The use of minimal topological differences to inspire the design of novel tetrahydroisoquinoline analogues with antimalarial activity.

A quantitative structure-activity relationship (QSAR) study was conducted using nineteen previously synthesized, and tested 1-aryl-6-hydroxy-1,2,3,4-tetrahydroisoquinolines with proven in vitro activities against Plasmodium falciparum. In order to computationally design and screen potent antimalarial agents, these compounds with known biological activity ranging from 0.697 to 35.978 µM were geometry optimized at the B3LYP/6-311 + G(d,p) level of theory, using the Gaussian 09W software. To calculate the topological differences, the series of the nineteen compounds was superimposed and a hypermolecule obtained with s ¯ = 17 and 20 vertices. Other molecular descriptors were considered in order to build a highly predictive QSAR model. These include the minimal topological differences (MTD), LogP, two dimensional polarity surface area (TDPSA), dipole moment (µ), chemical hardness (η), electrophilicity (ω), potential energy (Ep), electrostatic energy (Eele) and number of rotatable bonds (NRB). By using a training set composed of 15 randomly selected compounds from this series, several QSAR equations were derived. The QSAR equations obtained were then used to attempt to predict the IC50 values of 4 remaining compounds in a test (or validation) set. Ten analogues were proposed by a fragment search of a fragment library containing the pharmacophore model of the active compounds contained in the training set. The most active proposed analogue showed a predicted activity within the lower micromolar range.

Crystal structure and Hirshfeld surface analysis of 4-{2,2-di-chloro-1-[(E)-(4-chloro-phen-yl)diazen-yl]ethen-yl}-N,N-di-methyl-aniline.

The title compound, C16H14Cl3N3, comprises three mol-ecules of similar shape in the asymmetric unit. The crystal cohesion is ensured by inter-molecular C-H⋯N and C-H⋯Cl hydrogen bonds in addition to C-Cl⋯π inter-actions. Hirshfeld surface analysis and two-dimensional fingerprint plots reveal that Cl⋯H/H⋯Cl (33.6%), H⋯H (27.9%) and C⋯H/H⋯C (17.6%) are the most important contributors towards the crystal packing.

Crystal structure and Hirshfeld surface analysis of (E)-4-{[2,2-di-chloro-1-(4-meth-oxy-phen-yl)ethen-yl]diazen-yl}benzo-nitrile.

In the title compound, C16H11Cl2N3O, the 4-meth-oxy-substituted benzene ring makes a dihedral angle of 41.86 (9)° with the benzene ring of the benzo-nitrile group. In the crystal, mol-ecules are linked into layers parallel to (020) by C-H⋯O contacts and face-to-face π-π stacking inter-actions [centroid-centroid distances = 3.9116 (14) and 3.9118 (14) Å] between symmetry-related aromatic rings along the a-axis direction. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from Cl⋯H/H⋯Cl (22.8%), H⋯H (21.4%), N⋯H/H⋯N (16.1%), C⋯H/H⋯C (14.7%) and C⋯C (9.1%) inter-actions.

Crystal structures and Hirshfeld surface analyses of the two isotypic compounds (E)-1-(4-bromo-phen-yl)-2-[2,2-di-chloro-1-(4-nitro-phen-yl)ethen-yl]diazene and (E)-1-(4-chloro-phen-yl)-2-[2,2-di-chloro-1-(4-nitro-phen-yl)ethen-yl]diazene.

