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Twelve spiro thiazolidinone compounds (A–L) were synthesized via either conventional thermal or ultrasonication techniques using Fe2O3 nanoparticles. The modification of the traditional procedure by using Fe2O3 nanoparticles led to enhancement of the yield of the desired candidates to 78–93% in approximately half reaction time compared with 58–79% without catalyst. The products were fully characterized using different analytical and spectroscopic techniques. The structure of the two derivatives 4-phenyl-1-thia-4-azaspirodecan-3-one (A) and 4-(p-tolyl)-1-thia-4-azaspirodecan-3-one (B) were also determined using single crystal X-ray diffraction and Hirshfeld surface analysis. The two compounds (A and B) were crystallized in the orthorhombic system with Pbca and P212121 space groups, respectively. In addition, the crystal packing of compounds revealed the formation of supramolecular array with a net of intermolecular hydrogen bonding interactions. The energy optimized geometries of some selected derivatives were performed by density functional theory (DFT/B3LYP). The reactivity descriptors were also calculated and correlated with their biological properties. All the reported compounds were screened for antimicrobial inhibitions. The two derivatives, F and J, exhibited the highest levels of bacterial inhibition with an inhibition zone of 10–17 mm. Also, the two derivatives, F and J, displayed the most potent fungal inhibition with an inhibition zone of 15–23 mm. Molecular docking investigations of some selected derivatives were performed using a B-DNA (PDB: 1BNA) as a macromolecular target. Structure and activity relationship of the reported compounds were correlated with the data of antimicrobial activities and the computed reactivity parameters. [ABSTRACT FROM AUTHOR]

Abstract Twelve spiro thiazolidinone compounds (A–L) were synthesized via either conventional thermal or ultrasonication techniques using Fe2O3 nanoparticles. The modification of the traditional procedure by using Fe2O3 nanoparticles led to enhancement of the yield of the desired candidates to 78–93% in approximately half reaction time compared with 58–79% without catalyst. The products were fully characterized using different analytical and spectroscopic techniques. The structure of the two derivatives 4-phenyl-1-thia-4-azaspirodecan-3-one (A) and 4-(p-tolyl)-1-thia-4-azaspirodecan-3-one (B) were also determined using single crystal X-ray diffraction and Hirshfeld surface analysis. The two compounds (A and B) were crystallized in the orthorhombic system with Pbca and P2 1 2 1 2 1 space groups, respectively. In addition, the crystal packing of compounds revealed the formation of supramolecular array with a net of intermolecular hydrogen bonding interactions. The energy optimized geometries of some selected derivatives were performed by density functional theory (DFT/B3LYP). The reactivity descriptors were also calculated and correlated with their biological properties. All the reported compounds were screened for antimicrobial inhibitions. The two derivatives, F and J, exhibited the highest levels of bacterial inhibition with an inhibition zone of 10–17 mm. Also, the two derivatives, F and J, displayed the most potent fungal inhibition with an inhibition zone of 15–23 mm. Molecular docking investigations of some selected derivatives were performed using a B-DNA (PDB: 1BNA) as a macromolecular target. Structure and activity relationship of the reported compounds were correlated with the data of antimicrobial activities and the computed reactivity parameters.

The single crystal of the title compound Diethyl 1-(4-nitrobenzyl)-4-(4-nitrophenyl)-2,2-dioxooctahydro-2-pyrrolo[2,1-c]1,4thiazine-1,3-dicarboxylate was grown and characterized by single crystal X-ray diffraction technique. Further, Hirshfeld surface, quantum chemical, and molecular docking analyses of the compound were carried out. The title compound was crystallized in a triclinic crystal system with a centrosymmetric space group of P-1 and has one molecule in the asymmetric unit. The stability of the grown crystal structure was confirmed by the C-H...O and π...π interactions. The hydrogen bonding features were analyzed and the prominent intermolecular interactions present in the structure were investigated using Hirshfeld surface analysis. The interaction energy between pairs of the molecule was obtained from Energy Framework analysis. The molecular structure of the title compound was optimized using density functional theory calculation in the ground state and the calculated structural parameters of the compound were compared with the experimental XRD data. Mulliken atomic charge distribution and frontier molecular orbitals analyses were also carried out to validate the reactivity of the title molecule. Molecular docking studies confirm that the title compound has potent inhibitory nature against the human mutant HIV-1 reverse transcriptase protein. Thus, the present study paves the way for the development of a novel HIV-1 drug. [ABSTRACT FROM AUTHOR]

Context: The controlled slow evaporation process conducted at room temperature has produced a novel hybrid material denoted as (2-hydroxyethyl) trimethylammonium dihydrogen phosphate [2-HDETDHP] (C5H14NO+, H2PO4−), synthesized through the solution growth method. X-ray crystallography analysis reveals a triclinic structure with a filling rate of P and a Z value of 2. This hybrid material displays noteworthy absorption characteristics in the middle and far ultraviolet regions. UV-visible spectroscopy further establishes its transparency in the visible and near-visible ultraviolet domains. FT-IR spectroscopy examines various vibration modes, elucidating their relationships with the functional groups within the structure. Two- and three-dimensional fingerprint maps, coupled with three-dimensional crystal structures through Hirshfeld Surface Analysis, unveil the dominance of O•••H and H•••H interactions in the structure, comprising 49.40% and 50.40%, respectively. Fingerprint plots derived from the Hirshfeld surface assess the percentages of hydrogen bonding interactions, with 80.6% attributed to a fragment patch. The experiment of antimicrobial efficacy of a synthesized product, conducted in triplicate, demonstrated the synthesized product's potential antimicrobial activity. Methods: Hirshfeld surfaces are employed to investigate intermolecular hydrogen bonding, specifically within single phosphate groups. The molecular structure of 2-HDETDHP was refined using single-crystal X-ray analysis, while its optical characteristics were examined through UV-visible spectroscopy. FT-IR spectroscopy is employed for the assignment of molecular vibrations of functional groups in the affined structure. Quantum calculations were executed with the GAUSSIAN 09 software package at B3LYP/6-311G level of theory, to optimize the molecular geometries. The antimicrobial efficacy of a synthesized product was evaluated using the disc diffusion method against antibiotic-resistant Candida albicans, Candida tropicalis, Aspergillus niger, Staphylococcus aureus, and Escherichia coli. Microorganisms were cultured on nutrient agar, and inhibition zones were measured after incubation, with streptomycin and amphotericin as positive controls. [ABSTRACT FROM AUTHOR]

The 4′-(4-chlorobenzoyl)-3,-(2,6-dichlorophenyl)-1′-methylspiro(indole-3,2′-pyrrolidin)-2(1H)-one (SOD1) compound has been synthesized and the single crystals are grown by the slow evaporation method using ethanol. Initially, FT-IR and NMR (1H and 13C NMR) spectroscopic studies were used to confirm the structure of the compound. Single crystal X-ray diffraction data were used to determine the solid state structure of the grown single crystals. The title compound SOD1 crystallizes in the orthorhombic space group Pbca. The crystal packing analysis of the compound shows that distinct hydrogen bonding intermolecular interactions construct the R22(12), R22(8), and R12(8), supramolecular synthons to stabilize the packing modes. The propensity of intermolecular interactions is quantified by the Hirshfeld surface analysis, 2-D fingerprint plots and enrichment ratio analysis. Further, the 3-D packing topology of the molecular fragments is visualized through energy frameworks, which reveal the predominance of dispersion energy over other interaction energies. The optimized structure's geometric parameters were computed using DFT calculations using B3LYP/6–311+G(d,p) basis set and compared with the crystal structure parameters obtained by the X-ray diffraction studies. To explore the anticancer activity of the spiro compound, molecular docking with the 6FS1 protein was performed and the binding score of -7.7 kcal/mol was observed. Further, the binding interaction was explored by the dynamics simulation studies.

Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of β-diketones remains largely unexplored. β-Diketones and their complexes find broad applications as biologically active compounds. In this study, in silico molecular docking results revealed that two β-diketone derivatives, namely 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione and 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione, exhibit anti-COX-2 activities. However, recent docking results indicated that the relative anti-COX-2 activity of these two studied β-diketones was influenced by the employed docking programs. For improved design of COX-2 inhibitors from β-diketones, we conducted molecular dynamics simulations, density functional theory (DFT) calculations, Hirshfeld surface analysis, energy framework, and ADMET studies. The goal was to understand the interaction mechanisms and evaluate the inhibitory characteristics. The results indicate that 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione shows greater anti-COX-2 activity compared to 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione. [ABSTRACT FROM AUTHOR]

A novel compound (1E,1′E)-N,N′-(ethane-1,2-diyl)bis(1-(5-nitrothiophen-2-yl)methanimine) [EDNM] was synthesized from thiophene derivative in view to get multidentate ligand with potential biological activity. EDNM is characterized by FT-IR, 1H and 13C NMR and UV–Vis spectroscopic techniques and confirmed by SCXRD. EDNM crystallizes in the monoclinic system with P21/c space group with Z value 4 and unit cell parameters a = 5.6540(3) Å, b = 17.9249(8) Å and c = 7.5077(5) Å. DFT was employed for theoretical evaluations using B3LYP with the basis set 6–311 + + G (d,p). Geometry optimization, vibrational analysis, NMR, electronic absorption, MEP, FMO, Mulliken charges and NBO analysis were performed, thereby establishing the nature of reactive sites, band energy gap and atomic charges of EDNM. Theoretical values matched well with the experimental findings. NBO analysis revealed the donor acceptor interactions in molecule. Analysis of global reactivity descriptors along with Fukui indices outlines the elaborate scheme of reactive sites of the molecule, and Hirshfeld surface investigation revealed the intermolecular interactions in crystal packing. [ABSTRACT FROM AUTHOR]

A novel single crystal of (3-(4-chlorophenyl)-4,5-dihydroisoxazol-5-yl)methyl benzenesulfonate has been synthetized via a one-pot sequential strategy under sonication. The single crystal has been investigated using X-ray diffraction analysis. Hydrogen bonding between C–H···O and C–H···N produces a layer structure in the crystal. According to a Hirshfeld surface analysis, interactions H···H (28.9%), H···O/O···H (26.7%) and H···C/C···H (15.8%) make the largest contributions to crystal packing. The optimized structure and the solid-state structure that was obtained through experiments are compared using density functional theory at the B3LYP/6-311 G + (d,p) level. The computed energy difference between the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) is 4.6548 eV. [ABSTRACT FROM AUTHOR]

In this paper, we describe the synthesis and structural characterization of the 1-(cyclohex-1-en-1-yl)-3-(prop-2-yn-1-yl)-1,3-dihydro-2H-benzimidazol-2-one (2) via IR, NMR (1H and 13C), and HRMS. The crystal structure of the isolated organic compound 2 was confirmed through single-crystal X-ray diffraction analysis. The experimental results regarding the molecular geometry and intermolecular interactions within the crystal are in accordance with the DFT calculations and Hirshfeld surface analysis. [ABSTRACT FROM AUTHOR]

A new compound, 1,3‐bis(4‐chlorophenyl)‐5‐(4‐chlorobenzyl)‐1,3,5‐triazinane, C22H20Cl3N3 (I), was synthesized, and its structure was determined by X‐ray diffraction, along with various spectroscopic methods, UV‐VIS, FT‐IR, NMR 1H and 13C. The crystal belongs to the monoclinic system with a=7.1503 (5) Å; b=12.9506(10) Å; c=21.9709 (16) Å; β=96.637(2)° and space group P21/c. Hirshfeld surface analysis and two‐dimensional fingerprint plots were used to quantify the interatomic interactions present in the crystal. The molecular structure of (I) was determined by DFT calculations using the BP86‐D functional and a TZP basis set. The geometry optimizations and vibrational frequencies were calculated, and Natural atomic orbital charges were investigated using NBO 6.0 program. [ABSTRACT FROM AUTHOR]

Two novel N-alkylated isatin derivatives (2–3) were synthesized under phase-transfer catalysis conditions. Their condensation with hydrazine hydrate and phenylhydrazine in refluxing ethanol as solvent generates two series of isatin derivatives (3-hydrazono and 3-phenylhydrazono) (4–7). The structures synthesized are elucidated using UV/Vis, FTIR, 13C-NMR, 1H-NMR, and single crystal X-ray diffraction techniques of 2, 3, and 5. The experimental data were compared with the predicted ones obtained at the B3LYP/6-31G(d,p) level of theory. Relatively, good agreements were found between the calculated and experimental results. The intermolecular contacts in 2, 3, and 5 were investigated through the Hirshfeld surface analysis. The expected inhibitory efficiency of 2, 3, and 5 against cyclooxygenase-2 (COX-2) are investigated by their molecular docking into the binding site of COX-2, which revealed that 2 might have strong inhibition efficacy against COX-2 compared to 3. [ABSTRACT FROM AUTHOR]

The DFT approach has studied experimental spectroscopic molecular docking simulations of m-Phenylenediamine (m-PD) with quantum calculations. A molecular dynamics simulation is used to explore biomolecular stability. VEDA successfully carried out complete tasks for the distribution of potential energy. 1H-NMR and 13C-NMR shifts were assessed by the GIAO method, and results were compared with experimental spectra. TDDFT method and PCM solvent model were used to analyze electronic properties such as UV-Vis (in the gas phase, ethanol, and DMSO) and compared with the experimental UV-Vis spectra. The HOMO/LUMO energy results emphasize adequate charge transfer within the molecule. The electron excitation analysis was completed. Studies of donor-acceptor connections were performed using NBO analysis. The MEP surface analysis was carried out to show the charge distribution in the molecule. The degree of relative localization of electrons was analyzed using the ELF diagram. The Fukui functional analysis to find probable sites of attack by various substituents. Hirshfeld surface showed m-PD was stabilized primarily by forming H–H/H–N/C–H contacts. Biological studies like molecular docking were done with eight different receptors to find the best ligand-protein interactions. Molecular Dynamic Simulation was used to calculate the binding free energy of complex and to validate the inhibitory potency. This study helps in understanding the structural properties of compounds which in turn aids in elucidating the mechanism of a chemical reaction and helps in designing new reactions and catalysts. The main objective is to study structures and their properties by simulating chemical systems to provide accurate, reliable, and comprehensive data at an atomic level. [ABSTRACT FROM AUTHOR]

Ten new isatin derivatives (2–11) were synthesized by alkylation reactions under phase transfer catalysis (PTC) conditions. Structural characterization of all compounds was performed using 1H and 13C NMR spectroscopy. The molecular and crystal structures of three compounds (4, 7, and 8) were confirmed through single-crystal X-ray diffraction analysis. Spectral data were also calculated using density function theory (DFT) at the B3LYP/6–311++G(d, p) level and compared to the experimental results, to understand the non-binding intermolecular interactions in the solid phase crystal packing. The closest contacts between atoms of the three molecules studied were identified by 2D and 3D Hirshfeld surface analyses. The structures of 4, 7 and 8 are optimized and their HOMO and LUMO energies, as well as their orbital pictures were evaluated. The experimental results correlated well with the calculated results. Finally, molecular docking studies of 4, 7 and 8 were performed to investigate their binding patterns with inhibitory targets from the Protein Data Bank (PDB: 3G7B and PDB: 3T0T using the AutoDock Vina program. The antibacterial activities of 2–11 against Gram-positive and Gram-negative microbial strains, such as Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa were evaluated, and the findings indicated that 4 and 8 exhibited the highest efficacy, as reflected in their minimal inhibitory concentration (MIC) values.

