A database survey of molecular and crystallographic symmetry

2003 ◽  
Vol 59 (5) ◽  
pp. 634-640 ◽  
Author(s):  
Elna Pidcock ◽  
W. D. Samuel Motherwell ◽  
Jason C. Cole
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Relational Database ◽  
Acta Cryst ◽  
Wyckoff Position ◽  
Crystallographic Symmetry ◽  
Symmetry Of Molecules

The point of contact between molecular and crystallographic symmetries is that of the Wyckoff position, the position at which a molecule resides in a crystal structure. These Wyckoff positions may have the same symmetry as the molecules, some symmetry in common with the molecules or no symmetry at all. Using CSDSymmetry [Yao et al. (2002). Acta Cryst. B58, 640–646], a relational database containing information pertaining to the symmetry of molecules and the crystal structures that play host to them, the distribution of molecules over Wyckoff positions and the occupancy of Wyckoff positions in crystal structures is presented. Analysis of these data has led to the characterization of some relationships between molecular and crystallographic symmetry.

scholarly journals The preparation and characterization of SeCl3SbF6, improved syntheses of MCl3(As/Sb)F6 (M = S, Se), and the X-ray crystal structure determination of SeCl3AsF6 and a new phase of SBr3SbF6

1996 ◽  
Vol 74 (9) ◽  
pp. 1671-1681 ◽  
Author(s):  
Jack Passmore ◽  
Paul D. Boyle ◽  
Gabriele Schatte ◽  
Todd Way ◽  
T. Stanley Cameron
Keyword(s):  
Crystal Structure ◽  
Raman Spectroscopy ◽  
Crystal Structures ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Ft Raman Spectroscopy ◽  
New Phase ◽  
Ft Raman

Alternative and, in some cases, improved syntheses of the salts MX3(As/Sb)F6 (M = S, Se) and SCl3(SbCl6/AlCl4) are described. In addition, the synthesis of SeCl3SbF6 is reported. The compounds were characterized by FT–Raman spectroscopy and the X-ray crystal structures of SeCl3AsF6 (also 77Se NMR) and a new phase of SBr3SbF6 were determined. Crystals of SeCl3AsF6 and SBr3SbF6 are monoclinic, space group P21/c with [values for SBr3SbF6 in brackets] a = 7.678(1) [8.137(1)] Å, b = 9.380(3) [9.583(2)] Å, c = 11.920(3) [12.447(2)] Å, β = 98.19(2)° [97.36(1)]°, V = 849.72(3) [962.6(3)] Å3,z = 4, Dx = 2.925 [3.502] Mg m−3, R = 0.0525 [0.055], and Rw = 0.0554 [0.060] for 1151 [1472] observed reflections. Key words: MX3+ salts, FT–Raman spectroscopy, X-ray crystal structures of SeCl3AsF6, SBr3SbF6, and preparation of SeCl3SbF6.

Mono- and difunctional furan-based 1,2,3,5-dithiadiazolyl radicals; preparation and solid state structures of 2,5-[(S2N2C)OC4H2(CN2S2)] and 2,5-[(S2N2C)OC4H2(CN)]

1992 ◽  
Vol 70 (3) ◽  
pp. 919-925 ◽  
Author(s):  
A. Wallace Cordes ◽  
Charles M. Chamchoumis ◽  
Robin G. Hicks ◽  
Richard T. Oakley ◽  
Kelly M. Young ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Crystal Structures ◽  
Monoclinic Space Group ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
The Mean ◽  
Solid State Structures ◽  
Solid State Characterization

The preparation and solid state characterization of the bifunctional radical furan-2,5-bis(1,2,3,5-dithiadiazolyl) 2,5-[(S2N2C)OC4H2(CN2S2)] and the related monofunctional radical 2-cyanofuran-5-(1,2,3,5-dithiadiazolyl) 2,5-[(S2N2C)OC4H2(CN)] are described. The crystal structure of 2,5-[(S2N2C)OC4H2(CN2S2)] is orthorhombic, space group Pna21, and consists of interleaved arrays of dimers, for which the mean interannular [Formula: see text] contact is 3.137 Å. The crystal structure of the monofunctional radical 2,5-[(S2N2C)OC4H2(CN)] is monoclinic, space group P21/n, and consists of a ribbon-like network of dimers (mean interannular [Formula: see text] interconnected by close head-to-tail [Formula: see text] contacts. The dimer units form stacks parallel to z, with a mean interdimer [Formula: see text] separation of 3.956 Å. The similarities and differences between these two crystal structures and those of related benzene-substituted systems are discussed. Keywords: dithiadiazolyl radicals, furan-based diradicals, cyanofuran-based radicals, radical dimers, crystal structures.

