Solving crystal structures inP1: an automated procedure for finding an allowed origin in the correct space group

2000 ◽  
Vol 33 (2) ◽  
pp. 307-311 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Model ◽  
Structure Refinement ◽  
Human Intervention ◽  
Space Group ◽  
Space Groups ◽  
Structure Solution ◽  
Actual Space ◽  
Complex Crystal

Crystal structure solution inP1 may be particularly suitable for complex crystal structures crystallizing in other space groups. However, additional efforts and human intervention are often necessary to locate correctly the structural model so obtained with respect to an allowed origin of the actual space group. An automatic procedure is described which is able to perform such a task, allowing the routine passage to the correct space group and the subsequent structure refinement. Some tests are presented proving the effectiveness of the procedure.

Phosphanimin-Komplexe von Mangan(II)halogeniden. Die Kristallstrukturen von [MnCl2(Me3SiNPEt3)]2, [Mnl2(Me3SiNPEt3)2] und [MnI2(Me2Si(NPEt3)2)] / Phosphaneimine Complexes of Manganese(II)halides. The Crystal Structures of [MnCl2(Me3SiNPEt3)]2, [Mnl2(Me3SiNPEt3)2] and [MnI2(Me2Si(NPEt3)2)]

1995 ◽  
Vol 50 (8) ◽  
pp. 1215-1221 ◽  
Author(s):  
Hans-Joachim Mai ◽  
Sigrid Wocadlo ◽  
Werner Massa ◽  
Frank Weller ◽  
Kurt Dehnicke ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Decomposition ◽  
Ir Spectroscopy ◽  
Crystal Structures ◽  
Structure Refinement ◽  
Chelate Complex ◽  
Space Group ◽  
Bond Lengths ◽  
Structure Solution ◽  
Structure Determinations

The phosphaneimine complexes [MnCl2(Me3SiNPEt3)]2 (1) and [MnI2(Me3SiNPEt3)2] (2) have been prepared by the reaction of Me3SiNPEt3 with MnCl2 and Mnl2, respectively. Thermal decomposition of 2 leads to the chelate complex [MnI2(Me2Si(NPEt3)2)] (3) by cleaving SiMe4. The complexes are characterized by IR spectroscopy and by crystal structure determinations. 1: Space group P21/c, Z = 4, structure solution with 5062 observed unique reflections, R = 0.047. Lattice dimensions at -55 °C: a = 1175.8(5), b = 1634.5(2), c = 1740.2(8), β = 99.58(2)°. 1 forms dimeric molecules via chloro bridges and a cis-arrangement of the Me3SiNPEt3 donor molecules with Mn-N bond lengths of 210.4(5) and 208.2(4) pm. 2: Space group P 41212, Z = 4, structure refinement with 1633 independent reflections, 1072 observed unique reflections, R = 0.053. Lattice dimensions at -60 °C: a = b = 949.5(1), c = 3345.2(7) pm. 2 forms monomeric molecules with tetrahedrally coordinated Mn atoms and Mn-N bond lengths of 220.7(13) pm. 3: Space group P21/c, Z = 4, structure refinement with 8419 independent reflections, 4584 observed unique reflections, R = 0.047. Lattice dimensions at 20 °C: a = 1343.3(1), b = 2508.2(2), c = 1535.1(1) pm, β = 91.742(5)°. 3 forms monomeric molecules with the [Me2Si(NPEt3)2] ligand bound in a chelating fashion with Mn-N bond lengths of 212.9 pm in average.

μ2-Halogenokomplexe von N-Bromsuccinimid und N-Bromphthalimid. Die Kristallstrukturen von PPh4[X(N-Bromsuccinimid)2] und von PPh4[X(N-Bromphthalimid)2] mit X = CI und Br / μ2-Halogeno Complexes of N-Bromosuccinimide and N-Bromophthalimide. The Crystal Structures of PPh4 [X(N-Bromosuccinimide)2] and PPh4 [X(N-Brom ophthalimide)2] with X = Cl and Br