Using X-ray diffraction, FT-IR, 1H, 13C NMR, and UV–Vis spectra as well as theoretical DFT calculations, Ethyl-2-methyl-4-phenyl-3,4-dihydro-2H-benzo[4,5]thiazolo-[3,2-a]pyrimidine-3-carboxylate (T[3,2-a]P) has been synthesized and characterized. Physicochemical characteristics have been compared to examine stability. The most stable optimized structure was identified using the B3LYP/6–311++G(d,p) basis set, followed by UV–Vis and NMR analysis. TD-DFT analysis gave more information on how to estimate the electronic transitions in the UV–Vis spectra. In addition to the energy framework calculations, the Hirshfeld surface analyses have been demonstrated and discussed. The calculated band-gap energy of the pyrimidine derivative for various solvents and the estimated maximum wavelength (λ) absorbance were compared to the outcome of experiments. There were additional studies regarding the MEP map, surface area maps, and chemical reactivity. Additionally, topological and Mulliken charge distribution investigations were included. A pyrimidine derivative may be used as a chemotherapeutic and anticancer drug, according to docking experiments that were used to examine the interactions of the ligand (T[3,2-a]P]) with certain protein targets. The current study may lead to the identification of pyrimidine derivative as a possible therapeutic molecule. The practical and theoretical results were remarkably similar in terms of geometric and spectroscopic characteristics.

Detailed structural and noncovalent interactions in two thiazole derivatives (N-(4-Bromophenyl)-2-(methylthio)thiazole-5-carboxamide and Ethyl-5-((4-bromophenyl)carbamoyl)thiazole-4-carboxylate) are investigated by single crystal X-ray diffraction study and computational approaches. The structure investigation revealed that various interactions like C-H...O, N-H...O, and N-H...N hydrogen bonds and Br...Br interactions are involved in constructing ring motifs to stabilize the crystal packing. Hirshfeld surface analysis and fingerprint plots were carried out to study the differences and similarities in the relative contribution of noncovalent interactions in both the molecules. The FMOs and other global reactive parameters are analyzed for thiazole derivatives. The strength and nature of weak interactions present in the molecule were characterized by RDG-based NCI and QTAIM analyses. Natural bond orbital (NBO) analysis unravels the importance of non-covalent and hyperconjugative interactions for the stability of the molecules in their solid state. Further, molecular docking of N-(4-Bromophenyl)-2-(methylthio)thiazole-5-carboxamide and Ethyl-5-((4-bromophenyl)carbamoyl)thiazole-4-carboxylate with SARS-Covid-19 have been carried out. [ABSTRACT FROM AUTHOR]

In this study, two Schiff bases, (E)-2,4-di-tert-butyl-6-((4-fluorophenylimino)methyl)phenol (I) and (E)-2,4-di-tert-butyl-6-((3-iodo-4-methylphenylimino)methyl)phenol (II) are synthesized and characterized by XRD, FT-IR, UV-Vis and NMR techniques. (I) and (II) compounds display enol-imine form by O-H···N intramolecular hydrogen bonds. The title compounds are stabilized by C—H···π interactions. The presence of various inter molecular interactions and 2D-fingerprint regions are well supported by the Hirshfeld surface analysis. Also experimental optical energy band and gap studies are discussed. All chemical theoretical computations are calculated by Density Functional Theory (DFT) at B3LYP level by using 3-21 G basis set. Chemical activity analyses are showed that compounds have large energy gaps, higher values of hardness and lower values of softness support the title molecules are high kinetic stability. Also, chemical activity properties generate foresight about electrophilic and nucleophilic nature. The title compounds characterized by FT-IR, UV-Vis, NMR and XRD techniques. Local and global chemical activity analysis were investigated. Hirshfeld surface analysis revealed the nature of intermolecular contacts, the fingerprint plots and molecular surface contours. [ABSTRACT FROM AUTHOR]

In the present work, we report the experimental and computational investigations of 3-Hydroxy-4-nitrobenzaldehyde (3H4NB) were examined. Comparing observed and simulated vibrational spectra allowed for the identification of characteristic frequencies and the attribution of band names. For the density functional theory (DFT) calculations, the LSDA functional with 6-311 + G(d,p) degree of approximation was used. Furthermore, the same level of theory was used to calculate molecular orbitals such as natural bond orbitals (NBOs) and the HOMO-LUMO energy gap. The condensed Fukui function and the molecular electrostatic potential (MEP) surface were used to determine the relative electrophilicity and nucleophilicity of the current molecule. Intermolecular hydrogen bonding interactions are studied using Hirshfeld surface analysis and fingerprint plots. Molecular docking analysis was used to investigate the compound's biological activities. The hydrogen bond active binding residues and binding energy of a chosen chemical with carcinogenic activity targets were examined. [ABSTRACT FROM AUTHOR]

9-(4-hydroxyphenyl-tetramethyl-hexahydro-1H-xanthene-1,8(2H)-dione (OH-X) was synthesized and characterized experimentally using X-ray diffraction, FT-IR, 1H, 13 C NMR, and UV-Vis spectra, and theoretically using DFT calculations. To look at stability, different physicochemical properties have been compared. The most stable optimized structure was discovered using the B3LYP/6-311++G(d,p) basis set, followed by FTIR and NMR investigation. Further details on the estimation of the electronic transitions in the UV-Vis spectra were provided by TD-DFT analysis. The Hirshfeld surface analyses were presented and discussed, as well as the energy framework calculations. The estimated maximum wavelength (λ) absorbance and the band-gap energy of OH-X were computed for various solvents and compared to the outcomes of experiments. Investigations of chemical reactivity, MEP map, and surface area maps were also carried out. To show electron delocalization in the molecule, electron localization function (ELF) and the local orbital localizer (LOL) were used. Other topics included topological and Mulliken charge distribution studies. Utilizing certain vibrational modes, the vibrational assignments were accomplished and experimental data was compared. The docking studies were utilized to investigate the interactions of the ligand (OH-X) with certain protein targets, suggesting that OH-X could be employed as a potential cytotoxic and antibacterial agent. OH-X may be considered a potential medicinal molecule as a result of the current research. In terms of geometric and spectroscopic features, the findings from the experimental and theoretical were highly comparable. [ABSTRACT FROM AUTHOR]

The compound 2-(3-phenyl)-5-((m-toluloxy) methyl)-4H-1,2,4-triazole-4-yl) benzoic acid (PTMTBA) has been characterized using various analytical techniques such as NMR, FT-IR, and single crystal X-ray diffraction. The molecular structure reveals some fascinating features. The O1--H1...N4 and C--H...p intermolecular hydrogen bonding between molecules constitute a three-dimensional molecular network. The crystal structure has been optimized using both Hartree-Fock (HF) and Density functional theory (DFT) calculations. The molecular electrostatic potential (MEP) and frontier molecular orbitals (FMOs) of the molecule have been analyzed to gain insight into its physical and chemical properties. 3D Hirshfeld surfaces and allied 2D fingerprint plots have been analyzed for molecular interactions. The molecule docks very well with the target protein (PDB code: 3FFP), indicating it to be an effective inhibitor of carbonic anhydrase. [ABSTRACT FROM AUTHOR]