In the two isotypic title compounds, C14H8BrCl2N3O2, (I), and C14H8Cl3N3O2, (II), the substitution of one of the phenyl rings is different [Br for (I) and Cl for (II)]. Aromatic rings form dihedral angles of 60.9 (2) and 64.1 (2)°, respectively. Mol-ecules are linked through weak X⋯Cl contacts [X = Br for (I) and Cl for (II)], C-H⋯Cl and C-Cl⋯π inter-actions into sheets parallel to the ab plane. Additional van der Waals inter-actions consolidate the three-dimensional packing. Hirshfeld surface analysis of the crystal structures indicates that the most important contributions for the crystal packing for (I) are from C⋯H/H⋯C (16.1%), O⋯H/H⋯O (13.1%), Cl⋯H/H⋯Cl (12.7%), H⋯H (11.4%), Br⋯H/H⋯Br (8.9%), N⋯H/H⋯N (6.9%) and Cl⋯C/C⋯Cl (6.6%) inter-actions, and for (II), from Cl⋯H / H⋯Cl (21.9%), C⋯H/H⋯C (15.3%), O⋯H/H⋯O (13.4%), H⋯H (11.5%), Cl⋯C/C⋯Cl (8.3%), N⋯H/H⋯N (7.0%) and Cl⋯Cl (5.9%) inter-actions. The crystal of (I) studied was refined as an inversion twin, the ratio of components being 0.9917 (12):0.0083 (12).

Crystal structure and Hirshfeld surface analysis of dimethyl (1R*,3aS*,3a1 R*,6aS*,9R*,9aS*)-3a1,5,6,9a-tetra-hydro-1H,4H,9H-1,3a:6a,9-di-epoxy-phenalene-2,3-di-carboxyl-ate.

The title di-epoxy-phenalene derivative, C17H18O6, comprises a fused cyclic system containing four five-membered rings (two di-hydro-furan and two tetra-hydro-furan) and one six-membered ring (cyclo-hexa-ne). The five-membered di-hydro-furan and tetra-hydro-furan rings adopt envelope conformations, and the six-membered cyclo-hexane ring adopts a distorted chair conformation. Two methyl carboxyl-ate groups occupy adjacent positions (2- and 3-) on a tetra-hydro-furan ring. In the crystal, two pairs of C-H⋯O hydrogen bonds link the mol-ecules to form inversion dimers, enclosing two R 2 2(6) ring motifs, that stack along the a-axis direction and are arranged in layers parallel to the bc plane.

Crystal structure and Hirshfeld surface analysis of (E)-1-(4-chloro-phen-yl)-2-[2,2-di-chloro-1-(4-fluoro-phen-yl)ethen-yl]diazene.

In the title compound, C14H8Cl3FN2, the planes of the 4-fluoro-phenyl ring and the 4-chloro-phenyl ring make a dihedral angle of 56.13 (13)°. In the crystal, mol-ecules are stacked in a column along the a axis via a weak C-H⋯Cl hydrogen bond and face-to-face π-π stacking inter-actions [centroid-centroid distances = 3.8615 (18) and 3.8619 (18) Å]. The crystal packing is further stabilized by short Cl⋯Cl contacts. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from Cl⋯H/H⋯Cl (31.2%), H⋯H (14.8%), C⋯H/H⋯C (14.0%), F⋯H/H⋯F (12.8%), C⋯C (9.0%) and Cl⋯Cl (6.7%) inter-actions.

Crystal structure and Hirshfeld surface analysis of (E)-3-[(4-fluoro-benzyl-idene)amino]-5-phenyl-thia-zolidin-2-iminium bromide.

In the cation of the title salt, C16H15FN3S+·Br-, the phenyl ring is disordered over two sets of sites with a refined occupancy ratio of 0.503 (4):0.497 (4). The mean plane of the thia-zolidine ring makes dihedral angles of 13.51 (14), 48.6 (3) and 76.5 (3)° with the fluoro-phenyl ring and the major- and minor-disorder components of the phenyl ring, respectively. The central thia-zolidine ring adopts an envelope conformation. In the crystal, centrosymmetrically related cations and anions are linked into dimeric units via N-H⋯Br hydrogen bonds, which are further connected by weak C-H⋯Br hydrogen bonds into chains parallel to [110]. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (44.3%), Br⋯H/H⋯Br (16.8%), C⋯H/H⋯C (13.9%), F⋯H/H⋯F (10.3%) and S⋯H/H⋯S (3.8%) inter-actions.

Crystal structure of [1,3-bis-(2,4,6-tri-methyl-phen-yl)imidazolidin-2-yl-idene]di-chlorido-{2-[1-(di-methyl-amino)-eth-yl]benzyl-idene}ruthenium including an unknown solvate.

