Temperature Factors For Atoms Research Articles

Analysis of Atomic Thermal Vibration of CrN Based on Rietveld Refinement Method

The crystal structure of chromium nitride (CrN) is studied by X‐Ray diffraction from 25 to 600 °C. Based on the RIETAN‐2000 program of Rietveld refinement method, the experimental results are analyzed, and the crystal structure parameters of CrN powder crystals at different temperatures are refined. Atomic thermal vibration isotropic temperature factor B is directly obtained by the Rietveld refinement method. Using the maximum entropy method analytical procedure, the 3D and planar isoheight nuclear density distribution characteristics of CrN are derived, realizing the visualization of nuclear density distribution. It can help to calculate the thermal diffuse scattering.

Identifying Ligand Binding Sites of Proteins using Crystallographic Bfactors and Relative Pocket Sizes

The long-term goal of this project is to develop methods to predict the functional regions of proteins of unknown function. The results of previous studies have suggested that one of the largest pockets on a protein surface is most likely to be the ligand binding site. We tested if adding a measure related to local flexibility would make this prediction more accurate. We tested the hypothesis that considering the relative X-ray crystallographic B-factors (temperature factors) of atoms in a protein structure in addition to the relative sizes of surface pockets can help in identifying the functional regions of proteins.

Ti-based BCC Alloy: Dehydrogenation Characterization Using Synchrotron and Neutron Diffraction

Dehydrogenation of a BCC alloy of composition 52Ti-12V-36Cr doped with 4 wt.% Zr7Ni10 was studied by diffraction using synchrotron and neutron radiations. In the case of synchrotron radiation dehydrogenation was imposed by raising the temperature while keeping the sample under vacuum. We found that prior to final dehydrogenation the FCC dihydride phase is becoming metastable. Neutron in-situ experiment was done by keeping the deuterided sample at 200°C and slowly reducing the pressure. This lead to a reduction of the occupation factor of deuterium in the FCC phase and an increase of the isotropic atomic temperature factor of deuterium.

Effect of cation doping on ionic conductivity and crystal structure of oxyapatite-type lanthanum silicates

Crystal structures of oxyapatite-type lanthanum silicate (LSO), La9.667Si6O26.5, and Al- and Mg-doped LSOs; La9.667(Si5.8Al0.2)O26.4 and La9.667(Si5.5Mg0.5)O26.0, were refined using synchrotron powder X-ray diffraction (SXRD) data to investigate the origin of enhanced oxide ion (O2−) conducting behavior with Si-site doping. It was found that temperature factors of oxygen atoms largely increased with slight Al- or Mg-doping into the Si-site of LSO. Especially, that for the 2a-site oxygen located on the c axis (O4) was enhanced by doping. In addition, that for the 12i-site oxygen, O3, the constituent of an SiO4 tetrahedron in the LSO lattice increased with doping anisotropically toward O4. It was suggested that the ionic movement perpendicular to the c axis via SiO4 tetrahedron was activated by cation (M) doping, and that contributed to the ion conduction in addition to the fast ion channel along c axis.

Synthesis, structure and spectroscopic properties of Nd3+:SrY2O4 phosphor

In order to obtain new-type laser crystals, SrY2O4 is chosen as a host material. Because Y3+ ions in SrY2O4 occupy two non-equivalent sites, it might be possible to realize dual-wave laser and broadband emission at 1.06 m by partially replacing Y3+ with Nd3+. In this work, (3 at.%) Nd3+ doped SrY2O4 phosphor is synthesized by the conventional solid state reaction. The structure and luminescence properties in the visible and near-infrared ranges are studied. The peaks in the X-ray powder diffraction pattern of (3 at.%) Nd3+:SrY2O4 can be well indexed according to ICSD#25701. The lattice parameters, atomic coordinates, atomic temperature factors etc., are obtained by the Rietveld refinement with R_p of 4.68% and R_wp of 5.91%. According to the excitation spectra in a range of 220-380 nm, it can be seen that Nd3+:SrY2O4 is efficiently excited by 353 nm which is assigned to the 4I9/24D3/2+4D5/2+2I11/2+4D1/2 transition of Nd3+ ions. Under the 353 nm light excitation, Nd3+:SrY2O4 exhibits the strongest emission at 419 nm corresponding to the 2D15/24I9/2 transition of Nd3+ ions. What is more, Nd3+:SrY2O4 can be excited effectively by 824 nm light, which matches well with the commercial 830 nm diode laser. When excited with 824 nm, the strongest fluorescence peak is located at 1083 nm with a wide bandwidth of about 90 nm. Compared with that at 8~K, the bandwidth in the fluorescence spectrum at 300 K is broadened because of the homogeneous broadening induced by the increase of temperature. Additionally, the peaks corresponding to the 4F3/24I11/2 transition are split into two groups at 8~K, which results from the two non-equivalent sites of Nd3+ ions. Compared with Nd3+:YAG, Nd3+:SrY2O4 has more potential applications in the tunable and ultrashort lasers. The fluorescence lifetime of the 4F3/24I11/2 transition of (3 at.%) Nd3+:SrY2O4 is 281.7 s, which shows slight concentration quenching compared with that of (0.5 at.%) Nd3+:SrY2O4. The fluorescence lifetime of (3 at.%) Nd3+:SrY2O4 is much longer than that of (0.6 at.%) Nd3+:YAG which is beneficial to the energy storage. In conclusion, the wide emission band and the long decay time of 1.08 m indicate that Nd3+:SrY2O4 is a very promising new-wavelength and ultrashort laser material pumped by laser diode.

