Direct methods and refinement in electron and X-ray crystallography – diketopiperazine revisited

2010 ◽  
Vol 225 (2-3) ◽  
Author(s):  
Douglas L. Dorset
Keyword(s):  
Direct Methods ◽  
X Ray ◽  
X Ray Crystallography

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

Reminiscences and discoveries: Dorothy Hodgkin and the Indian connection

1996 ◽  
Vol 50 (1) ◽  
pp. 115-127 ◽  
Keyword(s):  
Large Angle ◽  
Direct Methods ◽  
Statistical Fluctuation ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Angle Scattering ◽  
Molecular Sizes ◽  
Indian Institute Of Science

Dorothy Hodgkin - as crystallographer, scientist and human being - far surpasses most, and so it is not easy to write about her many-splendoured personality. Instead, my aim here will he to discuss her influence on the growth of X-ray crystallography in India, directly through those who worked with her and indirectly by her travelling all over this country. In such an account, one must be pardoned for some personal element creeping in. In the twenties, India had developed a fairly strong tradition in X-ray physics. The six-week visit of C.V. Raman to Europe in 1921 greatly changed his research interests. On seeing the blue of the Mediterranean he started his researches on the scattering of light in liquids which finally culminated in the discovery of what is now called the Raman Effect. His encounter with Sir William Bragg and his work on naphthalene structure started three lines of research in India. First, Raman fabricated an X-ray tube and was amongst the earliest to use X-ray diffraction as a structural tool to study liquids. He showed that while in large-angle scattering the haloes reflected specific molecular sizes and packing shapes, small-angle scattering was directly related to the statistical fluctuation of density in a liquid. Second, Raman knew that Bragg’s first structure of naphthalene was not consistent with its birefringence, while the second one was. With this as cue he and his school launched extensive studies on the optical and magnetic anisotropy of organic crystals to get vital information on the arrangements of molecules in the crystalline state. Third, one of his students, Kedareshwar Bannerjee, was amongst the earliest to probe into the problem of phase determination by direct methods and for this he used Bragg’s data on naphthalene. Unfortunately, in spite of this early lead, it was not until 1951 that the first crystal structure was solved in India using Fourier methods by Gopinath Kartha. The Indian Institute of Science (IISc) had great hopes of starting a powerful school of X-ray crystallography when G.N. Ramachandran came back from Cambridge. But he went over to Madras, and there he established one of the most renowned Schools of Biophysics. With Gopinath Kartha he solved the structure of collagen.

The Direct Methods of X-ray Crystallography

Science ◽  
1986 ◽  
Vol 233 (4760) ◽  
pp. 178-183 ◽  
Author(s):  
H. HAUPTMAN
Keyword(s):  
Direct Methods ◽  
X Ray ◽  
X Ray Crystallography

Ulrich Wolfgang Arndt. 23 April 1924 — 24 March 2006

2014 ◽  
Vol 60 ◽  
pp. 39-55
Author(s):  
R. A. Crowther ◽  
A. G. W. Leslie
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Direct Methods ◽  
Biological Molecules ◽  
Data Generation ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
Whole Process ◽  
Wide Range

Ulrich (Uli) Arndt was a physicist and engineer whose contributions to the development of a wide range of instrumentation for X-ray crystallography played an important part in our ability to solve the atomic structure of large biological molecules. Such detailed information about protein structures has for the past 50 years underpinned the huge advances in the field of molecular biology. His innovations spanned all aspects of data generation and collection, from improvements in X-ray tubes, through novel designs for diffractometers and cameras to film scanners and more direct methods of X-ray detection. When he started in the field, the intensities of individual X-ray reflections were often estimated by eye from films. By the end of his career the whole process of collecting from a crystal a three-dimensional data set, possibly comprising hundreds of thousands of measurements, was fully automated and very rapid.

Synthesis of meso-phenyl-4,6-dipyrrins, preparation of their Cu(II), Ni(II), and Zn(II) chelates, and structural characterization of bis[meso-phenyl-4,6-dipyrrinato]Ni(II)

1996 ◽  
Vol 74 (11) ◽  
pp. 2182-2193 ◽  
Author(s):  
Christian Brückner ◽  
Veranja Karunaratne ◽  
Steven J. Rettig ◽  
David Dolphin
Keyword(s):  
Dihedral Angle ◽  
Direct Methods ◽  
Metal Chelates ◽  
Central Metal ◽  
Full Matrix ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transition Metal Chelates ◽  
Square Planar

meso-Phenyldipyrromethanes can be oxidized by 2,6-dicyano-3,5-dichloro-para-benzoquinone (DDQ) to the corresponding meso-phenyldipyrrins. As expected, these novel, stable bipyrrolic pigments readily form metal chelates with copper(II), nickel(II), and zinc(II). Their UV–VIS spectra are compared with a series of known alkyl-substituted dipyrrin chelates and, based on the UV–VIS spectral analysis, the dihedral angle between the two ligands in the bis[meso-phenyldipyrrinato]Ni(II) complex was calculated to be 42°. The molecular structure of this complex was determined by X-ray crystallography, essentially confirming the calculation. Crystals of C30H22N4Ni are orthorhombic, a = 17.156(3), b = 35.217(1), c = 7.886(1) Å, Z = 8, space group Fddd. The structure was solved by direct methods and refined by full-matrix least-squares procedures to R = 0.040 and Rw = 0.031 for 1058 reflections with I ≥ 3σ(F2). The central nickel is coordinated in a distorted square-planar fashion by four nitrogens. The pair of the planar dipyrrinato ligands enclose a dihedral angle of 38.5°. This is the lowest angle reported for nickel(II) complexes of this kind. As a result of this, and in sharp contrast to previously described nickel(II) dipyrrin chelates, the central metal is diamagnetic. Key words: meso-phenyldipyrromethanes, meso-phenyldipyrrins, meso-phenyldipyrrinato transition metal chelates, X-ray crystallography.