1994 ◽  
Vol 49 (5) ◽  
pp. 593-601 ◽  
Author(s):  
Mitra Ghassemzadeh ◽  
Klaus Harms ◽  
Kurt Dehnicke ◽  
Dieter Fenske
Keyword(s):  
Crystal Structure ◽  
Ir Spectroscopy ◽  
Crystal Structures ◽  
Yellow Crystal ◽  
Halide Ions ◽  
Space Group ◽  
Bond Angles ◽  
Structure Solution ◽  
Structure Determinations ◽  
Acetonitrile Solutions

The μ2-halogeno complexes PPh4[X(N-bromosuccinimide)2] and PPh4[X(N-bromophthali- mide)2] with X = Cl and Br have been prepared by reactions of N-bromosuccinimide and N-bromophthalimide, respectively, with the corresponding tetraphenylphosphonium halides PPh4X in acetonitrile solutions. The compounds form pale yellow crystal needles, which were characterized by IR spectroscopy and by crystal structure determinations. PPh4[Cl(N-Bromosuccinimide)2] (1): Space group P21/n, Z = 4, structure solution with 2516 observed unique reflections, R = 0.040. Lattice dimensions at -25 °C: a = 1775.9(1), b = 764.3(1), c = 2341.7(2) pm, β = 101.84(1)°. PPh4[Br(N-Bromosuccinimide)2] (2): Space group P21/n, Z = 4, structure solution with 5620 observed unique reflections, R = 0.061. Lattice dimensions at 20 °C: a = 1776.9(9), b = 762.2(3), c = 2331(1) pm, β = 103.02(3)°. PPh4[Cl(N-Bromophthalimide)2] (3): Space group P1̅, Z = 4, structure solution with 3812 observed unique reflections, R = 0.039. Lattice dimensions at -50 °C: a = 918.5(2), b = 1115.0(3), c = 2584.4(5) pm, α = 88.22(3)°, β = 83.20(3)°, γ = 85.10(3)°. PPh4[Br(N-Bromophthalimide)2] (4): Space group P1̅, Z = 2, structure solution with 3413 observed unique reflections, R = 0.044. Lattice dimensions at -50 °C: a = 1120.2(2), b = 1308.6(3), c = 1343.2(3) pm, α = 105.10(3)°, β = 104.16(3)°, γ = 92.99(3)°. The structures of 1-4 consist of PPh4+ ions, anions [X(N-bromosuccinimide)2]- and [X(N-bromophthalimide)2]-, respectively, in which the halide ions X- are coordinated by the bromine atoms of N-bromosuccinimide and N-bromophthalimide molecules, respectively. The bond angles Br···X···Br are 86.48(5)° for 1, 85.1(1)° for 2, 102.31(6)° and 93.61(6)° for 3, and 91.86(4)° for 4. The bond angles N-Br···X are nearly linear.

scholarly journals Crystal structure and XANES investigation of petzite, Ag3AuTe2

2019 ◽  
Vol 75 (2) ◽  
pp. 273-278
Author(s):  
Hidetomo Hongu ◽  
Akira Yoshiasa ◽  
Massimo Nespolo ◽  
Tsubasa Tobase ◽  
Makoto Tokuda ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Structures ◽  
Chemical Bonding ◽  
Structure Refinement ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Absolute Structure ◽  
Golden Mile

Petzite, Ag3AuTe2, crystallizes in the space group I4132, which is a Sohncke type of space group where chiral crystal structures can occur. The structure refinement of petzite reported long ago [Frueh (1959). Am. Mineral. 44, 693–701] did not provide any information about the absolute structure. A new single-crystal X-ray diffraction refinement has now been performed on a sample from Lake View Mine, Golden Mile, Kalgoorlie, Australia, which has resulted in a reliable absolute structure [a Flack parameter of 0.05 (3)], although this corresponds to the opposite enantiomorph reported previously. The minimum Te–Te distance is 3.767 (3) Å, slightly shorter than the van der Waals bonding distance, which suggests a weak interaction between the two chalcogens. XANES spectra near the Au and Te L III edges suggest that the chemical-bonding character of Au in petzite is more metallic than in other gold minerals.

