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.

A Comparison of Small Angle Neutron Scattering and X-Ray Diffraction Studies of Cobalt Precipitates in A Cu-0.95 at. % Co Alloy

1986 ◽  
Vol 82 ◽  
Author(s):  
S. Spooner ◽  
S. Iida ◽  
B. C. Larson
Keyword(s):  
Small Angle ◽  
Large Angle ◽  
Detailed Comparison ◽  
Scattering Data ◽  
Single Crystal Sample ◽  
X Ray Diffraction ◽  
Data Set ◽  
Crystal Sample ◽  
X Ray ◽  
Angle Scattering

ABSTRACTA detailed comparison of small-angle scattering (SANS) and large angle x-ray diffraction methods of characterization of precipitates was undertaken. Cobalt-rich precipitates on the order of 50 Å developed after a 17 hour anneal at 570°C were studied in a single crystal sample with SANS and with diffuse x-ray scattering near the (400)Bragg peak. Each scattering data set was analyzed independently in terms of a distribution of precipitate sizes; a detailed comparison is made of the size distribution obtained. A small interparticle interference effect is seen.

Large-angle convergent-beam setup for femtosecond X-ray crystallography

2003 ◽  
Vol 36 (2) ◽  
pp. 348-349 ◽  
Author(s):  
Davide Boschetto ◽  
Christian Rischel ◽  
I. Uschmann ◽  
J. Perez ◽  
S. Fourmaux ◽  
...  
Keyword(s):  
Small Molecule ◽  
Large Angle ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Beam Geometry ◽  
Convergent Beam ◽  
The Way

It is demonstrated how femtosecond plasma X-ray sources can be used to record X-ray diffraction images with many simultaneous reflections. A convergent-beam geometry was implemented and tested with a crystal of a small molecule [Fe-py3(tren)] as well as with a crystal of the protein lysozyme. The results pave the way for femtosecond X-ray crystallography.

Inorganic Crystal Structures Solved from EM Images and Refined to 0.02 À Accuracy Against Electron Diffraction Data

1997 ◽  
Vol 3 (S2) ◽  
pp. 1141-1142
Author(s):  
Sven Hovmöller ◽  
Xiaodong Zou ◽  
Thomas Weirich
Keyword(s):  
Single Crystal ◽  
Organic Molecules ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Crystal Data ◽  
Phase Problem ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Inorganic Crystal

Single crystal X-ray diffraction is the traditional method for accurate crystal structure determination. A major difficulty in X-ray crystallography is the phase problem; diffracted intensities contain amplitude information but no phases. In order to solve a structure, the phases of at least the strongest reflections must be estimated by Patterson techniques, so-called direct methods or in any other way. Once the structure has been solved (i.e. the atoms found to within about 0.2 Ångström of their correct positions), then refinement is rather straight-forward for single crystal data. Typically, single crystals diffract to about 1 Â resolution. After refinement, the atomic co-ordinates are obtained with an accuracy of about 0.01 Â for organic molecules and down to 0.001 Â for inorganic structures. One limitation of single crystal X-ray diffraction is that the crystals need to be at least about 10μm in all dimensions in order to diffract, even if the radiation source is a synchrotron.

Solid state and solution stereochemistry of crown ethers and models. ortho-Dimethoxydiphenyl ether and related dibenzo-15-crown-5 and tetrabenzo-30-crown-10 ethers as studied by X-ray crystallography and 1H and 13C NMR spectroscopy

1994 ◽  
Vol 72 (5) ◽  
pp. 1218-1224 ◽  
Author(s):  
G. W. Buchanan ◽  
A. Rodrigue ◽  
K. Bourque ◽  
A. C. Chiverton ◽  
I. R. Castleden ◽  
...  
Keyword(s):  
Solid Phase ◽  
Direct Methods ◽  
13C Nmr Spectroscopy ◽  
Structural Features ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
C Nmr

Solid phase 45.3 MHz 13C NMR spectra of ortho-dimethoxydiphenyl ether, 1, dibenzo[b,e]-15-crown-5- ether, 2, and tetrabenzo[b,e,q,t]-30-crown-10 ether, 3, have been obtained. Chemical shift trends are discussed in terms of the asymmetric units and structural features available from X-ray crystallographic data. Comparison with solution 13C spectra are made. The crystal structures of 1 and 3 were determined by X-ray diffraction at room temperature. 1 crystallizes in space group P21/a with a = 13.366(1), b = 8.230(1), c = 12.303(1) Å, β = 116.63(1)°, Z = 4. 3 crystallizes in space group P21/c with a = 7.903(1), b = 26.337(2), c = 7.852(1) Å, β = 97.28(1)°, Z = 2. The structures were solved by direct methods and refined by full-matrix least squares to residuals of 0.055 using 1727 reflections for 1 and of 0.042 using 2590 reflections for 3.

