无定形碳的逆向蒙特卡洛法建模

作为一种很有前景的建模方法,逆向蒙特卡洛法（Reverse Monte Carlo 简称RMC 法）在无定形碳结构研究中得到了广泛应用。本文阐述了RMC 法对于无定形碳材料结构识别的意义,简介了该法的基本原理,同时针对使用RMC 法建立无定形碳结构模型时遇到的两大难点：即模拟结构的真实性问题和大尺寸孔网络的建模问题,综述了该方法的改进和发展趋势。几何约束和能量约束的使用,提高了模拟结构的真实性;具有介孔的多孔碳模型的建立,将成为今后研究的热点。     

RMC_POT: A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity

An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness‐of‐fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard‐Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X‐ray structure factor‐based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future. © 2012 Wiley Periodicals, Inc.     

Fullrmc,a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

A new Reverse Monte Carlo (RMC) package “fullrmc” for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group. © 2016 Wiley Periodicals, Inc.     

Gadolinium acetylacetonate tetraphenyl monoporphyrinate complex and some of its derivatives: EXAFS study and molecular dynamics simulation

Many attempts to obtain single crystals appropriate for X-ray diffraction analysis of the Ln(tpp)(acac) derivatives (where Ln = Gd or Sm, tpp = tetraphenylporphyrin and acac = acetylacetonate) have failed so far. A suitable way to get structural parameters for these monoporphyrinates is to use extended X-ray absorption fine structure (EXAFS) spectroscopy. We recorded spectra of the monoporphyrins, Ln(tpp)(acac) and Gd(tpyp)(acac) (where tpyp = tetrapyridylporphyrin), and the bisporphyrin GdH(tpyp)2 in the solid state. We particularly focused our structural analysis on Gd(tpp)(acac), applying both molecular modeling and EXAFS, which allowed us to get accurate results about the local environment of the central atom. The Gd3+ ion of the complex at room temperature was found to be bonded to four monoporphyrin nitrogen atoms at an average distance R(Gd-N(av)) = 2.48 A and to three or four oxygen atoms at R(Gd-O(ac,w)) = 2.38 A from an acetylacetonato anion and a water molecule. The presence of the second water molecule in the coordination sphere was barely discernible by EXAFS analysis. Molecular modeling has provided further information about the coordination core geometry of the Gd(tpp)(acac) monoporphyrinate, including a bishydrated coordination sphere. Also, it has enabled the construction of a 3D structural model on which multiple scattering analyses were attempted. Monte Carlo simulation was used to validate the adjustments. EXAFS spectra analysis was carried out on the derivatives, displaying slight distortions in the lanthanide central-atom coordination geometry.     

Short- and long-range order in the positive electrode material, Li(NiMn)0.5O2: a joint X-ray and neutron diffraction, pair distribution function analysis and NMR study

The local environments and short-range ordering of LiNi(0.5)Mn(0.5)O(2), a potential Li-ion battery positive electrode material, were investigated by using a combination of X-ray and neutron diffraction and isotopic substitution (NDIS) techniques, (6)Li Magic Angle Spinning (MAS) NMR spectroscopy, and for the first time, X-ray and neutron Pair Distribution Function (PDF) analysis, associated with Reverse Monte Carlo (RMC) calculations. Three samples were studied: (6)Li(NiMn)(0.5)O(2), (7)Li(NiMn)(0.5)O(2), and (7)Li(NiMn)(0.5)O(2) enriched with (62)Ni (denoted as (7)Li(ZERO)Ni(0.5)Mn(0.5)O(2)), so that the resulting scattering length of Ni atoms is null. LiNi(0.5)Mn(0.5)O(2) adopts the LiCoO(2) structure (space group Rm) and comprises separate lithium layers, transition metal layers (Ni, Mn), and oxygen layers. NMR experiments and Rietveld refinements show that there is approximately 10% of Ni/Li site exchange between the Li and transition metal layers. PDF analysis of the neutron data revealed considerable local distortions in the layers that were not captured in the Rietveld refinements performed using the Bragg diffraction data and the LiCoO(2) structure, resulting in different M-O bond lengths of 1.93 and 2.07 Angstroms for Mn-O and Ni/Li-O, respectively. Large clusters of 2400-3456 atoms were built to investigate cation ordering. The RMC method was then used to improve the fit between the calculated model and experimental PDF data. Both NMR and RMC results were consistent with a nonrandom distribution of Ni, Mn, and Li cations in the transition metal layers; both the Ni and Li atoms are, on average, close to more Mn ions than predicted based on a random distribution of these ions in the transition metal layers. Constraints from both experimental methods showed the presence of short-range order in the transition metal layers comprising LiMn(6) and LiMn(5)Ni clusters combined with Ni and Mn contacts resembling those found in the so-called "flower structure" or structures derived from ordered honeycomb arrays.     