From structure topology to chemical composition. XI. Titanium silicates: crystal structures of innelite-1T and innelite-2M from the Inagli massif, Yakutia, Russia, and the crystal chemistry of innelite

2011 ◽  
Vol 75 (4) ◽  
pp. 2495-2518 ◽  
Author(s):  
E. Sokolova ◽  
F. Cámara ◽  
F. C. Hawthorne
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Microprobe Analysis ◽  
Electron Microprobe Analysis ◽  
Structure Refinement ◽  
Titanium Silicate ◽  
Space Group ◽  
Group Iii ◽  
Structure Topology ◽  
Titanium Silicates

AbstractThe crystal structures of two polytypes of innelite, ideally Ba4Ti2Na2M2+Ti(Si2O7)2[(SO4) (PO4)]O2[O(OH)] where M2+ = Mn, Fe2+, Mg, Ca: innelite-1T, a 5.4234(9), b 7.131(1), c 14.785(3) Å, α 98.442(4), β 94.579(3), γ 90.009(4)°, V 563.7(3) Å3, space group P1̄, Dcalc = 4.028 g/cm3, Z = 1; and innelite-2M, a 5.4206(8), b 7.125(1), c 29.314(4) Å, 0 94.698(3)°, V 1128.3(2) Å3, space group P2/c, Dcalc.= 4.024 g/cm3, Z = 2, from the Inagli massif, Yakutia, Russia, have been refined to R values of 8.99 and 7.60%, respectively. Electron-microprobe analysis gave the empirical formula for innelite as (Ba3.94Sr0.06)Σ4.00(Na2.16Mn0.382+Fe2+0.17Mg0.15Ca0.10☐0.04)Σ3(Ti2.97Nb0.02Al0.02)Σ3.01Si4.01 (S1.02P0.81☐0.17)Σ2H1.84O25.79F0.21 which is equivalent to (Ba3.94Sr0.06)Σ4.00(Ti1.97Nb0.02Al0.02)Σ2.01 [(OH0.99F0.21)Σ1.20O0.80], calculated on the basis of 26 (O + F) anions, with H2O calculated from structure refinement. The crystal structure of innelite is a combination of a TS (titanium silicate) block and an I (intermediate) block. The TS block consists of HOH sheets (H-heteropolyhedral, O-octahedral) and exhibits linkage and stereochemistry typical for Ti-disilicate minerals of Group III (Ti = 3 a.p.f.u.): two H sheets connect to the O sheet such that two (Si2O7) groups link to the trans edges of a Ti octahedron of the O sheet. The I block contains T sites, statistically occupied by S and P, and Ba atoms. In the structures of innelite-1T and innelite-2M, TS blocks are related by an inversion centre and a cy glide plane, respectively. HRTEM images show a coherent intergrowth of the two polytypes, together with an as-yet unidentified ∼10 Å phase.

scholarly journals Improved crystal structure solution from powder diffraction data by the use of conformational information

2017 ◽  
Vol 50 (5) ◽  
pp. 1421-1427 ◽  
Author(s):  
Elena A. Kabova ◽  
Jason C. Cole ◽  
Oliver Korb ◽  
Adrian C. Williams ◽  
Kenneth Shankland
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Structure Determination ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Structural Database ◽  
Complex Crystal

The effect of introducing conformational information to theDASHimplementation of crystal structure determination from powder diffraction data is investigated using 51 crystal structures, with the aim of allowing increasingly complex crystal structures to be solved more easily. The findings confirm that conformational information derived from the Cambridge Structural Database is indeed of value, considerably increasing the chances of obtaining a successful structure determination. Its routine use is therefore encouraged.

scholarly journals Symmetry Relations Between Space Groups in Layered Germanate Structures: Modeling Crystal Structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C1763-C1763
Author(s):  
Nelly Flores-Sanchez ◽  
Ivonne Rosales ◽  
Lauro Bucio
Keyword(s):  
Crystal Structures ◽  
Rietveld Refinement ◽  
Structural Model ◽  
Structural Data ◽  
X Rays ◽  
Monoclinic System ◽  
Space Group ◽  
Space Groups ◽  
Group Type ◽  
Symmetry Relations

