Data System (ADS)

Senabulya, Nancy

This work is motivated by the need for new visible frequency direct bandgap semiconductor materials that are earth abundant and low-cost to meet the increasing demand for optoelectronic device applications such as solid state lighting and photovoltaics. Zinc-Tin-Nitride (ZnSnN2), a member of the II-IV nitride semiconductor family has been proposed as an alternative to the more common III-nitride semiconductors for use in optoelectronic devices. This material has been synthesized under optimized conditions using plasma assisted molecular beam epitaxy. Though a lot of research has recently been done computationally to predict the electronic and structural properties of ZnSnN2, experimental verification of these theories in single crystal thin films is lacking and warrants investigation because the accurate determination of the crystal structure of ZnSnN2 is a fundamental prerequisite for controlling and optimizing optoelectronic properties. In this synchrotron x-ray diffraction study, we present experimental validation, through unit cell refinement and 3d reciprocal space maps, of the crystal structure of single domain ZnSnN2 films deposited on (111) Yttria stabilized zirconia (YSZ) and (001) Lithium gallate (LGO) substrates. We find that ZnSnN2 films grown on (111) YSZ can attain both the theoretically predicted disordered wurtzite and ordered orthorhombic Pna21 structures under carefully controlled MBE growth conditions, while films grown on (001) LGO have the ordered Pn21a orthorhombic crystal structure. Through a systematic annealing study, a temperature induced first order structural phase transition from the wurtzite to orthorhombic phase is realized, characterized by the appearance of superstructure reflections in.

Experimental correlation of melt structures, nucleation rates, and thermal histories of silicate melts

NASA Technical Reports Server (NTRS)

Boynton, W. V.; DRAKE; HILDEBRAND; JONES; LEWIS; TREIMAN; WARK

1987-01-01

The theory and measurement of the structure of liquids is an important aspect of modern metallurgy and igneous petrology. Liquid structure exerts strong controls on both the types of crystals that may precipitate from melts and on the chemical composition of those crystals. An interesting aspect of melt structure studies is the problem of melt memories; that is, a melt can retain a memory of previous thermal history. This memory can influence both nucleation behavior and crystal composition. This melt memory may be characterized quantitatively with techniques such as Raman, infrared and NMR spectroscopy to provide information on short-range structure. Melt structure studies at high temperature will take advantage of the microgravity conditions of the Space Station to perform containerless experiments. Melt structure determinations at high temperature (experiments that are greatly facilitated by containerless technology) will provide invaluable information for materials science, glass technology, and geochemistry. In conjunction with studies of nucleation behavior and nucleation rates, information relevant to nucleation in magma chambers in terrestrial planets will be acquired.

Structural characterisation of some vanillic Mannich bases: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Petrović, Vladimir P.; Simijonović, Dušica; Novaković, Sladjana B.; Bogdanović, Goran A.; Marković, Svetlana; Petrović, Zorica D.

2015-10-01

In this paper, synthesis and structural determination of 2-[1-(N-4-fluorophenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-F) is presented. To determine the structure of this new compound, IR and NMR spectral characterisation was performed experimentally and theoretically. Simulation of spectral data was carried out using three functionals: B3LYP, B3LYP-D2, and M06-2X. The results obtained for MB-F were compared to those attained for similar, known compound 2-[1-(N-phenylamino)-1-(4-hydroxy-3-methoxyphenyl)]methylcyclohexanone (MB-H), whose crystal structure is presented here. Taking into account all experimental and theoretical findings, the structure of MB-F was proposed.

Design and characterization of one-dimensional photonic crystals based on ZnS/Ge for infrared-visible compatible stealth applications

NASA Astrophysics Data System (ADS)

Qi, Dong; Wang, Xian; Cheng, Yongzhi; Gong, Rongzhou; Li, Bowen

2016-12-01

One-dimensional photonic crystals (1DPCs) based on ZnS/Ge for compatible stealth of infrared and visible were firstly proposed theoretically and investigated experimentally. Owing to the equal inclination interference, the designed 1DPCs structure can be fabricated with a certain color corresponding to the different responded wavelength. In addition, the average emissivity of the proposed structure can reach as low as 0.054 at infrared atmosphere window of 3-5 μm. The as-prepared structure indicates that it is feasible for 1DPC to achieve infrared-visible compatible stealth.

Tip-induced domain growth on the non-polar cuts of lithium niobate single-crystals

DOE PAGES

Alikin, Denis O.; Ievlev, Anton; Turigin, Anton P.; ...

2015-05-05

Currently ferroelectric materials with designed domain structures are considered as a perspective material for new generation of photonic, data storage and data processing devices. Application of external electric field is the most convenient way of the domain structure formation. Lots of papers are devoted to investigation of the domain kinetics on polar surface of crystals while the forward growth remains one of the most mysterious stages due to lack of experimental methods allowing to study it. Here we performed tip-induced polarization reversal on X- and Y-non-polar cuts in single-crystal of congruent lithium niobate allows us to study the forward growthmore » with high spatial resolution. The revealed difference in the shape and length of domains induced on X- and Y-cuts is beyond previously developed theoretical approaches used for the theoretical consideration of the domains growth at non-polar ferroelectric surfaces. Lastly, to explain experimental results we used kinetic approach with anisotropy of screening efficiency along different crystallographic directions.« less

Models of protein–ligand crystal structures: trust, but verify

PubMed Central

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.

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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.

Comparative theoretical and experimental study on novel tri-quinoline system and its anticancer studies

NASA Astrophysics Data System (ADS)

Gayathri, Kasirajan; Radhika, Ramachandran; Shankar, Ramasamy; Malathi, Mahalingam; Savithiri, Krishnaswamy; Sparkes, Hazel A.; Howard, Judith A. K.; Mohan, Palathurai Subramaniam

2017-04-01

A novel compound 2-chloro-3,6-bis-(quinolin-8-yloxymethyl)-quinoline 3 bearing a tri-quinoline moiety has been synthesized from 2-chloro-3,6-dimethyl quinoline 1 and 8-hydroxy quinoline 2 using dry acetone and K2CO3 as a base. 3 has been characterized by using FT-IR, FT-Raman, UV-Vis, 1H NMR, 13C NMR spectra and single crystal X-ray diffraction methods. We have also made a combined experimental and theoretical study on the molecular structure, vibrational spectra, NMR, FT-IR, FT-Raman and UV-Vis spectra of 2-chloro-3,6-bis-(quinolin-8-yloxymethyl)-quinoline. The theoretical studies of the title compound have been evaluated by using density functional theory calculations using B3LYP/6-31+G(d,p) and M06-2X/6-31+G(d,p) level of theories. The calculated theoretical values were found to be in good agreement with the experimental findings. The single crystal structure 3 crystallized in the orthorhombic space group Pna21. The compound 3 exhibits higher cytotoxicity in human cervical cancer cell lines (HeLa) than human breast cancer cell lines (MCF7).

Crystal Growth and Dissolution of Methylammonium Lead Iodide Perovskite in Sequential Deposition: Correlation between Morphology Evolution and Photovoltaic Performance.

PubMed

Hsieh, Tsung-Yu; Huang, Chi-Kai; Su, Tzu-Sen; Hong, Cheng-You; Wei, Tzu-Chien

2017-03-15

Crystal morphology and structure are important for improving the organic-inorganic lead halide perovskite semiconductor property in optoelectronic, electronic, and photovoltaic devices. In particular, crystal growth and dissolution are two major phenomena in determining the morphology of methylammonium lead iodide perovskite in the sequential deposition method for fabricating a perovskite solar cell. In this report, the effect of immersion time in the second step, i.e., methlyammonium iodide immersion in the morphological, structural, optical, and photovoltaic evolution, is extensively investigated. Supported by experimental evidence, a five-staged, time-dependent evolution of the morphology of methylammonium lead iodide perovskite crystals is established and is well connected to the photovoltaic performance. This result is beneficial for engineering optimal time for methylammonium iodide immersion and converging the solar cell performance in the sequential deposition route. Meanwhile, our result suggests that large, well-faceted methylammonium lead iodide perovskite single crystal may be incubated by solution process. This offers a low cost route for synthesizing perovskite single crystal.

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

PubMed

Derewenda, Zygmunt S; Godzik, Adam

2017-01-01

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.

Diffraction imaging (topography) with monochromatic synchrotron radiation

NASA Technical Reports Server (NTRS)

Steiner, Bruce; Kuriyama, Masao; Dobbyn, Ronald C.; Laor, Uri

1988-01-01

Structural information of special interest to crystal growers and device physicists is now available from high resolution monochromatic synchrotron diffraction imaging (topography). In the review, the importance of superior resolution in momentum transfer and in space is described, and illustrations are taken from a variety of crystals: gallium arsenide, cadmium telluride, mercuric iodide, bismuth silicon oxide, and lithium niobate. The identification and understanding of local variations in crystal growth processes are shown. Finally, new experimental opportunities now available for exploitation are indicated.

Thermoelectric properties of nanocrystalline Sb2Te3 thin films: experimental evaluation and first-principles calculation, addressing effect of crystal grain size.

PubMed

Morikawa, Satoshi; Inamoto, Takuya; Takashiri, Masayuki

2018-02-16

The effect of crystal grain size on the thermoelectric properties of nanocrystalline antimony telluride (Sb 2 Te 3 ) thin films was investigated by experiments and first-principles studies using a developed relaxation time approximation. The Sb 2 Te 3 thin films were deposited on glass substrates using radio-frequency magnetron sputtering. To change the crystal grain size of the Sb 2 Te 3 thin films, thermal annealing was performed at different temperatures. The crystal grain size, lattice parameter, and crystal orientation of the thin films were estimated using XRD patterns. The carrier concentration and in-plane thermoelectric properties of the thin films were measured at room temperature. A theoretical analysis was performed using a first-principles study based on density functional theory. The electronic band structures of Sb 2 Te 3 were calculated using different lattice parameters, and the thermoelectric properties were predicted based on the semi-classical Boltzmann transport equation in the relaxation time approximation. In particular, we introduced the effect of carrier scattering at the grain boundaries into the relaxation time approximation by estimating the group velocities from the electronic band structures. Finally, the experimentally measured thermoelectric properties were compared with those obtained by calculation. As a result, the calculated thermoelectric properties were found to be in good agreement with the experimental results. Therefore, we can conclude that introducing the effect of carrier scattering at the grain boundaries into the relaxation time approximation contributes to enhance the accuracy of a first-principles calculation relating to nanocrystalline materials.

Thermoelectric properties of nanocrystalline Sb2Te3 thin films: experimental evaluation and first-principles calculation, addressing effect of crystal grain size

NASA Astrophysics Data System (ADS)

Morikawa, Satoshi; Inamoto, Takuya; Takashiri, Masayuki

2018-02-01

The effect of crystal grain size on the thermoelectric properties of nanocrystalline antimony telluride (Sb2Te3) thin films was investigated by experiments and first-principles studies using a developed relaxation time approximation. The Sb2Te3 thin films were deposited on glass substrates using radio-frequency magnetron sputtering. To change the crystal grain size of the Sb2Te3 thin films, thermal annealing was performed at different temperatures. The crystal grain size, lattice parameter, and crystal orientation of the thin films were estimated using XRD patterns. The carrier concentration and in-plane thermoelectric properties of the thin films were measured at room temperature. A theoretical analysis was performed using a first-principles study based on density functional theory. The electronic band structures of Sb2Te3 were calculated using different lattice parameters, and the thermoelectric properties were predicted based on the semi-classical Boltzmann transport equation in the relaxation time approximation. In particular, we introduced the effect of carrier scattering at the grain boundaries into the relaxation time approximation by estimating the group velocities from the electronic band structures. Finally, the experimentally measured thermoelectric properties were compared with those obtained by calculation. As a result, the calculated thermoelectric properties were found to be in good agreement with the experimental results. Therefore, we can conclude that introducing the effect of carrier scattering at the grain boundaries into the relaxation time approximation contributes to enhance the accuracy of a first-principles calculation relating to nanocrystalline materials.

Structure, dielectric and electric properties of diisobutylammonium hydrogen sulfate crystal

NASA Astrophysics Data System (ADS)

Bednarchuk, Tamara J.; Kinzhybalo, Vasyl; Markiewicz, Ewa; Hilczer, Bożena; Pietraszko, Adam

2018-02-01

Diisobutylammonium hydrogen sulfate, a new organic-inorganic hybrid compound, was successfully synthesized and three structural phases in 298-433 K temperature range were revealed by differential scanning calorimetry and X-ray powder diffraction studies. Single crystal X-ray diffraction data were used to describe the crystal structures in each particular case. In phase III (below 336/319 K on heating/cooling) the crystal arrangement appears to be within the triclinic symmetry with P-1 space group. During heating in the 336-339 K region (and 319-337 K on cooling) the crystal exists in the phase II, characterized by monoclinic symmetry with P21/c space group. Consequently, above 339 K (during heating, and 337 K during cooling temperature sequences), i.e. in phase I the crystal exhibits orthorhombic symmetry (Cmce space group). Ferroelastic domain structure was observed in phase III. These phase boundaries (III→II and II→I) were accompanied by the presence of small anomalies, apparent in the dielectric permittivity and electric conductivity experimental data. Fast proton transport with activation energy of 0.23 eV was observed in the high temperature phase I and related to phonon assisted proton diffusion conditioned by disorder of diisobutylammonium (diba) cations, as well as by high thermal displacements of oxygen and sulfur atoms of hydrogen sulfate anion (hs).

Crystallization of sodium chloride from a concentrated calcium chloride-potassium chloride-sodium chloride solution in a CMSMPR crystallizer: Observation of crystal size distribution and model validation

NASA Astrophysics Data System (ADS)

Choi, Byung Sang

Compared to overwhelming technical data available in other advanced technologies, knowledge about particle technology, especially in particle synthesis from a solution, is still poor due to the lack of available equipment to study crystallization phenomena in a crystallizer. Recent technical advances in particle size measurement such as Coulter counter and laser light scattering have made in/ex situ study of some of particle synthesis, i.e., growth, attrition, and aggregation, possible with simple systems. Even with these advancements in measurement technology, to grasp fully the crystallization phenomena requires further theoretical and technical advances in understanding such particle synthesis mechanisms. Therefore, it is the motive of this work to establish the general processing parameters and to produce rigorous experimental data with reliable performance and characterization that rigorously account for the crystallization phenomena of nucleation, growth, aggregation, and breakage including their variations with time and space in a controlled continuous mixed-suspension mixed-product removal (CMSMPR) crystallizer. This dissertation reports the results and achievements in the following areas: (1) experimental programs to support the development and validation of the phenomenological models and generation of laboratory data for the purpose of testing, refining, and validating the crystallization process, (2) development of laboratory well-mixed crystallizer system and experimental protocols to generate crystal size distribution (CSD) data, (3) the effects of feed solution concentration, crystallization temperature, feed flow rate, and mixing speed, as well as different types of mixers resulting in the evolution of CSDs with time from a concentrated brine solution, (4) with statistically designed experiments the effects of processing variables on the resultant particle structure and CSD at steady state were quantified and related to each of those operating conditions by studying the detailed crystallization processes, such as nucleation, growth, and breakage, as well as agglomeration. The purification of CaCl2 solution involving the crystallization of NaCl from the solution mixture of CaCl2, KCl, and NaCl as shipped from Dow Chemical, Ludington, in a CMSMPR crystallizer was studied as our model system because of its nucleation and crystal growth tendencies with less agglomeration. This project also generated a significant body of experimental data that are available at URL that is http://www.che.utah.edu/˜ring/CrystallizationWeb.

Unraveling Complexity in the Solid Form Screening of a Pharmaceutical Salt: Why so Many Forms? Why so Few?

PubMed Central

2017-01-01

The solid form landscape of 5-HT2a antagonist 3-(4-(benzo[d]isoxazole-3-yl)piperazin-1-yl)-2,2-dimethylpropanoic acid hydrochloride (B5HCl) proved difficult to establish. Many crystalline materials were produced by solid form screening, but few forms readily grew high quality crystals to afford a clear picture or understanding of the solid form landscape. Careful control of crystallization conditions, a range of experimental methods, computational modeling of solvate structures, and crystal structure prediction were required to see potential arrangements of the salt in its crystal forms. Structural diversity in the solid form landscape of B5HCl was apparent in the layer structures for the anhydrate polymorphs (Forms I and II), dihydrate and a family of solvates with alcohols. The alcohol solvates, which provided a distinct packing from the neat forms and the dihydrate, form layers with conserved hydrogen bonding between B5HCl and the solvent, as well as stacking of the aromatic rings. The ability of the alcohol hydrocarbon moieties to efficiently pack between the layers accounted for the difficulty in growing some solvate crystals and the inability of other solvates to crystallize altogether. Through a combination of experiment and computation, the crystallization problems, form stability, and desolvation pathways of B5HCl have been rationalized at a molecular level. PMID:29018305

Segregation Phenomena on the Crystal Surface of Chemical Compounds

NASA Astrophysics Data System (ADS)

Tomashpol'skii, Yu. Ya.

2018-06-01

The current state of the theoretical and experimental studies of changes in the chemical structure and composition caused by segregation phenomena on the surface of chemical compounds was reviewed. The review considers the experimental data obtained exclusively on single crystals, which were studied by modern instrumental methods, including in situ Auger electron spectrometry, X-ray spectral microanalysis, high-resolution scanning and transmission electron microscopy, secondary electron emission, and atomic force microscopy. The models that suggest the crystal-chemical diffusion and liquid-phase mechanisms of segregation were described. The parameters of the theory include the type of chemical bond, elastic constants, and crystal-chemical characteristics of substances. The models make it possible to predict the nature of changes in the surface composition: segregation tendency, segregant type, and degree of nonstoichiometry. A new direction in surface segregation was considered, which is promising for nanoelectronics and emission electronics.

Magnetic properties of single crystal alpha-benzoin oxime: An EPR study

NASA Astrophysics Data System (ADS)

Sayin, Ulku; Dereli, Ömer; Türkkan, Ercan; Ozmen, Ayhan

2012-02-01

The electron paramagnetic resonance (EPR) spectra of gamma irradiated single crystals of alpha-benzoinoxime (ABO) have been examined between 120 and 440 K. Considering the dependence on temperature and the orientation of the spectra of single crystals in the magnetic field, we identified two different radicals formed in irradiated ABO single crystals. To theoretically determine the types of radicals, the most stable structure of ABO was obtained by molecular mechanic and B3LYP/6-31G(d,p) calculations. Four possible radicals were modeled and EPR parameters were calculated for the modeled radicals using the B3LYP method and the TZVP basis set. Calculated values of two modeled radicals were in strong agreement with experimental EPR parameters determined from the spectra. Additional simulated spectra of the modeled radicals, where calculated hyperfine coupling constants were used as starting points for simulations, were well matched with experimental spectra.

Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Pontelli, Enrico

2010-01-01

Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.

A facile approach towards synthesis, characterization, single crystal structure, and DFT study of 5-bromosalicylalcohol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rastogi, Rupali, E-mail: rastogirupali@ymail.com; Tarannum, Nazia; Butcher, R. J.

2016-03-15

5-Bromosalicylalcohol was prepared by the interaction of NaBH{sub 4} and 5-bromosalicylaldehyde. The use of sodium borohydride makes the reaction easy, facile, economic and does not require any toxic catalyst. The compound is characterized by FTIR, {sup 1}H NMR, {sup 13}C NMR, TEM and ESI-mass spectra. Crystal structure is determined by single crystal X-ray analysis. Quantum mechanical calculations of geometries, energies and thermodynamic parameters are carried out using density functional theory (DFT/B3LYP) method with 6-311G(d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data.

Optical control of light propagation in photonic crystal based on electromagnetically induced transparency

NASA Astrophysics Data System (ADS)

Dan, Wang; Jin-Ze, Wu; Jun-Xiang, Zhang

2016-06-01

A kind of photonic crystal structure with modulation of the refractive index is investigated both experimentally and theoretically for exploiting electromagnetically induced transparency (EIT). The combination of EIT with periodically modulated refractive index medium gives rise to high efficiency reflection as well as forbidden transmission in a three-level atomic system coupled by standing wave. We show an accurate theoretical simulation via transfer-matrix theory, automatically accounting for multilayer reflections, thus fully demonstrate the existence of photonic crystal structure in atomic vapor. Project supported by the National Natural Science Foundation of China (Grant No. 11574188) and the Project for Excellent Research Team of the National Natural Science Foundation of China (Grant No. 61121064).

Neutron Transmission of Single-crystal Sapphire Filters

NASA Astrophysics Data System (ADS)

Adib, M.; Kilany, M.; Habib, N.; Fathallah, M.

2005-05-01

An additive formula is given that permits the calculation of the nuclear capture, thermal diffuse and Bragg scattering cross-sections as a function of sapphire temperature and crystal parameters. We have developed a computer program that allows calculations of the thermal neutron transmission for the sapphire rhombohedral structure and its equivalent trigonal structure. The calculated total cross-section values and effective attenuation coefficient for single-crystalline sapphire at different temperatures are compared with measured values. Overall agreement is indicated between the formula and experimental data. We discuss the use of sapphire single crystal as a thermal neutron filter in terms of the optimum cystal thickness, mosaic spread, temperature, cutting plane and tuning for efficient transmission of thermal-reactor neutrons.

Al{sub 4}SiC{sub 4} wurtzite crystal: Structural, optoelectronic, elastic, and piezoelectric properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pedesseau, L., E-mail: laurent.pedesseau@insa-rennes.fr, E-mail: jacky.even@insa-rennes.fr; Even, J., E-mail: laurent.pedesseau@insa-rennes.fr, E-mail: jacky.even@insa-rennes.fr; Durand, O.

New experimental results supported by theoretical analyses are proposed for aluminum silicon carbide (Al{sub 4}SiC{sub 4}). A state of the art implementation of the density functional theory is used to analyze the experimental crystal structure, the Born charges, the elastic properties, and the piezoelectric properties. The Born charge tensor is correlated to the local bonding environment for each atom. The electronic band structure is computed including self-consistent many-body corrections. Al{sub 4}SiC{sub 4} material properties are compared to other wide band gap wurtzite materials. From a comparison between an ellipsometry study of the optical properties and theoretical results, we conclude thatmore » the Al{sub 4}SiC{sub 4} material has indirect and direct band gap energies of about 2.5 eV and 3.2 eV, respectively.« less

Prediction of new ground-state crystal structure of T a2O5

NASA Astrophysics Data System (ADS)

Yang, Yong; Kawazoe, Yoshiyuki

2018-03-01

Tantalum pentoxide (T a2O5 ) is a wide-gap semiconductor which has important technological applications. Despite the enormous efforts from both experimental and theoretical studies, the ground-state crystal structure of T a2O5 is not yet uniquely determined. Based on first-principles calculations in combination with evolutionary algorithm, we identify a triclinic phase of T a2O5 , which is energetically much more stable than any phases or structural models reported previously. Characterization of the static and dynamical properties of the phase reveals the common features shared with previous metastable phases of T a2O5 . In particular, we show that the d spacing of ˜3.8 Å found in the x-ray diffraction patterns of many previous experimental works is actually the radius of the second Ta-Ta coordination shell as defined by radial distribution functions.

A model for the solution structure of the rod arrestin tetramer.

PubMed

Hanson, Susan M; Dawson, Eric S; Francis, Derek J; Van Eps, Ned; Klug, Candice S; Hubbell, Wayne L; Meiler, Jens; Gurevich, Vsevolod V

2008-06-01

Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.

Transition from two-dimensional photonic crystals to dielectric metasurfaces in the optical diffraction with a fine structure

PubMed Central

Rybin, Mikhail V.; Samusev, Kirill B.; Lukashenko, Stanislav Yu.; Kivshar, Yuri S.; Limonov, Mikhail F.

2016-01-01

We study experimentally a fine structure of the optical Laue diffraction from two-dimensional periodic photonic lattices. The periodic photonic lattices with the C4v square symmetry, orthogonal C2v symmetry, and hexagonal C6v symmetry are composed of submicron dielectric elements fabricated by the direct laser writing technique. We observe surprisingly strong optical diffraction from a finite number of elements that provides an excellent tool to determine not only the symmetry but also exact number of particles in the finite-length structure and the sample shape. Using different samples with orthogonal C2v symmetry and varying the lattice spacing, we observe experimentally a transition between the regime of multi-order diffraction, being typical for photonic crystals to the regime where only the zero-order diffraction can be observed, being is a clear fingerprint of dielectric metasurfaces characterized by effective parameters. PMID:27491952

Towards predictive molecular dynamics simulations of DNA: electrostatics and solution/crystal environments

NASA Astrophysics Data System (ADS)

Babin, Volodymr; Baucom, Jason; Darden, Thomas; Sagui, Celeste

2006-03-01

We have investigated to what extend molecular dynamics (MD) simulatons can reproduce DNA sequence-specific features, given different electrostatic descriptions and different cell environments. For this purpose, we have carried out multiple unrestrained MD simulations of the duplex d(CCAACGTTGG)2. With respect to the electrostatic descriptions, two different force fields were studied: a traditional description based on atomic point charges and a polarizable force field. With respect to the cell environment, the difference between crystal and solution environments is emphasized, as well as the structural importance of divalent ions. By imposing the correct experimental unit cell environment, an initial configuration with two ideal B-DNA duplexes in the unit cell is shown to converge to the crystallographic structure. To the best of our knowledge, this provides the first example of a multiple nanosecond MD trajectory that shows and ideal structure converging to an experimental one, with a significant decay of the RMSD.

New structure type in the mixed-valent compound YbCu4Ga8.

PubMed

Subbarao, Udumula; Gutmann, Matthias J; Peter, Sebastian C

2013-02-18

The new compound YbCu(4)Ga(8) was obtained as large single crystals in high yield from reactions run in liquid gallium. Preliminary investigations suggest that YbCu(4)Ga(8) crystallizes in the CeMn(4)Al(8) structure type, tetragonal space group I4/mmm, and lattice constants are a = b = 8.6529(4) Å and c = 5.3976(11) Å. However, a detailed single-crystal XRD revealed a tripling of the c axis and crystallizing in a new structure type with lattice constants of a = b = 8.6529(4) Å and c = 15.465(1) Å. The structural model was further confirmed by neutron diffraction measurements on high-quality single crystal. The crystal structure of YbCu(4)Ga(8) is composed of pseudo-Frank-Kasper cages occupying one ytterbium atom in each ring which are shared through the corner along the ab plane, resulting in a three-dimensional network. The magnetic susceptibility of YbCu(4)Ga(8) investigated in the temperature range 2-300 K showed Curie-Weiss law behavior above 100 K, and the experimentally measured magnetic moment indicates mixed-valent ytterbium. Electrical resistivity measurements show the metallic nature of the compound. At low temperatures, variation of ρ as a function of T indicates a possible Fermi-liquid state at low temperatures.

Effect of an electric field on the orientation of a liquid crystal in a cell with a nonuniform director distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aksenova, E. V., E-mail: e.aksenova@spbu.ru; Karetnikov, A. A.; Karetnikov, N. A.

2016-05-15

The electric field-induced reorientation of a nematic liquid crystal in cells with a planar helicoidal or a homeoplanar structure of a director field is studied theoretically and experimentally. The dependences of the capacitances of these systems on the voltage in an applied electric field below and above the Fréedericksz threshold are experimentally obtained and numerically calculated. The calculations use the director distribution in volume that is obtained by direct minimization of free energy at various voltages. The inhomogeneity of the electric field inside a cell is taken into account. The calculation results are shown to agree with the experimental data.

Dependence of short and intermediate-range order on preparation in experimental and modeled pure a-Si

DOE PAGES

Holmstrom, Eero; Haberl, Bianca; Pakarinen, Olli H.; ...

2016-02-20

Variability in the short-to-intermediate range order of pure amorphous silicon prepared by different experimental and computational techniques is probed by measuring mass density, atomic coordination, bond-angle deviation, and dihedral angle deviation. It is found that there is significant variability in order parameters at these length scales in this archetypal covalently bonded, monoatomic system. This diversity strongly reflects preparation technique and thermal history in both experimental and simulated systems. Experiment and simulation do not fully quantitatively agree, partly due to differences in the way parameters are accessed. However, qualitative agreement in the trends is identified. Relaxed forms of amorphous silicon closelymore » resemble continuous random networks generated by a hybrid method of bond-switching Monte Carlo and molecular dynamics simulation. As-prepared ion implanted amorphous silicon can be adequately modeled using a structure generated from amorphization via ion bombardement using energetic recoils. Preparation methods which narrowly avoid crystallization such as experimental pressure-induced amorphization or simulated melt-quenching result in inhomogeneous structures that contain regions with significant variations in atomic ordering. Ad hoc simulated structures containing small (1 nm) diamond cubic crystal inclusions were found to possess relatively high bond-angle deviations and low dihedral angle deviations, a trend that could not be reconciled with any experimental material.« less

Complex Investigations of Sapphire Crystals Production

NASA Astrophysics Data System (ADS)

Malyukov, S. P.; Klunnikova, Yu V.

The problem of optimum conditions choice for processing sapphire substrates was solved with optimization methods and with combination of analytical simulation methods, experiment and expert system technology. The experimental results and software give rather full information on features of real structure of the sapphire crystal substrates and can be effectively used for optimization of technology of the substrate preparation for electronic devices.

Symmetry Groups of the Austenite Lattice and Construction of Self-Accommodation Complexes of Martensite Crystals in Alloys with the Shape-Memory Effect

NASA Astrophysics Data System (ADS)

Khundjua, A. G.; Ptitsin, A. G.; Brovkina, E. A.

2018-01-01

The internal structure of experimentally observed self-accommodation complexes of martensite crystals, which is determined by the system of twinning planes, is studied in this work. The direct correlation of the construction type of the complexes with the subgroups of the austenite lattice symmetry group is shown.

Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

PubMed

Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

2015-12-10

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

Experimental study on the sound absorption characteristics of continuously graded phononic crystals

NASA Astrophysics Data System (ADS)

Zhang, X. H.; Qu, Z. G.; He, X. C.; Lu, D. L.

2016-10-01

Novel three-dimensional (3D) continuously graded phononic crystals (CGPCs) have been designed, and fabricated by 3D printing. Each of the CGPCs is an entity instead of a combination of several other samples, and the porosity distribution of the CGPC along the incident direction is nearly linear. The sound absorption characteristics of CGPCs were experimentally investigated and compared with those of uniform phononic crystals (UPCs) and discretely stepped phononic crystals (DSPCs). Experimental results show that CGPCs demonstrate excellent sound absorption performance because of their continuously graded structures. CGPCs have higher sound absorption coefficients in the large frequency range and more sound absorption coefficient peaks in a specific frequency range than UPCs and DSPCs. In particular, the sound absorption coefficients of the CGPC with a porosity of 0.6 and thickness of 30 mm are higher than 0.56 when the frequency is 1350-6300 Hz and are all higher than 0.2 in the studied frequency range (1000-6300 Hz). CGPCs are expected to have potential application in noise control, especially in the broad frequency and low-frequency ranges.

An automated parallel crystallisation search for predicted crystal structures and packing motifs of carbamazepine.

PubMed

Florence, Alastair J; Johnston, Andrea; Price, Sarah L; Nowell, Harriott; Kennedy, Alan R; Shankland, Norman

2006-09-01

An automated parallel crystallisation search for physical forms of carbamazepine, covering 66 solvents and five crystallisation protocols, identified three anhydrous polymorphs (forms I-III), one hydrate and eight organic solvates, including the single-crystal structures of three previously unreported solvates (N,N-dimethylformamide (1:1); hemi-furfural; hemi-1,4-dioxane). Correlation of physical form outcome with the crystallisation conditions demonstrated that the solvent adopts a relatively nonspecific role in determining which polymorph is obtained, and that the previously reported effect of a polymer template facilitating the formation of form IV could not be reproduced by solvent crystallisation alone. In the accompanying computational search, approximately half of the energetically feasible predicted crystal structures exhibit the C=O...H--N R2(2)(8)dimer motif that is observed in the known polymorphs, with the most stable correctly corresponding to form III. Most of the other energetically feasible structures, including the global minimum, have a C=O...H--N C(4) chain hydrogen bond motif. No such chain structures were observed in this or any other previously published work, suggesting that kinetic, rather than thermodynamic, factors determine which of the energetically feasible crystal structures are observed experimentally, with the kinetics apparently favouring nucleation of crystal structures based on the CBZ-CBZ R2(2)(8) motif. (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association.

Study of the In2O3 molecule in the free state and in the crystal

NASA Astrophysics Data System (ADS)

Kaplan, Ilya G.; Miranda, Ulises; Trakhtenberg, Leonid I.

2018-03-01

The nanomaterials based on the In2O3 molecule are widely used as catalysts and sensors among other applications. In the present study, we discuss the possibility of using nanoclusters of In2O3 as molecular photomotors. A comparative analysis of the electronic structure of the In2O3 molecule in the free state and in the crystal is performed. For the free In2O3 molecule the geometry of its lowest structures, V-shape and linear, was optimised at the CCSD(T) level, which is the most precise computational method applied up to date to study In2O3. Using experimental crystallographic data, we determined the geometry of In2O3 in the crystal. It has a zigzag, not symmetric structure and possesses a dipole moment with magnitude slightly smaller than that of the V-structure of the free molecule (the linear structure due to its symmetry has no dipole moment). According to the Natural Atomic population analysis, the chemical structure of the linear In2O3 can be represented as O = In-O-In = O; the V-shaped molecule has the similar double- and single-bond structure. The construction of nanoclusters from ´bricksʼ of In2O3 with geometry extracted from crystal (or nanoclusters extracted directly from crystal) and their use as photo-driven molecular motors are discussed.

