FEBS JOURNAL, Issue 11 2009
Egon Persson
The initiation of blood coagulation involves tissue factor (TF)-induced allosteric activation of factor VIIa (FVIIa), which circulates in a zymogen-like state. In addition, the (most) active conformation of FVIIa presumably relies on a number of intramolecular interactions. We have characterized the role of Gly372(223) in FVIIa, which is the sole residue in activation loop 3 that is capable of forming backbone hydrogen bonds with the unusually long 170 loop and with activation loop 2, by studying the effects of replacement with Ala [G372(223)A]. G372A-FVIIa, both in the free and TF-bound form, exhibited reduced cleavage of factor X (FX) and of peptidyl substrates, and had increased Km values compared with wild-type FVIIa. Inhibition of G372A-FVIIa·sTF by p -aminobenzamidine was characterized by a seven-fold higher Ki than obtained with FVIIa·sTF. Crystallographic and modelling data suggest that the most active conformation of FVIIa depends on the backbone hydrogen bond between Gly372(223) and Arg315(170C) in the 170 loop. Despite the reduced activity and inhibitor susceptibility, native and active site-inhibited G372A-FVIIa bound sTF with the same affinity as the corresponding forms of FVIIa, and burial of the N-terminus of the protease domain increased similarly upon sTF binding to G372A-FVIIa and FVIIa. Thus Gly372(223) in FVIIa appears to play a critical role in maturation of the S1 pocket and adjacent subsites, but does not appear to be of importance for TF binding and the ensuing allostery. [source]

Substituent Effects on Crosslike Packing of 2,,7,-Diaryl- spiro(cyclopropane-1,9,-fluorene) Derivatives: Synthesis and Crystallographic, Optical, and Thermal Properties,

ADVANCED FUNCTIONAL MATERIALS, Issue 2 2007
Z. Wang
Abstract A series of 2,,7,-diarylspiro(cyclopropane-1,9,-fluorene) derivatives are efficiently synthesized and characterized to determine the reason for the "green-light" emission of these compounds. These compounds exhibit bright-violet to blue photoluminescence (PL) (,PLmax,=,353,419,nm) with excellent PL quantum efficiencies (,PL,=,83,100,%) in solution and show high thermal stabilities (Td,=,267,474,°C). The variation of the optical properties of these molecules in the solid state depends on the different stacking modes of these compounds containing different substituents, which are revealed by crystallographic analysis. CH,, hydrogen bonds instead of intermolecular ,,, interactions act as the driving force between adjacent fluorenes, even though a very small dialkyl group (cyclopropane) is introduced at the C-9 position of fluorene. The crosslike molecular stacking efficiently reduces the energy transfer between the herring-like aggregates and therefore results in the absence of a "green-light" emission tail. In order to determine the cause of the "green-light" emission tails, the fluorescence spectra of the films annealed in N2 or in air are recorded. Broad green-light emission tails were observed for the films annealed in air, which might be caused by fluorenone defects generated during processing or during the course of the photophysical analysis by reaction with residual oxygen. [source]

Order-disorder enantiotropy, monotropy, and isostructurality in a tetroxoprim-sulfametrole 1:1 molecular complex: Crystallographic and thermal studies

JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2003
Mino R. Caira
Abstract Two enantiotropic polymorphs of a tetroxoprim (TXP)-sulfametrole (SMTR) 1:1 molecular complex monohydrate and two isostructural TXP-SMTR 1:1 molecular complex solvates with methanol and ethanol were grown and studied by X-ray diffraction and thermal methods (thermogravimetric analysis and differential scanning calorimetry). Interconversion of the polymorphic hydrates is essentially an order/disorder transition involving a substituent on the TXP molecule. These hydrated phases may be described as "nearly isostructural" with the methanol and ethanol solvates. Thermal data for decomposition of the solvates were rationalized on the basis of the location and topologies of solvent crystallographic sites. Solid-state properties of two monotropic polymorphs of the unsolvated TXP-SMTR 1:1 molecular complex were also investigated and the theoretical and experimental phase diagrams of the individual components were assessed. The existence of polymorphic and pseudopolymorphic forms is determined by conformational flexibility of the TXP-SMTR bimolecular complex components, a tendency for molecular disorder in TXP, the ability of the drug complex to form intricate, highly stabilized hydrogen-bonded frameworks, and the competition between nonspecific van der Waals and specific hydrogen bond interactions. © 2003 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 92:2164,2176, 2003 [source]

Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function

PROTEIN SCIENCE, Issue 5 2008
Shira Albeck
Abstract Antizyme inhibitor (AzI) regulates cellular polyamine homeostasis by binding to the polyamine-induced protein, Antizyme (Az), with greater affinity than ornithine decarboxylase (ODC). AzI is highly homologous to ODC but is not enzymatically active. In order to understand these specific characteristics of AzI and its differences from ODC, we determined the 3D structure of mouse AzI to 2.05 Å resolution. Both AzI and ODC crystallize as a dimer. However, fewer interactions at the dimer interface, a smaller buried surface area, and lack of symmetry of the interactions between residues from the two monomers in the AzI structure suggest that this dimeric structure is nonphysiological. In addition, the absence of residues and interactions required for pyridoxal 5,-phosphate (PLP) binding suggests that AzI does not bind PLP. Biochemical studies confirmed the lack of PLP binding and revealed that AzI exists as a monomer in solution while ODC is dimeric. Our findings that AzI exists as a monomer and is unable to bind PLP provide two independent explanations for its lack of enzymatic activity and suggest the basis for its enhanced affinity toward Az. [source]

Towards a classification of icosahedral viruses in terms of indexed polyhedra

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2006
A. Janner
The standard Caspar & Klug classification of icosahedral viruses by means of triangulation numbers and the more recent novel characterization of Twarock leading to a Penrose-like tessellation of the capsid of viruses not obeying the Caspar,Klug rules can be obtained as a special case in a new approach to the morphology of icosahedral viruses. Considered are polyhedra with icosahedral symmetry and rational indices. The law of rational indices, fundamental for crystals, implies vertices at points of a lattice (here icosahedral). In the present approach, in addition to the rotations of the icosahedral group 235, crystallographic scalings play an important rôle. Crystallographic means that the scalings leave the icosahedral lattice invariant or transform it to a sublattice (or to a superlattice). The combination of the rotations with these scalings (linear, planar and radial) permits edge, face and vertex decoration of the polyhedra. In the last case, satellite polyhedra are attached to the vertices of a central polyhedron, the whole being generated by the icosahedral group from a finite set of points with integer indices. Three viruses with a polyhedral enclosing form given by an icosahedron, a dodecahedron and a triacontahedron, respectively, are presented as illustration. Their cores share the same polyhedron as the capsid, both being in a crystallographic scaling relation. [source]

ChemInform Abstract: Crystallographic, Magnetic and Magnetocaloric Properties of GdMgX Intermetallic Phases (X: Al, Ga, In).

CHEMINFORM, Issue 15 2001
F. Canepa
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

Isomeric Squaraine-Based [2]Pseudorotaxanes and [2]Rotaxanes: Synthesis, Optical Properties, and Their Tubular Structures in the Solid State

CHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2010
Min Xue
Abstract On the basis of formation of [2]pseudorotaxane complexes between triptycene-derived tetralactam macrocycles 1,a and 1,b and squaraine dyes, construction of squaraine-based [2]rotaxanes through clipping reactions were studied in detail. As a result, when two symmetrical squaraines 2,d and 2,e were utilized as templates, two pairs of isomeric [2]rotaxanes 3,a,b and 4,a,b as diastereomers were obtained, owing to the two possible linking modes of triptycene derivatives. It was also found, interestingly, that when a nonsymmetrical dye 2,g was involved, there existed simultaneously three isomers of [2]rotaxanes in one reaction due to the different directions of the guest threading. The 1H,NMR and 2D NOESY NMR spectra were used to distinguish the isomers, and the yield of [2]rotaxane 5,a with the benzyl group in the wider rim of the host 1,a was found to be higher than that of another isomer 5,b with an opposite direction of the guest, which indicated the partial selection of the threading direction. The X-ray structures of 3,b and 4,a showed that, except for the standard hydrogen bonds between the amide protons of the hosts and the carbonyl oxygen atoms of the guests, multiple ,,,,, stacking and CH,,,, interactions between triptycene subunits and aromatic rings of the guests also participated in the complexation. Crystallographic studies also revealed that the [2]rotaxane molecules 3,b and 4,a further self-assembled into tubular structures in the solid state with the squaraine dyes inside the channels. In the case of 4,a, all the nonsymmetrical macrocyclic molecules pointed in one direction, which suggests the formation of oriented tubular structures. Moreover, it was also found that the squaraines encapsulated in the triptycene-derived macrocycles were protected from chemical attack, and subsequently have potential applications in imaging probes and other biomedical areas. [source]

Crystallographic and Electrochemical Characteristics of La0.7Mg0.3Ni5.0,x(Al0.5Mo0.5)x Hydrogen-Storage Alloys,

CHEMPHYSCHEM, Issue 3 2005
Xin Bo Zhang Dr.
Abstract The structure, hydrogen-storage property and electrochemical characteristics of La0.7Mg0.3Ni5.0,x(Al0.5Mo0.5)x(x=0,0.8) hydrogen-storage alloys have been studied systematically. X-ray diffraction Rietveld analysis shows that all the alloys consist of an La(La,Mg)2Ni9 phase and an LaNi5 phase. The pressure,composition isotherms indicate that the hydrogen-storage capacity first increases and then decreases with increasing x, and the equilibrium pressure decreases with increasing x. Electrochemical measurements show that the maximum discharge capacity and the exchange-current density of the alloy electrodes increase as x increases from 0 to 0.6 and then decrease when x increases further from 0.6 to 0.8. Moreover, the low-temperature dischargeability of the alloy electrodes increases monotonically with increasing x in the alloys. [source]

Crystal growth and structural refinement of NaMn7O12

CRYSTAL RESEARCH AND TECHNOLOGY, Issue 10-11 2005
E. Gilioli
Abstract We report the crystal growth and the structural refinement of NaMn7O12, a manganite having a double perovskite structure. As in many similar compounds, there is coexistence of Mn3+ and Mn4+ but in this material they orderly occupy different sites for crystallographic reasons. Therefore, this peculiar structure can be considered as a model system for studying complex mechanisms such as charge, orbital and spin ordering. High purity bulk samples and "large" single crystals are needed to study tiny modifications in the crystallographic and magnetic structures associated to the ordering phenomena. Almost single phase (more than 96% pure) and single crystals (up to about 150 µm) of NaMn7O12 were synthesized by solid state reaction under pressure in a multi-anvil apparatus. Single crystal x-ray diffraction and SEM analysis have been used to characterize the crystals. The structure refinement indicates that NaMn7O12 crystallizes in the cubic Im3 space group, with a = 7.312 Å and Z = 2. Further studies are in progress to optimize the synthesis conditions, in order to grow larger crystals. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Benzylideneruthenium Complexes Bearing Pyridine-Based Ligands and Their Influence on the Formation of Mono- or Bis(pyridine) Complexes

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 34 2007
Wen-Zhen Zhang
Abstract Benzylideneruthenium complexes bearing the N-heterocyclic carbene (NHC) ligand 1,3-bis(2,6-dimethylphenyl)-4,5-dihydroimidazol-2-ylidene (H2IMe) and one or two pyridine-based ligands have been prepared by treating [RuCl2(=CHPh)(H2IMe)(PPh3)] with the corresponding pyridine derivative. X-ray crystallographic and mass spectrometric evidence is used to investigate the interconversion between mono- and bis(pyridine) complexes and the influence of the pyridine ligand on the formation of these complexes. The catalytic activity of these complexes has been tested in the ring-closing metathesis (RCM) reaction of diallylmalononitrile and the cross metathesis (CM) reaction of acrylonitrile with terminal olefins.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