Structural models for the new layered germanates ScInGe2O7 and ScFeGe2O7 were analyzed within the framework of symmetry relations between space groups. These compounds were supposed to be hettotypes of the thortveitite mineral, (Sc,Y)2Si2O7, which was considered as the aristotype. Thortveitite crystallizes in the monoclinic system, and the symmetry is described by the space group type C2/m. Other monoclinic hettotypes for the thortveitite are FeInGe2O7 (PDF 01-070-8447, ICSD - 94487), space group C2/m (No. 12); TbInGe2O7 (PDF 01-072-6515, ICSD - 96360), space group C2/c (No. 15); and FeYGe2O7 (PDF 01-072-6099, ICSD - 95935), space group P21/m (No. 11). All these space groups are related by symmetry. By the use of these relations, we proposed starting models for the crystal structures of ScInGe2O7 and ScFeGe2O7. For ScInGe2O7 this was found to be isostructural to FeInGe2O7 reported by our laboratory [1]. The structural data for this compound were obtained by conventional Rietveld refinement of the powder diffraction data of X-rays, using the GSAS program and EXPGUI [2, 3] interface. For ScFeGe2O7 the symmetry related structural model was found in the triclinic system by symmetry reduction from the space group C2/m (unique axis b) to the triclinic space group P1 (figure 1). Rietveld refinement was performed reaching to the following results: lattice parameters a = 5.3434 (8), b = 5.3145 (8), c = 4.8732 (7 ) Å, α = 99 468 (2), β = 97 257 (2), γ = 104 609 (2)0, V = 130.03 (5) A3, Z = 1; WRp = 0.047, Rp = 0.04 and reduced χ2 of 2.176 for 64 variables. This study was sponsored by CONACyT project CB-2011/167624.

scholarly journals Crystal chemistry of natural layered double hydroxides. 5. Single-crystal structure refinement of hydrotalcite, [Mg6Al2(OH)16](CO3)(H2O)4

2018 ◽  
Vol 83 (02) ◽  
pp. 269-280 ◽  
Author(s):  
Elena S. Zhitova ◽  
Sergey V. Krivovichev ◽  
Igor Pekov ◽  
H. Christopher Greenwell
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Structures ◽  
Structure Refinement ◽  
Unit Cell ◽  
Single Crystal Structure ◽  
Unit Cell Parameters ◽  
Diagnostic Features ◽  
Space Group ◽  
Cell Parameters

AbstractHydrotalcite, ideally [Mg6Al2(OH)16](CO3)(H2O)4, was studied in samples from Dypingdal, Snarum, Norway (3R and 2H), Zelentsovskaya pit (2H) and Praskovie–Evgenievskaya pit (2H) (both Southern Urals, Russia), Talnakh, Siberia, Russia (3R), Khibiny, Kola, Russia (3R), and St. Lawrence, New York, USA (3R and 2H). Two polytypes, 3R and 2H (both ‘classical’), were confirmed on the basis of single-crystal and powder X-ray diffraction data. Their chemical composition was studied by electron-microprobe analysis, infrared spectroscopy, differential scanning calorimetry, and thermogravimetric analysis. The crystal structure of hydrotalcite-3R was solved by direct methods in the space group R$ {\bar 3} $m on three crystals (two data collections at 290 K and one at 120 K). The unit-cell parameters are as follows (290/290/120 K): a = 3.0728(9)/3.0626(3)/3.0617(4), c = 23.326(9)/23.313(3)/23.203(3) Å and V = 190.7(1)/189.37(4)/188.36(4) Å3. The crystal structures were refined on the basis of 304/150/101 reflections to R1 = 0.075/0.041/0.038. Hydrotalcite-2H crystallises in the P63/mmc space group; unit-cell parameters for two crystals are (data collection at 290 K and 93 K): a = 3.046(1)/3.0521(9), c = 15.447(6)/15.439(4) Å, V = 124.39(8)/124.55(8) Å3. The crystal structures were refined on the basis of 160/142 reflections to R1 = 0.077/0.059. This paper reports the first single-crystal structure data on hydrotalcite. Hydrotalcite distribution in Nature, diagnostic features, polytypism, interlayer topology and localisation of M2+–M3+ cations within metal hydroxide layers are discussed.