Pharmaceutical polymorph control in a drug-mimetic supramolecular gel† †Electronic supplementary information (ESI) available: Synthetic and crystallographic experimental details, rheology, full crystallization and calculation details. See DOI: 10.1039/c6sc04126d Click here for additional data file.

PubMed Central

Foster, Jonathan A.; Damodaran, Krishna K.; Maurin, Antoine; Thompson, Hugh P. G.; Cameron, Gary J.; Bernal, Jenifer Cuesta

2017-01-01

We report the synthesis of a bis(urea) gelator designed to specifically mimic the chemical structure of the highly polymorphic drug substance ROY. Crystallization of ROY from toluene gels of this gelator results in the formation of the metastable red form instead of the thermodynamic yellow polymorph. In contrast, all other gels and solution control experiments give the yellow form. Conformational and crystal structure prediction methods have been used to propose the structure of the gel and show that the templation of the red form by the targeted gel results from conformational matching of the gelator to the ROY substrate coupled with overgrowth of ROY onto the local periodic structure of the gel fibres. PMID:28451150

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

PubMed Central

Fratanduono, Dayne E.; Coppari, Federica; Newman, Matthew G.; Duffy, Thomas S.

2018-01-01

The high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as 10 times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ x-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-Si alloy with 7 weight % (wt %) Si adopts the hexagonal close-packed structure over the measured pressure range, whereas Fe-15wt%Si is observed in a body-centered cubic structure. This study represents the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3–Earth mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for these planets. PMID:29707632

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

DOE PAGES

Wicks, June K.; Smith, Raymond F.; Fratanduono, Dayne E.; ...

2018-04-25

In this paper, the high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as ten times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ X-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-7wt.%Si adopts the hexagonal close packed (hcp) structure over the measured pressure range, whereas Fe-15wt.%Si is observed in a body-centered cubic (bcc) structure. This study representsmore » the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3 Earth-mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for such planets.« less

Crystal structure and equation of state of Fe-Si alloys at super-Earth core conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wicks, June K.; Smith, Raymond F.; Fratanduono, Dayne E.

In this paper, the high-pressure behavior of Fe alloys governs the interior structure and dynamics of super-Earths, rocky extrasolar planets that could be as much as ten times more massive than Earth. In experiments reaching up to 1300 GPa, we combine laser-driven dynamic ramp compression with in situ X-ray diffraction to study the effect of composition on the crystal structure and density of Fe-Si alloys, a potential constituent of super-Earth cores. We find that Fe-7wt.%Si adopts the hexagonal close packed (hcp) structure over the measured pressure range, whereas Fe-15wt.%Si is observed in a body-centered cubic (bcc) structure. This study representsmore » the first experimental determination of the density and crystal structure of Fe-Si alloys at pressures corresponding to the center of a ~3 Earth-mass terrestrial planet. Our results allow for direct determination of the effects of light elements on core radius, density, and pressures for such planets.« less

Fluid Physics and Macromolecular Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth" is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

PubMed

Ferraresi-Curotto, Verónica; Echeverría, Gustavo A; Piro, Oscar E; Pis-Diez, Reinaldo; González-Baró, Ana C

2015-02-25

Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory. Copyright © 2014 Elsevier B.V. All rights reserved.

Phononic crystal diffraction gratings

NASA Astrophysics Data System (ADS)

Moiseyenko, Rayisa P.; Herbison, Sarah; Declercq, Nico F.; Laude, Vincent

2012-02-01

When a phononic crystal is interrogated by an external source of acoustic waves, there is necessarily a phenomenon of diffraction occurring on the external enclosing surfaces. Indeed, these external surfaces are periodic and the resulting acoustic diffraction grating has a periodicity that depends on the orientation of the phononic crystal. This work presents a combined experimental and theoretical study on the diffraction of bulk ultrasonic waves on the external surfaces of a 2D phononic crystal that consists of a triangular lattice of steel rods in a water matrix. The results of transmission experiments are compared with theoretical band structures obtained with the finite-element method. Angular spectrograms (showing frequency as a function of angle) determined from diffraction experiments are then compared with finite-element simulations of diffraction occurring on the surfaces of the crystal. The experimental results show that the diffraction that occurs on its external surfaces is highly frequency-dependent and has a definite relation with the Bloch modes of the phononic crystal. In particular, a strong influence of the presence of bandgaps and deaf bands on the diffraction efficiency is found. This observation opens perspectives for the design of efficient phononic crystal diffraction gratings.

Analysis of crystallization data in the Protein Data Bank

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirkwood, Jobie; Hargreaves, David; O’Keefe, Simon

In a large-scale study using data from the Protein Data Bank, some of the many reported findings regarding the crystallization of proteins were investigated. The Protein Data Bank (PDB) is the largest available repository of solved protein structures and contains a wealth of information on successful crystallization. Many centres have used their own experimental data to draw conclusions about proteins and the conditions in which they crystallize. Here, data from the PDB were used to reanalyse some of these results. The most successful crystallization reagents were identified, the link between solution pH and the isoelectric point of the protein wasmore » investigated and the possibility of predicting whether a protein will crystallize was explored.« less

Large-volume protein crystal growth for neutron macromolecular crystallography.

PubMed

Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

2015-04-01

Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

Challenges and Solutions in Fabrication of Silica-Based Photonic Crystal Fibers: An Experimental Study

NASA Astrophysics Data System (ADS)

Amouzad Mahdiraji, G.; Chow, Desmond M.; Sandoghchi, S. R.; Amirkhan, F.; Dermosesian, E.; Shien Yeo, Kwok; Kakaei, Z.; Ghomeishi, M.; Poh, Soo Yong; Gang, Shee Yu; Mahamd Adikan, F. R.

2014-01-01

The fabrication process of photonic crystal fibers based on a stack-and-draw method is presented in full detail in this article. In addition, improved techniques of photonic crystal fiber preform preparation and fabrication are highlighted. A new method of connecting a handle to a preform using only a fiber drawing tower is demonstrated, which eliminates the need for a high-temperature glass working lathe. Also, a new technique of modifying the photonic crystal fiber structural pattern by sealing air holes of the photonic crystal fiber cane is presented. Using the proposed methods, several types of photonic crystal fibers are fabricated, which suggests potential for rapid photonic crystal fibers fabrication in laboratories equipped with and limited to only a fiber drawing tower.

Rational Self-Assembly of Nano-Colloids using DNA Interaction

NASA Astrophysics Data System (ADS)

Ung, Marie T.; Scarlett, Raynaldo; Sinno, Talid R.; Crocker, John C.

2010-03-01

DNA is an attractive tool to direct the rational self-assembly of nano-colloids since its interaction is specific and reversible. This tunable attractive interaction should lead to a diverse and rich phase diagram of higher ordered structures which would not otherwise be entropically favored.footnotetextTkachenko AV, Morphological Diversity of DNA-Colloidal Self-Assembly, Phys. Rev. Lett 89 (2002) We compare our latest experimental observations to a simulation framework that precisely replicates the experimental phase behavior and the crystal growth kinetics.footnotetextKim AJ, Scarlett R., Biancaniello PL, Sinno T, Crocker JC, Probing interfacial equilibration in microsphere crystals formed by DNA-directed assembly, Nature Materials 8, 52-55 (2009) We will discuss the crystallography of novel structures and address how particle size and heterogeneity affect nucleation and growth rates.

Lattice and Valence Electronic Structures of Crystalline Octahedral Molybdenum Halide Clusters-Based Compounds, Cs2[Mo6X14] (X = Cl, Br, I), Studied by Density Functional Theory Calculations.

PubMed

Saito, Norio; Cordier, Stéphane; Lemoine, Pierric; Ohsawa, Takeo; Wada, Yoshiki; Grasset, Fabien; Cross, Jeffrey S; Ohashi, Naoki

2017-06-05

The electronic and crystal structures of Cs 2 [Mo 6 X 14 ] (X = Cl, Br, I) cluster-based compounds were investigated by density functional theory (DFT) simulations and experimental methods such as powder X-ray diffraction, ultraviolet-visible spectroscopy, and X-ray photoemission spectroscopy (XPS). The experimentally determined lattice parameters were in good agreement with theoretically optimized ones, indicating the usefulness of DFT calculations for the structural investigation of these clusters. The calculated band gaps of these compounds reproduced those experimentally determined by UV-vis reflectance within an error of a few tenths of an eV. Core-level XPS and effective charge analyses indicated bonding states of the halogens changed according to their sites. The XPS valence spectra were fairly well reproduced by simulations based on the projected electron density of states weighted with cross sections of Al K α , suggesting that DFT calculations can predict the electronic properties of metal-cluster-based crystals with good accuracy.

Crystallization, dehydration and experimental phasing of WbdD, a bifunctional kinase and methyltransferase from Escherichia coli O9a

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hagelueken, Gregor; Huang, Hexian; Harlos, Karl

2012-10-01

The optimization of WbdD crystals using a novel dehydration protocol and experimental phasing at 3.5 Å resolution by cross-crystal averaging followed by molecular replacement of electron density into a non-isomorphous 3.0 Å resolution native data set are reported. WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 Å and most onlymore » to 8 Å) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 Å resolution were non-isomorphous with a lower (3.5 Å) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 Å resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 Å resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 Å resolution electron density yielded a successful molecular-replacement solution of the 3.0 Å resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 Å resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations.« less

Two-step crystal growth mechanism during crystallization of an undercooled Ni50Al50 alloy

NASA Astrophysics Data System (ADS)

An, Simin; Li, Jiahao; Li, Yang; Li, Shunning; Wang, Qi; Liu, Baixin

2016-08-01

Crystallization processes are always accompanied by the emergence of multiple intermediate states, of which the structures and transition dynamics are far from clarity, since it is difficult to experimentally observe the microscopic pathway. To insight the structural evolution and the crystallization dynamics, we perform large-scale molecular dynamics simulations to investigate the time-dependent crystallization behavior of the NiAl intermetallic upon rapid solidification. The simulation results reveal that the crystallization process occurs via a two-step growth mechanism, involving the formation of initial non-equilibrium long range order (NLRO) regions and of the subsequent equilibrium long range order (ELRO) regions. The formation of the NLRO regions makes the grains rather inhomogeneous, while the rearrangement of the NLRO regions into the ELRO regions makes the grains more ordered and compact. This two-step growth mechanism is actually controlled by the evolution of the coordination polyhedra, which are characterized predominantly by the transformation from five-fold symmetry to four-fold and six-fold symmetry. From liquids to NLRO and further to ELRO, the five-fold symmetry of these polyhedra gradually fades, and finally vanishes when B2 structure is distributed throughout the grain bulk. The energy decrease along the pathway further implies the reliability of the proposed crystallization processes.

Engineering a light-emitting planar defect within three-dimensional photonic crystals

PubMed Central

Liu, Guiqiang; Chen, Yan; Ye, Zhiqing

2009-01-01

Sandwich structures, constructed from a planar defect of rhodamine-B (RhB)-doped titania (TiO2) and two photonic crystals, were synthesized via the self-assembly method combined with spin-coating. The modification of the spontaneous emission of RhB molecules in such structures was investigated experimentally. The spontaneous emission of RhB-doped TiO2 film with photonic crystals was reduced by a factor of 5.5 over a large bandwidth of 13% of the first-order Bragg diffraction frequency when compared with that of RhB-doped TiO2 film without photonic crystals. The angular dependence of the modification and the photoluminescence lifetime of RhB molecules demonstrate that the strong and wide suppression of the spontaneous emission of the RhB molecules is due to the presence of the photonic band gap. PMID:27877309

Ellipsometry study of optical parameters of AgIn5S8 crystals

NASA Astrophysics Data System (ADS)

Isik, Mehmet; Gasanly, Nizami

2015-12-01

AgIn5S8 crystals grown by Bridgman method were characterized for optical properties by ellipsometry measurements. Spectral dependence of optical parameters; real and imaginary parts of the pseudodielectric function, pseudorefractive index, pseudoextinction coefficient, reflectivity and absorption coefficient were obtained from ellipsometry experiments carried out in the 1.2-6.2 eV range. Direct band gap energy of 1.84 eV was found from the analysis of absorption coefficient vs. photon energy. The oscillator energy, dispersion energy and zero-frequency refractive index, high-frequency dielectric constant values were found from the analysis of the experimental data using Wemple-DiDomenico and Spitzer-Fan models. Crystal structure and atomic composition ratio of the constituent elements in the AgIn5S8 crystal were revealed from structural characterization techniques of X-ray diffraction and energy dispersive spectroscopy.

Defect related electrical and optical properties of AlN bulk crystals grown by physical vapor transport

NASA Astrophysics Data System (ADS)

Irmscher, Klaus

AlN crystallizes thermodynamically stable in the wurtzite structure and possesses a direct band gap of about 6 eV. It is the ideal substrate for the epitaxial growth of Al-rich AlxGa1-xN films that enable deep ultraviolet (UV) emitters. Appropriate AlN bulk crystals can be grown by physical vapor transport (PVT). Besides high structural perfection, such substrate crystals should be highly UV transparent and ideally, electrically conductive. It is well known that point defects like impurities and intrinsic defects may introduce electronic energy levels within the bandgap, which lead to additional optical absorption or electrical compensation. Among the impurities, which may be incorporated into the AlN crystals during PVT growth at well above 2000 ° C, oxygen, carbon, and silicon play the major role. Based on our own experimental data as well as on experimental and theoretical results reported in literature, we discuss energy levels, charge states and possible negative-U behavior of these impurities and of vacancy-type defects. In particular, we develop a model that explains the absorption behavior of the crystals in dependence on the Fermi level that can be controlled by the growth conditions, including intentional doping. Further, we pay attention on spectroscopic investigations giving direct evidence for the chemical nature and atomic arrangement of the involved point defects. As examples local vibrational mode (LVM) spectroscopy of carbon related defects and recent reports of electron paramagnetic resonance (EPR) spectroscopy are discussed.

Solid-state NMR studies of theophylline co-crystals with dicarboxylic acids.

PubMed

Pindelska, Edyta; Sokal, Agnieszka; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Kolodziejski, Waclaw

2014-11-01

In this work, three polycrystalline materials containing co-crystals of theophylline with malonic, maleic, and glutaric acids were studied using (13)C, (15)N and (1)H solid-state NMR and FT-IR spectroscopy. The NMR assignments were supported by gauge including projector augmented waves (GIPAW) calculations of chemical shielding, performed using X-ray determined geometry. The experimental (13)C cross polarization/magic angle spinning (CP/MAS) NMR results and the calculated isotropic chemical shifts were in excellent agreement. A rapid and convenient method for theophylline co-crystals crystal structure analysis has been proposed for co-crystals, which are potentially new APIs. Copyright © 2014 Elsevier B.V. All rights reserved.

Insights into Hydrate Formation and Stability of Morphinanes from a Combination of Experimental and Computational Approaches

PubMed Central

2014-01-01

Morphine, codeine, and ethylmorphine are important drug compounds whose free bases and hydrochloride salts form stable hydrates. These compounds were used to systematically investigate the influence of the type of functional groups, the role of water molecules, and the Cl– counterion on molecular aggregation and solid state properties. Five new crystal structures have been determined. Additionally, structure models for anhydrous ethylmorphine and morphine hydrochloride dihydrate, two phases existing only in a very limited humidity range, are proposed on the basis of computational dehydration modeling. These match the experimental powder X-ray diffraction patterns and the structural information derived from infrared spectroscopy. All 12 structurally characterized morphinane forms (including structures from the Cambridge Structural Database) crystallize in the orthorhombic space group P212121. Hydrate formation results in higher dimensional hydrogen bond networks. The salt structures of the different compounds exhibit only little structural variation. Anhydrous polymorphs were detected for all compounds except ethylmorphine (one anhydrate) and its hydrochloride salt (no anhydrate). Morphine HCl forms a trihydrate and dihydrate. Differential scanning and isothermal calorimetry were employed to estimate the heat of the hydrate ↔ anhydrate phase transformations, indicating an enthalpic stabilization of the respective hydrate of 5.7 to 25.6 kJ mol–1 relative to the most stable anhydrate. These results are in qualitative agreement with static 0 K lattice energy calculations for all systems except morphine hydrochloride, showing the need for further improvements in quantitative thermodynamic prediction of hydrates having water···water interactions. Thus, the combination of a variety of experimental techniques, covering temperature- and moisture-dependent stability, and computational modeling allowed us to generate sufficient kinetic, thermodynamic and structural information to understand the principles of hydrate formation of the model compounds. This approach also led to the detection of several new crystal forms of the investigated morphinanes. PMID:25036525

Characterization of calcium deposition induced by Synechocystis sp. PCC6803 in BG11 culture medium

NASA Astrophysics Data System (ADS)

Yan, Huaxiao; Han, Zuozhen; Zhao, Hui; Zhou, Shixue; Chi, Naijie; Han, Mei; Kou, Xiaoyan; Zhang, Yan; Xu, Linlin; Tian, Chenchen; Qin, Song

2014-05-01

Calcium carbonate (CaCO3) crystals in their preferred orientation were obtained in BG11 culture media inoculated with Synechocystis sp. PCC6803 (inoculated BG11). In this study, the features of calcium carbonate deposition were investigated. Inoculated BG11 in different calcium ion concentrations was used for the experimental group, while the BG11 culture medium was used for the control group. The surface morphologies of the calcium carbonate deposits in the experimental and control groups were determined by scanning and transmission electron microscopy. The deposits were analyzed by electronic probe micro-analysis, Fourier transform infrared spectrum, X-ray diffraction, thermal gravimetric analysis and differential scanning calorimetry. The results show that the surfaces of the crystals in the experimental group were hexahedral in a scaly pattern. The particle sizes were micrometer-sized and larger than those in the control group. The deposits of the control group contained calcium (Ca), carbon (C), oxygen (O), phosphorus (P), iron (Fe), copper (Cu), zinc (Zn), and other elements. The deposits in the experimental group contained Ca, C, and O only. The deposits of both groups contained calcite. The thermal decomposition temperature of the deposits in the control group was lower than those in the experimental group. It showed that the CaCO3 deposits of the experimental group had higher thermal stability than those of the control group. This may be due to the secondary metabolites produced by the algae cells, which affect the carbonate crystal structure and result in a close-packed structure. The algae cells that remained after thermal weight loss were heavier in higher calcium concentrations in BG11 culture media. There may be more calcium-containing crystals inside and outside of these cells. These results shall be beneficial for understanding the formation mechanism of carbonate minerals.

Progress in thin-film silicon solar cells based on photonic-crystal structures

NASA Astrophysics Data System (ADS)

Ishizaki, Kenji; De Zoysa, Menaka; Tanaka, Yoshinori; Jeon, Seung-Woo; Noda, Susumu

2018-06-01

We review the recent progress in thin-film silicon solar cells with photonic crystals, where absorption enhancement is achieved by using large-area resonant effects in photonic crystals. First, a definitive guideline for enhancing light absorption in a wide wavelength range (600–1100 nm) is introduced, showing that the formation of multiple band edges utilizing higher-order modes confined in the thickness direction and the introduction of photonic superlattice structures enable significant absorption enhancement, exceeding that observed for conventional random scatterers. Subsequently, experimental evidence of this enhancement is demonstrated for a variety of thin-film Si solar cells: ∼500-nm-thick ultrathin microcrystalline silicon cells, few-µm-thick microcrystalline silicon cells, and ∼20-µm-thick thin single-crystalline silicon cells. The high short-circuit current densities and/or efficiencies observed for each cell structure confirm the effectiveness of using multiple band-edge resonant modes of photonic crystals for enhancing broadband absorption in actual solar cells.

Extended-Range Ultrarefractive 1D Photonic Crystal Prisms

NASA Technical Reports Server (NTRS)

Ting, David Z.

2007-01-01

A proposal has been made to exploit the special wavelength-dispersive characteristics of devices of the type described in One-Dimensional Photonic Crystal Superprisms (NPO-30232) NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 10a. A photonic crystal is an optical component that has a periodic structure comprising two dielectric materials with high dielectric contrast (e.g., a semiconductor and air), with geometrical feature sizes comparable to or smaller than light wavelengths of interest. Experimental superprisms have been realized as photonic crystals having three-dimensional (3D) structures comprising regions of amorphous Si alternating with regions of SiO2, fabricated in a complex process that included sputtering. A photonic crystal of the type to be exploited according to the present proposal is said to be one-dimensional (1D) because its contrasting dielectric materials would be stacked in parallel planar layers; in other words, there would be spatial periodicity in one dimension only. The processes of designing and fabricating 1D photonic crystal superprisms would be simpler and, hence, would cost less than do those for 3D photonic crystal superprisms. As in 3D structures, 1D photonic crystals may be used in applications such as wavelength-division multiplexing. In the extended-range configuration, it is also suitable for spectrometry applications. As an engineered structure or artificially engineered material, a photonic crystal can exhibit optical properties not commonly found in natural substances. Prior research had revealed several classes of photonic crystal structures for which the propagation of electromagnetic radiation is forbidden in certain frequency ranges, denoted photonic bandgaps. It had also been found that in narrow frequency bands just outside the photonic bandgaps, the angular wavelength dispersion of electromagnetic waves propagating in photonic crystal superprisms is much stronger than is the angular wavelength dispersion obtained by use of conventional prisms and diffraction gratings and is highly nonlinear.

Generalized Reliability Methodology Applied to Brittle Anisotropic Single Crystals. Degree awarded by Washington Univ., 1999

NASA Technical Reports Server (NTRS)

Salem, Jonathan A.

2002-01-01

A generalized reliability model was developed for use in the design of structural components made from brittle, homogeneous anisotropic materials such as single crystals. The model is based on the Weibull distribution and incorporates a variable strength distribution and any equivalent stress failure criteria. In addition to the reliability model, an energy based failure criterion for elastically anisotropic materials was formulated. The model is different from typical Weibull-based models in that it accounts for strength anisotropy arising from fracture toughness anisotropy and thereby allows for strength and reliability predictions of brittle, anisotropic single crystals subjected to multiaxial stresses. The model is also applicable to elastically isotropic materials exhibiting strength anisotropy due to an anisotropic distribution of flaws. In order to develop and experimentally verify the model, the uniaxial and biaxial strengths of a single crystal nickel aluminide were measured. The uniaxial strengths of the <100> and <110> crystal directions were measured in three and four-point flexure. The biaxial strength was measured by subjecting <100> plates to a uniform pressure in a test apparatus that was developed and experimentally verified. The biaxial strengths of the single crystal plates were estimated by extending and verifying the displacement solution for a circular, anisotropic plate to the case of a variable radius and thickness. The best correlation between the experimental strength data and the model predictions occurred when an anisotropic stress analysis was combined with the normal stress criterion and the strength parameters associated with the <110> crystal direction.

Chapter Eight - Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, Paul W; Mulder, David W; Artz, Jacob H.

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas-treatments. Other themesmore » presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.« less

Surface modes and reconstruction of diamond structure crystals

NASA Astrophysics Data System (ADS)

Goldammer, W.; Ludwig, W.; Zierau, W.

1986-08-01

Applying our recently proposed Green function method we calculate the surface phonon spectra for the (111) surfaces of the diamond structure crystals C, Si, Ge and α-Sn on the basis of a phenomenological force constant model. Allowing for changes in the surface force constants we investigate the possibility of a surface phonon softening. Relating these soft modes to surface reconstructions we find evidence for a Si (7 × 7), Ge (8 × 8) and α-Sn (3 × 3) reconstruction, while diamond does not exhibit a soft mode behavior at all. We can thus explain the occurrence of different surface structures in these geometrically identical crystals as being determined to a great extent already by bulk properties. Finally, we derive models of the reconstructed surfaces and discuss our model for the Si (7 × 7) surface with respect to experimental TED patterns.

Photonic crystals for improving light absorption in organic solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duché, D., E-mail: david.duche@im2np.fr; Le Rouzo, J.; Masclaux, C.

2015-02-07

We theoretically and experimentally study the structuration of organic solar cells in the shape of photonic crystal slabs. By taking advantage of the optical properties of photonic crystals slabs, we show the possibility to couple Bloch modes with very low group velocities in the active layer of the cells. These Bloch modes, also called slow Bloch modes (SBMs), allow increasing the lifetime of photons within the active layer. Finally, we present experimental demonstration performed by using nanoimprint to directly pattern the standard poly-3-hexylthiophène:[6,6]-phenyl-C61-butiryc acid methyl ester organic semiconductor blend in thin film form in the shape of a photonic crystalmore » able to couple SBMs. In agreement with the model, optical characterizations will demonstrate significant photonic absorption gains.« less

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

PubMed

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.

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

PubMed Central

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 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. PMID:25449625

The Stanford Automated Mounter: Enabling High-Throughput Protein Crystal Screening at SSRL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, C.A.; Cohen, A.E.

2009-05-26

The macromolecular crystallography experiment lends itself perfectly to high-throughput technologies. The initial steps including the expression, purification, and crystallization of protein crystals, along with some of the later steps involving data processing and structure determination have all been automated to the point where some of the last remaining bottlenecks in the process have been crystal mounting, crystal screening, and data collection. At the Stanford Synchrotron Radiation Laboratory, a National User Facility that provides extremely brilliant X-ray photon beams for use in materials science, environmental science, and structural biology research, the incorporation of advanced robotics has enabled crystals to be screenedmore » in a true high-throughput fashion, thus dramatically accelerating the final steps. Up to 288 frozen crystals can be mounted by the beamline robot (the Stanford Auto-Mounting System) and screened for diffraction quality in a matter of hours without intervention. The best quality crystals can then be remounted for the collection of complete X-ray diffraction data sets. Furthermore, the entire screening and data collection experiment can be controlled from the experimenter's home laboratory by means of advanced software tools that enable network-based control of the highly automated beamlines.« less

Spatial filtering with photonic crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maigyte, Lina; Staliunas, Kestutis; Institució Catalana de Recerca i Estudis Avançats

2015-03-15

Photonic crystals are well known for their celebrated photonic band-gaps—the forbidden frequency ranges, for which the light waves cannot propagate through the structure. The frequency (or chromatic) band-gaps of photonic crystals can be utilized for frequency filtering. In analogy to the chromatic band-gaps and the frequency filtering, the angular band-gaps and the angular (spatial) filtering are also possible in photonic crystals. In this article, we review the recent advances of the spatial filtering using the photonic crystals in different propagation regimes and for different geometries. We review the most evident configuration of filtering in Bragg regime (with the back-reflection—i.e., inmore » the configuration with band-gaps) as well as in Laue regime (with forward deflection—i.e., in the configuration without band-gaps). We explore the spatial filtering in crystals with different symmetries, including axisymmetric crystals; we discuss the role of chirping, i.e., the dependence of the longitudinal period along the structure. We also review the experimental techniques to fabricate the photonic crystals and numerical techniques to explore the spatial filtering. Finally, we discuss several implementations of such filters for intracavity spatial filtering.« less

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

OsN2: Crystal structure and electronic properties

NASA Astrophysics Data System (ADS)

Montoya, Javier A.; Hernandez, Alexander D.; Sanloup, Chrystèle; Gregoryanz, Eugene; Scandolo, Sandro

2007-01-01

Osmium nitride belongs to a family of nitrides synthesized recently at high pressures from their parent elements. Here we show, based on first-principles calculations, that the crystal structure of osmium nitride is isostructural to marcasite. Excellent agreement is obtained between the authors' results and x-ray, Raman, and compressibility measurements. In the OsN2 marcasite structure single-bonded N2 units occupy the interstitial sites of the Os close-packed lattice, giving rise to a metallic compound. A comparison between the formation energies of OsN2 and PtN2 explains the similar thermodynamic conditions of formation reported experimentally for the two compounds.

Corrosion

ERIC Educational Resources Information Center

Slabaugh, W. H.

1974-01-01

Presents some materials for use in demonstration and experimentation of corrosion processes, including corrosion stimulation and inhibition. Indicates that basic concepts of electrochemistry, crystal structure, and kinetics can be extended to practical chemistry through corrosion explanation. (CC)

The ‘Sticky Patch’ Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

PubMed Central

Derewenda, Zygmunt S.; Godzik, Adam

2017-01-01

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e. crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular ‘sticky patch’ model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer ‘sticky patches’ which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the ‘sticky patch’ model. We discuss state-of-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design of variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis. PMID:28573570

Towards engineered branch placement: Unreal™ match between vapour-liquid-solid glancing angle deposition nanowire growth and simulation

NASA Astrophysics Data System (ADS)

Taschuk, M. T.; Tucker, R. T.; LaForge, J. M.; Beaudry, A. L.; Kupsta, M. R.; Brett, M. J.

2013-12-01

The vapour-liquid-solid glancing angle deposition (VLS-GLAD) process is capable of producing complex nanotree structures with control over azimuthal branch orientation and height. We have developed a thin film growth simulation including ballistic deposition, simplified surface diffusion, and droplet-mediated cubic crystal growth for the VLS-GLAD process using the UnrealTM Development Kit. The use of a commercial game engine has provided an interactive environment while allowing a custom physics implementation. Our simulation's output is verified against experimental data, including a volumetric film reconstruction produced using focused ion beam and scanning-electron microscopy (SEM), crystallographic texture, and morphological characteristics such as branch orientation. We achieve excellent morphological and texture agreement with experimental data, as well as qualitative agreement with SEM imagery. The simplified physics in our model reproduces the experimental films, indicating that the dominant role flux geometry plays in the VLS-GLAD competitive growth process responsible for azimuthally oriented branches and biaxial crystal texture evolution. The simulation's successful reproduction of experimental data indicates that it should have predictive power in designing novel VLS-GLAD structures.

Biophysics of cadherin adhesion.

PubMed

Leckband, Deborah; Sivasankar, Sanjeevi

2012-01-01

Since the identification of cadherins and the publication of the first crystal structures, the mechanism of cadherin adhesion, and the underlying structural basis have been studied with a number of different experimental techniques, different classical cadherin subtypes, and cadherin fragments. Earlier studies based on biophysical measurements and structure determinations resulted in seemingly contradictory findings regarding cadherin adhesion. However, recent experimental data increasingly reveal parallels between structures, solution binding data, and adhesion-based biophysical measurements that are beginning to both reconcile apparent differences and generate a more comprehensive model of cadherin-mediated cell adhesion. This chapter summarizes the functional, structural, and biophysical findings relevant to cadherin junction assembly and adhesion. We emphasize emerging parallels between findings obtained with different experimental approaches. Although none of the current models accounts for all of the available experimental and structural data, this chapter discusses possible origins of apparent discrepancies, highlights remaining gaps in current knowledge, and proposes challenges for further study.

On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment.

PubMed

Burgess, Kevin M N; Bryce, David L

2015-02-01

The vaterite polymorph of CaCO3 has puzzled crystallographers for decades in part due to difficulties in obtaining single crystals. The multiple proposed structures for the vaterite polymorph of CaCO3 are assessed using a combined (43)Ca solid-state nuclear magnetic resonance (SSNMR) spectroscopic and computational approach. A combination of improved experimental and computational methods, along with a calibrated chemical shift scale and (43)Ca nuclear quadrupole moment, allow for improved insights relative to our earlier work (Bryce et al., J. Am. Chem. Soc. 2008, 130, 9282). Here, we synthesize a (43)Ca isotopically-enriched sample of vaterite and perform high-resolution quadrupolar SSNMR experiments including magic-angle spinning (MAS), double-rotation (DOR), and multiple-quantum (MQ) MAS experiments at magnetic field strengths of 9.4 and 21.1T. We identify one crystallographically unique Ca(2+) site in vaterite with a slight distribution in both chemical shifts and quadrupolar parameters. Both the experimental (43)Ca electric field gradient tensor and the isotropic chemical shift for vaterite are compared to those calculated with the gauge-including projector-augmented-wave (GIPAW) DFT method in an attempt to identify the model that best represents the crystal structure of vaterite. Simulations of (43)Ca DOR and MAS NMR spectra based on the NMR parameters computed for a total of 18 structural models for vaterite allow us to distinguish between these models. Among these 18, the P3221 and C2 structures provide simulated spectra and diffractograms in best agreement with all experimental data. Copyright © 2014 Elsevier Inc. All rights reserved.

Identification of Gravity-Related Effects on Crystal Growth From Melts With an Immiscibility Gap

NASA Technical Reports Server (NTRS)

Kassemi, M.; Sayir, A.; Farmer, S.

