Surface Structures from Direct Methods Using a Genetic Algorithm

1997 ◽  
Vol 3 (S2) ◽  
pp. 1047-1048
Author(s):  
E. Landree ◽  
C. Collazo-Davila ◽  
L. D. Marks
Keyword(s):  
Genetic Algorithm ◽  
Electron Scattering ◽  
Three Dimensional ◽  
Direct Methods ◽  
Surface Structures ◽  
Sampling Errors ◽  
X Ray Diffraction ◽  
X Ray ◽  
Search Routine ◽  
Surface Crystal

Two two-dimensional atomic models were constructed to test the application of Direct Methods for solving surface crystal structures (atomic positions are listed in Table 1). The use of Direct Methods to solve three dimensional structures from X-ray diffraction has been well established for several years. However to the best of our knowledge never before had this technique been applied to 2-D surface structures. A Genetic Algorithm (GA) search routine was implemented for exploring possible solutions.The models were constructed using electron scattering factors to calculate the intensities and phases for beams out to 1 Å resolution (Fig. 1). Since electron diffraction from surfaces has been shown to be nearly kinematical X-ray and electron scattering can be handled identically. An error term was applied to the generated intensities to simulate realistic sampling errors. The generated phases for each model were removed and later used to monitor the solutions calculated by the direct methods.

The crystal structure of gatehouseite

2011 ◽  
Vol 75 (6) ◽  
pp. 2823-2832
Author(s):  
P. Elliott ◽  
A. Pring
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
Chemical Analyses ◽  
X Ray Diffraction ◽  
X Ray ◽  
Manganese Phosphate ◽  
Phosphate Mineral ◽  
Unit Formula

AbstractThe crystal structure of the manganese phosphate mineral gatehouseite, ideally Mn52+(PO4)2(OH)4, space group P212121, a = 17.9733(18), b = 5.6916(11), c = 9.130(4) Å, V= 933.9(4) Å3, Z = 4, has been solved by direct methods and refined from single-crystal X-ray diffraction data (T = 293 K) to an R index of 3.76%. Gatehouseite is isostructural with arsenoclasite and with synthetic Mn52+(PO4)2(OH)4. The structure contains five octahedrally coordinated Mn sites, occupied by Mn plus very minor Mg with observed <Mn—O> distances from 2.163 to 2.239 Å. Two tetrahedrally coordinated P sites, occupied by P, Si and As, have <P—O> distances of 1.559 and 1.558 Å. The structure comprises two types of building unit. A strip of edge-sharing Mn(O,OH)6 octahedra, alternately one and two octahedra wide, extends along [010]. Chains of edge- and corner-shared Mn(O,OH)6 octahedra coupled by PO4 tetrahedra extend along [010]. By sharing octahedron and tetrahedron corners, these two units form a dense three-dimensional framework, which is further strengthened by weak hydrogen bonding. Chemical analyses by electron microprobe gave a unit formula of (Mn4.99Mg0.02)Σ5.01(P1.76Si0.07(As0.07)Σ2.03O8(OH)3.97.

scholarly journals SFX analysis of non-biological polycrystalline samples

IUCrJ ◽  
2015 ◽  
Vol 2 (3) ◽  
pp. 322-326 ◽  
Author(s):  
Tao Zhang ◽  
Shifeng Jin ◽  
Yuanxin Gu ◽  
Yao He ◽  
Ming Li ◽  
...  
Keyword(s):  
Single Crystal ◽  
Three Dimensional ◽  
Direct Methods ◽  
Test Sample ◽  
Monte Carlo Integration ◽  
X Ray Diffraction ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Serial Femtosecond Crystallography

Serial femtosecond crystallography (SFX) is capable of collecting three-dimensional single-crystal diffraction data using polycrystalline samples. This may dramatically enhance the power of X-ray powder diffraction. In this paper a test has been performed using simulated diffraction patterns. The test sample is a mixture of two zeolites with crystal grain sizes from 100 to 300 nm. X-ray diffraction snapshots by SFX were simulated and processed using the program suiteCrystFEL. Identification according to the primitive unit-cell volume determined from individual snapshots was able to separate the whole set of snapshots into two subsets, which correspond to the two zeolites in the sample. Monte Carlo integration inCrystFELwas then applied to them separately. This led to two sets of three-dimensional single-crystal diffraction intensities, based on which crystal structures of the two zeolites were solved easily by direct methods implemented in the programSHELXD.