The title compound, [RuCl2(C21H26N2)(C11H15N)], is an example of a new generation of N,N-dialkyl metallocomplex ruthenium catalysts with an N→Ru coordination bond as part of a six-membered chelate ring. The Ru atom has an Addison τ parameter of 0.234, which indicates a geometry inter-mediate between square-based pyramidal and trigonal-bipyramidal. The complex shows the usual trans arrangement of the two chloride ligands, with Ru-Cl bond lengths of 2.3397 (8) and 2.3476 (8) Å, and a Cl-Ru- Cl angle of 157.47 (3)°. The crystal structure features C-H⋯Cl, C-H⋯π and π-π stacking inter-actions. The solvent mol-ecules were found to be highly disordered and their contribution to the scattering was removed with the SQUEEZE procedure in PLATON [Spek (2015). Acta Cryst. C71, 9-18], which indicated a solvent cavity of volume 1096 Å3 containing approximately 419 electrons. These solvent mol-ecules are not considered in the given chemical formula and other crystal data.

Crystal structure and Hirshfeld surface analysis of (E)-1-[2,2-di-chloro-1-(4-nitro-phen-yl)ethen-yl]-2-(4-fluoro-phen-yl)diazene.

In the title compound, C14H8Cl2FN3O2, the 4-fluoro-phenyl ring and the nitro-substituted benzene ring form a dihedral angle of 63.29 (8)°. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds into chains running parallel to the c axis. The crystal packing is further stabilized by C-Cl⋯π, C-F⋯π and N-O⋯π inter-actions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯O/O⋯H (15.5%), H⋯H (15.3%), Cl⋯H/H⋯Cl (13.8%), C⋯H/H⋯C (9.5%) and F⋯H/H⋯F (8.2%) inter-actions.

Crystal structure and Hirshfeld surface analysis of dimethyl (3aS,6R,6aS,7S)-2-(2,2,2-tri-fluoro-acet-yl)-2,3-di-hydro-1H,6H,7H-3a,6:7,9a-di-epoxy-benzo[de]iso-quinoline-3a1,6a-di-carboxyl-ate.

The title mol-ecule, C18H16F3NO7, comprises a fused cyclic system containing four five-membered (two di-hydro-furan and two tetra-hydro-furan) rings and one six-membered (piperidine) ring. The five-membered di-hydro-furan and tetra-hydro-furan rings adopt envelope conformations, and the six-membered piperidine ring adopts a distorted chair conformation. Intra-molecular O⋯F inter-actions help to stabilize the conformational arrangement. In the crystal structure, mol-ecules are linked by weak C-H⋯O and C-H⋯F hydrogen bonds, forming a three-dimensional network. The Hirshfeld surface analysis confirms the dominant role of H⋯H contacts in establishing the packing.

IMDAV reaction between phenyl-maleic anhydride and thien-yl(fur-yl)allyl-amines: synthesis and mol-ecular structure of (3aSR,4RS,4aRS,7aSR)-5-oxothieno- and (3aSR,4SR,4aRS,7aSR)-5-oxofuro[2,3-f]iso-indole-4-carb-oxy-lic acids.

The title compounds C24H21NO3S, I, and C24H21NO4, II, are the products of the IMDAV reaction between phenyl-maleic anhydride and thien-yl(fur-yl)allyl-amines. Their mol-ecular structures comprise fused tricyclic systems containing thio-phene, cyclo-hexene and pyrrolidine rings (I) or furan, cyclo-hexene and pyrrolidine rings (II). The central cyclo-hexene and pyrrolidine rings in both compounds adopt slightly twisted boat and envelope conformations, respectively. The dihedral angles between the basal plane of the pyrrolidine ring and the thio-phene (in I) or furan (in II) ring plane are 22.74 (16) and 26.29 (5)°, respectively. The nitro-gen atom both in I and II has practically planar environment [the sums of the bond angles are 359.8 and 358.9°, respectively]. In the crystal of I, the mol-ecules form hydrogen-bonded zigzag chains along [010] through strong inter-molecular O-H⋯O hydrogen bonds involving carb-oxy-lic and keto groups, whereas in the crystal of II, the mol-ecules are joined into centrosymmetric dimers by strong O-H⋯O hydrogen bonds between the carb-oxy-lic groups. In II, the atoms involved into these hydrogen bonds (and hence the whole carb-oxy-lic group) are disordered over two sets of sites with an occupancy ratio of 0.6:0.4. Compounds I and II crystallize as racemates consisting of enanti-omeric pairs of the 3aSR,4RS,4aRS,7aSR and 3aSR,4SR,4aRS,7aSR diastereomers, respectively.