1999-01-01

This work involves an experimental-numerical approach to study the effects of natural and Marangoni convections on solidification of single crystals from a silicate melt with a liquid-liquid immiscibility gap. Industrial use of crystals grown from silicate melts is becoming increasingly important in electronic, optical, and high temperature structural applications. Even the simplest silicate systems like Al203-SiO2 have had, and will continue to have, a significant role in the development of traditional and advanced ceramics. A unique feature of crystals grown from the silicate systems is their outstanding linear electro-optic properties. They also exhibit exceptionally high optical rotativity. As a result, these crystals are attractive materials for dielectric, optical, and microwave applications. Experimental work in our laboratory has indicated that directional solidification of a single crystal mullite appears to be preceded by liquid-liquid phase separation in the melt. Disruption of the immiscible state results in crystallization of a two phase structure. There is also evidence that mixing in the melt caused by density-driven convection can significantly affect the stability of the immiscible liquid layers and result in poly-crystalline growth. On earth, the immiscible state has only been observed for small diameter crystals grown in float zone systems where natural convection is almost negligible. Therefore, it is anticipated that growth of large single crystals from silicate melts would benefit from microgravity conditions because of the reduction of the natural convective mixing. The main objective of this research is to determine the effects of transport processes on the phase separation in the melt during growth of a single crystal while addressing the following issues: (1) When do the immiscible layers form and are they real?; (2) What are the main physical characteristics of the immiscible liquids?; and (3) How mixing by natural or Marangoni convection affects the stability of the phase separated melt.

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Experimental (FTIR, Raman, UV-visible and PL) and theoretical (DFT and TDDFT) studies on bis(8-hydroxyquinolinium) tetrachlorocobaltate(II) compound

NASA Astrophysics Data System (ADS)

Chaouachi, Soumaya; Elleuch, Slim; Hamdi, Besma; Zouari, Ridha

2016-12-01

The purpose of this paper is to present the chemical preparation, crystal structure, vibrational study and optical features for new organic-inorganic compound [C9H8NO]2CoCl4 abbreviated [8-HQ]2CoCl4. The structural study by X-ray diffraction prove that this compound crystallize in a monoclinic unit-cell with space group C2/c (point group 2/m = C2h). It is built of tetrahedra [CoCl4]2- anions and (C9H8NO)+ cations in the 1/2 ratio. The crystal structure is stabilized by network three-dimensional of Nsbnd H⋯Cl, Nsbnd H⋯O, Osbnd H⋯Cl, Csbnd H⋯Cl hydrogen bonds, and offset π-π stacking interactions. Also, the Hirshfeld Surface projections and Fingerprint plots were elucidated the relative contribution of the type, nature and explore the H⋯Cl, C⋯H, C⋯C, C⋯N, H⋯O intermolecular contacts in the crystal in a visual manner. Furthermore, vibrational analysis of the structural groups in the compound was carried out by both Fourier transforms infrared (FT-IR) and Raman spectra. The spectral data are complemented by good information at the region characteristic of metal-ligand, which evidences coordination through the compound. The optical properties of the crystal were studied by using optical absorption UV-visible and photoluminescence (PL) spectroscopy studies. Theoretical calculations were performed using density functional theory (DFT) at (DFT/B3LYP/LanL2DZ) level in the aim of aiding in studying structural, vibrational and optical properties of the investigated compound. Good relationship consistency is found between the experimental and theoretical studies. Inspection of the optical properties has lead to confirm the exhibition of a green photoluminescence and the occurrence of charge transfer phenomenon in this material.

Photonic crystal Fano resonances for realizing optical switches, lasers, and non-reciprocal elements

NASA Astrophysics Data System (ADS)

Bekele, Dagmawi A.; Yu, Yi; Hu, Hao; Ding, Yunhong; Sakanas, Aurimas; Ottaviano, Luisa; Semenova, Elizaveta; Oxenløwe, Leif K.; Yvind, Kresten; Mork, Jesper

2017-08-01

We present our work on photonic crystal membrane devices exploiting Fano resonance between a line-defect waveguide and a side coupled nanocavity. Experimental demonstration of fast and compact all-optical switches for wavelength-conversion is reported. It is shown how the use of an asymmetric structure in combination with cavity-enhanced nonlinearity can be used to realize non-reciprocal transmission at ultra-low power and with large bandwidth. A novel type of laser structure, denoted a Fano laser, is discussed in which one of the mirrors is based on a Fano resonance. Finally, the design, fabrication and characterization of grating couplers for efficient light coupling in and out of the indium phosphide photonic crystal platform is discussed.

The evolution of structural and chemical heterogeneity during rapid solidification at gas atomization

NASA Astrophysics Data System (ADS)

Golod, V. M.; Sufiiarov, V. Sh

2017-04-01

Gas atomization is a high-performance process for manufacturing superfine metal powders. Formation of the powder particles takes place primarily through the fragmentation of alloy melt flow with high-pressure inert gas, which leads to the formation of non-uniform sized micron-scale particles and subsequent their rapid solidification due to heat exchange with gas environment. The article presents results of computer modeling of crystallization process, simulation and experimental studies of the cellular-dendrite structure formation and microsegregation in different size particles. It presents results of adaptation of the approach for local nonequilibrium solidification to conditions of crystallization at gas atomization, detected border values of the particle size at which it is possible a manifestation of diffusionless crystallization.

Structure and properties of fullerene molecular crystals with linear-scaling van der Waals density functional theory

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Andrinopoulos, Lampros; Hine, Nicholas

2014-03-01

Fullerene molecular crystals are of technological promise for their use in heterojunction photovoltaic cells. An improved theoretical understanding of their structure and properties would be a step towards the rational design of new devices. Simulations based on density-functional theory (DFT) are invaluable for developing such insight, but standard semi-local functionals do not capture the important inter-molecular van der Waals (vdW) interactions in fullerene crystals. Furthermore the computational cost associated with the large unit cells needed are at the limit or beyond the capabilities of traditional DFT methods. In this work we overcome these limitations by using our implementation of a number of vdW-DFs in the ONETEP linear-scaling DFT code to study the structural properties of C60 molecular crystals. Powder neutron diffraction shows that the low-temperature Pa-3 phase is orientationally ordered with individual C60 units rotated around the [111] direction. We fully explore the energy landscape associated with the rotation angle and find two stable structures that are energetically very close, one of which corresponds to the experimentally observed structure. We further consider the effect of orientational disorder in very large supercells of thousands of atoms.

The structural basis for enhanced silver reflectance in Koi fish scale and skin.

PubMed

Gur, Dvir; Leshem, Ben; Oron, Dan; Weiner, Steve; Addadi, Lia

2014-12-10

Fish have evolved biogenic multilayer reflectors composed of stacks of intracellular anhydrous guanine crystals separated by cytoplasm, to produce the silvery luster of their skin and scales. Here we compare two different variants of the Japanese Koi fish; one of them with enhanced reflectivity. Our aim is to determine how biology modulates reflectivity, and from this to obtain a mechanistic understanding of the structure and properties governing the intensity of silver reflectance. We measured the reflectance of individual scales with a custom-made microscope, and then for each individual scale we characterized the structure of the guanine crystal/cytoplasm layers using high-resolution cryo-SEM. The measured reflectance and the structural-geometrical parameters were used to calculate the reflectance of each scale, and the results were compared to the experimental measurements. We show that enhanced reflectivity is obtained with the same basic guanine crystal/cytoplasm stacks, but the structural arrangement between the stack, inside the stacks, and relative to the scale surface is varied when reflectivity is enhanced. Finally, we propose a model that incorporates the basic building block parameters, the crystal orientation inside the tissue, and the resulting reflectance and explains the mechanistic basis for reflectance enhancement.

Symmetry-lowering lattice distortion at the spin reorientation in MnBi single crystals

DOE PAGES

McGuire, Michael A.; Cao, Huibo; Chakoumakos, Bryan C.; ...

2014-11-18

Here we report structural and physical properties determined by measurements on large single crystals of the anisotropic ferromagnet MnBi. The findings support the importance of magnetoelastic effects in this material. X-ray diffraction reveals a structural phase transition at the spin reorientation temperature T SR = 90 K. The distortion is driven by magneto-elastic coupling, and upon cooling transforms the structure from hexagonal to orthorhombic. Heat capacity measurements show a thermal anomaly at the crystallographic transition, which is suppressed rapidly by applied magnetic fields. Effects on the transport and anisotropic magnetic properties of the single crystals are also presented. Increasing anisotropymore » of the atomic displacement parameters for Bi with increasing temperature above T SR is revealed by neutron diffraction measurements. It is likely that this is directly related to the anisotropic thermal expansion in MnBi, which plays a key role in the spin reorientation and magnetocrystalline anisotropy. Finally, the identification of the true ground state crystal structure reported here may be important for future experimental and theoretical studies of this permanent magnet material, which have to date been performed and interpreted using only the high temperature structure.« less

Semiconductor crystal growth and segregation problems on earth and in space

NASA Technical Reports Server (NTRS)

Gatos, H. C.

1982-01-01

Semiconductor crystal growth and segregation problems are examined in the context of their relationship to material properties, and some of the problems are illustrated with specific experimental results. The compositional and structural defects encountered in semiconductors are largely associated with gravity-induced convective currents in the melt; additional problems are introduced by variations in stoichiometry. It is demonstrated that in near-zero gravity environment, crystal growth and segregation takes place under ideal steady-state conditions with minimum convective interference. A discussion of the advantages of zero-gravity crystal growth is followed by a summary of problems arising from the absence of gravitational forces.

Tunable microwave bandpass filter integrated power divider based on the high anisotropy electro-optic nematic liquid crystal.

PubMed

Liu, Yupeng; Liu, Yang; Li, Haiyan; Jiang, Di; Cao, Weiping; Chen, Hui; Xia, Lei; Xu, Ruimin

2016-07-01

A novel, compact microwave tunable bandpass filter integrated power divider, based on the high anisotropy electro-optic nematic liquid crystal, is proposed in this letter. Liquid crystal, as the electro-optic material, is placed between top inverted microstrip line and the metal plate. The proposed structure can realize continuous tunable bandpass response and miniaturization. The proposed design concept is validated by the good performance of simulation results and experimental results. The electro-optic material has shown great potential for microwave application.

The statistical kinematical theory of X-ray diffraction as applied to reciprocal-space mapping

PubMed

Nesterets; Punegov

2000-11-01

The statistical kinematical X-ray diffraction theory is developed to describe reciprocal-space maps (RSMs) from deformed crystals with defects of the structure. The general solutions for coherent and diffuse components of the scattered intensity in reciprocal space are derived. As an example, the explicit expressions for intensity distributions in the case of spherical defects and of a mosaic crystal were obtained. The theory takes into account the instrumental function of the triple-crystal diffractometer and can therefore be used for experimental data analysis.

Synthesis, crystal structures and spectroscopic properties of triazine-based hydrazone derivatives; a comparative experimental-theoretical study.

PubMed

Arshad, Muhammad Nadeem; Bibi, Aisha; Mahmood, Tariq; Asiri, Abdullah M; Ayub, Khurshid

2015-04-03

We report here a comparative theoretical and experimental study of four triazine-based hydrazone derivatives. The hydrazones are synthesized by a three step process from commercially available benzil and thiosemicarbazide. The structures of all compounds were determined by using the UV-Vis., FT-IR, NMR (1H and 13C) spectroscopic techniques and finally confirmed unequivocally by single crystal X-ray diffraction analysis. Experimental geometric parameters and spectroscopic properties of the triazine based hydrazones are compared with those obtained from density functional theory (DFT) studies. The model developed here comprises of geometry optimization at B3LYP/6-31G (d, p) level of DFT. Optimized geometric parameters of all four compounds showed excellent correlations with the results obtained from X-ray diffraction studies. The vibrational spectra show nice correlations with the experimental IR spectra. Moreover, the simulated absorption spectra also agree well with experimental results (within 10-20 nm). The molecular electrostatic potential (MEP) mapped over the entire stabilized geometries of the compounds indicated their chemical reactivates. Furthermore, frontier molecular orbital (electronic properties) and first hyperpolarizability (nonlinear optical response) were also computed at the B3LYP/6-31G (d, p) level of theory.

The antifriction behaviours of ?

NASA Astrophysics Data System (ADS)

Yan, Feng-yuan; Xue, Qun-ji

1997-03-01

In this paper, the antifriction behaviours of 0022-3727/30/5/010/img2 (3:1) molecules and their crystal powder were evaluated by different methods. It was found that the 0022-3727/30/5/010/img2 crystal powder possessed hexagonal close packed (hcp) crystal structure with a = 10.1 Å and c = 16.55 Å, and a transformation of crystal structure from hcp to face centred cubic (fcc) occurred easily during friction (burnishing). It was confirmed that two kinds of process, breakage of 0022-3727/30/5/010/img2 powder coagulated by nanoscale single crystals and rearrangement of the molecules along the friction direction, had occurred under the friction force. The extreme pressure (EP) performance of 0022-3727/30/5/010/img2 as an additive in paraffin liquid was investigated on an SRV oscillating wear machine. It was found that the extreme pressure load (EP value) of paraffin liquid was increased by dispersion of 0022-3727/30/5/010/img2 powder, accompanied by a slight improvement in the antifriction behaviour. it was confirmed that the improvement in EP value and antifriction behaviour of oil was dependent on the crystal structure of 0022-3727/30/5/010/img2 powder, but independent of the spherical molecular structure of 0022-3727/30/5/010/img8 or 0022-3727/30/5/010/img9. The burnishing experimental results also proved that the antifriction behaviour was determined by the crystal structure and had no relation to the molecular structure. It was also found that fullerenes possessed some physical properties similar to those of graphite. Since the formation of compact fullerenes with high shear strength during friction can be effectively prevented by some other lubricants, it is suggested that fullerenes should be mixed with other lubricants for tribological application.

Nonreciprocity of spin waves in magnonic crystals created by surface acoustic waves in structures with yttrium iron garnet

NASA Astrophysics Data System (ADS)

Kryshtal, R. G.; Medved, A. V.

2015-12-01

Experimental results of investigations of nonreciprocity for surface magnetostatic spin waves (SMSW) in the magnonic crystal created by surface acoustic waves (SAW) in yttrium iron garnet films on a gallium gadolinium garnet substrate as without metallization and with aluminum films with different electrical conductivities (thicknesses) are presented. In structures without metallization, the frequency of magnonic gaps is dependent on mutual directions of propagation of the SAW and SMSW, showing nonreciprocal properties for SMSW in SAW - magnonic crystals even with the symmetrical dispersion characteristic. In metalized SAW - magnonic crystals the shift of the magnonic band gaps frequencies at the inversion of the biasing magnetic field was observed. The frequencies of magnonic band gaps as functions of SAW frequency are presented. Measured dependencies, showing the decrease of magnonic gaps frequency and the expansion of the magnonic band gap width with the decreasing of the metal film conductivity are given. Such nonreciprocal properties of the SAW - magnonic crystals are promising for signal processing in the GHz range.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Haishuang; Krysiak, Yaşar; Hoffmann, Kristin

The crystal structure and disorder phenomena of Al{sub 4}B{sub 2}O{sub 9}, an aluminum borate from the mullite-type family, were studied using automated diffraction tomography (ADT), a recently established method for collection and analysis of electron diffraction data. Al{sub 4}B{sub 2}O{sub 9}, prepared by sol-gel approach, crystallizes in the monoclinic space group C2/m. The ab initio structure determination based on three-dimensional electron diffraction data from single ordered crystals reveals that edge-connected AlO{sub 6} octahedra expanding along the b axis constitute the backbone. The ordered structure (A) was confirmed by TEM and HAADF-STEM images. Furthermore, disordered crystals with diffuse scattering along themore » b axis are observed. Analysis of the modulation pattern implies a mean superstructure (AAB) with a threefold b axis, where B corresponds to an A layer shifted by ½a and ½c. Diffraction patterns simulated for the AAB sequence including additional stacking disorder are in good agreement with experimental electron diffraction patterns. - Graphical abstract: Crystal structure and disorder phenomena of B-rich Al{sub 4}B{sub 2}O{sub 9} studied by automated electron diffraction tomography (ADT) and described by diffraction simulation using DISCUS. - Highlights: • Ab-initio structure solution by electron diffraction from single nanocrystals. • Detected modulation corresponding mainly to three-fold superstructure. • Diffuse diffraction streaks caused by stacking faults in disordered crystals. • Observed streaks explained by simulated electron diffraction patterns.« less

Large-volume protein crystal growth for neutron macromolecular crystallography

DOE PAGES

Ng, Joseph D.; Baird, James K.; Coates, Leighton; ...

2015-03-30

Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for themore » growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.« less

Large-volume protein crystal growth for neutron macromolecular crystallography

PubMed Central

Ng, Joseph D.; Baird, James K.; Coates, Leighton; Garcia-Ruiz, Juan M.; Hodge, Teresa A.; Huang, Sijay

2015-01-01

Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations. PMID:25849493

Large-volume protein crystal growth for neutron macromolecular crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ng, Joseph D.; Baird, James K.; Coates, Leighton

Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for themore » growth of crystals to significant dimensions that are now relevant to NMC are revisited. We report that these include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.« less

Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography.

PubMed

Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N

2016-11-15

Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1 H, 13 C, and 15 N nuclei. Due to their higher sensitivity to polarization effects, 17 O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.

The MORPHEUS II protein crystallization screen

PubMed Central

Gorrec, Fabrice

2015-01-01

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions. PMID:26144227

The MORPHEUS II protein crystallization screen.

PubMed

Gorrec, Fabrice

2015-07-01

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

Experimental determination of the kinetics of formation of the benzene-ethane co-crystal and implications for Titan

NASA Astrophysics Data System (ADS)

Cable, Morgan L.; Vu, Tuan H.; Hodyss, Robert; Choukroun, Mathieu; Malaska, Michael J.; Beauchamp, Patricia

2014-08-01

Benzene is found on Titan and is a likely constituent of the putative evaporite deposits formed around the hydrocarbon lakes. We have recently demonstrated the formation of a benzene-ethane co-crystal under Titan-like surface conditions. Here we investigate the kinetics of formation of this new structure as a function of temperature. We show that the formation process would reach completion under Titan surface conditions in ~18 h and that benzene precipitates from liquid ethane as the co-crystal. This suggests that benzene-rich evaporite basins around ethane/methane lakes and seas may not contain pure crystalline benzene, but instead benzene-ethane co-crystals. This co-crystalline form of benzene with ethane represents a new class of materials for Titan's surface, analogous to hydrated minerals on Earth. This new structure may also influence evaporite characteristics such as particle size, dissolution rate, and infrared spectral properties.

Nonlinear coherent structures in granular crystals

NASA Astrophysics Data System (ADS)

Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

2017-10-01

The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

Experimental evidence of low-density liquid water upon rapid decompression

PubMed Central

Lin, Chuanlong; Smith, Jesse S.; Sinogeikin, Stanislav V.; Shen, Guoyin

2018-01-01

Water is an extraordinary liquid, having a number of anomalous properties which become strongly enhanced in the supercooled region. Due to rapid crystallization of supercooled water, there exists a region that has been experimentally inaccessible for studying deeply supercooled bulk water. Using a rapid decompression technique integrated with in situ X-ray diffraction, we show that a high-pressure ice phase transforms to a low-density noncrystalline (LDN) form upon rapid release of pressure at temperatures of 140–165 K. The LDN subsequently crystallizes into ice-Ic through a diffusion-controlled process. Together with the change in crystallization rate with temperature, the experimental evidence indicates that the LDN is a low-density liquid (LDL). The measured X-ray diffraction data show that the LDL is tetrahedrally coordinated with the tetrahedral network fully developed and clearly linked to low-density amorphous ices. On the other hand, there is a distinct difference in structure between the LDL and supercooled water or liquid water in terms of the tetrahedral order parameter. PMID:29440411

Unidirectional Wave Vector Manipulation in Two-Dimensional Space with an All Passive Acoustic Parity-Time-Symmetric Metamaterials Crystal

NASA Astrophysics Data System (ADS)

Liu, Tuo; Zhu, Xuefeng; Chen, Fei; Liang, Shanjun; Zhu, Jie

2018-03-01

Exploring the concept of non-Hermitian Hamiltonians respecting parity-time symmetry with classical wave systems is of great interest as it enables the experimental investigation of parity-time-symmetric systems through the quantum-classical analogue. Here, we demonstrate unidirectional wave vector manipulation in two-dimensional space, with an all passive acoustic parity-time-symmetric metamaterials crystal. The metamaterials crystal is constructed through interleaving groove- and holey-structured acoustic metamaterials to provide an intrinsic parity-time-symmetric potential that is two-dimensionally extended and curved, which allows the flexible manipulation of unpaired wave vectors. At the transition point from the unbroken to broken parity-time symmetry phase, the unidirectional sound focusing effect (along with reflectionless acoustic transparency in the opposite direction) is experimentally realized over the spectrum. This demonstration confirms the capability of passive acoustic systems to carry the experimental studies on general parity-time symmetry physics and further reveals the unique functionalities enabled by the judiciously tailored unidirectional wave vectors in space.

[Machinable property of a novel dental mica glass-ceramic].

PubMed

Chen, Ji-hua; Li, Na; Ma, Xin-pei; Zhao, Ying-hua; Sun, Xiang; Li, Guang-xin

2007-12-01

To investigate the machinability of a novel dental mica glass-ceramic and analyze the effect of heat-treatment on its ductile machinable behavior. The drilling and turning experiment were used to measure the machinabilities of the control group (feldspar ceramic: Vita Mark II) and 7 experiment groups treated with different crystallization techniques. The microstructures were analyzed using scanning electron microscopy (SEM) and X-ray diffraction (XRD). The average drilling depths in 30 s of the experimental groups ranged from (0.5 +/- 0.1) mm to (7.1 +/- 0.8) mm. There were significant differences between the control [(0.8 +/- 0.1) mm] and the experimental groups (P < 0.05) except the group crystallized at 740 degrees C for 60 min. When crystallized at 650 degrees C (60 min), continuous band chips could formed in machining at a high velocity and cut depth. The crystal portion of this group is only about 40%. This material has a satisfactory machinability. The mechanism could be attributed to a combination of the interlocked structure of mica crystals and the low viscosity of glassy phase.

Back to basics: history of photonic crystals and metamaterials

NASA Astrophysics Data System (ADS)

Soukoulis, Costas M.

2018-04-01

We will review the history of photonic crystals and overview of the theoretical and experimental efforts in obtaining a photonic bandgap, a frequency band in three-dimensional dielectric structures in which electromagnetic (EM) waves are forbidden, is presented. Many experimental groups all over the world still employ this woodpile structure to fabricate PCs at optical wavelengths, waveguides, enhance nanocavities, and produce nanolasers with a low threshold limit. We have been focused on a new class of materials, the so-called metamaterials (MMs) or negative-index materials, which exhibit highly unusual electromagnetic properties and hold promise for new device applications. Metamaterials can be designed to exhibit both electric and magnetic resonances that can be separately tuned to occur in frequency bands from megahertz to terahertz frequencies, and hope-fully to the visible region of the EM spectrum.

Ab initio calculations of the electronic structure and specific optical features of β-LiNH4SO4 single crystals

NASA Astrophysics Data System (ADS)

Rudysh, M. Ya.; Brik, M. G.; Stadnyk, V. Yo.; Brezvin, R. S.; Shchepanskyi, P. A.; Fedorchuk, A.; Khyzhun, O. Y.; Kityk, I. V.; Piasecki, M.

2018-01-01

In the present work complex experimental and theoretical studies of electronic and optical properties for β-lithium-ammonium sulfate crystals of good optical quality are performed using the X-ray photoelectron spectroscopy (XPS) and X-ray emission spectroscopy (XES). Standard immersion and spectroscopic techniques accompanied by the theoretical quantum-chemical calculations in the density functional theory (DFT) framework were applied. Calculations of band structure and related properties were carried out within a framework of local density and generalized gradient approximations as well as hybrid B3LYP functionals. The energy levels features and their origin are established from the DFT calculations and they were ferified by XPS and XES measurements. Theoretical and experimental refractive indices dispersions along the principal crystallographic directions (nx, ny and nz) as well as birefringence dispersion (Δnx, Δny and Δnz) in the visible spectral range are obtained. It was found a closeness of nx and ny curves for the titled crystals. More precise birefringence examining predicts their intersection at λ ≈ 190 nm.

Vibrational, DFT, and thermal analysis of 2,4,6-triamino-1,3,5-triazin-1-ium 3-(prop-2-enoyloxy) propanoate acrylic acid monosolvate monohydrate

NASA Astrophysics Data System (ADS)

Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Anbalagan, G.

2013-12-01

New organic crystals of 2,4,6-triamino-1,3,5-triazin-1-ium 3-(prop-2-enoyloxy) propanoate acrylic acid monosolvate monohydrate (MAC) have been obtained from aqueous solution by the slow solvent evaporation method at room temperature. Single crystal X-ray diffraction analysis reveals that the compound crystallises in the triclinic system with centrosymmetric space group P-1. FT-IR and FT-Raman spectra of MAC have been recorded and analyzed. The molecular geometry and vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-31G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction data. The theoretical results show that the optimized geometry can well reproduce the crystal structure, and the calculated vibrational frequency values show good agreement with experimental values. A study of the electronic properties, such as HOMO and LUMO energies and Molecular electrostatic potential (MEP) were performed. Mulliken charges and NBO charges of the title molecule were also calculated and interpreted. Thermogravimetric analysis has been done to study the thermal behaviour of MAC. The 13C and 1H nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

PubMed

Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

2014-12-11

The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Stabilizing subnanometer Ag(0) nanoclusters by thiolate and diphosphine ligands and their crystal structures

NASA Astrophysics Data System (ADS)

Yang, Huayan; Wang, Yu; Zheng, Nanfeng

2013-03-01

The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions.The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions. Electronic supplementary information (ESI) available: Experimental details, more pictures of the structure and XPS spectra of the clusters. CCDC 916463 and 916464. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr34328f

Linear and nonlinear properties of photonic crystal fibers filled with nematic liquid crystals

NASA Astrophysics Data System (ADS)

Brzdąkiewicz, K. A.; Laudyn, U. A.; Karpierz, M. A.; Woliński, T. R.; Wójcik, J.

2006-12-01

We investigate linear and nonlinear light propagation in the photonic crystal fibers infiltrated with nematic liquid crystals. Such a photonic structure, with periodic modulation of refractive index, which could be additionally controlled by the temperature and by the optical power, allows for the study of discrete optical phenomena. Our theoretical investigations, carried out with the near infrared wavelength of 830 nm, for both focusing and defocusing Kerr-type nonlinearity, show the possibility of the transverse light localization, which can result in the discrete soliton generation. In addition, we present the preliminary experimental results on the linear light propagation in the photonic crystal fiber with the glycerin-water solution and 6CHBT nematics, as the guest materials.

Research on Lead Acid Battery Electrodes.

DTIC Science & Technology

1982-02-26

electrode. Changes in electrode structure caused by the use of lignin derivatives have also been reported (12). The use of lignin derivatives and other... lignin derivative. R-2761d) 24 2. Description of Experimental Procedure The positive and negative plates used in this investiga- tion were...sisted of crystals in the 3-8 pm range, although many crystals 31 Fig. 11 - A negative plate immediately after for-f mation where a lignin derivative

Temperature Dependence of the Luminescence Decay Time of a PbWO4 Scintillator

NASA Astrophysics Data System (ADS)

Shi, Chao-shu; Deng, Jie; Han, Zheng-fu; Xie, Zhi-jian; Liao, Jing-ying; G, Zimmerer; J, Beker; M, Kamada; M, Runne; A, Schröder

1998-06-01

Experimental results are given for the temperature dependence of the decay time of the emission at 430 nm from PbWO4 crystal under vacuum-ultraviolet (82 nm) photon excitation in the temperature range of 80-300 K. The structures in the curve are interpreted for the first time by studying the thermoluminescence of PbWO4, which originates from the traps in the crystal.

Quartz substrate infrared photonic crystal

NASA Astrophysics Data System (ADS)

Ghadiri, Khosrow; Rejeb, Jalel; Vitchev, Vladimir N.

2003-01-01

This paper presents the fabrication of a planar photonic crystal (p2c) made of a square array of dielectric rods embedded in air, operating in the infrared spectrum. A quartz substrate is employed instead of the commonly used silicon or column III-V substrate. Our square structure has a normalized cylinder radius-to-pitch ratio of r/a = 0.248 and dielectric material contrast ɛr of 4.5. We choose a Z-cut synthetic quartz for its cut (geometry), and etching properties. Then a particular Z-axis etching process is employed in order to ensure the sharp-edged verticality of the rods and fast etching speed. We also present the computer simulations that allowed the establishment of the photonic band gaps (PBG) of our photonic crystal, as well as the actual measurements. An experimental measurement have been carried out and compared with different simulations. It was found that experimental results are in good agreement with different simulation results. Finally, a frequency selective device for optical communication based on the introduction of impurity sites in the photonic crystal is presented. With our proposed structure Optical System on a Chip (OsoC) with micro-cavity based active devices such as lasers, diodes, modulators, couplers, frequency selective emitters, add-drop filters, detectors, mux/demuxes and polarizers connected by passive waveguide links can be realized.

Theoretical and experimental studies on vibrational and nonlinear optic properties of guanidinium 3-nitrobenzoate. Differences and similarity between guanidinium 3-nitrobenzoate and guanidinium 4-nitrobenzoate complexes

NASA Astrophysics Data System (ADS)

Drozd, Marek

2018-03-01

According to literature data two structures of guanidine with nitrobenzoic acids are known. For guanidinium 4-nitrobenzoate the detailed studies of X-ray structure, vibrational and theoretical properties were performed. This compound was classified as second harmonic generator with efficiency of 3.3 times that KDP, standard crystal. On the contrary to mentioned above results for the guanidinium 3-nitrobenzoate the basic X-ray diffraction study was performed, only. On the basis of established crystallographic results, the detailed investigation of geometry and vibrational properties were made on the basis of theoretical calculation. According to this data the equilibrium geometry of investigated molecule was established. On the basis of this calculation the detailed computational studies of vibrational properties were performed. The theoretical IR and Raman frequencies, intensities and PED analysis are presented. Additionally, the NBO charges, HOMO and LUMO shapes and NLO properties of titled crystal were calculated. On the basis of these results the crystal was classified as second order generator in NLO but with bigger efficiency that guanidinium 4-nitorobenzoate compound. The obtained data are compared with experimental crystallographic and vibrational results for real crystal of guanidinium 3-nitrobenzoate. Additionally, the theoretical vibrational spectra are compared with literature calculations of guanidinium 4-nitrobenzoate compound.

Relation between the structural parameters of metallic glasses at the onset crystallization temperatures and threshold values of the effective diffusion coefficients

NASA Astrophysics Data System (ADS)

Tkatch, V. I.; Svyrydova, K. A.; Vasiliev, S. V.; Kovalenko, O. V.

2017-08-01

Using the results of differential scanning calorimetry and X-ray diffractometry, an analysis has been carried out of the initial stages of the eutectic and primary mechanisms of crystallization of a series of metallic glasses based on Fe and Al with the established temperature dependences of the effective diffusion coefficients. Analytical relationships, which relate the volume density of crystallites formed in the glasses at the temperatures of the onset of crystallization with the values of the effective diffusion coefficients at these temperatures have been proposed. It has been established that, in the glasses, the crystallization of which begins at the lower boundary of the threshold values of the effective diffusion coefficients ( 10-20 m2/s), structures are formed with the volume density of crystallites on the order of 1023-1024 m-3 and, at the upper boundary (10-18 m2/s), of the order of 1018 and 1020 m-3 in the glasses that are crystallized via the eutectic and primary mechanisms, respectively. Good agreement between the calculated and experimental estimates indicates that the threshold values of the effective diffusion coefficients are the main factors that determine the structure of glasses at the initial stages of crystallization.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

X-Ray Structure determination of the Glycine Cleavage System Protein H of Mycobacterium tuberculosis Using An Inverse Compton Synchrotron X-Ray Source

PubMed Central

Abendroth, Jan; McCormick, Michael S.; Edwards, Thomas E.; Staker, Bart; Loewen, Roderick; Gifford, Martin; Rifkin, Jeff; Mayer, Chad; Guo, Wenjin; Zhang, Yang; Myler, Peter; Kelley, Angela; Analau, Erwin; Hewitt, Stephen Nakazawa; Napuli, Alberto J.; Kuhn, Peter; Ruth, Ronald D.; Stewart, Lance J.

2010-01-01

Structural genomics discovery projects require ready access to both X-ray and NMR instrumentation which support the collection of experimental data needed to solve large numbers of novel protein structures. The most productive X-ray crystal structure determination laboratories make extensive frequent use of tunable synchrotron X-ray light to solve novel structures by anomalous diffraction methods. This requires that frozen cryo-protected crystals be shipped to large government-run synchrotron facilities for data collection. In an effort to eliminate the need to ship crystals for data collection, we have developed the first laboratory-scale synchrotron light source capable of performing many of the state-of-the-art synchrotron applications in X-ray science. This Compact Light Source is a first-in-class device that uses inverse Compton scattering to generate X-rays of sufficient flux, tunable wavelength and beam size to allow high-resolution X-ray diffraction data collection from protein crystals. We report on benchmarking tests of X-ray diffraction data collection with hen egg white lysozyme, and the successful high-resolution X-ray structure determination of the Glycine cleavage system protein H from Mycobacterium tuberculosis using diffraction data collected with the Compact Light Source X-ray beam. PMID:20364333

Effect of impurities and post-experimental purification in SAD phasing with serial femtosecond crystallography data.