Die Kristallstrukturen von Verbindungen des Typs A2TeX6 (A = K, NH4, Rb, Cs; X = Cl, Br, I) / The Crystal Structures of Compounds A2TeX6 (A = K, NH4, Rb, Cs; X = Cl, Br, I)

1989 ◽  
Vol 44 (10) ◽  
pp. 1187-1194 ◽  
Author(s):  
Walter Abriel ◽  
André du Bois
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Crystal Structures ◽  
Soft Mode ◽  
Type Structure ◽  
Ionic Radii ◽  
Space Group ◽  
Space Groups ◽  
Structure Space

With the determination of the crystal structure of (NH4)2TeI6 the list of the descriptions of A2TeX6 structures is further completed. At 293 K three structure types are observed with an antifluorite packing of cations and anions: The cubic K2PtCl6 type structure (space group Fm 3̄ m, Z = 4), the tetragonal Rb2TeI6 type structure (space group P4/mnc, Z = 2), and the monoclinic K2TeBr6 type structure (space group P21/n, Z = 2). The latter type was found for (NH4)2TeI6 with a = 8.0694(7), b = 8.0926(9), c = 11.7498(8) Å and β = 89.605(8)° and refined to a final Rw of 0.065. From ionic radii ratios the symmetry of the A2MX6 type structures can be predicted including a prediction of low temperature instability (soft mode condensation). Group-subgroup relationships connect the corresponding space groups and the space groups of the high/low temperature polymorphs.

scholarly journals One molecule, three crystal structures: conformational trimorphism of N-[(1S)-1-phenylethyl]benzamide

2020 ◽  
Vol 76 (8) ◽  
pp. 1229-1233
Author(s):  
Fermin Flores Manuel ◽  
Martha Sosa Rivadeneyra ◽  
Sylvain Bernès
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Solvent Mixtures ◽  
Screw Axis ◽  
Intermolecular Hydrogen Bonds ◽  
Space Group ◽  
Space Groups ◽  
Compound C ◽  
Chain Axis ◽  
Phenyl Rings

The title compound, C15H15NO, is an enantiopure small molecule, which has been synthesized many times, although its crystal structure was never determined. By recrystallization from a variety of solvent mixtures (pure acetonitrile, ethanol–water, toluene–ethanol, THF–methanol), we obtained three unsolvated polymorphs, in space groups P21 and P212121. Form I is obtained from acetonitrile, without admixture of other forms, whereas forms II and III are obtained simultaneously by concomitant crystallizations from alcohol-based solvent mixtures. All forms share the same supramolecular structure, based on infinite C 1 1(4) chain motifs formed by N—H...O intermolecular hydrogen bonds, as usual for non-sterically hindered amides. However, a conformational modification of the molecular structure, related to the rotation of the phenyl rings, alters the packing of the chains in the crystal structures. The orientation of the chain axis is perpendicular and parallel to the crystallographic twofold screw axis of space group P21 in forms I and II, respectively. As for form III, the asymmetric unit contains two independent molecules forming parallel chains in space group P212121, and the crystal structure combines features of monoclinic forms I and II.

Structure refinement of a twinned pseudo-symmetric crystal of [Mn(C10H24N4)(NCO)2]+·ClO_4^-

2005 ◽  
Vol 61 (4) ◽  
pp. 407-417 ◽  
Author(s):  
Alan David Rae ◽  
Susanne Mossin ◽  
Henning Osholm Sørensen
Keyword(s):  
Structure Refinement ◽  
Irreducible Representations ◽  
Minor Components ◽  
Hierarchical Approach ◽  
Space Group ◽  
Space Groups ◽  
Final Structure ◽  
Structure Solution

The crystal studied is a 0.545 (1):0.455 twin, space group C\bar 1, Z = 16, and is a commensurate occupational and displacive modulation of a Z = 4 idealized parent structure with the space group A2/a and a p = a/2, b p = b/2, c p = c. A hierarchical approach to solution and refinement led sequentially to structures in the space groups A2/a, P21/n, P\bar 1 and finally C\bar 1. The major and minor components of the reflection intensities could be identified using irreducible representations of A2/a and P21/n, which in turn suggested suitable constraints and restraints for optimizing the refinement pathway. Comparative refinement was used to show the correctness of the final structure solution and how appropriately chosen constrained refinement allowed an escape from a false minima.

Sign in / Sign up

Export Citation Format

Share Document