scholarly journals Synthesis and Crystal Structure of Benzyl 4-(2-fluoro-4-(trifluoromethyl)phenyl)- 2,6,6-trimethyl-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and Its DFT Analysis Combined with Bond Order Modeling in Terms of The Bond Critical Point Quantities

2021 ◽  
Author(s):  
Zeki Büyükmumcu ◽  
Sema OZTURK YILDIRIM ◽  
Gökalp Çetin ◽  
Rahime Şimşek ◽  
Ray J. Butcher
Keyword(s):  
Crystal Structure ◽  
Critical Point ◽  
Bond Order ◽  
Mass Density ◽  
3D Structure ◽  
Molecular Surface ◽  
Bond Critical Point ◽  
Symmetry Code ◽  
Boat Conformation ◽  
Correlation Degree

Abstract Inflammation is the underlying cause of many diseases such as cardiovascular diseases, cancer and autoimmune diseases. Recently 1,4-dihydropyridine (1,4-DHP) compounds were found effective to reduce inflammation which contributes to development of inflammation associated diseases. Based on these data we synthesized to investigate this type of action of annulated 1,4-DHP molecule, benzyl 4-(2-fluoro-4-(trifluoromethyl)phenyl)-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and proved the structure of this molecule by IR, 1H-NMR, 13C-NMR, HMRS and X-ray crystallography.X-ray analyses were conducted to find out the exact 3D structure of the mentioned molecule. The molecular structure crystallizes in triclinic space group, P-1, with a = 7.0889(11) Å, b = 12.4861(18) Å, c = 14.338(2) Å, α = 66.899(4)°, β = 89.025(4)°, γ = 85.101(4)° and V = 1162.9(3) Å3. In the title molecule, C27H25F4NO3, the cyclohexene ring is in a sofa conformation and the 1,4-dihydropyridine ring is in a slight boat conformation. In the 2-fluoro phenyl and benzyl rings form a dihedral angle of 13.6(1)°. In the crystal structure stabilized by the intra- and intermolecular N—H···O, C—H···O and C—H···F interactions. The molecules are linked together to form a dimer by N(1)—H(1N) ···O(1)i and C(2)—H(2A) ···O(1)i hydrogen bonds [symmetry code: (i) x+1,y,z ], producing two R12(6) rings.Natural charge, QTAIM, bond order, molecular planarity and molecular surface analyses have been performed on the optimized geometry by DFT. Considering the quantities obtained at the bond critical poins, the chemical bonds are discussed for classification. The correlation between bond critical point quantities and the bond orders based on different definitions have been explored considering different bond order models from the literature. The Laplacian Bond Order (LBO) gives best correlation for four of five bond order models. All the bond order models with an exception of the model with parameter G have approximately same correlation degree for C-C bonds. For C-H bonds, only bond model with parameters of electron density and the principle curvatures for LBO gives relatively good correlation with R2 value of 0.943. The two phenyl rings of the structure have aromaticity comparable to benzene as deduced from QTAIM quantities and molecular planarity metrics. As a result of molecular surface analysis, the mass density, molecular polarity index, v (the measure of charge balance), σ2tot .v (measure of intermolecular interactions) were calculated and compared with literature values.

Crystal Structure and Conformation of Ring A of 2β-Bromo-19β,28-epoxy-18α-oleanan-3-one

1993 ◽  
Vol 58 (11) ◽  
pp. 2737-2744 ◽  
Author(s):  
Jiří Novotný ◽  
Jaroslav Podlaha ◽  
Jiří Klinot
Keyword(s):  
Crystal Structure ◽  
Opposite Direction ◽  
Chair Conformation ◽  
Boat Conformation ◽  
Form Ring ◽  
Twist Boat

The crystal structure of β-bromo-19β,28-epoxy-18α-oleanan-3-one was elucidated. The crystal is orthorhombic, P212121, a = 9.686(1), b = 14.355(2), c = 19.687(4) Å, Z = 4, R = 0.042 for 2 410 observed reflections. Rings B, C, D and E adopt the chair conformation, the five membered ether cycle in ring E occurs in the envelope form. Ring A takes the twist-boat conformation turned towards the classical boat with C2 and C5 in the stem-stern position, in contrast to the conformation in solution, which is turned in the opposite direction towards the classical boat with C3 and C10 in the stem-stern positions.

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.

