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Tuberculosis (TB) is a deadly disease of global concern. The previous work studies the geometric optimization, vibrational analysis, TDDFT, and electronic properties of the TB pathogen drug isoniazid (ISO). This communication will discuss the changes in geometry, electronic properties, and shielding parameters of ISO‐absorbed carbon nanotube (CNT) (CNT‐ISO, C56H16). This study has used the DFT/B3LYP/6–311G (d, p) method for the first time to report ISO's electronic structure and interaction parameters on the CNT surface. The same level theory is used to discuss the thermodynamic stability of CNT‐ISO. The calculated UV spectra of CNT are compared with UV spectra of CNT‐ISO by using the same level theory in a water solvent, which provides a better comprehension of CNT as a drug delivery system after absorption of the ISO in the human body. The nature and strength of interactions have been discussed with the help of NBO and AIM analysis, and the frontier orbital highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO‐LUMO) gap, chemical softness, and chemical hardness have been calculated to understand its complete chemical properties. The characters of the frontier molecular orbitals are discussed and analyzed by comparing the DOS spectra of CNT with CNT‐ISO. It has also examined the scan plot of interaction with time using ab‐initio dynamics simulation (ADMP) calculations. [ABSTRACT FROM AUTHOR]

Three N‐substituted benzimidazole cobalt(II) complexes have been synthesized and fully characterized by elemental analysis, FT‐IR spectroscopy, and X‐ray crystallography. The crystal packing formation features were studied by AIM analysis, and the energy and nature of both weak noncovalent interactions in the crystal and metal–ligand coordination bonds were assessed. These N‐coordinated cobalt(II) complexes were screened for antimicrobial activities against Gram‐negative (Escherichia coli, Bacillus subtilis) and Gram‐positive (Enterococcus durans) bacteria. Minimal inhibitory concentrations (MIC = 6.2 mg/mL) were found for complex cobalt chloride with allylbenzimidazole ligands against E. durans and E. coli. Its antimicrobial activity is several times higher compared to the reference gentamicin. Molecular docking made it possible to consider the nature of binding of cobalt metal complexes with vinyl‐, allyl‐ and styrylbenzimidazole ligands to biological targets and estimate their energy. The binding energy meanings depend on protein and ligand type, and reaches 8 kcal/mol. [ABSTRACT FROM AUTHOR]

Homogeneous catalysis involving a transition metal agostic interaction (TM...H...C) is an attractive strategy for C–H bond activation, in which the transition metal agostic intermediates serve as the critical component. To investigate the roles of manganese agostic intermediates in the unusual migration of the Mn(CO)3 fragment in the (exo-phenyl)(η3-cyclohexenyl)manganese tricarbonyl [(Ph)(η3-C6H8)Mn(CO)3] (complex 1) under the protonation of tetrafluoroboric acid–diethyl ether (HBF4.Et2O), a comprehensive density functional theory (DFT) theoretical study was performed. The computational results showed that formation of the [(cyclohex-3-enyl)-η6-benzene]manganese tricarbonyl complex [(C6H9)(η6-Ph)Mn(CO)3+][BF4] (complex 2) was achieved via a series of mono-agostic and di-agostic intermediates. The overall rate-limiting step for this unusual migration of the Mn(CO)3 fragment is the formation of the di-agostic (η2-phenyl)manganese complex 8 (4 → 5 → 8) with a Gibbs barrier of 15.4 kcal mol−1. The agostic intermediates with TM...H...C agostic interactions were well-characterized by geometry parameters, Atoms-In-Molecules (AIM) analyses, and the Natural Adaptive Orbitals (NAdOs). The located pathways in the current study successfully explained the experimental observations, and the findings on the TM...H...C agostic interaction provided a new aspect of the catalytic reaction with the manganese complex. [ABSTRACT FROM AUTHOR]

This study addresses a comprehensive assessment of the interaction between chemical warfare agents (CWA) and acetylcholinesterase (AChE) systems, focus on the intriguing pnictogen‐bond interaction (PnB). Utilizing the crystallographic data from the Protein Data Bank pertaining to the AChE‐CWA complex involving Sarin (GB), Cyclosarin (GF), 2‐[fluoro(methyl)phosphoryl]oxy‐1,1‐dimethylcyclopentane (GP) and venomous agent X (VX) agents, the CWA is systematically displaced by increments of 0.1 Å along the PO bond axis, extending its distance by 4 Å from the original position. The AIM analysis was carried out and consistently revealed the presence of a significant interaction along the PO bond. Investigating the intrinsic nature of the PnB, the NBO and the EDA analysis unearthed the contribution of orbital factors to the overall energy of the system. Strikingly, this observation challenges the conventional σ‐hole explanation commonly associated with such interactions. This finding adds a layer of complexity to understanding of PnB, encouraging further exploration into the underlying mechanisms governing these intriguing chemical phenomena. [ABSTRACT FROM AUTHOR]