Phase determination in protein x-ray crystallography at low resolution – 6.0 Å Data from rubredoxin via the pseudoatom glob approximation

1999 ◽  
Vol 214 (10) ◽  
Author(s):  
D. L. Dorset ◽  
M. P. McCourt
Keyword(s):  
Phase Error ◽  
Direct Methods ◽  
Basis Set ◽  
X Ray Diffraction ◽  
Screening Criteria ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein X ◽  
Scattering Factor ◽  
The Fourier Transform

AbstractWith a re-scaled pseudoatom scattering factor approximation to the Fourier transform of globular density units in the protein, the crystal structure of rubredoxin was determined from experimental x-ray diffraction data by direct methods at 6 Å resolution. The Sayre equation expanded a relatively small basis set and screening criteria, such as density flatness and a Patterson correlation coefficient, selected the best of several possible solutions. In the two-dimensional determination, principal peak positions were located in the maps, giving a mean phase error of 57.6° for all 17

Fractionation of polymethylene chains: An electron crystallographic investigation

1986 ◽  
Vol 44 ◽  
pp. 794-795
Author(s):  
Douglas L. Dorset
Keyword(s):  
Cross Section ◽  
Binary Systems ◽  
Linear Chain ◽  
Pure Component ◽  
Organic Substrates ◽  
Crystallographic Investigation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Molecular Sizes ◽  
The Stability

A variety of linear chain materials exist as polydisperse systems which are difficultly purified. The stability of continuous binary solid solutions assume that the Gibbs free energy of the solution is lower than that of either crystal component, a condition which includes such factors as relative molecular sizes and shapes and perhaps the symmetry of the pure component crystal structures.Although extensive studies of n-alkane miscibility have been carried out via powder X-ray diffraction of bulk samples we have begun to examine binary systems as single crystals, taking advantage of the well-known enhanced scattering cross section of matter for electrons and also the favorable projection of a paraffin crystal structure posited by epitaxial crystallization of such samples on organic substrates such as benzoic acid.

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.

Organic Crystals in the Tracheids of Torreya Yunnanensis

IAWA Journal ◽  
1996 ◽  
Vol 17 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Yuki Kondo ◽  
Tomoyuki Fujii ◽  
Yoshioki Hayashi ◽  
Atsushi Kato
Keyword(s):  
Phase Contrast ◽  
Growth Ring ◽  
Uv Spectra ◽  
Resonance Spectroscopy ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
Cinnamic Aldehyde ◽  
X Ray ◽  
Polarised Light ◽  
Contrast Microscopy

Organic crystals were found in tracheid lumina of some samples of Torreya yunnanensis Chen ' L. K. Fu imported from Yunnan, China. Tracheids with crystals were found in short to long tangential bands along the growth ring boundaries. Because the crystals were rapidly dissolved with ethanol and xylene, cross and tangential sections were mounted in de-ionized water without staining and observed by biological, polarised light, and phase-contrast microscopy. The crystals were sublimated under vacuum during routine sample preparation for conventional SEM and only the peripheral parts remained. With the aid of low vacuum-SEM and modified cryo-SEM procedure, the shape of the crystals was revealed. Some were styloid and large enough to fill tracheid lumina, while others were stacked appearing as slates filling tracheid lumina. X-ray diffraction applied to sections and isolated crystals showed that they were single crystals and orientated along the cell wall. UV spectra on isolated crystals and methanol dissolution of crystals suggested that they were composed of phenolic compounds. Crystals that were recrystallized from methanol were analysed by 1H and l3C nuclear magnetic resonance spectroscopy. These two techniques revealed that the major and minor components were o-methoxy cinnamic acid and o-methoxy cinnamic aldehyde.

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.

Synthesis and characterization of a linked, π-π stacked organotin compound of 2-mercapto-6-nitrobenzothiazolyl diphenyltin chloride with 2-ethoxyl-6-nitrobenzothiazole

2003 ◽  
Vol 81 (7) ◽  
pp. 825-831 ◽  
Author(s):  
Chunlin Ma ◽  
Qin Jiang ◽  
Rufen Zhang
Keyword(s):  
Title Compound ◽  
Organotin Compound ◽  
X Ray Diffraction ◽  
X Ray ◽  
Stacking Interaction ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Molecular Components

The new organotin compound, Ph2Sn(Cl)[S(C7H3N2O2S)]·[(C7H3N2O2S)OEt], assembled by an intermolecular aromatic benzothiazole–benzothiazole π-π stacking interaction, has been synthesized by the reaction of diphenyltin dichloride with 2-mercapto-6-nitrobenzothiazole. The title compound was characterized by elemental, IR, 1H NMR, and X-ray crystallography analyses. Single-crystal X-ray diffraction data reveals that the title compound has two different molecular components. The component Ph2Sn(Cl)[S(C7H3N2O2S)] has a pentacoordinate tin, which further forms an infinite one-dimensional chain by intermolecular non-bonded Cl···S interactions, resulting in an intercalation lattice that holds (C7H3N2O2S)OEt molecules. The formation of the molecule (C7H3N2O2S)OEt as well as its intercalated mechanism has also been discussed.Key words: organotin, assemble, π-π stacking interaction, 2-mercapto-6-nitrobenzothiazole, non-bonded interaction, crystal structure.

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