Electronegativity and Bader's bond critical point

1992 ◽  
Vol 13 (7) ◽  
pp. 912-918 ◽  
Author(s):  
Sanchita Hati ◽  
Dipankar Datta
Keyword(s):  
Critical Point ◽  
Bond Critical Point

scholarly journals Crystal structure of human mARC1 reveals its exceptional position among eukaryotic molybdenum enzymes

2018 ◽  
Vol 115 (47) ◽  
pp. 11958-11963 ◽  
Author(s):  
Christian Kubitza ◽  
Florian Bittner ◽  
Carsten Ginsel ◽  
Antje Havemeyer ◽  
Bernd Clement ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Full Range ◽  
3D Structure ◽  
Cytochrome P450 Enzymes ◽  
Oxygenated Compounds ◽  
Online Databases ◽  
Starting Point ◽  
Wide Range ◽  
Nitrogen Containing Compounds

Biotransformation enzymes ensure a viable homeostasis by regulating reversible cycles of oxidative and reductive reactions. The metabolism of nitrogen-containing compounds is of high pharmaceutical and toxicological relevance because N-oxygenated metabolites derived from reactions mediated by cytochrome P450 enzymes or flavin-dependent monooxygenases are in some cases highly toxic or mutagenic. The molybdenum-dependent mitochondrial amidoxime-reducing component (mARC) was found to be an extremely efficient counterpart, which is able to reduce the full range of N-oxygenated compounds and thereby mediates detoxification reactions. However, the 3D structure of this enzyme was unknown. Here we present the high-resolution crystal structure of human mARC. We give detailed insight into the coordination of its molybdenum cofactor (Moco), the catalytic mechanism, and its ability to reduce a wide range of N-oxygenated compounds. The identification of two key residues will allow future discrimination between mARC paralogs and ensure correct annotation. Since our structural findings contradict in silico predictions that are currently made by online databases, we propose domain definitions for members of the superfamily of Moco sulfurase C-terminal (MOSC) domain-containing proteins. Furthermore, we present evidence for an evolutionary role of mARC for the emergence of the xanthine oxidase protein superfamily. We anticipate the hereby presented crystal structure to be a starting point for future descriptions of MOSC proteins, which are currently poorly structurally characterized.

scholarly journals Crystal structure, Hirshfeld surface analysis and interaction energy calculation of 4-(furan-2-yl)-2-(6-methyl-2,4-dioxopyran-3-ylidene)-2,3,4,5-tetrahydro-1H-1,5-benzodiazepine

2021 ◽  
Vol 77 (8) ◽  
pp. 834-838
Author(s):  
Mohamed El Hafi ◽  
Sanae Lahmidi ◽  
Lhoussaine El Ghayati ◽  
Tuncer Hökelek ◽  
Joel T. Mague ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Surface Analysis ◽  
Crystal Packing ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Energy Calculation ◽  
Boat Conformation ◽  
Stacking Interactions ◽  
Π Stacking

The title compound {systematic name: (S,E)-3-[4-(furan-2-yl)-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepin-2-ylidene]-6-methyl-2H-pyran-2,4(3H)-dione}, C19H16N2O4, is constructed from a benzodiazepine ring system linked to furan and pendant dihydropyran rings, where the benzene and furan rings are oriented at a dihedral angle of 48.7 (2)°. The pyran ring is modestly non-planar [largest deviation of 0.029 (4) Å from the least-squares plane] while the tetrahydrodiazepine ring adopts a boat conformation. The rotational orientation of the pendant dihydropyran ring is partially determined by an intramolecular N—HDiazp...ODhydp (Diazp = diazepine and Dhydp = dihydropyran) hydrogen bond. In the crystal, layers of molecules parallel to the bc plane are formed by N—HDiazp...ODhydp hydrogen bonds and slipped π–π stacking interactions. The layers are connected by additional slipped π–π stacking interactions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H...H (46.8%), H...O/O...H (23.5%) and H...C/C...H (15.8%) interactions, indicating that van der Waals interactions are the dominant forces in the crystal packing. Computational chemistry indicates that in the crystal the N—H...O hydrogen-bond energy is 57.5 kJ mol−1.

scholarly journals Unusual formation of (E)-11-(aminomethylene)-8,9,10,11-tetrahydropyrido[2′,3′:4,5]pyrimido[1,2-a]azepin-5(7H)-one and its crystal structure

