Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

PubMed

McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

2009-11-17

Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

PubMed

Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

2016-02-26

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

PubMed

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

Solution Structures of Mycobacterium tuberculosis Thioredoxin C and Models of the Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

PubMed Central

Olson, Andrew L.; Neumann, Terrence S.; Cai, Sheng; Sem, Daniel S.

2012-01-01

Here we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared to the solution structure. Based on these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function. PMID:23229911

[Crystal structure of SMU.2055 protein from Streptococcus mutans and its small molecule inhibitors design and selection].

PubMed

Xiaodan, Chen; Xiurong, Zhan; Xinyu, Wu; Chunyan, Zhao; Wanghong, Zhao

2015-04-01

The aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied. The three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures. The crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected. Protein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model.

PubMed

Gabriëlse, Alexander; Löwen, Hartmut; Smallenburg, Frank

2017-11-07

In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO) lattices not previously considered for the square shoulder model.

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

PubMed

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

2017-02-14

Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

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

Sabin, Charles; Plevka, Pavel, E-mail: pavel.plevka@ceitec.muni.cz

Molecular replacement and noncrystallographic symmetry averaging were used to detwin a data set affected by perfect hemihedral twinning. The noncrystallographic symmetry averaging of the electron-density map corrected errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of themore » domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C{sup α} atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.« less

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

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

PubMed

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

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

How to tackle protein structural data from solution and solid state: An integrated approach.

PubMed

Carlon, Azzurra; Ravera, Enrico; Andrałojć, Witold; Parigi, Giacomo; Murshudov, Garib N; Luchinat, Claudio

2016-02-01

Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule. Copyright © 2016 Elsevier B.V. All rights reserved.

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Modelling sodium cobaltate by mapping onto magnetic Ising model

NASA Astrophysics Data System (ADS)

Gemperline, Patrick; Morris, David Jonathan Pryce

Fast Ion conductors are a class of crystals that are frequently used as battery materials, especially in smart phones, laptops, and other portable devices. Sodium Cobalt Oxide, NaxCoO2, falls into this class of crystals, but is unique because it possesses the ability to act as a thermoelectric material and a superconductor at different concentrations of Na+. The crystal lattice is mapped onto an Ising Magnetic Spin model and a Monte-Carol Simulation is used to find the most energetically favorable configuration of spins. This spin configuration is mapped back to the crystal lattice resulting in the most stable crystal structure of Sodium Cobalt Oxide at various concentrations. Knowing the atomic structures of the crystals will aid in the research of the materials capabilities and the possible uses of the material commercially. Ohio Supercomputer Center. 1987. Ohio Supercomputer Center. Columbus OH: Ohio Supercomputer Center. and the John Hauck Foundation.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Raman, AFM and SNOM high resolution imaging of carotene crystals in a model carrot cell system.

PubMed

Rygula, Anna; Oleszkiewicz, Tomasz; Grzebelus, Ewa; Pacia, Marta Z; Baranska, Malgorzata; Baranski, Rafal

2018-05-15

Three non-destructive and complementary techniques, Raman imaging, Atomic Force Microscopy and Scanning Near-field Optical Microscopy were used simultaneously to show for the first time chemical and structural differences of carotenoid crystals. Spectroscopic and microscopic scanning probe measurements were applied to the released crystals or to crystals accumulated in a unique, carotenoids rich callus tissue growing in vitro that is considered as a new model system for plant carotenoid research. Three distinct morphological crystal types of various carotenoid composition were identified, a needle-like, rhomboidal and helical. Raman imaging using 532 and 488 nm excitation lines provided evidence that the needle-like and rhomboidal crystals had similar carotenoid composition and that they were composed mainly of β-carotene accompanied by α-carotene. However, the presence of α-carotene was not identified in the helical crystals, which had the characteristic spatial structure. AFM measurements of crystals identified by Raman imaging revealed the crystal topography and showed the needle-like and rhomboidal crystals were planar but they differed in all three dimensions. Combining SNOM and Raman imaging enabled indication of carotenoid rich structures and visualised their distribution in the cell. The morphology of identified subcellular structures was characteristic for crystalline, membraneous and tubular chromoplasts that are plant organelles responsible for carotenoid accumulation in cells. Copyright © 2018 Elsevier B.V. All rights reserved.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

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

Zhou, X. Edward; Gao, Xiang; Barty, Anton

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE PAGES

Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

2016-04-12

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

Gaia: automated quality assessment of protein structure models.

PubMed

Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V

2011-08-15

Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures. In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement. We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures. dokh@unc.edu Supplementary data are available at Bioinformatics online.

MAIN software for density averaging, model building, structure refinement and validation

PubMed Central

Turk, Dušan

2013-01-01

MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms. PMID:23897458

Thermal crystallization mechanism of silk fibroin protein

NASA Astrophysics Data System (ADS)

Hu, Xiao

In this thesis, the thermal crystallization mechanism of silk fibroin protein from Bombyx mori silkworm, was treated as a model for the general study of protein based materials, combining theories from both biophysics and polymer physics fields. A systematic and scientific path way to model the dynamic beta-sheet crystallization process of silk fibroin protein was presented in the following sequence: (1) The crystallinity, fractions of secondary structures, and phase compositions in silk fibroin proteins at any transition stage were determined. Two experimental methods, Fourier transform infrared spectroscopy (FTIR) with Fourier self-deconvolution, and specific reversing heat capacity, were used together for the first time for modeling the static structures and phases in the silk fibroin proteins. The protein secondary structure fractions during the crystallization were quantitatively determined. The possibility of existence of a "rigid amorphous phase" in silk protein was also discussed. (2) The function of bound water during the crystallization process of silk fibroin was studied using heat capacity, and used to build a silk-water dynamic crystallization model. The fundamental concepts and thermal properties of silk fibroin with/without bound water were discussed. Results show that intermolecular bound water molecules, acting as a plasticizer, will cause silk to display a water-induced glass transition around 80°C. During heating, water is lost, and the change of the microenvironment in the silk fibroin chains induces a mesophase prior to thermal crystallization. Real time FTIR during heating and isothermal holding above Tg show the tyrosine side chain changes only during the former process, while beta sheet crystallization occurs only during the latter process. Analogy is made between the crystallization of synthetic polymers according to the four-state scheme of Strobl, and the crystallization process of silk fibroin, which includes an intermediate precursor stage before crystallization. (3) The beta-sheet crystallization kinetics in silk fibroin protein were measured using X-ray, FTIR and heat flow, and the structure reveals the formation mechanism of the silk crystal network. Avrami kinetics theories, which were established for studies of synthetic polymer crystal growth, were for the first time extended to investigate protein self-assembly in multiblock silk fibroin samples. The Avrami exponent, n, was close to two for all methods, indicating formation of beta sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in most synthetic homopolymers. A microphase separation pattern after chymotrypsin enzyme biodegradation was shown in the protein structures using scanning electron microscopy. A model was then used to explain the crystallization of silk fibroin protein by analogy to block copolymers. (4) The effects of metal ions during the crystallization of silk fibroin was investigated using thermal analysis. Advanced thermal analysis methods were used to analyze the thermal protein-metallic ion interactions in silk fibroin proteins. Results show that K+ and Ca2+ metallic salts play different roles in silk fibroin proteins, which either reduce (K+) or increase (Ca2+ ) the glass transition (Tg) of pure silk protein and affect the thermal stability of this structure.

Increasing low frequency sound attenuation using compounded single layer of sonic crystal

NASA Astrophysics Data System (ADS)

Gulia, Preeti; Gupta, Arpan

2018-05-01

Sonic crystals (SC) are man-made periodic structures where sound hard scatterers are arranged in a crystalline manner. SC reduces noise in a particular range of frequencies called as band gap. Sonic crystals have a promising application in noise shielding; however, the application is limited due to the size of structure. Particularly for low frequencies, the structure becomes quite bulky, restricting its practical application. This paper presents a compounded model of SC, which has the same overall area and filling fraction but with increased low frequency sound attenuation. Two cases have been considered, a three layer SC and a compounded single layer SC. Both models have been analyzed using finite element simulation and plane wave expansion method. Band gaps for periodic structures have been obtained using both methods which are in good agreement. Further, sound transmission loss has been evaluated using finite element method. The results demonstrate the use of compounded model of Sonic Crystal for low frequency sound attenuation.

Psychological Separation, Attachment Security, Vocational Self-Concept Crystallization, and Career Indecision: A Structural Equation Analysis.

ERIC Educational Resources Information Center

Tokar, David M.; Withrow, Jason R.; Hall, Rosalie J.; Moradi, Bonnie

2003-01-01

Structural equation modeling was used to test theoretically based models in which psychological separation and attachment security variables were related to career indecision and those relations were mediated through vocational self-concept crystallization. Results indicated that some components of separation and attachment security did relate to…

Multiscale Modeling of Structurally-Graded Materials Using Discrete Dislocation Plasticity Models and Continuum Crystal Plasticity Models

NASA Technical Reports Server (NTRS)

Saether, Erik; Hochhalter, Jacob D.; Glaessgen, Edward H.

2012-01-01

A multiscale modeling methodology that combines the predictive capability of discrete dislocation plasticity and the computational efficiency of continuum crystal plasticity is developed. Single crystal configurations of different grain sizes modeled with periodic boundary conditions are analyzed using discrete dislocation plasticity (DD) to obtain grain size-dependent stress-strain predictions. These relationships are mapped into crystal plasticity parameters to develop a multiscale DD/CP model for continuum level simulations. A polycrystal model of a structurally-graded microstructure is developed, analyzed and used as a benchmark for comparison between the multiscale DD/CP model and the DD predictions. The multiscale DD/CP model follows the DD predictions closely up to an initial peak stress and then follows a strain hardening path that is parallel but somewhat offset from the DD predictions. The difference is believed to be from a combination of the strain rate in the DD simulation and the inability of the DD/CP model to represent non-monotonic material response.

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Key structure-activity relationships in the vanadium phosphorus oxide catalyst system

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

Thompson, M.R.; Ebner, J.R.

1990-04-01

The crystal structure of vanadyl pyrophosphate has been redetermined using single crystals obtained from a near solidified melt of a microcrystalline catalyst sample. Crystals that index as vanadyl pyrophosphate obtained from this melt are variable in color. Crystallographic refinement of the single crystal x-ray diffraction data indicates that structural differences among these materials can be described in terms of crystal defects associated with linear disorder of the vanadium atoms. The importance of the disorder is outlined in the context of its effect on the proposed surface topology parallel to (1,0,0). Models of the surface topology simply and intuitively account formore » the non-stoichometric surface atomic P/V ratio exhibited by selective catalysts of this phase. These models also point to the possible role of the excess phosphorus in providing site isolation of reactive centers at the surface. 33 refs., 7 figs.« less

Computational modelling of mesoscale dislocation patterning and plastic deformation of single crystals

NASA Astrophysics Data System (ADS)

Xia, Shengxu; El-Azab, Anter

2015-07-01

We present a continuum dislocation dynamics model that predicts the formation of dislocation cell structure in single crystals at low strains. The model features a set of kinetic equations of the curl type that govern the space and time evolution of the dislocation density in the crystal. These kinetic equations are coupled to stress equilibrium and deformation kinematics using the eigenstrain approach. A custom finite element method has been developed to solve the coupled system of equations of dislocation kinetics and crystal mechanics. The results show that, in general, dislocations self-organize in patterns under their mutual interactions. However, the famous dislocation cell structure has been found to form only when cross slip is implemented in the model. Cross slip is also found to lower the yield point, increase the hardening rate, and sustain an increase in the dislocation density over the hardening regime. Analysis of the cell structure evolution reveals that the average cell size decreases with the applied stress, which is consistent with the similitude principle.

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

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

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

The rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP.

PubMed

Pletnev, Sergei; Subach, Fedor V; Verkhusha, Vladislav V; Dauter, Zbigniew

2014-01-01

The rotational order-disorder (OD) structure of the reversibly photoswitchable fluorescent protein rsTagRFP is discussed in detail. The structure is composed of tetramers of 222 symmetry incorporated into the lattice in two different orientations rotated 90° with respect to each other around the crystal c axis and with tetramer axes coinciding with the crystallographic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates the rotational OD structure with statistically averaged I422 symmetry. Despite order-disorder pathology, the structure of rsTagRFP has electron-density maps of good quality for both non-overlapping and overlapping parts of the model. The crystal contacts, crystal internal architecture and a possible mechanism of rotational OD crystal formation are discussed.

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.

Structural and Functional Mechanisms of Adaptations of WrbA in Extremophilic Organisms

DTIC Science & Technology

2010-05-11

organisms adapt to high temperature. A model of the thermophilic enzyme was constructed based on the crystal Structure of the mesophilie counterpart to...binding for the thermophilic enzyme was independent of ligand concentration. Comparison of enzyme activities between the two proteins with a variety of...extremophilic organisms adapt to high temperature. A model of the thermophilic enzyme was constructed based on the crystal structure of the mesophilic

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

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

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

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

PubMed

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

2017-09-25

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

On crystal versus fiber formation in dipeptide hydrogelator systems.

PubMed

Houton, Kelly A; Morris, Kyle L; Chen, Lin; Schmidtmann, Marc; Jones, James T A; Serpell, Louise C; Lloyd, Gareth O; Adams, Dave J

2012-06-26

Naphthalene dipeptides have been shown to be useful low-molecular-weight gelators. Here we have used a library to explore the relationship between the dipeptide sequence and the hydrogelation efficiency. A number of the naphthalene dipeptides are crystallizable from water, enabling us to investigate the comparison between the gel/fiber phase and the crystal phase. We succeeded in crystallizing one example directly from the gel phase. Using X-ray crystallography, molecular modeling, and X-ray fiber diffraction, we show that the molecular packing of this crystal structure differs from the structure of the gel/fiber phase. Although the crystal structures may provide important insights into stabilizing interactions, our analysis indicates a rearrangement of structural packing within the fibers. These observations are consistent with the fibrillar interactions and interatomic separations promoting 1D assembly whereas in the crystals the peptides are aligned along multiple axes, allowing 3D growth. This observation has an impact on the use of crystal structures to determine supramolecular synthons for gelators.

Micromechanical models for the stiffness and strength of UHMWPE macrofibrils

NASA Astrophysics Data System (ADS)

Dong, Hai; Wang, Zheliang; O'Connor, Thomas C.; Azoug, Aurelie; Robbins, Mark O.; Nguyen, Thao D.

2018-07-01

Ultrahigh molecular weight polyethylene (UHMWPE) fibers have a complex hierarchical structure that at the micron-scale is composed of oriented chain crystals, lamellar crystals, and amorphous domains organized into macrofibrils. We developed a computational micromechanical modeling study of the effects of the morphological structure and constituent material properties on the deformation mechanisms, stiffness and strength of the UHMWPE macrofibrils. Specifically, we developed four representative volume elements, which differed in the arrangement and orientation of the lamellar crystals, to describe the various macrofibrillar microstructures observed in recent experiments. The stiffness and strength of the crystals were determined from molecular dynamic simulations of a pure PE crystal. A finite deformation crystal plasticity model was used to describe the crystals and an isotropic viscoplastic model was used for the amorphous phase. The results show that yielding in UHMWPE macrofibrils under axial tension is dominated by the slip in the oriented crystals, while yielding under transverse compression and shear is dominated by slips in both the oriented and lamellar crystals. The results also show that the axial modulus and strength are mainly determined by the volume fraction of the oriented crystals and are insensitive to the arrangements of the lamellar crystals when the modulus of the amorphous phase is significantly smaller than that of the crystals. In contrast, the arrangement and size of the lamellar crystals have a significant effect on the stiffness and strength under transverse compression and shear. These findings can provide a guide for new materials and processing design to improve the properties of UHMWPE fibers by controlling the macrofibrillar morphologies.

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.

Thick strings, the liquid crystal blue phase, and cosmological large-scale structure

NASA Technical Reports Server (NTRS)

Luo, Xiaochun; Schramm, David N.

1992-01-01

A phenomenological model based on the liquid crystal blue phase is proposed as a model for a late-time cosmological phase transition. Topological defects, in particular thick strings and/or domain walls, are presented as seeds for structure formation. It is shown that the observed large-scale structure, including quasi-periodic wall structure, can be well fitted in the model without violating the microwave background isotropy bound or the limits from induced gravitational waves and the millisecond pulsar timing. Furthermore, such late-time transitions can produce objects such as quasars at high redshifts. The model appears to work with either cold or hot dark matter.

Study on sensing property of one-dimensional ring mirror-defect photonic crystal

NASA Astrophysics Data System (ADS)

Chen, Ying; Luo, Pei; Cao, Huiying; Zhao, Zhiyong; Zhu, Qiguang

2018-02-01

Based on the photon localization and the photonic bandgap characteristics of photonic crystals (PCs), one-dimensional (1D) ring mirror-defect photonic crystal structure is proposed. Due to the introduction of mirror structure, a defect cavity is formed in the center of the photonic crystal, and then the resonant transmission peak can be obtained in the bandgap of transmission spectrum. The transfer matrix method is used to establish the relationship model between the resonant transmission peak and the structure parameters of the photonic crystals. Using the rectangular air gate photonic crystal structure, the dynamic monitoring of the detected gas sample parameters can be achieved from the shift of the resonant transmission peak. The simulation results show that the Q-value can attain to 1739.48 and the sensitivity can attain to 1642 nm ṡ RIU-1, which demonstrates the effectiveness of the sensing structure. The structure can provide certain theoretical reference for air pollution monitoring and gas component analysis.

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.

The Cytoplasmic Permeation Pathway of Neurotransmitter Transporters†

PubMed Central

Rudnick, Gary

2011-01-01

Ion-coupled solute transporters are responsible for transporting nutrients, ions and signaling molecules across a variety of biological membranes. Recent high-resolution crystal structures of several transporters from protein families that were previously thought to be unrelated show common structural features indicating a large structural family representing transporters from all kingdoms of life. This review describes studies that led to an understanding of the conformational changes required for solute transport in this family. The first structure in this family showed the bacterial amino acid transporter LeuT, which is homologous to neurotransmitter transporters, in an extracellularly-oriented conformation with a molecule of leucine occluded at the substrate site. Studies with the mammalian serotonin transporter identified positions, buried in the LeuT structure, that defined a potential pathway leading from the cytoplasm to the substrate binding site. Modeling studies utilized an inverted structural repeat within the LeuT crystal structure to predict the conformation of LeuT in which the cytoplasmic permeation pathway, consisting of positions identified in SERT, was open for substrate diffusion to the cytoplasm. From the difference between the model and the crystal structures, a simple “rocking bundle” mechanism was proposed, in which a 4-helix bundle changed its orientation with respect to the rest of the protein to close the extracellular pathway and open the cytoplasmic one. Subsequent crystal structures from structurally related proteins provide evidence supporting this model for transport. PMID:21774491

Discovery of a diamond-based photonic crystal structure in beetle scales.

PubMed

Galusha, Jeremy W; Richey, Lauren R; Gardner, John S; Cha, Jennifer N; Bartl, Michael H

2008-05-01

We investigated the photonic crystal structure inside iridescent scales of the weevil Lamprocyphus augustus. By combining a high-resolution structure analysis technique based on sequential focused ion beam milling and scanning electron microscopy imaging with theoretical modeling and photonic band-structure calculations, we discovered a natural three-dimensional photonic structure with a diamond-based crystal lattice operating at visible wavelengths. Moreover, we found that within individual scales, the diamond-based structure is assembled in the form of differently oriented single-crystalline micrometer-sized pixels with only selected lattice planes facing the scales' top surface. A comparison of results obtained from optical microreflectance measurements with photonic band-structure calculations reveals that it is this sophisticated microassembly of the diamond-based crystal lattice that lends Lamprocyphus augustus its macroscopically near angle-independent green coloration.

Microgravity

NASA Image and Video Library

2001-06-06

X-rays diffracted from a well-ordered protein crystal create sharp patterns of scattered light on film. A computer can use these patterns to generate a model of a protein molecule. To analyze the selected crystal, an X-ray crystallographer shines X-rays through the crystal. Unlike a single dental X-ray, which produces a shadow image of a tooth, these X-rays have to be taken many times from different angles to produce a pattern from the scattered light, a map of the intensity of the X-rays after they diffract through the crystal. The X-rays bounce off the electron clouds that form the outer structure of each atom. A flawed crystal will yield a blurry pattern; a well-ordered protein crystal yields a series of sharp diffraction patterns. From these patterns, researchers build an electron density map. With powerful computers and a lot of calculations, scientists can use the electron density patterns to determine the structure of the protein and make a computer-generated model of the structure. The models let researchers improve their understanding of how the protein functions. They also allow scientists to look for receptor sites and active areas that control a protein's function and role in the progress of diseases. From there, pharmaceutical researchers can design molecules that fit the active site, much like a key and lock, so that the protein is locked without affecting the rest of the body. This is called structure-based drug design.

Crystallization of PTP Domains.

PubMed

Levy, Colin; Adams, James; Tabernero, Lydia

2016-01-01

Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed.

‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

PubMed Central

Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

2015-01-01

The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

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.

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

NASA Astrophysics Data System (ADS)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

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.

Influence of computational domain size on the pattern formation of the phase field crystals

NASA Astrophysics Data System (ADS)

Starodumov, Ilya; Galenko, Peter; Alexandrov, Dmitri; Kropotin, Nikolai

2017-04-01

Modeling of crystallization process by the phase field crystal method (PFC) represents one of the important directions of modern computational materials science. This method makes it possible to research the formation of stable or metastable crystal structures. In this paper, we study the effect of computational domain size on the crystal pattern formation obtained as a result of computer simulation by the PFC method. In the current report, we show that if the size of a computational domain is changed, the result of modeling may be a structure in metastable phase instead of pure stable state. The authors present a possible theoretical justification for the observed effect and provide explanations on the possible modification of the PFC method to account for this phenomenon.

The application of inverse Broyden's algorithm for modeling of crack growth in iron crystals.

PubMed

Telichev, Igor; Vinogradov, Oleg

2011-07-01

In the present paper we demonstrate the use of inverse Broyden's algorithm (IBA) in the simulation of fracture in single iron crystals. The iron crystal structure is treated as a truss system, while the forces between the atoms situated at the nodes are defined by modified Morse inter-atomic potentials. The evolution of lattice structure is interpreted as a sequence of equilibrium states corresponding to the history of applied load/deformation, where each equilibrium state is found using an iterative procedure based on IBA. The results presented demonstrate the success of applying the IBA technique for modeling the mechanisms of elastic, plastic and fracture behavior of single iron crystals.

Homogenous Nucleation and Crystal Growth in a Model Liquid from Direct Energy Landscape Sampling Simulation

NASA Astrophysics Data System (ADS)

Walter, Nathan; Zhang, Yang

Nucleation and crystal growth are understood to be activated processes involving the crossing of free-energy barriers. Attempts to capture the entire crystallization process over long timescales with molecular dynamic simulations have met major obstacles because of molecular dynamics' temporal constraints. Herein, we circumvent this temporal limitation by using a brutal-force, metadynamics-like, adaptive basin-climbing algorithm and directly sample the free-energy landscape of a model liquid Argon. The algorithm biases the system to evolve from an amorphous liquid like structure towards an FCC crystal through inherent structure, and then traces back the energy barriers. Consequently, the sampled timescale is macroscopically long. We observe that the formation of a crystal involves two processes, each with a unique temperature-dependent energy barrier. One barrier corresponds to the crystal nucleus formation; the other barrier corresponds to the crystal growth. We find the two processes dominate in different temperature regimes. Compared to other computation techniques, our method requires no assumptions about the shape or chemical potential of the critical crystal nucleus. The success of this method is encouraging for studying the crystallization of more complex

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.

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.

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

Measuring and modelling the structure of chocolate

NASA Astrophysics Data System (ADS)

Le Révérend, Benjamin J. D.; Fryer, Peter J.; Smart, Ian; Bakalis, Serafim

2015-01-01

The cocoa butter present in chocolate exists as six different polymorphs. To achieve the desired crystal form (βV), traditional chocolate manufacturers use relatively slow cooling (<2°C/min). A newer generation of rapid cooling systems has been suggested requiring further understanding of fat crystallisation. To allow better control and understanding of these processes and newer rapid cooling processes, it is necessary to understand both heat transfer and crystallization kinetics. The proposed model aims to predict the temperature in the chocolate products during processing as well as the crystal structure of cocoa butter throughout the process. A set of ordinary differential equations describes the kinetics of fat crystallisation. The parameters were obtained by fitting the model to a set of DSC curves. The heat transfer equations were coupled to the kinetic model and solved using commercially available CFD software. A method using single crystal XRD was developed using a novel subtraction method to quantify the cocoa butter structure in chocolate directly and results were compared to the ones predicted from the model. The model was proven to predict phase change temperature during processing accurately (±1°C). Furthermore, it was possible to correctly predict phase changes and polymorphous transitions. The good agreement between the model and experimental data on the model geometry allows a better design and control of industrial processes.

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.

Interatomic Potentials for Structure Simulation of Alkaline-Earth Cuprates

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

Eremin, N.N.; Leonyuk, L.I.; Urusov, V.S.

2001-05-01

A specific potential model of interionic interactions was derived in which the crystal structures of alkaline-earth cuprates were satisfactorily described and some of their physical properties were predicted. It was found that a harmonic three-particle O-Cu-O potential and some Morse-type contributions to the simple Buckingham-type Cu-O repulsive potential enable one to improve essentially the results of crystal structure modeling for cuprates. The obtained potential set seems to be well transferable for different cuprates, despite the variety in linkages of the CuO{sub 4} groups. In the present work this potential set model was applied in the crystal structure modeling for Ca{submore » 2}CuO{sub 3}, CaCuO{sub 2}, SrCuO{sub 3}, (Sr{sub 1.19}Ca{sub 0.73})Cu{sub 2}O{sub 4}, and BaCuO{sub 2}. Some elastic and energetic properties of the compounds under question were predicted.« less

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

PubMed

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

PubMed

Wall, Michael E

2018-03-01

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

Melt Flow before Crystal Seeding in Cz Si Growth with Transversal MF

NASA Astrophysics Data System (ADS)

Iizuka, Masaya; Mukaiyama, Yuji; Demina, S. E.; Kalaev, V. V.

2017-06-01

Industrial Cz growth of Si crystal of 300 mm and higher diameter usually requires DC magnetic fields (MFs) to suppress turbulence in the melt. We present 3D unsteady analysis of melt turbulent convection in an industrial Cz system coupled with the effect of the transversal MF for different argon gas flow rates for the stage before crystal seeding. We have performed detailed 2D axisymmetric modeling of global heat transfer in the whole Cz furnace. Radiative heat fluxes obtained in 2D modeling have been used in detailed 3D steady and unsteady modeling of crystallization zone. LES method is applied as a predictive approach for modeling of turbulent flow of silicon melt. We have obtained flow structure and temperature distribution in the melt, which were different from previously reported data. We have observed a well-fixed dark spike which includes low temperature melt area on the melt free surface in MF cases. These results indicates that MF and argon flow rate conditions are important to achieve stable positioning of the dark spike on the melt free surface for optimized crystal seeding without uncontrollable meltdown and single crystal structure loss.

A crystal plasticity model for slip in hexagonal close packed metals based on discrete dislocation simulations

NASA Astrophysics Data System (ADS)

Messner, Mark C.; Rhee, Moono; Arsenlis, Athanasios; Barton, Nathan R.

2017-06-01

This work develops a method for calibrating a crystal plasticity model to the results of discrete dislocation (DD) simulations. The crystal model explicitly represents junction formation and annihilation mechanisms and applies these mechanisms to describe hardening in hexagonal close packed metals. The model treats these dislocation mechanisms separately from elastic interactions among populations of dislocations, which the model represents through a conventional strength-interaction matrix. This split between elastic interactions and junction formation mechanisms more accurately reproduces the DD data and results in a multi-scale model that better represents the lower scale physics. The fitting procedure employs concepts of machine learning—feature selection by regularized regression and cross-validation—to develop a robust, physically accurate crystal model. The work also presents a method for ensuring the final, calibrated crystal model respects the physical symmetries of the crystal system. Calibrating the crystal model requires fitting two linear operators: one describing elastic dislocation interactions and another describing junction formation and annihilation dislocation reactions. The structure of these operators in the final, calibrated model reflect the crystal symmetry and slip system geometry of the DD simulations.

Littelmann path model for geometric crystals, Whittaker functions on Lie groups and Brownian motion

NASA Astrophysics Data System (ADS)

Chhaibi, Reda

2013-02-01

Generally speaking, this thesis focuses on the interplay between the representations of Lie groups and probability theory. It subdivides into essentially three parts. In a first rather algebraic part, we construct a path model for geometric crystals in the sense of Berenstein and Kazhdan, for complex semi-simple Lie groups. We will mainly describe the algebraic structure, its natural morphisms and parameterizations. The theory of total positivity will play a particularly important role. Then, we anticipate on the probabilistic part by exhibiting a canonical measure on geometric crystals. It uses as ingredients the superpotential for the flag manifold and a measure invariant under the crystal actions. The image measure under the weight map plays the role of Duistermaat-Heckman measure. Its Laplace transform defines Whittaker functions, providing an interesting formula for all Lie groups. Then it appears clearly that Whittaker functions are to geometric crystals, what characters are to combinatorial crystals. The Littlewood-Richardson rule is also exposed. Finally we present the probabilistic approach that allows to find the canonical measure. It is based on the fundamental idea that the Wiener measure will induce the adequate measure on the algebraic structures through the path model. In the last chapter, we show how our geometric model degenerates to the continuous classical Littelmann path model and thus recover known results. For example, the canonical measure on a geometric crystal of highest weight degenerates into a uniform measure on a polytope, and recovers the parameterizations of continuous crystals.

The Structure of Human Intelligence: It Is Verbal, Perceptual, and Image Rotation (VPR), Not Fluid and Crystallized

ERIC Educational Resources Information Center

Johnson, W.; Bouchard, T.J.

2005-01-01

In a heterogeneous sample of 436 adult individuals who completed 42 mental ability tests, we evaluated the relative statistical performance of three major psychometric models of human intelligence-the Cattell-Horn fluid-crystallized model, Vernon's verbal-perceptual model, and Carroll's three-strata model. The verbal-perceptual model fit…

X-ray crystallography

NASA Technical Reports Server (NTRS)

2001-01-01

X-rays diffracted from a well-ordered protein crystal create sharp patterns of scattered light on film. A computer can use these patterns to generate a model of a protein molecule. To analyze the selected crystal, an X-ray crystallographer shines X-rays through the crystal. Unlike a single dental X-ray, which produces a shadow image of a tooth, these X-rays have to be taken many times from different angles to produce a pattern from the scattered light, a map of the intensity of the X-rays after they diffract through the crystal. The X-rays bounce off the electron clouds that form the outer structure of each atom. A flawed crystal will yield a blurry pattern; a well-ordered protein crystal yields a series of sharp diffraction patterns. From these patterns, researchers build an electron density map. With powerful computers and a lot of calculations, scientists can use the electron density patterns to determine the structure of the protein and make a computer-generated model of the structure. The models let researchers improve their understanding of how the protein functions. They also allow scientists to look for receptor sites and active areas that control a protein's function and role in the progress of diseases. From there, pharmaceutical researchers can design molecules that fit the active site, much like a key and lock, so that the protein is locked without affecting the rest of the body. This is called structure-based drug design.

Crystal Model Kits for Use in the General Chemistry Laboratory.

ERIC Educational Resources Information Center

Kildahl, Nicholas J.; And Others

1986-01-01

Dynamic crystal model kits are described. Laboratory experiments in which students use these kits to build models have been extremely successful in providing them with an understanding of the three-dimensional structures of the common cubic unit cells as well as hexagonal and cubic closest-packing of spheres. (JN)

Structure of the mixed-metal carbonate KAgCO₃ revisited: order-disorder (OD) polytypism and allotwinning.

PubMed

Hans, Philipp; Stöger, Berthold; Weil, Matthias; Zobetz, Erich

2015-04-01

Crystals of KAgCO3 belong to an order-disorder (OD) family of structures composed of layers of two kinds. There are two polytypes with a maximum degree of order [MDO1: Pccb; MDO2: Ibca, doubled a-axis compared with MDO1], which are both realised to a different extent in two crystals under investigation [volume fraction MDO1:MDO2 in crystal (I): 0.0216:0.9784 (3) and in crystal (II): 0.9657:0.0343 (3)]. Sharp diffraction spots and the absence of diffuse scattering indicate highly ordered macroscopic domains. The structure of KAgCO3 was refined concurrently against all reflections using an allotwin model (addition of the intensities of both domains). It is shown that a disorder model refined against reflections of only one domain can lead to a significant overestimation of the volume fraction of this domain.

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

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

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

DIFFRACTION FROM MODEL CRYSTALS

USDA-ARS?s Scientific Manuscript database

Although calculating X-ray diffraction patterns from atomic coordinates of a crystal structure is a widely available capability, calculation from non-periodic arrays of atoms has not been widely applied to cellulose. Non-periodic arrays result from modeling studies that, even though started with at...

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.

Workflow for Integrating Mesoscale Heterogeneities in Materials Structure with Process Simulation of Titanium Alloys (Postprint)

DTIC Science & Technology

2014-10-01

offer a practical solution to calculating the grain -scale hetero- geneity present in the deformation field. Consequently, crystal plasticity models...process/performance simulation codes (e.g., crystal plasticity finite element method). 15. SUBJECT TERMS ICME; microstructure informatics; higher...iii) protocols for direct and efficient linking of materials models/databases into process/performance simulation codes (e.g., crystal plasticity

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins.

PubMed

Wathen, Brent; Kuiper, Michael; Walker, Virginia; Jia, Zongchao

2003-01-22

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.

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.

X-ray structure determination at low resolution

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

Brunger, Axel T., E-mail: brunger@stanford.edu; Department of Molecular and Cellular Physiology, Stanford University; Department of Neurology and Neurological Sciences, Stanford University

2009-02-01

Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alonemore » was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible.« less

SIMBAD : a sequence-independent molecular-replacement pipeline

DOE PAGES

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

2018-06-08

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

SIMBAD : a sequence-independent molecular-replacement pipeline

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

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less

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

NASA Technical Reports Server (NTRS)

Landis, W. J.

1995-01-01

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

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

PubMed

Landis, W J

1995-05-01

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

Structural analysis according to reduced data: VIII. Refinement of the extended model of aspherical atoms

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

Dudka, A. P.

A program for the refinement of the model of aspherical atoms within the Stewart-Hansen-Coppens formalism has been developed. Deformation scattering up to the 8th expansion order in multipoles has been taken into account for the first time. The program was tested for 11 crystals. The effect of the result of interpolation of radial scattering curves on the model parameters is considered. The importance of introduction of multipoles of high (5th-8th) orders into the model for a number of crystals is shown. The use of the extended multipole model for a silicon crystal revealed some new specific features of the electronicmore » structure: consideration of multipoles up to the 7th order makes it possible to explain the intensity of the forbidden 222 reflection.« less

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.

Protein purification and crystallization artifacts: The tale usually not told.

PubMed

Niedzialkowska, Ewa; Gasiorowska, Olga; Handing, Katarzyna B; Majorek, Karolina A; Porebski, Przemyslaw J; Shabalin, Ivan G; Zasadzinska, Ewelina; Cymborowski, Marcin; Minor, Wladek

2016-03-01

The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non-reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building. © 2016 The Protein Society.

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

PubMed

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

2014-03-01

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

Molecular modeling studies of novel retro-binding tripeptide active-site inhibitors of thrombin.

PubMed

Lau, W F; Tabernero, L; Sack, J S; Iwanowicz, E J

1995-08-01

A novel series of retro-binding tripeptide thrombin active-site inhibitors was recently developed (Iwanowicz, E. I. et al. J. Med. Chem. 1994, 37, 2111(1)). It was hypothesized that the binding mode for these inhibitors is similar to that of the first three N-terminal residues of hirudin. This binding hypothesis was subsequently verified when the crystal structure of a member of this series, BMS-183,507 (N-[N-[N-[4-(Aminoiminomethyl)amino[-1-oxobutyl]-L- phenylalanyl]-L-allo-threonyl]-L-phenylalanine, methyl ester), was determined (Taberno, L.J. Mol. Biol. 1995, 246, 14). The methodology for developing the binding models of these inhibitors, the structure-activity relationships (SAR) and modeling studies that led to the elucidation of the proposed binding mode is described. The crystal structure of BMS-183,507/human alpha-thrombin is compared with the crystal structure of hirudin/human alpha-thrombin (Rydel, T.J. et al. Science 1990, 249,227; Rydel, T.J. et al. J. Mol Biol. 1991, 221, 583; Grutter, M.G. et al. EMBO J. 1990, 9, 2361) and with the computational binding model of BMS-183,507.

Modeling of the structure of ribosomal protein L1 from the archaeon Haloarcula marismortui

NASA Astrophysics Data System (ADS)

Nevskaya, N. A.; Kljashtorny, V. G.; Vakhrusheva, A. V.; Garber, M. B.; Nikonov, S. V.

2017-07-01

The halophilic archaeon Haloarcula marismortui proliferates in the Dead Sea at extremely high salt concentrations (higher than 3 M). This is the only archaeon, for which the crystal structure of the ribosomal 50S subunit was determined. However, the structure of the functionally important side protuberance containing the abnormally negatively charged protein L1 (HmaL1) was not visualized. Attempts to crystallize HmaL1 in the isolated state or as its complex with RNA using normal salt concentrations (≤500 mM) failed. A theoretical model of HmaL1 was built based on the structural data for homologs of the protein L1 from other organisms, and this model was refined by molecular dynamics methods. Analysis of this model showed that the protein HmaL1 can undergo aggregation due to the presence of a cluster of positive charges unique for proteins L1. This cluster is located at the RNA-protein interface, which interferes with the crystallization of HmaL1 and the binding of the latter to RNA.

Premature melt solidification during mold filling and its influence on the as-cast structure

NASA Astrophysics Data System (ADS)

Wu, M.; Ahmadein, M.; Ludwig, A.

2018-03-01

Premature melt solidification is the solidification of a melt during mold filling. In this study, a numerical model is used to analyze the influence of the pouring process on the premature solidification. The numerical model considers three phases, namely, air, melt, and equiaxed crystals. The crystals are assumed to have originated from the heterogeneous nucleation in the undercooled melt resulting from the first contact of the melt with the cold mold during pouring. The transport of the crystals by the melt flow, in accordance with the socalled "big bang" theory, is considered. The crystals are assumed globular in morphology and capable of growing according to the local constitutional undercooling. These crystals can also be remelted by mixing with the superheated melt. As the modeling results, the evolutionary trends of the number density of the crystals and the volume fraction of the solid crystals in the melt during pouring are presented. The calculated number density of the crystals and the volume fraction of the solid crystals in the melt at the end of pouring are used as the initial conditions for the subsequent solidification simulation of the evolution of the as-cast structure. A five-phase volume-average model for mixed columnar-equiaxed solidification is used for the solidification simulation. An improved agreement between the simulation and experimental results is achieved by considering the effect of premature melt solidification during mold filling. Finally, the influences of pouring parameters, namely, pouring temperature, initial mold temperature, and pouring rate, on the premature melt solidification are discussed.