Reactions of lignin model compounds with pulp bleaching chemicals. Cannizzaro-type reaction of tetrachloro-o-benzoquinone with alkali

1992 ◽  
Vol 70 (6) ◽  
pp. 1706-1710 ◽  
Author(s):  
A. Bruce McKague ◽  
Douglas W. Reeve ◽  
Steven J. Rettig ◽  
James Trotter
Keyword(s):  
Direct Methods ◽  
Aqueous Sodium Hydroxide ◽  
Pulp Bleaching ◽  
Model Compounds ◽  
Lignin Model Compounds ◽  
Full Matrix ◽  
Aqueous Sodium ◽  
X Ray ◽  
X Ray Crystallography ◽  
Lignin Model

Reaction of tetrachloro-o-benzoquinone 1 with aqueous sodium hydroxide resulted in a Cannizzaro-type disproportionation into tetrachloromuconic acid and tetrachlorocatechol. The tetrachloromuconic acid was isolated and identified by X-ray crystallography as the methyl ester of the cyclized lactone 3. Crystals of C7H3Cl3O4, 4, are orthorhombic, a = 9.991 (2), b = 7.981 (1), c = 24.626(2) Å, Z = 8, space group Pna21. The structure was solved by direct methods and was refined by full-matrix least-squares procedures to R = 0.033 for 1609 reflections with I ≥ 3σ(I).

scholarly journals X-ray crystal structure analysis of 5-bromospiro[indoline-3,7'-pyrano[3,2-C:5,6-C']dichromene]-2,6',8'-trione

2021 ◽  
Vol 12 (2) ◽  
pp. 187-191
Author(s):  
Varun Sharma ◽  
Bubun Banerjee ◽  
Gurpreet Kaur ◽  
Vivek Kumar Gupta
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
Crystal Structure Analysis ◽  
One Pot ◽  
X Ray ◽  
X Ray Crystallography ◽  
Naturally Occurring ◽  
Three Component Reaction ◽  
Ft Ir ◽  
Solvent Molecules

An analog of spirooxindole[pyrano-bis-2H-l-benzopyran] derivatives namely 5-bromospiro [indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione was synthesized via one-pot pseudo three-component reaction of one equivalent of 5-bromoisatin and two equivalents of 4-hydroxycoumarin using mandelic acid as a naturally occurring organo catalyst in aqueous ethanol under reflux conditions. The synthesized compound was characterized by FT-IR, 1H NMR, 13C NMR, and HRMS data. Crystal structure was determined by using single X-ray crystallography technique. It was found that the crystals are triclinic with space group P-1, C108H60Br4N4O29S2: a = 11.8333(6) Å, b = 12.8151(6) Å, c = 17.1798(8) Å, α = 77.317(4)°, β = 74.147(4)°, γ = 66.493(5)°, V = 2280.0(2) Å3, Z = 1, T = 149.99(10) K, μ(MoKα) = 1.902 mm-1, Dcalc = 1.647 g/cm3, 11545 reflections measured (3.836° ≤ 2Θ ≤ 50.998°), 8310 unique (Rint = 0.0488, Rsigma = 0.0875) which were used in all calculations. The final R1 was 0.0622 (I > 2σ(I)) and wR2 was 0.1994 (all data). The crystal structure was solved by direct methods and refined by full-matrix least-squares procedure to a final R-value of 0.0622 for 6264 observed reflections. The crystal structure was stabilized by an elaborate system of N-H···O, O-H···O, C-H···π, and π···π interactions involving solvent molecules to form supramolecular structure.

X-Ray structure determination of 1,2-anhydro-3,4:5,6-di-O-isopropylidene-1-C-nitro-D-mannitol

1988 ◽  
Vol 66 (7) ◽  
pp. 1600-1604 ◽  
Author(s):  
Walter A. Szarek ◽  
George W. Hay ◽  
Ramesh K. Sood ◽  
Konia Trouton ◽  
Suzanne Fortier
Keyword(s):  
Crystal Structure ◽  
Hydrogen Peroxide ◽  
Direct Methods ◽  
Major Product ◽  
Calculated Density ◽  
Aqueous Sodium ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cell Dimensions

The structure of the major product of the reaction of 1,2-dideoxy-3,4:5,6-di-O-isopropylidene-1-C-nitro-D-arabino-hex-1-enitol with 30% hydrogen peroxide and aqueous sodium hydrogencarbonate has been confirmed by X-ray crystallography to be that of 1,2-anhydro-3,4:5,6-di-O-isopropylidene-1-C-nitro-D-mannitol (2). The crystal structure of 2, C12H19NO7, is orthorhombic, P212121, with cell dimensions a = 10.269(3), b = 15.115(7), c = 9.295(8) Å, and Z = 4. The calculated density is Dx = 1.336 gcm−3. The structure was solved by direct methods and refined to a residual R = 0.052. The molecule has a 2G− conformation having bond lengths and angles in agreement with those observed in related structures, except for the C(1)—C(2), C(2)—C(3), and O(2N)—N bond distances which were found to be unusually small.

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