X-ray absorption spectroscopy of hemes and hemeproteins in solution: multiple scattering analysis

A full quantitative analysis of Fe K-edge X-ray absorption spectra has been performed for hemes in two porphynato complexes, that is, iron(III) tetraphenylporphyrin chloride (Fe(III)TPPCl) and iron(III) tetraphenylporphyrin bis(imidazole) (Fe(III)TPP(Imid)2), in two protein complexes whose X-ray structure is known at atomic resolution (1.0 A), that is, ferrous deoxy-myoglobin (Fe(II)Mb) and ferric aquo-myoglobin (Fe(III)MbH2O), and in ferric cyano-myoglobin (Fe(III)MbCN), whose X-ray structure is known at lower resolution (1.4 A). The analysis has been performed via the multiple scattering approach, starting from a muffin tin approximation of the molecular potential. The Fe-heme structure has been obtained by analyzing independently the Extended X-ray Absorption Fine Structure (EXAFS) region and the X-ray Absorption Near Edge Structure (XANES) region. The EXAFS structural results are in full agreement with the crystallographic values of the models, with an accuracy of +/- 0.02 A for Fe-ligand distances, and +/-6 degrees for angular parameters. All the XANES features above the theoretical zero energy (in the lower rising edge) are well accounted for by single-channel calculations, for both Fe(II) and Fe(III) hemes, and the Fe-N p distance is determined with the same accuracy as EXAFS. XANES evaluations of Fe-5th and Fe-6th ligand distances are determined with 0.04-0.07 A accuracy; a small discrepancy with EXAFS (0.01 to 0.05 A beyond the statistical error), is found for protein compounds. Concerns from statistical correlation among parameters and multiple minima in the parameter space are discussed. As expected, the XANES accuracy is slightly lower than what was found for polarized XANES on Fe(III)MbCN single crystal (0.03-0.04 A), and states the actual state-of-the-art of XANES analysis when used to extract heme-normal parameters in a solution spectrum dominated by heme-plane scattering.     

The X-ray absorption spectroscopic model of the copper(II) imidazole complex ion in liquid aqueous solution: a strongly solvated square pyramid

Cu K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near-edge structure (MXAN) analyses were combined to evaluate the structure of the copper(II) imidazole complex ion in liquid aqueous solution. Both methods converged to the same square-pyramidal inner coordination sphere [Cu(Im)(4)L(ax)](2+) (L(ax) indeterminate) with four equatorial nitrogen atoms at EXAFS, 2.02 ± 0.01 ?, and MXAN, 1.99 ± 0.03 ?. A short-axial N/O scatterer (L(ax)) was found at 2.12 ± 0.02 ? (EXAFS) or 2.14 ± 0.06 ? (MXAN). A second but very weak axial Cu-N/O interaction was found at 2.9 ± 0.1 ? (EXAFS) or 3.0 ± 0.1 ? (MXAN). In the MXAN fits, only a square-pyramidal structural model successfully reproduced the doubled maximum of the rising K-edge X-ray absorption spectrum, specifically excluding an octahedral model. Both EXAFS and MXAN also found eight outlying oxygen scatterers at 4.2 ± 0.3 ? that contributed significant intensity over the entire spectral energy range. Two prominent rising K-edge shoulders at 8987.1 and 8990.5 eV were found to reflect multiple scattering from the 3.0 ? axial scatterer and the imidazole rings, respectively. In the MXAN fits, the imidazole rings took in-plane rotationally staggered positions about copper. The combined (EXAFS and MXAN) model for the unconstrained cupric imidazole complex ion in liquid aqueous solution is an axially elongated square-pyramidal core, with a weak nonbonded interaction at the second axial coordination position and a solvation shell of eight nearest-neighbor water molecules. This core square-pyramidal motif has persisted through [Cu(H(2)O)(5)](2+), [Cu(NH(3))(4)(NH(3),H(2)O)](2+), (1, 2) and now [Cu(Im)(4)L(ax))](2+) and appears to be the geometry preferred by unconstrained aqueous-phase copper(II) complex ions.     

