Structure determination of riboflavin by synchrotron high-resolution powder X-ray diffraction (original) (raw)
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Pakistan journal of pharmaceutical sciences, 2013
Riboflavin (vitamin B2) belongs to a group of respiratory enzymes that occur widely in animals and plants participating in vital oxidation- reduction processes in the body. A computational study was conducted on riboflavin by ArgusLab 4.0.1 to obtain the most active conformation of riboflavin and to analyze its excited-state properties. The best conformation of riboflavin was found to be -199.2173 kcal/mol which is the minimum potential energy calculated by geometry convergence function by ArgusLab software; performed according to Hartree-Fock calculation method. Electronic transition states (ground and excited), were also calculated and visualized by semi-empirical ZINDO method by ArgusLab from which molecular properties such as energies, wave function and dipole moments were established. All the results obtained from geometry optimization and excited-state properties lead us to delineate the active sites with charged groups of riboflavin to interact with the receptors. Such types ...
CrystEngComm, 2011
The crystal structure of propylthiouracil, a drug used in the treatment of hyperthyroidism, was determined by means of high-resolution synchrotron X-ray powder diffraction data. The Rietveld method was employed to refine the structure. This drug crystallizes in an orthorhombic (Pcab) space group, with unit cell parameters a 1⁄4 28.67338(23) A#, b 1⁄4 11.15287(6) A#, c 1⁄4 10.66821(5) A#, V 1⁄4 3411.59 (4) A#3, Z 1⁄4 16, Z0 1⁄4 2, M 1⁄4 170.23 g mol1, rcalc 1⁄4 1.3258(1) g cm3. The goodness-of-fit and R-factors were, respectively: c2 1⁄4 1.599, RBragg 1⁄4 1.57%, Rwp 1⁄4 8.85% and Rexp 1⁄4 5.53%. Four hydrogen bonds involving the atoms N(6)–H(12)/S(39), N(19)–H(21)/O(41), N(27)–H(33)/S(18) and N(40)–H (42)/O(20) form a network of molecular aggregates in propylthiouracil.
EXPO software for solving crystal structures by powder diffraction data: methods and application
Crystal Research and Technology, 2015
Innovative methodologies, introduced in the software EXPO and working both in the reciprocal and in the direct space, can be successfully adopted for solving crystal structure by X-ray powder diffraction data. The principles underlying these methodologies are summarized. Three representative examples of crystal structure solution of the peptides Z-(Aib) 2-OH, Z-(Aib) 3-O-t-Bu and Z-(Aib) 4-OH are discussed in relation to their different degree of structure complexity.
2021
The crystal structure of 6-amino nicotinic acid (6-ANA) which is a derivative of vitamin B3, was determined from a sample having an additional crystalline phase using both laboratory and synchrotron X-ray powder diffraction data. The nature of intermolecular interactions in 6-ANA has been analysed through Hirshfeld surfaces and 2-dimensional fingerprint plots and compared with those in some other nicotinic acid derivatives.A pair of intermolecular N–H⋯O and O–H⋯N hydrogen bonds generated cyclic R22(8) rings in 6-ANA forming one dimensional molecular strips, which are further connected through N–H⋯O hydrogen bonds to produce a three dimensional supramolecular framework. Geometry optimization of 6-ANA was carried out along with the molecular electrostatic potential calculations. The enrichment ratio of various contacts, calculated for 6-ANA and some other related compounds retrieved from the CSD, show an increased propensity of O∙∙∙H and N∙∙∙H contacts to form, which is consistent wit...
Structure of β-trimyristin and β-tristearin from high-resolution X-ray powder diffraction data
Acta Crystallographica Section B Structural Science, 2001
The crystal structures of β-1,2,3-tritetradecanoylglycerol (β-trimyristin or β-MMM) and β-1,2,3-trioctadecanoylglycerol (β-tristearin or β-SSS) have been determined from high-resolution synchrotron X-ray powder diffraction data. Grid search and Rietveld refinement have been used to determine and refine the structure, respectively. Both substances crystallize in space group P\\bar 1 with Z = 2. The unit-cell parameters for β-MMM are a = 12.0626 (6), b = 41.714 (1), c = 5.4588 (3) Å, α = 73.388 (4), β = 100.408 (5) and γ = 118.274 (4)°. For β-SSS the unit-cell parameters are a = 12.0053 (7), b = 51.902 (2), c = 5.4450 (3) Å, α = 73.752 (5), β = 100.256 (6) and γ = 117.691 (5)°. Soft-distance restraints have been applied to the molecules during refinement. For β-MMM the final Rp value obtained is 0.053 and for β-SSS the final Rp value is 0.041.
Synthesis, characterization and film formation of modified riboflavin
Materials Science and Engineering: C, 1995
Riboflavin (RBF) is not naturally imbued with an amphiphilic character. To impart amphiphilicity the hydroxyl groups of the ribose moiety have been esterified using steak acid, The compound thus modified, 2',3',4',5'-tetrastearoyl riboflavin (SRBF), has been characterized using optical absorption and fluoreslcence spectroscopy, NMR and cyclic voltammetry. Thin films of SRBF have been deposited on IT0 glass using the LB technique. These films exhibit fluorescence properties which are similar to RBF in solution. X-ray diffraction results indicate that the molecules are organized in a highly ordered fashion.
Structure determination from powder diffraction data
Acta Crystallographica Section A Foundations of Crystallography, 2007
Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.
Journal of Molecular Structure, 2019
The structure determination from laboratory X-ray powder diffraction data of oxamic acid, a derivative of the biologically active oxalic acid and the simplest organic acid containing an amide group, is presented in this contribution. An energy minimization analysis by DFT-D was carried out. The structure was determined with the program TALP and refined by the Rietveld method with GSAS-II in space group Cc (No. 9). The final unit-cell parameters are a = 9.4989(6), b = 5.43796(9), c = 6.8637(9) Å, = 107.152(5)°, V = 338.772(10) Å 3 , Z = 4. The refinement converged to the figures of merit: R e = 0.01674, R p = 0.03270, R wp = 0.05652 and GoF = 3.378 with a good fit between the calculated pattern of the structural model and the experimental pattern. The DFT-D calculations show an excellent reproduction of the experimental structure, validating the correctness of the structure. The non-centrosymmetric nature of the structure was confirmed by SHG measurements. In the crystal structure, the molecules are close to planar and form a complex infinite 2D hydrogen-bonding pattern based on the cyclic amide-acid heterosynthon.
The Crystal Structure of D-Ribose-At Last!
Angewandte Chemie International Edition, 2010
Among the half-million or so chemical compounds whose crystal structures have been determined by X-ray or neutron diffraction, the crystal structure of d-ribose is conspicuously absent. [1] Thus, although most modern chemistry textbooks and handbooks show the molecule of d-ribose in the bfuranose form, as present in countless biochemically important ribose derivatives, it has been known for more than forty years from early NMR observations that d-ribose exists in aqueous solution as a mixture of a-and b-pyranoses and aand b-furanoses with the b-pyranose form predominating (Scheme 1).
Crystal structure of chicken riboflavin-binding protein
The EMBO Journal, 1997
specific riboflavin-binding proteins and that these proteins 27100 Pavia, Italy in the same positions: Asn36 and Asn147. The primary Keywords: crystal structure/fluorescence quenching/ structures of the carbohydrates attached to plasma (Rohrer folate-binding protein/phosphoglycoprotein/riboflavinand White, 1992) and yolk ) RfBP binding protein have been determined and shown to be identical. Although the carbohydrate composition of the egg white RfBP is known, the primary structure of its oligosaccharide chains