Layered [BaM(C3H2O4)2(H2O)4] (M = Fe or Co) Complexes , Spectroscopic, Magnetic and Thermal Study

EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2003
Izaskun Gil de Muro
Abstract Complexes with formula [BaM(C3H2O4)2(H2O)4], where M = Fe or Co, were synthesised and characterised. These two types of complexes are isostructural and crystallise in the Pccn space group. Their structure consists of two-dimensional networks of octahedral MO6 polyhedra in which the transition metal ions are coordinated by bridging malonate ligands, through the O-C-O atoms. These M-malonate units are extended along the crystallographic [101] plane. Spectroscopic data are consistent with the cations being in a high-spin octahedral symmetry. The two types of compounds exhibit 2D antiferromagnetic interactions as well as weak ferromagnetism below the Néel temperature, as a result of an intralayer misalignment of the spins. Thermal treatment of the metallo-organic precursors gave rise to BaMO3,y oxides at lower temperatures and reaction times than those found in the literature using the ceramic method. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003). [source]

Architecture of Supramolecular Soft Functional Materials: From Understanding to Micro-/Nanoscale Engineering

ADVANCED FUNCTIONAL MATERIALS, Issue 19 2010
Jing-Liang Li
Abstract This article gives an overview of the current progress of a class of supramolecular soft materials consisting of fiber networks and the trapped liquid. After discussing the up-to-date knowledge on the types of fiber networks and the correlation to the rheological properties, the gelation mechanism turns out to be one of the key subjects for this review. In this concern, the following two aspects will be focused upon: the single fiber network formation and the multi-domain fiber network formation of this type of material. Concerning the fiber network formation, taking place via nucleation, and the nucleation-mediated growth and branching mechanism, the theoretical basis of crystallographic mismatch nucleation that governs fiber branching and formation of three-dimensional fiber networks is presented. In connection to the multi-domain fiber network formation, which is governed by the primary nucleation and the subsequent formation of single fiber networks from nucleation centers, the control of the primary nucleation rate will be considered. Based on the understanding on the the gelation mechanism, the engineering strategies of soft functional materials of this type will be systematically discussed. These include the control of the nucleation and branching-controlled fiber network formation in terms of tuning the thermodynamic driving force of the gelling system and introducing suitable additives, as well as introducing ultrasound. Finally, a summary and the outlook of future research on the basis of the nucleation-growth-controlled fiber network formation are given. [source]

Architecture of Supramolecular Soft Functional Materials: From Understanding to Micro-/Nanoscale Engineering

Structural and functional insights into Erwinia carotovora l -asparaginase

FEBS JOURNAL, Issue 17 2008
Anastassios C. Papageorgiou
Bacterial l -asparaginases are enzymes that catalyze the hydrolysis of l -asparagine to aspartic acid. For the past 30 years, these enzymes have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. Their intrinsic low-rate glutaminase activity, however, causes serious side-effects, including neurotoxicity, hepatitis, coagulopathy, and other dysfunctions. Erwinia carotovora asparaginase shows decreased glutaminase activity, so it is believed to have fewer side-effects in leukemia therapy. To gain detailed insights into the properties of E. carotovora asparaginase, combined crystallographic, thermal stability and cytotoxic experiments were performed. The crystal structure of E. carotovoral -asparaginase in the presence of l -Asp was determined at 2.5 Å resolution and refined to an Rcryst of 19.2 (Rfree = 26.6%) with good stereochemistry. Cytotoxicity measurements revealed that E. carotovora asparaginase is 30 times less toxic than the Escherichia coli enzyme against human leukemia cell lines. Moreover, denaturing experiments showed that E. carotovora asparaginase has decreased thermodynamic stability as compared to the E. coli enzyme and is rapidly inactivated in the presence of urea. On the basis of these results, we propose that E. carotovora asparaginase has limited potential as an antileukemic drug, despite its promising low glutaminase activity. Our analysis may be applicable to the therapeutic evaluation of other asparaginases as well. [source]