Crystal structure and Hirshfeld surface analysis of (E)-5-phenyl-3-[(pyridin-4-yl-methyl-idene)amino]-thia-zolidin-2-iminium bromide monohydrate.

In the cation of the title salt, C15H15N4S+·Br-·H2O, the central thia-zolidine ring adopts an envelope conformation with puckering parameters Q(2) = 0.279 (4) Šand φ(2) = 222.5 (9)°. The mean plane of the thia-zolidine ring makes dihedral angles of 12.4 (2) and 66.8 (3)° with the pyridine and phenyl rings, respectively. The pyridine ring in the title mol-ecule is essentially planar (r.m.s deviation = 0.005 Å). In the crystal, the cations, anions and water mol-ecules are linked into a three-dimensional network, which forms cross layers parallel to the (120) and (20) planes via O-H⋯Br, N-H⋯Br and N-H⋯N hydrogen bonds. C-H⋯π inter-actions also help in the stabilization of the mol-ecular packing. Hirshfeld surface analysis and 2D (two-dimensional) fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (35.5%), C⋯H/H⋯C (23.9%), Br⋯H/H⋯Br (16.4%), N⋯H/H⋯N (10.6%) and S⋯H/H⋯S (7.9%) inter-actions.

Three-component reaction between isatoic anhydride, amine and meth-yl-subs-tituted furyl-acryl-alde-hydes: crystal structures of 3-benzyl-2-[(E)-2-(5-methylfuran-2-yl)vin-yl]-2,3-di-hydro-quinazolin-4(1H)-one, 3-benzyl-2-[(E)-2-(furan-2-yl)-1-methyl-vin-yl]-2,3-di-hydro-quinazolin-4(1H)-one and 3-(furan-2-ylmeth-yl)-2-[(E)-2-(furan-2-yl)-1-methyl-vin-yl]-2,3-di-hydro-quinazolin-4(1H)-one.

Compounds (I), C22H20N2O2, (II), C22H20N2O2 and (III), C20H18N2O3 are the products of three-component reactions between isatoic anhydride, the corresponding amine and 3-(5-methylfuran-2-yl)- or (furan-2-yl)-2-methyl-acryl-aldehyde. Compound (I) crystallizes in the monoclinic space group P21/n, while compounds (II) and (III) are isostructural and crystallize in the ortho-rhom-bic space group Pbca. The tetra-hydro-pyrimidine ring in (I)-(III) adopts a sofa conformation. The NH nitro-gen atom has a trigonal-pyramidal geometry, whereas the N(R) nitro-gen atom is flattened. The furyl-vinyl substituents in (I)-(III) are practically planar and have an E configuration at the C=C double bond. In (I), this bulky fragment occupies the axial position at the quaternary carbon atom of the tetra-hydro-pyrimidine ring, whereas in (II) and (III) it is equatorially disposed. In the crystal of (I), mol-ecules form hydrogen-bonded chains propagating along [001] by strong inter-molecular N-H⋯O hydrogen bonds. The chains are packed in stacks along the a-axis direction. In the crystals of (II) and (III), mol-ecules also form hydrogen-bonded chains propagating along [100] by strong inter-molecular N-H⋯O hydrogen bonds. However, despite the fact that compounds (II) and (III) are isostructural, steric differences between the phenyl and furyl substituents result in chains with different geometries. Thus in the crystal of (II) the chains have a zigzag-like structure, whereas in the crystal of (III), they are almost linear. In both (II) and (III), the hydrogen-bonded chains are further packed in stacks along the b-axis direction.

