Crystal growth, structural, optical, spectral and thermal studies of tris(L-phenylalanine)L-phenylalaninium nitrate: a new organic nonlinear optical material.

PubMed

Prakash, M; Geetha, D; Lydia Caroline, M

2011-10-15

Tris(L-phenylalanine)L-phenylalaninium nitrate, C(9)H(12)NO(2)(+)·NO(3)(-)·3C(9)H(11)NO(2) (TPLPN), a new organic nonlinear optical material was grown from aqueous solution by slow evaporation solution growth at room temperature. The grown crystals were subjected to powder X-ray diffraction and single crystal X-ray diffraction studies to confirm the crystalline nature and crystal structure. The modes of vibration of different molecular groups present in TPLPN have been identified by FTIR spectral analysis. The presence of hydrogen and carbon in the grown crystal were confirmed by using proton and carbon nuclear magnetic resonance (NMR) spectral analyses. The optical transmission spectral study establishes good transmitting ability of the crystal in the entire visible region. The thermogravimetric (TG) and differential thermal analyses (DTA) were carried out to understand the thermal stability of the sample. The nonlinear optical property of the compound observed using Kurtz powder second harmonic generation test assets the suitability of the grown material for the frequency conversion of laser radiation of Nd:YAG. Copyright © 2011 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxin components in the Rieske nonhaem iron oxygenase carbazole 1,9a-dioxygenase

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

Matsuzawa, Jun; Aikawa, Hiroki; Umeda, Takashi

2014-09-25

A crystal was obtained of the complex between reduced terminal oxygenase and oxidized ferredoxin components of carbazole 1,9a-dioxygenase. The crystal belonged to space group P2{sub 1} and diffracted to 2.25 Å resolution. The initial reaction in bacterial carbazole degradation is catalyzed by carbazole 1,9a-dioxygenase, which consists of terminal oxygenase (Oxy), ferredoxin (Fd) and ferredoxin reductase components. The electron-transfer complex between reduced Oxy and oxidized Fd was crystallized at 293 K using the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant under anaerobic conditions. The crystal diffracted to a maximum resolution of 2.25 Å and belonged to space group P2{submore » 1}, with unit-cell parameters a = 97.3, b = 81.6, c = 116.2 Å, α = γ = 90, β = 100.1°. The V{sub M} value is 2.85 Å{sup 3} Da{sup −1}, indicating a solvent content of 56.8%.« less

Synthesis, growth, structural, thermal and optical studies of pyrrolidinium-2-carboxylate-4-nitrophenol single crystals.

PubMed

Swarna Sowmya, N; Sampathkrishnan, S; Vidyalakshmi, Y; Sudhahar, S; Mohan Kumar, R

2015-06-15

Organic nonlinear optical material, pyrrolidinium-2-carboxylate-4-nitrophenol (PCN) was synthesized and single crystals were grown by slow evaporation solution growth method. Single crystal X-ray diffraction analysis confirmed the structure and lattice parameters of PCN crystals. Infrared, Raman and NMR spectral analyses were used to elucidate the functional groups present in the compound. The thermal behavior of synthesized compound was studied by thermogravimetric and differential scanning calorimetry (TG-DSC) analyses. The photoluminescence property was studied by exciting the crystal at 360 nm. The relative second harmonic generation (SHG) efficiency of grown crystal was estimated by using Nd:YAG laser with fundamental wavelength of 1,064 nm. Copyright © 2015 Elsevier B.V. All rights reserved.

Growth and characterization of organic material 4-dimethylaminobenzaldehyde single crystal.

PubMed

Jebin, R P; Suthan, T; Rajesh, N P; Vinitha, G; Madhusoodhanan, U

2015-01-25

The organic material 4-dimethylaminobenzaldehyde single crystals were grown by slow evaporation technique. The grown crystal was confirmed by the single crystal and powder X-ray diffraction analyses. The functional groups of the crystal have been identified from the Fourier Transform Infrared (FTIR) and FT-Raman studies. The optical property of the grown crystal was analyzed by UV-Vis-NIR and photoluminescence (PL) spectral measurements. The thermal behavior of the grown crystal was analyzed by thermogravimetric (TG) and differential thermal analyses (DTA). Dielectric measurements were carried out with different frequencies by using parallel plate capacitor method. The third order nonlinear optical properties of 4-dimethylaminobenzaldehyde was measured by the Z-scan technique using 532 nm diode pumped continuous wave (CW) Nd:YAG laser. Copyright © 2014 Elsevier B.V. All rights reserved.

Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490(963-1138) domain of TamB from Escherichia coli.

PubMed

Josts, Inokentijs; Grinter, Rhys; Kelly, Sharon M; Mosbahi, Khedidja; Roszak, Aleksander; Cogdell, Richard; Smith, Brian O; Byron, Olwyn; Walker, Daniel

2014-09-01

TamB is a recently described inner membrane protein that, together with its partner protein TamA, is required for the efficient secretion of a subset of autotransporter proteins in Gram-negative bacteria. In this study, the C-terminal DUF490963-1138 domain of TamB was overexpressed in Escherichia coli K-12, purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the primitive trigonal space group P3121, with unit-cell parameters a = b = 57.34, c = 220.74 Å, and diffracted to 2.1 Å resolution. Preliminary secondary-structure and X-ray diffraction analyses are reported. Two molecules are predicted to be present in the asymmetric unit. Experimental phasing using selenomethionine-labelled protein will be undertaken in the future.

Screening and structural elucidation of the zwitterionic cocrystal o-picolinic acid with p-nitro aniline

NASA Astrophysics Data System (ADS)

Mekala, R.; Jagdish, P.; Mathammal, R.; Sangeetha, K.

2017-04-01

The cocrystal was screened by solvent drop grinding method and the crystals were grown by slow evaporation method at ambient conditions. The cocrystal formation of o-picolinic acid with p-nitro aniline was initially analysed by powder X-ray diffraction. Further the structural properties of the grown crystal were confirmed by the single X-ray diffraction which indicates that the cocrystal were connected by the strong N+sbnd H-⋯O hydrogen bond interaction. The cell parameters of the grown crystal were a = 14.2144(5) Å, b = 5.7558(2) Å, c = 16.0539(6) Å. The functional groups were identified using Fourier transform infrared and Raman spectral analysis. The excitation and emission state of the sample was analysed by the UV-Visible and Fluorescence studies. The red emission was observed from the Fluorescence studies. NMR studies revealed the chemical shift of the cocrystal. Thermal stability and its melting behaviour were studied by TGA and DSC analytical techniques. Electrical behaviour was studied using the dielectric studies. The intermolecular charge transfer within the molecule were analysed using HOMO- LUMO plots.

Crystal structure determination of new antimitotic agent bis(p-fluorobenzyl)trisulfide.

PubMed

An, Haoyun; Hu, Xiurong; Gu, Jianming; Chen, Linshen; Xu, Weiming; Mo, Xiaopeng; Xu, Wanhong; Wang, Xiaobo; Xu, Xiao

2008-01-01

The purpose of this research was to investigate the physical characteristics and crystalline structure of bis(p-fluorobenzyl)trisulfide, a new anti-tumor agent. Methods used included X-ray single crystal diffraction, X-ray powder diffraction (XRPD), Fourier-transform infrared (FT-IR) spectroscopy, differential scanning calorimetric (DSC) and thermogravimetric (TG) analyses. The findings obtained with X-ray single crystal diffraction showed that a monoclinic unit cell was a = 12.266(1) A, b = 4.7757(4) A, c = 25.510(1) A, beta = 104.25(1) degrees ; cell volume = 1,448.4(2) A(3), Z = 4, and space group C2/c. The XRPD studies of the four crystalline samples, obtained by recrystallization from four different solvents, indicated that they had the same diffraction patterns. The diffraction pattern stimulated from the crystal structure data is in excellent agreement with the experimental results. In addition, the identical FT-IR spectra of the four crystalline samples revealed absorption bands corresponding to S-S and C-S stretching as well as the characteristic aromatic substitution. Five percent weight loss at 163.3 degrees C was observed when TG was used to study the decomposition process in the temperature range of 20-200 degrees C. DSC also allowed for the determination of onset temperatures at 60.4(1)-60.7(3) degrees C and peak temperatures at 62.1(3)-62.4(3) degrees C for the four crystalline samples studied. The results verified that the single crystal structure shared the same crystal form with the four crystalline samples investigated.

Syntheses, structural characterization, and DPPH radical scavenging activity of cocrystals of caffeine with 1- and 2-naphthoxyacetic acids

NASA Astrophysics Data System (ADS)

Suresh Kumar, G. S.; Seethalakshmi, P. G.; Sumathi, D.; Bhuvanesh, N.; Kumaresan, S.

2013-03-01

Caffeine:1-naphthoxyacetic acid [(caf)(1-naa)] and caffeine:2-naphthoxyacetic acid [(caf)(2-naa)] cocrystals have been synthesized and single crystals were grown by slow evaporation technique. The structures of the grown crystals were elucidated using single crystal X-ray diffraction analysis. Both the cocrystals belong to the monoclinic crystallographic system with space group P21/c, Z = 4, and α = γ = 90°, whereas β = 111.4244(18)° for [(caf)(1-naa)] and β = 109.281(6)° for [(caf)(2-naa)]. The crystal packing is predominantly stabilized by hydrogen bonding and π-π stacking interactions. The presence of unionized -COOH functional group in both the cocrystals was identified by FTIR spectral analysis. Thermal behavior and stability of both the cocrystals were studied by TGA/DTA analyses. Solvent-free formation of these cocrystals was confirmed by powder X-ray diffraction analyses. The theoretical energy of cocrystals showed that the formers have higher energy than cocrystals 1 and 2. DPPH radical scavenging activity of cocrystals 1 and 2 is slightly greater than the formers.

Crystal structure, thermal and optical properties of Benzimidazole benzimidazolium picrate crystal

NASA Astrophysics Data System (ADS)

Jagadesan, A.; Peramaiyan, G.; Srinivasan, T.; Kumar, R. Mohan; Arjunan, S.

2016-02-01

A new organic framework of benzimidazole with picric acid has been synthesized. A single crystal with a size of 38×10×4 mm3 was grown by a slow evaporation solution growth technique. X-ray diffraction study revealed that the BZP crystal belongs to triclinic system with space group P-1. High resolution X-ray diffraction study shows the absence of grain boundaries without any defects. The thermal stability and specific heat capacity of BZP were investigated by TG/DT and TG/DSC analyses. From the UV-vis-NIR spectral study, optical transmission window and band gap of BZP were found out. The nonlinear refractive index (n2) and third order susceptibility Re(χ(3)) values of BZP crystal are estimated to be 1.73×10-7 cm2/W and 1.26×10-5 esu, respectively using a Z-scan technique.

Synthesis, growth, structural, optical, spectral, thermal and mechanical studies of 4-methoxy 4-nitrostilbene (MONS): a new organic nonlinear optical single crystal.

PubMed

Dinakaran, Paul M; Bhagavannarayana, G; Kalainathan, S

2012-11-01

4-Methoxy 4-nitrostilbene (MONS), a new organic nonlinear optical material has been synthesized. Based on the solubility data good quality single crystal with dimensions up to 38×11×3 mm(3) has been grown by slow evaporation method using ethyl methyl ketone (MEK) as a solvent. Powder XRD confirms the crystalline property and also the diffraction planes have been indexed. The lattice parameters for the grown MONS crystals were determined by using single crystal X-ray diffraction analysis and it reveals that the crystal lattice system is triclinic. The crystalline perfection of the grown crystals has been analysed by high resolution X-ray diffraction (HRXRD) rocking curve measurements. Fourier transform infrared (FTIR) spectrum for powdered MONS sample confirms the functional groups present in the grown crystal. The UV-vis absorption spectrum has been recorded in the range of 190-1100 nm and the cut off wavelength 499 nm has been determined. The optical constants of MONS have been determined through UV-vis-NIR spectroscopy. The MONS crystals were further subjected to other characterizations. i.e., (1)H NMR, TG/DTA, photoluminescence and microhardness test. The Kurtz and Perry powder technique confirms the NLO property of the grown crystal and the SHG efficiency of MONS was found to be 1.55× greater than that of KDP crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

A Novel Coordination Polymer Based on Trinuclear Cobalt Building Blocks Cluster: Synthesis, Crystal Structure, and Properties

NASA Astrophysics Data System (ADS)

Lu, J. F.; Tang, Z. H.; Shi, J.; Ge, H. G.; Jiang, M.; Song, J.; Jin, L. X.

2017-12-01

The title compound {[Co3(μ3-OH)(μ2-H2O)2(H2O)5(BTC)2] · 6H2O} n (H3BTC is a 1,3,5-benzenetricarboxylic acid) was prepared and characterized by single crystal and powder X-ray diffraction, Fourier transform infrared spectroscopy, thermogravimetric and elemental analyses. The single crystal X-ray diffraction reveals that the title compound consists of 1D infinite zigzag chains which were constructed by trinuclear cobalt cluster and BTC3- ligand. Neighbouring above-mentioned 1D infinite zigzag chains are further linked by intermolecular hydrogen bonding to form a 3D supermolecular structure. In addition, the luminescent properties of the title compound were investigated.

Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

NASA Astrophysics Data System (ADS)

Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

2018-04-01

The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

Comparison of quartz crystallographic preferred orientations identified with optical fabric analysis, electron backscatter and neutron diffraction techniques.

PubMed

Hunter, N J R; Wilson, C J L; Luzin, V

2017-02-01

Three techniques are used to measure crystallographic preferred orientations (CPO) in a naturally deformed quartz mylonite: transmitted light cross-polarized microscopy using an automated fabric analyser, electron backscatter diffraction (EBSD) and neutron diffraction. Pole figure densities attributable to crystal-plastic deformation are variably recognizable across the techniques, particularly between fabric analyser and diffraction instruments. Although fabric analyser techniques offer rapid acquisition with minimal sample preparation, difficulties may exist when gathering orientation data parallel with the incident beam. Overall, we have found that EBSD and fabric analyser techniques are best suited for studying CPO distributions at the grain scale, where individual orientations can be linked to their source grain or nearest neighbours. Neutron diffraction serves as the best qualitative and quantitative means of estimating the bulk CPO, due to its three-dimensional data acquisition, greater sample area coverage, and larger sample size. However, a number of sampling methods can be applied to FA and EBSD data to make similar approximations. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Advanced Structural Analyses by Third Generation Synchrotron Radiation Powder Diffraction

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

Sakata, M.; Aoyagi, S.; Ogura, T.

2007-01-19

Since the advent of the 3rd generation Synchrotron Radiation (SR) sources, such as SPring-8, the capabilities of SR powder diffraction increased greatly not only in an accurate structure refinement but also ab initio structure determination. In this study, advanced structural analyses by 3rd generation SR powder diffraction based on the Large Debye-Scherrer camera installed at BL02B2, SPring-8 is described. Because of high angular resolution and high counting statistics powder data collected at BL02B2, SPring-8, ab initio structure determination can cope with a molecular crystals with 65 atoms including H atoms. For the structure refinements, it is found that a kindmore » of Maximum Entropy Method in which several atoms are omitted in phase calculation become very important to refine structural details of fairy large molecule in a crystal. It should be emphasized that until the unknown structure is refined very precisely, the obtained structure by Genetic Algorithm (GA) or some other ab initio structure determination method using real space structural knowledge, it is not possible to tell whether the structure obtained by the method is correct or not. In order to determine and/or refine crystal structure of rather complicated molecules, we cannot overemphasize the importance of the 3rd generation SR sources.« less

Syntheses, structures and properties of two new coordination polymers based on D-camphoric acid and 2-phenyl-4,6-diamino-1,3,5-triazine

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

Lun, Huijie; Yang, Jinghe; Jin, Linyu

2015-05-15

By hydrothermal method, two new coordination polymers [Co(ca)(phdat)]{sub n} (1), [Ni(ca)(phdat).0.125H{sub 2}O]{sub n} (2) (H{sub 2}ca=D-camphoric acid, phdat=2-phenyl-4,6-diamino-1,3,5-triazine) have been achieved and structurally characterized by IR, elemental analyses, X-ray single-crystal diffraction and TGA. The X-ray single-crystal diffraction reveals that compounds 1 and 2 are isostructural, both of which exhibit two-dimensional layered network built up from paddle-wheel Co{sub 2}(CO{sub 2}){sub 4}/Ni{sub 2}(CO{sub 2}){sub 4} SBUs by ca{sup 2−} ligand. In the existence of π…π stacking interactions between triazine rings and phenyl rings, the 3D networks are constructed with the hanging phdat filled between the neighboring layers. Furthermore, compounds 1–2 exhibit antiferromagneticmore » behavior and compound 2 displays a good activity for methanol oxidation. - Graphical abstract: Two new coordination compounds 1–2 have been synthesized and characterized by single-crystal X-ray diffractions, IR spectra, elemental analyses, thermogravimetric analyses, magnetic and electrochemical measurement. - Highlights: • This paper reports two new coordination polymers based on D-camphoric acid. • Both the compounds feather two-dimensional layered networks built up from paddle-wheel SBUs. • The magnetism and electrochemical property are investigated.« less

X-ray diffraction studies of enkephalins. Crystal structure of [(4'-bromo) Phe4,Leu5]enkephalin.

PubMed Central

Ishida, T; Kenmotsu, M; Mino, Y; Inoue, M; Fujiwara, T; Tomita, K; Kimura, T; Sakakibara, S

1984-01-01

In order to investigate the structure-activity relationship of [Leu5]- and [Met5]enkephalins, [(4'-bromo)Phe4, Leu5]-, [(4'-bromo)Phe4, Met5]- and [Met5] enkephalins were synthesized and crystallized. The crystal structure of [(4'-bromo) Phe4, Leu5]- enkephalin was determined by X-ray diffraction method using the heavy atom method and refined to R = 0.092 by the least-squares method. The molecule in this crystal took essentially the same type I' beta-turn conformation found in [Leu5]enkephalin [Smith & Griffin (1978) Science 199, 1214-1216). On the other hand, the preliminary three-dimensional Patterson analyses showed that the most probable conformations of [(4'-bromo)Phe4,Met5]- and [Met5]enkephalins are both the dimeric extended forms. Based on these insights, the biologically active conformation of enkephalin was discussed in relation to the mu- and delta-receptors. PMID:6721829

Synthesis, structural, spectroscopic and optical studies of charge transfer complex salts.

PubMed

Manikandan, Maruthappan; Mahalingam, Thaiyan; Hayakawa, Yasuhiro; Ravi, Ganesan

2013-01-15

New charge transfer molecular complex adducts of picric acid (C6H3N3O7) with triethylamine (C6H15N) and dimethylformamide (HCON(CH3)2) were synthesized successfully for the first time. Chemical composition and stoichiometry of the synthesized complex salts were verified by CHN elemental analysis. Solubility of the complex salts have been determined by gravimetric method and single crystals of two new salts were grown by low temperature solution growth technique. Crystal system, crystalline nature and cell parameters of the grown crystals were determined by single crystal X-ray diffraction (SXRD) and powder X-ray diffraction (PXRD) analyses. The formations of the charge-transfer complex, functional groups and the modes of vibrations have been confirmed by Fourier transform infrared (FTIR) spectroscopy. In order to know the linear and nonlinear optical suitability for device fabrication, UV-Vis (UV) spectral analysis and relative second harmonic generation (SHG) efficiency test were performed for the grown crystals. Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis, structural, spectroscopic and optical studies of charge transfer complex salts

NASA Astrophysics Data System (ADS)

Manikandan, Maruthappan; Mahalingam, Thaiyan; Hayakawa, Yasuhiro; Ravi, Ganesan

2013-01-01

New charge transfer molecular complex adducts of picric acid (C6H3N3O7) with triethylamine (C6H15N) and dimethylformamide (HCON(CH3)2) were synthesized successfully for the first time. Chemical composition and stoichiometry of the synthesized complex salts were verified by CHN elemental analysis. Solubility of the complex salts have been determined by gravimetric method and single crystals of two new salts were grown by low temperature solution growth technique. Crystal system, crystalline nature and cell parameters of the grown crystals were determined by single crystal X-ray diffraction (SXRD) and powder X-ray diffraction (PXRD) analyses. The formations of the charge-transfer complex, functional groups and the modes of vibrations have been confirmed by Fourier transform infrared (FTIR) spectroscopy. In order to know the linear and nonlinear optical suitability for device fabrication, UV-Vis (UV) spectral analysis and relative second harmonic generation (SHG) efficiency test were performed for the grown crystals.

Growth, structural, optical, thermal and mechanical properties of ammonium pentaborate single crystal.

PubMed

Balakrishnan, T; Bhagavannarayana, G; Ramamurthi, K

2008-11-15

Nonlinear optical single crystals of ammonium pentaborate (APB) were grown by the slow cooling method from aqueous solution. Grown crystal was characterized by powder X-ray diffraction (PXRD) and FT-IR spectral analysis. Perfection of the grown crystal was evaluated by high-resolution X-ray diffractometry (HRXRD). The effect of nylon threading on the perfection of the grown bigger crystal was also studied by HRXRD. The range and percentage of optical transmission was ascertained by recording UV-vis-NIR spectrum. Thermal properties were investigated by TG-DTA and DSC analyses. Its mechanical hardness was estimated by Vickers microhardness tester.

Growth and dielectric, mechanical, thermal and etching studies of an organic nonlinear optical L-arginine trifluoroacetate (LATF) single crystal

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

Arjunan, S.; Department of Physics, Presidency College, Chennai 600005; Mohan Kumar, R.

2008-08-04

L-arginine trifluoroacetate, an organic nonlinear optical material, has been synthesized from aqueous solution. Bulk single crystal of dimension 57 mm x 5 mm x 3 mm has been grown by temperature lowering technique. Powder X-ray diffraction studies confirmed the monoclinic structure of the grown L-arginine trifluoroacetate crystal. Linear optical property of the grown crystal has been studied by UV-vis spectrum. Dielectric response of the L-arginine trifluoroacetate crystal was analysed for different frequencies and temperatures in detail. Microhardness study on the sample reveals that the crystal possesses relatively higher hardness compared to many organic crystals. Thermal analyses confirmed that the L-argininemore » trifluoroacetate material is thermally stable upto 212 deg. C. The etching studies have been performed to assess the perfection of the L-arginine trifluoroacetate crystal. Kurtz powder second harmonic generation test confirms the nonlinear optical properties of the as-grown L-arginine trifluoroacetate crystal.« less

Synthesis, growth, structural and optical studies of a novel organic Piperazine (bis) p-toluenesulfonate single crystal.

PubMed

Rekha, P; Peramaiyan, G; NizamMohideen, M; Kumar, R Mohan; Kanagadurai, R

2015-03-15

A novel organic single crystal of Piperazinium (bis) p-toluenesulfonate (PPTS) was grown by a slow evaporation solution growth technique. The structure of the grown crystal was determined using single crystal X-ray diffraction analysis. The PPTS crystal belongs to the triclinic crystal system with space group of P1¯. The presence of functional groups was confirmed by FTIR spectral analysis. The optical transmittance range and cut-off wavelength were identified by UV-vis-NIR spectral studies. The luminescent properties of PPTS crystal were investigated. The thermal behavior of PPTS crystal was studied by TG-DT analyses. Copyright © 2014 Elsevier B.V. All rights reserved.

Reduction of glycine particle size by impinging jet crystallization.

PubMed

Tari, Tímea; Fekete, Zoltán; Szabó-Révész, Piroska; Aigner, Zoltán

2015-01-15

The parameters of crystallization processes determine the habit and particle size distribution of the products. A narrow particle size distribution and a small average particle size are crucial for the bioavailability of poorly water-soluble pharmacons. Thus, particle size reduction is often required during crystallization processes. Impinging jet crystallization is a method that results in a product with a reduced particle size due to the homogeneous and high degree of supersaturation at the impingement point. In this work, the applicability of the impinging jet technique as a new approach in crystallization was investigated for the antisolvent crystallization of glycine. A factorial design was applied to choose the relevant crystallization factors. The results were analysed by means of a statistical program. The particle size distribution of the crystallized products was investigated with a laser diffraction particle size analyser. The roundness and morphology were determined with the use of a light microscopic image analysis system and a scanning electron microscope. Polymorphism was characterized by differential scanning calorimetry and powder X-ray diffraction. Headspace gas chromatography was utilized to determine the residual solvent content. Impinging jet crystallization proved to reduce the particle size of glycine. The particle size distribution was appropriate, and the average particle size was an order of magnitude smaller (d(0.5)=8-35 μm) than that achieved with conventional crystallization (d(0.5)=82-680 μm). The polymorphic forms of the products were influenced by the solvent ratio. The quantity of residual solvent in the crystallized products was in compliance with the requirements of the International Conference on Harmonization. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.; Park, YongKeun

2014-01-01

We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

PubMed Central

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.

2013-01-01

Abstract. We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated. PMID:23797986

Crystal growth of carbonate apatite using a CaCO3 flux.

PubMed

Suetsugu, Y; Tanaka, J

1999-09-01

Single crystals of carbonate apatite were grown using a CaCO3 flux under an Ar gas pressure of 55 MPa. The crystals obtained were observed by scanning electron microscopy, optical microscopy and X-ray diffraction. Electron probe microanalyses and thermal analyses were performed. CO3 ions in planar triangle form replaced both OH sites and PO4 tetrahedral sites in the apatite structure: in particular, the OH sites were perfectly substituted by CO3 ions using this method.

Crystal growth, structural, optical, mechanical and thermal properties of a new nonlinear optical single crystal: L-Ornithine monohydrochloride.

PubMed

Balakrishnan, T; Ramamurthi, K

2009-03-01

Amino acid family crystals exhibit excellent nonlinear optical and electro optical properties. l-Ornithine monohydrochloride single crystal, belongs to the amino acid group, was grown by the slow evaporation solution growth technique at room temperature. The grown crystals were characterized by single crystal and powder X-ray diffraction analysis, Fourier transform infrared (FTIR) spectroscopy, TGA, DTA and DSC analyses. UV-vis-NIR spectrum shows excellent transmission in the UV, visible and NIR region (300-1600nm). The mechanical properties of grown crystals were studied using Vickers microhardness tester. Its second harmonic generation efficiency was tested using Nd:YAG laser and is 1.25 times that of KDP.

Solid-state reaction kinetics of neodymium doped magnesium hydrogen phosphate system

NASA Astrophysics Data System (ADS)

Gupta, Rashmi; Slathia, Goldy; Bamzai, K. K.

2018-05-01

Neodymium doped magnesium hydrogen phosphate (NdMHP) crystals were grown by using gel encapsulation technique. Structural characterization of the grown crystals has been carried out by single crystal X-ray diffraction (XRD) and it revealed that NdMHP crystals crystallize in orthorhombic crystal system with space group Pbca. Kinetics of the decomposition of the grown crystals has been studied by non-isothermal analysis. The estimation of decomposition temperatures and weight loss has been made from the thermogravimetric/differential thermo analytical (TG/DTA) in conjuncture with DSC studies. The various steps involved in the thermal decomposition of the material have been analysed using Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova equations for evaluating various kinetic parameters.

Vibrational spectra, powder X-ray diffractions and physical properties of cyanide complexes with 1-ethylimidazole

NASA Astrophysics Data System (ADS)

Kürkçüoğlu, Güneş Süheyla; Kiraz, Fulya Çetinkaya; Sayın, Elvan

2015-10-01

The heteronuclear tetracyanonickelate(II) complexes of the type [M(etim)Ni(CN)4]n (hereafter, abbreviated as M-Ni-etim, M = Mn(II), Fe(II) or Co(II); etim = 1-ethylimidazole, C5H8N2) were prepared in powder form and characterized by FT-IR and Raman spectroscopy, powder X-ray diffraction (PXRD), thermal (TG; DTG and DTA), and elemental analysis techniques. The structures of these complexes were elucidated using vibrational spectra and powder X-ray diffraction patterns with the peak assignment to provide a better understanding of the structures. It is shown that the spectra are consistent with a proposed crystal structure for these compounds derived from powder X-ray diffraction measurements. Vibrational spectra of the complexes were presented and discussed with respect to the internal modes of both the etim and the cyanide ligands. The C, H and N analyses were carried out for all the complexes. Thermal behaviors of these complexes were followed using TG, DTG and DTA curves in the temperature range 30-700 °C in the static air atmosphere. The FT-IR, Raman spectra, thermal and powder X-ray analyses revealed no significant differences between the single crystal and powder forms. Additionally, electrical and magnetic properties of the complexes were investigated. The FT-IR and Raman spectroscopy, PXRD, thermal and elemental analyses results propose that these complexes are similar in structure to the Hofmann-type complexes.

Multi-crystal native SAD analysis at 6 keV.

PubMed

Liu, Qun; Guo, Youzhong; Chang, Yanqi; Cai, Zheng; Assur, Zahra; Mancia, Filippo; Greene, Mark I; Hendrickson, Wayne A

2014-10-01

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.

Radiation damage and annealing in plutonium tetrafluoride

NASA Astrophysics Data System (ADS)

McCoy, Kaylyn; Casella, Amanda; Sinkov, Sergey; Sweet, Lucas; McNamara, Bruce; Delegard, Calvin; Jevremovic, Tatjana

2017-12-01

A sample of plutonium tetrafluoride that was separated prior to 1966 at the Hanford Site in Washington State was analyzed at the Pacific Northwest National Laboratory (PNNL) in 2015 and 2016. The plutonium tetrafluoride, as received, was an unusual color and considering the age of the plutonium, there were questions about the condition of the material. These questions had to be answered in order to determine the suitability of the material for future use or long-term storage. Therefore, thermogravimetric/differential thermal analysis and X-ray diffraction evaluations were conducted to determine the plutonium's crystal structure, oxide content, and moisture content; these analyses reported that the plutonium was predominately amorphous and tetrafluoride, with an oxide content near ten percent. Freshly fluorinated plutonium tetrafluoride is known to be monoclinic. During the initial thermogravimetric/differential thermal analyses, it was discovered that an exothermic event occurred within the material near 414 °C. X-ray diffraction analyses were conducted on the annealed tetrafluoride. The X-ray diffraction analyses indicated that some degree of recrystallization occurred in conjunction with the 414 °C event. The following commentary describes the series of thermogravimetric/differential thermal and X-ray diffraction analyses that were conducted as part of this investigation at PNNL.

X-ray characterization of curved crystals for hard x-ray astronomy

NASA Astrophysics Data System (ADS)

Buffagni, Elisa; Bonnini, Elisa; Ferrari, Claudio; Virgilli, Enrico; Frontera, Filippo

2015-05-01

Among the methods to focus photons the diffraction in crystals results as one of the most effective for high energy photons. An assembling of properly oriented crystals can form a lens able to focus x-rays at high energy via Laue diffraction in transmission geometry; this is a Laue lens. The x-ray diffraction theory provides that the maximum diffraction efficiency is achieved in ideal mosaic crystals, but real mosaic crystals show diffraction efficiencies several times lower than the ideal case due to technological problems. An alternative and convenient approach is the use of curved crystals. We have recently optimized an efficient method based on the surface damage of crystals to produce self-standing uniformly curved Si, GaAs and Ge tiles of thickness up to 2-3 mm and curvature radii R down to a few meters. We show that, for curved diffracting planes, such crystals have a diffraction efficiency nearly forty times higher than the diffraction efficiency of perfect similar flat crystals, thus very close to that of ideal mosaic crystals. Moreover, in an alternative configuration where the diffracting planes are perpendicular to the curved ones, a focusing effect occurs and will be shown. These results were obtained for several energies between 17 and 120 keV with lab sources or at high energy facilities such as LARIX at Ferrara (Italy), ESRF at Grenoble (France), and ANKA at Karlsruhe (Germany).

Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.

PubMed

San Martin, Fabiana; Mechaly, Ariel E; Larrieux, Nicole; Wunder, Elsio A; Ko, Albert I; Picardeau, Mathieu; Trajtenberg, Felipe; Buschiazzo, Alejandro

2017-03-01

The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.

Clay pigment structure characterisation as a guide for provenance determination--a comparison between laboratory powder micro-XRD and synchrotron radiation XRD.

PubMed

Švarcová, Silvie; Bezdička, Petr; Hradil, David; Hradilová, Janka; Žižak, Ivo

2011-01-01

Application of X-ray diffraction (XRD)-based techniques in the analysis of painted artworks is not only beneficial for indisputable identification of crystal constituents in colour layers, but it can also bring insight in material crystal structure, which can be affected by their geological formation, manufacturing procedure or secondary changes. This knowledge might be helpful for art historic evaluation of an artwork as well as for its conservation. By way of example of kaolinite, we show that classification of its crystal structure order based on XRD data is useful for estimation of its provenance. We found kaolinite in the preparation layer of a Gothic wall painting in a Czech church situated near Karlovy Vary, where there are important kaolin deposits. Comparing reference kaolin materials from eight various Czech deposits, we found that these can be differentiated just according to the kaolinite crystallinity. Within this study, we compared laboratory powder X-ray micro-diffraction (micro-XRD) with synchrotron radiation X-ray diffraction analysing the same real sample. We found that both techniques led to the same results.

Crystal Structure Variations of Sn Nanoparticles upon Heating

NASA Astrophysics Data System (ADS)

Mittal, Jagjiwan; Lin, Kwang-Lung

2018-04-01

Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

Phononic crystal diffraction gratings

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

A new series of lanthanide coordination polymers with 2,2‧-bipyridine and glutaric acid: Synthesis, crystal structures and properties of [Ln(bipy)(glut)(NO3)

NASA Astrophysics Data System (ADS)

Wang, Chunguang; Xing, Yongheng; Li, Zhangpeng; Li, Jing; Zeng, Xiaoqing; Ge, Maofa; Niu, Shuyun

2009-08-01

A series of new lanthanide coordination polymers, with the formula [Ln(bipy)(glut)(NO 3)] (Ln = Eu ( 1), Tb ( 2), Sm ( 3), Pr ( 4); bipy = 2,2'-bipyridine; H 2glut = glutaric acid), have been synthesized under the hydrothermal condition and characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction, and single-crystal X-ray diffraction. Structural analyses reveal that all four complexes are isostructural and crystallized in monoclinic system, P2 1/ c space group. For these complexes, the Ln 3+ are all linked through glutaric acid ligands to form 1D chain-like polymeric structures, and bipy and NO3- are coordinated on two sides of the chains. The thermogravimetric analysis of 1 and photoluminescent properties of 1 and 2 are discussed in detail.

Growth, optical, ICP and thermal studies of nonlinear optical single crystal: Sodium acid phthalate (NaAP)

NASA Astrophysics Data System (ADS)

Mahadevan, M.; Arivanandhan, M.; Elangovan, K.; Anandan, P.; Ramachandran, K.

2017-07-01

Good quality single crystals of sodium acid phthalate (NaAP) were grown by slow evaporation technique. Single crystal X-ray diffraction study of the grown crystal reveals that the crystal belongs to orthorhombic system with space group B2ab. Fourier transform infrared spectrum confirms the presence of the functional groups of the grown material. Inductively coupled plasma emission spectroscopy analysis is used to confirm the presence of Na element in the sample. Thermal analysis of the NaAP crystal shows that the crystal is stable up to 140°C. Optical transmittance of the grown crystal was recorded in the wavelength range from 200 and 800 nm using UV-Vis-NIR spectrophotometer. The second harmonic generation of NaAP was analysed using Kurtz powder technique.

Growth, density functional theory (DFT) and spectral studies on L-2-aminobutyric acid -biologically active material

NASA Astrophysics Data System (ADS)

Usha, C.; Santhakumari, R.; Meenakshi, R.; Jayasree, R.; Bhuvaneswari, M.

2017-12-01

Single crystal of L-2-aminobutyric acid (ABA) was grown from water by slow evaporation at room temperature. The crystalline nature of the grown crystal was confirmed using powder X-ray diffraction studies. The grown crystal was subjected to FT-IR, FT-Raman, 1H NMR and 13C NMR spectral analyses to confirm the presence of functional group and molecular structure respectively. Thermal properties were investigated by thermogravimetric and differential thermal analyses. The range and percentage of optical transmission was ascertained by recording UV-vis-NIR spectrum. The electronic charge distribution and reactivity of the molecules within the crystal were studied by HOMO and LUMO analysis and the molecular electrostatic potential (MEP) of the grown crystal was performed using the B3LYP method. The anti-bacterial activities of the crystal were performed by disk diffusion method against the standard bacteria E. coli. The crystal exhibits good anti-bacterial activity. Second harmonic generation efficiency of the powdered ABA crystal was tested using Nd:YAG laser and it is found to be ∼3.3 times that of potassium dihydrogen orthophosphate.

Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals

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

Frank, Matthias; Carlson, David B.; Hunter, Mark

2014-02-28

Here we present femtosecond x-ray diffraction patterns from two-dimensional (2-D) protein crystals using an x-ray free electron laser (XFEL). To date it has not been possible to acquire x-ray diffraction from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permits a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy methodology at the Linac Coherent Light Source, we observed Bragg diffraction to better than 8.5 Å resolution for two different 2-D protein crystal samples that were maintained at room temperature. These proof-of-principle results show promisemore » for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.« less

Structural, thermal and optical properties of a semiorganic nonlinear optical single crystal: glycine zinc sulphate.

PubMed

Balakrishnan, T; Ramamurthi, K

2007-10-01

Glycine zinc sulphate salt was synthesized and the solubility and metastable zonewidth were estimated from the aqueous solution. Single crystals of glycine zinc sulphate were grown by solvent evaporation method from aqueous solution. Grown crystals were characterized by X-ray diffraction and FT-IR spectral analyses. The range and percentage of optical transmission was ascertained by recording UV-vis-NIR spectrum. Thermal properties of the crystal were investigated by thermogravimetric analysis. Microhardness study was carried out on (01-1) face of the grown crystal. Its powder second harmonic generation efficiency was measured using Nd:YAG laser and the value was observed to be 0.7 times that of potassium dihydrogen orthophosphate.

Crystal structure, molecular docking, and biological activity of the zinc complexes with 2-thenoyltrifluoroacetone and N-donor heterocyclic ligands

NASA Astrophysics Data System (ADS)

Eshaghi Malekshah, Rahime; Salehi, Mehdi; Kubicki, Maciej; Khaleghian, Ali

2017-12-01

Two novel mononuclear complexes, [Zn (TTA) (bipy)Cl] (1) and [Zn (TTA) (phen)Cl] (2) (TTA = 4,4,4-Trifluoro-1-(2-furyl)-1,3-butanedione, phen = 1,10-phenanthroline and bipy 2, 2ʹ-bipyridine), were synthesized and fully characterized by elemental analyses, 1H NMR, UV-Vis, FTIR spectroscopy, and conductivity measurements. The crystal structures of these two mono-nuclear zinc (II) complexes were determined by X-ray single-crystal diffraction. The result of X-ray diffraction analyses revealed that both complexes have distorted tetragonal-pyramid structures. In MTT cytotoxicity studies, these Zn (II) complexes exhibited antitumor activity against MCF-7 and MKN-45 cell lines. It was also found that the proliferation rate of MCF-7 and MKN-45 cells decreased after treatment with the above-mentioned complexes. In addition, the apoptosis-inducing activity was assessed by AO/EB (Acridine Orange/Ethidium bromide) staining assay and found that they have the potential to act as effective metal-based anticancer drugs. Finally, the molecular docking studies showed that complex 2 strongly binds through minor groove with DNA by relative binding energy -7.33 kcal mol-1.

Synthesis, growth, structural, spectroscopic and optical studies of a new semiorganic nonlinear optical crystal: L-valine hydrochloride.

PubMed

Kirubavathi, K; Selvaraju, K; Valluvan, R; Vijayan, N; Kumararaman, S

2008-04-01

Single crystals of a new semiorganic nonlinear optical (NLO) material, L-valine hydrochloride (LVHCl), having dimensions up to 20 mm x 6 mm x 4 mm have been grown by slow evaporation solution growth technique. Single crystal X-ray diffraction studies confirm that the grown crystal belongs to the monoclinic system. The functional groups presented in the crystal were confirmed by Fourier transform infrared (FTIR) technique. Optical transmission spectrum shows very low absorption in the entire visible region. Differential thermal and thermogravimetric analyses confirmed that the crystal is stable up to 211 degrees C. The powder second harmonic generation (SHG) efficiency of LVHCl is 1.7 times efficient as potassium dihydrogen phosphate (KDP).

Diffraction Correlation to Reconstruct Highly Strained Particles

NASA Astrophysics Data System (ADS)

Brown, Douglas; Harder, Ross; Clark, Jesse; Kim, J. W.; Kiefer, Boris; Fullerton, Eric; Shpyrko, Oleg; Fohtung, Edwin

2015-03-01

Through the use of coherent x-ray diffraction a three-dimensional diffraction pattern of a highly strained nano-crystal can be recorded in reciprocal space by a detector. Only the intensities are recorded, resulting in a loss of the complex phase. The recorded diffraction pattern therefore requires computational processing to reconstruct the density and complex distribution of the diffracted nano-crystal. For highly strained crystals, standard methods using HIO and ER algorithms are no longer sufficient to reconstruct the diffraction pattern. Our solution is to correlate the symmetry in reciprocal space to generate an a priori shape constraint to guide the computational reconstruction of the diffraction pattern. This approach has improved the ability to accurately reconstruct highly strained nano-crystals.

Radiation damage and annealing in plutonium tetrafluoride

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

McCoy, Kaylyn; Casella, Amanda; Sinkov, Sergey

Plutonium tetrafluoride that was separated prior to 1966 at the Hanford Site in Washington State was analyzed at the Pacific Northwest National Laboratory (PNNL) in 2015 and 2016. The plutonium tetrafluoride, as received, was an off-normal color and considering the age of the plutonium, there were questions about the condition of the material. These questions had to be answered in order to determine the suitability of the material for future use or long-term storage. Therefore, Thermogravimetric/Differential Thermal Analysis and X-ray Diffraction evaluations were conducted to determine the plutonium’s crystal structure, oxide content, and moisture content; these analyses reported that themore » plutonium was predominately amorphous and tetrafluoride, with an oxide content near ten percent. Freshly fluorinated plutonium tetrafluoride is known to be monoclinic. During the initial Thermogravimetric/Differential Thermal analyses, it was discovered that an exothermic event occurred within the material near 414°C. X-ray Diffraction analyses were conducted on the annealed tetrafluoride. The X-ray Diffraction analyses indicated that some degree of recrystallization occurred in conjunction with the 414°C event. The following commentary describes the series of Thermogravimetric/Differential Thermal and X-ray Diffraction analyses that were conducted as part of this investigation at PNNL, in collaboration with the University of Utah Nuclear Engineering Program.« less

Synthesis, structural, optical and thermal studies of an organic nonlinear optical 4-aminopyridinium maleate single crystal.

PubMed

Pandi, P; Peramaiyan, G; Kumar, M Krishna; Kumar, R Mohan; Jayavel, R

2012-03-01

Synthesis and growth of a novel organic nonlinear optical (NLO) crystal of 4-aminopyridinium maleate (4APM) in larger size by the slow evaporation solution growth technique are reported. Single crystal and powder X-ray diffraction analyses reveal that 4APM crystallizes in monoclinic system with space group P2(1) with cell parameters a=8.140(4)Å, b=5.457(5)Å, c=10.926(10)Å and volume=481.4(7)Å(3). The grown crystal has been characterized by Fourier transform infrared and UV-visible spectral analyses. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) have been carried out to study its thermal properties. Dielectric measurements have been carried out to study the distribution of charges within the crystal. The mechanical strength of the crystal has been studied by using Vickers' microhardness test. The etching studies have been carried out on the grown crystal. The Kurtz and Perry powder SHG technique confirms the NLO property of the grown crystal and the SHG efficiency of 4APM was found to be 4.8 times greater than that of KDP crystal. Copyright © 2011 Elsevier B.V. All rights reserved.

Grazing-incidence X-ray diffraction from a crystal with subsurface defects

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

Gaevskii, A. Yu., E-mail: transilv@mail.ru; Golentus, I. E.

2015-03-15

The diffraction of X rays incident on a crystal surface under grazing angles under conditions of total external reflection has been investigated. An approach is proposed in which exact solutions to the dynamic problem of grazing-incidence diffraction in an ideal crystal are used as initial functions to calculate the diffuse component of diffraction in a crystal with defects. The diffuse component of diffraction is calculated for a crystal with surface defects of a dilatation-center type. Exact formulas of the continuum theory which take into account the mirror-image forces are used for defect-induced atomic displacements. Scattering intensity maps near Bragg peaksmore » are constructed for different scan modes, and the conditions for detecting primarily the diffuse component are determined. The results of dynamic calculations of grazing-incidence diffraction in defect-containing crystals are compared with calculations in the kinematic approximation.« less

Maximizing Macromolecule Crystal Size for Neutron Diffraction Experiments

NASA Technical Reports Server (NTRS)

Judge, R. A.; Kephart, R.; Leardi, R.; Myles, D. A.; Snell, E. H.; vanderWoerd, M.; Curreri, Peter A. (Technical Monitor)

2002-01-01

A challenge in neutron diffraction experiments is growing large (greater than 1 cu mm) macromolecule crystals. In taking up this challenge we have used statistical experiment design techniques to quickly identify crystallization conditions under which the largest crystals grow. These techniques provide the maximum information for minimal experimental effort, allowing optimal screening of crystallization variables in a simple experimental matrix, using the minimum amount of sample. Analysis of the results quickly tells the investigator what conditions are the most important for the crystallization. These can then be used to maximize the crystallization results in terms of reducing crystal numbers and providing large crystals of suitable habit. We have used these techniques to grow large crystals of Glucose isomerase. Glucose isomerase is an industrial enzyme used extensively in the food industry for the conversion of glucose to fructose. The aim of this study is the elucidation of the enzymatic mechanism at the molecular level. The accurate determination of hydrogen positions, which is critical for this, is a requirement that neutron diffraction is uniquely suited for. Preliminary neutron diffraction experiments with these crystals conducted at the Institute Laue-Langevin (Grenoble, France) reveal diffraction to beyond 2.5 angstrom. Macromolecular crystal growth is a process involving many parameters, and statistical experimental design is naturally suited to this field. These techniques are sample independent and provide an experimental strategy to maximize crystal volume and habit for neutron diffraction studies.

Optical-diffraction method for determining crystal orientation

DOEpatents

Sopori, B.L.

1982-05-07

Disclosed is an optical diffraction technique for characterizing the three-dimensional orientation of a crystal sample. An arbitrary surface of the crystal sample is texture etched so as to generate a pseudo-periodic diffraction grating on the surface. A laser light beam is then directed onto the etched surface, and the reflected light forms a farfield diffraction pattern in reflection. Parameters of the diffraction pattern, such as the geometry and angular dispersion of the diffracted beam are then related to grating shape of the etched surface which is in turn related to crystal orientation. This technique may be used for examining polycrystalline silicon for use in solar cells.

Optical devices combining an organic semiconductor crystal with a two-dimensional inorganic diffraction grating

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

Kitazawa, Takenori; Yamao, Takeshi, E-mail: yamao@kit.ac.jp; Hotta, Shu

2016-02-01

We have fabricated optical devices using an organic semiconductor crystal as an emission layer in combination with a two-dimensional (2D) inorganic diffraction grating used as an optical cavity. We formed the inorganic diffraction grating by wet etching of aluminum-doped zinc oxide (AZO) under a 2D cyclic olefin copolymer (COC) diffraction grating used as a mask. The COC diffraction grating was fabricated by nanoimprint lithography. The AZO diffraction grating was composed of convex prominences arranged in a triangular lattice. The organic crystal placed on the AZO diffraction grating indicated narrowed peaks in its emission spectrum under ultraviolet light excitation. These aremore » detected parallel to the crystal plane. The peaks were shifted by rotating the optical devices around the normal to the crystal plane, which reflected the rotational symmetries of the triangular lattice through 60°.« less

Dynamic X-ray diffraction sampling for protein crystal positioning

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

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction,more » significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Furthermore, by usingin situtwo-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.« less

Dynamic X-ray diffraction sampling for protein crystal positioning

DOE PAGES

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye; ...

2017-01-01

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction,more » significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Furthermore, by usingin situtwo-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.« less

Dynamic X-ray diffraction sampling for protein crystal positioning

PubMed Central

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye; Kissick, David J.; Zhang, Shijie; Newman, Justin A.; Sheedlo, Michael J.; Chowdhury, Azhad U.; Fischetti, Robert F.; Das, Chittaranjan; Buzzard, Gregery T.; Bouman, Charles A.; Simpson, Garth J.

2017-01-01

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations. PMID:28009558

Dynamic X-ray diffraction sampling for protein crystal positioning.

PubMed

Scarborough, Nicole M; Godaliyadda, G M Dilshan P; Ye, Dong Hye; Kissick, David J; Zhang, Shijie; Newman, Justin A; Sheedlo, Michael J; Chowdhury, Azhad U; Fischetti, Robert F; Das, Chittaranjan; Buzzard, Gregery T; Bouman, Charles A; Simpson, Garth J

2017-01-01

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.

Hemoglobin redux: combining neutron and X-ray diffraction with mass spectrometry to analyse the quaternary state of oxidized hemoglobins

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

Mueser, Timothy C., E-mail: timothy.mueser@utoledo.edu; Griffith, Wendell P.; Kovalevsky, Andrey Y.

2010-11-01

X-ray and neutron diffraction studies of cyanomethemoglobin are being used to evaluate the structural waters within the dimer–dimer interface involved in quaternary-state transitions. Improvements in neutron diffraction instrumentation are affording the opportunity to re-examine the structures of vertebrate hemoglobins and to interrogate proton and solvent position changes between the different quaternary states of the protein. For hemoglobins of unknown primary sequence, structural studies of cyanomethemoglobin (CNmetHb) are being used to help to resolve sequence ambiguity in the mass spectra. These studies have also provided additional structural evidence for the involvement of oxidized hemoglobin in the process of erythrocyte senescence. X-raymore » crystal studies of Tibetan snow leopard CNmetHb have shown that this protein crystallizes in the B state, a structure with a more open dyad, which possibly has relevance to RBC band 3 protein binding and erythrocyte senescence. R-state equine CNmetHb crystal studies elaborate the solvent differences in the switch and hinge region compared with a human deoxyhemoglobin T-state neutron structure. Lastly, comparison of histidine protonation between the T and R state should enumerate the Bohr-effect protons.« less

Bis (3-methoxy-4-hydroxybenzaldehyde-2,4,6-trinitrophenol) organic cocrystal: Synthesis and physico-chemical properties

NASA Astrophysics Data System (ADS)

Sudharsana, N.; Krishnakumar, V.; Nagalakshmi, R.