Chemical Reduction of Nd1.85Ce0.15CuO4−δPowders in Supercritical Sodium Ammonia Solutions

Nd1.85Ce0.15CuO4−δpowders are chemically reduced in supercritical sodium ammonia solutions from room temperature to 350°C. The crystallographic structure of the reduced powders is investigated from Rietveld refinement of X-ray powder diffraction. The atomic positions are maintained constant within experimental errors while temperature factors of all atoms increase significantly after the chemical treatments, especially of Nd/Ce atoms. The ammonothermally reduced Nd1.85Ce0.15CuO4−δpowders show diamagnetic below 24 K which is contributed to the lower oxygen content and higher temperature factors of atoms in the treated compound. The ammonothermal method paves a new way to reduce oxides in supercritical solutions near room temperature.

Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor

AbstractComputational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors so there is less chance that errors are playing roles in temperature factors. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution and R-factor. Programs and scripts were written for extracting the temperature factors for the beta strands, loops and turns so that the analysis could be done for different atom-types and residue-types. The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel (the lower wall or ‘inner’ wall comprising the trimer interface in the case of the 16 stranded barrels) was more rigid and the other half of the barrel (the higher or ‘outer’ wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.

New Organic Ferroelectrics: Cocrystal of 5,5′-Dimethyl-2,2′-bipyridine and Bromanilic Acid

Abstract Cocrystal 55DMBP–H2ba was synthesized and characterized. The crystal structure is isostructural to cocrystal 55DMBP–H2ia with iodanilic acid. The heat capacity, dielectric permittivity, and polarization–electric field hysteresis showed that the 55DMBP–H2ba undergoes a paraelectric–ferroelectic phase transition at 253 K on cooling. The transition mechanism is discussed through the analysis of isotropic temperature factors of atoms.

The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

ChemInform Abstract: Structure of Capnoidine, a Phthalide Isoquinoline Alkaloid

I n t r o d u c t i o n . In the course of our studies of natural products we investigated the crystal and molecular structure of capnoidine isolated from Corydalis cava collected from Vojvodinas Danube region. Extraction, isolation, separation and identification of capnoidine were performed as described by Slavik & Slavikova (1961), Preininger, gimanek, GaSi6 & gantavy (1973) and Ga~i6, Popovi6 & Dragutinovi6 (1985). The interest in this work lies in the accurate determination of molecular conformation of the compound which might assist in a better understanding of its biological action, studies of which are in progress. 0108-2701/91 / 102191-03503.00 Experimental. A crystal 0.22 × 0.35 × 0.15 mm was mounted on a CAD-4 diffractometer (University of Berne) using graphite-monochromated Mo Ka radiation. Cell constants were refined by a leastsquares fit for 22 centered reflections with 0 range from 4.2 to 8.5 ° . Intensity data were collected with w-20 scan in the range 20 3.5tr(/) were considered as observed. Data were corrected for Lorentz and polarization effects. The structure was solved using SHELXS86 (Sheldrick, 1986) with all non-H atoms obtained from the E map (R = 0-173). Full-matrix least-squares (on F) isotropic (R = 0.096) and anisotropic refinement with program SHELX76 (Sheldrick, 1976) minimized ~'.w(AF) 2 for 245 parameters with unit weights. Final R=0 .038 , wR=0.038, (A/tr)max = 0007. Positions of H atoms were generated from assumed geometries and their positions were taken into account without refinement in structure-factor calculations with common isotropic temperature factor U = 0.072 (4)/~2. A final © 1991 International Union of Crystallography 2192 C 2 o H I T N O 6 Table 1. Fractional atomic coordinates (× 104) and equivalent isotropic temperature factors ( x 10 3) I U v~= ~( , , + u~+ v~).