Theoretical investigations on the structures and properties of CL-20/TNT cocrystal and its defective models by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao

2018-06-09

"Perfect" and defective models of CL-20/TNT cocrystal explosive were established. Molecular dynamics methods were introduced to determine the structures and predict the comprehensive performances, including stabilities, sensitivity, energy density and mechanical properties, of the different models. The influences of crystal defects on the properties of these explosives were investigated and evaluated. The results show that, compared with the "perfect" model, the rigidity and toughness of defective models are decreased, while the ductility, tenacity and plastic properties are enhanced. The binding energies, interaction energy of the trigger bond, and the cohesive energy density of defective crystals declined, thus implying that stabilities are weakened, the explosive molecule is activated, trigger bond strength is diminished and safety is worsened. Detonation performance showed that, owing to the influence of crystal defects, the density is lessened, detonation pressure and detonation velocity are also declined, i.e., the power of defective explosive is decreased. In a word, the crystal defects may have a favorable effect on the mechanical properties, but have a disadvantageous influence on sensitivity, stability and energy density of CL-20/TNT cocrystal explosive. The results could provide theoretical guidance and practical instructions to estimate the properties of defective crystal models.

Probing the crystal structure landscape by doping: 4-bromo, 4-chloro and 4-methylcinnamic acids.

PubMed

Desiraju, Gautam R; Chakraborty, Shaunak; Joseph, Sumy

2018-06-11

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br-atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii and others, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of pi...pi interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera).

PubMed

Jin, Tengchuan; Wang, Cheng; Zhang, Caiying; Wang, Yang; Chen, Yu-Wei; Guo, Feng; Howard, Andrew; Cao, Min-Jie; Fu, Tong-Jen; McHugh, Tara H; Zhang, Yuzhu

2017-08-30

Coconut (Cocos nucifera) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. The structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

Continuous structural evolution of calcium carbonate particles: a unifying model of copolymer-mediated crystallization.

PubMed

Kulak, Alex N; Iddon, Peter; Li, Yuting; Armes, Steven P; Cölfen, Helmut; Paris, Oskar; Wilson, Rory M; Meldrum, Fiona C

2007-03-28

Two double-hydrophilic block copolymers, each comprising a nonionic block and an anionic block comprising pendent aromatic sulfonate groups, were used as additives to modify the crystallization of CaCO3. Marked morphological changes in the CaCO3 particles were observed depending on the reaction conditions used. A poly(ethylene oxide)-b-poly(sodium 4-styrenesulfonate) diblock copolymer was particularly versatile in effecting a morphological change in calcite particles, and a continuous structural transition in the product particles from polycrystalline to mesocrystal to single crystal was observed with variation in the calcium concentration. The existence of this structural sequence provides unique insight into the mechanism of polymer-mediated crystallization. We propose that it reflects continuity in the crystallization mechanism itself, spanning the limits from nonoriented aggregation of nanoparticles to classical ion-by-ion growth. The various pathways to polycrystalline, mesocrystal, and single-crystal particles, which had previously been considered to be distinct, therefore all form part of a unifying crystallization framework based on the aggregation of precursor subunits.

Predicting patchy particle crystals: variable box shape simulations and evolutionary algorithms.

PubMed

Bianchi, Emanuela; Doppelbauer, Günther; Filion, Laura; Dijkstra, Marjolein; Kahl, Gerhard

2012-06-07

We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.

Multistep modeling of protein structure: application to bungarotoxin

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Shibata, M.; Rein, R.

1986-01-01

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

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

Wong, Jaslyn E. M. M.; Midtgaard, Søren Roi; Gysel, Kira

The crystal and solution structures of the T. thermophilus NlpC/P60 d, l-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan. LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of themore » Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.« less

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.

Semi-analytical model for a slab one-dimensional photonic crystal

NASA Astrophysics Data System (ADS)

Libman, M.; Kondratyev, N. M.; Gorodetsky, M. L.

2018-02-01

In our work we justify the applicability of a dielectric mirror model to the description of a real photonic crystal. We demonstrate that a simple one-dimensional model of a multilayer mirror can be employed for modeling of a slab waveguide with periodically changing width. It is shown that this width change can be recalculated to the effective refraction index modulation. The applicability of transfer matrix method of reflection properties calculation was demonstrated. Finally, our 1-D model was employed to analyze reflection properties of a 2-D structure - a slab photonic crystal with a number of elliptic holes.

New simulation model of multicomponent crystal growth and inhibition.

PubMed

Wathen, Brent; Kuiper, Michael; Walker, Virginia; Jia, Zongchao

2004-04-02

We review a novel computational model for the study of crystal structures both on their own and in conjunction with inhibitor molecules. The model advances existing Monte Carlo (MC) simulation techniques by extending them from modeling 3D crystal surface patches to modeling entire 3D crystals, and by including the use of "complex" multicomponent molecules within the simulations. These advances makes it possible to incorporate the 3D shape and non-uniform surface properties of inhibitors into simulations, and to study what effect these inhibitor properties have on the growth of whole crystals containing up to tens of millions of molecules. The application of this extended MC model to the study of antifreeze proteins (AFPs) and their effects on ice formation is reported, including the success of the technique in achieving AFP-induced ice-growth inhibition with concurrent changes to ice morphology that mimic experimental results. Simulations of ice-growth inhibition suggest that the degree of inhibition afforded by an AFP is a function of its ice-binding position relative to the underlying anisotropic growth pattern of ice. This extended MC technique is applicable to other crystal and crystal-inhibitor systems, including more complex crystal systems such as clathrates.

A Novel Probabilistic Multi-Scale Modeling and Sensing Framework for Fatigue Life Prediction of Aerospace Structures and Materials: DCT Project

DTIC Science & Technology

2012-08-25

Accel- erated Crystal Plasticity FEM Simulations (submitted). 5. M. Anahid, M. Samal and S. Ghosh, Dwell fatigue crack nucleation model based on using...4] M. Anahid, M. K. Samal , and S. Ghosh. Dwell fatigue crack nucleation model based on crystal plasticity finite element simulations of

Control of DNA-Functionalized Nanoparticle Assembly

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries, and drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, as well as the parameters to develop colloidal models that reproduce both the shape of single crystals and their growth kinetics.

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

Investigation of the cluster formation in lithium niobate crystals by computer modeling method

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

Voskresenskii, V. M.; Starodub, O. R., E-mail: ol-star@mail.ru; Sidorov, N. V.

The processes occurring upon the formation of energetically equilibrium oxygen-octahedral clusters in the ferroelectric phase of a stoichiometric lithium niobate (LiNbO{sub 3}) crystal have been investigated by the computer modeling method within the semiclassical atomistic model. An energetically favorable cluster size (at which a structure similar to that of a congruent crystal is organized) is shown to exist. A stoichiometric cluster cannot exist because of the electroneutrality loss. The most energetically favorable cluster is that with a Li/Nb ratio of about 0.945, a value close to the lithium-to-niobium ratio for a congruent crystal.

A short review of theoretical and empirical models for characterization of optical materials doped with the transition metal and rare earth ions

NASA Astrophysics Data System (ADS)

Su, P.; Ma, C.-G.; Brik, M. G.; Srivastava, A. M.

2018-05-01

In this paper, a brief retrospective review of the main developments in crystal field theory is provided. We have examined how different crystal field models are applied to solve the problems that arise in the spectroscopy of optically active ions. Attention is focused on the joint application of crystal field and density functional theory (DFT) based models, which takes advantages of strong features of both individual approaches and allows for obtaining a complementary picture of the electronic properties of a doped crystal with impurity energy levels superimposed onto the host band structure.

Concentration and structure inhomogeneities in GaSb(Si) single crystals grown at different heat and mass transfer conditions

NASA Astrophysics Data System (ADS)

Serebryakov, Yu. A.; Prokhorov, I. A.; Vlasov, V. N.; Korobeynikova, E. N.; Zakharov, B. G.; Shul'pina, I. L.; Marchenko, M. P.; Fryazinov, I. V.

2007-06-01

Results of ground-based experiments on crystallization of gallium antimonide on the POLIZON facility carried out within the framework of space experiment preparation aboard FOTON satellite are submitted. Technical and technological opportunities of suppression of disturbing factors for improvement of quality of grown crystals in space are substantiated. Features of formation of concentration and structure inhomogeneities in GaSb:Si crystals grown under non-stationary and stationary convection conditions are investigated. Experimental data about structure and dopant distribution inhomogeneities are discussed taking into account results of numerical researches of GaSb:Si crystallization. Also earlier received results of modeling of GaSb:Te crystallization under close temperature conditions are used. Correlation between computational and experimental data is shown. The data on intensity of flows close to crystallization front are received at which non-stationary or stationary conditions of crystallization are realized. The forecast for space conditions is made. The influence of a rotating magnetic field on convection in melt for application in space experiment projected is investigated.

Understanding the structure of chocolate

NASA Astrophysics Data System (ADS)

Schenk, H.; Peschar, R.

2004-10-01

Crystallization of cocoa-butter in the β phase from the melt under static conditions is only possible using the memory effect of cocoa-butter. Under all other conditions polymorphs with lower melting temperatures develop, whereas the β phase is the preferred one in chocolate. SAXS experiments proved 1,3-distearoyl-2-oleoylglycerol seeds with triple chain-length packing initiate the β-crystallization. Models for the different phases may be based on the crystal structure determinations of triacylglycerols. A new, patented, way of chocolate making is in development in which the traditional tempering process is replaced by another pre-crystallization process. The process is based on the use of seed crystals in the liquid phase and driven by a feedback system.

Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

Crystal field analysis of the energy level structure of Cs2NaAlF6:Cr3+

NASA Astrophysics Data System (ADS)

Rudowicz, C.; Brik, M. G.; Avram, N. M.; Yeung, Y. Y.; Gnutek, P.

2006-06-01

An analysis of the energy level structure of Cr3+ ions in Cs2NaAlF6 crystal is performed using the exchange charge model (ECM) together with the crystal field analysis/microscopic spin Hamiltonian (CFA/MSH) computer package. Utilizing the crystal structure data, our approach enables modelling of the crystal field parameters (CFPs) and thus the energy level structure for Cr3+ ions at the two crystallographically inequivalent sites in Cs2NaAlF6. Using the ECM initial adjustment procedure, the CFPs are calculated in the crystallographic axis system centred at the Cr3+ ion at each site. Additionally the CFPs are also calculated using the superposition model (SPM). The ECM and SPM predicted CFP values match very well. Consideration of the symmetry aspects for the so-obtained CFP datasets reveals that the latter axis system matches the symmetry-adapted axis system related directly to the six Cr-F bonds well. Using the ECM predicted CFPs as an input for the CFA/MSH package, the complete energy level schemes are calculated for Cr3+ ions at the two sites. Comparison of the theoretical results with the experimental spectroscopic data yields satisfactory agreement. Our results confirm that the actual symmetry at both impurity sites I and II in the Cs2NaAlF6:Cr3+ system is trigonal D3d. The ECM predicted CFPs may be used as the initial (starting) parameters for simulations and fittings of the energy levels for Cr3+ ions in structurally similar hosts.

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

PubMed Central

Schneidman-Duhovny, Dina; Hammel, Michal

2018-01-01

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex. PMID:29605933

Distribution function of random strains in an elastically anisotropic continuum and defect strengths of T m3 + impurity ions in crystals with zircon structure

NASA Astrophysics Data System (ADS)

Malkin, B. Z.; Abishev, N. M.; Baibekov, E. I.; Pytalev, D. S.; Boldyrev, K. N.; Popova, M. N.; Bettinelli, M.

2017-07-01

We construct a distribution function of the strain-tensor components induced by point defects in an elastically anisotropic continuum, which can be used to account quantitatively for many effects observed in different branches of condensed matter physics. Parameters of the derived six-dimensional generalized Lorentz distribution are expressed through the integrals computed over the array of strains. The distribution functions for the cubic diamond and elpasolite crystals and tetragonal crystals with the zircon and scheelite structures are presented. Our theoretical approach is supported by a successful modeling of specific line shapes of singlet-doublet transitions of the T m3 + ions doped into AB O4 (A =Y , Lu; B =P , V) crystals with zircon structure, observed in high-resolution optical spectra. The values of the defect strengths of impurity T m3 + ions in the oxygen surroundings, obtained as a result of this modeling, can be used in future studies of random strains in different rare-earth oxides.

Purification, crystallization and preliminary X-ray diffraction analysis of the glyoxalase II from Leishmania infantum

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

Trincão, José; Sousa Silva, Marta; Barata, Lídia

2006-08-01

A glyoxalase II from L. infantum was cloned, purified and crystallized and its structure was solved by X-ray crystallography. In trypanosomatids, trypanothione replaces glutathione in all glutathione-dependent processes. Of the two enzymes involved in the glyoxalase pathway, glyoxalase I and glyoxalase II, the latter shows absolute specificity towards trypanothione thioester, making this enzyme an excellent model to understand the molecular basis of trypanothione binding. Cloned glyoxalase II from Leishmania infantum was overexpressed in Escherichia coli, purified and crystallized. Crystals belong to space group C222{sub 1} (unit-cell parameters a = 65.6, b = 88.3, c = 85.2 Å) and diffract beyondmore » 2.15 Å using synchrotron radiation. The structure was solved by molecular replacement using the human glyoxalase II structure as a search model. These results, together with future detailed kinetic characterization using lactoyltrypanothione, should shed light on the evolutionary selection of trypanothione instead of glutathione by trypano-somatids.« less

Crystal structure of spinach plastocyanin at 1.7 A resolution.

PubMed Central

Xue, Y.; Okvist, M.; Hansson, O.; Young, S.

1998-01-01

The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins. PMID:9792096

Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

NASA Astrophysics Data System (ADS)

Koley, Biplab; Chatterjee, S.; Jana, Partha P.

2017-02-01

A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

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

PubMed

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

2016-08-01

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

Magnetic and structural instabilities in CePd 2Al 2 and LaPd 2Al 2

NASA Astrophysics Data System (ADS)

Chapon, L. C.; Goremychkin, E. A.; Osborn, R.; Rainford, B. D.; Short, S.

2006-05-01

We have investigated the crystal and magnetic structure of the RPd 2Al 2 compounds (R=La, Ce) by neutron powder diffraction (ND) and inelastic neutron scattering (INS). The ND study shows that both compounds undergo a structural phase transition from tetragonal to orthorhombic symmetry at 91.5 K (La) and 13.5 K (Ce). In the case of CePd 2Al 2 the crystal field excitation spectrum, which has an extra peak that cannot be explained by a standard crystal field model, indicates the presence of strong magneto-elastic coupling.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

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

Wall, Michael E.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.

2018-01-25

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Emission behaviors of unsymmetrical 1,3-diaryl-β-diketones: A model perfectly disclosing the effect of molecular conformation on luminescence of organic solids

NASA Astrophysics Data System (ADS)

Cheng, Xiao; Li, Feng; Han, Shenghua; Zhang, Yufei; Jiao, Chuanjun; Wei, Jinbei; Ye, Kaiqi; Wang, Yue; Zhang, Hongyu

2015-03-01

A series of unsymmetrical 1,3-diaryl-β-diketones 1-6 displaying molecular conformation-dependent fluorescence quantum yields have been synthesized. Crystals with planar molecular conformation such as 1, 2, 3 and 4 are highly fluorescent (φf: 39-53%), and the one holding slightly twisted conformation (5) is moderately luminescent (φf = 17%), while crystal 6 possessing heavily bent structure is completely nonluminous (φf ~ 0). The distinct fluorescence efficiencies are ascribed to their different molecular conformations, since all the crystals hold the same crystal system, space group and crystal packing structures. Additionally, the fluorescent crystals 1-5 display low threshold amplified spontaneous emission (ASE) with small full widths at half-maximum (FWHM: 3-7 nm), indicating their potential as candidates for organic crystal lasing devices.

Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility

PubMed Central

Loving, Kathryn A.; Lin, Andy; Cheng, Alan C.

2014-01-01

Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets. PMID:25079060

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

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

Thompson, Michael C.; Cascio, Duilio; Yeates, Todd O.

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the datamore » sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less

The importance of proper crystal-chemical and geometrical reasoning demonstrated using layered single and double hydroxides

PubMed Central

Richardson, Ian G.

2013-01-01

Atomistic modelling techniques and Rietveld refinement of X-ray powder diffraction data are widely used but often result in crystal structures that are not realistic, presumably because the authors neglect to check the crystal-chemical plausibility of their structure. The purpose of this paper is to reinforce the importance and utility of proper crystal-chemical and geometrical reasoning in structural studies. It is achieved by using such reasoning to generate new yet fundamental information about layered double hydroxides (LDH), a large, much-studied family of compounds. LDH phases are derived from layered single hydroxides by the substitution of a fraction (x) of the divalent cations by trivalent. Equations are derived that enable calculation of x from the a parameter of the unit cell and vice versa, which can be expected to be of widespread utility as a sanity test for extant and future structure determinations and computer simulation studies. The phase at x = 0 is shown to be an α form of divalent metal hydroxide rather than the β polymorph. Crystal-chemically sensible model structures are provided for β-Zn(OH)2 and Ni- and Mg-based carbonate LDH phases that have any trivalent cation and any value of x, including x = 0 [i.e. for α-M(OH)2·mH2O phases]. PMID:23719702

Phase field model of the nanoscale evolution during the explosive crystallization phenomenon

NASA Astrophysics Data System (ADS)

Lombardo, S. F.; Boninelli, S.; Cristiano, F.; Deretzis, I.; Grimaldi, M. G.; Huet, K.; Napolitani, E.; La Magna, A.

2018-03-01

Explosive crystallization is a well known phenomenon occurring due to the thermodynamic instability of strongly under-cooled liquids, which is particularly relevant in pulsed laser annealing processes of amorphous semiconductor materials due to the globally exothermic amorphous-to-liquid-to-crystal transition pathway. In spite of the assessed understanding of this phenomenon, quantitative predictions of the material kinetics promoted by explosive crystallization are hardly achieved due to the lack of a consistent model able to simulate the concurrent kinetics of the amorphous-liquid and liquid-crystal interfaces. Here, we propose a multi-well phase-field model specifically suited for the simulation of explosive crystallization induced by pulsed laser irradiation in the nanosecond time scale. The numerical implementation of the model is robust despite the discontinuous jumps of the interface speed induced by the phenomenon. The predictive potential of the simulations is demonstrated by means of comparisons of the modelling predictions with experimental data in terms of in situ reflectivity measurements and ex-situ micro-structural and chemical characterization.

A Capped Dipeptide Which Simultaneously Exhibits Gelation and Crystallization Behavior.

PubMed

Martin, Adam D; Wojciechowski, Jonathan P; Bhadbhade, Mohan M; Thordarson, Pall

2016-03-08

Short peptides capped at their N-terminus are often highly efficient gelators, yet notoriously difficult to crystallize. This is due to strong unidirectional interactions within fibers, resulting in structure propagation only along one direction. Here, we synthesize the N-capped dipeptide, benzimidazole-diphenylalanine, which forms both hydrogels and single crystals. Even more remarkably, we show using atomic force microscopy the coexistence of these two distinct phases. We then use powder X-ray diffraction to investigate whether the single crystal structure can be extrapolated to the molecular arrangement within the hydrogel. The results suggest parallel β-sheet arrangement as the dominant structural motif, challenging existing models for gelation of short peptides, and providing new directions for the future rational design of short peptide gelators.

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

Modelling of Surfaces. Part 1: Monatomic Metallic Surfaces Using Equivalent Crystal Theory

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John; Rodriguez, Agustin M.

1994-01-01

We present a detailed description of equivalent crystal theory focusing on its application to the study of surface structure. While the emphasis is in the structure of the algorithm and its computational aspects, we also present a comprehensive discussion on the calculation of surface energies of metallic systems with equivalent crystal theory and other approaches. Our results are compared to experiment and other semiempirical as well as first-principles calculations for a variety of fcc and bcc metals.

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.

Invited review liquid crystal models of biological materials and silk spinning.

PubMed

Rey, Alejandro D; Herrera-Valencia, Edtson E

2012-06-01

A review of thermodynamic, materials science, and rheological liquid crystal models is presented and applied to a wide range of biological liquid crystals, including helicoidal plywoods, biopolymer solutions, and in vivo liquid crystals. The distinguishing characteristics of liquid crystals (self-assembly, packing, defects, functionalities, processability) are discussed in relation to biological materials and the strong correspondence between different synthetic and biological materials is established. Biological polymer processing based on liquid crystalline precursors includes viscoelastic flow to form and shape fibers. Viscoelastic models for nematic and chiral nematics are reviewed and discussed in terms of key parameters that facilitate understanding and quantitative information from optical textures and rheometers. It is shown that viscoelastic modeling the silk spinning process using liquid crystal theories sheds light on textural transitions in the duct of spiders and silk worms as well as on tactoidal drops and interfacial structures. The range and consistency of the predictions demonstrates that the use of mesoscopic liquid crystal models is another tool to develop the science and biomimetic applications of mesogenic biological soft matter. Copyright © 2011 Wiley Periodicals, Inc.

Effect of surface modification of cellulose nanocrystal on nonisothermal crystallization of poly(β-hydroxybutyrate) composites.

PubMed

Chen, Jianxiang; Wu, Defeng; Tam, Kam C; Pan, Keren; Zheng, Zhigong

2017-02-10

Ring-opening polymerization of l-lactide from cellulose nanocrystal (CNC) surface yielded polylactide-grafted CNC (CNC-g-PLA). The structure and chemical composition of the CNC-g-PLA were characterized by FT-IR, 1 H NMR, XPS and XRD. The crystallization behavior and lamellar structure of poly(β-hydroxybutyrate) (PHB) in the presence of pristine CNC and CNC-g-PLA were elucidated via DSC and SAXS, and Babinet's reciprocity theory was applied. Crystallization kinetics were further analyzed using Ozawa, Mo and Kissinger models. In the presence of pristine CNC, nucleation of PHB crystals led to an increase in the crystallization temperature (T c ) of PHB; while CNC-g-PLA acted as antinucleation agent, resulting in a remarkable reduction in T c of PHB. Accordingly, the composite with pristine CNC possessed a higher crystallization rate than neat PHB, while CNC-g-PLA displayed the lowest crystallization rate. However, the lamellar structure of PHB was not affected by the presence of pristine and modified CNCs, and almost identical crystallization activation energies as the neat PHB were observed, indicating that nucleation is dominant during PHB crystallization, instead of crystal growth. This study offers a promising approach of using pristine and modified CNCs to control the crystallization of biodegradable aliphatic polyesters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complex assembly, crystallization and preliminary X-ray crystallographic studies of rhesus macaque MHC Mamu-A*01 complexed with an immunodominant SIV-Gag nonapeptide

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

Chu, Fuliang; Graduate School, Chinese Academy of Sciences, Beijing; Lou, Zhiyong

2005-06-01

Crystallization of the first rhesus macaque MHC class I complex. Simian immunodeficiency virus (SIV) infection in rhesus macaques has been used as the best model for the study of human immunodeficiency virus (HIV) infection in humans, especially in the cytotoxic T-lymphocyte (CTL) response. However, the structure of rhesus macaque (or any other monkey model) major histocompatibility complex class I (MHC I) presenting a specific peptide (the ligand for CTL) has not yet been elucidated. Here, using in vitro refolding, the preparation of the complex of the rhesus macaque MHC I allele (Mamu-A*01) with human β{sub 2}m and an immunodominant peptide,more » CTPYDINQM (Gag-CM9), derived from SIV Gag protein is reported. The complex (45 kDa) was crystallized; the crystal belongs to space group I422, with unit-cell parameters a = b = 183.8, c = 155.2 Å. The crystal contains two molecules in the asymmetric unit and diffracts X-rays to 2.8 Å resolution. The structure is being solved by molecular replacement and this is the first attempt to determined the crystal structure of a peptide–nonhuman primate MHC complex.« less

Substituent effect on the thermodynamic solubility of structural analogs: relative contribution of crystal packing and hydration.

PubMed

Ozaki, Shunsuke; Nakagawa, Yoshiaki; Shirai, Osamu; Kano, Kenji

2014-11-01

Thermodynamic analysis of the solubility of benzoylphenylurea (BPU) derivatives was conducted to investigate the relative importance of crystal packing and hydration for improving solubility with minor structural modification. The contribution of crystal packing to solubility was evaluated from the change in Gibbs energy on the transition from the crystalline to liquid state. Hydration Gibbs energy was estimated using a linear free-energy relationship between octanol-water partition coefficients and gas-water partition coefficients. The established solubility model satisfactorily explained the relative thermodynamic solubility of the model compounds and revealed that crystal packing and hydration equally controlled solubility of the structural analogs. All hydrophobic substituents were undesirable for solubility in terms of hydration, as expected. On the other hand, some of these hydrophobic substituents destabilized crystal packing and improved the solubility of the BPU derivatives when their impact on crystal packing exceeded their negative influence on hydration. The replacement of a single substituent could cause more than a 10-fold enhancement in thermodynamic solubility; this degree of improvement was comparable to that generally achieved by amorphous formulations. Detailed analysis of thermodynamic solubility will allow us to better understand the true substituent effect and design drug-like candidates efficiently. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Monoclinic crystal structure of α - RuCl 3 and the zigzag antiferromagnetic ground state

DOE PAGES

Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; ...

2015-12-10

We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, inmore » contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition around 8 T for in-plane fields followed by a gradual, asymptotic approach to magnetization saturation, as characteristic of strongly anisotropic exchange interactions.« less

Practical quantum mechanics-based fragment methods for predicting molecular crystal properties.

PubMed

Wen, Shuhao; Nanda, Kaushik; Huang, Yuanhang; Beran, Gregory J O

2012-06-07

Significant advances in fragment-based electronic structure methods have created a real alternative to force-field and density functional techniques in condensed-phase problems such as molecular crystals. This perspective article highlights some of the important challenges in modeling molecular crystals and discusses techniques for addressing them. First, we survey recent developments in fragment-based methods for molecular crystals. Second, we use examples from our own recent research on a fragment-based QM/MM method, the hybrid many-body interaction (HMBI) model, to analyze the physical requirements for a practical and effective molecular crystal model chemistry. We demonstrate that it is possible to predict molecular crystal lattice energies to within a couple kJ mol(-1) and lattice parameters to within a few percent in small-molecule crystals. Fragment methods provide a systematically improvable approach to making predictions in the condensed phase, which is critical to making robust predictions regarding the subtle energy differences found in molecular crystals.

“Skin-Core-Skin” Structure of Polymer Crystallization Investigated by Multiscale Simulation

PubMed Central

Ruan, Chunlei

2018-01-01

“Skin-core-skin” structure is a typical crystal morphology in injection products. Previous numerical works have rarely focused on crystal evolution; rather, they have mostly been based on the prediction of temperature distribution or crystallization kinetics. The aim of this work was to achieve the “skin-core-skin” structure and investigate the role of external flow and temperature fields on crystal morphology. Therefore, the multiscale algorithm was extended to the simulation of polymer crystallization in a pipe flow. The multiscale algorithm contains two parts: a collocated finite volume method at the macroscopic level and a morphological Monte Carlo method at the microscopic level. The SIMPLE (semi-implicit method for pressure linked equations) algorithm was used to calculate the polymeric model at the macroscopic level, while the Monte Carlo method with stochastic birth-growth process of spherulites and shish-kebabs was used at the microscopic level. Results show that our algorithm is valid to predict “skin-core-skin” structure, and the initial melt temperature and the maximum velocity of melt at the inlet mainly affects the morphology of shish-kebabs. PMID:29659516

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.

Polymorphism in molecular solids: an extraordinary system of red, orange, and yellow crystals.

PubMed

Yu, Lian

2010-09-21

Diamond and graphite are polymorphs of each other: they have the same composition but different structures and properties. Many other substances exhibit polymorphism: inorganic and organic, natural and manmade. Polymorphs are encountered in studies of crystallization, phase transition, materials synthesis, and biomineralization and in the manufacture of specialty chemicals. Polymorphs can provide valuable insights into crystal packing and structure-property relationships. 5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, known as ROY for its red, orange, and yellow crystals, has seven polymorphs with solved structures, the largest number in the Cambridge Structural Database. First synthesized by medicinal chemists, ROY has attracted attention from solid-state chemists because it demonstrates the remarkable diversity possible in organic solids. Many structures of ROY polymorphs and their thermodynamic properties are known, making ROY an important model system for testing computational models. Though not the most polymorphic substance on record, ROY is extraordinary in that many of its polymorphs can crystallize simultaneously from the same liquid and are kinetically stable under the same conditions. Studies of ROY polymorphs have revealed a new crystallization mechanism that invalidates the common view that nucleation defines the polymorph of crystallization. A slow-nucleating polymorph can still dominate the product if it grows rapidly and nucleates on another polymorph. Studies of ROY have also helped understand a new, surprisingly fast mode of crystal growth in organic liquids cooled to the glass transition temperature. This growth mode exists only for those polymorphs that have more isotropic, and perhaps more liquid-like, packing. The rich polymorphism of ROY results from a combination of favorable thermodynamics and kinetics. Not only must there be many polymorphs of comparable energies or free energies, many polymorphs must be kinetically stable and crystallize at comparable rates to be observed. This system demonstrates the unique insights that polymorphism provides into solid-state structures and properties, as well as the inadequacy of our current understanding of the phenomenon. Despite many studies of ROY, it is still impossible to predict the next molecule that is equally or more polymorphic. ROY is a lucky gift from medicinal chemists.

Beyond the Flipped Classroom: A Highly Interactive Cloud-Classroom (HIC) Embedded into Basic Materials Science Courses

ERIC Educational Resources Information Center

Liou, Wei-Kai; Bhagat, Kaushal Kumar; Chang, Chun-Yen

2016-01-01

The present study compares the highly interactive cloud-classroom (HIC) system with traditional methods of teaching materials science that utilize crystal structure picture or real crystal structure model, in order to examine its learning effectiveness across three dimensions: knowledge, comprehension and application. The aim of this study was to…

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.

Cylindrically symmetric Green's function approach for modeling the crystal growth morphology of ice.

PubMed

Libbrecht, K G

1999-08-01

We describe a front-tracking Green's function approach to modeling cylindrically symmetric crystal growth. This method is simple to implement, and with little computer power can adequately model a wide range of physical situations. We apply the method to modeling the hexagonal prism growth of ice crystals, which is governed primarily by diffusion along with anisotropic surface kinetic processes. From ice crystal growth observations in air, we derive measurements of the kinetic growth coefficients for the basal and prism faces as a function of temperature, for supersaturations near the water saturation level. These measurements are interpreted in the context of a model for the nucleation and growth of ice, in which the growth dynamics are dominated by the structure of a disordered layer on the ice surfaces.

Gradient Plasticity Model and its Implementation into MARMOT

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

Barker, Erin I.; Li, Dongsheng; Zbib, Hussein M.

2013-08-01

The influence of strain gradient on deformation behavior of nuclear structural materials, such as boby centered cubic (bcc) iron alloys has been investigated. We have developed and implemented a dislocation based strain gradient crystal plasticity material model. A mesoscale crystal plasticity model for inelastic deformation of metallic material, bcc steel, has been developed and implemented numerically. Continuum Dislocation Dynamics (CDD) with a novel constitutive law based on dislocation density evolution mechanisms was developed to investigate the deformation behaviors of single crystals, as well as polycrystalline materials by coupling CDD and crystal plasticity (CP). The dislocation density evolution law in thismore » model is mechanism-based, with parameters measured from experiments or simulated with lower-length scale models, not an empirical law with parameters back-fitted from the flow curves.« less

Ge K-Edge Extended X-Ray Absorption Fine Structure Study of the Local Structure of Amorphous GeTe and the Crystallization

NASA Astrophysics Data System (ADS)

Maeda, Yoshihito; Wakagi, Masatoshi

1991-01-01

The local structure and crystallization of amorphous GeTe (a-GeTe) were examined by means of Ge K-edge EXAFS. In a-GeTe, both Ge-Ge and Ge-Te bonds were observed to exist in nearest neighbors of Ge. The average coordination number around Ge is 3.7, which is close to the tetrahedral structure. A random covalent network (RCN) model seems to be suitable for the local Structure. After a-GeTe crystallizes at 129°C, the Ge-Ge bond disappears and the Ge-Te bond length increases considerably. As temperature rises, in a-GeTe the Debye-Waller factor of the Ge-Te bond increases greatly, while that of the Ge-Ge bond increases only slightly. At the crystallization, it is found that the fluctuation of the Ge-Te bond length plays a major role in the change of the local structure and bonding state around Ge.

Medium-range structure and glass forming ability in Zr–Cu–Al bulk metallic glasses

DOE PAGES

Zhang, Pei; Maldonis, Jason J.; Besser, M. F.; ...

2016-03-05

Fluctuation electron microscopy experiments combined with hybrid reverse Monte Carlo modeling show a correlation between medium-range structure at the nanometer scale and glass forming ability in two Zr–Cu–Al bulk metallic glass (BMG) alloys. Both Zr 50Cu 35Al 15 and Zr 50Cu 45Al 5 exhibit two nanoscale structure types, one icosahedral and the other more crystal-like. In Zr 50Cu 35Al 15, the poorer glass former, the crystal-like structure is more stable under annealing below the glass transition temperature, T g, than in Zr 50Cu 45Al 5. Variable resolution fluctuation microscopy of the MRO clusters show that in Zr 50Cu 35Al 15more » on sub-Tg annealing, the crystal-like clusters shrink even as they grow more ordered, while icosahedral-like clusters grow. Furthermore, the results suggest that achieving better glass forming ability in this alloy system may depend more on destabilizing crystal-like structures than enhancing non-crystalline structures.« less

Characterisation of calcium phosphate crystals on calcified human aortic vascular smooth muscle cells and potential role of magnesium.

PubMed

Louvet, Loïc; Bazin, Dominique; Büchel, Janine; Steppan, Sonja; Passlick-Deetjen, Jutta; Massy, Ziad A

2015-01-01

Cardiovascular disease including vascular calcification (VC) remains the leading cause of death in patients suffering from chronic kidney disease (CKD). The process of VC seems likely to be a tightly regulated process where vascular smooth muscle cells are playing a key role rather than just a mere passive precipitation of calcium phosphate. Characterisation of the chemical and crystalline structure of VC was mainly led in patients or animal models with CKD. Likewise, Mg2+ was found to be protective in living cells although a potential role for Mg2+ could not be excluded on crystal formation and precipitation. In this study, the crystal formation and the role of Mg2+ were investigated in an in vitro model of primary human aortic vascular smooth muscle cells (HAVSMC) with physical techniques. In HAVSMC incubated with increased Ca x Pi medium, only calcium phosphate apatite crystals (CPA) were detected by Micro-Fourier Transform InfraRed spectroscopy (µFTIR) and Field Effect Scanning Electron Microscope (FE-SEM) and Energy Dispersive X-ray spectrometry (EDX) at the cell layer level. Supplementation with Mg2+ did not alter the crystal composition or structure. The crystal deposition was preferentially positioned near or directly on cells as pictured by FE-SEM observations and EDX measurements. Large µFTIR maps revealed spots of CPA crystals that were associated to the cellular layout. This qualitative analysis suggests a potential beneficial effect of Mg2+ at 5 mM in noticeably reducing the number and intensities of CPA µFTIR spots. For the first time in a model of HAVSMC, induced calcification led to the formation of the sole CPA crystals. Our data seems to exclude a physicochemical role of Mg2+ in altering the CPA crystal growth, composition or structure. Furthermore, Mg2+ beneficial role in attenuating VC should be linked to an active cellular role.

Characterisation of Calcium Phosphate Crystals on Calcified Human Aortic Vascular Smooth Muscle Cells and Potential Role of Magnesium

PubMed Central

Louvet, Loïc; Bazin, Dominique; Büchel, Janine; Steppan, Sonja; Passlick-Deetjen, Jutta; Massy, Ziad A.

2015-01-01

Background Cardiovascular disease including vascular calcification (VC) remains the leading cause of death in patients suffering from chronic kidney disease (CKD). The process of VC seems likely to be a tightly regulated process where vascular smooth muscle cells are playing a key role rather than just a mere passive precipitation of calcium phosphate. Characterisation of the chemical and crystalline structure of VC was mainly led in patients or animal models with CKD. Likewise, Mg2+ was found to be protective in living cells although a potential role for Mg2+ could not be excluded on crystal formation and precipitation. In this study, the crystal formation and the role of Mg2+ were investigated in an in vitro model of primary human aortic vascular smooth muscle cells (HAVSMC) with physical techniques. Methodology/Principal Findings In HAVSMC incubated with increased Ca x Pi medium, only calcium phosphate apatite crystals (CPA) were detected by Micro-Fourier Transform InfraRed spectroscopy (µFTIR) and Field Effect Scanning Electron Microscope (FE — SEM) and Energy Dispersive X-ray spectrometry (EDX) at the cell layer level. Supplementation with Mg2+ did not alter the crystal composition or structure. The crystal deposition was preferentially positioned near or directly on cells as pictured by FE — SEM observations and EDX measurements. Large µFTIR maps revealed spots of CPA crystals that were associated to the cellular layout. This qualitative analysis suggests a potential beneficial effect of Mg2+ at 5 mM in noticeably reducing the number and intensities of CPA µFTIR spots. Conclusions/Significance For the first time in a model of HAVSMC, induced calcification led to the formation of the sole CPA crystals. Our data seems to exclude a physicochemical role of Mg2+ in altering the CPA crystal growth, composition or structure. Furthermore, Mg2+ beneficial role in attenuating VC should be linked to an active cellular role. PMID:25607936

In situ data collection and structure refinement from microcapillary protein crystallization

PubMed Central

Yadav, Maneesh K.; Gerdts, Cory J.; Sanishvili, Ruslan; Smith, Ward W.; Roach, L. Spencer; Ismagilov, Rustem F.; Kuhn, Peter; Stevens, Raymond C.

2007-01-01

In situ X-ray data collection has the potential to eliminate the challenging task of mounting and cryocooling often fragile protein crystals, reducing a major bottleneck in the structure determination process. An apparatus used to grow protein crystals in capillaries and to compare the background X-ray scattering of the components, including thin-walled glass capillaries against Teflon, and various fluorocarbon oils against each other, is described. Using thaumatin as a test case at 1.8 Å resolution, this study demonstrates that high-resolution electron density maps and refined models can be obtained from in situ diffraction of crystals grown in microcapillaries. PMID:17468785

Reduced-temperature crystallization of thin amorphous Fe80B20 films studied via empirical modeling of extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Oliver, S. A.; Ayers, J. D.; Das, B. N.; Koon, N. C.

1996-04-01

The evolution of the local atomic environment around Fe atoms in very thin (15 nm), amorphous, partially crystallized and fully crystallized films of Fe80B20 was studied using extended x-ray absorption fine structure (EXAFS) measurements. The relative atomic fraction of each crystalline phase present in the annealed samples was extracted from the Fe EXAFS data by a least-squares fitting procedure, using data collected from t-Fe3B, t-Fe2B, and α-Fe standards. The type and relative fraction of the crystallization products follows the trends previously measured in Fe80B20 melt-spun ribbons, except for the fact that crystallization temperatures are ≊200 K lower than those measured in bulk equivalents. This greatly reduced crystallization temperature may arise from the dominant role of surface nucleation sites in the crystallization of very thin amorphous films.

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

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.

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.