High Purity GaAs Nanowires Free of Planar Defects: Growth and Characterization,

ADVANCED FUNCTIONAL MATERIALS, Issue 23 2008
Hannah J. Joyce
Abstract We investigate how to tailor the structural, crystallographic and optical properties of GaAs nanowires. Nanowires were grown by Au nanoparticle-catalyzed metalorganic chemical vapor deposition. A high arsine flow rate, that is, a high ratio of group V to group III precursors, imparts significant advantages. It dramatically reduces planar crystallographic defects and reduces intrinsic carbon dopant incorporation. Increasing V/III ratio further, however, instigates nanowire kinking and increases nanowire tapering. By choosing an intermediate V/III ratio we achieve uniform, vertically aligned GaAs nanowires, free of planar crystallographic defects, with excellent optical properties and high purity. These findings will greatly assist the development of future GaAs nanowire-based electronic and optoelectronic devices, and are expected to be more broadly relevant to the rational synthesis of other III,V nanowires. [source]

Quantum chemical study of leaving group activation in T. vivax nucleoside hydrolase

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2006
Stefan Loverix
Abstract General acid catalysis is a powerful and widely used strategy in enzymatic nucleophilic displacement reactions. However, in the nucleoside hydrolase of the parasite Trypanosoma vivax, crystallographic and mutagenesis studies failed to identify a general acid. The only groups in the vicinity of the leaving group that contribute to catalysis are (i) the indole side chain of Trp260, and (ii) the 5,-group of the substrate's ribose moiety. The x-ray structure of the slow Asp10Ala mutant of nucleoside hydrolase with the substrate inosine bound in the active site displays a face-to-face aromatic stacking interaction between Trp260 and the purine base of the substrate, as well as a peculiar C4,-endo ribose pucker that allows the 5,-OH group to accept an intramolecular hydrogen bond from the C8 of the purine. The first interaction (aromatic stacking) has been shown to raise the pKa of the leaving purine. Here, we present a DFT study showing that the 5,-OH group of ribose fulfills a similar role, rather than stabilizing the oxocarbenium-like transition state. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source]

DFT calculations of light-induced excited states and comparison with time-resolved crystallographic results

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2005
Philip Coppens
Abstract DFT calculations of the ground and first excited states of several transition metal complexes have been performed to complement time-resolved diffraction experiments. The results from different functionals and relativistic treatments are tested against both diffraction and spectroscopic values. Calculations of the d8,d8 complex [Pt2(pyrophosphite)4]4, quantitatively reproduce metal,metal shortening on excitation to the triplet state and support bond formation between the two metal centers, as do calculations on [Rh2(1,3-diisocyanopropane)4]2+. Results on homoleptic and heteroleptic copper(I) 2,9-dimethyl,1,10-phenanthroline (dmp) complexes, which are investigated because of their potential for solar energy capture, confirm considerable molecular deformations on excitation. The distortion calculated for the isolated complex [Cu(dmp)(dmpe)]+ (dmpe=1,2-bis(dimethylphosphino)ethane) is significantly larger than observed in the crystal, indicating the constraining effect of the crystalline environment. The change in the net charge of the Cu atom upon photo-induced metal-to-ligand charge transfer is less than 0.2 e, showing the limitations of the formal Cu(I),Cu(II) designation. Electron density difference maps show a pronounced change in electronic structure of the Cu atom on excitation. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source]

Effective Chiral Ferrocenyl Phosphine-Thioether Ligands in Enantioselective Palladium-Catalyzed Allylic Alkylations

ADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 9 2009
Hong Yee Cheung
Abstract Chiral ferrocene-derived phosphine-thioether mixed donor ligands supported by heterocycles effected the palladium-catalyzed enantioselective allylic alkylations with excellent yields and enantioselectivities (up to 96% ee). With cyclic and unsymmetrical allylic acetates as substrate, the corresponding alkylated products with enantioselectivities up to 87% ee were obtained. Based on X-ray crystallographic and NMR studies, the origin of the observed enantioselectivities is discussed. [source]

