scholarly journals NMR and X-ray studies of apetalic acid isolated from Calophyllum brasiliense and of its chiral amides

2021 ◽  
Author(s):  
Marie-Rose Van Calsteren ◽  
Ricardo Reyes-Chilpa ◽  
Chistopher K Jankowski ◽  
Fleur Gagnon ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Antimycobacterial Activity ◽  
Side Chain ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Rain Forests ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calophyllum Brasiliense ◽  
Derivatives Of

The tropical tree Calophyllum brasiliense (Clusiaceae) grows in the rain forests from Brazil to Mexico. Its leaves, as well as those of other Calophyllum species, are rich sources of chromanone acids, such as apetalic acid, isoapetalic acid, and their derivatives. Apetalic acid has shown significant antimycobacterial activity. The biological activity of apetalic acid has been related to the configuration of three asymmetric centers and the stereochemistry of the molecule; however, the C-19 configuration in the acidic side chain has not been fully resolved. For this reason, the unequivocal determination of the absolute configuration by means of X-ray crystallography in a sample of unique homogeneous apetalic acid stereoisomer was the most important point to start this study. We prepared some chiral amides using the carboxyl group. We determined the C-19 stereochemistry of apetalic acid, and its specific chiral derivatives, using NMR, X-ray diffraction methods, and molecular mechanics. Finally, we observed that steric hindrance in the side chain of apetalic acid leads to restriction of rotation around the pivotal link C-10 and C-19 establishing chiral centers at C2(R), C3(S), and C19(R). We were able to separate derivatives of these two high-rotatory-barrier conformers of apetalic acid by forming diastereoisomeric amides with phenylglycine methyl ester having a chiral center at C-2’. Our results allowed the conclusion of the existence of atropisomerism in the apetalic acid molecule.

Structural studies on monofluorinated derivatives of the phytohormone indole-3-acetic acid (auxin)

1996 ◽  
Vol 52 (4) ◽  
pp. 651-661 ◽  
Author(s):  
A. Antolić ◽  
B. Kojić-Prodić ◽  
S. Tomić ◽  
B. Nigović ◽  
V. Magnus ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Side Chain ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Molecular Conformations ◽  
X Ray ◽  
Structure Activity ◽  
Planar Conformation ◽  
Derivatives Of ◽  
Indole 3 Acetic Acid

As part of the molecular recognition studies on the phytohormone indole-3-acetic acid (IAA) a series of fluorinated IAA's has been examined. The phenyl ring substitution at positions 4, 5, 6 and 7 resulted in four compounds, which were analyzed. Structure–activity correlation includes the analysis of their molecular conformations, based on the X-ray diffraction and computational chemistry results, and bioactivity determinations in the Avena coleoptile and the Pisum sativum stem straight-growth tests, lipophilicity and UV absorbance. The conformations of monofluorinated IAA's and a free hormone are defined by rotations about two bonds: one describes the relative orientation of a side chain towards the indole plane and the second the orientation of the carboxylic group. The results of X-ray structure analysis revealed the folded shape of the molecules in all compounds studied. Molecular mechanics and dynamics located the folded conformation as the local minimum, but failed to detect the planar conformation as one of the local minima, which according to ab initio results on IAA and 4-CI-IAA could also be possible. Crystal data at 295 K for 4-F-IAA and at 297 K for 5-F-IAA, and at 100 K for 6-F-IAA and 7-F-IAA using Mo Kα radiation (λ = 0.71073 Å) and Cu Kα (λ = 1.5418 Å, for 7-F-IAA), are as follows: 4-F-IAA, C10H8NO2F, Mr = 193.18, monoclinic, C2/c, a = 17.294 (5), b = 13.875 (4), c = 7.442 (4) Å, β = 103.88 (6)°, V = 1734 (1) Å3, Z = 8, Dx = 1.480 g cm−3, μ = 1.1 cm−1, F(000) = 800, R = 0.043, wR = 0.044 for 823 symmetry-independent [I ≥ 3σ(I)] reflections; 5-F-IAA, C10H8NO2F, monoclinic, P21/c, a = 19.284 (5), b = 5.083 (4), c = 9.939 (4) Å, β = 117.28 (6)°, V = 865.9 (1) Å3, Z = 4, Dx = 1.482 g cm−3, μ = 1.1  cm−1, F(000) = 400, R = 0.062, wR = 0.057 for 729 symmetry-independent [I ≥ 3σ(I)] reflections; 6-F-IAA, C10H8NO2F, monoclinic, P21/a, a = 9.360 (1), b = 5.167 (4), c = 17.751 (4) Å, β = 93.75 (1)°, V = 856.7 (8) Å3, Z = 4, Dx = 1.498 g cm−3, μ = 1.1 cm−1, F(000) = 400, R = 0.048, wR = 0.048 for 1032 symmetry-independent [I ≥ 2σ(I)] reflections; 7-F-IAA, C10H8NO2F, monoclinic, P21/a, a = 9.935 (5), b = 5.0059 (4), c = 17.610 (1) Å, β = 102.13 (1)°, V = 856.3 (1) Å3, Z = 4, Dx = 1.498 g cm−3, μ = 9.8 cm−1 (Cu Kα, F(000) = 400, R = 0.035, wR = 0.040 for 1504 symmetry-independent [I ≥ 2σ(I)] reflections.