2016-10-01

A 3-methoxy-4-hydroxybenzaldehyde-2,4,6-trinitrophenol (mhba-tnp) cocrystal was grown by the slow evaporation solution growth technique using ethanol as a solvent. As-grown crystals were characterized by single crystal X-ray diffraction (XRD) study and crystallized with a centrosymmetric space group. Optical properties of the grown crystal have been studied by Ultraviolet-Visible (UV-Vis) absorption spectra in the range from 200 to 800nm and the band gap energy of the crystal was obtained as 2.8eV. Fourier transform infrared (FTIR) and micro Raman spectral analyses have been carried out to confirm the functional groups present in the title compound. Differential scanning calorimetry (DSC) and polarized light thermomicroscopy (PLTM) analyses were carried out to find the melting point. In addition, the optimized geometric parameters and the molecular orbitals were calculated using density functional theory (DFT) with the help of the Gaussian 03W software.

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).

Hydrothermal synthesis, crystal structures, and enantioselective adsorption property of bis(L-histidinato)nickel(II) monohydrate

NASA Astrophysics Data System (ADS)

Ramos, Christian Paul L.; Conato, Marlon T.

2018-05-01

Despite the numerous researches in metal-organic frameworks (MOFs), there are only few reports on biologically important amino acids, histidine in particular, on its use as bridging ligand in the construction of open-framework architectures. In this work, hydrothermal synthesis was used to prepare a compound based on Ni2+ and histidine. The coordination assembly of imidazole side chain of histidine with divalent nickel ions in aqueous condition yielded purple prismatic solids. Single crystal X-ray diffraction (XRD) analysis of the product revealed structure for Ni(C6H8N3O2)2 • H2O that has a monoclinic (C2) structure with lattice parameters, a = 29.41, b = 8.27, c = 6.31 Å, β = 90.01 ˚. Circular dichroism - optical rotatory dispersion (CD-ORD), Powder X-ray diffraction (PXRD) and Fourier transform - infrared spectroscopy (FT-IR) analyses are conducted to further characterize the crystals. Enantioselective adsorption analysis using racemic mixture of 2-butanol confirmed bis(L-histidinato)nickel(II) monohydrate MOF crystal's enantioselective property preferentially favoring the adsorption of (S)-2-butanol isomer.

Effects of carbon dioxide, Nd:YAG and carbon dioxide-Nd:YAG combination lasers at high energy densities on synthetic hydroxyaptite.

PubMed

Meurman, J H; Voegel, J C; Rauhamaa-Mäkinen, R; Gasser, P; Thomann, J M; Hemmerle, J; Luomanen, M; Paunio, I; Frank, R M

1992-01-01

The aim of this study was to determine the crystalline structure and chemical alterations of synthetic hydroxyapatite after irradiation with either CO2, Nd:YAG or CO2-Nd:YAG combination lasers at high energy densities of 500-3,230 J.cm2. Further, dissolution kinetics of the lased material were analysed and compared with those of unlased apatite. Electron microscopy showed that the lased material consisted of two kinds of crystals. From the micrographs their diameters varied from 600 to 1,200 A and from 3,000 to 6,000 A, respectively. The larger crystals showed 6.9-Angström periodic lattice fringes in the transmission electron microscope. alpha-Tricalcium phosphate (TCP) was identified by X-ray diffraction. Selective-area electron diffraction identified the large crystals to consist of tricalcium phosphate while the smaller crystals were probably hydroxyapatite. Assays of dissolution kinetics showed that at these high energy densities lased material dissolved more rapidly than unlased synthetic hydroxyapatite due to the higher solubility of TCP.

Growth, structural, optical and thermal properties of gamma-glycine crystal.

PubMed

Balakrishnan, T; Babu, R Ramesh; Ramamurthi, K

2008-04-01

Single crystals of gamma-glycine were grown from a mixture of glycine, water and lithium bromide. Single crystal X-ray diffraction analysis confirmed the growth of gamma-glycine phase. Presence of various functional groups of gamma-glycine was identified by FTIR spectrum. Optical absorbance spectrum recorded in the wavelength range of UV-vis-NIR revealed that this crystal has good optical transparency in the range 250-1500 nm. Vickers microhardness values were estimated on the prominent (100) face. Thermogravimetric and differential scanning calorimetric analyses were carried out to study the thermal properties of gamma-glycine. Second harmonic generation efficiency of the crystal measured by Kurtz's powder method using Nd:YAG laser is about three times that of KDP.

Growth, structural, spectral, optical, and thermal studies on amino acid based new NLO single crystal: L-phenylalanine-4-nitrophenol.

PubMed

Prakash, M; Lydia Caroline, M; Geetha, D

2013-05-01

A new organic nonlinear optical single crystal, L-phenylalanine-4-nitrophenol (LPAPN) belonging to the amino acid group has been successfully grown by slow evaporation technique. The lattice parameters of the grown crystal have been determined by X-ray diffraction studies. FT-IR spectrum was recorded to identify the presence of functional group and molecular structure was confirmed by NMR spectrum. Thermal strength of the grown crystal has been studied using TG-DTA analyses. The grown crystals were found to be transparent in the entire visible region. The existence of second harmonic generation signals was observed using Nd:YAG laser with fundamental wavelength of 1064 nm. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of Ultrasonic Surface Treatment on the Transparency and Orientation of Fresnoite Surface Crystallization

NASA Astrophysics Data System (ADS)

Endo, A.; Sakida, S.; Benino, Y.; Nanba, T.

2011-10-01

Surface crystallized glass ceramics with fresnoite (Ba2TiSi2O8) phase were prepared by conventional heat treatment of 30BaO-20TiO2-50SiO2 glass together with ultrasonic surface treatment (UST) technique. The precursor glass was fully crystallized in a bulk form without any cracks, and the optical transparency and crystallographic orientation of the crystalline layers were evaluated by UV-Vis spectroscopy and XRD diffraction analyses, respectively. These properties were both enhanced significantly by applying UST using fresnoite/water suspension before the crystallization process, which is advantage for nonlinear optical applications of bulk glass ceramics. The effects of UST on the crystallization behavior were investigated by applying UST with various conditions.

Synthesis, crystal growth, structural, thermal, optical and mechanical properties of solution grown 4-methylpyridinium 4-hydroxybenzoate single crystal.

PubMed

Sudhahar, S; Krishna Kumar, M; Sornamurthy, B M; Mohan Kumar, R

2014-01-24

Organic nonlinear optical material, 4-methylpyridinium 4-hydroxybenzoate (4MPHB) was synthesized and single crystal was grown by slow evaporation solution growth method. Single crystal and powder X-ray diffraction analyses confirm the structure and crystalline perfection of 4MPHB crystal. Infrared, Raman and NMR spectroscopy techniques were used to elucidate the functional groups present in the compound. TG-DTA analysis was carried out in nitrogen atmosphere to study the decomposition stages, endothermic and exothermic reactions. UV-visible and Photoluminescence spectra were recorded for the grown crystal to estimate the transmittance and band gap energy respectively. Linear refractive index, birefringence, and SHG efficiency of the grown crystal were studied. Laser induced surface damage threshold and mechanical properties of grown crystal were studied to assess the suitability of the grown crystals for device applications. Copyright © 2013 Elsevier B.V. All rights reserved.

A top-down approach to crystal engineering of a racemic Δ2-isoxazoline.

PubMed

Lombardo, Giuseppe M; Rescifina, Antonio; Chiacchio, Ugo; Bacchi, Alessia; Punzo, Francesco

2014-02-01

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top-down approach to be a useful tool for crystal engineering.

Solid-state reaction kinetics and optical studies of cadmium doped magnesium hydrogen phosphate crystals

NASA Astrophysics Data System (ADS)

Verma, Madhu; Gupta, Rashmi; Singh, Harjinder; Bamzai, K. K.

2018-04-01

The growth of cadmium doped magnesium hydrogen phosphate was successfully carried out by using room temperature solution technique i.e., gel encapsulation technique. Grown crystals were confirmed by single crystal X-ray diffraction (XRD). The structure of the grown crystal belongs to orthorhombic crystal system and crystallizes in centrosymmetric space group. Kinetics of the decomposition of the grown crystals were studied by non-isothermal analysis. Thermo gravimetric / differential thermo analytical (TG/DTA) studies revealed that the grown crystal is stable upto 119 °C. The various steps involved in the thermal decomposition of the material have been analysed using Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova equations for evaluating various kinetic parameters. The optical studies shows that the grown crystals possess wide transmittance in the visible region and significant optical band gap of 5.5ev with cut off wavelength of 260 nm.

Luminescent properties under X-ray excitation of Ba(1-x)PbxWO4 disordered solid solution

NASA Astrophysics Data System (ADS)

Bakiz, B.; Hallaoui, A.; Taoufyq, A.; Benlhachemi, A.; Guinneton, F.; Villain, S.; Ezahri, M.; Valmalette, J.-C.; Arab, M.; Gavarri, J.-R.

2018-02-01

A series of polycrystalline barium-lead tungstate Ba1-xPbxWO4 with 0 ≤ x ≤ 1 was synthesized using a classical solid-state method with thermal treatment at 1000 °C. These materials were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier Transform Raman (FT-Raman) spectroscopy. X-ray diffraction profile analyses were performed using Rietveld method. These materials crystallized in the scheelite tetragonal structure and behaved as quasi ideal solid solution. Raman spectroscopy confirmed the formation of the solid solution. Structural distortions were evidenced in X-ray diffraction profiles and in vibration Raman spectra. The scanning electron microscopy experiments showed large and rounded irregular grains. Luminescence experiments were performed under X-ray excitation. The luminescence emission profiles have been interpreted in terms of four Gaussian components, with a major contribution of blue emission. The integrated intensity of luminescence reached a maximum value in the composition range x = 0.3-0.6, in relation with distortions of crystal lattice.

Spherical quartz crystals investigated with synchrotron radiation

DOE PAGES

Pereira, N. R.; Macrander, A. T.; Hill, K. W.; ...

2015-10-27

The quality of x-ray spectra and images obtained from plasmas with spherically bent crystals depends in part on the crystal's x-ray diffraction across the entire crystal surface. We employ the energy selectivity and high intensity of synchrotron radiation to examine typical spherical crystals from alpha-quartz for their diffraction quality, in a perpendicular geometry that is particularly convenient to examine sagittal focusing. The crystal's local diffraction is not ideal: the most noticeable problems come from isolated regions that so far have failed to correlate with visible imperfections. In conclusion, excluding diffraction from such problem spots has little effect on the focusmore » beyond a decrease in background.« less

Low-resolution structure of Drosophila translin

PubMed Central

Kumar, Vinay; Gupta, Gagan D.

2012-01-01

Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to Rwork (Rfree) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin–TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers. PMID:23650579

Synthesis, structural, thermal and optical studies of 1-ethyl-2,6-dimethyl-4-hydroxy pyridinium halides.

PubMed

Dhanuskodi, S; Manivannan, S; Kirschbaum, K

2006-05-15

1-Ethyl-2,6-dimethyl-4-hydroxy pyridinium chloride dihydrate and bromide dihydrate salts have been synthesized and their single crystals were grown by the slow evaporation of aqueous solution at 30 degrees C. The grown crystals were characterized by elemental analysis, FT-NMR and FT-IR techniques to confirm the formation of the expected compound. Optical transmittance window in aqueous solution was found to be 275-1100 nm by UV-vis-NIR technique. Thermogravimetric and differential thermal analyses reveal thermal stability and the presence of two water molecules in the crystal lattices. The crystal structure of chloride salt was also determined by X-ray diffraction method.

Synthesis, Structural and Antioxidant Studies of Some Novel N-Ethyl Phthalimide Esters

PubMed Central

Chandraju, Siddegowda; Win, Yip-Foo; Tan, Weng Kang; Quah, Ching Kheng; Fun, Hoong-Kun

2015-01-01

A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity. PMID:25742494

Synthesis, structural and antioxidant studies of some novel N-ethyl phthalimide esters.

PubMed

Chidan Kumar, C S; Loh, Wan-Sin; Chandraju, Siddegowda; Win, Yip-Foo; Tan, Weng Kang; Quah, Ching Kheng; Fun, Hoong-Kun

2015-01-01

A series of N-ethyl phthalimide esters 4(a-n) were synthesized and characterized by spectroscopic studies. Further, the molecular structure of majority of compounds were analysed by single crystal X-ray diffraction studies. The X-ray analysis revealed the importance of substituents on the crystal stability and molecular packing. All the synthesized compounds were tested for in vitro antioxidant activity by DPPH radical scavenging, FRAP and CUPRAC methods. Few of them have shown good antioxidant activity.

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

Luong Thi, T. T., E-mail: thuyltt@hnue.edu.vn; Nguyen Bich, N.; Nguyen, H.

Two 4-substituted 2,2'-bipyridines, namely 4-(ferrocenylethynyl)-2,2'-bipyridine (I) and 4-ferrocenyl-2,2'-bipyridine (II) have been synthesized and fully characterized via single-crystal X-ray diffraction and {sup 1}H and {sup 13}C NMR analyses. The π-conjugated system designed from 2,2'-bipyridine modified with the ferrocenylethynyl and ferrocenyl groups shows the desired planarity. In the crystal packing of I and II, the molecules arrange themselves in head-to-tail and head-to-head motifs, respectively, resulting in consecutive layers of ferrocene and pyridine moieties.

Rietveld analysis using powder diffraction data with anomalous scattering effect obtained by focused beam flat sample method

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

Tanaka, Masahiko, E-mail: masahiko@spring8.or.jp; Katsuya, Yoshio, E-mail: katsuya@spring8.or.jp; Sakata, Osami, E-mail: SAKATA.Osami@nims.go.jp

2016-07-27

Focused-beam flat-sample method (FFM) is a new trial for synchrotron powder diffraction method, which is a combination of beam focusing optics, flat shape powder sample and area detectors. The method has advantages for X-ray diffraction experiments applying anomalous scattering effect (anomalous diffraction), because of 1. Absorption correction without approximation, 2. High intensity X-rays of focused incident beams and high signal noise ratio of diffracted X-rays 3. Rapid data collection with area detectors. We applied the FFM to anomalous diffraction experiments and collected synchrotron X-ray powder diffraction data of CoFe{sub 2}O{sub 4} (inverse spinel structure) using X-rays near Fe K absorptionmore » edge, which can distinguish Co and Fe by anomalous scattering effect. We conducted Rietveld analyses with the obtained powder diffraction data and successfully determined the distribution of Co and Fe ions in CoFe{sub 2}O{sub 4} crystal structure.« less

The crystallization behavior of amorphous Ge2Sb2Te5 films induced by a multi-pulsed nanosecond laser

NASA Astrophysics Data System (ADS)

Fan, T.; Liu, F. R.; Li, W. Q.; Guo, J. C.; Wang, Y. H.; Sun, N. X.; Liu, F.

2017-09-01

In this paper, accumulated crystallization of amorphous Ge2Sb2Te5 (a-GST) films induced by a multi-pulsed nanosecond (ns) excimer laser was investigated by x-ray diffraction (XRD), atomic force microscopy, field-emission scanning electron microscopy, x-ray photoelectron spectroscopy (XPS) and a spectrophotometer. XRD analyses revealed that detectable crystallization was firstly observed in the preferred orientation (200), followed by the orientations (220) and (111) after two pulses. Optical contrast, determined by crystallinity as well as surface roughness, was found to retain a linear relation within the first three pulses. A layered growth mechanism from the top surface to the interior of a-GST films was used to explain the crystallization behavior induced by the multi-pulse ns laser. XPS analyses for bond rearrangement and electronic structure further suggested that the crystallization process was performed by generating new bonds of Ge-Te and Sb-Te after laser irradiations. This paper presents the potential of multi-level devices and tunable thermal emitters based on controllable crystallization of phase-change materials.

Radiation damage and annealing in plutonium tetrafluoride

DOE PAGES

McCoy, Kaylyn; Casella, Amanda; Sinkov, Sergey; ...

2017-08-03

A sample of plutonium tetrafluoride that was separated prior to 1966 at the Hanford Site in Washington State was analyzed at the Pacific Northwest National Laboratory (PNNL) in 2015 and 2016. The plutonium tetrafluoride, as received, was an unusual color and considering the age of the plutonium, there were questions about the condition of the material. These questions had to be answered in order to determine the suitability of the material for future use or long-term storage. Therefore, thermogravimetric/differential thermal analysis and X-ray diffraction evaluations were conducted to determine the plutonium's crystal structure, oxide content, and moisture content; these analysesmore » reported that the plutonium was predominately amorphous and tetrafluoride, with an oxide content near ten percent. Freshly fluorinated plutonium tetrafluoride is known to be monoclinic. And during the initial thermogravimetric/differential thermal analyses, it was discovered that an exothermic event occurred within the material near 414 °C. X-ray diffraction analyses were conducted on the annealed tetrafluoride. The X-ray diffraction analyses indicated that some degree of recrystallization occurred in conjunction with the 414 °C event. This commentary describes the series of thermogravimetric/differential thermal and X-ray diffraction analyses that were conducted as part of this investigation at PNNL.« less

High Resolution X-Ray Diffraction of Macromolecules with Synchrotron Radiation

NASA Technical Reports Server (NTRS)

Stojanoff, Vivian; Boggon, Titus; Helliwell, John R.; Judge, Russell; Olczak, Alex; Snell, Edward H.; Siddons, D. Peter; Rose, M. Franklin (Technical Monitor)

2000-01-01

We recently combined synchrotron-based monochromatic X-ray diffraction topography methods with triple axis diffractometry and rocking curve measurements: high resolution X-ray diffraction imaging techniques, to better understand the quality of protein crystals. We discuss these methods in the light of results obtained on crystals grown under different conditions. These non destructive techniques are powerful tools in the characterization of the protein crystals and ultimately will allow to improve, develop, and understand protein crystal growth. High resolution X-ray diffraction imaging methods will be discussed in detail in light of recent results obtained on Hen Egg White Lysozyme crystals and other proteins.

A drunken search in crystallization space.

PubMed

Fazio, Vincent J; Peat, Thomas S; Newman, Janet

2014-10-01

The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the PDB. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40% of the crystallization conditions found currently in the PDB are identical or very similar to a commercial condition.

Crystallization and preliminary X-ray diffraction study of the protealysin precursor belonging to the peptidase family M4

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

Gromova, T. Yu., E-mail: duk@img.ras.ru; Demidyuk, I. V.; Kostrov, S. V.

2008-09-15

A protealysin precursor (the enzyme of the peptidase family M4) was crystallized for the first time. The crystal-growth conditions were found, and single crystals of the protein with dimensions of 0.3-0.5 mm were grown. The preliminary X-ray diffraction study of the enzyme was performed. The protealysin precursor was shown to crystallize in two crystal modifications suitable for the X-ray diffraction study of the three-dimensional structure of the protein molecule at atomic resolution.

Synthesis, growth, structural, spectral, thermal, chemical etching, linear and nonlinear optical and mechanical studies of an organic single crystal 4-chloro 4-nitrostilbene (CONS): a potential NLO material.

PubMed

Dinakaran, Paul M; Kalainathan, S

2013-07-01

4-Chloro 4-nitrostilbene (CONS) a new organic nonlinear optical material has been synthesized. Employing slow evaporation method, good optical quality single crystals (dimensions up to 6×2×3 mm(3)) have been grown using ethyl methyl ketone (EMK) as a solvent. The grown crystals have been subjected to various characterizations such as single crystal X-ray diffraction, powder XRD, Fourier Transform Infrared spectroscopy (FTIR), proton NMR, solid UV absorption, SHG studies. Single crystal X-ray diffraction reveals that the crystal system belongs to monoclinic with noncentrosymmetric space group P21. The UV-Vis absorption spectrum has been recorded and found that the cut off wavelength is 380 nm. Functional groups and the structure of the title compound have been confirmed by FTIR and (1)H NMR spectroscopic analyses respectively. Molecular mass of the CONS confirmed by the high resolution mass spectral analysis .The thermal behavior of the grown crystal has been studied by TG/DTA analysis and it shows the melting point is at 188.66 °C. Dislocations and growth pattern present in the grown crystal revealed by the etching study. The mechanical strength of the CONS crystal has been studied by Vicker's hardness measurement. The SHG efficiency of the grown crystal has been determined by Kurtz and Perry powder test which revealed that the CONS crystal (327 mV) has 15 times greater efficiency than that of KDP (21.7 mV). Copyright © 2013 Elsevier B.V. All rights reserved.

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

Zhao, Haishuang; Krysiak, Yaşar; Hoffmann, Kristin

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

A new Keggin-type polyoxometalate catalyst for degradation of aqueous organic contaminants

NASA Astrophysics Data System (ADS)

Olgun, Asim; Çolak, Alper Tolga; Gübbük, İ. Hilal; Şahin, Onur; Kanar, Ebru

2017-04-01

In this study, a new polyoxometalate, K16[Ni(H2O)6]2[BW12O40]4·48H2O (1) was synthesized at room temperature and characterized by X-ray single crystal diffractions, elemental analyses, IR spectra, and thermo gravimetric analyses (TGA). Crystal structure analysis reveals that compound 1 exhibits a supramolecular structure containing one Keggin-type [BW12O40]4 heteropoly anion. The catalytic properties of this molecule for the degradation of Methyl red (MR), Rhodamine B (RhB), Methyl orange (MO) and Congo red (CR) were investigated. The results show that the compound 1 is a promising catalyst candidate for dye degradation.

Improving the diffraction of apoA-IV crystals through extreme dehydration.

PubMed

Deng, Xiaodi; Davidson, W Sean; Thompson, Thomas B

2012-01-01

Apolipoproteins are the protein component of high-density lipoproteins (HDL), which are necessary for mobilizing lipid-like molecules throughout the body. Apolipoproteins undergo self-association, especially at higher concentrations, making them difficult to crystallize. Here, the crystallization and diffraction of the core fragment of apolipoprotein A-IV (apoA-IV), consisting of residues 64-335, is presented. ApoA-IV(64-335) crystallized readily in a variety of hexagonal (P6) morphologies with similar unit-cell parameters, all containing a long axis of nearly 550 Å in length. Preliminary diffraction experiments with the different crystal morphologies all resulted in limited streaky diffraction to 3.5 Å resolution. Crystal dehydration was applied to the different morphologies with variable success and was also used as a quality indicator of crystal-growth conditions. The results show that the morphologies that withstood the most extreme dehydration conditions showed the greatest improvement in diffraction. One morphology in particular was able to withstand dehydration in 60% PEG 3350 for over 12 h, which resulted in well defined intensities to 2.7 Å resolution. These results suggest that the approach of integrating dehydration with variation in crystal-growth conditions might be a general technique to optimize diffraction. © 2012 International Union of Crystallography. All rights reserved.

Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

PubMed

Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

2014-05-05

Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. Copyright © 2014 Elsevier B.V. All rights reserved.

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements

DOE PAGES

Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.; ...

2017-08-08

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here, in this paper, a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focusedmore » ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Lastly, our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.« less

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements

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

Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here, in this paper, a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focusedmore » ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Lastly, our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.« less

Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements.

PubMed

Hofmann, Felix; Phillips, Nicholas W; Harder, Ross J; Liu, Wenjun; Clark, Jesse N; Robinson, Ian K; Abbey, Brian

2017-09-01

Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focused ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.

Micro-beam Laue Alignment of Multi-Reflection Bragg Coherent Diffraction Imaging Measurements

PubMed Central

Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.; Liu, Wenjun; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian

2017-01-01

Multi-reflection Bragg coherent diffraction imaging has the potential to allow 3D resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here we demonstrate a different approach, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focussed ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples. PMID:28862628

Mesoscopic monodisperse ferromagnetic colloids enable magnetically controlled photonic crystals.

PubMed

Xu, Xiangling; Majetich, Sara A; Asher, Sanford A

2002-11-20

We report here the first synthesis of mesoscopic, monodisperse particles which contain nanoscopic inclusions of ferromagnetic cobalt ferrites. These monodisperse ferromagnetic composite particles readily self-assemble into magnetically responsive photonic crystals that efficiently Bragg diffract incident light. Magnetic fields can be used to control the photonic crystal orientation and, thus, the diffracted wavelength. We demonstrate the use of these ferromagnetic particles to fabricate magneto-optical diffracting fluids and magnetically switchable diffracting mirrors.

[Effect of K2O addition on the crystallization property of dental glass-ceramics].

PubMed

Liu, Xiao-Qiu; Song, Wen-Zhi; Sun, Hong-Chen; Yang, Hai-Bin; Zou, Guang-Tian; Wang, Jing-Yun; Ye, Chang-Li

2006-10-01

To evaluate the effect of K2O addition on the crystallization property of dental glass-ceramics in the Li2O-SiO2-Al2O3-P2O5-ZnO system. Different content of K2O was added into Li2O-SiO2-Al2O3-P2O5-ZnO glass system. The heat-treated system of the glass-ceramics was determined by differential thermal analyses (DTA), then the crystallization components and the microstmcture of the glass-ceramics with different content of K2O were investigated from X-ray diffraction (XRD) analyses and scanning electron microscopy (SEM). Addition of K2O helped to reduce the viscosity of the glass system and improved crystallization. More lithium disilicate crystals appeared after heated-treatment of the glass system which contained 5.3 wt% addition of K2O, and the homogeneously lath-shaped crystals were 4 gm in length. Certain content of K2O can improve the crystallization property of dental glass-ceramics in the Li2O-SiO2-Al2O3-P2O5-ZnO system.

Inclined monochromator for high heat-load synchrotron x-ray radiation

DOEpatents

Khounsary, A.M.

1994-02-15

A double crystal monochromator is described including two identical, parallel crystals, each of which is cut such that the normal to the diffraction planes of interest makes an angle less than 90 degrees with the surface normal. Diffraction is symmetric, regardless of whether the crystals are symmetrically or asymmetrically cut, enabling operation of the monochromator with a fixed plane of diffraction. As a result of the inclination of the crystal surface, an incident beam has a footprint area which is elongated both vertically and horizontally when compared to that of the conventional monochromator, reducing the heat flux of the incident beam and enabling more efficient surface cooling. Because after inclination of the crystal only a fraction of thermal distortion lies in the diffraction plane, slope errors and the resultant misorientation of the diffracted beam are reduced. 11 figures.

Inclined monochromator for high heat-load synchrotron x-ray radiation

DOEpatents

Khounsary, Ali M.

1994-01-01

A double crystal monochromator including two identical, parallel crystals, each of which is cut such that the normal to the diffraction planes of interest makes an angle less than 90 degrees with the surface normal. Diffraction is symmetric, regardless of whether the crystals are symmetrically or asymmetrically cut, enabling operation of the monochromator with a fixed plane of diffraction. As a result of the inclination of the crystal surface, an incident beam has a footprint area which is elongated both vertically and horizontally when compared to that of the conventional monochromator, reducing the heat flux of the incident beam and enabling more efficient surface cooling. Because after inclination of the crystal only a fraction of thermal distortion lies in the diffraction plane, slope errors and the resultant misorientation of the diffracted beam are reduced.

Structural and Functional Analyses of the Six1 Transcriptional Complex for Anti-Breast Cancer Drug Design

DTIC Science & Technology

2011-04-01

of structurally highly related initial hits. 
 Fig. 8. A malachite green based secondary assay confirmed the top two initial hits do inhibit ED’s...Crystals (left) and diffraction pattern (right) of ED. using a malachite -green based phosphatase assay (Fig. 8). We further demonstrated that these

Comparative Analysis of Thaumatin Crystals Grown on Earth and in Microgravity. Experiment 23

NASA Technical Reports Server (NTRS)

Ng, Joseph D.; Lorber, Bernard; Giege, Richard; Koszelak, Stanley; Day, John; Greenwood, Aaron; McPherson, Alexander

1998-01-01

The protein thaumatin was studied as a model macromolecule for crystallization in microgravity environment experiments conducted on two U.S. Space Shuttle missions (second United States Microgravity Laboratory (USML-2) and Life and Microgravity Spacelab (LMS)). In this investigation we evaluated and compared the quality of space- and Earth-grown thaumatin crystals using x-ray diffraction analysis and characterized them according to crystal size, diffraction resolution limit, and mosaicity. Two different approaches for growing thaumatin crystals in the microgravity environment, dialysis and liquid-liquid diffusion, were employed as a joint experiment by our two investigative teams. Thaumatin crystals grown under a microgravity environment were generally larger in volume with fewer total crystals. They diffracted to significantly higher resolution and with improved diffraction properties as judged by relative Wilson plots. The mosaicity for space-grown crystals was significantly less than for those grown on Earth. Increasing concentrations of protein in the crystallization chambers under microgravity lead to larger crystals. The data presented here lend further support to the idea that protein crystals of improved quality can be obtained in a microgravity environment.

Occurrence and characterisation of calcium oxalate crystals in stems and fruits of Hylocereus costaricensis and Selenicereus megalanthus (Cactaceae: Hylocereeae).

PubMed

Viñas, María; Jiménez, Víctor M

2016-10-01

Detailed description about occurrence of calcium oxalate (CaOx) crystals in the edible vine cactus species Hylocereus costaricensis and Selenicereus megalanthus is scarce. Therefore, we evaluated and characterized the presence, morphology and composition of CaOx crystals in both species. Crystals were isolated from greenhouse and in vitro vegetative stems, and from ripe fruit peels and pulp by enzymatic digestion and density centrifugation and quantified with a haemocytometer. Morphologies were studied using scanning electron microscopy, elemental composition with energy-dispersive X-ray spectroscopy and salt composition with X-ray powder diffraction. Analyses conducted confirmed that isolated crystals were exclusively composed by CaOx, both mono- and dihydrated. Highest crystal contents were measured in greenhouse stems, followed by the fruit peels. While very few crystals were quantified in in vitro plants, they were not detected in the fruit pulp at all, which is of advantage for its human consumption and could be linked to mechanisms of seed dispersal through animals. Different crystal morphologies were observed, sometimes varying between genotypes and tissues analysed. This is the first work known to the authors with a detailed characterization of CaOx crystals in vine cacti. Copyright © 2016 Elsevier Ltd. All rights reserved.

Three pharmaceuticals cocrystals of adefovir: Syntheses, structures and dissolution study

NASA Astrophysics Data System (ADS)

Zhang, Xiaoming; Sun, Fuxing; Zhang, Tingting; Jia, Jiangtao; Su, Hongmin; Wang, Chenhui; Zhu, Guangshan

2015-11-01

We report here three novel cocrystals, which are composed of adefovir as the API (Active Pharmaceutical Ingredient) with p-aminobenzoic acid (1, 2C8H12N5O4P·C7H6NO2·3H2O), 3,5-dihydroxybenzoic acid (2, C8H12N5O4P·C7H6O4·H2O) and 2,6-pyridinedicarboxlic acid (3, C8H12N5O4P·C7H5NO4) as CCFs (cocrystal formers) respectively by crystal engineering strategy. Their structures were characterized by single crystal X-ray diffraction, powder X-ray diffraction (PXRD) analysis, thermogravimetric analyses (TGA), elemental analysis (EA) and infrared spectral analysis (IR). The analysis of single crystal X-ray diffraction demonstrate that cocrystal 1 and 2 form a strong hydrogen-bonded assembly through the phosphoric acids of API with water in the lattice and carboxylic acids of CCF respectively. Cocrystal 3 is formed in which the phosphoric acid groups of API are also held by the carboxylic acid groups of CCF. The PXRD results indicate their high purity of as-synthesized samples. The TGA, EA, IR and dissolution study of API and the cocrystals were also measured and discussed.

Synthesis, characterization and dissolution of three pharmaceutical cocrystals based on deferiprone

NASA Astrophysics Data System (ADS)

Zhang, Xiaoming; Tian, Yuyang; Jia, Jiangtao; Zhang, Tingting; Zhu, Guangshan

2016-03-01

In this paper we present three new cocrystals based on deferiprone which is the first oral medicine as iron chelator. Solitary deferiprone possesses some known problems due to its good solubility and frequent dosing side effects. For these three novel co crystals, deferiprone is the active pharmaceutical ingredient (API), p-hydroxybenzoic acid (1, C7H9NO2·C7H6O3), 2, 5-dihydroxybenzoic acid (2, C7H9NO2·C7H6O4) and maleic acid (3, C7H9NO2·C4H4O4) are used as cocrystal formers (CCFs), respectively. Their structures were characterized by single crystal X-ray diffraction, powder X-ray diffraction (PXRD) analysis, thermogravimetric analyses (TGA), differential thermal analysis (DTA), elemental analysis (EA) and infrared spectral analysis (IR). Single crystal X-ray diffraction demonstrates that all three cocrystals (1-3) possess strong hydrogen-bondings assembled through hydroxyl of API and carboxylic acids of CCFs. The PXRD results indicate their high purity of as-synthesized samples. TGA, DTA, EA, IR and dissolution study of API and cocrystals were also measured and discussed, respectively. The results suggest that the cocrystals exhibit low dissolution rates comparing with solitary deferiprone, which is very advantageous for the oral medicine with frequent dosing side effects.

Research Associate | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). KEY ROLES/RESPONSIBILITIES - Research Associate III Dr. Zbigniew Dauter is the head investigator of the Synchrotron Radiation Research Section (SRRS) of CCR’s Macromolecular Crystallography Laboratory. The Synchrotron Radiation Research Section is located at Argonne National Laboratory, Argonne, Illinois; this is the site of the largest U.S. synchrotron facility. The SRRS uses X-ray diffraction technique to solve crystal structures of various proteins and nucleic acids of biological and medical relevance. The section is also specializing in analyzing crystal structures at extremely high resolution and accuracy and in developing methods of effective diffraction data collection and in using weak anomalous dispersion effects to solve structures of macromolecules. The areas of expertise are: Structural and molecular biology Macromolecular crystallography Diffraction data collection Dr. Dauter requires research support in these areas, and the individual will engage in the purification and preparation of samples, crystallize proteins using various techniques, and derivatize them with heavy atoms/anomalous scatterers, and establish conditions for cryogenic freezing. Individual will also participate in diffraction data collection at the Advanced Photon Source. In addition, the candidate will perform spectroscopic and chromatographic analyses of protein and nucleic acid samples in the context of their purity, oligomeric state and photophysical properties.

Diffractive-refractive optics: X-ray splitter.

PubMed

Hrdý, Jaromír

2010-01-01

The possibility of splitting a thin (e.g. undulator) X-ray beam based on diffraction-refraction effects is discussed. The beam is diffracted from a crystal whose diffracting surface has the shape of a roof with the ridge lying in the plane of diffraction. The crystal is cut asymmetrically. One half of the beam impinges on the left-hand part of the roof and the other half impinges on the right-hand side of the roof. Owing to refraction the left part of the beam is deviated to the left whereas the right part is deviated to the right. The device proposed consists of two channel-cut crystals with roof-like diffraction surfaces; the crystals are set in a dispersive position. The separation of the beams after splitting is calculated at a distance of 10 m from the crystals for various asymmetry and inclination angles. It is shown that such a splitting may be utilized for long beamlines. Advantages and disadvantages of this method are discussed.

Effect of Li and NH4 doping on the crystal perfection, second harmonic generation efficiency and laser damage threshold of potassium pentaborate crystals

NASA Astrophysics Data System (ADS)

Vigneshwaran, A. N.; Kalainathan, S.; Raja, C. Ramachandra

2018-03-01

Potassium pentaborate (KB5) is an excellent nonlinear optical material especially in the UV region. In this work, Li and NH4 doped KB5 crystals were grown using slow evaporation solution growth method. The incorporation of dopant has been confirmed and analysed by Energy dispersive X-ray analysis (EDAX), Inductively coupled plasma (ICP) analysis and Raman spectroscopy. The crystalline perfection of pure and doped KB5 crystals was studied by High resolution X-ray diffraction (HRXRD) analysis. Structural grain boundaries were observed in doped crystals. Second harmonic generation was confirmed for pure and doped crystals and output values revealed the enhancement of SHG efficiency in doped crystals. Resistance against laser damage was carried out using 1064 nm Nd-YAG laser of pulse width 10 ns. The laser damage threshold value is increased in Li doped crystal and decreased in NH4 doped crystal when compared to pure KB5 crystal.

Synchrotron X-ray reciprocal-space mapping, topography and diffraction resolution studies of macromolecular crystal quality.

PubMed

Boggon, T J; Helliwell, J R; Judge, R A; Olczak, A; Siddons, D P; Snell, E H; Stojanoff, V

2000-07-01

A comprehensive study of microgravity and ground-grown chicken egg-white lysozyme crystals is presented using synchrotron X-ray reciprocal-space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed reduced intrinsic mosaicities on average, but no differences in terms of strain over their ground-grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the ground-control case only a small volume of the crystal contributed to the intensity at the diffraction peak. The techniques prove to be highly complementary, with the reciprocal-space mapping providing a quantitative measure of the crystal mosaicity and strain (or variation in lattice spacing) and the topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out at the synchrotron.

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin

PubMed Central

Jaimohan, S. M.; Naresh, M. D.; Arumugam, V.; Mandal, A. B.

2009-01-01

Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemo­globins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 Å resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 Å, β = 109.35°. Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit. PMID:19851014

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin.

PubMed

Jaimohan, S M; Naresh, M D; Arumugam, V; Mandal, A B

2009-10-01

Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 A resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 A, beta = 109.35 degrees . Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

NASA Technical Reports Server (NTRS)

Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

2000-01-01

A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

Growth and characterization of a third order nonlinear optical single crystal: Ethylenediamine-4-nitrophenolate monohydrate

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

Dhanalakshmi, B.; Ponnusamy, S., E-mail: suruponnus@gmail.com; Muthamizhchelvan, C.

2015-10-15

Highlights: • EDA4NPH crystal possesses negative nonlinear refractive index. • The crystal exhibits high third-order NLO susceptibility. • Wide transparency of the crystal makes it suitable for NLO applications. • Dielectric studies substantiate the suitability for electro-optic applications. • The crystal possesses suitable mechanical strength for device fabrication. - Abstract: Bulk crystals of the charge-transfer complex, ethylenediamine-4-nitrophenolate monohydrate, were grown by slow solvent evaporation method from aqueous solution at room temperature. The X-ray diffraction measurements showed that the crystal belongs to centrosymmetric space group C2/c of monoclinic system. The functional groups in the complex were identified using FTIR, FTRaman andmore » FTNMR analyses. The Z-scan measurements revealed the negative nonlinear refractive index of the crystal. The nonlinear absorption coefficient and third order nonlinear optical susceptibility calculated from the measurements were −3.5823 × 10{sup −3} cm/W and 2.3762 × 10{sup −6} esu respectively. The crystal was shown to be highly transparent above 366 nm by UV–vis spectroscopy and a yellow fluorescence was observed from PL spectrum. The TG–DTA and DSC analyses showed that the crystal is thermally stable up to 117.4 °C. The crystals were characterized by dielectric, etching and microhardness studies.« less

Application of a real-space three-dimensional image reconstruction method in the structural analysis of noncrystalline biological macromolecules enveloped by water in coherent x-ray diffraction microscopy.

PubMed

Kodama, Wataru; Nakasako, Masayoshi

2011-08-01

Coherent x-ray diffraction microscopy is a novel technique in the structural analyses of particles that are difficult to crystallize, such as the biological particles composing living cells. As water is indispensable for maintaining particles in functional structures, sufficient hydration of targeted particles is required during sample preparation for diffraction microscopy experiments. However, the water enveloping particles also contributes significantly to the diffraction patterns and reduces the electron-density contrast of the sample particles. In this study, we propose a protocol for the structural analyses of particles in water by applying a three-dimensional reconstruction method in real space for the projection images phase-retrieved from diffraction patterns, together with a developed density modification technique. We examined the feasibility of the protocol through three simulations involving a protein molecule in a vacuum, and enveloped in either a droplet or a cube-shaped water. The simulations were carried out for the diffraction patterns in the reciprocal planes normal to the incident x-ray beam. This assumption and the simulation conditions corresponded to experiments using x-ray wavelengths of shorter than 0.03 Å. The analyses demonstrated that our protocol provided an interpretable electron-density map. Based on the results, we discuss the advantages and limitations of the proposed protocol and its practical application for experimental data. In particular, we examined the influence of Poisson noise in diffraction patterns on the reconstructed three-dimensional electron density in the proposed protocol.

Synthesis and characterization of 3-acetoxy-2-methyl-N-(phenyl)benzamide and 3-acetoxy-2-methyl-N-(4- methylphenyl)benzamide

NASA Astrophysics Data System (ADS)

Kırca, Başak Koşar; Çakmak, Şükriye; Kütük, Halil; Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2018-01-01

This study treats about two successfully synthesized secondary amide compounds 3-Acetoxy-2-methyl-N-(phenyl)benzamide, I and 3-Acetoxy-2-methyl-N-(4-methylphenyl)benzamide, II. Compounds were characterized by FTIR, 1H NMR, 13C NMR and X-ray single crystal diffraction analysis techniques. Single crystal X-ray diffraction analyses show that while I crystallized in the orthorhombic system with space group Pbca, II crystallized in the triclinic system with space group P-1 and the asymmetric unit of II consists of two crystallographically independent molecules. Lattice constants are a = 7.9713 (3) Å, b = 9.5059 (3) Å, c = 37.1762 (2) Å, Z = 8 for I and a = 7.5579 (8) Å, b = 8.8601 (8) Å, c = 23.363 (3) Å, α = 97.011 (9) °, β = 96.932 (9)°, γ = 90.051 (8)°, Z = 4 for II. Crystallographic studies also show that the supramolecular structures were stabilized by intramolecular, intermolecular hydrogen bonds and Csbnd H … π interactions for both compounds. Characteristic amide bonds were observed in IR and NMR spectra.

1D cyanide complexes with 2-pyridinemethanol: Synthesis, crystal structures and spectroscopic properties

NASA Astrophysics Data System (ADS)

Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer

2015-12-01

Two new one-dimensional coordination polymers, [Cu(hmpH)2Pd(μ-CN)2(CN)2]n (1) and [Cu(hmpH)2Pt(μ-CN)2(CN)2]n (2), (hmpH = 2-pyridinemethanol), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. Single crystal X-ray diffraction analysis indicates that complexes 1 and 2 are isomorphous and isostructural, and crystallize in the triclinic system and P-1 space group. The Pd(II) or Pt(II) ions are four coordinated with four cyanide-carbon atoms in a square planar geometry. Cu(II) ion displays a distorted octahedral coordination by two N-atoms and two O-atoms of hmpH ligands, two bridging cyanide groups. In one dimensional structure of the complexes, [M(CN)4]2- (M = Pd(II) or Pt(II)) anions and [Cu(hmpH)2]2+ cations are linked via bridging cyanide ligands. In the complexes, the presence of intramolecular C-H⋯M (M = Pd(II) or Pt(II)) interactions with distance values of 3.00-2.95 Å are established, respectively.

Crystal structure, spectral property, antimicrobial activity and DFT calculation of N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea

NASA Astrophysics Data System (ADS)

Zhang, Hong-Song; Zhang, Kong-Yan; Chen, Li-Chuan; Li, Yao-Xin; Chai, Lan-Qin

2017-10-01

N-(coumarin-3-yl)-N‧-(2-amino-5-phenyl-1,3,4-thiadiazol-2-yl) urea was synthesized and characterized by elemental analysis, IR, 1H NMR, 13C NMR, UV-Vis and emission spectroscopy, as well as by single-crystal X-ray diffraction. X-ray crystallographic analyses have indicated that the crystal structure consists of two dimethyl sulfoxide (DMSO) solvent molecules and the structural geometry of DMSO is a trigonal pyramid in shape. In the crystal structure, a self-assembling two-dimensional (2-D) layer supramolecular architecture is formed through intermolecular hydrogen bonds, Cdbnd O···π (thiadiazole ring) and π···π stacking interactions. The geometry of the compound has been optimized by the DFT method and the results are compared with the X-ray diffraction data. The electronic transitions and spectral features of the compound were carried out by using DFT/B3LYP method. In addition, the antimicrobial activity was also studied, and the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and HOMO-LUMO gap were also calculated.

Observing the overall rocking motion of a protein in a crystal

NASA Astrophysics Data System (ADS)

Ma, Peixiang; Xue, Yi; Coquelle, Nicolas; Haller, Jens D.; Yuwen, Tairan; Ayala, Isabel; Mikhailovskii, Oleg; Willbold, Dieter; Colletier, Jacques-Philippe; Skrynnikov, Nikolai R.; Schanda, Paul

2015-10-01

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall `rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Synthesis, nucleation, growth, structural, spectral, thermal, linear and nonlinear optical studies of novel organic NLO crystal: 4-fluoro 4-nitrostilbene (FONS).

PubMed

Dinakaran, Paul M; Kalainathan, S

2013-03-15

A novel organic nonlinear optical material 4-fluoro 4-nitrostilbene (FONS), with molecular formula (C(14)H(10)FNO(2)) has been synthesized. Using ethyl methyl ketone as solvent, the synthesized material has been repeatedly recrystallized to minimize the impurities and good optical quality single crystals were harvested by slow evaporation method. Single crystal X-ray diffraction analysis reveals that the grown FONS crystal belongs to monoclinic system with noncentrosymmetric space group "P2(1)". The powder X-ray diffraction pattern of FONS has been recorded. Functional groups of the title compound were confirmed by FTIR and the molecular structure was confirmed by (1)HNMR. The UV-vis-NIR absorption study reveals no absorption in the visible region and the cut-off wavelength was found to be at 408 nm. Optical band gap (E(g)) of the grown crystal was found to be 3.27 eV and also the optical constants were determined. Thermal behaviour of the FONS has been studied by TGA/DTA analyses. From the mass spectrum, the ratio of compound formation of FONS was analyzed. The NLO property has been confirmed by Kurtz and Perry powder SHG technique and the SHG efficiency of FONS (262 mV) crystal was found to be 12 times greater than that of KDP (21.7 mV). Copyright © 2013 Elsevier B.V. All rights reserved.

Hemispherical Laue camera

DOEpatents

Li, James C. M.; Chu, Sungnee G.

1980-01-01

A hemispherical Laue camera comprises a crystal sample mount for positioning a sample to be analyzed at the center of sphere of a hemispherical, X-radiation sensitive film cassette, a collimator, a stationary or rotating sample mount and a set of standard spherical projection spheres. X-radiation generated from an external source is directed through the collimator to impinge onto the single crystal sample on the stationary mount. The diffracted beam is recorded on the hemispherical X-radiation sensitive film mounted inside the hemispherical film cassette in either transmission or back-reflection geometry. The distances travelled by X-radiation diffracted from the crystal to the hemispherical film are the same for all crystal planes which satisfy Bragg's Law. The recorded diffraction spots or Laue spots on the film thereby preserve both the symmetry information of the crystal structure and the relative intensities which are directly related to the relative structure factors of the crystal orientations. The diffraction pattern on the exposed film is compared with the known diffraction pattern on one of the standard spherical projection spheres for a specific crystal structure to determine the orientation of the crystal sample. By replacing the stationary sample support with a rotating sample mount, the hemispherical Laue camera can be used for crystal structure determination in a manner previously provided in conventional Debye-Scherrer cameras.

Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

DOE PAGES

Dao, E. Han; Sierra, Raymond G.; Laksmono, Hartawan; ...

2015-04-30

In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS) using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecondmore » X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.« less

Optical, mechanical and thermal behaviors of Nitrilotriacetic acid single crystal

NASA Astrophysics Data System (ADS)

Deepa, B.; Philominathan, P.

2017-11-01

An organic nonlinear single crystal of Nitrilotriacetic acid (NTAA) was grown for the first time by employing a simple slow evaporation technique. Single crystal X-ray diffraction (XRD) analysis reveals that the grown crystal belongs to the monoclinic system with noncentrosymmetric space group CC. Fourier transform infrared (FTIR) spectral study ascertains the presence of functional groups in NTAA. The molecular structure of the grown crystal was confirmed by Nuclear Magnetic Resonance (NMR) spectral analysis. The optical parameters such as transmittance, absorption coefficient and band gap were calculated from UV-Visible and fluorescence studies. Dielectric measurements were carried out for different frequency and temperature. The mechanical strength of the grown crystal was measured using Vickers microhardness test. The high thermal stability and the melting point of the grown crystal were also estimated using thermogravimetric (TGA) and differential thermal analyses (DTA). The confirmation of the grown crystals belonging to nonlinear optical crystals was performed by Kurtz-Perry technique and found as suitable candidate for optoelectronics applications.

Dynamical effects in Bragg coherent x-ray diffraction imaging of finite crystals

NASA Astrophysics Data System (ADS)

Shabalin, A. G.; Yefanov, O. M.; Nosik, V. L.; Bushuev, V. A.; Vartanyants, I. A.

2017-08-01

We present simulations of Bragg coherent x-ray diffractive imaging (CXDI) data from finite crystals in the frame of the dynamical theory of x-ray diffraction. The developed approach is based on a numerical solution of modified Takagi-Taupin equations and can be applied for modeling of a broad range of x-ray diffraction experiments with finite three-dimensional crystals of arbitrary shape also in the presence of strain. We performed simulations for nanocrystals of a cubic and hemispherical shape of different sizes and provided a detailed analysis of artifacts in the Bragg CXDI reconstructions introduced by the dynamical diffraction. Based on our theoretical analysis we developed an analytical procedure to treat effects of refraction and absorption in the reconstruction. Our results elucidate limitations for the kinematical approach in the Bragg CXDI and suggest a natural criterion to distinguish between kinematical and dynamical cases in coherent x-ray diffraction on a finite crystal.

Microporous Cd(II) metal-organic framework as fluorescent sensor for nitroaromatic explosives at the sub-ppm level

NASA Astrophysics Data System (ADS)

Wang, Xing-Po; Han, Lu-Lu; Wang, Zhi; Guo, Ling-Yu; Sun, Di

2016-03-01

A novel Cd(II) metal-organic framework (MOF) based on a rigid biphenyltetracarboxylic acid, [Cd4(bptc)2(DMA)4(H2O)2·4DMA] (1) was successfully synthesized under the solvothermal condition and characterized by single-crystal X-ray diffraction and further consolidated by elemental analyses, powder X-ray diffraction (PXRD), infrared spectra (IR) and luminescent measurements. Single crystal X-ray diffraction analysis reveals that compound 1 is 4-connected PtS (Point symbol: {42·84}) network based on [Cd2(COO)4] secondary building units (SBUs). Its inherent porous and emissive characteristics make them to be a suitable fluorescent probe to sense small solvents and nitroaromatic explosives. Compound 1 shows obviously solvent-dependent emissive behaviors, especially for acetone with very high fluorescence quenching effect. Moreover, compound 1 displays excellent sensing of nitroaromatic explosives at sub-ppm level, giving a detection limit of 0.43 ppm and 0.37 ppm for nitrobenzene (NB) and p-nitrotoluene (PNT), respectively. This shows this Cd(II) MOF can be used as fluorescence probe for the detection of nitroaromatic explosives.

