Investigation of the molecular basis of halogenated Schiff base derivative by combined crystallographic and computational studies

Halogenated Schiff base derivatives are gaining more popularity in supramolecular chemistry due to the synergistic effect of hydrogen and halogen-based noncovalent interactions, which helps to design novel therapeutic materials. In this work, we have examined the nature of molecular interactions to investigate the structure-functional relationship of a halogen-based derivative. The FTIR, HRMS and NMR spectroscopic techniques confirmed the formation of the desired novel Schiff base compound. Further, crystal structure studies showed an infinite 1D supramolecular chain formed by type-I halogen…halogen interaction. The Hirshfeld surface and enrichment ratio analyses were performed to visualize and assess the role of diverse interactions involved in crystal packing. The QTAIM, NCI, LOL and ELF studies were conducted extensively to comprehend the strength of interaction constructed based on electron density distribution. The global and local reactive indices were determined using DFT studies to analyze the molecular properties of the compound. Antibacterial activity against MRSA bacteria was performed and showed a good zone of inhibition. The docking analysis was performed for 1mwt protein and validated. The in silico molecular docking studies of the halogenated Schiff base structure with the penicillin-binding protein showed a good docking affinity of -7.5 kcal/mol and supported by in vitro studies. The ligand binding stability within the protein's active site was further demonstrated by molecular dynamics (MD) simulation studies for the Schiff base molecule.Communicated by Ramaswamy H. Sarma.

Structure-property relationship in thioxotriaza-spiro derivative: Crystal structure and molecular docking analysis against SARS-CoV-2 main protease

Detailed structural and non-covalent interactions in thioxotriaza-spiroderivative (DZ2) are investigated by single crystal structure anslysis and computational approaches. Its results were compared with the previously reported spiroderivative (DZ1). The crystal structure analysis revealed various C–H…O, N–H…O, C–H…N and N–H…S hydrogen bonds involved in constructing several dimeric motifs to stabilize the crystal packing. The differences and similarities in the relative contribution of non-covalent interactions in DZ1 and DZ2 compounds are compared using the Hirshfeld surface analysis and 2D fingerprint plots. The binding energies of specific molecular pairs and homodimers have been obtained using molecule–molecule interaction energy calculation. The hierarchy and topology of pair-wise intermolecular interactions are visualized through energy frameworks. The nature and strength of intra and intermolecular interactions were characterized using non-covalent interaction index analysis and the quantum theory of atoms in molecule approach. Further, molecular docking of compounds (DZ1 and DZ2) with SARS-CoV-2 main protease for COVID-19 is performed. And the superposition of these ligands and inhibitor N3, which is docked into the binding pocket of 7BQY, is presented. The binding affinity of −6.7 kcal/mol is observed, attributed to hydrogen bonding and hydrophobic interactions between the ligand and the amino acid residues of the receptor.

4-acetamido-3-nitrobenzoic acid - structural, quantum chemical studies, ADMET and molecular docking studies of SARS-CoV2

In December 2019, a new type of SARS corona virus emerged from China and caused a globally pandemic corona virus disease (COVID-19). This highly infectious virus has been named as SARS-CoV-2 by the International Committee of the Taxonomy of Viruses. It has severely affected a large population and economy worldwide. Globally various scientific communities have been involved in studying this newly emerged virus and is lifecycle. Multiple diverse studies are in progress to design novel therapeutic agents, in which understanding of interactions between the target and drug ligand is a significant key for this challenge. Structures of proteins involved in the life cycle of the virus have been revealed in RCSB PDB by researchers. In this study, we employed molecular docking study of 4-Acetamido-3-nitrobenzoic acid (ANBA) with corona virus proteins (spike protein, spike binding domain with ACE2 receptor and Main protease, RNA-dependent RNA polymerase). Single crystal X-ray analysis and density functional theory calculations were carried out for ANBA to explore the structural and chemical-reactive parameters. Intermolecular interactions which are involved in the ligand-protein binding process are validated by Hirshfeld surface analysis. To study the behaviour of ANBA in a living organism and to calculate the physicochemical parameters, ADMET analysis was done using SwissADME and Osiris data warrior tools. Further, Toxicity of ANBA was predicted using pkCSM online software. Based on the molecular docking analysis, we introduce here a potent drug molecule that binds to the COVID-19 proteins.Communicated by Ramaswamy H. Sarma.

Design, crystal structure determination, molecular dynamic simulation and MMGBSA calculations of novel p38-alpha MAPK inhibitors for combating Alzheimer's disease