New approach to twin interfaces of modulated martensite

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2010
Zongbin Li
In Ni,Mn,Ga ferromagnetic shape memory alloys, the crystallographic nature of martensitic variant interfaces is one of the key factors governing the variant reorientation through field-induced interface motion and hence the shape memory performance. So far, the crystal structure studies of these materials , conducted by means of transmission electron microscopy , have suffered from uncertainties in determining the number of unit cells of modulated superstructure, and consequently improper interpretations of orientation correlations of martensitic variants. In this paper a new approach is presented for comprehensive analysis of crystallographic and morphological information of modulated martensite, using automated electron backscatter diffraction. As a first attempt, it has been applied for the unambiguous determination of the orientation relationships of adjacent martensitic variants and their twin interface characters in an incommensurate 7M modulated Ni,Mn,Ga alloy, from which a clear and full-featured image of the crystallographic nature of constituent twin interfaces is built up. Certainly, this new approach will make it feasible not only to generalize the statistical analysis of martensitic variant distributions for various materials with modulated superstructure, but also to give insight into the crystallographic characteristics of martensitic variant interfaces and the variant reorientation mechanism of new advanced materials for interface engineering. [source]

Local atomic structure in tetragonal pure ZrO2 nanopowders

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2010
Leandro M. Acuña
The local atomic structures around the Zr atom of pure (undoped) ZrO2 nanopowders with different average crystallite sizes, ranging from 7 to 40,nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2 nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr,O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye,Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. [source]

An ab initio theoretical study of electronic structure and properties of 2,-deoxyguanosine in gas phase and aqueous media

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2002
S. K. Mishra
Abstract Molecular geometries of two structural forms of 2,-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2,-endo and C3,-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2,-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2,-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water,air interface. Though the normal Watson,Crick-type base pairing would not be possible with the keto-N7R form of 2,-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti -conformation of 2,-deoxyguanosine including the dihedral angle ,CN agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2,-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H+ and OH, fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH, group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2,-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 530,540, 2002; DOI 10.1002/jcc.10046 [source]

A comparison of crystallographic and NMR data for thieno[2,3- b:4,5- b,]dipyridine and its monohydroperchlorate salt

JOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2000
Leroy H. Klemm
X-ray crystallographic studies of thieno[2,3- b:4,5- b,]dipyridine (1) and its monohydroperchlorate salt (1a) show that 1 is protonated at N1 in ring A and not at N6 in ring C. In each compound individual rings are planar, but there is a small dihedral angle-of-twist between the A and C rings. On going from 1 to 1a the largest changes in bond angles and bond lengths occur in ring A. 1H and l3C nmr spectra of 1 plus the 13C nmr spectrum of 1a are reported. [source]

Raman phonons and Raman Jahn,Teller bands in perovskite-like manganites

JOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2001
Milko N. Iliev
The perovskite-like manganites R1,xAxMnO3, where R is a trivalent rare earth or Y and A is a divalent alkaline earth element, are characterized by a strong interplay of magnetism, electric transport and crystallographic distortion. At doping levels 0.15 < x < 0.45 the materials exhibit colossal magnetoresistance near the concomitant ferromagnetic and insulator,metal transitions. At a fractional doping level, such as x = 0.5, the crystallographic and magnetic environment is strongly modified and charge ordering between Mn3+ and Mn4+ or phase separation takes place. In this work, the polarized Raman spectra of the orthorhombic and rhombohedral phases of parent RMnO3 compound were analyzed in close comparison with results of lattice dynamic calculations. We argue that the strong high-wavenumber bands between 400 and 700 cm,1, which dominate the Raman spectra of rhombohedral RMnO3 and magnetoresistive La1,xAxMnO3 are not proper Raman modes for the R3c or Pnma structures. Rather, the bands are of phonon density-of-states origin and correspond to oxygen phonon branches activated by the non-coherent Jahn,Teller distortions of the Mn3+O6 octahedra. The reduction of these bands upon doping of La1,xAxMnO3 and their disappearance in the ferromagnetic metallic phase support the model. The variation with temperature of the Raman spectra of La0.5Ca0.5MnO3 is also discussed. The results give a strong indication for charge and orbital ordering and formation of superstructure at low temperatures. Copyright © 2001 John Wiley & Sons, Ltd. [source]