Invited Review Article: Development of crystal lenses for energetic photons

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

Smither, Robert K.

2014-08-15

This paper follows the development of crystal diffraction lenses designed to focus energetic photons. It begins with the search for a solution to the astrophysics problem of how to detect weak astrophysics sources of gamma rays and x-rays. This led to the basic designs for a lens and to the understanding of basic limitations of lens design. The discussion of the development of crystal diffraction lenses is divided into two parts: lenses using crystals with mosaic structure, and lenses that use crystals with curved crystal planes. This second group divides into two sub-groups: (1) Curved crystals that are used tomore » increase the acceptance angle of the diffraction of a monochromatic beam and to increase the energy bandwidth of the diffraction. (2) Curved crystals used to focus gamma ray beams. The paper describes how these two types of crystals affect the design of the corresponding crystal lenses in different fields: astrophysics, medical imaging, detection of weak, distant, gamma-ray sources, etc. The designs of crystal lenses for these applications are given in enough detail to allow the reader to design a lens for his own application.« less

Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystals

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

Haugh, M. J., E-mail: haughmj@nv.doe.gov; Jacoby, K. D.; Wu, M.

2014-11-15

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals thatmore » we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories in Albuquerque, New Mexico. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a double crystal diffractometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.« less

Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O -demethylase crystals by the microseeding method

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

Harada, Ayaka; Sato, Yukari; Kamimura, Naofumi

2016-11-30

A tetrahydrofolate-dependentO-demethylase, LigM, from Sphingobiumsp. SYK-6 was crystallized by the hanging-drop vapour-diffusion method. However, the obtained P3 121 orP3 221 crystals, which diffracted to 2.5–3.3 Å resolution, were hemihedrally twinned. To overcome the twinning problem, microseeding using P3 121/P3 2 21 crystals as microseeds was performed with optimization of the reservoir conditions. As a result, another crystal form was obtained. The newly obtained crystal diffracted to 2.5–3.0 Å resolution and belonged to space group P2 12 12, with unit-cell parametersa= 102.0,b= 117.3,c = 128.1 Å. The P2 12 12 crystals diffracted to better than 2.0 Å resolution after optimizing themore » cryoconditions. Phasing using the single anomalous diffraction method was successful at 3.0 Å resolution with a Pt-derivative crystal. This experience suggested that microseeding is an effective method to overcome the twinning problem, even when twinned crystals are utilized as microseeds.« less

Phase diagram of a crystalline protein: Determination of the solubility of concanavalin A by a microquantitation assay

NASA Astrophysics Data System (ADS)

Mikol, Vincent; Giegé, Richard

1989-09-01

A quick and miniature method has been devised for determining protein solubility and used to investigate the equilibrium solubility of concanavalin A from the Jack Bean with its crystals as a function of ammonium sulfate concentration, temperature and pH. The crystals were characterized by X-ray diffraction and their morphologies related to the corresponding solubilities. The protein solution concentration was estimated out of small crystallizing drops using a rapid and sensitive microassay. Measurements of protein quantity were carried out in 96-well microplates in an automatic spectrophotometer. The resulting phase diagram has permitted to analyse the solubility of concanavalin A, to estimate supersaturation and to devise readily new ways of crystal growth of this lectin, namely by pH and temperature variations. Moreover, the approach is proved to be a valuable tool to design crystallization experiments of new molecules and to improve and control protein crystal growth.

Unique isothermal crystallization behavior of novel polyphenylene sulfide/inorganic fullerene-like WS2 nanocomposites.

PubMed

Naffakh, Mohammed; Marco, Carlos; Gómez, Marián A; Jiménez, Ignacio

2008-11-27

The isothermal crystallization of polyphenylene sulfide (PPS) nanocomposites with inorganic fullerene-like tungsten disulfide nanoparticles (IF-WS2) has been studied from a thermal and morphological point of view, using differential scanning calorimetry (DSC), scanning electron microscopy (SEM), polarized optical microscopy (POM) and time-resolved synchrotron X-ray diffraction. All the analyses revealed that the incorporation of the IF-WS2 altered significantly the crystallization behavior of PPS, in a way strongly dependent with the nanocomposite composition. The addition of IF-WS2 in 0.1 wt % proportion retarded the crystallization of PPS by increasing its fold surface free energy in a 10%. However, addition of the nanoparticles in excess of 1 wt % results in a promotion of the crystallization rate with reduction of the fold surface free energy to half the value of pure PPS.

Observation of divergent-beam X-ray diffraction from a crystal of diamond using synchrotron radiation.

PubMed

Glazer, A M; Collins, S P; Zekria, D; Liu, J; Golshan, M

2004-03-01

In 1947 Kathleen Lonsdale conducted a series of experiments on X-ray diffraction using a divergent beam external to a crystal sample. Unlike the Kossel technique, where divergent X-rays are excited by the presence of fluorescing atoms within the crystal, the use of an external divergent source made it possible to study non-fluorescing crystals. The resulting photographs not only illustrated the complexity of X-ray diffraction from crystals in a truly beautiful way, but also demonstrated unprecedented experimental precision. This long-forgotten work is repeated here using a synchrotron radiation source and, once again, considerable merit is found in Lonsdale's technique. The results of this experiment suggest that, through the use of modern 'third-generation' synchrotron sources, divergent-beam diffraction could soon enjoy a renaissance for high-precision lattice-parameter determination and the study of crystal perfection.

Surface-treated self-standing curved crystals as high-efficiency elements for X- and γ-ray optics: theory and experiment.

PubMed

Bonnini, Elisa; Buffagni, Elisa; Zappettini, Andrea; Doyle, Stephen; Ferrari, Claudio

2015-06-01

The efficiency of a Laue lens for X- and γ-ray focusing in the energy range 60-600 keV is closely linked to the diffraction efficiency of the single crystals composing the lens. A powerful focusing system is crucial for applications like medical imaging and X-ray astronomy where wide beams must be focused. Mosaic crystals with a high density, such as Cu or Au, and bent crystals with curved diffracting planes (CDPs) are considered for the realization of a focusing system for γ-rays, owing to their high diffraction efficiency in a predetermined angular range. In this work, a comparison of the efficiency of CDP crystals and Cu and Au mosaic crystals was performed on the basis of the theory of X-ray diffraction. Si, GaAs and Ge CDP crystals with optimized thicknesses and moderate radii of curvature of several tens of metres demonstrate comparable or superior performance with respect to the higher atomic number mosaic crystals generally used. In order to increase the efficiency of the lens further, a stack of several CDP crystals is proposed as an optical element. CDP crystals were obtained by a surface-damage method, and a stack of two surface-damaged bent Si crystals was prepared and tested. Rocking curves of the stack were performed with synchrotron radiation at 19 keV to check the lattice alignment: they exhibited only one diffraction peak.

Diffraction of real and virtual photons in a pyrolytic graphite crystal as source of intensive quasimonochromatic X-ray beam

NASA Astrophysics Data System (ADS)

Bogomazova, E. A.; Kalinin, B. N.; Naumenko, G. A.; Padalko, D. V.; Potylitsyn, A. P.; Sharafutdinov, A. F.; Vnukov, I. E.

2003-01-01

A series of experiments on the parametric X-rays radiation (PXR) generation and radiation soft component diffraction of relativistic electrons in pyrolytic graphite (PG) crystals have been carried out at the Tomsk synchrotron. It is shown that the experimental results with PG crystals are explained by the kinematic PXR theory if we take into account a contribution of the real photons diffraction (transition radiation, bremsstrahlung and PXR photons as well). The measurements of the emission spectrum of channeled electrons in the photon energy range much smaller than the characteristic energy of channeling radiation have been performed with a crystal-diffraction spectrometer. For electrons incident along the <1 1 0> axis of a silicon crystal, the radiation intensity in the energy range 30⩽ ω⩽360 keV exceeds the bremsstrahlung one almost by an order of magnitude. Different possibilities to create an effective source of the monochromatic X-ray beam based on the real and virtual photons diffraction in the PG crystals have been considered.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of α-11 giardin from Giardia lamblia

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

Pathuri, Puja; Nguyen, Emily Tam; Luecke, Hartmut, E-mail: hudel@uci.edu

2006-11-01

α-11 giardin from the intestinal protozoan parasite, G. lamblia has been cloned, expressed, purified and crystallized under two different conditions and in two different space groups. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group and crystals obtained in the second condition diffracted to 2.93 Å and belong to a primitive monoclinic space group. α-11 Giardin, a protein from the annexin superfamily, is a 35.0 kDa protein from the intestinal protozoan parasite Giardia lamblia which triggers a form of diarrhea called giardiasis. Here, the cloning, expression, purification and the crystallization of α-11more » giardin under two different conditions and in two different space groups is reported. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group, while crystals from the second condition, which included calcium in the crystallization solution, diffracted to 2.93 Å and belong to a primitive monoclinic space group. Determination of the detailed atomic structure of α-11 giardin will provide a better insight into its biological function and might establish whether this class of proteins is a potential drug target against giardiasis.« less

One-step aluminium-assisted crystallization of Ge epitaxy on Si by magnetron sputtering

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

Liu, Ziheng, E-mail: ziheng.liu@unsw.edu.au; Hao, Xiaojing; Ho-Baillie, Anita

In this work, one-step aluminium-assisted crystallization of Ge on Si is achieved via magnetron sputtering by applying an in-situ low temperature (50 °C to 150 °C) heat treatment in between Al and Ge depositions. The effect of heat treatment on film properties and the growth mechanism of Ge epitaxy on Si are studied via X-ray diffraction, Raman and transmission electron microscopy analyses. Compared with the conventional two-step process, the one-step aluminium-assisted crystallization requires much lower thermal budget and results in pure Ge epitaxial layer, which may be suitable for use as a virtual substrate for the fabrication of III-V solar cells.

Synthesis, Characterization, Crystal Structure, and Biological Studies of a Cadmium(II) Complex with a Tridentate Ligand 4′-Chloro-2,2′:6′,2′′-Terpyridine

PubMed Central

Saghatforoush, L. A.; Valencia, L.; Chalabian, F.; Ghammamy, Sh.

2011-01-01

A new Cd(II) complex with the ligand 4′-chloro-2,2′6′,2′′-terpyridine (Cltpy), [Cd(Cltpy)(I)2], has been synthesized and characterized by CHN elemental analysis, 1H-NMR, 13C-NMR, and IR spectroscopy and structurally analyzed by X-ray single-crystal diffraction. The single-crystal X-ray analyses show that the coordination number in complex is five with three terpyridine (Cltpy) N-donor atoms and two iodine atoms. The antibacterial activities of Cltpy and its Cd(II) complex are tested against different bacteria. PMID:21738495

Guidelines for the successful generation of protein–ligand complex crystals

PubMed Central

Müller, Ilka

2017-01-01

With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein–ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make a good crystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting. PMID:28177304

A drunken search in crystallization space

PubMed Central

Fazio, Vincent J.; Peat, Thomas S.; Newman, Janet

2014-01-01

The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the PDB. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40% of the crystallization conditions found currently in the PDB are identical or very similar to a commercial condition. PMID:25286930

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

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

Measuring the X-ray Resolving Power of Bent Potassium Acid Phthalate Diffraction Crystals

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

Haugh, M. J.; Wu, M.; Jacoby, K. D.

2014-11-01

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals thatmore » we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories (SNL) in Albuquerque, NM. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a dual goniometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.« less

Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystalsa)

NASA Astrophysics Data System (ADS)

Haugh, M. J.; Wu, M.; Jacoby, K. D.; Loisel, G. P.

2014-11-01

This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals that we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories in Albuquerque, New Mexico. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a double crystal diffractometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography.

PubMed

Gicquel, Yannig; Schubert, Robin; Kapis, Svetlana; Bourenkov, Gleb; Schneider, Thomas; Perbandt, Markus; Betzel, Christian; Chapman, Henry N; Heymann, Michael

2018-04-24

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 µm grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources.

PubMed

Tang, M X; Zhang, Y Y; E, J C; Luo, S N

2018-05-01

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic-plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

Three-dimensional Bragg diffraction in growth-disordered opals

NASA Astrophysics Data System (ADS)

Baryshev, A. V.; Kaplyanskii, Alexander A.; Kosobukin, Vladimir A.; Limonov, M. F.; Samusev, K. B.; Usvyat, D. E.

2003-06-01

After artificial opals as well as opal-based infilled and inverted composites are considered to be promising representatives of photonic crystal materials. Earlier, photonic stop gaps in opals were studied mainly in transmission or specular reflection geometries corresponding to "one-dimensional" Bragg diffraction. On the contrary, this work was aimed at observing the typical patterns of optical Bragg diffraction in which phenomenon opal crystal structure acts as a three-dimensional diffraction grating. Although our experiments were performed for artificial opals possessing unavoidable imperfections a well-pronounced diffraction peaks were observed characteristic of a crystal structure. Each of the diffraction maxima reveals a photonic stop gap in the specified direction, while the spectral width of the peak is a measure of the photonic stop gap width.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources

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

Tang, M. X.; Zhang, Y. Y.; E, J. C.

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of themore » diffraction patterns is discussed.« less

Effect of niobium content on the microstructure and thermal properties of fluorapatite glass-ceramics.

PubMed

Denry, I L; Holloway, J A; Nakkula, R J; Walters, J D

2005-10-01

Niobium oxide has been shown to improve biocompatibility and promote bioactivity. The purpose of this study was to evaluate the effect of niobium oxide additions on the microstructure and thermal properties of fluorapatite glass-ceramics for biomedical applications. Four glass-ceramic compositions with increasing amounts of niobium oxide from 0 to 5 wt % were prepared. The glass compositions were melted at 1,525 degrees C for 3 h, quenched, ground, melted again at 1,525 degrees C for 3 h and furnace cooled. The coefficient of thermal expansion was measured by dilatometry. The crystallization behavior was evaluated by differential thermal analysis. The nature of the crystalline phases was investigated by X-ray diffraction. The microstructure was studied by SEM. In addition, the cytotoxicity of the ceramics was evaluated according to the ASTM standard F895--84. The results from X-ray diffraction analyses showed that fluorapatite was the major crystalline phase in all glass-ceramics. Differential thermal analyses revealed that fluorapatite crystallization occurred between 800 and 934 degrees C depending on the composition. The coefficient of thermal expansion varied from 7.6 to 9.4 x 10(-6)/ degrees C. The microstructure after heat treatment at 975 degrees C for 30 min consisted of submicroscopic fluorapatite crystals (200--300 nm) for all niobium-containing glass-ceramics, whereas the niobium-free glass-ceramic contained needle-shaped fluorapatite crystals, 2 microm in length. None of the glass-ceramics tested exhibited any cytotoxic activity as tested by ASTM standard F895--84. (c) 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2005.

Growth, structural, optical, thermal and laser damage threshold studies of an organic single crystal: 1,3,5 – triphenylbenzene (TPB)

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

Raja, R. Subramaniyan; Babu, G. Anandha; Ramasamy, P., E-mail: E-mail-ramasamyp@ssn.edu.in

2016-05-23

Good quality single crystals of pure hydrocarbon 1,3,5-Triphenylbenzene (TPB) have been successfully grown using toluene as a solvent using controlled slow cooling solution growth technique. TPB crystallizes in orthorhombic structure with the space group Pna2{sub 1}. The structural perfection of the grown crystal has been analysed by high resolution X-ray diffraction measurements. The range and percentage of the optical transmission are ascertained by recording the UV-vis spectrum. Thermo gravimetric analysis (TGA) and differential thermal analysis (DTA) were used to study its thermal properties. Powder second harmonic generation studies were carried out to explore its NLO properties. Laser damage threshold valuemore » has been determined using Nd:YAG laser operating at 1064 nm.« less

Crystal regularity with high-resolution synchrotron X-radiation diffraction imaging

NASA Technical Reports Server (NTRS)

Steiner, Bruce; Dobbyn, Ronald C.

1991-01-01

New, high-resolution sources of X-radiation such as monochromatic synchrotron radiation beams with subarcsec divergence allow observation of regularities in a range of crystals with sufficient clarity for comprehensive analyses, whose results can deepen understanding of the nature of various crystal irregularities, their sources, and their effects on device performance. An account is presented of the results thus achievable with irregularities encountered in lattice orientation and strain, grain and subgrain boundaries, dislocations, domain boundaries, additional phases, and surface scratches. Significant achievements to date encompass the observation of critical anomalies in lead tin telluride, the reconciliation of disparate observations of GaAs, the determination of the performance effects of irregularities in mercuric iodide, and the characterization of the origins of crystal growth in bismuth silicon oxide.

Diffraction and Imaging Study of Imperfections of Protein Crystals with Coherent X-rays

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Thomas, B. R.; Chernov, A. A.; Chu, Y. S.; Lai, B.

2004-01-01

High angular-resolution x-ray diffraction and phase contrast x-ray imaging were combined to study defects and perfection of protein crystals. Imperfections including line defects, inclusions and other microdefects were observed in the diffraction images of a uniformly grown lysozyme crystal. The observed line defects carry distinct dislocation features running approximately along the <110> growth front and have been found to originate mostly in a central growth area and occasionally in outer growth regions. Slow dehydration led to the broadening of a fairly symmetric 4 4 0 rocking curve by a factor of approximately 2.6, which was primarily attributed to the dehydration-induced microscopic effects that are clearly shown in diffraction images. X-ray imaging and diffraction characterization of the quality of apoferritin crystals will also be discussed in the presentation.

Crystallization of human nicotinamide phosphoribosyltransferase

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

Takahashi, Ryo; Nakamura, Shota; Yoshida, Takuya

2007-05-01

Human nicotinamide phosphoribosyltransferase has been crystallized using microseeding methods and X-ray diffraction data have been collected at 2.0 Å resolution. In the NAD biosynthetic pathway, nicotinamide phosphoribosyltransferase (NMPRTase; EC 2.4.2.12) plays an important role in catalyzing the synthesis of nicotinamide mononucleotide from nicotinamide and 5′-phosphoribosyl-1′-pyrophosphate. Because the diffraction pattern of the initally obtained crystals was not suitable for structure analysis, the crystal quality was improved by successive use of the microseeding technique. The resultant crystals diffracted to 2.0 Å resolution. These crystals belonged to space group P21, with unit-cell parameters a = 60.56, b = 106.40, c = 82.78 Å.more » Here, the crystallization of human NMPRTase is reported in the free form; the crystals should be useful for inhibitor-soaking experiments on the enzyme.« less

Continuous diffraction of molecules and disordered molecular crystals

PubMed Central

Yefanov, Oleksandr M.; Ayyer, Kartik; White, Thomas A.; Barty, Anton; Morgan, Andrew; Mariani, Valerio; Oberthuer, Dominik; Pande, Kanupriya

2017-01-01

The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities. This situation arises in the continuous diffraction of laser-aligned molecules or translationally disordered molecular crystals. This paper develops the analysis of the intensity statistics of such continuous diffraction to obtain parameters such as scaling, beam coherence and the number of contributing independent object orientations. When measured, continuous molecular diffraction is generally weak and accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities or their mean value to guide the subtraction of the background, it is shown how all measured values can be utilized to estimate the background, noise and signal, by employing a modified ‘noisy Wilson’ distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously published continuous diffraction data measured from crystals of photosystem II [Ayyer et al. (2016 ▸), Nature, 530, 202–206]. PMID:28808434

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

Structural, optical, mechanical and dielectric studies of pure and doped L-Prolinium trichloroacetate single crystals.

PubMed

Renuka, N; Ramesh Babu, R; Vijayan, N; Vasanthakumar, Geetha; Krishna, Anuj; Ramamurthi, K

2015-02-25

In the present work, pure and metal substituted L-Prolinium trichloroacetate (LPTCA) single crystals were grown by slow evaporation method. The grown crystals were subjected to single crystal X-ray diffraction (XRD), powder X-ray diffraction, FTIR, UV-Visible-NIR, hardness, photoluminescence and dielectric studies. The dopant concentration in the crystals was measured by inductively coupled plasma (ICP) analysis. Single crystal X-ray diffraction studies of the pure and metal substituted LPTCA revealed that the grown crystals belong to the trigonal system. Ni(2+) and Co(2+) doping slightly altered the lattice parameters of LPTCA without affecting the basic structure of the crystal. FTIR spectral analysis confirms the presence of various functional groups in the grown crystals. The mechanical behavior of pure and doped crystals was analyzed by Vickers's microhardness test. The optical transmittance, dielectric and photoluminescence properties of the pure and doped crystals were analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

Crystal growth, differential gas adsorption, high thermal stability, and reversible coordination of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O)

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

Halake, Shobha; Ok, Kang Min, E-mail: kmok@cau.ac.kr

2015-11-15

Single crystals of two barium-organic framework materials, Ba(SBA)(DMF){sub 4} (CAUMOF-15) and Ba{sub 2}(BTEC)(H{sub 2}O) (CAUMOF-16), have been grown through solvothermal reactions (H{sub 2}SBA=4,4′-sulfonyldibenzoic acid and H{sub 4}BTEC=1,2,4,5-benzenetetracarboxylic acid). The crystal structures of the reported frameworks have been determined by single-crystal X-ray diffraction. The materials have been fully characterized by powder X-ray diffraction (PXRD), elemental analyses, Infrared (IR) spectroscopy, and thermogravimetric analyses (TGA). CAUMOF-15 reveals a three-dimensional open-framework that comprises of an inorganic motif with one-dimensional chains and the SBA linkers. CAUMOF-16 shows another three-dimensional backbone consisting of layers of edge-shared BaO{sub 9} and BaO{sub 10} polyhedra, and BTEC pillars. Bothmore » of the 3D frameworks exhibit relatively high thermal stabilities. The PXRD and IR spectral data confirm that CAUMOF-15 and CAUMOF-16 reveal reversible coordinations of the respective solvent molecules, DMF and H{sub 2}O. Gas adsorption properties towards nitrogen, hydrogen, and carbon dioxide have been also investigated. - Graphical abstract: Crystals of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O), exhibiting a differential gas adsorption, a high thermal stability, and a reversible coordination of solvent molecules have been grown. - Highlights: • Crystals of two new 3D Ba-MOFs are grown. • The two Ba-MOFs reveal very high thermal stabilities up to ca. 400 °C. • Ba(SBA)(DMF){sub 4} exhibits differential gas adsorption properties. • The two Ba-MOFs show reversible coordination of the solvent molecules.« less

Further Improvement of the RITS Code for Pulsed Neutron Bragg-edge Transmission Imaging

NASA Astrophysics Data System (ADS)

Sato, H.; Watanabe, K.; Kiyokawa, K.; Kiyanagi, R.; Hara, K. Y.; Kamiyama, T.; Furusaka, M.; Shinohara, T.; Kiyanagi, Y.

The RITS code is a unique and powerful tool for a whole Bragg-edge transmission spectrum fitting analysis. However, it has had two major problems. Therefore, we have proposed methods to overcome these problems. The first issue is the difference in the crystallite size values between the diffraction and the Bragg-edge analyses. We found the reason was a different definition of the crystal structure factor. It affects the crystallite size because the crystallite size is deduced from the primary extinction effect which depends on the crystal structure factor. As a result of algorithm change, crystallite sizes obtained by RITS drastically approached to crystallite sizes obtained by Rietveld analyses of diffraction data; from 155% to 110%. The second issue is correction of the effect of background neutrons scattered from a specimen. Through neutron transport simulation studies, we found that the background components consist of forward Bragg scattering, double backward Bragg scattering, and thermal diffuse scattering. RITS with the background correction function which was developed through the simulation studies could well reconstruct various simulated and experimental transmission spectra, but refined crystalline microstructural parameters were often distorted. Finally, it was recommended to reduce the background by improving experimental conditions.

Ionothermal synthesis, crystal structure, and magnetic study of Co2PO4OH isostructural with caminite.

PubMed

Wang, Guangmei; Valldor, Martin; Spielberg, Eike T; Mudring, Anja-Verena

2014-03-17

A new framework cobalt(II) hydroxyl phosphate, Co2PO4OH, was prepared by ionothermal synthesis using 1-butyl-4-methyl-pyridinium hexafluorophosphate as the ionic liquid. As the formation of Co2PO4F competes in the synthesis, the synthesis conditions have to be judiciously chosen to obtain well-crystallized, single phase Co2PO4OH. Single-crystal X-ray diffraction analyses reveal Co2PO4OH crystallizes with space group I41/amd (a = b = 5.2713(7) Å, c = 12.907(3) Å, V = 358.63(10) Å(3), and Z = 4). Astonishingly, it does not crystallize isotypically with Co2PO4F but rather isotypically with the hydroxyl minerals caminite Mg1.33[SO4(OH)0.66(H2O)0.33] and lipscombite Fe(2–y)PO4(OH) (0 ≤ y ≤ 2/3). Phosphate tetrahedra groups interconnect four rod-packed face-sharing ∞(1){CoO(6/2)} octahedra chains to form a three-dimensional framework structure. The compound Co2PO4OH was further characterized by powder X-ray diffraction, Fourier transform–infrared, and ultraviolet–visible spectroscopy, confirming the discussed structure. The magnetic measurement reveals that Co2PO4OH undergoes a magnetic transition and presents at low temperatures a canted antiferromagnetic spin order in the ground state.

Quantitative analysis of crystalline pharmaceuticals in tablets by pattern-fitting procedure using X-ray diffraction pattern.

PubMed

Takehira, Rieko; Momose, Yasunori; Yamamura, Shigeo

2010-10-15

A pattern-fitting procedure using an X-ray diffraction pattern was applied to the quantitative analysis of binary system of crystalline pharmaceuticals in tablets. Orthorhombic crystals of isoniazid (INH) and mannitol (MAN) were used for the analysis. Tablets were prepared under various compression pressures using a direct compression method with various compositions of INH and MAN. Assuming that X-ray diffraction pattern of INH-MAN system consists of diffraction intensities from respective crystals, observed diffraction intensities were fitted to analytic expression based on X-ray diffraction theory and separated into two intensities from INH and MAN crystals by a nonlinear least-squares procedure. After separation, the contents of INH were determined by using the optimized normalization constants for INH and MAN. The correction parameter including all the factors that are beyond experimental control was required for quantitative analysis without calibration curve. The pattern-fitting procedure made it possible to determine crystalline phases in the range of 10-90% (w/w) of the INH contents. Further, certain characteristics of the crystals in the tablets, such as the preferred orientation, size of crystallite, and lattice disorder were determined simultaneously. This method can be adopted to analyze compounds whose crystal structures are known. It is a potentially powerful tool for the quantitative phase analysis and characterization of crystals in tablets and powders using X-ray diffraction patterns. Copyright 2010 Elsevier B.V. All rights reserved.

Quasi van der Waals epitaxy of copper thin film on single-crystal graphene monolayer buffer

NASA Astrophysics Data System (ADS)

Lu, Zonghuan; Sun, Xin; Washington, Morris A.; Lu, Toh-Ming

2018-03-01

Quasi van der Waals epitaxial growth of face-centered cubic Cu (~100 nm) thin films on single-crystal monolayer graphene is demonstrated using thermal evaporation at an elevated substrate temperature of 250 °C. The single-crystal graphene was transferred to amorphous (glass) and crystalline (quartz) SiO2 substrates for epitaxy study. Raman analysis showed that the thermal evaporation method had minimal damage to the graphene lattice during the Cu deposition. X-ray diffraction and electron backscatter diffraction analyses revealed that both Cu films are single-crystal with (1 1 1) out-of-plane orientation and in-plane Σ3 twin domains of 60° rotation. The crystallinity of the SiO2 substrates has a negligible effect on the Cu crystal orientation during the epitaxial growth, implying the strong screening effect of graphene. We also demonstrate the epitaxial growth of polycrystalline Cu on a commercial polycrystalline monolayer graphene consisting of two orientation domains offset 30° to each other. It confirms that the crystal orientation of the epitaxial Cu film follows that of graphene, i.e. the Cu film consists of two orientation domains offset 30° to each other when deposited on polycrystalline graphene. Finally, on the contrary to the report in the literature, we show that the direct current and radio frequency flip sputtering method causes significant damage to the graphene lattice during the Cu deposition process, and therefore neither is a suitable method for Cu epitaxial growth on graphene.

Crystal structure and density of helium to 232 kbar

NASA Technical Reports Server (NTRS)

Mao, H. K.; Wu, Y.; Jephcoat, A. P.; Hemley, R. J.; Bell, P. M.; Bassett, W. A.

1988-01-01

The properties of helium and hydrogen at high pressure are topics of great interest to the understanding of planetary interiors. These materials constitute 95 percent of the entire solar system. A technique was presented for the measurement of X-ray diffraction from single-crystals of low-Z condenses gases in a diamond-anvil cell at high pressure. The first such single-crystal X-ray diffraction measurements on solid hydrogen to 26.5 GPa were presented. The application of this technique to the problem of the crystal structure, equation of state, and phase diagram of solid helium is reported. Crucial for X-ray diffraction studies of these materials is the use of a synchrotron radiation source which provides high brillance, narrow collimation of the incident and diffracted X-ray beams to reduce the background noise, and energy-dispersive diffraction techniques with polychromatic (white) radiation, which provides high detection efficiency.

Controlled nucleation and growth of CdS nanoparticles in a polymer matrix.

PubMed

Di Luccio, Tiziana; Laera, Anna Maria; Tapfer, Leander; Kempter, Susanne; Kraus, Robert; Nickel, Bert

2006-06-29

In-situ synchrotron X-ray diffraction (XRD) was used to monitor the thermal decomposition (thermolysis) of Cd thiolates precursors embedded in a polymer matrix and the nucleation of CdS nanoparticles. A thiolate precursor/polymer solid foil was heated to 300 degrees C in the X-ray diffraction setup of beamline W1.1 at Hasylab, and the diffraction curves were each recorded at 10 degrees C. At temperatures above 240 degrees C, the precursor decomposition is complete and CdS nanoparticles grow within the polymer matrix forming a nanocomposite with interesting optical properties. The nanoparticle structural properties (size and crystal structure) depend on the annealing temperature. Transmission electron microscopy (TEM) and photoluminescence (PL) analyses were used to characterize the nanoparticles. A possible mechanism driving the structural transformation of the precursor is inferred from the diffraction features arising at the different temperatures.

A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids.

PubMed

Zipper, Lauren E; Aristide, Xavier; Bishop, Dylan P; Joshi, Ishita; Kharzeev, Julia; Patel, Krishna B; Santiago, Brianna M; Joshi, Karan; Dorsinvil, Kahille; Sweet, Robert M; Soares, Alexei S

2014-12-01

A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under different conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63-82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. The results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations.

Inelastic neutron scattering experiments with the monochromatic imaging mode of the RITA-II spectrometer

NASA Astrophysics Data System (ADS)

Bahl, C. R. H.; Lefmann, K.; Abrahamsen, A. B.; Rønnow, H. M.; Saxild, F.; Jensen, T. B. S.; Udby, L.; Andersen, N. H.; Christensen, N. B.; Jakobsen, H. S.; Larsen, T.; Häfliger, P. S.; Streule, S.; Niedermayer, Ch.

2006-05-01

Recently a monochromatic multiple data taking mode has been demonstrated for diffraction experiments using a RITA type cold neutron spectrometer with a multi-bladed analyser and a position-sensitive detector. Here, we show how this mode can be used in combination with a flexible radial collimator to perform real inelastic neutron scattering experiments. We present the results from inelastic powder, single crystal dispersion and single crystal constant energy mapping experiments. The advantages and complications of performing these experiments are discussed along with a comparison between the imaging mode and the traditional monochromatic focussing mode.

Spectroscopic investigations using density functional theory on 2-methoxy- 4(phenyliminomethyl)phenol: A non linear optical material

NASA Astrophysics Data System (ADS)

Hijas, K. M.; Madan Kumar, S.; Byrappa, K.; Geethakrishnan, T.; Jeyaram, S.; Nagalakshmi, R.

2018-03-01

Single crystals of 2-methoxy-4(phenyliminomethyl)phenol were grown from ethanol by slow evaporation solution growth technique. Single crystal X-ray diffraction experiment reveals the crystallization in orthorhombic system having non-centrosymmetric space group C2221. Geometrical optimization by density functional theory method was carried out using Gaussian program and compared with experimental results. Detailed experimental and theoretical vibrational analyses were carried out and the results were correlated to find close agreement. Thermal analyses show the material is thermally stable with a melting point of 159 °C. Natural bond orbital analysis was carried out to explain charge transfer interactions through hydrogen bonding. Relatively smaller HOMO-LUMO band gap favors the non linear optical activity of the molecule. Natural population analysis and molecular electrostatic potential calculations visualize the charge distribution in an isolated molecule. Calculated first-order molecular hyperpolarizability and preliminary second harmonic generation test carried out using Kurtz-Perry technique establish 2-methoxy-4(phenyliminomethyl)phenol crystal as a good non linear optical material. Z-scan proposes the material for reverse saturable absorption.

One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

NASA Astrophysics Data System (ADS)

Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

2016-11-01

Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

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.

High resolution synchrotron X-radiation diffraction imaging of crystals grown in microgravity and closely related terrestrial crystals

NASA Technical Reports Server (NTRS)

Steiner, Bruce; Dobbyn, Ronald C.; Black, David; Burdette, Harold; Kuriyama, Masao; Fripp, Archibald; Simchik, Richard

1991-01-01

Irregularities in three crystals grown in space and in four terrestrial crystals grown under otherwise comparable conditions have been observed in high resolution diffraction imaging. The images provide important new clues to the nature and origins of irregularities in each crystal. For two of the materials, mercuric iodide and lead tin telluride, more than one phase (an array of non-diffracting inclusions) was observed in terrestrial samples; but the formation of these multiple phases appears to have been suppressed in directly comparable crystals grown in microgravity. The terrestrial seed crystal of triglycine sulfate displayed an unexpected layered structure, which propagated during directly comparable space growth. Terrestrial Bridgman regrowth of gallium arsenide revealed a mesoscopic structure substantially different from that of the original Czochralski material. A directly comparable crystal is to be grown shortly in space.

Imperfection and radiation damage in protein crystals studied with coherent radiation

PubMed Central

Nave, Colin; Sutton, Geoff; Evans, Gwyndaf; Owen, Robin; Rau, Christoph; Robinson, Ian; Stuart, David Ian

2016-01-01

Fringes and speckles occur within diffraction spots when a crystal is illuminated with coherent radiation during X-ray diffraction. The additional information in these features provides insight into the imperfections in the crystal at the sub-micrometre scale. In addition, these features can provide more accurate intensity measurements (e.g. by model-based profile fitting), detwinning (by distinguishing the various components), phasing (by exploiting sampling of the molecular transform) and refinement (by distinguishing regions with different unit-cell parameters). In order to exploit these potential benefits, the features due to coherent diffraction have to be recorded and any change due to radiation damage properly modelled. Initial results from recording coherent diffraction at cryotemperatures from polyhedrin crystals of approximately 2 µm in size are described. These measurements allowed information about the type of crystal imperfections to be obtained at the sub-micrometre level, together with the changes due to radiation damage. PMID:26698068

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

Li, Na; Mu, Bao; Lv, Lei

Four new polyoxometalate(POM)–templated metal–organic frameworks based on flexible ligands, namely, [Cu{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}Mo{sup VI}{sub 11}O{sub 40}O{sub 2})]·8H{sub 2}O(1), [Cu{sup I}{sub 3}Cu{sup II}{sub 3}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40}){sub 2}(PMo{sup V}{sub 12}O{sub 34})]·8H{sub 2}O(2), [Ni{sub 6}(bip){sub 12}(PMo{sup VI}{sub 12}O{sub 40})(PMo{sup VI}{sub 11}Mo{sup V}O{sub 40}){sub 2}]Cl·6H{sub 2}O(3), [Co{sup II}{sub 3}Co{sup III}{sub 2}(H{sub 2}bib){sub 2}(Hbib){sub 2}(PW{sub 9}O{sub 34}){sub 2}(H{sub 2}O){sub 6}]·6H{sub 2}O(4) (bip=1,3-bis(imidazolyl)propane, bib=1,4-bis(imidazolyl)butane) have been obtained under hydrothermal condition and characterized by single-crystal X-ray diffraction analyses, elemental analyses, and thermogravimetric (TG) analyses. The studies of single crystal X-ray indicate that compounds 1–3 crystallize in the trigonal space groupmore » P-3, and compound 4 crystallizes in the triclinic space group P-1. Compounds 1 and 3 represent 3D frameworks, and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals, while compounds 2 and 4 show 3D frameworks by hydrogen bonds. This compounds provide new examples of host–guest compounds based on flexible bis(imidazole) ligands. In addition, the electrochemical property and the catalytic property of compound 1 have also been investigated. - Graphical abstract: Four inorganic–organic hybrid compounds based polyoxometalates (POMs) and flexible ligands, namely, have been obtained under hydrothermal conditions and characterized by single-crystal X-ray diffraction analyses, elemental analyses, IR spectra, and thermogravimetric (TG) analyses. Compounds 1–3 are new examples of host–guest compounds based on flexible bis(imidazole) ligands and POMs as the guest molecules are incorporated into the cages which are composed of the ligands and metals. - Highlights: • Polyoxometalate–templated metal–organic frameworks have been prepared. • POMs as the guest molecules are incorporated into the cages. • The cages are flexibility based on flexible bis(imidazole) ligands.« less

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

Yin, Fei; Chen, Jing; Liang, Yongfeng

Two coordination polymers [Co(dnbab){sub 2}(bimb)](H{sub 2}O){sub 4} (1) and [Zn(dnbab){sub 2}(bimb)](H{sub 2}O){sub 5} (2) (Hdnbab=4-[(3,5-dinitrobenzoyl)amino]benzoic acid, bimb=1,4-bis(1-imidazolyl) benzene) have been solvothermally synthesized. Their structures have been determined by single-crystal X-ray diffraction analyses and further characterized by powder X-ray diffraction (PXRD) and thermogravimetric (TG) analyses. Complexes 1 and 2 are isostructures and each displays an one-dimensional (1D) zigzag chain, which further forms a 3D supramolecular architecture with 1-D channels via inter-chain π–π interactions and hydrogen bonds. Moreover, the magnetic properties of 1 and fluorescent properties of 2 have been investigated. - Graphical abstract: Two coordination supramolecular frameworks [Co(dnbab){sub 2}(bimb)](H{sub 2}O){sub 4}(1)more » and [Zn(dnbab){sub 2}(bimb)](H{sub 2}O){sub 5}(2) (Hdnbab=4-[(3,5-dinitrobenzoyl)amino]benzoic acid, bimb=1,4-bis(1-imidazolyl) benzene) have been synthesized and characterized by X-ray single-crystal diffraction. Their thermal, magnetic and fluorescent properties have also been studied. - Highlights: • Two isomorphic Co(II)/Zn(II) complexes with the mixed-ligands have been synthesized. • Hydrogen bonds and π–π stacking interactions directed the final 3-D architecture assembly. • Both Co(II) and Zn(II) complexes show good thermal stability. • Co complex exhibits antiferromagnetic interaction. • The fluorescent property of Zn(II) complex has been investigated in the solid state.« less

Crystallization and X-ray diffraction of crystals formed in water-plasticized amorphous lactose.

PubMed

Jouppila, K; Kansikas, J; Roos, Y H

1998-01-01

Effects of storage time and relative humidity on crystallization and crystal forms produced from amorphous lactose were investigated. Crystallization was observed from time-dependent loss of sorbed water and increasing intensities of peaks in X-ray diffraction patterns. The rate of crystallization increased with increasing storage relative humidity. Lactose crystallized mainly as alpha-lactose monohydrate and anhydrous crystals with alpha- and beta-lactose in a molar ratio of 5:3. The results suggested that the crystal form was defined by the early nucleation process. The crystallization data are important in modeling of crystallization phenomena and prediction of stability of lactose-containing food and pharmaceutical materials.

Energy-dispersive neutron imaging and diffraction of magnetically driven twins in a Ni2MnGa single crystal magnetic shape memory alloy

NASA Astrophysics Data System (ADS)

Kabra, Saurabh; Kelleher, Joe; Kockelmann, Winfried; Gutmann, Matthias; Tremsin, Anton

2016-09-01

Single crystals of a partially twinned magnetic shape memory alloy, Ni2MnGa, were imaged using neutron diffraction and energy-resolved imaging techniques at the ISIS spallation neutron source. Single crystal neutron diffraction showed that the crystal produces two twin variants with a specific crystallographic relationship. Transmission images were captured using a time of flight MCP/Timepix neutron counting detector. The twinned and untwinned regions were clearly distinguishable in images corresponding to narrow-energy transmission images. Further, the spatially-resolved transmission spectra were used to elucidate the orientations of the crystallites in the different volumes of the crystal.

Crystallization of Mitochondrial Respiratory Complex II from Chicken Heart: a Membrane Protein Complex Diffracting to 2.0 Å.

PubMed Central

Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward

2006-01-01

Synopsis A multi-subunit mitochondrial membrane protein complex involved in the Krebs Cycle and respiratory chain has been crystallized in a form suitable for near-atomic resolution structure determination. A procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Å with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites. PMID:15805592

Crystallization and X-ray diffraction analysis of a catalytic domain of hyperthermophilic chitinase from Pyrococcus furiosus

PubMed Central

Mine, Shouhei; Nakamura, Tsutomu; Hirata, Kunio; Ishikawa, Kazuhiko; Hagihara, Yoshihisa; Uegaki, Koichi

2006-01-01

The crystallization and preliminary X-ray diffraction analysis of a catalytic domain of chitinase (PF1233 gene) from the hyperthermophilic archaeon Pyrococcus furiosus is reported. The recombinant protein, prepared using an Escherichia coli expression system, was crystallized by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected at the undulator beamline BL44XU at SPring-8 to a resolution of 1.50 Å. The crystals belong to space group P212121, with unit-cell parameters a = 90.0, b = 92.8, c = 107.2 Å. PMID:16880559

Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 β-xylosidase from Geobacillus thermoleovorans IT-08

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

Rohman, Ali; Oosterwijk, Niels van; Kralj, Slavko

2007-11-01

The β-xylosidase was crystallized using PEG 6000 as precipitant. 5% PEG 6000 yielded bipyramid-shaped tetragonal crystals diffracting to 1.55 Å resolution, and 13% PEG 6000 gave rectangular monoclinic crystals diffracting to 1.80 Å resolution. The main enzymes involved in xylan-backbone hydrolysis are endo-1,4-β-xylanase and β-xylosidase. β-Xylosidase converts the xylo-oligosaccharides produced by endo-1,4-β-xylanase into xylose monomers. The β-xylosidase from the thermophilic Geobacillus thermoleovorans IT-08, a member of glycoside hydrolase family 43, was crystallized at room temperature using the hanging-drop vapour-diffusion method. Two crystal forms were observed. Bipyramid-shaped crystals belonging to space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = bmore » = 62.53, c = 277.4 Å diffracted to 1.55 Å resolution. The rectangular crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 57.94, b = 142.1, c = 153.9 Å, β = 90.5°, and diffracted to 1.80 Å resolution.« less

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

NASA Astrophysics Data System (ADS)

Karthigha, S.; Krishnamoorthi, C.

2018-03-01

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

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.

Crystallization of multiple forms of bovine seminal ribonuclease in the liganded and unliganded state

NASA Astrophysics Data System (ADS)

Sica, F.; Adinolfi, S.; Berisio, R.; De Lorenzo, C.; Mazzarella, L.; Piccoli, R.; Vitagliano, L.; Zagari, A.

1999-01-01

Bovine seminal ribonuclease (BS-RNase) is an intriguing homodimeric enzyme which exists as two conformational isomers, characterized by distinct catalytic and biological properties, referred to as M×M and M=M. Reduction of inter-chain disulfide bridges produces a stable monomeric derivative (M) which is still active. This paper reports the screening and optimization of crystallization conditions for growing single diffraction-quality crystals for the various BS-RNase forms. The crystallization trials were performed using both the vapor diffusion and microbatch methods. The M×M dimer was crystallized in the free form from polyethylene glycol (PEG) 4000 at pH 8.5 and as a complex with the substrate analog uridylyl(2'- 5')guanosine (UpG) from an unbuffered ammonium sulfate (AS) solution. These two crystal types diffract X-rays to 2.5 and 1.9 Å resolution, respectively. Two different crystal types were obtained both for the M=M dimer and for the monomeric derivative. (M=M)a crystals, grown from PEG 4000 (8% w/v) at pH 5.6, diffract X-rays to 4.0 Å. At higher PEG concentration (15% w/v) a different crystal type was obtained, (M=M)b, which showed a better diffraction limit (2.5 Å). For the monomer, type (M)a and (M)b crystals, diffracting X-rays to 2.5 Å resolution, were obtained from AS at pH 6.5 and from PEG 4000 at pH 8.5, respectively. A comparison with previously crystallized forms of the dimer M×M and its complexes with uridylyl(2'-5')adenosine and 2'-deoxycytidylyl(3'-5')-2'-deoxyadenosine is also presented. The three-dimensional structure analysis of (M×M)·UpG and (M=M)b is in progress.

Observation of sagittal X-ray diffraction by surface acoustic waves in Bragg geometry.

PubMed

Vadilonga, Simone; Zizak, Ivo; Roshchupkin, Dmitry; Evgenii, Emelin; Petsiuk, Andrei; Leitenberger, Wolfram; Erko, Alexei

2017-04-01

X-ray Bragg diffraction in sagittal geometry on a Y-cut langasite crystal (La 3 Ga 5 SiO 14 ) modulated by Λ = 3 µm Rayleigh surface acoustic waves was studied at the BESSY II synchrotron radiation facility. Owing to the crystal lattice modulation by the surface acoustic wave diffraction, satellites appear. Their intensity and angular separation depend on the amplitude and wavelength of the ultrasonic superlattice. Experimental results are compared with the corresponding theoretical model that exploits the kinematical diffraction theory. This experiment shows that the propagation of the surface acoustic waves creates a dynamical diffraction grating on the crystal surface, and this can be used for space-time modulation of an X-ray beam.

Observation of sagittal X-ray diffraction by surface acoustic waves in Bragg geometry1

PubMed Central

Vadilonga, Simone; Zizak, Ivo; Roshchupkin, Dmitry; Evgenii, Emelin; Petsiuk, Andrei; Leitenberger, Wolfram; Erko, Alexei

2017-01-01

X-ray Bragg diffraction in sagittal geometry on a Y-cut langasite crystal (La3Ga5SiO14) modulated by Λ = 3 µm Rayleigh surface acoustic waves was studied at the BESSY II synchrotron radiation facility. Owing to the crystal lattice modulation by the surface acoustic wave diffraction, satellites appear. Their intensity and angular separation depend on the amplitude and wavelength of the ultrasonic superlattice. Experimental results are compared with the corresponding theoretical model that exploits the kinematical diffraction theory. This experiment shows that the propagation of the surface acoustic waves creates a dynamical diffraction grating on the crystal surface, and this can be used for space–time modulation of an X-ray beam. PMID:28381976

Crystallization and preliminary X-ray diffraction analysis of a chitin-binding domain of hyperthermophilic chitinase from Pyrococcus furiosus

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

Nakamura, Tsutomu; Ishikawa, Kazuhiko; Hagihara, Yoshihisa

The expression, purification and preliminary X-ray diffraction studies of a chitin-binding domain of the chitinase from P. furiosus are reported. The crystallization and preliminary X-ray diffraction analysis of the chitin-binding domain of chitinase from a hyperthermophilic archaeon, Pyrococcus furiosus, are reported. The recombinant protein was prepared using an Escherichia coli overexpression system and was crystallized by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected to 1.70 Å resolution. The crystal belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2. The unit-cell parameters were determined to be a = b = 48.8, c = 85.0 Å.

Highly efficient acousto-optic diffraction in Sn2P2S6 crystals.

PubMed

Martynyuk-Lototska, I Yu; Mys, O G; Grabar, A A; Stoika, I M; Vysochanskii, Yu M; Vlokh, R O

2008-01-01

We have studied the acousto-optic (AO) diffraction in Sn2P2S6 crystals and found that they manifest high values of an AO figure of merit. The above crystals may therefore be used as highly efficient materials in different AO applications.

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

Zipper, Lauren E.; Aristide, Xavier; Bishop, Dylan P.

A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under differentmore » conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63–82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. Ultimately, the results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations.« less

Synthesis, crystal structures and luminescence properties of new multi-component co-crystals of isostructural Co(II) and Zn(II) complexes

NASA Astrophysics Data System (ADS)

Tella, Adedibu C.; Owalude, Samson O.; Omotoso, Mary F.; Olatunji, Sunday J.; Ogunlaja, Adeniyi S.; Alimi, Lukman O.; Popoola, Olugbenga K.; Bourne, Susan A.

2018-04-01

Two novel isostructural compounds containing multi-component co-crystals [M(C6H4NO2)2(H2O)2](C9H6O6)2 (M = Co (1), Zn (2), C6H4NO2 = Picolinic acid, C9H6O6 = Trimesic acid) have been synthesized. The compounds were characterized by elemental analysis, FT-IR, UV-Visible and 1H NMR spectroscopies as well as thermal and single crystal X-ray diffraction analyses. Single crystal X-ray diffraction analysis reveals that 1 and 2 are isostructural. Compound 1 crystallizes in triclinic space group (P-1, with a = 5.154 (10) Å, b = 11.125 (2) Å, c = 14.113 (3) Å, α = 91.01 (3)°, β = 100.54 (3)°, and γ = 102.71 (3)°). In a similar fashion, compound 2 crystallizes in triclinic space group (P-1, with a = 5.1735 (3) Å, b = 11.0930 (10) Å, c = 14.1554 (8) Å, α = 91.70 (3)°, β = 100.26 (3)°, γ = 102.90 (3)°). The metal (II) cation presents distorted MN2O4 octahedral geometry with H2O molecules coordinated to the metal in equatorial position while the picolinic acid molecules are axially coordinated through the pyridine N atom. The two trimesic acid molecules are not part of the first coordination sphere. Compounds 1 and 2 constitute an example of a class of coordination compound of multicomponent crystals having trimesic acid outside the coordination sphere where it is neither protonated or deprotonated. The two compounds were investigated for luminiscence properties.

Preparation and Analysis of RNA Crystals

NASA Technical Reports Server (NTRS)

Todd, Paul

2000-01-01

The crystallization of RiboNucleic Acids (RNA) was studied from the standpoint of mechanisms of crystal growth in three tasks: (1) preparation of high-quality crystals of oligonuclotides for X-ray diffraction, (2) finding pathways to the growth of high-quality crystals for X-ray diffraction and (3) investigation of mechanisms of action of inertial acceleration on crystal growth. In these tasks: (1) RNA crystals were prepared and studied by X-ray diffraction; (2) a pathway to high-quality crystals was discovered and characterized; a combination of kinetic and equilibrium factors could be optimized as described below; and (3) an interplay between purity and gravity was found in a combination of space and ground experiments with nucleic acids and proteins. Most significantly, the rate of concentration of precipitant and RNA can be controlled by membrane-based methods of water removal or by diffusion of multivalent cations across an interface stabilized by a membrane. Oligonucleotide solutions are electrokinetically stabilized colloids, and crystals can form by the controlled addition of multivalent cations.