Superspace description of wagnerite-group minerals (Mg,Fe,Mn)2(PO4)(F,OH)

PubMed Central

Lazic, Biljana; Armbruster, Thomas; Chopin, Christian; Grew, Edward S.; Baronnet, Alain; Palatinus, Lukas

2014-01-01

Reinvestigation of more than 40 samples of minerals belonging to the wagnerite group (Mg, Fe, Mn)2(PO4)(F,OH) from diverse geological environments worldwide, using single-crystal X-ray diffraction analysis, showed that most crystals have incommensurate structures and, as such, are not adequately described with known polytype models (2b), (3b), (5b), (7b) and (9b). Therefore, we present here a unified superspace model for the structural description of periodically and aperiodically modulated wagnerite with the (3+1)-dimensional superspace group C2/c(0β0)s0 based on the average triplite structure with cell parameters a ≃ 12.8, b ≃ 6.4, c ≃ 9.6 Å, β ≃ 117° and the modulation vectors q = β b*. The superspace approach provides a way of simple modelling of the positional and occupational modulation of Mg/Fe and F/OH in wagnerite. This allows direct comparison of crystal properties. PMID:24675594

Monitoring of Batch Industrial Crystallization with Growth, Nucleation, and Agglomeration. Part 2: Structure Design for State Estimation with Secondary Measurements

PubMed Central

2017-01-01

This work investigates the design of alternative monitoring tools based on state estimators for industrial crystallization systems with nucleation, growth, and agglomeration kinetics. The estimation problem is regarded as a structure design problem where the estimation model and the set of innovated states have to be chosen; the estimator is driven by the available measurements of secondary variables. On the basis of Robust Exponential estimability arguments, it is found that the concentration is distinguishable with temperature and solid fraction measurements while the crystal size distribution (CSD) is not. Accordingly, a state estimator structure is selected such that (i) the concentration (and other distinguishable states) are innovated by means of the secondary measurements processed with the geometric estimator (GE), and (ii) the CSD is estimated by means of a rigorous model in open loop mode. The proposed estimator has been tested through simulations showing good performance in the case of mismatch in the initial conditions, parametric plant-model mismatch, and noisy measurements. PMID:28890604

Monitoring of Batch Industrial Crystallization with Growth, Nucleation, and Agglomeration. Part 2: Structure Design for State Estimation with Secondary Measurements.

PubMed

Porru, Marcella; Özkan, Leyla

2017-08-30

This work investigates the design of alternative monitoring tools based on state estimators for industrial crystallization systems with nucleation, growth, and agglomeration kinetics. The estimation problem is regarded as a structure design problem where the estimation model and the set of innovated states have to be chosen; the estimator is driven by the available measurements of secondary variables. On the basis of Robust Exponential estimability arguments, it is found that the concentration is distinguishable with temperature and solid fraction measurements while the crystal size distribution (CSD) is not. Accordingly, a state estimator structure is selected such that (i) the concentration (and other distinguishable states) are innovated by means of the secondary measurements processed with the geometric estimator (GE), and (ii) the CSD is estimated by means of a rigorous model in open loop mode. The proposed estimator has been tested through simulations showing good performance in the case of mismatch in the initial conditions, parametric plant-model mismatch, and noisy measurements.

Radiating dipoles in photonic crystals

PubMed

Busch; Vats; John; Sanders

2000-09-01

The radiation dynamics of a dipole antenna embedded in a photonic crystal are modeled by an initially excited harmonic oscillator coupled to a non-Markovian bath of harmonic oscillators representing the colored electromagnetic vacuum within the crystal. Realistic coupling constants based on the natural modes of the photonic crystal, i.e., Bloch waves and their associated dispersion relation, are derived. For simple model systems, well-known results such as decay times and emission spectra are reproduced. This approach enables direct incorporation of realistic band structure computations into studies of radiative emission from atoms and molecules within photonic crystals. We therefore provide a predictive and interpretative tool for experiments in both the microwave and optical regimes.

Relationship between crystal structure and solid-state properties of pharmaceuticals

NASA Astrophysics Data System (ADS)

Sheth, Agam R.

This thesis strives to understand the structure-property relationships of some pharmaceutical crystals at the molecular level with emphasis on the effect of secondary processing on the solid phase. Using single crystal X-ray diffractometry (SCXRD), the structure of warfarin sodium 2-propanol adduct (W) was established to be a true solvate, contrary to previous reports. Using dynamic water vapor sorption, optical and environmental scanning electron microscopy, SCXRD, powder X-ray diffractometry (PXRD), volume computations and molecular modeling, the effect of relative humidity and temperature on the crystal structure of W was investigated. Ab initio calculations on piroxicam showed that the difference in energy between the two polymorphs, I and II, arises predominantly from the difference between their lattice energies. The detailed hydrogen bonding networks of the two polymorphs are described and compared using graph sets. Despite stabilization of the polymorphs by hydrogen bonds, pair-wise distribution function transforms show a loss of polymorphic memory upon cryogrinding the two polymorphs, leading to a difference in recrystallization behavior between amorphous piroxicam prepared from polymorphs I and II. Structural and solid-state changes of piroxicam polymorphs under mechanical stress were investigated using cryogenic grinding, PXRD, diffuse-reflectance solid-state ultraviolet-visible spectroscopy, 13C solid-state nuclear magnetic resonance spectroscopy, and diffuse-reflectance solid-state Fourier-transform infrared spectroscopy. Intermolecular proton transfer was found to accompany changes in phase and color observed upon cryogrinding the two polymorphs. Model-free and model-fitting studies of the dehydration kinetics of piroxicam monohydrate (PM) showed the dependence of activation energy ( Ea) on both isothermal and non-isothermal heating conditions, and on the fraction of conversion. In the constant-E a region, isothermal dehydration follows the two-dimensional phase boundary model, while non-isothermal dehydration follows a mechanism intermediate between two- and three-dimensional diffusion that cannot be described by any of the common models. Structural studies suggest that the complex hydrogen bond pattern in PM is responsible for the observed dehydration behavior. Ab initio calculations provide an explanation for the changes in the molecular and crystal structures accompanying the reversible change in hydration state between anhydrous piroxicam Form I and PM. The thesis further demonstrates the utility of model-free analysis in describing complex dehydration kinetics.

Improved performance of HgCdTe infrared detector focal plane arrays by modulating light field based on photonic crystal structure

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

Liang, Jian; Hu, Weida, E-mail: wdhu@mail.sitp.ac.cn; Ye, Zhenhua

2014-05-14

An HgCdTe long-wavelength infrared focal plane array photodetector is proposed by modulating light distributions based on the photonic crystal. It is shown that a promising prospect of improving performance is better light harvest and dark current limitation. To optimize the photon field distributions of the HgCdTe-based photonic crystal structure, a numerical method is built by combining the finite-element modeling and the finite-difference time-domain simulation. The optical and electrical characteristics of designed HgCdTe mid-wavelength and long-wavelength photon-trapping infrared detector focal plane arrays are obtained numerically. The results indicate that the photon crystal structure, which is entirely compatible with the large infraredmore » focal plane arrays, can significantly reduce the dark current without degrading the quantum efficiency compared to the regular mesa or planar structure.« less

Refined structures of three crystal forms of toxic shock syndrome toxin-1 and of a tetramutant with reduced activity.

PubMed Central

Prasad, G. S.; Radhakrishnan, R.; Mitchell, D. T.; Earhart, C. A.; Dinges, M. M.; Cook, W. J.; Schlievert, P. M.; Ohlendorf, D. H.

1997-01-01

The structure of toxic shock syndrome toxin-1 (TSST-1), the causative agent in toxic shock syndrome, has been determined in three crystal forms. The three structural models have been refined to R-factors of 0.154, 0.150, and 0.198 at resolutions of 2.05 A, 2.90 A, and 2.75 A, respectively. One crystal form of TSST-1 contains a zinc ion bound between two symmetry-related molecules. Although not required for biological activity, zinc dramatically potentiates the mitogenicity of TSST-1 at very low concentrations. In addition, the structure of the tetramutant TSST-1H [T69I, Y80W, E132K, I140T], which is nonmitogenic and does not amplify endotoxin shock, has been determined and refined in a fourth crystal form (R-factor = 0.173 to 1.9 A resolution). PMID:9194182

Determining crystal structures through crowdsourcing and coursework

NASA Astrophysics Data System (ADS)

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-09-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Determining crystal structures through crowdsourcing and coursework.

PubMed

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

2016-09-16

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

Structure modeling and manufacturing PCFs for the range of 2-25 μm

NASA Astrophysics Data System (ADS)

Lvov, Alexandr; Salimgareev, Dmitrii; Korsakov, Michail; Korsakov, Alexandr; Zhukova, Liya

2017-11-01

Photostable and flexible materials transparent at the wide spectral range are necessary for the development of optical fiber units. Solid solutions of silver and monadic thallium halides are the most suitable crystal media for this purpose. The goal of our research was the search of optimum structure for the fibers with a single mode operation and a rather large core diameter. We modelled fiber structures (solid-core, hollow-core, active-core PCF) with various ratio of inserts diameters and increments between the inserts, basing on two crystal systems: AgCl-AgBr and AgBr-TlI. Then we chose the single mode fiber structure and manufactured it by means of extrusion.

A possible molecular basis for photoprotection in the minor antenna proteins of plants.

PubMed

Fox, Kieran F; Ünlü, Caner; Balevičius, Vytautas; Ramdour, Baboo Narottamsing; Kern, Carina; Pan, Xiaowei; Li, Mei; van Amerongen, Herbert; Duffy, Christopher D P

2018-07-01

The bioenergetics of light-harvesting by photosynthetic antenna proteins in higher plants is well understood. However, investigation into the regulatory non-photochemical quenching (NPQ) mechanism, which dissipates excess energy in high light, has led to several conflicting models. It is generally accepted that the major photosystem II antenna protein, LHCII, is the site of NPQ, although the minor antenna complexes (CP24/26/29) are also proposed as alternative/additional NPQ sites. LHCII crystals were shown to exhibit the short excitation lifetime and several spectral signatures of the quenched state. Subsequent structure-based models showed that this quenching could be explained by slow energy trapping by the carotenoids, in line with one of the proposed models. Using Fluorescence Lifetime Imaging Microscopy (FLIM) we show that the crystal structure of CP29 corresponds to a strongly quenched conformation. Using a structure-based theoretical model we show that this quenching may be explained by the same slow, carotenoid-mediated quenching mechanism present in LHCII crystals. Copyright © 2018 Elsevier B.V. All rights reserved.

Tuning hardness in calcite by incorporation of amino acids

NASA Astrophysics Data System (ADS)

Kim, Yi-Yeoun; Carloni, Joseph D.; Demarchi, Beatrice; Sparks, David; Reid, David G.; Kunitake, Miki E.; Tang, Chiu C.; Duer, Melinda J.; Freeman, Colin L.; Pokroy, Boaz; Penkman, Kirsty; Harding, John H.; Estroff, Lara A.; Baker, Shefford P.; Meldrum, Fiona C.

2016-08-01

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit--mineral single crystals containing embedded macromolecules--remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

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.

Discrete structures in continuum descriptions of defective crystals

PubMed Central

2016-01-01

I discuss various mathematical constructions that combine together to provide a natural setting for discrete and continuum geometric models of defective crystals. In particular, I provide a quite general list of ‘plastic strain variables’, which quantifies inelastic behaviour, and exhibit rigorous connections between discrete and continuous mathematical structures associated with crystalline materials that have a correspondingly general constitutive specification. PMID:27002070

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

Treesearch

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

1993-01-01

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

Low-Ca pyroxenes from LL group chondritic meteorites: Crystal structural studies and implications for their thermal histories

NASA Astrophysics Data System (ADS)

Artioli, G.; Davoli, G.

1994-12-01

Crystal structural refinements of one orthorhombic (Pbca) and two monoclinic (P21/c) single crystals, from chondrules of low-Ca pyroxenes from unequilibrated chondritic meteorites of the LL group, were carried out. The intracrystalline Fe-Mg distribution between the M1 and M2 crystallographic sites of the Parnallee (LL-3) orthoenstatite is suggestive of very rapid cooling, whereas both the structural state and intracrystalline Fe-Mg distribution in the Soko Banja (LL-4) and Jolomba (LL-6) clinoenstaties indicate rapid cooling from the high temperature polymorphs, with no significant re-equilibration at lower temperatures. These results imply that thermal metamorphism in the parent body, if present, was insufficient to allow re-equilibration of the pyroxene minerals to low temperature, ordered crystal structures. The data also indicate that, assuming low or mild pressure and shock effects, there is no well defined correlation between equilibrium temperature of the mineral phases and the alleged petrologic type of the meteorites. This evidence is consistent with a rubble pile model for the parent body accretional history, or with an onion shell model with very low thermal peak metamorphism, as is assumed for a very small object.

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.

Exploration of N-arylpiperazine Binding Sites of D2 Dopaminergic Receptor.

PubMed

Soskic, Vukic; Sukalovic, Vladimir; Kostic-Rajacic, Sladjana

2015-01-01

The crystal structures of the D3 dopamine receptor and several other G-protein coupled receptors (GPCRs) were published in recent times. Those 3D structures are used by us and other scientists as a template for the homology modeling and ligand docking analysis of related GPCRs. Our main scientific interest lies in the field of pharmacologically active N-arylpiperazines that exhibit antipsychotic and/or antidepressant properties, and as such are dopaminergic and serotonergic receptor ligands. In this short review article we are presenting synthesis and biological data on the new N-arylpipereazine as well our results on molecular modeling of the interactions of those N-arylpiperazines with the model of D2 dopamine receptors. To obtain that model the crystal structure of the D3 dopamine receptor was used. Our results show that the N-arylpiperazines binding site consists of two pockets: one is the orthosteric binding site where the N-arylpiperazine part of the ligand is docked and the second is a non-canonical accessory binding site for N-arylpipereazine that is formed by a second extracellular loop (ecl2) of the receptor. Until now, the structure of this receptor region was unresolved in crystal structure analyses of the D3 dopamine receptor. To get a more complete picture of the ligand - receptor interaction, DFT quantum mechanical calculations on N-arylpiperazine were performed and the obtained models were used to examine those interactions.

Ab initio solution of macromolecular crystal structures without direct methods.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

2017-04-04

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

NASA Technical Reports Server (NTRS)

Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.

2003-01-01

One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin microfilament system to be restructured in a controlled manner via polymerization, depolymerization, severing, cross-linking, and anchorage. The structure the semicrystalline state of profilin:actin will challenge and validate current models of muscle contraction and cell motility. The methodology and theory under development will be easily extendable to other systems.

[Development of intelligence in old age].

PubMed

Rott, C

1990-01-01

This article attempts to find the structure of a selected spectrum of intelligence. A combination of longitudinal and cross-sectional methods is applied. Two dimensions were found, which can be named as "crystallized" and "fluid" abilities (in the sense of Horn & Cattell). Whereas, the crystallized abilities do not show any systematic variation from age 61 to 83, fluid abilities decline with age. Schaie's three-component-model is not able to describe differences and variations of crystallized intelligence. Within fluid intelligence, age changes are more important than cohort differences. There are hints that structural changes take place.

The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry.

PubMed

Noya, Eva G; Vega, Carlos; Doye, Jonathan P K; Louis, Ard A

2010-06-21

The phase diagram of model anisotropic particles with four attractive patches in a tetrahedral arrangement has been computed at two different values of the range of the potential, with the aim of investigating the conditions under which a diamond crystal can be formed. We find that the diamond phase is never stable for our longer-ranged potential. At low temperatures and pressures, the fluid freezes into a body-centered-cubic solid that can be viewed as two interpenetrating diamond lattices with a weak interaction between the two sublattices. Upon compression, an orientationally ordered face-centered-cubic crystal becomes more stable than the body-centered-cubic crystal, and at higher temperatures, a plastic face-centered-cubic phase is stabilized by the increased entropy due to orientational disorder. A similar phase diagram is found for the shorter-ranged potential, but at low temperatures and pressures, we also find a region over which the diamond phase is thermodynamically favored over the body-centered-cubic phase. The higher vibrational entropy of the diamond structure with respect to the body-centered-cubic solid explains why it is stable even though the enthalpy of the latter phase is lower. Some preliminary studies on the growth of the diamond structure starting from a crystal seed were performed. Even though the diamond phase is never thermodynamically stable for the longer-ranged model, direct coexistence simulations of the interface between the fluid and the body-centered-cubic crystal and between the fluid and the diamond crystal show that at sufficiently low pressures, it is quite probable that in both cases the solid grows into a diamond crystal, albeit involving some defects. These results highlight the importance of kinetic effects in the formation of diamond crystals in systems of patchy particles.

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.

Structural morphology of crystals with the barite (BaSO 4) structure: A revision and extension

NASA Astrophysics Data System (ADS)

Hartman, P.; Strom, C. S.

1989-09-01

The structural morphology of crystals with the barite (BaSO 4) structure (sulphates, chromates, perchlorates, permanganates and tetrafluoroborates) has been determined with the use of computer programs. Uniquely defined F forms are {002}, {210}, {211}, {020} and {201}. Two different F slices were found for {101} and {200}, 33 for {011}. Attachment energies and specific surface energies have been calculated for an electrostatic point charge model as a function of the charge distribution in the anion. On this basis it is concluded that {101} behaves as an F form, {200} as an S form and {011} as a K form. The theoretical growth form shows {210}, {101} and {002} as main forms. A comparison is made with habits of natural and synthetic crystals. Experiments on KCIO 4 show that {011} appears at high supersaturations (>38; ;20%). It is shown that a broken bond model provides relative attachment energies that are higher by a factor of about three.

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

A model for the study of ligand binding to the ribosomal RNA helix h44

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

Dibrov, Sergey M.; Parsons, Jerod; Hermann, Thomas

2010-09-02

Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand-RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structuralmore » model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region.« less

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

Zhang, Pei; Maldonis, Jason J.; Besser, M. F.

Fluctuation electron microscopy experiments combined with hybrid reverse Monte Carlo modeling show a correlation between medium-range structure at the nanometer scale and glass forming ability in two Zr–Cu–Al bulk metallic glass (BMG) alloys. Both Zr 50Cu 35Al 15 and Zr 50Cu 45Al 5 exhibit two nanoscale structure types, one icosahedral and the other more crystal-like. In Zr 50Cu 35Al 15, the poorer glass former, the crystal-like structure is more stable under annealing below the glass transition temperature, T g, than in Zr 50Cu 45Al 5. Variable resolution fluctuation microscopy of the MRO clusters show that in Zr 50Cu 35Al 15more » on sub-Tg annealing, the crystal-like clusters shrink even as they grow more ordered, while icosahedral-like clusters grow. Furthermore, the results suggest that achieving better glass forming ability in this alloy system may depend more on destabilizing crystal-like structures than enhancing non-crystalline structures.« less

Triboluminescence and crystal structure of the complex [Eu(NО3 )3 (HMPA)3 ]: role of cleavage planes.

PubMed

Bukvetskii, B V; Mirochnik, A G; Zhikhareva, P A

2017-05-01

The atomic structure of crystals of the [Eu(NО 3 ) 3 (HMPA) 3 ] [hexamethylphosphotriamide (HMPA)] complex characterized by an intensive luminescence and triboluminescence was determined using X-ray structural analysis. Noncentrosymmetric crystals have a monoclinic syngony: a = 16.0686 (3), b = 11.0853 (2), c = 20.9655 Å (4), β = 93.232° (1), space group P2 1 , Z = 4, ρ calc  = 1.560 g/cm 3 . The crystal structure is represented by individual С 18 Н 54 EuN 12 O 12 P 3 complexes linked through van der Waals interactions with clearly expressed cleavage planes. The Eu(III) atom coordination polyhedron reflected the state of a distorted square antiprism. Structural aspects of the suggested model, including formation of triboluminescence properties, were considered and the role of the cleavage planes was discussed. Copyright © 2016 John Wiley & Sons, Ltd.

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

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.

Highly robust crystalsome via directed polymer crystallization at curved liquid/liquid interface

PubMed Central

Wang, Wenda; Qi, Hao; Zhou, Tian; Mei, Shan; Han, Lin; Higuchi, Takeshi; Jinnai, Hiroshi; Li, Christopher Y.

2016-01-01

Lipids and amphiphilic block copolymers spontaneously self-assemble in water to form a plethora of micelles and vesicles. They are typically fluidic in nature and often mechanically weak for applications such as drug delivery and gene therapeutics. Mechanical properties of polymeric materials could be improved by forming crystalline structures. However, most of the self-assembled micelles and vesicles have curved surfaces and precisely tuning crystallization within a nanoscale curved space is challenging, as the curved geometry is incommensurate with crystals having three-dimensional translational symmetry. Herein, we report using a miniemulsion crystallization method to grow nanosized, polymer single-crystal-like capsules. We coin the name crystalsome to describe this unique structure, because they are formed by polymer lamellar crystals and their structure mimics liposomes and polymersomes. Using poly(L-lactic acid) (PLLA) as the model polymer, we show that curved water/p-xylene interface formed by the miniemulsion process can guide the growth of PLLA single crystals. Crystalsomes with the size ranging from ∼148 nm to over 1 μm have been formed. Atomic force microscopy measurement demonstrate a two to three orders of magnitude increase in bending modulus compared with conventional polymersomes. We envisage that this novel structure could shed light on investigating spherical crystallography and drug delivery. PMID:26837260

Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

PubMed

Corbett, Michael S P; Mark, Alan E; Poger, David

2017-02-28

Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Fundamental Studies of Crystal Growth of Microporous Materials

NASA Technical Reports Server (NTRS)

Dutta, P.; George, M.; Ramachandran, N.; Schoeman, B.; Curreri, Peter A. (Technical Monitor)

2002-01-01

Microporous materials are framework structures with well-defined porosity, often of molecular dimensions. Zeolites contain aluminum and silicon atoms in their framework and are the most extensively studied amongst all microporous materials. Framework structures with P, Ga, Fe, Co, Zn, B, Ti and a host of other elements have also been made. Typical synthesis of microporous materials involve mixing the framework elements (or compounds, thereof) in a basic solution, followed by aging in some cases and then heating at elevated temperatures. This process is termed hydrothermal synthesis, and involves complex chemical and physical changes. Because of a limited understanding of this process, most synthesis advancements happen by a trial and error approach. There is considerable interest in understanding the synthesis process at a molecular level with the expectation that eventually new framework structures will be built by design. The basic issues in the microporous materials crystallization process include: (1) Nature of the molecular units responsible for the crystal nuclei formation; (2) Nature of the nuclei and nucleation process; (3) Growth process of the nuclei into crystal; (4) Morphological control and size of the resulting crystal; (5) Surface structure of the resulting crystals; (6) Transformation of frameworks into other frameworks or condensed structures. The NASA-funded research described in this report focuses to varying degrees on all of the above issues and has been described in several publications. Following is the presentation of the highlights of our current research program. The report is divided into five sections: (1) Fundamental aspects of the crystal growth process; (2) Morphological and Surface properties of crystals; (3) Crystal dissolution and transformations; (4) Modeling of Crystal Growth; (5) Relevant Microgravity Experiments.

The effect of tailor-made additives on crystal growth of methyl paraben: Experiments and modelling

NASA Astrophysics Data System (ADS)

Cai, Zhihui; Liu, Yong; Song, Yang; Guan, Guoqiang; Jiang, Yanbin

2017-03-01

In this study, methyl paraben (MP) was selected as the model component, and acetaminophen (APAP), p-methyl acetanilide (PMAA) and acetanilide (ACET), which share the similar molecular structure as MP, were selected as the three tailor-made additives to study the effect of tailor-made additives on the crystal growth of MP. HPLC results indicated that the MP crystals induced by the three additives contained MP only. Photographs of the single crystals prepared indicated that the morphology of the MP crystals was greatly changed by the additives, but PXRD and single crystal diffraction results illustrated that the MP crystals were the same polymorph only with different crystal habits, and no new crystal form was found compared with other references. To investigate the effect of the additives on the crystal growth, the interaction between additives and facets was discussed in detail using the DFT methods and MD simulations. The results showed that APAP, PMAA and ACET would be selectively adsorbed on the growth surfaces of the crystal facets, which induced the change in MP crystal habits.

Crystallinity of tellurium capping and epitaxy of ferromagnetic topological insulator films on SrTiO 3

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

Park, Jihwey; Soh, Yeong-Ah; Aeppli, Gabriel

2015-06-30

Thin films of topological insulators are often capped with an insulating layer since topological insulators are known to be fragile to degradation. However, capping can hinder the observation of novel transport properties of the surface states. To understand the influence of capping on the surface states, it is crucial to understand the crystal structure and the atomic arrangement at the interfaces. Here, we use x-ray diffraction to establish the crystal structure of magnetic topological insulator Cr-doped (Bi,Sb) 2Te 3 (CBST) films grown on SrTiO 3 (1 1 1) substrates with and without a Te capping layer. We find that bothmore » the film and capping layer are single crystal and that the crystal quality of the film is independent of the presence of the capping layer, but that x-rays cause sublimation of the CBST film, which is prevented by the capping layer. Our findings show that the different transport properties of capped films cannot be attributed to a lower crystal quality but to a more subtle effect such as a different electronic structure at the interface with the capping layer. Our results on the crystal structure and atomic arrangements of the topological heterostructure will enable modelling the electronic structure and design of topological heterostructures.« less

Shear sensitive monomer-polymer laminate structure and method of using same

NASA Technical Reports Server (NTRS)

Singh, Jag J. (Inventor); Eftekhari, Abe (Inventor); Parmar, Devendra S. (Inventor)

1993-01-01

Monomer cholesteric liquid crystals have helical structures which result in a phenomenon known as selective reflection, wherein incident white light is reflected in such a way that its wavelength is governed by the instantaneous pitch of the helix structure. The pitch is dependent on temperature and external stress fields. It is possible to use such monomers in flow visualization and temperature measurement. However, the required thin layers of these monomers are quickly washed away by a flow, making their application time dependent for a given flow rate. The laminate structure according to the present invention comprises a liquid crystal polymer substrate attached to a test surface of an article. A light absorbing coating is applied to the substrate and is thin enough to permit bonding steric interaction between the liquid crystal polymer substrate and an overlying liquid crystal monomer thin film. Light is directed through and reflected by the liquid crystal monomer thin film and unreflected light is absorbed by the underlying coating. The wavelength of the reflected light is indicative of the shear stress experienced by the test surface. Novel aspects of the invention include its firm bonding of a liquid crystal monomer to a model and its use of a coating to reduce interference from light unreflected by the monomer helical structure.

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

Ben Smida, Youssef; Marzouki, Riadh; Georges, Samuel

A new sodium cobalt (II) arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6} has been synthesized by a solid-state reaction and its crystal structure determined from single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group C2/m, with a=10.7098(9) Å, b=14.7837(9) Å, c=6.6845(7) Å, and β=105.545(9)°. The structure is described as a three-dimensional framework built up of corner-edge sharing CoO{sub 6}, CoO{sub 4} and AsO{sub 4} polyhedra, with interconnecting channels along [100] in which the Na{sup +} cations are located. The densest ceramics with relative density of 94% was obtained by ball milling and optimization of sintering temperature, andmore » its microstructure characterized by scanning electron microscopy. The electrical properties of the ceramics were studied over a temperature interval from 280 °C to 560 °C using the complex impedance spectroscopy over the range of 13 MHz–5 Hz. The ionic bulk conductivity value of the sample at 360 °C is 2.51 10{sup −5} S cm{sup −1} and the measured activation energy is Ea=1 eV. The sodium migration pathways in the crystal structure were investigated computationally using the bond valence site energy (BVSE) model and classical molecular dynamics (MD) simulations. - Graphical abstract: Correlation between crystal structure, microstructure and ionic conductivity . Display Omitted - Highlights: • A new arsenate Na{sub 4}Co{sub 7}(AsO{sub 4}){sub 6} was prepared by solid state reaction. • Its crystal structure was determined by powder X-ray diffraction. • Na{sup +} ionic conductivity was probed by complex impedance spectroscopy. • Na{sup +} conduction pathways were modeled by bond-valence method and molecular dynamics.« less

Favoured local structures in liquids and solids: a 3D lattice model.

PubMed

Ronceray, Pierre; Harrowell, Peter

2015-05-07

We investigate the connection between the geometry of Favoured Local Structures (FLS) in liquids and the associated liquid and solid properties. We introduce a lattice spin model - the FLS model on a face-centered cubic lattice - where this geometry can be arbitrarily chosen among a discrete set of 115 possible FLS. We find crystalline groundstates for all choices of a single FLS. Sampling all possible FLS's, we identify the following trends: (i) low symmetry FLS's produce larger crystal unit cells but not necessarily higher energy groundstates, (ii) chiral FLS's exhibit peculiarly poor packing properties, (iii) accumulation of FLS's in supercooled liquids is linked to large crystal unit cells, and (iv) low symmetry FLS's tend to find metastable structures on cooling.

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.

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

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

Yennawar, Hemant; Møller, Magda; University of Copenhagen, DK-2100 Copenhagen

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

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.

Active crystals on a sphere

NASA Astrophysics Data System (ADS)

Praetorius, Simon; Voigt, Axel; Wittkowski, Raphael; Löwen, Hartmut

2018-05-01

Two-dimensional crystals on curved manifolds exhibit nontrivial defect structures. Here we consider "active crystals" on a sphere, which are composed of self-propelled colloidal particles. Our work is based on a phase-field-crystal-type model that involves a density and a polarization field on the sphere. Depending on the strength of the self-propulsion, three different types of crystals are found: a static crystal, a self-spinning "vortex-vortex" crystal containing two vortical poles of the local velocity, and a self-translating "source-sink" crystal with a source pole where crystallization occurs and a sink pole where the active crystal melts. These different crystalline states as well as their defects are studied theoretically here and can in principle be confirmed in experiments.

Discrete structures in continuum descriptions of defective crystals.

PubMed

Parry, G P

2016-04-28

I discuss various mathematical constructions that combine together to provide a natural setting for discrete and continuum geometric models of defective crystals. In particular, I provide a quite general list of 'plastic strain variables', which quantifies inelastic behaviour, and exhibit rigorous connections between discrete and continuous mathematical structures associated with crystalline materials that have a correspondingly general constitutive specification. © 2016 The Author(s).

Chemistry Notes.

ERIC Educational Resources Information Center

School Science Review, 1982

1982-01-01

Discusses laboratory procedures, classroom materials, and demonstrations including: a model for metallic/ionic structures; Friedel-Crafts acylation reaction; aids to teaching crystal structure; a metal displacement project; silver recovery from fixer and silver residues; iodine sublimation; nature of acids; card models for teaching bonding; and…

On the Relationship Between Scintillation Anisotropy and Crystal Structure in Pure Crystalline Organic Scintillator Materials

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

Schuster, Patricia; Feng, Patrick; Brubaker, Erik

We report the scintillation anisotropy effect for proton recoil events has been investigated in five pure organic crystalline materials: anthracene, trans-stilbene, p-terphenyl, bibenzyl, and diphenylacetylene. These measurements include characterization of the scintillation response for one hemisphere of proton recoil directions in each crystal. In addition to standard measurements of the total light output and pulse shape at each angle, the prompt and delayed light anisotropies are analyzed, allowing for investigation of the singlet and triplet molecular excitation behaviors independently. This work provides new quantitative and qualitative observations that make progress toward understanding the physical mechanisms behind the scintillation anisotropy. Thesemore » measurements show that the relationship between the prompt and delayed light anisotropies is correlated with crystal structure, as it changes between the pi-stacked crystal structure materials (anthracene and p-terphenyl) and the herringbone crystal structure materials (stilbene, bibenzyl, and diphenylacetylene). The observations are consistent with a model in which there are preferred directions of kinetic processes for the molecular excitations. Finally, these processes and the impact of their directional dependencies on the scintillation anisotropy are discussed.« less

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature.

PubMed

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-06

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

NASA Astrophysics Data System (ADS)

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

PubMed Central

Tsujino, Soichiro; Tomizaki, Takashi

2016-01-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography. PMID:27150272

On the Relationship Between Scintillation Anisotropy and Crystal Structure in Pure Crystalline Organic Scintillator Materials

DOE PAGES

Schuster, Patricia; Feng, Patrick; Brubaker, Erik

2018-05-03

We report the scintillation anisotropy effect for proton recoil events has been investigated in five pure organic crystalline materials: anthracene, trans-stilbene, p-terphenyl, bibenzyl, and diphenylacetylene. These measurements include characterization of the scintillation response for one hemisphere of proton recoil directions in each crystal. In addition to standard measurements of the total light output and pulse shape at each angle, the prompt and delayed light anisotropies are analyzed, allowing for investigation of the singlet and triplet molecular excitation behaviors independently. This work provides new quantitative and qualitative observations that make progress toward understanding the physical mechanisms behind the scintillation anisotropy. Thesemore » measurements show that the relationship between the prompt and delayed light anisotropies is correlated with crystal structure, as it changes between the pi-stacked crystal structure materials (anthracene and p-terphenyl) and the herringbone crystal structure materials (stilbene, bibenzyl, and diphenylacetylene). The observations are consistent with a model in which there are preferred directions of kinetic processes for the molecular excitations. Finally, these processes and the impact of their directional dependencies on the scintillation anisotropy are discussed.« less

Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1

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

El Omari, Kamel; Iourin, Oleg; Kadlec, Jan

2014-08-01

The sulfur SAD phasing method was successfully used to determine the structure of the N-terminal domain of HCV E1 from low-resolution diffracting crystals by combining data from 32 crystals. Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffractedmore » very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.« less

Possible Mechanisms for Turbofan Engine Ice Crystal Icing at High Altitude

NASA Technical Reports Server (NTRS)

Tsao, Jen-Ching; Struk, Peter M.; Oliver, Michael

2014-01-01

A thermodynamic model is presented to describe possible mechanisms of ice formation on unheated surfaces inside a turbofan engine compression system from fully glaciated ice crystal clouds often formed at high altitude near deep convective weather systems. It is shown from the analysis that generally there could be two distinct types of ice formation: (1) when the "surface freezing fraction" is in the range of 0 to 1, dominated by the freezing of water melt from fully or partially melted ice crystals, the ice structure is formed from accretion with strong adhesion to the surface, and (2) when the "surface melting fraction" is the range of 0 to 1, dominated by the further melting of ice crystals, the ice structure is formed from accumulation of un-melted ice crystals with relatively weak bonding to the surface. The model captures important qualitative trends of the fundamental ice-crystal icing phenomenon reported earlier1,2 from the research collaboration work by NASA and the National Research Council (NRC) of Canada. Further, preliminary analysis of test data from the 2013 full scale turbofan engine ice crystal icing test3 conducted in the NASA Glenn Propulsion Systems Laboratory (PSL) has also suggested that (1) both types of ice formation occurred during the test, and (2) the model has captured some important qualitative trend of turning on (or off) the ice crystal ice formation process in the tested engine low pressure compressor (LPC) targeted area under different icing conditions that ultimately would lead to (or suppress) an engine core roll back (RB) event.

Possible Mechanisms for Turbofan Engine Ice Crystal Icing at High Altitude

NASA Technical Reports Server (NTRS)

Tsao, Jen-Ching; Struk, Peter M.; Oliver, Michael J.

2016-01-01

A thermodynamic model is presented to describe possible mechanisms of ice formation on unheated surfaces inside a turbofan engine compression system from fully glaciated ice crystal clouds often formed at high altitude near deep convective weather systems. It is shown from the analysis that generally there could be two distinct types of ice formation: (1) when the "surface freezing fraction" is in the range of 0 to 1, dominated by the freezing of water melt from fully or partially melted ice crystals, the ice structure is formed from accretion with strong adhesion to the surface, and (2) when the "surface melting fraction" is the range of 0 to 1, dominated by the further melting of ice crystals, the ice structure is formed from accumulation of un-melted ice crystals with relatively weak bonding to the surface. The model captures important qualitative trends of the fundamental ice-crystal icing phenomenon reported earlier (Refs. 1 and 2) from the research collaboration work by NASA and the National Research Council (NRC) of Canada. Further, preliminary analysis of test data from the 2013 full scale turbofan engine ice crystal icing test (Ref. 3) conducted in the NASA Glenn Propulsion Systems Laboratory (PSL) has also suggested that (1) both types of ice formation occurred during the test, and (2) the model has captured some important qualitative trend of turning on (or off) the ice crystal ice formation process in the tested engine low pressure compressor (LPC) targeted area under different icing conditions that ultimately would lead to (or suppress) an engine core roll back (RB) event.

Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties

NASA Astrophysics Data System (ADS)

Xie, Tian; Grossman, Jeffrey C.

2018-04-01

The use of machine learning methods for accelerating the design of crystalline materials usually requires manually constructed feature vectors or complex transformation of atom coordinates to input the crystal structure, which either constrains the model to certain crystal types or makes it difficult to provide chemical insights. Here, we develop a crystal graph convolutional neural networks framework to directly learn material properties from the connection of atoms in the crystal, providing a universal and interpretable representation of crystalline materials. Our method provides a highly accurate prediction of density functional theory calculated properties for eight different properties of crystals with various structure types and compositions after being trained with 1 04 data points. Further, our framework is interpretable because one can extract the contributions from local chemical environments to global properties. Using an example of perovskites, we show how this information can be utilized to discover empirical rules for materials design.

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

Synthesis and crystal structure analysis of uranyl triple acetates

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

Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com; Department of Chemistry, Samara National Research University, 443086 Samara; Serezhkina, Larisa B.

2016-12-15

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

Picosecond fluorescence of intact and dissolved PSI-LHCI crystals.

PubMed

van Oort, Bart; Amunts, Alexey; Borst, Jan Willem; van Hoek, Arie; Nelson, Nathan; van Amerongen, Herbert; Croce, Roberta

2008-12-15

Over the past several years, many crystal structures of photosynthetic pigment-protein complexes have been determined, and these have been used extensively to model spectroscopic results obtained on the same proteins in solution. However, the crystal structure is not necessarily identical to the structure of the protein in solution. Here, we studied picosecond fluorescence of photosystem I light-harvesting complex I (PSI-LHCI), a multisubunit pigment-protein complex that catalyzes the first steps of photosynthesis. The ultrafast fluorescence of PSI-LHCI crystals is identical to that of dissolved crystals, but differs considerably from most kinetics presented in the literature. In contrast to most studies, the data presented here can be modeled quantitatively with only two compartments: PSI core and LHCI. This yields the rate of charge separation from an equilibrated core (22.5 +/- 2.5 ps) and rates of excitation energy transfer from LHCI to core (k(LC)) and vice versa (k(CL)). The ratio between these rates, R = k(CL)/k(LC), appears to be wavelength-dependent and scales with the ratio of the absorption spectra of LHCI and core, indicating the validity of a detailed balance relation between both compartments. k(LC) depends slightly but nonsystematically on detection wavelength, averaging (9.4 +/- 4.9 ps)(-1). R ranges from 0.5 (<690 nm) to approximately 1.3 above 720 nm.

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

2016-09-01

Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

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.

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

PubMed Central

Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

2013-01-01

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

Photonic crystals, light manipulation, and imaging in complex nematic structures

NASA Astrophysics Data System (ADS)

Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

2016-03-01

Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

Tuning hardness in calcite by incorporation of amino acids.