scholarly journals 2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

2015 ◽  
Vol 11 ◽  
pp. 2179-2188 ◽  
Author(s):  
Yury A Sayapin ◽  
Inna O Tupaeva ◽  
Alexandra A Kolodina ◽  
Eugeny A Gusakov ◽  
Vitaly N Komissarov ◽  
...  
Keyword(s):  
Density Functional ◽  
Acetic Acid Solution ◽  
Intramolecular Proton Transfer ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
Derivatives Of

A series of derivatives of 2-hetaryl-1,3-tropolone (β-tropolone) was prepared by the acid-catalyzed reaction of 2-methylbenzoxazoles, 2-methylbenzothiazoles and 2,3,3-trimethylindoline with 3,4,5,6-tetrachloro-1,2-benzoquinone. The molecular structures of the three representative compounds were determined by X-ray crystallography. In crystal and (as shown by the DFT PBE0/6-311+G** calculations) in solution, 2-hetaryl-4,5,6,7-tetrachloro- and 2-hetaryl-5,6,7-trichloro-1,3-tropolones exist in the NH-tautomeric form with a strong resonance-assisted intramolecular N–H···O hydrogen bond. The mechanism of the formation of 1,3-tropolones in the reaction of methylene-active five-membered heterocycles with o-chloranil in acetic acid solution has been studied using density functional theory (DFT) methods. The reaction of 2-(2-benzoxa(thia)zolyl)-5,6,7-trichloro(4,5,6,7-tetrachloro)-1,3-tropolones with alcohols leads to the contraction of the seven-membered tropone ring with the formation of 2-(2-benzoxa(thia)zolyl)-6-alkoxycarbonylphenols. The molecular structure of 2-(2-ethoxycarbonyl-6-hydroxy-3,4,5-trichlorophenyl)benzoxazole has been determined by X-ray diffraction. 2-(2-Benzoxa(thia)zolyl)-6-alkoxycarbonylphenols display intense green fluorescence with anomalous Stokes shifts caused by the excited state intramolecular proton transfer (ESIPT) effects.

LauePt, a graphical-user-interface program for simulating and analyzing white-beam X-ray diffraction Laue patterns

2010 ◽  
Vol 43 (4) ◽  
pp. 926-928 ◽  
Author(s):  
X. R. Huang
Keyword(s):  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
White Beam ◽  
Diffraction Geometry ◽  
Wide Range ◽  
User Friendly ◽  
Beam Diffraction ◽  
Laue Method

LauePtis a robust and extremely easy-to-use Windows application for accurately simulating, indexing and analyzing white-beam X-ray diffraction Laue patterns of any crystals under arbitrary diffraction geometry. This program has a user-friendly graphic interface and can be conveniently used by nonspecialists with little X-ray diffraction or crystallography knowledge. Its wide range of applications include (1) determination of single-crystal orientation with the Laue method, (2) white-beam topography, (3) white-beam microdiffraction, (4) X-ray studies of twinning, domains and heterostructures, (5) verification or determination of crystal structures from white-beam diffraction, and (6) teaching of X-ray crystallography.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

2010 ◽  
Vol 66 (5) ◽  
pp. 558-567 ◽  
Author(s):  
Anna S. Gardberg ◽  
Alexis Rae Del Castillo ◽  
Kevin L. Weiss ◽  
Flora Meilleur ◽  
Matthew P. Blakeley ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Electron Density ◽  
Pyrococcus Furiosus ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Improved Model

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3-protonated perdeuterated crystals ofPyrococcus furiosusrubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 Å resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the σ level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 Å resolution RT neutron data for perdeuterated rubredoxin are ∼8 times more likely overall to provide high-confidence positions for D atoms than 1.1 Å resolution X-ray data at 100 K or RT. At or above the 1.0σ level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 Å resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0σ level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

scholarly journals History of protein crystallography in China

2007 ◽  
Vol 362 (1482) ◽  
pp. 1035-1042 ◽  
Author(s):  
Zihe Rao
Keyword(s):  
Protein Crystallography ◽  
Three Dimensional ◽  
Porcine Insulin ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Subsequent Determination ◽  
History Of

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

scholarly journals Structural properties of methoxy derivatives of benzyl bromide, determined from powder X-ray diffraction data