Structural diversity of silver (I) azine complexes - Effect of substituents and counter anions

NASA Astrophysics Data System (ADS)

Patra, Goutam Kumar; Mukherjee, Anindita; Mitra, Partha; Adarsh, N. N.

2011-08-01

Three new Ag(I) complexes, 1, 2, and 3 of two azine ligands diacetyl dihydrazone ( L1) and benzil dihydrazone ( L2) have been synthesized and characterized by single crystal X-ray diffraction studies (for 2 and 3), X-ray powder diffraction studies( 1 and 2), elemental analyses, IR and UV-VIS spectroscopy and TGA analysis. They represent one-dimensional polymeric assemblies and discrete dinuclear Ag(I) complex depending on functionality of the ligands and the counter anions. Tetrahedral as well as square pyramidal coordination motifs of the silver (I) ions have been observed in the supramolecular designing of such hybrid organic-inorganic materials.

Structure flexibility of the Cu2ZnSnS4 absorber in low-cost photovoltaic cells: from the stoichiometric to the copper-poor compounds.

PubMed

Choubrac, L; Lafond, A; Guillot-Deudon, C; Moëlo, Y; Jobic, S

2012-03-19

Here we present for the very first time a single-crystal investigation of the Cu-poor Zn-rich derivative of Cu(2)ZnSnS(4). Nowadays, this composition is considered as the one that delivers the best photovoltaic performances in the specific domain of Cu(2)ZnSnS(4)-based thin-film solar cells. The existence of this nonstoichiometric phase is definitely demonstrated here in an explicit and unequivocal manner on the basis of powder and single-crystal X-ray diffraction analyses coupled with electron microprobe analyses. Crystals are tetragonal, space group I ̅4, Z = 2, with a = 5.43440(15) Å and c = 10.8382(6) Å for Cu(2)ZnSnS(4) and a = 5.43006(5) Å and c = 10.8222(2) Å for Cu(1.71)Zn(1.18)Sn(0.99)S(4). © 2012 American Chemical Society

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

X-ray plane-wave diffraction effects in a crystal with third-order nonlinearity

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

Balyan, M. K., E-mail: mbalyan@ysu.am

The two-wave dynamical diffraction in the Laue geometry has been theoretically considered for a plane X-ray wave in a crystal with a third-order nonlinear response to the external field. An analytical solution to the problem stated is found for certain diffraction conditions. A nonlinear pendulum effect is analyzed. The nonlinear extinction length is found to depend on the incident-wave intensity. A pendulum effect of a new type is revealed: the intensities of the transmitted and diffracted waves periodically depend on the incidentwave intensity at a fixed crystal thickness. The rocking curves and Borrmann nonlinear effect are numerically calculated.

Synthesis, structure and characterization of a hybrid centrosymmetric material (4-dimethylaminopyridinium nitrate gallic acid monohydrate) well-designed for non-linear optics

NASA Astrophysics Data System (ADS)

Ennaceur, Nasreddine; Jalel, Boutheina; Henchiri, Rokaya; Cordier, Marie; Ledoux-Rak, Isabelle

2018-01-01

Hybrid material: 4-Dimethylaminopyridinium nitrate gallic acid monohydrate abbreviated DNGA monohydrate has been successfully synthesized by slow evaporation method at room temperature. X-ray diffraction (XRD) on a single crystal showed that the latter was crystallized in P-1 space group. Likewise, thermal analyses demonstrated the stability of our crystal up to 80 °C. Besides, the analysis of the infrared spectrum (FTIR), allowed us to confirm the presence of the different groups present in the structure. Furthermore, by studying the UV-Visible spectrum, the transparency of our crystal was proven. Despite the fact that of having a centrosymmetric structure, the nonlinear optical properties of our single crystal, which was tested by Kurtz-Perry technique, proved that its second harmonic generation efficiency was 1.22 times more than that of KDP (potassium dihydrogen phosphate) single crystal. This nonlinear optical behavior of the studied compound was also determined through the calculations of polarizability and first hyperpolarizability values.

Towards protein-crystal centering using second-harmonic generation (SHG) microscopy

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

Kissick, David J.; Dettmar, Christopher M.; Becker, Michael

2013-05-01

The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals has been explored. The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals was explored. These studies included (i) comparison of microcrystal positions in cryoloops as determined by SHG imaging and by X-ray diffraction rastering and (ii) X-ray structure determinations of selected proteins to investigate the potential for laser-induced damage from SHG imaging. In studies using β{sub 2} adrenergic receptor membrane-protein crystals prepared in lipidic mesophase, the crystal locations identified by SHGmore » images obtained in transmission mode were found to correlate well with the crystal locations identified by raster scanning using an X-ray minibeam. SHG imaging was found to provide about 2 µm spatial resolution and shorter image-acquisition times. The general insensitivity of SHG images to optical scatter enabled the reliable identification of microcrystals within opaque cryocooled lipidic mesophases that were not identified by conventional bright-field imaging. The potential impact of extended exposure of protein crystals to five times a typical imaging dose from an ultrafast laser source was also assessed. Measurements of myoglobin and thaumatin crystals resulted in no statistically significant differences between structures obtained from diffraction data acquired from exposed and unexposed regions of single crystals. Practical constraints for integrating SHG imaging into an active beamline for routine automated crystal centering are discussed.« less

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

Sathyalakshmi, R.; Bhagavannarayana, G.; Ramasamy, P.

L-(+)-Glutamic acid hydro bromide, an isomorphic salt of L-glutamic acid hydrochloride, was synthesized and the synthesis was confirmed using Fourier transform infrared analysis. Solubility of the material in water was determined. L-Glutamic acid hydro bromide crystals were grown by low temperature solution growth using the solvent evaporation technique. Single crystal X-ray diffraction studies were carried out and the cell parameters, atomic co-ordinates, bond lengths and bond angles were reported. High-resolution X-ray diffraction studies were carried out and good crystallinity for the grown crystal was observed from the diffraction curve. The grown crystals were subjected to dielectric studies. Ultraviolet-visible-near infrared spectralmore » analysis shows good optical transmission in the visible and infrared region of the grown crystals. The second harmonic generation efficiency of L-glutamic acid hydro bromide crystal was determined using the Kurtz powder test and it was found that it had efficiency comparable with that of the potassium di-hydrogen phosphate crystal.« less

Sequential x-ray diffraction topography at 1-BM x-ray optics testing beamline at the advanced photon source

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

Stoupin, Stanislav, E-mail: sstoupin@aps.anl.gov; Shvyd’ko, Yuri; Trakhtenberg, Emil

2016-07-27

We report progress on implementation and commissioning of sequential X-ray diffraction topography at 1-BM Optics Testing Beamline of the Advanced Photon Source to accommodate growing needs of strain characterization in diffractive crystal optics and other semiconductor single crystals. The setup enables evaluation of strain in single crystals in the nearly-nondispersive double-crystal geometry. Si asymmetric collimator crystals of different crystallographic orientations were designed, fabricated and characterized using in-house capabilities. Imaging the exit beam using digital area detectors permits rapid sequential acquisition of X-ray topographs at different angular positions on the rocking curve of a crystal under investigation. Results on sensitivity andmore » spatial resolution are reported based on experiments with high-quality Si and diamond crystals. The new setup complements laboratory-based X-ray topography capabilities of the Optics group at the Advanced Photon Source.« less

The collection of MicroED data for macromolecular crystallography.

PubMed

Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

2016-05-01

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids

PubMed Central

Zipper, Lauren E.; Aristide, Xavier; Bishop, Dylan P.; Joshi, Ishita; Kharzeev, Julia; Patel, Krishna B.; Santiago, Brianna M.; Joshi, Karan; Dorsinvil, Kahille; Sweet, Robert M.; Soares, Alexei S.

2014-01-01

A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under different conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63–82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. The results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations. PMID:25484231

A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids

DOE PAGES

Zipper, Lauren E.; Aristide, Xavier; Bishop, Dylan P.; ...

2014-11-28

A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under differentmore » conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63–82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. Ultimately, the results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations.« less

Growth and physicochemical properties of second-order nonlinear optical 2-amino-5-chloropyridinium trichloroacetate single crystals

NASA Astrophysics Data System (ADS)

Renugadevi, R.; Kesavasamy, R.

2015-09-01

The growth of organic nonlinear optical (NLO) crystal 2-amino-5-chloropyridinium trichloroacetate (2A5CPTCA) has been synthesized and single crystals have been grown from methanol solvent by slow evaporation technique. The grown crystals were subjected to various characterization analyses in order to find out the suitability for device fabrication. Single crystal X-ray diffraction analysis reveals that 2A5CPTCA crystallizes in monoclinic system with the space group Cc. The grown crystal was further characterized by Fourier transform infrared spectral analysis to find out the functional groups. The nuclear magnetic resonance spectroscopy is a research technique that exploits the magnetic properties of certain atomic nuclei. The optical transparency window in the visible and near-IR (200--1100 nm) regions was found to be good for NLO applications. Thermogravimetric analysis and differential thermal analysis were used to study its thermal properties. The powder second harmonic generation efficiency measurement with Nd:YAG laser (1064 nm) radiation shows that the highest value when compared with the standard potassium dihydrogen phosphate crystal.

Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Popov, V. O.

2017-11-01

The spatial organization of the genome is controlled by a special class of architectural proteins, including proteins containing BTB domains that are able to dimerize or multimerize. The centrosomal protein 190 is one of such architectural proteins. The purification, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 are reported. The crystallization conditions were found by the vapor-diffusion technique. The crystals diffracted to 1.5 Å resolution and belonged to sp. gr. P3221. The structure was solved by the molecular replacement method. The structure refinement is currently underway.

Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp. strain ADP

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

Balotra, Sahil; Newman, Janet; French, Nigel G.

2014-02-19

The amidase domain of the allophanate hydrolase AtzF from Pseudomonas sp. strain ADP has been crystallized and preliminary X-ray diffraction data have been collected. The allophanate hydrolase from Pseudomonas sp. strain ADP was expressed and purified, and a tryptic digest fragment was subsequently identified, expressed and purified. This 50 kDa construct retained amidase activity and was crystallized. The crystals diffracted to 2.5 Å resolution and adopted space group P2{sub 1}, with unit-cell parameters a = 82.4, b = 179.2, c = 112.6 Å, β = 106.6°.

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

DOE PAGES

Jakobi, Arjen J.; Passon, Daniel M.; Knoops, Kevin; ...

2016-03-01

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. Furthermore, the observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

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

Jakobi, Arjen J.; Passon, Daniel M.; Knoops, Kevin

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. Furthermore, the observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

PubMed Central

Jakobi, Arjen J.; Passon, Daniel M.; Knoops, Kèvin; Stellato, Francesco; Liang, Mengning; White, Thomas A.; Seine, Thomas; Messerschmidt, Marc; Chapman, Henry N.; Wilmanns, Matthias

2016-01-01

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined. PMID:27006771

Connecting heterogeneous single slip to diffraction peak evolution in high-energy monochromatic X-ray experiments

PubMed Central

Pagan, Darren C.; Miller, Matthew P.

2014-01-01

A forward modeling diffraction framework is introduced and employed to identify slip system activity in high-energy diffraction microscopy (HEDM) experiments. In the framework, diffraction simulations are conducted on virtual mosaic crystals with orientation gradients consistent with Nye’s model of heterogeneous single slip. Simulated diffraction peaks are then compared against experimental measurements to identify slip system activity. Simulation results compared against diffraction data measured in situ from a silicon single-crystal specimen plastically deformed under single-slip conditions indicate that slip system activity can be identified during HEDM experiments. PMID:24904242

Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

PubMed Central

Heymann, Michael; Opthalage, Achini; Wierman, Jennifer L.; Akella, Sathish; Szebenyi, Doletha M. E.; Gruner, Sol M.; Fraden, Seth

2014-01-01

An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation. PMID:25295176

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

Aoki, Ken-ichi; Tanaka, Nobutada, E-mail: ntanaka@pharm.showa-u.ac.jp; Ishikura, Shuhei

Pig heart carbonyl reductase has been crystallized in the presence of NADPH. Diffraction data have been collected using synchrotron radiation. Pig heart carbonyl reductase (PHCR), which belongs to the short-chain dehydrogenase/reductase (SDR) family, has been crystallized by the hanging-drop vapour-diffusion method. Two crystal forms (I and II) have been obtained in the presence of NADPH. Form I crystals belong to the tetragonal space group P4{sub 2}, with unit-cell parameters a = b = 109.61, c = 94.31 Å, and diffract to 1.5 Å resolution. Form II crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2, with unit-cell parameters amore » = b = 120.10, c = 147.00 Å, and diffract to 2.2 Å resolution. Both crystal forms are suitable for X-ray structure analysis at high resolution.« less

On capturing the grain-scale elastic and plastic anisotropy of alpha-Ti with spherical nanoindentation and electron back-scattered diffraction

DOE PAGES

Weaver, Jordan S.; Priddy, Matthew W.; McDowell, David L.; ...

2016-09-01

Here, spherical nanoindentation combined with electron back-scattered diffraction has been employed to characterize the grain-scale elastic and plastic anisotropy of single crystal alpha-Ti of two different compositions (in two different titanium alloys). Data analyses protocols needed to reliably extract the desired properties of interest are extended and demonstrated in this paper. Specifically, the grain-scale mechanical response is extracted in the form of indentation stress-strain curves for commercially pure (CP-Ti) alpha-Ti and alloyed (Ti-64) titanium from measurements on polycrystalline samples. The results are compared with responses of single crystals and nanoindentation tests (hardness and modulus) from the literature, and the measuredmore » indentation moduli are validated using crystal-elastic finite element simulations. The results obtained in this study show that (i) it is possible to characterize reliably the elastic and plastic anisotropy of alpha-Ti (hcp) of varying alloying contents with spherical nanoindentation stress-strain curves, (ii) the indentation modulus of alpha-Ti-64 is 5–10% less than CP-Ti, and (iii) the indentation yield strength of alpha-Ti-64 is 50–80% higher than CP-Ti.« less

Diffractive-refractive optics: (+,-,-,+) X-ray crystal monochromator with harmonics separation.

PubMed

Hrdý, Jaromír; Mikulík, Petr; Oberta, Peter

2011-03-01

A new kind of two channel-cut crystals X-ray monochromator in dispersive (+,-,-,+) position which spatially separates harmonics is proposed. The diffracting surfaces are oriented so that the diffraction is inclined. Owing to refraction the diffracted beam is sagittally deviated. The deviation depends on wavelength and is much higher for the first harmonics than for higher harmonics. This leads to spatial harmonics separation. The idea is supported by ray-tracing simulation.

Crystallization and preliminary X-ray diffraction studies of the ferredoxin reductase component in the Rieske nonhaem iron oxygenase system carbazole 1,9a-dioxygenase

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

Ashikawa, Yuji; Uchimura, Hiromasa; Fujimoto, Zui

2007-06-01

The NAD(P)H:ferredoxin oxidoreductase in carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3 was crystallized and diffraction data were collected to 2.60 Å resolution. Carbazole 1,9a-dioxygenase (CARDO), which consists of an oxygenase component (CARDO-O) and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), catalyzes dihydroxylation at the C1 and C9a positions of carbazole. CARDO-R was crystallized at 277 K using the hanging-drop vapour-diffusion method with the precipitant PEG 8000. Two crystal types (types I and II) were obtained. The type I crystal diffracted to a maximum resolution of 2.80 Å and belonged to space group P4{sub 2}2{sub 1}2, with unit-cell parameters amore » = b = 158.7, c = 81.4 Å. The type II crystal was obtained in drops from which type I crystals had been removed; it diffracted to 2.60 Å resolution and belonged to the same space group, with unit-cell parameters a = b = 161.8, c = 79.5 Å.« less

Neutron and X-ray single-crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels.

PubMed

Tsukui, Shu; Kimura, Fumiko; Kusaka, Katsuhiro; Baba, Seiki; Mizuno, Nobuhiro; Kimura, Tsunehisa

2016-07-01

Protein microcrystals magnetically aligned in D2O hydrogels were subjected to neutron diffraction measurements, and reflections were observed for the first time to a resolution of 3.4 Å from lysozyme microcrystals (∼10 × 10 × 50 µm). This result demonstrated the possibility that magnetically oriented microcrystals consolidated in D2O gels may provide a promising means to obtain single-crystal neutron diffraction from proteins that do not crystallize at the sizes required for neutron diffraction structure determination. In addition, lysozyme microcrystals aligned in H2O hydrogels allowed structure determination at a resolution of 1.76 Å at room temperature by X-ray diffraction. The use of gels has advantages since the microcrystals are measured under hydrated conditions.

Preliminary crystallographic analysis of ADP-glucose pyrophosphorylase from Agrobacterium tumefaciens

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

Cupp-Vickery, Jill R., E-mail: jvickery@uci.edu; Igarashi, Robert Y.; Meyer, Christopher R.

2005-03-01

Crystallization and X-ray diffraction methods for native A. tumefaciens ADP-glucose pyrophosphorylase and its selenomethionyl derivative are described. Two crystal forms are identified, both of which diffract to 2 Å.

Crystallization and preliminary X-ray diffraction analysis of the peripheral light-harvesting complex LH2 from Marichromatium purpuratum.

PubMed

Cranston, Laura J; Roszak, Aleksander W; Cogdell, Richard J

2014-06-01

LH2 from the purple photosynthetic bacterium Marichromatium (formerly known as Chromatium) purpuratum is an integral membrane pigment-protein complex that is involved in harvesting light energy and transferring it to the LH1-RC `core' complex. The purified LH2 complex was crystallized using the sitting-drop vapour-diffusion method at 294 K. The crystals diffracted to a resolution of 6 Å using synchrotron radiation and belonged to the tetragonal space group I4, with unit-cell parameters a=b=109.36, c=80.45 Å. The data appeared to be twinned, producing apparent diffraction symmetry I422. The tetragonal symmetry of the unit cell and diffraction for the crystals of the LH2 complex from this species reveal that this complex is an octamer.

Crystallization and preliminary X-ray diffraction analysis of the peripheral light-harvesting complex LH2 from Marichromatium purpuratum

PubMed Central

Cranston, Laura J.; Roszak, Aleksander W.; Cogdell, Richard J.

2014-01-01

LH2 from the purple photosynthetic bacterium Marichromatium (formerly known as Chromatium) purpuratum is an integral membrane pigment–protein complex that is involved in harvesting light energy and transferring it to the LH1–RC ‘core’ complex. The purified LH2 complex was crystallized using the sitting-drop vapour-diffusion method at 294 K. The crystals diffracted to a resolution of 6 Å using synchrotron radiation and belonged to the tetragonal space group I4, with unit-cell parameters a = b = 109.36, c = 80.45 Å. The data appeared to be twinned, producing apparent diffraction symmetry I422. The tetragonal symmetry of the unit cell and diffraction for the crystals of the LH2 complex from this species reveal that this complex is an octamer. PMID:24915099

Three-dimensional reconstruction of the size and shape of protein microcrystals using Bragg coherent diffractive imaging

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

Coughlan, H. D.; Darmanin, C.; Kirkwood, H. J.

2016-03-14

Three-dimensional imaging of protein crystals during X-ray diffraction experiments opens up a range of possibilities for optimising crystal quality and gaining new insights into the fundamental processes that drive radiation damage. Obtaining this information at the appropriate lengthscales however is extremely challenging. One approach that has been recently demonstrated as a promising avenue for charactering the size and shape of protein crystals at nanometre lengthscales is Bragg Coherent Diffractive Imaging (BCDI). BCDI is a recently developed technique that is able to recover the phase of the continuous diffraction intensity signal around individual Bragg peaks. When data is collected at multiplemore » points on a rocking curve a Reciprocal Space Map (RSM) can be assembled and then inverted using BCDI to obtain a three-dimensional image of the crystal. The first demonstration of two-dimensional BCDI of protein crystals was reported by Boutet at al., recently this work was extended to the study of radiation damage of micron-sized crystals. Here we present the first three-dimensional reconstructions of a Lysozyme protein crystal using BDI. The results are validated against RSM and TEM data and have implications for both radiation damage studies and for developing new approaches to structure retrieval from micron-sized protein crystals.« less

Crystallization of the C-terminal domain of the addiction antidote CcdA in complex with its toxin CcdB

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

Buts, Lieven; De Jonge, Natalie; Loris, Remy, E-mail: reloris@vub.ac.be

2005-10-01

The CcdA C-terminal domain was crystallized in complex with CcdB in two crystal forms that diffract to beyond 2.0 Å resolution. CcdA and CcdB are the antidote and toxin of the ccd addiction module of Escherichia coli plasmid F. The CcdA C-terminal domain (CcdA{sub C36}; 36 amino acids) was crystallized in complex with CcdB (dimer of 2 × 101 amino acids) in three different crystal forms, two of which diffract to high resolution. Form II belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 37.6, b = 60.5, c = 83.8 Å and diffracts to 1.8more » Å resolution. Form III belongs to space group P2{sub 1}, with unit-cell parameters a = 41.0, b = 37.9, c = 69.6 Å, β = 96.9°, and diffracts to 1.9 Å resolution.« less

Purification, crystallization and preliminary X-ray diffraction analysis of royal palm tree (Roystonea regia) peroxidase

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

Watanabe, Leandra; Nascimento, Alessandro S.; Zamorano, Laura S.

2007-09-01

The purification, crystallization, X-ray diffraction data acquisition and molecular-replacement results of royal palm tree (R. regia) peroxidase are described. Royal palm tree peroxidase (RPTP), which was isolated from Roystonea regia leaves, has an unusually high stability that makes it a promising candidate for diverse applications in industry and analytical chemistry [Caramyshev et al. (2005 ▶), Biomacromolecules, 6, 1360–1366]. Here, the purification and crystallization of this plant peroxidase and its X-ray diffraction data collection are described. RPTP crystals were obtained by the hanging-drop vapour-diffusion method and diffraction data were collected to a resolution of 2.8 Å. The crystals belong to themore » trigonal space group P3{sub 1}21, with unit-cell parameters a = b = 116.83, c = 92.24 Å, and contain one protein molecule per asymmetric unit. The V{sub M} value and solvent content are 4.07 Å{sup 3} Da{sup −1} and 69.8%, respectively.« less

Growth and characterization of 4-chloro-3-nitrobenzophenone single crystals using vertical Bridgman technique

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

Aravinth, K., E-mail: anandcgc@gmail.com; Babu, G. Anandha, E-mail: anandcgc@gmail.com; Ramasamy, P., E-mail: anandcgc@gmail.com

2014-04-24

4-chloro-3-nitrobenzophenone (4C3N) has been grown by using vertical Bridgman technique. The grown crystal was confirmed by Powder X-ray diffraction analysis. The crystalline perfection of the grown crystal was examined by high-resolution X-ray diffraction study. The fluorescence spectra of grown 4C3N single crystals exhibit emission peak at 575 nm. The micro hardness measurements were used to analyze the mechanical property of the grown crystal.

Temperature-controlled two new Co(II) compounds with distinct topological networks: Syntheses, crystal structures and catalytic properties

NASA Astrophysics Data System (ADS)

Meng, Qing-Hua; Long, Xu; Liu, Jing-Li; Zhang, Shuan; Zhang, Guang-Hui

2018-04-01

Two new Co(II) coordination compounds, namely [Co2(bptc)(bpp)2]n (1) and [Co(bptc)0.5(bpp)]n (2) (H4bptc = biphenyl-3,3‧,5,5‧-tetracarboxylic acid, bpp = 1,3-di(4-pyridyl)propane), have been hydrothermally synthesized from the same reactants via tuning the reaction temperature. Single crystal X-ray diffraction analyses revealed that both 1 and 2 feature 2D sheet motifs. Topological analyses revealed that compounds 1 and 2 show distinct topological networks. Under the weak Van der Waals interactions, the 2D sheet motifs of compounds 1 and 2 are further packed into 2D→3D interdigitated supramolecular frameworks. Moreover, the two Co(II) compounds show high catalytic activities for degradation of methyl orange (MO) in a Fenten-like process.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein.

PubMed

Rahaman, Siti Nurulnabila A; Mat Yusop, Jastina; Mohamed-Hussein, Zeti-Azura; Ho, Kok Lian; Teh, Aik-Hong; Waterman, Jitka; Ng, Chyan Leong

2016-03-01

C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), including overexpression and purification, verification by mass spectrometry and a Western blot using anti-C1ORF123 antibodies, crystallization and X-ray diffraction analysis of the protein crystals, are reported here. The rC1ORF123 protein was crystallized by the hanging-drop vapor-diffusion method with a reservoir solution comprised of 20% PEG 3350, 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate pH 6.5. The crystals diffracted to 1.9 Å resolution and belonged to an orthorhombic space group with unit-cell parameters a = 59.32, b = 65.35, c = 95.05 Å. The calculated Matthews coefficient (VM) value of 2.27 Å(3) Da(-1) suggests that there are two molecules per asymmetric unit, with an estimated solvent content of 45.7%.

Macromolecular diffractive imaging using imperfect crystals

PubMed Central

Ayyer, Kartik; Yefanov, Oleksandr; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Lourdu Xavier, Paulraj; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

2016-01-01

The three-dimensional structures of macromolecules and their complexes are predominantly elucidated by X-ray protein crystallography. A major limitation is access to high-quality crystals, to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields sufficiently high-resolution information that the crystal structure can be solved. The observation that crystals with shrunken unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks1,2 hints that crystallographic resolution for some macromolecules may be limited not by their heterogeneity but rather by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern, equal to the incoherent sum of diffraction from rigid single molecular complexes aligned along several discrete crystallographic orientations and hence with an increased information content3. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins4 —they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5 Å limit of measurable Bragg peaks, which allows us to directly phase5 the pattern. With the molecular envelope conventionally determined at 4.5 Å as a constraint, we then obtain a static image of the photosystem II dimer at 3.5 Å resolution. This result shows that continuous diffraction can be used to overcome long-supposed resolution limits of macromolecular crystallography, with a method that puts great value in commonly encountered imperfect crystals and opens up the possibility for model-free phasing6,7. PMID:26863980

Crystal Structure of 17α-Dihydroequilin, C18H22O2, from Synchrotron Powder Diffraction Data and Density Functional Theory

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

Kaduk, James; Gindhart, Amy; Blanton, Thomas

The crystal structure of 17α-dihydroequilin has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. 17α-dihydroequilin crystallizes in space group P212121 (#19) with a = 6.76849(1) Å, b = 8.96849(1) Å, c = 23.39031(5) Å, V = 1419.915(3) Å3, and Z = 4. Both hydroxyl groups form hydrogen bonds to each other, resulting in zig-zag chains along the b-axis. The powder diffraction pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ as the entry 00-066-1608.

Formation of Superhard Chromium Carbide Crystal Microrods in Ni-Cr-C Systems

NASA Astrophysics Data System (ADS)

Val'chuk, V. P.; Zmienko, D. S.; Kolesov, V. V.; Chernozatonskii, L. A.

2018-04-01

Ni-Cr-C materials with a high hardness determined by the presence of regions consisting of Cr3C2 microrods with a record microhardness reaching 3200 kg/mm2 have been obtained. Their self-organization in a powder consisting of Ni, Cr, and carbon microparticles with a high weight percentage occurs in the process of its sintering at a temperature of 1300°C and the subsequent sharp cooling of the resulting alloy. A model has been proposed for the process of formation of such crystal microrods whose characteristics have been determined by hardness measurement, electron microscopy, and microchemical and X-ray diffraction analyses.

Photorefractive detection of tagged photons in ultrasound modulated optical tomography of thick biological tissues.

PubMed

Ramaz, F; Forget, B; Atlan, M; Boccara, A C; Gross, M; Delaye, P; Roosen, G

2004-11-01

We present a new and simple method to obtain ultrasound modulated optical tomography images in thick biological tissues with the use of a photorefractive crystal. The technique offers the advantage of spatially adapting the output speckle wavefront by analysing the signal diffracted by the interference pattern between this output field and a reference beam, recorded inside the photorefractive crystal. Averaging out due to random phases of the speckle grains vanishes, and we can use a fast single photodetector to measure the ultrasound modulated optical contrast. This technique offers a promising way to make direct measurements within the decorrelation time scale of living tissues.

Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

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

Kimminau, G; Nagler, B; Higginbotham, A

2008-06-19

Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

Cyanide bridged hetero-metallic polymeric complexes: Syntheses, vibrational spectra, thermal analyses and crystal structures of complexes [M(1,2-dmi)2Ni(μ-CN)4]n (M = Zn(II) and Cd(II))

NASA Astrophysics Data System (ADS)

Kürkçüoğlu, Güneş Süheyla; Sayın, Elvan; Şahin, Onur

2015-12-01

Two cyanide bridged hetero-metallic complexes of general formula, [M(1,2-dmi)2Ni(μ-CN)4]n (1,2-dmi = 1,2-dimethylimidazole and M = Zn(II) or Cd(II)) have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal analyses and elemental analyses. The crystallographic analyses reveal that the complexes, [Zn(1,2-dmi)2Ni(μ-CN)4] (1) and [Cd(1,2-dmi)2Ni(μ-CN)4] (2), have polymeric 2D networks. In the complexes, four cyanide groups of [Ni(CN)4]2- coordinated to the adjacent M(II) ions and distorted octahedral geometries of complexes are completed by two nitrogen atoms of trans 1,2-dmi ligands. The structures of 1 and 2 are similar and linked via intermolecular hydrogen bonding, C-H⋯Ni interactions to give rise to 3D networks. Vibration assignments are given for all the observed bands and the spectral features also supported to the crystal structures of heteronuclear complexes. The FT-IR and Raman spectra of the complexes are very much consistent with the structural data presented.

Unique Chiral Interpenetrating d-f Heterometallic MOFs as Luminescent Sensors.

PubMed

Wu, Zhi-Lei; Dong, Jie; Ni, Wei-Yan; Zhang, Bo-Wen; Cui, Jian-Zhong; Zhao, Bin

2015-06-01

One novel three-dimensional (3D) 3d-4f metal-organic framework (MOF), [TbZn(L)(CO3)2(H2O)]n (1) [HL = 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine], has been successfully synthesized and structurally characterized. Structural analysis shows that compound 1 features a unique chiral interpenetrating 3D framework for the first time. The resulting crystals of 1 are composed of enantiomers 1a (P41) and 1b (P43), as was clearly confirmed by the crystal structure and the corresponding circular dichroism (CD) analyses of eight randomly selected crystals. The investigations on CD spectra based on every single crystal clearly assigned the Cotton effect signals. The powder X-ray diffraction measurement of 1 after being immersed in common solvents reveals that 1 possess excellent solvent stability. Furthermore, luminescent studies imply that 1 displays highly selective luminescent sensing of aldehydes, such as formol, acetaldehyde, and propanal.

X-ray diffraction imaging (topography) of electroopticcrystals by synchrotron radiation

NASA Technical Reports Server (NTRS)

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

1988-01-01

Information of special interest to crystal growers and device physicists now available from monochromatic synchrotron diffraction imaging (topography) is reviewed. Illustrations are taken from a variety of electro-optic crystals. Aspects of the detailed understanding of crystal growth processes obtainable from carefully selected samples are described. Finally, new experimental opportunities now available for exploitation are indicated.

An Excel Spreadsheet for a One-Dimensional Fourier Map in X-ray Crystallography

ERIC Educational Resources Information Center

Clegg, William

2004-01-01

The teaching of crystal structure determination with single-crystal X-ray diffraction at undergraduate level faces numerous challenges. Single-crystal X-ray diffraction is used in a vast range of chemical research projects and forms the basis for a high proportion of structural results that are presented to high-school, undergraduate, and graduate…

Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

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

Mitchell, M.; Nam, H; Carter, A

2009-01-01

Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetricmore » unit capsid have been determined by molecular-replacement methods and structure determination is in progress.« less

Effect of Mg2+ on acidic calcium phosphate phases grown by electrodeposition

NASA Astrophysics Data System (ADS)

Correia, Matheus Bento; Júnior, José Pedro Gualberto; Macedo, Michelle Cardinale S. S.; Resende, Cristiane Xavier; dos Santos, Euler Araujo

2017-10-01

In this work, the effect of Mg2+ ions on the electrodeposition of dicalcium phosphate dihydrate (DCPD), octacalcium phosphate (OCP) and calcium-deficient hydroxyapatite (CDHA) crystals on a commercially pure titanium (cp-Ti) substrate was evaluated. We demonstrated that Mg2+ ions could change the morphology of the coatings by inhibiting the growth rate of the OCP and CDHA crystals and diminishing the crystallite size of DCPD. The inhibition effect on OCP and CDHA was most likely due to a surface adsorption mechanism since no evidence of a doping process was observed using Rietveld refinement and electron diffraction analyses. Conversely, the presence of Mg2+ ions generated a favorable condition for the nucleation of a new Mg2+-rich DCPD crystal population, presenting smaller crystallite sizes.

Polymorphism of Alprazolam (Xanax): a review of its crystalline phases and identification, crystallographic characterization, and crystal structure of a new polymorph (form III).

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Van den Mooter, Guy; Blaton, Norbert

2007-05-01

A new polymorphic form of Alprazolam (Xanax), 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo-[4,3-alpha][1,4]benzodiazepine, C(17)H(13)ClN(4), has been investigated by means of X-ray powder diffraction (XRPD), single crystal X-ray diffraction, and differential scanning calorimetry (DSC). This polymorphic form (form III) was obtained during DSC experiments after the exothermic recrystallization of the melt of form I. The crystal unit cell dimensions for form III were determined from diffractometer methods. The monoclinic unit cell found for this polymorph using XRPD after indexing the powder diffractogram was confirmed by the cell parameters obtained from single crystal X-ray diffractometry on a crystal isolated from the DSC pans. The single crystal unit cell parameters are: a = 28.929(9), b = 13.844(8), c = 7.361(3) angstroms, beta = 92.82(3) degrees , V = 2944(2) angstroms(3), Z = 8, space group P2(1) (No.4), Dx = 1.393 Mg/m(3). The structure obtained from single crystal X-ray diffraction was used as initial model for Rietveld refinement on the powder diffraction data of form III. The temperature phase transformations of alprazolam were also studied using high temperature XRPD. A review of the different phases available in the Powder Diffraction File (PDF) database for this drug is described bringing some clarification and corrections. (c) 2007 Wiley-Liss, Inc. and the American Pharmacists Association.

Overcoming a hemihedral twinning problem in tetrahydrofolate-dependent O -demethylase crystals by the microseeding method

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

Harada, Ayaka; Sato, Yukari; Kamimura, Naofumi

2016-11-30

A tetrahydrofolate-dependentO-demethylase, LigM, fromSphingobiumsp. SYK-6 was crystallized by the hanging-drop vapour-diffusion method. However, the obtainedP3 121 orP3 221 crystals, which diffracted to 2.5–3.3 Å resolution, were hemihedrally twinned. To overcome the twinning problem, microseeding usingP3 121/P3 221 crystals as microseeds was performed with optimization of the reservoir conditions. As a result, another crystal form was obtained. The newly obtained crystal diffracted to 2.5–3.0 Å resolution and belonged to space groupP2 12 12, with unit-cell parametersa= 102.0,b= 117.3,c= 128.1 Å. TheP2 12 12 crystals diffracted to better than 2.0 Å resolution after optimizing the cryoconditions. Phasing using the single anomalous diffractionmore » method was successful at 3.0 Å resolution with a Pt-derivative crystal. This experience suggested that microseeding is an effective method to overcome the twinning problem, even when twinned crystals are utilized as microseeds.« less

Crystallization and preliminary crystallographic analysis of the Clostridium perfringens enterotoxin

PubMed Central

Briggs, David C.; Smedley, James G.; McClane, Bruce A.; Basak, Ajit K.

2010-01-01

Clostridium perfringens is a Gram-positive anaerobic species of bacterium that is notable for its ability to produce a plethora of toxins, including membrane-active toxins (α-toxins), pore-forming toxins (∊-toxins) and binary toxins (ι-toxins). Here, the crystallization of the full-length wild-type C. perfringens enterotoxin is reported, which is the causative agent of the second most prevalent food-borne illness in the United States and has been implicated in many other gastrointestinal pathologies. Several crystal forms were obtained. However, only two of these optimized crystal forms (I and II) were useable for X-ray diffraction data collection. The form I crystals diffracted to d min = 2.7 Å and belonged to space group C2, while the form II crystals diffracted to d min = 4 Å and belonged to space group P213. PMID:20606275

Investigations on structural, optical, electrical, mechanical and third-order nonlinear behaviour of 3-aminopyridinium 2,4-dinitrophenolate single crystal

NASA Astrophysics Data System (ADS)

Mohanbabu, B.; Bharathikannan, R.; Siva, G.

2017-10-01

The single crystals of 3-aminopyridinium 2,4-dinitrophenolate (APDP) have been synthesized and grown by slow evaporation technique at room temperature. The crystal system was identified and lattice dimensions were measured from the single-crystal X-ray diffraction (SXRD) analysis. UV-visible absorption and transmittance spectra have been recorded in the region between 250 and 1100 nm. The different vibrational modes of the molecule were studied by Fourier transform infrared (FTIR) spectroscopic analysis. The decreasing tendency of dielectric constant with increasing frequency was analysed in dielectric study. The polarizability value calculated using Penn analysis well agrees with the value calculated using Clausius-Mossotti equation. The photoconductivity and photoluminescence behaviour were also studied on grown APDP crystal. The mechanical strength of the crystal has been studied using a Vickers' microhardness test. The stiffness constant and yield strength of the crystal were also calculated from the microhardness test. The third-order nonlinear optical parameters such as refractive index, absorption coefficient and third-order susceptibility were estimated by Z-scan studies.

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Theoretical and experimental morphologies of 4-aminobenzophenone (ABP) crystals

NASA Astrophysics Data System (ADS)

Wang, Qingwu; Sheen, D. B.; Shepherd, E. E. A.; Sherwood, J. N.; Simpson, G. S.; Hammond, R. B.

1997-11-01

The lattice energy (Elatt), slice energies (Eslice) and attachment energies (Eatt) of the different habit faces of ABP crystals have been calculated using the computer program HABIT. On the basis of the attachment energies of different crystal faces, the morphology was defined as {1 0 0}, {0 0 1}, {1 1 0}, {11bar0} and {1 01bar}. To confirm this theoretical prediction, we have grown ABP films and ABP crystals from the vapour phase. In both cases, the morphologically most important face was defined as {1 0 0} face using X-ray diffraction techniques. The remaining faces of the vapour-grown crystals were defined using a projection method, while the crystallites in the films were morphologically analysed by means of atomic force microscopy (AFM). The experimental morphologies are basically in agreement with the computation. Deviations from the equilibrium morphology can be ascribed to departure from equilibrium conditions during growth. For completeness, the results are compared with those for crystals grown from solutions for which deviations in morphology from the theoretical predictions can be ascribed to interaction between the crystal faces and solvent molecules.

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

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

Kusakizako, Tsukasa; Tanaka, Yoshiki; Hipolito, Christopher J.

A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-raymore » diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.« less

Purification, crystallization and preliminary X-ray diffraction studies of N-acetylglucosamine-phosphate mutase from Candida albicans

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

Nishitani, Yuichi; Maruyama, Daisuke; Nonaka, Tsuyoshi

2006-04-01

Preliminary X-ray diffraction studies on N-acetylglucosamine-phosphate mutase from C. albicans are reported. N-acetylglucosamine-phosphate mutase (AGM1) is an essential enzyme in the synthesis of UDP-N-acetylglucosamine (UDP-GlcNAc) in eukaryotes and belongs to the α-d-phosphohexomutase superfamily. AGM1 from Candida albicans (CaAGM1) was purified and crystallized by the sitting-drop vapour-diffusion method. The crystals obtained belong to the primitive monoclinic space group P2{sub 1}, with unit-cell parameters a = 60.2, b = 130.2, c = 78.0 Å, β = 106.7°. The crystals diffract X-rays to beyond 1.8 Å resolution using synchrotron radiation.

Crystallization and preliminary X-ray diffraction analysis of West Nile virus

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

Kaufmann, Barbel; Plevka, Pavel; Kuhn, Richard J.

2010-05-25

West Nile virus, a human pathogen, is closely related to other medically important flaviviruses of global impact such as dengue virus. The infectious virus was purified from cell culture using polyethylene glycol (PEG) precipitation and density-gradient centrifugation. Thin amorphously shaped crystals of the lipid-enveloped virus were grown in quartz capillaries equilibrated by vapor diffusion. Crystal diffraction extended at best to a resolution of about 25 {angstrom} using synchrotron radiation. A preliminary analysis of the diffraction images indicated that the crystals had unit-cell parameters a {approx_equal} b {approx_equal} 480 {angstrom}, {gamma} = 120{sup o}, suggesting a tight hexagonal packing of onemore » virus particle per unit cell.« less

Photoluminescent lead(II) coordination polymers stabilised by bifunctional organoarsonate ligands

NASA Astrophysics Data System (ADS)

Lin, Jian-Di; Onet, Camelia I.; Schmitt, Wolfgang

2015-04-01

Four lead(II) coordination polymers were isolated under hydro(solvo)thermal conditions. The applied synthetic methodology takes advantage of the coordination behaviour of a new bifunctional organoarsonate ligand, 4-(1, 2, 4-triazol-4-yl)phenylarsonic acid (H2TPAA) and involves the variation of lead(II) reactants, metal/ligand mole ratios, and solvents. The constitutional composition of the four lead(II) coordination polymers can be formulated as [Pb2(TPAA)(HTPAA)(NO3)]·6H2O (1), [Pb2(TPAA)(HTPAA)2]·DMF·0.5H2O (DMF = N, N-Dimethylformamide) (2), [Pb2Cl2(TPAA)H2O] (3), and [Pb3Cl(TPAA)(HTPAA)2H2O]Cl (4). The compounds were characterized by single-crystal and powder x-ray diffraction techniques, thermogravimetric analyses, infra-red spectroscopy, and elemental analyses. Single-crystal x-ray diffraction reveals that 1 and 2 represent two-dimensional (2D) layered structures whilst 3 and 4 form three-dimensional (3D) frameworks. The structures of 1, 2, and 4 contain one-dimensional (1D) {PbII/AsO3} substructures, while 3 is composed of 2D {PbII/AsO3} arrays. Besides their interesting topologies, 1-4 all exhibit photoluminescence properties in the solid state at room temperature.

Use of a miniature diamond-anvil cell in high-pressure single-crystal neutron Laue diffraction

PubMed Central

Binns, Jack; Kamenev, Konstantin V.; McIntyre, Garry J.; Moggach, Stephen A.; Parsons, Simon

2016-01-01

The first high-pressure neutron diffraction study in a miniature diamond-anvil cell of a single crystal of size typical for X-ray diffraction is reported. This is made possible by modern Laue diffraction using a large solid-angle image-plate detector. An unexpected finding is that even reflections whose diffracted beams pass through the cell body are reliably observed, albeit with some attenuation. The cell body does limit the range of usable incident angles, but the crystallographic completeness for a high-symmetry unit cell is only slightly less than for a data collection without the cell. Data collections for two sizes of hexamine single crystals, with and without the pressure cell, and at 300 and 150 K, show that sample size and temperature are the most important factors that influence data quality. Despite the smaller crystal size and dominant parasitic scattering from the diamond-anvil cell, the data collected allow a full anisotropic refinement of hexamine with bond lengths and angles that agree with literature data within experimental error. This technique is shown to be suitable for low-symmetry crystals, and in these cases the transmission of diffracted beams through the cell body results in much higher completeness values than are possible with X-rays. The way is now open for joint X-ray and neutron studies on the same sample under identical conditions. PMID:27158503

Blazed vector gratings fabricated using photosensitive polymer liquid crystals and control of polarization diffraction

NASA Astrophysics Data System (ADS)

Ono, Hiroshi; Kuzuwata, Mitsuru; Sasaki, Tomoyuki; Noda, Kohei; Kawatsuki, Nobuhiro

2014-03-01

The blazed vector grating possessing antisymmetric distributions of the birefringence were fabricated by exposing the line-focused linearly polarized ultraviolet light on the photosensitive polymer liquid crystals. The polarization states of the diffraction beams can be highly and widely controlled by designing the blazed structures, and the diffraction properties were well-explained by Jones calculus.

Instrument and method for focusing X-rays, gamma rays and neutrons

DOEpatents

Smither, Robert K.

1984-01-01

A crystal diffraction instrument or diffraction grating instrument with an improved crystalline structure or grating spacing structure having a face for receiving a beam of photons or neutrons and diffraction planar spacing or grating spacing along that face with the spacing increasing progressively along the face to provide a decreasing Bragg diffraction angle for a monochromatic radiation and thereby increasing the usable area and acceptance angle. The increased planar spacing for the diffraction crystal is provided by the use of a temperature differential across the crystalline structure, by assembling a plurality of crystalline structures with different compositions, by an individual crystalline structure with a varying composition and thereby a changing planar spacing along its face, and by combinations of these techniques. The increased diffraction grating element spacing is generated during the fabrication of the diffraction grating by controlling the cutting tool that is cutting the grooves or controlling the laser beam, electron beam or ion beam that is exposing the resist layer, etc. It is also possible to vary this variation in grating spacing by applying a thermal gradient to the diffraction grating in much the same manner as is done in the crystal diffraction case.

Instrument and method for focusing x rays, gamma rays, and neutrons

DOEpatents

Smither, R.K.

1982-03-25

A crystal-diffraction instrument or diffraction-grating instrument is described with an improved crystalline structure or grating spacing structure having a face for receiving a beam of photons or neutrons and diffraction planar spacing or grating spacing along that face with the spacing increasing progressively along the face to provide a decreasing Bragg diffraction angle for a monochromatic radiation and thereby increasing the usable area and acceptance angle. The increased planar spacing for the diffraction crystal is provided by the use of a temperature differential across the line structures with different compositions, by an individual crystalline structure with a varying composition and thereby a changing planar spacing along its face, and by combinations of these techniques. The increased diffraction grating element spacing is generated during the fabrication of the diffraction grating by controlling the cutting tool that is cutting the grooves or controlling the laser beam, electron beam, or ion beam that is exposing the resist layer, etc. It is also possible to vary this variation in grating spacing by applying a thermal gradient to the diffraction grating in much the same manner as is done in the crystal-diffraction case.

Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction

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

O'Dell, William B.; Swartz, Paul D.; Weiss, Kevin L.

Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bondsviaan oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 fromNeurospora crassa(NcPMO-2) was heterologously expressed inPichia pastoristo facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressingNcPMO-2 from a glycoengineered strain ofP. pastorisand by the use of crystal seeding methods, respectively. These improvements resulted in high-resolution (1.20 Å) X-ray diffraction data collection at 100 K and themore » production of a largeNcPMO-2 crystal suitable for room-temperature neutron diffraction data collection to 2.12 Å resolution.« less

Data Exploration Toolkit for serial diffraction experiments

DOE PAGES

Zeldin, Oliver B.; Brewster, Aaron S.; Hattne, Johan; ...

2015-01-23

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the 'diffraction before destruction' nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography datamore » sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.« less

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.

PubMed

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-12-01

Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, β=95.2°. Diffraction images were processed to a resolution of 1.74 Å with an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto

PubMed Central

Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

2010-01-01

Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27 724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a = 74.3, b = 49.9, c = 56.3 Å, β = 95.2°. Diffraction images were processed to a resolution of 1.74 Å with an R merge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase. PMID:21139221

Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus.

PubMed

Chander, M; Setlow, P; Lamani, E; Jedrzejas, M J

1999-06-15

Phosphoglycerate mutase (PGM), an important enzyme in the glycolytic pathway, catalyzes the transfer of a phosphate group between the 2 and the 3 positions of glyceric acid. The gene coding for the 2, 3-diphosphoglycerate independent monomeric PGM from Bacillus stearothermophilus (57 kDa), whose activity is extremely pH sensitive and has an absolute and specific requirement for Mn2+, has been cloned and the enzyme overexpressed and purified to homogeneity. Circular dichroism studies showed at most only small secondary structure changes in the enzyme upon binding to Mn2+ or its 3-phosphoglycerate substrate, but thermal unfolding analyses revealed that Mn2+ but not 3-phosphoglycerate caused a large increase in the enzyme's stability. Diffraction-quality crystals of the enzyme were obtained at neutral pH in the presence of 3-phosphoglyceric acid with ammonium sulfate as the precipitating agent; these crystals diffract X rays to beyond 2.5-A resolution and belong to the orthorhombic space group C2221 with unit cell dimensions, a = 58.42, b = 206.08, c = 124.87 A, and alpha = beta = gamma = 90.0 degrees. The selenomethionyl version of the B. stearothermophilus protein has also been overexpressed, purified, and crystallized. Employing these crystals, the determination of the three-dimensional structure of this PGM by the multiwavelength anomalous dispersion method is in progress. Copyright 1999 Academic Press.

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

Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystals

PubMed Central

Wojdyla, Justyna Aleksandra; Panepucci, Ezequiel; Martiel, Isabelle; Ebner, Simon; Huang, Chia-Ying; Caffrey, Martin; Bunk, Oliver; Wang, Meitian

2016-01-01

A fast continuous grid scan protocol has been incorporated into the Swiss Light Source (SLS) data acquisition and analysis software suite on the macromolecular crystallography (MX) beamlines. Its combination with fast readout single-photon counting hybrid pixel array detectors (PILATUS and EIGER) allows for diffraction-based identification of crystal diffraction hotspots and the location and centering of membrane protein microcrystals in the lipid cubic phase (LCP) in in meso in situ serial crystallography plates and silicon nitride supports. Diffraction-based continuous grid scans with both still and oscillation images are supported. Examples that include a grid scan of a large (50 nl) LCP bolus and analysis of the resulting diffraction images are presented. Scanning transmission X-ray microscopy (STXM) complements and benefits from fast grid scanning. STXM has been demonstrated at the SLS beamline X06SA for near-zero-dose detection of protein crystals mounted on different types of sample supports at room and cryogenic temperatures. Flash-cooled crystals in nylon loops were successfully identified in differential and integrated phase images. Crystals of just 10 µm thickness were visible in integrated phase images using data collected with the EIGER detector. STXM offers a truly low-dose method for locating crystals on solid supports prior to diffraction data collection at both synchrotron microfocusing and free-electron laser X-ray facilities. PMID:27275141

Characterization of monoclinic crystals in tablets by pattern-fitting procedure using X-ray powder diffraction data.