PubMed

Kim, Yi-Yeoun; Carloni, Joseph D; Demarchi, Beatrice; Sparks, David; Reid, David G; Kunitake, Miki E; Tang, Chiu C; Duer, Melinda J; Freeman, Colin L; Pokroy, Boaz; Penkman, Kirsty; Harding, John H; Estroff, Lara A; Baker, Shefford P; Meldrum, Fiona C

2016-08-01

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

Determining crystal structures through crowdsourcing and coursework

PubMed Central

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-01-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

Optomechanics of two- and three-dimensional soft photonic crystals

NASA Astrophysics Data System (ADS)

Krishnan, Dwarak

Soft photonic crystals are a class of periodic dielectric structures that undergo highly nonlinear deformation due to strain or other external stimulus such as temperature, pH etc. This can in turn dramatically affect optical properties such as light transmittance. Moreover certain classes of lithographically fabricated structures undergo some structural distortion due to the effects of processing, eventually affecting the optical properties of the final photonic crystal. In this work, we study the deformation mechanics of soft photonic crystal structures using realistic physics-based models and leverage that understanding to explain the optomechanics of actual 2-D and 3-D soft photonic crystals undergoing similar symmetry breaking nonlinear deformations. We first study the optomechanics of two classes of 3-D soft photonic crystals: (1) hydrogel and (2) elastomer based material systems. The hydrogel based inverse face-centered-cubic structure undergoes swelling with change in pH of the surrounding fluid. The inverse structure is a network of bulky domains with thin ligament-like connections, and it undergoes a pattern transformation from FCC to L11 as a result of swelling. A continuum scale poroelasticity based coupled fluid-diffusion FEM model is developed to accurately predict this mechanical behavior. Light transmittance simulation results qualitatively explain the experimentally observed trends in the optical behavior with pH change. The elastomer based, lithographically fabricated material experiences shrinkage induced distortion upon processing. This behavior is modeled using FEM with the material represented by a neo-Hookean constitutive law. The light transmittance calculations for normal incidence are carried out using the transfer matrix method and a good comparison is obtained for the positions of first and second order reflectance peaks. A unit cell based approach is taken to compute the photonic bandstructure to estimate light propagation through the structure for other angles of light incidence. To obtain a detailed picture of the change in optical properties due to a pattern transformation, we study simple 2-D elastomer photonic crystals which undergo an interesting structural pattern transformation from simple circular holes to alternately oriented ellipses in a square lattice due to uniaxial compression. The incident light does not have any effect on the properties of the elastomer material. A decomposition of the deformation gradient quickly shows that the pattern transformation is induced by alternating rotations of the interstitial regions and the bending of interconnecting ligaments. Numerical simulations of light transmittance using vector element based FEM analysis of Maxwells equations shows changes in the light energy localization within the material especially in the high energy/low wavelength regions of the spectra. Additionally, with bandstructure calculations on a unit cell of the structure, the optomechanical behavior is completely explained. Finally, computational evidence is provided for a hypothetical 2-D photonic crystal made of a light-sensitive material, which undergoes a structural pattern transformation primarily due to the effect of incident light. The model takes into account the order kinetics of optically induced isomerization (of trans to cis configuration) in the azobenzene-liquid crystal elastomer to compute the transformational strain. This strain, in turn, deforms the structure and hence changes its periodicity and dielectric properties and thus affects the manner in which light gets localized within the material system. This consequently changes the profile of the imposed transformational strain on the deformed structure. The macroscopic strain history shows that prior to the mechanical instability that causes the pattern transformation, there is a period of structural relaxation which initiates the pattern transformation. After the symmetry breaking pattern transformation, the photonic bandstructure is altered significantly. Light does not get localized in the spot regions anymore and stress relaxation dominates. Due to this, the compressive macroscopic strain of the pattern transformed structure starts to decrease indicating a possible cyclical behavior.

Pauli structures arising from confined particles interacting via a statistical potential

NASA Astrophysics Data System (ADS)

Batle, Josep; Ciftja, Orion; Farouk, Ahmed; Alkhambashi, Majid; Abdalla, Soliman

2017-09-01

There have been suggestions that the Pauli exclusion principle alone can lead a non-interacting (free) system of identical fermions to form crystalline structures dubbed Pauli crystals. Single-shot imaging experiments for the case of ultra-cold systems of free spin-polarized fermionic atoms in a two-dimensional harmonic trap appear to show geometric arrangements that cannot be characterized as Wigner crystals. This work explores this idea and considers a well-known approach that enables one to treat a quantum system of free fermions as a system of classical particles interacting with a statistical interaction potential. The model under consideration, though classical in nature, incorporates the quantum statistics by endowing the classical particles with an effective interaction potential. The reasonable expectation is that possible Pauli crystal features seen in experiments may manifest in this model that captures the correct quantum statistics as a first order correction. We use the Monte Carlo simulated annealing method to obtain the most stable configurations of finite two-dimensional systems of confined particles that interact with an appropriate statistical repulsion potential. We consider both an isotropic harmonic and a hard-wall confinement potential. Despite minor differences, the most stable configurations observed in our model correspond to the reported Pauli crystals in single-shot imaging experiments of free spin-polarized fermions in a harmonic trap. The crystalline configurations observed appear to be different from the expected classical Wigner crystal structures that would emerge should the confined classical particles had interacted with a pair-wise Coulomb repulsion.

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.

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.

Carboplatin binding to histidine

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

Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.

An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the brominemore » form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.« less

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

The Crystal and Molecular Structure of an Asymmetric Diacetylene Monomer, 6-(2-methyl-4-nitroanilino)-2,4-hexadiyne-1-ol

NASA Technical Reports Server (NTRS)

Vlasse, Marcus; Paley, Mark S.

1993-01-01

The crystal and molecular structure of an asymmetric diacetylene monomer has been determined from x-ray diffraction data. The crystals, obtained from an acetone/pentane solution, are orthorhombic, Fdd2 with Z = 16 in a unit cell having dimensions of a = 42.815(6) A, b = 22.224(5) A, c = 4.996(l) A. The structure was solved by direct methods and refined by least- squares techniques to an R(sub F) of 6.4% for 988 reflections and 171 variables. The diacetylene chains are disposed in the unit cell in a complex manner in order to satisfy the hydrogen- bonding, crystal packing, and symmetry requirements of the system. The solid state polymerization mechanism is discussed with respect to the geometric disposition of the diacetylene chains. These chains are far apart and incorrectly oriented with respect to each other to permit polymerization in the crystal by means of 1,4-addition, consistent with the Baughman mechanistic model.

Topological Characterization of Carbon Graphite and Crystal Cubic Carbon Structures.

PubMed

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

2017-09-07

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

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.

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.

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

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

PubMed Central

Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

2013-01-01

The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

The nature of geometric frustration in the Kob-Andersen mixture

NASA Astrophysics Data System (ADS)

Crowther, Peter; Turci, Francesco; Royall, C. Patrick

2015-07-01

Geometric frustration is an approach to the glass transition based upon the consideration of locally favoured structures (LFS), which are geometric motifs which minimise the local free energy. Geometric frustration proposes that a transition to a crystalline state is frustrated because these LFS do not tile space. However, this concept is based on icosahedra which are not always the LFS for a given system. The LFS of the popular Kob-Andersen (KA) model glassformer are the bicapped square antiprism, which does tile space. Such a LFS-crystal is indeed realised in the Al2Cu structure, which is predicted to be a low energy state for the KA model with a 2:1 composition. We, therefore, hypothesise that upon changing the composition in the KA model towards 2:1, geometric frustration may be progressively relieved, leading to larger and larger domains of LFS which would ultimately correspond to the Al2Cu crystal. Remarkably, rather than an increase, upon changing composition we find a small decrease in the LFS population, and the system remains impervious to nucleation of LFS crystals. We suggest that this may be related to the composition of the LFS, as only a limited subset is compatible with the crystal. We further demonstrate that the Al2Cu crystal will grow from a seed in the KA model with 2:1 composition and identify the melting temperature to be 0.447(2).

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

Artificial Hip Simulator with Crystal Models

NASA Image and Video Library

1966-06-21

Robert Johnson, top, sets the lubricant flow while Donald Buckley adjusts the bearing specimen on an artificial hip simulator at the National Aeronautics and Space Administration (NASA) Lewis Research Center. The simulator was supplemented by large crystal lattice models to demonstrate the composition of different bearing alloys. This this image by NASA photographer Paul Riedel was used for the cover of the August 15, 1966 edition of McGraw-Hill Product Engineering. Johnson was chief of Lubrication Branch and Buckley head of the Space Environment Lubrication Section in the Fluid System Components Division. In 1962 they began studying the molecular structure of metals. Their friction and wear testing revealed that the optimal structure for metal bearings was a hexagonal crystal structure with proper molecular space. Bearing manufacturers traditionally preferred cubic structures over hexagonal arrangements. Buckley and Johnson found that even though the hexagonal structural was not as inherently strong as its cubic counterpart, it was less likely to cause a catastrophic failure. The Lewis researchers concentrated their efforts on cobalt-molybdenum and titanium alloys for high temperatures applications. The alloys had a number of possible uses, included prosthetics. The alloys were similar in composition to the commercial alloys used for prosthetics, but employed the longer lasting hexagonal structure.

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

Microphase Separation Controlled Beta Sheet Crystallization Kinetics in Silk Fibroin Protein.

NASA Astrophysics Data System (ADS)

Hu, Xiao; Lu, Qiang; Kaplan, David; Cebe, Peggy

2009-03-01

We investigate the mechanism of isothermal crystallization kinetics of beta-sheet crystals in silk multiblock fibrous proteins. The Avrami analysis kinetic theory, for studies of synthetic polymer crystal growth, is for the first time extended to investigate protein self-assembly in beta-sheet rich Bombyx mori silk fibroin samples, using time-resolved Fourier transform infrared spectroscopy, differential scanning calorimetry and synchrotron real-time wide-angle X-ray scattering. Results indicate formation of beta sheet crystals in silk proteins is different from the 3-D spherulitic crystal growth found in synthetic homopolymers. Observations by scanning electron microscopy support the view that the protein structures vary during the different stages of crystal growth, and show a microphase separation pattern after chymotrypsin enzyme biodegradation. We present a model to explain the crystallization of the multiblock silk fibroin protein, by analogy to synthetic block copolymers. This model could be widely applicable in other proteins with multiblock (i.e., crystallizable and non-crystallizable) domains.

Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule.

PubMed

Mandal, Taraknath; Marson, Ryan L; Larson, Ronald G

2016-10-04

We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, a coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal. With the force field obtained by this method, we show that CG simulations of the drug phenytoin predict growth of a crystalline slab from a melt of phenytoin, allowing determination of the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology. By applying meta-dynamics to the coarse-grained model, a new crystalline form of phenytoin (monoclinic, space group P2 1 ) was predicted which is different from the experimentally known crystal structure (orthorhombic, space group Pna2 1 ). Atomistic simulations and quantum calculations then showed the polymorph to be meta-stable at ambient temperature and pressure, and thermodynamically more stable than the conventional orthorhombic crystal at high pressure. The results suggest an efficient route to study crystal growth of small organic molecules that could also be useful for identification of possible polymorphs as well.

Modeling the SHG activities of diverse protein crystals

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

Haupert, Levi M.; DeWalt, Emma L.; Simpson, Garth J., E-mail: gsimpson@purdue.edu

2012-11-01

The origins of the diversity in the SHG signal from protein crystals are investigated and potential protein-crystal coverage by SHG microscopy is assessed. A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much ofmore » the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ∼84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.« less

Calcium Oxalate Accumulation in Malpighian Tubules of Silkworm (Bombyx mori)

NASA Astrophysics Data System (ADS)

Wyman, Aaron J.; Webb, Mary Alice

2007-04-01

Silkworm provides an ideal model system for study of calcium oxalate crystallization in kidney-like organs, called Malpighian tubules. During their growth and development, silkworm larvae accumulate massive amounts of calcium oxalate crystals in their Malpighian tubules with no apparent harm to the organism. This manuscript reports studies of crystal structure in the tubules along with analyses identifying molecular constituents of tubule exudate.

Recent Advances in the Understanding of the Influence of Electric and Magnetic Fields on Protein Crystal Growth

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

Pareja-Rivera, Carina; Cuéllar-Cruz, Mayra; Esturau-Escofet, Nuria

Here, in this contribution we use nonconventional methods that help to increase the success rate of a protein crystal growth, and consequently of structural projects using X-ray diffraction techniques. In order to achieve this purpose, this contribution presents new approaches involving more sophisticated techniques of protein crystallization, not just for growing protein crystals of different sizes by using electric fields, but also for controlling crystal size and orientation. Also, this latter was possible through the use of magnetic fields that allow to obtain protein crystals suitable for both high-resolution X-ray and neutron diffraction crystallography where big crystals are required. Thismore » contribution discusses some pros, cons and realities of the role of electromagnetic fields in protein crystallization research, and their effect on protein crystal contacts. Additionally, we discuss the importance of room and low temperatures during data collection. Finally, we also discuss the effect of applying a rather strong magnetic field of 16.5 T, for shorts and long periods of time, on protein crystal growth, and on the 3D structure of two model proteins.« less

Recent Advances in the Understanding of the Influence of Electric and Magnetic Fields on Protein Crystal Growth

DOE PAGES

Pareja-Rivera, Carina; Cuéllar-Cruz, Mayra; Esturau-Escofet, Nuria; ...

2016-12-05

Here, in this contribution we use nonconventional methods that help to increase the success rate of a protein crystal growth, and consequently of structural projects using X-ray diffraction techniques. In order to achieve this purpose, this contribution presents new approaches involving more sophisticated techniques of protein crystallization, not just for growing protein crystals of different sizes by using electric fields, but also for controlling crystal size and orientation. Also, this latter was possible through the use of magnetic fields that allow to obtain protein crystals suitable for both high-resolution X-ray and neutron diffraction crystallography where big crystals are required. Thismore » contribution discusses some pros, cons and realities of the role of electromagnetic fields in protein crystallization research, and their effect on protein crystal contacts. Additionally, we discuss the importance of room and low temperatures during data collection. Finally, we also discuss the effect of applying a rather strong magnetic field of 16.5 T, for shorts and long periods of time, on protein crystal growth, and on the 3D structure of two model proteins.« less

Superlattice Structures, Electronic Properties, and Spin Dynamics of the Partially Cu-Extracted Phase for the Composite Crystal System CuxV4O11

NASA Astrophysics Data System (ADS)

Onoda, Masashige; Tamura, Asato

2017-02-01

The crystal structures, electronic properties, and spin dynamics of CuxV4O11 with 1.2 ≤ x < 2, classified as the partially Cu-extracted phase for the composite crystal system, are explored through measurements of x-ray four-circle diffraction, electrochemistry, electrical resistivity, thermoelectric power, magnetization, and electron paramagnetic resonance. This system has superlattice structures mainly ascribed to the partial ordering of Cu ions. Cu1.78V4O11 is triclinic with space group Pbar{1} and the double supercell of the V4O11 substructure of the composite crystal. The significantly Cu-extracted crystal Cu1.40V4O11 has a quadruple supercell with space group P1. The electron transport for V ions is nonmetallic owing to the polaronic nature and/or phonon softening and to the random potential of Cu ions. The Curie-Weiss-type paramagnetism basically originates from the Cu2+ chain coordinated octahedrally, and the EPR relaxation at low temperatures is understood through the exchange mechanism for the dipole-dipole and anisotropic exchange interactions. The near absence of paramagnetic behaviors of V4+ ions might be due to the spin-singlet ladder model or alternating-exchange chain model depending on the superlattice structure and valence distribution. The electrochemical performance of Li rechargeable batteries using this superlattice system is about 300 A h kg-1 at voltages above 2 V.

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

Prediction of the As-Cast Structure of Al-4.0 Wt Pct Cu Ingots

NASA Astrophysics Data System (ADS)

Ahmadein, Mahmoud; Wu, M.; Li, J. H.; Schumacher, P.; Ludwig, A.

2013-06-01

A two-stage simulation strategy is proposed to predict the as-cast structure. During the first stage, a 3-phase model is used to simulate the mold-filling process by considering the nucleation, the initial growth of globular equiaxed crystals and the transport of the crystals. The three considered phases are the melt, air and globular equiaxed crystals. In the second stage, a 5-phase mixed columnar-equiaxed solidification model is used to simulate the formation of the as-cast structure including the distinct columnar and equiaxed zones, columnar-to-equiaxed transition, grain size distribution, macrosegregation, etc. The five considered phases are the extradendritic melt, the solid dendrite, the interdendritic melt inside the equiaxed grains, the solid dendrite, and the interdendritic melt inside the columnar grains. The extra- and interdendritic melts are treated as separate phases. In order to validate the above strategy, laboratory ingots (Al-4.0 wt pct Cu) are poured and analyzed, and a good agreement with the numerical predictions is achieved. The origin of the equiaxed crystals by the "big-bang" theory is verified to play a key role in the formation of the as-cast structure, especially for the castings poured at a low pouring temperature. A single-stage approach that only uses the 5-phase mixed columnar-equiaxed solidification model and ignores the mold filling can predict satisfactory results for a casting poured at high temperature, but it delivers false results for the casting poured at low temperature.

Crystal-Packing Trends for a Series of 6,9,12,15,18-Pentaaryl-1-hydro[60]fullerenes

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

Kennedy, Robert D.; Halim, Merissa; Khan, Saeed I.

2012-06-11

The relationship between the size of the substituents of aryl groups in a series of fifteen 6,9,12,15,18-pentaaryl-1-hydro[60]fullerenes and the solid-state structures and packing motifs of these compounds has been analyzed. Pentaarylfullerenes have a characteristic “badminton shuttlecock” shape that causes several derivatives to crystallize into columnar stacks. However, many pentaarylfullerenes form non-stacked structures with, for example, dimeric, layered, diamondoid, or feather-in-cavity relationships between molecules. Computational modeling gave a qualitative estimate of the best shape match between the ball and socket surfaces of each pentaarylfullerene. The best match was for pentaarylfullerenes with large, spherically shaped para-substituents on the aryl groups. The seriesmore » of pentaarylfullerenes was characterized by single-crystal X-ray diffraction. A total of 34 crystal structures were obtained as various solvates and were categorized by their packing motifs.« less

Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor

PubMed Central

Suzuki, Kano; Mizutani, Kenji; Maruyama, Shintaro; Shimono, Kazumi; Imai, Fabiana L.; Muneyuki, Eiro; Kakinuma, Yoshimi; Ishizuka-Katsura, Yoshiko; Shirouzu, Mikako; Yokoyama, Shigeyuki; Yamato, Ichiro; Murata, Takeshi

2016-01-01

V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model. PMID:27807367

Low-temperature nanodoping of protonated LiNbO3 crystals by univalent ions

NASA Astrophysics Data System (ADS)

Borodin, Yu. V.

2015-01-01

In the nanocomposite model developed here, crystals are treated as subordinate aggregate of pro- ton-selected structural elements, their blocks, and proton-containing quantum sublattices with preferred transport effects separating them. The formation of stratified reversible hexagonal structures is accompanied with protonation and formation of a dense network of H-bonds ensuring the nanocomposite properties. Nanodoping with H+ ions occurs during processing of crystals and glasses in melts as well as in aqueous solutions of Ag, Tl, Rb, and Cs salts. The isotope exchange H+ ↔ D+ and ion exchange H+ ↔ M+ lead to nanodoping of protonated materials with D+ and M+ ions. This is manifested especially clearly in Li-depleted nonequilibrium LiNbO3 and LiTaO3 crystals. Low-temperature proton-ion nanodoping over superlattices is a basically new approach to analysis of the structure and properties of extremely nonequilibrium materials.

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.

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.

Satellite Tobacco Mosaic Virus Structure

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Viurus (STMV)--one of the smallest viruses known--has been successfully reduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystals grown on Earth, the crystals grown under microgravity conditions were visually perfect, with no striations or clumping of crystals. Furthermore, the x-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This stylized ribbon model shows the protein coat in white and the nucleic acid in yellow. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, University of California at Irvin.

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Building a three-dimensional model of CYP2C9 inhibition using the Autocorrelator: an autonomous model generator.

PubMed

Lardy, Matthew A; Lebrun, Laurie; Bullard, Drew; Kissinger, Charles; Gobbi, Alberto

2012-05-25

In modern day drug discovery campaigns, computational chemists have to be concerned not only about improving the potency of molecules but also reducing any off-target ADMET activity. There are a plethora of antitargets that computational chemists may have to consider. Fortunately many antitargets have crystal structures deposited in the PDB. These structures are immediately useful to our Autocorrelator: an automated model generator that optimizes variables for building computational models. This paper describes the use of the Autocorrelator to construct high quality docking models for cytochrome P450 2C9 (CYP2C9) from two publicly available crystal structures. Both models result in strong correlation coefficients (R² > 0.66) between the predicted and experimental determined log(IC₅₀) values. Results from the two models overlap well with each other, converging on the same scoring function, deprotonated charge state, and predicted the binding orientation for our collection of molecules.

Model of melting (crystallization) process of the condensed disperse phase in the smoky plasmas

NASA Astrophysics Data System (ADS)

Dragan, G. S.; Kolesnikov, K. V.; Kutarov, V. V.

2018-01-01

The paper presents an analysis of the causes of a formation of spatial ordered grain structures in a smoky plasma. We are modeling the process of melting (crystallization) of a condensed phase in this environment taking into account the screened electrostatic interaction and the diffusion-drift force. We discuss an influence of the charge on the melting temperatures.

The Crystal Structure of GXGD Membrane Protease FlaK

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

J Hu; Y Xue; S Lee

2011-12-31

The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices.more » The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.« less

The crystal structure of GXGD membrane protease FlaK

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

Hu, Jian; Xue, Yi; Lee, Sangwon

2011-09-20

The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices.more » The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.« less

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.

Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal

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

Zhu, Jin-Yi; Fu, Zheng-Qing; Argonne National Laboratory, Argonne, Illinois

2012-09-01

The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using data collected from a moderately diffracting crystal and 1.9 Å synchrotron X-rays. The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent amore » novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF{sub anom}/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R{sub free} = 26.8%) to 2.3 Å resolution. High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R{sub free} = 21.4%) to 1.85 Å resolution. AF1382 has a winged-helix–turn–helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1–82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.« less

Controlled dehydration improves the diffraction quality of two RNA crystals.

PubMed

Park, HaJeung; Tran, Tuan; Lee, Jun Hyuck; Park, Hyun; Disney, Matthew D

2016-11-03

Post-crystallization dehydration methods, applying either vapor diffusion or humidity control devices, have been widely used to improve the diffraction quality of protein crystals. Despite the fact that RNA crystals tend to diffract poorly, there is a dearth of reports on the application of dehydration methods to improve the diffraction quality of RNA crystals. We use dehydration techniques with a Free Mounting System (FMS, a humidity control device) to recover the poor diffraction quality of RNA crystals. These approaches were applied to RNA constructs that model various RNA-mediated repeat expansion disorders. The method we describe herein could serve as a general tool to improve diffraction quality of RNA crystals to facilitate structure determinations.

Covering complete proteomes with X-ray structures: A current snapshot

DOE PAGES

Mizianty, Marcin J.; Fan, Xiao; Yan, Jing; ...

2014-10-23

Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtainedmore » through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.« less

Phase-Field Modeling of Polycrystalline Solidification: From Needle Crystals to Spherulites—A Review

NASA Astrophysics Data System (ADS)

Gránásy, László; Rátkai, László; Szállás, Attila; Korbuly, Bálint; Tóth, Gyula I.; Környei, László; Pusztai, Tamás

2014-04-01

Advances in the orientation-field-based phase-field (PF) models made in the past are reviewed. The models applied incorporate homogeneous and heterogeneous nucleation of growth centers and several mechanisms to form new grains at the perimeter of growing crystals, a phenomenon termed growth front nucleation. Examples for PF modeling of such complex polycrystalline structures are shown as impinging symmetric dendrites, polycrystalline growth forms (ranging from disordered dendrites to spherulitic patterns), and various eutectic structures, including spiraling two-phase dendrites. Simulations exploring possible control of solidification patterns in thin films via external fields, confined geometry, particle additives, scratching/piercing the films, etc. are also displayed. Advantages, problems, and possible solutions associated with quantitative PF simulations are discussed briefly.

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

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

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s −1 . At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensitymore » within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5–2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

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

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s –1. At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution ofmore » diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ~1.5–2 compared with those observed at conventional dose rates. As a result, improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures

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

Gao, Jianzhao; Wu, Zhonghua; Hu, Gang

Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community. We empirically evaluated and compared the predictive performance of seven representative methods. The analysis suggests that these methods produce quite accuratemore » propensities for the diffraction-quality crystallization. We also summarized results of the first study of the relation between these predictive propensities and the resolution of the crystallizable proteins. We found that the propensities predicted by several methods are significantly higher for proteins that have high resolution structures compared to those with the low resolution structures. Moreover, we tested a new meta-predictor, MetaXXC, which averages the propensities generated by the three most accurate predictors of the diffraction-quality crystallization. MetaXXC generates putative values of resolution that have modest levels of correlation with the experimental resolutions and it offers the lowest mean absolute error when compared to the seven considered methods. We conclude that protein sequences can be used to fairly accurately predict whether their corresponding protein structures can be solved using X-ray crystallography. Moreover, we also ascertain that sequences can be used to reasonably well predict the resolution of the resulting protein crystals.« less

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

DOE PAGES

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.; ...

2017-10-13

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s –1. At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution ofmore » diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ~1.5–2 compared with those observed at conventional dose rates. As a result, improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« less

Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams

DOE PAGES

Warkentin, Matthew A.; Atakisi, Hakan; Hopkins, Jesse B.; ...

2017-10-13

Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s −1 . At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensitymore » within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5–2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.« 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

Raman Spectroscopy Adds Complementary Detail to the High-Resolution X-Ray Crystal Structure of Photosynthetic PsbP from Spinacia oleracea

PubMed Central

Lapkouski, Mikalai; Hofbauerova, Katerina; Sovova, Zofie; Ettrichova, Olga; González-Pérez, Sergio; Dulebo, Alexander; Kaftan, David; Kuta Smatanova, Ivana; Revuelta, Jose L.; Arellano, Juan B.; Carey, Jannette; Ettrich, Rüdiger

2012-01-01

Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR) exploits an intermediate phase that, although nominally “dry,” has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å) x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein. PMID:23071614

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

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.

A model for finite-deformation nonlinear thermomechanical response of single crystal copper under shock conditions

NASA Astrophysics Data System (ADS)

Luscher, Darby J.; Bronkhorst, Curt A.; Alleman, Coleman N.; Addessio, Francis L.

2013-09-01

A physically consistent framework for combining pressure-volume-temperature equations of state with crystal plasticity models is developed for the application of modeling the response of single and polycrystals under shock conditions. The particular model is developed for copper, thus the approach focuses on crystals of cubic symmetry although many of the concepts in the approach are applicable to crystals of lower symmetry. We employ a multiplicative decomposition of the deformation gradient into isochoric elastic, thermoelastic dilation, and plastic parts leading to a definition of isochoric elastic Green-Lagrange strain. This finite deformation kinematic decomposition enables a decomposition of Helmholtz free-energy into terms reflecting dilatational thermoelasticity, strain energy due to long-range isochoric elastic deformation of the lattice and a term reflecting energy stored in short range elastic lattice deformation due to evolving defect structures. A model for the single crystal response of copper is implemented consistent with the framework into a three-dimensional Lagrangian finite element code. Simulations exhibit favorable agreement with single and bicrystal experimental data for shock pressures ranging from 3 to 110 GPa.

Accessing protein conformational ensembles using room-temperature X-ray crystallography

PubMed Central

Fraser, James S.; van den Bedem, Henry; Samelson, Avi J.; Lang, P. Therese; Holton, James M.; Echols, Nathaniel; Alber, Tom

2011-01-01

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation. PMID:21918110

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.

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.

Evolution of Nano-structured Quasicrystals from Amorphous alloys

NASA Astrophysics Data System (ADS)

Xing, L. Q.; Kelton, K. F.

2002-03-01

Ta shows a significant effect on the precipitation of quasicrystals in (Zr_1-xTa_x)_64Cu_18Ni_8Al_10 amorphous alloys. The amorphous alloy made without Ta forms precipitates of tetragonal Zr_2Cu primary phases upon annealing. The addition of a small amount of Ta ( ~ 3 at%) to the alloy initiates the precipitation of primary icosahedral quasicrystal phases. Moreover, as the Ta concentration increases, the size of the precipitates decreases dramatically. To study the effect of Ta in this alloy system and to understand the mechanism for the precipitation of nano-structured quasicrystals, we have investigated the crystallization characteristics of the alloys made with different Ta concentration using DSC, checked the structures of the annealed samples with TEM and X-ray diffraction, and analyzed the kinetics of the crystallization processes. The kinetic parameter and the measured crystal size distribution will be compared with theoretical predictions from conventional nucleation and growth model and from a new model for nucleation that couples the long-range diffusion flux with the interfacial attachment processes.

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.

Organic Crystal Engineering of Thermosetting Cyanate Ester Monomers: Influence of Structure on Melting Point

DTIC Science & Technology

2016-05-27

often discussed in the field of thermosetting materials, crystal engineering1-4 plays a key role in facilitating the successful utilization of these...not to alter the desirable properties of the polymerized networks. Fortunately, the field of crystal engineering provides examples where even very...Chickos and Acree.26 For molecular modeling, methods ranging from atomistic simulations with semi-empirical force fields to density functional

X-ray Diffraction from Membrane Protein Nanocrystals

PubMed Central

Hunter, M.S.; DePonte, D.P.; Shapiro, D.A.; Kirian, R.A.; Wang, X.; Starodub, D.; Marchesini, S.; Weierstall, U.; Doak, R.B.; Spence, J.C.H.; Fromme, P.

2011-01-01

Membrane proteins constitute >30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is <300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain <100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain <200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells. PMID:21190672

Exploring Molecular Speciation and Crystallization Mechanism of Amorphous 2-Phenylamino Nicotinic Acid.

PubMed

Kalra, Arjun; Lubach, Joseph W; Munson, Eric J; Li, Tonglei

2018-02-07

Molecular understanding of phase stability and transition of the amorphous state helps in formulation and manufacturing of poorly-soluble drugs. Crystallization of a model compound, 2-phenylamino nicotinic acid (2PNA), from the amorphous state was studied using solid-state analytical methods. Our previous report suggests that 2PNA molecules mainly develop intermolecular -COOH∙∙∙pyridine N (acid-pyridine) interactions in the amorphous state. In the current study, the molecular speciation is explored with regard to the phase transition from the amorphous to the crystalline state. Using spectroscopic techniques, the molecular interactions and structural evolvement during the recrystallization from the glassy state were investigated. The results unveiled that the structurally heterogeneous amorphous state contains acid-pyridine aggregates - either as hydrogen-bonded neutral molecules or as zwitterions - as well as a population of carboxylic acid dimers. Phase transition from the amorphous state results in crystal structures composed of carboxylic acid dimer (acid-acid) synthon or acid-pyridine chains depending on the crystallization conditions employed. The study underlines the structural evolvement, as well as its impact on the metastability, of amorphous samples from local, supramolecular assemblies to long-range intermolecular ordering through crystallization.

Light-Activated Gigahertz Ferroelectric Domain Dynamics

NASA Astrophysics Data System (ADS)

Akamatsu, Hirofumi; Yuan, Yakun; Stoica, Vladimir A.; Stone, Greg; Yang, Tiannan; Hong, Zijian; Lei, Shiming; Zhu, Yi; Haislmaier, Ryan C.; Freeland, John W.; Chen, Long-Qing; Wen, Haidan; Gopalan, Venkatraman

2018-03-01

Using time- and spatially resolved hard x-ray diffraction microscopy, the striking structural and electrical dynamics upon optical excitation of a single crystal of BaTiO3 are simultaneously captured on subnanoseconds and nanoscale within individual ferroelectric domains and across walls. A large emergent photoinduced electric field of up to 20 ×106 V /m is discovered in a surface layer of the crystal, which then drives polarization and lattice dynamics that are dramatically distinct in a surface layer versus bulk regions. A dynamical phase-field modeling method is developed that reveals the microscopic origin of these dynamics, leading to gigahertz polarization and elastic waves traveling in the crystal with sonic speeds and spatially varying frequencies. The advances in spatiotemporal imaging and dynamical modeling tools open up opportunities for disentangling ultrafast processes in complex mesoscale structures such as ferroelectric domains.

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.

Synthesis, crystal structure, and magnetic properties of two-dimensional divalent metal glutarate/dipyridylamine coordination polymers, with a single crystal-to-single crystal transformation in the copper derivative

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

Montney, Matthew R.; Supkowski, Ronald M.; Staples, Richard J.

Hydrothermal reaction of divalent metal chlorides with glutaric acid and 4,4'-dipyridylamine (dpa) has afforded an isostructural family of coordination polymers with formulation [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate). Square pyramidal coordination is seen in 1-3, with semi-ligation of a sixth donor to produce a '5+1' extended coordination sphere. Neighboring metal atoms are linked into 1D [M(glu)]{sub n} neutral chains through chelating/monodentate bridging glutarate moieties with a syn-anti binding mode, and semi-chelation of the pendant carboxylate oxygen. These chains further connect into 2D layers through dipodal dpa ligands. Neighboring layers stack into the pseudo 3D crystal structure ofmore » 1-3 through supramolecular hydrogen bonding between dpa amine units and the semi-chelated glutarate oxygen atoms. The variable temperature magnetic behavior of 1-3 was explored and modeled as infinite 1D Heisenberg chains. Notably, complex 3 undergoes a thermally induced single crystal-to-single crystal transformation between centric and acentric space groups, with a conformationally disordered unilayer structure at 293 K and an ordered bilayer structure at 173 K. All materials were further characterized via infrared spectroscopy and elemental and thermogravimetric analyses. - Graphical abstract: The coordination polymers [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate, dpa=4,4'-dipyridylamine) exhibit 2D layer structures based on 1D [M(glu)]{sub n} chains linked through dpa tethers. Antiferromagnetic coupling is observed for 2 and 3, while ferromagnetism is predominant in 1. Compound 3 undergoes a thermally induced single crystal-to-single crystal transformation from an acentric to a centrosymmetric space group.« less

Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions

PubMed Central

Maréchal, J-D; Kemp, C A; Roberts, G C K; Paine, M J I; Wolf, C R; Sutcliffe, M J

2008-01-01

The cytochromes P450 (CYPs) comprise a vast superfamily of enzymes found in virtually all life forms. In mammals, xenobiotic metabolizing CYPs provide crucial protection from the effects of exposure to a wide variety of chemicals, including environmental toxins and therapeutic drugs. Ideally, the information on the possible metabolism by CYPs required during drug development would be obtained from crystal structures of all the CYPs of interest. For some years only crystal structures of distantly related bacterial CYPs were available and homology modelling techniques were used to bridge the gap and produce structural models of human CYPs, and thereby obtain useful functional information. A significant step forward in the reliability of these models came seven years ago with the first crystal structure of a mammalian CYP, rabbit CYP2C5, followed by the structures of six human enzymes, CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2D6 and CYP3A4, and a second rabbit enzyme, CYP2B4. In this review we describe as a case study the evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism. This work has led directly to the successful design of CYP2D6 mutants with novel activity—including creating a testosterone hydroxylase, converting quinidine from inhibitor to substrate, creating a diclofenac hydroxylase and creating a dextromethorphan O-demethylase. Our modelling-derived hypothesis-driven integrated interdisciplinary studies have given key insight into the molecular determinants of CYP2D6 and other important drug metabolizing enzymes. PMID:18026129

Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers

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

Lenz, Dominic A.; Likos, Christos N.; Blaak, Ronald

We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, amore » transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed.« less

Structural, thermal, laser damage, photoconductivity, NLO and mechanical properties of modified vertical Bridgman method grown AgGa0.5In0.5Se2 single crystal

NASA Astrophysics Data System (ADS)

Vijayakumar, P.; Ramasamy, P.

2016-08-01

AgGa0.5In0.5Se2 single crystal was grown using modified vertical Bridgman method. The structural perfection of the AgGa0.5In0.5Se2 single crystal has been analyzed by high-resolution X-ray diffraction rocking curve measurements. The structural and compositional uniformities of AgGa0.5In0.5Se2 were studied using Raman scattering spectroscopy at room temperature. The FWHM of the Γ1 (W1) and Γ5L (Γ15) measured at different regions of the crystal confirms that the composition throughout its length is fairly uniform. Thermal properties of the as-grown crystal, including specific heat, thermal diffusivity and thermal conductivity have been investigated. The multiple shot surface laser damage threshold value was measured using Nd:YAG laser. Photoconductivity measurements with different temperatures have confirmed the positive photoconducting behavior. Second harmonic generation (SHG) on powder samples has been measured using the Kurtz and Perry technique and the results display that AgGa0.5In0.5Se2 is a phase-matchable NLO material. The hardness behavior has been measured using Vickers micro hardness measurement and the indentation size effect has been observed. The classical Meyer's law, propositional resistance model and modified propositional resistance model have been used to analyse the micro hardness behavior.

Deciphering chemical order/disorder and material properties at the single-atom level.

PubMed

Yang, Yongsoo; Chen, Chien-Chun; Scott, M C; Ophus, Colin; Xu, Rui; Pryor, Alan; Wu, Li; Sun, Fan; Theis, Wolfgang; Zhou, Jihan; Eisenbach, Markus; Kent, Paul R C; Sabirianov, Renat F; Zeng, Hao; Ercius, Peter; Miao, Jianwei

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling 'real' materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily on average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. This work combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure-property relationships at the fundamental level.

Packing interface energetics in different crystal forms of the λ Cro dimer.

PubMed

Ahlstrom, Logan S; Miyashita, Osamu

2014-07-01

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. © 2013 Wiley Periodicals, Inc.

Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2014-01-01

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them, in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ~5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. PMID:24218107

Testing the limits of sensitivity in a solid-state structural investigation by combined X-ray powder diffraction, solid-state NMR, and molecular modelling.

PubMed

Filip, Xenia; Borodi, Gheorghe; Filip, Claudiu

2011-10-28

A solid state structural investigation of ethoxzolamide is performed on microcrystalline powder by using a multi-technique approach that combines X-ray powder diffraction (XRPD) data analysis based on direct space methods with information from (13)C((15)N) solid-state Nuclear Magnetic Resonance (SS-NMR) and molecular modeling. Quantum chemical computations of the crystal were employed for geometry optimization and chemical shift calculations based on the Gauge Including Projector Augmented-Wave (GIPAW) method, whereas a systematic search in the conformational space was performed on the isolated molecule using a molecular mechanics (MM) approach. The applied methodology proved useful for: (i) removing ambiguities in the XRPD crystal structure determination process and further refining the derived structure solutions, and (ii) getting important insights into the relationship between the complex network of non-covalent interactions and the induced supra-molecular architectures/crystal packing patterns. It was found that ethoxzolamide provides an ideal case study for testing the accuracy with which this methodology allows to distinguish between various structural features emerging from the analysis of the powder diffraction data. This journal is © the Owner Societies 2011

Thermal tuning on band gaps of 2D phononic crystals considering adhesive layers

NASA Astrophysics Data System (ADS)

Zhou, Xiaoliang; Chen, Jialin; Li, Yuhang; Sun, Yuxin; Xing, Yufeng

2018-02-01

Phononic crystals are very attractive in many applications, such as noise reduction, filters and vibration isolation, due to their special forbidden band gap structures. In the present paper, the investigation of tunable band gaps of 2D phononic crystals with adhesive layers based on thermal changing is conducted. Based on the lumped-mass method, an analytical model of 2D phononic crystals with relatively thin adhesive layers is established, in which the in-plane and out-of-plane modes are both in consideration. The adhesive material is sensitive to temperature so that the band structure can be tuned and controlled by temperature variation. As temperature increases from 20 °C-80 °C, the first band gap shifts to the frequency zone around 10 kHz, which is included by the audible frequency range. The results propose an important guideline for applications, such as noise suppression using the 2D phononic crystals.

The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers

NASA Astrophysics Data System (ADS)

Hu, Yufeng; Chen, Zhenhang; Fu, Yanjun; He, Qingzhong; Jiang, Lun; Zheng, Jiangge; Gao, Yina; Mei, Pinchao; Chen, Zhongzhou; Ren, Xueqin

2015-03-01

Flexibility is an intrinsic property of proteins and essential for their biological functions. However, because of structural flexibility, obtaining high-quality crystals of proteins with heterogeneous conformations remain challenging. Here, we show a novel approach to immobilize traditional precipitants onto molecularly imprinted polymers (MIPs) to facilitate protein crystallization, especially for flexible proteins. By applying this method, high-quality crystals of the flexible N-terminus of human fragile X mental retardation protein are obtained, whose absence causes the most common inherited mental retardation. A novel KH domain and an intermolecular disulfide bond are discovered, and several types of dimers are found in solution, thus providing insights into the function of this protein. Furthermore, the precipitant-immobilized MIPs (piMIPs) successfully facilitate flexible protein crystal formation for five model proteins with increased diffraction resolution. This highlights the potential of piMIPs for the crystallization of flexible proteins.