Elucidating the domain structure of the cobalt oxide water splitting catalyst by X-ray pair distribution function analysis

Pair distribution function (PDF) analysis was applied for structural characterization of the cobalt oxide water-splitting catalyst films using high energy X-ray scattering. The catalyst was found to be composed of domains consistent with a cobalt dioxide lattice sheet structure, possibly containing a Co(4)O(4) cubane-type "defect". The analysis identifies the film to consist of domains composed of 13-14 cobalt atoms with distorted coordination geometries that can be modeled by alteration in terminal oxygen atom positions at the domain edge. Phosphate is seen as a disordered component in the films. This work establishes an approach that can be applied to study the structure of in situ cobalt oxide water-splitting film under functional catalytic conditions.     

A washboard with moment of inertia model of gas-surface scattering

A washboard with moment of inertia (WBMI) model for gas atom scattering from a flexible surface is proposed and applied. This model is a direct extension of the washboard model [J. Chem. Phys. 92, 680 (1990)] proposed for gas atom scattering from relatively rigid, corrugated surfaces. In addition, a moment of inertia is incorporated in the original washboard model to describe the flexibility of softer, more highly corrugated surfaces such as polymer or liquid surfaces. The moment of inertia of the effective surface object introduces a dependence of the efficiency of energy transfer on the position and direction of impact, a feature that has been shown to be critical by molecular dynamics simulations. The WBMI model is solved numerically by Monte Carlo integration, which makes the implementation of multiple impacts between a colliding atom and the surface very efficient. The model is applied to Ne and Ar atoms scattering from an alkylthiolate self-assembled monolayer surface and reproduces the major results obtained by classical trajectory simulation of the same system, i.e., a bimodal translation energy distribution P(E(f)) with the low-energy component well-fit with a Boltzmann distribution, but with a temperature that may (Ar) or may not (Ne) be the same as the surface temperature. This indicates that the WBMI model, with well-motivated physical assumptions and simplified interaction, reveals many of the major aspects of the gas-surface collision dynamics, though it does not take into account the real-time dynamics explicitly.     

Nine absorbed components pharmacokinetic of raw and processed Moutan Cortex in normal and blood-heat and hemorrhage syndrome model rats

Raw Moutan Cortex (RMC) and Processed Moutan Cortex (PMC) have a long history of use in China and other Asian countries. In this study, a rapid and accurate ultra-high-pressure liquid chromatography coupled with diode array detector (UHPLC–DAD) method was developed and validated for the simultaneous determination of nine absorbed compounds of RMC/PMC. After extraction by protein precipitation with methanol from plasma, the analytes were separated on an Acquity UPLC® BEH Shield RP₁₈ column (2.1 × 100 mm, 1.7 μm, Waters, USA). Acetonitrile (A) and 0.1% (v/v) formic acid in water (B) were selected as the mobile phase to perform gradient elution. The linearity of nine analytes was >0.9915. The intra- and inter-assay precision (RSD) values were within 11.18%, and accuracy ranged from 91.32 to 101.29%. Suitable stability, matrix effect and extraction recoveries were also obtained. The validated method was applied to compare the pharmacokinetics of RMC and PMC in Blood-Heat and Hemorrhage Syndrome Model and normal rats. The results revealed that processing and the pathological state could influence the pharmacokinetic characteristics of compounds in RMC/PMC. The study willbe useful for further studies on pharmacokinetics and clinical application of raw and processed Moutan Cortex.     

New lipophilic 3-hydroxy-4-pyridinonate iron(III) complexes: synthesis and EXAFS structural characterisation

New tris-iron(III) chelates of 3-hydroxy-4-pyridinone ligands derived from maltol (3-hydroxy-2-methyl-4-pyrone) or ethylmaltol (2-ethyl-3-hydroxy-4-pyrone), including a variety of N-aryl (phenyl, 4'-tolyl, 4'-(n-butyl)phenyl, 4'-(n-hexyl)phenyl) and N-benzyl (4'-methylbenzyl, 4'-fluorobenzyl and 4'-(trifluoromethyl)benzylamine) substituents on the nitrogen atom of the pyridinone ring, have been prepared. Characterization by C,H,N elemental analysis and thermogravimetric measurements indicates that most of the complexes are obtained as hydrates of general formula ML3.xH2O. Structural characterization of these difficult to crystallize lipophilic complexes has been achieved by EXAFS spectroscopy. Solutions of iron(III) complexes of maltol, ethylmaltol, 1,2-dimethyl-3-hydroxy-4-pyridinone and 1-phenyl-2-methyl-3-hydroxy-4-pyridinone in methanol-water mixtures were also examined by EXAFS. Distances from the central atom to ligand atoms, within 6 A of the metal, have been determined in the solid and solution samples and the results show that the structure observed in the powder is maintained in solution. The local structure around the metal centre, bond distances and bond angles, does not change significantly with variable lipophilicity, thus indicating that ligands may be tailored according to specific needs without altering their chelation properties. EXAFS data analysis for this set of tris-iron(III) compounds illustrates the important contribution of both intra-ligand and inter-ligand multiple scattering pathways through the metal centre to a peak observed in the FT spectrum at twice the metal ligand distance (approximately 4 A). The present results demonstrate that EXAFS features at twice the metal-ligand distance are valuable in the assignment of molecular geometry and that location of hydration water molecules, by EXAFS analysis, is limited by the geometry of the complexes, in particular for those in which ligands containing phenyl rings are present.     