Citrulline is a non-protein amino acid that acts as a metabolic intermediate in the urea cycle and arginine synthesis. It is present in some foods, although its name derives from watermelon (Citrullus vulgaris), from which it was first identified. Under normal conditions, Citrulline exists as a zwitterion in aqueous solutions since its carboxylic and amine groups can act as Lewis donors to chelate metal cations. In addition, Citrulline possesses in the aliphatic chain a terminal ureide group, which could also coordinate. Although Citrulline is comparable to other classical amino acids, its coordination chemistry has yet to be explored. Only two metal complexes have been reported, and the copper complex is a polymeric and insoluble material. As part of our search for active Casiopeina® analogs, we created a more soluble complex by combining 2,2′-Bipyridine into a new mixed material, resulting in the mononuclear complex [Cu(Bipy)(Citr)(H2O)(NO3)]·H2O. Single-crystal X-ray diffraction, spectroscopic methods (FT-IR, UV-Vis, Raman), and mass spectrometry characterized the material. Interestingly, both isomers of Citrulline, R(D), and S(L) are present in the same crystal. In addition, the molecular structure and electronic properties of the complex were calculated using density functional theory (DFT). Non-covalent interactions were characterized using the atoms-in-molecules (AIM) approach and Hirshfeld surface (HS) analysis. This ternary complex containing Citrulline and 2,2′-Bipyridine will be used for docking calculations and preliminary biological studies using calf thymus DNA (CT-DNA) and plasmid pUC19 as a first approximation to cytotoxic activity against cancer cell lines. [ABSTRACT FROM AUTHOR]

3-ferrocenyl-estra-1,3,5 (10)-triene-17-one (2), [Fe(C5H5)(C24H25O3)], crystallizes in the monoclinic space group C2. The cyclopentadienyl (Cp) rings adopt a nearly eclipsed conformation, and the Cp plane is tilted by 87.66° with respect to the substituted phenyl plane. An average Fe-C(Cp) bond length of 2.040(13) Å was determined, similar to the one reported for ferrocene. Hirshfeld surfaces and two-dimensional fingerprint plots were generated to analyze weak intermolecular C-H···π and C-H···O interactions. Density functional theory studies revealed a 1.15 kcal/mol rotational barrier for the C3-O1 single bound. Fluorescence quenching studies and in silico docking studies suggest that human serum albumin forms a complex with 2 via a static mechanism dominated by van der Waals interactions and hydrogen bonding interactions. [ABSTRACT FROM AUTHOR]

Context: The design and synthesis of safe and highly active sulfonylurea herbicides is still a challenge. Therefore, following some principles of structure-activity relationship (SAR) of sulfonylurea herbicides, this work focuses on evaluating two sulfonylurea derivatives bearing electron-withdrawing substituents, namely, –(CO)OCH3 and –NO2 on the aryl group, on herbicidal activity. To understand the effects caused by the substituent groups, the molecular and electronic structures of the sulfonylureas were evaluated by density functional theory. Likewise, the crystalline supramolecular arrangements of both compounds were analyzed by Hirshfeld surface, QTAIM, and NBO, with the aim of verifying changes in intermolecular interactions caused by substituent groups. Finally, through a toxicophoric analysis, we were able to predict the interacting groups in their biological target, acetolactate synthase, and verify the interactions with the binding site. Methods: All theoretical calculations were conducted using the highly parameterized empirical exchange-correlation functional M06-2X accompanied by the diffuse and polarized basis set 6-311++G(d,p). The atomic coordinates were obtained directly from the crystalline structures, and from the energies of the frontier molecular orbitals (HOMO and LUMO), chemical descriptors were obtained that indicated the influence of the functional groups in the sulfonylureas on the reactivity of the molecules. The intermolecular interactions in the crystals were analyzed using the Hirshfeld, QTAIM, and NBO surfaces. Toxicophoric modeling was performed by the PharmaGist webserver and molecular docking calculations were performed by the GOLD 2022.1.0 software package so that the ligand was fitted to the binding site in a 10 Å sphere. For this, genetic algorithm parameters were used using the ChemPLP scoring function for docking and ASP for redocking. [ABSTRACT FROM AUTHOR]

The quantum chemical properties of hydantoin (imidazolidine-2,4-dione) have been studied by the DFT method (density functional theory) and experimentally by FT-IR, UV–Vis, 1H, and 13 C NMR. The B3LYP technique is used to determine HOMO-LUMO, vibrational frequency, and other parameters as well as to optimize the structure. Along with that vibrational mode assessment, the estimated vibrational frequencies were compared to experimental FT-IR spectra. MEP (molecular electrostatic potential) analysis and a Fukui function analysis were both done to look into the reactive regions of the molecule in order to look into the charge distribution of the molecule. Additionally, the electron localization function (ELF) value was examined to reveal details about the chemical composition, molecular bonding, and reactivity. The calculation of UV–visible spectra using the TD-DFT/PCM approach is done, and the results are contrasted with UV spectra that have been calculated experimentally. From HOMO to LUMO orbitals, electron excitation analysis was carried out. Hole and Electron density distribution (EDD and HDD) maps were created in an excited state using various solvents. The intermolecular interactions on the crystal surface were described and evaluated using fingerprint plots and Hirshfeld surface analyses. The Hirshfeld surface was used to identify different kinds of intermolecular interactions, including N–C, N–H, N–O, O–C, and O–H. The 1H-NMR and 13 C-NMR shifts were calculated using the GIAO method, and the results were compared to experimental spectra. In a biological investigation utilizing several receptors, molecular docking was employed to identify the most effective ligand-protein interactions. The stability of biomolecular systems was investigated using a molecular dynamics simulation. [ABSTRACT FROM AUTHOR]

In this investigation a single crystal of (4-oxo-piperidinium ethylene acetal) trioxonitrate (4-OPEAN) was synthesized by modifying the mechanism of gradual evaporation at ambient temperature. The operational groupings are found in the complex material in the elaborate substance, according to the infrared spectrum. Single crystal X-ray diffraction suggests, (4-OPEAN) with the chemical formula (C7H12NO2)NO3 belongs to the orthorhombic space group Pnma and is centrosymmetric in three dimensions with the aforementioned network configurations, a = 11.7185(8) Å, b = 7.2729(6) Å, c = 11.0163(8) Å, Z = 4, V = 938.89(12) Å3, R = 0.0725 and wR = 0.1762. Many NH…O and CH…O hydrogen bridges, both bifurcated and non-bifurcated, link the 4-oxo-piperidinium ethylene acetal cations to the trigonal (NO3−) anions. Molecular geometry and optimal parameters of (4-OPEAN) have been determined via DFT computations at the theory-level B3LYP/6-311 ++ G(d, p), these have been contrasted with the X-ray data already available. Hirshfeld surface analysis has made it possible for the visualization and quantification of relationships between molecules in the crystal composition. Quantum theory atoms in molecules, electron location function, decreased density gradient, and localized orbital locator research have all been used to explore non-covalent interactions in crystal structure. In order to pinpoint both the nucleophilic and electrophilic locations that support hydrogen bond formation, the molecule electrostatic potential was determined. The greatest and lowest energies of occupied and unfilled molecular orbitals, together with additional derived atomic characteristics, show the material to be extremely stable and hard. According to a molecular docking study, 4-OPEAN may exhibit inhibiting effects on the 6Y84 and 7EJY virus proteins from corona (COVID-19).

The multicomponent reaction of 4-nitrobenzaldehyde with acetophenone and urea in the presence of HCl was investigated, and, as a result, 4,5-bis(4-nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione was synthesized. The structure of the synthesized compound was confirmed by the X-ray method. We performed Hirshfeld surfaces (HS) analysis and two-dimensional (2D) fingerprint plots for the studied compound to obtain surface reactivity and intermolecular interactions. The H∙∙∙H interactions were found to be higher, up to 32.2%, while the percentage C∙∙∙O contact was found to be the lowest among the reported interactions for single crystal packing. The energy framework analysis shows the strength of interaction energy within fragments of a single crystal at 3.08 A distances. The DFT study shows structural reactivity and a reduced HOMO-LUMO gap up to 4.0 eV. The NPA study reveals the reactivity and excellent charge transfer within the structure. The TD-DFT study reveals the absorbance in the UV region and excited state parameters during crucial transitions (transitions with maximum oscillator strength). The investigated compound shows excellent optical and nonlinear optical (NLO) properties, as indicated by its polarizability (αo) and hyperpolarizability (βo) values. [ABSTRACT FROM AUTHOR]

This study focuses on selected members of the general salen-analogues family possessing two O-H⋯N hydrogen bonds, namely three isomers of N,N'-bis(salicylidene)-X-phenylenediamine, denoted as ortho, meta and para. Two of the isomers are not planar in the published crystal structures. The current study tackles the problem of symmetry and interactions within the molecules, as well as in the crystal lattice. The aromaticity of the phenyl rings is evaluated using the Harmonic Oscillator Model of Aromaticity (HOMA) index. Intra- and inter-molecular non-covalent interactions are studied via Hirshfeld surface analysis, Independent Gradient Model (IGM), Quantum Theory of Atoms in Molecules (QTAIM), Non-Covalent Interaction (NCI) index, Electron Localisation Function (ELF), Core-Valence Bifurcation (CVB) index and Symmetry-Adapted Perturbation Theory (SAPT). Density Functional Theory (DFT) simulations were carried out in vacuo and with solvent reaction field based on Polarisable Continuum Model (IEF-PCM formulation) at the ω B97XD/6-311+G(2d,2p) level. Crystal structure analyses were performed for the data reported previously in the literature. The obtained results demonstrate that the three isomers differ greatly in their structural properties (molecular symmetry is broken for the ortho and meta isomers in the solid state) and ability to form intermolecular interactions, while retaining overall similar physico-chemical characteristics, e.g., aromaticity of the phenyl rings. It was found that the presence of the polar solvent does not significantly affect the structure of the studied compounds. An application of the Hirshfeld surface analysis revealed the nature of the non-covalent interactions present in the investigated crystals. The SAPT results showed that the stability of the dimers extracted from the crystals of the Schiff base derivatives arises from electrostatics and dispersion. [ABSTRACT FROM AUTHOR]

In this paper, we describe the synthesis and structural characterization of the 1-(cyclohex-1-en-1-yl)-3-(prop-2-yn-1-yl)-1,3-dihydro-2H-benzimidazol-2-one (2) via IR, NMR (1H and 13C), and HRMS. The crystal structure of the isolated organic compound 2 was confirmed through single-crystal X-ray diffraction analysis. The experimental results regarding the molecular geometry and intermolecular interactions within the crystal are in accordance with the DFT calculations and Hirshfeld surface analysis.

Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of β-diketones remains largely unexplored. β-Diketones and their complexes find broad applications as biologically active compounds. In this study, in silico molecular docking results revealed that two β-diketone derivatives, namely 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione and 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione, exhibit anti-COX-2 activities. However, recent docking results indicated that the relative anti-COX-2 activity of these two studied β-diketones was influenced by the employed docking programs. For improved design of COX-2 inhibitors from β-diketones, we conducted molecular dynamics simulations, density functional theory (DFT) calculations, Hirshfeld surface analysis, energy framework, and ADMET studies. The goal was to understand the interaction mechanisms and evaluate the inhibitory characteristics. The results indicate that 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione shows greater anti-COX-2 activity compared to 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione.

The molecular structure of Schiff base ZIm was investigated using spectroscopic (NMR, UV–vis) techniques. Theoretical calculations of the mentioned compound have been carried out using density functional theory at the B3LYP/6-31G(d) level of theory. Geometrical parameters such as bond lengths (Å) and angles (°) obtained by DFT calculations show excellent agreement with X-ray analysis result. The Hirshfeld surface (HS) analysis shows the different percentage interactions: H/H (49.8%), H/C (28.7%), N/H (15.2%) and O/H (5.7%) interactions. The 1H and 13C NMR chemical shifts with respect to TMS were calculated using the gauge-independent atomic orbital (GIAO) method in CDCl3 and compared with the experimental data. The UV–Vis spectrum of ZIm was computed with the B3LYP and CAMB3LYP functionals and the 6-31G(d) basis set in different solvents such as CHCl3, CH3CN, MeOH and DMSO. The frontier molecular orbital's (FMO's) analysis and molecular electrostatic potential surface (MEP) were investigated using theoretical calculations. The theoretical results show good agreement with the experimental results. [ABSTRACT FROM AUTHOR]

Here, a new cyano-bridged 3d–4f compound, a Dy(III)–Fe(III) molecular assembly ([Dy(DMF)4(H2O)3(μ-CN)Fe(CN)5.H2O] (1)), having a structure consisting of neutral one-dimensional (1D) chains, as well as an unbound aqua molecule, was synthesized and characterized using single crystal X-ray diffraction (XRD), infrared (IR), and elemental analyses. We then examined its structural topologies and studied its density functional theory (DFT), Hirshfeld surface analyses, and photophysical properties. The 1D chains were further linked by H-bond interactions, generating a three-dimensional (3D) motif which stabilizes the whole molecule. The weak interactions in 1 were assessed using Hirshfeld surface analyses, as well as fingerprint plots and DFT studies. Additionally, Hirshfeld surface analysis was performed to elucidate the roles of the weak interactions, such as the H⋯H, C⋯H, C–H⋯π, and van der Waals (vdW) interactions which are pivotal to stabilizing the crystal environment. Furthermore, the DFT studies were used to elucidate the bonding structure within the complex system. Complex 1 exhibits characteristic fluorescence as the Dy(III) complex is an excellent lime green luminescent material. Thus, it is considered to be a suitable material for preparing photoluminescent material. [ABSTRACT FROM AUTHOR]

Optically transparent organic single crystals of (E)-N'-(2,4-dimethoxybenzylidene) benzohydrazide (DMBBH) have been grown by slow evaporation technique. The detailed crystal structure of DMBBH was determined from Single crystal X-ray diffraction (SCXRD) study. The presence of active functional groups in the compound was identified by the experimental and computational Fourier transform infrared (FTIR) and NMR analyses. The UV–Vis Spectrum reveals the optical transparency of the grown crystal in the visible region. The natural bond orbital (NBO) analysis results show that the interaction between the donor π(C2-C7) and acceptor π*(C1-N8) has the highest stabilization energy (111.9 kJ/mol) and it shows the hyperconjugation within the –CONH‒ group. The first order hyperpolarizability value β0 = 2.8501 × 10–30 esu of the synthesized compound was eight times greater than that of urea (0.3728 × 10–30 esu). The Z-scan approach revealed the nonlinear optical (NLO) behaviour and optical limiting characteristics of the molecule. [ABSTRACT FROM AUTHOR]