3D coherent X-ray diffractive imaging of an Individual colloidal crystal grain

NASA Astrophysics Data System (ADS)

Shabalin, A.; Meijer, J.-M.; Sprung, M.; Petukhov, A. V.; Vartanyants, I. A.

Self-assembled colloidal crystals represent an important model system to study nucleation phenomena and solid-solid phase transitions. They are attractive for applications in photonics and sensorics. We present results of a coherent x-ray diffractive imaging experiment performed on a single colloidal crystal grain. The full three-dimensional (3D) reciprocal space map measured by an azimuthal rotational scan contained several orders of Bragg reflections together with the coherent interference signal between them. Applying the iterative phase retrieval approach, the 3D structure of the crystal grain was reconstructed and positions of individual colloidal particles were resolved. We identified an exact stacking sequence of hexagonal close-packed layers including planar and linear defects. Our results open up a breakthrough in applications of coherent x-ray diffraction for visualization of the inner 3D structure of different mesoscopic materials, such as photonic crystals. Present address: University of California - San Diego, USA.

Crystal Engineering; How molecules build solids

NASA Astrophysics Data System (ADS)

Williams, Jeffrey H.

2017-09-01

There are more than 20 million chemicals in the literature, with new materials being synthesized each week. Most of these molecules are stable, and the 3-dimensional arrangement of the atoms in the molecules, in the various solids may be determined by routine x-ray crystallography. When this is done, it is found that this vast range of molecules, with varying sizes and shapes can be accommodated by only a handful of solid structures. This limited number of architectures for the packing of molecules of all shapes and sizes, to maximize attractive intermolecular forces and minimizing repulsive intermolecular forces, allows us to develop simple models of what holds the molecules together in the solid. In this volume we look at the origin of the molecular architecture of crystals; a topic that is becoming increasingly important and is often termed, crystal engineering. Such studies are a means of predicting crystal structures, and of designing crystals with particular properties by manipulating the structure and interaction of large molecules. That is, creating new crystal architectures with desired physical characteristics in which the molecules pack together in particular architectures; a subject of particular interest to the pharmaceutical industry.

Illustrating and homology modeling the proteins of the Zika virus

PubMed Central

Ekins, Sean; Liebler, John; Neves, Bruno J.; Lewis, Warren G.; Coffee, Megan; Bienstock, Rachelle; Southan, Christopher; Andrade, Carolina H.

2016-01-01

The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening. PMID:27746901

One-step model of photoemission from single-crystal surfaces

DOE PAGES

Karkare, Siddharth; Wan, Weishi; Feng, Jun; ...

2017-02-28

In our paper, we present a three-dimensional one-step photoemission model that can be used to calculate the quantum efficiency and momentum distributions of electrons photoemitted from ordered single-crystal surfaces close to the photoemission threshold. Using Ag(111) as an example, we also show that the model can not only calculate the quantum efficiency from the surface state accurately without using any ad hoc parameters, but also provides a theoretical quantitative explanation of the vectorial photoelectric effect. This model in conjunction with other band structure and wave function calculation techniques can be effectively used to screen single-crystal photoemitters for use as electronmore » sources for particle accelerator and ultrafast electron diffraction applications.« less

Effects of rotation on crystal settling in a terrestrial magma ocean: Spherical shell model

NASA Astrophysics Data System (ADS)

Maas, C.; Hansen, U.

2015-12-01

Like Moon or Mars, Earth experienced one or several deep magma ocean periods of globalextent in a later stage of its accretion. The crystallization of these magma oceans is of keyimportance for the chemical structure of Earth, the mantle evolution and the onset of platetectonics. Due to the fast rotation of early Earth and the small magma viscosity, rotationprobably had a profound effect on differentiation processes. For example, Matyska et al.[1994] propose that the distribution of heterogeneities like the two large low shear velocityprovinces (LLSVP) at the core mantle boundary is influenced by rotational dynamicsof early Earth. Further Garnero and McNamara [2008] suggest that the LLSVPs arevery long-living anomalies, probably reaching back to the time of differentiation andsolidification of Earth. However, nearly all previous studies neglect the effects of rotation.In our previous work using a Cartesian model, a strong influence of rotation as well asof latitude on the differentiation processes in an early magma ocean was revealed. Weshowed that crystal settling in an early stage of magma ocean crystallization cruciallydepends on latitude as well as on rotational strength and crystal density.In order to overcome the restrictions as to the geometry of the Cartesian model, we arecurrently developing a spherical model to simulate crystal settling in a rotating sphericalshell. This model will allow us not only to investigate crystal settling at the poles andthe equator, but also at latitudes in-between these regions, as well as the migration ofcrystals between poles and equator. ReferencesE. J. Garnero and A. K. McNamara. Structure and dynamics of earth's lower mantle.Science, 320(5876):626-628, 2008.C. Matyska, J. Moser, and D. A. Yuen. The potential influence of radiative heat transferon the formation of megaplumes in the lower mantle. Earth and Planetary ScienceLetters, 125(1):255-266, 1994.

Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

PubMed

Horrell, Sam; Antonyuk, Svetlana V; Eady, Robert R; Hasnain, S Samar; Hough, Michael A; Strange, Richard W

2016-07-01

Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

Crystal structure of low-symmetry rondorfite

NASA Astrophysics Data System (ADS)

Rastsvetaeva, R. K.; Zadov, A. E.; Chukanov, N. V.

2008-03-01

The crystal structure of an aluminum-rich variety of the mineral rondorfite with the composition Ca16[Mg2(Si7Al)(O31OH)]Cl4 from the skarns of the Verkhne-Chegemskoe plateau (the Kabardino-Balkarian Republic, the Northern Caucasus Region, Russia) was solved in the triclinic space group with the unit-cell parameters a = 15.100(2) Å, b = 15.110(2) Å, c = 15.092(2) Å, α = 90.06(1)°, β = 90.01(1)°, γ = 89.93(1)°, Z = 4, sp. gr. P1. The structural model consisting of 248 independent atoms was determined by the phase-correction method and refined to R = 3.8% with anisotropic displacement parameters based on all 7156 independent reflections with 7156 F > 3σ( F). The crystal structure is based on pentamers consisting of four Si tetrahedra linked by the central Mg tetrahedron. The structure can formally be refined in the cubic space group ( a = 15.105 Å, sp. gr. Fd overline 3 , seven independent positions) with anisotropic displacement parameters to R = 2.74% based on 579 reflections with F > 3σ( F) without accounting for more than 1000 observed reflections, which are inconsistent with the cubic symmetry of the crystal structure.

Three-Dimensional Model of Holographic Formation of Inhomogeneous PPLC Diffraction Structures

NASA Astrophysics Data System (ADS)

Semkin, A. O.; Sharangovich, S. N.

2018-05-01

A three-dimensional theoretical model of holographic formation of inhomogeneous diffraction structures in composite photopolymer - liquid crystal materials is presented considering both the nonlinearity of recording and the amplitude-phase inhomogeneity of the recording light field. Based on the results of numerical simulation, the kinematics of formations of such structures and their spatial profile are investigated.

The mechanical properties of as-grown noncubic organic molecular crystals assessed by nanoindentation

DOE PAGES

Taw, Matthew R.; Yeager, John D.; Hooks, Daniel E.; ...

2017-06-19

Organic molecular crystals are often noncubic and contain significant steric hindrance within their structure to resist dislocation motion. Plastic deformation in these systems can be imparted during processing (tableting and comminution of powders), and the defect density impacts subsequent properties and performance. This paper measured the elastic and plastic properties of representative monoclinic, orthorhombic, and triclinic molecular crystalline structures using nanoindentation of as-grown sub-mm single crystals. The variation in modulus due to in-plane rotational orientation, relative to a Berkovich tip, was approximately equal to the variation of a given crystal at a fixed orientation. The onset of plasticity occurs consistentlymore » at shear stresses between 1 and 5% of the elastic modulus in all three crystal systems, and the hardness to modulus ratio suggests conventional Berkovich tips do not generate fully self-similar plastic zones in these materials. Finally, this provides guidance for mechanical models of tableting, machining, and property assessment of molecular crystals.« less

The phosphorylation site in double helical amylopectin as investigated by a combined approach using chemical synthesis, crystallography and molecular modeling.

PubMed

Engelsen, Søren Balling; Madsen, Anders Østergaard; Blennow, Andreas; Motawia, Mohammed Saddik; Møller, Birger Lindberg; Larsen, Sine

2003-04-24

The only known in planta substitution of starch is phosphorylation. Whereas the function of starch phosphorylation is poorly understood, phosphorylated starch possesses improved functionality in vitro. Molecular models of native crystalline starch are currently being developed and the starch phosphorylating enzyme has recently been discovered. Accordingly, it is desirable to obtain a more exact description of the molecular structures of phosphorylated starch. We have determined the crystal structure of methyl alpha-D-glucopyranoside 6-O-phosphate as its potassium salt which is thought to be the starch phosphate counterion in vivo. From this structure and previously known glucophosphate structures we describe the possible 6-O-phosphate geometries and through modeling extrapolate the results to the double helical structure of the crystalline part of amylopectin. The geometries of the existing crystal structures of 6-O-phosphate groups were found to belong to two main adiabatic valleys. One of these conformations could be fitted into the double helical amylopectin part without perturbing the double helical amylopectin structure and without creating steric problems for the hexagonal chain-chain packing.

Theoretical explanation of spin-Hamiltonian parameters and local structure for the orthorhombic MnO2 -4 clusters in K2CrO4 : Mn6 + crystal

NASA Astrophysics Data System (ADS)

Wang, Ning; Xie, Linhua

2017-12-01

In this paper, the spin-Hamiltonian parameters (g factors gx, gy, gz and hyperfine structure constants A Ax, Ay, Az) and the absorption spectrum of K2CrO4 : Mn6 + crystal are theoretically explained by using the high-order perturbation theory, the double-spin-orbit-coupling model theory and the double-mechanism theory (the crystal field mechanism and the charge-transfer (CT) mechanism). The calculation results show that the contribution of the CT mechanism cannot be neglected for Mn6 + ions in orthorhombic clusters with the ground state ?.

Electron density distribution and disordered crystal structure of 15R-SiAlON, SiAl{sub 4}O{sub 2}N{sub 4}

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

Banno, Hiroki; Hanai, Takaaki; Asaka, Toru

2014-03-15

The crystal structure of SiAl{sub 4}O{sub 2}N{sub 4} was characterized by laboratory X-ray powder diffraction (CuKα{sub 1}). The title compound is trigonal with space group R3-bar m. The hexagonal unit-cell dimensions (Z=3) are a=0.301332(3) nm, c=4.18616(4) nm and V=0.3291825(5) nm{sup 3}. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of one of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensitymore » partitioning was minimized. The reliability indices calculated from the MPF were R{sub wp}=5.05%, S (=R{sub wp}/R{sub e})=1.21, R{sub p}=3.77%, R{sub B}=1.29% and R{sub F}=1.01%. The disordered crystal structure was successfully described by overlapping three types of domains with ordered atom arrangements. The distribution of atomic positions in one of the three types of domains can be achieved in the space group R3-bar m. The atom arrangements in the other two types of domains are noncentrosymmetrical with the space group R3m. These two structural configurations are related by the pseudo-symmetry inversion. -- Graphical abstract: A bird's eye view of electron densities up to 75.3% (0.133 nm{sup −3}) of the maximum on the plane parallel to (110) with the corresponding atomic arrangements of SiAl{sub 4}O{sub 2}N{sub 4}. Highlights: • Crystal structure of SiAl{sub 4}O{sub 2}N{sub 4} is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • The maximum-entropy method-based pattern fitting method is used to confirm the validity of the model. • The disordered structure is described by overlapping three types of domains with ordered atom arrangements.« less

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

Duke, B. J.; O'Leary, Brian

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

Persistent Self-Association of Solute Molecules in Solution.

PubMed

Tang, Weiwei; Mo, Huaping; Zhang, Mingtao; Parkin, Sean; Gong, Junbo; Wang, Jingkang; Li, Tonglei

2017-11-02

The structural evolvement of a solute determines the crystallization outcome. The self-association mechanism leading to nucleation, however, remains poorly understood. Our current study explored the solution chemistry of a model compound, tolfenamic acid (TFA), in three different solvents mainly by solution NMR. It was found that hydrogen-bonded pairs of solute-solute or solute-solvent stack with each through forming a much weaker π-π interaction as the concentration increases. Depending on the solvent, configurations of the solution species may be retained in the resultant crystal structure or undergo rearrangement. Yet, the π-π stacking is always retained in the crystal regardless of the solvent used for the crystallization. The finding suggests that nucleation not only involves the primary intermolecular interaction (hydrogen bonding) but also engages the secondary forces in the self-assembly process.

Direct imaging of isofrequency contours in photonic structures

DOE PAGES

Regan, E. C.; Igarashi, Y.; Zhen, B.; ...

2016-11-25

The isofrequency contours of a photonic crystal are important for predicting and understanding exotic optical phenomena that are not apparent from high-symmetry band structure visualizations. We demonstrate a method to directly visualize the isofrequency contours of high-quality photonic crystal slabs that show quantitatively good agreement with numerical results throughout the visible spectrum. Our technique relies on resonance-enhanced photon scattering from generic fabrication disorder and surface roughness, so it can be applied to general photonic and plasmonic crystals or even quasi-crystals. We also present an analytical model of the scattering process, which explains the observation of isofrequency contours in our technique.more » Furthermore, the isofrequency contours provide information about the characteristics of the disorder and therefore serve as a feedback tool to improve fabrication processes.« less

Rapid crystallization of externally produced ions in a Penning trap

NASA Astrophysics Data System (ADS)

Murböck, T.; Schmidt, S.; Birkl, G.; Nörtershäuser, W.; Thompson, R. C.; Vogel, M.

2016-10-01

We have studied the cooling dynamics, formation process, and geometric structure of mesoscopic crystals of externally produced magnesium ions in a Penning trap. We present a cooling model and measurements for a combination of buffer gas cooling and laser cooling which has been found to reduce the ion kinetic energy by eight orders of magnitude from several hundreds of eV to μ eV and below within seconds. With ion numbers of the order of 1 ×103 to 1 ×105 , such cooling leads to the formation of ion Coulomb crystals which display a characteristic shell structure in agreement with the theory of non-neutral plasmas. We show the production and characterization of two-species ion crystals as a means of sympathetic cooling of ions lacking a suitable laser-cooling transition.

Soft matter perspective on protein crystal assembly.

PubMed

Fusco, Diana; Charbonneau, Patrick

2016-01-01

Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter physics to understand colloidal assembly offer some insights into the problem of crystallizing proteins. This topical review describes the various analogies that have been made between proteins and colloids in that context. We highlight the explanatory power of patchy particle models, but also the challenges of providing guidance for crystallizing specific proteins. We conclude with a presentation of possible future research directions. This review is intended for soft matter scientists interested in protein crystallization as a self-assembly problem, and as an introduction to the pertinent physics literature for protein scientists more generally. Copyright © 2015 Elsevier B.V. All rights reserved.

Discovery of black dye crystal structure polymorphs: Implications for dye conformational variation in dye-sensitized solar cells

DOE PAGES

Cole, Jacqueline M.; Low, Kian Sing; Gong, Yun

2015-11-24

Here, we present the discovery of a new crystal structure polymorph (1) and pseudopolymorph (2) of the Black Dye, one of the world’s leading dyes for dye-sensitized solar cells, DSSCs (10.4% device performance efficiency). This reveals that Black Dye molecules can adopt multiple low-energy conformers. This is significant since it challenges existing models of the Black Dye···TiO 2 adsorption process that renders a DSSC working electrode; these have assumed a single molecular conformation that refers to the previously reported Black Dye crystal structure (3). The marked structural differences observed between 1, 2, and 3 make the need for modeling multiplemore » conformations more acute. Additionally, the ordered form of the Black Dye (1) provides a more appropriate depiction of its anionic structure, especially regarding its anchoring group and NCS bonding descriptions. The tendency toward NCS ligand isomerism, evidenced via the disordered form 2, has consequences for electron injection and electron recombination in Black Dye embedded DSSC devices. Dyes 2 and 3 differ primarily by the absence or presence of a solvent of crystallization, respectively; solvent environment effects on the dye are thereby elucidated. This discovery of multiple Black Dye conformers from diffraction, with atomic-level definition, complements recently reported nanoscopic evidence for multiple dye conformations existing at a dye···TiO 2 interface, for a chemically similar DSSC dye; those results emanated from imaging and spectroscopy, but were unresolved at the submolecular level. Taken together, these findings lead to the general notion that multiple dye conformations should be explicitly considered when modeling dye···TiO 2 interfaces in DSSCs, at least for ruthenium-based dye complexes.« less

Shear-induced partial translational ordering of a colloidal solid

NASA Astrophysics Data System (ADS)

Ackerson, B. J.; Clark, N. A.

1984-08-01

Highly charged submicrometer plastic spheres suspended in water at low ionic strength will order spontaneously into bcc crystals or polycrystals. A simple linear shear orients and disorders these crystals by forcing (110) planes to stack normal to the shear gradient and to slide relative to each other with a <111> direction parallel to the solvent flow. In this paper we analyze in detail the disordering and flow processes occurring beyond the intrinsic elastic limit of the bcc crystal. We are led to a model in which the flow of a colloidal crystal is interpreted as a fundamentally different process from that found in atomic crystals. In the colloidal crystal the coupling of particle motion to the background fluid forces a homogeneous flow, where every layer is in motion relative to its neighboring layers. In contrast, the plastic flow in an atomic solid is defect mediated flow. At the lowest applied stress, the local bcc order in the colloidal crystal exhibits shear strains both parallel and perpendicular to the direction of the applied stress. The magnitude of these deformations is estimated using the configurational energy for bcc and distorted bcc crystals, assuming a screened Coulomb pair interaction between colloidal particles. As the applied stress is increased, the intrinsic elastic limit of the crystal is exceeded and the crystal begins to flow with adjacent layers executing an oscillatory path governed by the balance of viscous and screened Coulomb forces. The path takes the structure from the bcc1 and bcc2 twins observed at zero shear to a distorted two-dimensional hcp structure at moderate shear rates, with a loss of interlayer registration as the shear is increased. This theoretical model is consistent with other experimental observations, as well.

Crystal Structure of a Ube2S-Ubiquitin Conjugate

PubMed Central

Lorenz, Sonja; Bhattacharyya, Moitrayee; Feiler, Christian; Rape, Michael; Kuriyan, John

2016-01-01

Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a “donor” ubiquitin and a primary amino group of an “acceptor” ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface. PMID:26828794

Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A.

PubMed

Kita, Shunsuke; Matsubara, Haruki; Kasai, Yoshiyuki; Tamaoki, Takaharu; Okabe, Yuki; Fukuhara, Hideo; Kamishikiryo, Jun; Krayukhina, Elena; Uchiyama, Susumu; Ose, Toyoyuki; Kuroki, Kimiko; Maenaka, Katsumi

2015-06-01

Emerging evidence has revealed the pivotal roles of C-type lectin-like receptors (CTLRs) in the regulation of a wide range of immune responses. Human natural killer cell receptor-P1A (NKRP1A) is one of the CTLRs and recognizes another CTLR, lectin-like transcript 1 (LLT1) on target cells to control NK, NKT and Th17 cells. The structural basis for the NKRP1A-LLT1 interaction was limitedly understood. Here, we report the crystal structure of the ectodomain of LLT1. The plausible receptor-binding face of the C-type lectin-like domain is flat, and forms an extended β-sheet. The residues of this face are relatively conserved with another CTLR, keratinocyte-associated C-type lectin, which binds to the CTLR member, NKp65. A LLT1-NKRP1A complex model, prepared using the crystal structures of LLT1 and the keratinocyte-associated C-type lectin-NKp65 complex, reasonably satisfies the charge consistency and the conformational complementarity to explain a previous mutagenesis study. Furthermore, crystal packing and analytical ultracentrifugation revealed dimer formation, which supports a complex model. Our results provide structural insights for understanding the binding modes and signal transduction mechanisms, which are likely to be conserved in the CTLR family, and for further rational drug design towards regulating the LLT1 function. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic and optical holonomic manipulation of colloids, structures and topological defects in liquid crystals for characterization of mesoscale self-assembly and dynamics

NASA Astrophysics Data System (ADS)

Varney, Michael C. M.

Colloidal systems find important applications ranging from fabrication of photonic crystals to direct probing of phenomena encountered in atomic crystals and glasses; topics of great interest for physicists exploring a broad range of scientific, industrial and biomedical fields. The ability to accurately control particles of mesoscale size in various liquid host media is usually accomplished through optical trapping methods, which suffer limitations intrinsic to trap laser intensity and force generation. Other limitations are due to colloid properties, such as optical absorptivity, and host properties, such as viscosity, opacity and structure. Therefore, alternative and/or novel methods of colloidal manipulation are of utmost importance in order to advance the state of the art in technical applications and fundamental science. In this thesis, I demonstrate a magnetic-optical holonomic control system to manipulate magnetic and optical colloids in liquid crystals and show that the elastic structure inherent to nematic and cholesteric liquid crystals may be used to assist in tweezing of particles in a manner impossible in other media. Furthermore, I demonstrate the utility of this manipulation in characterizing the structure and microrheology of liquid crystals, and elucidating the energetics and dynamics of colloids interacting with these structures. I also demonstrate the utility of liquid crystal systems as a table top model system to probe topological defects in a manner that may lead to insights into topologically related phenomena in other fields, such as early universe cosmology, sub-atomic and high energy systems, or Skrymionic structures. I explore the interaction of colloid surface anchoring with the structure inherent in cholesteric liquid crystals, and how this affects the periodic dynamics and localization metastability of spherical colloids undergoing a "falling" motion within the sample. These so called "metastable states" cause colloidal dynamics to deviate from Stokes-like behavior at very low Reynolds numbers and is understood by accounting for periodic landscapes of elastic interaction potential between the particle and cholesteric host medium due to surface anchoring. This work extends our understanding of how colloids interact with liquid crystals and topological defects, and introduces a powerful method of colloidal manipulation with many potential applications.

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

DOE PAGES

Peck, Ariana; Poitevin, Frederic; Lane, Thomas Joseph

2018-02-21

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signalmore » reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.« less

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

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

Peck, Ariana; Poitevin, Frederic; Lane, Thomas Joseph

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signalmore » reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.« less

Machine learning for the structure-energy-property landscapes of molecular crystals.

PubMed

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

Potassium-cobalt sulphate crystal growth assisted by low frequency vibrations

NASA Astrophysics Data System (ADS)

Sadovsky, A.; Ermochenkov, I.; Dubovenko, E.; Sukhanova, E.; Bebyakin, M.; Dubov, V.; Avetissov, I.

2018-02-01

Single crystals of K2Co(SO4)2·6H2O were grown from solution using the temperature reduction method enhanced by the axial low frequency vibration control technique (AVC-technique). Physical modeling of heat-mass transfer in solution under the AVC action was performed. The growth rate of the AVC grown crystal was found to be twice that of the crystal grown under natural convection conditions. Analysis of spectral characteristics (absorption and Raman spectra) as well as structural properties (dislocation density and microhardness) of the grown crystals showed the significant superiority of the AVC technique for the growth of K2Co(SO4)2·6H2O crystals.

Filtering properties of Thue-Morse nano-photonic crystals containing high-temperature superconductor

NASA Astrophysics Data System (ADS)

Talebzadeh, Robabeh; Bavaghar, Mehrdad

2018-05-01

In this paper, we introduced new design of quasi-periodic layered structures by choosing order two of ternary Thue-Morse structure. We considered Superconductor-dielectric photonic crystal with mirror symmetric as (ABSSAB)N(BASSBA)N composed of two kinds of nano-scale dielectric layers (A and B) and high-temperature superconductor layers where N is the number of period. This structure is assumed to be the free space. By using the transfer matrix method and the two fluid model, we theoretically study the transmission spectrum of ternary Thue-Morse superconducting photonic crystals with mirror symmetry and introduce this structure as a narrow optical filter. We showed that transmission peak so-called defect mode appears itself inside the transmission spectrum of suggested structure as same as defective layered structure. Also, we analyzed the influence of various related parameters such as the operating temperature of superconductor layer on position of defect mode. The redshift of defect mode with increasing the operating temperature was observed.

Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus , Sulfolobus tokodaii and Methanocaldococcus jannaschii

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

Watanabe, Yuzo; Yanai, Hisaaki; Kanagawa, Mayumi

2016-07-27

The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, fromThermus thermophilus,Sulfolobus tokodaiiandMethanocaldococcus jannaschiiwere determined and their structural characteristics were analyzed. For PurS fromT. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the interaction site with PurL and PurQ, the other subunits of the formylglycinamide ribonucleotide amidotransferase. Molecular-dynamics simulations ofmore » the PurS dimer as well as a model of the complex of the PurS dimer, PurL and PurQ suggest that PurS plays some role in the catalysis of the enzyme by its bending motion.« less

Lattice Entertain You: Paper Modeling of the 14 Bravais Lattices on Youtube

ERIC Educational Resources Information Center

Sein, Lawrence T., Jr.; Sein, Sarajane E.

2015-01-01

A system for the construction of double-sided paper models of the 14 Bravais lattices, and important crystal structures derived from them, is described. The system allows the combination of multiple unit cells, so as to better represent the overall three-dimensional structure. Students and instructors can view the models in use on the popular…

Modeling the SHG activities of diverse protein crystals

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

Haupert, Levi M.; DeWalt, Emma L.; Simpson, Garth J.

2012-10-18

A symmetry-additiveab initiomodel for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much of the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within themore » crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ~84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.« less

The mechanism of color change in the neon tetra fish: a light-induced tunable photonic crystal array.

PubMed

Gur, Dvir; Palmer, Benjamin A; Leshem, Ben; Oron, Dan; Fratzl, Peter; Weiner, Steve; Addadi, Lia

2015-10-12

The fresh water fish neon tetra has the ability to change the structural color of its lateral stripe in response to a change in the light conditions, from blue-green in the light-adapted state to indigo in the dark-adapted state. The colors are produced by constructive interference of light reflected from stacks of intracellular guanine crystals, forming tunable photonic crystal arrays. We have used micro X-ray diffraction to track in time distinct diffraction spots corresponding to individual crystal arrays within a single cell during the color change. We demonstrate that reversible variations in crystal tilt within individual arrays are responsible for the light-induced color variations. These results settle a long-standing debate between the two proposed models, the "Venetian blinds" model and the "accordion" model. The insight gained from this biogenic light-induced photonic tunable system may provide inspiration for the design of artificial optical tunable systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

PubMed Central

Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

2014-01-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

Computational Modeling of Bloch Surface Waves in One-Dimensional Periodic and Aperiodic Multilayer Structures

NASA Astrophysics Data System (ADS)

Koju, Vijay

Photonic crystals and their use in exciting Bloch surface waves have received immense attention over the past few decades. This interest is mainly due to their applications in bio-sensing, wave-guiding, and other optical phenomena such as surface field enhanced Raman spectroscopy. Improvement in numerical modeling techniques, state of the art computing resources, and advances in fabrication techniques have also assisted in growing interest in this field. The ability to model photonic crystals computationally has benefited both the theoretical as well as experimental communities. It helps the theoretical physicists in solving complex problems which cannot be solved analytically and helps to acquire useful insights that cannot be obtained otherwise. Experimentalists, on the other hand, can test different variants of their devices by changing device parameters to optimize performance before fabrication. In this dissertation, we develop two commonly used numerical techniques, namely transfer matrix method, and rigorous coupled wave analysis, in C++ and MATLAB, and use two additional software packages, one open-source and another commercial, to model one-dimensional photonic crystals. Different variants of one-dimensional multilayered structures such as perfectly periodic dielectric multilayers, quasicrystals, aperiodic multilayer are modeled, along with one-dimensional photonic crystals with gratings on the top layer. Applications of Bloch surface waves, along with new and novel aperiodic dielectric multilayer structures that support Bloch surface waves are explored in this dissertation. We demonstrate a slow light configuration that makes use of Bloch Surface Waves as an intermediate excitation in a double-prism tunneling configuration. This method is simple compared to the more usual techniques for slowing light using the phenomenon of electromagnetically induced transparency in atomic gases or doped ionic crystals operated at temperatures below 4K. Using a semi-numerical approach, we show that a 1D photonic crystal, a multilayer structure composed of alternating layers of TiO2 and SiO2 , can be used to slow down light by a factor of up to 400. The results also show that better control of the speed of light can be achieved by changing the number of bilayers and the air-gap thickness appropriately. The existence of Bloch surface waves in periodic dielectric multilayer structures with a surface defect is well-known. Not yet recognized is that quasi-crystals and aperiodic dielectric multilayers can also support Bloch-like surface waves. We numerically show the excitation of Bloch-like surface waves in Fibonacci quasi-crystals, Thue-Morse aperiodic dielectric multilayers using the prism coupling method. We report improved surface electric field intensity and penetration depth of Bloch-like surface waves in the air side in such structures compared to their periodic counterparts. Bloch surface waves have also demonstrated significant potential in the field of bios-ensing technology. We further extend our study into a new type of multilayer structure based on Maximal-length sequence, which is a pseudo random sequence. We study the characteristics of Bloch surface waves in a 32 layered Maximal-length sequence multilayer and perform angular, as well as spectral sensitivity analysis for refractive index change detection. We demonstrate numerically that Maximal-length sequence multilayers significantly enhance the sensitivity of Bloch surface waves. Another type of structure that support Bloch surface waves are dielectric multilayer structures with a grating profile on the top-most layer. The grating profile adds an additional degree of freedom to the phase matching conditions for Bloch surface wave excitation. In such structures, the conditions for Bloch surface wave coupling can also be achieved by rotating both polar and azimuthal angles. The generation of Bloch surface waves as a function of azimuthal angle have similar characteristics to conventional grating coupled Bloch surface waves. However, azimuthal generated Bloch surface waves have enhanced angular sensitivity compared to conventional polar angle coupled modes, which makes them appropriate for detecting tiny variations in surface refractive index due to the addition of nano-particles such as protein molecules.

Disorder in Ag7GeSe5I, a superionic conductor: temperature-dependent anharmonic structural study.

PubMed

Albert, Stéphanie; Pillet, Sébastien; Lecomte, Claude; Pradel, Annie; Ribes, Michel

2008-02-01

A temperature-dependent structural investigation of the substituted argyrodite Ag(7)GeSe(5)I has been carried out on a single crystal from 15 to 475 K, in steps of 50 K, and correlated to its conductivity properties. The argyrodite crystallizes in a cubic cell with the F\\bar 43m space group. The crystal structure exhibits high static and dynamic disorder which has been efficiently accounted for using a combination of (i) Gram-Charlier development of the Debye-Waller factors for iodine and silver, and (ii) a split-atom model for Ag(+) ions. An increased delocalization of the mobile d(10) Ag(+) cations with temperature has been clearly shown by the inspection of the joint probability-density functions; the corresponding diffusion pathways have been determined.

Microwave Diffraction Techniques from Macroscopic Crystal Models

ERIC Educational Resources Information Center

Murray, William Henry

1974-01-01

Discusses the construction of a diffractometer table and four microwave models which are built of styrofoam balls with implanted metallic reflecting spheres and designed to simulate the structures of carbon (graphite structure), sodium chloride, tin oxide, and palladium oxide. Included are samples of Bragg patterns and computer-analysis results.…

Correlation between surface reconstruction and polytypism in InAs nanowire selective area epitaxy

NASA Astrophysics Data System (ADS)

Liu, Ziyang; Merckling, Clement; Rooyackers, Rita; Richard, Olivier; Bender, Hugo; Mols, Yves; Vila, María; Rubio-Zuazo, Juan; Castro, Germán R.; Collaert, Nadine; Thean, Aaron; Vandervorst, Wilfried; Heyns, Marc

2017-12-01

The mechanism of widely observed intermixing of wurtzite and zinc-blende crystal structures in InAs nanowire (NW) grown by selective area epitaxy (SAE) is studied. We demonstrate that the crystal structure in InAs NW grown by SAE can be controlled using basic growth parameters, and wurtzitelike InAs NWs are achieved. We link the polytypic InAs NWs SAE to the reconstruction of the growth front (111)B surface. Surface reconstruction study of InAs (111) substrate and the following homoepitaxy experiment suggest that (111) planar defect nucleation is related to the (1 × 1) reconstruction of InAs (111)B surface. In order to reveal it more clearly, a model is presented to correlate growth temperature and arsenic partial pressure with InAs NW crystal structure. This model considers the transition between (1 × 1) and (2 × 2) surface reconstructions in the frame of adatom atoms adsorption/desorption, and the polytypism is thus linked to reconstruction quantitatively. The experimental data fit well with the model, which highly suggests that surface reconstruction plays an important role in the polytypism phenomenon in InAs NWs SAE.

Theoretical modeling of zircon's crystal morphology according to data of atomistic calculations

NASA Astrophysics Data System (ADS)

Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

2017-04-01

Zircon is an essential mineral that is used in the U-Pb dating. Moreover, zircon is highly resistant to radioactive exposure. It is of great interest in solving both fundamental and applied problems associated with the isolation of high-level radioactive waste. There is significant progress in forecasting of the most energetically favorable crystal structures at the present time. Unfortunately, the theoretical forecast of crystal morphology at high technological level is under-explored nowadays, though the estimation of crystal equilibrium habit is extremely important in studying the physical and chemical properties of new materials. For the first time, the thesis about relation of the equilibrium shape of a crystal with its crystal structure was put forward in the works by O.Brave. According to it, the idealized habit is determined in the simplest case by a correspondence with the reticular densities Rhkl of individual faces. This approach, along with all subsequent corrections, does not take into account the nature of atoms and the specific features of the chemical bond in crystals. The atomistic calculations of crystal surfaces are commonly performed using the energetic characteristics of faces, namely, the surface energy (Esurf), which is a measure of the thermodynamic stability of the crystal face. The stable crystal faces are characterized by small positive values of Esurf. As we know from our previous research (Gromalova et al.,2015) one of the constitutive factors affecting the value of the surface energy in calculations is a choice of potentials model. In this regard, we studied several sets of parameters of atomistic interatomic potentials optimized previously. As the first test model («Zircon 1») were used sets of interatomic potentials of interaction Zr-O, Si-O and O-O in the form of Buckingham potentials. To improve playback properties of zircon additionally used Morse potential for a couple of Zr-Si, as well as the three-particle angular harmonic potential. The other sets of interatomic potentials («Zircon 2, Zircon 3») differed from the first in that parameters was found with the help of quantum-chemical calculations of the structure «ab initio».The surface energies for different faces of zircon were calculated using Metadise code (Watson et al., 1996) at P4-3000 personal computer with Windows XP operating system. The computation time for one simple form was from 30 minutes to 12 hours. Calculations have shown that depending on the chosen model the surface energy of zircons faces several changes. For example, Esurf of face (331) obtained using models of potentials «Zircon 2», «Zircon 3» sufficiently similar (2.82 and 3.01 J/mol2 respectively). Meaning of Esurf of this face, calculated on the basis of set «Zircon 1» significantly lower (1,54 J/mol2). With regard to the face (100), it has low surface energies when selecting all three models, with a minimum value (1,14 J/mol2) in the model «Zircon 1». References: Gromalova N.A., Eremin N.N., Urusov V.S. Atomistic computer modeling of the crystal-morpology of corundum group minerals // Zapiski RMO. V. 144. №4. 2015. p. 84-92. Watson G.W., Kelsey E.T., de Leeuw N.H., Harris D.J, Parker S.C. Atomistic simulation of dislocations, surfaces and interfaces in MgO. Journal of the Chemical Society Faraday Transactions. 1996. V.92 P. 433-438.

Random close packing in protein cores

NASA Astrophysics Data System (ADS)

Gaines, Jennifer C.; Smith, W. Wendell; Regan, Lynne; O'Hern, Corey S.

2016-03-01

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ≈0.75 , a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ ≈0.56 , which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.

Random close packing in protein cores.

PubMed

Gaines, Jennifer C; Smith, W Wendell; Regan, Lynne; O'Hern, Corey S

2016-03-01

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ≈ 0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ ≈ 0.56, which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.

Interactions of biomacromolecules with reverse hexagonal liquid crystals: drug delivery and crystallization applications.

PubMed

Libster, Dima; Aserin, Abraham; Garti, Nissim

2011-04-15

Recently, self-assembled lyotropic liquid crystals (LLCs) of lipids and water have attracted the attention of both scientific and applied research communities, due to their remarkable structural complexity and practical potential in diverse applications. The phase behavior of mixtures of glycerol monooleate (monoolein, GMO) was particularly well studied due to the potential utilization of these systems in drug delivery systems, food products, and encapsulation and crystallization of proteins. Among the studied lyotropic mesophases, reverse hexagonal LLC (H(II)) of monoolein/water were not widely subjected to practical applications since these were stable only at elevated temperatures. Lately, we obtained stable H(II) mesophases at room temperature by incorporating triacylglycerol (TAG) molecules into the GMO/water mixtures and explored the physical properties of these structures. The present feature article summarizes recent systematic efforts in our laboratory to utilize the H(II) mesophases for solubilization, and potential release and crystallization of biomacromolecules. Such a concept was demonstrated in the case of two therapeutic peptides-cyclosporin A (CSA) and desmopressin, as well as RALA peptide, which is a model skin penetration enhancer, and eventually a larger macromolecule-lysozyme (LSZ). In the course of the study we tried to elucidate relationships between the different levels of organization of LLCs (from the microstructural level, through mesoscale, to macroscopic level) and find feasible correlations between them. Since the structural properties of the mesophase systems are a key factor in drug release applications, we investigated the effects of these guest molecules on their conformations and the way these molecules partition within the domains of the mesophases. The examined H(II) mesophases exhibited great potential as transdermal delivery vehicles for bioactive peptides, enabling tuning the release properties according to their chemical composition and physical properties. Furthermore, we showed a promising opportunity for crystallization of CSA and LSZ in single crystal form as model biomacromolecules for crystallographic structure determination. The main outcomes of our research demonstrated that control of the physical properties of hexagonal LLC on different length scales is key for rational design of these systems as delivery vehicles and crystallization medium for biomacromolecules. Copyright © 2011 Elsevier Inc. All rights reserved.

Spontaneous polarization and dielectric relaxation dynamics of ferroelectric liquid crystals derived from 2(S)-[2(S)-ethylhexyolxy] propionic acid and its (S, R)-diastereomer

NASA Astrophysics Data System (ADS)

Huang, Lei-Ching; Fu, Chao-Ming

2015-09-01

The spontaneous polarization and molecular dynamics of four ferroelectric liquid crystals (FLCs) with two different kinds of core rings and two types of diastereomeric structures were investigated in this study. The FLCs with a biphenyl ring core structure showed higher spontaneous polarization than the FLCs with a naphthalene ring core structure. The complex dielectric spectra exhibited the Goldstone mode in the ferroelectric (SmC*) phase for all FLCs. The complex dielectric spectra of the four FLCs can be optimally fitted by the Debye model and the Cole-Cole model. Moreover, the Goldstone mode was enhanced under low DC bias fields for the FLCs with the (S, R)- diastereomeric structure, whereas the mode was suppressed for the FLCs with the (S, S)- diastereomeric structure. A microscopic molecular dynamic model is proposed to describe the underlying mechanism of the particular enhancement of the Goldstone mode. The experimental results of dielectric spectra and spontaneous polarization are explained in the discussion of the mesomorphic properties related to the FLC molecular structure.

The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph.