scholarly journals Crystal structures of three functionalized chalcones: 4′-dimethylamino-3-nitrochalcone, 3-dimethylamino-3′-nitrochalcone and 3′-nitrochalcone

2020 ◽  
Vol 76 (10) ◽  
pp. 1599-1604
Author(s):  
Charlie L. Hall ◽  
Victoria Hamilton ◽  
Jason Potticary ◽  
Matthew E. Cremeens ◽  
Natalie E. Pridmore ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Functional Groups ◽  
Organic Molecules ◽  
Two Dimensional ◽  
Large Dataset ◽  
Acta Cryst ◽  
Small Organic Molecules ◽  
Hydrogen Bonding Interactions

The structure of three functionalized chalcones (1,3-diarylprop-2-en-1-ones), containing combinations of nitro and dimethylamino functional groups, are presented, namely, 1-[4-(dimethylamino)phenyl]-3-(3-nitrophenyl)prop-2-en-1-one, C17H16N2O3, Gp8m, 3-[3-(dimethylamino)phenyl]-1-(3-nitrophenyl)prop-2-en-1-one, C17H16N2O3, Hm7m and 1-(3-nitrophenyl)-3-phenylprop-2-en-1-one, C15H11NO3, Hm1-. Each of the molecules contains bonding motifs seen in previously solved crystal structures of functionalized chalcones, adding to the large dataset available for these small organic molecules. The structures of all three of the title compounds contain similar bonding motifs, resulting in two-dimensional planes of molecules formed via C—H...O hydrogen-bonding interactions involving the nitro- and ketone groups. The structure of Hm1- is very similar to the crystal structure of a previously solved isomer [Jing (2009). Acta Cryst. E65, o2510].

scholarly journals DSR: enhanced modelling and refinement of disordered structures withSHELXL

2015 ◽  
Vol 48 (3) ◽  
pp. 933-938 ◽  
Author(s):  
Daniel Kratzert ◽  
Julian J. Holstein ◽  
Ingo Krossing
Keyword(s):  
Crystal Structure ◽  
Computer Program ◽  
Crystal Structures ◽  
Model Building ◽  
Structure Refinement ◽  
Crystal Structure Refinement ◽  
Molecular Fragments ◽  
Acta Cryst ◽  
Disordered Structures ◽  
Placement Procedure

One of the remaining challenges in single-crystal structure refinement is the proper description of disorder in crystal structures. This paper describes a computer program that performs semi-automatic modelling of disordered moieties inSHELXL[Sheldrick (2015).Acta Cryst.C71, 3–8.]. The new program contains a database that includes molecular fragments and their corresponding stereochemical restraints, and a placement procedure to place these fragments on the desired position in the unit cell. The program is also suitable for speeding up model building of well ordered crystal structures.

Preparation and characterization of a series of bromodiphenyl(N,N-dialkyldithiocarbamato)tellurium(IV) compounds where R=Me, Et, i-Pr, Bu, and of chlorodiphenyl(N,N-dibutyldithiocarbamato)tellurium(IV) and diphenylbis(N,N-dibutyldithiocarbamato)tellurium(IV). Crystal structure of Ph2TeBr[S2CNEt2] and Ph2Te[S2CNBu2]2

1991 ◽  
Vol 69 (12) ◽  
pp. 1948-1956 ◽  
Author(s):  
Jane H. E. Bailey ◽  
John E. Drake ◽  
Maria L. Y. Wong
Keyword(s):  
Crystal Structure ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Crystal Structures ◽  
Vibrational Spectroscopy ◽  
Elemental Analysis ◽  
Reductive Elimination ◽  
Cell Parameters ◽  
Nuclear Magnetic Resonance Spectra

