Experimental Structure Factors Research Articles

Determination of partial structure factors by reverse Monte Carlo modelling—a test of themethod

The reverse Monte Carlo modelling technique is commonly applied for theanalysis of the atomic structure of liquid and amorphous substances. Inparticular, partial structure factors of multi-component alloys can be determinedusing this method. In the present study we use the example of the liquidNi33Ge67 alloy to investigate the impact of different input data on the result of RMC modelling. Itwas found that even two experimental structure factors might be sufficient to obtainreliable partial structure factors if the contrast between them is high enough.

Crystal structure of TM1367 from Thermotoga maritima at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

Crystal structure of TM1367 from <i>Thermotoga maritima</i> at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from <i>Thermotoga maritima</i> at 2.15 Å resolution

New insights into optical Fourier transforms, radial distribution function, and Glatter’smethod

We address several subtle issues concerning the static scattering of light or x-rays fromphysical/chemical/biological systems. In the context of Fourier integrals we point out thatthe Glatter–Moore algorithms can efficiently perform sine inversion between two functionsJ(q) andL(r) of calculus, andthe structure factor S(q) can be correct only if the asymptotic value of the pair correlation function differs from unity. Next, concerning the radial distributionfunction g(r), we derive a new integral equation for and use it to find the effective potential when the input pair potential is parabolic. Finally, turning to data analysis,we demonstrate that a bump in the underlying distance distribution functionP(r) plays a major role in producing attenuated oscillations in the experimental structure factor,and also in the study of a subtle convolution integral.

Crystal structure of a single‐stranded DNA‐binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution

Crystal structure of a single‐stranded DNA‐binding protein (TM0604) from <i>Thermotoga maritima</i> at 2.60 Å resolution

Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 Å resolution

Introduction. As part of a structural genomics program, we are determining structures of proteins from the causative agent of anthrax, Bacillus anthracis, a Grampositive spore-forming bacterium. Among our initial candidates for crystallographic analysis are the products of essential genes based on knock-out studies in Bacillus subtilis. The BA3935 gene of B. anthracis (www.tigr.org), annotated as DapA2, encodes a putative protein consisting of 292 amino acid residues with a subunit molecular weight of 31,233 Da. The predicted protein has 60% identity with dihydrodipicolinate synthase (DHDPS or DapA) from B. subtilis and 40% amino acid sequence identity to its orthologue in Escherichia coli. dapA is one of only 271 out of the total of 4118 genes in B. subtilis that are indispensable for growth of the organism on standard laboratory media. 1 DHDPS catalyses the condensation of aspartate semialdehyde and pyruvate and is the first committed step on the pathway to diaminopimelate and L-lysine in prokaryotes, some fungi, and higher plants (Scheme 1). The product released from the E. coli enzyme has been shown to be 4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTDPA) rather than L-2,3-dihydrodipicolinic acid (DHDPA); as the name of the enzyme suggests, 2 DHDPA can be formed spontaneously from HTDPA by elimination of water. The steps of aspartate semialdehyde synthesis from aspartate are shared with the biosynthetic pathways leading methionine and threonine. The diaminopimelate/ lysine pathway is thought to be of particular importance in Gram-positive bacteria because diaminopimelate makes up a higher proportion of the dry cell weight than it does in Gram-negative bacteria, a consequence of the thicker cell wall in the former. In Bacilli, the product of the DHDPS reaction is further reduced by dipicolinate synthase to dipicolinate, which makes up 10% of the dry weight of spores. Crystal structures have been determined of DHDPS from E. coli, 3 Nicotiana sylvestris, 4 and most recently from Thermotoga maritima. 5 In this article, we report the crystal structure of DHDPS from B. anthracis (Ba DHDPS), the first structure of a dihydrodipicolinate synthase from a Gram-positive bacterium. The structure of Ba DHDPS was determined by molecular replacement using the coordinate set for the E. coli orthologue (PDB code 1DHP) as the search model. 3 Two structures have been determined to 1.9 and 2.2 A resolution in different orthorhombic crystal forms. Data collection, refinement, and model-building statistics are summarized in Table I. The structures in the two crystal forms are very similar and unless otherwise stated, the commentary here will refer to the structure refined to higher resolution

Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 Å resolution reveals a new fold

Crystal structure of virulence factor CJ0248 from <i>Campylobacter jejuni</i> at 2.25 Å resolution reveals a new fold

Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 Å resolution

Crystal structure of PurE (BA0288) from <i>Bacillus anthracis</i> at 1.8 Å resolution

Model-independent one-dimensional imaging of interfacial structures at&lt;1Åresolution

The feasibility of model-independent error-correction algorithms is established for imaging buried interfacial structures in one dimension. Using the experimental structure factor modulus from x-ray specular reflectivity data, we directly compare structures derived by a modified Fienup algorithm using a known reference structure and that derived by traditional (model-dependent) least-squares fitting. This demonstrates the utility of this approach for determining one-dimensional interfacial electron density profiles with spatial resolution of $&lt;1\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$. The potential applications and limitations of this approach are discussed.

Neutron Scattering Experiments on Fully Deuterated Liquid N-Methylformamide DCONDCD3 at Various Temperatures and under Pressure. Comparison to X-ray Results

Neutron scattering experiments are performed on fully deuterated liquid N-methylformamide (C2D5NO) at various temperatures and under pressure. The recorded data at atmospheric pressure and room temperature are analyzed to yield the molecular form factor and the distinct pair correlation function. Our measurements clearly show that the hydrogen-bond network, of which the parameters are deduced, persists locally in the liquid. The experimental structure factor could be explained in terms of short-range crystal structure. The r(N...O) distance decreases with increasing temperature from 293 to 398 K, whereas no significant variation of the intermolecular structure is detected when varying pressure from 1 bar to 4 kbar. Along the study, some comparison is made with complementary X-ray results.

Modeling the atomic structure of very high-density amorphous ice

The structure of very high-density amorphous (VHDA) ice has been modeled by positionally disordering three crystalline phases, namely ice IV, VI, and XII. These phases were chosen because only they are stable or metastable in the region of the ice phase diagram where VHDA ice is formed, and their densities are comparable to that of VHDA ice. An excellent fit to the medium range of the experimentally observed pair-correlation function $g(r)$ of VHDA ice was obtained by introducing disorder into the positions of the ${\mathrm{H}}_{2}\mathrm{O}$ molecules, as well as small amounts of molecular rotational disorder, disorder in the $\mathrm{O}\mathrm{H}$ bond lengths and disorder in the $\mathrm{H}\mathrm{O}\mathrm{H}$ bond angles. The low-$k$ behavior of the experimental structure factor, $S(k)$, is also very well reproduced by this disordered-crystal model. The fraction of each phase present in the best-fit disordered model is very close to that observed in the probable crystallization products of VHDA ice. In particular, only negligible amounts of ice IV are predicted, in accordance with the experimental observation.

An effective pair potential for liquid semiconductor, Se: Structure and related dynamical properties

The effective pair potential of liquid semiconductor Se is extracted from its experimental structure factor data using an accurate liquid state theory and this shows important basic features. A model potential incorporating the basic features of the structure factor extracted potential is suggested. This model potential is then used to describe through low-order perturbation theory, the structure and related dynamical properties like self-diffusion coefficient and shear viscosity of this complex liquid over a wide range of temperatures.

Effects of Activation on the Structure and Adsorption Properties of a Nanoporous Carbon Using Molecular Simulation

We present a study on the effects of activation on a saccharose-based carbon using molecular simulation. A constrained Reverse Monte Carlo method is used to build molecular models that match the experimental structure factors of both activated and unactivated carbon, using appropriate constraints for bond angle and coordination number to describe the three body correlation. The semi-coke sample, that is named CS1000, is obtained by pyrolyzing pure saccharose at 1000∘C under nitrogen flow. An activated form of this carbon, CS1000a, was obtained by heating CS1000 in an atmosphere of CO2 for 20 hours. We built molecular models for CS1000 and CS1000a and also simulated the TEM images of the model. We perform GCMC simulation of a Lennard-Jones model of Argon on the resulting models to obtain the adsorption isotherms. We then study the difference in the morphology of CS1000 and CS1000a that lead to different adsorption properties in carbon upon activation.

Modelling studies of carbon nanotubes—Comparison of simulations and X-ray diffraction data

Computer simulations of the powder diffraction profiles for multi-wall carbon nanotubes were performed using the Debye equation including a generalized Debye–Waller factor. The X-ray diffraction data were recorded using high-energy synchrotron radiation and an image plate as a detector for the carbon nanotubes produced by a template chemical vapour deposition (CVD) process. The computed and experimental structure factors were converted to real-space via the Fourier transform. The results of computation, obtained in the form of the structure factor and the pair correlation function, are compared with the X-ray experimental data in both reciprocal and real-space. The nanotube model consisting of five layers with the length of 12 Å has proved to account very well for the experimental data.