The hallmark of the Alzheimer's disease (AD) is the accumulation of aggregated, misfolded proteins. The cause for this accumulation is increased production of misfolded proteins and impaired clearance of them. Amyloid aggregation and tau hyperphosphorylation are the two proteinopathies which accomplish deprivation of cell and tissue hemostasis during neuropathological process of the AD, as a result of which progressive neuronal degeneration and the loss of cognitive functions. p38 mitogen-activated protein kinase (p38 MAPK) has been implicated in both the events associated with AD: tau protein phosphorylation and inflammation. p38α MAPK pathway is activated by a dual phosphorylation at Thr180 and Tyr182 residues. Clinical and preclinical evidence implicates the stress related kinase p38α MAPK as a potential neurotherapeutic target. Drug design of p38α MAPK inhibitors is mainly focused on small molecules that compete for Adenosine triphosphate in the catalytic site. Here we have carried out the synthesis of phenyl sulfonamide derivatives Sulfo (I) and Sulfo (II). Crystal structures of Sulfo (I) and Sulfo (II) were solved by direct methods using SHELXS-97. Sulfo (I) and Sulfo (II) have R_int values of 0.0283 and 0.0660, respectively, indicating good quality of crystals and investigated their ability against p38α MAPK. Docking studies revealed that the Sulfo (I) had better binding affinity (-62.24 kcal/mol) as compared to Sulfo (II) and cocrystal having binding affinity of -54.61 kcal/mol and -59.84 kcal/mol, respectively. Molecular dynamics simulation studies of Sulfo (I) and cocrystal of p38α MAPK suggest that during the course of 30 ns simulation run, compound Sulfo (I) attained stability, substantiating the consistency of its binding to p38α MAPK compared to cocrystal. Binding free energy analysis suggests that the compound Sulfo (I) is better than the cocrystal. Thus, this study corroborates the therapeutic potential of synthesized Sulfo (I) in combatting AD.Communicated by Ramaswamy H. Sarma.

Theoretical and experimental solid state studies of Ethyl 1-benzyl-2-(thiophen-3-yl)-1H-benzo[d]imidazole-5-carboxylate

The title compound Ethyl 1-benzyl-2-(thiophen-3-yl)-1H-benzo[d]imidazole-5-carboxylate (BI) is prepared and characterized using spectroscopic methods. The theoretical optimization and three dimensional molecular structure are confirmed by X-ray diffraction method (single crystal). The C–H…π intermolecular interactions stabilize the crystal structure. The intermolecular contacts in the crystal structure are quantified using Hirshfeld surfaces and the crystal packing is elucidated using 3D energy frameworks analysis. In the frameworks, the dispersion energy term is dominated over the electrostatic energy term. The structural optimization was carried out with B3LYP/6-311++G (d, p) level of theory. The visual representations of positive and negative potentials (electrostatic potential) are mapped on the electron density isosurface. The band gap energy (HOMO-LUMO) of the molecule is calculated to be 4.36 eV. Structural conformation of BI is compared with similar structures.

I2-Catalyzed transformation of o-aminobenzamide to o-ureidobenzonitrile using isothiocyanates

The present work describes an unexpected and unique protocol for the iodine catalysed synthesis of o-ureidobenzonitriles using o-aminobenzamides and isothiocyanates via intramolecular rearrangement. The metal-free route achieved here is insensitive to moisture and applicable to the synthesis of a wide variety of o-ureidobenzonitriles with excellent yields even in a scalable fashion.

Crystal structure, Hirshfeld surfaces, topology, energy frameworks and dielectric studies of 1-(2-chlorophenyl)- 3,3-bis(methylthio)prop-2-en-1-one

The title compound 1-(2-chlorophenyl)-3,3-bis(methylthio)prop-2-en-1-one (1) have been synthesized, crystallized and characterized using FT-IR, 1H NMR, 13C NMR, LCMS and confirmed by single crystal X-ray diffraction method. In addition, the intermolecular interactions in the crystal structure are analyzed using Hirshfeld surfaces computational method. The (1) crystallizes in a monoclinic crystal system (space group P 21/ c) with cell parameters a = 17.0132(9) Å, b = 8.6521(4) Å, c = 8.2815(7) Å, β = 95.512(6) ° and Z = 4. Intermolecular hydrogen bonds/interactions of the type C · · · H · · · O, C–H · · · S, C–H · · · Cg and C–Cl · · · Cg stabilize the crystal structure. The intermolecular interactions responsible for crystal packing are analyzed using Hirshfeld surfaces computational method, 2D finger print plots, electrostatic potential surfaces, toplogy surfaces [curvedness (C) and shape index (S), enrichment ratio (E) and 3D energy frameworks]. In addition the dielectric studies were performed for the title molecule. The crystal structure database (CSD) analysis was carried out for structural conformation and crystal packing confirmation. Overall structural studies confirmed that the intermolecular interactions of the type S · · · S chalocogen bonds are involved in crystal packing in addition to the C11–H11 · · · O1, C10–H10B · · · O1, two C10–H10 · · · S1, C4–H11 · · · Cg1 and C1–Cl1 · · · Cg1 interactions.