Context: Herein, we compare and contrast the dual roles of Cun clusters (n = 3, 5, and 7 atoms) in scavenging or generating RO• free radicals from ROH at the theoretical levels (where R = H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). This investigation is performed in water media to mimic the actual environment in the biological system. In the presence of the Cun clusters, bond dissociation energy (BDE) of RO–H and R–OH is reduced. This is clear evidence for the increased possibility of both the RO–H and R–OH bonds breakage and scavenging of RO• radicals. The nature of anchoring bonds responsible for the interaction of Cun clusters with ROH and RO• are interpreted using the quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) analysis. The DFT results indicate that the O•⋅⋅⋅•Cu bond is stronger and has more covalent character in RO•⋅⋅⋅•Cun radical complexes than in ROH⋅⋅⋅•Cun. Therefore, the interactions of Cun clusters with RO• radicals (antioxidant) are more pronounced than their interactions with ROH non-radicals (pro-oxidant). Methods: The GAMESS software package was utilized in this paper. The B3LYP and M06 functions with the 6–311 + + G(d,p), and LANL2DZ/SDD basis sets was used to perform the important geometrical parameters of RO•⋅⋅⋅•Cun and ROH⋅⋅⋅•Cun, binding energy (Eb), and bond dissociation energy (BDE). [ABSTRACT FROM AUTHOR]

The compound 3,4‐diaminopyridine (3,4‐AP), a derivative of 4‐aminopyridine (4‐AP), is used in the symptomatic treatment of fatigue in multiple sclerosis as well as Lambert–Eaton myasthenia syndrome whereas the parent compound 4‐AP is used as an acetylcholine‐releasing drug, in serum, saliva, and urine. 4‐AP is an experimental drug that may reduce symptoms in some people with multiple sclerosis, particularly those who are more sensitive to heat. The carbon nanotubes (CNTs) have inside cavity tethering on the surface upon functionalization and adsorption on the walls of CNTs, which provides extra ability to carry pharmaceutical agents through multiple ways. Due to these benefits, this communication will discuss the comparative changes in geometry, electronic properties, and shielding parameters of 4‐AP and 3,4‐AP absorbed C56H16. The DFT/B3LYP/6–31G (d, p) method is used for the first time to report electronic structure and interaction parameters on the CNT surface. The same level theory is used to discuss the thermodynamic stability of CNT‐4‐AP/3,4‐AP. The calculated UV spectra of CNT are compared with UV spectra of CNT‐4‐AP and 3,4‐AP by using the same level theory in a water solvent, which provides a better comprehension of CNT as a drug delivery system after absorption of the 4‐AP and 3,4‐AP in the human body. The nature and strength of interactions have been discussed with the help of AIM analysis, and the frontier orbital highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) gap, chemical softness, and chemical hardness have been calculated to understand its complete chemical properties. The characters of the frontier molecular orbitals are discussed and analyzed by comparing the DOS spectra of CNT with CNT‐4‐AP/3,4‐AP. [ABSTRACT FROM AUTHOR]

N-propargylimidazole and N-propargyl-2-methylimidazole complexes of zinc(II) chloride and acetate were synthesized and studied by X-ray analysis, NMR, and FTIR spectroscopy. Molecular structures of compounds under study represent a configuration of the ZnN2O2 or ZnN2Cl2 type where the zinc(II) ion is coordinated by two nitrogen atoms from the N-propargylimidazole ligands and two atoms of the co-complexing agent. All complexes crystallize in the monoclinic system, the molecules of N-propargyl-2-methylimidazole complexes of zinc(II) chloride and acetate have the C2 symmetry axis passing through the zinc atom. The atoms in molecules (AIM) analysis method were used for investigation of the nature and energy of coordination bonding between metal and ligand and non-covalent interactions in the crystal. An evaluation of the antimicrobial activity of N-propargylimidazole complexes of zinc(II) chloride and acetate in relation to Enterococcus durans, Bacillus subtilis and Escherichia coli was carried out. The studied metal complexes were practically inactive against the test microorganisms. [ABSTRACT FROM AUTHOR]