2017 ◽  
Vol 73 (10) ◽  
pp. 1497-1500
Author(s):  
Khamid U. Khodjaniyazov ◽  
Utkir S. Makhmudov ◽  
Kambarali K. Turgunov ◽  
Burkhon Z. Elmuradov
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Aqueous Ammonia ◽  
Boat Conformation ◽  
X Ray ◽  
First Time ◽  
Twist Boat ◽  
Unusual Formation

Selective C-formylation of 8,9,10,11-tetrahydropyrido[2′,3′:4,5]pyrimido[1,2-a]-azepin-5(7H)-one has been studied for the first time. It was revealed that formylation proceeds by the formation of an intermediate salt, which due to the re-amination process on treatment with aqueous ammonia transformed into the corresponding (E)-11-(aminomethylene)-8,9,10,11-tetrahydropyrido[2′,3′:4,5]-pyrimido[1,2-a]azepin-5(7H)-one, C13H14N4O, as anE-isomer. Formylation was carried out by Vilsmeier–Haack reagent and the structure of the synthesized compound was confirmed by X-ray structural analysis, spectroscopic and LC–MS methods. In the molecule, the seven-membered pentamethylene ring adopts a twist-boat conformation.

scholarly journals (Z)-3-Benzyl-1,5-benzothiazepin-4(5H)-one

2012 ◽  
Vol 68 (8) ◽  
pp. o2329-o2329
Author(s):  
V. Sabari ◽  
R. Selvakumar ◽  
M. Bakthadoss ◽  
S. Aravindhan
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Membered Ring ◽  
Boat Conformation ◽  
Compound C

In the crystal structure of the title compound, C16H13NOS, molecules are linked into cyclic centrosymmetricR22(8) dimersviapairs of N—H...O hydrogen bonds. The seven-membered ring adopts a boat conformation.

scholarly journals The characterisation and X-ray crystal structure of pentabromodiselenium hexafluoroarsenate, Se2Br5AsF6; some thermodynamic considerations and the nonexistence of Se2I5AsF6

1987 ◽  
Vol 65 (7) ◽  
pp. 1584-1593 ◽  
Author(s):  
Michael P. Murchie ◽  
Jack Passmore ◽  
Peter S. White
Keyword(s):  
Crystal Structure ◽  
Bond Order ◽  
Room Temperature ◽  
Bromine Atom ◽  
Elemental Selenium ◽  
Analogous Reaction ◽  
X Ray Diffraction ◽  
X Ray ◽  
Final Agreement ◽  
Anion Interaction

The crystal structure of Se2Br5AsF6 was determined by low-temperature X-ray diffraction methods. Single crystals of Se2Br5AsF6 are rhombohedral, space group R3 with a = 13.367(4) Å, c = 19.000(6) Å, V = 2940 Å3, and Z = 9. The structure was refined to final agreement indices of R = 0.087, Rw = 0.093 for 604 observed (I > 3σ(I)) reflections and 71 parameters. The structure consists of essentially discrete Se2Br5+ cations and AsF6− anions with some cation–anion interaction. The Se2Br5+ cation, of essentially C2h symmetry contains two trans SeBr2 units, linked by a bridging bromine atom. The two terminal selenium–bromine bond distances are 2.291(7) and 2.268(6) Å, of bond order 1, and the angle between them is 100.0(3)°. The bridging bromine atom lies at the inversion centre of the Se2Br5+ cation, with an Se—Br distance of 2.582(3) Å, corresponding to a bond order of about 0.5. The two angles between the bridging Se—Br and terminal Se—Br bonds are 97.4(1)° and 98.9(2)°. Se2Br5AsF6 decomposes slowly at room temperature and rapidly at 100 °C leading to the formation of SeBr3AsF6, SeBr4, and elemental selenium. It reacts with Br2 to give SeBr3AsF6 and SeBr4. Se2Br5AsF6 is prepared by the reaction of Se4(AsF6)2 and the appropriate quantity of Br2. The analogous reaction with I2 leads to I2SeSeSeSeI2(AsF6)2 and not Se2I5AsF6. These differences have been accounted for on the basis of estimates of the appropriate bond and crystal lattice energies. The 77Se nmr of SeBr3+ and Se2Br5+ in SO2 solution, and the Raman spectrum of SeBr4 are reported.

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