PubMed

Zhang, Tao; Gu, Yuanxin; Fan, Haifu

2016-06-01

In serial crystallography (SX) with either an X-ray free-electron laser (XFEL) or synchrotron radiation as the light source, huge numbers of micrometre-sized crystals are used in diffraction data collection. For a SAD experiment using a derivative with introduced heavy atoms, it is difficult to completely exclude crystals of the native protein from the sample. In this paper, simulations were performed to study how the inclusion of native crystals in the derivative sample could affect the result of SAD phasing and how the post-experimental purification proposed by Zhang et al. [(2015), Acta Cryst. D71, 2513-2518] could be used to remove the impurities. A gadolinium derivative of lysozyme and the corresponding native protein were used in the test. Serial femtosecond crystallography (SFX) diffraction snapshots were generated by CrystFEL. SHELXC/D, Phaser, DM, ARP/wARP and REFMAC were used for automatic structure solution. It is shown that a small amount of impurities (snapshots from native crystals) in the set of derivative snapshots can strongly affect the SAD phasing results. On the other hand, post-experimental purification can efficiently remove the impurities, leading to results similar to those from a pure sample.

A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition

NASA Astrophysics Data System (ADS)

Woutersen, Sander; Ensing, Bernd; Hilbers, Michiel; Zhao, Zuofeng; Angell, C. Austen

2018-03-01

Simulations and theory suggest that the thermodynamic anomalies of water may be related to a phase transition between two supercooled liquid states, but so far this phase transition has not been observed experimentally because of preemptive ice crystallization. We used calorimetry, infrared spectroscopy, and molecular dynamics simulations to investigate a water-rich hydrazinium trifluoroacetate solution in which the local hydrogen bond structure surrounding a water molecule resembles that in neat water at elevated pressure, but which does not crystallize upon cooling. Instead, this solution underwent a sharp, reversible phase transition between two homogeneous liquid states. The hydrogen-bond structures of these two states are similar to those established for high- and low-density amorphous (HDA and LDA) water. Such structural similarity supports theories that predict a similar sharp transition in pure water under pressure if ice crystallization could be suppressed.

Revealing the preferred interlayer orientations and stackings of two-dimensional bilayer gallium selenide crystals

DOE PAGES

Li, Xufan; Basile Carrasco, Leonardo A.; Yoon, Mina; ...

2015-01-21

Characterizing and controlling the interlayer orientations and stacking order of bilayer two-dimensional (2D) crystals and van der Waals (vdW) heterostructure is crucial to optimize their electrical and optoelectronic properties. The four polymorphs of layered gallium selenide (GaSe) that result from different layer stacking provide an ideal platform to study the stacking configurations in bilayer 2D crystals. Here, through a controllable vapor-phase deposition method we selectively grow bilayer GaSe crystals and investigate their two preferred 0° or 60° interlayer rotations. The commensurate stacking configurations (AA' and AB-stacking) in as-grown 2D bilayer GaSe crystals are clearly observed at the atomic scale andmore » the Ga-terminated edge structure are identified for the first time by using atomic-resolution scanning transmission electron microscopy (STEM). Theoretical analysis of the interlayer coupling energetics vs. interlayer rotation angle reveals that the experimentally-observed orientations are energetically preferred among the bilayer GaSe crystal polytypes. Here, the combined experimental and theoretical characterization of the GaSe bilayers afforded by these growth studies provide a pathway to reveal the atomistic relationships in interlayer orientations responsible for the electronic and optical properties of bilayer 2D crystals and vdW heterostructures.« less

Observation of Dirac-like energy band and ring-torus Fermi surface associated with the nodal line in topological insulator CaAgAs

NASA Astrophysics Data System (ADS)

Takane, Daichi; Nakayama, Kosuke; Souma, Seigo; Wada, Taichi; Okamoto, Yoshihiko; Takenaka, Koshi; Yamakawa, Youichi; Yamakage, Ai; Mitsuhashi, Taichi; Horiba, Koji; Kumigashira, Hiroshi; Takahashi, Takashi; Sato, Takafumi

2018-01-01

One of key challenges in current material research is to search for new topological materials with inverted bulk-band structure. In topological insulators, the band inversion caused by strong spin-orbit coupling leads to opening of a band gap in the entire Brillouin zone, whereas an additional crystal symmetry such as point-group and nonsymmorphic symmetries sometimes prohibits the gap opening at/on specific points or line in momentum space, giving rise to topological semimetals. Despite many theoretical predictions of topological insulators/semimetals associated with such crystal symmetries, the experimental realization is still relatively scarce. Here, using angle-resolved photoemission spectroscopy with bulk-sensitive soft-x-ray photons, we experimentally demonstrate that hexagonal pnictide CaAgAs belongs to a new family of topological insulators characterized by the inverted band structure and the mirror reflection symmetry of crystal. We have established the bulk valence-band structure in three-dimensional Brillouin zone, and observed the Dirac-like energy band and ring-torus Fermi surface associated with the line node, where bulk valence and conducting bands cross on a line in the momentum space under negligible spin-orbit coupling. Intriguingly, we found that no other bands cross the Fermi level and therefore the low-energy excitations are solely characterized by the Dirac-like band. CaAgAs provides an excellent platform to study the interplay among low-energy electron dynamics, crystal symmetry, and exotic topological properties.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Liquid crystals of carbon nanotubes and graphene.

PubMed

Zakri, Cécile; Blanc, Christophe; Grelet, Eric; Zamora-Ledezma, Camilo; Puech, Nicolas; Anglaret, Eric; Poulin, Philippe

2013-04-13

Liquid crystal ordering is an opportunity to develop novel materials and applications with spontaneously aligned nanotubes or graphene particles. Nevertheless, achieving high orientational order parameter and large monodomains remains a challenge. In addition, our restricted knowledge of the structure of the currently available materials is a limitation for fundamental studies and future applications. This paper presents recent methodologies that have been developed to achieve large monodomains of nematic liquid crystals. These allow quantification and increase of their order parameters. Nematic ordering provides an efficient way to prepare conductive films that exhibit anisotropic properties. In particular, it is shown how the electrical conductivity anisotropy increases with the order parameter of the nematic liquid crystal. The order parameter can be tuned by controlling the length and entanglement of the nanotubes. In the second part of the paper, recent results on graphene liquid crystals are reported. The possibility to obtain water-based liquid crystals stabilized by surfactant molecules is demonstrated. Structural and thermodynamic characterizations provide indirect but statistical information on the dimensions of the graphene flakes. From a general point of view, this work presents experimental approaches to optimize the use of nanocarbons as liquid crystals and provides new methodologies for the still challenging characterization of such materials.

Structural and magnetic investigations of single-crystalline neodymium zirconate pyrochlore Nd2Zr2O7

NASA Astrophysics Data System (ADS)

Hatnean, M. Ciomaga; Lees, M. R.; Petrenko, O. A.; Keeble, D. S.; Balakrishnan, G.; Gutmann, M. J.; Klekovkina, V. V.; Malkin, B. Z.

2015-05-01

We report structural and magnetic properties studies of large high-quality single crystals of the frustrated magnet Nd2Zr2O7 . Powder x-ray diffraction analysis confirms that Nd2Zr2O7 adopts the pyrochlore structure. Room-temperature x-ray diffraction and time-of-flight neutron-scattering experiments show that the crystals are stoichiometric in composition with no measurable site disorder. The temperature dependence of the magnetic susceptibility shows no magnetic ordering at temperatures down to 0.5 K. Fits to the magnetic susceptibility data using a Curie-Weiss law reveal a ferromagnetic coupling between the Nd moments. Magnetization versus field measurements show a local Ising anisotropy along the <111 > axes of the Nd3 + ions in the ground state. Specific heat versus temperature measurements in zero applied magnetic field indicate the presence of a thermal anomaly below T ˜7 K, but no evidence of magnetic ordering is observed down to 0.5 K. The experimental temperature dependence of the single-crystal bulk dc susceptibility and isothermal magnetization are analyzed using crystal field theory and the crystal field parameters and exchange coupling constants determined.

Analytical coupled-wave model for photonic crystal surface-emitting quantum cascade lasers.

PubMed

Wang, Zhixin; Liang, Yong; Yin, Xuefan; Peng, Chao; Hu, Weiwei; Faist, Jérôme

2017-05-15

An analytical coupled-wave model is developed for surface-emitting photonic-crystal quantum cascade lasers (PhC-QCLs). This model provides an accurate and efficient analysis of full three-dimensional device structure with large-area cavity size. Various laser properties of interest including the band structure, mode frequency, cavity loss, mode intensity profile, and far field pattern (FFP), as well as their dependence on PhC structures and cavity size, are investigated. Comparison with numerical simulations confirms the accuracy and validity of our model. The calculated FFP and polarization profile well explain the previously reported experimental results. In particular, we reveal the possibility of switching the lasing modes and generating single-lobed FFP by properly tuning PhC structures.

1-Formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline: Synthesis, characterization, antimicrobial activity and DFT studies

NASA Astrophysics Data System (ADS)

Sid, Assia; Messai, Amel; Parlak, Cemal; Kazancı, Nadide; Luneau, Dominique; Keşan, Gürkan; Rhyman, Lydia; Alswaidan, Ibrahim A.; Ramasami, Ponnadurai

2016-10-01

The structure of 1-formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline synthesized as single crystal was investigated by FTIR, NMR, XRD. Experimental data were complemented by quantum mechanical calculations. XRD data show that the compound crystallizes in the triclinic system (P-1) via trans isomer (a = 6.4267(4) Å, b = 10.9259(12) Å, c = 12.4628(9) Å and α = 102.894(8)°, β = 102.535(6)°, γ = 101.633(7)°). Anti-microbial screening results indicate that the compound shows promising activity. The theoretically predicted and experimentally obtained parameters reveal further insight into pyrazoline systems.

Calculation of photonic bandgap for 2D hexagonal and square structure base on hybrid polymer material

NASA Astrophysics Data System (ADS)

Hidayat, S.; Riveli, N.

2018-05-01

We have calculated 2D photonic crystal band gap using plane-wave expansion method. The studied model of structures is hexagonal lattice and square lattice of rod cylinder in air. We have simulated the dispersion relation of it structure using hybrid polymer as rod material. The parameter structures are nrod = 1.5, nhole = 1, and rrod = 0.25a, where a is lattice constant. We found the distributed feedback occurs at the edge of upper band or frequency at 0.66 (a/λ). In our experimental work, we have successfully fabricated the 2D photonic crystal from hybrid polymer incorporated with organic dye laser. The lasing characteristics ware investigated using strip-line excitation light of SHG Nd-YAG laser (λ=532 nm). The lasing wavelengths for hexagonal structure are observed at 606 nm and 621 nm for photonic crystal period of 400 nm and 410 nm, respectively. λ=532 nm). Whereas the square structure, the lasing wavelengths are observed at (588 nm ± 2) and (606 nm ± 2 nm) for grating period of 391 nm and 405 nm.

Molecular engineering of colloidal liquid crystals using DNA origami

NASA Astrophysics Data System (ADS)

Siavashpouri, Mahsa; Wachauf, Christian; Zakhary, Mark; Praetorius, Florian; Dietz, Hendrik; Dogic, Zvonimir

Understanding the microscopic origin of cholesteric phase remains a foundational, yet unresolved problem in the field of liquid crystals. Lack of experimental model system that allows for the systematic control of the microscopic chiral structure makes it difficult to investigate this problem for several years. Here, using DNA origami technology, we systematically vary the chirality of the colloidal particles with molecular precision and establish a quantitative relationship between the microscopic structure of particles and the macroscopic cholesteric pitch. Our study presents a new methodology for predicting bulk behavior of diverse phases based on the microscopic architectures of the constituent molecules.

Enhancement of second harmonic generation in NaNO{sub 2}-infiltrated opal photonic crystal using structural light focusing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaytsev, Kirill I., E-mail: kirzay@gmail.com; Yurchenko, Stanislav O., E-mail: st.yurchenko@mail.ru

Experimental and numerical results for second harmonic generation (SHG) in photonic crystal (PC) based on NaNO{sub 2}-infiltrated opal matrix are presented. SHG is performed in reflection mode; thus, the direction of the SHG maximum is equal to the angle of mirror reflection. The PC was pumped with femtosecond optical pulses at different angles of incidence, allowing the dependence of the SHG efficiency on the location of the fundamental wavelength toward the PC band gap (BG) to be examined. The most efficient SHG was observed when pumping the BG of the PC. To interpret the experimental results, finite-difference time-domain numerical simulationsmore » of the light interaction with the PC were conducted. The observed effect of highly efficient SHG is associated with structural light focusing, and, as a consequence, with strong optical field localization within certain near-surface PC regions. Thus, SHG enhancement based on structural light focusing in PC was demonstrated.« less

Long-wavelength macromolecular crystallography - First successful native SAD experiment close to the sulfur edge

NASA Astrophysics Data System (ADS)

Aurelius, O.; Duman, R.; El Omari, K.; Mykhaylyk, V.; Wagner, A.

2017-11-01

Phasing of novel macromolecular crystal structures has been challenging since the start of structural biology. Making use of anomalous diffraction of natively present elements, such as sulfur and phosphorus, for phasing has been possible for some systems, but hindered by the necessity to access longer X-ray wavelengths in order to make most use of the anomalous scattering contributions of these elements. Presented here are the results from a first successful experimental phasing study of a macromolecular crystal structure at a wavelength close to the sulfur K edge. This has been made possible by the in-vacuum setup and the long-wavelength optimised experimental setup at the I23 beamline at Diamond Light Source. In these early commissioning experiments only standard data collection and processing procedures have been applied, in particular no dedicated absorption correction has been used. Nevertheless the success of the experiment demonstrates that the capability to extract phase information can be even further improved once data collection protocols and data processing have been optimised.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Synthesis, crystal structure, spectroscopic characterization, docking simulation and density functional studies of 1-(3,4-dimethoxyphenyl) -3-(4-flurophenyl)-propan-1-one

NASA Astrophysics Data System (ADS)

Khamees, Hussien Ahmed; Jyothi, Mahima; Khanum, Shaukath Ara; Madegowda, Mahendra

2018-06-01

The compound 1-(3,4-dimethoxyphenyl)-3-(4-flurophenyl)-propan-1-one (DFPO) was synthesized by Claisen-Schmidt condensation reaction and the single crystals were obtained by slow evaporation method. Three-dimensional structure was confirmed by single crystal X-ray diffraction method and exhibiting the triclinic crystal system with space group P-1. The crystal structure is stabilized by Csbnd H⋯O intermolecular and weak interactions. Computed molecular geometry has been obtained by density functional theory (DFT) and compared with experimental results. The spectra of both FT-IR in the range (4000-400 cm-1) and FT- Raman (3500-50 cm-1) of DFPO were recorded experimentally and computed by (DFT) using B3LYP/6-311G (d,p) as basis sets. Intramolecular charge transfer has been scanned using natural bond orbital (NBO) analysis and revealed the various contribution of bonding and lone pair to the stabilization of molecule. Nonlinear optical activity (NLO) of the title compound has been determined by second harmonic generation (SHG) and computed using DFT method. Hyperpolarizability, HOMO-LUMO energy gap, hardness, softness electronegativity and others Global reactivity descriptors of DFPO has been calculated and revealed complete picture of chemical reactivity of DFPO. Hirshfeld surface analyses were applied to investigate the intermolecular interactions and revealed that more than two-thirds of the inter contacts are associated with O⋯H, C⋯H and H⋯H interactions. Docking studies of DFPO showed inhibition of Vascular endothelial growth Factor human receptor (VEGFR-2) signalling pathway, which indicates DFPO as anti-angiogenesis, that play pivotal role in cancer, so we suggest it for clinical studies to evaluate its potential to treat human cancers.

Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil.

PubMed

Pöppler, Ann Christin; Corlett, Emily K; Pearce, Harriet; Seymour, Mark P; Reid, Matthew; Montgomery, Mark G; Brown, Steven P

2017-03-01

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C 14 H 4 N 2 O 2 S 2 ·C 12 H 13 N 2 ]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental 1 H and 13 C chemical shifts are determined from two-dimensional 1 H- 13 C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C-H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a 1 H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the 1 H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N-H...O and C-H...O hydrogen bonding, while changes of -2.7 and -1.5 ppm are due to ring current effects associated with C-H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

Manipulation of photons at the surface of three-dimensional photonic crystals.

PubMed

Ishizaki, Kenji; Noda, Susumu

2009-07-16

In three-dimensional (3D) photonic crystals, refractive-index variations with a periodicity comparable to the wavelength of the light passing through the crystal give rise to so-called photonic bandgaps, which are analogous to electronic bandgaps for electrons moving in the periodic electrostatic potential of a material's crystal structure. Such 3D photonic bandgap crystals are envisioned to become fundamental building blocks for the control and manipulation of photons in optical circuits. So far, such schemes have been pursued by embedding artificial defects and light emitters inside the crystals, making use of 3D bandgap directional effects. Here we show experimentally that photons can be controlled and manipulated even at the 'surface' of 3D photonic crystals, where 3D periodicity is terminated, establishing a new and versatile route for photon manipulation. By making use of an evanescent-mode coupling technique, we demonstrate that 3D photonic crystals possess two-dimensional surface states, and we map their band structure. We show that photons can be confined and propagate through these two-dimensional surface states, and we realize their localization at arbitrary surface points by designing artificial surface-defect structures through the formation of a surface-mode gap. Surprisingly, the quality factors of the surface-defect mode are the largest reported for 3D photonic crystal nanocavities (Q up to approximately 9,000). In addition to providing a new approach for photon manipulation by photonic crystals, our findings are relevant for the generation and control of plasmon-polaritons in metals and the related surface photon physics. The absorption-free nature of the 3D photonic crystal surface may enable new sensing applications and provide routes for the realization of efficient light-matter interactions.

Crystal structure refinement of ReSi1.75 with an ordered arrangement of silicon vacancies

NASA Astrophysics Data System (ADS)

Harada, Shunta; Hoshikawa, Hiroaki; Kuwabara, Kosuke; Tanaka, Katsushi; Okunishi, Eiji; Inui, Haruyuki

2011-08-01

The crystal structure and microstructure of ReSi1.75 were investigated by synchrotron X-ray diffraction combined with scanning transmission electron microscopy. ReSi1.75 contains an ordered arrangement of vacancies in Si sites in the underlying tetragonal C11b lattice of the MoSi2-type and the crystal structure is monoclinic with the space group Cm. Atomic positions of Si atoms near vacancies are considerably displaced from the corresponding positions in the parent C11b structure, and they exhibit anomalously large local thermal vibration accompanied by large values of atomic displacement parameter. There are four differently-oriented domains with two of them being related to each other by the 90° rotation about the c-axis of the underlying C11b lattice and the other two being their respective twins. The habit planes for domain boundaries observed experimentally are consistent with those predicted with ferroelastic theory.

Molecular and electronic structure of terminal and alkali metal-capped uranium(V) nitride complexes

PubMed Central

King, David M.; Cleaves, Peter A.; Wooles, Ashley J.; Gardner, Benedict M.; Chilton, Nicholas F.; Tuna, Floriana; Lewis, William; McInnes, Eric J. L.; Liddle, Stephen T.

2016-01-01

Determining the electronic structure of actinide complexes is intrinsically challenging because inter-electronic repulsion, crystal field, and spin–orbit coupling effects can be of similar magnitude. Moreover, such efforts have been hampered by the lack of structurally analogous families of complexes to study. Here we report an improved method to U≡N triple bonds, and assemble a family of uranium(V) nitrides. Along with an isoelectronic oxo, we quantify the electronic structure of this 5f1 family by magnetometry, optical and electron paramagnetic resonance (EPR) spectroscopies and modelling. Thus, we define the relative importance of the spin–orbit and crystal field interactions, and explain the experimentally observed different ground states. We find optical absorption linewidths give a potential tool to identify spin–orbit coupled states, and show measurement of UV···UV super-exchange coupling in dimers by EPR. We show that observed slow magnetic relaxation occurs via two-phonon processes, with no obvious correlation to the crystal field. PMID:27996007

Predicting crystal structures and properties of matter under extreme conditions via quantum mechanics: The pressure is on

DOE PAGES

Zurek, Eva; Grochala, Wojciech

2014-11-27

Experimental studies of compressed matter are now routinely conducted at pressures exceeding 1 mln atm (100 GPa) and occasionally they even surpass 10 mln atm (1 TPa). The structure and properties of solids that have been so significantly squeezed differ considerably from those know at ambient pressures (1 atm), often times leading to new and unexpected physics. Chemical reactivity is also substantially altered in the extreme pressure regime. In this feature paper we describe how synergy between theory and experiment can pave the road towards new experimental discoveries. Because chemical rules-of-thumb established at 1 atm often fail to predict themore » structures of solids under high pressure, automated crystal structure prediction (CSP) methods have been increasingly employed. After outlining the most important CSP techniques, we showcase a few examples from the recent literature that exemplify just how useful theory can be as an aid in the interpretation of experimental data, describe exciting theoretical predictions that are guiding experiment, and discuss when the computational methods that are currently routinely employed fail. Lastly, we forecast important problems that will be targeted by theory as theoretical methods undergo rapid development, along with the simultaneous increase of computational power.« less

The single crystal elastic constants of hexagonal SiC to 1000 C

NASA Technical Reports Server (NTRS)

Li, Z.; Bradt, R. C.

1988-01-01

The relationships between the sound velocities in the cubic and hexagonal crystal structures and the tensor transformations for the two structures are applied to determine the elastic stiffnesses for the hexagonal structures of SiC to 1000 C. These results are then applied to calculate the polycrystalline elastic moduli, E and G, and their temperature variations. The calculated values for E and G at 20 C are 420 and 180 GPa; for (dE/dT) and (dG/dT), the values are -0.020 and -0.007 GPa/C, respectively.These agree well with published experimental values for E and G of dense polycrystalline alpha silicon carbides.

Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of manganese (II) complex of picolinate: A combined experimental and computational study

NASA Astrophysics Data System (ADS)

Tamer, Ömer; Avcı, Davut; Atalay, Yusuf; Çoşut, Bünyemin; Zorlu, Yunus; Erkovan, Mustafa; Yerli, Yusuf

2016-02-01

A novel manganese (II) complex with picolinic acid (pyridine 2-carboxylic acid, Hpic), namely, [Mn(pic)2(H2O)2] was prepared and its crystal structure was fully characterized by using single crystal X-ray diffraction. Picolinate (pic) ligands were coordinated to the central manganese(II) ion as bidentate N,O-donors through the nitrogen atoms of pyridine rings and the oxygen atoms of carboxylate groups forming five-membered chelate rings. The spectroscopic characterization of Mn(II) complex was performed by the applications of FT-IR, Raman, UV-vis and EPR techniques. In order to support these studies, density functional theory (DFT) calculations were carried out by using B3LYP level. IR and Raman spectra were simulated at B3LYP level, and obtained results indicated that DFT calculations generally give compatible results to the experimental ones. The electronic structure of the Mn(II) complex was predicted using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength were investigated by applying natural bond orbital (NBO) analysis. Nonlinear optical properties of Mn(II) complex were investigated by the determining of molecular polarizability (α) and hyperpolarizability (β) parameters.

The bifoil photodyne: a photonic crystal oscillator.

PubMed

Lugo, J E; Doti, R; Sanchez, N; de la Mora, M B; del Rio, J A; Faubert, J

2014-01-15

Optical tweezers is an example how to use light to generate a physical force. They have been used to levitate viruses, bacteria, cells, and sub cellular organisms. Nonetheless it would be beneficial to use such force to develop a new kind of applications. However the radiation pressure usually is small to think in moving larger objects. Currently, there is some research investigating novel photonic working principles to generate a higher force. Here, we studied theoretically and experimentally the induction of electromagnetic forces in one-dimensional photonic crystals when light impinges on the off-axis direction. The photonic structure consists of a micro-cavity like structure formed of two one-dimensional photonic crystals made of free-standing porous silicon, separated by a variable air gap and the working wavelength is 633 nm. We show experimental evidence of this force when the photonic structure is capable of making auto-oscillations and forced-oscillations. We measured peak displacements and velocities ranging from 2 up to 35 microns and 0.4 up to 2.1 mm/s with a power of 13 mW. Recent evidence showed that giant resonant light forces could induce average velocity values of 0.45 mm/s in microspheres embedded in water with 43 mW light power.

The bifoil photodyne: a photonic crystal oscillator

PubMed Central

Lugo, J. E.; Doti, R.; Sanchez, N.; de la Mora, M. B.; del Rio, J. A.; Faubert, J.

2014-01-01

Optical tweezers is an example how to use light to generate a physical force. They have been used to levitate viruses, bacteria, cells, and sub cellular organisms. Nonetheless it would be beneficial to use such force to develop a new kind of applications. However the radiation pressure usually is small to think in moving larger objects. Currently, there is some research investigating novel photonic working principles to generate a higher force. Here, we studied theoretically and experimentally the induction of electromagnetic forces in one-dimensional photonic crystals when light impinges on the off-axis direction. The photonic structure consists of a micro-cavity like structure formed of two one-dimensional photonic crystals made of free-standing porous silicon, separated by a variable air gap and the working wavelength is 633 nm. We show experimental evidence of this force when the photonic structure is capable of making auto-oscillations and forced-oscillations. We measured peak displacements and velocities ranging from 2 up to 35 microns and 0.4 up to 2.1 mm/s with a power of 13 mW. Recent evidence showed that giant resonant light forces could induce average velocity values of 0.45 mm/s in microspheres embedded in water with 43 mW light power. PMID:24423985

Structural evolution of gypsum under high pressure: single-crystal X-ray experiments revisited

NASA Astrophysics Data System (ADS)

Li, Tsung-Lung; Lee, Pei-Lun

2018-05-01

The structures of gypsum at pressures up to approximately 4 GPa are studied with density functional theory (DFT) and thoroughly compared with single-crystal X-ray diffraction experiments reported in the literature [Comodi et al. in (Am Miner 93:1530-1537, 2008)]. It is found that the exchange-correlation density functional revPBE (revised Perdew-Burke-Ernzerhof) in conjunction with a nonlocal van der Waals (vdW) correction is capable of modeling the lattice constants, axial compressibility, and bulk modulus with good accuracy, suggesting that the inclusion of the vdW functional is crucially important for understanding the structure of hydrous minerals. To gain further physical insights, the geometric parameters associated with the constituting components of gypsum (water molecules, SO4 tetrahedra, and CaO8 polyhedra) are analyzed and compared with the experimental values. DFT simulations show that, under pressure, the polyhedral layers remain as nearly planar sheets of interconnecting SO4 tetrahedra and CaO8 polyhedra without further crinkling. DFT analysis on the layer compressibility along the major crystal axis reveals that, in contrast to experimental reports, the hydrous interlayer is less compressible than the polyhedral layer. Squeezed by the lateral pressure, the water molecules in the hydrous interlayer become better affixed along the major axis, making the interlayer harder to compress along this axis.

Growth Twinning and Generation of High-Frequency Surface Nanostructures in Ultrafast Laser-Induced Transient Melting and Resolidification.

PubMed

Sedao, Xxx; Shugaev, Maxim V; Wu, Chengping; Douillard, Thierry; Esnouf, Claude; Maurice, Claire; Reynaud, Stéphanie; Pigeon, Florent; Garrelie, Florence; Zhigilei, Leonid V; Colombier, Jean-Philippe

2016-07-26

The structural changes generated in surface regions of single crystal Ni targets by femtosecond laser irradiation are investigated experimentally and computationally for laser fluences that, in the multipulse irradiation regime, produce sub-100 nm high spatial frequency surface structures. Detailed experimental characterization of the irradiated targets combining electron back scattered diffraction analysis with high-resolution transmission electron microscopy reveals the presence of multiple nanoscale twinned domains in the irradiated surface regions of single crystal targets with (111) surface orientation. Atomistic- and continuum-level simulations performed for experimental irradiation conditions reproduce the generation of twinned domains and establish the conditions leading to the formation of growth twin boundaries in the course of the fast transient melting and epitaxial regrowth of the surface regions of the irradiated targets. The observation of growth twins in the irradiated Ni(111) targets provides strong evidence of the role of surface melting and resolidification in the formation of high spatial frequency surface structures. This also suggests that the formation of twinned domains can be used as a sensitive measure of the levels of liquid undercooling achieved in short pulse laser processing of metals.

Effect of H{sup +} implantation on the optical properties of semi-insulating GaAs crystals in the IR spectral region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klyui, N. I.; Lozinskii, V. B., E-mail: lvb@isp.kiev.ua; Liptuga, A. I.

2017-03-15

The optical properties of semi-insulating GaAs crystals subjected to multienergy hydrogen-ion implantation and treatment in a high-frequency electromagnetic field are studied in the infrared spectral region. It is established that such combined treatment provides a means for substantially increasing the transmittance of GaAs crystals to values characteristic of crystals of high optical quality. On the basis of analysis of the infrared transmittance and reflectance data, Raman spectroscopy data, and atomic-force microscopy data on the surface morphology of the crystals, a physical model is proposed to interpret the effects experimentally observed in the crystals. The model takes into account the interactionmore » of radiation defects with the initial structural defects in the crystals as well as the effect of compensation of defect centers by hydrogen during high-frequency treatment.« less

NMR crystallography of 2-acylamino-6-[1 H]-pyridones: Solid-state NMR, GIPAW computational, and single crystal X-ray diffraction studies

NASA Astrophysics Data System (ADS)

Ośmiałowski, Borys; Kolehmainen, Erkki; Ikonen, Satu; Ahonen, Kari; Löfman, Miika

2011-12-01

2-Acylamino-6-[1 H]-pyridones [acyl = RCO, where R = methyl ( 1), ethyl ( 2), iso-propyl ( 3), tert-butyl ( 4), and 1-adamantyl ( 5)] have been synthesized and characterized by NMR spectroscopy. From three congeners, 2, 3 and 5, also single crystal X-ray structures have been solved. For these derivatives GIPAW calculations acts as a "bridge" between solid-state NMR data and calculated chemical shifts based on X-ray determined geometry. In crystals all three compounds exist as pyridone tautomers possessing similar six-membered ring structure stabilized by intramolecular C dbnd O⋯HN hydrogen bond. Theoretical GIPAW calculated and experimental 13C and 15N CPMAS NMR shifts are in excellent agreement with each other.

Experimental Observation of Three-Component New Fermions in Topological Semimetal MoP

NASA Astrophysics Data System (ADS)

Lv, B. Q.; Feng, Z.-L.; Xu, Q.-N.; Ma, J.-Z.; Kong, L.-Y.; Richard, Pierre; Huang, Y.-B.; Strocov, V. N.; Fang, C.; Weng, H.-M.; Shi, Y.-G.; Qian, Tian; Ding, Hong; Paul Scherrer Institute, Swiss Light Source, CH-5232 Villigen PSI, Switzerland Team; Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics Team; University of Chinese Academy of Sciences, Beijing 100190, China Team; Collaborative Innovation Center of Quantum Matter, Beijing, China Collaboration; Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China Team

Condensed matter systems can host quasiparticle excitations that are analogues to elementary particles such as Majorana, Weyl, and Dirac fermions. Recent advances in band theory have expanded the classification of fermions in crystals, and revealed crystal symmetry-protected electron excitations that have no high-energy counterparts. Here, using angle-resolved photoemission spectroscopy, we demonstrate the existence of a triply degenerate point in the electronic structure of MoP crystal, where the quasiparticle excitations are beyond the Majorana-Weyl-Dirac classification. Furthermore, we observe pairs of Weyl points in the bulk electronic structure coexisting with the new fermions, thus introducing a platform for studying the interplay between different types of fermions. We thank Binbin Fu, Nan Xu, and Xin Gao for the assistance in the ARPES experiments.

Synthesis, crystal structure and DFT studies of N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide

NASA Astrophysics Data System (ADS)

Gautam, P.; Gautam, D.; Chaudhary, R. P.

2013-12-01

The title compound N-(4-acetyl-5,5-dimethyl-4,5-dihydro-1,3,4-thiadiazol-2-yl)acetamide ( III) was obtained from the reaction of 2-(propan-2-ylidene)hydrazinecarbothioamide ( II) with acetic anhydride instead of formation of the desired thiosemcarbazide derivative of Meldrum acid. The structures of II and III were established by elemental analysis, IR, NMR, Mass and X-ray crystallographic studies. II crystallizes in triclinic system, sp. gr. Z = 2; III crystallizes in the monoclinic system, sp. gr. P21/ c, Z = 8. Density functional theory (DFT) calculations have been carried out for III. 1H and 13C NMR of III has been calculated and correlated with experimental results.

Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

NASA Astrophysics Data System (ADS)

McBriarty, Martin E.

Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

High resolution electron microscopy study of crystal growth mechanisms in chicken bone composites

NASA Astrophysics Data System (ADS)

Cuisinier, F. J. G.; Steuer, P.; Brisson, A.; Voegel, J. C.