One-dimensional copper(II) coordination polymers based on 1,3-bis(pyridin-4-yl)propane and diimine ligands

Two one-dimensional (1D) coordination polymers (CPs), namely catena-poly[[[aqua(2,2'-bipyridine-κ²N,N')(nitrato-κO)copper(II)]-μ-1,3-bis(pyridin-4-yl)propane-κ²N:N'] nitrate], {[Cu(NO₃)(C₁₀H₈N₂)(C₁₃H₁₄N₂)(H₂O)]·NO₃}_n (1), and catena-poly[[[aqua(nitrato-κO)(1,10-phenanthroline-κ²N,N')copper(II)]-μ-1,3-bis(pyridin-4-yl)propane-κ²N:N'] nitrate], {[Cu(NO₃)(C₁₂H₈N₂)(C₁₃H₁₄N₂)(H₂O)]·NO₃}_n (2), have been synthesized using [Cu(NO₃)(NN)(H₂O)₂]NO₃, where NN = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen), as a linker in a 1:1 molar ratio. The CPs were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis and single-crystal X-ray structure determination. The 1,3-bis(pyridin-4-yl)propane (dpp) ligand acts as a bridging ligand, leading to the formation of a 1D polymer. The octahedral coordination sphere around copper consists of two N atoms from bpy for 1 or phen for 2, two N atoms from dpp, one O atom from water and one O atom from a coordinated nitrate anion. Each structure contains two crystallographically independent chains in the asymmetric unit and the chains are linked via hydrogen bonds into a three-dimensional network.

Design and Amberlyst-15 mediated synthesis of novel thienyl-pyrazole carboxamides that potently inhibit Phospholipase A2 by binding to an allosteric site on the enzyme

Inflammation-mediated disorders are on the rise and hence, there is an urgent need for the design and synthesis of new anti-inflammatory drugs with higher affinity and specificity for their potential targets. The current study presents an effective and new protocol for the synthesis of thienyl-pyrazoles through 3 + 2 annulations using a recyclable heterogeneous catalyst Amberlyst-15. Chalcones 3(a-g) prepared from 3-methylthiophene-2-carbaldehyde and acetophenones by Claisen-Schmidt approach reacted with semicarbazide hydrochloride 4 in the presence of Amberlyst-15 in acetonitrile at room temperature producing thienyl-pyrazole carboxamides 5(a-h) in good yields. Alternatively, the compounds 5(a-h) were prepared by conventional method using acetic acid (30%) medium. Structures of synthesized new pyrazoles were confirmed by spectral and crystallographic studies. All the new compounds were evaluated for their in vitro inhibition of Phospholipase A2 from Vipera russelli and preliminary studies revealed that, amongst the designed series, compounds 5b, 5c and 5h showed promising inhibition. Further, the compounds exhibited linear mixed-type inhibition behavior for the sPLA2 enzyme indicating that they bind to an allosteric site distinct from either the calcium or substrate binding site on the enzyme. These kinetic conclusions were further validated by macromolecular rigid-body docking whereby compounds 5c and 5h showed binding to distinct pockets on the protein. These findings present a promising series of lead molecules that can serve as prototypes for the treatment of inflammatory related disorders.

Synthesis of cocrystals/salts of flucytosine: Structure and stability

Three molecular salts and two cocrystals of FLC were synthesized with superior solid state stability.

Different supramolecular architectures mediated by different weak interactions in the crystals of three N-aryl-2,5-dimethoxybenzenesulfonamides

The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N-aryl-2,5-dimethoxybenzenesulfonamides, namely N-(2,3-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C₁₄H₁₃Cl₂NO₄S, (I), N-(2,4-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C₁₄H₁₃Cl₂NO₄S, (II), and N-(2,4-dimethylphenyl)-2,5-dimethoxybenzenesulfonamide, C₁₆H₁₉NO₄S, (III), are described. The asymmetric unit of (I) consists of two symmetry-independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C-H...O interactions in (I), N-H...Cl and C-H...O interactions in (II), and C-H...O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C-H...O, C-H...Cl, C-H...π(aryl), π(aryl)-π(aryl) and Cl...Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The d_norm and shape-index surfaces of (I)-(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H...H contacts, followed by H...O/O...H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N-H...O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N-H...O hydrogen bonds form either C(4) chain motifs or R₂²(8) rings. Further comparison reveals that the characteristics of the N-H...O hydrogen-bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the benzenesulfonyl ring, with the nature and position of the substituents on the aniline ring exerting little effect. On the other hand, the crystal structures of (I)-(III) display several weak interactions other than the common N-H...O hydrogen bonds, resulting in supramolecular architectures varying from one- to three-dimensional depending on the nature and position of the substituents on the aniline ring.

A fluorophore-labelled copper complex: crystal structure, hybrid cyclic water-perchlorate cluster and biological properties

A fluorophore-labelled copper(II) complex, aquabis(dimethylformamide-κO)(perchlorato-κO)[2-(quinolin-2-yl)-1,3-oxazolo[4,5-f][1,10]phenanthroline]copper(II) perchlorate monohydrate, [Cu(ClO₄)(C₂₂H₁₂N₄O)(C₃H₇NO)₂(H₂O)]ClO₄·H₂O, has been synthesized and characterized. A cyclic hydrogen-bonded water-perchlorate anionic cluster, i.e. [(ClO₄)₂(H₂O)₂]^2-, has been identified within the structure. Each cyclic anionic cluster unit is interconnected by hydrogen bonding to the cation. The cations join into an infinite hydrogen-bonded chain running in the [010] direction. Furthermore, interaction of the complex with calf-thymus DNA (CT-DNA) and cellular localization within the cells was explored. Spectroscopic studies indicate that the compound has a good affinity for DNA and stains the nucleus of the cells.