PubMed

Yamamura, Shigeo; Momose, Yasunori

2003-06-18

The purpose of this study is to characterize the monoclinic crystals in tablets by using X-ray powder diffraction data and to evaluate the deformation feature of crystals during compression. The monoclinic crystals of acetaminophen and benzoic acid were used as the samples. The observed X-ray diffraction intensities were fitted to the analytic expression, and the fitting parameters, such as the lattice parameters, the peak-width parameters, the preferred orientation parameter and peak asymmetric parameter were optimized by a non-linear least-squares procedure. The Gauss and March distribution functions were used to correct the preferred orientation of crystallites in the tablet. The March function performed better in correcting the modification of diffraction intensity by preferred orientation of crystallites, suggesting that the crystallites in the tablets had fiber texture with axial orientation. Although a broadening of diffraction peaks was observed in acetaminophen tablets with an increase of compression pressure, little broadening was observed in the benzoic tablets. These results suggest that "acetaminophen is a material consolidating by fragmentation of crystalline particles and benzoic acid is a material consolidating by plastic deformation then occurred rearrangement of molecules during compression". A pattern-fitting procedure is the superior method for characterizing the crystalline drugs of monoclinic crystals in the tablets, as well as orthorhombic isoniazid and mannitol crystals reported in the previous paper.

An X-ray diffractometer using mirage diffraction

PubMed Central

Fukamachi, Tomoe; Jongsukswat, Sukswat; Ju, Dongying; Negishi, Riichirou; Hirano, Keiichi; Kawamura, Takaaki

2014-01-01

Some characteristics are reported of a triple-crystal diffractometer with a (+, −, +) setting of Si(220) using mirage diffraction. The first crystal is flat, while the second and third crystals are bent. Basically, the first crystal is used as a collimator, the second as a monochromator and the third as the sample. The third crystal also works as an analyzer. The advantages of this diffractometer are that its setup is easy, its structure is simple, the divergence angle from the second crystal is small and the energy resolution of the third crystal is high, of the order of sub-meV. PMID:25242911

High resolution diffraction imaging of crystals grown in microgravity and closely related terrestrial crystals

NASA Technical Reports Server (NTRS)

Steiner, B.; Dobbyn, R.; Black, D.; Burdette, H.; Kuriyama, M.; Spal, R.; Vandenberg, L.; Fripp, A.; Simchick, R.; Lal, R.

1991-01-01

Irregularities found in three crystals grown in space, in four crystals grown entirely on the ground were examined and compared. Irregularities were observed in mercuric iodide, lead tin telluride, triglycine sulfate, and gallium arsenide by high resolution synchrotron x radiation diffraction imaging. Radiation detectors made from mercuric iodide crystals grown in microgravity were reported to perform far better than conventional detectors grown from the same material under full gravity. Effort is now underway to reproduce these 'space' crystals, optimize their properties, and extend comparable superiority to other types of materials.

Growth and characterization of organic NLO material: Clobetasol propionate

NASA Astrophysics Data System (ADS)

Purusothaman, R.; Rajesh, P.; Ramasamy, P.

2015-06-01

Single crystals of clobetasol propionate (CP) have been grown by slow evaporation solution technique using mixed solvent of methanol-acetone. The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm their lattice parameter and space group. The powder X-ray diffraction pattern of the grown CP has been indexed. Thermal analysis was performed to study the thermal stability of the grown crystals. Photoluminescence spectrum shows broad emission peak observed at 421 nm. Nonlinear optical studies were carried out for the grown crystal and second harmonic generation (SHG) efficiency was found in the crystal.

Crystallization and preliminary X-ray diffraction analysis of restriction endonuclease EcoRII

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Meehan, E.; Pusey, M. L.; Chen, L.

1999-01-01

Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal asymmetric unit contains two protein molecules, and self-rotation function analysis shows a pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of crystal diffraction and to search for heavy-atom derivatives are under way.

Saturated fatty acids and fatty acid esters promote the polymorphic transition of clarithromycin metastable form I crystal.

PubMed

Watanabe, Miteki; Mizoguchi, Midori; Aoki, Hajime; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

2016-10-15

The phase transition of active pharmaceutical ingredients should be taken into account during manufacturing, processing- and storage, because different crystal forms lead to different physical properties of formulations. The phase transition of clarithromycin (CAM) metastable form I to stable form II was investigated on heating with additives such as fatty acids or fatty acid esters. Differential scanning calorimetry analyses revealed that when form I was heated with additives, the phase transition temperature of form I decreased close to the melting points of the additives. Powder X-ray diffraction analyses indicated the tentative presence of a non-crystalline component during the transition of form I to form II on heating with additives. These observations implied that CAM form I dissolved in the melted additives on heating and the dissolved CAM crystallized to form II. Reduction of transition temperatures in the presence of additives were also observed for the crystals of nifedipine form B and carbamazepine form III. These results suggested that the phenomena can be widely applicable for simultaneous crystalline phase transition and granulation using binder additives. Copyright © 2016 Elsevier B.V. All rights reserved.

A comparative study on the crystal structure of bicycle analogues to the natural phytotoxin helminthosporins

NASA Astrophysics Data System (ADS)

Barbosa, Luiz Cláudio de Almeida; Teixeira, Robson Ricardo; Nogueira, Leonardo Brandão; Maltha, Celia Regina Alvares; Doriguetto, Antônio Carlos; Martins, Felipe Terra

2016-02-01

Herein we described structural insights of a series of analogues to helminthosporin phytotoxins. The key reaction used to prepare the compounds corresponded to the [3 + 4] cycloaddition between the oxyallyl cation generated from 2,4-dibromopentan-3-one and different furans. Their structures were confirmed upon IR, NMR and X-ray diffraction analyses. While bicycles 7, 8 and 9 crystallize in the centrosymmetric monoclinic space group P21/c, compound 10 was solved in the noncentrosymmetric orthorhombic space group P212121. The solid materials obtained were shown to be racemic crystals (7, 8, 9) or racemic conglomerate (10). In all compounds, there is formation of a bicycle featured by fused tetrahydropyranone and 2,5-dihydrofuran rings. They adopt chair and envelope conformations, respectively. Crystal packing of all compounds is stabilized through C-H•••O contacts. Conformational aspects as well as similarities and differences among the crystal structures of the synthesized analogues are discussed.

Supernucleation and Orientation of Poly(butylene terephthalate) Crystals in Nanocomposites Containing Highly Reduced Graphene Oxide

PubMed Central

2017-01-01

The ring-opening polymerization of cyclic butylene terephthalate into poly(butylene terephthalate) (pCBT) in the presence of reduced graphene oxide (RGO) is an effective method for the preparation of polymer nanocomposites. The inclusion of RGO nanoflakes dramatically affects the crystallization of pCBT, shifting crystallization peak temperature to higher temperatures and, overall, increasing the crystallization rate. This was due to a supernucleating effect caused by RGO, which is maximized by highly reduced graphene oxide. Furthermore, combined analyses by differential scanning calorimetry (DSC) experiments and wide-angle X-ray diffraction (WAXS) showed the formation of a thick α-crystalline form pCBT lamellae with a melting point of ∼250 °C, close to the equilibrium melting temperature of pCBT. WAXS also demonstrated the pair orientation of pCBT crystals with RGO nanoflakes, indicating a strong interfacial interaction between the aromatic rings of pCBT and RGO planes, especially with highly reduced graphene oxide. PMID:29296028

Crystallization and preliminary crystallographic investigation of a low-pH native insulin monomer with flexible behaviour.

PubMed

Zhang, Youshang; Whittingham, Jean L; Turkenburg, Johan P; Dodson, Eleanor J; Brange, Jens; Dodson, G Guy

2002-01-01

Insulin naturally aggregates as dimers and hexamers, whose structures have been extensively analysed by X-ray crystallography. Structural determination of the physiologically relevant insulin monomer, however, is an unusual challenge owing to the difficulty in finding solution conditions in which the concentration of insulin is high enough for crystallization yet the molecule remains monomeric. By utilizing solution conditions known to inhibit insulin assembly, namely 20% acetic acid, crystals of insulin in the monomeric state have been obtained. The crystals are strongly diffracting and a data set extending to 1.6 A has recently been collected. The crystals nominally belong to the space group I422, with unit-cell parameters a = b = 57.80, c = 54.61 A, giving rise to one molecule in the asymmetric unit. Preliminary electron-density maps show that whilst most of the insulin monomer is well ordered and similar in conformation to other insulin structures, parts of the B-chain C-terminus main chain adopt more than one conformation.

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

Kuz'micheva, G. M., E-mail: galkuz@mitht.ru; Zaharko, O.; Tyunina, E. A.

Langatate crystals of the general composition La{sub 3}(Ga{sub 0.5}Ta{sub 0.5})Ga{sub 5}O{sub 14}, grown by the Czochralski method, have been investigated by neutron diffraction (single crystals) and X-ray diffraction (ground single crystals). The crystals were grown in an atmosphere of 99% Ar + 1% O{sub 2} in the Y54{sup o} direction (rotation by 54{sup o} with respect to the y axis), without subsequent annealing (orange crystal) or with vacuum annealing (colorless crystal). It is established that colorless crystals have a higher gallium content and, therefore, a larger number of oxygen vacancies in comparison with colored crystals; this is a possible reasonmore » for their lower microhardness.« less

The syntheses, molecular structure analyses and DFT studies on new benzil monohydrazone based Schiff bases

NASA Astrophysics Data System (ADS)

Elmacı, Gökhan; Duyar, Halil; Aydıner, Burcu; Seferoğlu, Nurgül; Naziri, Mir Abolfazl; Şahin, Ertan; Seferoğlu, Zeynel

2018-06-01

Benzil monohydrazone based Schiff bases were synthesized and characterized by 1H NMR, 13C NMR, HRMS as well as by single crystal X-ray diffraction. The geometries of the compounds was optimized by the DFT method and the results were compared with the X-ray diffraction data. The HOMO and LUMO energy gap and also related parameters (electronic chemical potential (μ) and global hardness (η), global electrophilicity index (ω) and softness (s)) were obtained from ground state calculations. In addition, the thermal properties of the compounds were investigated by DTA-TGA. The results showed that the compounds have good thermal properties for practical applications as optic dye.

Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate

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

Mise, Takeshi; Matsunami, Hideyuki; Samatey, Fadel A.

The periplasmic domain of the E. coli aspartate receptor Tar was cloned, expressed, purified and crystallized with and without bound ligand. The crystals obtained diffracted to resolutions of 1.58 and 1.95 Å, respectively. The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni{sup 2+}. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 weremore » grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-Tar2 were grown and diffracted to resolutions of 1.95 and 1.58 Å, respectively. Crystals of apo-Tar1 and Asp-Tar1 adopted space group P4{sub 1}2{sub 1}2, while those of apo-Tar2 and Asp-Tar2 adopted space groups P2{sub 1}2{sub 1}2{sub 1} and C2, respectively.« less

Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa

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

Taguchi, Chiho; Quantum Beam Science Directorate, Japan Atomic Energy Agency; Taura, Futoshi

Polyketide synthase-1 from C. sativa has been crystallized. The crystal diffracted to 1.55 Å resolution with sufficient quality for further structure determination. Polyketide synthase-1 (PKS-1) is a novel type III polyketide synthase that catalyzes the biosynthesis of hexanoyl triacetic acid lactone in Cannabis sativa (Mexican strain). PKS-1 was overproduced in Escherichia coli, purified and finally crystallized in two different space groups. The crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M calcium acetate and 20%(w/v) polyethylene glycol 3350 diffracted to 1.65 Å resolution and belonged to space group P1, with unit-cell parameters a = 54.3, b =more » 59.3, c = 62.6 Å, α = 69, β = 81, γ = 80°. Another crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M sodium chloride and 20%(w/v) polyethylene glycol 3350 diffracted to 1.55 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 54.3, b = 110, c = 130 Å. These data will enable us to determine the crystal structure of PKS-1.« less

Diffraction crystal for sagittally focusing x-rays

DOEpatents

Ice, Gene E.; Sparks, Jr., Cullie J.

1984-01-01

The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

Diffraction crystals for sagittally focusing x-rays

DOEpatents

Ice, G.E.; Sparks, C.J. Jr.

1982-06-07

The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis

PubMed Central

Vyas, Rajan; Kumar, Vijay; Panjikar, Santosh; Karthikeyan, Subramanian; Kishan, K. V. Radha; Tewari, Rupinder; Weiss, Manfred S.

2008-01-01

Aspartate semialdehyde dehydrogenase from Mycobacterium tuberculosis (Asd, ASADH, Rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in Escherichia coli. The enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form A and of one or two monomers in the cubic crystal form B. PMID:18323599

7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

PubMed Central

Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S.; Zatsepin, Nadia A.; Barty, Anton; Benner, W. Henry; Boutet, Sébastien; Feld, Geoffrey K.; Hau-Riege, Stefan P.; Kirian, Richard A.; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I.; Pardini, Tommaso; Segelke, Brent; Williams, Garth J.; Spence, John C. H.; Abela, Rafael; Coleman, Matthew; Evans, James E.; Schertler, Gebhard F. X.; Frank, Matthias; Li, Xiao-Dan

2014-01-01

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution. PMID:24914166

A simple X-ray source of two orthogonal beams for small samples imaging

NASA Astrophysics Data System (ADS)

Hrdý, J.

2018-04-01

A simple method for simultaneous imaging of small samples by two orthogonal beams is proposed. The method is based on one channel-cut crystal which is oriented such that the beam is diffracted on two crystallographic planes simultaneously. These planes are symmetrically inclined to the crystal surface. The beams are three times diffracted. After the first diffraction the beam is split. After the second diffraction the split beams become parallel. Finally, after the third diffraction the beams become convergent and may be used for imaging. The corresponding angular relations to obtain orthogonal beams are derived.

Crystallization and preliminary X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex

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

Huet, Joëlle, E-mail: jhuet@ulb.ac.be; Azarkan, Mohamed; Looze, Yvan

2008-05-01

A chitinase isolated from the latex of the tropical species Carica papaya has been crystallized. The addition of N-acetyl-d-glucosamine to the crystallization solution has improved the diffraction quality resolution of the crystal to 1.8 Å resolution. A chitinase isolated from the latex of the tropical species Carica papaya has been purified to homogeneity and crystallized. This enzyme belongs to glycosyl hydrolase family 19 and exhibits exceptional resistance to proteolysis. The initially observed crystals, which diffracted to a resolution of 2.0 Å, were improved through modification of the crystallization protocol. Well ordered crystals were subsequently obtained using N-acetyl-d-glucosamine, the monomer resultingmore » from the hydrolysis of chitin, as an additive to the crystallization solution. Here, the characterization of a chitinase crystal that belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 69.08, b = 44.79, c = 76.73 Å, β = 95.33° and two molecules per asymmetric unit, is reported. Diffraction data were collected to a resolution of 1.8 Å. Structure refinement is currently in progress.« less

Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study.

PubMed

Dupraz, Maxime; Beutier, Guillaume; Rodney, David; Mordehai, Dan; Verdier, Marc

2015-06-01

Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and 'relaxed' after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal.

Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study1

PubMed Central

Dupraz, Maxime; Beutier, Guillaume; Rodney, David; Mordehai, Dan; Verdier, Marc

2015-01-01

Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and ‘relaxed’ after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal. PMID:26089755

Phase modulation due to crystal diffraction by ptychographic imaging

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

Civita, M.; Diaz, A.; Bean, R. J.

Solving the phase problem in x-ray crystallography has occupied a considerable scientific effort in the 20th century and led to great advances in structural science. Here we use x-ray ptychography to demonstrate an interference method which measures the phase of the beam transmitted through a crystal, relative to the incoming beam, when diffraction takes place. The observed phase change of the direct beam through a small gold crystal is found to agree with both a quasikinematical model and full dynamical theories of diffraction. Our discovery of a diffraction contrast mechanism will enhance the interpretation of data obtained from crystalline samplesmore » using the ptychography method, which provides some of the most accurate x-ray phase-contrast images.« less

Phase modulation due to crystal diffraction by ptychographic imaging

DOE PAGES

Civita, M.; Diaz, A.; Bean, R. J.; ...

2018-03-06

Solving the phase problem in x-ray crystallography has occupied a considerable scientific effort in the 20th century and led to great advances in structural science. Here we use x-ray ptychography to demonstrate an interference method which measures the phase of the beam transmitted through a crystal, relative to the incoming beam, when diffraction takes place. The observed phase change of the direct beam through a small gold crystal is found to agree with both a quasikinematical model and full dynamical theories of diffraction. Our discovery of a diffraction contrast mechanism will enhance the interpretation of data obtained from crystalline samplesmore » using the ptychography method, which provides some of the most accurate x-ray phase-contrast images.« less

Phase modulation due to crystal diffraction by ptychographic imaging

NASA Astrophysics Data System (ADS)

Civita, M.; Diaz, A.; Bean, R. J.; Shabalin, A. G.; Gorobtsov, O. Yu.; Vartanyants, I. A.; Robinson, I. K.

2018-03-01

Solving the phase problem in x-ray crystallography has occupied a considerable scientific effort in the 20th century and led to great advances in structural science. Here we use x-ray ptychography to demonstrate an interference method which measures the phase of the beam transmitted through a crystal, relative to the incoming beam, when diffraction takes place. The observed phase change of the direct beam through a small gold crystal is found to agree with both a quasikinematical model and full dynamical theories of diffraction. Our discovery of a diffraction contrast mechanism will enhance the interpretation of data obtained from crystalline samples using the ptychography method, which provides some of the most accurate x-ray phase-contrast images.

Spectrally-Narrowed Emissions from Organic Crystals Having a One-Dimensional Grating on Their Surface.

PubMed

Yamamoto, Hiroyuki; Obara, Keiji; Higashihara, Shohei; Obama, Yuki; Yamao, Takeshi; Hotta, Shu

2016-04-01

We have succeeded in directly engraving one-dimensional diffraction gratings on the surface of organic semiconducting oligomer crystals by using focused ion beam (FIB) lithography and laser ablation (LA) methods. The FIB method enabled us to shape the gratings with varying periods down to ~150 nm. With the LA method a large-area grating with a ~500-nm period was readily accessible. All the above crystals indicated spectrally-narrowed emission (SNE) lines even in the case of shallow groove depths ~2-4 nm. In particular, we definitively observed the SNE pertinent to the first-order diffraction with the crystal having the diffraction grating of a 148.3-nm average period. The present results indicate utility of the built-in gratings that can directly be fabricated on the surface of the crystals.

Crystallization and preliminary X-ray diffraction studies of θ-toxin (perfringolysin O), a pore-forming cytolysin of Clostridium perfringens

NASA Astrophysics Data System (ADS)

Sugahara, Mitsuaki; Sekino-Suzuki, Naoko; Ohno-Iwashita, Yoshiko; Miki, Kunio

1996-10-01

θ-Toxin (perfringolysin O), a cholesterol-binding, pore-forming cytolysin of Clostridium perfringens type A was crystallized by the vapor diffusion procedure using polyethyleneglycol 4000 and sodium chloride as precipitants in 2-(cyclohexylamino)ethanesulfonic acid (CHES) buffer at pH 9.5. The diffraction patterns of precession photographs indicated that the crystals belong to the orthorhombic system and the space group C222 1 with unit-cell dimensions of a = 47.7 Å, b = 182.0 Å and c = 175.8 Å. Assuming that the asymmetric unit contains one or two molecules (Mw 52 700), the Vm value is calculated as 3.6 or 1.8 Å 3/dalton, respectively. The crystals diffract X-rays to at least 3 Å resolution and are suitable for high resolution X-ray crystal structure determination.

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

NASA Astrophysics Data System (ADS)

Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

2016-11-01

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P1211 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

Diffractive optical devices produced by light-assisted trapping of nanoparticles.

PubMed

Muñoz-Martínez, J F; Jubera, M; Matarrubia, J; García-Cabañes, A; Agulló-López, F; Carrascosa, M

2016-01-15

One- and two-dimensional diffractive optical devices have been fabricated by light-assisted trapping and patterning of nanoparticles. The method is based on the dielectrophoretic forces appearing in the vicinity of a photovoltaic crystal, such as Fe:LiNbO3, during or after illumination. By illumination with the appropriate light distribution, the nanoparticles are organized along patterns designed at will. One- and two-dimensional diffractive components have been achieved on X- and Z-cut Fe:LiNbO3 crystals, with their polar axes parallel and perpendicular to the crystal surface, respectively. Diffraction gratings with periods down to around a few micrometers have been produced using metal (Al, Ag) nanoparticles with radii in the range of 70-100 nm. Moreover, several 2D devices, such as Fresnel zone plates, have been also produced showing the potential of the method. The diffractive particle patterns remain stable when light is removed. A method to transfer the diffractive patterns to other nonphotovoltaic substrates, such as silica glass, has been also reported.

Characterisation of the rare cadmium chromate pigment in a 19th century tube colour by Raman, FTIR, X-ray and EPR

NASA Astrophysics Data System (ADS)

Christiansen, Marie Bitsch; Sørensen, Mikkel Agerbæk; Sanyova, Jana; Bendix, Jesper; Simonsen, Kim Pilkjær

2017-03-01

In an investigation of the artists' materials used by P. S. Krøyer the contents of the tube colours found in Krøyer's painting cabinet were examined. In most cases, the results of the pigment analyses were as expected based on our knowledge of artists' colours used in the late 1800s and early 1900s. However, in one of the tube colours labelled "Jaune de Cadmium Citron" (cadmium lemon yellow) an extremely rare cadmium chromate pigment was found. The pigment was analysed and characterised by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), powder X-ray diffraction (PXRD), single-crystal X-ray crystallography, and electron paramagnetic resonance (EPR) spectroscopy. Cadmium chromate was synthesised by precipitation from an aqueous solution of cadmium nitrate and potassium chromate, and the resulting yellow crystals proved identical to the pigment found in the tube colour "Jaune de Cadmium Citron". The structure determined by single-crystal X-ray diffraction identified the pigment as 2CdCrO4·KOH·H2O or more accurately as KCd2(CrO4)2(H3O2) illustrating the μ-H3O2- species. The yellow colour of the paint sample taken from the tube had a greenish hue, which became even more prominent upon storage and drying. EPR analysis of the sample showed the presence of paramagnetic degradation products containing Cr(III) and Cr(V).

Characterisation of the rare cadmium chromate pigment in a 19th century tube colour by Raman, FTIR, X-ray and EPR.

PubMed

Christiansen, Marie Bitsch; Sørensen, Mikkel Agerbæk; Sanyova, Jana; Bendix, Jesper; Simonsen, Kim Pilkjær

2017-03-15

In an investigation of the artists' materials used by P. S. Krøyer the contents of the tube colours found in Krøyer's painting cabinet were examined. In most cases, the results of the pigment analyses were as expected based on our knowledge of artists' colours used in the late 1800s and early 1900s. However, in one of the tube colours labelled "Jaune de Cadmium Citron" (cadmium lemon yellow) an extremely rare cadmium chromate pigment was found. The pigment was analysed and characterised by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), powder X-ray diffraction (PXRD), single-crystal X-ray crystallography, and electron paramagnetic resonance (EPR) spectroscopy. Cadmium chromate was synthesised by precipitation from an aqueous solution of cadmium nitrate and potassium chromate, and the resulting yellow crystals proved identical to the pigment found in the tube colour "Jaune de Cadmium Citron". The structure determined by single-crystal X-ray diffraction identified the pigment as 2CdCrO 4 ·KOH·H 2 O or more accurately as KCd 2 (CrO 4 ) 2 (H 3 O 2 ) illustrating the μ-H 3 O 2 - species. The yellow colour of the paint sample taken from the tube had a greenish hue, which became even more prominent upon storage and drying. EPR analysis of the sample showed the presence of paramagnetic degradation products containing Cr(III) and Cr(V). Copyright © 2016 Elsevier B.V. All rights reserved.

Purification, crystallization and preliminary X-ray structural studies of a 7.2 kDa cytotoxin isolated from the venom of Daboia russelli russelli of the Viperidae family

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

Roy Choudhury, Subhasree; Gomes, Aparna; Gomes, Antony

2006-03-01

A cytotoxin from Indian Russell’s viper (D. russelli russelli) venom having multifunctional activity has been crystallized in space group P4{sub 1}. Larger crystals diffracted to 1.5 Å but were found to be twinned; preliminary data were therefore collected (2.93 Å) from a smaller crystal. A cytotoxin (MW 7.2 kDa) from Indian Russell’s viper (Daboia russelli russelli) venom possessing antiproliferative activity, cardiotoxicity, neurotoxicity and myotoxicity has been purified, characterized and crystallized. The crystals belong to the tetragonal space group P4{sub 1}, with unit-cell parameters a = b = 47.94, c = 50.2 Å. Larger crystals, which diffracted to 1.5 Å, weremore » found to be twinned; diffraction data were therefore collected to 2.93 Å resolution using a smaller crystal. Molecular-replacement calculations identified two molecules of the protein in the asymmetric unit, which is in accordance with the calculated V{sub M} value.« less

Increasing dissolution of trospium chloride by co-crystallization with urea

NASA Astrophysics Data System (ADS)

Skořepová, Eliška; Hušák, Michal; Čejka, Jan; Zámostný, Petr; Kratochvíl, Bohumil

2014-08-01

The search for various solid forms of an active pharmaceutical ingredient (API) is an important step in drug development. Our aim was to prepare co-crystals of trospium chloride, an anticholinergic drug used for the treatment of incontinence, and to investigate if they have advantageous properties for drug formulation. Phase identification was done by powder X-ray diffraction and single-crystal X-ray diffraction. The chemical composition was verified by solution NMR and the dissolution rate of the prepared phases was studied by IDR (intrinsic dissolution rate). For further analysis of phase stability and transitions, combined thermal analysis and temperature-resolved X-ray powder diffraction were used. Urea was selected as a co-crystallization partner. Trospium chloride urea (1:1) co-crystal was prepared by a solvent evaporation. From single-crystal data, the co-crystal structure was solved in a space group P21/c and compared to previously published structures of trospium chloride. Intrinsic dissolution rate revealed that the co-crystal dissolves 32% faster than pure API. However, its low thermal and pressure stability makes it a challenging choice for the final drug formulation.

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...

Method of Generating X-Ray Diffraction Data for Integral Detection of Twin Defects in Super-Hetero-Epitaxial Materials

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang Hyouk (Inventor); King, Glen C. (Inventor); Elliott, James R. (Inventor)

2009-01-01

A method provides X-ray diffraction (XRD) data suitable for integral detection of a twin defect in a strained or lattice-matched epitaxial material made from components having crystal structures having symme try belonging to different space groups. The material is mounted in a n X-ray diffraction (XRD) system. In one embodiment, the XRD system's goniometer angle Omega is set equal to (Theta(sub B)-Beta) where The ta(sub B) is a Bragg angle for a designated crystal plane of the allo y that is disposed at a non-perpendicular orientation with respect to the {111) crystal plane, and Beta is the angle between the designate d crystal plane and a { 111 } crystal plane of one of the epitaxial components. The XRD system's detector angle is set equal to (Theta(su b B)+Beta). The material can be rotated through an angle of azimuthal rotation Phi about the axis aligned with the material. Using the det ector, the intensity of the X-ray diffraction is recorded at least at the angle at which the twin defect occurs.

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography.

PubMed

Coughlan, H D; Darmanin, C; Kirkwood, H J; Phillips, N W; Hoxley, D; Clark, J N; Vine, D J; Hofmann, F; Harder, R J; Maxey, E; Abbey, B

2017-01-01

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed.

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography

DOE PAGES

Coughlan, H. D.; Darmanin, C.; Kirkwood, H. J.; ...

2017-01-01

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals. Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to themore » diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. As a result, a possible mechanism to account for these observations is proposed.« less

Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography

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

Coughlan, H. D.; Darmanin, C.; Kirkwood, H. J.

The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals. Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to themore » diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. As a result, a possible mechanism to account for these observations is proposed.« less

In situ high-pressure measurement of crystal solubility by using neutron diffraction

NASA Astrophysics Data System (ADS)

Chen, Ji; Hu, Qiwei; Fang, Leiming; He, Duanwei; Chen, Xiping; Xie, Lei; Chen, Bo; Li, Xin; Ni, Xiaolin; Fan, Cong; Liang, Akun

2018-05-01

Crystal solubility is one of the most important thermo-physical properties and plays a key role in industrial applications, fundamental science, and geoscientific research. However, high-pressure in situ measurements of crystal solubility remain very challenging. Here, we present a method involving high-pressure neutron diffraction for making high-precision in situ measurements of crystal solubility as a function of pressure over a wide range of pressures. For these experiments, we designed a piston-cylinder cell with a large chamber volume for high-pressure neutron diffraction. The solution pressures are continuously monitored in situ based on the equation of state of the sample crystal. The solubility at a high pressure can be obtained by applying a Rietveld quantitative multiphase analysis. To evaluate the proposed method, we measured the high-pressure solubility of NaCl in water up to 610 MPa. At a low pressure, the results are consistent with the previous results measured ex situ. At a higher pressure, more reliable data could be provided by using an in situ high-pressure neutron diffraction method.

Anisotropic light diffraction in crystals with a large acoustic-energy walk-off

NASA Astrophysics Data System (ADS)

Balakshy, V. I.; Voloshin, A. S.; Molchanov, V. Ya.

2014-11-01

The influence of energy walk-off in an acoustic beam on the characteristic of anisotropic Bragg diffraction of light has been investigated by the example of paratellurite crystal. The angular and frequency characteristics of acousto-optic diffraction have been calculated in wide ranges of ultrasound frequencies and Bragg angles using the modified Raman-Nath equations. It is shown that the walk-off of an acoustic beam may change (either widen or narrow) significantly the frequency and angular ranges. The calculation results have been experimentally checked on an acousto-optic cell made of 10.5°-cut paratellurite crystal.

X-Ray Topography of Tetragonal Lysozyme Grown by the Temperature-Controlled Technique

NASA Technical Reports Server (NTRS)

Stojanoff, V.; Siddons, D. P.; Monaco, Lisa A.; Vekilov, Peter; Rosenberger, Franz

1997-01-01

Growth-induced defects in lysozyme crystals were observed by white-beam and monochromatic X-ray topography at the National Synchrotron Light Source (NSLS) at the Brookhaven National Laboratory (BNL). The topographic methods were non-destructive to the extent that traditional diffraction data collection could be performed to high resolution after topography. It was found that changes in growth parameters, defect concentration as detected by X-ray topography, and the diffraction quality obtainable from the crystals were all strongly correlated. In addition, crystals with fewer defects showed lower mosaicity and higher diffraction resolution as expected.

Diffraction and imaging study of imperfections of crystallized lysozyme with coherent X-rays

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Chu, Y. S.; Lai, B.; Thomas, B. R.; Chernov, A. A.

2004-01-01

Phase-contrast X-ray diffraction imaging and high-angular-resolution diffraction combined with phase-contrast radiographic imaging were employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in the symmetric Laue case. The full-width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal was approximately 16.7 arcsec and imperfections including line defects, inclusions and other microdefects were observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <1 1 0> growth front and have been found to originate mostly in a central growth area and occasionally in outer growth regions. Inclusions of impurities or formations of foreign particles in the central growth region are resolved in the images with high sensitivity to defects. Slow dehydration led to the broadening of a fairly symmetric 4 4 0 rocking curve by a factor of approximately 2.6, which was primarily attributed to the dehydration-induced microscopic effects that are clearly shown in X-ray diffraction images. The details of the observed defects and the significant change in the revealed microstructures with drying provide insight into the nature of imperfections, nucleation and growth, and the properties of protein crystals.

Structural, mechanical and light yield characterisation of heat treated LYSO:Ce single crystals for medical imaging applications

NASA Astrophysics Data System (ADS)

Mengucci, P.; André, G.; Auffray, E.; Barucca, G.; Cecchi, C.; Chipaux, R.; Cousson, A.; Davì, F.; Di Vara, N.; Rinaldi, D.; Santecchia, E.

2015-06-01

Five single crystals of cerium-doped lutetium yttrium oxyorthosilicate (LYSO:Ce) grown by the Czochralski method were submitted to structural characterisation by X-ray (XRD) and neutron (ND) diffraction, scanning (SEM) and transmission (TEM) electron microscopy and energy dispersive microanalysis (EDS). The Ultimate Tensile Strength (UTS), the Young Modulus (YM) and the Light Yield (LY) of the samples were also measured in order to correlate the mechanical and the optical behaviour of the crystals with the characteristics of their microstructure. Two of the samples analysed were also heat treated at 300 °C for 10 h to evidence possible variations induced by the temperature in the optical and mechanical response of the crystals. Results showed that the mean compositional variations evidenced by the structural analyses do not affect the mechanical and optical behaviour of the samples. On the contrary, the thermal treatment could induce the formation of coherent spherical particles (size 10 to 15 nm), not uniformly distributed inside the sample, that strongly reduce the UTS and YM values, but it does not affect the optical response of the crystal. This latter result was attributed to the low value of the heating temperature (300 °C) that is not sufficiently high to induce annealing of the oxygen vacancies traps that are responsible of the deterioration of the scintillation properties of the LYSO:Ce crystals. This study was carried out in the framework of the Crystal Clear Collaboration (CCC).

Three-dimensional electron diffraction of plant light-harvesting complex

PubMed Central

Wang, Da Neng; Kühlbrandt, Werner

1992-01-01

Electron diffraction patterns of two-dimensional crystals of light-harvesting chlorophyll a/b-protein complex (LHC-II) from photosynthetic membranes of pea chloroplasts, tilted at different angles up to 60°, were collected to 3.2 Å resolution at -125°C. The reflection intensities were merged into a three-dimensional data set. The Friedel R-factor and the merging R-factor were 21.8 and 27.6%, respectively. Specimen flatness and crystal size were critical for recording electron diffraction patterns from crystals at high tilts. The principal sources of experimental error were attributed to limitations of the number of unit cells contributing to an electron diffraction pattern, and to the critical electron dose. The distribution of strong diffraction spots indicated that the three-dimensional structure of LHC-II is less regular than that of other known membrane proteins and is not dominated by a particular feature of secondary structure. ImagesFIGURE 1FIGURE 2 PMID:19431817

Structural characterization and aging of glassy pharmaceuticals made using acoustic levitation.

PubMed

Benmore, Chris J; Weber, J K R; Tailor, Amit N; Cherry, Brian R; Yarger, Jeffery L; Mou, Qiushi; Weber, Warner; Neuefeind, Joerg; Byrn, Stephen R

2013-04-01

Here, we report the structural characterization of several amorphous drugs made using the method of quenching molten droplets suspended in an acoustic levitator. (13) C NMR, X-ray, and neutron diffraction results are discussed for glassy cinnarizine, carbamazepine, miconazole nitrate, probucol, and clotrimazole. The (13) C NMR results did not find any change in chemical bonding induced by the amorphization process. High-energy X-ray diffraction results were used to characterize the ratio of crystalline to amorphous material present in the glasses over a period of 8 months. All the glasses were stable for at least 6 months except carbamazepine, which has a strong tendency to crystallize within a few months. Neutron and X-ray pair distribution function analyses were applied to the glassy materials, and the results were compared with their crystalline counterparts. The two diffraction techniques yielded similar results in most cases and identified distinct intramolecular and intermolecular correlations. The intramolecular scattering was calculated based on the crystal structure and fit to the measured X-ray structure factor. The resulting intermolecular pair distribution functions revealed broad-nearest and next-nearest neighbor molecule-molecule correlations. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 102:1290-1300, 2013. Copyright © 2013 Wiley Periodicals, Inc.

Preliminary morphological and X-ray diffraction studies of the crystals of the DNA cetyltrimethylammonium salt.

PubMed

Osica, V D; Pyatigorskaya, T L; Polyvtsev, O F; Dembo, A T; Kliya, M O; Vasilchenko, V N; Verkin, B I; Sukharevskya, B Y

1977-04-01

Double-stranded DNA molecules (molecular weight 2.5 X 10(5) - 5 X 10(5) daltons) have been crystallized from water-salt solutions as cetyltrimethylammonium salts (CTA-DNA). Variation of crystallization conditions results in a production of different types of CTA-DNA crystals: spherulits, dendrites, needle-shaped and faceted rhombic crystals, the latter beeing up to 0.3 mm on a side. X-ray diffraction data indicate that DNA molecules in the crystals form a hexagonal lattice which parameters vary slightly with the morphological type of the crystal. Comparison of the melting curves of the DNA preparation before and after crystallization suggests that DNA molecules are partially fractionated in the course of crystallization. Crystals of the CTA-DNA-proflavine complex have also been obtained.

Preliminary morphological and X-ray diffraction studies of the crystals of the DNA cetyltrimethylammonium salt.

PubMed Central

Osica, V D; Pyatigorskaya, T L; Polyvtsev, O F; Dembo, A T; Kliya, M O; Vasilchenko, V N; Verkin, B I; Sukharevskya, B Y

1977-01-01

Double-stranded DNA molecules (molecular weight 2.5 X 10(5) - 5 X 10(5) daltons) have been crystallized from water-salt solutions as cetyltrimethylammonium salts (CTA-DNA). Variation of crystallization conditions results in a production of different types of CTA-DNA crystals: spherulits, dendrites, needle-shaped and faceted rhombic crystals, the latter beeing up to 0.3 mm on a side. X-ray diffraction data indicate that DNA molecules in the crystals form a hexagonal lattice which parameters vary slightly with the morphological type of the crystal. Comparison of the melting curves of the DNA preparation before and after crystallization suggests that DNA molecules are partially fractionated in the course of crystallization. Crystals of the CTA-DNA-proflavine complex have also been obtained. Images PMID:866188

Crystallization and x-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase [Crysallization and preliminary x-ray diffraction analysis of a bacterial class I labdane-related diterpene synthase

DOE PAGES

Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia; ...

2015-08-25

Here, labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg 2+ (LrdC-Mg 2+) and in complex with inorganic pyrophosphate (PP i) (LrdC-Mg 2+–PP i). Crystals of native LrdC-Mg 2+ diffracted to 2.50 Å resolution and belonged to the trigonal space group P3 221, with unit-cell parameters a = b = 107.1, c = 89.2 Å.more » Crystals of the LrdC-Mg 2+–PP i complex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36 Å resolution and also belonged to the trigonal space group P3 221. Crystals of the LrdC-Mg 2+–PP i complex grown in a second crystallization condition with PEG 3350 diffracted to 2.57 Å resolution and belonged to the monoclinic space group P2 1, with unit-cell parameters a = 49.9, b = 104.1, c = 66.5 Å, β = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.« less

The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

2017-10-01

A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.

HANFORD WASTE MINERALOGY REFERENCE REPORT

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

DISSELKAMP RS

2010-06-29

This report lists the observed mineral phases present in the Hanford tanks. This task was accomplished by performing a review of numerous reports that used experimental techniques including, but not limited to: x-ray diffraction, polarized light microscopy, scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, electron energy loss spectroscopy, and particle size distribution analyses. This report contains tables that can be used as a quick reference to identify the crystal phases observed in Hanford waste.

HANFORD WASTE MINEROLOGY REFERENCE REPORT

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

DISSELKAMP RS

2010-06-18

This report lists the observed mineral phase phases present in the Hanford tanks. This task was accomplished by performing a review of numerous reports using experimental techniques including, but not limited to: x-ray diffraction, polarized light microscopy, scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, electron energy loss spectroscopy, and particle size distribution analyses. This report contains tables that can be used as a quick reference to identify the crystal phases present observed in Hanford waste.

Growth, structural, optical, mechanical and quantum chemical analysis of unidirectional grown bis(guanidinium) 5-sulfosalicylate (BGSSA) single crystal

NASA Astrophysics Data System (ADS)

Sreedevi, R.; Saravana Kumar, G.; Amarsingh Bhabu, K.; Balu, T.; Murugakoothan, P.; Rajasekaran, T. R.

2018-02-01

Bis(guanidinium) 5-sulfosalicylate single crystal was grown by using Sankaranarayanan-Ramasamy (SR) method from the solution of methanol and water in equimolar ratio. Good quality crystal with 50 mm length and 10 mm in diameter was grown. The grown crystal was subjected to single crystal X-ray diffraction analysis to confirm the crystal structure and it was found to be orthorhombic. UV-Vis-NIR spectroscopic study revealed that the SR method grown crystal had good optical transparency with wide optical band gap of 4.4 eV. The presence of the functional groups and modes of vibrations were identified by FTIR spectroscopy recorded in the range 4000-400 cm-1. The mechanical strength of the grown crystal was confirmed using Vickers microhardness tester by applying load from 25 g to 100 g. Density functional theory (DFT) method with B3LYP/6-31-G (d,p) level basis set was employed and hence the optimized molecular geometry, first order hyperpolarizability, dipole moment, thermodynamic functions, molecular electrostatic potential and frontier molecular orbital analysis of the grown BGSSA sample was computed and analysed.

Improving the dissolution and bioavailability of 6-mercaptopurine via co-crystallization with isonicotinamide.

PubMed

Wang, Jian-Rong; Yu, Xueping; Zhou, Chun; Lin, Yunfei; Chen, Chen; Pan, Guoyu; Mei, Xuefeng

2015-03-01

6-Mercaptopurine (6-MP) is a clinically important antitumor drug. The commercially available form was provided as monohydrate and belongs to BCS class II category. Co-crystallization screening by reaction crystallization method (RCM) and monitored by powder X-ray diffraction led to the discovery of a new co-crystal formed between 6-MP and isonicotinamide (co-crystal 1). Co-crystal 1 was thoroughly characterized by X-ray diffraction, FT-IR and Raman spectroscopy, and thermal analysis. Noticeably, the in vitro and in vivo studies revealed that co-crystal 1 possesses improved dissolution rate and superior bioavailability on animal model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthesis, structural and spectral characterization of a novel NLO crystal N,N‧-diphenylguanidinium picrate: diacetone solvate

NASA Astrophysics Data System (ADS)

Shanmugavadivu, T.; Dhandapani, M.; Naveen, S.; Lokanath, N. K.

2017-09-01

An organic NLO active material N,N‧-diphenylguanidinium picrate: diacetone solvate (C13H14N3+. C6H2N3O7-. 2C3H6O) (DPGPD) was synthesized and single crystals were grown by slow evaporation-solution growth technique at room temperature. DPGPD crystallizes in monoclinic crystal system with noncentrosymmetric space group, Cc confirmed by single crystal X-ray diffraction analysis. The presence of various functional groups was identified from FT-IR spectral analysis and the proton transfer during the formation of compound was confirmed by NMR spectroscopic techniques. The thermal stability was investigated by TG/DTA analyses. Optical transmittance was measured by UV-Vis-NIR spectroscopy and band gap energy was calculated. Photoluminescence spectrum was used to explore its applicability towards laser diodes. Dielectric property of the material was ascertained at different temperatures and it is found that the grown crystal has higher dielectric constant in low frequencies. Photoconductivity study revealed that DPGPD exhibits positive photoconductivity. SHG property was found to be 0.6 times higher than that of KDP.

Structural, thermal and optical characterization of an organic NLO material--benzaldehyde thiosemicarbazone monohydrate single crystals.

PubMed

Santhakumari, R; Ramamurthi, K

2011-02-01

Single crystals of the organic NLO material, benzaldehyde thiosemicarbazone (BTSC) monohydrate, were grown by slow evaporation method. Solubility of BTSC monohydrate was determined in ethanol at different temperatures. The grown crystals were characterized by single crystal X-ray diffraction analysis to determine the cell parameters and by FT-IR technique to study the presence of the functional groups. Thermogravimetric and differential thermal analyses reveal the thermal stability of the crystal. UV-vis-NIR spectrum shows excellent transmission in the region of 200-1100 nm. Theoretical calculations were carried out to determine the linear optical constants such as extinction coefficient and refractive index. Further the optical nonlinearities of BTSC have been investigated by Z-scan technique with He-Ne laser radiation of wavelength 632.8 nm. Mechanical properties of the grown crystal were studied using Vickers microhardness tester. Second harmonic generation efficiency of the powdered BTSC monohydrate was tested using Nd:YAG laser and it is found to be ∼5.3 times that of potassium dihydrogen orthophosphate. Copyright © 2010 Elsevier B.V. All rights reserved.

Structure analysis on synthetic emerald crystals

NASA Astrophysics Data System (ADS)

Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

2013-05-01

Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

High Pressure Single Crystal Diffraction at PX 2

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

Zhang, Dongzhou; Dera, Przemyslaw K.; Eng, Peter J.

2017-01-01

In this report, we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell at the GSECARS 13-BM-C beamline at the Advanced Photon Source. ATREX and RSV programs are used to analyze the data.

Idealized powder diffraction patterns for cellulose polymorphs

USDA-ARS?s Scientific Manuscript database

Cellulose samples are routinely analyzed by X-ray diffraction to determine their crystal type (polymorph) and crystallinity. However, the connection is seldom made between those efforts and the crystal structures of cellulose that have been determined with synchrotron X-radiation and neutron diffrac...

The new HMI beamline MAGS: an instrument for hard X-ray diffraction at BESSY.

PubMed

Dudzik, Esther; Feyerherm, Ralf; Diete, Wolfgang; Signorato, Riccardo; Zilkens, Christopher

2006-11-01

The Hahn-Meitner-Institute Berlin is operating the new hard X-ray diffraction beamline MAGS at the Berlin synchrotron radiation source BESSY. The beamline is intended to complement the existing neutron instrumentation at the Berlin Neutron Scattering Centre. The new beamline uses a 7 T multipole wiggler to produce photon fluxes in the 10(11)-10(12) photons s(-1) (100 mA)(-1) (0.1% bandwidth)(-1) range at energies from 4 to 30 keV at the experiment. It has active bendable optics to provide flexible horizontal and vertical focusing and to compensate the large heat load from the wiggler source. The experimental end-station consists of a six-circle Huber diffractometer which can be used with an additional (polarization) analyser and different sample environments. The beamline is intended for single-crystal diffraction and resonant magnetic scattering experiments for the study of ordering phenomena, phase transitions and materials science.

Curved focusing crystals for hard X-ray astronomy

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

Ferrari, C., E-mail: ferrari@imem.cnr.it; Buffagni, E.; Bonnini, E.

A lens made by a properly arranged array of crystals can be used to focus x-rays of energy ranging from 30 to 500 keV for x-ray astronomy. Mosaic or curved crystals can be employed as x-ray optical elements. In this work self standing curved focusing Si and GaAs crystals in which the lattice bending is induced by a controlled damaging process on one side of planar crystals are characterized. Diffraction profiles in Laue geometry have been measured in crystals at x-ray energies E = 17, 59 and 120 keV. An enhancement of diffraction efficiency is found in asymmetric geometries.

X-ray transparent microfluidic chip for mesophase-based crystallization of membrane proteins and on-chip structure determination

DOE PAGES

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; ...

2014-08-21

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. In addition, we validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

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

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.

2014-10-01

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

Two novel transition metal-organic frameworks based on 1,3,5-benzenetricarboxylate ligand: Syntheses, structures and thermal properties

NASA Astrophysics Data System (ADS)

Fu, Ying; Li, Guobao; Liao, Fuhui; Xiong, Ming; Lin, Jianhua

2011-10-01

Two novel transition metal-organic frameworks, [Zn 6(OH) 3(BTC) 3(H 2O) 3]ṡ7H 2O ( 1) and [Cd(BTC)(H 2O)]ṡ[HIM] ( 2) (H 3BTC = 1,3,5-benzenetricarboxylic acid), have been synthesized under hydrothermal conditions and characterized by single crystal and variable temperature powder X-ray diffraction (VTPXRD), IR spectroscopy, elemental analyses, ICP measurements, and coupled TG-MS analyses. Compound 1 crystallizes in the trigonal space group R3 c, and could be described as a 3D porous network consisting of (Zn 2O 8) n zigzag chains and bridging BTC ligands with 1D channels along c axis. Compound 2 crystallizes in the monoclinic space group P2 1/ c, and exhibits a 2D framework made up of CdO 6 octahedra and BTC ligands parallel the bc plane. TG-MS and VTPXRD studies reveal that 1 is stable up to 320 °C under air, and 2 stable up to 220 °C.

Amorphous Calcium Carbonate Precipitation by Cellular Biomineralization in Mantle Cell Cultures of Pinctada fucata

PubMed Central

Xiang, Liang; Kong, Wei; Su, Jingtan; Liang, Jian; Zhang, Guiyou; Xie, Liping; Zhang, Rongqing

2014-01-01

The growth of molluscan shell crystals is generally thought to be initiated from the extrapallial fluid by matrix proteins, however, the cellular mechanisms of shell formation pathway remain unknown. Here, we first report amorphous calcium carbonate (ACC) precipitation by cellular biomineralization in primary mantle cell cultures of Pinctada fucata. Through real-time PCR and western blot analyses, we demonstrate that mantle cells retain the ability to synthesize and secrete ACCBP, Pif80 and nacrein in vitro. In addition, the cells also maintained high levels of alkaline phosphatase and carbonic anhydrase activity, enzymes responsible for shell formation. On the basis of polarized light microscopy and scanning electron microscopy, we observed intracellular crystals production by mantle cells in vitro. Fourier transform infrared spectroscopy and X-ray diffraction analyses revealed the crystals to be ACC, and de novo biomineralization was confirmed by following the incorporation of Sr into calcium carbonate. Our results demonstrate the ability of mantle cells to perform fundamental biomineralization processes via amorphous calcium carbonate, and these cells may be directly involved in pearl oyster shell formation. PMID:25405357

A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids

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

Zipper, Lauren E.; Binghamton University, 4400 Vestal Parkway East, Vestal, NY 13902; Aristide, Xavier

This article describes the use of evaporation control lids that are fitted to crystallization plates to improve the reproducibility of trials using as little as 5 nl. The plate lids contain apertures which are large enough for the transfer of protein containing droplets, but small enough to greatly reduce the rate of evaporation during the time needed to prepare the plate. A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fittingmore » the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under different conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63–82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. The results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations.« less

Application of powder X-ray diffraction in studying the compaction behavior of bulk pharmaceutical powders.