Radiation damage in protein crystals examined under various conditions by different methods

JOURNAL OF SYNCHROTRON RADIATION, Issue 2 2009
Elspeth F. Garman
Investigation of radiation damage in protein crystals has progressed in several directions over the past couple of years. There have been improvements in the basic procedures such as calibration of the incident X-ray intensity and calculation of the dose likely to be deposited in a crystal of known size and composition with this intensity. There has been increased emphasis on using additional techniques such as optical, Raman or X-ray spectroscopy to complement X-ray diffraction. Apparent discrepancies between the results of different techniques can be explained by the fact that they are sensitive to different length scales or to changes in the electronic state rather than to movement of atoms. Investigations have been carried out at room temperature as well as cryo-temperatures and, in both cases, with the introduction of potential scavenger molecules. These and other studies are leading to an overall description of the changes which can occur when a protein crystal is irradiated with X-rays at both cryo- and room temperatures. Results from crystallographic and spectroscopic radiation-damage experiments can be reconciled with other studies in the field of radiation physics and chemistry. [source]

XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysis

JOURNAL OF SYNCHROTRON RADIATION, Issue 1 2003
Richard W. Strange
This paper reports a three-dimensional EXAFS refinement of the Mo coordination sphere of the FeMoco cluster of the dithionite-reduced MoFe protein from Klebsiella pneumoniae nitrogenase (Kp1) using the 1.6,Å-resolution crystallographic coordinates. At this resolution, the positions of the heavy (Fe and S) atoms of the cluster are well determined and there is excellent agreement between the crystallographic and EXAFS models. However, the lighter homocitrate and histidine ligands are poorly determined in the crystal structure, and it is shown that the application of EXAFS-derived distance restraints during the early stages of crystallographic refinement provides a means of substantially improving (by ,0.1,Å) the final crystallographic model. The consistency of the EXAFS analysis with the crystallographic information in this case justifies applications of EXAFS to cases where protein crystal structures are absent. Thus, the VFe protein of V-nitrogenase has been shown by EXAFS to possess a V-atom site catalytically similar to the well characterized MoFe-nitrogenases, with V replacing Mo. [source]

Controlled Crystallization of Calcite Under Surface Electric Field Due to Polarized Hydroxyapatite Ceramics

JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 7 2009
Norio Wada
We examined effects of surface electric fields for the crystallization of calcite on polarized hydroxyapatite ceramics with and without polyacrylic acid (PAA) as soluble additive. Both on negatively and positively charged surfaces without PAA, the only precipitates were rhombohedra calcite crystals with the face of the {10.4} plane favorably oriented parallel to the surfaces. This oriented growth was explained by the nucleation theory in the presence of an external electric field. However, the addition of PAA drastically changed the situation of the calcite crystals, i.e., the crystallites were the hemispheric aggregates of calcite needles with a facetted rhombohedral {10.4} end face and flat island-shaped aggregates of ones with a rough (00.1) end face having a triangular shape. The calcite needles grew along the crystallographic [00.1] axis. This oriented growth was explained by epitaxy on the PAA,Ca2+ complexes adsorbing on the surfaces. The morphology of the PAA,Ca2+ complex assemblies adsorbing on the surfaces before the calcite nucleation was an important factor to control the structure of calcite aggregates formed following. This morphology was controlled by properties of the surface electric field and the spatial distribution of the negatively and positively charged sites in the PAA,Ca2+ complexes. [source]