The series Ph2TeBr[S2CNR2], where R = Bu, Pr, i-Pr, Et, and Me, as well as Ph2TeCl[S2CNR2] and Ph2Te[S2CNR2]2, where R=Bu, Pr, have been synthesized and characterized by elemental analysis and vibrational spectroscopy. Comparisons of the effect of changing R groups and halogen atoms can be made based on the two crystal structures determined herein along with earlier work. The geometry about tellurium is consistent with that of a distorted sawhorse structure where the dithiocarbamate groups are monodentate (or anisobidentate). The crystal structures of Ph2TeBr[S2CNEt2], 4, and Ph2Te[S2CNBu2]2, 7, were completed. The cell parameters for 4 are a = 11.204(3) Å, b = 14.106(11) Å, c = 13.867(10) Å, α = 99.62(6)°, β = 102.76(5)°, γ = 87.73(4)°, V = 2107 Å3, Z = 4, R = 0.0448, and Rw = 0.0489 and for 7 are a = 19.392(6) Å, b = 9.622(2) Å, c = 19.089(6) Å, β = 104.70(2)°, V = 3445(2) Å3, Z = 4, R = 0.0397, and Rw = 0.0439. Nuclear magnetic resonance spectra are not simple and indicate that several species are present in solution, as rearrangements and reductive elimination take place. Key words: structure, tellurium, bromo, diphenyl, dialkyldithiocarbamato.

scholarly journals Crystal structures of bis(phenoxy)silicon phthalocyanines: increasing π–π interactions, solubility and disorder and no halogen bonding observed

2016 ◽  
Vol 72 (7) ◽  
pp. 988-994 ◽  
Author(s):  
Benoît H. Lessard ◽  
Alan J. Lough ◽  
Timothy P. Bender
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Structures ◽  
Halogen Bonding ◽  
X Ray Diffraction ◽  
X Ray ◽  
Π Interactions ◽  
Silicon Phthalocyanines ◽  
Solution Processable

We report the syntheses and characterization of three solution-processable phenoxy silicon phthalocyanines (SiPcs), namely bis(3-methylphenoxy)(phthalocyanine)silicon [(3MP)2-SiPc], C46H30N8O2Si, bis(2-sec-butylphenoxy)(phthalocyanine)silicon [(2secBP)2-SiPc], C44H24I2N8O2Si, and bis(3-iodophenoxy)(phthalocyanine)silicon [(3IP)2-SiPc], C52H42N8O2Si. Crystals grown of these compounds were characterized by single-crystal X-ray diffraction and the π–π interactions between the aromatic SiPc cores were studied. It was determined that (3MP)2-SiPc has similar interactions to previously reported bis(3,4,5-trifluorophenoxy)silicon phthalocyanines [(345 F)2-SiPc] with significant π–π interactions between the SiPc groups. (3IP)2-SiPc and (2secBP)2-SiPc both experienced a parallel stacking of two of the peripheral aromatic groups. In all three cases, the solubility of these molecules was increased by the addition of phenoxy groups while maintaining π–π interactions between the aromatic SiPc groups. The solubility of (2secBP)2-SiPc was significantly higher than other bis-phenoxy-SiPcs and this was exemplified by the higher observed disorder within the crystal structure.

Polymorphism of 7-dimethylaminocyclopenta[c]coumarin: packing analysis and generation of trial crystal structures

1996 ◽  
Vol 52 (1) ◽  
pp. 201-208 ◽  
Author(s):  
A. Gavezzotti
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Acta Cryst ◽  
Structure Generation ◽  
Space Groups ◽  
Energy Hypersurface ◽  
Packing Analysis ◽  
Potential Energy Hypersurface

The crystal structures of two polymorphs of the title compound [Pbca and Pna21; Jasinski & Woudenberg (1995). Acta Cryst. C51, 107–109] were analysed. Packing energies and indices were compared. Molecules in the two forms show a slight conformational difference; both conformers were packed in some of the most frequent space groups for organic molecules (P21, P21/c, P212121 and Pna21) using a computer program for crystal structure generation and prediction (PROMET3). The results of such calculations are used to provide tentative explanations for the preference of the two conformers for centrosymmetric and non-centrosymmetric space groups. Several comments on general problems encountered in crystal structure prediction are also presented, concerning in particular the multi-minima structure of the potential energy hypersurface.