2005 ◽  
Vol 20 (4) ◽  
pp. 345-352 ◽  
Author(s):  
Zhigang Pan ◽  
Eugene Y. Cheung ◽  
Kenneth D. M. Harris ◽  
Edwin C. Constable ◽  
Catherine E. Housecroft
Keyword(s):  
Structural Properties ◽  
Diffraction Data ◽  
Benzyl Bromide ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Derivatives Of ◽  
Potential Use

Structure determination of 3,5-dimethoxybenzyl bromide and 3,4,5-trimethoxybenzyl bromide has been carried out from laboratory powder X-ray diffraction data using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. These two compounds are of interest for their potential use as building blocks for the synthesis of dendritic materials. Although the two molecules differ only in the presence/absence of the methoxy group at the 4-position of the aromatic ring, the structural properties of the two materials are significantly different.

scholarly journals Determination of the relative configuration of tropinone and granatanone aldols by using TBDMS ethers

2012 ◽  
Vol 8 ◽  
pp. 1877-1883 ◽  
Author(s):  
Ryszard Lazny ◽  
Aneta Nodzewska ◽  
Katarzyna Sidorowicz ◽  
Przemyslaw Kalicki
Keyword(s):  
Coupling Constants ◽  
Side Chain ◽  
X Ray Diffraction ◽  
Relative Configuration ◽  
X Ray ◽  
Vicinal Coupling Constants ◽  
Nmr Data ◽  
And Shifts ◽  
Solventless Reaction

The relative configurations oftert-butyldimethylsilyl (TBDMS) ethers of all four diastereomers of the aldols of tropinone (8-methyl-8-azabicyclo[3.2.1]octan-3-one), as well as of granatanone (9-methyl-9-azabicyclo[3.3.1]nonan-3-one), were determined from NMR data, and from the observed interconversion of the diastereomers (exo,antitoendo,synandexo,syntoendo,anti). Theexoforms invert toendoisomers in the presence of silica gel. The relative configuration of a new isomer of tropinone aldol accessible synthetically through the direct solventless reaction of tropinone and benzaldehyde in the presence of water was determined asexo,synby comparison of NMR data of the aldol isomers, in particular vicinal coupling constants and shifts corresponding to the side-chain CH group, with data of related TBDMS derivatives and confirmed by single-crystal X-ray diffraction.

Sem and X-Ray Analysis of Renal and Biliary Calculi

1976 ◽  
Vol 34 ◽  
pp. 306-307
Author(s):  
R. J. Narconis ◽  
G. L. Johnson
Keyword(s):  
Chemical Constituents ◽  
Natural State ◽  
X Ray Diffraction ◽  
Chemical Methods ◽  
X Ray ◽  
Additional Dimension ◽  
Biliary Calculi ◽  
Calculus Formation ◽  
Scanning Electron

Analysis of the constituents of renal and biliary calculi may be of help in the management of patients with calculous disease. Several methods of analysis are available for identifying these constituents. Most common are chemical methods, optical crystallography, x-ray diffraction, and infrared spectroscopy. The application of a SEM with x-ray analysis capabilities should be considered as an additional alternative.A scanning electron microscope equipped with an x-ray “mapping” attachment offers an additional dimension in its ability to locate elemental constituents geographically, and thus, provide a clue in determination of possible metabolic etiology in calculus formation. The ability of this method to give an undisturbed view of adjacent layers of elements in their natural state is of advantage in determining the sequence of formation of subsequent layers of chemical constituents.

Structural Study of a new Compound Based on Acid 1,4-Cyclohexanedicarboxylic (1,4-CDC)

2010 ◽  
Vol 6 (1) ◽  
pp. 891-896
Author(s):  
Manel Halouani ◽  
M. Dammak ◽  
N. Audebrand ◽  
L. Ktari
Keyword(s):  
Aqueous Solution ◽  
Water Molecules ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Compound I ◽  
Unit Cell Parameters ◽  
Monoclinic System ◽  
X Ray ◽  
Cell Parameters ◽  
Cyclohexanedicarboxylic Acid

One nickel 1,4-cyclohexanedicarboxylate coordination polymers, Ni2 [(O10C6H4)(COO)2].2H2O  (I), was hydrothermally synthesized from an aqueous solution of Ni (NO3)2.6H2O, (1,4-CDC) (1,4-CDC = 1,4-cyclohexanedicarboxylic acid) and tetramethylammonium nitrate. Compound (I) crystallizes in the monoclinic system with the C2/m space group. The unit cell parameters are a = 20.1160 (16) Å, b = 9.9387 (10) Å, c = 6.3672 (6) Å, β = 97.007 (3) (°), V= 1263.5 (2) (Å3) and Dx= 1.751g/cm3. The refinement converged into R= 0.036 and RW = 0.092. The structure, determined by single crystal X-ray diffraction, consists of two nickel atoms Ni (1) and Ni (2). Lots of ways of which is surrounded by six oxygen atoms, a carboxyl group and two water molecules.

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