N-(4-Iodo-1,3-diphenylbutyl)acetamide was obtained. Structure of the amide was confirmed by single crystal X-ray diffraction analysis; the nature and strength of the hydrogen bonds formed by the compound in the crystal and solutions were studied by quantum chemical calculations (DFT, AIM analysis). The hydrogen bond energy was assessed by two methods and compared with each other. A comparison was made of the experimental and theoretical infrared spectrum of the compound under study. PASS analysis was performed to predict the biological activity of N-(4-iodo-1,3-diphenylbutyl)acetamide. [ABSTRACT FROM AUTHOR]

Homogeneous catalysis involving a transition metal agostic interaction (TM…H…C) is an attractive strategy for C–H bond activation, in which the transition metal agostic intermediates serve as the critical component. To investigate the roles of manganese agostic intermediates in the unusual migration of the Mn(CO)3 fragment in the (exo-phenyl)(η3-cyclohexenyl)manganese tricarbonyl [(Ph)(η3-C6H8)Mn(CO)3] (complex 1) under the protonation of tetrafluoroboric acid–diethyl ether (HBF4.Et2O), a comprehensive density functional theory (DFT) theoretical study was performed. The computational results showed that formation of the [(cyclohex-3-enyl)-η6-benzene]manganese tricarbonyl complex [(C6H9)(η6-Ph)Mn(CO)3+][BF4] (complex 2) was achieved via a series of mono-agostic and di-agostic intermediates. The overall rate-limiting step for this unusual migration of the Mn(CO)3 fragment is the formation of the di-agostic (η2-phenyl)manganese complex 8 (4 → 5 → 8) with a Gibbs barrier of 15.4 kcal mol−1. The agostic intermediates with TM…H…C agostic interactions were well-characterized by geometry parameters, Atoms-In-Molecules (AIM) analyses, and the Natural Adaptive Orbitals (NAdOs). The located pathways in the current study successfully explained the experimental observations, and the findings on the TM…H…C agostic interaction provided a new aspect of the catalytic reaction with the manganese complex.

The mechanistic pathways for nucleophilic aromatic substitution of the nitro groups of 5,7-dinitro-3H-quinazolin-4-one and 1,3-dinitro-10H-dibenzo[b,f][1,4]oxazepin-11-one with 1H-1,2,3-triazole have been studied in both gas and solvent phase employing DFT/B3LYP calculations using 6-31G(d,p) basis set. The energetic parameters, i.e., free energy profiles along the reaction route and H-bond energy, charge analysis, and structural parameters have supported mechanistic pathway involving one-step concerted mechanism via formation of transition state during the reaction course. Despite substantial steric hindrance at adjacent position to fusion point, the regioselective attack of 1H-1,2,3-triazole has been observed at peri-position of benzannulated heterocycles. This regioselectivity is credited to intramolecular hydrogen bond C–H···O = C which stabilizes peri-transition state formation rather than para-transition state. The hydrogen bond acceptor–donor interactions have been studied using AIM method. The DFT and AIM analysis-derived results are compared for different sized dinitro-substituted benzannulated heterocycles and these studies have confirmed the contribution of substantial steric hindrance at peri-position with increased size of heterocycle. As benzannulated heterocycles are quite significant from the perspective of medicinal and natural product chemistry, this work will fulfill the need to find an efficient synthetic method for benzannulated heterocycles. [ABSTRACT FROM AUTHOR]

An advanced organic–inorganic hybrid compound 1,1,4,7,7-pentamethyldiethylenetriammonium trinitrate (PMDT) has been synthesized and characterized by X-ray diffractometry. The title molecule is abbreviated as PMDT has been investigated using experimental and computational techniques. The quantum chemical study was carried out using DFT calculation with B3LYP/6–31++G(d, p) basis set. Different methods have been performed to quantify the non covalent interactions within the title molecule. Atoms In Molecules (AIM) approach at bond critical points BCP's of the hydrogen bonds (C–H…O and N–H…O) in PMDT have been applied. Electron localization Function (ELF) and Local Orbital Locator (LOL) methods were studied in order to detect the electron density at bonding and anti-bonding sites of the title compound. The Hirshfeld surface analysis exposes important information on the inter and intramolecular interactions present in the crystal structure. Further characterization of the non covalent interactions has been shown by reduced Density of Gradient (RDG) and Independent Gradient Model (IGM). In addition, to map and analyze the weak-interaction regions, the interaction region indicators (IRI) have been used. The effect of polar solvents for the electrophilic and nucleophilic sites has been investigated. The ChELPG and Mulliken population analyses have been carried out. Frontier molecular orbital's (HOMO-LUMO) was discussed to afford the information about the reactivity of the PMDT molecule in gas, water and DMSO solvation. The temperature behavior and conductivity of the title molecule have been analyzed. Finally, in order to estimate the antibacterial mechanism of the PMDT compound action, molecular docking calculations were carried out on the active sites of various proteins.