1995-12-01

The present study describes the early stages of chicken bone crystal growth, followed by high resolution electron microscopy (HREM). We have developed an original analysis procedure to determine the crystal structure. Images were first digitalized and selected areas were fast Fourier transformed. Numerical masks were selected around the most intense spots and the filtered signal was retransformed back to real space. The filtered images were then compared to computer calculated images to identify the inorganic mineral phase. Nanometer-sized particles were observed on amorphous areas. These particles have a structure loosely related to hydroxyapatite (HA) and a specific orientation. In a more advanced situation, the nanoparticles appeared to grow in two dimensions and to form plate-like crystals. These crystals seem, in a last growth step, to fuse by their (100) faces. These experimental observations allowed us to propose a four-step model for the development and growth of chicken bone crystals. The two initial stages are the ionic adsorption onto the organic substrate followed by the nucleation of nanometer-sized particles. The two following steps, i.e. two-dimensional growth of the nanoparticles leading to the formation of needle-like crystals, and the lateral fusion of these crystals by their (100) faces, are controlled only by spatial constraints inside the extracellular organic matrix.

Splitting Fermi Surfaces and Heavy Electronic States in Non-Centrosymmetric U3Ni3Sn4

NASA Astrophysics Data System (ADS)

Maurya, Arvind; Harima, Hisatomo; Nakamura, Ai; Shimizu, Yusei; Homma, Yoshiya; Li, DeXin; Honda, Fuminori; Sato, Yoshiki J.; Aoki, Dai

2018-04-01

We report the single-crystal growth of the non-centrosymmetric paramagnet U3Ni3Sn4 by the Bridgman method and the Fermi surface properties detected by de Haas-van Alphen (dHvA) experiments. We have also investigated single-crystal U3Ni3Sn4 by single-crystal X-ray diffraction, magnetization, electrical resistivity, and heat capacity measurements. The angular dependence of the dHvA frequencies reveals many closed Fermi surfaces, which are nearly spherical in topology. The experimental results are in good agreement with local density approximation (LDA) band structure calculations based on the 5f-itinerant model. The band structure calculation predicts many Fermi surfaces, mostly with spherical shape, derived from 12 bands crossing the Fermi energy. To our knowledge, the splitting of Fermi surfaces due to the non-centrosymmetric crystal in 5f-electron systems is experimentally detected for the first time. The temperature dependence of the dHvA amplitude reveals a large cyclotron effective mass of up to 35 m0, indicating the heavy electronic state of U3Ni3Sn4 due to the proximity of the quantum critical point. From the field dependence of the dHvA amplitude, a mean free path of conduction electrons of up to 1950 Å is detected, reflecting the good quality of the grown crystal. The small splitting energy related to the antisymmetric spin-orbit interaction is most likely due to the large cyclotron effective mass.

Crystal Structure and Photocatalytic Activity of Al-Doped TiO2 Nanofibers for Methylene Blue Dye Degradation.

PubMed

Lee, Deuk Yong; Lee, Myung-Hyun; Kim, Bae-Yeon; Cho, Nam-Ihn

2016-05-01

Al-TiO2 nanofibers were prepared using a sol-gel derived electrospinning by varying the Al/Ti molar ratio from 0 to 0.73 to investigate the effect of Al doping on the crystal structure and the photocatalytic activity of Al-TiO2 for methylene blue (MB) degradation. XRD results indicated that as the Al/Ti molar ratio rose, crystal structure of Al-TiO2 was changed from anatase/rutile (undoped), anatase (0.07-0.18), to amorphous phase (0.38-0.73), which was confirmed by XPS and Raman analysis. The degradation kinetic constant increased from 7.3 x 10(-4) min(-1) to 4.5 x 10(-3) min(-1) with the increase of Al/Ti molar ratios from 0 to 0.38, but decreased to 3.4 x 10(-3) min(-1) when the Al/Ti molar ratio reached 0.73. The Al-TiO2 catalyst doped with 0.38 Al/Ti molar ratio demonstrated the best MB degradation. Experimental results indicated that the Al doping in Al-TiO2 was mainly attributed to the crystal structure of TiO2 and the photocatalytic degradation of MB.

Tunable two-dimensional photonic crystals using liquid crystal infiltration

NASA Astrophysics Data System (ADS)

Leonard, S. W.; Mondia, J. P.; van Driel, H. M.; Toader, O.; John, S.; Busch, K.; Birner, A.; Gösele, U.; Lehmann, V.

2000-01-01

The photonic band gap of a two-dimensional photonic crystal is continuously tuned using the temperature dependent refractive index of a liquid crystal. Liquid crystal E7 was infiltrated into the air pores of a macroporous silicon photonic crystal with a triangular lattice pitch of 1.58 μm and a band gap wavelength range of 3.3-5.7 μm. After infiltration, the band gap for the H polarized field shifted dramatically to 4.4-6.0 μm while that of the E-polarized field collapsed. As the sample was heated to the nematic-isotropic phase transition temperature of the liquid crystal (59 °C), the short-wavelength band edge of the H gap shifted by as much as 70 nm while the long-wavelength edge was constant within experimental error. Band structure calculations incorporating the temperature dependence of the liquid crystal birefringence can account for our results and also point to an escaped-radial alignment of the liquid crystal in the nematic phase.

Face-selective crystal growth behavior of L-aspartic acid in the presence of L-asparagine

NASA Astrophysics Data System (ADS)

Sato, Hiroyasu; Doki, Norihito; Yoshida, Saki; Yokota, Masaaki; Shimizu, Kenji

2016-02-01

The kinetic mechanism of L-asparagine (L-Asn) action on L-aspartic acid (L-Asp) crystal growth, namely the face-selective effect of L-Asn on the L-Asp crystal growth rate in each direction, was examined. In the a-axis direction, the effect of L-Asn on the L-Asp crystal growth rate was small. Enhancement and inhibition of L-Asp crystal growth, and interestingly the dissolution of the L-Asp crystal face, were observed in the b-axis direction, depending on the amount of L-Asn added. In the c-axis direction, the L-Asp crystal growth rate decreased with the increase in the amount of L-Asn added, and the experimental results were well fitted with a Langmuir adsorption isotherm. The study showed that there were crystal growth conditions where enhancement and inhibition, as well as inhibition and dissolution, coexisted in the presence of an additive with a structure similar to the growing crystal.

Real-time molecular scale observation of crystal formation.

PubMed

Schreiber, Roy E; Houben, Lothar; Wolf, Sharon G; Leitus, Gregory; Lang, Zhong-Ling; Carbó, Jorge J; Poblet, Josep M; Neumann, Ronny

2017-04-01

How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.

Molecular Modeling and Experimental Study of Nonlinear Optical Compounds: Mono-Substituted Derivatives of Dicyanovinylbenzene

NASA Technical Reports Server (NTRS)

Timofeeva, Tatyana V.; Nesterov, Vladimir N.; Antipin, Mikhael Y.; Clark, R. D.; Sanghadasa, M.; Cardelino, B. H.; Moore, C. E.; Frazier, Donald O.

2000-01-01

A search for potential nonlinear optical (NLO) compounds has been performed using the Cambridge Structural Database and molecular modeling. We have studied a series of mono-substituted derivatives of dicyanovinylbenzene as the NLO properties of one of its derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were described earlier. The molecular geometry in the series of the compounds studied was investigated with an X- ray analysis and discussed along with results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the molecular planarity has been revealed. Two new compounds from the series studied were found to be active for second harmonic generation (SHG) in the powder. The measurements of SHG efficiency have shown that the o-F- and p-Cl-derivatives of dicyanovinylbenzene are about 10 and 20- times more active than urea, respectively. The peculiarities of crystal structure formation in the framework of balance between the van der Waals and electrostatic interactions have been discussed. The crystal morphology of DIVA and two new SHG-active compounds have been calculated on the basis of their known crystal structures.

Synthesis, structural characterization, and DFT calculations of 3-buthyl-4-(3-methyl-3-mesitylcyclobut-1-yl)-1,3-thiazole-2(3H)-thione

DOE Office of Scientific and Technical Information (OSTI.GOV)

Şen, B.; Barim, E.; Kirilmis, C.

2016-03-15

The title compound, C{sub 21}H{sub 29}NS{sub 2}, has been synthesized and its crystal structure has been determined from single crystal X-ray diffraction data. Crystals are monoclinic, a = 11.4923(8), b = 13.1842(7), c = 14.6583(8) Å, β = 109.983(6)°, sp. gr. P2{sub 1}/c, Z = 4. Mesityl and thiazole groups are in cis positions with respect to the cyclobutane ring. The cyclobutane ring is puckered, with a dihedral angle of 26.6(2)° between the two three-atom planes. The crystal structure involves one weak intermolecular C–H···S hydrogen-bond. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,more » p) basis set in ground state. Geometric parameters (bond lengths, bond angles and torsion angles) and vibrational assignments have been calculated theoretically and compared with the experimental data.« less

Three-dimensional magnetophotonic crystals based on artificial opals

NASA Astrophysics Data System (ADS)

Baryshev, A. V.; Kodama, T.; Nishimura, K.; Uchida, H.; Inoue, M.

2004-06-01

We fabricated and experimentally investigated three-dimensional magnetophotonic crystals (3D MPCs) based on artificial opals. Opal samples with three-dimensional dielectric lattices were impregnated with different types of magnetic material. Magnetic and structural properties of 3D MPCs were studied by field emission scanning electron microscopy, x-ray diffraction analysis, and vibrating sample magnetometer. We have shown that magnetic materials synthesized in voids of opal lattices and the composites obtained have typical magnetic properties.

Effect of the mechanical activation of a cathode on the structure of electrolytic copper single crystals

NASA Astrophysics Data System (ADS)

Gryzunova, N. N.; Vikarchuk, A. A.; Gryzunov, A. M.; Denisova, A. G.

2017-10-01

The morphology of the electrolytic copper single crystals formed under the mechanical activation of a cathode is described. Pentagonal pyramids and conical microcrystals with high growth steps are shown to form during electrocrystallization under these conditions. It is experimentally found that microcrystals grow on disclination defects, in particular, at the sites of termination of twin growth boundaries, and mechanical activation causes the formation of such defects.

Electronic structure of multi-walled carbon fullerenes

NASA Astrophysics Data System (ADS)

Doore, Keith; Cook, Matthew; Clausen, Eric; Lukashev, Pavel V.; Kidd, Tim E.; Stollenwerk, Andrew J.

2017-02-01

Despite an enormous amount of research on carbon based nanostructures, relatively little is known about the electronic structure of multi-walled carbon fullerenes, also known as carbon onions. In part, this is due to the very high computational expense involved in estimating electronic structure of large molecules. At the same time, experimentally, the exact crystal structure of the carbon onion is usually unknown, and therefore one relies on qualitative arguments only. In this work we present the results of a computational study on a series of multi-walled fullerenes and compare their electronic structures to experimental data. Experimentally, the carbon onions were fabricated using ultrasonic agitation of isopropanol alcohol and deposited onto the surface of highly ordered pyrolytic graphite using a drop cast method. Scanning tunneling microscopy images indicate that the carbon onions produced using this technique are ellipsoidal with dimensions on the order of 10 nm. The majority of differential tunneling spectra acquired on individual carbon onions are similar to that of graphite with the addition of molecular-like peaks, indicating that these particles span the transition between molecules and bulk crystals. A smaller, yet sizable number exhibited a semiconducting gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) levels. These results are compared with the electronic structure of different carbon onion configurations calculated using first-principles. Similar to the experimental results, the majority of these configurations are metallic with a minority behaving as semiconductors. Analysis of the configurations investigated here reveals that each carbon onion exhibiting an energy band gap consisted only of non-metallic fullerene layers, indicating that the interlayer interaction is not significant enough to affect the total density of states in these structures.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

NASA Astrophysics Data System (ADS)

Hofmann, D. W. M.; Kuleshova, L. N.

2018-05-01

Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

Electrical and Thermal Conductivity of Solid Solution Sn1- x Mn x Te (0 ≥ x ≥ 0.04)

NASA Astrophysics Data System (ADS)

Akhundova, N. M.

2018-01-01

Electrical and thermal properties of the Sn1-xMnxTe single crystals (0 ≥ x ≥ 0.04) with contacts of eutectic alloy 57Bi + 43Sn (in mass%) are investigated at temperatures from 77 to 300 K. Experimental results show that this alloy with specified single crystals forms ohmic contact with a sufficiently low contact resistance. The electronic thermal conductivity in some samples reaches about 50% of the total thermal conductivity, and structural defects contribute significantly to the thermal resistance of the crystals.

Experimental vizualization of 2D photonic crystal equi-frequency contours

NASA Astrophysics Data System (ADS)

Senderakova, Dagmar; Drzik, Milan; Pisarcik, Matej

2017-12-01

Photonic crystals have been extensively studied for their unique optical properties that promise interesting novel devices. Our contribution is focused on a 2D photonic crystal structure formed by Al2O3 layer on silicon substrate, patterned with periodic hexagonal lattice of deep air holes. Azimuthal angle dependences of the specular light reflection were recorded photo-electrically at various angles of icidence and wavelengths. Data obtained were processed via mapping in reciprocal k-space. The method promises a possibility to visualize the equi-frequency contours and get more detailed information about the properties of the sample used.

Tandem differential mobility analysis-mass spectrometry reveals partial gas-phase collapse of the GroEL complex.

PubMed

Hogan, Christopher J; Ruotolo, Brandon T; Robinson, Carol V; Fernandez de la Mora, Juan

2011-04-07

A parallel-plate differential mobility analyzer and a time-of-flight mass spectrometer (DMA-MS) are used in series to measure true mobility in dry atmospheric pressure air for mass-resolved electrosprayed GroEL tetradecamers (14-mers; ~800 kDa). Narrow mobility peaks are found (2.6-2.9% fwhm); hence, precise mobilities can be obtained for these ions without collisional activation, just following their generation by electrospray ionization. In contrast to previous studies, two conformers are found with mobilities (Z) differing by ~5% at charge state z ~ 79. By extrapolating to small z, a common mobility/charge ratio Z(0)/z = 0.0117 cm(2) V(-1) s(-1) is found for both conformers. When interpreted as if the GroEL ion surface were smooth and the gas molecule-protein collisions were perfectly elastic and specular, this mobility yields an experimental collision cross section, Ω, 11% smaller than in an earlier measurement, and close to the cross section, A(C,crystal), expected for the crystal structure (determined by a geometric approximation). However, the similarity between Ω and A(C,crystal) does not imply a coincidence between the native and gas-phase structures. The nonideal nature of protein-gas molecule collisions introduces a drag enhancement factor, ξ = 1.36, with which the true cross section A(C) is related to Ω via A(C) = Ω/ξ. Therefore, A(C) for GroEL 14-mer ions determined by DMA measurements is 0.69A(C,crystal). The factor 1.36 used here is based on the experimental Stokes-Millikan equation, as well as on prior and new numerical modeling accounting for multiple scattering events via exact hard-sphere scattering calculations. Therefore, we conclude that the gas-phase structure of the GroEL complex as electrosprayed is substantially more compact than the corresponding X-ray crystal structure.

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

Erbium ion implantation into diamond - measurement and modelling of the crystal structure.

PubMed

Cajzl, Jakub; Nekvindová, Pavla; Macková, Anna; Malinský, Petr; Sedmidubský, David; Hušák, Michal; Remeš, Zdeněk; Varga, Marián; Kromka, Alexander; Böttger, Roman; Oswald, Jiří

2017-02-22

Diamond is proposed as an extraordinary material usable in interdisciplinary fields, especially in optics and photonics. In this contribution we focus on the doping of diamond with erbium as an optically active centre. In the theoretical part of the study based on DFT simulations we have developed two Er-doped diamond structural models with 0 to 4 carbon vacancies in the vicinity of the Er atom and performed geometry optimizations by the calculation of cohesive energies and defect formation energies. The theoretical results showed an excellent agreement between the calculated and experimental cohesive energies for the parent diamond. The highest values of cohesive energies and the lowest values of defect formation energies were obtained for models with erbium in the substitutional carbon position with 1 or 3 vacancies in the vicinity of the erbium atom. From the geometry optimization the structural model with 1 vacancy had an octahedral symmetry whereas the model with 3 vacancies had a coordination of 10 forming a trigonal structure with a hexagonal ring. In the experimental part, erbium doped diamond crystal samples were prepared by ion implantation of Er + ions using ion implantation fluences ranging from 1 × 10 14 ions per cm 2 to 5 × 10 15 ions per cm 2 . The experimental results revealed a high degree of diamond structural damage after the ion implantation process reaching up to 69% of disordered atoms in the samples. The prepared Er-doped diamond samples annealed at the temperatures of 400, 600 and 800 °C in a vacuum revealed clear luminescence, where the 〈110〉 cut sample has approximately 6-7 times higher luminescence intensity than the 〈001〉 cut sample with the same ion implantation fluence. The reported results are the first demonstration of the Er luminescence in the single crystal diamond structure for the near-infrared spectral region.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivas, Blanca de las; Rodríguez, Héctor; Angulo, Iván

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. Crystalsmore » 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.« less

Gradient-index phononic crystal lens-based enhancement of elastic wave energy harvesting

NASA Astrophysics Data System (ADS)

Tol, S.; Degertekin, F. L.; Erturk, A.

2016-08-01

We explore the enhancement of structure-borne elastic wave energy harvesting, both numerically and experimentally, by exploiting a Gradient-Index Phononic Crystal Lens (GRIN-PCL) structure. The proposed GRIN-PCL is formed by an array of blind holes with different diameters on an aluminum plate, where the blind hole distribution is tailored to obtain a hyperbolic secant gradient profile of refractive index guided by finite-element simulations of the lowest asymmetric mode Lamb wave band diagrams. Under plane wave excitation from a line source, experimentally measured wave field validates the numerical simulation of wave focusing within the GRIN-PCL domain. A piezoelectric energy harvester disk located at the first focus of the GRIN-PCL yields an order of magnitude larger power output as compared to the baseline case of energy harvesting without the GRIN-PCL on the uniform plate counterpart.

Solid-state modeling of the terahertz spectrum of the high explosive HMX.

PubMed

Allis, Damian G; Prokhorova, Darya A; Korter, Timothy M

2006-02-09

The experimental solid-state terahertz (THz) spectrum (3-120 cm(-1)) of the beta-crystal form of the high explosive octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) has been analyzed using solid-state density functional theory calculations. Various density functionals (both generalized gradient approximation and local density approximation) are compared in terms of their abilities to reproduce the experimentally observed solid-state structure and low-frequency vibrational motions. Good-to-excellent agreement between solid-state theory and experiment can be achieved in the THz region where isolated-molecule calculations fail to reproduce the observed spectral features, demonstrating a clear limitation of using isolated-molecule calculations for the assignment of THz frequency motions in molecular solids. The deficiency of isolated-molecule calculations is traced to modification of the molecular structure in the solid state through crystal packing effects and the formation of weak C-H...O hydrogen bonds.

Temperature insensitive curvature sensor based on cascading photonic crystal fiber

NASA Astrophysics Data System (ADS)

Fu, Guangwei; Li, Yunpu; Fu, Xinghu; Jin, Wa; Bi, Weihong

2018-03-01

A temperature insensitive curvature sensor is proposed based on cascading photonic crystal fiber. Using the arc fusion splicing method, this sensor is fabricated by cascading together a single-mode fiber (SMF), a three layers air holes structure of photonic crystal fiber (3PCF), a five layers air holes structure of photonic crystal fiber (5PCF) and a SMF in turn. So the structure SMF-3PCF-5PCF-SMF can be obtained with a total length of 20 mm. During the process of fabrication, the splicing machine parameters and the length of each optical fiber are adjusted to obtain a high sensitivity curvature sensor. The experimental results show that the curvature sensitivity is -8.40 nm/m-1 in the curvature variation range of 0-1.09 m-1, which also show good linearity. In the range of 30-90 °C, the temperature sensitivity is only about 3.24 pm/°C, indicating that the sensor is not sensitive to temperature. The sensor not only has the advantages of easy fabricating, simple structure, high sensitivity but also can solve the problem of temperature measurement cross sensitivity, so it can be used for different areas including aerospace, large-scale bridge, architectural structure health monitoring and so on.

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Characterization of photonic colloidal crystals in real and reciprocal space

NASA Astrophysics Data System (ADS)

Thijssen, J. H. J.

2007-05-01

In this thesis, we present experimental work on the characterization of photonic colloidal crystals in real and reciprocal space. Photonic crystals are structures in which the refractive index varies periodically in space on the length scale of the wavelength of light. Self-assembly of colloidal particles is a promising route towards three-dimensional (3-D) photonic crystals. However, fabrication of photonic band-gap materials remains challenging, so calculations that predict their optical properties are indispensable. Our photonic band-structure calculations on binary Laves phases have led to a proposed route towards photonic colloidal crystals with a band gap in the visible region. Furthermore, contrary to results in literature, we found that there is no photonic band gap for inverse BCT crystals. Finally, optical spectra of colloidal crystals were analyzed using band-structure calculations. Self-assembled photonic crystals are fabricated in multiple steps. Each of these steps can significantly affect the 3-D structure of the resulting crystal. X-rays are an excellent probe of the internal structure of photonic crystals, even if the refractive-index contrast is large. In Chapter 3, we demonstrate that an angular resolution of 0.002 mrad is achievable at a third-generation synchrotron using compound refractive optics. As a result, the position and the width of Bragg reflections in 2D diffraction patterns can be resolved, even for lattice spacings larger than a micrometer (corresponding to approximately 0.1 mrad). X-ray diffraction patterns and electron-microscopy images are used in Chapter 4 to determine the orientation of hexagonal layers in convective-assembly colloidal crystals. Quantitative analysis revealed that, in our samples, the layers were not exactly hexagonal and the stacking sequence was that of face-centered cubic (FCC) crystals, though stacking faults may have been present. In Chapter 5, binary colloidal crystals of organic spheres (polystyrene, PMMA) and/or inorganic spheres (silica) are introduced as promising templates for strongly photonic crystals. To prevent melting of the template, we used atomic layer deposition (ALD) to infiltrate polystyrene and PMMA templates with alumina, after which chemical vapor deposition (CVD) was used to further enhance the refractive-index contrast. Binary colloidal crystals of silica spheres can be infiltrated by CVD directly, but they often have a layer of colloidal fluid on top. Preliminary etching experiments demonstrated that it may be possible to etch silica templates with plasmas or with adhesive tape. As described in Chapter 6, sedimentation of colloidal silica spheres in an external, high-frequency electric field lead to mm-scale BCT crystals with up to 25 layers. In addition, electric fields were used as an external control to switch between BCT and close-packed (CP) crystal structures within seconds. We also developed two procedures to invert BCT crystals without loss of structure - colloidal particles were immobilized by diffusion-polymerization or photo-induced polymerization of the surrounding solvent. Some BCT crystals were even infiltrated with silicon using CVD. We demonstrate in Chapter 7 that X-ray diffraction can be used to determine the 3-D structure of such photonic colloidal crystals at the various stages of their fabrication. Excellent agreement was found with confocal and electron-microscopy images.

DFT calculations in the assignment of solid-state NMR and crystal structure elucidation of a lanthanum(iii) complex with dithiocarbamate and phenanthroline.

PubMed

Gowda, Vasantha; Laitinen, Risto S; Telkki, Ville-Veikko; Larsson, Anna-Carin; Antzutkin, Oleg N; Lantto, Perttu

2016-12-06

The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state 13 C and 15 N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and 13 C and 15 N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P2 1 /n. Both 13 C and 15 N CP-MAS NMR revealed the presence of six structurally different dithiocarbamate groups in the asymmetric unit cell, implying a non-centrosymmetric packing arrangement of molecules. This was supported by single-crystal X-ray crystallography showing that the title compound crystallised in the triclinic space group P1[combining macron]. In addition, the crystal structure also revealed that one of the dithiocarbamate ligands has a conformational disorder. NMR chemical shift calculations employing the periodic gauge including projector augmented wave (GIPAW) approach supported the assignment of the experimental 13 C and 15 N NMR spectra. However, the best correspondences were obtained with the structure where the atomic positions in the X-ray unit cell were optimised at the DFT level. The roles of the scalar and spin-orbit relativistic effects on NMR shielding were investigated using the zeroth-order regular approximation (ZORA) method with the outcome that already the scalar relativistic level qualitatively reproduces the experimental chemical shifts. The electronic properties of the complex were evaluated based on the results of the natural bond orbital (NBO) and topology of the electron density analyses. Overall, we apply a multidisciplinary approach acquiring comprehensive information about the solid-state structure and the metal-ligand bonding of the heteroleptic lanthanum complex.

WinPSSP : a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pagola, Silvina; Polymeros, Alekos; Kourkoumelis, Nikolaos

2017-02-01

The direct-space methods softwarePowder Structure Solution Program(PSSP) [Pagola & Stephens (2010).J. Appl. Cryst.43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs.WinPSSPis a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinatesmore » into the Rietveld analysis softwareGSAS. WinPSSPperformance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.« less

Crystal structure prediction supported by incomplete experimental data

NASA Astrophysics Data System (ADS)

Tsujimoto, Naoto; Adachi, Daiki; Akashi, Ryosuke; Todo, Synge; Tsuneyuki, Shinji

2018-05-01

We propose an efficient theoretical scheme for structure prediction on the basis of the idea of combining methods, which optimize theoretical calculation and experimental data simultaneously. In this scheme, we formulate a cost function based on a weighted sum of interatomic potential energies and a penalty function which is defined with partial experimental data totally insufficient for conventional structure analysis. In particular, we define the cost function using "crystallinity" formulated with only peak positions within the small range of the x-ray-diffraction pattern. We apply this method to well-known polymorphs of SiO2 and C with up to 108 atoms in the simulation cell and show that it reproduces the correct structures efficiently with very limited information of diffraction peaks. This scheme opens a new avenue for determining and predicting structures that are difficult to determine by conventional methods.

Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

NASA Astrophysics Data System (ADS)

Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

2018-04-01

A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

Experimental and density functional theory (DFT): A dual approach to probe the key properties of creatininium L-tartrate monohydrate single crystal for nonlinear optical applications

NASA Astrophysics Data System (ADS)

Thirumurugan, R.; Babu, B.; Anitha, K.; Chandrasekaran, J.

2017-12-01

A novel organic nonlinear optical (NLO) material, creatininium L-tartrate monohydrate (CTM) was synthesized and it was grown as single crystals with optical quality. 1H and 13C NMR spectral studies were performed and molecular structure of synthesized CTM compound was confirmed. Single crystal X-ray diffraction (SXRD) analysis confirmed that CTM was crystallized in orthorhombic system with non-centrosymmetric (NCS), P212121, space group. The grown crystal exhibited admirable properties such as second harmonic generation efficiency (SHG) (1.9 times KDP), and high laser damage threshold (LDT) value of 3.7 GW cm-2. CTM crystal displayed high transparency (∼60%) in the visible and near-IR region with low cut-off wavelength at 249 nm. Photoluminescence study confirmed blue wavelength emission (∼463 nm) of grown crystal. Thermal and mechanical behaviours have been successfully analysed for grown crystals. The dielectric studies were carried out for grown crystal as a function of frequencies at different temperatures. Hirshfeld surface and fingerprint plots provided the percentage of individual interactions contributed by each atom. Moreover, density functional theory (DFT) calculations have been employed to probe the frontier molecular orbitals (FMOs) and first hyperpolarizability (β) analysis of the optimized CTM structure. These results validated CTM as a suitable NLO candidate and were discussed in this work.

Radiation coloring of nonstoichiometric M(1-x)R(x)F(2+x) single crystals with a fluorite defect structure

NASA Astrophysics Data System (ADS)

Rustamov, Ia.; Tavshunskii, G. A.; Khabibullaev, P. K.; Bessonova, T. S.; Sobolev, B. P.

1985-06-01

Experimental results are reported concerning the radiation coloring of nonstoichiometric crystals of the M(1-x)R(x)F(2+x) type in the presence of fluorite defects. Samples of the crystals are cut using the Stockbarger technique in a chemically active fluoridating atmosphere generated by pyrolysis of tetrafluoroethylene. The samples were irradiated at 77 and 300 K using a Co-60 gamma-ray source and the total doses were in the range 10 to the 6th to 10 to the 7th roentgen. Absorption spectra of the crystals were analogous spectra for MF2-RF3 single crystals with RF 3 contents of less than 1 mole percent. It is shown that the properties of radiation coloring of the two types of crystal are very different: F-centers formed at 300 K in Ca(1-x)R(x) F(2+x), but not at 77 K. Complex color centers were observed at 77 K in Ca(1-x)R(x)F(2+x) single crystals and the intensity of the centers was determined by the competition among the electron trapping processes involving the r3(+) ions. It is concluded that the coloring characteristics of the M(1-x)R(x)F(2+x) crystals are related to their structural characteristics as compared with the MF2-RF3 crystals.

Density functional theory in the solid state

PubMed Central

Hasnip, Philip J.; Refson, Keith; Probert, Matt I. J.; Yates, Jonathan R.; Clark, Stewart J.; Pickard, Chris J.

2014-01-01

Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure–property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program. PMID:24516184

Electronic structure and orientation relationship of Li nanoclusters embedded in MgO studied by depth-selective positron annihilation two-dimensional angular correlation

NASA Astrophysics Data System (ADS)

Falub, C. V.; Mijnarends, P. E.; Eijt, S. W.; van Huis, M. A.; van Veen, A.; Schut, H.

2002-08-01

Quantum-confined positrons are sensitive probes for determining the electronic structure of nanoclusters embedded in materials. In this work, a depth-selective positron annihilation 2D-ACAR (two-dimensional angular correlation of annihilation radiation) method is used to determine the electronic structure of Li nanoclusters formed by implantation of 1016-cm-2 30-keV 6Li ions in MgO (100) and (110) crystals and by subsequent annealing at 950 K. Owing to the difference between the positron affinities of lithium and MgO, the Li nanoclusters act as quantum dots for positrons. 2D-ACAR distributions for different projections reveal a semicoherent fitting of the embedded metallic Li nanoclusters to the host MgO lattice. Ab initio Korringa-Kohn-Rostoker calculations of the momentum density show that the anisotropies of the experimental distributions are consistent with an fcc crystal structure of the Li nanoclusters. The observed reduction of the width of the experimental 2D-ACAR distribution is attributed to positron trapping in vacancies associated with Li clusters. This work proposes a method for studying the electronic structure of metallic quantum dots embedded in an insulating material.

Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex

PubMed Central

Tsurumura, Toshiharu; Tsumori, Yayoi; Qiu, Hao; Oda, Masataka; Sakurai, Jun; Nagahama, Masahiro; Tsuge, Hideaki

2013-01-01

Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Recently, we solved the crystal structure of Ia in complex with actin and the nonhydrolyzable NAD+ analog βTAD (thiazole-4-carboxamide adenine dinucleotide); however, the structures of the NAD+-bound form (NAD+-Ia-actin) and the ADP ribosylated form [Ia-ADP ribosylated (ADPR)-actin] remain unclear. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystallized the NAD+-Ia-actin complex. Here we report high-resolution structures of NAD+-Ia-actin and Ia-ADPR-actin obtained by soaking apo-Ia-actin crystal with NAD+ under different conditions. The structures of NAD+-Ia-actin and Ia-ADPR-actin represent the pre- and postreaction states, respectively. By assigning the βTAD-Ia-actin structure to the transition state, the strain-alleviation model of ADP ribosylation, which we proposed previously, is experimentally confirmed and improved. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases. PMID:23382240

A Practical Approach to Protein Crystallography.

PubMed

Ilari, Andrea; Savino, Carmelinda

2017-01-01

Macromolecular crystallography is a powerful tool for structural biology. The resolution of a protein crystal structure is becoming much easier than in the past, thanks to developments in computing, automation of crystallization techniques and high-flux synchrotron sources to collect diffraction datasets. The aim of this chapter is to provide practical procedures to determine a protein crystal structure, illustrating the new techniques, experimental methods, and software that have made protein crystallography a tool accessible to a larger scientific community.It is impossible to give more than a taste of what the X-ray crystallographic technique entails in one brief chapter and there are different ways to solve a protein structure. Since the number of structures available in the Protein Data Bank (PDB) is becoming ever larger (the protein data bank now contains more than 100,000 entries) and therefore the probability to find a good model to solve the structure is ever increasing, we focus our attention on the Molecular Replacement method. Indeed, whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set and a search model downloaded from the PDB, with the aid only of computer work.

Spontaneous formation and dynamics of half-skyrmions in a chiral liquid-crystal film

NASA Astrophysics Data System (ADS)

Nych, Andriy; Fukuda, Jun-Ichi; Ognysta, Uliana; Žumer, Slobodan; Muševič, Igor

2017-12-01

Skyrmions are coreless vortex-like excitations emerging in diverse condensed-matter systems, and real-time observation of their dynamics is still challenging. Here we report the first direct optical observation of the spontaneous formation of half-skyrmions. In a thin film of a chiral liquid crystal, depending on experimental conditions including film thickness, they form a hexagonal lattice whose lattice constant is a few hundred nanometres, or appear as isolated entities with topological defects compensating their charge. These half-skyrmions exhibit intriguing dynamical behaviour driven by thermal fluctuations. Numerical calculations of real-space images successfully corroborate the experimental observations despite the challenge because of the characteristic scale of the structures close to the optical resolution limit. A thin film of a chiral liquid crystal thus offers an intriguing platform that facilitates a direct investigation of the dynamics of topological excitations such as half-skyrmions and their manipulation with optical techniques.

