Crystal structure, DFT and Hirshfeld surface analysis of N-acetyl-t-3-methyl-r-2,c-6-diphenylpiperidine

In the title compound [systematic name: 1-(3-methyl-2,6-diphenylpiperidin-1-yl)ethanone], C20H23NO, the piperidine ring adopts a distorted boat conformation, while the phenyl rings subtend a dihedral angle 65.1 (2)°. In the crystal, molecules are linked by C—H...O hydrogen bonds into chains extending along the b-axis direction. The DFT/B3LYP/6–311 G(d,p) method was used to determine the HOMO–LUMO energy levels. A Hirshfeld surface analysis was conducted to verify the contributions of the different intermolecular interactions, indicating that the important contributions to the crystal packing are from H...H (73.2%), C...H (18.4%) and O...H (8.4%) interactions.

Crystal structure and Hirshfeld surface analysis of 6-((E)-2-{4-[2-(4-chlorophenyl)-2-oxoethoxy]phenyl}ethenyl)-4,5-dihydropyridazin-3(2H)-one

The pyridazine ring in the title compound, C20H17ClN2O3, adopts a screw-boat conformation. The whole molecule is flattened, the dihedral angles subtended by the least-squares plane of the central aromatic ring with those of the terminal benzene and pyridazine rings being 15.18 (19) and 11.23 (19)°, respectively. In the crystal, the molecules are linked by pairs of N—H...O bonds into centrosymmetric dimers and by C—H...π contacts into columns. The results of the Hirshfeld surface analysis show that the most prominent interactions are H...H, accounting for 36.5% of overall crystal packing, and H...O/O...H (18.6% contribution) contacts.

Optimization of N-piperidinyl-benzimidazolone derivatives as potent and selective inhibitors of 8-Oxo Guanine DNA Glycosylase 1

8-oxo Guanine DNA Glycosylase 1 is the initiating enzyme within base excision repair and removes oxidized guanines from damaged DNA. Since unrepaired 8-oxoG could lead to G:C→T:A transversion, base removal is of the utmost importance for cells to ensure genomic integrity. For cells with elevat-ed levels of reactive oxygen species this dependency is further increased. In the past we and others have validated OGG1 as a target for inhibitors to treat cancer and inflammation. Here, we present the optimization campaign that led to the broadly used tool compound TH5487. Based on a high-throughput screen, we performed hit to lead expansion and arrived at potent and selective substituted N-piperidinyl-benzimidazolones. Using X-ray crystallography data, we describe the surprising bind-ing mode of the most potent member of the class, TH8535. Here, the N-Piperidinyl-linker adopts a chair instead of a boat conformation which was found for weaker analogues. We further demonstrate cellular target engagement and efficacy of TH8535 against a number of cancer cell lines.

Two Compounds of 1-((4-Bromothiophen-2-Yl)Methylene)-2-(Perfluorophenyl)Hydrazine, and 1-((4-Bromo-5-Methylthiophen-2-Yl)Methylene)-2-(Perfluorophenyl)Hydrazine and They Crystal, Molecular and Electronic Properties

The crystals, C11H4BrF5N2S, (I), 1-((4-bromothiophen-2-yl)methylene)-2-(perfluorophenyl)hydrazine and C12H6BrF5N2S, (II), 1-((4-bromo-5-methylthiophen-2-yl)methylene)-2-(perfluorophenyl)hydrazine are molecules with two rings and hydrazone part like a centre of the molecule. The compounds have been synthesized and characterized by elemental, spectroscopic (1H-NMR) analysis. The crystal structures of the solid phase were determined by single crystal X-ray diffraction method. They crystallize in the monoclinic space group with Z = 4 and Z = 2 molecules per unit-cell. The compound (I) crystallizes as a racemate in the centrosymmetric space group and the compound (II) crystallizes as a non-racemate in the non-centrosymmetric space group. The “absolute configuration and conformation for bond values” were derived from the anomalous dispersion (ad) for (II). The crystal structures are revealed diverse non-covalent interactions such as intra- and interhydrogen bonding, π-ring···π-ring, C-H···π-ring and they were investigated. The expected stereochemistry of hydrazones atoms C7, N2 and N1 were confirmed for (I) and (II). The hole molecule of the (I), and (II) possesses “a boat conformation” like a 6-membered ring. The results of the single crystal studies are reproduced with the help of Hirshfeld surface study and Gaussian software.

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

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.