Theoretical calculations of the temperature dependence of the electrical and thermal conductivities of liquid gallium

Abstract The electrical and thermal resistivities of liquid gallium are calculated over a range of temperatures above the melting point using the solutions of the Boltzmann equation. The experimental x-ray structure factor of Waseda and the form factor derived using the Heine-Abarenkov model potential are used in these calculations. The ratio of the electrical and thermal conductivities is calculated and compared to experimental values and to the theoretical Lorenz number.

Comparison of the structures of evaporated and ion-implanted amorphous siliconsamples

The experimental structure factors of evaporated and ion-implanted amorphous silicon havebeen modelled by reverse Monte Carlo modelling. A detailed comparison, in terms of thepair correlation function and the distribution (of the cosines) of bond angles, is reportedhere for the two materials. It is found that for an acceptable reproduction of the measuredstructure factors the evaporated models must contain more ‘small’ bond angles, of the order of75°, than their necessary abundance in the implanted models.

Crystal structure of an indigoidine synthase A (IndA)‐like protein (TM1464) from Thermotoga maritima at 1.90 Å resolution reveals a new fold

Crystal structure of an indigoidine synthase A (IndA)‐like protein (TM1464) from <i>Thermotoga maritima</i> at 1.90 Å resolution reveals a new fold

Real and reciprocal space structural correlations contributing to the first sharp diffraction peak in silica glass

We have applied a ``real-reciprocal space analysis,'' using the continuous wavelet transform technique, to the experimental neutron and x-ray structure factors of silica glass to elucidate a correlation between the ``first sharp diffraction peak (FSDP)'' in reciprocal space and the corresponding length scale in real space. The present analysis allows us to obtain compelling evidence that the dominant interatomic distance linked to the FSDP in silica glass is $\ensuremath{\sim}5\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$, although longer distances are also important, making an exponentially decreasing contribution. Further analysis using molecular-dynamics simulations demonstrates that the interatomic spatial correlations at $r\ensuremath{\sim}5\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$ are associated with a couple of local ``pseudo-Bragg'' planes having an interlayer separation of $\ensuremath{\sim}4\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$, accounting for the origin of structural ordering on the medium-range length scale in silica glass.

Study on the cluster of floating dross before nucleating during hot-dipping process

During hot-dipping in molten Zn-55AI, the forming of “floating” dross is closely related with the interaction between the Al and the Fe atoms. Utilizing the thita-thita X-ray diffraction and the Percus-Yevick hard sphere model, this paper investigates the structure of molten AI3Fe that is an approximant of partial melt in practical Zn-55AI alloy melt. It is found that in the melt there exist clusters that resemble the structure of intermetallic compound Af3Fe. The strong interaction between Al and Fe atoms is also indicated by the deficiency of the coordination number from 12 and the shrinkage of averaged atomic diameter. Based on such information, it is speculated that in the molten Zn-55AI, with the accumulation of Fe, Al3Fe-like clusters form with priority, then grow into dross. On the other hand, after deflating of the effective hard sphere diameter of pure Al atom and enlarging that of the pure Fe atom, the modified model can achieve reasonable fit to the experimental structure factor. Hard sphere modeling also gave a good estimation of the mass density 3.65 g/cm3 of liquid Al3Fe alloy at 1550°C. Compared with the density of 3.7 g/cm3 of Zn-55AI, the reason for dross floating is satisfactorily understood.

A new orbital-based model for the analysis of experimental molecular charge densities: an application to (Z)-N-methyl-C-phenylnitrone

An alternative to the usual atom-centred multipole expansion is presented for the analysis of high resolution, low-temperature X-ray scattering data. The molecular electron density is determined in a fixed basis of molecular orbitals with variable orbital occupation numbers, i.e. the same form which is used to represent the density in ab initio electron-correlated calculations. The advantages of such an approach include linear scaling (in the sense that the number of parameters to be determined by fitting varies linearly with system size) and ease of property calculation. The method is applied to experimental high-resolution structure factors for a phenylnitrone, and compared to the results of a multipole model of the same data. Finally, the model is critically compared with several related, published orbital-based models.