Magneto-optical spectra and electron structure of Nd0.5Gd0.5Fe3(BO3)4 single crystal

NASA Astrophysics Data System (ADS)

Malakhovskii, A. V.; Gnatchenko, S. L.; Kachur, I. S.; Piryatinskaya, V. G.; Sukhachev, A. L.; Temerov, V. L.

2016-03-01

Polarized absorption spectra and magnetic circular dichroism (MCD) spectra of Nd0.5Gd0.5Fe3(BO3)4 single crystal were measured in the range of 10000-21000 cm-1 and at temperatures 2-300 K. On the basis of these data, in the paramagnetic state of the crystal, the 4f states of the Nd3+ ion were identified in terms of the irreducible representations and in terms of | J , ±MJ 〉 wave functions of the free atom. The changes of the Landé factor during f-f transitions were found theoretically in the | J , ±MJ 〉 wave functions approximation and were determined experimentally with the help of the measured MCD spectra. In the majority of cases the experimentally found values are close to the theoretically predicted ones.

Phase diagram of supercooled water confined to hydrophilic nanopores

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2012-07-01

We present a phase diagram for water confined to cylindrical silica nanopores in terms of pressure, temperature, and pore radius. The confining cylindrical wall is hydrophilic and disordered, which has a destabilizing effect on ordered water structure. The phase diagram for this class of systems is derived from general arguments, with parameters taken from experimental observations and computer simulations and with assumptions tested by computer simulation. Phase space divides into three regions: a single liquid, a crystal-like solid, and glass. For large pores, radii exceeding 1 nm, water exhibits liquid and crystal-like behaviors, with abrupt crossovers between these regimes. For small pore radii, crystal-like behavior is unstable and water remains amorphous for all non-zero temperatures. At low enough temperatures, these states are glasses. Several experimental results for supercooled water can be understood in terms of the phase diagram we present.

Summary of theoretical and experimental investigation of grating type, silicon photovoltaic cells. [using p-n junctions on light receiving surface of base crystal

NASA Technical Reports Server (NTRS)

Chen, L. Y.; Loferski, J. J.

1975-01-01

Theoretical and experimental aspects are summarized for single crystal, silicon photovoltaic devices made by forming a grating pattern of p/n junctions on the light receiving surface of the base crystal. Based on the general semiconductor equations, a mathematical description is presented for the photovoltaic properties of such grating-like structures in a two dimensional form. The resulting second order elliptical equation is solved by computer modeling to give solutions for various, reasonable, initial values of bulk resistivity, excess carrier concentration, and surface recombination velocity. The validity of the computer model is established by comparison with p/n devices produced by alloying an aluminum grating pattern into the surface of n-type silicon wafers. Current voltage characteristics and spectral response curves are presented for cells of this type constructed on wafers of different resistivities and orientations.

Investigation of hydrogen interaction with defects in zirconia

NASA Astrophysics Data System (ADS)

Melikhova, O.; Kuriplach, J.; Čížek, J.; Procházka, I.; Brauer, G.; Anwand, W.

2010-04-01

Defect studies of a ZrO2 + 9 mol. % Y2O3 single crystal were performed in this work using a high resolution positron lifetime spectroscopy combined with slow positron implantation spectroscopy. In order to elucidate the nature of positron trapping sites observed experimentally, the structural relaxations of several types of vacancy-like defects in zirconia were performed and positron characteristics for them were calculated. Relaxed atomic configurations of studied defects were obtained by means of ab initio pseudopotential method within the supercell approach. Theoretical calculations indicated that neither oxygen vacancies nor their neutral complexes with substitute yttrium atoms are capable of positron trapping. On the other hand, zirconium vacancies are deep positron traps and are most probably responsible for the saturated positron trapping observed in yttria stabilized zirconia single crystals. However, the calculated positron lifetime for zirconium vacancy is apparently longer than the experimental value corresponding to a single-component spectrum measured for the cubic ZrO2 + 9 mol. % Y2O3 single crystal. It was demonstrated that this effect can be explained by hydrogen trapped in zirconium vacancies. On the basis of structure relaxations, we found that zirconium vacancy - hydrogen complexes represent deep positron traps with the calculated lifetime close to the experimental one. In zirconium vacancy - hydrogen complexes the hydrogen atom forms an O-H bond with one of the nearest neighbour oxygen atoms. The calculated bond length is close to 1 Å.

The electronic structure of RbTiOPO4 and the effects of the A-site cation substitution in KTiOPO4-family crystals

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Meng, Guangsi; Lin, Z. S.

2012-10-01

The electronic structure of RbTiOPO4 has been investigated with x-ray photoemission spectroscopy. Detailed photoemission spectra of the element core levels have been recorded under excitation by nonmonochromatic Al Kα radiation (1486.6 eV). The chemical bonding parameters are compared to those reported for complex titanates and phosphates. The band structures of KTiOPO4, RbTiOPO4, K0.535R0.465TiOPO4 and TlTiOPO4 have been calculated by ab initio methods and compared to available experimental results. It is found that the band structure of KTP-type phosphate crystals is weakly dependent on the nature of the A-site (A=K, Rb, Tl) element.

Synthesis, spectroscopic characterization and crystallographic behavior of a biologically relevant novel indole-fused heterocyclic compound - Experimental and theoretical (DFT) studies

NASA Astrophysics Data System (ADS)

Sharma, Sakshi; Brahmachari, Goutam; Banerjee, Bubun; Nurjamal, Khondekar; Kumar, Abhishek; Srivastava, Ambrish Kumar; Misra, Neeraj; Pandey, Sarvesh Kumar; Rajnikant; Gupta, Vivek K.

2016-08-01

The present communication deals with the eco-friendly synthesis, spectral properties and X-ray crystal structure of an indole derivative - Ethyl 2'-amino-3'-cyano-6'-methyl-5-nitro-2-oxospiro [indoline-3,4'-pyran]-5'-carboxylate. The title compound was synthesized in 87% yield. The crystal structure of the molecule is stabilized by intermolecular Nsbnd H … N, Nsbnd H … O and Csbnd H … π interactions. The molecule is organized in the crystal lattice forming sheet like structure. To interpret the experimental data, ab initio computations of the vibrational frequencies were carried out using the Gaussian 09 program followed by the full optimizations done using Density Functional Theory (DFT) at B3LYP/6-31 + G(d,p) level. The combined use of experiments and computations allowed a firm assignment of the majority of observed bands for the compound. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap were presented. The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs) and density of states (DOS). From the optimized geometry of the molecule, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMOs) of the title compound have been calculated in the ground state theoretically. The theoretical results showed good agreement with the experimental values. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compound.

Crystal orientation dependence of band matching in all-B2-trilayer current-perpendicular-to-plane giant magnetoresistance pseudo spin-valves using Co{sub 2}Fe(Ge{sub 0.5}Ga{sub 0.5}) Heusler alloy and NiAl spacer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jiamin; Hono, K., E-mail: kazuhiro.hono@nims.go.jp; Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-2-1, Sengen, Tsukuba 305-0047

2015-05-07

We have experimentally investigated the crystal orientation dependence of band matching in current-perpendicular-to-plane giant magnetoresistance (CPP-GMR) pseudo-spin-valves using Co{sub 2}Fe(Ge{sub 0.5}Ga{sub 0.5}) (CFGG) Heusler alloy ferromagnetic layer and NiAl spacer. The high quality epitaxial CFGG/NiAl/CFGG all-B2-trilayers structure devices were fabricated on both MgO(001) and sapphire (112{sup ¯}0) single crystal substrates to create (001) and (110) crystal orientations. Same magneto-transport properties were observed from these two differently orientated devices indicating that there is no or little orientation dependence of band matching on MR output. We also found that all-B2-trilayer structure was free of lattice matching influence depending on the crystal orientation,more » which made it a good candidate for CPP-GMR device.« less

Experimental and quantum chemical studies of a new organic proton transfer compound, 1H-imidazole-3-ium-3-hydroxy-2,4,6-trinitrophenolate

NASA Astrophysics Data System (ADS)

Dhamodharan, P.; Sathya, K.; Dhandapani, M.

2018-02-01

A new proton transfer compound, 1H-imidazole-3-ium-3-hydroxy-2,4,6-trinitrophenolate (IMHTP), was crystallized by slow evaporation-solution growth technique. 1H and 13C NMR spectral studies confirm the molecular structure of the grown crystal. Single crystal X-ray diffraction study confirms that IMHTP crystallizes in monoclinic system with space group P21/c. Thermal curves (TG/DTA) show that the material is thermally stable up to 198 °C. The crystal emits fluorescence at 510 nm, proving its utility in making green light emitting materials in optical applications. The stable molecular structure was optimized by Gaussian 09 program with B3LYP/6-311++G(d,p) level of basis set. The frontier molecular orbital study shows that the charge transfer interaction occurs within the complex. The calculated first-order hyperpolarizability value of IMHTP is 44 times higher than that the reference material, urea. The electrostatic potential map was used to probe into electrophilic and nucleophilic reactive sites present in the molecule.

Theoretical research on the spin-Hamiltonian parameters of the rhombic W5+ centers in CaWO4:Y3+ crystal

NASA Astrophysics Data System (ADS)

Mei, Yang; Wei, Cheng-Fu; Zheng, Wen-Chen

2016-02-01

Detailed theoretical calculations for the spin-Hamiltonian parameters (g factors gi and hyperfine structure constants Ai, where i=x, y, z) of the rhombic W5+ center in CaWO4:Y3+ crystal are performed by using the high-order perturbation formulas for d1 ions in rhombic tetrahedral clusters with the ground state |dz2>. These formulas consist of the contributions from two mechanisms, the crystal-field (CF) mechanism connected with CF excited states in the vastly-used CF theory and the frequently-neglected charge-transfer (CT) mechanism related to CT excited states. The calculated results agree well with the experimental values. The calculations indicate that for W5+ ion (or other high valence state dn ions) in crystals, the model calculations of spin-Hamiltonian parameters should take both the CF and CT mechanisms into account. The signs of hyperfine structure constants Ai are suggested and the forming (or defect model) of rhombic W5+ center in CaWO4:Y3+ crystal is confirmed from the calculations.

Keto-enol tautomerism of (E)-2-[(3,4-dimethylphenylimino)methyl]-4-nitrophenol: Synthesis, X-ray, FT-IR, UV-Vis, NMR and quantum chemical characterizations

NASA Astrophysics Data System (ADS)

Özek Yıldırım, Arzu; Yıldırım, M. Hakkı; Albayrak Kaştaş, Çiǧdem

2017-01-01

(E)-2-((3,4-dimethylphenylimino)methyl)-4-nitrophenol, which is a new Schiff base compound, was synthesized and characterized by experimental and computational methods. Molecular geometry, harmonic oscillator model of aromaticity (HOMA) indices, intra- and inter-molecular interactions in the crystal structure were determined by using single crystal X-ray diffraction technique. The optimized structures, which are obtained by Gaussian and Slater type orbitals, were compared to experimental structures to determine how much correlation is found between the experimental and the calculated properties. Intramolecular and hyperconjugative interactions of bonds have been found by Natural Bond Orbital analysis. The experimental infrared spectrum of the compound has been analyzed in detail by the calculated infrared spectra and Potential Energy Distribution analysis. To find out about the correlation between the solvent polarity and the enol-keto equilibrium, experimental UV-Visible spectra of the compound were obtained in benzene, CHCl3, EtOH and DMSO solvents. In these solvents, the UV-Vis spectra and relaxed potential energy surface scan (PES) calculations have been performed to get more insight into the equilibrium dynamics. Solvent effects in UV-Vis and PES calculations have been taken into account by using Polarizable Continuum Modelling method. 1H and 13C NMR spectra of the compound (in DMSO) were analyzed. The computational study of nonlinear optical properties shows that the compound can be used for the development of nonlinear optical materials.

Radiation-induced hydroxyl addition to purine molecules: EPR and ENDOR study of hypoxanthine hydrochloride monohydrate single crystals.

PubMed

Tokdemir, Sibel; Nelson, William H

2005-06-01

Three radical species were detected in an EPR/ENDOR study of X-irradiated hypoxanthine.HCl.H2O single crystals at room temperature: RI was identified as the product of net H addition to C8, RII was identified as the product of net H addition to C2, and RIII was identified as the product of OH addition to C8. The observed set of radicals was the same for room-temperature irradiation as for irradiation at 10 K followed by warming the crystals to room temperature; however, the C2 H-addition and C8 OH-addition radicals were not detectable after storage of the crystals for about 2 months at room temperature. Use of selectively deuterated crystals permitted unique assignment of the observed hyperfine couplings, and results of density functional theory calculations on each of the radical structures were consistent with the experimental results. Comparison of these experimental results with others from previous crystal-based systems and model system computations provides insight into the mechanisms by which the biologically important purine C8 hydroxyl addition products are formed. The evidence from solid systems supports the mechanism of net water addition to one-electron oxidized purine bases and demonstrates the importance of a facial approach between the reactants.

Developments in the Implementation of Acoustic Droplet Ejection for Protein Crystallography.

PubMed

Wu, Ping; Noland, Cameron; Ultsch, Mark; Edwards, Bonnie; Harris, David; Mayer, Robert; Harris, Seth F

2016-02-01

Acoustic droplet ejection (ADE) enables crystallization experiments at the low-nanoliter scale, resulting in rapid vapor diffusion equilibration dynamics and efficient reagent usage in the empirical discovery of structure-enabling protein crystallization conditions. We extend our validation of this technology applied to the diverse physicochemical property space of aqueous crystallization reagents where dynamic fluid analysis coupled to ADE aids in accurate and precise dispensations. Addition of crystallization seed stocks, chemical additives, or small-molecule ligands effectively modulates crystallization, and we here provide examples in optimization of crystal morphology and diffraction quality by the acoustic delivery of ultra-small volumes of these cofactors. Additional applications are discussed, including set up of in situ proteolysis and alternate geometries of crystallization that leverage the small scale afforded by acoustic delivery. Finally, we describe parameters of a system of automation in which the acoustic liquid handler is integrated with a robotic arm, plate centrifuge, peeler, sealer, and stacks, which allows unattended high-throughput crystallization experimentation. © 2015 Society for Laboratory Automation and Screening.

Towards TiO2 nanotubes modified by WO3 species: influence of ex situ crystallization of precursor on the photocatalytic activities of WO3/TiO2 composites

NASA Astrophysics Data System (ADS)

Sun, Hui; Dong, Bohua; Su, Ge; Gao, Rongjie; Liu, Wei; Song, Liang; Cao, Lixin

2015-09-01

TiO2 nanotubes (TNT) crystallized at different temperatures were loaded with WO3 hydrate through the reaction between (NH4)6W7O24·6H2O and an aqueous solution of HCl. The photocatalytic activities of nanocomposites firstly increase and then decrease as a function of the crystallized temperature of the TNT precursor. The structural, morphologic and optical properties of WO3/TiO2 nanocomposites were also investigated in this study. The samples, initially anatase titania (573 K-773 K), presented phase transition to rutile titania at 873 K. With the crystallized temperature increasing, an evolution of samples morphology changing from nanotube-like structure to nanorod-like structure was observed. Meanwhile, the absorption edge of samples exhibited a red shift, and correspondingly their band gap decreased. Consistent with x-ray diffraction diffractograms, the existence of rutile titania as an impurity in the precursor TNT, crystallized at higher than 873 K, depressed photocatalytic activity evidently. As a result, the degradation rate of methyl orange (MO) increased with the samples crystallinity firstly, and then reduced due to the appearance of rutile titania. In our experimental conditions, the optimal photocatalytic activity was achieved for the sample crystalized at 773 K. Its degradation rate could reach 98.76% after 90 min UV light irradiation.

Probing and characterizing the growth of a crystal of ultracold bosons and light

NASA Astrophysics Data System (ADS)

Ostermann, S.; Piazza, F.; Ritsch, H.

2017-12-01

The non-linear coupled particle light dynamics of an ultracold gas in the field of two independent counter-propagating laser beams can lead to the dynamical formation of a self-ordered lattice structure as presented in (2016) Phys. Rev. X 6 021026. Here we present new numerical studies on experimentally observable signatures to monitor the growth and properties of such a crystal in real time. While, at least theoretically, optimal non-destructive observation of the growth dynamics and the hallmarks of the crystalline phase can be performed by analyzing scattered light, monitoring the evolution of the particle’s momentum distribution via time-of-flight probing is an experimentally more accessible choice. In this work we show that both approaches allow us to unambiguously distinguish the crystal from independent collective scattering as it occurs in matter wave super-radiance. As a clear crystallization signature, we identify spatial locking between the two emerging standing laser waves, together creating the crystal potential. For sufficiently large systems, the system allows reversible adiabatic ramping into the crystalline phase as an alternative to a quench across the phase transition and growth from fluctuations.

Experimental and theoretical studies of the molecular structure of 7-Methyl-3-[(3-methyl-3-mesityl-cyclobutyl]-5-phenyl-5H-thiazolo[3,2-α]pyrimidine-6-carboxylic acid ethyl ester

NASA Astrophysics Data System (ADS)

Acar, Betül; Yilmaz, Ibrahim; Çalışkan, Nezihe; Cukurovali, Alaaddin

2017-07-01

In this work, the title molecule, 7-Methyl-3-[(3-methyl-3-mesityl-cyclobutyl]-5-phenyl-5H-thiazolo[3,2-α]pyrimidine-6-carboxylic acid ethyl ester (C30H34N2O2S1), was synthesized and characterized by FT-IR spectroscopy and single crystal X-ray diffraction. The compound crystallizes in the triclinic space group P21/c. with Z = 4, a = 14.1988(6), b = 19.0893(5), c = 10.1325(4) Å, V = 2674.56(17) A3. The optimized structure parameters of the studied molecule was determined theoretically using HF/6-31G(d) and B3LYP/6-31G(d) methods for ground state, and compared with previously reported experimental findings. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental frequencies obtained by FT-IR spectra. The electronic properties, such as HOMO and LUMO energies, and molecular electrostatic potential (MEP) are also performed.

GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

PubMed

Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

2018-04-10

We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

Carbon agent chemical vapor transport growth of Ga2O3 crystal

NASA Astrophysics Data System (ADS)

Jie, Su; Tong, Liu; Jingming, Liu; Jun, Yang; Guiying, Shen; Yongbiao, Bai; Zhiyuan, Dong; Youwen, Zhao

2016-10-01

Beta-type gallium oxide (β-Ga2O3) is a new attractive material for optoelectronic devices. Different methods had been tried to grow high quality β-Ga2O3 crystals. In this work, crystal growth of Ga2O3 has been carried out by chemical vapor transport (CVT) method in a closed quartz tube using C as transport agent and sapphire wafer as seed. The CVT mass flux has been analyzed by theoretical calculations based on equilibrium thermodynamics and 1D diffusional mass transport. The crystal growth experimental results are in agreement with the theoretical predictions. Influence factors of Ga2O3 crystal growth, such as temperature distribution, amount of C as transport agent used, have also been discussed. Structural (XRD) and optical (Raman spectroscopy, photoluminescence spectrum) properties of the CVT-Ga2O3 crystal are presented. Project supported by the National Natural Science Foundation of China (Nos. 61474104, 61504131).

A molecular dynamics simulation of solvent effects on the crystal morphology of HMX.

PubMed

Duan, Xiaohui; Wei, Chunxue; Liu, Yonggang; Pei, Chonghua

2010-02-15

The solvent has a large effect on the crystal morphology of the organic explosive compound octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX, C(4)H(8)N(8)O(8)). The attachment energy calculations predict a growth morphology in vacuum dominated by (020), (011), (102 ), (111 ) and (100) crystal forms. Molecular dynamics simulations are performed for these crystal faces of HMX in contact with acetone solvent. A corrected attachment energy model, accounting for the surface chemistry and the associated topography (step structure) of the habit crystal plane, is applied to predict the morphological importance of a crystal surface in solvent. From the solvent-effected attachment energy calculations it follows that the (100) face becomes morphologically more important compared with that in vacuum, while the (020) and (102 ) are not visible at all. This agrees well with the observed experimental HMX morphology grown from the acetone solution.

Experimental and theoretical studies of the crystal structures of bis-isoxazole-bis-methylene dinitrate (BIDN) and bis-isoxazole tetramethylene tetranitrate (BITN) by x-ray crystallography and density functional theory

NASA Astrophysics Data System (ADS)

Taylor, Decarlos E.; Sausa, Rosario C.

2018-06-01

The determination of crystal structures plays an important role for model testing and validation, and understanding intra and intermolecular interactions that influence crystal packing. Here, we report the molecular structure of two recently synthesized energetic molecules, 3,3-bis-isoxazole-5,5‧-bis-methylene dinitrate (C8H6N4O8, BIDN) and bis-isoxazole tetramethylene tetranitrate (C10H8N6O14, BITN) determined by single crystal x-ray diffraction and solid state density functional theory (DFT). BIDN is composed of two planar alkyl nitrate groups (r.m.s deviation = 0.0004 (1) Å) bonded to two planar azole rings (r.m.s deviation = 0.001 (1) Å, whereas BITN is composed of four planar alkyl nitrate groups (average r.m.s deviation = 0.002 (1) Å) bonded to two planar azole rings (average r.m.s deviation = 0.002 (1) Å). The theoretical calculations predict very well the planarity of both the alkyl nitrate groups and rings for both compounds. Furthermore, they predict well the bond lengths and angles of both molecules with mean deviation values of 0.018 Å (BIDN) and 0.017 Å (BITN) and 0.481° (BIDN) and 0.747° (BITN). Overall, the DFT determined torsion angles agree well with those determined experimentally for both BIDN (average deviation = 1.139°) and BITN (average deviation = 0.604°). The theoretical cell constant values are in excellent agreement with those determined experimentally for both molecules, with the BIDN a cell value and β angle showing the largest deviation, 2.1% and -1.3%, respectively. Contacts between the atoms N and H dominate the intermolecular interactions of BIDN, whereas contacts involving the atoms O and H dominate the BITN intermolecular interactions. Electrostatic potential calculations at the B3LYP/6-31G* level reveal BIDN exhibits a lower sensitivity to impact compared to BITN.

Exploration on anion ordering, optical properties and electronic structure in K3WO3F3 elpasolite

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Isaenko, L. I.; Kesler, V. G.; Lin, Z. S.; Molokeev, M. S.; Yelisseyev, A. P.; Zhurkov, S. A.

2012-03-01

Room-temperature modification of potassium oxyfluorotungstate, G2-K3WO3F3, has been prepared by low-temperature chemical route and single crystal growth. Wide optical transparency range of 0.3-9.4 μm and forbidden band gap Eg=4.32 eV have been obtained for G2-K3WO3F3 crystal. Meanwhile, its electronic structure has been calculated with the first-principles calculations. The good agreement between the theorectical and experimental results have been achieved. Furthermore, G2-K3WO3F3 is predicted to possess the relatively large nonlinear optical coefficients.

Alkyltributylphosphonium chloride ionic liquids: synthesis, physicochemical properties and crystal structure.

PubMed

Adamová, Gabriela; Gardas, Ramesh L; Nieuwenhuyzen, Mark; Puga, Alberto V; Rebelo, Luís Paulo N; Robertson, Allan J; Seddon, Kenneth R

2012-07-21

A series of alkyltributylphosphonium chloride ionic liquids, prepared from tributylphosphine and the respective 1-chloroalkane, C(n)H(2n+1)Cl (where n = 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12 or 14), is reported. This work is a continuation of an extended series of tetraalkylphosphonium ionic liquids, where the focus is on the variability of n and its impact on the physical properties, such as melting points/glass transitions, thermal stability, density and viscosity. Experimental density and viscosity data were interpreted using QPSR and group contribution methods and the crystal structure of propyl(tributyl)phosphonium chloride is detailed.

Atomistic insights into the nanosecond long amorphization and crystallization cycle of nanoscale G e2S b2T e5 : An ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Branicio, Paulo S.; Bai, Kewu; Ramanarayan, H.; Wu, David T.; Sullivan, Michael B.; Srolovitz, David J.

2018-04-01

The complete process of amorphization and crystallization of the phase-change material G e2S b2T e5 is investigated using nanosecond ab initio molecular dynamics simulations. Varying the quench rate during the amorphization phase of the cycle results in the generation of a variety of structures from entirely crystallized (-0.45 K/ps) to entirely amorphized (-16 K/ps). The 1.5-ns annealing simulations indicate that the crystallization process depends strongly on both the annealing temperature and the initial amorphous structure. The presence of crystal precursors (square rings) in the amorphous matrix enhances nucleation/crystallization kinetics. The simulation data are used to construct a combined continuous-cooling-transformation (CCT) and temperature-time-transformation (TTT) diagram. The nose of the CCT-TTT diagram corresponds to the minimum time for the onset of homogenous crystallization and is located at 600 K and 70 ps. That corresponds to a critical cooling rate for amorphization of -4.5 K/ps. The results, in excellent agreement with experimental observations, suggest that a strategy that utilizes multiple quench rates and annealing temperatures may be used to effectively optimize the reversible switching speed and enable fast and energy-efficient phase-change memories.

Mechanical and structural model of fractal networks of fat crystals at low deformations.

PubMed

Narine, S S; Marangoni, A G

1999-12-01

Fat-crystal networks demonstrate viscoelastic behavior at very small deformations. A structural model of these networks is described and supported by polarized light and atomic-force microscopy. A mechanical model is described which allows the shear elastic modulus (G') of the system to be correlated with forces acting within the network. The fractal arrangement of the network at certain length scales is taken into consideration. It is assumed that the forces acting are due to van der Waals forces. The final expression for G' is related to the volume fraction of solid fat (Phi) via the mass fractal dimension (D) of the network, which agrees with the experimental verification of the scaling behavior of fat-crystal networks [S. S. Narine and A. G. Marangoni, Phys. Rev. E 59, 1908 (1999)]. G' was also found to be inversely proportional to the diameter of the primary particles (sigma approximately equal to 6 microm) within the network (microstructural elements) as well as to the diameter of the microstructures (xi approximately equal to 100 microm) and inversely proportional to the cube of the intermicrostructural element distance (d(0)). This formulation of the elastic modulus agrees well with experimental observations.

Electronic structure of LiGaS 2

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Isaenko, L. I.; Kesler, V. G.; Lobanov, S.; Huang, H.; Lin, Z. S.

2009-04-01

X-ray photoelectron spectroscopy (XPS) measurement has been performed to determine the valence band structure of LiGaS 2 crystals. The experimental measurement is compared with the electronic structure obtained from the density functional calculations. It is found that the Ga 3d states in the XPS spectrum are much higher than the calculated results. In order to eliminate this discrepancy, the LDA+ U method is employed and reasonable agreement is achieved. Further calculations show that the difference of the linear and nonlinear optical coefficients between LDA and LDA+ U calculations is negligibly small, indicating that the Ga 3d states are actually independent of the excited properties of LiGaS 2 crystals since they are located at a very deep position in the valence bands.

Electronic Structure of Energetic Molecules and Crystals Under Compression

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

Understanding how the electronic structure of energetic materials change under compression is important to elucidating mechanisms of shock-induced reactions and detonation. In this presentation, the electronic structure of prototypical energetic crystals are examined under high degrees of compression using ab initio quantum chemical calculations. The effects of compression on and interactions between the constituent molecules are examined in particular. The insights these results provide into previous experimental observations and theoretical predictions of energetic materials under high pressure are discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Allowing for crystalline structure effects in Geant4

DOE PAGES

Bagli, Enrico; Asai, Makoto; Dotti, Andrea; ...

2017-03-24

In recent years, the Geant4 toolkit for the Monte Carlo simulation of radiation with matter has seen large growth in its divers user community. A fundamental aspect of a successful physics experiment is the availability of a reliable and precise simulation code. Geant4 currently does not allow for the simulation of particle interactions with anything other than amorphous matter. To overcome this limitation, the GECO (GEant4 Crystal Objects) project developed a general framework for managing solid-state structures in the Geant4 kernel and validate it against experimental data. As a result, accounting for detailed geometrical structures allows, for example, simulation ofmore » diffraction from crystal planes or the channeling of charged particle.« less

Bis(tetraphenylarsonium) hexachloridozirconate(IV) acetonitrile tetrasolvate

DOE PAGES

Borjas, Rosendo; Mariappan Balasekaran, Samundeeswari; Poineau, Frederic

2018-04-06

The bis(tetraphenylarsonium) hexachloridozirconate(IV) salt, (AsPh 4 ) 2 [ZrCl 6 ] (Ph = C 6 H 5 ), was prepared more than 25 years ago [Esmadi & Sutcliffe (1991). Indian J. Chem. 30 A , 99–101], but its crystal structure was never reported. By following a similar experimental procedure, the compound was synthesized and its crystal structure was investigated as a acetonitrile tetrasolvate, (As(C 6 H 5 ) 4 ) 2 [ZrCl 6 ]·4CH 3 CN, by single-crystal X –ray diffraction. The [ZrCl 6 ] 2− anion adopts a slightly distorted octahedral coordination sphere, with Zr—Cl bond lengths of 2.4586 (6), 2.4723 (6),more » and 2.4818 (5) Å, and Cl—Zr—Cl angles ranging from 89.602 (19) to 90.397 (19)°.« less

Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

NASA Astrophysics Data System (ADS)

Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

2017-10-01

A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

Computer modelling of BaY2F8: defect structure, rare earth doping and optical behaviour

NASA Astrophysics Data System (ADS)

Amaral, J. B.; Couto Dos Santos, M. A.; Valerio, M. E. G.; Jackson, R. A.

2005-10-01

BaY2F8, when doped with rare earth elements, is a material of interest in the development of solid-state laser systems, especially for use in the infrared region. This paper presents the application of a computational technique, which combines atomistic modelling and crystal field calculations, in a study of rare earth doping of the material. Atomistic modelling is used to calculate the intrinsic defect structure and the symmetry and detailed geometry of the dopant ion-host lattice system, and this information is then used to calculate the crystal field parameters, which are an important indicator in assessing the optical behaviour of the dopant-crystal system. Energy levels are then calculated for the Dy3+-substituted material, and comparisons with the results of recent experimental work are made.

Bis(tetraphenylarsonium) hexachloridozirconate(IV) acetonitrile tetrasolvate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borjas, Rosendo; Mariappan Balasekaran, Samundeeswari; Poineau, Frederic

The bis(tetraphenylarsonium) hexachloridozirconate(IV) salt, (AsPh 4 ) 2 [ZrCl 6 ] (Ph = C 6 H 5 ), was prepared more than 25 years ago [Esmadi & Sutcliffe (1991). Indian J. Chem. 30 A , 99–101], but its crystal structure was never reported. By following a similar experimental procedure, the compound was synthesized and its crystal structure was investigated as a acetonitrile tetrasolvate, (As(C 6 H 5 ) 4 ) 2 [ZrCl 6 ]·4CH 3 CN, by single-crystal X –ray diffraction. The [ZrCl 6 ] 2− anion adopts a slightly distorted octahedral coordination sphere, with Zr—Cl bond lengths of 2.4586 (6), 2.4723 (6),more » and 2.4818 (5) Å, and Cl—Zr—Cl angles ranging from 89.602 (19) to 90.397 (19)°.« less

Process of negative-muon-induced formation of an ionized acceptor center ({sub μ}A){sup –} in crystals with the diamond structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belousov, Yu. M., E-mail: theorphys@phystech.edu

The formation of an ionized acceptor center by a negative muon in crystals with the diamond structure is considered. The negative muon entering a target is captured by a nucleus, forming a muonic atom {sub μ}A coupled to a lattice. The appearing radiation-induced defect has a significant electric dipole moment because of the violation of the local symmetry of the lattice and changes the phonon spectrum of the crystal. The ionized acceptor center is formed owing to the capture of an electron interacting with the electric dipole moment of the defect and with the radiation of a deformation-induced local-mode phonon.more » Upper and lower bounds of the formation rate of the ionized acceptor center in diamond, silicon, and germanium crystals are estimated. It is shown that the kinetics of the formation of the acceptor center should be taken into account when processing μSR experimental data.« less

Dynamic Properties of DNA-Programmable Nanoparticle Crystallization.

PubMed

Yu, Qiuyan; Zhang, Xuena; Hu, Yi; Zhang, Zhihao; Wang, Rong

2016-08-23

The dynamics of DNA hybridization is very important in DNA-programmable nanoparticle crystallization. Here, coarse-grained molecular dynamics is utilized to explore the structural and dynamic properties of DNA hybridizations for a self-complementary DNA-directed nanoparticle self-assembly system. The hexagonal close-packed (HCP) and close-packed face-centered cubic (FCC) ordered structures are identified for the systems of different grafted DNA chains per nanoparticle, which are in good agreement with the experimental results. Most importantly, the dynamic crystallization processes of DNA hybridizations are elucidated by virtue of the mean square displacement, the percentage of hybridizations, and the lifetime of DNA bonds. The lifetime can be modeled by the DNA dehybridization, which has an exponential form. The lifetime of DNA bonds closely depends on the temperature. A suitable temperature for the DNA-nanoparticle crystallization is obtained in the work. Moreover, a too large volume fraction hinders the self-assembly process due to steric effects. This work provides some essential information for future design of nanomaterials.