Crystal structure and Hirshfeld surface analysis of (E)-3-[(2,3-di-chloro-benzyl-idene)amino]-5-phenyl-thia-zolidin-2-iminium bromide.

In the cation of the title salt, C16H14Cl2N3S+·Br-, the central thia-zolidine ring adopts an envelope conformation. The phenyl ring is disordered over two sites with a refined occupancy ratio of 0.541 (9):0.459 (9). In the crystal, C-H⋯Br and N-H⋯Br hydrogen bonds link the components into a three-dimensional network with the cations and anions stacked along the b-axis direction. Weak C-H⋯π inter-actions, which only involve the minor disorder component of the ring, also contribute to the mol-ecular packing. In addition, there are also inversion-related Cl⋯Cl halogen bonds and C-Cl⋯π (ring) contacts. A Hirshfeld surface analysis was conducted to verify the contributions of the different inter-molecular inter-actions.

Crystal structure and Hirshfeld surface analysis of ethane-1,2-diaminium 3-[2-(1,3-dioxo-1,3-di-phenyl-propan-2-yl-idene)hydrazin-yl]-5-nitro-2-oxido-benzene-sulfonate dihydrate.

In the anion of the title hydrated salt, C2H10N22+·C21H13N3O8S2-·2H2O, the planes of the phenyl rings and the benzene ring of the 5-nitro-2-oxido-benzene-sulfonate group are inclined to one another by 44.42 (11), 56.87 (11) and 77.70 (12)°. In the crystal, the anions are linked to the cations and the water mol-ecules by N-H⋯O and O-H⋯O hydrogen bonds, forming a three-dimensional network. Furthermore, there are face-to-face π-π stacking inter-actions between the centroids of one phenyl ring and the benzene ring of the 5-nitro-2-oxido-benzene-sulfonate group [centroid-centroid distance = 3.8382 (13) Šand slippage = 1.841 Å]. A Hirshfeld surface analysis was conducted to verify the contributions of the different inter-molecular inter-actions.

Crystal structure and Hirshfeld surface analysis of 3,3',3''-[(1,3,5-triazine-2,4,6-tri-yl)tris-(-oxy)]tris-(5,5-di-methyl-cyclo-hex-2-en-1-one).

The three cyclo-hexenone rings of the title compound, C27H33N3O6, adopt slightly distorted envelope conformations, with the C atom bearing two methyl groups as the flap atom in each case. These cyclo-hexenone mean planes form dihedral angles of 87.41 (11), 70.73 (11) and 70.47 (11)° with the 1,3,5-triazine ring, while the dihedral angle between the cyclo-hexenone mean planes are 57.52 (12), 23.75 (12) and 53.21 (12)°. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming a three-dimensional network.

Design of new anti-Alzheimer drugs: ring-expansion synthesis and synchrotron X-ray diffraction study of dimethyl 4-ethyl-11-fluoro-1,4,5,6,7,8-hexa-hydro-azonino[5,6-b]indole-2,3-di-carboxyl-ate.

The title compound, C20H23FN2O4, is the product of a ring-expansion reaction from a seven-membered fluorinated hexa-hydro-azepine to a nine-membered azonine. The nine-membered azonine ring of the mol-ecule adopts a chair-boat conformation. The C=C and C-N bond lengths [1.366 (3) and 1.407 (3) Å, respectively] indicate the presence of conjugation within the enamine CH2-C=C-N-CH2 fragment. The substituent planes at the C=C double bond of this fragment are twisted by 16.0 (3)° as a result of steric effects. The amine N(Et) N atom has a trigonal-pyramidal configuration (sum of the bond angles = 346.3°). The inter-planar angle between the two carboxyl-ate substituents is 60.39 (8)°. In the crystal, mol-ecules form zigzag chains along [010] by inter-molecular N-H⋯O hydrogen-bonding inter-actions, which are further packed in stacks toward [100]. The title azonino-indole might be considered as a candidate for the design of new Alzheimer drugs.