PubMed

Guizard, C; Chanzy, H; Sarko, A

1985-06-05

The crystal and molecular structure of a dextran hydrate has been determined through combined electron and X-ray diffraction analysis, aided by stereochemical model refinement. A total of 65 hk0 electron diffraction intensities were measured on frozen single crystals held at the temperature of liquid nitrogen, to a resolution limit of 1.6 A. The X-ray intensities were measured from powder patterns recorded from collections of the single crystals. The structure crystallizes in a monoclinic unit cell with parameters a = 25.71 A, b = 10.21 A, c (chain axis) = 7.76 A and beta = 91.3 degrees. The space group is P2(1) with b axis unique. The unit cell contains six chains and eight water molecules, with three chains of the same polarity and four water molecules constituting the asymmetric unit. Along the chain direction the asymmetric unit is a dimer residue; however, the individual glucopyranose residues are very nearly related by a molecular 2-fold screw axis. The conformation of the chain is very similar to that in the anhydrous structure, but the chain packing differs in the two structures in that the rotational positions of the chains about the helix axes (the chain setting angles) are considerably different. The chains still pack in the form of sheets that are separated by water molecules. The difference in the chain setting angles between the anhydrous and hydrate structures corresponds to the angle between like unit cell axes observed in the diffraction diagrams recorded from hybrid crystals containing both polymorphs. Despite some beam damage effects, the structure was determined to a satisfactory degree of agreement, with the residuals R''(electron diffraction) = 0.258 and R(X-ray) = 0.127.

Light-activated Gigahertz Ferroelectric Domain Dynamics

DOE PAGES

Akamatsu, Hirofumii; Yuan, Yakun; Stoica, Vladimir A.; ...

2018-02-26

Using time- and spatially-resolved hard X-ray diffraction microscopy, the striking structural and electrical dynamics upon optical excitation of a single crystal of BaTiO 3 are simultaneously captured on sub-nanoseconds and nanoscale within individual ferroelectric domains and across walls. A large emergent photo-induced electric field of up to 20 million volts per meter is discovered in a surface layer of the crystal, which then drives polarization and lattice dynamics that are dramatically distinct in a surface layer versus bulk regions. A dynamical phase-field modeling (DPFM) method is developed that reveals the microscopic origin of these dynamics, leading to GHz polarization andmore » elastic waves travelling in the crystal with sonic speeds and spatially varying frequencies. The advance of spatiotemporal imaging and dynamical modeling tools open opportunities of disentangling ultrafast processes in complex mesoscale structures such as ferroelectric domains« less

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

PubMed

Copeland, Kari L; Anderson, Julie A; Farley, Adam R; Cox, James R; Tschumper, Gregory S

2008-11-13

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.

Phonon conductivity metrics for compact, linked-cage, layered, and filled-cage crystals, using ab initio, molecular dynamics and Boltzmann transport treatments

NASA Astrophysics Data System (ADS)

Huang, Baoling

Atomic-level thermal transport in compact, layered, linked-cage, and filled-cage crystals is investigated using a multiscale approach, combines the ab initio calculation, molecular dynamics (MD), Boltzman transport equations (BTE), and the kinetic theory. These materials are of great interests in energy storage, transport, and conversion. The structural metrics of phonon conductivity of these crystals are then explored. An atomic structure-based model is developed for the understanding the relationship between the atomic structure and phonon transport in compact crystals at high temperatures. The elemental electronegativity, element mass, and the arrangement of bonds are found to be the dominant factors to determine the phonon conductivity. As an example of linked-cage crystals, the phonon conductivity of MOF-5 is investigated over a wide temperature range using MD simulations and the Green-Kubo method. The temperature dependence of the thermal conductivity of MOF-5 is found to be weak at high temperatures, which results from the suppression of the long-range acoustic phonon transport by the special linked-cage structure. The mean free path of the majority of phonons in MOF-5 is limited by the cage size. The phonon and electron transport in layered Bi2Te3 structure are investigated using the first-principle calculations, MD, and BTE. Strong anisotropy has been found for both phonon and electron transport due to the special layered structure. The long-range acoustic phonons dominate the phonon transport with a strong temperature and direction dependence. Temperature dependence of the energy gap and appropriate modelling of relaxation times are found to be important for the prediction of the electrical transport in the intrinsic regime. The scattering by the acoustic, optical, and polar-optical phonons are found to dominate the electron transport. For filled skutterudite structure, strong coupling between the filler and the host is found, which contradicts the traditional "rattler" concept. The interatomic bonds of the host are significantly affected by the filler. It is shown that without changing the interatomic potentials for the host, the filler itself can not result in a lower phonon conductivity for the filled structure. It is also found that the behavior of partially-filled skutterudites can be better understood by treating the partially-filled structure as a solid solution of the empty structure and fully-filled structure. The combination of theoretical-analysis methods used in this work, provides for comparative insight into the role of atomic structure on the phonon transport in a variety of crystals used in energy storage, transport, and conversion.

Rapid assessment of crystal orientation in semi-crystalline polymer films using rotational zone annealing and impact of orientation on mechanical properties

DOE PAGES

Ye, Changhuai; Wang, Chao; Wang, Jing; ...

2017-08-17

Crystal orientation in semi-crystalline polymers tends to enhance their performance, such as increased yield strength and modulus, along the orientation direction. Zone annealing (ZA) orients the crystal lamellae through a sharp temperature gradient that effectively directs the crystal growth, but the sweep rate (V ZA) of this gradient significantly impacts the extent of crystal orientation. Here in this work, we demonstrate rotational zone annealing (RZA) as an efficient method to elucidate the influence of V ZA on the crystal morphology of thin films in a single experiment using isotactic poly(1-butene), PB-1, as a model semi-crystalline polymer. These RZA results aremore » confirmed using standard, serial linear ZA to tune the structure from an almost unidirectional oriented morphology to weakly oriented spherulites. The overall crystallinity is only modestly changed in comparison to isothermal crystallization (maximum of 55% from ZA vs. 48% for isothermal crystallization). However, the average grain size increases and the spherulites become anisotropic from ZA. Due to these structural changes, the Young's modulus of the oriented films, both parallel and perpendicular to the spherulite orientation direction, is significantly increased by ZA. The modulus does become anisotropic after ZA due to the directionality in the crystal structure, with more than a threefold increase in the modulus parallel to the orientation direction for the highest oriented film in comparison to the modulus from isothermal crystallization. Lastly, RZA enables rapid identification of conditions to maximize orientation of crystals in thin polymer films, which could find utility in determining conditions to improve crystallinity and performance in organic electronics.« less

Rapid assessment of crystal orientation in semi-crystalline polymer films using rotational zone annealing and impact of orientation on mechanical properties

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

Ye, Changhuai; Wang, Chao; Wang, Jing

Crystal orientation in semi-crystalline polymers tends to enhance their performance, such as increased yield strength and modulus, along the orientation direction. Zone annealing (ZA) orients the crystal lamellae through a sharp temperature gradient that effectively directs the crystal growth, but the sweep rate (V ZA) of this gradient significantly impacts the extent of crystal orientation. Here in this work, we demonstrate rotational zone annealing (RZA) as an efficient method to elucidate the influence of V ZA on the crystal morphology of thin films in a single experiment using isotactic poly(1-butene), PB-1, as a model semi-crystalline polymer. These RZA results aremore » confirmed using standard, serial linear ZA to tune the structure from an almost unidirectional oriented morphology to weakly oriented spherulites. The overall crystallinity is only modestly changed in comparison to isothermal crystallization (maximum of 55% from ZA vs. 48% for isothermal crystallization). However, the average grain size increases and the spherulites become anisotropic from ZA. Due to these structural changes, the Young's modulus of the oriented films, both parallel and perpendicular to the spherulite orientation direction, is significantly increased by ZA. The modulus does become anisotropic after ZA due to the directionality in the crystal structure, with more than a threefold increase in the modulus parallel to the orientation direction for the highest oriented film in comparison to the modulus from isothermal crystallization. Lastly, RZA enables rapid identification of conditions to maximize orientation of crystals in thin polymer films, which could find utility in determining conditions to improve crystallinity and performance in organic electronics.« less

Fluorescent Applications to Crystallization

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Forsythe, Elizabeth; Achari, Aniruddha

2006-01-01

By covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and tests with model proteins have shown that labeling u to 5 percent of the protein molecules does not affect the X-ray data quality obtained . The presence of the trace fluorescent label gives a number of advantages. Since the label is covalently attached to the protein molecules, it "tracks" the protein s response to the crystallization conditions. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a darker background. Non-protein structures, such as salt crystals, do not show up under fluorescent illumination. Crystals have the highest protein concentration and are readily observed against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. Preliminary tests, using model proteins, indicates that we can use high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that more rapid amorphous precipitation kinetics may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Experiments are now being carried out to test this approach using a wider range, of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons.

Synthesis, crystal structure and electrical properties of N,N-dimethylanilinium trichloridostannate (II): (C8H12N)SnCl3

NASA Astrophysics Data System (ADS)

Chouaib, H.; Kamoun, S.; Costa, L. C.; Graça, M. P. F.

2015-12-01

A new (C8H12N)SnCl3 crystal of the general formula AMX3 was grown by soft chemistry method. X-ray study shows that the crystal crystallized in a monoclinic system with the space group P21/a. The structure was solved by Patterson method and refined to a final value of R = 0.0304 for 1157 independent observed reflections. The cohesion and the stability of the atomic arrangement result from the N-H … Cl hydrogen bonds between (C8H12N)+ cations and isolated (SnCl3)- anions. At high temperature this compound exhibits a structural phase transition at 340 K. This transition has been characterized by differential scanning calorimetric and impedance spectroscopy. The impedance data were well fitted to an Rp//CPE equivalent electrical circuit model. The close values of activation energies, obtained from the thermal behavior of the conductivity and the relaxation time confirm the presence of a hopping transport mechanism.

The crystal structure of the regulatory domain of the human sodium-driven chloride/bicarbonate exchanger.

PubMed

Alvadia, Carolina M; Sommer, Theis; Bjerregaard-Andersen, Kaare; Damkier, Helle Hasager; Montrasio, Michele; Aalkjaer, Christian; Morth, J Preben

2017-09-21

The sodium-driven chloride/bicarbonate exchanger (NDCBE) is essential for maintaining homeostatic pH in neurons. The crystal structure at 2.8 Å resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif. The VTVLP motif is highly conserved and likely to be the physiologically relevant interface for all other members of the SLC4 family. A novel conserved Zn 2+ -binding motif present in the N-terminal domain of NDCBE is identified and characterized in vitro. Cellular studies confirm the Zn 2+ dependent transport of two electroneutral bicarbonate transporters, NCBE and NBCn1. The Zn 2+ site is mapped to a cluster of histidines close to the conserved ETARWLKFEE motif and likely plays a role in the regulation of this important motif. The combined structural and bioinformatics analysis provides a model that predicts with additional confidence the physiologically relevant interface between the cytoplasmic domain and the transmembrane domain.

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.

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

Inhibitor-based validation of a homology model of the active-site of tripeptidyl peptidase II.

PubMed

De Winter, Hans; Breslin, Henry; Miskowski, Tamara; Kavash, Robert; Somers, Marijke

2005-04-01

A homology model of the active site region of tripeptidyl peptidase II (TPP II) was constructed based on the crystal structures of four subtilisin-like templates. The resulting model was subsequently validated by judging expectations of the model versus observed activities for a broad set of prepared TPP II inhibitors. The structure-activity relationships observed for the prepared TPP II inhibitors correlated nicely with the structural details of the TPP II active site model, supporting the validity of this model and its usefulness for structure-based drug design and pharmacophore searching experiments.

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

A Multiscale Computational Model Combining a Single Crystal Plasticity Constitutive Model with the Generalized Method of Cells (GMC) for Metallic Polycrystals.

PubMed

Ghorbani Moghaddam, Masoud; Achuthan, Ajit; Bednarcyk, Brett A; Arnold, Steven M; Pineda, Evan J

2016-05-04

A multiscale computational model is developed for determining the elasto-plastic behavior of polycrystal metals by employing a single crystal plasticity constitutive model that can capture the microstructural scale stress field on a finite element analysis (FEA) framework. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, the stand-alone GMC is applied for studying simple material microstructures such as a repeating unit cell (RUC) containing single grain or two grains under uniaxial loading conditions. For verification, the results obtained by the stand-alone GMC are compared to those from an analogous FEA model incorporating the same single crystal plasticity constitutive model. This verification is then extended to samples containing tens to hundreds of grains. The results demonstrate that the GMC homogenization combined with the crystal plasticity constitutive framework is a promising approach for failure analysis of structures as it allows for properly predicting the von Mises stress in the entire RUC, in an average sense, as well as in the local microstructural level, i.e. , each individual grain. Two-three orders of saving in computational cost, at the expense of some accuracy in prediction, especially in the prediction of the components of local tensor field quantities and the quantities near the grain boundaries, was obtained with GMC. Finally, the capability of the developed multiscale model linking FEA and GMC to solve real-life-sized structures is demonstrated by successfully analyzing an engine disc component and determining the microstructural scale details of the field quantities.

A Multiscale Computational Model Combining a Single Crystal Plasticity Constitutive Model with the Generalized Method of Cells (GMC) for Metallic Polycrystals

PubMed Central

Ghorbani Moghaddam, Masoud; Achuthan, Ajit; Bednarcyk, Brett A.; Arnold, Steven M.; Pineda, Evan J.

2016-01-01

A multiscale computational model is developed for determining the elasto-plastic behavior of polycrystal metals by employing a single crystal plasticity constitutive model that can capture the microstructural scale stress field on a finite element analysis (FEA) framework. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, the stand-alone GMC is applied for studying simple material microstructures such as a repeating unit cell (RUC) containing single grain or two grains under uniaxial loading conditions. For verification, the results obtained by the stand-alone GMC are compared to those from an analogous FEA model incorporating the same single crystal plasticity constitutive model. This verification is then extended to samples containing tens to hundreds of grains. The results demonstrate that the GMC homogenization combined with the crystal plasticity constitutive framework is a promising approach for failure analysis of structures as it allows for properly predicting the von Mises stress in the entire RUC, in an average sense, as well as in the local microstructural level, i.e., each individual grain. Two–three orders of saving in computational cost, at the expense of some accuracy in prediction, especially in the prediction of the components of local tensor field quantities and the quantities near the grain boundaries, was obtained with GMC. Finally, the capability of the developed multiscale model linking FEA and GMC to solve real-life-sized structures is demonstrated by successfully analyzing an engine disc component and determining the microstructural scale details of the field quantities. PMID:28773458

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

Theoretical Calculations of Refractive Properties for Hg3Te2Cl2 Crystals

NASA Astrophysics Data System (ADS)

Bokotey, O. V.

2016-05-01

This paper reviews the optical properties, such as refractive index, optical dielectric constant, and reflection coefficient of the Hg3Te2Cl2 crystals. The applications of the Hg3X2Y2 crystals as electronic, optical, and optoelectronic devices are very much determined by the nature and magnitude of these fundamental material properties. The origin of chemical bonding in the crystals is very important for definition of the physical and chemical properties. The main structural feature of the Hg3X2Y2 crystals is the presence of covalent pyramids [XHg3] and linear X-Hg-X groups. Optical properties are calculated according to the model proposed by Harrison. The refractive index in the spectral region far from the absorption edge is determined within the generalized single-oscillator model. The calculated results are found to be in good agreement with experimental data.

Novel Crystal Structure C60 Nanowire

NASA Astrophysics Data System (ADS)

Mickelson, William; Aloni, Shaul; Han, Weiqiang; Cumings, John; Zettl, Alex

2003-03-01

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride (BN) nanotubes. For small-diameter BN tubes, the wire consists of a linear chain of C60's. With increasing BN tube inner diameter, novel C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) which are unknown for bulk or thin film forms of C60. C60 in BN nanotubes presents a model system for studying the properties of new dimensionally-constrained "silo" crystal structures.

Semiconductor nanowhiskers: Synthesis, properties, and applications

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

Dubrovskii, V. G., E-mail: dubrovskii@mail.ioffe.ru; Cirlin, G. E., E-mail: Cirlin@beam.ioffe.ru; Ustinov, V. M., E-mail: Vmust@beam.ioffe.ru

2009-12-15

Recent results of studying the semiconductor's whisker nanocrystals are reviewed. Physical grounds of growing whisker nanocrystals using the mechanism vapor-liquid-crystal are given and the main epitaxial technologies of synthesis of whisker nanocrystals are described. Thermodynamic and kinetic factors controlling the morphological properties, composition, and crystal structure of whisker nanocrystals are considered in detail. The main theoretical models of the growth and structure of whisker nanocrystals are described. The data on physical properties of whisker nanocrystals and possibilities of their use in nanophotonics, nanoelectronics, and nanobiotechnology are presented.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

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.

Crystallization processes in Ge{sub 2}Sb{sub 2}Se{sub 4}Te glass

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

Svoboda, Roman, E-mail: roman.svoboda@upce.cz; Bezdička, Petr; Gutwirth, Jan

2015-01-15

Highlights: • Crystallization kinetics of Ge{sub 2}Sb{sub 2}Se{sub 4}Te glass was studied in dependence on particle size by DSC. • All studied fractions were described in terms of the SB autocatalytic model. • Relatively high amount of Te enhances manifestation of bulk crystallization mechanisms. • XRD analysis of samples crystallized under different conditions showed correlation with DSC data. • XRD analysis revealed a new crystallization mechanism indistinguishable by DSC. - Abstract: Differential scanning calorimetry (DSC) and X-ray diffraction (XRD) analysis were used to study crystallization in Ge{sub 2}Sb{sub 2}Se{sub 4}Te glass under non-isothermal conditions as a function of the particlemore » size. The crystallization kinetics was described in terms of the autocatalytic Šesták–Berggren model. An extensive discussion of all aspects of a full-scale kinetic study of a crystallization process was undertaken. Dominance of the crystallization process originating from mechanically induced strains and heterogeneities was confirmed. Substitution of Se by Te was found to enhance the manifestation of the bulk crystallization mechanisms (at the expense of surface crystallization). The XRD analysis showed significant dependence of the crystalline structural parameters on the crystallization conditions (initial particle size of the glassy grains and applied heating rate). Based on this information, a new microstructural crystallization mechanism, indistinguishable by DSC, was proposed.« less

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.

Left-right correlation in coupled F-center defects.

PubMed

Janesko, Benjamin G

2016-08-07

This work explores how left-right correlation, a textbook problem in electronic structure theory, manifests in a textbook example of electrons trapped in crystal defects. I show that adjacent F-center defects in lithium fluoride display symptoms of "strong" left-right correlation, symptoms similar to those seen in stretched H2. Simulations of UV/visible absorption spectra qualitatively fail to reproduce experiment unless left-right correlation is taken into account. This is of interest to both the electronic structure theory and crystal-defect communities. Theorists have a new well-behaved system to test their methods. Crystal-defect groups are cautioned that the approximations that successfully model single F-centers may fail for adjacent F-centers.

Outer-sphere Pb(II) adsorbed at specific surface sites on single crystal α-alumina

USGS Publications Warehouse

Bargar, John R.; Towle, Steven N.; Brown, Gordon E.; Parks, George A.

1996-01-01

Solvated Pb(II) ions were found to adsorb as structurally well-defined outer-sphere complexes at specific sites on the α-Al2O3 (0001) single crystal surface, as determined by grazing-incidence X-ray absorption fine structure (GI-XAFS) measurements. The XAFS results suggest that the distance between Pb(II) adions and the alumina surface is approximately 4.2 Å. In contrast, Pb(II) adsorbs as more strongly bound inner-sphere complexes on α-Al2O3 (102). The difference in reactivities of the two alumina surfaces has implications for modeling surface complexation reactions of contaminants in natural environments, catalysis, and compositional sector zoning of oxide crystals.

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.

Peculiarities of thermoelectric half-Heusler phase formation in Gd-Ni-Sb and Lu-Ni-Sb ternary systems

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

Romaka, V.V., E-mail: romakav@lp.edu.ua; Romaka, L.; Horyn, A.

The phase equilibria in the Gd–Ni–Sb and Lu-Ni-Sb ternary systems were studied at 873 K by X-ray and metallographic analyses in the whole concentration range. The interaction of the elements in the Gd–Ni–Sb system results the formation of five ternary compounds at investigated temperature: Gd{sub 5}Ni{sub 2}Sb (Mo{sub 5}SiB{sub 2}-type), Gd{sub 5}NiSb{sub 2} (Yb{sub 5}Sb{sub 3}-type), GdNiSb (MgAgAs-type), Gd{sub 3}Ni{sub 6}Sb{sub 5} (Y{sub 3}Ni{sub 6}Sb{sub 5}-type), and GdNi{sub 0.72}Sb{sub 2} (HfCuSi{sub 2}-type). At investigated temperature the Lu-Ni-Sb system is characterized by formation of the LuNiSb (MgAgAs-type), Lu{sub 5}Ni{sub 2}Sb (Mo{sub 5}SiB{sub 2}-type), and Lu{sub 5}Ni{sub 0.56}Sb{sub 2.44} (Yb{sub 5}Sb{sub 3}-type)more » compounds. The disordering in the crystal structure of half-Heusler GdNiSb and LuNiSb was revealed by EPMA and studied by means of Rietveld refinement and DFT modeling. The performed electronic structure calculations are in good agreement with electrical transport property studies. - Graphical abstract: Crystal structure model and electron localization function of Lu{sub 5}Ni{sub 2}Sb. Display Omitted - Highlights: • Gd-Ni-Sb and Lu-Ni-Sb phase diagrams were constructed at 873 K. • GdNiSb and LuNiSb are characterized by disordered crystal structure. • Crystal structure optimization with DFT calculations confirmed crystal structure disorder in GdNiSb and LuNiSb.« less

Effect of anisotropic MoS2 nanoparticles on the blue phase range of a chiral liquid crystal.

PubMed

Lavrič, Marta; Cordoyiannis, George; Kralj, Samo; Tzitzios, Vassilios; Nounesis, George; Kutnjak, Zdravko

2013-08-01

Liquid-crystalline blue phases are attracting significant interest due to their potential for applications related to tunable photonic crystals and fast optical displays. In this work a brief theoretical model is presented accounting for the impact of anisotropic nanoparticles on the blue phase stability region. This model is tested by means of high-resolution calorimetric and optical measurements of the effect of anisotropic, surface-functionalized MoS2 nanoparticles on the blue phase range of a chiral liquid crystal. The addition of these nanoparticles effectively increases the temperature range of blue phases and especially the cubic structure of blue phase I.

Poly(acrylic acid) to induce competitive crystallization of a theophylline/oxalic acid cocrystal and a theophylline polymorph

NASA Astrophysics Data System (ADS)

Jang, Jisun; Kim, Il Won

2016-01-01

Polymeric additives to induce competitive crystallization of pharmaceutical compounds were explored. A cocrystal of theophylline and oxalic acid was used as a model system, and poly(acrylic acid), poly(caprolactone), and poly(ethylene glycol) were the additives. The cocrystal formation was selectively hindered with addition of poly(acrylic acid). First the size of the cocrystals were reduced, and eventually the cocrystallization was inhibited to generate neat theophylline crystals. The theophylline crystals were of a distinctively different crystal structure from known polymorphs, based on powder X-ray diffraction. They were also obtained in nanoscale size, when millimeter-scale crystals formed without poly(acrylic acid). Polymeric additives that could form specific interactions with crystallizing compounds seem to be useful tools for the phase and size control of pharmaceutical crystals.

Glassy phases and driven response of the phase-field-crystal model with random pinning.

PubMed

Granato, E; Ramos, J A P; Achim, C V; Lehikoinen, J; Ying, S C; Ala-Nissila, T; Elder, K R

2011-09-01

We study the structural correlations and the nonlinear response to a driving force of a two-dimensional phase-field-crystal model with random pinning. The model provides an effective continuous description of lattice systems in the presence of disordered external pinning centers, allowing for both elastic and plastic deformations. We find that the phase-field crystal with disorder assumes an amorphous glassy ground state, with only short-ranged positional and orientational correlations, even in the limit of weak disorder. Under increasing driving force, the pinned amorphous-glass phase evolves into a moving plastic-flow phase and then, finally, a moving smectic phase. The transverse response of the moving smectic phase shows a vanishing transverse critical force for increasing system sizes.

The iron-nickel-phosphorus system: Effects on the distribution of trace elements during the evolution of iron meteorites

NASA Astrophysics Data System (ADS)

Corrigan, Catherine M.; Chabot, Nancy L.; McCoy, Timothy J.; McDonough, William F.; Watson, Heather C.; Saslow, Sarah A.; Ash, Richard D.

2009-05-01

To better understand the partitioning behavior of elements during the formation and evolution of iron meteorites, two sets of experiments were conducted at 1 atm in the Fe-Ni-P system. The first set examined the effect of P on solid metal/liquid metal partitioning behavior of 22 elements, while the other set explored the effect of the crystal structures of body-centered cubic (α)- and face-centered cubic (γ)-solid Fe alloys on partitioning behavior. Overall, the effect of P on the partition coefficients for the majority of the elements was minimal. As, Au, Ga, Ge, Ir, Os, Pt, Re, and Sb showed slightly increasing partition coefficients with increasing P-content of the metallic liquid. Co, Cu, Pd, and Sn showed constant partition coefficients. Rh, Ru, W, and Mo showed phosphorophile (P-loving) tendencies. Parameterization models were applied to solid metal/liquid metal results for 12 elements. As, Au, Pt, and Re failed to match previous parameterization models, requiring the determination of separate parameters for the Fe-Ni-S and Fe-Ni-P systems. Experiments with coexisting α and γ Fe alloy solids produced partitioning ratios close to unity, indicating that an α versus γ Fe alloy crystal structure has only a minor influence on the partitioning behaviors of the trace element studied. A simple relationship between an element's natural crystal structure and its α/γ partitioning ratio was not observed. If an iron meteorite crystallizes from a single metallic liquid that contains both S and P, the effect of P on the distribution of elements between the crystallizing solids and the residual liquid will be minor in comparison to the effect of S. This indicates that to a first order, fractional crystallization models of the Fe-Ni-S-P system that do not take into account P are appropriate for interpreting the evolution of iron meteorites if the effects of S are appropriately included in the effort.

Phase-field crystal modeling of heteroepitaxy and exotic modes of crystal nucleation

NASA Astrophysics Data System (ADS)

Podmaniczky, Frigyes; Tóth, Gyula I.; Tegze, György; Pusztai, Tamás; Gránásy, László

2017-01-01

We review recent advances made in modeling heteroepitaxy, two-step nucleation, and nucleation at the growth front within the framework of a simple dynamical density functional theory, the Phase-Field Crystal (PFC) model. The crystalline substrate is represented by spatially confined periodic potentials. We investigate the misfit dependence of the critical thickness in the StranskiKrastanov growth mode in isothermal studies. Apparently, the simulation results for stress release via the misfit dislocations fit better to the PeopleBean model than to the one by Matthews and Blakeslee. Next, we investigate structural aspects of two-step crystal nucleation at high undercoolings, where an amorphous precursor forms in the first stage. Finally, we present results for the formation of new grains at the solid-liquid interface at high supersaturations/supercoolings, a phenomenon termed Growth Front Nucleation (GFN). Results obtained with diffusive dynamics (applicable to colloids) and with a hydrodynamic extension of the PFC theory (HPFC, developed for simple liquids) will be compared. The HPFC simulations indicate two possible mechanisms for GFN.

Stacking fault density and bond orientational order of fcc ruthenium nanoparticles

NASA Astrophysics Data System (ADS)

Seo, Okkyun; Sakata, Osami; Kim, Jae Myung; Hiroi, Satoshi; Song, Chulho; Kumara, Loku Singgappulige Rosantha; Ohara, Koji; Dekura, Shun; Kusada, Kohei; Kobayashi, Hirokazu; Kitagawa, Hiroshi

2017-12-01

We investigated crystal structure deviations of catalytic nanoparticles (NPs) using synchrotron powder X-ray diffraction. The samples were fcc ruthenium (Ru) NPs with diameters of 2.4, 3.5, 3.9, and 5.4 nm. We analyzed average crystal structures by applying the line profile method to a stacking fault model and local crystal structures using bond orientational order (BOO) parameters. The reflection peaks shifted depending on rules that apply to each stacking fault. We evaluated the quantitative stacking faults densities for fcc Ru NPs, and the stacking fault per number of layers was 2-4, which is quite large. Our analysis shows that the fcc Ru 2.4 nm-diameter NPs have a considerably high stacking fault density. The B factor tends to increase with the increasing stacking fault density. A structural parameter that we define from the BOO parameters exhibits a significant difference from the ideal value of the fcc structure. This indicates that the fcc Ru NPs are highly disordered.

Sponge-like nanoporous single crystals of gold

PubMed Central

Khristosov, Maria Koifman; Bloch, Leonid; Burghammer, Manfred; Kauffmann, Yaron; Katsman, Alex; Pokroy, Boaz

2015-01-01

Single crystals in nature often demonstrate fascinating intricate porous morphologies rather than classical faceted surfaces. We attempt to grow such crystals, drawing inspiration from biogenic porous single crystals. Here we show that nanoporous single crystals of gold can be grown with no need for any elaborate fabrication steps. These crystals are found to grow following solidification of a eutectic composition melt that forms as a result of the dewetting of nanometric thin films. We also present a kinetic model that shows how this nano-porous single-crystalline structure can be obtained, and which allows the potential size of the porous single crystal to be predicted. Retaining their single-crystalline nature is due to the fact that the full crystallization process is faster than the average period between two subsequent nucleation events. Our findings clearly demonstrate that it is possible to form single-crystalline nano porous metal crystals in a controlled manner. PMID:26554856

Immersion Freezing of Aluminas: The Effect of Crystallographic Properties on Ice Nucleation

NASA Astrophysics Data System (ADS)

King, M.; Chong, E.; Freedman, M. A.

2017-12-01

Atmospheric aerosol particles serve as the nuclei for heterogeneous ice nucleation, a process that allows for ice to form at higher temperatures and lower supersaturations with respect to ice. This process is essential to the formation of ice in cirrus clouds. Heterogeneous ice nucleation is affected by many factors including the composition, crystal structure, porosity, and surface area of the particles. However, these factors are not well understood and, as such, are difficult to account for in climate models. To test the effects of crystal structure on ice nucleation, a system of transition aluminas (Al2O3) that differ only in their crystal structure, despite being compositionally similar, were tested using immersion freezing. Particles were immersed in water and placed into a temperature controlled chamber. Freezing events were then recorded as the chamber was cooled to negative 30 °. Alpha-alumina, which is a member of the hexagonal crystal system, showed a significantly higher temperature at which all particles froze in comparison to other samples. This supports the hypothesis that, since a hexagonal crystal structure is the lowest energy state for ice, hexagonal surface structures would best facilitate ice nucleation. However, a similar sample of hexagonal chi-alumina did not show the same results. Further analysis of the samples will be done to characterize surface structures and composition. These conflicting data sets raise interesting questions about the effect of other surface features, such as surface area and porosity, on ice nucleation.

Synthesis, crystal structure and electronic structure of the binary phase Rh{sub 2}Cd{sub 5}

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

Koley, Biplab; Chatterjee, S.; Jana, Partha P., E-mail: ppj@chem.iitkgp.ernet.in

2017-02-15

A new phase in the Rh-Cd binary system - Rh{sub 2}Cd{sub 5} has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh{sub 2}Cd{sub 5} crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh{sub 2}Cd{sub 5} can be described as a defect form of the In{sub 3}Pd{sub 5} structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist ofmore » (3{sup 5}) (3{sup 7})- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh{sub 2}Cd{sub 5}. - Graphical abstract: (3.6.3.6)-Kagomé nets of cadmium atoms (top) and (3{sup 5}) (3{sup 7})- nets of both cadmium and rhodium atoms (bottom) in the structure of Rh{sub 2}Cd{sub 5}.« less

Structure of Greyhound hemoglobin: origin of high oxygen affinity.

PubMed

Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F

2011-05-01

This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure.

Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals

PubMed Central

Gonzalez-Gutierrez, Giovanni; Lukk, Tiit; Agarwal, Vinayak; Papke, David; Nair, Satish K.; Grosman, Claudio

2012-01-01

The determination of structural models of the various stable states of an ion channel is a key step toward the characterization of its conformational dynamics. In the case of nicotinic-type receptors, different structures have been solved but, thus far, these different models have been obtained from different members of the superfamily. In the case of the bacterial member ELIC, a cysteamine-gated channel from Erwinia chrisanthemi, a structural model of the protein in the absence of activating ligand (and thus, conceivably corresponding to the closed state of this channel) has been previously generated. In this article, electrophysiological characterization of ELIC mutants allowed us to identify pore mutations that slow down the time course of desensitization to the extent that the channel seems not to desensitize at all for the duration of the agonist applications (>20 min). Thus, it seems reasonable to conclude that the probability of ELIC occupying the closed state is much lower for the ligand-bound mutants than for the unliganded wild-type channel. To gain insight into the conformation adopted by ELIC under these conditions, we solved the crystal structures of two of these mutants in the presence of a concentration of cysteamine that elicits an intracluster open probability of >0.9. Curiously, the obtained structural models turned out to be nearly indistinguishable from the model of the wild-type channel in the absence of bound agonist. Overall, our findings bring to light the limited power of functional studies in intact membranes when it comes to inferring the functional state of a channel in a crystal, at least in the case of the nicotinic-receptor superfamily. PMID:22474383

Diffusion paths formation for Cu + ions in superionic Cu 6PS 5I single crystals studied in terms of structural phase transition

NASA Astrophysics Data System (ADS)

Gągor, A.; Pietraszko, A.; Kaynts, D.

2005-11-01

In order to understand the structural transformations leading to high ionic conductivity of Cu + ions in Cu 6PS 5I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T=(144-169) K Cu 6PS 5I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above Tc delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43 c ( a'=19.528 Å, z=32). Finally, above T1=274 K increasing disordering of the Cu + ions heightens the symmetry to F-43 m ( a=9.794 Å, z=4). In this work, the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions ( R1=0.0397 for F-43 c phase, and 0.0245 for F-43 m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.

Local order and crystallization of dense polydisperse hard spheres

NASA Astrophysics Data System (ADS)

Coslovich, Daniele; Ozawa, Misaki; Berthier, Ludovic

2018-04-01

Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap for a class of models of size polydisperse fluids, which we successfully equilibrate beyond laboratory time scales by means of the swap Monte Carlo algorithm. In this contribution, we study the interplay between compositional and geometric local orders in a model of polydisperse hard spheres equilibrated with this algorithm. Local compositional order has a weak state dependence, while local geometric order associated to icosahedral arrangements grows more markedly but only at very high density. We quantify the correlation lengths and the degree of sphericity associated to icosahedral structures and compare these results to those for the Wahnström Lennard-Jones mixture. Finally, we analyze the structure of very dense samples that partially crystallized following a pattern incompatible with conventional fractionation scenarios. The crystal structure has the symmetry of aluminum diboride and involves a subset of small and large particles with size ratio approximately equal to 0.5.

Theoretical modeling on the laser-induced phase deformation of liquid crystal optical phased shifter

NASA Astrophysics Data System (ADS)

Zhou, Zhuangqi; Wang, Xiangru; Zhuo, Rusheng; He, Xiaoxian; Wu, Liang; Wang, Xiaolin; Tan, Qinggui; Qiu, Qi

2018-03-01

To improve the working condition of liquid crystal phase shifter on incident laser power, a theoretical model on laser induced phase distortion is built on the physics of heat deposition and heat transfer. Four typical factors (absorption, heat sink structure, cooling fluid rate, and substrate) are analyzed to evaluate the influence of phase distortion when a relative high-power laser is pumped into the liquid crystal phase shifter. Flow rate of cooling fluid and heat sink structure are the most important two factors on improving the limit of incident laser power. Meanwhile, silicon wafer is suggested to replace the back glass contacting the heat sink, because of its higher heat transfer coefficient. If the device is fabricated on the conditions that: the total absorption is 5% and it has a strong heat sink structure with a flow rate of 0.01 m/s, when the incident laser power is 110W, the laser-induced phase deformation on the center is diminished to be less than 0.06, and the maximum temperature increase on the center is less than 1K degree.

Interacting quasi-band model for electronic states in compound semiconductor alloys: Zincblende structure

NASA Astrophysics Data System (ADS)

Shinozuka, Yuzo; Oda, Masato

2015-09-01

The interacting quasi-band model proposed for electronic states in simple alloys is extended for compound semiconductor alloys with general lattice structures containing several atoms per unit cell. Using a tight-binding model, a variational electronic wave function for quasi-Bloch states yields a non-Hermitian Hamiltonian matrix characterized by matrix elements of constituent crystals and concentration of constituents. Solving secular equations for each k-state yields the alloy’s energy spectrum for any type of randomness and arbitrary concentration. The theory is used to address III-V (II-VI) alloys with a zincblende lattice with crystal band structures well represented by the sp3s* model. Using the resulting 15 × 15 matrix, the concentration dependence of valence and conduction bands is calculated in a unified scheme for typical alloys: Al1-xGaxAs, GaAs1-xPx, and GaSb1-xPx. Results agree well with experiments and are discussed with respect to the concentration dependence, direct-indirect gap transition, and band-gap-bowing origin.

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.

Sulfur hexafluoride plasma surface modification of Gly-Ala and Ala-Gly as Bombyx mori silk model compounds: Mechanism investigations

NASA Astrophysics Data System (ADS)

Sangprasert, W.; Lee, V. S.; Boonyawan, D.; Tashiro, K.; Nimmanpipug, P.

2010-01-01

Low-pressure plasma has been used to improve the hydrophobicity of Thai silk. In this study, Glycine-Alanine (GA) and Alanine-Glycine (AG) were chosen to represent model compounds of Bombyx mori silk. Single crystals of the simplified model compounds were characterized by polarizing microscopy and X-ray diffraction. The space groups of P2 12 12 1 and P2 1 were found for AG and GA, respectively. The initial structures for calculation were obtained from the experimental crystal structures. Density functional theory at the BHandHLYP levels was used to investigate possible mechanisms of fluorine radicals reacting with AG and GA in the SF 6 plasma treatment. The results indicate that hydrogen atoms of silk model compounds were most likely to be abstracted from the alanine residue.

Quantum effect on the nucleation of plastic deformation carriers and destruction in crystals

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

Khon, Yury A., E-mail: khon@ispms.tsc.ru; Kaminskii, Petr P., E-mail: ppk@ispms.tsc.ru

2015-10-27

New concepts on the irreversible crystal deformation as a structure transformation caused by a change in interatomic interactions at fluctuations of the electron density under loading are described. The change in interatomic interactions lead to the excitation of dynamical displacements of atoms. A model and a theory of a deformable pristine crystal taking into account the excitation of thermally activated and dynamical displacements of atoms are suggested. New mechanisms of the nucleation of plastic deformation carriers and destruction in pristine crystals at the real value of the deforming stress are studied.

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.

van der Waals three-body force shell model (VTSM) for the lattice dynamical studies of thallous bromide

NASA Astrophysics Data System (ADS)

Tiwari, Sarvesh K.; Pandey, L. K.; Shukla, Lal Ji; Upadhyaya, K. S.

2009-12-01

The van der Waals three-body force shell model (VTSM) has been developed by modifying the three-body force shell model (TSM) for the lattice dynamics of ionic crystals with cesium chloride (CsCl) structure. This new model incorporates van der Waals interactions along with long-range Coulomb interactions, three-body interactions and short-range second neighbour interactions in the framework of a rigid shell model (RSM). In the present paper, VTSM has been used to study the lattice dynamics of thallous bromide (TlBr), from which adequacy of VTSM has been established. A comparative study of the dynamical behaviour of TlBr has also been done between the present model and TSM, the model over which modification has been made to obtain the present model VTSM. Good agreement has been observed between the theoretical and experimental results, which give confidence that it is an appropriate model for the complete description of ionic crystals with CsCl structure.

DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography.