Computational crystallization

PubMed Central

Altan, Irem; Charbonneau, Patrick; Snell, Edward H.

2016-01-01

Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed. PMID:26792536

Multi-temperature study of potassium uridine-5'-monophosphate: electron density distribution and anharmonic motion modelling.

PubMed

Jarzembska, Katarzyna N; Řlepokura, Katarzyna; Kamiński, Radosław; Gutmann, Matthias J; Dominiak, Paulina M; Woźniak, Krzysztof

2017-08-01

Uridine, a nucleoside formed of a uracil fragment attached to a ribose ring via a β-N1-glycosidic bond, is one of the four basic components of ribonucleic acid. Here a new anhydrous structure and experimental charge density distribution analysis of a uridine-5'-monophosphate potassium salt, K(UMPH), is reported. The studied case constitutes the very first structure of a 5'-nucleotide potassium salt according to the Cambridge Structural Database. The excellent crystal quality allowed the collection of charge density data at various temperatures, i.e. 10, 100, 200 and 300 K on one single crystal. Crystal structure and charge density data were analysed thoroughly in the context of related literature-reported examples. Detailed analysis of the charge density distribution revealed elevated anharmonic motion of part of the uracil ring moiety relatively weakly interacting with the neighbouring species. The effect was manifested by alternate positive and negative residual density patterns observed for these atoms, which `disappear' at low temperature. It also occurred that the potassium cation, quite uniformly coordinated by seven O atoms from all molecular fragments of the UMPH - anion, including the O atom from the ribofuranose ring, can be treated as spherical in the charge density model which was supported by theoretical calculations. Apart from the predominant electrostatic interactions, four relatively strong hydrogen bond types further support the stability of the crystal structure. This results in a compact and quite uniform structure (in all directions) of the studied crystal, as opposed to similar cases with layered architecture reported in the literature.

Magnetic and crystal structures of the honeycomb lattice Na2IrO3 and single layer Sr2IrO4

NASA Astrophysics Data System (ADS)

Ye, Feng

2013-03-01

5 d based iridates have recently attracted great attention due to the large spin-orbit coupling (SOC). It is now recognized that the SOC that competes with other relevant energies, particularly the on-site Coulomb interaction U, and have driven novel electronic and magnetic phases. Combining single crystal neutron and x-ray diffractions, we have investigated the magnetic and crystal structures of the honeycomb lattice Na2IrO3. The system orders magnetically below 18.1 K with Ir4+ ions forming zigzag spin chains within the layered honeycomb network with ordered moment of 0.22 μB /Ir site. Such a configuration sharply contrasts the Neel or stripe states proposed in the Kitaev-Heisenberg model. The structure refinement reveals that the Ir atoms form nearly ideal 2D honeycomb lattice while the IrO6 octahedra experience a trigonal distortion that is critical to the ground state. The results of this study provide much-needed experimental insights into the magnetic and crystal structure crucial to the understanding of the exotic magnetic order and possible topological characteristics in the 5 d-electron based honeycomb lattice. Neutron diffraction experiments are also performed to investigate the magnetic and crystal structure of the single layer iridate Sr2IrO4, where new structural information and spin order are obtained that is not available from previous neutron powder diffraction measurement. This work was sponsored in part by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy.

Spanning the scales of mechanical metamaterials using time domain simulations in transformed crystals, graphene flakes and structured soils

NASA Astrophysics Data System (ADS)

Aznavourian, Ronald; Puvirajesinghe, Tania M.; Brûlé, Stéphane; Enoch, Stefan; Guenneau, Sébastien

2017-11-01

We begin with a brief historical survey of discoveries of quasi-crystals and graphene, and then introduce the concept of transformation crystallography, which consists of the application of geometric transforms to periodic structures. We consider motifs with three-fold, four-fold and six-fold symmetries according to the crystallographic restriction theorem. Furthermore, we define motifs with five-fold symmetry such as quasi-crystals generated by a cut-and-projection method from periodic structures in higher-dimensional space. We analyze elastic wave propagation in the transformed crystals and (Penrose-type) quasi-crystals with the finite difference time domain freeware SimSonic. We consider geometric transforms underpinning the design of seismic cloaks with square, circular, elliptical and peanut shapes in the context of honeycomb crystals that can be viewed as scaled-up versions of graphene. Interestingly, the use of morphing techniques leads to the design of cloaks with interpolated geometries reminiscent of Victor Vasarely’s artwork. Employing the case of transformed graphene-like (honeycomb) structures allows one to draw useful analogies between large-scale seismic metamaterials such as soils structured with columns of concrete or grout with soil and nanoscale biochemical metamaterials. We further identify similarities in designs of cloaks for elastodynamic and hydrodynamic waves and cloaks for diffusion (heat or mass) processes, as these are underpinned by geometric transforms. Experimental data extracted from field test analysis of soil structured with boreholes demonstrates the application of crystallography to large scale phononic crystals, coined as seismic metamaterials, as they might exhibit low frequency stop bands. This brings us to the outlook of mechanical metamaterials, with control of phonon emission in graphene through extreme anisotropy, attenuation of vibrations of suspension bridges via low frequency stop bands and the concept of transformed meta-cities. We conclude that these novel materials hold strong applications spanning different disciplines or across different scales from biophysics to geophysics.

Experimental Observation of Bulk Liquid Water Structure in ``No Man's Land''

NASA Astrophysics Data System (ADS)

Sellberg, Jonas; McQueen, Trevor; Huang, Congcong; Loh, Duane; Laksmono, Hartawan; Sierra, Raymond; Hampton, Christina; Starodub, Dmitri; Deponte, Daniel; Martin, Andrew; Barty, Anton; Wikfeldt, Thor; Schlesinger, Daniel; Pettersson, Lars; Beye, Martin; Nordlund, Dennis; Weiss, Thomas; Feldkamp, Jan; Caronna, Chiara; Seibert, Marvin; Messerschmidt, Marc; Williams, Garth; Boutet, Sebastien; Bogan, Michael; Nilsson, Anders

2013-03-01

Experiments on pure bulk water below about 235 K have so far been difficult: water crystallization occurs very rapidly below the homogeneous nucleation temperature of 232 K and above 160 K, leading to a ``no man's land'' devoid of experimental results regarding the structure. Here, we demonstrate a new, general experimental approach to study the structure of liquid states at supercooled conditions below their limit of homogeneous nucleation. We use femtosecond x-ray pulses generated by the LCLS x-ray laser to probe evaporatively cooled droplets of supercooled bulk water and find experimental evidence for the existence of metastable bulk liquid water down to temperatures of 223 K in the previously largely unexplored ``no man's land''. We acknoweledge NSF (CHE-0809324), Office of Basic Energy Sciences, and the Swedish Research Council for financial support.

Anisotropic crystal deformation measurements determined using powder X-ray diffraction and a new in situ compression stage.

PubMed

Haware, Rahul V; Kim, Paul; Ruffino, Lauren; Nimi, Brian; Fadrowsky, Catherine; Doyle, Michael; Boerrigter, Stephan X M; Cuitino, Alberto; Morris, Ken

2011-10-14

This report addresses the development of experimental and computational estimations of the anisotropic elastic moduli (EM) of single crystals to aid in the a priori (i.e., starting with the crystal structure) prediction of the trend as a function of the direction of applied stress. Experimentally EM values in the normal direction to the X-, Y- and Z-planes of block shaped aspirin and acetaminophen crystals were determined using data generated by the newly designed compression stage housed in our powder X-ray diffractometer. Computational estimations of EM were made using the applicable modules in Material Studio 5.5. The measured EM values normal to the (100), (020) and (002) planes of aspirin, and (20-1), (020) and (001) planes of acetaminophen crystals by both methods succeeded in detected the anisotropic behavior. However, disparity in the relative values between measured EM values by different techniques was observed. This may be attributed to deformation sources other than lattice compression including inelastic processes such as local failure and plasticity as well as deformation at the crystal-probe interfaces due to crystal surface roughness (asperities). The trend of the ratio of the values from the respective methods showed reasonable agreement and promise for the technique. The present approach demonstrated the suitability of the compression stage to determine and predict anisotropic EM of subjected small molecular organic crystals. Copyright © 2011 Elsevier B.V. All rights reserved.

Structural phase transition in monolayer MoTe2 driven by electrostatic doping

NASA Astrophysics Data System (ADS)

Wang, Ying; Xiao, Jun; Zhu, Hanyu; Li, Yao; Alsaid, Yousif; Fong, King Yan; Zhou, Yao; Wang, Siqi; Shi, Wu; Wang, Yuan; Zettl, Alex; Reed, Evan J.; Zhang, Xiang

2017-10-01

Monolayers of transition-metal dichalcogenides (TMDs) exhibit numerous crystal phases with distinct structures, symmetries and physical properties. Exploring the physics of transitions between these different structural phases in two dimensions may provide a means of switching material properties, with implications for potential applications. Structural phase transitions in TMDs have so far been induced by thermal or chemical means; purely electrostatic control over crystal phases through electrostatic doping was recently proposed as a theoretical possibility, but has not yet been realized. Here we report the experimental demonstration of an electrostatic-doping-driven phase transition between the hexagonal and monoclinic phases of monolayer molybdenum ditelluride (MoTe2). We find that the phase transition shows a hysteretic loop in Raman spectra, and can be reversed by increasing or decreasing the gate voltage. We also combine second-harmonic generation spectroscopy with polarization-resolved Raman spectroscopy to show that the induced monoclinic phase preserves the crystal orientation of the original hexagonal phase. Moreover, this structural phase transition occurs simultaneously across the whole sample. This electrostatic-doping control of structural phase transition opens up new possibilities for developing phase-change devices based on atomically thin membranes.

Effects of scandium substitution on the crystal structure and luminescence properties of LuBO{sub 3}: Ce{sup 3+}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yuntao, E-mail: caswyt@hotmail.com; Ren, Guohao, E-mail: rgh@mail.sic.ac.cn; Ding, Dongzhou

2012-10-15

The calcite phase of LuBO{sub 3} and ScBO{sub 3} polycrystalline powders were synthesized by solid state reaction method, and the Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce (x=0.2, 0.5, 0.7) single crystals were grown by the Czochralski method. A large composition deviation between the initial polycrystalline powders and final single crystal was confirmed by electron probe micro-analysis. Raman spectroscopy revealed that moderate lattice disorder was induced by scandium substitution. However, based on the single crystal X-ray study, we finally concluded that the crystal structure of lutetium scandium orthoborate still crystallized in the rhombohedral system belonging to R3{sup -}c. Furthermore, the relationship between themore » energies of the five 5d levels of Ce{sup 3+} and the crystalline environment was revealed. The total redshift, total crystal field splitting, and centroid shift of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce{sup 3+} were calculated based on their VUV excitation spectra. The variations trend of these observed spectroscopic parameters was in accordance with the predicted ones. - Graphical abstract: The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. The relationship between the energies of the five Ce{sup 3+} 5d levels and the crystalline environment is established. Highlights: Black-Right-Pointing-Pointer Moderate lattice disorder is induced by scandium doping. Black-Right-Pointing-Pointer The crystal structure of Lu{sub 1-x}Sc{sub x}BO{sub 3}:Ce is rhombohedral system with R3{sup -}c space group. Black-Right-Pointing-Pointer Relationship between energies of Ce{sup 3+} 5d levels and crystalline environment is established. Black-Right-Pointing-Pointer The spectroscopic parameters are experimentally and theoretically calculated.« less

Photonic crystal fiber modal interferometer based on thin-core-fiber mode exciter.

PubMed

Miao, Yinping; Ma, Xixi; Wu, Jixuan; Song, Binbin; Zhang, Hao; Liu, Bo; Yao, Jianquan

2015-11-10

A thin-core-fiber excited photonic crystal fiber modal interferometer has been proposed and experimentally demonstrated. By employing a thin-core fiber as the mode exciter, both of the core and cladding modes propagate in the photonic crystal fiber and interfere with each other. The experimental results show that the transmission dips corresponding to different-order modes have various strain responses with opposite shift directions. The strain sensitivity could be improved to 58.57  pm/με for the applied strain from 0 to 491 με by utilizing the wavelength interval between the dips with opposite shift directions. Moreover, due to the pure silica property of the employed photonic crystal fiber, the proposed fiber modal interferometer exhibits a low-temperature sensitivity of about 0.56  pm/°C within a temperature range from 26.4°C (room temperature) to 70°C. Additionally, the proposed fiber modal interferometer has several advantages, such as good stability, compact structure, and simple fabrication. Therefore, it is more applicable for strain measurement with reducing temperature cross-sensitivity.

Growth of zinc selenide single crystals by physical vapor transport in microgravity

NASA Technical Reports Server (NTRS)

Rosenberger, Franz

1993-01-01

The goals of this research were the optimization of growth parameters for large (20 mm diameter and length) zinc selenide single crystals with low structural defect density, and the development of a 3-D numerical model for the transport rates to be expected in physical vapor transport under a given set of thermal and geometrical boundary conditions, in order to provide guidance for an advantageous conduct of the growth experiments. In the crystal growth studies, it was decided to exclusively apply the Effusive Ampoule PVT technique (EAPVT) to the growth of ZnSe. In this technique, the accumulation of transport-limiting gaseous components at the growing crystal is suppressed by continuous effusion to vacuum of part of the vapor contents. This is achieved through calibrated leaks in one of the ground joints of the ampoule. Regarding the PVT transport rates, a 3-D spectral code was modified. After introduction of the proper boundary conditions and subroutines for the composition-dependent transport properties, the code reproduced the experimentally determined transport rates for the two cases with strongest convective flux contributions to within the experimental and numerical error.

EPR study of a gamma-irradiated (2-hydroxyethyl)triphenylphosphonium chloride single crystal

NASA Astrophysics Data System (ADS)

Karakaş, E.; Türkkan, E.; Dereli, Ö.; Sayιn, Ü.; Tapramaz, R.

2011-12-01

In this study, gamma-irradiated single crystals of (2-hydroxyethyl)triphenylphosphonium chloride [CH2CH2OH P(C6H5)3Cl] were investigated with electron paramagnetic resonance (EPR) spectroscopy at room temperature for different orientations in the magnetic field. The single crystals were irradiated with a 60Co-γ-ray source at 0.818 kGy/h for about 36 h. Taking the chemical structure and the experimental spectra of the irradiated single crystal of the title compound into consideration, a paramagnetic species was produced with the unpaired electron delocalized around 31P and several 1H nuclei. The anisotropic hyperfine values due to the 31P nucleus, slightly anisotropic hyperfine values due to the 1H nuclei and the g-tensor of the radical were measured from the spectra. Depending on the molecular structure and measured parameters, three possible radicals were modeled using the B3LYP/6-31+G(d) level of density-functional theory, and EPR parameters were calculated for modeled radicals using the B3LYP/TZVP method/basis set combination. The calculated hyperfine coupling constants were found to be in good agreement with the observed EPR parameters. The experimental and theoretically simulated spectra for each of the three crystallographic axes were well matched with one of the modeled radicals (discussed in the text). We thus identified the radical C˙H2CH2 P(C 6H5)3 Cl as a paramagnetic species produced in a single crystal of the title compound in two magnetically distinct sites. The experimental g-factor and hyperfine coupling constants of the radical were found to be anisotropic, with the isotropic values g iso = 2.0032, ? G, ? G, ? G and ? G for site 1 and g iso=2.0031, ? G, ? G ? G and ? G for site 2.

Protein Crystallization: Specific Phenomena and General Insights on Crystallization Kinetics

NASA Technical Reports Server (NTRS)

Rosenberger, F.

1998-01-01

Experimental and simulation studies of the nucleation and growth kinetics of proteins have revealed phenomena that are specific for macromolecular crystallization, and others that provide a more detailed understanding of solution crystallization in general. The more specific phenomena, which include metastable liquid-liquid phase separations and gelation prior to solid nucleation, are due to the small ratio of the intermolecular interaction-range to the size of molecules involved. The apparently more generally applicable mechanisms include the cascade-like formation of macrosteps, as an intrinsic morphological instability that roots in the coupled bulk transport and nonlinear interface kinetics in systems with mixed growth rate control. Analyses of this nonlinear response provide (a) criteria for the choice of bulk transport conditions to minimize structural defect formation, and (b) indications that the "slow" protein crystallization kinetics stems from the mutual retardation of growth steps.

Crystallization and preliminary X-ray diffraction analysis of the lectin from Dioclea rostrata Benth seeds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delatorre, Plínio; Departamento de Ciências Biológicas, Universidade Regional do Cariri, Crato, CE 63195-000; Nascimento, Kyria Santiago

2006-02-01

D. rostrata lectin was crystallized by hanging-drop vapor diffusion. The crystal belongs to the orthorhombic space group I222 and diffracted to 1.87 Å resolution. Lectins from the Diocleinae subtribe (Leguminosae) are highly similar proteins that promote various biological activities with distinctly differing potencies. The structural basis for this experimental data is not yet fully understood. Dioclea rostrata lectin was purified and crystallized by hanging-drop vapour diffusion at 293 K. The crystal belongs to the orthorhombic space group I222, with unit-cell parameters a = 61.51, b = 88.22, c = 87.76 Å. Assuming the presence of one monomer per asymmetric unit,more » the solvent content was estimated to be about 47.9%. A complete data set was collected at 1.87 Å resolution.« less

Phase behavior of binary and polydisperse suspensions of compressible microgels controlled by selective particle deswelling

NASA Astrophysics Data System (ADS)

Scotti, A.; Gasser, U.; Herman, E. S.; Han, Jun; Menzel, A.; Lyon, L. A.; Fernandez-Nieves, A.

2017-09-01

We investigate the phase behavior of suspensions of poly(N -isopropylacrylamide) (pNIPAM) microgels with either bimodal or polydisperse size distribution. We observe a shift of the fluid-crystal transition to higher concentrations depending on the polydispersity or the fraction of large particles in suspension. Crystallization is observed up to polydispersities as high as 18.5%, and up to a number fraction of large particles of 29% in bidisperse suspensions. The crystal structure is random hexagonal close-packed as in monodisperse pNIPAM microgel suspensions. We explain our experimental results by considering the effect of bound counterions. Above a critical particle concentration, these cause deswelling of the largest microgels, which are the softest, changing the size distribution of the suspension and enabling crystal formation in conditions where incompressible particles would not crystallize.

Probing vacancy-type free-volume defects in Li2B4O7 single crystal by positron annihilation lifetime spectroscopy

NASA Astrophysics Data System (ADS)

Shpotyuk, O.; Adamiv, V.; Teslyuk, I.; Ingram, A.; Demchenko, P.

2018-01-01

Vacancy-type free-volume defects in lithium tetraborate Li2B4O7 single crystal, grown by the Czochralski technique, are probed with positron annihilation spectroscopy in the lifetime measuring mode. The experimental positron lifetime spectrum is reconstructed within the three-component fitting, involving channels of positron and positronium Ps trapping, as well as within the two-component fitting with a positronium-compensating source input. Structural configurations of the most efficient positron traps are considered using the crystallographic specificity of lithium tetraborate with the main accent on cation-type vacancies. Possible channels of positron trapping are visualized using the electronic structure calculations with density functional theory at the basis of structural parameters proper to Li2B4O7. Spatially-extended positron-trapping complexes involving singly-ionized lithium vacancies, with character lifetime close to 0.32 ns, are responsible for positron trapping in the nominally undoped lithium tetraborate Li2B4O7 crystal.

A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition.

PubMed

Woutersen, Sander; Ensing, Bernd; Hilbers, Michiel; Zhao, Zuofeng; Angell, C Austen

2018-03-09

Simulations and theory suggest that the thermodynamic anomalies of water may be related to a phase transition between two supercooled liquid states, but so far this phase transition has not been observed experimentally because of preemptive ice crystallization. We used calorimetry, infrared spectroscopy, and molecular dynamics simulations to investigate a water-rich hydrazinium trifluoroacetate solution in which the local hydrogen bond structure surrounding a water molecule resembles that in neat water at elevated pressure, but which does not crystallize upon cooling. Instead, this solution underwent a sharp, reversible phase transition between two homogeneous liquid states. The hydrogen-bond structures of these two states are similar to those established for high- and low-density amorphous (HDA and LDA) water. Such structural similarity supports theories that predict a similar sharp transition in pure water under pressure if ice crystallization could be suppressed. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate*

PubMed Central

Knihtila, Ryan; Holzapfel, Genevieve; Weiss, Kevin; Meilleur, Flora; Mattos, Carla

2015-01-01

RAS GTPase is a prototype for nucleotide-binding proteins that function by cycling between GTP and GDP, with hydrogen atoms playing an important role in the GTP hydrolysis mechanism. It is one of the most well studied proteins in the superfamily of small GTPases, which has representatives in a wide range of cellular functions. These proteins share a GTP-binding pocket with highly conserved motifs that promote hydrolysis to GDP. The neutron crystal structure of RAS presented here strongly supports a protonated γ-phosphate at physiological pH. This counters the notion that the phosphate groups of GTP are fully deprotonated at the start of the hydrolysis reaction, which has colored the interpretation of experimental and computational data in studies of the hydrolysis mechanism. The neutron crystal structure presented here puts in question our understanding of the pre-catalytic state associated with the hydrolysis reaction central to the function of RAS and other GTPases. PMID:26515069

Neutron crystal structure of RAS GTPase puts in question the protonation state of the GTP γ-phosphate

DOE PAGES

Knihtila, Ryan; Holzapfel, Genevieve; Weiss, Kevin; ...

2015-10-29

RAS GTPase is a prototype for nucleotide-binding proteins that function by cycling between GTP and GDP, with hydrogen atoms playing an important role in the GTP hydrolysis mechanism. It is one of the most well studied proteins in the superfamily of small GTPases, which has representatives in a wide range of cellular functions. These proteins share a GTP-binding pocket with highly conserved motifs that promote hydrolysis to GDP. The neutron crystal structure of RAS presented here strongly supports a protonated gamma-phosphate at physiological pH. This counters the notion that the phosphate groups of GTP are fully deprotonated at the startmore » of the hydrolysis reaction, which has colored the interpretation of experimental and computational data in studies of the hydrolysis mechanism. As a result, the neutron crystal structure presented here puts in question our understanding of the pre-catalytic state associated with the hydrolysis reaction central to the function of RAS and other GTPases.« less

Structure of free radicals in irradiated acetyl-L-leucine single crystals at 77 K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almanov, G.A.; Bogdanchikov, G.A.; Usov, O.M.

1988-09-01

By using the EPR method, two types of radicals are observed, which are formed in acetyl-L-leucine single crystals irradiated at 77K. These are alkyl type radicals (CH/sub 3/)/sub 2/CCH/sub 2/CH(NHCOCH/sub 3/)COOH and peptide group radicals. When the crystals are defrozen to room temperatures, the radicals of the second type disappear without formation of paramagnetic particles. Two possible structures of the peptide group radicals were studied by the INDO method. On defreezing to room temperature, the alkyl group radical is retained, while the peptide radical disappears without formation of paramagnetic particles. For the protonated form of the anion-radical, a better agreementmore » is observed between the theoretically calculated and the experimentally obtained HFI constants. The quantum chemical analysis of the possible structures of the peptide group radicals indicates that the formation of the protonated form of the anion-radical is energetically favorable.« less

Field-Effects in Large Axial Ratio Liquid Crystals

NASA Astrophysics Data System (ADS)

Lonberg, Franklin J.

This paper consists of an introduction and four chapters, the abstracts of which are presented below. Chapter 2. The subject of this chapter is the dynamic periodic structures which are observed in the twist Frederiks transition. It is found that, for fields above a material dependent level, a transient periodic distortion is observed. The wave vector is parallel to the unperturbed director and increases with increasing field. A theoretical model and experimental data are presented. Chapter 3. The subject of this chapter is the discovery of a new equilibrium structure in the splay Frederiks transition. Experimental observation has shown that the imposition of a field, just above the critical strength, produces a periodic distortion in the polymer liquid crystal PBG. This periodic state is not dynamic in origin but it is a true ground state. An analysis of the energy of a liquid crystal, in the splay Frederiks transition geometry, shows that in materials with K(,1)/K(,3) > 3.3 the periodic distortion will have a lower critical field than the uniform distortion. Chapter 4. The subject of this chapter is the dynamics of the bend Frederiks transition in large axial ratio nematics. Experimental evidence is presented to show that there is a distortion mode which occurs at field greater than 2H(,c), which is very fast and does not grow exponentially. An analysis of the equations of motion shows that a mode with wave length half that of the static equilibrium mode will have these properties. Chapter 5. The bend Frederiks transition is use to show that the bend and splay elastic constants are linear in concentration in PBG. Interpretation of this result is made in connection with models of the elastic energy in liquid crystal made of semi-flexible partiles.

Synthesis, Crystal and Electronic Structures, and Optical Properties of (CH 3NH 3) 2CdX 4 (X = Cl, Br, I)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roccanova, Rachel; Ming, Wenmei; Whiteside, Vincent R.

Here, we report the synthesis, crystal and electronic structures, as well as optical properties of the hybrid organic–inorganic compounds MA 2CdX 4 (MA = CH 3NH 3; X = Cl, Br, I). MA 2CdI 4 is a new compound, whereas, for MA 2CdCl 4 and MA 2CdBr 4, structural investigations have already been conducted but electronic structures and optical properties are reported here for the first time. Single crystals were grown through slow evaporation of MA 2CdX 4 solutions with optimized conditions yielding mm-sized colorless (X = Cl, Br) and pale yellow (X = I) crystals. Single crystal and variablemore » temperature powder X-ray diffraction measurements suggest that MA 2CdCl 4 forms a 2D layered perovskite structure and has two structural transitions at 283 and 173 K. In contrast, MA 2CdBr 4 and MA 2CdI 4 adopt 0D K 2SO 4-derived crystal structures based on isolated CdX 4 tetrahedra and show no phase transitions down to 20 K. The contrasting crystal structures and chemical compositions in the MA 2CdX 4 family impact their air stabilities, investigated for the first time in this work; MA 2CdCl 4 is air-stable, whereas MA 2CdBr 4 and MA 2CdI 4 partially decompose when left in air. Optical absorption measurements suggest that MA 2CdX 4 have large optical band gaps above 3.9 eV. Room temperature photoluminescence spectra of MA 2CdX 4 yield broad peaks in the 375–955 nm range with full width at half-maximum values up to 208 nm. These PL peaks are tentatively assigned to self-trapped excitons in MA 2CdX 4 following the crystal and electronic structure considerations. The bands around the Fermi level have small dispersions, which is indicative of high charge localization with significant exciton binding energies in MA 2CdX 4. On the basis of our combined experimental and computational results, MA 2CdX 4 and related compounds may be of interest for white-light-emitting phosphors and scintillator applications.« less

Synthesis, Crystal and Electronic Structures, and Optical Properties of (CH 3NH 3) 2CdX 4 (X = Cl, Br, I)

DOE PAGES

Roccanova, Rachel; Ming, Wenmei; Whiteside, Vincent R.; ...

2017-11-02

Here, we report the synthesis, crystal and electronic structures, as well as optical properties of the hybrid organic–inorganic compounds MA 2CdX 4 (MA = CH 3NH 3; X = Cl, Br, I). MA 2CdI 4 is a new compound, whereas, for MA 2CdCl 4 and MA 2CdBr 4, structural investigations have already been conducted but electronic structures and optical properties are reported here for the first time. Single crystals were grown through slow evaporation of MA 2CdX 4 solutions with optimized conditions yielding mm-sized colorless (X = Cl, Br) and pale yellow (X = I) crystals. Single crystal and variablemore » temperature powder X-ray diffraction measurements suggest that MA 2CdCl 4 forms a 2D layered perovskite structure and has two structural transitions at 283 and 173 K. In contrast, MA 2CdBr 4 and MA 2CdI 4 adopt 0D K 2SO 4-derived crystal structures based on isolated CdX 4 tetrahedra and show no phase transitions down to 20 K. The contrasting crystal structures and chemical compositions in the MA 2CdX 4 family impact their air stabilities, investigated for the first time in this work; MA 2CdCl 4 is air-stable, whereas MA 2CdBr 4 and MA 2CdI 4 partially decompose when left in air. Optical absorption measurements suggest that MA 2CdX 4 have large optical band gaps above 3.9 eV. Room temperature photoluminescence spectra of MA 2CdX 4 yield broad peaks in the 375–955 nm range with full width at half-maximum values up to 208 nm. These PL peaks are tentatively assigned to self-trapped excitons in MA 2CdX 4 following the crystal and electronic structure considerations. The bands around the Fermi level have small dispersions, which is indicative of high charge localization with significant exciton binding energies in MA 2CdX 4. On the basis of our combined experimental and computational results, MA 2CdX 4 and related compounds may be of interest for white-light-emitting phosphors and scintillator applications.« less

Structural investigation of (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid: X-ray crystal structure, spectroscopy and DFT

NASA Astrophysics Data System (ADS)

Venkatesan, Perumal; Rajakannan, Venkatachalam; Venkataramanan, Natarajan S.; Ilangovan, Andivelu; Sundius, Tom; Thamotharan, Subbiah

2016-09-01

The title compound, (2E)-2-(ethoxycarbonyl)-3-[(4-methoxyphenyl)amino]prop-2-enoic acid is characterized by means of X-ray crystallography, spectroscopic methods and quantum chemical calculations. The title compound crystallizes in centrosymmetric space group P21/c. Moreover, the crystal structure is primarily stabilized through intramolecular Nsbnd H⋯O and Osbnd H⋯O and intermolecular Nsbnd H⋯O and Csbnd H⋯O interactions along with carbonyl⋯carbonyl and Csbnd H⋯C contacts. These intermolecular interactions are analysed and quantified by using Hirshfeld surface analysis, PIXEL energy, NBO, AIM and DFT calculations. The overall lattice energies of the title and parent compounds suggest that the title compound is stabilized by a 4.5 kcal mol-1 higher energy than the parent compound. The additional stabilization force comes from the methoxy substitution on the title molecule, which is evident since the methoxy group is involved in the intermolecular Csbnd H⋯O interaction as an acceptor. The vibrational modes of the interacting groups are investigated using both experimental and theoretical FT-IR and FT-Raman spectra. The experimental and theoretical UV-Vis spectra agree well. The time dependent DFT spectra show that the ligand-to-ligand charge transfer is responsible for the intense absorbance of the compound.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Thermal desorption of metals from tungsten single crystal surfaces

NASA Technical Reports Server (NTRS)

Bauer, E.; Bonczek, F.; Poppa, H.; Todd, G.

1975-01-01

After a short review of experimental methods used to determine desorption energies and frequencies the assumptions underlying the theoretical analysis of experimental data are discussed. Recent experimental results on the flash desorption of Cu, Ag, and Au from clean, well characterized W (110) and (100) surfaces are presented and analyzed in detail with respect to the coverage dependence. The results obtained clearly reveal the limitations of previous analytical methods and of the experimental technique per se (such as structure and phase changes below and in the temperature region in which desorption occurs).

Defect types and room-temperature ferromagnetism in undoped rutile TiO2 single crystals

NASA Astrophysics Data System (ADS)

Li, Dong-Xiang; Qin, Xiu-Bo; Zheng, Li-Rong; Li, Yu-Xiao; Cao, Xing-Zhong; Li, Zhuo-Xin; Yang, Jing; Wang, Bao-Yi

2013-03-01

Room-temperature ferromagnetism has been experimentally observed in annealed rutile TiO2 single crystals when a magnetic field is applied parallel to the sample plane. By combining X-ray absorption near the edge structure spectrum and positron annihilation lifetime spectroscopy, Ti3+—VO defect complexes (or clusters) have been identified in annealed crystals at a high vacuum. We elucidate that the unpaired 3d electrons in Ti3+ ions provide the observed room-temperature ferromagnetism. In addition, excess oxygen ions in the TiO2 lattice could induce a number of Ti vacancies which obviously increase magnetic moments.

Infrared photonic bandgap materials and structures

NASA Astrophysics Data System (ADS)

Sundaram, S. K.; Keller, P. E.; Riley, B. J.; Martinez, J. E.; Johnson, B. R.; Allen, P. J.; Saraf, L. V.; Anheier, N. C., Jr.; Liau, F.