Crystal structure of 3-benzyl-2-[(E)-2-(furan-2-yl)ethen-yl]-2,3-di-hydro-quinazolin-4(1H)-one and 3-benzyl-2-[(E)-2-(thio-phen-2-yl)ethen-yl]-2,3-di-hydro-quinazolin-4(1H)-one from synchrotron X-ray diffraction.

The chiral title compounds, C21H18N2O2, (I), and C21H18N2OS, (II) - products of the three-component reaction between benzyl-amine, isatoic anhydride and furyl- or thienyl-acrolein - are isostructural and form isomorphous racemic crystals. The tetra-hydro-pyrimidine ring in (I) and (II) adopts a sofa conformation. The amino N atom has a trigonal-pyramidal geometry [sum of the bond angles is 347.0° for both (I) and (II)], whereas the amido N atom is flat [sum of the bond angles is 359.3° for both (I) and (II)]. The furyl- and thienylethenyl substituents in (I) and (II) are planar and the conformation about the bridging C=C bond is E. These bulky fragments occupy the axial position at the quaternary C atom of the tetra-hydro-pyrimidine ring, apparently, due to steric reasons. In the crystals, mol-ecules of (I) and (II) form hydrogen-bonded helicoidal chains propagating along [010] by strong inter-molecular N-H⋯O hydrogen bonds.

Crystal structures of (5RS)-(Z)-4-[5-(furan-2-yl)-3-phenyl-4,5-di-hydro-1H-pyrazol-1-yl]-4-oxobut-2-enoic acid and (5RS)-(Z)-4-[5-(furan-2-yl)-3-(thio-phen-2-yl)-4,5-di-hydro-1H-pyrazol-1-yl]-4-oxobut-2-enoic acid.

The title compounds, C17H14N2O4 (I) and C15H12N2O4S (II), possess very similar mol-ecular geometries. In both mol-ecules, the central 1,3,5-tris-ubstituted di-hydro-pyrazole ring adopts an envelope conformation. The oxobutenoic acid fragment has an almost planar Z conformation [r.m.s. deviations of 0.049 and 0.022 Å, respectively, for (I) and (II)] which is determined by the both bond conjugation and the strong intra-molecular O-H⋯O hydrogen bond. The substituents in positions 1 and 3 of the di-hydro-pyrazole ring [oxobutenoic acid and phenyl in (I) and oxobutenoic acid and thienyl in (II)] are nearly coplanar with its basal plane [the corresponding dihedral angles are 6.14 (9) and 2.22 (11)° in (I) and 6.27 (12) and 3.91 (11)° in (II)]. The furyl ring plane is twisted relative to the basal plane of the di-hydro-pyrazole ring by 85.51 (8) and 88.30 (7)° in (I) and (II), respectively. In the crystal of (I), mol-ecules form zigzag hydrogen-bonded chains along [001] by C-H⋯O hydrogen bonds, which are further packed in stacks along [100]. Unlike (I), the crystal of (II) contains centrosymmetric hydrogen-bonded dimers formed by pairs of C-H⋯S hydrogen bonds, which are further linked by weak C-H⋯O hydrogen bonds into a three-dimensional framework.

A New Ceramide and Biflavonoid from the Leaves of Parinari hypochrysea (Chrysobalanaceae).

A new ceramide and a new biflavonoid named parinaramide (1) and sparinaritin (2), respectively, have been isolated along with ten known compounds, kaempferol, quercetin, taxifolin, taxifolin-3-O-rhamnoside, lupeol, betulinic acid, ursolic acid, 2α-hydroxy-ursolic acid, 2,3-dihydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl)-1-propanone, and sucrose, from the leaves of Parinari hypochrysea (Chrysobalanaceae). Structures were determined using 1D- and 2D-NMR, MS and by chemical analysis. The methanol extract of leaves, stem bark and roots of P. hypochrysea were screened for their antioxidant and lipoxygenase inhibition potential and found to be inactive.