PubMed

Bandyopadhyay, Rebanta; Selbo, Jon; Amidon, Gregory E; Hawley, Michael

2005-11-01

This study investigates the effects of crystal lattice deformation on the powder X-ray diffraction (PXRD) patterns of compressed polycrystalline specimen (compacts/tablets) made from molecular, crystalline powders. The displacement of molecules and the corresponding adjustment of interplanar distances (d-spacings) between diffracting planes of PNU-288034 and PNU-177553, which have crystal habits with a high aspect ratio favoring preferred orientation during tableting, are demonstrated by shifts in the diffracted peak positions. The direction of shift in diffracted peak positions suggests a reduction of interplanar d-spacing in the crystals of PNU-288034 and PNU-177553 following compaction. There is also a general reduction of peak intensities following compression at the different compressive loads. The lattice strain representing the reduction in d-spacing is proportional to the original d-spacing of the uncompressed sample suggesting that, as with systems that obey a simple Hooke's law relationship, the further apart the planes of atoms/molecules within the lattice are, the easier it is for them to approach each other under compressive stresses. For a third model compound comprising more equant-shaped crystals of PNU-141659, the shift in diffracted peak positions are consistent with an expansion of lattice spacing after compression. This apparent anomaly is supported by the PXRD studies of the bulk powder consisting of fractured crystals where also, the shift in peak position suggests expansion of the lattice planes. Thus the crystals of PNU-141659 may be fracturing under the compressive loads used to produce the compacts. Additional studies are underway to relate the PXRD observations with the bulk tableting properties of these model compounds.

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

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

Dynamical electron diffraction simulation for non-orthogonal crystal system by a revised real space method.

PubMed

Lv, C L; Liu, Q B; Cai, C Y; Huang, J; Zhou, G W; Wang, Y G

2015-01-01

In the transmission electron microscopy, a revised real space (RRS) method has been confirmed to be a more accurate dynamical electron diffraction simulation method for low-energy electron diffraction than the conventional multislice method (CMS). However, the RRS method can be only used to calculate the dynamical electron diffraction of orthogonal crystal system. In this work, the expression of the RRS method for non-orthogonal crystal system is derived. By taking Na2 Ti3 O7 and Si as examples, the correctness of the derived RRS formula for non-orthogonal crystal system is confirmed by testing the coincidence of numerical results of both sides of Schrödinger equation; moreover, the difference between the RRS method and the CMS for non-orthogonal crystal system is compared at the accelerating voltage range from 40 to 10 kV. Our results show that the CMS method is almost the same as the RRS method for the accelerating voltage above 40 kV. However, when the accelerating voltage is further lowered to 20 kV or below, the CMS method introduces significant errors, not only for the higher-order Laue zone diffractions, but also for zero-order Laue zone. These indicate that the RRS method for non-orthogonal crystal system is necessary to be used for more accurate dynamical simulation when the accelerating voltage is low. Furthermore, the reason for the increase of differences between those diffraction patterns calculated by the RRS method and the CMS method with the decrease of the accelerating voltage is discussed. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

On the nature of the reversibility of hydration-dehydration on the crystal structure and magnetism of the ferrimagnet [MnII(enH)(H2O)][CrIII(CN)6].H2O.

PubMed

Yoshida, Yusuke; Inoue, Katsuya; Kurmoo, Mohamedally

2009-01-05

We report the synthesis, crystal structure, and thermal and magnetic properties of the two-dimensional achiral soft ferrimagnet [Mn(II)(enH)(H(2)O)][Cr(III)(CN)(6)].H(2)O (1), en = 1,2-diaminoethane, as well as the recyclability of the dehydration and rehydration and their influence on the crystal structure and its magnetic properties. Unlike [Mn(S-pnH)(H(2)O)][Cr(CN)(6)].H(2)O (2S, pn = 1,2-diaminopropane), which is a chiral (P2(1)2(1)2(1)) enantiopure ferrimagnet (T(C) = 38 K), 1 crystallizes in the achiral orthorhombic Pcmn space group, having a similar two-dimensional square network of Mn-Cr with bridging cyanide, and 1 behaves also as a soft ferrimagnet (T(C) = 42 K). X-ray diffraction experiments on a single crystal of 1 indicate a transformation from a single crystal to an amorphous phase upon dehydrataion and partial recovery of its crystallinity upon rehydration. The dehydrated phase 1-DP exhibits long-range ordering at 75 K to a ferrimagnetic state and coercive field at 2 K of 100 Oe, which are a higher critical temperature and coercive field than for the virgin sample (H(C) = 60 Oe). Thermogravimetric analyses indicate that the crystallinity deteriorates upon hydration-dehydration cycling, with persistence toward the amorphous phase, as also seen by magnetization measurements. This effect is associated with an increase of statistical disorder inherent in the dehydration-rehydration process. X-ray powder diffraction suggests that 1-DP may retain order within the layers but loses coherence in the stacking of the layers.

In-situ neutron diffraction and crystal plasticity finite element modeling to study the kinematic stability of retained austenite in bearing steels

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

Voothaluru, Rohit; Bedekar, Vikram; Xie, Qingge

This work integrates in-situ neutron diffraction and crystal plasticity finite element modeling to study the kinematic stability of retained austenite in high carbon bearing steels. The presence of a kinematically metastable retained austenite in bearing steels can significantly affect the macro-mechanical and micro-mechanical material response. Mechanical characterization of metastable austenite is a critical component in accurately capturing the micro-mechanical behavior under typical application loads. Traditional mechanical characterization techniques are unable to discretely quantify the micro-mechanical response of the austenite, and as a result, the computational predictions rely heavily on trial and error or qualitative descriptions of the austenite phase. Inmore » order to overcome this, in the present work, we use in-situ neutron diffraction of a uniaxial tension test of an A485 Grade 1 bearing steel specimen. The mechanical response determined from the neutron diffraction analysis was incorporated into a hybrid crystal plasticity finite element model that accounts for the martensite's crystal plasticity and the stress-assisted transformation from austenite to martensite in bearing steels. Here, the modeling response was used to estimate the single crystal elastic constants of the austenite and martensite phases. Finally, the results show that using in-situ neutron diffraction, coupled with a crystal plasticity model, can successfully predict both the micro-mechanical and macro-mechanical responses of bearing steels while accounting for the martensitic transformation of the retained austenite.« less

In-situ neutron diffraction and crystal plasticity finite element modeling to study the kinematic stability of retained austenite in bearing steels

DOE PAGES

Voothaluru, Rohit; Bedekar, Vikram; Xie, Qingge; ...

2018-11-21

This work integrates in-situ neutron diffraction and crystal plasticity finite element modeling to study the kinematic stability of retained austenite in high carbon bearing steels. The presence of a kinematically metastable retained austenite in bearing steels can significantly affect the macro-mechanical and micro-mechanical material response. Mechanical characterization of metastable austenite is a critical component in accurately capturing the micro-mechanical behavior under typical application loads. Traditional mechanical characterization techniques are unable to discretely quantify the micro-mechanical response of the austenite, and as a result, the computational predictions rely heavily on trial and error or qualitative descriptions of the austenite phase. Inmore » order to overcome this, in the present work, we use in-situ neutron diffraction of a uniaxial tension test of an A485 Grade 1 bearing steel specimen. The mechanical response determined from the neutron diffraction analysis was incorporated into a hybrid crystal plasticity finite element model that accounts for the martensite's crystal plasticity and the stress-assisted transformation from austenite to martensite in bearing steels. Here, the modeling response was used to estimate the single crystal elastic constants of the austenite and martensite phases. Finally, the results show that using in-situ neutron diffraction, coupled with a crystal plasticity model, can successfully predict both the micro-mechanical and macro-mechanical responses of bearing steels while accounting for the martensitic transformation of the retained austenite.« less

Crystallization and characterization of human chorionic gonadotropin in chemically deglycosylated and enzymatically desialylated states

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

Lustbader, J.W.; Birken, S.; Pileggi, N.F.

1989-11-28

Crystals suitable for X-ray diffraction studies at moderate resolution have been grown from two forms of human chorionic gonadotropin (hCG): HF-treated hCG and neuraminidase-treated hCG. The enzymatically desialylated form of hCG produced crystals that diffract to 2.8 {angstrom} as compared to the HF-treated hCG crystals that diffract to 3.0 {angstrom}. Although it was assumed that the high and heterogeneous carbohydrate content of the glycoprotein hormones inhibited their crystallization, this report suggests that it is the negatively charged surface sugars and neither the total carbohydrate content nor its heterogeneity which interferes with crystal formation. Chemical deglycosylation resulted in significantly increased proteinmore » degradation during crystal growth. Such peptide bond cleavages were observed to a much lesser extent in the crystals grown from neuraminidase-digested hCG. Sequence analysis of the HF-treated hCG crystals suggested that up to 45% of the molecules within the crystal had an acid-labile peptide bond cleaved. In contrast, the neuraminidase-treated hCG exhibited less than 9% of this type of cleavage. The manner in which hCG was treated prior to crystallization was found to be a very important factor in the extent of peptide bound cleavages occurring during crystal growth. HF treatment of glycoproteins may render glycoproteins more susceptible to peptide bond cleavage during crystal growth.« less

An evaluation of adhesive sample holders for advanced crystallographic experiments

PubMed Central

Mazzorana, Marco; Sanchez-Weatherby, Juan; Sandy, James; Lobley, Carina M. C.; Sorensen, Thomas

2014-01-01

The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed. PMID:25195752

Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain

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

Nishimura, Mitsuhiro; Protein Research Group, RIKEN Yokohama Institute, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045; Kaminishi, Tatsuya

2007-11-01

A truncated variant of human ribosomal protien L10 was prepared and crystallized. Diffraction data were collected to 2.5 Å resolution. Eukaryotic ribosomal protein L10 is an essential component of the large ribosomal subunit, which organizes the architecture of the aminoacyl-tRNA binding site. The human L10 protein is also called the QM protein and consists of 214 amino-acid residues. For crystallization, the L10 core domain (L10CD, Phe34–Glu182) was recombinantly expressed in Escherichia coli and purified to homogeneity. A hexagonal crystal of L10CD was obtained by the sitting-drop vapour-diffusion method. The L10CD crystal diffracted to 2.5 Å resolution and belongs to spacemore » group P3{sub 1}21 or P3{sub 2}21.« less

Purification, crystallization and preliminary X-ray diffraction studies of UDP-N-acetylglucosamine pyrophosphorylase from Candida albicans

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

Maruyama, Daisuke; Nishitani, Yuichi; Nonaka, Tsuyoshi

2006-12-01

UDP-N-acetylglucosamine pyrophosphorylase was purified and crystallized and X-ray diffraction data were collected to 2.3 Å resolution. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is an essential enzyme in the synthesis of UDP-N-acetylglucosamine. UAP from Candida albicans was purified and crystallized by the sitting-drop vapour-diffusion method. The crystals of the substrate and product complexes both diffract X-rays to beyond 2.3 Å resolution using synchrotron radiation. The crystals of the substrate complex belong to the triclinic space group P1, with unit-cell parameters a = 47.77, b = 62.89, c = 90.60 Å, α = 90.01, β = 97.72, γ = 92.88°, whereas those of the productmore » complex belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.95, b = 90.87, c = 94.88 Å.« less

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

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

Abramchik, Yu. A.; Timofeev, V. I., E-mail: tostars@mail.ru; Muravieva, T. I.

2016-11-15

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12{sub 1}1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, βmore » = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.« less

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.

Order and disorder in crystals of hexameric NTPases from dsRNA bacteriophages.

PubMed

Mancini, Erika J; Grimes, Jonathan M; Malby, Robyn; Sutton, Geoffrey C; Kainov, Denis E; Juuti, Jarmo T; Makeyev, Eugene V; Tuma, Roman; Bamford, Dennis H; Stuart, David I

2003-12-01

The packaging of genomic RNA in members of the Cystoviridae is performed by P4, a hexameric protein with NTPase activity. Across family members such as Phi6, Phi8 and Phi13, the P4 proteins show low levels of sequence identity, but presumably have similar atomic structures. Initial structure-determination efforts for P4 from Phi6 and Phi8 were hampered by difficulties in obtaining crystals that gave ordered diffraction. Diffraction from crystals of full-length P4 showed a variety of disorder and anisotropy. Subsequently, crystals of Phi13 P4 were obtained which yielded well ordered diffraction to 1.7 A. Comparison of the packing arrangements of P4 hexamers in different crystal forms and analysis of the disorder provides insights into the flexibility of this family of proteins, which might be an integral part of their biological function.

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.

Goniometer-based femtosecond crystallography with X-ray free electron lasers

DOE PAGES

Cohen, Aina E.; Soltis, S. Michael; González, Ana; ...

2014-10-31

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were usedmore » to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β 2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.« less

Goniometer-based femtosecond crystallography with X-ray free electron lasers

PubMed Central

Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; Calero, Guillermo; Chang, Joseph F.; Chollet, Matthieu; Ehrensberger, Paul; Eriksson, Thomas L.; Feng, Yiping; Hattne, Johan; Hedman, Britt; Hollenbeck, Michael; Holton, James M.; Keable, Stephen; Kobilka, Brian K.; Kovaleva, Elena G.; Kruse, Andrew C.; Lemke, Henrik T.; Lin, Guowu; Lyubimov, Artem Y.; Manglik, Aashish; Mathews, Irimpan I.; McPhillips, Scott E.; Nelson, Silke; Peters, John W.; Sauter, Nicholas K.; Smith, Clyde A.; Song, Jinhu; Stevenson, Hilary P.; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Vinetsky, Vladimir; Wakatsuki, Soichi; Weis, William I.; Zadvornyy, Oleg A.; Zeldin, Oliver B.; Zhu, Diling; Hodgson, Keith O.

2014-01-01

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources. PMID:25362050

Purification, crystallization and X-ray crystallographic analysis of a putative exopolyphosphatase from Zymomonas mobilis

PubMed Central

Zhang, Aili; Guo, Erhong; Qian, Lanfang; Tang, Nga-Yeung; Watt, Rory M.; Bartlam, Mark

2016-01-01

Exopolyphosphatase (PPX) enzymes degrade inorganic polyphosphate (poly-P), which is essential for the survival of microbial cells in response to external stresses. In this study, a putative exopolyphosphatase from Zymomonas mobilis (ZmPPX) was crystallized. Crystals of the wild-type enzyme diffracted to 3.3 Å resolution and could not be optimized further. The truncation of 29 amino acids from the N-terminus resulted in crystals that diffracted to 1.8 Å resolution. The crystals belonged to space group C2, with unit-cell parameters a = 122.0, b = 47.1, c = 89.5 Å, α = γ = 90, β = 124.5°. An active-site mutant that crystallized in the same space group and with similar unit-cell parameters diffracted to 1.56 Å resolution. One molecule was identified per asymmetric unit. Analytical ultracentrifugation confirmed that ZmPPX forms a dimer in solution. It was confirmed that ZmPPX possesses exopolyphosphatase activity against a synthetic poly-P substrate. PMID:26919520

Purification, crystallization and X-ray crystallographic analysis of a putative exopolyphosphatase from Zymomonas mobilis.

PubMed

Zhang, Aili; Guo, Erhong; Qian, Lanfang; Tang, Nga-Yeung; Watt, Rory M; Bartlam, Mark

2016-03-01

Exopolyphosphatase (PPX) enzymes degrade inorganic polyphosphate (poly-P), which is essential for the survival of microbial cells in response to external stresses. In this study, a putative exopolyphosphatase from Zymomonas mobilis (ZmPPX) was crystallized. Crystals of the wild-type enzyme diffracted to 3.3 Å resolution and could not be optimized further. The truncation of 29 amino acids from the N-terminus resulted in crystals that diffracted to 1.8 Å resolution. The crystals belonged to space group C2, with unit-cell parameters a = 122.0, b = 47.1, c = 89.5 Å, α = γ = 90, β = 124.5°. An active-site mutant that crystallized in the same space group and with similar unit-cell parameters diffracted to 1.56 Å resolution. One molecule was identified per asymmetric unit. Analytical ultracentrifugation confirmed that ZmPPX forms a dimer in solution. It was confirmed that ZmPPX possesses exopolyphosphatase activity against a synthetic poly-P substrate.

Evanescent Properties of Optical Diffraction from 2-Dimensional Hexagonal Photonic Crystals and Their Sensor Applications.

PubMed

Liao, Yu-Yang; Chen, Yung-Tsan; Chen, Chien-Chun; Huang, Jian-Jang

2018-04-03

The sensitivity of traditional diffraction grating sensors is limited by the spatial resolution of the measurement setup. Thus, a large space is required to improve sensor performance. Here, we demonstrate a compact hexagonal photonic crystal (PhC) optical sensor with high sensitivity. PhCs are able to diffract optical beams to various angles in azimuthal space. The critical wavelength that satisfies the phase matching or becomes evanescent was used to benchmark the refractive index of a target analyte applied on a PhC sensor. Using a glucose solution as an example, our sensor demonstrated very high sensitivity and a low limit of detection. This shows that the diffraction mechanism of hexagonal photonic crystals can be used for sensors when compact size is a concern.

Flat liquid crystal diffractive lenses with variable focus and magnification

NASA Astrophysics Data System (ADS)

Valley, Pouria

Non-mechanical variable lenses are important for creating compact imaging devices. Various methods employing dielectrically actuated lenses, membrane lenses, and liquid crystal lenses were previously proposed [1-4]. In This dissertation the design, fabrication, and characterization of innovative flat tunable-focus liquid crystal diffractive lenses (LCDL) are presented. LCDL employ binary Fresnel zone electrodes fabricated on Indium-Tin-Oxide using conventional micro-photolithography. The light phase can be adjusted by varying the effective refractive index of a nematic liquid crystal sandwiched between the electrodes and a reference substrate. Using a proper voltage distribution across various electrodes the focal length can be changed between several discrete values. Electrodes are shunted such that the correct phase retardation step sequence is achieved. If the number of 2pi zone boundaries is increased by a factor of m the focal length is changed from f to f/m based on the digitized Fresnel zone equation: f = rm2/2mlambda, where r m is mth zone radius, and lambda is the wavelength. The chromatic aberration of the diffractive lens is addressed and corrected by adding a variable fluidic lens. These LCDL operate at very low voltage levels (+/-2.5V ac input), exhibit fast switching times (20-150 ms), can have large apertures (>10 mm), and small form factor, and are robust and insensitive to vibrations, gravity, and capillary effects that limit membrane and dielectrically actuated lenses. Several tests were performed on the LCDL including diffraction efficiency measurement, switching dynamics, and hybrid imaging with a refractive lens. Negative focal lengths are achieved by adjusting the voltages across electrodes. Using these lenses in combination, magnification can be changed and zoom lenses can be formed. These characteristics make LCDL a good candidate for a variety of applications including auto-focus and zoom lenses in compact imaging devices such as camera phones. A business plan centered on this technology was developed as part of the requirements for the minor in entrepreneurship from the Eller College of Management. An industrial analysis is presented in this study that involves product development, marketing, and financial analyses (Appendix I).

Graphene as a protein crystal mounting material to reduce background scatter.

PubMed

Wierman, Jennifer L; Alden, Jonathan S; Kim, Chae Un; McEuen, Paul L; Gruner, Sol M

2013-10-01

The overall signal-to-noise ratio per unit dose for X-ray diffraction data from protein crystals can be improved by reducing the mass and density of all material surrounding the crystals. This article demonstrates a path towards the practical ultimate in background reduction by use of atomically thin graphene sheets as a crystal mounting platform for protein crystals. The results show the potential for graphene in protein crystallography and other cases where X-ray scatter from the mounting material must be reduced and specimen dehydration prevented, such as in coherent X-ray diffraction imaging of microscopic objects.

Graphene as a protein crystal mounting material to reduce background scatter

PubMed Central

Wierman, Jennifer L.; Alden, Jonathan S.; Kim, Chae Un; McEuen, Paul L.; Gruner, Sol M.

2013-01-01

The overall signal-to-noise ratio per unit dose for X-ray diffraction data from protein crystals can be improved by reducing the mass and density of all material surrounding the crystals. This article demonstrates a path towards the practical ultimate in background reduction by use of atomically thin graphene sheets as a crystal mounting platform for protein crystals. The results show the potential for graphene in protein crystallography and other cases where X-ray scatter from the mounting material must be reduced and specimen dehydration prevented, such as in coherent X-ray diffraction imaging of microscopic objects. PMID:24068843

A novel Monte Carlo algorithm for simulating crystals with McStas

NASA Astrophysics Data System (ADS)

Alianelli, L.; Sánchez del Río, M.; Felici, R.; Andersen, K. H.; Farhi, E.

2004-07-01

We developed an original Monte Carlo algorithm for the simulation of Bragg diffraction by mosaic, bent and gradient crystals. It has practical applications, as it can be used for simulating imperfect crystals (monochromators, analyzers and perhaps samples) in neutron ray-tracing packages, like McStas. The code we describe here provides a detailed description of the particle interaction with the microscopic homogeneous regions composing the crystal, therefore it can be used also for the calculation of quantities having a conceptual interest, as multiple scattering, or for the interpretation of experiments aiming at characterizing crystals, like diffraction topographs.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein

PubMed Central

Rahaman, Siti Nurulnabila A.; Mat Yusop, Jastina; Mohamed-Hussein, Zeti-Azura; Ho, Kok Lian; Teh, Aik-Hong; Waterman, Jitka; Ng, Chyan Leong

2016-01-01

C1ORF123 is a human hypothetical protein found in open reading frame 123 of chromosome 1. The protein belongs to the DUF866 protein family comprising eukaryote-conserved proteins with unknown function. Recent proteomic and bioinformatic analyses identified the presence of C1ORF123 in brain, frontal cortex and synapses, as well as its involvement in endocrine function and polycystic ovary syndrome (PCOS), indicating the importance of its biological role. In order to provide a better understanding of the biological function of the human C1ORF123 protein, the characterization and analysis of recombinant C1ORF123 (rC1ORF123), including overexpression and purification, verification by mass spectrometry and a Western blot using anti-C1ORF123 antibodies, crystallization and X-ray diffraction analysis of the protein crystals, are reported here. The rC1ORF123 protein was crystallized by the hanging-drop vapor-diffusion method with a reservoir solution comprised of 20% PEG 3350, 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate pH 6.5. The crystals diffracted to 1.9 Å resolution and belonged to an orthorhombic space group with unit-cell parameters a = 59.32, b = 65.35, c = 95.05 Å. The calculated Matthews coefficient (V M) value of 2.27 Å3 Da−1 suggests that there are two molecules per asymmetric unit, with an estimated solvent content of 45.7%. PMID:26919524

Does the thermal evolution of molecular structures critically affect the magnetic anisotropy?† †Electronic supplementary information (ESI) available. CCDC 1045631–1045633. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01245g

PubMed Central

Qian, Kang; Baldoví, José J.; Zhang, Yi-Quan; Overgaard, Jacob; Wang, Bing-Wu

2015-01-01

A dysprosium based single-ion magnet is synthesized and characterized by the angular dependence of the single-crystal magnetic susceptibility. Ab initio and effective electrostatic analyses are performed using the molecular structures determined from single crystal X-ray diffraction at 20 K, 100 K and 300 K. Contrary to the common assumption, the results reveal that the structural thermal effects that may affect the energy level scheme and magnetic anisotropy below 100 K are negligible. PMID:29568416

Synthesis, crystal structure investigation, spectroscopic characterizations and DFT computations on a novel 1-(2-chloro-4-phenylquinolin-3-yl)ethanone

NASA Astrophysics Data System (ADS)

Murugavel, S.; Stephen, C. S. Jacob Prasanna; Subashini, R.; Reddy, H. Raveendranatha; AnanthaKrishnan, Dhanabalan

2016-10-01

The title compound 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE) was synthesised effectively by chlorination of 3-acetyl-4-phenylquinolin-2(1H)-one (APQ) using POCl3 reagent. Structural and vibrational spectroscopic studies were performed by utilizing single crystal X-ray diffraction, FTIR and NMR spectral analysis along with DFT method utilizing GAUSSIAN‧ 03 software. Veda program has been employed to perform a detailed interpretation of vibrational spectra. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NBO, Global chemical reactivity descriptors and thermodynamic properties have been examined by (DFT/B3LYP) method with the 6-311G(d,p) basis set level.

Ultra-low thermal conductivity of TlIn5Se8 and structure of the new complex chalcogenide Tl0.98In13.12Se16.7Te2.3

NASA Astrophysics Data System (ADS)

Lefèvre, Robin; Berthebaud, David; Pérez, Olivier; Pelloquin, Denis; Boudin, Sophie; Gascoin, Franck

2017-06-01

TlIn5Se8 has been synthesized by means of solid-state reaction and densified by Spark Plasma Sintering. The compound is a semiconductor with a band gap of 1.62 eV estimated from reflectance measurements. Its thermal conductivity is about 0.45 W m-1. K-1 in the temperature range 300-673 K, an extremely low value attributed to its complex pseudo-1D structure reminiscent of the pseudo-hollandite. While attempting to dope TlIn5Se8 with Te, a new complex chalcogenide was discovered and characterized by the combination of TEM and XRD diffraction. It belongs to the A2In12X19 family, crystallizing in the R 3 ̅:H space group. Single crystal X-ray diffraction study led to a refined composition of Tl0.98In13.12Se16.7Te2.3 with cell parameters: a=13.839(5) Å and c=35.18(3) Å. A static disorder is found on one indium site situated in an octahedral environment. The single crystal XRD study is in agreement with TEM analyses in STEM-HAADF image mode that do not show any extended defects or disorder at atomic scale.

Optical Crystals

ERIC Educational Resources Information Center

Bergsten, Ronald

1974-01-01

Discusses the production and structure of a sequence of optical crystals which can serve as one-, two-, and three-dimensional diffraction plates to illustrate diffraction patterns by using light rather than x-rays or particles. Applications to qualitative presentations of Laue theory at the secondary and college levels are recommended. (CC)

Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

PubMed Central

Sawaya, Michael R.; Cascio, Duilio; Gingery, Mari; Rodriguez, Jose; Goldschmidt, Lukasz; Colletier, Jacques-Philippe; Messerschmidt, Marc M.; Boutet, Sébastien; Koglin, Jason E.; Williams, Garth J.; Brewster, Aaron S.; Nass, Karol; Hattne, Johan; Botha, Sabine; Doak, R. Bruce; Shoeman, Robert L.; DePonte, Daniel P.; Park, Hyun-Woo; Federici, Brian A.; Sauter, Nicholas K.; Schlichting, Ilme; Eisenberg, David S.

2014-01-01

It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information. PMID:25136092

The significance of Bragg's law in electron diffraction and microscopy, and Bragg's second law.

PubMed

Humphreys, C J

2013-01-01

Bragg's second law, which deserves to be more widely known, is recounted. The significance of Bragg's law in electron diffraction and microscopy is then discussed, with particular emphasis on differences between X-ray and electron diffraction. As an example of such differences, the critical voltage effect in electron diffraction is described. It is then shown that the lattice imaging of crystals in high-resolution electron microscopy directly reveals the Bragg planes used for the imaging process, exactly as visualized by Bragg in his real-space law. Finally, it is shown how in 2012, for the first time, on the centennial anniversary of Bragg's law, single atoms have been identified in an electron microscope using X-rays emitted from the specimen. Hence atomic resolution X-ray maps of a crystal in real space can be formed which give the positions and identities of the different atoms in the crystal, or of a single impurity atom in the crystal.

Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase.

PubMed

Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia; Stojanoff, Vivian; Rodríguez-Sanoja, Romina; Rudiño-Piñera, Enrique; Sánchez, Sergio

2015-09-01

Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg(2+) (LrdC-Mg(2+)) and in complex with inorganic pyrophosphate (PPi) (LrdC-Mg(2+)-PPi). Crystals of native LrdC-Mg(2+) diffracted to 2.50 Å resolution and belonged to the trigonal space group P3221, with unit-cell parameters a = b = 107.1, c = 89.2 Å. Crystals of the LrdC-Mg(2+)-PPi complex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36 Å resolution and also belonged to the trigonal space group P3221. Crystals of the LrdC-Mg(2+)-PPi complex grown in a second crystallization condition with PEG 3350 diffracted to 2.57 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 49.9, b = 104.1, c = 66.5 Å, β = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.

Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns

PubMed Central

Lan, Ti-Yen; Wierman, Jennifer L.; Tate, Mark W.; Philipp, Hugh T.; Elser, Veit

2017-01-01

Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such ‘sparse’ frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009). Phys. Rev. E, 80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources. PMID:28808431

Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya

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

Azarkan, Mohamed; Garcia-Pino, Abel; Dibiani, Rachid

2006-12-01

The Kunitz-type trypsin/chymotrypsin inhibitor isolated from C. papaya latex has been crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms are observed, diffracting to 2.6 and 1.7 Å. A Kunitz-type protease inhibitor purified from the latex of green papaya (Carica papaya) fruits was crystallized in the presence and absence of divalent metal ions. Crystal form I, which is devoid of divalent cations, diffracts to a resolution of 2.6 Å and belongs to space group P3{sub 1} or P3{sub 2}. This crystal form is a merohedral twin with two molecules in the asymmetric unit and unit-cell parameters a = bmore » = 74.70, c = 78.97 Å. Crystal form II, which was grown in the presence of Co{sup 2+}, diffracts to a resolution of 1.7 Å and belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 44.26, b = 81.99, c = 140.89 Å.« less

Specific features of two diffraction schemes for a widely divergent X-ray beam

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

Avetyan, K. T.; Levonyan, L. V.; Semerjian, H. S.

2015-03-15

We investigated the specific features of two diffraction schemes for a widely divergent X-ray beam that use a circular diaphragm 30–50 μm in diameter as a point source of characteristic radiation. In one of the schemes, the diaphragm was set in front of the crystal (the diaphragm-crystal (d-c) scheme); in the other, it was installed behind the crystal (the crystal-diaphragm (c-d) scheme). It was established that the diffraction image in the c-d scheme is a topographic map of the investigated crystal area. In the d-c scheme at L = 2l (l and L are the distances between the crystal andmore » the diaphragm and between the photographic plate and the diaphragm, respectively), the branches of hyperbolas formed in this family of planes (hkl) by the characteristic K{sub α} and K{sub β} radiations, including higher order reflections, converge into one straight line. It is experimentally demonstrated that this convergence is very sensitive to structural inhomogeneities in the crystal under study.« less

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

NASA Astrophysics Data System (ADS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D. M.; Conway, Barbara R.; Timmins, Peter

2007-03-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2NC(CH 3) 3-n(CH 2OH) n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family ( n=0, 1, 2), but significantly contrasting structural properties for the member with n=3.

Purification, crystallization and preliminary X-ray diffraction of the N-terminal calmodulin-like domain of the human mitochondrial ATP-Mg/P{sub i} carrier SCaMC1

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

Yang, Qin, E-mail: yang@crystal.harvard.edu; Brüschweiler, Sven; Chou, James J., E-mail: yang@crystal.harvard.edu

2013-12-24

The N-terminal calmodulin-like domain of the human mitochondrial ATP-Mg/P{sub i} carrier SCaMC1 was crystallized in the presence of Ca{sup 2+}. X-ray diffraction data were collected to 2.9 Å resolution from crystals which belonged to space group P6{sub 2}22.

The effect of laser radiation on the diffraction of X-rays in crystals

NASA Astrophysics Data System (ADS)

Trushin, V. N.; Chuprunov, E. V.; Khokhlov, A. F.

1988-10-01

The effect of laser radiation on the intensity of the X-ray diffraction peaks of KDP, ADP, and CuSO4-5H2O crystals was studied experimentally. This intensity was found to increase as a function of the laser beam power. This result suggests that it is possible to use laser beams to control X-ray intensity in the crystals considered.

Crystallization and preliminary X-ray diffraction analysis of the arginine repressor of the hyperthermophile Thermotoga neapolitana

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

Massant, Jan, E-mail: jan.massant@vub.ac.be; Peeters, Eveline; Charlier, Daniel

2006-01-01

The arginine repressor of the hyperthermophile T. neapolitana was crystallized with and without its corepressor arginine. Both crystals diffracted to high resolution and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with similar unit-cell parameters. The arginine repressor of Thermotoga neapolitana (ArgRTnp) is a member of the family of multifunctional bacterial arginine repressors involved in the regulation of arginine metabolism. This hyperthermophilic repressor shows unique DNA-binding features that distinguish it from its homologues. ArgRTnp exists as a homotrimeric protein that assembles into hexamers at higher protein concentrations and/or in the presence of arginine. ArgRTnp was crystallized with andmore » without its corepressor arginine using the hanging-drop vapour-diffusion method. Crystals of the aporepressor diffracted to a resolution of 2.1 Å and belong to the orthorhombic P2{sub 1}2{sub 1}2{sub 1} space group, with unit-cell parameters a = 117.73, b = 134.15, c = 139.31 Å. Crystals of the repressor in the presence of its corepressor arginine diffracted to a resolution of 2.4 Å and belong to the same space group, with similar unit-cell parameters.« less

X-Ray Diffraction and Imaging Study of Imperfections of Crystallized Lysozyme with Coherent X-Rays

NASA Technical Reports Server (NTRS)

Hu, Zheng-Wei; Chu, Y. S.; Lai, B.; Cai, Z.; Thomas, B. R.; Chernov, A. A.

2003-01-01

Phase-sensitive x-ray diffraction imaging and high angular-resolution diffraction combined with phase contrast radiographic imaging are employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in symmetric Laue case. The fill width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal is approximately 16.7 arcseconds, and defects, which include point defects, line defects, and microscopic domains, have been clearly observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <110> growth front, and they have been found to originate mostly at a central growth area and occasionally at outer growth regions. Individual point defects trapped at a crystal nucleus are resolved in the images of high sensitivity to defects. Slow dehydration has led to the broadening of the 4 4 0 rocking curve by a factor of approximately 2.4. A significant change of the defect structure and configuration with drying has been revealed, which suggests the dehydration induced migration and evolution of dislocations and lattice rearrangements to reduce overall strain energy. The sufficient details of the observed defects shed light upon perfection, nucleation and growth, and properties of protein crystals.

Growth, structural, spectral, mechanical, thermal and dielectric characterization of phosphoric acid admixtured L-alanine (PLA) single crystals.

PubMed

Rose, A S J Lucia; Selvarajan, P; Perumal, S

2011-10-15

Phosphoric acid admixtured L-alanine (PLA) single crystals were grown successfully by solution method with slow evaporation technique at room temperature. Crystals of size 18 mm×12 mm×8 mm have been obtained in 28 days. The grown crystals were colorless and transparent. The solubility of the grown samples has been found out at various temperatures. The lattice parameters of the grown crystals were determined by X-ray diffraction technique. The reflection planes of the sample were confirmed by the powder X-ray diffraction study and diffraction peaks were indexed. Fourier transform infrared (FTIR) studies were used to confirm the presence of various functional groups in the crystals. UV-visible transmittance spectrum was recorded to study the optical transparency of grown crystal. The nonlinear optical (NLO) property of the grown crystal was confirmed by Kurtz-Perry powder technique and a study of its second harmonic generation efficiency in comparison with potassium dihydrogen phosphate (KDP) has been made. The mechanical strength of the crystal was estimated by Vickers hardness test. The grown crystals were subjected to thermo gravimetric and differential thermal analysis (TG/DTA). The dielectric behavior of the sample was also studied. Copyright © 2011 Elsevier B.V. All rights reserved.

Thaumatin crystallization aboard the International Space Station using liquid-liquid diffusion in the Enhanced Gaseous Nitrogen Dewar (EGN).

PubMed

Barnes, Cindy L; Snell, Edward H; Kundrot, Craig E

2002-05-01

This paper reports results from the first biological crystal-growth experiment on the International Space Station (ISS). Crystals of thaumatin were grown using liquid-liquid diffusion in Tygon tubing transported in the Enhanced Gaseous Nitrogen Dewar (EGN). Different volume ratios and concentrations of protein and precipitant were used to test different adaptations of the vapor-diffusion crystallization recipe to the liquid-liquid diffusion method. The EGN warmed up from 77 to 273 K in about 4 d, about the same time it took to warm from 273 to 293 K. The temperature within the EGN was 293-297 K for the majority of the experiment. Air gaps that blocked liquid-liquid diffusion formed in the tubes. Nonetheless, crystals were grown. Synchrotron diffraction data collected from the best space-grown crystal extended to 1.28 A, comparable to previous studies of space-grown thaumatin crystals. The resolution of the best ground-control crystal was only 1.47 A. It is not clear if the difference in diffraction limit arises from factors other than crystal size. Improvements in temperature control and the elimination of air gaps are needed, but the results show that the EGN on the ISS can be used to produce space-grown crystals that diffract to high resolution.

Thaumatin Crystallization Aboard the International Space Station Using Liquid-Liquid Diffusion in the Enhanced Gaseous Nitrogen Dewar (EGN)

NASA Technical Reports Server (NTRS)

Kundrot, Craig; Barnes, Cindy L.; Snell, Edward H.; Stinson, Thomas N. (Technical Monitor)

2002-01-01

This paper reports results from the first biological crystal growth experiment on the International Space Station (ISS). Crystals of thaumatin were grown using liquid-liquid diffusion in Tygon tubing transported in the Enhanced Gaseous Nitrogen Dewar (EGN). Different Volume ratios and concentrations of protein and precipitant were used to test different adaptations of the vapor diffusion crystallization recipe to the liquid-liquid diffusion method. The EGN warmed up from -196 C to 0 C in about four days, about the same time it took to warm from 0 C to 20 C. The temperature within the EGN was 20 - 24 C for the majority of the experiment. Air gaps that blocked liquid-liquid diffusion formed in the tubes. Nonetheless, crystals were grown. Synchrotron diffraction data collected from the best space grown crystal extended to 1.28 Angstroms, comparable to previous studies of space-grown thaumatin crystals. The resolution of the best ground control crystal was only 1.47 Angstroms. It is not clear if the difference in diffraction limit is due to factors other than crystal size. Improvements in temperature control and the elimination of air gaps are needed, but the results show that EGN on the ISS can be used to produce space grown crystals that diffract to high resolution.

Method for detecting a mass density image of an object

DOEpatents

Wernick, Miles N [Chicago, IL; Yang, Yongyi [Westmont, IL

2008-12-23

A method for detecting a mass density image of an object. An x-ray beam is transmitted through the object and a transmitted beam is emitted from the object. The transmitted beam is directed at an angle of incidence upon a crystal analyzer. A diffracted beam is emitted from the crystal analyzer onto a detector and digitized. A first image of the object is detected from the diffracted beam emitted from the crystal analyzer when positioned at a first angular position. A second image of the object is detected from the diffracted beam emitted from the crystal analyzer when positioned at a second angular position. A refraction image is obtained and a regularized mathematical inversion algorithm is applied to the refraction image to obtain a mass density image.

3-D microstructure of olivine in complex geological materials reconstructed by correlative X-ray μ-CT and EBSD analyses.

PubMed

Kahl, W-A; Dilissen, N; Hidas, K; Garrido, C J; López-Sánchez-Vizcaíno, V; Román-Alpiste, M J

2017-11-01

We reconstruct the 3-D microstructure of centimetre-sized olivine crystals in rocks from the Almirez ultramafic massif (SE Spain) using combined X-ray micro computed tomography (μ-CT) and electron backscatter diffraction (EBSD). The semidestructive sample treatment involves geographically oriented drill pressing of rocks and preparation of oriented thin sections for EBSD from the μ-CT scanned cores. The μ-CT results show that the mean intercept length (MIL) analyses provide reliable information on the shape preferred orientation (SPO) of texturally different olivine groups. We show that statistical interpretation of crystal preferred orientation (CPO) and SPO of olivine becomes feasible because the highest densities of the distribution of main olivine crystal axes from EBSD are aligned with the three axes of the 3-D ellipsoid calculated from the MIL analyses from μ-CT. From EBSD data we distinguish multiple CPO groups and by locating the thin sections within the μ-CT volume, we assign SPO to the corresponding olivine crystal aggregates, which confirm the results of statistical comparison. We demonstrate that the limitations of both methods (i.e. no crystal orientation data in μ-CT and no spatial information in EBSD) can be overcome, and the 3-D orientation of the crystallographic axes of olivines from different orientation groups can be successfully correlated with the crystal shapes of representative olivine grains. Through this approach one can establish the link among geological structures, macrostructure, fabric and 3-D SPO-CPO relationship at the hand specimen scale even in complex, coarse-grained geomaterials. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Streaking images that appear only in the plane of diffraction in undoped GaAs single crystals: Diffraction imaging (topography) by monochromatic synchrotron radiation

NASA Technical Reports Server (NTRS)

Kuriyama, Masao; Steiner, Bruce; Dobbyn, Ronald C.; Laor, Uri; Larson, David; Brown, Margaret

1988-01-01

Streaking images restricted to the direction of the diffraction (scattering) vector have been observed on transmission through undoped GaAs. These disruption images (caused by the reduction of diffraction in the direction of observation) appear both in the forward and in Bragg diffracted directions in monochromatic synchrontron radiation diffraction imaging. This previously unobserved phenomenon can be explained in terms of planar defects (interfaces) or platelets which affects the absorption coefficient in anomalous transmission. Such regions of the crystal look perfect despite the presence of imperfections when the scattering vector is not perpendicular to the normal of the platelets. The observed crystallographic orientation of these interfaces strongly indicates that they are antiphase boundaries.

Unified structure theory of icosahedral quasicrystals: Evidence from neutron powder diffraction patterns that AlCrFeMnSi, AlCuLiMg, and TiNiFeSi icosahedral quasicrystals are twins of cubic crystals containing about 820 or 1012 atoms in a primitive unit cube

PubMed Central

Pauling, Linus

1988-01-01

A unified structure theory of icosahedral quasicrystals, combining the twinned-cubic-crystal theory and the Penrose-tiling-six-dimensional-projection theory, is described. Values of the primitive-cubic lattice constant for several quasicrystals are evaluated from x-ray and neutron diffraction data. The fact that the low-angle diffraction maxima can be indexed with cubic unit cells provides additional support for the twinned-cubic-crystal theory of icosahedral quasicrystals. PMID:16593990

Time-resolved in situ neutron diffraction under supercritical hydrothermal conditions: a study of the synthesis of KTiOPO4.

PubMed

Ok, Kang Min; Lee, Dong Woo; Smith, Ronald I; O'Hare, Dermot

2012-10-31

In the first in situ neutron powder diffraction study of a supercritical hydrothermal synthesis, the crystallization of KTiOPO(4) (KTP) at 450 °C and 380 bar has been investigated. The time-resolved diffraction data suggest that the crystallization of KTP occurs by the reaction between dissolved K(+)(aq), PO(4)(3-)(aq), and [Ti(OH)(x)]((4-x)+)(aq) species.

Using Strong Magnetic Fields to Control Solutal Convection

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2003-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity , we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagnetic salts and solutions in magnetic fields and compare them to analytical predictions.

Countering Solutal Buoyant Convection with High Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemist, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitant, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity, we have been able to dramatically effect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the current status of the investigation and discuss results from the experimental and modeling efforts.

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

PubMed Central

Baba, Seiki; Hoshino, Takeshi; Ito, Len; Kumasaka, Takashi

2013-01-01

Protein crystals are fragile, and it is sometimes difficult to find conditions suitable for handling and cryocooling the crystals before conducting X-ray diffraction experiments. To overcome this issue, a protein crystal-mounting method has been developed that involves a water-soluble polymer and controlled humid air that can adjust the moisture content of a mounted crystal. By coating crystals with polymer glue and exposing them to controlled humid air, the crystals were stable at room temperature and were cryocooled under optimized humidity. Moreover, the glue-coated crystals reproducibly showed gradual transformations of their lattice constants in response to a change in humidity; thus, using this method, a series of isomorphous crystals can be prepared. This technique is valuable when working on fragile protein crystals, including membrane proteins, and will also be useful for multi-crystal data collection. PMID:23999307

Structural, mechanical, electrical and optical properties of a new lithium boro phthalate NLO crystal synthesized by a slow evaporation method

NASA Astrophysics Data System (ADS)

Mohanraj, K.; Balasubramanian, D.; Jhansi, N.

2017-11-01

A new non-linear optical (NLO) single crystal of lithium boro phthalate (LiBP) was grown by slow solvent evaporation technique. The powder sample was subjected to powder X-ray diffraction (PXRD) to find its crystalline nature and the crystal structure of the grown crystal was determined using single crystal X-ray (SXRD) diffraction analysis. The Fourier Transform Infrared (FTIR) spectrum was recorded for grown crystal to identify the various functional groups present in the compound. The mechanical property of the LiBP single crystal was studied using Vickers microhardness tester. The dielectric constant and dielectric loss measurements were carried out for the grown crystal at various temperatures. The grown crystal was subjected to UV-Visible Spectral Studies to analyze the linear optical behavior of the grown crystal. The Kurtz-Perry Powder technique was employed to measure the Second Harmonic Generation efficiency of the grown crystal.

Crystallization and preliminary crystallographic analysis of two Streptococcus agalactiae proteins: the family II inorganic pyrophosphatase and the serine/threonine phosphatase

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

Rantanen, Mika K.; Lehtiö, Lari; Rajagopal, Lakshmi

Two S. agalactiae proteins, the inorganic pyrophosphatase and the serine/threonine phosphatase, were crystallized and diffraction data were collected and processed from these crystals. The data from the two protein crystals extended to 2.80 and 2.65 Å, respectively. Streptococcus agalactiae, which infects human neonates and causes sepsis and meningitis, has recently been shown to possess a eukaryotic-like serine/threonine protein phosphorylation signalling cascade. Through their target proteins, the S. agalactiae Ser/Thr kinase and Ser/Thr phosphatase together control the growth as well as the morphology and virulence of this organism. One of the targets is the S. agalactiae family II inorganic pyrophosphatase. Themore » inorganic pyrophosphatase and the serine/threonine phosphatase have therefore been purified and crystallized and diffraction data have been collected from their crystals. The data were processed using XDS. The inorganic pyrosphosphatase crystals diffracted to 2.80 Å and the Ser/Thr phosphatase crystals to 2.65 Å. Initial structure-solution experiments indicate that structure solution will be successful in both cases. Solving the structure of the proteins involved in this cascade is the first step towards understanding this phenomenon in atomic detail.« less

Two-dimensional microsphere quasi-crystal: fabrication and properties

NASA Astrophysics Data System (ADS)

Noginova, Natalia E.; Venkateswarlu, Putcha; Kukhtarev, Nickolai V.; Sarkisov, Sergey S.; Noginov, Mikhail A.; Caulfield, H. John; Curley, Michael J.

1996-11-01

2D quasi-crystals were fabricated from polystyrene microspheres and characterized for their structural, diffraction, and non-linear optics properties. The quasi- crystals were produced with the method based on Langmuir- Blodgett thin film technique. Illuminating the crystal with the laser beam, we observed the diffraction pattern in the direction of the beam propagation and in the direction of the back scattering, similar to the x-ray Laue pattern observed in regular crystals with hexagonal structure. The absorption spectrum of the quasi-crystal demonstrated two series of regular maxima and minima, with the spacing inversely proportional to the microspheres diameter. Illumination of the dye-doped microspheres crystal with Q- switched radiation of Nd:YAG laser showed the enhancement of non-linear properties, in particular, second harmonic generation.

Synthesis and crystal structure determination of yttrium ultraphosphate YP 5O 14

NASA Astrophysics Data System (ADS)

Mbarek, A.; Graia, M.; Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

2009-03-01

The crystal structure of monoclinic YP 5O 14 (space group C2/ c, a=12.919(2) Å, b=12.796(4) Å, c=12.457(2) Å, β=91.30(1)°, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F2 using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ( ωR=0.069). The structure is isotypic with HoP 5O 14. This structure is built up from infinite layers of PO 4 tetrahedra linked through isolated YO 8 polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu 3+ ion incorporated in the monoclinic C2/ c polymorph of YP 5O 14 as local structural probe show that in YP 5O 14: 5% Eu 3+ sample, the Eu 3+ ions are distributed over the two Y 3+ crystallographic sites of C 2 symmetry of this structure.

Synthesis, crystal structure and antimicrobial activities of two isomeric gold(I) complexes with nitrogen-containing heterocycle and triphenylphosphine ligands, [Au(L)(PPh3)] (HL = pyrazole and imidazole).

PubMed

Nomiya, K; Noguchi, R; Ohsawa, K; Tsuda, K; Oda, M

2000-03-01

Two isomeric gold(I)-triphenylphosphine complexes with nitrogen-containing heterocycles, [Au(L)(PPh3) (HL = pyrazole (1), imidazole (2)) were isolated as colorless cubic crystals for 1 and colorless plate crystals for 2, respectively. The crystal structures of 1 and 2 were determined by single-crystal X-ray diffraction. These complexes were also fully characterized by complete elemental analyses, thermogravimetric/differential thermal analyses (TG/DTA) and FT-IR in the solid state and by solution NMR (31P, 1H and 13C) spectroscopy and molecular weight measurements in acetone solution. These complexes consisted of a monomeric 2-coordinate AuNP core both in the solid state and in solution. The molecular structures of 1 and 2 were compared with those of related gold(I) complexes, [Au(1,2,3-triz)(PPh3)] (3, Htriz = triazole), [Au(1,2,4-triz)(PPh3)]2 (4) as a dimer through a gold(I)-gold(I) bond in the solid state, and [Au(tetz)(PPh3)] (5, Htetz = tetrazole). Selective and effective antimicrobial activities against two gram-positive bacteria (B. subtilis, S. aureus) and modest activities against one yeast (C. albicans) found in these gold(I) complexes 1-4 are noteworthy, in contrast to poor activities observed in the corresponding silver(I) complexes.

7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source

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

Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido

2014-06-09

Membrane proteins arranged as two-dimensional (2D) crystals in the lipid en- vironment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. X-ray diffraction from individual 2D crystals did not represent a suitable investigation tool because of radiation damage. The recent availability of ultrashort pulses from X-ray Free Electron Lasers (X-FELs) has now provided a mean to outrun the damage. Here we report on measurements performed at the LCLS X-FEL on bacteriorhodopsin 2D crystals mounted on a solid support and kept at room temperature. By merg- ing data from about a dozen of single crystalmore » diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 °A, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase of resolution. The presented results pave the way to further X-FEL studies on 2D crystals, which may include pump-probe experiments at subpicosecond time resolution.« less

Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiations.

PubMed

León-Reina, L; García-Maté, M; Álvarez-Pinazo, G; Santacruz, I; Vallcorba, O; De la Torre, A G; Aranda, M A G

2016-06-01

This study reports 78 Rietveld quantitative phase analyses using Cu  K α 1 , Mo  K α 1 and synchrotron radiations. Synchrotron powder diffraction has been used to validate the most challenging analyses. From the results for three series with increasing contents of an analyte (an inorganic crystalline phase, an organic crystalline phase and a glass), it is inferred that Rietveld analyses from high-energy Mo  K α 1 radiation have slightly better accuracies than those obtained from Cu  K α 1 radiation. This behaviour has been established from the results of the calibration graphics obtained through the spiking method and also from Kullback-Leibler distance statistic studies. This outcome is explained, in spite of the lower diffraction power for Mo radiation when compared to Cu radiation, as arising because of the larger volume tested with Mo and also because higher energy allows one to record patterns with fewer systematic errors. The limit of detection (LoD) and limit of quantification (LoQ) have also been established for the studied series. For similar recording times, the LoDs in Cu patterns, ∼0.2 wt%, are slightly lower than those derived from Mo patterns, ∼0.3 wt%. The LoQ for a well crystallized inorganic phase using laboratory powder diffraction was established to be close to 0.10 wt% in stable fits with good precision. However, the accuracy of these analyses was poor with relative errors near to 100%. Only contents higher than 1.0 wt% yielded analyses with relative errors lower than 20%.