担载Ni2（C5H5）2（CO）2催化剂的EXAFS表征

以Ni_2Cp_2(CO)_2(Cp=C_5H_5)为催化剂母体化合物,γ-Al_2O_3,SiO_2为担体制备了担载型镍催化剂,对母体化合物及热分解处理前后的催化剂样品在同步辐射装置上进行了外延X-光精细结构(Extended X-ray Absorpdon Fine Structure)测定,以先进的球面波理论对实验结果进行拟合,标样拟合结果与文献XRD完全一致。催化剂的EXAFS表征结果表明,母体化合物与氧化物担体表面发生了较强的化学作用,镍组分具有较高的分散度,镍在氧化硅表面存在Ni[(O)_8]_n,Ni—Ni两种配位,而在氧化铝表面几乎只存在Ni[(O)s)_n配位,催化剂上Ni—Ni键长比母体化合物Ni—Ni键长增加0.01nm左右,Ni—Ni键的伸长及其配位状态可能对其催化行为有重要影响。     

Experimental evidence for a variable first coordination shell of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea solution

A combined extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS) investigation has been performed to evaluate the coordination structure of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea (dmpu) solutions. This approach has singled out the existence of a flexible coordination shell around the cadmium(II) ion in aqueous and dimethyl sulfoxide solutions, whereas a regular octahedral complex is detected in dmpu. The EXAFS and LAXS techniques provide different values of the Cd-O first shell distance (2.27(1) A and 2.302(5) A, respectively) for the hydrated and dimethyl sulfoxide solvated complexes, and this discrepancy is originated by the simultaneous presence of hexa- and heptacoordinated complexes in solution, giving rise to a broad distribution of distances around the ion. These findings demonstrate that, in solution, the cadmium(II) ion forms quite flexible hydration and dimethyl sulfoxide solvate complexes undergoing a solvent exchange with unusually stable seven-coordinated intermediate complexes, and therefore the mean ion-solvent distance is longer in solution than in the solid state. In the dmpu solution, due to the bulkiness of the solvent molecules, the octahedral cadmium(II) solvate is extremely crowded and it is not possible for a seventh ligand to enter the inner-coordination shell. This investigation shows that the combined analysis of the EXAFS and LAXS data allows a reliable determination of the structural properties of electrolyte solutions, also in the presence of flexible coordination shell with a variable number of coordinating molecules.     

Quantitative adsorption and local structures of gallium(III) at the water-alpha-FeOOH interface

The adsorption of Ga(III) at the water-alpha-FeOOH (goethite) interface has been investigated by means of quantitative adsorption experiments, extended X-ray absorption fine structure (EXAFS) spectroscopy, and surface complexation modeling. Under the conditions studied, pH range 3-11 and surface coverages of 0.9-3.2 micromol/m2, Ga(III) was found to adsorb strongly to alpha-FeOOH, and the surface species were more resistant toward hydrolysis and formation of soluble Ga(OH)4- than either solid gallium hydroxides or soluble polynuclear complexes. The EXAFS measurements revealed the presence of octahedral Ga(III) complexes at the water-alpha-FeOOH interface, with practically no structural variations as a function of pH or total gallium concentration. Analysis of the first coordination shell required an anharmonic model indicating a distorted geometry of the GaO6 octahedra, with mean Ga-O distances at 1.96-1.98 angstroms. A method based on the continuous Cauchy wavelet transforms (CCWT) was used to identify backscattering atoms in the higher coordination shells. This analysis indicated predominately Fe backscattering, and the quantitative data fitting resulted in three Ga-Fe paths at 3.05, 3.2, and 3.55 angstroms, which correspond to two edge-sharing and one corner-sharing linkage, respectively. The collective results from EXAFS spectroscopy showed that Ga(III) adsorbs to Fe equivalent sites at the surface alpha-FeOOH as an extension of the rows of Fe octahedra in the bulk structure. This interpretation was further corroborated by a Ga-Fe-Fe multiple scattering path at 6.13 angstroms. The quantitative adsorption and proton data were modeled using a surface complexation formalism based on a 1 pK(a) constant capacitance model. In agreement with the EXAFS results, the model obtained included one predominating surface complex with the stoichiometry [triple bond]FeOGa(OH)2(-0.5) and the stability constant log beta(intr.) = -2.55 +/- 0.04 ([triple bond]FeOH(-0.5) + Ga3+ + 2H2O <--> [triple bond]FeOGa(OH)2(-0.5) + 3H+).     