Crystal structures of a β-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulfide bond-mediated dimeric forms

Glycobiology ◽  
2020 ◽  
Vol 30 (7) ◽  
pp. 474-488 ◽  
Author(s):  
Farha Khan ◽  
Devanshu Kurre ◽  
K Suguna
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Entamoeba Histolytica ◽  
Disulfide Bond ◽  
Structural Basis ◽  
Free Form ◽  
Biophysical Characterization ◽  
Biophysical Studies ◽  
First Time

Abstract β-Trefoil lectins are galactose/N-acetyl galactosamine specific lectins, which are widely distributed across all kingdoms of life and are known to perform several important functions. However, there is no report available on the characterization of these lectins from protozoans. We have performed structural and biophysical studies on a β-trefoil lectin from Entamoeba histolytica (EntTref), which exists as a mixture of monomers and dimers in solution. Further, we have determined the affinities of EntTref for rhamnose, galactose and different galactose-linked sugars. We obtained the crystal structure of EntTref in a sugar-free form (EntTref_apo) and a rhamnose-bound form (EntTref_rham). A novel Cys residue-mediated dimerization was revealed in the crystal structure of EntTref_apo while the structure of EntTref_rham provided the structural basis for the recognition of rhamnose by a β-trefoil lectin for the first time. To the best of our knowledge, this is the only report of the structural, functional and biophysical characterization of a β-trefoil lectin from a protozoan source and the first report of Cys-mediated dimerization in this class of lectins.

Synthesis, Crystal Structures and Characterization of a New Antitumor Cu(II) Complex with N-sulfonamide Ligand

2018 ◽  
Vol 69 (6) ◽  
pp. 1407-1410
Author(s):  
Adriana Corina Hangan ◽  
Alexandru Turza ◽  
Roxana Liana Stan ◽  
Luminita Simona Oprean
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Metal Ion ◽  
Planar Geometry ◽  
X Ray ◽  
Magnetic Methods ◽  
Square Planar ◽  
Ft Ir

A new Cu(II) complex with N-sulfonamide ligand, [Cu(N-(5-(4-methylphenyl)-[1,3,4]-thiadiazole-2-yl)-toluenesulfonamidate)4]((CH3)2NH2+)2(complex) has been synthesized and characterized. The X-ray crystal structure of the complex has been determined. The Cu(II) ion is four-coordinated, forming a CuN4 chromophore. The ligand acts as monodentate, coordinating the metal ion through a single Nthiadiazole atom. The complex has a square planar geometry. The characterization of the complex has been studied by FT-IR, electronic, EPR spectroscopic and magnetic methods.

An enantiomerically pure P-stereogenic bisphosphine: (S,S)-ethylenebis[(2-methylphenyl)phenylphosphine] (o-tolyl-DiPAMP)

2014 ◽  
Vol 70 (12) ◽  
pp. 1174-1177
Author(s):  
Wioletta Bendzińska-Berus ◽  
Magdalena Kaik-King ◽  
Gary King ◽  
Urszula Rychlewska
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Research Program ◽  
Structure Determination ◽  
Title Compound ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
Enantiomerically Pure ◽  
X Ray

In connection with a research program involving the synthesis, structure determination, reactivity and ability to coordinate to metal centres of chiral bisphosphine ligands, we have synthesized and structurally characterized, by means of single-crystal X-ray diffraction analysis, the title compound {systematic name: (S,S)-(ethane-1,2-diyl)bis[(2-methylphenyl)phenylphosphane], abbreviated aso-tolyl-DiPAMP}, C28H28P2. So far, neither the free bisphosphine (DiPAMP) nor analogues that incorporate the ethylenebisphosphine frame have had their crystal structures reported. The investigated compound forms crystals which are isostructural with the bisphosphine dioxide analogue [Kinget al.(2007).Acta Cryst.E63, o3278], despite the involvement of the dioxide in C—H...O(=P) hydrogen bonds and the lack of similar hydrogen bonds in the investigated crystal structure. In both molecules, the P—C—C—P chain is in atransconformation, extended further at both ends by one of the two P—Cipsobonds. The planes of the phenyl ando-tolyl rings attached to the same P atom are nearly perpendicular to one another. Both crystal structures are mainly stabilized by dispersive interactions.

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