The crystal and molecular structure of three derivatives of carbonyl 2-substituted pyrroles was determined by the single crystal X-ray diffraction. There are 2,2-dichloro-1-(1-methyl-1H-pyrrol-2-yl)ethan-1-one (I), 2-chloro-1-(1H-pyrrol-2-yl)ethan-1-one (II) and methyl 1H-pyrrole-2-carboxylate (III). All compounds crystallize with one molecule in the asymmetric unit in P212121 for I and II, and P21/c group for III. Despite the similar structures of the investigated compounds, the hydrogen bonds formed in their crystal structures adopt different H-bond motifs. In structure I, the dimers R12(5) and R21(7) form a chain along the b-axis, while in structures II and III, chain C(5) structural motifs are formed. The single point calculations at a ωB97XD/6-311++G(d,p) level of theory indicate that systems with N-H⋯O bonds have greater interaction energies (are more stable) compared with systems featuring C-H⋯O/Cl bonds. A descriptive Hirshfeld analysis showed that the greatest differences are visible for the H⋯H interactions. These H⋯H interactions predominate in structure III, accounting for 45% of the intermolecular interactions, while in structures I and II, they account for only 25%. Although compounds I-II contain Cl-atoms, the percentage of Cl⋯Cl interactions is rather low. In structure with two Cl-atoms (I), the contribution of the Cl⋯Cl contacts is 8.7% and for II, the contribution accounts for only 0.4% of the interactions. [ABSTRACT FROM AUTHOR]

• The AHMP+.AMBA− compound was synthesized by the slow evaporation technique. • The present compound was characterized by SCXRD, FTIR and DFT analyses. • The O⋅⋅⋅H and H⋅⋅⋅H contacts are observed as significant interactions. • TG and DTA analyses show thermal stability up to 168 ºC of the present salt. • AHMP+.AMBA− is suitable for the fabrication of optoelectronic and photonic devices. The organic crystal (AHMP+.AMBA−) of the AHMP and AMBA organic compounds was successfully synthesized and grown by the slow evaporation solution process. The present work focuses on the crystal structure, Hirshfeld surface, spectroscopic and DFT analyses of the title salt. The crystal geometry of AHMP+.AMBA− monohydrated salt was characterized by the single-crystal XRD technique. The synthesized salt crystallizes in the triclinic crystal system and P-1 space group. The identification of the functional groups of the compound has been done by FTIR spectroscopy and DFT/B3LYP-D3/6–311++ G (d,p) level of theory. Further, Hirshfeld surface mapping and its associated two-dimensional fingerprint plots predict that the O⋅⋅⋅H and H⋅⋅⋅H interactions are dominant for stabilizing the crystal structure. TG-DTA reveals the crystal is thermally stable up to 168 ºC. The optical studies have been performed by the time-dependent DFT (TD-DFT) and UV–Vis spectroscopic methods. Moreover, the Z-scan experiment has been done to obtain third-order NLO properties. Additionally, the HOMO-LUMO energy gap, MEP maps and theoretical NLO parameters have also been calculated. [Display omitted] [ABSTRACT FROM AUTHOR]

• A new tetrachlorocobaltate(II) salt with 4-nitrobenzyl-4-methylpyridinium was synthesized and characterized. • Hirshfeld surfaces and fingerprint plots represented the weak interactions. • The HOMO-LUMO energy gap and UV–visible diffuse reflectance spectrum explained the charge transfer interactions in the molecules. • The first hyperpolarizability (β tot) was 342 times higher than that of standard KDP crystal (β KDP = 6.85 × 10−31 esu). • As-synthesized salt exhibited good antibacterial activity against S. aureus and E. coli. This paper presented the synthesis, composition analysis, and structural characterization of a new organo-inorganic metal halide, 4-nitrobenzyl-4-methylpyridinium tetrachlorocobaltate(II) [4NO 2 Bz-4-MePy] 2 [CoCl 4 ](1). The single-crystal X-ray diffraction analysis displayed that the compound crystallized in the monoclinic space group P 2 1 / c , consisting of two [4NO 2 Bz-4-MePy]+ cations and a [CoCl 4 ]2− anion. The energy gap between the HOMO and LUMO orbitals, the polarizability, and the first hyperpolarizability were carried out based on the DFT calculation. The HOMO-LUMO energy gap and UV-visible diffuse reflectance spectrum illustrated the charge transfer interactions between the [CoCl 4 ]2− anions and the [4NO 2 Bz-4-MePy]+ cations. In addition, the low band gap values (1.64 eV for the Tauc formula, 1.62 eV for the truncated line method, and 2.73 eV for the calculated value) indicated that the crystal was appropriate for optical applications. The first hyperpolarizability (β tot) was 342 times higher than that of standard KDP crystal (β KDP = 6.85 × 10−31 esu), suggesting that crystal 1 was a premium material for NLO applications. The scanning electron microscopy and energy dispersive spectrometer determined the morphology and elemental distribution of the crystal. Hirshfeld surface analysis was performed to quantify the contributions of the different intermolecular interactions. The result of antimicrobial experiments displayed that the compound had excellent antimicrobial activity against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). [Display omitted] [ABSTRACT FROM AUTHOR]

• Detailed quantitative analysis of the different intermolecular interactions present in methyl (E)-2-(2-hydroxybenzylidene)hydrazine-1-carboxylate (a), methyl (E)-2-(3- hydroxybenzylidene)hydrazine-1-carboxylate (b) and methyl (E)-2-(4- hydroxybenzylidene)hydrazine-1-carboxylate (c). • The structure investigation revealed that various interactions like C H...O, N H...O and pi stacking interactions are involved in constructing ring motifs to stabilize the crystal packing. • Their solid-state structures have been analysed through Hirshfeld surface analysis, including the evaluation of the different energy frameworks, indicating that the molecular structures are primarily formed by hydrogen bonds and the stabilization is dominated via the electrostatic energy contribution. • The chemically active regions of the aldimines were identified by the analysis of molecular electrostatic potential surface. • Further, from PASS analysis and literature reports, molecular docking of title compounds was carried out with testosterone 17beta-dehydrogenase (NADP+) (PDB-ID 3KLP). Interactions present in differently substituted hydroxy based imine derivatives were characterised and identified by the utilisation of spectroscopic techniques in conjunction with X-ray crystallography and theoretical computations. All the target compounds ' a - c ' crystallises in monoclinic crystal system with P21/c and C2/c space groups. CH...Pi and Pi...Pi interaction are the characteristic interactions present in the target compounds ' a - c ' The most significant contributions to the crystal packing were found using Hirshfeld surface analysis, and potential contact points were identified. H...H, O...H and C...H contacts and π stacking interactions are the dominant contacts observed in all the crystals these results showed that hydrogen bonding and hydrophobic interactions were significantly present. Furthermore, investigations related to calculations of the molecular electrostatic potential and frontier molecular orbital (highest occupied–lowest unoccupied) were carried out for the optimised structure. The HOMO-LUMO energy gap made it possible to determine the molecule's chemical hardness, chemical inertness, electronegativity, and electrophilicity index, which showed its possible kinetic stability and reactivity. The target compounds' predicted activity spectra (PASS) showed that these compounds exhibit significant Testosterone 17beta-dehydrogenase (NADP+) inhibition activity, with Pa 7.18–7.95. Finally, Testosterone 17beta-dehydrogenase (NADP+) (PDB-ID 3KLP) was used to conduct molecular docking investigations of compounds ' a - c '. Due to their tiny size and lack of rigidity, which enable them to bind well at any position, a and b exhibit higher binding free energies of -7.08 and -7.00 kcal/mol and inhibition constants of 0.1 and 1.2 µM than compound c. [Display omitted] [ABSTRACT FROM AUTHOR]