Synthesis and crystal structure of racemic (R*,R*)-2,2′-(1,4-phenylene)bis(3-phenyl-2,3,5,6-tetrahydro-4H-1,3-thiazin-4-one)

In the racemic title compound, C26H24N2O2S2, one of the thiazine rings shows a twisted boat conformation (Q = 0.743 Å, θ = 92.1°) and the other a half-chair puckering (Q = 0.669 Å, θ = 54.3°). The terminal phenyl rings are almost parallel to each other [dihedral angle 21.71 (10)°]. Both of these rings are orthogonal to the central phenyl ring, subtending a dihedral angle of about 78° in each case. The extended structure is consolidated by C—H...O and C—H...S hydrogen bonds as well as aromatic ring interactions of parallel-displaced and T-type. The molecule has approximate C2 local symmetry but this is not carried over to its three-dimensional structure or the intermolecular interactions.

Crystal structure, Hirshfeld surface and frontier molecular orbital analysis of 9-(3-bromo-4-hydroxy-5-methoxyphenyl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione

In the fused ring system of the title compound, C24H27BrO5, the mean plane and maximum deviations of the central pyran ring are 0.0384 (2) and 0.0733 (2) Å, respectively. The cyclohexenone rings both adopt envelope conformations with the tetra-substituted C atoms as flap atoms, whereas the central pyran ring adopts a flattened boat conformation. The central pyran and phenyl substituent rings are almost perpendicular to each other, making a dihedral angle of 89.71 (2)°. In the crystal, pairs of molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with an R 2 2(20) ring motif. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (50.6%), O...H/H...O (22.9%) and C...H/H...C (11.1%) contacts. Quantum chemical calculations for the frontier molecular orbitals were undertaken to determine the chemical reactivity of the title compound.

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

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.

Ferroptosis-Inhibitory Difference between Chebulagic Acid and Chebulinic Acid Indicates Beneficial Role of HHDP

The search for a safe and effective inhibitor of ferroptosis, a recently described cell death pathway, has attracted increasing interest from scientists. Two hydrolyzable tannins, chebulagic acid and chebulinic acid, were selected for the study. Their optimized conformations were calculated using computational chemistry at the B3LYP-D3(BJ)/6-31G and B3LYP-D3(BJ)/6-311 + G(d,p) levels. The results suggested that (1) chebulagic acid presented a chair conformation, while chebulinic acid presented a skew-boat conformation; (2) the formation of chebulagic acid requires 762.1729 kcal/mol more molecular energy than chebulinic acid; and (3) the 3,6-HHDP (hexahydroxydiphenoyl) moiety was shown to be in an (R)- absolute stereoconfiguration. Subsequently, the ferroptosis inhibition of both tannins was determined using a erastin-treated bone marrow-derived mesenchymal stem cells (bmMSCs) model and compared to that of ferrostatin-1 (Fer-1). The relative inhibitory levels decreased in the following order: Fer-1 > chebulagic acid > chebulinic acid, as also revealed by the in vitro antioxidant assays. The UHPLC–ESI-Q-TOF-MS analysis suggested that, when treated with 16-(2-(14-carboxytetradecyl)-2-ethyl-4,4-dimethyl-3-oxazolidinyloxy free radicals, Fer-1 generated dimeric products, whereas the two acids did not. In conclusion, two hydrolyzable tannins, chebulagic acid and chebulinic acid, can act as natural ferroptosis inhibitors. Their ferroptosis inhibition is mediated by regular antioxidant pathways (ROS scavenging and iron chelation), rather than the redox-based catalytic recycling pathway exhibited by Fer-1. Through antioxidant pathways, the HHDP moiety in chebulagic acid enables ferroptosis-inhibitory action of hydrolyzable tannins.

Crystal structure and Hirshfeld surface analysis of (3aR,4S,7S,7aS)-4,5,6,7,8,8-hexachloro-2-{6-[(3aR,4R,7R,7aS)-4,5,6,7,8,8-hexachloro-1,3-dioxo-1,3,3a,4,7,7a-hexahydro-2H-4,7-methanoisoindol-2-yl]hexyl}-3a,4,7,7a-tetrahydro-1H-4,7-methanoisoindole-1,3(2H)-dione

The molecule of the title compound, C24H16Cl12N2O4, is generated by a crystallographic inversion centre at the midpoint of the central C—C bond. A kink in the molecule is defined by a torsion angle of −169.86 (15)° about this central bond of the alkyl bridge. The pyrrolidine ring is essentially planar [max. deviation = 0.014 (1) Å]. The cyclohexane ring has a boat conformation, while both cyclopentane rings adopt an envelope conformation. In the crystal structure, molecules are linked by intermolecular C—H...O, C—H...Cl and C—Cl...π interactions, and short intermolecular Cl...O and Cl...Cl contacts, forming a three-dimensional network.