Quantitative prediction of the thermal motion and intrinsic disorder of protein cofactors in crystalline state: A case study on halide anions

The thermal motion and intrinsic disorder of protein cofactors are highly correlated with their biological functions and can be at least in part measured by atomic temperature factor or B-factor. However, this crystallographic parameter, which actually shares the equal importance with the atomic coordinate in describing the complete profile of crystal structures, has long been underappreciated in the field of biology. In the present study, we attempt to put the first step towards the quantitative prediction of the B-factor values of halide anions, which were recently found to play a fundamental role in conferring stability and specificity to the architecture of proteins and their complexes with nucleic acids and small ligands. In this procedure, the local nonbonding landscapes of halide anions bound in proteins are characterized by electrostatic and dispersion potentials, and then the resulting descriptors of the characterization are statistically correlated with experimentally measured B-factors by using both linear and nonlinear machine learning approaches. From the modeling results and the comparison of these results to those obtained previously for predicting protein B-factors, we demonstrate that the dynamic behavior of halide anions in protein crystals is primarily governed by the local features of nonbonding potential landscapes and, owing to the non-ignorable noise existing in experimental data, the relationship between the B-factor values and the local nonbonding landscapes can only be modeled at a moderate level of accuracy even using the complicated nonlinear methods. These findings are consistent well with that concluding from previous studies of protein B-factors.

Direct methods and refinement in electron and X-ray crystallography – diketopiperazine revisited

AbstractTexture diffraction data in pioneering Russian electron crystallographic studies inspired the invention of modern precession methods for collecting single crystal data. (Although oblique texture patterns contain overlapped reflections, the similarity to precession methods is a result of averaging intensities over an angular distribution of crystallites within the large area sampled by the incident electron beam.) Using texture diffraction amplitudes originally measured by Vainshtein, the crystal structure of diketopiperazine has been re-determined using automated direct methods (SIR97) and refined by block diagonal least squares. This determination was carried out in parallel with an equivalent direct methods study of a larger X-ray data set from the same material published by Degeilh and Marsh, followed by least squares refinement, reproducing the original results. After both refinements, the electron crystallographic bonding parameters for heavy atoms are found to be similar to derived X-ray crystallographic parameters. On the other hand, C–H and N–H distances are more accurately determined by electron crystallography than by X-ray crystallography since the light atom positions are more easily detected in ensuing maps. Surprisingly the least squares refinement against the electron diffraction data did not require a restraint on the magnitude of atomic incremental movement; moreover the atomic temperature factors could be refined, producing results that were more reasonable than expected from the very low overall B value found from a Wilson plot.

Topological atomic displacements, Kirchhoff and Wiener indices of molecules

We provide a physical interpretation of the Kirchhoff index of any molecules as well as of the Wiener index of acyclic ones. For the purpose, we use a local vertex invariant that is obtained from first principles and describes the atomic displacements due to small vibrations/oscillations of atoms from their equilibrium positions. In addition, we show that the topological atomic displacements correlate with the temperature factors (B-factors) of atoms obtained by X-ray crystallography for both organic molecules and biological macromolecules.

Structural Basis for Phototoxicity of the Genetically Encoded Photosensitizer KillerRed

KillerRed is the only known fluorescent protein that demonstrates notable phototoxicity, exceeding that of the other green and red fluorescent proteins by at least 1,000-fold. KillerRed could serve as an instrument to inactivate target proteins or to kill cell populations in photodynamic therapy. However, the nature of KillerRed phototoxicity has remained unclear, impeding the development of more phototoxic variants. Here we present the results of a high resolution crystallographic study of KillerRed in the active fluorescent and in the photobleached non-fluorescent states. A unique and striking feature of the structure is a water-filled channel reaching the chromophore area from the end cap of the beta-barrel that is probably one of the key structural features responsible for phototoxicity. A study of the structure-function relationship of KillerRed, supported by structure-based, site-directed mutagenesis, has also revealed the key residues most likely responsible for the phototoxic effect. In particular, Glu(68) and Ser(119), located adjacent to the chromophore, have been assigned as the primary trigger of the reaction chain.

Structural analysis of outer membrane beta-stranded porins using B-factor

AbstractComputational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins that allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have lesser possibilities of errors so there is lesser chance that errors are playing roles in temperature factors. Structures of six porins (four 16-stranded beta barrel porins and two 8-stranded beta barrel porins) were taken from the PDB for the analysis based on resolution and R-factor. Programs and scripts were written for extracting the temperature factors for the beta strands, loops and turns so that the analysis could be done for different atom-types and residue-types. The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8-stranded barrels it was found one part of the barrel (the lower wall or 'inner' wall comprising the trimer interface in the case of the 16-stranded barrels) was more rigid and the other half of the barrel (the higher or 'outer' wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.

Temperature factor analysis of outer membrane β-stranded porin crystal structures suggests the pore is not uniformly rigid

AbstractOuter membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than 3.0 Å) and R-factor (< 0.23). The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops (L2 and L3) that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel (the lower wall or 'inner' wall comprising the trimer interface in the case of the 16 stranded barrels) was more rigid and the other half of the barrel (the higher or 'outer' wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.