Faster acquisition of structure-factor amplitudes in surface X-ray diffraction experiments

2004 ◽  
Vol 37 (3) ◽  
pp. 395-398 ◽  
Author(s):  
X. Torrelles ◽  
J. Rius
Keyword(s):  
Three Dimensional ◽  
Direct Methods ◽  
Lorentz Factor ◽  
Test Material ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Lack Of Information ◽  
Unit Cells ◽  
Order Of Magnitude

The traditional way of measuring intensities in surface X-ray diffraction experiments is by performing rocking scans. Owing to experimental time limitations, this rather slow procedure leads to incomplete data sets for large surface unit cells. This lack of information not only may affect adversely the accuracy of the refined atomic positions, but also hinders the application of three-dimensional direct methods of structure solution. Here the viability of the alternative data collection strategy proposed by Specht & Walker [J. Appl. Cryst.(1993),26, 166–171] is investigated by using as test material a 50 Å thick NBCO thin film grown on an SrTiO3(001) substrate. This procedure, which is based on stationaryLscans,i.e.the sample is kept fixed during theLscan, shortens the measuring time by an order of magnitude. In this study, special attention has been paid to the validation of the predicted theoretical Lorentz factor, which is specific for this experimental setup.

Crystal structure of 9-Oxofluorene-4-carboxylic acid

1981 ◽  
Vol 34 (5) ◽  
pp. 1143 ◽  
Author(s):  
CHL Kennard ◽  
G Smith ◽  
GF Katekar
Keyword(s):  
Crystal Structure ◽  
Carboxylic Acid ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
A Cell

The crystal structure of 9-oxofluorene-4-carboxylic acid has been determined by direct methods using three-dimensional X-ray diffraction data, and refined to R0·068 for 1323 'observed' reflections. Crystals are monoclinic, space group P21/c with 24 in a cell of dimensions a 3·843(3), b 7·986(5), c 3269(2) �, β 96·64(4)�. The molecules form centrosymmetric hydrogen-bonded cyclic dimers [O···O 2·642(3) �] with the plane of the carboxylic acid making an angle of 26·5� with that of the 9-oxofluorene group. Stacks of molecules form down the a axis with 3.843 �. separation.

Four interpenetrating hydrogen-bonded three-dimensional networks in divanillin

2018 ◽  
Vol 74 (12) ◽  
pp. 1768-1773
Author(s):  
Marcos R. Imer ◽  
Virginia Aldabalde ◽  
Silvina Pagola ◽  
Jacco van de Streek ◽  
Leopoldo Suescun
Keyword(s):  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
X Ray Diffraction ◽  
Interpenetrating Networks ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Translation Equivalent ◽  
Hydrogen Bonding Networks ◽  
Space Approach

The crystal structure of divainillin (systematic name: 6,6′-dihydroxy-5,5′-dimethoxy-[1,1′-biphenyl]-3,3′-dicarbaldehyde), C16H14O6, was determined from laboratory powder X-ray diffraction data using the software EXPO2013 (direct methods) and WinPSSP (direct-space approach). Divanillin molecules crystallize in the orthorhombic space group Pba2 (No. 32), with two molecules per unit cell (Z′ = 1 \over 2). Each divanillin molecule, with twofold symmetry, is linked through strong alcohol–aldehyde hydrogen bonds to four equivalent molecules, defining a three-dimensional hydrogen-bonding network, with rings made up of six divanillin units (a diamond-like arrangement). Each molecule is also connected through π–π interactions to a translation-equivalent molecule along c. Four consecutive molecules stacked along [001] belong to four different three-dimensional hydrogen-bonding networks defining a quadruple array of interpenetrating networks. This complex hydrogen-bonding array is proposed as an explanation for the aging process experienced by divanillin powders.