Crystal engineering: co-crystals of cinnamic acid derivatives with a pyridyl derivative co-crystallizer.

PubMed

Lorenzo, Daniel A; Forrest, Sebastian J K; Sparkes, Hazel A

2016-02-01

A number of hydrogen-bonded co-crystals, consisting of a cinnamic acid derivative and a pyridyl co-crystallizer, have been synthesized and their properties investigated by X-ray diffraction. Samples were prepared by recrystallization or solvent drop grinding of trans-cinnamic acid (1), 4-methylcinnamic acid (2), 4-methoxy cinnamic acid (3) or 3,4-methoxy cinnamic acid (4), with 4,4-dipyridyl (A), iso-nicotinamide (B) or nicotinamide (C). The X-ray single-crystal structures of seven novel co-crystals, obtained through recrystallization, are examined and the hydrogen-bonding interactions discussed. Consistent hydrogen-bonding motifs were observed for samples prepared when using 4,4-dipyridyl (A) or iso-nicotinamide (B) as the co-crystallizing agent. Powder X-ray diffraction analysis of the samples prepared by solvent drop grinding suggests the formation of ten co-crystals.

Characterization of calcium crystals in Abelia using x-ray diffraction and electron microscopes

USDA-ARS?s Scientific Manuscript database

Localization, chemical composition, and morphology of calcium crystals in leaves and stems of Abelia mosanensis and A. ×grandiflora were analyzed with a variable pressure scanning electron microscope (VP-SEM) equipped with an X-ray diffraction system, low temperature SEM (LT-SEM) and a transmission ...

Using Two-Dimensional Colloidal Crystals to Understand Crystallography

ERIC Educational Resources Information Center

Bosse, Stephanie A.; Loening, Nikolaus M.

2008-01-01

X-ray crystallography is an essential technique for modern chemistry and biochemistry, but it is infrequently encountered by undergraduate students owing to lack of access to equipment, the time-scale for generating diffraction-quality molecular crystals, and the level of mathematics involved in analyzing the resulting diffraction patterns.…

The Influence of Surface Morphology and Diffraction Resolution of Canavalin Crystals

NASA Technical Reports Server (NTRS)

Plomp, M.; Thomas, B. R.; Day, J. S.; McPherson, A.; Chernov, A. A.; Malkin, A.

2003-01-01

Canavalin crystals grown from material purified and not purified by High Performance Liquid Chromatography were studied by atomic force microscopy and x-ray diffraction. After purification, resolution was improved from 2.55Angstroms to 2.22Angstroms and jagged isotropic spiral steps transformed into regular, well polygonized steps.

Structure and stability of hydrous minerals at high pressure

NASA Technical Reports Server (NTRS)

Duffy, T. S.; Fei, Y.; Meade, C.; Hemley, R. J.; Mao, H. K.

1994-01-01

The presence of even small amounts of hydrogen in the Earth's deep interior may have profound effects on mantle melting, rheology, and electrical conductivity. The recent discovery of a large class of high-pressure H-bearing silicates further underscores the potentially important role for hydrous minerals in the Earth's mantle. Hydrogen may also be a significant component of the Earth's core, as has been recently documented by studies of iron hydride at high pressure. In this study, we explore the role of H in crystal structures at high pressure through detailed Raman spectroscopic and x ray diffraction studies of hydrous minerals compressed in diamond anvil cells. Brucite, Mg(OH)2, has a simple structure and serves as an analogue for the more complex hydrous silicates. Over the past five years, this material has been studied at high pressure using shock-compression, powder x ray diffraction, infrared spectroscopy, Raman spectroscopy, and neutron diffraction. In addition, we have recently carried out single-crystal synchrotron x-ray diffraction on Mg(OH)2 and Raman spectroscopy on Mg(OD)2 at elevated pressure. From all these studies, an interesting picture of the crystal chemical behavior of this material at high pressure is beginning to emerge. Some of the primary conclusions are as follows: First, hydrogen bonding is enhanced by the application of pressure. Second, layered minerals which are elastically anisotropic at low pressure may not be so at high pressure. Furthermore, the brucite data place constraints on the effect of hydrogen on seismic velocities and density at very high pressure. Third, the stability of hydrous minerals may be enhanced at high P by subtle structural rearrangements that are difficult to detect using traditional probes and require detailed spectroscopic analyses. Finally, brucite appears to be unique in that it undergoes pressure-induced disordering that is confined solely to the H-containing layers of the structure.

Single-drop optimization of protein crystallization.

PubMed

Meyer, Arne; Dierks, Karsten; Hilterhaus, Dierk; Klupsch, Thomas; Mühlig, Peter; Kleesiek, Jens; Schöpflin, Robert; Einspahr, Howard; Hilgenfeld, Rolf; Betzel, Christian

2012-08-01

A completely new crystal-growth device has been developed that permits charting a course across the phase diagram to produce crystalline samples optimized for diffraction experiments. The utility of the device is demonstrated for the production of crystals for the traditional X-ray diffraction data-collection experiment, of microcrystals optimal for data-collection experiments at a modern microbeam insertion-device synchrotron beamline and of nanocrystals required for data collection on an X-ray laser beamline.

Discovery of a metastable Al20Sm4 phase

NASA Astrophysics Data System (ADS)

Ye, Z.; Zhang, F.; Sun, Y.; Mendelev, M. I.; Ott, R. T.; Park, E.; Besser, M. F.; Kramer, M. J.; Ding, Z.; Wang, C.-Z.; Ho, K.-M.

2015-03-01

We present an efficient genetic algorithm, integrated with experimental diffraction data, to solve a nanoscale metastable Al20Sm4 phase that evolves during crystallization of an amorphous magnetron sputtered Al90Sm10 alloy. The excellent match between calculated and experimental X-ray diffraction patterns confirms an accurate description of this metastable phase. Molecular dynamic simulations of crystal growth from the liquid phase predict the formation of disordered defects in the devitrified crystal.

Crystallization screening test for the whole-cell project on Thermus thermophilus HB8

PubMed Central

Iino, Hitoshi; Naitow, Hisashi; Nakamura, Yuki; Nakagawa, Noriko; Agari, Yoshihiro; Kanagawa, Mayumi; Ebihara, Akio; Shinkai, Akeo; Sugahara, Mitsuaki; Miyano, Masashi; Kamiya, Nobuo; Yokoyama, Shigeyuki; Hirotsu, Ken; Kuramitsu, Seiki

2008-01-01

It was essential for the structural genomics of Thermus thermophilus HB8 to efficiently crystallize a number of proteins. To this end, three conventional robots, an HTS-80 (sitting-drop vapour diffusion), a Crystal Finder (hanging-drop vapour diffusion) and a TERA (modified microbatch) robot, were subjected to a crystallization condition screening test involving 18 proteins from T. thermophilus HB8. In addition, a TOPAZ (microfluidic free-interface diffusion) designed specifically for initial screening was also briefly examined. The number of diffraction-quality crystals and the time of appearance of crystals increased in the order HTS-80, Crystal Finder, TERA. With the HTS-80 and Crystal Finder, the time of appearance was short and the rate of salt crystallization was low. With the TERA, the number of diffraction-quality crystals was high, while the time of appearance was long and the rate of salt crystallization was relatively high. For the protein samples exhibiting low crystallization success rates, there were few crystallization conditions that were common to the robots used. In some cases, the success rate depended greatly on the robot used. The TOPAZ showed the shortest time of appearance and the highest success rate, although the crystals obtained were too small for diffraction studies. These results showed that the combined use of different robots significantly increases the chance of obtaining crystals, especially for proteins exhibiting low crystallization success rates. The structures of 360 of 944 purified proteins have been successfully determined through the combined use of an HTS-80 and a TERA. PMID:18540056

Arizona porphyry copper/hydrothermal deposits II: Crystal structure of ajoite, (K + Na)3Cu20Al3Si29O76(OH)16⋅∼8H2O

PubMed Central

Pluth, Joseph J.; Smith, Joseph V.

2002-01-01

A crystal from the type locality Ajo, AZ, yielded just enough intensity from streaked diffractions using synchrotron x-rays at the Advanced Photon Source to solve the crystal structure with composition (K + Na)3Cu20Al3Si29O76(OH)16⋅∼8H2O; triclinic, P1̄, a = 13.634(5) Å, b = 13.687(7), c = 14.522(7), α = 110.83(1)°, β = 107.21(1), γ = 105.68(1); refined to a final R = 12.5%. Electron microprobe analysis yielded a similar chemical composition that is slightly different from the combined chemical and electron microprobe analyses in the literature. The ajoite structure can be described as a zeolitic octahedral-tetrahedral framework that combines the alternate stacking of edge-sharing octahedral CuO6 layers and curved aluminosilicate layers and strings. Channels bounded by elliptical 12-rings and circular 8-rings of tetrahedra contain (K and Na) ions and water. The Al atoms occupy some of the Si tetrahedral sites. Each Cu atom has near-planar bonds to four oxygen atoms plus two longer distances that generate a distorted octahedron. Valence bond estimates indicate that 8 oxygen atoms of 46 are hydroxyl. Only one alkali atom was located in distorted octahedral coordination, and electron microprobe analyses indicate K and Na as major substituents. The water from chemical analysis presumably occurs as disordered molecules of zeolitic type not giving electron density from diffraction. The high R factor results from structural disorder and many weak intensities close to detection level. The crystal chemistry is compared with shattuckite, Cu5(SiO3)4(OH)2, and planchéite, Cu8Si8O22(OH)4⋅H2O, both found in oxidized copper deposits of Arizona but only the former directly with ajoite. PMID:12177404

Arizona porphyry copper/hydrothermal deposits II: crystal structure of ajoite, (K + Na)3Cu20Al3Si29O76(OH)16*~8H2O.

PubMed

Pluth, Joseph J; Smith, Joseph V

2002-08-20

A crystal from the type locality Ajo, AZ, yielded just enough intensity from streaked diffractions using synchrotron x-rays at the Advanced Photon Source to solve the crystal structure with composition (K + Na)3Cu20Al3Si29O76(OH)16* approximately 8H2O; triclinic, P1, a = 13.634(5) A, b = 13.687(7), c = 14.522(7), alpha = 110.83(1) degrees, beta = 107.21(1), gamma = 105.68(1); refined to a final R = 12.5%. Electron microprobe analysis yielded a similar chemical composition that is slightly different from the combined chemical and electron microprobe analyses in the literature. The ajoite structure can be described as a zeolitic octahedral-tetrahedral framework that combines the alternate stacking of edge-sharing octahedral CuO6 layers and curved aluminosilicate layers and strings. Channels bounded by elliptical 12-rings and circular 8-rings of tetrahedra contain (K and Na) ions and water. The Al atoms occupy some of the Si tetrahedral sites. Each Cu atom has near-planar bonds to four oxygen atoms plus two longer distances that generate a distorted octahedron. Valence bond estimates indicate that 8 oxygen atoms of 46 are hydroxyl. Only one alkali atom was located in distorted octahedral coordination, and electron microprobe analyses indicate K and Na as major substituents. The water from chemical analysis presumably occurs as disordered molecules of zeolitic type not giving electron density from diffraction. The high R factor results from structural disorder and many weak intensities close to detection level. The crystal chemistry is compared with shattuckite, Cu5(SiO3)4(OH)2, and planchéite, Cu8Si8O22(OH)4.H2O, both found in oxidized copper deposits of Arizona but only the former directly with ajoite.

Gelator-doped liquid-crystal phase grating with multistable and dynamic modes

NASA Astrophysics Data System (ADS)

Lin, Hui-Chi; Yang, Meng-Ru; Tsai, Sheng-Feng; Yan, Shih-Chiang

2014-01-01

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.

Gelator-doped liquid-crystal phase grating with multistable and dynamic modes

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

Lin, Hui-Chi, E-mail: huichilin@nfu.edu.tw; Yang, Meng-Ru; Tsai, Sheng-Feng

2014-01-06

We demonstrate a gelator-doped nematic liquid-crystal (LC) phase grating, which can be operated in both the multistable mode and the dynamic mode. Thermoreversible association and dissociation of the gelator molecules can vary and fix the multistable diffraction efficiencies of the gratings. A voltage (V) can also be applied to modulate dynamically the diffraction efficiencies of the grating, which behaves as a conventional LC grating. Experimental results show that the variations of the diffraction efficiencies in the multistable and dynamic modes are similar. The maximum diffraction efficiency is approximately 30% at V = 2 V.

Ultra-fast switching blue phase liquid crystals diffraction grating stabilized by chiral monomer

NASA Astrophysics Data System (ADS)

Manda, Ramesh; Pagidi, Srinivas; Sarathi Bhattacharya, Surjya; Yoo, Hyesun; T, Arun Kumar; Lim, Young Jin; Lee, Seung Hee

2018-05-01

We have demonstrated an ultra-fast switching and efficient polymer stabilized blue phase liquid crystal (PS-BPLC) diffraction grating utilizing a chiral monomer. We have obtained a 0.5 ms response time by a novel polymer stabilization method which is three times faster than conventional PS-BPLC. In addition, the diffraction efficiency was improved 2% with a much wider phase range and the driving voltage to switch the device is reduced. The polarization properties of the diffracted beam are unaffected by this novel polymer stabilization. This device can be useful for future photonic applications.

X-ray Microscopic Characterization of Protein Crystals

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Holmes, A.; Thomas, B.R.; Chernov, a. A.; Chu, Y. S.; Lai, B.

2004-01-01

The microscopic mapping of the variation in degree of perfection and in type of defects in entire protein crystals by x-rays may well be a prerequisite for better understanding causes of lattice imperfections, the growth history, and properties of protein crystals. However, x-ray microscopic characterization of bulk protein crystals, in the as-grown state, is frequently more challenging than that of small molecular crystals due to the experimental difficulties arising largely from the unique features possessed by protein crystals. In this presentation, we will illustrate ssme recent activities in employing coherence-based phase contrast x-ray imaging and high-angular-resolution diffraction techniques for mapping microdefects and the degree of perfection of protein crystals, and demonstrate a correlation between crystal perfection, diffraction phenomena., and crystallization conditions. The observed features and phenomena will be discussed in context to gain insight into the nature of defects, nucleation and growth, and the properties of protein crystals.

Macromolecule Crystal Quality Improvement in Microgravity: The Role of Impurities

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, Edward H.; Pusey, Marc L.; Sportiello, Michael G.; Todd, Paul; Bellamy, Henry; Borgstahl, Gloria E.; Pokros, Matt; Cassanto, John M.

2000-01-01

While macromolecule impurities may affect crystal size and morphology the over-riding question is; "How do macromolecule impurities effect crystal X-ray quality and diffraction resolution?" In the case of chicken egg white lysozyme, crystals can be grown in the presence of a number of impurities without affecting diffraction resolution. One impurity however, the lysozyme dimer, does negatively impact the X-ray crystal properties. Crystal quality improvement as a result of better partitioning of this impurity during crystallization in microgravity has been reported'. In our recent experimental work dimer partitioning was found to be not significantly different between the two environments. Mosaicity analysis of pure crystals showed a reduced mosaicity and increased signal to noise for the microgravity grown crystals. Dimer incorporation however, did greatly reduce the resolution limit in both ground and microgravity grown crystals. These results indicate that impurity effects in microgravity are complex and may rely on the conditions or techniques employed.

Photonic crystal borax competitive binding carbohydrate sensing motif†

PubMed Central

Cui, Qingzhou; Muscatello, Michelle M. Ward; Asher, Sanford A.

2009-01-01

We developed a photonic crystal sensing method for diol containing species such as carbohydrates based on a poly(vinyl alcohol) (PVA) hydrogel containing an embedded crystalline colloidal array (CCA). The polymerized CCA (PCCA) diffracts visible light. We show that in the presence of borax the diffraction wavelength shifts as the concentration of glucose changes. The diffraction shifts result from the competitive binding of glucose to borate, which reduces the concentration of borate bound to the PVA diols. PMID:19381378

Investigation of Renal Stones by X-ray and Neutron Diffraction

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

Baeva, M.; Boianova, A.; Beskrovnyi, A. I.

2007-04-23

Renal stones were investigated by X-ray diffraction. The obtained results showed only one crystal phase in every sample. With the aim to verify eventual availability of second phase (under 3 volume %) the same renal stones were investigated by neutron diffraction. The neutron spectra proved that additional crystal phase was absent in the renal stones. The obtained results are scientific-practical, in aid of the medicine, especially in the case of renal stone disease.

Cross-linked lysozyme crystal templated synthesis of Au nanoparticles as high-performance recyclable catalysts.

PubMed

Liang, Miao; Wang, Libing; Liu, Xia; Qi, Wei; Su, Rongxin; Huang, Renliang; Yu, Yanjun; He, Zhimin

2013-06-21

Bio-nanomaterials fabricated using a bioinspired templating technique represent a novel class of composite materials with diverse applications in biomedical, electronic devices, drug delivery, and catalysis. In this study, Au nanoparticles (NPs) are synthesized within the solvent channels of cross-linked lysozyme crystals (CLLCs) in situ without the introduction of extra chemical reagents or physical treatments. The as-prepared AuNPs-in-protein crystal hybrid materials are characterized by light microscopy, transmission electron microscopy, x-ray diffraction, and Fourier-transform infrared spectroscopy analyses. Small AuNPs with narrow size distribution reveal the restriction effects of the porous structure in the lysozyme crystals. These composite materials are proven to be active heterogeneous catalysts for the reduction of 4-nitrophenol to 4-aminophenol. These catalysts can be easily recovered and reused at least 20 times because of the physical stability and macro-dimension of CLLCs. This work is the first to use CLLCs as a solid biotemplate for the preparation of recyclable high-performance catalysts.

Cross-linked lysozyme crystal templated synthesis of Au nanoparticles as high-performance recyclable catalysts

NASA Astrophysics Data System (ADS)

Liang, Miao; Wang, Libing; Liu, Xia; Qi, Wei; Su, Rongxin; Huang, Renliang; Yu, Yanjun; He, Zhimin

2013-06-01

Bio-nanomaterials fabricated using a bioinspired templating technique represent a novel class of composite materials with diverse applications in biomedical, electronic devices, drug delivery, and catalysis. In this study, Au nanoparticles (NPs) are synthesized within the solvent channels of cross-linked lysozyme crystals (CLLCs) in situ without the introduction of extra chemical reagents or physical treatments. The as-prepared AuNPs-in-protein crystal hybrid materials are characterized by light microscopy, transmission electron microscopy, x-ray diffraction, and Fourier-transform infrared spectroscopy analyses. Small AuNPs with narrow size distribution reveal the restriction effects of the porous structure in the lysozyme crystals. These composite materials are proven to be active heterogeneous catalysts for the reduction of 4-nitrophenol to 4-aminophenol. These catalysts can be easily recovered and reused at least 20 times because of the physical stability and macro-dimension of CLLCs. This work is the first to use CLLCs as a solid biotemplate for the preparation of recyclable high-performance catalysts.

One-Dimensional Photonic Crystal Superprisms

NASA Technical Reports Server (NTRS)

Ting, David

2005-01-01

Theoretical calculations indicate that it should be possible for one-dimensional (1D) photonic crystals (see figure) to exhibit giant dispersions known as the superprism effect. Previously, three-dimensional (3D) photonic crystal superprisms have demonstrated strong wavelength dispersion - about 500 times that of conventional prisms and diffraction gratings. Unlike diffraction gratings, superprisms do not exhibit zero-order transmission or higher-order diffraction, thereby eliminating cross-talk problems. However, the fabrication of these 3D photonic crystals requires complex electron-beam substrate patterning and multilayer thin-film sputtering processes. The proposed 1D superprism is much simpler in structural complexity and, therefore, easier to design and fabricate. Like their 3D counterparts, the 1D superprisms can exhibit giant dispersions over small spectral bands that can be tailored by judicious structure design and tuned by varying incident beam direction. Potential applications include miniature gas-sensing devices.

Expression, crystallization and preliminary X-ray crystallographic analyses of two N-terminal acetyltransferase-related proteins from Thermoplasma acidophilum

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

Han, Sang Hee; Ha, Jun Yong; Kim, Kyoung Hoon

2006-11-01

An N-terminal acetyltransferase ARD1 subunit-related protein (Ta0058) and an N-terminal acetyltransferase-related protein (Ta1140) from T. acidophilum were crystallized. X-ray diffraction data were collected to 2.17 and 2.40 Å, respectively. N-terminal acetylation is one of the most common protein modifications in eukaryotes, occurring in approximately 80–90% of cytosolic mammalian proteins and about 50% of yeast proteins. ARD1 (arrest-defective protein 1), together with NAT1 (N-acetyltransferase protein 1) and possibly NAT5, is responsible for the NatA activity in Saccharomyces cerevisiae. In mammals, ARD1 is involved in cell proliferation, neuronal development and cancer. Interestingly, it has been reported that mouse ARD1 (mARD1{sup 225}) mediatesmore » ∊-acetylation of hypoxia-inducible factor 1α (HIF-1α) and thereby enhances HIF-1α ubiquitination and degradation. Here, the preliminary X-ray crystallographic analyses of two N-terminal acetyltransferase-related proteins encoded by the Ta0058 and Ta1140 genes of Thermoplasma acidophilum are reported. The Ta0058 protein is related to an N-terminal acetyltransferase complex ARD1 subunit, while Ta1140 is a putative N-terminal acetyltransferase-related protein. Ta0058 shows 26% amino-acid sequence identity to both mARD1{sup 225} and human ARD1{sup 235}.The sequence identity between Ta0058 and Ta1140 is 28%. Ta0058 and Ta1140 were overexpressed in Escherichia coli fused with an N-terminal purification tag. Ta0058 was crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium acetate pH 4.6, 8%(w/v) polyethylene glycol 4000 and 35%(v/v) glycerol. X-ray diffraction data were collected to 2.17 Å. The Ta0058 crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 49.334, c = 70.384 Å, α = β = γ = 90°. The asymmetric unit contains a monomer, giving a calculated crystal volume per protein weight (V{sub M}) of 2.13 Å{sup 3} Da{sup −1} and a solvent content of 42.1%. Ta1140 was also crystallized at 297 K using a reservoir solution consisting of 0.1 M trisodium citrate pH 5.6, 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000 and 0.2 M sodium chloride. X-ray diffraction data were collected to 2.40 Å. The Ta1140 crystals belong to space group R3, with hexagonal unit-cell parameters a = b = 75.174, c = 179.607 Å, α = β = 90, γ = 120°. Two monomers are likely to be present in the asymmetric unit, with a V{sub M} of 2.51 Å{sup 3} Da{sup −1} and a solvent content of 51.0%.« less

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer.

PubMed

Vogel, Sven C; Biwer, Chris M; Rogers, David H; Ahrens, James P; Hackenberg, Robert E; Onken, Drew; Zhang, Jianzhong

2018-06-01

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U-Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr 3 . A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download.

Interactive visualization of multi-data-set Rietveld analyses using Cinema:Debye-Scherrer

PubMed Central

Biwer, Chris M.; Rogers, David H.; Ahrens, James P.; Hackenberg, Robert E.; Onken, Drew; Zhang, Jianzhong

2018-01-01

A tool named Cinema:Debye-Scherrer to visualize the results of a series of Rietveld analyses is presented. The multi-axis visualization of the high-dimensional data sets resulting from powder diffraction analyses allows identification of analysis problems, prediction of suitable starting values, identification of gaps in the experimental parameter space and acceleration of scientific insight from the experimental data. The tool is demonstrated with analysis results from 59 U–Nb alloy samples with different compositions, annealing times and annealing temperatures as well as with a high-temperature study of the crystal structure of CsPbBr3. A script to extract parameters from a series of Rietveld analyses employing the widely used GSAS Rietveld software is also described. Both software tools are available for download. PMID:29896062

Syntheses, structures and properties of three new two-dimensional Cu(I)-Ln(III) heterometallic coordination polymers based on 2,2'-dipyridyl-5,5'-dicarboxylate ligands.

PubMed

Zhao, Junwei; Cheng, Yamin; Shang, Sensen; Zhang, Fang; Chen, Li; Chen, Lijuan

2013-12-01

Three new two-dimensional Cu(I)-Ln(III) heterometallic coordination polymers [Ln(III)Cu2(I)(Hbpdc)4] · Cl · xH2O [Ln(III) = La(III), x = 8 (1); Ln(III) = Pr(III), x=9 (2); Ln(III) = Eu(III), x = 8 (3)] (H2bpdc = 2,2'-bipyridyl-5,5'-dicarboxylic acid) have been prepared under hydrothermal conditions and structurally characterized by elemental analyses, inductively coupled plasma atomic emission spectrometry (ICP-AES) analyses, IR spectra, X-ray photoelectron spectroscopy (XPS) and single-crystal X-ray diffraction. X-ray diffraction indicates that the isomorphic 1-3 display the two-dimensional sheet structure constructed from [Cu(I)(Hbpdc)2](-) fragments through Ln(3+) connectors. Moreover, the solid-state photoluminescence measurements of 3 indicate that the Eu(III) ions, Hbpdc(-) ligands and Cu(I) cations make contributions to its luminescent properties simultaneously. Copyright © 2013 Elsevier B.V. All rights reserved.

Design and synthesis of two luminescent Zn(II)-based coordination polymers with different structures regulated by different solvent system

NASA Astrophysics Data System (ADS)

Wu, Wei-Ping; Wen, Gui-Lin; Liao, Yi; Wang, Jun; Lu, Lu; Wu, Yu; Xie, Bin

2016-08-01

Two new coordination polymers (CPs) [Zn(HL)(H2O)]n (1) and [Zn3(L)2(H2O)2]n·(H2O)n (2), based on a multifunctional ligand combined carboxylate groups and a nitrogen donor group 5-(6-carboxypyridin-2-yl)isophthalic acid (H3L), have been synthesized under different solvent media and fully characterized by powder X-ray diffraction (PXRD), infrared (IR) spectra, elemental analyses (EA) and thermogravimetric analyses (TGA). Single-crystal X-ray diffraction analysis reveals that 1 shows 1D dimeric chain structure, while 2 gives a 3D dense packing framework. Topology analysis illustrates that 2 can be simplified as a 3-nodal net (4, 5, 6-connected net) with the point symbol of {44·62}{46·64}2{48·66·8}. In addition, solid state luminescent properties of two complexes have also been studied in detail, which may act as the potential optical materials.

CdO-NPs; synthesis from 1D new nano Cd coordination polymer, characterization and application as anti-cancer drug for reducing the viability of cancer cells

NASA Astrophysics Data System (ADS)

Afzalian Mend, Behnaz; Delavar, Mahmoud; Darroudi, Majid

2017-04-01

The hexagonal CdO nano-particles (CdO-NPs) was prepared using new nano Cd coordination polymer, [Cd(NO3)(bipy)(pzca)]n (1) as a precursor, through direct calcination process at 500 °C. The precursor (1) was synthesized by sonochemical method. The new nano compound (1) was characterized by IR spectroscopy, elemental analyses, X-ray powder diffraction (XRD), transmission electron microscopy (TEM) and thermal gravimetric analyses. The structure of nano coordination polymer was determined by comparing the XRD pattern of nano and single-crystal of compound (1). The nano CdO was characterized by scanning electron microscopy (SEM) and X-ray powder diffraction (XRD). In addition, the activity and efficiency of nano CdO as an anti-cancer drug was studied on cancer cells with different concentration. The results shows that the viability of cancer cells reduced above 2 μg/mL of CdO-NPs concentration.

Trinuclear organooxotin assemblies from solvothermal synthesis reaction: Crystal structure, hydrogen bonding and π π stacking interaction

NASA Astrophysics Data System (ADS)

Ma, Chunlin; Sun, Junshan; Zhang, Rufen

2007-05-01

Two new trinuclear mono-organooxotin(IV) complexes with 2,3,4,5-tetrafluorobenzoic acid and sodium perchlorate of the types: [(SnR) 3(OH)(2,3,4,5-F 4C 6HCO 2) 4 · ClO 4] · [O 2CC 6HF 4](R = PhCH 2, 1; o- F-PhCH 2 for 2), have been solvothermally synthesized and structurally characterized by elemental, IR, 1H, 13C and 119Sn NMR and X-ray crystallography diffraction analyses. Complex 2 is also characterized by X-ray crystallography diffraction analyses. In complex 2, four carboxyl groups and a perchlorate bridged three tin atoms in a cyclohexane chair arrangement and form the basic framework. A hydroxyl group comprises the oxygen components of the stannoxane ring system. In these complexes, weak but significant intramolecular hydrogen bonding and π-π stacking interaction are also shown. These contacts lead to aggregation and supramolecular assembly of complexes 1 and 2 into 1D or 2D framework.

Preliminary small-angle X-ray scattering and X-ray diffraction studies of the BTB domain of lola protein from Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Boyko, K. M.; Nikolaeva, A. Yu.; Kachalova, G. S.; Bonchuk, A. N.; Dorovatovskii, P. V.; Popov, V. O.

2017-11-01

The Drosophila genome has several dozens of transcription factors (TTK group) containing BTB domains assembled into octamers. The LOLA protein belongs to this family. The purification, crystallization, and preliminary X-ray diffraction and small-angle X-ray scattering (SAXS) studies of the BTB domain of this protein are reported. The crystallization conditions were found by the vapor-diffusion technique. A very low diffraction resolution (8.7 Å resolution) of the crystals was insufficient for the determination of the threedimensional structure of the BTB domain. The SAXS study demonstrated that the BTB domain of the LOLA protein exists as an octamer in solution.

Liquid crystal devices especially for use in liquid crystal point diffraction interferometer systems

NASA Technical Reports Server (NTRS)

Marshall, Kenneth L. (Inventor)

2009-01-01

Liquid crystal point diffraction interferometer (LCPDI) systems that can provide real-time, phase-shifting interferograms that are useful in the characterization of static optical properties (wavefront aberrations, lensing, or wedge) in optical elements or dynamic, time-resolved events (temperature fluctuations and gradients, motion) in physical systems use improved LCPDI cells that employ a "structured" substrate or substrates in which the structural features are produced by thin film deposition or photo resist processing to provide a diffractive element that is an integral part of the cell substrate(s). The LC material used in the device may be doped with a "contrast-compensated" mixture of positive and negative dichroic dyes.

Liquid crystal devices especially for use in liquid crystal point diffraction interferometer systems

DOEpatents

Marshall, Kenneth L [Rochester, NY

2009-02-17

Liquid crystal point diffraction interferometer (LCPDI) systems that can provide real-time, phase-shifting interferograms that are useful in the characterization of static optical properties (wavefront aberrations, lensing, or wedge) in optical elements or dynamic, time-resolved events (temperature fluctuations and gradients, motion) in physical systems use improved LCPDI cells that employ a "structured" substrate or substrates in which the structural features are produced by thin film deposition or photo resist processing to provide a diffractive element that is an integral part of the cell substrate(s). The LC material used in the device may be doped with a "contrast-compensated" mixture of positive and negative dichroic dyes.

Beam-splitter switches based on zenithal bistable liquid-crystal gratings.

PubMed

Zografopoulos, Dimitrios C; Beccherelli, Romeo; Kriezis, Emmanouil E

2014-10-01

The tunable optical diffractive properties of zenithal bistable nematic liquid-crystal gratings are theoretically investigated. The liquid-crystal orientation is rigorously solved via a tensorial formulation of the Landau-de Gennes theory and the optical transmission properties of the gratings are investigated via full-wave finite-element frequency-domain simulations. It is demonstrated that by proper design the two stable states of the grating can provide nondiffracting and diffracting operation, the latter with equal power splitting among different diffraction orders. An electro-optic switching mechanism, based on dual-frequency nematic materials, and its temporal dynamics are further discussed. Such gratings provide a solution towards tunable beam-steering and beam-splitting components with extremely low power consumption.

Three-dimensional Bragg coherent diffraction imaging of an extended ZnO crystal.

PubMed

Huang, Xiaojing; Harder, Ross; Leake, Steven; Clark, Jesse; Robinson, Ian

2012-08-01

A complex three-dimensional quantitative image of an extended zinc oxide (ZnO) crystal has been obtained using Bragg coherent diffraction imaging integrated with ptychography. By scanning a 2.5 µm-long arm of a ZnO tetrapod across a 1.3 µm X-ray beam with fine step sizes while measuring a three-dimensional diffraction pattern at each scan spot, the three-dimensional electron density and projected displacement field of the entire crystal were recovered. The simultaneously reconstructed complex wavefront of the illumination combined with its coherence properties determined by a partial coherence analysis implemented in the reconstruction process provide a comprehensive characterization of the incident X-ray beam.

Deterministic Bragg Coherent Diffraction Imaging.

PubMed

Pavlov, Konstantin M; Punegov, Vasily I; Morgan, Kaye S; Schmalz, Gerd; Paganin, David M

2017-04-25

A deterministic variant of Bragg Coherent Diffraction Imaging is introduced in its kinematical approximation, for X-ray scattering from an imperfect crystal whose imperfections span no more than half of the volume of the crystal. This approach provides a unique analytical reconstruction of the object's structure factor and displacement fields from the 3D diffracted intensity distribution centred around any particular reciprocal lattice vector. The simple closed-form reconstruction algorithm, which requires only one multiplication and one Fourier transformation, is not restricted by assumptions of smallness of the displacement field. The algorithm performs well in simulations incorporating a variety of conditions, including both realistic levels of noise and departures from ideality in the reference (i.e. imperfection-free) part of the crystal.

Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom.

PubMed

Ullah, Anwar; Magalhães, Geraldo Santana; Masood, Rehana; Mariutti, Ricardo Barros; Coronado, Monika Aparecida; Murakami, Mário Tyago; Barbaro, Katia Cristina; Arni, Raghuvir Krishnaswamy

2014-10-01

Brown spider envenomation results in dermonecrosis, intravascular coagulation, haemolysis and renal failure, mainly owing to the action of sphingomyelinases D (SMases D), which catalyze the hydrolysis of sphingomyelin to produce ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidylcholine to produce lysophosphatidic acid. Here, the heterologous expression, purification, crystallization and preliminary X-ray diffraction analysis of LgRec1, a novel SMase D from Loxosceles gaucho venom, are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 52.98, b = 62.27, c = 84.84 Å and diffracted to a maximum resolution of 2.6 Å.

Crystallization and preliminary X-ray diffraction analysis of a novel sphingomyelinase D from Loxosceles gaucho venom

PubMed Central

Ullah, Anwar; Magalhães, Geraldo Santana; Masood, Rehana; Mariutti, Ricardo Barros; Coronado, Monika Aparecida; Murakami, Mário Tyago; Barbaro, Katia Cristina; Arni, Raghuvir Krishnaswamy

2014-01-01

Brown spider envenomation results in dermonecrosis, intravascular coagulation, haemolysis and renal failure, mainly owing to the action of sphingomyelinases D (SMases D), which catalyze the hydrolysis of sphingomyelin to produce ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidylcholine to produce lysophosphatidic acid. Here, the heterologous expression, purification, crystallization and preliminary X-ray diffraction analysis of LgRec1, a novel SMase D from Loxosceles gaucho venom, are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 52.98, b = 62.27, c = 84.84 Å and diffracted to a maximum resolution of 2.6 Å. PMID:25286953

Studies on the growth, structural, optical, mechanical properties of 8-hydroxyquinoline single crystal by vertical Bridgman technique

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

Prabhakaran, SP.; Babu, R. Ramesh, E-mail: rampap2k@yahoo.co.in; Velusamy, P.

2011-11-15

Highlights: {yields} Growth of bulk single crystal of 8-hydroxyquinoline (8-HQ) by vertical Bridgman technique for the first time. {yields} The crystalline perfection is reasonably good. {yields} The photoluminescence spectrum shows that the material is suitable for blue light emission. -- Abstract: Single crystal of organic nonlinear optical material, 8-hydroxyquinoline (8-HQ) of dimension 52 mm (length) x 12 mm (dia.) was grown from melt using vertical Bridgman technique. The crystal system of the material was confirmed by powder X-ray diffraction analysis. The crystalline perfection of the grown crystal was examined by high-resolution X-ray diffraction study. Low angular spread around 400'' ofmore » the diffraction curve and the low full width half maximum values show that the crystalline perfection is reasonably good. The recorded photoluminescence spectrum shows that the material is suitable for blue light emission. Optical transmittance for the UV and visible region was measured and mechanical strength was estimated from Vicker's microhardness test along the growth face of the grown crystal.« less

A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

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

Yap, Thai Leong; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551; Chen, Yen Liang

Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents anmore » interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.« less

Supercritical carbon dioxide treatment as a method for polymorph preparation of deoxycholic acid.

PubMed

Tozuka, Yuichi; Kawada, Dai; Oguchi, Toshio; Yamamoto, Keiji

2003-09-16

A new polymorph of deoxycholic acid (DCA) was formed by using a supercritical carbon dioxide treatment. Deoxycholic acid crystals were stored in a pressure vessel purged with carbon dioxide at 12MPa, 60 degrees C for definite intervals. After storage for 1h in supercritical carbon dioxide (SC-CO2), new X-ray diffraction (XRD) peaks, not found in the bulk DCA crystal, were observed at 2theta = 7.4 degrees, 9.7 degrees and 14.0 degrees. The intensities of the new diffraction peaks increased with an increase in storage time, whereas the intensities of the diffraction peaks due to bulk DCA crystal decreased. On the DSC curves, the crystals obtained showed an exothermic peak at around 155 degrees C followed by the melting peak of bulk DCA crystal at 175 degrees C. By the temperature-controlled powder XRD measurement, the crystals obtained were found to be a metastable form of DCA. The polymorphs of DCA have not been reported; therefore, the SC-CO2 treatment would be a peculiar method to obtain a DCA polymorph.

A new method to evaluate the quality of single crystal Cu by an X-ray diffraction butterfly pattern method

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

Xu Zhenming; Guo Zhenqi; Li Jianguo

2004-12-15

A new method for the evaluation of the quality of an Ohno continuous cast (OCC) Cu single crystal by X-ray diffraction (XRD) butterfly pattern was brought forward. Experimental results show that the growth direction of single crystal Cu is inclined from both sides of the single crystal Cu rod to the axis and is axially symmetric. The degree of deviation from the [100] orientation from the crystal axis is less than 5 deg. with a casting speed 10-40 mm/min. The orientation of single crystal Cu does not have a fixed direction but is in a regular range. Moreover, the orientationmore » of stray grains in the single crystal Cu is random from continuous casting.« less

Microseed matrix screening for optimization in protein crystallization: what have we learned?

PubMed

D'Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W; Marsh, May

2014-09-01

Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems.

Microseed matrix screening for optimization in protein crystallization: what have we learned?

PubMed Central

D’Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W.; Marsh, May

2014-01-01

Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems. PMID:25195878

X-ray evaluation of crystals for stellar spectrometers

NASA Technical Reports Server (NTRS)

Alexandropolos, N. G. (Editor)

1974-01-01

The report consists of three parts. The first part is an analysis of the principles involved in X-ray crystal evaluation and how they are applied to a number of crystals. The principles of crystal evaluation analysis as they apply to the special problems of X-ray astronomy are presented. A number of crystals were evaluated, and the energy dependence of the diffraction properties of (002) PET, (111) Ge, (101) ADP, (001) KAP, and (001) RAP are reported. The second part is a compilation of the diffraction properties of a number of crystals as reported by other authors. In the third part some technical details of a triple crystal spectrometer built by the author at Polytechnic Institute of Brooklyn are given. This spectrometer seems to be a most appropriate instrument for evaluation of crystal properties. (Modified author abstract)

Structural and optical properties of WTe2 single crystals synthesized by DVT technique

NASA Astrophysics Data System (ADS)

Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

2018-05-01

Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

Sequential Linker Installation: Precise Placement of Functional Groups in Multivariate Metal-Organic Frameworks

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

Yuan, S; Lu, WG; Chen, YP

2015-03-11

A unique strategy, sequential linker installation (SLI), has been developed to construct multivariate MOFs with functional groups precisely positioned. PCN-700, a Zr-MOF with eight-connected Zr6O4(OH)(8)(H2O)(4) clusters, has been judiciously designed; the Zr-6 clusters in this MOF are arranged in such a fashion that, by replacement of terminal OH-/H2O ligands, subsequent insertion of linear dicarboxylate linkers is achieved. We demonstrate that linkers with distinct lengths and functionalities can be sequentially installed into PCN-700. Single-crystal to single-crystal transformation is realized so that the positions of the subsequently installed linkers are pinpointed via single-crystal X-ray diffraction analyses. This methodology provides a powerful toolmore » to construct multivariate MOFs with precisely positioned functionalities in the desired proximity, which would otherwise be difficult to achieve.« less

Pure rhombohedral Bi1-x EuxPO4 nano-/micro-structures: fast synthesis, shape evolution and luminescence properties.

PubMed

Yu, Dongyan; Liang, Yujun; Zhang, Mengfei; Li, Guogang; Yan, Chunjie

2016-02-01

BiPO4 and Eu-doped BiPO4 crystals were synthesized via a simple precipitation route at room temperature, employing Bi(NO3)3 and (NH4)2HPO4 as the reactants, Eu2O3 as the dopant and citric acid as a template. X-ray powder diffraction analyses showed that pure rhombohedral BiPO4 form was obtained, and was the preferential orientation growth of the crystal. Field emission scanning electron microscope observations showed that the concentration of Bi(3+) obviously changed the products' morphologies from nanosphere, hollow sphere to hexagonal prism. The acidity of the solution and the contents of citric acid and Eu(3+) ion tailored the size of the final crystals. Effects of concentration of Eu(3+) ion on the luminescence emission intensity were also investigated. Copyright © 2015 John Wiley & Sons, Ltd.

Asymmetric flavone-based liquid crystals: synthesis and properties

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

Timmons, Daren J.; Jordan, Abraham J.; Kirchon, Angelo A.

2017-02-01

A series of flavones (n-F) substituted at the 4', and 6 positions was prepared, characterised by NMR (1H,13C), HRMS, and studied for liquid crystal properties. The 4'-alkoxy,6-methoxyflavones (4-F–16-F) exhibit varying ranges of nematic and smectic A phases as evidenced by polarised optical microscopy and differential scanning calorimetry (DSC). As the tail length is increased, the smectic phase becomes more prevalent. Smectic phases for (8-F–16-F) were further analysed by powder X-ray diffraction (XRD), and the rate of structural transformations was explored by combined DSC/XRD studies. Flavonol 6-F–OH was also prepared but no mesogenic behaviour was observed. The molecular structures of 6-Fmore » and 6-F–OH were determined by single-crystal XRD and help to explain the differences in material properties. Additionally, fluorescence and electrochemical studies were conducted on solutions of n-F.« less

Series of chiral interpenetrating 3d-4f heterometallic MOFs: Luminescent sensors and magnetic properties

NASA Astrophysics Data System (ADS)

Zhang, Xiaolei; Chen, Chen; Liu, Xiaoli; Gao, Peng; Hu, Ming

2017-09-01

Series of chiral 3d-4f heterometallic MOFs based on a multidentate terpyridyl carboxylic acid ligand have been synthesized under the solvothermal conditions, namely, [LnZnL(CO3)2(H2O)]n (Ln = Eu (1), Gd (2), Dy (3), Ho (4), Er (5), Tm (6), Yb (7), Lu (8)) (HL = 4‧-(4-carboxyphenyl)-2,2‧:6‧,2″-terpyridine). Compounds 1-8 were structurally characterized by the elemental analyses, infrared spectra, and single crystal X-ray diffractions. Compounds 1-8 exhibit the chiral interpenetrating 3D frameworks. Interestingly, 1 can serve as the luminescent sensor to detect nitrobenzene molecules with high sensitivity. The investigations on CD spectra of single crystals clearly assigned the Cotton effect, indicating that there exist two chiral enantiomers of 1-8 in the course of crystallization. The magnetic properties of 2 and 7 were exploited, respectively.

Synthesis, crystal structure, biological activity and theoretical calculations of novel isoxazole derivatives

NASA Astrophysics Data System (ADS)

Jin, R. Y.; Sun, X. H.; Liu, Y. F.; Long, W.; Chen, B.; Shen, S. Q.; Ma, H. X.

2016-01-01

Series of isoxazole derivatives were synthesized by substituted chalcones and 2-chloro-6-fluorobenzene formaldehyde oxime with 1,3-dipolar cycloaddition. The target compounds were determined by melting point, IR, 1H NMR, elemental analyses and HRMS. The crystal structure of compound 3a was detected by X-ray diffraction and it crystallizes in the triclinic space group p2(1)/c with z = 4. The molecular geometry of compound 3a was optimized using density functional theory (DFT/B3LYP) method with the 6-31G+(d,p) basis set in the ground state. From the optimized geometry of the molecule, FT-IR, FT-Raman, HOMO-LUMO and natural bond orbital (NBO) were calculated at B3LYP/6-31G+(d,p) level. Finally, the antifungal activity of the synthetic compounds were evaluated against Pythium solani, Gibberella nicotiancola, Fusarium oxysporium f.sp. niveum and Gibberella saubinetii.

Structure determination and characterization of two rare-earth molybdenum borate compounds: LnMoBO(6) (Ln = La, Ce).

PubMed

Zhao, Dan; Cheng, Wen-Dan; Zhang, Hao; Hang, Shu-Ping; Fang, Ming

2008-07-28

The structural, optical, and electronic properties of two rare-earth molybdenum borate compounds, LnMoBO(6) (Ln = La, Ce), have been investigated by means of single-crystal X-ray diffraction, elemental analyses, and spectral measurements, as well as calculations of energy band structures, density of states, and optical response functions by the density functional method. The title compounds, which crystallize in monoclinic space group P2(1)/c, possess a similar network of interconnected [Ce(2)(MoO(4))(2)](2+) chains and [BO(2)](-) wavy chains. Novel 1D molybdenum oxide chains are contained in their three-dimensional (3D) networks. The calculated results of crystal energy band structure by the density functional theory (DFT) method show that the solid-state compound LaMoBO(6) is a semiconductor with indirect band gaps.

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.

Characterization of potassium bromide crystals grown in the aqueous solution of picric acid

NASA Astrophysics Data System (ADS)

Maheswari, J. Uma; Krishnan, C.; Kalyanaraman, S.; Selvarajan, P.

2016-12-01

Potassium bromide crystals were grown in the aqueous solution of picric acid by slow evaporation technique at room temperature. X-ray Diffraction (XRD) analysis ensures that the grown sample is in Fm3m space group and FCC structure. Energy Dispersive X-ray Spectroscopy (EDX) reveals the presence of elements in the title compound. UV-Vis-NIR spectrum reveals that the grown sample is a promising nonlinear optical (NLO) material. FTIR analysis confirms the functional groups present in the sample. The thermogravimetric (TG) and differential thermogravimetric (DTA) analyses ensure that the sample material is thermally stable up to 160 °C. The second harmonic efficiency of the sample is 1.3 times greater than that of standard KDP. The mechanical strength of the grown sample is estimated by Vickers microhardness tester. The electrical properties were investigated by impedance analysis and the results of various studies of the grown crystals are discussed.

Additional evidence from x-ray powder diffraction patterns that icosahedral quasi-crystals of intermetallic compounds are twinned cubic crystals

PubMed Central

Pauling, Linus

1988-01-01

Analysis of the measured values of Q for the weak peaks (small maxima, usually considered to be background fluctuations, “noise”) on the x-ray powder diffraction curves for 17 rapidly quenched alloys leads directly to the conclusion that they are formed by an 820-atom or 1012-atom primitive cubic structure that by icosahedral twinning produces the so-called icosahedral quasi-crystals. PMID:16593948

Crystallization and preliminary X-ray crystallographic analysis of the heterodimeric crotoxin complex and the isolated subunits crotapotin and phospholipase A{sub 2}

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

Santos, K. F.; Murakami, M. T.; Cintra, A. C. O.

2007-04-01

Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A{sub 2} and a catalytically inactive acidic phospholipase A{sub 2} analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained. Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A{sub 2} and a catalytically inactive acidic phospholipase A{sub 2} analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained.more » The crotoxin complex crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 38.2, b = 68.7, c = 84.2 Å, and diffracted to 1.75 Å resolution. The crystal of the phospholipase A{sub 2} domain belongs to the hexagonal space group P6{sub 1}22 (or its enantiomorph P6{sub 5}22), with unit-cell parameters a = b = 38.7, c = 286.7 Å, and diffracted to 2.6 Å resolution. The crotapotin crystal diffracted to 2.3 Å resolution; however, the highly diffuse diffraction pattern did not permit unambiguous assignment of the unit-cell parameters.« less

Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins

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

Renzi, Fabiana; Panetta, Gianna; Vallone, Beatrice

Recombinant His-tagged XendoU, a eukaryotic endoribonuclease, appeared to aggregate in the presence of divalent cations. Monodisperse protein which yielded crystals diffracting to 2.2 Å was obtained by addition of EDTA. XendoU is the first endoribonuclease described in higher eukaryotes as being involved in the endonucleolytic processing of intron-encoded small nucleolar RNAs. It is conserved among eukaryotes and its viral homologue is essential in SARS replication and transcription. The large-scale purification and crystallization of recombinant XendoU are reported. The tendency of the recombinant enzyme to aggregate could be reversed upon the addition of chelating agents (EDTA, imidazole): aggregation is a potentialmore » drawback when purifying and crystallizing His-tagged proteins, which are widely used, especially in high-throughput structural studies. Purified monodisperse XendoU crystallized in two different space groups: trigonal P3{sub 1}21, diffracting to low resolution, and monoclinic C2, diffracting to higher resolution.« less

Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection

NASA Technical Reports Server (NTRS)

Hu, Z. W.; Thomas, B. R.; Chernov, A. A.

2001-01-01

Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.

Laboratory multiple-crystal X-ray topography and reciprocal-space mapping of protein crystals: influence of impurities on crystal perfection.