Two binary cocrystals of 1,4‐diiodotetrafluorobenzene (1,4‐DITFB, C6F4I2) and 1,3,5‐trifluoro‐2,4,6‐triiodobenzene (1,3,5‐TITFB, C6F3I3) with the flexible 2‐{[(naphthalen‐2‐yl)methyl]sulfanyl}pyridine 1‐oxide (NTPO, C16H13NOS) molecule were successfully prepared and characterized by X‐ray diffraction and quantum chemistry calculation methods. X‐ray diffraction analysis reveals that the conformation of the flexible NTPO molecule has been changed significantly after introducing the 1,4‐DITFB or 1,3,5‐TITFB molecule into the NTPO lattice. Also the formation of the binary cocrystals is driven mainly by robust C—I...−O—N+ halogen bonds and π‐hole...π‐bond interactions, and they possess 'sandwich' structural frameworks. Moreover, interaction energy analysis and AIM analysis were used to explore the contribution of different fragments to the structural stability and the corresponding electronic properties, which reveals that the robust halogen bonds with shorter bonding lengths [2.768 (4) and 2.789 (3) Å] are suggested to be covalent to a certain degree. [ABSTRACT FROM AUTHOR]

• Single crystal X-ray structure determination of complex 2 confirms that dibutyltin(IV) complex has a bicapped tetrahedron. • Experimental and calculated electronic spectra have similarity, with a slight difference in λ max due to the solvent environment. • Global reactivity descriptors and MEP explain that the interaction between organotin(IV) complexes and CT-DNA is a type of groove and electrostatic interaction. • NBO analysis suggests that organotin(IV) complexes have ligand-to-metal (donation) and metal-to-ligand (back donation), that stabilize the complexes. The present study describes the detailed DFT-based electronic structure calculations without any symmetry constraints being performed on di- and triorganotin derivatives of 4-fluoroanthranilic acid (AFA), viz. Me 2 SnL 2 (1), n -Bu 2 SnL 2 (2), Me 3 SnL (3), and Ph 3 SnL (4) (where L = monoanion of AFA). The structural and atomic charge analysis have confirmed the previously reported our experimental results, i.e. bicapped tetrahedral and distorted tetrahedral geometry for di- and triorganotin derivatives, respectively, and all the complexes 1–4 contain a positively charged central tin atom surrounded by a negatively charged system. The single crystal X-ray structure of complex 2 (n -Bu 2 SnL 2) also suggests that AFA acts as a monoanion and bidentate ligand resulting a bicapped tetrahedral environment around tin. Various population analysis such as Mulliken (MPA), Hirshfeld (HPA), and natural population analysis (NPA) have been employed to calculate the charges at all the atoms. A finite difference approximation method has been used to explain the charge distribution within the studied complexes 1–4 based on the conceptual global and local reactivity DFT-based descriptions, frontier molecular-orbital analysis (FMOA), and molecular electrostatic potential maps (MEP). Further, the conceptual DFT-based global reactivity descriptors and frontier molecular orbital analysis show that the interactions between CT-DNA and complexes 1–4 may be groove binding or electrostatic. The integral equation formalism-polarizable continuum model (IEF-PCM) has been employed to calculate the UV–visible spectra of 1–4 in the solvent field, whereas the same in the gas phase has been obtained with the help of time-dependent DFT (TD-DFT) at the same level of theory. The intramolecular charge distribution in 1–4 has been investigated with the help of natural bond orbital (NBO) analysis. The topological and energetic parameters at the selected bond critical points in the coordination sphere of complexes 1–4 have been calculated using atoms-in-molecules (AIM) theory. The analysis of different kinds of non-covalent interactions (NCI) in complexes 1 – 4 has also been investigated. X-ray crystallography of complex 2 (n-Bu2SnL2) suggests that AFA is a monoanion and bidentate ligand. DFT-based quantum chemical calculations have been used to explore the structure and reactivity of organotin(IV) complexes 1 – 4 through global and local reactivity descriptors, and the various interactions between AFA and organotin(IV) moiety (R2Sn/R3Sn) have been explored by NBO and AIM analysis. [Display omitted] [ABSTRACT FROM AUTHOR]