PubMed

Batyuk, Alexander; Wu, Yufan; Honegger, Annemarie; Heberling, Matthew M; Plückthun, Andreas

2016-04-24

DARPin libraries, based on a Designed Ankyrin Repeat Protein consensus framework, are a rich source of binding partners for a wide variety of proteins. Their modular structure, stability, ease of in vitro selection and high production yields make DARPins an ideal starting point for further engineering. The X-ray structures of around 30 different DARPin complexes demonstrate their ability to facilitate crystallization of their target proteins by restricting flexibility and preventing undesired interactions of the target molecule. However, their small size (18 kDa), very hydrophilic surface and repetitive structure can limit the DARPins' ability to provide essential crystal contacts and their usefulness as a search model for addressing the crystallographic phase problem in molecular replacement. To optimize DARPins for their application as crystallization chaperones, rigid domain-domain fusions of the DARPins to larger proteins, proven to yield high-resolution crystal structures, were generated. These fusions were designed in such a way that they affect only one of the terminal capping repeats of the DARPin and do not interfere with residues involved in target binding, allowing to exchange at will the binding specificities of the DARPin in the fusion construct. As a proof of principle, we designed rigid fusions of a stabilized version of Escherichia coli TEM-1 β-lactamase to the C-terminal capping repeat of various DARPins in six different relative domain orientations. Five crystal structures representing four different fusion constructs, alone or in complex with the cognate target, show the predicted relative domain orientations and prove the validity of the concept. Copyright © 2016 Elsevier Ltd. All rights reserved.

3-D Structure of Molecules of Biological Significance

ERIC Educational Resources Information Center

Bennett, Alice S.; Schwenk, Karl

1974-01-01

Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

σ-Hole and π-Hole Synthon Mimicry in Third-Generation Crystal Engineering: Design of Elastic Crystals.

PubMed

Saha, Subhankar; Desiraju, Gautam R

2017-04-06

Designing elastic crystals is a difficult task and is of relevance in potential applications from materials to biology. Here, multi-step crystal engineering based on σ-hole and π-hole synthon mimicry is performed to obtain binary organic molecular crystals with a high degree of flexibility. A structural model is proposed based only on σ-hole-oriented type-II halogen bonds with their characteristic orthogonal geometry. These σ-hole contacts are then partly replaced by chemically and geometrically similar π-hole synthons to obtain new crystals in the second step. In the final step, all the σ-hole interactions are replaced with π-hole interactions and elastic crystals of non-halogenated compounds are obtained. All the crystals obtained according to our protocols are found to be elastic. When crystals that do not conform to the desired structure type appeared, they were found to be brittle. This underlines the role of orthogonal-type interactions, whether they are of the σ-hole or π-hole type, in achieving elasticity. This is the first report in which π-hole interactions are used for property engineering. This example may illustrate a new generation of crystal engineering in which a particular property is associated more with topological rather than chemical attributes, although the significance of the latter cannot be completely excluded. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Elastico-mechanoluminescence and crystal-structure relationships in persistent luminescent materials and II-VI semiconductor phosphors

NASA Astrophysics Data System (ADS)

Chandra, B. P.; Chandra, V. K.; Jha, Piyush

2015-04-01

Elastico-mechanoluminescence (EML) has recently attracted the attention of a large number of researchers because of its potential in different types of mechano-optical devices. For understanding the mechanism of EML the relationships between elastico-mechanoluminescence (EML) and crystal-structure of a large number of persistent luminescent materials and II-VI semiconductor phosphors known to date are investigated. It is found that, although most of the non-centrosymmetric crystals exhibit EML, certain non-centrosymmetric crystals do not show EML. Whereas, many centrosymmetric crystals do not exhibit EML, certain centrosymmetric crystals exhibit EML. Piezoelectric ZnS:Cu,Cl single crystals do not show EML, but piezoelectric ZnS:Cu,Cl microcrystalline phosphors show very intense EML. Piezoelectric single crystals of undoped ZnS do not show EML. It seems that EML is related to local piezoelectrification near the impurities in crystals where piezoelectric constant is high. Suitable piezoelectric field near the local piezoelectric region and stable charge carriers in traps are required for appearance of EML. The EML of persistent luminescent materials and II-VI semiconductor phosphors can be understood on the basis of piezoelectrically-induced trap-depth reduction model of EML. Using suitable dopants both in non-centrosymmetric and centrosymmetric crystals intense elastico-mechanoluminescent materials emitting desired colours can be tailored, which may find applications in several mechano-optical devices.

Relationship Between Equilibrium Forms of Lysozyme Crystals and Precipitant Anions

NASA Technical Reports Server (NTRS)

Nadarajah, Arunan

1996-01-01

Molecular forces, such as electrostatic, hydrophobic, van der Waals and steric forces, are known to be important in determining protein interactions. These forces are affected by the solution conditions and changing the pH, temperature or the ionic strength of the solution can sharply affect protein interactions. Several investigations of protein crystallization have shown that this process is also strongly dependent on solution conditions. As the ionic strength of the solution is increased, the initially soluble protein may either crystallize or form an amorphous precipitate at high ionic strengths. Studies done on the model protein hen egg white lysozyme have shown that different crystal forms can be easily and reproducibly obtained, depending primarily on the anion used to desolubilize the protein. In this study we employ pyranine to probe the effect of various anions on the water structure. Additionally, lysozyme crystallization was carried out at these conditions and the crystal form was determined by X-ray crystallography. The goal of the study was to understand the physico-chemical basis for the effect of changing the anion concentration on the equilibrium form of lysozyme crystals. It will also verify the hypothesis that the anions, by altering the bulk water structure in the crystallizing solutions, alter the surface energy of the between the crystal faces and the solution and, consequently, the equilibrium form of the crystals.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

PubMed

Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

2014-07-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. © 2014 Sripathi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.

PubMed

Gay, Sean C; Shah, Manish B; Talakad, Jyothi C; Maekawa, Keiko; Roberts, Arthur G; Wilderman, P Ross; Sun, Ling; Yang, Jane Y; Huelga, Stephanie C; Hong, Wen-Xu; Zhang, Qinghai; Stout, C David; Halpert, James R

2010-04-01

The structure of the K262R genetic variant of human cytochrome P450 2B6 in complex with the inhibitor 4-(4-chlorophenyl)imidazole (4-CPI) has been determined using X-ray crystallography to 2.0-A resolution. Production of diffraction quality crystals was enabled through a combination of protein engineering, chaperone coexpression, modifications to the purification protocol, and the use of unique facial amphiphiles during crystallization. The 2B6-4-CPI complex is virtually identical to the rabbit 2B4 structure bound to the same inhibitor with respect to the arrangement of secondary structural elements and the placement of active site residues. The structure supports prior P450 2B6 homology models based on other mammalian cytochromes P450 and is consistent with the limited site-directed mutagenesis studies on 2B6 and extensive studies on P450 2B4 and 2B1. Although the K262R genetic variant shows unaltered binding of 4-CPI, altered binding affinity, kinetics, and/or product profiles have been previously shown with several other ligands. On the basis of new P450 2B6 crystal structure and previous 2B4 structures, substitutions at residue 262 affect a hydrogen-bonding network connecting the G and H helices, where subtle differences could be transduced to the active site. Docking experiments indicate that the closed protein conformation allows smaller ligands such as ticlopidine to bind to the 2B6 active site in the expected orientation. However, it is unknown whether 2B6 undergoes structural reorganization to accommodate bulkier molecules, as previously inferred from multiple P450 2B4 crystal structures.

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

A simple analytical thermo-mechanical model for liquid crystal elastomer bilayer structures

NASA Astrophysics Data System (ADS)

Cui, Yun; Wang, Chengjun; Sim, Kyoseung; Chen, Jin; Li, Yuhang; Xing, Yufeng; Yu, Cunjiang; Song, Jizhou

2018-02-01

The bilayer structure consisting of thermal-responsive liquid crystal elastomers (LCEs) and other polymer materials with stretchable heaters has attracted much attention in applications of soft actuators and soft robots due to its ability to generate large deformations when subjected to heat stimuli. A simple analytical thermo-mechanical model, accounting for the non-uniform feature of the temperature/strain distribution along the thickness direction, is established for this type of bilayer structure. The analytical predictions of the temperature and bending curvature radius agree well with finite element analysis and experiments. The influences of the LCE thickness and the heat generation power on the bending deformation of the bilayer structure are fully investigated. It is shown that a thinner LCE layer and a higher heat generation power could yield more bending deformation. These results may help the design of soft actuators and soft robots involving thermal responsive LCEs.

Crystal structure of the human astrovirus capsid spike.

PubMed

Dong, Jinhui; Dong, Liping; Méndez, Ernesto; Tao, Yizhi

2011-08-02

Astroviruses are single-stranded, plus-sense RNA viruses that infect both mammals and birds, causing gastroenteritis and other extraintestinal diseases. Clinical studies have established astroviruses as the second leading cause of viral diarrhea in young children. Here we report the crystal structure of the human astrovirus dimeric surface spike determined to 1.8-Å resolution. The overall structure of each spike/projection domain has a unique three-layered β-sandwiches fold, with a core, six-stranded β-barrel structure that is also found in the hepatitis E virus capsid protrusions, suggesting a closer phylogenetic relationship between these two viruses than previously acknowledged. Based on a hepatitis E virus capsid model, we performed homology modeling and produced a complete, T = 3 astrovirus capsid model with features remarkably similar to those observed in a cryoelectron microscopy reconstruction image of a human astrovirus. Mapping conserved residues onto the astrovirus projection domain revealed a putative receptor binding site with amino acid compositions characteristic for polysaccharide recognition. Our results will have an important impact on future characterization of astrovirus structure and function, and will likely have practical applications in the development of vaccines and antivirals.

Research on bandgaps in two-dimensional phononic crystal with two resonators.

PubMed

Gao, Nansha; Wu, Jiu Hui; Yu, Lie

2015-02-01

In this paper, the bandgap properties of a two-dimensional phononic crystal with the two resonators is studied and embedded in a homogenous matrix. The resonators are not connected with the matrix but linked with connectors directly. The dispersion relationship, transmission spectra, and displacement fields of the eigenmodes of this phononic crystal are studied with finite-element method. In contrast to the phononic crystals with one resonators and hollow structure, the proposed structures with two resonators can open bandgaps at lower frequencies. This is a very interesting and useful phenomenon. Results show that, the opening of the bandgaps is because of the local resonance and the scattering interaction between two resonators and matrix. An equivalent spring-pendulum model can be developed in order to evaluate the frequencies of the bandgap edge. The study in this paper is beneficial to the design of opening and tuning bandgaps in phononic crystals and isolators in low-frequency range. Copyright © 2014 Elsevier B.V. All rights reserved.

Mitigating cold flow problems of biodiesel: Strategies with additives

NASA Astrophysics Data System (ADS)

Mohanan, Athira

The present thesis explores the cold flow properties of biodiesel and the effect of vegetable oil derived compounds on the crystallization path as well as the mechanisms at play at different stages and length scales. Model systems including triacylglycerol (TAG) oils and their derivatives, and a polymer were tested with biodiesel. The goal was to acquire the fundamental knowledge that would help design cold flow improver (CFI) additives that would address effectively and simultaneously the flow problems of biodiesel, particularly the cloud point (CP) and pour point (PP). The compounds were revealed to be fundamentally vegetable oil crystallization modifiers (VOCM) and the polymer was confirmed to be a pour point depressant (PPD). The results obtained with the VOCMs indicate that two cis-unsaturated moieties combined with a trans-/saturated fatty acid is a critical structural architecture for depressing the crystallization onset by a mechanism wherein while the straight chain promotes a first packing with the linear saturated FAMEs, the kinked moieties prevent further crystallization. The study of model binary systems made of a VOCM and a saturated FAME with DSC, XRD and PLM provided a complete phase diagram including the thermal transformation lines, crystal structure and microstructure that impact the phase composition along the different crystallization stages, and elicited the competing effects of molecular mass, chain length mismatch and isomerism. The liquid-solid boundary is discussed in light of a simple thermodynamic model based on the Hildebrand equation and pair interactions. In order to test for synergies, the PP and CP of a biodiesel (Soy1500) supplemented with several VOCM and PLMA binary cocktails were measured using a specially designed method inspired by ASTM standards. The results were impressive, the combination of additives depressed CP and PP better than any single additive. The PLM and DSC results suggest that the cocktail additives are most effective when the right molecular structure and optimal concentration are provided. The cocktail mixture achieves then tiny crystals that are prevented from aggregating for an extended temperature range. The results of the study can be directly used for the design of functional and economical CFI from vegetable oils and their derivatives.

The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

PubMed

Tavanti, Michele; Porter, Joanne L; Levy, Colin W; Gómez Castellanos, J Rubén; Flitsch, Sabine L; Turner, Nicholas J

2018-07-02

The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes. Copyright © 2018 Elsevier Inc. 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

[A prediction model for the activity of insecticidal crystal proteins from Bacillus thuringiensis based on support vector machine].

PubMed

Lin, Yi; Cai, Fu-Ying; Zhang, Guang-Ya

2007-01-01

A quantitative structure-property relationship (QSPR) model in terms of amino acid composition and the activity of Bacillus thuringiensis insecticidal crystal proteins was established. Support vector machine (SVM) is a novel general machine-learning tool based on the structural risk minimization principle that exhibits good generalization when fault samples are few; it is especially suitable for classification, forecasting, and estimation in cases where small amounts of samples are involved such as fault diagnosis; however, some parameters of SVM are selected based on the experience of the operator, which has led to decreased efficiency of SVM in practical application. The uniform design (UD) method was applied to optimize the running parameters of SVM. It was found that the average accuracy rate approached 73% when the penalty factor was 0.01, the epsilon 0.2, the gamma 0.05, and the range 0.5. The results indicated that UD might be used an effective method to optimize the parameters of SVM and SVM and could be used as an alternative powerful modeling tool for QSPR studies of the activity of Bacillus thuringiensis (Bt) insecticidal crystal proteins. Therefore, a novel method for predicting the insecticidal activity of Bt insecticidal crystal proteins was proposed by the authors of this study.

Comparing pharmacophore models derived from crystallography and NMR ensembles

NASA Astrophysics Data System (ADS)

Ghanakota, Phani; Carlson, Heather A.

2017-11-01

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the "extra" pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.

Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors

NASA Astrophysics Data System (ADS)

Miguet, Laurence; Zhang, Ziding; Barbier, Maryse; Grigorov, Martin G.

2006-02-01

Human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) catalyzes the interconversion of cortisone into active cortisol. 11βHSD1 inhibition is a tempting target for the treatment of a host of human disorders that might benefit from blockade of glucocorticoid action, such as obesity, metabolic syndrome, and diabetes type 2. Here, we report an in silico screening study aimed at identifying new selective inhibitors of human 11βHSD1 enzyme. In the first step, homology modeling was employed to build the 3D structure of 11βHSD1. Further, molecular docking was used to validate the predicted model by showing that it was able to discriminate between known 11βHSD1 inhibitors or substrates and non-inhibitors. The homology model was found to reproduce closely the crystal structure that became publicly available in the final stages of this work. Finally, we carried out structure-based virtual screening experiments on both the homology model and the crystallographic structure with a database of 114'000 natural molecules. Among these, 15 molecules were consistently selected as inhibitors based on both the model and crystal structures of the enzyme, implying a good quality for the homology model. Among these putative 11βHSD1 inhibitors, two were flavonone derivatives that have already been shown to be potent inhibitors of the enzyme.

Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

PubMed

Chakravorty, Arghya; Jia, Zhe; Li, Lin; Zhao, Shan; Alexov, Emil

2018-02-13

Typically, the ensemble average polar component of solvation energy (ΔG polar solv ) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔG polar solv ) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔG polar solv (⟨ΔG polar solv ⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.

Modeling G Protein-Coupled Receptors: a Concrete Possibility

PubMed Central

Costanzi, Stefano

2010-01-01

G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that are involved in the regulation of a wide range of physiological functions and constitute the most common target for therapeutic intervention. Due to the paucity of crystal structures, homology modeling has become a widespread technique for the construction of GPCR models, which have been applied to the study of their structure-function relationships and to the identification of lead ligands through virtual screening. Rhodopsin has been for years the only available template. However, recent breakthroughs in GPCR crystallography have led to the solution of the structures of a few additional receptors. In light of these newly elucidated crystal structures, we have been able to produce a substantial amount of data to demonstrate that accurate models of GPCRs in complex with their ligands can be constructed through homology modeling followed by fully flexible molecular docking. These results have been confirmed by our success in the first blind assessment of GPCR modeling and docking, organized in coordination with the solution of the X-ray structure of the adenosine A2A receptor. Taken together, these data indicate that: a) the transmembrane helical bundle can be modeled with considerable accuracy; b) predicting the binding mode of a ligand, although doable, is challenging; c) modeling of the extracellular and intracellular loops is still problematic. PMID:21253444

Crystal Structure Studies of Low-Ca Pyroxenes from LL-Group Chondritic Meteorites

NASA Astrophysics Data System (ADS)

Artioli, G.; Davoli, G.; Sighinolfi, G. P.

1993-07-01

One orthorhombic (Pbca) and two monoclinic (P2(sub)1/c) single crystals of low-Ca pyroxenes were extracted from unequilibrated chondritic meteorites of the LL-group. The results of the crystal structure refinements performed using x-ray diffraction data indicate that: (1) the intracrystalline Fe-Mg distribution over the M1 and M2 crystallographic sites of the Parnallee (LL-3) orthoenstatite is consistent with a temperature of 960 degrees C for the closure of the exchange equilibrium process; and (2) the structural state and intracristalline Fe-Mg order in the Soko Banja (LL-4) and Jolomba (LL-6) clinoenstatites indicate a closing temperature of at least 1000-1100 degrees C, with no significant reequilibration at lower temperatures. The present data represent the first detailed crystallographic investigation of pyroxenes from LL-chondrites and support the hypothesis that the chondrule pyroxenes bear a distinct memory of rapid cooling in the solar nebular and that thermal metamorphism in the parent body, if present, was totally unsufficient to allow reequilibration of the pyroxene minerals to the low-temperature ordered crystal structures. The data also indicate that, assuming low or mild pressure and shock effects, there is no well-defined correlation between equilibrium temperature of the mineral phases and the alleged petrologic type of the meteorites. This evidence is consistent with a rubble-pile model for the parent body accretional history, or with an onion-shell model with very low thermal-peak metamorphism, as it is assumed for a very small object.

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.

Optical parameters and dispersion behavior of potassium magnesium chloride sulfate single crystals doped with Co+2 ions

NASA Astrophysics Data System (ADS)

Abu El-Fadl, A.; Abd-Elsalam, A. M.

2018-05-01

Single crystals of potassium magnesium chloride sulfate (KMCS) doped with cobalt ions were grown by slow cooling method. Powder XRD study confirmed the monoclinic structure of the grown crystals. The functional group vibrations were checked through FTIR spectroscopy measurements. In optical studies, the absorbance behavior of the crystals and their optical energy gap were established by Tauc plot. The refractive index, the extinction coefficient and other optical constants were calculated for the grown crystals. The normal dispersion of the refractive index was analyzed according to single oscillator Sellmeier's model. The Urbach's rule was applied to analyze the localized states density in the forbidden gap.

Growth of semimetallic ErAs films epitaxially embedded in GaAs

NASA Astrophysics Data System (ADS)

Crook, Adam M.; Nair, Hari P.; Lee, Jong H.; Ferrer, Domingo A.; Akinwande, Deji; Bank, Seth R.

2011-10-01

We present models for the growth and electrical conductivity of ErAs films grown with the nanoparticle-seeded film growth technique. This growth mode overcomes the mismatch in rotational symmetry between the rocksalt ErAs crystal structure and the zincblende GaAs crystal structure. This results in films of ErAs grown through a thin film of GaAs that preserves the symmetry of the substrate. The conductivity of the films, as a function of film thickness, are investigated and a surface roughness model is used to explain observed trends. Transmission electron micrographs confirm the suppression of anti-phase domains. A simple diffusion model is developed to describe the diffusion and incorporation of surface erbium into subsurface ErAs layers and predict potential failure mechanisms of the growth method.

Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major

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

Arakaki, Tracy; Le Trong, Isolde; Structural Genomics of Pathogenic Protozoa

2006-03-01

The crystal structure of a conserved hypothetical protein from L. major, Pfam sequence family PF04543, structural genomics target ID Lmaj006129AAA, has been determined at a resolution of 1.6 Å. The gene product of structural genomics target Lmaj006129 from Leishmania major codes for a 164-residue protein of unknown function. When SeMet expression of the full-length gene product failed, several truncation variants were created with the aid of Ginzu, a domain-prediction method. 11 truncations were selected for expression, purification and crystallization based upon secondary-structure elements and disorder. The structure of one of these variants, Lmaj006129AAH, was solved by multiple-wavelength anomalous diffraction (MAD)more » using ELVES, an automatic protein crystal structure-determination system. This model was then successfully used as a molecular-replacement probe for the parent full-length target, Lmaj006129AAA. The final structure of Lmaj006129AAA was refined to an R value of 0.185 (R{sub free} = 0.229) at 1.60 Å resolution. Structure and sequence comparisons based on Lmaj006129AAA suggest that proteins belonging to Pfam sequence families PF04543 and PF01878 may share a common ligand-binding motif.« less

Application of Powder Diffraction Methods to the Analysis of the Atomic Structure of Nanocrystals: The Concept of the Apparent Lattice Parameter (ALP)

NASA Technical Reports Server (NTRS)

Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.; Curreri, Peter A. (Technical Monitor)

2002-01-01

The applicability of standard methods of elaboration of powder diffraction data for determination of the structure of nano-size crystallites is analysed. Based on our theoretical calculations of powder diffraction data we show, that the assumption of the infinite crystal lattice for nanocrystals smaller than 20 nm in size is not justified. Application of conventional tools developed for elaboration of powder diffraction data, like the Rietveld method, may lead to erroneous interpretation of the experimental results. An alternate evaluation of diffraction data of nanoparticles, based on the so-called 'apparent lattice parameter' (alp) is introduced. We assume a model of nanocrystal having a grain core with well-defined crystal structure, surrounded by a surface shell with the atomic structure similar to that of the core but being under a strain (compressive or tensile). The two structural components, the core and the shell, form essentially a composite crystal with interfering, inseparable diffraction properties. Because the structure of such a nanocrystal is not uniform, it defies the basic definitions of an unambiguous crystallographic phase. Consequently, a set of lattice parameters used for characterization of simple crystal phases is insufficient for a proper description of the complex structure of nanocrystals. We developed a method of evaluation of powder diffraction data of nanocrystals, which refers to a core-shell model and is based on the 'apparent lattice parameter' methodology. For a given diffraction pattem, the alp values are calculated for every individual Bragg reflection. For nanocrystals the alp values depend on the diffraction vector Q. By modeling different a0tomic structures of nanocrystals and calculating theoretically corresponding diffraction patterns using the Debye functions we showed, that alp-Q plots show characteristic shapes which can be used for evaluation of the atomic structure of the core-shell system. We show, that using a simple model of a nanocrystal with spherical shape and centro-symmetric strain at the surface shell we obtain theoretical alp-Q values which match very well the alp-Q plots determined experimentally for Sic, GaN, and diamond nanopowders. The theoretical models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the surface shell. According to our calculations, the part of the diffraction pattern measured at relatively low diffraction vectors Q (below 10/angstrom) provides information on the surface strain, whle determination of the lattice parameters in the grain core requires measurements at large Q-values (above 15 - 20/angstrom).

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

PubMed

Hayakawa, Daichi; Nishiyama, Yoshiharu; Mazeau, Karim; Ueda, Kazuyoshi

2017-09-08

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A). Copyright © 2017 Elsevier Ltd. All rights reserved.

Toda hierarchies and their applications

NASA Astrophysics Data System (ADS)

Takasaki, Kanehisa

2018-05-01

The 2D Toda hierarchy occupies a central position in the family of integrable hierarchies of the Toda type. The 1D Toda hierarchy and the Ablowitz–Ladik (aka relativistic Toda) hierarchy can be derived from the 2D Toda hierarchy as reductions. These integrable hierarchies have been applied to various problems of mathematics and mathematical physics since 1990s. A recent example is a series of studies on models of statistical mechanics called the melting crystal model. This research has revealed that the aforementioned two reductions of the 2D Toda hierarchy underlie two different melting crystal models. Technical clues are a fermionic realization of the quantum torus algebra, special algebraic relations therein called shift symmetries, and a matrix factorization problem. The two melting crystal models thus exhibit remarkable similarity with the Hermitian and unitary matrix models for which the two reductions of the 2D Toda hierarchy play the role of fundamental integrable structures.

Field-controlled structures in ferromagnetic cholesteric liquid crystals.

PubMed

Medle Rupnik, Peter; Lisjak, Darja; Čopič, Martin; Čopar, Simon; Mertelj, Alenka

2017-10-01

One of the advantages of anisotropic soft materials is that their structures and, consequently, their properties can be controlled by moderate external fields. Whereas the control of materials with uniform orientational order is straightforward, manipulation of systems with complex orientational order is challenging. We show that a variety of structures of an interesting liquid material, which combine chiral orientational order with ferromagnetic one, can be controlled by a combination of small magnetic and electric fields. In the suspensions of magnetic nanoplatelets in chiral nematic liquid crystals, the platelet's magnetic moments orient along the orientation of the liquid crystal and, consequently, the material exhibits linear response to small magnetic fields. In the absence of external fields, orientations of the liquid crystal and magnetization have wound structure, which can be either homogeneously helical, disordered, or ordered in complex patterns, depending on the boundary condition at the surfaces and the history of the sample. We demonstrate that by using different combinations of small magnetic and electric fields, it is possible to control reversibly the formation of the structures in a layer of the material. In such a way, different periodic structures can be explored and some of them may be suitable for photonic applications. The material is also a convenient model system to study chiral magnetic structures, because it is a unique liquid analog of a solid helimagnet.

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.

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.

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

Wang, Bingnan

Photonic crystals and metamaterials, both composed of artificial structures, are two interesting areas in electromagnetism and optics. New phenomena in photonic crystals and metamaterials are being discovered, including some not found in natural materials. This thesis presents my research work in the two areas. Photonic crystals are periodically arranged artificial structures, mostly made from dielectric materials, with period on the same order of the wavelength of the working electromagnetic wave. The wave propagation in photonic crystals is determined by the Bragg scattering of the periodic structure. Photonic band-gaps can be present for a properly designed photonic crystal. Electromagnetic waves withmore » frequency within the range of the band-gap are suppressed from propagating in the photonic crystal. With surface defects, a photonic crystal could support surface modes that are localized on the surface of the crystal, with mode frequencies within the band-gap. With line defects, a photonic crystal could allow the propagation of electromagnetic waves along the channels. The study of surface modes and waveguiding properties of a 2D photonic crystal will be presented in Chapter 1. Metamaterials are generally composed of artificial structures with sizes one order smaller than the wavelength and can be approximated as effective media. Effective macroscopic parameters such as electric permittivity ϵ, magnetic permeability μ are used to characterize the wave propagation in metamaterials. The fundamental structures of the metamaterials affect strongly their macroscopic properties. By designing the fundamental structures of the metamaterials, the effective parameters can be tuned and different electromagnetic properties can be achieved. One important aspect of metamaterial research is to get artificial magnetism. Metallic split-ring resonators (SRRs) and variants are widely used to build magnetic metamaterials with effective μ < 1 or even μ < 0. Varactor based nonlinear SRRs are built and modeled to study the nonlinearity in magnetic metamaterials and the results will be presented in Chapter 3. Negative refractive index n is one of the major target in the research of metamaterials. Negative n can be obtained with a metamaterial with both ϵ and μ negative. As an alternative, negative index for one of the circularly polarized waves could be achieved with metamaterials having a strong chirality ?. In this case neither ϵ} nor μ negative is required. My work on chiral metamaterials will be presented in Chapter 4.« less

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.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

NASA Astrophysics Data System (ADS)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

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.

Theoretical research of the spin-Hamiltonian parameters for two rhombic W5+ centers in KTiOPO4 (KTP) crystal through a two-mechanism model

NASA Astrophysics Data System (ADS)

Mei, Yang; Chen, Bo-Wei; Wei, Chen-Fu; Zheng, Wen-Chen

2016-09-01

The high-order perturbation formulas based on the two-mechanism model are employed to calculate the spin-Hamiltonian parameters (g factors gi and hyperfine structure constants Ai, where i=x, y, z) for two approximately rhombic W5+ centers in KTiOPO4 (KTP) crystal. In the model, both the widely-applied crystal-field (CF) mechanism concerning the interactions of CF excited states with the ground state and the generally-neglected charge-transfer (CT) mechanism concerning the interactions of CT excited states with the ground state are included. The calculated results agree with the experimental values, and the signs of constants Ai are suggested. The calculations indicate that (i) for the high valence state dn ions in crystals, the contributions to spin-Hamiltonian parameters should take into account both the CF and CT mechanisms and (ii) the large g-shifts |Δgi | (=|gi-ge |, where ge≈ 2.0023) for W5+ centers in crystals are due to the large spin-orbit parameter of free W5+ ion.

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.

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.

Pressure relaxation and diffusion of vacancies in rapidly grown helium crystals

NASA Astrophysics Data System (ADS)

Birchenko, A. P.; Mikhin, N. P.; Rudavskii, E. Ya.; Smirnov, S. N.; Fysun, Ya. Yu.

2018-04-01

An experimental study of the features of pressure relaxation in rapidly grown crystals of a diluted solid solution 3He-4He, at temperatures above 1.3 K, was performed. A cylindrical cell with capacitive pressure sensors at the ends was used for measurements. It was found that, when the helium crystals were grown at cooling rates ≳4 mK/s, the difference in pressure ΔP registered by the sensors at 1.3 K reached 2.4 bars. The ΔP value decreased with subsequent stepwise increase in temperature, but reached zero only after thorough annealing at the premelting temperatures. The kinetics of pressure changes at the sample ends at different temperatures was recorded. The results obtained were interpreted within the framework of the structural relaxation model based on the monovacancy diffusion mechanism. The proposed model made it possible to explain the dependence of ΔP on the time and temperature recorded in the experiment, as well as to determine the activation energy of the structural relaxation process and the diffusion coefficient of vacancies. The details of the vacancy model are described in the Appendix.

How grain boundaries affect the efficiency of poly-CdTe solar-cells: A fundamental atomic-scale study of grain boundary dislocation cores using CdTe bi-crystal thin films.

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

Klie, Robert

It is now widely accepted that grain boundaries in poly-crystalline CdTe thin film devices have a detrimental effect on the minority carrier lifetimes, the open circuit voltage and therefore the overall solar-cell performance. The goal of this project was to develop a fundamental understanding of the role of grain boundaries in CdTe on the carrier life-time, open-circuit voltage, Voc, and the diffusion of impurities. To achieve this goal, i) CdTe bi-crystals were fabricated with various misorientation angels, ii) the atomic- and electronic structures of the grain boundaries were characterized using scanning transmission electron microscopy (STEM), and iii) first-principles density functionalmore » theory modeling was performed on the structures determined by STEM to predict the grain boundary potential. The transport properties and minority carrier lifetimes of the bi-crystal grain boundaries were measured using a variety of approaches, including TRPL, and provided feedback to the characterization and modeling effort about the effectiveness of the proposed models.« less

Ice cream structure modification by ice-binding proteins.

PubMed

Kaleda, Aleksei; Tsanev, Robert; Klesment, Tiina; Vilu, Raivo; Laos, Katrin

2018-04-25

Ice-binding proteins (IBPs), also known as antifreeze proteins, were added to ice cream to investigate their effect on structure and texture. Ice recrystallization inhibition was assessed in the ice cream mixes using a novel accelerated microscope assay and the ice cream microstructure was studied using an ice crystal dispersion method. It was found that adding recombinantly produced fish type III IBPs at a concentration 3 mg·L -1 made ice cream hard and crystalline with improved shape preservation during melting. Ice creams made with IBPs (both from winter rye, and type III IBP) had aggregates of ice crystals that entrapped pockets of the ice cream mixture in a rigid network. Larger individual ice crystals and no entrapment in control ice creams was observed. Based on these results a model of ice crystals aggregates formation in the presence of IBPs was proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Chirality-controlled crystallization via screw dislocations.

PubMed

Sung, Baeckkyoung; de la Cotte, Alexis; Grelet, Eric

2018-04-11

Chirality plays an important role in science from enantiomeric separation in chemistry to chiral plasmonics in nanotechnology. However, the understanding of chirality amplification from chiral building blocks to ordered helical superstructures remains a challenge. Here, we demonstrate that topological defects, such as screw dislocations, can drive the chirality transfer from particle to supramolecular structure level during the crystallization process. By using a model system of chiral particles, which enables direct imaging of single particle incorporation into growing crystals, we show that the crystallization kinetic pathway is the key parameter for monitoring, via the defects, the chirality amplification of the crystalline structures from racemic to predominantly homohelical. We provide an explanation based on the interplay between geometrical frustration, racemization induced by thermal fluctuations, and particle chirality. Our results demonstrate that screw dislocations not only promote the growth, but also control the chiral morphology and therefore the functionality of crystalline states.

Control of the conformations of ion Coulomb crystals in a Penning trap

PubMed Central

Mavadia, Sandeep; Goodwin, Joseph F.; Stutter, Graham; Bharadia, Shailen; Crick, Daniel R.; Segal, Daniel M.; Thompson, Richard C.

2013-01-01

Laser-cooled atomic ions form ordered structures in radiofrequency ion traps and in Penning traps. Here we demonstrate in a Penning trap the creation and manipulation of a wide variety of ion Coulomb crystals formed from small numbers of ions. The configuration can be changed from a linear string, through intermediate geometries, to a planar structure. The transition from a linear string to a zigzag geometry is observed for the first time in a Penning trap. The conformations of the crystals are set by the applied trap potential and the laser parameters, and agree with simulations. These simulations indicate that the rotation frequency of a small crystal is mainly determined by the laser parameters, independent of the number of ions and the axial confinement strength. This system has potential applications for quantum simulation, quantum information processing and tests of fundamental physics models from quantum field theory to cosmology. PMID:24096901

Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

NASA Astrophysics Data System (ADS)

Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

2017-10-01

DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

Crystal Structure of the Catalytic Domain of Drosophila [beta]1,4-Galactosyltransferase-7

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

Ramakrishnan, Boopathy; Qasba, Pradman K.

2010-11-03

The {beta}1,4-galactosyltransferase-7 ({beta}4Gal-T7) enzyme, one of seven members of the {beta}4Gal-T family, transfers in the presence of manganese Gal from UDP-Gal to an acceptor sugar (xylose) that is attached to a side chain hydroxyl group of Ser/Thr residues of proteoglycan proteins. It exhibits the least protein sequence similarity with the other family members, including the well studied family member {beta}4Gal-T1, which, in the presence of manganese, transfers Gal from UDP-Gal to GlcNAc. We report here the crystal structure of the catalytic domain of {beta}4Gal-T7 from Drosophila in the presence of manganese and UDP at 1.81 {angstrom} resolution. In the crystalmore » structure, a new manganese ion-binding motif (HXH) has been observed. Superposition of the crystal structures of {beta}4Gal-T7 and {beta}4Gal-T1 shows that the catalytic pocket and the substrate-binding sites in these proteins are similar. Compared with GlcNAc, xylose has a hydroxyl group (instead of an N-acetyl group) at C2 and lacks the CH{sub 2}OH group at C5; thus, these protein structures show significant differences in their acceptor-binding site. Modeling of xylose in the acceptor-binding site of the {beta}4Gal-T7 crystal structure shows that the aromatic side chain of Tyr{sup 177} interacts strongly with the C5 atom of xylose, causing steric hindrance to any additional group at C5. Because Drosophila Cd7 has a 73% protein sequence similarity to human Cd7, the present crystal structure offers a structure-based explanation for the mutations in human Cd7 that have been linked to Ehlers-Danlos syndrome.« less

Simulation of the as-cast structure of Al-4.0wt.%Cu ingots with a 5-phase mixed columnar-equiaxed solidification model

NASA Astrophysics Data System (ADS)

Wu, M.; Ahmadein, M.; Kharicha, A.; Ludwig, A.; Li, J. H.; Schumacher, P.

2012-07-01

Empirical knowledge about the formation of the as-cast structure, mostly obtained before 1980s, has revealed two critical issues: one is the origin of the equiaxed crystals; one is the competing growth of the columnar and equiaxed structures, and the columnar-to-equiaxed transition (CET). Unfortunately, the application of empirical knowledge to predict and control the as-cast structure was very limited, as the flow and crystal transport were not considered. Therefore, a 5-phase mixed columnar-equiaxed solidification model was recently proposed by the current authors based on modeling the multiphase transport phenomena. The motivation of the recent work is to determine and evaluate the necessary modeling parameters, and to validate the mixed columnar-equiaxed solidification model by comparison with laboratory castings. In this regard an experimental method was recommended for in-situ determination of the nucleation parameters. Additionally, some classical experiments of the Al-Cu ingots were conducted and the as-cast structural information including distinct columnar and equiaxed zones, macrosegregation, and grain size distribution were analysed. The final simulation results exhibited good agreement with experiments in the case of high pouring temperature, whereas disagreement in the case of low pouring temperature. The reasons for the disagreement are discussed.

Structural Basis for the Inhibition of Gas Hydrates by α-Helical Antifreeze Proteins

PubMed Central

Sun, Tianjun; Davies, Peter L.; Walker, Virginia K.

2015-01-01

Kinetic hydrate inhibitors (KHIs) are used commercially to inhibit gas hydrate formation and growth in pipelines. However, improvement of these polymers has been constrained by the lack of verified molecular models. Since antifreeze proteins (AFPs) act as KHIs, we have used their solved x-ray crystallographic structures in molecular modeling to explore gas hydrate inhibition. The internal clathrate water network of the fish AFP Maxi, which extends to the protein’s outer surface, is remarkably similar to the {100} planes of structure type II (sII) gas hydrate. The crystal structure of this water web has facilitated the construction of in silico models for Maxi and type I AFP binding to sII hydrates. Here, we have substantiated our models with experimental evidence of Maxi binding to the tetrahydrofuran sII model hydrate. Both in silico and experimental evidence support the absorbance-inhibition mechanism proposed for KHI binding to gas hydrates. Based on the Maxi crystal structure we suggest that the inhibitor adsorbs to the gas hydrate lattice through the same anchored clathrate water mechanism used to bind ice. These results will facilitate the rational design of a next generation of effective green KHIs for the petroleum industry to ensure safe and efficient hydrocarbon flow. PMID:26488661

Density functional study for the bridged dinuclear center based on a high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus thermophilus.

PubMed

Du, Wen-Ge Han; Noodleman, Louis

2013-12-16

Strong electron density for a peroxide type dioxygen species bridging the Fea3 and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 Å) X-ray crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus. The crystals represent the as-isolated X-ray photoreduced CcO structures. The bridging peroxide was proposed to arise from the recombination of two radiation-produced HO(•) radicals formed either very near to or even in the space between the two metals of the DNC. It is unclear whether this peroxide species is in the O2(2-), O2(•)(-), HO2(-), or the H2O2 form and what is the detailed electronic structure and binding geometry including the DNC. In order to answer what form of this dioxygen species was observed in the DNC of the 1.8 Å X-ray CcO crystal structure (3S8G), we have applied broken-symmetry density functional theory (BS-DFT) geometric and energetic calculations (using OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and spin states and with O2(2-), O2(•)(-), HO2(-), or H2O2 in the bridging position. By comparing the DFT optimized geometries with the X-ray crystal structure (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal structure is likely to represent the superposition of the Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), intermediate spin (IS), or high spin (HS)) with the majority species having the proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations show that the side chain of Tyr237 is likely trapped in the deprotonated Tyr237(-) anion form in the 3S8G X-ray crystal structure.