YIG thin films for magneto-optical and microwave applications

PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 12 2004
T. Boudiar
Abstract Thin films of Yttrium Iron Garnet (YIG) are grown by radio frequency magnetron non reactive sputtering system on quartz and Gadolinium Gallium Garnet (GGG) for optical applications or alumina substrates for microwave applications. A post deposition annealing is needed to obtain the crystallization of YIG films and the magnetic properties which are correlated with the magneto-optical properties. Their crystallographic, morphologic and magnetic properties are explored. The variation of Faraday rotation is studied versus the wavelength. For both optical substrates, quartz and GGG, results are comparable with the literature for bulk material. A microwave isolator was realized with YIG thin film on alumina substrate in a coplanar configuration. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Louis Pasteur's discovery of molecular chirality and spontaneous resolution in 1848, together with a complete review of his crystallographic and chemical work

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2009
H. D. Flack
Pasteur's chemical and crystallographic work is described. The article commences with a brief overview of related science (chemical structure, crystallography, optical activity) before and after 1848, the year of the discovery of molecular chirality and spontaneous resolution. Concerning this discovery, three separate and varying reports are described. These are: (i) the publications in the scientific literature, (ii) the early (auto)biographies and (iii) Pasteur's handwritten laboratory notebooks. The three versions give differing views on the topic. Subsequently all of Pasteur's crystallographic and chemical work is passed in review, a topic very rarely broached. Pasteur's view in later life on this part of his work is examined. The article concludes with a discussion of the term dissymmetry used by Pasteur. [source]

Large-scale preparation of the homogeneous LolA,lipoprotein complex and efficient in vitro transfer of lipoproteins to the outer membrane in a LolB-dependent manner

PROTEIN SCIENCE, Issue 12 2007
Shoji Watanabe
Abstract An ATP-binding cassette transporter LolCDE complex of Escherichia coli releases lipoproteins destined to the outer membrane from the inner membrane as a complex with a periplasmic chaperone, LolA. Interaction of the LolA,lipoprotein complex with an outer membrane receptor, LolB, then causes localization of lipoproteins to the outer membrane. As far as examined, formation of the LolA,lipoprotein complex strictly depends on ATP hydrolysis by the LolCDE complex in the presence of LolA. It has been speculated, based on crystallographic and biochemical observations, that LolA undergoes an ATP-dependent conformational change upon lipoprotein binding. Thus, preparation of a large amount of the LolA,lipoprotein complex is difficult. Moreover, lipoproteins bound to LolA are heterogeneous. We report here that the coexpression of LolA and outer membrane-specific lipoprotein Pal from a very efficient plasmid causes the unusual accumulation of the LolA,Pal complex in the periplasm. The complex was purified to homogeneity and shown to be a functional intermediate of the lipoprotein localization pathway. In vitro incorporation of Pal into outer membranes revealed that a single molecule of LolB catalyzes the incorporation of more than 100 molecules of Pal into outer membranes. Moreover, the LolB-dependent incorporation of Pal was not affected by excess-free LolA, indicating that LolB specifically interacts with liganded LolA. Finally, the LolB depletion caused the accumulation of a significant amount of Pal in the periplasm, thereby establishing the conditions for preparation of the homogeneous LolA,lipoprotein complex. [source]

The ankyrin repeat as molecular architecture for protein recognition

PROTEIN SCIENCE, Issue 6 2004
Leila K. Mosavi
Abstract The ankyrin repeat is one of the most frequently observed amino acid motifs in protein databases. This protein,protein interaction module is involved in a diverse set of cellular functions, and consequently, defects in ankyrin repeat proteins have been found in a number of human diseases. Recent biophysical, crystallographic, and NMR studies have been used to measure the stability and define the various topological features of this motif in an effort to understand the structural basis of ankyrin repeat-mediated protein,protein interactions. Characterization of the folding and assembly pathways suggests that ankyrin repeat domains generally undergo a two-state folding transition despite their modular structure. Also, the large number of available sequences has allowed the ankyrin repeat to be used as a template for consensus-based protein design. Such projects have been successful in revealing positions responsible for structure and function in the ankyrin repeat as well as creating a potential universal scaffold for molecular recognition. [source]