The crystal structure of zwitterionic 2-{[(4-imin-iumyl-3-methyl-1,4-di-hydro-pyridin-1-yl)meth-yl]carbamo-yl}benzoate hemihydrate

The asymmetric unit of the title compound, C₁₅H₁₅N₃O₃·0.5H₂O, comprises two 2-{[(4-iminiumyl-3-methyl-1,4-di-hydro-pyridin-1-yl)meth-yl]carbamo-yl}benzoate zwitterions (A and B) and a water mol-ecule. The dihedral angles between the pyridine and phenyl rings in the zwitterions are 53.69 (10) and 73.56 (11)° in A and B, respectively. In the crystal, mol-ecules are linked by N-H⋯O, O-H⋯O, C-H⋯O and C-H⋯π(ring) hydrogen bonds into a three-dimensional network. The crystal structure also features π-π inter-actions involving the centroids of the pyridine and phenyl rings [centroid-centroid distances = 3.5618 (12) Å in A and 3.8182 (14) Å in B].

Three closely related (2E,2'E)-3,3'-(1,4-phenyl-ene)bis-[1-(meth-oxy-phen-yl)prop-2-en-1-ones]: supra-molecular assemblies in one dimension mediated by hydrogen bonding and C-H⋯π inter-actions

The three title compounds are centrosymmetric. Their packing features chains linked by either pairwise C—H⋯O or C—H⋯π inter­actions.

In the title compounds, (2E,2′E)-3,3′-(1,4-phenyl­ene)bis­[1-(2-meth­oxy­phen­yl)prop-2-en-1-one], C₂₆H₂₂O₄ (I), (2E,2′E)-3,3′-(1,4-phenyl­ene)bis­[1-(3-meth­oxy­phen­yl)prop-2-en-1-one], C₂₆H₂₂O₄ (II) and (2E,2′E)-3,3′-(1,4-phenyl­ene)bis­[1-(3,4-di­meth­oxy­phen­yl)prop-2-en-1-one], C₂₈H₂₆O₆ (III), the asymmetric unit consists of a half-mol­ecule, completed by crystallographic inversion symmetry. The dihedral angles between the central and terminal benzene rings are 56.98 (8), 7.74 (7) and 7.73 (7)° for (I), (II) and (III), respectively. In the crystal of (I), mol­ecules are linked by pairs of C—H⋯π inter­actions into chains running parallel to [101]. The packing for (II) and (III), features inversion dimers linked by pairs of C—H⋯O hydrogen bonds, forming R₂²(16) and R₂²(14) ring motifs, respectively, as parts of [201] and [101] chains, respectively.

Supramolecular architectures in N-(4-bromobenzoyl)-arylsulfonamides: crystal structures and Hirshfeld surface analysis

A detailed analysis of the molecular packing of five N-(4-bromobenzoyl)-substituted benzenesulfonamides, i-X~4-Br (1–5) [i-X=H, 2-CH3, 4-CH3, 2-Cl, 4-Cl] is presented. The intermolecular interactions and the packing patterns are evaluated along with an analysis of their Hirshfeld surfaces and fingerprint plots (FP). The crystals feature molecular self-assembly through N–H···O hydrogen-bonds forming three types of supramolecular synthon:  C 1 1 ( 4 ) ${\rm{C}}_1^1(4)$ chain, R 4 4 ( 16 ) ${\rm{R}}_4^4(16)$ tetramer and R 2 2 ( 8 ) ${\rm{R}}_2^2(8)$ ring. These molecular assemblies extend to form one-dimensional (1D), 2D or 3D supramolecular architectures via diverse intermolecular interactions. A study of 33 i-X~4-Y (Y=H, CH3, OCH3, NO2, F, Cl, Br) structures shows the substituent on the sulfonamide ring modulates the intermolecular interactions and the subsequent supramolecular architectures drastically, with the fluoro- and bromo-substituted analogues providing distinctive self-assemblies. The R 4 4 ( 16 ) ${\rm{R}}_4^4(16)$ synthon produced by N–H···O hydrogen-bonds in the 4-CH3~4-Br derivative is a rare phenomenon amongst a set of 74 i-X~j-Y structures.

Crystal structures of isomeric 4-bromo-N-[(2-nitro-phen-yl)sulfon-yl]benzamide and 4-bromo-N-[(4-nitro-phen-yl)sulfon-yl]benzamide

The isomeric title compounds both display three-dimensional supra­molecular architectures arising from N—H⋯O, C—H⋯O, C—H⋯π and π–π inter­actions.

The syntheses and crystal structures of the isomeric 4-bromo-N-[(2-nitro­phen­yl)sulfon­yl]benzamide, (I), and 4-bromo-N-[(4-nitro­phen­yl)sulfon­yl]benzamide, (II), are described (mol­ecular formula = C₁₃H₉BrN₂O₅S in each case). The asymmetric unit of (I) contains two independent mol­ecules [(IA) and (IB)], while that of (II) contains one mol­ecule. The benzoic acid aromatic ring of mol­ecule (IA) is disordered due to rotation about the C_ar—C(=O) bond over two orientations in a 0.525 (9):0.475 (9) ratio. The dihedral angle between the benzene rings is 85.9 (3)° in (IA) and 65.22 (19)° in (IB), while in (II), the corresponding value is 56.7 (7)°. In the crystals of (I) and (II), N—H⋯O, C—H⋯O and C—H⋯π inter­actions generate three-dimensional networks.

Crystal structures of 3-fluoro-N-[2-(tri-fluoro-meth-yl)phen-yl]benzamide, 3-bromo-N-[2-(tri-fluoro-meth-yl)phen-yl]benzamide and 3-iodo-N-[2-(tri-fluoro-meth-yl)phen-yl]benzamide

The crystal structures of three N-[2-(tri­fluoro­meth­yl)phen­yl]benzamides are reported. The 3-fluoro­benzamide crystallized with two independent mol­ecules in the asymmetric unit; the dihedral angles between the two benzene rings are 43.94 (8) and 55.66 (7)°. In the 3-bromo­benzamide and the 3-iodo­benzamide, this dihedral angle is much smaller, viz. 10.40 (12) and 12.5 (2)°, respectively.

In the title compounds, C₁₄H₉F₄NO, (I), C₁₄H₉BrF₃NO, (II), and C₁₄H₉F₃INO, (III), the two benzene rings are inclined to one another by 43.94 (8)° in mol­ecule A and 55.66 (7)° in mol­ecule B of compound (I), which crystallizes with two independent mol­ecules in the asymmetric unit, but by only 10.40 (12)° in compound (II) and 12.5 (2)° in compound (III). In the crystals of all three compounds, N—H⋯O hydrogen bonds link the mol­ecules to form chains propagating along the a-axis direction for (I), and along the b-axis direction for (II) and (III). In the crystal of (I), –A–B–A–B– chains are linked by C—H⋯O hydrogen bonds, forming layers parallel to (010). Within the layers there are weak offset π–π inter­actions present [inter­centroid distances = 3.868 (1) and 3.855 (1) Å]. In the crystals of (II) and (III), the chains are linked via short halogen–halogen contacts [Br⋯Br = 3.6141 (4) Å in (II) and I⋯I = 3.7797 (5) Å in (III)], resulting in the formation of ribbons propagating along the b-axis direction.

Investigation of the crystal structures and Hirshfeld surfaces of three closely related N-(2-fluorobenzoyl)-arylsulfonamides

The investigation of the crystal structures of three closely related sulfonamides, namely N-(2-fluorobenzoyl)-2-methylbenzenesulfonamide (I), N-(2-fluorobenzoyl)-4-methylbenzenesulfonamide (II) and N-(2-fluorobenzoyl)-2-chlorobenzenesulfonamide (III) by analysing intermolecular interactions and the packing patterns, and also by Hirshfeld surface analyses is presented. Compound (I) has a three-dimensional (3D) network, in which N–H···O and C–H···F chains build up two-dimensional (2D) arrays, which are extended into a 3D network through C–H···π interactions. In (II), alternating N–H···O and C–H···O rings form one-dimensional (1D) ribbons, which are interconnected by C–H···π interactions to build a 2D network. In (III), 2D sheets comprising N–H···O rings, C–H···π chains, Cl···F and F···F contacts are stacked by π···π interactions to form a 3D network. Hirshfeld surface analyses, comprising dnorm surfaces, curvedness and 2D fingerprint (FP) plots, for all three molecules were also conducted to verify the importance of the different intermolecular interactions.

Crystal structures of three N-(aryl-sulfon-yl)-4-fluoro-benzamides

The crystal structures of three N-(aryl­sulfon­yl)-4-fluoro­benzamides, namely 4-fluoro-N-(2-methyl­phenyl­sulfon­yl)­benzamide, (I), N-(2-chloro­phenyl­sulfon­yl)-4-fluoro­benzamide, (II), and N-(4-chloro­phenyl­sulfon­yl)-4-fluoro­benzamide monohydrate, (III), are described and compared with related structures. The conformation of the three mol­ecules is very similar with the aromatic rings being inclined to one another by 82.83 (11) and 85.01 (10)° in the two independent mol­ecules of (I), 89.91 (10)° in (II) and 81.82 (11)° in (III).

The crystal structures of three N-aryl­sulfonyl-4-fluoro­benzamides, namely 4-fluoro-N-(2-methyl­phenyl­sulfon­yl)benzamide, C₁₄H₁₂FNO₃S, (I), N-(2-chloro­phenyl­sulfon­yl)-4-fluorobenzamide, C₁₃H₉ClFNO₃S, (II), and N-(4-chloro­phenyl­sulfon­yl)-4-fluoro­benzamide monohydrate, C₁₃H₉ClFNO₃S·H₂O, (III), are described and compared with related structures. The asymmetric unit of (I) contains two independent mol­ecules (A and B), while that of (II) contains just one mol­ecule, and that of (III) contains a mol­ecule of water in addition to one main mol­ecule. The dihedral angle between the benzene rings is 82.83 (11)° in mol­ecule A and 85.01 (10)° in mol­ecule B of (I), compared to 89.91 (10)° in (II) and 81.82 (11)° in (III). The crystal structure of (I) features strong N—H⋯O hydrogen bonds between the A and B mol­ecules, resulting in an R₄⁴(16) tetra­meric unit. These tetra­meric units are connected into sheets in the bc plane by various C—H⋯O inter­actions, and adjacent sheets are further inter­linked via C—H⋯π_ar­yl inter­actions, forming a three-dimensional architecture. The crystal structure is further stabilized by π_ar­yl–π_ar­yl and S=O⋯π_ar­yl inter­actions. In the crystal of (II), mol­ecules are connected into R₂²(8) and R₂²(14) dimers via N—H⋯O hydrogen bonds and C—H⋯O inter­actions, respectively; the dimers are further inter­connected via a weak C=O⋯π_ar­yl inter­action, leading to the formation of chains along [1-10]. In the crystal of (III), N—H⋯O and O—H⋯O hydrogen bonds involving both the main mol­ecule and the solvent water mol­ecule results in the formation of sheets parallel to the bc plane. The sheets are further connected by C—H⋯O inter­actions and weak C—Cl⋯π_ar­yl, C—F⋯π_ar­yl and S=O⋯π_ar­yl inter­actions, forming a three-dimensional architecture.

Crystal structure of 3-(thiophen-2-yl)-5-(p-tolyl)-4,5-dihydro-1H-pyrazole-1-carboxamide

C15H15N3OS, monoclinic, P21/c (No. 14), a = 10.2852(5) Å, b = 10.1649(5) Å, c = 14.7694(8) Å, β = 107.442(2)°, V = 1473.12(13) Å3, Z = 4, R gt (F) = 0.0449, wR ref (F 2 ) = 0.1275, T = 293(2) K.

Crystal structure of 2-(4-methyl-piperazin-1-yl)quinoline-3-carbaldehyde

In the title compound, C₁₅H₁₇N₃O, the aldehyde group is twisted relative to the quinoline group by17.6 (2)° due to the presence of a bulky piperazinyl group in the ortho position. The piperazine N atom attached to the aromatic ring is sp³-hybridized and the dihedral angle between the mean planes through the the six piperazine ring atoms and through the quinoline ring system is 40.59 (7)°. Both piperazine substituents are in equatorial positions.

Crystal structure of 8-eth-oxy-3-(4-nitro-phen-yl)-2H-chromen-2-one

In the title compound, C17H13NO5, the coumarin ring system is essentially planar (r.m.s. deviation = 0.008 Å). The nitro-phenyl ring makes a dihedral angle of 25.27 (9)° with the coumarin ring plane. The nitro group is almost coplanar with the phenyl ring to which it is attached, making a dihedral angle of 4.3 (3)°. The eth-oxy group is inclined to the coumarin ring plane by 4.1 (2)°. Electron delocalization was found at the short bridging C-C bond with a bond length of 1.354 (2) Å. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming sheets in the bc plane. The sheets are linked via π-π stacking [centroid-centroid distances = 3.5688 (13) and 3.7514 (13) Å], forming a three-dimensional structure.

Crystal structure of (2R)-1-[(methyl-sulfon-yl)-oxy]propan-2-aminium chloride: a chiral mol-ecular salt

In the title chiral mol­ecular salt, C₄H₁₂NO₃S⁺·Cl⁻, the cation is protonated at the N atom, producing [RNH₃]⁺, where R is CH₃SO₂OCH₂C(H)CH₃. The N atom in the cation is sp³-hybridized. In the crystal, cations and anions are connected by strong N—H⋯Cl hydrogen bonds to generate edge-shared 12-membered rings of the form {⋯Cl⋯HNH}₃. This pattern of hydrogen bonding gives rise to zigzag supra­molecular layers in the ab plane. The layers are connected into a three-dimensional architecture by C—H⋯O hydrogen bonds. The structure was refined as an inversion twin.

Crystal structures of three N-ar-yl-2,2,2-tri-bromo-acetamides

Three N-(ar­yl)-2,2,2-tri­bromo­acetamides show different weak inter­actions in their crystal structures.

Three N-ar­yl-2,2,2-tri­bromo­acetamides, namely, 2,2,2-tri­bromo-N-(2-fluoro­phen­yl)­acetamide, C₈H₅Br₃FNO, (I), 2,2,2-tri­bromo-N-[3-(tri­fluoro­methyl)­phen­yl]­acetamide, C₉H₅Br₃F₃NO, (II) and 2,2,2-tri­bromo-N-(4-fluoro­phen­yl)­acetamide, C₈H₅Br₃FNO, (III) were synthesized and their crystal structures were analysed. In the crystal structure of (I), C—Br⋯π_ar­yl inter­actions connect the mol­ecules into dimers, which in turn are connected via Br⋯Br contacts [3.6519 (12) Å], leading to the formation of a one-dimensional ladder-type architecture. The crystal structure of (II) features chains linked by N—H⋯O and C—H⋯O hydrogen bonds. Two such chains are inter­linked to form ribbons through Br⋯Br [3.6589 (1) Å] and Br⋯F [3.0290 (1) Å] inter­actions. C—Br⋯π_ar­yl and C—F⋯π_ar­yl inter­actions between the ribbons extend the supra­molecular architecture of (II) from one dimension to two. In (III), the mol­ecules are connected into R₂²(8) dimers via pairs of C—H⋯F inter­actions and these dimers form ribbons through Br⋯Br [3.5253 (1) Å] contacts. The ribbons are further inter­linked into columns via C—Br⋯O=C contacts, forming a two-dimensional architecture.

Investigation of the crystal structures of N-(4-fluorobenzoyl)benzenesulfonamide and N-(4-fluoro-benzoyl)-4-methylbenzenesulfonamide

The crystal structures of two closely related compounds, namely, N-(4-fluorobenzoyl)-benzenesulfonamide (I) and N-(4-fluorobenzoyl)-4-methylbenzenesulfonamide (II) are investigated by analysing the packing patterns and intermolecular interactions, and also by Hirshfeld surface analysis. The crystal structure of each of (I) and (II) displays a two-dimensional architecture. Hirshfeld surfaces comprising dnorm surface and 2D fingerprint plots were analysed for both molecules in order to understand the relationship between the crystal structures. The analysis shows that the lengths of the observed hydrogen bonds and other intermolecular interactions in (II) are relatively shorter than those observed in (I). Further, the analysis demonstrates the predominant participation of the sulfonyl-O atom and the carbonyl-O atom as the hydrogen bond acceptors in (I) and (II), respectively.

Crystal structure of 3-(thio-phen-2-yl)-5-p-tolyl-4,5-di-hydro-1H-pyrazole-1-carbo-thio-amide

In the title compound, the central pyrazole ring adopts a twisted conformation on the –CH—CH₂– bond and its mean plane makes dihedral angles of 7.19 (12) and 71.13 (11)° with the attached thio­phene and toluene rings, respectively. In the crystal, mol­ecules are linked by N—H⋯S hydrogen bonds, forming chains propagating along [010].

In the title compound, C₁₅H₁₅N₃S₂, the central pyrazole ring adopts a twisted conformation on the –CH—CH₂– bond. Its mean plane makes dihedral angles of 7.19 (12) and 71.13 (11)° with those of the thio­phene and toluene rings, respectively. The carbothi­amide group [C(=S)—N] is inclined to the pyrazole ring mean plane by 16.8 (2)°. In the crystal, mol­ecules are linked by N—H⋯S hydrogen bonds, forming chains propagating along [010]. Within the chains, there are N—H⋯π inter­actions present. Between the chains there are weak parallel slipped π–π inter­actions involving inversion-related thio­phene and pyrazole rings [inter-centroid distance = 3.7516 (14) Å; inter-planar distance = 3.5987 (10) Å; slippage = 1.06 Å].

Crystal structure of (1E,1'E)-N,N'-(ethane-1,2-di-yl)bis-[(pyridin-2-yl)methanimine]

The whole mol-ecule of the title compound, C14H14N4, is generated by twofold rotation symmetry. The twofold axis bis-ects the central -CH2-CH2- bond and the planes of the pyridine rings are inclined to one another by 65.60 (7)°. In the crystal, there are no significant inter-molecular inter-actions present.

Crystal structure of 2-chloro-N-(3-fluoro-phen-yl)acetamide

In the title compound, C₈H₇ClFNO, the F atom is disordred over the meta positions of the benzene ring in a 0.574 (4):0.426 (4) ratio and the Cl atom is syn to the O atom [O—C—C—Cl = 5.6 (3)°]. A short intra­molecular C—H⋯O contact occurs. In the crystal, mol­ecules are linked into amide C(4) chains propagating in [101] by N—H⋯O hydrogen bonds.

Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus

The ATP binding cassette (ABC) transporters, represent one of the largest superfamilies of primary transporters, which are very essential for various biological functions. The crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus has been determined at 1.77 Å resolution. The crystal structure revealed that the protomer has two thick arms, (arm I and II), which resemble 'L' shape. The ATP-binding pocket is located close to the end of arm I. ATP molecule is docked into the active site of the protein. The dimeric crystal structure of ATP-binding subunit of ABC transporter from G. kaustophilus has been compared with the previously reported crystal structure of ATP-binding subunit of ABC transporter from Salmonella typhimurium.

Design, synthesis, anticonvulsant and analgesic studies of new pyrazole analogues: a Knoevenagel reaction approach

Compounds1a,4aand7a(76.58, 79.76 and 78 94% protection) shows potent anticonvulsant activity compounds1b,5a,5b,7aand7bshowed good analgesic property.

Crystal structure of ethyl (6-hy-droxy-1-benzo-furan-3-yl)acetate sesquihydrate

In the title hydrate, C12H12O4·1.5H2O, one of the water mol-ecules in the asymmetric unit is located on a twofold rotation axis. The mol-ecule of the benzo-furan derivative is essentially planar (r.m.s. deviation for the non-H atoms = 0.021 Å), with the ester group adopting a fully extended conformation. In the crystal, O-H⋯O hydrogen bonds between the water mol-ecules and the hy-droxy groups generate a centrosymmetric R 6 (6)(12) ring motif. These R 6 (6)(12) rings are fused, forming a one-dimensional motif extending along the c-axis direction.