2006-02-01

Three-dimensional periodic dielectric structure can be described by band theory, analogous to electron waves in a crystal. Photonic band gap (PBG) structures were introduced in 1987. The PBG is an energy band in which optical modes, spontaneous emission, and zero-point fluctuations are all absent. It was first theoretically predicted that a three-dimensional photonic crystal could have a complete band gap. E. Yablonovitch built the first three-dimensional photonic crystal (Yablonovite) on microwave length scale, with a complete PBG. In nature, photonic crystals occur as semiprecious opal and the microscopic structures on the wings of some tropical butterflies, which are repeating structures (PBG structure/materials) that inhibit the propagation of some frequencies of light. Pacific Northwest National Laboratory (PNNL) has been developing tunable (between 3.5 and 16 μm) quantum cascade lasers (QCL), chalcogenides, and all other components for an integrated approach to chemical sensing. We have made significant progress in modeling and fabrication of infrared photonic band gap (PBG) materials and structures. We modeled several 2-D designs and defect configurations. Transmission spectra were computed by the Finite Difference Time Domain Method (with FullWAVE TM). The band gaps were computed by the Plane Wave Expansion Method (with BandSOLVE TM). The modeled designs and defects were compared and the best design was identified. On the experimental front, chalcogenide glasses were used as the starting materials. As IIS 3, a common chalcogenide, is an important infrared (IR) transparent material with a variety of potential applications such as IR sensors, waveguides, and photonic crystals. Wet-chemical lithography has been extended to PBG fabrication and challenges identified. An overview of results and challenges will be presented.

Quantification of photoinduced bending of dynamic molecular crystals: from macroscopic strain to kinetic constants and activation energies.

PubMed

Chizhik, Stanislav; Sidelnikov, Anatoly; Zakharov, Boris; Naumov, Panče; Boldyreva, Elena

2018-02-28

Photomechanically reconfigurable elastic single crystals are the key elements for contactless, timely controllable and spatially resolved transduction of light into work from the nanoscale to the macroscale. The deformation in such single-crystal actuators is observed and usually attributed to anisotropy in their structure induced by the external stimulus. Yet, the actual intrinsic and external factors that affect the mechanical response remain poorly understood, and the lack of rigorous models stands as the main impediment towards benchmarking of these materials against each other and with much better developed soft actuators based on polymers, liquid crystals and elastomers. Here, experimental approaches for precise measurement of macroscopic strain in a single crystal bent by means of a solid-state transformation induced by light are developed and used to extract the related temperature-dependent kinetic parameters. The experimental results are compared against an overarching mathematical model based on the combined consideration of light transport, chemical transformation and elastic deformation that does not require fitting of any empirical information. It is demonstrated that for a thermally reversible photoreactive bending crystal, the kinetic constants of the forward (photochemical) reaction and the reverse (thermal) reaction, as well as their temperature dependence, can be extracted with high accuracy. The improved kinematic model of crystal bending takes into account the feedback effect, which is often neglected but becomes increasingly important at the late stages of the photochemical reaction in a single crystal. The results provide the most rigorous and exact mathematical description of photoinduced bending of a single crystal to date.

Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Mary X.; Brodin, Jeffrey D.; Millan, Jaime A.

Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the co-assembly of DNA-conjugated proteins and spherical gold 2 nanoparticles (AuNPs) as a model system, we explore how steric repulsion between non-complementary, neighboring DNA-NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that by changing factors related to NP repulsion, two structurally distinctmore » outcomes can be achieved. When steric repulsion between DNA-AuNPs is significantly greater than that between DNA-proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA-hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar and the structural outcome can be adjusted using the density of DNA duplexes on DNA-AuNPs and by screening the Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.« less

Crystal structure determination of new antimitotic agent bis(p-fluorobenzyl)trisulfide.

PubMed

An, Haoyun; Hu, Xiurong; Gu, Jianming; Chen, Linshen; Xu, Weiming; Mo, Xiaopeng; Xu, Wanhong; Wang, Xiaobo; Xu, Xiao

2008-01-01

The purpose of this research was to investigate the physical characteristics and crystalline structure of bis(p-fluorobenzyl)trisulfide, a new anti-tumor agent. Methods used included X-ray single crystal diffraction, X-ray powder diffraction (XRPD), Fourier-transform infrared (FT-IR) spectroscopy, differential scanning calorimetric (DSC) and thermogravimetric (TG) analyses. The findings obtained with X-ray single crystal diffraction showed that a monoclinic unit cell was a = 12.266(1) A, b = 4.7757(4) A, c = 25.510(1) A, beta = 104.25(1) degrees ; cell volume = 1,448.4(2) A(3), Z = 4, and space group C2/c. The XRPD studies of the four crystalline samples, obtained by recrystallization from four different solvents, indicated that they had the same diffraction patterns. The diffraction pattern stimulated from the crystal structure data is in excellent agreement with the experimental results. In addition, the identical FT-IR spectra of the four crystalline samples revealed absorption bands corresponding to S-S and C-S stretching as well as the characteristic aromatic substitution. Five percent weight loss at 163.3 degrees C was observed when TG was used to study the decomposition process in the temperature range of 20-200 degrees C. DSC also allowed for the determination of onset temperatures at 60.4(1)-60.7(3) degrees C and peak temperatures at 62.1(3)-62.4(3) degrees C for the four crystalline samples studied. The results verified that the single crystal structure shared the same crystal form with the four crystalline samples investigated.

Density functional theory determination of structural and electronic properties of struvite.

PubMed

Romanowski, Zbigniew; Kempisty, Paweł; Prywer, Jolanta; Krukowski, Stanisław; Torzewska, Agnieszka

2010-07-29

Crystallographic structure, total energy, electronic structure, and the most important elastic properties of struvite, NH(4)MgPO(4).6H(2)O, the main component of infectious urinary stones, are presented. The calculations were performed using ab initio full-electron calculations within the density functional theory-generalized gradient approximation (DFT-GGA) framework. The obtained crystallographic symmetry and the calculated lattice parameters and also the elastic constants are in good agreement with the experimental data. The elastic properties are essential for establishing an optimal response of urinary stones during shock-wave lithotripsy. The calculated electronic charge distribution confirms the layered structure of the struvite crystals. The polar character of the crystal, well-known from crystal growth experiments, was also confirmed by the magnitude of spontaneous polarization which was obtained from direct determination of the electrical dipole density. The calculated value of spontaneous polarization is equal to -8.8 microC cm(-2). This feature may play a key role in struvite crystallization, electrically binding the charged active impurities and other active species, and consequently determining urinary stone formation. We also present the results of our own experiment of the mineralization of struvite induced to growth by Proteus bacteria which are mainly isolated from infectious urinary stones.

Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

NASA Astrophysics Data System (ADS)

Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

2013-01-01

The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

Crystal structure, electronic structure, and photoluminescent properties of SrMoO{sub 4}:Tb{sup 3+} phosphors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Sung Wook; Moon, Byung Kee; Jeong, Jung Hyun, E-mail: jhjeong@pknu.ac.kr

2015-10-15

Highlights: • SrMoO{sub 4}:Tb{sup 3+} phosphor samples were synthesized at different temperatures. • The crystal and electronic structures, and luminescence properties were studied. • The excitation peak shifts to red with increasing the sintering temperature. • The luminescence mechanism of SrMoO{sub 4}:Tb{sup 3+} was suggested. - Abstract: The experimental and theoretical studies of the optical properties of SrMoO{sub 4}:Tb{sup 3+} phosphors were carried out. The structural, optical, and electronical properties of the phosphors were systematically studied. The phosphor samples were crystallized at different temperatures via a sol–gel method. Excitation spectra of SrMoO{sub 4}:Tb{sup 3+} powder samples exhibited gradual red shiftmore » and luminescent intensity changed with increasing the sintering temperature. Such spectral changes depend strongly on the crystallographic properties such as lattice parameters and crystallinity. The shift of the excitation spectra is mainly ascribed to the covalent bond interaction between Mo−O bonds. An energy band model was demonstrated to describe the luminescence mechanism in the material.« less

X-ray crystal structure and theoretical study of a new dinuclear Cu(II) complex with two different geometry centers bridged with an oxo group

NASA Astrophysics Data System (ADS)

Golbedaghi, Reza; Azimi, Saeid; Molaei, Atefeh; Hatami, Masoud; Notash, Behrouz

2017-10-01

A new Schiff base ligand HL, 1,3-bis(2-((Z)-(2-aminoethylimino)methyl)phenoxy)ethylene di amine, has been synthesized from the reaction of a new aldehyde and ethylenediamine. After preparation the Schiff base, a new dinuclear Cu(II) complex with two different geometry for each metal ion was synthesized. Single crystal X-ray structure analysis of the complex Cu(II) showed that the complex is binuclear and all nitrogen and oxygen atoms of ligand (N4O3) are coordinated to two Cu(II) center ions. The crystal structure studying shows, a perchlorate ion has been coordinated to the two Cu(II) metal centers as bridged and another perchlorate coordinated to the one of Cu(II) ion as terminal. However, two interesting structures square pyramidal and distorted octahedral Cu(II) ions are bridged asymmetrically by a perchlorate ion and oxygen of hydroxyl group of Schiff base ligand. In addition, we had a theoretical study to have a comparison of experimental and theoretical results we determined the HOMO and LUMO orbitals.

Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination.

PubMed

Avilov, A; Kuligin, K; Nicolopoulos, S; Nickolskiy, M; Boulahya, K; Portillo, J; Lepeshov, G; Sobolev, B; Collette, J P; Martin, N; Robins, A C; Fischione, P

2007-01-01

We have developed a new fast electron diffractometer working with high dynamic range and linearity for crystal structure determinations. Electron diffraction (ED) patterns can be scanned serially in front of a Faraday cage detector; the total measurement time for several hundred ED reflections can be tens of seconds having high statistical accuracy for all measured intensities (1-2%). This new tool can be installed to any type of TEM without any column modification and is linked to a specially developed electron beam precession "Spinning Star" system. Precession of the electron beam (Vincent-Midgley technique) reduces dynamical effects allowing also use of accurate intensities for crystal structure analysis. We describe the technical characteristics of this new tool together with the first experimental results. Accurate measurement of electron diffraction intensities by electron diffractometer opens new possibilities not only for revealing unknown structures, but also for electrostatic potential determination and chemical bonding investigation. As an example, we present detailed atomic bonding information of CaF(2) as revealed for the first time by precise electron diffractometry.

Structural and electron charge density studies of a nonlinear optical compound 4,4 di-methyl amino cyano biphenyl

NASA Astrophysics Data System (ADS)

Naima, Boubegra; Abdelkader, Chouaih; Mokhtaria, Drissi; Fodil, Hamzaoui

2014-01-01

The 4,4 dimethyl amino cyano biphenyl crystal (DMACB) is characterized by its nonlinear activity. The intra molecular charge transfer of this molecule results mainly from the electronic transmission of the electro-acceptor (cyano) and electro-donor (di-methyl-amino) groups. An accurate electron density distribution around the molecule has been calculated based on a high-resolution X-ray diffraction study. The data were collected at 123 K using graphite-monochromated Mo K α radiation to sin(β)/λ = 1.24 Å-1. The integrated intensities of 13796 reflections were measured and reduced to 6501 independent reflections with I >= 3σ(I). The crystal structure was refined using the experimental model of Hansen and Coppens (1978). The crystal structure has been validated and deposited at the Cambridge Crystallographic Data Centre with the deposition number CCDC 876507. In this article, we present the thermal motion and the structural analysis obtained from the least-square refinement based on F2 and the electron density distribution obtained from the multipolar model.

Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

NASA Astrophysics Data System (ADS)

Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

2017-02-01

Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators

PubMed Central

Moeder, Katelyn E.; Ho, Chris M. W.; Zimmerman, Maxwell I.; Frederick, Thomas E.; Bowman, Gregory R.

2017-01-01

Allosteric drugs, which bind to proteins in regions other than their main ligand-binding or active sites, make it possible to target proteins considered “undruggable” and to develop new therapies that circumvent existing resistance. Despite growing interest in allosteric drug discovery, rational design is limited by a lack of sufficient structural information about alternative binding sites in proteins. Previously, we used Markov State Models (MSMs) to identify such “cryptic pockets,” and here we describe a method for identifying compounds that bind in these cryptic pockets and modulate enzyme activity. Experimental tests validate our approach by revealing both an inhibitor and two activators of TEM β-lactamase (TEM). To identify hits, a library of compounds is first virtually screened against either the crystal structure of a known cryptic pocket or an ensemble of structures containing the same cryptic pocket that is extracted from an MSM. Hit compounds are then screened experimentally and characterized kinetically in individual assays. We identify three hits, one inhibitor and two activators, demonstrating that screening for binding to allosteric sites can result in both positive and negative modulation. The hit compounds have modest effects on TEM activity, but all have higher affinities than previously identified inhibitors, which bind the same cryptic pocket but were found, by chance, via a computational screen targeting the active site. Site-directed mutagenesis of key contact residues predicted by the docking models is used to confirm that the compounds bind in the cryptic pocket as intended. Because hit compounds are identified from docking against both the crystal structure and structures from the MSM, this platform should prove suitable for many proteins, particularly targets whose crystal structures lack obvious druggable pockets, and for identifying both inhibitory and activating small-molecule modulators. PMID:28570708

Structural, vibrational and NMR spectroscopic investigations of newly synthesized 3-((ethylthio)(4-nitrophenyl)methyl)-1H-indole

NASA Astrophysics Data System (ADS)

Bhat, Sheeraz Ahmad; Dar, Ajaz A.; Ahmad, Shabbir; Khan, Abu T.

2017-10-01

The compound 3-((ethylthio)(4-nitrophenyl)methyl)-1H-indole was synthesized at room temperature through one-pot three-component reaction from 1H-indole, 4-nitrobenzaldehyde, and ethanethiol using hydrated ferric sulfate as a Lewis acid catalyst. The structure was characterised by single crystal XRD, FTIR (4000-400 cm-1), FT-Raman (4000-50 cm-1) and 1H and 13C NMR analysis. The compound crystallizes in the monoclinic with volume 3238.3(9) Å3. The experimental vibrational data find the theoretical support through anharmonic frequency calculations using DFT/B3LYP level of theory in combination with 6-31G(d,p) basis set. It is observed that the predicted geometry well reproduces the XRD structural parameters. The experimental 1H and 13C NMR spectra in CDCl3 solvent and the simulated spectra predicted using gauge independent atomic orbital (GIAO) approach are also found in agreement with each other. HOMO-LUMO, MEP, atomic charges and various other thermodynamic and NLO properties of the title molecule are also reported in this paper.

Three-dimensional photonic crystals as intermediate filter for thin-film tandem solar cells

NASA Astrophysics Data System (ADS)

Bielawny, Andreas; Miclea, Paul T.; Wehrspohn, Ralf B.; Lee, Seung-Mo; Knez, Mato; Rockstuhl, Carsten; Lisca, Marian; Lederer, Falk L.; Carius, Reinhard

2008-04-01

The concept of a 3D photonic crystal structure as diffractive and spectrally selective intermediate filter within 'micromorphous' (a-Si/μc-Si) tandem solar cells has been investigated numerically and experimentally. Our device aims for the enhancement of the optical pathway of incident light within the amorphous silicon top cell in its spectral region of low absorption. From our previous simulations, we expect a significant improvement of the tandem cell efficiency of about absolutely 1.3%. This increases the efficiency for a typical a-Si / μc-Si tandem cell from 11.1% to 12.4%, as a result of the optical current-matching of the two junctions. We suggest as wavelength-selective optical element a 3D-structured optical thin-film, prepared by self-organized artificial opal templates and replicated with atomic layer deposition. The resulting samples are highly periodic thin-film inverted opals made of conducting and transparent zinc-oxide. We describe the fabrication processes and compare experimental data on the optical properties in reflection and transmission with our simulations and photonic band structure calculations.

Role of Molecular Structure on X-ray Diffraction in Thermotropic Uniaxial and Biaxial Nematic Liquid Crystal Phases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-08-27

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Role of Molecular Structure on X-ray Diffraction in Uniaxial and Biaxial Phases of Thermotropic Liquid Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-04-29

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Lunar and Planetary Science XXXV: Effects of Impacts: Shock and Awe

NASA Technical Reports Server (NTRS)

Kyte, F. T.; Koeberl, C.

2004-01-01

This document discusses the following topics: Zircon as a Shock Indicator in Impactites of Drill Core Yaxcopoil-1, Chicxulub Impact Structure, Mexico; Experimental Investigation of Shock Effects in a Metapelitic Granulite; Experimental Reproduction of Shock Veins in Single-Crystal Minerals; Post-Shock Crystal-Plastic Processes in Quartz from Crystalline Target Rocks of the Charlevoix Impact Structure; Shock Reequilibration of Fluid Inclusions; How Does Tektite Glass Lose Its Water?; Assessing the Role of Anhydrite in the KT Mass Extinction: Hints from Shock-loading Experiments; A Mineralogical and Geochemical Study of the Nonmarine Permian/Triassic Boundary in the Southern Karoo Basin, South Africa; Extraterrestrial Chromium in the Permian-Triassic Boundary at Graphite Peak, Antarctica; Magnetic Fe,Si,Al-rich Impact Spherules from the P-T Boundary Layer at Graphite Peak, Antarctica; A Newly Recognized Late Archean Impact Spherule Layer in the Reivilo Formation, Griqualand West Basin, South Africa; Initial Cr-Isotopic and Iridium Measurements of Concentrates from Late Eocene Cpx-Spherule Deposits; An Ordinary Chondrite Impactor Composition for the Bosumtwi Impact Structure, Ghana, West Africa: Discussion of Siderophile Element Contents and Os and Cr Isotope Data.

Investigation on the growth and characterization of 4-aminobenzophenone single crystal by the vertical dynamic gradient freeze technique

NASA Astrophysics Data System (ADS)

Prabhakaran, SP.; Ramesh Babu, R.; Sukumar, M.; Bhagavannarayana, G.; Ramamurthi, K.

2014-03-01

Growth of bulk single crystal of 4-Aminobenzophenone (4-ABP) from the vertical dynamic gradient freeze (VDGF) setup designed with eight zone furnace was investigated. The experimental parameters for the growth of 4-ABP single crystal with respect to the design of VDGF setup are discussed. The eight zones were used to generate multiple temperature gradients over the furnace, and video imaging system helped to capture the real time growth and solid-liquid interface. 4-ABP single crystal with the size of 18 mm diameter and 40 mm length was grown from this investigation. Structural and optical quality of grown crystal was examined by high resolution X-ray diffraction and UV-visible spectral analysis, respectively and the blue emission was also confirmed from the photoluminescence spectrum. Microhardness number of the crystal was estimated at different loads using Vicker's microhardness tester. The size and quality of single crystal grown from the present investigation are compared with the vertical Bridgman grown 4-ABP.

Transient quantum coherent effects in the acetylene-filled hollow-core photonic crystal fiber

NASA Astrophysics Data System (ADS)

Stepanov, S.; Rodríguez Casillas, N.; Ocegueda Miramontes, M.; Hernández Hernández, E.

2017-02-01

Low-pressure acetylene in the hollow-core photonic crystal structure fibers is an excellent medium for the room-temperature investigation of the coherent quantum effects in communication wavelength region. Pulsed excitation enables observation of new coherent phenomena like optical nutation or photon echo and evaluation of important temporal characteristics of the light-molecule interactions. We also report original experimental results on the pulsed excitation of the electromagnetically induced transparency in co- and counter-propagation configurations.

Light-assisted, templated self-assembly using a photonic-crystal slab.

PubMed

Jaquay, Eric; Martínez, Luis Javier; Mejia, Camilo A; Povinelli, Michelle L

2013-05-08

We experimentally demonstrate the technique of light-assisted, templated self-assembly (LATS). We excite a guided-resonance mode of a photonic-crystal slab with 1.55 μm laser light to create an array of optical traps. We demonstrate assembly of a square lattice of 520 nm diameter polystyrene particles spaced by 860 nm. Our results demonstrate how LATS can be used to fabricate reconfigurable structures with symmetries different from traditional colloidal self-assembly, which is limited by free energetic constraints.

High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

NASA Astrophysics Data System (ADS)

Snigireva, I.; Snigirev, A.

2013-10-01

We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals.

Structure and energetics of high index Fe, Al, Cu and Ni surfaces using equivalent crystal theory

NASA Technical Reports Server (NTRS)

Rodriguez, Agustin M.; Bozzolo, Guillermo; Ferrante, John

1993-01-01

Equivalent crystal theory (ECT) is applied to the study of multilayer relaxations and surface energies of high-index faces of Fe, Al, Ni, and Cu. Changes in interplanar spacing as well as registry of planes close to the surface and the ensuing surface energies changes are discussed in reference to available experimental data and other theoretical calculations. Since ECT is a semiempirical method, the dependence of the results on the variation of the input used was investigated.

Theoretical and Experimental Studies of the Electro-Optic Effect: Toward a Microscopic Understanding.

DTIC Science & Technology

1981-08-01

electro - optic effect is investigated both theoretically and experimentally. The theoretical approach is based upon W.A. Harrison’s ’Bond-Orbital Model’. The separate electronic and lattice contributions to the second-order, electro - optic susceptibility are examined within the context of this model and formulae which can accommodate any crystal structure are presented. In addition, a method for estimating the lattice response to a low frequency (dc) electric field is outlined. Finally, experimental measurements of the electro -

Twice electric field poling for engineering multiperiodic Hex-PPLN microstructures

NASA Astrophysics Data System (ADS)

Pagliarulo, Vito; Gennari, Oriella; Rega, Romina; Mecozzi, Laura; Grilli, Simonetta; Ferraro, Pietro

2018-05-01

Satellite bulk ferroelectric domains were observed everywhere around the larger main inverted ferroelectric domains when a Twice Electric Field Poling (TEFP) process is applied on a z-cut lithium niobate substrate. TEFP approach can be very advantageous for engineering multiperiodic poled microstructures in ferroelectrics. In fact, it is very difficult in the experimental practice to avoid underpoling and/or overpoling when structures with different sizes are requested in the same crystal. TEFP was applied to photoresist patterned crystal with 100 μm period and then a second EP step, with a ten-times smaller periodicity of 10 μm, was accomplished on the same sample. The intriguing fact is that the shorter 10 μm pattern disappeared everywhere except that around the larger satellite ferroelectric domains. The formation of this double-periodicity in the reversed ferroelectric domains occurs very easily and in repeatedly way. We have experimentally investigated the formation of such HePPLN structures by an interference microscopy in digital holography (DH) modality. The reported results demonstrate the possibility of fabricating multi-periodic structures and open the way to investigate the possibility to achieve hierarchical PPLN structures by multiple subsequent electric poling processes.

Vibrational signatures in the THz spectrum of 1,3-DNB: A first-principles and experimental study

NASA Astrophysics Data System (ADS)

Ahmed, Towfiq; Azad, Abul K.; Chellappa, Raja; Higginbotham-Duque, Amanda; Dattelbaum, Dana M.; Zhu, Jian-Xin; Moore, David; Graf, Matthias J.

2016-05-01

Understanding the fundamental processes of light-matter interaction is important for detection of explosives and other energetic materials, which are active in the infrared and terahertz (THz) region. We report a comprehensive study on electronic and vibrational lattice properties of structurally similar 1,3-dinitrobenzene (1,3-DNB) crystals through first-principles electronic structure calculations and THz spectroscopy measurements on polycrystalline samples. Starting from reported x-ray crystal structures, we use density-functional theory (DFT) with periodic boundary conditions to optimize the structures and perform linear response calculations of the vibrational properties at zero phonon momentum. The theoretically identified normal modes agree qualitatively with those obtained experimentally in a frequency range up to 2.5 THz and quantitatively at much higher frequencies. The latter frequencies are set by intra-molecular forces. Our results suggest that van der Waals dispersion forces need to be included to improve the agreement between theory and experiment in the THz region, which is dominated by intermolecular modes and sensitive to details in the DFT calculation. An improved comparison is needed to assess and distinguish between intra- and intermolecular vibrational modes characteristic of energetic materials.

Investigation of phononic crystals for dispersive surface acoustic wave ozone sensors

NASA Astrophysics Data System (ADS)

Westafer, Ryan S.

The object of this research was to investigate dispersion in surface phononic crystals (PnCs) for application to a newly developed passive surface acoustic wave (SAW) ozone sensor. Frequency band gaps and slow sound already have been reported for PnC lattice structures. Such engineered structures are often advertised to reduce loss, increase sensitivity, and reduce device size. However, these advances have not yet been realized in the context of surface acoustic wave sensors. In early work, we computed SAW dispersion in patterned surface structures and we confirmed that our finite element computations of SAW dispersion in thin films and in one dimensional surface PnC structures agree with experimental results obtained by laser probe techniques. We analyzed the computations to guide device design in terms of sensitivity and joint spectral operating point. Next we conducted simulations and experiments to determine sensitivity and limit of detection for more conventional dispersive SAW devices and PnC sensors. Finally, we conducted extensive ozone detection trials on passive reflection mode SAW devices, using distinct components of the time dispersed response to compensate for the effect of temperature. The experimental work revealed that the devices may be used for dosimetry applications over periods of several days.

A structural analysis of small vapor-deposited 'multiply twinned' gold particles

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Heinemann, K.; Yacaman, M. J.; Poppa, H.

1979-01-01

High resolution selected zone dark field, Bragg reflection imaging and weak beam dark field techniques of transmission electron microscopy were used to determine the structure of small gold particles vapor deposited on NaCl substrates. Attention was focused on the analysis of those particles in the 50-150 A range that have pentagonal or hexagonal bright field profiles. These particles have been previously described as multiply twinned crystallites composed of face-centered cubic tetrahedra. The experimental evidence of the present studies can be interpreted on the assumption that the particle structure is a regular icosahedron or decahedron for the hexagonal or the pentagonal particles respectively. The icosahedron is a multiply twinned rhombohedral crystal and the decahedron is a multiply twinned body-centered orthorhombic crystal, each of which constitutes a slight distortion from the face-centered cubic structure.

A study of tantalum pentoxide Ta 2O 5 structures up to 28 GPa

DOE PAGES

Stavrou, Elissaios; Zaug, Joseph M.; Bastea, Sorin; ...

2017-05-02

In this study, tantalum pentoxide Ta 2O 5 with the orthorhombic L-Ta 2O 5 structure has been experimentally studied up to 28.3 GPa (at ambient temperature) using synchrotron angle-dispersive powder X-ray diffraction (XRD). The ambient pressure phase remains stable up to 25 GPa where with increased pressure a crystalline to amorphous phase transition occurs. A detailed equation of state (EOS), including pressure dependent lattice parameters, is reported. The results of this study were compared with a previous high-pressure XRD study by Li et al. A clear discrepancy between the ambient-pressure crystal structures and, consequently, the reported EOSs between the twomore » studies was revealed. Finally, he origin of this discrepancy is attributed to two different crystal structures used to index the XRD patterns.« less

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

A combined crystallographic, thermal, Raman and computational study on polymorphism and phase transition in 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

PubMed

Suárez, Sebastián; Manzano, Veronica E; Fantoni, Adolfo C; Halac, Emilia; Baggio, Ricardo; Cukiernik, Fabio D

2017-12-01

The crystal structure of the triclinic polymorph of 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C 14 H 20 O 3 , differs markedly from that of the orthorhombic polymorph [Manzano et al. (2015). Acta Cryst. C71, 1022-1027]. The two molecular structures are alike with respect to their bond lengths and angles, but differ in their spatial arrangement. This gives rise to quite different packing schemes, even if built up by similar chains having the hydroxy-ethanone O-H...O hydrogen-bond synthon in common. Both phases were found to be related by a first-order thermally driven phase transformation at 338-340 K, which is discussed in detail. The relative stabilities of both polymorphs are explained on the basis of both the noncovalent interactions operating in each structure and quantum chemical calculations. The polymorphic phase transition has also been studied experimentally by means of differential scanning calorimetry (DSC) experiments, conducted on individual single crystals, Raman spectroscopy and controlled heating under a microscope of individual single crystals, which were further characterized by powder and single-crystal X-ray diffraction.

Crystal structure, spectroscopic study, photoluminescent properties and DFT calculations of the 2-guanidinobenzimidazolium dichloride and dibromide monohydrate salts

NASA Astrophysics Data System (ADS)

Hassen, S.; Chebbi, H.; Zid, M. F.; Arfaoui, Y.

2018-09-01

Two organic salts compounds C8H13Cl2N5O(1) and C8H13Br2N5O(2) were prepared by slow evaporation at room temperature and characterized through single-crystal X-ray diffraction, photoluminescence, IR and UV-Vis diffuse reflectance spectroscopy (UV/DRS) from which the optical properties were determined. The asymmetric unit of (1) and (2) consists of a discrete guanidinobenzimidazolium, two halide anions X- (X = Cl, Br) and one crystallization water molecule. The crystal structures of the two title salts are stabilized by Nsbnd H … X, Osbnd H … X, Nsbnd H⋯O and Csbnd H … X hydrogen bonds. Moreover, the protonated 2-guanidobenzimidazole shows a π-π interaction adding extra stability to the three-dimensional architecture. The ground state geometries of the two compounds were optimized using density functional theory (DFT) at the 6-311+G(2d, 2p) level of theory. In order to study the excited states, time-depending density functional theory calculations were performed on the optimized structures at the same level of theory. The calculated electronic absorption and infrared spectra were in good agreement with the experimental ones.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheligovskaya, E. A., E-mail: lmm@phyche.ac.ru

Structural mechanisms are proposed for experimentally observed phase transitions between crystalline modifications of aqueous ice, Ih and II, as well as II and Ic. It is known that the Ih–II transition occurs with the conservation of large structural units (hexagonal channels) common for these ices. It is shown that the Ih → II transition may occur with the conservation of 5/6 of all hydrogen bonds in crystal, including all hydrogen bonds in the retained channels (3/4 of the total number of bonds in crystal) and 1/3 of the bonds between these channels (1/12 of the total number). The transformation ofmore » other hydrogen bonds between the retained channels leads to the occurrence of proton order in ice II. A structural mechanism is proposed to explain the transformation of single crystals of ice Ih either into single crystals of ice II or into crystalline twins of ice II with c axes rotated by 180° with respect to each other, which is often observed at the Ih → II transition. It is established that up to 7/12 of all hydrogen bonds are retained at the irreversible cooperative II → Ic transition.« less

Steady distribution structure of point defects near crystal-melt interface under pulling stop of CZ Si crystal

NASA Astrophysics Data System (ADS)

Abe, T.; Takahashi, T.; Shirai, K.

2017-02-01

In order to reveal a steady distribution structure of point defects of no growing Si on the solid-liquid interface, the crystals were grown at a high pulling rate, which Vs becomes predominant, and the pulling was suddenly stopped. After restoring the variations of the crystal by the pulling-stop, the crystals were then left in prolonged contact with the melt. Finally, the crystals were detached and rapidly cooled to freeze point defects and then a distribution of the point defects of the as-grown crystals was observed. As a result, a dislocation loop (DL) region, which is formed by the aggregation of interstitials (Is), was formed over the solid-liquid interface and was surrounded with a Vs-and-Is-free recombination region (Rc-region), although the entire crystals had been Vs rich in the beginning. It was also revealed that the crystal on the solid-liquid interface after the prolonged contact with the melt can partially have a Rc-region to be directly in contact with the melt, unlike a defect distribution of a solid-liquid interface that has been growing. This experimental result contradicts a hypothesis of Voronkov's diffusion model, which always assumes the equilibrium concentrations of Vs and Is as the boundary condition for distribution of point defects on the growth interface. The results were disscussed from a qualitative point of view of temperature distribution and thermal stress by the pulling-stop.

Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist

NASA Astrophysics Data System (ADS)

Marmolejo-Valencia, A. F.; Martínez-Mayorga, K.

2017-05-01

Modulation of opioid receptors is the primary choice for pain management and structural information studies have gained new horizons with the recently available X-ray crystal structures. Herkinorin is one of the most remarkable salvinorin A derivative with high affinity for the mu opioid receptor, moderate selectivity and lack of nitrogen atoms on its structure. Surprisingly, binding models for herkinorin are lacking. In this work, we explore binding models of herkinorin using automated docking, molecular dynamics simulations, free energy calculations and available experimental information. Our herkinorin D-ICM-1 binding model predicted a binding free energy of -11.52 ± 1.14 kcal mol-1 by alchemical free energy estimations, which is close to the experimental values -10.91 ± 0.2 and -10.80 ± 0.05 kcal mol-1 and is in agreement with experimental structural information. Specifically, D-ICM-1 molecular dynamics simulations showed a water-mediated interaction between D-ICM-1 and the amino acid H2976.52, this interaction coincides with the co-crystallized ligands. Another relevant interaction, with N1272.63, allowed to rationalize herkinorin's selectivity to mu over delta opioid receptors. Our suggested binding model for herkinorin is in agreement with this and additional experimental data. The most remarkable observation derived from our D-ICM-1 model is that herkinorin reaches an allosteric sodium ion binding site near N1503.35. Key interactions in that region appear relevant for the lack of β-arrestin recruitment by herkinorin. This interaction is key for downstream signaling pathways involved in the development of side effects, such as tolerance. Future SAR studies and medicinal chemistry efforts will benefit from the structural information presented in this work.

The MORPHEUS II protein crystallization screen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorrec, Fabrice, E-mail: fgorrec@mrc-lmb.cam.ac.uk

2015-06-27

MORPHEUS II is a 96-condition initial crystallization screen formulated de novo. The screen incorporates reagents selected from the Protein Data Bank to yield crystals that are not observed in traditional conditions. In addition, the formulation facilitates the optimization and cryoprotection of crystals. High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected frommore » the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.« less

Development of a ReaxFF reactive force field for ammonium nitrate and application to shock compression and thermal decomposition.

PubMed

Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P

2014-02-27

We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings.