Crystal structure, Hirshfeld surface analysis, calculations of inter-molecular inter-action energies and energy frameworks and the DFT-optimized mol-ecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)meth-yl]-3-(prop-1-en-2-yl)-1H-benzimidazol-2-one.

The benzimidazole entity of the title mol-ecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C-H⋯O hydrogen bonds link individual mol-ecules into layers extending parallel to the ac plane. Two weak C-H⋯π(ring) inter-actions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The mol-ecular structure optimized by density functional theory (DFT) at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state.

Crystal structure, Hirshfeld surface analysis, calculations of crystal voids, inter-action energy and energy frameworks as well as density functional theory (DFT) calculations of 3-[2-(morpholin-4-yl)eth-yl]-5,5-di-phenyl-imidazolidine-2,4-dione.

In the title mol-ecule, C21H23N3O3, the imidazolidine ring slightly deviates from planarity and the morpholine ring exhibits the chair conformation. In the crystal, N-H⋯O and C-H⋯O hydrogen bonds form helical chains of mol-ecules extending parallel to the c axis that are connected by C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis reveals that the most important contributions for the crystal packing are from H⋯H (55.2%), H⋯C/C⋯H (22.6%) and H⋯O/O⋯H (20.5%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated to be 236.78 Å3 and 12.71%, respectively. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the nearly equal electrostatic and dispersion energy contributions. The DFT-optimized mol-ecular structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state. Moreover, the HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure and Hirshfeld surface analysis of (Z)-N-{chloro-[(4-ferrocenylphen-yl)imino]-meth-yl}-4-ferrocenylaniline N,N-di-methyl-formamide monosolvate.

The title mol-ecule, [Fe2(C5H5)2(C23H17ClN2)]·C3H7NO, is twisted end to end and the central N/C/N unit is disordered. In the crystal, several C-H⋯π(ring) inter-actions lead to the formation of layers, which are connected by further C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (60.2%) and H⋯C/C⋯H (27.0%) inter-actions. Hydrogen bonding, C-H⋯π(ring) inter-actions and van der Waals inter-actions dominate the crystal packing.

Crystal structure, Hirshfeld surface analysis, crystal voids, inter-action energy calculations and energy frameworks, and DFT calculations of 1-(4-methyl-benz-yl)in-do-line-2,3-dione.

The in-do-line portion of the title mol-ecule, C16H13NO2, is planar. In the crystal, a layer structure is generated by C-H⋯O hydrogen bonds and C-H⋯π(ring), π-stacking and C=O⋯π(ring) inter-actions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (43.0%), H⋯C/C⋯H (25.0%) and H⋯O/O⋯H (22.8%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 120.52 Å3 and 9.64%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state.

Crystal structure, Hirshfeld surface analysis, crystal voids, inter-action energy calculations and energy frameworks and DFT calculations of ethyl 2-cyano-3-(3-hy-droxy-5-methyl-1H-pyrazol-4-yl)-3-phen-yl-propano-ate.

The title compound, C16H17N3O3, is racemic as it crystallizes in a centrosymmetric space group (P ), although the trans disposition of substituents about the central C-C bond is established. The five- and six-membered rings are oriented at a dihedral angle of 75.88 (8)°. In the crystal, N-H⋯N hydrogen bonds form chains of mol-ecules extending along the c-axis direction that are connected by inversion-related pairs of O-H⋯N into ribbons. The ribbons are linked by C-H⋯π(ring) inter-actions, forming layers parallel to the ab plane. A Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (45.9%), H⋯N/N⋯H (23.3%), H⋯C/C⋯H (16.2%) and H⋯O/O⋯H (12.3%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 100.94 Å3 and 13.20%, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure, Hirshfeld surface and crystal void analysis, inter-molecular inter-action energies, DFT calculations and energy frameworks of 2H-benzo[b][1,4]thia-zin-3(4H)-one 1,1-dioxide.

In the title mol-ecule, C8H7NO3S, the nitro-gen atom has a planar environment, and the thia-zine ring exhibits a screw-boat conformation. In the crystal, corrugated layers of mol-ecules parallel to the ab plane are formed by N-H⋯O and C-H⋯O hydrogen bonds together with C-H⋯π(ring) and S=O⋯π(ring) inter-actions. The layers are connected by additional C-H⋯O hydrogen bonds and π-stacking inter-actions. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯O/O⋯H (49.4%), H⋯H (23.0%) and H⋯C/C⋯H (14.1%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated as 75.4 Å3 and 9.3%. Density functional theory (DFT) computations revealed N-H⋯O and C-H⋯O hydrogen-bonding energies of 43.3, 34.7 and 34.4 kJ mol-1, respectively. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via the electrostatic energy contribution. Moreover, the DFT-optimized structure at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Synthesis, crystal structure and Hirshfeld surface analysis of 1-(12-bromo-dodec-yl)indoline-2,3-dione.

In the title compound, C20H28BrNO2, the indoline portion is almost planar and the 12-bromo-dodecyl chain adopts an all-trans conformation apart from the gauche terminal C-C-C-Br fragment. A micellar-like structure is generated in the crystal by C-H⋯O hydrogen bonds and π-stacking inter-actions between indolinedione head groups and inter-calation of the 12-bromo-dodecyl tails. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (58.9%), H⋯O/O⋯H (17.9%) and H⋯Br/Br⋯H (9.5%) contacts. A density functional theory (DFT) optimized structure at the B3LYP/ 6-311 G(d,p) level shows good agreement with the experimentally determined mol-ecular structure in the solid state.

Synthesis, crystal structure, spectroscopic characterization, DFT calculations, Hirshfeld surface analysis, molecular docking, and molecular dynamics simulation investigations of novel pyrazolopyranopyrimidine derivatives.

A series of new pyrazolopyranopyrimidine derivatives (3-9) were synthesized from 5-amino-2,4-dihydro-3-methyl-4-phenylpyrano-[2,3-c]pyrazole-5-carbonitrile (2) by multicomponent reactions (MCR) involving malononitrile, benzaldehyde, and pyrazolone under refluxing ethanol in the presence of piperidine. Compound (2) was then converted to 2-acetylpyrazolopyranopyrimidine (3) through a reaction with acetic anhydride. The deprotection of 3 using ammonium hydroxide in ethanol, leads to 4. Subsequent chlorination of 4 by phosphorus oxychloride affords 5 which was alkylated using methyl iodide and ethyl bromoacetate in DMF, leading to regioisomers 6-9. The products were characterized by spectroscopic techniques (1H and 13C NMR) and confirmed by single crystal X-ray diffraction (XRD) studies for 2, 5, 6, and 9. Moreover, the geometrical parameters, molecular orbital calculations, and spectral data of 2, 5, 6, and 9 were compared by DFT at the B3LYP/6-311G(d,p) level of theory. There is good agreement between the calculated results and the experimental data. The intermolecular contacts for 2, 5, 6, and 9 were studied by Hirshfeld surface analysis. In addition, the molecular docky study was conducted to investigate the binding patterns of 2, 5, 6, and 9 within the binding site of cyclin-dependent kinase 2 (CDK2) and penicillin-binding protein 1 A. After the docking process, molecular dynamics (MD) simulations for 100 ns were performed on CDK2 and PBP 1 A proteins in the complex with 5.Communicated by Ramaswamy H. Sarma.

Crystal structure and Hirshfeld surface analysis of 3-eth-oxy-1-ethyl-6-nitro-quinoxalin-2(1H)-one.

The asymmetric unit of the title compound, C12H13N3O4, consists of two mol-ecules differing to a small degree in their conformations. In the crystal, layers of mol-ecules are connected by weak C-H⋯O hydrogen bonds and slipped π-stacking inter-actions. These layers lie parallel to (10) and are stacked along the normal to that plane. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing arise from H⋯H (43.5%) and H⋯O/O⋯H (30.8%) contacts. The density functional theory (DFT) optimized structure of the title compound at the B3LYP/ 6-311 G(d,p) level agrees well with the experimentally determined mol-ecular structure in the solid state.

Crystal structure, Hirshfeld surface analysis, inter-action energy and energy framework calculations, as well as density functional theory (DFT) com-putation, of methyl 2-oxo-1-(prop-2-yn-yl)-1,2-di-hydro-quinoline-4-carboxyl-ate.

In the title mol-ecule, C14H11NO3, the di-hydro-quinoline core deviates slightly from planarity, indicated by the dihedral angle of 1.07 (3)° between the two six-membered rings. In the crystal, layers of mol-ecules almost parallel to the bc plane are formed by C-H⋯O hydro-gen bonds. These are joined by π-π stacking inter-actions. A Hirshfeld surface analysis revealed that the most important contributions to the crystal packing are from H⋯H (36.0%), H⋯C/C⋯H (28.9%) and H⋯O/O⋯H (23.5%) inter-actions. The evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the dispersion energy contribution. Moreover, the mol-ecular structure optimized by density functional theory (DFT) at the B3LYP/6-311G(d,p) level is com-pared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Synthesis, crystal structure and Hirshfeld surface analysis of (E)-benzo[d][1,3]dioxole-5-carbaldehyde oxime.

The asymmetric unit of the title mol-ecule, C8H7NO3, consists of two mol-ecules differing slightly in conformation and in their inter-molecular inter-actions in the solid. The dihedral angle between the benzene and dioxolane rings is 0.20 (7)° in one mol-ecule and 0.31 (7)° in the other. In the crystal, the two mol-ecules are linked into dimers through pairwise O-H⋯N hydrogen bonds, with these units being formed into stacks by two different sets of aromatic π-stacking inter-actions. The stacks are connected by C-H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most significant contacts in the crystal packing are H⋯O/O⋯H (36.7%), H⋯H (32.2%) and C⋯H/H⋯C (12.7%).

Synthesis, structure elucidation, Hirshfeld surface analysis, DFT, and molecular docking of new 6-bromo-imidazo[4,5-b]pyridine derivatives as potential tyrosyl-tRNA synthetase inhibitors.

Novel 6-bromo-imidazo[4,5-b]pyridine derivatives (2-4, 5a-13a, and 6b, 8b-13b) have been synthesized based on a developed systematic approach involving the condensation of 5-Bromo-2,3-diaminopyridine with a suitable aromatic aldehyde in the presence of molecular iodine in water, followed by alkylation reactions using different alkyl dibromide agents. The synthesized compounds were characterized by the NMR spectroscopy technique. The structures of 8a, 9a, 12a, and 11b were confirmed using monocrystalline X-ray crystallography. Theoretical calculations have been carried out using DFT and TD-DFT methods at the B3LYP/6-31G++(d,p) level of theory. Intermolecular contacts between units of 8a, 9a, 12a, and 11b were determined through the Hirshfeld surface analysis. The molecular docking study has been performed to determine the binding affinity of 8a, 9a, 12a, and 11b into the binding site of S. aureus tyrosyl-tRNA synthetase as a target enzyme, and the results revealed that 9a is the most potent compound among the selected compounds with a binding affinity of -8.74 Kcal/mol.Communicated by Ramaswamy H. Sarma.

Synthesis, structure and Hirshfeld surface analysis of 1,3-bis-[(1-octyl-1H-1,2,3-triazol-4-yl)meth-yl]-1H-benzo[d]imidazol-2(3H)-one.

The title mol-ecule, C29H44N8O, adopts a conformation resembling a two-bladed fan with the octyl chains largely in fully extended conformations. In the crystal, C-H⋯O hydrogen bonds form chains of mol-ecules extending along the b-axis direction, which are linked by weak C-H⋯N hydrogen bonds and C-H⋯π inter-actions to generate a three-dimensional network. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (68.3%), H⋯N/N⋯H (15.7%) and H⋯C/C⋯H (10.4%) inter-actions.

Crystal structure, Hirshfeld surface analysis, inter-molecular inter-action energies, energy frameworks and DFT calculations of 4-amino-1-(prop-2-yn-1-yl)pyrimidin-2(1H)-one.

In the title mol-ecule, C7H7N3O, the pyrimidine ring is essentially planar, with the propynyl group rotated out of this plane by 15.31 (4)°. In the crystal, a tri-periodic network is formed by N-H⋯O, N-H⋯N and C-H⋯O hydrogen-bonding and slipped π-π stacking inter-actions, leading to narrow channels extending parallel to the c axis. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (36.2%), H⋯C/C⋯H (20.9%), H⋯O/O⋯H (17.8%) and H⋯N/N⋯H (12.2%) inter-actions, showing that hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions. The mol-ecular structure optimized by density functional theory (DFT) calculations at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The HOMO-LUMO behaviour was also elucidated to determine the energy gap.

Crystal structure determination, Hirshfeld surface, crystal void, inter-molecular inter-action energy analyses, as well as DFT and energy framework calculations of 2-(4-oxo-4,5-di-hydro-1H-pyra-zolo[3,4-d]pyrimidin-1-yl)acetic acid.

In the title mol-ecule, C7H6N4O3, the bicyclic ring system is planar with the carb-oxy-methyl group inclined by 81.05 (5)° to this plane. In the crystal, corrugated layers parallel to (010) are generated by N-H⋯O, O-H⋯N and C-H⋯O hydrogen-bonding inter-actions. The layers are associated through C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯O/O⋯H (34.8%), H⋯N/N⋯H (19.3%) and H⋯H (18.1%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated to be 176.30 Å3 and 10.94%, showing that there is no large cavity in the crystal packing. Computational methods revealed O-H⋯N, N-H⋯O and C-H⋯O hydrogen-bonding energies of 76.3, 55.2, 32.8 and 19.1 kJ mol-1, respectively. Evaluations of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via dispersion energy contributions. Moreover, the optimized mol-ecular structure, using density functional theory (DFT) at the B3LYP/6-311G(d,p) level, was compared with the experimentally determined one. The HOMO-LUMO energy gap was determined and the mol-ecular electrostatic potential (MEP) surface was calculated at the B3LYP/6-31G level to predict sites for electrophilic and nucleophilic attacks.

Crystal structure, Hirshfeld surface analysis and DFT calculations of (E)-3-[1-(2-hy-droxy-phenyl-anilino)ethyl-idene]-6-methyl-pyran-2,4-dione.

The asymmetric unit of the title compound, C14H13NO4, contains three independent mol-ecules, which differ slightly in conformation. Each contains an intra-molecular N-H⋯O hydrogen bond. In the crystal, O-H⋯O hydrogen bonds form chains of mol-ecules, which are linked into corrugated sheets parallel to (03) plane by C-H⋯O hydrogen bonds together with π inter-actions between the carbonyl groups and the 2-hy-droxy-phenyl rings. The layers are linked by further C-H⋯O hydrogen bonds. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.0%), H⋯O/O⋯H (28.3%) and H⋯C/C⋯H (10.9%) inter-actions. van der Waals inter-actions are the dominant inter-actions in the crystal packing. Moreover, density functional theory (DFT) optimized structures at the B3LYP/ 6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behavior was elucidated to determine the energy gap of 4.53 eV.

Crystal structure, Hirshfeld surface analysis, inter-action energy and DFT calculations and energy frameworks of methyl 6-chloro-1-methyl-2-oxo-1,2-di-hydro-quinoline-4-carboxyl-ate.

In the title compound, C12H10ClNO3, the di-hydro-quinoline moiety is not planar with a dihedral angle between the two ring planes of 1.61 (6)°. An intra-molecular C-H⋯O hydrogen bond helps to establish the rotational orientation of the carboxyl group. In the crystal, sheets of mol-ecules parallel to (10) are generated by C-H⋯O and C-H⋯Cl hydrogen bonds, and are stacked through slipped π-stacking inter-actions between inversion-related di-hydro-quinoline units. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (34.2%), H⋯O/O⋯H (19.9%), H⋯Cl/Cl⋯H (12.8%), H⋯C/C⋯H (10.3%) and C⋯C (9.7%) inter-actions. Computational chemistry indicates that in the crystal, the C-H⋯Cl hydrogen-bond energy is -37.4 kJ mol-1, while the C-H⋯O hydrogen-bond energies are -45.4 and -29.2 kJ mol-1. An evaluation of the electrostatic, dispersion and total energy frameworks revealed that the stabilization is dominated via the dispersion energy contribution. Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state, and the HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure and Hirshfeld surface analysis study of (E)-1-(4-chloro-phen-yl)-N-(4-ferrocenylphen-yl)methanimine.

The substituted cyclo-penta-dienyl ring in the title mol-ecule, [Fe(C5H5)(C18H13ClN)], is nearly coplanar with the phenyl-1-(4-chloro-phen-yl)methanimine substituent, with dihedral angles between the planes of the phenyl-ene ring and the Cp and 4-(chloro-phen-yl)methanimine units of 7.87 (19) and 9.23 (10)°, respectively. The unsubstituted cyclo-penta-dienyl ring is rotationally disordered, the occupancy ratio for the two orientations refined to a 0.666 (7)/0.334 (7) ratio. In the crystal, the mol-ecules pack in 'bilayers' parallel to the ab plane with the ferrocenyl groups on the outer faces and the substituents directed towards the regions between them. The ferrocenyl groups are linked by C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (46.1%), H⋯C/C⋯ H (35.4%) and H⋯Cl/Cl⋯H (13.8%) inter-actions. Thus C-H⋯π(ring) and van der Waals inter-actions are the dominant inter-actions in the crystal packing.

Crystal structure, Hirshfeld surface analysis and inter-action energy calculation of 4-(furan-2-yl)-2-(6-methyl-2,4-dioxo-pyran-3-yl-idene)-2,3,4,5-tetra-hydro-1H-1,5-benzodiazepine.

The title compound {systematic name: (S,E)-3-[4-(furan-2-yl)-2,3,4,5-tetra-hydro-1H-benzo[b][1,4]diazepin-2-yl-idene]-6-methyl-2H-pyran-2,4(3H)-dione}, C19H16N2O4, is constructed from a benzodiazepine ring system linked to furan and pendant di-hydro-pyran 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) Šfrom the least-squares plane] while the tetra-hydro-diazepine ring adopts a boat conformation. The rotational orientation of the pendant di-hydro-pyran ring is partially determined by an intra-molecular N-HDiazp⋯ODhydp (Diazp = diazepine and Dhydp = di-hydro-pyran) hydrogen bond. In the crystal, layers of mol-ecules parallel to the bc plane are formed by N-HDiazp⋯ODhydp hydrogen bonds and slipped π-π stacking inter-actions. The layers are connected by additional slipped π-π stacking inter-actions. 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%) inter-actions, indicating that van der Waals inter-actions 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.

Crystal structure, Hirshfeld surface analysis and inter-action energy calculation of 1-decyl-2,3-di-hydro-1H-benzimidazol-2-one.

The title mol-ecule, C17H26N2O, adopts an L-shaped conformation, with the straight n-decyl chain positioned nearly perpendicular to the di-hydro-benzimidazole moiety. The di-hydro-benzimidazole portion is not quite planar as there is a dihedral angle of 1.20 (6)° between the constituent planes. In the crystal, N-H⋯O hydrogen bonds form inversion dimers, which are connected into the three-dimensional structure by C-H⋯O hydrogen bonds and C-H⋯π(ring) inter-actions. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (75.9%), H⋯C/C⋯H (12.5%) and H⋯O/O⋯H (7.0%) inter-actions. Based on computational chemistry using the CE-B3LYP/6-31 G(d,p) energy model, C-H⋯O hydrogen bond energies are -74.9 (for N-H⋯O) and -42.7 (for C-H⋯O) kJ mol-1.