• Structural investigation of sulfonamide derivative using crystal X-ray diffraction technique. • N H...S and C-Br...S interaction is studied. • HOMO-LUMO and MEP analysis helped to understand the physical properties of the molecule. • The nature of non-covalent bonding characteristics were revealed by the QTAIM and NCI analysis. In this research paper, the compound (E)-2-(4-bromobenzylidene)hydrazinecarbothioamide (NC2) was synthesized and characterized by spectroscopic techniques and crystal structure was elucidated using single crystal X-ray diffraction method. The Hirshfeld surface analysis revealed the relative contributions of different intermolecular interactions to crystal packing, while the 2D fingerprint plots provided a visual representation of the intermolecular interactions via the surface area corresponding to each type of interaction. The findings revealed that the crystal packing of the molecule is mostly determined by H...H, C-Br...S and N H...S interactions. We investigated the structural and electronic properties of the compound NC2 using density functional theory (DFT). The optimized geometry, total energy, HOMO-LUMO gap, and vibrational spectra were calculated at the ωB97X/6–311+ G (d,p) level of theory. The calculated results showed that the molecule has a stable geometry with a trans-conformation. The HOMO-LUMO gap of 3.813 eV indicates that the molecule has moderate stability. The nature of noncovalent interactions are investigated using the methods reduced density gradient (RDG) and topology analysis like quantum theory of atoms in molecules (QTAIM) proposed by Bader et al. The compound NC2 is found to adhere to the Lipinski's rule of five and exhibit good pharmacokinetic properties. [ABSTRACT FROM AUTHOR]

• A strontium thiocyanate coordination compound templated by hexamethylenetetramine [Sr(H 2 O) 6 (SCN) 2 ]·2HMTA synthesized for the first time. • Synthesis method is benign and employing cost-effective and ecofriendly reagents. • A highly intricate H-bonding (O–H···C HMTA , O–H···N HMTA , C12–H12···S1 and C–H···N) network between [Sr(H 2 O) 6 (SCN) 2 ] and HMTA molecules leading to chains and rings of different sizes, which leads to 3D supramolecular framework. • H—H interactions contribute the highest (30.5 %) to the HS of the repeating unit. • The complex could be a suitable precursor for SrO or SrS nanoparticles. The synthesis and structural characterization of a strontium thiocyanate coordination compound with hexamethylenetetramine [Sr(H 2 O) 6 (SCN) 2 ]·2HMTA has been reported. The complex crystallizes in the monoclinic space group P2 1 /c. This air-stable and water-soluble complex undergoes thermal decomposition in several steps. The molecules are assembled into a stable 3D supramolecular assembly via O–H···S and O–H···N stacking interactions. The supramolecular contacts in the complex were investigated and visualized through a detailed analysis of the Hirshfeld surface (HS) and 2D fingerprint plots to quantify the interactions within the crystal structure. The noncovalent interactions were analysed using the Bader's quantum theory of "atoms in molecules" (QTAIM) and the noncovalent interaction plot (NCI plot) and rationalized using molecular electrostatic potential surface calculations. The binding energies associated with the noncovalent interactions observed in the crystal structures and the interplay between them have been calculated using theoretical DFT calculations. The AIM, NCI and HOMO-LUMO profiles substantiate the H-bond classification. This study demonstrated a good correlation between experimental and theoretical data. [Display omitted] [ABSTRACT FROM AUTHOR]

Citrulline is a non-protein amino acid that acts as a metabolic intermediate in the urea cycle and arginine synthesis. It is present in some foods, although its name derives from watermelon (Citrullus vulgaris), from which it was first identified. Under normal conditions, Citrulline exists as a zwitterion in aqueous solutions since its carboxylic and amine groups can act as Lewis donors to chelate metal cations. In addition, Citrulline possesses in the aliphatic chain a terminal ureide group, which could also coordinate. Although Citrulline is comparable to other classical amino acids, its coordination chemistry has yet to be explored. Only two metal complexes have been reported, and the copper complex is a polymeric and insoluble material. As part of our search for active Casiopeina® analogs, we created a more soluble complex by combining 2,2′-Bipyridine into a new mixed material, resulting in the mononuclear complex [Cu(Bipy)(Citr)(H2O)(NO3)]·H2O. Single-crystal X-ray diffraction, spectroscopic methods (FT-IR, UV-Vis, Raman), and mass spectrometry characterized the material. Interestingly, both isomers of Citrulline, R(D), and S(L) are present in the same crystal. In addition, the molecular structure and electronic properties of the complex were calculated using density functional theory (DFT). Non-covalent interactions were characterized using the atoms-in-molecules (AIM) approach and Hirshfeld surface (HS) analysis. This ternary complex containing Citrulline and 2,2′-Bipyridine will be used for docking calculations and preliminary biological studies using calf thymus DNA (CT-DNA) and plasmid pUC19 as a first approximation to cytotoxic activity against cancer cell lines.

3-ferrocenyl-estra-1,3,5 (10)-triene-17-one (2), [Fe(C5H5)(C24H25O3)], crystallizes in the monoclinic space group C2. The cyclopentadienyl (Cp) rings adopt a nearly eclipsed conformation, and the Cp plane is tilted by 87.66° with respect to the substituted phenyl plane. An average Fe-C(Cp) bond length of 2.040(13) Å was determined, similar to the one reported for ferrocene. Hirshfeld surfaces and two-dimensional fingerprint plots were generated to analyze weak intermolecular C-H···π and C-H···O interactions. Density functional theory studies revealed a 1.15 kcal/mol rotational barrier for the C3-O1 single bound. Fluorescence quenching studies and in silico docking studies suggest that human serum albumin forms a complex with 2 via a static mechanism dominated by van der Waals interactions and hydrogen bonding interactions.

As part of this study, the vibrational properties of 3H4NB were examined. Comparing observed and simulated vibrational spectra allowed for the identification of characteristic frequencies and the attribution of band names. For the density functional theory (DFT) calculations, the LSDA functional with 6-311++G(d,p) degree of approximation was used. Furthermore, the same level of theory was used to calculate molecular orbitals such as natural bond orbitals (NBOs) and the HOMO-LUMO energy gap. The condensed Fukui function and the molecular electrostatic potential (MEP) surface were used to determine the relative electrophilicity and nucleophilicity of the current molecule. Intermolecular hydrogen bonding interactions are studied using Hirshfeld surface analysis and fingerprint plots. Molecular docking analysis was used to investigate the compound's biological activities. The hydrogen bond active binding residues and binding energy of a chosen chemical with carcinogenic activity targets were examined. [ABSTRACT FROM AUTHOR]

The multicomponent reaction of 4-nitrobenzaldehyde with acetophenone and urea in the presence of HCl was investigated, and, as a result, 4,5-bis(4-nitrophenyl)-8a-phenyl-decahydro-[1,3]diazino[4,5-d]pyrimidine-2,7-dione was synthesized. The structure of the synthesized compound was confirmed by the X-ray method. We performed Hirshfeld surfaces (HS) analysis and two-dimensional (2D) fingerprint plots for the studied compound to obtain surface reactivity and intermolecular interactions. The H∙∙∙H interactions were found to be higher, up to 32.2%, while the percentage C∙∙∙O contact was found to be the lowest among the reported interactions for single crystal packing. The energy framework analysis shows the strength of interaction energy within fragments of a single crystal at 3.08 A distances. The DFT study shows structural reactivity and a reduced HOMO-LUMO gap up to 4.0 eV. The NPA study reveals the reactivity and excellent charge transfer within the structure. The TD-DFT study reveals the absorbance in the UV region and excited state parameters during crucial transitions (transitions with maximum oscillator strength). The investigated compound shows excellent optical and nonlinear optical (NLO) properties, as indicated by its polarizability (αo) and hyperpolarizability (βo) values.