End-of-life textile recycling presents a real economic and environmental challenge. From a circular economy perspective, we attempt to evaluate the chitosan–ZnO nanocomposite efficiency in the recycling of cotton-used fabric, accompanied by the electroanalytic and the optoelectronic investigation of the resulting nanocomposites. For comparison, the precipitation and the sonochemical pathways were used as in situ treatment methods. The effect of chitosan characteristics on the antibacterial sustainability of the treated fabrics and the properties of the resulting nanocomposites were studied. The chemical bonding, crystal structure, morphology, optical and optoelectronic properties, intermolecular interactions and antibacterial properties of the resulting free nanocomposites were investigated. The treated used fabrics were characterized by Fourier-transform infrared spectroscopy and scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy before and after 20 washes. Density functional theory study and atoms in molecules analysis of cellulose–nanocomposite interaction were carried out. The results indicate an effective dose of 2 mg against tested bacteria for all the nanocomposites. The nanocomposites have an orange-red emission with no Zn defects and large oscillator strength (ƒ) values. Medium molecular weight chitosan-based nanocomposites showed more intense orange-red emission and higher ƒ values. Sustainable antibacterial properties of treated fabrics are generated with high molecular weight chitosan-based nanocomposites. More than 83% of the antibacterial activity is retained after 20 washes. The theoretical study confirms the stability of the free nanocomposite (chitosan–ZnO) and its destabilization by contacting the fabric when ZnO is a rod shaped, which generates its growth-promoting. [ABSTRACT FROM AUTHOR]

• Palladium(II) (1,2) and platinum(II) (3,4) long chain dithiocarbamate complexes were prepared. • X-ray analysis of 1 and 4 revealed the square planar coordination geometry around the metal centre. • Complex 4 revealed intermolecular anagostic C-H∙∙∙Pt interactions. • C-H∙∙∙Pt interactions were characterized using DFT, Hirshfeld surface analysis and AIM analysis. • Platinum complexes (3,4) show better anticancer activity than those of palladium complexes (1,2). Four new homoleptic complexes bis(N-dodecyl-N-benzyl)dithiocarbamato-S,S')M(II) (where M=palladium (1), platinum (3)) and bis(N-dodecyl-N-(2-hydroxybenzyl)dithiocarbamato-S,S')M(II) (where M=palladium (2), platinum (4)) were synthesized and characterized using elemental analysis, FTIR and NMR spectra. The crystal structures of 1 and 4 were solved by single crystal X-ray diffraction technique. Single crystal X-ray analysis of the two of the complexes (1 and 4) revealed the presence of a distorted square planar coordination geometry (S 4) about the metal centre. Complex 4 revealed two intermolecular anagostic C-H∙∙∙Pt interactions which were characterized through a comprehensive set analysis using single crystal X-ray diffraction (experimental) and DFT, Hirshfeld surface analysis and AIM (theoretical) analysis. The electronic behavior, MEP surfaces, FMO and DOS studies of the complexes 1 and 4 were investigated employing DFT. A strong correlation has been found between both experimental and theoretical bond parameters. MTT assay was used to study the antitumor activities of 1 – 4 against MCF7 cancer cells. The results reveal that all complexes have fine anticancer activities. [Display omitted] [ABSTRACT FROM AUTHOR]

[Display omitted] New six-coordinated N -propargylimidazole complexes with cobalt(II), nickel(II) and copper(II) chlorides, [M(N -propargylimidazole) 4 Cl 2 ], were obtained in good yields by the reaction of N -propargylimidazole with corresponding metal chlorides. Molecular and crystal structures of compounds 1 – 3 were studied by X-ray analysis. Numerous non-covalent interactions including halogen bonds and π-stacking forms in the crystal were analyzed in the framework of quantum theory Atom in molecules. An evaluation of the antimicrobial activity of N -propargylimidazole complexes with Co(II), Ni(II) and Cu(II) chlorides in relation to E. durans , B. subtilis and E. coli showed that the complexes of nickel exhibit antimicrobial activity comparable to gentamicin in relation to E. coli. To explore the inhibitory activity mechanism the molecular docking was carry out. [ABSTRACT FROM AUTHOR]