Reverse Monte Carlo simulations, Raman scattering, and thermal studies of an amorphous Ge30Se70 alloy produced by mechanical alloying

The short- and intermediate-range orders of an amorphous Ge30Se70 alloy produced by mechanical alloying were studied by reverse Monte Carlo simulations of its x-ray total structure factor, Raman scattering, and differential scanning calorimetry. The simulations were used to compute the G(Ge-Ge) (RMC)(r), G(Ge-Se) (RMC)(r), and G(Se-Se) (RMC)(r) partial distribution functions and the S(Ge-Ge) (RMC)(K), S(Ge-Se) (RMC)(K), and S(Se-Se) (RMC)(K) partial structure factors. We calculated the coordination numbers and interatomic distances for the first and second neighbors and the bond-angle distribution functions Theta(ijl)(cos theta). The data obtained indicate that the structure of the alloy has important differences when compared to alloys prepared by other techniques. There are a high number of Se-Se pairs in the first shell, and some of the tetrahedral units formed seemed to be connected by Se-Se bridges.     

Three-dimensional structure of nanocomposites from atomic pair distribution function analysis: study of polyaniline and (polyaniline)(0.5)V(2)O(5) x 1.0 H(2)O

The three-dimensional structures of emeraldine base polyaniline (PANI) and (polyaniline)(0.5)V(2)O(5) x 1.0 H(2)O have been determined by total X-ray scattering experiments. Atomic pair distribution functions (PDF) were measured to obtain experimental observables against which structural models were tested and refined. The PDF approach is necessary because of the limited structural coherence in these nanostructured materials. Polyaniline possesses a well-defined local atomic arrangement that can be described in terms of an 84-atom orthorhombic unit cell. The nanocomposite (PANI)(0.5)V(2)O(5) x 1.0 H(2)O too is locally well ordered and may be described in terms of a small number of structure-sensible parameters. The PDF approach allows the construction of structure models of PANI and (PANI)(0.5)V(2)O(5) x 1.0 H(2)O on the basis of which important materials' properties can be explained predicted and possibly improved.     

A combined density functional and x-ray diffraction study of Pt nanoparticle structure

The structure of 1.7 nm Pt nanoparticles is investigated using x-ray diffraction (XRD) measurements and density functional theory (DFT) calculations. Two types of particles are compared, those made by solution chemistry which are capped either by thiol or amine ligands, and dendrimer encapsulated particles (DENs) which do not have capping ligands. All particles were dried before analyzing their structure. Pair distribution function (PDF) data from XRD measurements show that the ligand-capped particles are more disordered than the DENs. To determine the structure of the particles and the nature of the ligand-induced disorder, we use a hybrid reverse Monte Carlo approach. A weighted average of the calculated binding energy of the particles and a goodness-of-fit parameter to the PDF data is taken as the object function, which is minimized to determine the optimal structure. A scan over different weights gives the set of pareto optimal structures, which show how well simultaneous agreement can be reached to both experiment and theory. Using an embedded atom potential to sample configuration space and DFT to refine the optimal structures, we show that the DEN structure is most consistent with a face centered cubic lattice of truncated octahedral shape. The disorder induced by the capping ligands is consistent with surface relaxation of the particle rather than disorder of the crystal structure.     

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study.

The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.     

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study

The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.     

Cl/GaAs(111)表面近边X射线吸收精细结构的多重散射研究

利用多重散射团簇方法（MSC）计算了Cl/GaAs(111)吸附表面的Cl原子k边X射线吸收精细结构谱（NEXAFS）.阐明了NEXAFS谱中各个弱结构的物理起源.根据模型计算的结果与实验比较,求得吸附在顶位的氯原子和最近邻的镓原子的键长为（0.213±0.005）nm.这个结果在0.005 nm的误差范围内将广延X射线吸收精细结构（EXFAS）实验谱的Fourier变换结果（0.217 nm）和Slab模型计算的结果（0.208 nm）合理地联系起来.此外,MSC计算求得衬底表面层Ga－As键长为（0.235±0.005）nm,证实Cl吸附引起GaAs(111)表面驰豫.