Crystal structure of (R)-6'-bromo-3,3-dimethyl-3',4'-di-hydro-2'H-spiro-[cyclo-hexane-1,3'-1,2,4-benzo-thia-diazine] 1',1'-dioxide

In the title compound, C14H19BrN2O2S, the 1,2,4-thia-diazinane ring adopts an envelope conformation with the N atom (attached to the sulfonyl group) as the flap, while the cyclo-hexane ring adopts a chair conformation. The mean plane of the cyclo-hexane ring is almost normal to the benzene ring and the mean plane of the 1,2,4-thia-diazinane ring, making dihedral angles of 70.4 (2) and 71.43 (19)°, respectively. Furthermore, the dihedral angle between the benzene ring and the mean plane of the 1,2,4-thia-diazinane ring is 4.91 (18)°. The mol-ecular structure is stabilized by an intra-molecular C-H⋯O hydrogen bond, which encloses an S(6) ring motif. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds into chains along [10-1], forming a C(6) graph-set motif. These chains are inter-connected via C-H⋯π inter-actions, leading to chains along [-101], so finally forming sheets parallel to (010).

Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

UDP-N-acetyl-d-mannosamine dehydrogenase (UDP-d-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-d-mannosamine (UDP-d-ManNAc) to Uridine-diphospho-N-acetyl-d-mannosaminuronic acid (UDP-d-ManNAcA) through twofold oxidation of NAD(+). In order to reveal the structural features of the Pyrococcus horikoshii UDP-d-ManNAcADH, we have determined the crystal structure of the product-bound enzyme by X-ray diffraction to resolution of 1.55Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-d-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.

Crystal structure of N-(3-hy-droxy-phenyl)succinimide

In the title compound, C10H9NO3, the dihedral angle between the benzene and pyrrolidine rings is 53.9 (1)°. In the crystal, mol-ecules are linked through strong O-H⋯O hydrogen bonds into zigzag C(8) chains running along [010]. The chains are linked by C-H⋯π inter-actions forming sheets lying parallel to (100).

Crystal structure of cis-1-(2-methyl-1,2,3,4-tetra-hydro-quinolin-4-yl)azepan-2-one

In the title compound, C₁₆H₂₂N₂O, the azepan-2-one ring adopts a chair conformation, while the 1,2,3,4-tetra­hydro­pyridine ring adopts a half-chair conformation. In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, forming supra­molecular chains propagated along [10-1], with weak C—H⋯O inter­actions occurring between the chains.

Crystal structure of 1'-(2-methyl-prop-yl)-2,3-di-hydro-spiro-[1-benzo-thio-pyran-4,4'-imidazolidine]-2',5'-dione

In the title compound, C₁₅H₁₈N₂O₂S, the 2,3-di­hydro-1-benzo­thio­pyran ring adopts a sofa conformation and the hydantoin ring is twisted with respect to the benzene ring at 78.73 (17)°. In the crystal, pairs of N—H⋯O hydrogen bonds link the mol­ecules into inversion dimers.

Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles

In the L-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77Å and 1.95Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type IIIH and such PGDHs structures having this type are reported for the first time.

Bis(2-bromo-benz-yl) ether

In the title compound, C₁₄H₁₂Br₂O, the dihedral angle between the aromatic rings is 2.7 (3)° and the Br atoms lie on the same side of the mol­ecule. No inter­molecular inter­actions occur in the crystal beyond van der Waals contacts.

Molecular docking studies of benzimidazopyrimidine and coumarin substituted benzimidazopyrimidine derivatives: As potential human Aurora A kinase inhibitors

Protein kinases are important drug targets in human cancers, inflammation and metabolic diseases. Docking studies was performed for all the benzimidazopyrimidine and coumarin substituted benzimidazopyridimine derivatives with human Aurora A kinase target (3FDN) employing flexible ligand docking approach by using AutoDock 4.2. All the compounds were found to have minimum binding energy ranging from -6.26 to -9.29 kJ/mol. Among the molecules tested for docking study, 10-(6-Bromo-2-oxo- 2H-chromen-4-ylmethyl)-2-isopropyl-10H-benzo[4,5]imidazo[1,2-a]pyrimidin-4-one (2k) showed minimum binding energy (-9.29 kJ/mol) with ligand efficiency of -0.31. All the ligands were docked deeply within the binding pocket region of 3FDN showing hydrogen bonds with Ala 213 and Asn 261. The docking study results showed that these derivatives are excellent inhibitor of human Aurora A kinase target; and also all these docked compounds have good inhibition constant, vdW + Hbond + desolv energy with best RMSD value.

5-(4-Chloro-phen-oxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde

In the title compound, C₁₇H₁₃ClN₂O₂, the phenyl and chloro­benzene rings are inclined to the central pyrazole ring at 40.84 (9) and 65.30 (9)°, respectively. In the crystal, pairs of C—H⋯π inter­actions link the mol­ecules into inversion dimers and C—H⋯O hydrogen bonds link these dimers into columns extended in [010]. The crystal packing exhibits short inter­molecular O⋯Cl contacts of 3.0913 (16) Å.

2-Nitro-benzyl methane-sulfonate

In the title compound, C₈H₉NO₅S, the dihedral angle between the benzene ring and the nitro group is 5.86 (15)° and the C—C—O—S group adopts an anti conformation [torsion angle = −168.44 (15)°]. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds, generating a three-dimensional network.