Based on single crystal X-ray diffraction studies for 1-(4-nitrophenyl)-3,5-di-thiophen-2-yl-1H-pyrazole (2a), monoclinic crystal system with a space group of C2/c was determined, where a final residual value of R equals to 0.058. The synthesized compounds were characterized through 1H and 13C NMR spectroscopy, and its intermolecular interactions were considered utilizing 2D and 3D Hirshfeld surface studies. The optimized molecular geometry, vibrational frequencies, and frontier molecular orbital energies of the title molecule were explored using density functional theory. Molecular modeling study revealed feasible binding modes of the title compound to protein targets, which showed small binding free energies. The X-ray structure and Hirshfeld surface analysis of the titled compound (2a) employed to identify intermolecular interactions within the structure are reported below. [ABSTRACT FROM AUTHOR]

Short peptides have great potential as safe and effective anticancer drug leads. Herein, the influence of short cyclic peptides containing the Pro-Pro-Phe-Phe sequence on patient-derived melanoma cells was investigated. Cyclic peptides such as cyclo(Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe-), called CLA, and cyclo(Pro-homoPro-β3homoPhe-Phe-), called P11, exert the cytotoxic and the cytostatic effects in melanoma cells, respectively. CLA was the most active peptide as it reduced the viability of melanoma cells to 50% of control at about 10 µM, whereas P11 at about 40 µM after 48 h incubation. Interestingly, a linear derivative of P11 did not induce any effect in melanoma cells confirming previous studies showing that cyclic peptides exert better biological activity compared to their linear counterparts. According to in silico predictions, cyclic tetrapeptides show a better pharmacokinetic and toxic profile to humans than CLA. Notably, the spatial structure of those peptides containing synthetic amino acids has not been explored yet. In the Cambridge Structural Database, there is only one such cyclic tetrapeptide, cyclo((R)-β2homoPhe-D-Pro-Lys-Phe-), while in the Protein Data Bank—none. Therefore, we report the first crystal structure of cyclo(Pro-Pro-β3homoPhe-Phe-), denoted as 4B8M, a close analog of P11, which is crucial for drug discovery. Comparative molecular and supramolecular analysis of both structures was performed. The DFT findings revealed that 4B8M is well interpreted in the water solution. The results of complex Hirshfeld surface investigations on the cooperativity of interatomic contacts in terms of electrostatic and energetic features are provided. In short, the enrichment ratio revealed O...H/H...O and C...H/H...C as privileged intercontacts in the crystals in relation to basic and large supramolecular H-bonding synthon patterns. Furthermore, the ability of self-assemble 4B8M leading to a nanotubular structure is also discussed. [ABSTRACT FROM AUTHOR]

In the present study, N‐(thiophen‐2‐ylmethyl)thiophene‐2‐carboxamide, C10H9NOS2, (I), was obtained by the reaction of thiophene‐2‐carbonyl chloride and thiophen‐2‐ylmethanamine. Characterization of (I) was carried out using X‐ray diffraction, spectroscopic techniques and elemental analyses. The DFT/B3LYP/6‐311++G(d,p) theoretical level was successfully applied to calculate the optimized geometry and the local and global chemical activity parameters. The results obtained show good agreement between the experimental and theoretical geometrical parameters. The local and global chemical activity parameters were examined to determine the electrophilic and nucleophilic sites in (I). The natural bond orbital (NBO) analysis of (I) gives an efficient methodology for investigating the inter‐ and intramolecular bonding, as well as giving a convenient basis for investigating charge transfer or conjugative interactions in molecular systems. Also, the antimicrobial activity of (I) was investigated against eight microorganisms using the microdilution method and it is found to have an effective antibacterial activity. In addition, molecular docking studies were calculated in order to understand the nature of the binding of (I) with a lung cancer protein (PDB entry 1x2j). [ABSTRACT FROM AUTHOR]

The molecular structure of Thiosemicarbazide 5 Sulfosalicylate – a semi organic single crystal (T5SS) was investigated by density functional theory employing Becke’s three parameter hybrid exchange functional with Lee– Yang–Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted on the finite field approach to reveal the nonlinear optical property of the chosen crystal T5SS. The calculated first order hyperpolarizability (β) of T5SS is found to be 3.267 times that of urea which suggests that the material may be a suitable candidate for nonlinear optical applications. The Natural Bond Orbital (NBO) analysis confirms the occurrences of strong inter and intramolecular charge transfer or conjugative interaction in the molecule which enhance the increase in hyperpolarizability (β) value. Frontier molecular orbital analysis explains the eventual charge transfer occurrence between the molecules and the energy gap reflects the chemical reactivity of the molecule. The percentage of intermolecular contacts contributing to the Hirshfeld surface in T5SS crystal was obtained by Hirshfeld surface analyses with 2D fingerprint plots. [ABSTRACT FROM AUTHOR]

In this work, three new alkyl substituted imidazo[4,5-b]pyridine derivatives have been synthesized by alkylation reactions under phase transfer catalysis conditions. The compounds (4 and 7) obtained were characterized using 1H NMR and 13C NMR spectroscopy. Their molecular and crystal structures have been confirmed by single-crystal X-ray diffraction. The global and local reactivities of the derivatives were investigated using the DFT/B3LYP method with the 6-31G(d,p) basis set. In addition, the closest contacts between the active atoms of the compounds were identified through the Hirshfeld surface analysis. Furthermore, the affinity of these derivatives to adsorb onto different metallic surfaces was estimated using Monte Carlo simulations. It was found that both compounds exhibit a remarkable tendency to adsorb onto an iron surface in comparison with other metal surfaces. It is expected that 7 will act as an effective corrosion inhibitor compared to 4 in acidic environments. [ABSTRACT FROM AUTHOR]

• Structural determination of a new cadmium thiocyanate coordination polymer [Cd(µ-2-Ampy) 2 (µ 1,3 -SCN) 2 ] n. • Synthesis method is benign and employing cost-effective and ecofriendly reagents. • Cooperative N H—H and N H—S hydrogen bonds, as well as weak C H—π and π—π stacking interactions assembles the polymer into a 3D supramolecular framework. • Molecular docking was performed in relation to the activity towards breast, lung, and liver cancers. • PLIP analysis indicates mostly hydrophobic interactions and hydrogen bond interactions between proteins and the complex. A one-dimensional [Cd(SCN) 2 ] n coordination polymer doubly bridged by 2-aminopyridine has been synthesized via slow evaporation method at low temperature and it was characterized by single-crystal X-ray diffraction, Fourier Transform Infrared (FT-IR) spectroscopy, electronic spectroscopy, thermogravimetric analysis (TGA), and elemental analysis. The polymeric complex crystallizes in the triclinic crystal system with space group P-1. An analysis of the crystal structure as well as Hirshfeld surfaces (HS) associated with 2D fingerprint plots, indicates the existence of C–H· · · π and π-stacking interactions alongside N H—N and N H—S H-bonding interactions contributing to the stabilization of the layered assembly of the compound. Theoretical Density Functional Theory (DFT) Calculations (using different levels of theory) were done on the asymmetric unit of the polymer and a polymer fragment that reflects the coordination environment of Cd2+ in the polymer, to gain more information about the coordination environment of Cd2+ in the polymer. This also permitted a quantification of the interaction energies associated with hydrogen bonding and non-covalent interactions, as well as other quantum chemical parameters. Good consistency was found between the calculated results and the experimental structure. All the levels of theory used predict that the polymer fragment was less stable compared to the asymmetric unit except at the B3LYP/SSD level of theory. Analysis of the HOMO and LUMO was used to explain the charge transfer within the polymer. Thermal analysis of the polymer indicates it decomposes in two steps resulting in a residue indexed to the hexagonal phase of CdS JCPDS [06–0314]. The activity of the metal complex against breast, lung, and liver cancer was measured. The interactions occurring in the docking calculation were examined in detail with PLIP (Protein-Ligand Interaction Profiler) analysis. Lastly, Swiss- ADME (absorption, distribution, metabolism and excretion) analysis was performed to examine the pharmacological properties of the metal complex. [Display omitted] [ABSTRACT FROM AUTHOR]