Dynamical properties and temperature induced molecular disordering ofLiBH4andLiBD4

We report on neutron powder-diffraction experiments, inelastic incoherent neutron-scattering experiments, and density-functional calculations on dynamics, order and disorder properties of ${\text{LiBH}}_{4}$ and ${\text{LiBD}}_{4}$. From refinement of ${\text{LiBD}}_{4}$ structure at 10 and 302 K, we found an almost ideal tetrahedral geometry of ${\text{BD}}_{4}$ ions (difference between shortest and longest interatomic distances is less than 4% for B-D bond, and less than 3% for D-D bond), close to the calculated geometry. A quantitative agreement was found between experimental and calculated anisotropic temperature factors of individual atoms. For phonon energies $<15\text{ }\text{meV}$, the phonon density of states of ${\text{LiBH}}_{4}$ in the low-temperature phase depends quadratically on the phonon energy while for the high-temperature phase a linear dependence is observed, revealing a high lattice anharmonicity in the high-temperature phase. Moreover, an increased phonon density of states at low energies in the high-temperature phase compared to the low-temperature phase give a direct evidence for disorder in the high-temperature phase of ${\text{LiBH}}_{4}$ of the hydrogen sublattice which can originate from orientational disorder of ${\text{BH}}_{4}$ units. Potential energy landscape for rotation of ${\text{BH}}_{4}$ indicates that fairly localized minima and barriers higher than 0.6 eV exist in the low-temperature phase, i.e., ordered ${\text{BH}}_{4}$ ions. The high-temperature structure shows shallow barriers of $\ensuremath{\sim}0.2\text{ }\text{eV}$ without distinct energy minima, i.e., orientation of a single ${\text{BH}}_{4}$ unit cannot be precisely defined. This corroborates the large thermal displacements observed in diffraction studies and high disorder of ${\text{BH}}_{4}$ ions deduced from experimental partial phonon density of states in the high-temperature phase.

Crystal Engineering on Industrial Diaryl Pigments Using Lattice Energy Minimizations and X-ray Powder Diffraction

Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was found experimentally as a metastable gamma phase of PY12. Calculations on mixed crystals (solid solutions) showed that mixed crystals of PY12 and PY13 should adopt the PY13 structure with planar molecules, resulting in high color strengths; this was proven experimentally (Pigment Yellow 188). Similarly, the high color strength of mixed crystals consisting of PY13 and PY14 (Pigment Yellow 174), and PY13/PY83 (Pigment Yellow 176) is explained by the crystal structures.

The application of the in situ high-temperature X-ray diffraction quantitative analysis

An extending RQA standardless method is applied to in situ high-temperature quantitative analysis of Cu 2O–Al 2O 3–SiO 2 pseudo-ternary system. By carrying out the refinement of the in situ high-temperature XRD data according to the designed uniform refining strategy, we analyzed the influences of the refined variables on the analytical results such as the phase fraction and the residuals. It indicates that the thermal diffuse scattering function gives a satisfactory fitting for the background. The refinements of temperature factors of atoms and lattice parameters of unit cells are the prerequisite for the refinements of the other structure factors, and the preferred orientation can be effectively reduced in the RQA method for anisotropic crystalline phases. The reliable results were obtained and the precision has reached 0.1–2.3%.

Li 2B 4O 7 crystal structure in anharmonic approximation at 20, 200, 400 and 500 °C

Li 2B 4O 7 crystal structure was studied at elevated temperatures and refined in anharmonic approximation: 20 °C, a = 9.475(3), c = 10.283(6) Å, 883 F( h k l), R = 0.015; 200 °C, a = 9.501(3), c = 10.275(6) Å, 826 F( h k l), R = 0.021; 400 °C, a = 9.535(3), c = 10.295(8) Å, 809 F( h k l), R = 0.022; and 500 °C, a = 9.550(3), c = 10.295(6) Å, 779 F( h k l), R = 0.029. B O bond lengths were corrected in a view of O and B atomic vibrations. Refinement of anharmonic components of atomic temperature factors has revealed high asymmetry of Li thermal vibrations. The behaviour of tetraborate groups was studied. A stability of rigid B O groups configuration was indicated, as in the case of β CsB 5O 8, LiB 3O 5 and β-Na 2B 8O 13, studied by us earlier. The boron–oxygen framework expands as a three-dimensional hinge; B O B and O B O angles inside tetraborate groups practically do not change, while B1 O1 B2 angles between the groups increase to 1.6° on heating up to 500 °C due to O1 atoms shifts letting Li atom to fall through oxygen atoms along c-axis causing the contraction in this direction.