PubMed

Hu, Z W; Thomas, B R; Chernov, A A

2001-06-01

Double-axis multiple-crystal X-ray topography, rocking-curve measurements and triple-axis reciprocal-space mapping have been combined to characterize protein crystals using a laboratory source. Crystals of lysozyme and lysozyme crystals doped with acetylated lysozyme impurities were examined. It was shown that the incorporation of acetylated lysozyme into crystals of lysozyme induces mosaic domains that are responsible for the broadening and/or splitting of rocking curves and diffraction-space maps along the direction normal to the reciprocal-lattice vector, while the overall elastic lattice strain of the impurity-doped crystals does not appear to be appreciable in high angular resolution reciprocal-space maps. Multiple-crystal monochromatic X-ray topography, which is highly sensitive to lattice distortions, was used to reveal the spatial distribution of mosaic domains in crystals which correlates with the diffraction features in reciprocal space. Discussions of the influence of acetylated lysozyme on crystal perfection are given in terms of our observations.

The plug-based nanovolume Microcapillary Protein Crystallization System (MPCS)

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

Gerdts, Cory J.; Elliott, Mark; Lovell, Scott

2012-02-08

The Microcapillary Protein Crystallization System (MPCS) embodies a new semi-automated plug-based crystallization technology which enables nanolitre-volume screening of crystallization conditions in a plasticware format that allows crystals to be easily removed for traditional cryoprotection and X-ray diffraction data collection. Protein crystals grown in these plastic devices can be directly subjected to in situ X-ray diffraction studies. The MPCS integrates the formulation of crystallization cocktails with the preparation of the crystallization experiments. Within microfluidic Teflon tubing or the microfluidic circuitry of a plastic CrystalCard, {approx}10-20 nl volume droplets are generated, each representing a microbatch-style crystallization experiment with a different chemical composition.more » The entire protein sample is utilized in crystallization experiments. Sparse-matrix screening and chemical gradient screening can be combined in one comprehensive 'hybrid' crystallization trial. The technology lends itself well to optimization by high-granularity gradient screening using optimization reagents such as precipitation agents, ligands or cryoprotectants.« less

Studies on 2-amino-5-nitropyridinium nitrate (2A5NPN): A semi-organic third order nonlinear optical single crystal

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

Sivasubramani, V.; Pandian, Muthu Senthil, E-mail: senthilpandianm@ssn.edu.in; Ramasamy, P.

2016-05-23

2-amino-5-nitropyridinium nitrate (2A5NPN) is a semi-organic nonlinear optical crystal and optically good quality 2A5NPN single crystals were successfully grown by slow evaporation solution growth technique (SEST) at ambient temperature. The crystallographic structure of the grown crystal was determined by single crystal X-Ray diffraction analysis and it belongs to Monoclinic crystal system with centro symmetric crystalline nature. The crystallinity of the grown crystal was confirmed by powder X-ray diffraction analysis. The other physical properties of grown crystals are also characterized using TG-DTA, UV-Visible NIR, chemical etching, photoconductivity and Z-scan measurements. The Z-scan method reveals that the 2A5NPN crystal possesses multi photonmore » absorption behaviour and the significantly higher third order susceptibility and it is a promising potential NLO material.« less

Crystallization of Δ{sup 1}-tetrahydrocannabinolic acid (THCA) synthase from Cannabis sativa

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

Shoyama, Yoshinari; Takeuchi, Ayako; Taura, Futoshi

Δ{sup 1}-Tetrahydrocannabinolic acid (THCA) synthase from C. sativa was crystallized. The crystal diffracted to 2.7 Å resolution with sufficient quality for further structure determination. Δ{sup 1}-Tetrahydrocannabinolic acid (THCA) synthase is a novel oxidoreductase that catalyzes the biosynthesis of the psychoactive compound THCA in Cannabis sativa (Mexican strain). In order to investigate the structure–function relationship of THCA synthase, this enzyme was overproduced in insect cells, purified and finally crystallized in 0.1 M HEPES buffer pH 7.5 containing 1.4 M sodium citrate. A single crystal suitable for X-ray diffraction measurement was obtained in 0.09 M HEPES buffer pH 7.5 containing 1.26 Mmore » sodium citrate. The crystal diffracted to 2.7 Å resolution at beamline BL41XU, SPring-8. The crystal belonged to the primitive cubic space group P432, with unit-cell parameters a = b = c = 178.2 Å. The calculated Matthews coefficient was approximately 4.1 or 2.0 Å{sup 3} Da{sup −1} assuming the presence of one or two molecules of THCA synthase in the asymmetric unit, respectively.« less

An evaluation of adhesive sample holders for advanced crystallographic experiments

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

Mazzorana, Marco; Sanchez-Weatherby, Juan, E-mail: juan.sanchez-weatherby@diamond.ac.uk; Sandy, James

Commercially available adhesives have been evaluated for crystal mounting when undertaking complex macromolecular crystallography experiments. Here, their use as tools for advanced sample mounting and cryoprotection is assessed and their suitability for room-temperature data-collection and humidity-controlled studies is investigated. The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposingmore » it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed.« less

Crystallization, optimization and preliminary X-ray characterization of a metal-dependent PI-PLC from Streptomyces antibioticus

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

Jackson, Michael R.; Selby, Thomas L.

2012-10-30

A recombinant metal-dependent phosphatidylinositol-specific phospholipase C (PI-PLC) fromStreptomyces antibioticushas been crystallized by the hanging-drop method with and without heavy metals. The native crystals belonged to the orthorhombic space groupP222, with unit-cell parametersa= 41.26,b= 51.86,c = 154.78 Å. The X-ray diffraction results showed significant differences in the crystal quality of samples soaked with heavy atoms. Additionally, drop pinning, which increases the surface area of the drops, was also used to improve crystal growth and quality. The combination of heavy-metal soaks and drop pinning was found to be critical for producing high-quality crystals that diffracted to 1.23 Å resolution.

The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments

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

Brockhauser, Sandor; UJF–EMBL–CNRS UMI 3265, 6 Rue Jules Horowitz, 38043 Grenoble; Ravelli, Raimond B. G.

2013-07-01

Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented. Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitatemore » the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.« less

Aqueous Nucleation and Growth of Titanium Oxides Using Time-Resolved Synchrotron X- ray Diffraction

NASA Astrophysics Data System (ADS)

Hummer, D. R.; Heaney, P. J.; Post, J. E.

2006-05-01

The inorganic precipitation of oxide minerals in soil environments has profound effects on a variety of geochemical processes. These include the removal of metals from the aqueous phase, the production of coatings that reduce the reactive surface area of pre-existing mineral grains, and the generation of feedstocks for microbial metabolic reactions. Recent observations of transient, metastable phases during the growth of oxide crystallites has raised questions about their role in crystallization mechanisms, and created a need for more detailed structural measurements. To better understand the process of nucleation and growth, we investigated the crystallization of Ti oxides from aqueous 0.5 M TiCl4 solutions using synchrotron X-ray diffraction at temperatures of 100 and 150 °C. Solutions were heated in a 1.0 mm internal diameter quartz glass capillary sealed with epoxy. Powder diffraction patterns of the growing crystallites were collected using image plate technology with a time step of ~ 4 minutes, providing high resolution in situ measurements of structural changes during the crystallization process. The data indicate a co-precipitation of the two crystalline phases anatase and rutile within the first 30 minutes of heating, followed by a gradual phase transition from anatase to rutile during particle coarsening throughout the 10 hour duration of an experiment. The co-existence of anatase and rutile at the onset of crystallization lends additional support to the assertion of nearly identical free energies for anatase and rutile at the nanoscale, believed to be due to the prominence of surface energy effects (Ranade et al., 2001). Whole pattern analyses using the Rietveld refinement method also documented previously unobserved changes in lattice parameters of both phases during growth, on the order of 0.2-0.3 % expansion for each axis. The trends in lattice parameters are observed to be temperature dependent, generally having lower values at higher crystallization temperature. In addition to increased surface energy, these small but measurable structural changes may be partially responsible for the observed reversals in thermodynamic stability between crystalline Ti oxide phases at very small particle sizes.

Structures of Astromaterials Revealed by EBSD

NASA Technical Reports Server (NTRS)

Zolensky, M.

2018-01-01

Groups at the Johnson Space Center and the University of Tokyo have been using electron back-scattered diffraction (EBSD) to reveal the crystal structures of extraterrestrial minerals for many years. Even though we also routinely use transmission electron microscopy, synchrotron X-ray diffraction (SXRD), and conventional electron diffraction, we find that EBSD is the most powerful technique for crystal structure elucidation in many instances. In this talk I describe a few of the cases where we have found EBSD to provide crucial, unique information. See attachment.

Optical pendulum effect in one-dimensional diffraction-thick porous silicon based photonic crystals

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

Novikov, V. B., E-mail: vb.novikov@physics.msu.ru; Svyakhovskiy, S. E.; Maydykovskiy, A. I.

We present the realization of the multiperiodic optical pendulum effect in 1D porous silicon photonic crystals (PhCs) under dynamical Bragg diffraction in the Laue scheme. The diffraction-thick PhC contained 360 spatial periods with a large variation of the refractive index of adjacent layers of 0.4. The experiments reveal switching of the light leaving the PhC between the two spatial directions, which correspond to Laue diffraction maxima, as the fundamental wavelength or polarization of the incident light is varied. A similar effect can be achieved when the temperature of the sample or the intensity of the additional laser beam illuminating themore » crystal are changed. We show that in our PhC structures, the spectral period of the pendulum effect is down to 5 nm, while the thermal period is about 10 °C.« less

Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C61-butyric acid methyl ester

NASA Astrophysics Data System (ADS)

Lazzerini, Giovanni Mattia; Paternò, Giuseppe Maria; Tregnago, Giulia; Treat, Neil; Stingelin, Natalie; Yacoot, Andrew; Cacialli, Franco

2016-02-01

We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surface topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of "molecular terraces" whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.

Growth and characterization of Melaminium bis (trichloroacetate) dihydrate

NASA Astrophysics Data System (ADS)

Kanagathara, N.; Renganathan, N. G.; Marchewka, M. K.; Sivakumar, N.; Gayathri, K.; Krishnan, P.; Gunasekaran, S.; Anbalagan, G.

2013-01-01

Single crystals of melaminium bis (trichloroacetate) dihydrate have been grown successfully by slow evaporation solution growth technique at room temperature. Single crystal X-ray diffraction analysis reveals that the compound crystallizes in monoclinic system with non -centrosymmetric space group C2 with lattice parameters a = 17.70 Å, b = 8.44 Å, c = 6.09 Å, α = 90°, β = 100.24°, γ = 90° and V = 900 (Å)3. The UV-Vis transmittance spectrum shows that the crystal has a good optical transmittance in the entire visible region with lower cutoff wavelength of 351 nm. The vibrational frequencies of various functional groups present in the crystal have been derived from FI-IR, FT-Raman and Confocal Raman analyses. The chemical structure of the compound was established by 1H and 13C NMR spectrum. TGA-DTA analysis reveals that the materials have good thermal stability and the melting point of the crystal is found to be 195 °C. The dielectric response of the crystals was studied in the frequency range 50 Hz to 5 MHz at different temperatures and the results are discussed. Etching studies show the growth pattern of the crystals. The second harmonic generation efficiency was measured in comparison with KDP by employing powder Kurtz method.

Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester

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

Lazzerini, Giovanni Mattia; Yacoot, Andrew; Paternò, Giuseppe Maria

2016-02-01

We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surfacemore » topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of “molecular terraces” whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.« less

Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands.

PubMed

Stsiapanava, Alena; Chaloupkova, Radka; Fortova, Andrea; Brynda, Jiri; Weiss, Manfred S; Damborsky, Jiri; Smatanova, Ivana Kuta

2011-02-01

Haloalkane dehalogenases make up an important class of hydrolytic enzymes which catalyse the cleavage of carbon-halogen bonds in halogenated aliphatic compounds. There is growing interest in these enzymes owing to their potential use in environmental and industrial applications. The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 can slowly detoxify the industrial pollutant 1,2,3-trichloropropane (TCP). Structural analysis of this enzyme complexed with target ligands was conducted in order to obtain detailed information about the structural limitations of its catalytic properties. In this study, the crystallization and preliminary X-ray analysis of complexes of wild-type DhaA with 2-propanol and with TCP and of complexes of the catalytically inactive variant DhaA13 with the dye coumarin and with TCP are described. The crystals of wild-type DhaA were plate-shaped and belonged to the triclinic space group P1, while the variant DhaA13 can form prism-shaped crystals belonging to the orthorhombic space group P2(1)2(1)2(1) as well as plate-shaped crystals belonging to the triclinic space group P1. Diffraction data for crystals of wild-type DhaA grown from crystallization solutions with different concentrations of 2-propanol were collected to 1.70 and 1.26 Å resolution, respectively. A prism-shaped crystal of DhaA13 complexed with TCP and a plate-shaped crystal of the same variant complexed with the dye coumarin diffracted X-rays to 1.60 and 1.33 Å resolution, respectively. A crystal of wild-type DhaA and a plate-shaped crystal of DhaA13, both complexed with TCP, diffracted to atomic resolutions of 1.04 and 0.97 Å, respectively.

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

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

Brewster, Aaron S.; Sawaya, Michael R.; University of California, Los Angeles, CA 90095-1570

2015-02-01

Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data setmore » from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

PubMed Central

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

2016-01-01

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

Crystallization and preliminary X-ray studies of a non-haemorrhagic fibrin(ogen)olytic metalloproteinase from the venom of Agkistrodon acutus

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

Hou, Jing; Li, Ming; Chen, Jiashu

Crystals of a non-haemorrhagic fibrin(ogen)olytic metalloproteinase from the venom of A. acutus have been obtained and characterized by X-ray diffraction. A non-haemorrhagic fibrin(ogen)olytic metalloproteinase from the venom of Agkistrodon acutus has been crystallized by the hanging-drop method. The crystals belong to space group P3{sub 1}21, with unit-cell parameters a = b = 80.57, c = 66.77 Å and one molecule in the asymmetric unit. X-ray diffraction data were collected to 1.86 Å resolution.

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis

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

Lu, Feifei; Gao, Feng; Li, Honglin

The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of Rv3705c from M. tuberculosis are described. The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 198.0, c = 364.1 Å, α = β = 90, γ = 120°, and diffracted to a resolution of 3.3 Å.

Preparation of crystals for characterizing the Grb7 SH2 domain before and after complex formation with a bicyclic peptide antagonist.

PubMed

Ambaye, Nigus D; Gunzburg, Menachem J; Traore, Daouda A K; Del Borgo, Mark P; Perlmutter, Patrick; Wilce, Matthew C J; Wilce, Jacqueline A

2014-02-01

Human growth factor receptor-bound protein 7 (Grb7) is an adapter protein involved in cell growth, migration and proliferation. It is now recognized that Grb7 is an emerging therapeutic target in specific cancer subtypes. Recently, the discovery of a bicyclic peptide inhibitor that targets the Grb7 SH2 domain, named G7-B1, was reported. In an attempt to probe the foundation of its interaction with Grb7, the crystallization and preliminary data collection of both the apo and G7-B1-bound forms of the Grb7 SH2 domain are reported here. Diffraction-quality crystals were obtained using the hanging-drop vapour-diffusion method. After several rounds of microseeding, crystals of the apo Grb7 SH2 domain were obtained that diffracted to 1.8 Å resolution, while those of the G7-B1-Grb7 SH2 domain complex diffracted to 2.2 Å resolution. The apo Grb7 SH2 domain crystallized in the trigonal space group P63, whereas the G7-B1-Grb7 SH2 domain complex crystallized in the monoclinic space group P21. The experimental aspects of crystallization, crystal optimization and data collection and the preliminary data are reported.

Colloidal crystal growth monitored by Bragg diffraction interference fringes.

PubMed

Bohn, Justin J; Tikhonov, Alexander; Asher, Sanford A

2010-10-15

We monitored the crystal growth kinetics of crystallization of a shear melted crystalline colloidal array (CCA). The fcc CCA heterogeneously nucleates at the flow cell wall surface. We examined the evolution of the (1 1 1) Bragg diffraction peak, and, for the first time, quantitatively monitored growth by measuring the temporal evolution of the Bragg diffraction interference fringes. Modeling of the evolution of the fringe patterns exposes the time dependence of the increasing crystal thickness. The initial diffusion-driven linear growth is followed by ripening-driven growth. Between 80 and 90 microM NaCl concentrations the fcc crystals first linearly grow at rates between 1.9 and 4.2 microm/s until they contact homogeneously nucleated crystals in the bulk. At lower salt concentrations interference fringes are not visible because the strong electrostatic interactions between particles result in high activation barriers, preventing defect annealing and leading to a lower crystal quality. The fcc crystals melt to a liquid phase at >90 microM NaCl concentrations. Increasing NaCl concentrations slow the fcc CCA growth rate consistent with the expectation of the classical Wilson-Frenkel growth theory. The final thickness of wall-nucleated CCA, that is determined by the competition between growth of heterogeneously and homogenously nucleated CCA, increases with higher NaCl concentrations. Copyright 2010 Elsevier Inc. All rights reserved.

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

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

Vogeley, Lutz; Luecke, Hartmut, E-mail: hudel@uci.edu

2006-04-01

Crystals of Anabaena sensory rhodopsin transducer, the transducer for the cyanobacterial photosensor Anabaena sensory rhodopsin, obtained in the space groups P4, C2 and P2{sub 1}2{sub 1}2{sub 1} diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for these crystal forms were obtained by SIRAS phasing using an iodide quick-soak derivative (P4) and molecular replacement (C2 and P2{sub 1}2{sub 1}2{sub 1}). Anabaena sensory rhodopsin transducer (ASRT) is a 14.7 kDa soluble signaling protein associated with the membrane-embedded light receptor Anabaena sensory rhodopsin (ASR) from Anabaena sp., a freshwater cyanobacterium. Crystals of ASRT were obtained in three different space groups, P4, C2more » and P2{sub 1}2{sub 1}2{sub 1}, which diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for one of these crystal forms (P4) were obtained by SIRAS phasing using an iodide quick-soak derivative and a partial model was built. Phases for the remaining crystal forms were obtained by molecular replacement using the partial model from the P4 crystal form.« less

A preliminary neutron diffraction study of rasburicase, a recombinant urate oxidase enzyme, complexed with 8-azaxanthin

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

Budayova-Spano, Monika, E-mail: spano@embl-grenoble.fr; Institut Laue-Langevin, 6 Rue Jules Horowitz, BP 156, 38042 Grenoble; Bonneté, Françoise

2006-03-01

Neutron diffraction data of hydrogenated recombinant urate oxidase enzyme (Rasburicase), complexed with a purine-type inhibitor 8-azaxanthin, was collected to 2.1 Å resolution from a crystal grown in D{sub 2}O by careful control and optimization of crystallization conditions via knowledge of the phase diagram. Deuterium atoms were clearly seen in the neutron-scattering density map. Crystallization and preliminary neutron diffraction measurements of rasburicase, a recombinant urate oxidase enzyme expressed by a genetically modified Saccharomyces cerevisiae strain, complexed with a purine-type inhibitor (8-azaxanthin) are reported. Neutron Laue diffraction data were collected to 2.1 Å resolution using the LADI instrument from a crystal (grownmore » in D{sub 2}O) with volume 1.8 mm{sup 3}. The aim of this neutron diffraction study is to determine the protonation states of the inhibitor and residues within the active site. This will lead to improved comprehension of the enzymatic mechanism of this important enzyme, which is used as a protein drug to reduce toxic uric acid accumulation during chemotherapy. This paper illustrates the high quality of the neutron diffraction data collected, which are suitable for high-resolution structural analysis. In comparison with other neutron protein crystallography studies to date in which a hydrogenated protein has been used, the volume of the crystal was relatively small and yet the data still extend to high resolution. Furthermore, urate oxidase has one of the largest primitive unit-cell volumes (space group I222, unit-cell parameters a = 80, b = 96, c = 106 Å) and molecular weights (135 kDa for the homotetramer) so far successfully studied with neutrons.« less

5-Arylidene derivatives of Meldrum's acid: Synthesis, structural characterization using single crystal and powder crystal X-ray diffraction, and electronic properties

NASA Astrophysics Data System (ADS)

Dey, Tanusri; Ghosh, Soumen; Ghosh, Somnath; Mukherjee, Alok Kumar

2015-07-01

Four 5-arylidene derivatives of Meldrum's acid, 5-(4-chlorobenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (2), 5-(3-hydroxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (3), 5-(3,4-dimethoxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (4) and 5-(2,4-dimethoxy benzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (5) have been synthesized and their crystal structures have been determined using single crystal X-ray diffractometry for 2, 4 and 5 and X-ray powder diffraction for 3. The nature of intermolecular interactions in 2-5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots. The DFT optimized molecular geometries in 2-5 agree closely with those obtained from the crystallographic studies. The crystal packing in 2-5 exhibits an interplay of Osbnd H⋯O, Csbnd H⋯O, Csbnd H⋯Cl and Csbnd H⋯π (arene) hydrogen bonds and π⋯π interactions, which assemble molecules into three-dimensional architecture in 2, 3 and 5 and two-dimensional framework in 4. The Hirshfeld surface analyses of 2-5, Meldrum's acid (1) and a few related 5-arylidene derivatives of Meldrum's acid retrieved from the Cambridge Structural Database (CSD) indicate that about 85% of the Hirshfeld surface area (72% in 2 where H⋯Cl contribution is about 13%) in this class of compounds are due to H⋯H, O⋯H and C⋯H contacts. The HOMO-LUMO energy gap (>2.2 eV) in 2-5 indicates a significant degree of internal charge transfer within the molecule.

(+)- and (-)-Cajanusine, a pair of new enantiomeric stilbene dimers with a new skeleton from the leaves of Cajanus cajan.

PubMed

Li, Xiao-Long; Zhao, Bing-Xin; Huang, Xiao-Jun; Zhang, Dong-Mei; Jiang, Ren-Wang; Li, Ying-Jie; Jian, Yu-Qing; Wang, Ying; Li, Yao-Lan; Ye, Wen-Cai

2014-01-03

A pair of new enantiomeric stilbene dimers, (+)- and (-)-cajanusine [(+)-1 and (-)-1], with a unique coupling pattern were isolated from the leaves of Cajanus cajan . Their structures including absolute configurations were elucidated on the basis of comprehensive spectroscopic and single-crystal X-ray diffraction analyses, as well as CD calculations. The plausible biogenetic pathway of 1 was also proposed. Additionally, (±)-1, (+)-1, and (-)-1 exhibited inhibitory activities on the growth of human hepatocellular carcinoma cells.

Projection of the Liquidus Surface of the Co - Sn - Bi System

NASA Astrophysics Data System (ADS)

Abilov, Ch. I.; Allazov, M. R.; Sadygova, S. G.

2016-11-01

The crystallization behavior of phases in alloys of the Co - Sn - Bi system is studied by the methods of differential thermal (DTA), x-ray phase (XRP) and x-ray diffraction (XRD) analyses and hardness measurement. The projection of the liquidus surface is plotted. The boundaries of layering, the development of the monovariant processes, and the coordinates of the nonvariant equilibrium compositions are determined. Compositions of (Co3Sn2)1 - x Bi x solid solutions suitable for the production of antifriction materials are suggested.

Growth and characterization of Methyl 2-amino-5-bromobenzoate crystal for NLO applications

NASA Astrophysics Data System (ADS)

Parthasarathy, M.; Gopalakrishnan, R.

2012-11-01

Good quality single crystal of organic Methyl 2-amino-5-bromobenzoate (M2A5B) was grown using slow evaporation solution growth technique. The grown crystal was confirmed by single crystal X-ray diffraction. The functional groups and vibrational frequencies were identified using FT-IR and FT-Raman spectral analyses. The presence of hydrogen and carbon atoms in the grown sample was confirmed with proton and carbon NMR spectral studies. The optical energy band gap of the title compound is found to be 2.7 eV from the optical transmission spectra. The refractive indices nx, ny, and nz were found to be 1.569, 1.587 and 1.600, respectively using Brewster's angle method. The melting point of the material obtained with melting point apparatus is 74 °C. Thermal stability of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The mechanical behaviour of the grown crystal was analyzed with Vicker's microhardness tester. The particle size dependent second harmonic generation efficiency for M2A5B was evaluated by Kurtz-Perry powder method using Nd:YAG laser, which established the existence of phase matching.

A Test of Macromolecular Crystallization in Microgravity: Large, Well-Ordered Insulin Crystals

NASA Technical Reports Server (NTRS)

Borgstahl, Gloria E. O.; Vahedi-Faridi, Ardeschir; Lovelace, Jeff; Bellamy, Henry D.; Snell, Edward H.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Crystals of insulin grown in microgravity on space shuttle mission STS-95 were extremely well-ordered and unusually large (many > 2 mm). The physical characteristics of six microgravity and six earth-grown crystals were examined by X-ray analysis employing superfine f slicing and unfocused synchrotron radiation. This experimental setup allowed hundreds of reflections to be precisely examined for each crystal in a short period of time. The microgravity crystals were on average 34 times larger, had 7 times lower mosaicity, had 54 times higher reflection peak heights and diffracted to significantly higher resolution than their earth grown counterparts. A single mosaic domain model could account for reflections in microgravity crystals whereas reflections from earth crystals required a model with multiple mosaic domains. This statistically significant and unbiased characterization indicates that the microgravity environment was useful for the improvement of crystal growth and resultant diffraction quality in insulin crystals and may be similarly useful for macromolecular crystals in general.

Study of structural and optical properties of YAG and Nd:YAG single crystals

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

Kostić, S.; Lazarević, Z.Ž., E-mail: lzorica@yahoo.com; Radojević, V.

2015-03-15

Highlights: • Transparent YAG and pale pink Nd:YAG single crystals were produced by the Czochralski technique. • Growth mechanisms and shape of the liquid/solid interface and incorporation of Nd{sup 3+} were studied. • The structure of the crystals was investigated by X-ray diffraction, Raman and IR spectroscopy. • The 15 Raman and 17 IR modes were observed. • The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. - Abstract: Yttrium aluminum garnet (YAG, Y{sub 3}Al{sub 5}O{sub 12}) and yttrium aluminum garnet doped with neodymium (Nd:YAG) single crystals were grown by the Czochralski technique. Themore » critical diameter and the critical rate of rotation were calculated. Suitable polishing and etching solutions were determined. As a result of our experiments, the transparent YAG and pale pink Nd:YAG single crystals were produced. The obtained crystals were studied by X-ray diffraction, Raman and IR spectroscopy. The crystal structure was confirmed by XRD. The 15 Raman and 17 IR modes were observed. The Raman and IR spectroscopy results are in accordance with X-ray diffraction analysis. The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. The absence of a core was confirmed by viewing polished crystal slices. Also, it is important to emphasize that the obtained Nd:YAG single crystal has a concentration of 0.8 wt.% Nd{sup 3+} that is characteristic for laser materials.« less

Racemic & quasi-racemic protein crystallography enabled by chemical protein synthesis.

PubMed

Kent, Stephen Bh

2018-04-04

A racemic protein mixture can be used to form centrosymmetric crystals for structure determination by X-ray diffraction. Both the unnatural d-protein and the corresponding natural l-protein are made by total chemical synthesis based on native chemical ligation-chemoselective condensation of unprotected synthetic peptide segments. Racemic protein crystallography is important for structure determination of the many natural protein molecules that are refractory to crystallization. Racemic mixtures facilitate the crystallization of recalcitrant proteins, and give diffraction-quality crystals. Quasi-racemic crystallization, using a single d-protein molecule, can facilitate the determination of the structures of a series of l-protein analog molecules. Copyright © 2018 Elsevier Ltd. All rights reserved.

Isolation, purification, crystallization, and preliminary X-ray diffraction study of the crystals of HU protein from M. gallisepticum

NASA Astrophysics Data System (ADS)

Nikolaeva, A. Yu.; Timofeev, V. I.; Boiko, K. M.; Korzhenevskii, D. A.; Rakitina, T. V.; Dorovatovskii, P. V.; Lipkin, A. V.

2015-11-01

HU proteins are involved in bacterial DNA and RNA repair. Since these proteins are absent in cells of higher organisms, inhibitors of HU proteins can be used as effective and safe antibiotics. The crystallization conditions for the M. gallisepticum HU protein were found and optimized by the vapor-diffusion method. The X-ray diffraction data set was collected to 2.91 Å resolution from the crystals grown by the vapor-diffusion method on a synchrotron source. The crystals of the HU protein belong to sp. gr. P41212 and have the following unit-cell parameters: a = b = 97.94 Å, c = 77.92 Å, α = β = γ = 90°.

Curved crystals for high-resolution focusing of X and gamma rays through a Laue lens

NASA Astrophysics Data System (ADS)

Guidi, Vincenzo; Bellucci, Valerio; Camattari, Riccardo; Neri, Ilaria

2013-08-01

Crystals with curved diffracting planes have been investigated as high-efficiency optical components for the realization of a Laue lens for satellite-borne experiments in astrophysics. At Sensor and Semiconductor Laboratory (Ferrara, Italy) a research and development plan to implement Si and Ge curved crystals by surface grooving technique has been undertaken. The method of surface grooving allows obtaining Si and Ge curved crystals with self-standing curvature, i.e., with no need for external bending device, which is a mandatory issue in satellite-borne experiments. Si and Ge grooved crystals have been characterized by X-ray diffraction at ESRF and ILL to prove their functionality for a high-reflectivity Laue lens.

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.

Growth of high quality and large-sized Rb 0.3MoO 3 single crystals by molten salt electrolysis method

NASA Astrophysics Data System (ADS)

Wang, Junfeng; Xiong, Rui; Yi, Fan; Yin, Di; Ke, Manzhu; Li, Changzhen; Liu, Zhengyou; Shi, Jing

2005-05-01

High quality and large-sized Rb 0.3MoO 3 single crystals were synthesized by molten salt electrolysis method. X-ray diffraction (XRD) patterns and rocking curves, as well as the white beam Laue diffraction of X-ray images show the crystals grown by this method have high quality. The lattice constants evaluated from XRD patterns are a0=1.87 nm, b0=0.75 nm, c0=1.00 nm, β=118.83∘. The in situ selected area electron diffraction (SAED) patterns along the [101¯], [11¯1¯] and [103¯] zone axes at room temperature indicate that the Rb 0.3MoO 3 crystal possess perfect C-centered symmetry. Temperature dependence of the resistivity shows this compound undergoes a metal to semiconductor transition at 183 K.

In-situ data collection at the photon factory macromolecular crystallography beamlines

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

Yamada, Yusuke, E-mail: yusuke.yamada@kek.jp; Matsugaki, Naohiro; Kato, Ryuichi

Crystallization trial is one of the most important but time-consuming steps in macromolecular crystallography, and in-situ diffraction experiment has a capability to make researchers to proceed this step more efficiently. At the Photon Factory, a new tabletop diffractometer for in-situ diffraction experiments has been developed. It consists of XYZ translation stages with a plate handler, an on-axis viewing system and a plate rack with a capacity for ten crystallization plates. These components sit on a common plate and are able to be placed on the existing diffractometer table. The CCD detector with a large active area and a pixel arraymore » detector with a small active area are used for acquiring diffraction images from crystals. Dedicated control software and a user interface have also been developed. The new diffractometer has been operational for users and used for evaluation of crystallization screening since 2014.« less

Applications of the diffraction and interference of light and electronic waves

NASA Astrophysics Data System (ADS)

Bahrim, Cristian; Lanning, Robert

2010-10-01

As part of a NSF sponsored program, called STAIRSTEP, at Lamar University we work on improving the basic knowledge of our physics majors in topics with broader impact in various areas of science and engineering [1]. The purpose is to facilitate a deeper understanding of some fundamental concepts in the field of optics through hands-on experience [2]. We choose to study the interference/diffraction of light and matter waves, because of its fundamental importance in physics with many applications. We target multiple goals in our field of study such as to understand the formation of electronic waves (wave packets) and their interaction with atoms in crystals (electron diffraction); the Fourier analysis of light with applications in spectroscopy, etc. We can show that a crystal lattice Fourier transforms the sinusoidal waves associated to free electrons fired toward the crystal. Our studies led to a simple and instructive recipe for discovering the arrangement of atoms in crystals from the analysis of the diffraction patterns produced by radiation or by electrons transmitted through crystals. [1] Doerschuk P. et al., 39th ASEE/IEEE Frontiers in Education Conference, San Antonio 2009, M3F-1. [2] Bahrim C, Innovation 2006 -- World Innovations in Engineering Education and Research, Chapter 17, iNEER Innovation Series, ISBN 0-9741252-5-3.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa

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

Kraschnefski, Mark J.; Scott, Stacy A.; Holloway, Gavan

2005-11-01

The carbohydrate-binding component (VP8*{sub 64–223}) of the human Wa rotavirus spike protein has been overexpressed in E. coli, purified and crystallized in two different crystal forms. X-ray diffraction data have been collected that have enabled determination of the Wa VP8*{sub 64–223} structure by molecular replacement. Rotaviruses exhibit host-specificity and the first crystallographic information on a rotavirus strain that infects humans is reported here. Recognition and attachment to host cells, leading to invasion and infection, is critically linked to the function of the outer capsid spike protein of the rotavirus particle. In some strains the VP8* component of the spike proteinmore » is implicated in recognition and binding of sialic-acid-containing cell-surface carbohydrates, thereby enabling infection by the virus. The cloning, expression, purification, crystallization and initial X-ray diffraction analysis of the VP8* core from human Wa rotavirus is reported. Two crystal forms (trigonal P3{sub 2}21 and monoclinic P2{sub 1}) have been obtained and X-ray diffraction data have been collected, enabling determination of the VP8*{sub 64–223} structure by molecular replacement.« less

Femtosecond X-ray protein nanocrystallography.

PubMed

Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

2011-02-03

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

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.

Growth of single crystalline delafossite LaCuO2 by the travelling-solvent floating zone method

NASA Astrophysics Data System (ADS)

Mohan, A.; Büchner, B.; Wurmehl, S.; Hess, C.

2014-09-01

Single crystals of LaCuO2 have been grown for the first time using the travelling-solvent floating zone method. The crystal was grown in an Ar-atmosphere by reduction of La2Cu2O5, which was used as the feed rod composition for the growth. The grown crystal has been characterized with regard to phase purity and single crystallinity using powder X-ray diffraction, energy dispersive X-ray analysis, Laue diffraction and scanning electron microscopy.

Diffraction imaging (topography) with monochromatic synchrotron radiation

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

Study of silicon strip waveguides with diffraction gratings and photonic crystals tuned to a wavelength of 1.5 µm

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

Barabanenkov, M. Yu., E-mail: barab@iptm.ru; Vyatkin, A. F.; Volkov, V. T.

2015-12-15

Single-mode submicrometer-thick strip waveguides on silicon-on-insulator substrates, fabricated by silicon-planar-technology methods are considered. To solve the problem of 1.5-µm wavelength radiation input-output and its frequency filtering, strip diffraction gratings and two-dimensional photonic crystals are integrated into waveguides. The reflection and transmission spectra of gratings and photonic crystals are calculated. The waveguide-mode-attenuation coefficient for a polycrystalline silicon waveguide is experimentally estimated.

Crystallographic analysis of ground and space thermostable T1 lipase crystal obtained via counter diffusion method approach.

PubMed

Mohamad Aris, Sayangku Nor Ariati; Thean Chor, Adam Leow; Mohamad Ali, Mohd Shukuri; Basri, Mahiran; Salleh, Abu Bakar; Raja Abd Rahman, Raja Noor Zaliha

2014-01-01

Three-dimensional structure of thermostable lipase is much sought after nowadays as it is important for industrial application mainly found in the food, detergent, and pharmaceutical sectors. Crystallization utilizing the counter diffusion method in space was performed with the aim to obtain high resolution diffracting crystals with better internal order to improve the accuracy of the structure. Thermostable T1 lipase enzyme has been crystallized in laboratory on earth and also under microgravity condition aboard Progress spacecraft to the ISS in collaboration with JAXA (Japanese Aerospace Exploration Agency). This study is conducted with the aims of improving crystal packing and structure resolution. The diffraction data set for ground grown crystal was collected to 1.3 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.40 Å, b = 80.95 Å, and c = 99.81 Å, whereas the diffraction data set for space grown crystal was collected to 1.1 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.31 Å, b = 80.85 Å, and c = 99.81 Å. The major difference between the two crystal growth systems is the lack of convection and sedimentation in microgravity environment resulted in the growth of much higher quality crystals of T1 lipase.

Improved crystallization of the coxsackievirus B3 RNA-dependent RNA polymerase

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

Jabafi, Ilham; Selisko, Barbara; Coutard, Bruno

2007-06-01

The first crystal of a coxsackievirus RNA-dependent RNA polymerase is reported. The Picornaviridae virus family contains a large number of human pathogens such as poliovirus, hepatitis A virus and rhinoviruses. Amongst the viruses belonging to the genus Enterovirus, several serotypes of coxsackievirus coexist for which neither vaccine nor therapy is available. Coxsackievirus B3 is involved in the development of acute myocarditis and dilated cardiomyopathy and is thought to be an important cause of sudden death in young adults. Here, the first crystal of a coxsackievirus RNA-dependent RNA polymerase is reported. Standard crystallization methods yielded crystals that were poorly suited tomore » X-ray diffraction studies, with one axis being completely disordered. Crystallization was improved by testing crystallization solutions from commercial screens as additives. This approach yielded crystals that diffracted to 2.1 Å resolution and that were suitable for structure determination.« less

The MORPHEUS II protein crystallization screen

PubMed Central

Gorrec, Fabrice

2015-01-01

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

Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains

PubMed Central

DeWalt, Emma L.; Begue, Victoria J.; Ronau, Judith A.; Sullivan, Shane Z.; Das, Chittaranjan; Simpson, Garth J.

2013-01-01

Polarization-resolved second-harmonic generation (PR-SHG) microscopy is described and applied to identify the presence of multiple crystallographic domains within protein-crystal conglomerates, which was confirmed by synchrotron X-ray diffraction. Principal component analysis (PCA) of PR-SHG images resulted in principal component 2 (PC2) images with areas of contrasting negative and positive values for conglomerated crystals and PC2 images exhibiting uniformly positive or uniformly negative values for single crystals. Qualitative assessment of PC2 images allowed the identification of domains of different internal ordering within protein-crystal samples as well as differentiation between multi-domain conglomerated crystals and single crystals. PR-SHG assessments of crystalline domains were in good agreement with spatially resolved synchrotron X-ray diffraction measurements. These results have implications for improving the productive throughput of protein structure determination through early identification of multi-domain crystals. PMID:23275165

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

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

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

The MORPHEUS II protein crystallization screen.

PubMed

Gorrec, Fabrice

2015-07-01

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

Origins of contrasting copper coordination geometries in crystalline copper sulfate pentahydrate.

PubMed

Ruggiero, Michael T; Erba, Alessandro; Orlando, Roberto; Korter, Timothy M

2015-12-14

Metal-aqua ion ([M(H2O)n](X+)) formation is a fundamental step in mechanisms that are central to enzymatic and industrial catalysis. Past investigations of such ions have yielded a wealth of information regarding their properties, however questions still exist involving the exact structures of these complexes. A prominent example of this is hexaaqua copper(II) ([Cu(H2O)6](2+)), with the solution versus gas-phase configurations under debate. The differences are often attributed to the intermolecular interactions between the bulk solvent and the aquated complex, resulting in structures stabilized by extended hydrogen-bonding networks. Yet solution phase systems are difficult to study due to the lack of atomic-level positional details. Crystalline solids are ideal models for comparative study, as they contain fixed structures that can be fully characterized using diffraction techniques. Here, crystalline copper sulfate pentahydrate (CuSO4·5H2O), which contains two unique copper-water geometries, was studied in order to elucidate the origin of these contrasting hydrated metal envrionments. A combination of solid-state density functional theory and low-temperature X-ray diffraction was used to probe the electronic origins of this phenomenon. This was accomplished through implementation of crystal orbital overlap population and crystal orbital Hamiltonian population analyses into a developmental version of the CRYSTAL14 software. These new computational methods help highlight the delicate interplay between electronic structure and metal-water geometries.

Cloning, purification, crystallization and preliminary crystallographic analysis of SecA from Enterococcus faecalis

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

Meining, Winfried, E-mail: wim@csb.ki.se; Scheuring, Johannes; Fischer, Markus

2006-06-01

SecA ATPase from E. faecalis has been cloned, overexpressed, purified and crystallized. Crystals belong to space group C2 and diffract to 2.4 Å resolution. The gene coding for SecA from Enterococcus faecalis was cloned and overexpressed in Escherichia coli. In this protein, the lysine at position 6 was replaced by an asparagine in order to reduce sensitivity towards proteases. The modified protein was purified and crystallized. Crystals diffracting to 2.4 Å resolution were obtained using the vapour-diffusion technique. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 203.4, b = 49.8, c = 100.8 Å,more » α = γ = 90.0, β = 119.1°. A selenomethionine derivative was prepared and is currently being tested in crystallization trials.« less

High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

DOEpatents

Smither, Robert K [Hinsdale, IL

2011-05-17

A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

Band structure and optical properties of opal photonic crystals

NASA Astrophysics Data System (ADS)

Pavarini, E.; Andreani, L. C.; Soci, C.; Galli, M.; Marabelli, F.; Comoretto, D.

2005-07-01

A theoretical approach for the interpretation of reflectance spectra of opal photonic crystals with fcc structure and (111) surface orientation is presented. It is based on the calculation of photonic bands and density of states corresponding to a specified angle of incidence in air. The results yield a clear distinction between diffraction in the direction of light propagation by (111) family planes (leading to the formation of a stop band) and diffraction in other directions by higher-order planes (corresponding to the excitation of photonic modes in the crystal). Reflectance measurements on artificial opals made of self-assembled polystyrene spheres are analyzed according to the theoretical scheme and give evidence of diffraction by higher-order crystalline planes in the photonic structure.

Magnetic Control of Convection during Protein Crystallization

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2004-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular Crystals for diffraction analyses has been the central focus for bio-chemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and Sedimentation as is achieved in "microgravity", we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, f o d o n of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with counteracts on for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteract terrestrial gravity. The genera1 objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagentic salts and solutions in magnetic fields and compare them to analyticalprctions.

Excitation of surface waves on one-dimensional solid–fluid phononic crystals and the beam displacement effect

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

Moiseyenko, Rayisa P.; Georgia Institute of Technology, UMI Georgia Tech – CNRS, George W. Woodruff School of Mechanical Engineering, Georgia Tech Lorraine, 2 rue Marconi, 57070 Metz-Technopole; Liu, Jingfei

The possibility of surface wave generation by diffraction of pressure waves on deeply corrugated one-dimensional phononic crystal gratings is studied both theoretically and experimentally. Generation of leaky surface waves, indeed, is generally invoked in the explanation of the beam displacement effect that can be observed upon reflection on a shallow grating of an acoustic beam of finite width. True surface waves of the grating, however, have a dispersion that lies below the sound cone in water. They thus cannot satisfy the phase-matching condition for diffraction from plane waves of infinite extent incident from water. Diffraction measurements indicate that deeply corrugatedmore » one-dimensional phononic crystal gratings defined in a silicon wafer are very efficient diffraction gratings. They also confirm that all propagating waves detected in water follow the grating law. Numerical simulations however reveal that in the sub-diffraction regime, acoustic energy of a beam of finite extent can be transferred to elastic waves guided at the surface of the grating. Their leakage to the specular direction along the grating surface explains the apparent beam displacement effect.« less

Single beam write and/or replay of spatial heterodyne holograms

DOEpatents

Thomas, Clarence E.; Hanson, Gregory R.

2007-11-20

A method of writing a spatially heterodyne hologram having spatially heterodyne fringes includes: passing a single write beam through a spatial light modulator that digitally modulates said single write beam; and focusing the single write beam at a focal plane of a lens to impose a holographic diffraction grating pattern on the photorefractive crystal, the holographic diffraction grating pattern including the spatially heterodyne hologram having spatially heterodyne fringes, wherein only said single write beam is incident on said photorefractive crystal without a reference beam. A method of replaying a spatially heterodyne hologram having spatially heterodyne fringes at a replay angle includes: illuminating a photorefractive crystal having a holographic diffraction grating with a beam from a laser at an illumination angle, the holographic diffraction grating pattern including the spatially heterodyne hologram having spatially heterodyne fringes, wherein a difference between said illumination angle and said replay angle defines a diffraction angle .alpha. that is a function of a plane wave mathematically added to original object wave phase and amplitude data of said spatially heterodyne hologram having spatially heterodyne fringes.

Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate

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

Pauwels, Kris, E-mail: krpauwel@vub.ac.be; Loris, Remy; Vandenbussche, Guy

2005-08-01

Crystals of the lipase of B. glumae in complex with its specific foldase were obtained in two forms. Crystallization, crystal manipulation and preliminary X-ray diffraction analysis are described. Bacterial lipases that are secreted via the type II secretion pathway require a lipase-specific foldase in order to obtain their native and biologically active conformation in the periplasmic space. The lipase–foldase complex from Burkholderia glumae (319 and 333 residues, respectively) was crystallized in two crystal forms. One crystal form belongs to space group P3{sub 1}21 (P3{sub 2}21), with unit-cell parameters a = b = 122.3, c = 98.2 Å. A procedure ismore » presented which improved the diffraction of these crystals from ∼5 to 2.95 Å. For the second crystal form, which belonged to space group C2 with unit-cell parameters a = 183.0, b = 75.7, c = 116.6 Å, X-ray data were collected to 1.85 Å.« less

Crystallization and preliminary X-ray analysis of gamma-glutamyltranspeptidase from Escherichia coli K-12.

PubMed

Kumagai, H; Nohara, S; Suzuki, H; Hashimoto, W; Yamamoto, K; Sakai, H; Sakabe, K; Fukuyama, K; Sakabe, N

1993-12-20

gamma-Glutamyltranspeptidase (EC 2.3.2.2) from Escherichia coli K-12 has been purified and crystallized by means of vapor diffusion in hanging drops. Two kinds of crystals on cell dimensions were found for X-ray diffraction analysis, one from ammonium sulfate and the other from polyethylene glycol 6000 as precipitants. The crystals of the orthorhombic form grown in the presence of 15% polyethylene glycol and 20 mM sodium acetate buffer were chosen for further analysis. The crystals belonged to space group P2(1)2(1)2(1), with cell dimensions of a = 128.1, b = 129.9 and c = 79.2 A, and two molecules constitute an asymmetric unit. These crystals diffracted to 2.0 A resolution and were suitable for X-ray crystallographic studies.

Growth and characterization of Cadmium Thiosemicarbazide Bromide crystals for antibacterial and nonlinear optical applications

NASA Astrophysics Data System (ADS)

Thomas Joseph Prakash, J.; Martin Sam Gnanaraj, J.

2015-01-01

Semiorganic nonlinear optical crystals of Cadmium Thiosemicarbazide Bromide was grown by slow evaporation solution growth technique. The unit cell parameters were estimated by subjecting the crystals to single crystal X-ray diffraction. The grown crystals were subjected to Powder X-ray diffraction for analyzing the crystalline nature of the sample. FTIR studies reveal the functional groups and the optical characters were analyzed by UV-Vis spectral studies. Mechanical stability of the sample was assessed by Vicker's micro hardness test. The presence of surface dislocations was identified by chemical etching technique. Antibacterial study was carried out against ACDP declared harmful pathogens. SHG efficiency of CTSB crystal was tested using Nd: YAG laser and it was found to be ∼1.8 times that of potassium dihydrogen phosphate.

Influence of hydroxypropylmethylcellulose addition and homogenization conditions on properties and ageing of corn starch based films.

PubMed

Jiménez, Alberto; Fabra, María José; Talens, Pau; Chiralt, Amparo

2012-06-20

Edible films based on corn starch, hydroxypropyl methylcellulose (HPMC) and their mixtures were prepared by using two different procedures to homogenize the film forming dispersions (rotor-stator and rotor-stator plus microfluidizer). The influence of both HPMC-starch ratio and the homogenization method on the structural, optical, tensile and barrier properties of the films was analysed. The ageing of the films was also studied by characterizing them after 5 weeks' storage. Starch re-crystallization in newly prepared and stored films was analysed by means of X-ray diffraction. HPMC-corn starch films showed phase separation of polymers, which was enhanced when microfluidization was applied to the film forming dispersion. Nevertheless, HPMC addition inhibited starch re-crystallization during storage, giving rise to more flexible films at the end of the period. Water barrier properties of starch films were hardly affected by the addition of HPMC, although oxygen permeability increased due to its poorer oxygen barrier properties. Copyright © 2012 Elsevier Ltd. All rights reserved.

Magnetic and neutron diffraction study on quaternary oxides MTeMoO6 (M = Mn and Zn)

NASA Astrophysics Data System (ADS)

Doi, Yoshihiro; Suzuki, Ryo; Hinatsu, Yukio; Ohoyama, Kenji

2009-01-01

Crystal structures and magnetic properties of quaternary oxides MTeMoO6 (M = Mn and Zn) were investigated. From the Rietveld analyses for the powder x-ray and neutron diffraction measurements, their detailed structures have been determined. Both compounds have orthorhombic structure with space group P 21212 and a charge configuration of M2+Te4+Mo6+O6. ZnTeMoO6 shows diamagnetic behavior. In this structure, M ions are arranged in a square-planar manner. The temperature dependence of the magnetic susceptibility for MnTeMoO6 shows a broad peak at ~33 K, which is due to a two-dimensional characteristic of the magnetic interaction. In addition, this compound shows an antiferromagnetic transition at 20 K. The magnetic structure was determined by the powder neutron diffraction measurement at 3.3 K. The magnetic moments of Mn2+ ions (4.45 μB) order in a collinear antiferromagnetic arrangement along the b axis.

Purification, crystallization and preliminary X-ray diffraction analysis of the kinase domain of human tousled-like kinase 2

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

Garrote, Ana M.; Redondo, Pilar; Montoya, Guillermo, E-mail: gmontoya@cnio.es

2014-02-19

The C-terminal kinase domain of TLK2 (a human tousled-like kinase) has been cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. Tousled-like kinases (TLKs) are an evolutionarily conserved family of serine/threonine protein kinases involved in chromatin dynamics, including DNA replication and repair, transcription and chromosome segregation. The two members of the family reported in humans, namely TLK1 and TLK2, localize to the cell nucleus and are capable of forming homo- ormore » hetero-oligomers by themselves. To characterize the role of TLK2, its C-terminal kinase domain was cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. The latter produced the best diffracting crystal (3.4 Å resolution using synchrotron radiation), with unit-cell parameters a = b = c = 126.05 Å, α = β = γ = 90°. The asymmetric unit contained one protein molecule, with a Matthews coefficient of 4.59 Å{sup 3} Da{sup −1} and a solvent content of 73.23%.« less

Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27

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

Abramchik, Yu. A.; Timofeev, V. I., E-mail: tostars@mail.ru; Muravieva, T. I.

2017-01-15

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°Ð¡, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample,more » which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unitcell parameters: a = 107.7 Å, b = 112.6 Å, c = 110.2 Å, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-Å resolution.« less