Theory of liquid crystal orientation under action of light wave field and aligning surfaces

NASA Astrophysics Data System (ADS)

Dadivanyan, A. K.; Chausov, D. N.; Belyaev, V. V.; Barabanova, N. N.; Chausova, O. V.; Kuleshova, Yu D.

2018-03-01

Theoretical models developed in the MRSU group under leadership of Professor Artem Dadivanyan in area of the LC orientation and photo-induced effects are presented. Angular distribution functions of the dye and liquid crystal molecules under action of intensive light beam have been derived. The number of molecules in cluster is estimated. A model of dimers formation in the photoalignment dye is suggested that explains influence of the dye molecular structure on both polar and azimuthal anchoring energy.

Concurrent display of both α- and β-turns in a model peptide.

PubMed

Srinivas, Deekonda; Vijayadas, Kuruppanthara N; Gonnade, Rajesh; Phalgune, Usha D; Rajamohanan, Pattuparambil R; Sanjayan, Gangadhar J

2011-08-21

This article describes a model peptide that concurrently displays both α- and β-turns, as demonstrated by structural investigations using single crystal X-ray crystallography and solution-state NMR studies. The motif reported herein has the potential for the design of novel conformationally ordered synthetic oligomers with structural architectures distinct from those classically observed.

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

PubMed Central

Eyal, Zohar; Matzov, Donna; Krupkin, Miri; Wekselman, Itai; Paukner, Susanne; Zimmerman, Ella; Rozenberg, Haim; Bashan, Anat; Yonath, Ada

2015-01-01

The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus. PMID:26464510

Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

PubMed

Lobley, Carina M C; Aller, Pierre; Douangamath, Alice; Reddivari, Yamini; Bumann, Mario; Bird, Louise E; Nettleship, Joanne E; Brandao-Neto, Jose; Owens, Raymond J; O'Toole, Paul W; Walsh, Martin A

2012-12-01

The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.

ROY Revisited, Again: The Eighth Solved Structure

DOE PAGES

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai; ...

2018-01-01

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

ROY Revisited, Again: The Eighth Solved Structure

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

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

Left-right correlation in coupled F-center defects

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

Janesko, Benjamin G., E-mail: b.janesko@tcu.edu

This work explores how left-right correlation, a textbook problem in electronic structure theory, manifests in a textbook example of electrons trapped in crystal defects. I show that adjacent F-center defects in lithium fluoride display symptoms of “strong” left-right correlation, symptoms similar to those seen in stretched H{sub 2}. Simulations of UV/visible absorption spectra qualitatively fail to reproduce experiment unless left-right correlation is taken into account. This is of interest to both the electronic structure theory and crystal-defect communities. Theorists have a new well-behaved system to test their methods. Crystal-defect groups are cautioned that the approximations that successfully model single F-centersmore » may fail for adjacent F-centers.« less

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.

Crystal structure and phase stability in Fe{sub 1{minus}x}Co{sub x} from AB initio theory

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

Soederlind, P.; Abrikosov, I.A.; James, P.

1996-06-01

For alloys between Fe and Co, their magnetic properties determine their structure. From the occupation of d states, a phase diagram is expected which depend largely on the spin polarization. A method more elaborate than canonical band models is used to calculate the spin moment and crystal structure energies. This method was the multisublattice generalization of the coherent potential approximation in conjunction with the Linear-Muffin-Tin-Orbital method in the atomic sphere approximation. To treat itinerant magnetism, the Vosko-Wilk-Nusair parameterization was used for the local spin density approximation. The fcc, bcc, and hcp phases were studied as completely random alloys, while themore » {alpha}{prime} phase for off-stoichiometries were considered as partially ordered. Results are compared with experiment and canonical band model.« less

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

On the origin of fiber calcite crystals in moonmilk deposits.

PubMed

Cañaveras, Juan Carlos; Cuezva, Soledad; Sanchez-Moral, Sergio; Lario, Javier; Laiz, Leonila; Gonzalez, Juan Miguel; Saiz-Jimenez, Cesareo

2006-01-01

In this study, we show that moonmilk subaerial speleothems in Altamira Cave (Spain) consist of a network of fiber calcite crystals and active microbial structures. In Altamira moonmilks, the study of the typology and distribution of fiber crystals, extracellular polymeric substances, and microorganisms allowed us to define the initial stages of fiber crystal formation in recent samples as well as the variations in the microstructural arrangement in more evolved stages. Thus, we have been able to show the existence of a relationship among the different types of fiber crystals and their origins. This allowed us to outline a model that illustrates the different stages of formation of the moonmilk, developed on different substrata, concluding that microbes influence physicochemical precipitation, resulting in a variety of fiber crystal morphologies and sizes.

Crystallization tendencies of modelled Lennard-Jones liquids with different attractions

NASA Astrophysics Data System (ADS)

Valdès, L.-C.; Gerges, J.; Mizuguchi, T.; Affouard, F.

2018-01-01

Molecular dynamics simulations are performed on simple models composed of monoatomic Lennard-Jones atoms for which the repulsive interaction is the same but the attractive part is tuned. We investigate the precise role of the attractive part of the interaction potential on different structural, dynamical, and thermodynamical properties of these systems in the liquid and crystalline states. It includes crystallization trends for which the main physical ingredients involved have been computed: the diffusion coefficient, the Gibbs energy difference between the liquid and the crystalline state, and the crystal-liquid interfacial free energy. Results are compared with predictions from the classical nucleation theory including transient and steady-state regimes at moderate and deeper undercooling. The question of the energetic and entropic impact of the repulsive and attractive part of the interaction potential towards crystallization is also addressed.

Troublesome Crystal Structures: Prevention, Detection, and Resolution

PubMed Central

Harlow, Richard L.

1996-01-01

A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures. PMID:27805169

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1.

PubMed

Hosaka, Toshiaki; Okazaki, Masateru; Kimura-Someya, Tomomi; Ishizuka-Katsura, Yoshiko; Ito, Kaori; Yokoyama, Shigeyuki; Dodo, Kosuke; Sodeoka, Mikiko; Shirouzu, Mikako

2017-09-01

Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P22 1 2 1 , which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P22 1 2 1 were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family. © 2017 The Protein Society.

Crystal structure of human tooth enamel studied by neutron diffraction

NASA Astrophysics Data System (ADS)

Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

2015-02-01

Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

Entangled photon pair generation by spontaneous parametric down-conversion in finite-length one-dimensional photonic crystals

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

Centini, M.; Sciscione, L.; Sibilia, C.

A description of spontaneous parametric down-conversion in finite-length one-dimensional nonlinear photonic crystals is developed using semiclassical and quantum approaches. It is shown that if a suitable averaging is added to the semiclassical model, its results are in very good agreement with the quantum approach. We propose two structures made with GaN/AlN that generate both degenerate and nondegenerate entangled photon pairs. Both structures are designed so as to achieve a high efficiency of the nonlinear process.

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation

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

Xu, Kai; Olsen, Olav; Tzvetkova-Robev, Dorothea

The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

Nucleic acid binding drugs. Part XIII. Molecular motion in a drug-nucleic acid model system: thermal motion analysis of a proflavine-dinucleoside crystal structure.

PubMed Central

Aggarwal, A K; Neidle, S

1985-01-01

The high-resolution crystal structure of the intercalation complex between proflavine and cytidylyl-3',5'-guanosine (CpG) has been studied by thermalmotion analysis. This has provided information on the translational and librational motions of individual groups in the complex. Many of these motions are similar to, though of larger magnitude than in uncomplexed dinucleosides. Pronounced librational effects were observed along the base pairs and in the plane of the drug chromophore. PMID:4034394

The crystal structure of DR6 in complex with the amyloid precursor protein provides insight into death receptor activation

DOE PAGES

Xu, Kai; Olsen, Olav; Tzvetkova-Robev, Dorothea; ...

2015-04-02

The amyloid precursor protein (APP) has garnered considerable attention due to its genetic links to Alzheimer's disease. Death receptor 6 (DR6) was recently shown to bind APP via the protein extracellular regions, stimulate axonal pruning, and inhibit synapse formation. Here, we report the crystal structure of the DR6 ectodomain in complex with the E2 domain of APP and show that it supports a model for APP-induced dimerization and activation of cell surface DR6.

Hybrid transfer-matrix FDTD method for layered periodic structures.

PubMed

Deinega, Alexei; Belousov, Sergei; Valuev, Ilya

2009-03-15

A hybrid transfer-matrix finite-difference time-domain (FDTD) method is proposed for modeling the optical properties of finite-width planar periodic structures. This method can also be applied for calculation of the photonic bands in infinite photonic crystals. We describe the procedure of evaluating the transfer-matrix elements by a special numerical FDTD simulation. The accuracy of the new method is tested by comparing computed transmission spectra of a 32-layered photonic crystal composed of spherical or ellipsoidal scatterers with the results of direct FDTD and layer-multiple-scattering calculations.

Ultra-structural defects cause low bone matrix stiffness despite high mineralization in osteogenesis imperfecta mice☆

PubMed Central

Vanleene, Maximilien; Porter, Alexandra; Guillot, Pascale-Valerie; Boyde, Alan; Oyen, Michelle; Shefelbine, Sandra

2012-01-01

Bone is a complex material with a hierarchical multi-scale organization from the molecule to the organ scale. The genetic bone disease, osteogenesis imperfecta, is primarily caused by mutations in the collagen type I genes, resulting in bone fragility. Because the basis of the disease is molecular with ramifications at the whole bone level, it provides a platform for investigating the relationship between structure, composition, and mechanics throughout the hierarchy. Prior studies have individually shown that OI leads to: 1. increased bone mineralization, 2. decreased elastic modulus, and 3. smaller apatite crystal size. However, these have not been studied together and the mechanism for how mineral structure influences tissue mechanics has not been identified. This lack of understanding inhibits the development of more accurate models and therapies. To address this research gap, we used a mouse model of the disease (oim) to measure these outcomes together in order to propose an underlying mechanism for the changes in properties. Our main finding was that despite increased mineralization, oim bones have lower stiffness that may result from the poorly organized mineral matrix with significantly smaller, highly packed and disoriented apatite crystals. Using a composite framework, we interpret the lower oim bone matrix elasticity observed as the result of a change in the aspect ratio of apatite crystals and a disruption of the crystal connectivity. PMID:22449447

Ultra-structural defects cause low bone matrix stiffness despite high mineralization in osteogenesis imperfecta mice.

PubMed

Vanleene, Maximilien; Porter, Alexandra; Guillot, Pascale-Valerie; Boyde, Alan; Oyen, Michelle; Shefelbine, Sandra

2012-06-01

Bone is a complex material with a hierarchical multi-scale organization from the molecule to the organ scale. The genetic bone disease, osteogenesis imperfecta, is primarily caused by mutations in the collagen type I genes, resulting in bone fragility. Because the basis of the disease is molecular with ramifications at the whole bone level, it provides a platform for investigating the relationship between structure, composition, and mechanics throughout the hierarchy. Prior studies have individually shown that OI leads to: 1. increased bone mineralization, 2. decreased elastic modulus, and 3. smaller apatite crystal size. However, these have not been studied together and the mechanism for how mineral structure influences tissue mechanics has not been identified. This lack of understanding inhibits the development of more accurate models and therapies. To address this research gap, we used a mouse model of the disease (oim) to measure these outcomes together in order to propose an underlying mechanism for the changes in properties. Our main finding was that despite increased mineralization, oim bones have lower stiffness that may result from the poorly organized mineral matrix with significantly smaller, highly packed and disoriented apatite crystals. Using a composite framework, we interpret the lower oim bone matrix elasticity observed as the result of a change in the aspect ratio of apatite crystals and a disruption of the crystal connectivity. Copyright © 2012 Elsevier Inc. All rights reserved.

Temperature Dependence of Density, Viscosity and Electrical Conductivity for Hg-Based II-VI Semiconductor Melts

NASA Technical Reports Server (NTRS)

Li, C.; Ban, H.; Lin, B.; Scripa, R. N.; Su, C.-H.; Lehoczky, S. L.

2004-01-01

The relaxation phenomenon of semiconductor melts, or the change of melt structure with time, impacts the crystal growth process and the eventual quality of the crystal. The thermophysical properties of the melt are good indicators of such changes in melt structure. Also, thermophysical properties are essential to the accurate predication of the crystal growth process by computational modeling. Currently, the temperature dependent thermophysical property data for the Hg-based II-VI semiconductor melts are scarce. This paper reports the results on the temperature dependence of melt density, viscosity and electrical conductivity of Hg-based II-VI compounds. The melt density was measured using a pycnometric method, and the viscosity and electrical conductivity were measured by a transient torque method. Results were compared with available published data and showed good agreement. The implication of the structural changes at different temperature ranges was also studied and discussed.

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.

Neutron diffraction study of antiferromagnetic ErNi3Ga9 in magnetic fields

NASA Astrophysics Data System (ADS)

Ninomiya, Hiroki; Sato, Takaaki; Matsumoto, Yuji; Moyoshi, Taketo; Nakao, Akiko; Ohishi, Kazuki; Kousaka, Yusuke; Akimitsu, Jun; Inoue, Katsuya; Ohara, Shigeo

2018-05-01

We report specific heat, magnetization, magnetoresistance, and neutron diffraction measurements of single crystals of ErNi3Ga9. This compound crystalizes in a chiral structure with space group R 32 . The erbium ions form a two-dimensional honeycomb structure. ErNi3Ga9 displays antiferromagnetic order below 6.4 K. We determined that the magnetic structure is slightly amplitude-modulated as well as antiferromagnetic with q = (0 , 0 , 0.5) . The magnetic properties are described by an Ising-like model in which the magnetic moment is always along the c-axis owing to the large uniaxial anisotropy caused by the crystalline electric field effect in the low temperature region. When the magnetic field is applied along the c-axis, a metamagnetic transition is observed around 12 kOe at 2 K. ErNi3Ga9 possesses crystal chirality, but the antisymmetric magnetic interaction, the so-called Dzyaloshinskii-Moriya (DM) interaction, does not contribute to the magnetic structure, because the magnetic moments are parallel to the DM-vector.

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

Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation

DOE PAGES

Kim, Jeong Joo; Lorenz, Robin; Arold, Stefan T.; ...

2016-04-07

Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Here, although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-raymore » scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG.« less

The random field Blume-Capel model revisited

NASA Astrophysics Data System (ADS)

Santos, P. V.; da Costa, F. A.; de Araújo, J. M.

2018-04-01

We have revisited the mean-field treatment for the Blume-Capel model under the presence of a discrete random magnetic field as introduced by Kaufman and Kanner (1990). The magnetic field (H) versus temperature (T) phase diagrams for given values of the crystal field D were recovered in accordance to Kaufman and Kanner original work. However, our main goal in the present work was to investigate the distinct structures of the crystal field versus temperature phase diagrams as the random magnetic field is varied because similar models have presented reentrant phenomenon due to randomness. Following previous works we have classified the distinct phase diagrams according to five different topologies. The topological structure of the phase diagrams is maintained for both H - T and D - T cases. Although the phase diagrams exhibit a richness of multicritical phenomena we did not found any reentrant effect as have been seen in similar models.

Studies on Aspirin Crystals Generated by a Modified Vapor Diffusion Method.

PubMed

Mittal, Amit; Malhotra, Deepak; Jain, Preeti; Kalia, Anupama; Shunmugaperumal, Tamilvanan

2016-08-01

The objectives of the current investigation were (1) to study the influence of selected two different non-solvents (diethylether and dichloromethane) on the drug crystal formation of a model drug, aspirin (ASP-I) by the modified vapor diffusion method and (2) to characterize and compare the generated crystals (ASP-II and ASP-III) using different analytical techniques with that of unprocessed ASP-I. When compared to the classical vapor diffusion method which consumes about 15 days to generate drug crystals, the modified method needs only 12 h to get the same. Fourier transform-infrared spectroscopy (FT-IR) reveals that the internal structures of ASP-II and ASP-III crystals were identical when compared with ASP-I. Although the drug crystals showed a close similarity in X-ray diffraction patterns, the difference in the relative intensities of some of the diffraction peaks (especially at 2θ values of around 7.7 and 15.5) could be attributed to the crystal habit or crystal size modification. Similarly, the differential scanning calorimetry (DSC) study speculates that only the crystal habit modifications might occur but without involving any change in internal structure of the generated drug polymorphic form I. This is further substantiated from the scanning electron microscopy (SEM) pictures that indicated the formation of platy shape for the ASP-II crystals and needle shape for the ASP-III crystals. In addition, the observed slow dissolution of ASP crystals should indicate polymorph form I formation. Thus, the modified vapor diffusion method could routinely be used to screen and legally secure all possible forms of other drug entities too.

Crystallization, structural relaxation and thermal degradation in Poly(L-lactide)/cellulose nanocrystal renewable nanocomposites.

PubMed

Lizundia, E; Vilas, J L; León, L M

2015-06-05

In this work, crystallization, structural relaxation and thermal degradation kinetics of neat Poly(L-lactide) (PLLA) and its nanocomposites with cellulose nanocrystals (CNC) and CNC-grafted-PLLA (CNC-g-PLLA) have been studied. Although crystallinity degree of nanocomposites remains similar to that of neat homopolymer, results reveal an increase on the crystallization rate by 1.7-5 times boosted by CNC, which act as nucleating agents during the crystallization process. In addition, structural relaxation kinetics of PLLA chains has been drastically reduced by 53% and 27% with the addition of neat and grafted CNC, respectively. The thermal degradation activation energy (E) has been determined from thermogravimetric analysis in the light of Kissinger's and Ozawa-Flynn-Wall theoretical models. Results reveal a reduction on the thermal stability when in presence of CNC-g-PLLA, while raw CNC slightly increases the thermal stability of PLLA. Fourier transform infrared spectroscopy and energy dispersive X-ray spectroscopy results confirm that the presence of residual catalyst in CNC-g-PLLA plays a pivotal role in the thermal degradation behavior of nanocomposites. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

DOE PAGES

Taddei, Keith M.; Sturza, M.; Chung, Duck -Yung; ...

2015-09-14

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate frommore » the majority phase. In order to better understand this minority phase, a series of high-quality Cs xFe 2–ySe 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.« less

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

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

Taddei, K. M.; Sturza, M.; Chung, D. Y.

2015-09-01

By simultaneously displaying magnetism and superconductivity in a single phase, the iron based superconductors provide a model system for the study of magnetism’s role in superconductivity. The class of intercalated iron selenide superconductors is unique amongst these in having the additional property of phase separation and coexistence of two distinct phases - one majority phase with iron vacancy ordering and strong antiferromagnetism and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfullymore » synthesized separate from the majority phase. In order to better understand this minority phase, a series of high quality CsxFe2-ySe2 single crystals with (0.8 ≤ x ≤ 1; 0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show the average structure of the minority phase to be I4/mmm, however, the temperature evolution of its lattice parameters shows it to be distinct from the high temperature I4/mmm parent structure. Neutron and x-ray diffraction experiments performed on single crystal samples reveal the presence of previously unobserved discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body-centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from a three-dimensional Cs vacancy ordering in the minority phase. This model predicts a 25% vacancy of the Cs site which is consistent with the site’s refined occupancy. Magnetization measurements performed in tandem with neutron single crystal diffraction provide evidence that the minority phase is the host of superconductivity. Our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the valence of iron.« less

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.

Growing Larger Crystals for Neutron Diffraction

NASA Technical Reports Server (NTRS)

Pusey, Marc

2003-01-01

Obtaining crystals of suitable size and high quality has been a major bottleneck in macromolecular crystallography. With the advent of advanced X-ray sources and methods the question of size has rapidly dwindled, almost to the point where if one can see the crystal then it was big enough. Quality is another issue, and major national and commercial efforts were established to take advantage of the microgravity environment in an effort to obtain higher quality crystals. Studies of the macromolecule crystallization process were carried out in many labs in an effort to understand what affected the resultant crystal quality on Earth, and how microgravity improved the process. While technological improvements are resulting in a diminishing of the minimum crystal size required, neutron diffraction structural studies still require considerably larger crystals, by several orders of magnitude, than X-ray studies. From a crystal growth physics perspective there is no reason why these 'large' crystals cannot be obtained: the question is generally more one of supply than limitations mechanism. This talk will discuss our laboratory s current model for macromolecule crystal growth, with highlights pertaining to the growth of crystals suitable for neutron diffraction studies.

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

Ramadhar, Timothy R.; Zheng, Shao-Liang; Chen, Yu-Sheng

This report describes complete practical guidelines and insights for the crystalline sponge method, which have been derived through the first use of synchrotron radiation on these systems, and includes a procedure for faster synthesis of the sponges. These guidelines will be applicable to crystal sponge data collected at synchrotrons or in-house facilities, and will allow researchers to obtain reliable high-quality data and construct chemically and physically sensible models for guest structural determination. A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported.more » The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.« less

Magmatic structures in the Krkonoše Jizera Plutonic Complex, Bohemian Massif: evidence for localized multiphase flow and small-scale thermal mechanical instabilities in a granitic magma chamber

NASA Astrophysics Data System (ADS)

Žák, Jiří; Klomínský, Josef

2007-08-01

The present paper examines magmatic structures in the Jizera and Liberec granites of the Krkonoše-Jizera Plutonic Complex, Bohemian Massif. The magmatic structures are here interpreted to preserve direct field evidence for highly localized magma flow and other processes in crystal-rich mushes, and to capture the evolution of physical processes in an ancient granitic magma chamber. We propose that after chamber-wide mixing and hybridization, as suggested by recent petrological studies, laminar magma flow became highly localized to weaker channel-like domains within the higher-strength crystal framework. Mafic schlieren formed at flow rims, and their formation presumably involved gravitational settling and velocity gradient flow sorting coupled with interstitial melt escape. Local thermal or compositional convection may have resulted in the formation of vertical schlieren tubes and ladder dikes whereas subhorizontal tubes or channels formed during flow driven by lateral gradients in magma pressure. After the cessation or deceleration of channel flow, gravity-driven processes (settling of crystals and enclaves, gravitational differentiation, development of downward dripping instabilities), accompanied by compaction, filter pressing and melt segregation, dominated in the crystal mush within the flow channels. Subsequently, magmatic folds developed in schlieren layers and the magma chamber recorded complex, late magmatic strains at high magma crystallinities. Late-stage magma pulsing into localized submagmatic cracks represents the latest events of magmatic history of the chamber prior to its final crystallization. We emphasize that the most favorable environments for the formation and preservation of magmatic structures, such as those hosted in the Jizera and Liberec granites, are slowly cooling crystal-rich mushes. Therefore, where preserved in plutons, these structures may lend strong support for a "mush model" of magmatic systems.

Crystal structure of an orthomyxovirus matrix protein reveals mechanisms for self-polymerization and membrane association.

PubMed

Zhang, Wenting; Zheng, Wenjie; Toh, Yukimatsu; Betancourt-Solis, Miguel A; Tu, Jiagang; Fan, Yanlin; Vakharia, Vikram N; Liu, Jun; McNew, James A; Jin, Meilin; Tao, Yizhi J

2017-08-08

Many enveloped viruses encode a matrix protein. In the influenza A virus, the matrix protein M1 polymerizes into a rigid protein layer underneath the viral envelope to help enforce the shape and structural integrity of intact viruses. The influenza virus M1 is also known to mediate virus budding as well as the nuclear export of the viral nucleocapsids and their subsequent packaging into nascent viral particles. Despite extensive studies on the influenza A virus M1 (FLUA-M1), only crystal structures of its N-terminal domain are available. Here we report the crystal structure of the full-length M1 from another orthomyxovirus that infects fish, the infectious salmon anemia virus (ISAV). The structure of ISAV-M1 assumes the shape of an elbow, with its N domain closely resembling that of the FLUA-M1. The C domain, which is connected to the N domain through a flexible linker, is made of four α-helices packed as a tight bundle. In the crystal, ISAV-M1 monomers form infinite 2D arrays with a network of interactions involving both the N and C domains. Results from liposome flotation assays indicated that ISAV-M1 binds membrane via electrostatic interactions that are primarily mediated by a positively charged surface loop from the N domain. Cryoelectron tomography reconstruction of intact ISA virions identified a matrix protein layer adjacent to the inner leaflet of the viral membrane. The physical dimensions of the virion-associated matrix layer are consistent with the 2D ISAV-M1 crystal lattice, suggesting that the crystal lattice is a valid model for studying M1-M1, M1-membrane, and M1-RNP interactions in the virion.

William Barlow and the Determination of Atomic Arrangement in Crystals.

PubMed

Mauskopf, Seymour H

2015-04-01

William Barlow (1845-1934) was an important if unconventional scientist, known for having developed the 'closest-packing' atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the 'success' of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

Crystal structure control of aluminized clay minerals on the mobility of caesium in contaminated soil environments

NASA Astrophysics Data System (ADS)

Dzene, Liva; Ferrage, Eric; Viennet, Jean-Christophe; Tertre, Emmanuel; Hubert, Fabien

2017-02-01

Radioactive caesium pollution resulting from Fukushima Dai-ichi and Chernobyl nuclear plant accidents involves strong interactions between Cs+ and clays, especially vermiculite-type minerals. In acidic soil environments, such as in Fukushima area, vermiculite is subjected to weathering processes, resulting in aluminization. The crystal structure of aluminized clays and its implications for Cs+ mobility in soils remain poorly understood due to the mixture of these minerals with other clays and organic matter. We performed acidic weathering of a vermiculite to mimic the aluminization process in soils. Combination of structure analysis and Cs+ extractability measurements show that the increase of aluminization is accompanied by an increase in Cs+ mobility. Crystal structure model for aluminized vermiculite is based on the interstratification of unaltered vermiculite layers and aluminized layers within the same particle. Cs+ in vermiculite layers is poorly mobile, while the extractability of Cs+ is greatly enhanced in aluminized layers. The overall reactivity of the weathered clay (cation exchange capacity, Cs+ mobility) is then governed by the relative abundance of the two types of layers. The proposed layer model for aluminized vermiculite with two coexisting populations of caesium is of prime importance for predicting the fate of caesium in contaminated soil environments.

Modulus and yield stress of drawn LDPE

NASA Astrophysics Data System (ADS)

Thavarungkul, Nandh

Modulus and yield stress were investigated in drawn low density polyethylene (LDPE) film. Uniaxially drawn polymeric films usually show high values of modulus and yield stress, however, studies have normally only been conducted to identify the structural features that determine modulus. In this study small-angle x-ray scattering (SAXS), thermal shrinkage, birefringence, differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA) were used to examine, directly and indirectly, the structural features that determine both modulus and yield stress, which are often closely related in undrawn materials. Shish-kebab structures are proposed to account for the mechanical properties in drawn LDPE. The validity of this molecular/morphological model was tested using relationships between static mechanical data and structural and physical parameters. In addition, dynamic mechanical results are also in line with static data in supporting the model. In the machine direction (MD), "shish" and taut tie molecules (TTM) anchored in the crystalline phase account for E; whereas crystal lamellae with contributions from "shish" and TTM determine yield stress. In the transverse direction (TD), the crystalline phase plays an important roll in both modulus and yield stress. Modulus is determined by crystal lamellae functioning as platelet reinforcing elements in the amorphous matrix with an additional contributions from TTM and yield stress is determined by the crystal lamellae's resistance to deformation.

Reply to “Structural and magnetic behavior of the cubic oxyfluoride SrFeO{sub 2}F studied by neutron diffraction”

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

Clemens, Oliver, E-mail: oliver.clemens@kit.edu; Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen; Berry, Frank J.

2015-03-15

In this article we comment on the results published by Thompson et al. (, J. Solid State Chem. 219 (2014) 173–178) on the crystal structure of SrFeO{sub 2}F, who claim the compound to crystallize in the cubic space group Pm-3m. We give a more detailed explanation of the determination of our previously reported structural model with Imma symmetry (Clemens et al., J. Solid State Chem. 206 (2013) 158–169), with addition of variable temperature XRD measurements with high counting time to provide unambiguous evidence for the Imma model being correct for our sample. - Graphical abstract: The crystal structure of SrFeO{submore » 2}F is discussed with regards to previous reports. - Highlights: • SrFeO{sub 2}F was synthesized by polymer based fluorination of SrFeO{sub 3}. • Evaluation of the diffraction data shows a pseudocubic cell metric. • Superstructure reflections at low d-spacings indicate deviation from cubic symmetry. • The phase transition temperature from orthorhombic to cubic was determined using variable temperature X-ray diffraction. • Results published by Thompson et al. are critically discussed with respect to those observations.« less

Current trends in protein crystallization.

PubMed

Gavira, José A

2016-07-15

Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale. Copyright © 2015 Elsevier Inc. All rights reserved.

Structural models of the MscL gating mechanism

NASA Technical Reports Server (NTRS)

Sukharev, S.; Durell, S. R.; Guy, H. R.

2001-01-01

Three-dimensional structural models of the mechanosensitive channel of large conductance, MscL, from the bacteria Mycobacterium tuberculosis and Escherichia coli were developed for closed, intermediate, and open conformations. The modeling began with the crystal structure of M. tuberculosis MscL, a homopentamer with two transmembrane alpha-helices, M1 and M2, per subunit. The first 12 N-terminal residues, not resolved in the crystal structure, were modeled as an amphipathic alpha-helix, called S1. A bundle of five parallel S1 helices are postulated to form a cytoplasmic gate. As membrane tension induces expansion, the tilts of M1 and M2 are postulated to increase as they move away from the axis of the pore. Substantial expansion is postulated to occur before the increased stress in the S1 to M1 linkers pulls the S1 bundle apart. During the opening transition, the S1 helices and C-terminus amphipathic alpha-helices, S3, are postulated to dock parallel to the membrane surface on the perimeter of the complex. The proposed gating mechanism reveals critical spatial relationships between the expandable transmembrane barrel formed by M1 and M2, the gate formed by S1 helices, and "strings" that link S1s to M1s. These models are consistent with numerous experimental results and modeling criteria.

Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges

PubMed Central

Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

2015-01-01

Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca2+-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca2+-binding sites of Ca2+-ATPase and that of the iron atom in the heme in catalase. PMID:25730881

Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

PubMed

Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

2015-03-17

Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

NH2-terminal sequence truncation decreases the stability of bovine rhodanese, minimally perturbs its crystal structure, and enhances interaction with GroEL under native conditions.

PubMed

Trevino, R J; Gliubich, F; Berni, R; Cianci, M; Chirgwin, J M; Zanotti, G; Horowitz, P M

1999-05-14

The NH2-terminal sequence of rhodanese influences many of its properties, ranging from mitochondrial import to folding. Rhodanese truncated by >9 residues is degraded in Escherichia coli. Mutant enzymes with lesser truncations are recoverable and active, but they show altered active site reactivities (Trevino, R. J., Tsalkova, T., Dramer, G., Hardesty, B., Chirgwin, J. M., and Horowitz, P. M. (1998) J. Biol. Chem. 273, 27841-27847), suggesting that the NH2-terminal sequence stabilizes the overall structure. We tested aspects of the conformations of these shortened species. Intrinsic and probe fluorescence showed that truncation decreased stability and increased hydrophobic exposure, while near UV CD suggested altered tertiary structure. Under native conditions, truncated rhodanese bound to GroEL and was released and reactivated by adding ATP and GroES, suggesting equilibrium between native and non-native conformers. Furthermore, GroEL assisted folding of denatured mutants to the same extent as wild type, although at a reduced rate. X-ray crystallography showed that Delta1-7 crystallized isomorphously with wild type in polyethyleneglycol, and the structure was highly conserved. Thus, the missing NH2-terminal residues that contribute to global stability of the native structure in solution do not significantly alter contacts at the atomic level of the crystallized protein. The two-domain structure of rhodanese was not significantly altered by drastically different crystallization conditions or crystal packing suggesting rigidity of the native rhodanese domains and the stabilization of the interdomain interactions by the crystal environment. The results support a model in which loss of interactions near the rhodanese NH2 terminus does not distort the folded native structure but does facilitate the transition in solution to a molten globule state, which among other things, can interact with molecular chaperones.

Nonclassical crystallization in vivo et in vitro (II): Nanogranular features in biomimetic minerals disclose a general colloid-mediated crystal growth mechanism.

PubMed

Rodríguez-Navarro, Carlos; Ruiz-Agudo, Encarnación; Harris, Joe; Wolf, Stephan E

2016-11-01

Recent research has shown that biominerals and their biomimetics (i) typically form via an amorphous precursor phase, and (ii) commonly display a nanogranular texture. Apparently, these two key features are closely related, underlining the fact that the formation of biominerals and their biomimetics does not necessarily follow classical crystallization routes, and leaves a characteristic nanotextural imprint which may help to disclose their origins and formation mechanisms. Here we present a general overview of the current theories and models of nonclassical crystallization and their applicability for the advance of our current understanding of biomineralization and biomimetic mineralization. We pay particular attention to the link between nonclassical crystallization routes and the resulting nanogranular textures of biomimetic CaCO 3 mineral structures. After a general introductory section, we present an overview of classical nucleation and crystal growth theories and their limitations. Then, we introduce the Ostwald's step rule as a general framework to explain nonclassical crystallization. Subsequently, we describe nonclassical crystallization routes involving stable prenucleation clusters, dense liquid and solid amorphous precursor phases, as well as current nonclassical crystal growth models. The latter include oriented attachment, mesocrystallization and the new model based on the colloidal growth of crystals via attachment of amorphous nanoparticles. Biomimetic examples of nanostructured CaCO 3 minerals formed via these nonclassical routes are presented which help us to show that colloid-mediated crystal growth can be regarded as a wide-spread growth mechanism. Implications of these observations for the advance in the current understanding on the formation of biomimetic materials and biominerals are finally outlined. Copyright © 2016 Elsevier Inc. All rights reserved.

A Bullet-Shaped Tray To Demonstrate the Particle Model of Matter.

ERIC Educational Resources Information Center

Douma, Sander

1999-01-01

Describes a model that (1) convincingly demonstrates a particle model of gas behavior, (2) can be used by students, (3) can be mass produced, and (4) illustrates other properties of matter such as simple crystal structures and states of matter. (WRM)

Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with Alpha-Alpha Domain Architecture that Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence

PubMed Central

Harris, Golda G.; Lombardi, Patrick M.; Pemberton, Travis A.; Matsui, Tsutomu; Weiss, Thomas M.; Cole, Kathryn E.; Köksal, Mustafa; Murphy, Frank V.; Vedula, L. Sangeetha; Chou, Wayne K.W.; Cane, David E.; Christianson, David W.

2015-01-01

Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with 3 Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed based on ~36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis. PMID:26598179

The influence of the long-range order on the vibrational spectra of structures based on sodalite cage.

PubMed

Mikuła, A; Król, M; Koleżyński, A

2015-06-05

Zeolites are a group of tecto-aluminosilicates with numerous practical applications, e.g. gas separators, molecular sieves and sorbents. The unique properties result from porous structure of channels and cages which are built from smaller units - the so-called Secondary Building Units (SBU), and sometimes also larger groups (Breck, 1974; Ciciszwili et al., 1974; Mozgawa, 2008; Čejka and van Bekkum, 2005). The aim of this study was the examination of the influence of long-range order on vibrational spectra of sodalite and zeolite A. Ab initio calculations (geometry optimizations and vibrational spectra calculations) of sodalite cage and selected SBU were carried out by means of Gaussian09 (Frisch et al., 2009) (in the case of isolated clusters) and Crystal09 (Dovesi et al., 2005, 2009) (for periodic structures). The obtained results were compared with the experimental spectra of sodalite and zeolite A crystal structures, synthesized under hydrothermal conditions. These results allowed analyzing of the long-range ordering influence on the vibrational spectra, as well as the identification of the characteristic vibrations in β cage based frameworks. It has been found, that based on small structural fragment (SBU) models a characteristic vibrations can be identify. However, full spectra analysis and especially the interpretation of far-infrared region of the spectra require using periodic models under the influence of translational crystal lattice. Copyright © 2015 Elsevier B.V. All rights reserved.

Diffusion paths formation for Cu{sup +} ions in superionic Cu{sub 6}PS{sub 5}I single crystals studied in terms of structural phase transition

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

Gagor, A.; Pietraszko, A.; Kaynts, D.

2005-11-15

In order to understand the structural transformations leading to high ionic conductivity of Cu{sup +} ions in Cu{sub 6}PS{sub 5}I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T{sub c}=(144-169)K Cu{sub 6}PS{sub 5}I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above T{sub c} delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43c (a{sup '}=19.528A, z=32). Finally, above T{sub 1}=274K increasing disordering of the Cu{sup +} ions heightens the symmetry to F-43m (a=9.794A, z=4). In this work,more » the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions (R{sub 1}=0.0397 for F-43c phase, and 0.0245 for F-43m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.« less

Modelling inhibition of avian aromatase by azole pesticides.

PubMed

Saxena, A K; Devillers, J; Bhunia, S S; Bro, E

2015-01-01

The potential effects of pesticides and their metabolites on the endocrine system are of major concern to wildlife and human health. In this context, the azole pesticides have earned special attention due to their cytochrome P450 aromatase inhibition potential. Cytochrome P450 aromatase (CYP19) catalyses the conversion of androstenedione and testosterone into oestrone and oestradiol, respectively. Thus, aromatase modulates the oestrogenic balance essential not only for females, but also for male physiology, including gonadal function. Its inhibition affects reproductive organs, fertility and sexual behaviour in humans and wildlife species. Several studies have shown that azole pesticides are able to inhibit human and fish aromatases but the information on birds is lacking. Consequently, it appeared to be of interest to estimate the aromatase inhibition of azoles in three different avian species, namely Gallus gallus, Coturnix coturnix japonica and Taeniopygia guttata. In the absence of the crystal structure of the aromatase enzyme in these bird species, homology models for the individual avian species were constructed using the crystal structure of human aromatase (hAr) (pdb: 3EQM) that showed high sequence similarity for G. gallus (82.0%), T. guttata (81.9%) and C. japonica (81.2%). A homology model with Oncorhynchus mykiss (81.9%) was also designed for comparison purpose. The homology-modelled aromatase for each avian and fish species and crystal structure of human aromatase were selected for docking 46 structurally diverse azoles and related compounds. We showed that the docking behaviour of the chemicals on the different aromatases was broadly the same. We also demonstrated that there was an acceptable level of correlation between the binding score values and the available aromatase inhibition data. This means that the homology models derived on bird and fish species can be used to approximate the potential inhibitory effects of azoles on their aromatase.

Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions

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

Krishnan, Vengadesan; Dwivedi, Prabhat; Kim, Brandon J.

The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. The crystal structure of a 75 kDa central fragment of GBS104, a tip pilin from the 2063V/R strain of Streptococcus agalactiae (group B streptococcus; GBS), is reported. In addition, a homology model of the remaining two domains of GBS104 was built and a model of full-length GBS104 was generated by combining the homology model (the N1 and N4 domains) and the crystal structure of the 75 kDa fragment (the N2 and N3 domains).more » This rod-shaped GBS104 model is constructed of three IgG-like domains (the N1, N2 and N4 domains) and one vWFA-like domain (the N3 domain). The N1 and N2 domains of GBS104 are assembled with distinct and remote segments contributed by the N- and C-termini. The metal-binding site in the N3 domain of GBS104 is in the closed/low-affinity conformation. Interestingly, this domain hosts two long arms that project away from the metal-binding site. Using site-directed mutagenesis, two cysteine residues that lock the N3 domain of GBS104 into the open/high-affinity conformation were introduced. Both wild-type and disulfide-locked recombinant proteins were tested for binding to extracellular matrix proteins such as collagen, fibronectin, fibrinogen and laminin, and an increase in fibronectin binding affinity was identified for the disulfide-locked N3 domain, suggesting that induced conformational changes may play a possible role in receptor binding.« less

Polarizable atomic multipole X-ray refinement: application to peptide crystals

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

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less