[Display omitted] • The chalcogen-bonded and tetrel-bonded complexes between the singlet metallylenes and carbonyl chalcogenides are investigated and compared. • The dual binding behavior of the metallylenes and carbonyl chalcogenides can be explained on the basis of the molecular electrostatic potential surfaces. • The nature of the complexes has been investigated by the NBO, AIM and SAPT analysis. The intermolecular interactions between the singlet metallylenes XH 2 (X = Si, Ge, Sn, Pb) and carbonyl chalcogenides OCY (Y = S, Se, Te) have been studied by the high-level quantum chemical calculations. The chalcogen-bonded and tetrel-bonded complexes can be formed between XH 2 and OCY due to their ambiphilic character. The structure and binding strength of the complexes have been explored on the basis of the MEP surfaces of the monomers, and geometrical parameters and interaction energies of the complexes. The nature of the complexes has been investigated by the NBO, AIM and SAPT analysis. The tetrel-bonded complexes exhibit a much stronger binding strength with larger interaction energies and shorter binding distances compared to the chalcogen-bonded complexes. The interaction energies of the complexes become larger with the increase of the Y atomic number, but become smaller with the increase of the X atomic number. NBO analysis reveals that the dominant orbital interactions in the chalcogen-bonded and tetrel-bonded complexes are LP(X) → σ*(C-Y) and LP(Y) → LP*(X), respectively. AIM analysis suggests that the chalcogen-bonded complexes are the purely noncovalent, but the tetrel-bonded complexes have partial covalent character. SAPT analysis indicates that the contribution of the energy component decreases in the order of E ele > E disp > E ind for most chalcogen-bonded complexes, and this order is E ele > E ind > E disp for most tetrel-bonded complexes. [ABSTRACT FROM AUTHOR]

The compounds m‐Tolylacetic acid and 2‐amino‐4‐Picoline were used as a precursor to synthesize the molecular complex 2‐amino‐4‐methylpyridinium 2‐(3‐methylphenyl)‐acetate by means of proton transfer. High‐resolution X‐ray diffraction data were collected for the crystallized complex at 100 K. The structure was solved spherically and further an aspherical model refinement was performed using Hansen and Coppens multipole formalism. Topological properties using AIM analysis were carried out for the title compound to understand the atom–atom interactions and the strength of the bond. The structure exhibits interesting patterns of N–H...O and C–H...O hydrogen bonds. A pair of N–H...O hydrogen bonds links the anion and cation of the molecular complex generating an R22(8) ring motif. These ring motifs are linked to adjacent anions and cations through another intermolecular N–H...O hydrogen bond generating a bifurcated R22(8)ring motif. Hirshfeld surface analysis was carried out to understand the types of inter‐molecular interactions and their strengths. [ABSTRACT FROM AUTHOR]

The coordination complex bis(1H-benzimidazole-κN3)cadmium(II) dibenzoate has been synthesized and characterized by single crystal diffraction analysis. Cadmium center is six coordinated and formed a distorted octahedron coordinated geometry. The Hirshfeld analysis shows that in the dnorm-surface of the compound, there are dark red spots near the hydrogen-bonds acceptor and donor atoms, while intermolecular interactions result in faint-red spots. The AIM analysis was performed, there exist a BCP in each N(C)–H∙∙∙O hydrogen bond, the bond paths also can be seen, the |V(b)|/G(b) < 1 and the H(b) > 0, the interaction is indicative of being a closed shell. The TG results are consistent with the X-ray diffraction structure

Quantum-chemical study (B3PW91/6-311G** and MP2/6-311G**) of structural and spectral criteria of the intramolecular coordination bond N→Si existence in [methoxy(methyl)silyl] derivatives of 8-mercaptoquinoline C9H6NSSi(OMe)nMe3–n (n = 1–3) has been carried out. Quantum topological analysis of electron distribution (AIM) has been performed to determine the physical nature of the hypervalent interaction. It has been found that the energy of the N→Si hypervalent bond depends on the number of the methoxy groups in the Si(OMe)3 fragment. [ABSTRACT FROM AUTHOR]