Crystal structure of (±)-2-[4-(4-chlorophenoxymethyl)phenoxy]propionic acid

1982 ◽  
Vol 35 (10) ◽  
pp. 2151 ◽  
Author(s):  
G Smith ◽  
CHL Kennard ◽  
WL Duax ◽  
DC Swenson
Keyword(s):  
Crystal Structure ◽  
Propionic Acid ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Side Chain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bonded

The crystal structure of (�)-2-[4-(4-chlorophenoxymethyl)phenoxy]propionic acid has been determined by direct methods using three-dimensional X-ray diffraction data. The crystals are triclinic, P1, Z 2, a 9.345(2), b 12,602(2), c 6.741(1) �, α 101.37(1), β 97.42(1), γ 101.75(1)�. The structure refined to give a final R 0.084 for 2172 observed reflections. The acid molecules form centrosymmetric hydrogen bonded cyclic dimers [O. . .O,2.619(4) �] about a centre of symmetry in the cell. The oxopropionic acid side chain has a synplanar-synplanar (carbonyl) conformation while the planar p-chlorophenoxymethyl substituent in the p-position has a synclinal orientation relative to the primary phenoxy residue.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

Chemical modification of the bacterial wall to determine sites of metal deposition

1978 ◽  
Vol 36 (2) ◽  
pp. 350-351
Author(s):  
T. J. Beveridge
Keyword(s):  
Electron Scattering ◽  
Metal Salt ◽  
Metal Deposition ◽  
Suitable Model ◽  
X Ray Diffraction ◽  
Subtilis Cell ◽  
Thin Sections ◽  
X Ray ◽  
Section Data ◽  
Metal Impregnation

The Bacillus subtilis cell wall provides a protective sacculus about the vital constituents of the bacterium and consists of a collection of anionic hetero- and homopolymers which are mainly polysaccharidic. We recently demonstrated that unfixed walls were able to trap and retain substantial amounts of metal when suspended in aqueous metal salt solutions. These walls were briefly mixed with low concentration metal solutions (5mM for 10 min at 22°C), were well washed with deionized distilled water, and the quantity of metal uptake (atomic absorption and X-ray fluorescence), the type of staining response (electron scattering profile of thin-sections), and the crystallinity of the deposition product (X-ray diffraction of embedded specimens) determined.Since most biological material possesses little electron scattering ability electron microscopists have been forced to depend on heavy metal impregnation of the specimen before obtaining thin-section data. Our experience with these walls suggested that they may provide a suitable model system with which to study the sites of reaction for this metal deposition.

Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

1985 ◽  
Vol 63 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
John F. Richardson ◽  
Ted S. Sorensen
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Chair Conformation ◽  
Molecular Structures ◽  
Boat Conformation ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

scholarly journals An investigation of polyhedral deformation in two mixed-metal diarsenates: SrZnAs2O7and BaCuAs2O7

2015 ◽  
Vol 71 (4) ◽  
pp. 330-337 ◽  
Author(s):  
Sabina Kovač ◽  
Ljiljana Karanović ◽  
Tamara Đorđević
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
General Formula ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Open Framework ◽  
Geometrical Characteristics ◽  
Barium Copper

Two isostructural diarsenates, SrZnAs2O7(strontium zinc diarsenate), (I), and BaCuAs2O7[barium copper(II) diarsenate], (II), have been synthesized under hydrothermal conditions and characterized by single-crystal X-ray diffraction. The three-dimensional open-framework crystal structure consists of corner-sharingM2O5(M2 = Zn or Cu) square pyramids and diarsenate (As2O7) groups. Each As2O7group shares its five corners with five differentM2O5square pyramids. The resulting framework delimits two types of tunnels aligned parallel to the [010] and [100] directions where the large divalent nine-coordinatedM1 (M1 = Sr or Ba) cations are located. The geometrical characteristics of theM1O9,M2O5and As2O7groups of known isostructural diarsenates, adopting the general formulaM1IIM2IIAs2O7(M1II= Sr, Ba, Pb;M2II= Mg, Co, Cu, Zn) and crystallizing in the space groupP21/n, are presented and discussed.

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