In this study, cyclic peptide (CP) with cyclooctaglycine model and gold nanoparticles (AuNP) with Au6 cluster model were used to examin the function of penicillamine (PCA) drug on ten different configurations of cyclic peptide-gold nanoparticles (CPAuNP). Binding energies, quantum molecular descriptors such as electrophilicity power (ω), global hardness (η), and solubility energies were studied in aqueous solution and gas phase at the M06-2X density functional level. The binding energy analysis was performed on (CPAuNP/PCA1-10) structures to determine the most stable structure. The obtained values for solvation energies indicate that CPAuNPs can have an effective performance when used along with PCA drug, which is a major factor in drug delivery. The quantum molecular descriptors reveal that the reactivity of cyclic peptide (CP) and PCA drug increases in (CPAuNP/PCA1-10) structures. AIM calculations for all structures show that intermolecular hydrogen bonding and Au-L (L = H, O, S, C, N) interactions play an important role for this drug delivery system. When the PCA drug is parallel to the CPAuNP carrier, interacting simultaneously with CP and AuNP, the structure is more stable than the structures in which the drug has interactions only with the CP or AuNP. DOI: http://dx.doi.org/10.17807/orbital.v12i3.1519

Karanjin, phytochemical from Pongamia pinnata is reported to be effective against HIV that causes AIDS in humans, however, the delivery of this therapeutic molecule still needs improvement. Hence, this study provides a better understanding of the nonbonded interaction between an anti-HIV drug karanjin and carbon nanotube (CNT) (C56H16). The electronic structure and interaction properties of the molecule karanjin over the surface of CNT were theoretically studied in the gas phase by DFT/B3LYP/6-31G (d , p) level of theory for the first time. The UV–Vis spectra and transitions of the karanjin drug, CNT (C56H16) and complex CNT (C-56)/karanjin in gas phase have been calculated by time-dependent density functional theory (TDDFT) for the investigation of adsorption effect. To support our hypothesis, we have performed quantum chemical analysis for CNT (C56H16)/karanjin in water and DMSO solvent. In this process, this CNT (C-56)/karanjin complex enters into affected cell in liquid medium. After that, the drug delivery system CNT (C-56) unloads karanjin at the affected site. The binding character interactive species have been determined by NBO and AIM analysis. The frontier orbital HOMO–LUMO gap, chemical softness, chemical hardness have also been calculated to understand its complete chemical properties. The outcomes from our interaction of drug karanjin with CNT (C56H16) will be instrumental for better drug delivery potential in the upcoming future. The absorption of the anti-HIV agent Karanjin, found from the seeds of the Karanja plant, by carbon nanotubes (CNT C56H16) has been studied using density functional theory (DFT). During absorption, NBO analysis, the value of Electrophilic charge transfer (ECT), HOMO, LUMO plot revealed that the charge flows from Karanjin (μ = 3.86 D) to CNT56 (μ = 0.00 D) and the whole system (μ = 6.285D) gets polarized, which results in a weak Van der Waals interaction of Karanjin with CNT. The bathochromic shift appears in UV spectra after the absorption process. This study provides a new pathway for researchers to design a new drug delivery system. [ABSTRACT FROM AUTHOR]

Studies have shown that hydrazides and thier derivatives are used for pharmaceutical and medicinal purposes. At present, the whole world is suffering for COVID-19 virus. There are some vaccines or medicines available to treat this disease all over the world. Today the one fourth of the world's population is under lockdown condition. In this scenario, scientists from the whole world are doing different types of research on this disease. Being a molecular modeller, this inspires us to design new types of species (may be drugs) which may be capable for COVID-19 Protease. In the present effort, we have performed docking studies of title compounds with COVID-19 protein (6LU7) for anti-COVID-19 activity. A comparative quantum chemical calculations of molecular geometries (bond lengths and bond angles) of 4-Hydroxy Benzo Hydrazide (4HBH) and its newly designed derivatve [(E)-N′-((1H-Pyrrol-2-YL)Methylene) –4-Hydroxy Benzo Hydrazide and its isomers (I, II and III)] in the ground state have also been carried out due to its biological importance and compared with the similer type of compound found in literature i.e. benzohydrazide. The optimized geometry and wavenumber of the vibrational bands of the molecules have been calculated by density functional theory (DFT) using Becke's three-parameters hybrid functional (B3LYP/CAM-B3LYP) with 6–311G (d, p) as the basis set. Vibrational wavenumbers are compared with the observed FT-IR and FTRaman spectra of 4-Hydroxy Benzo Hydrazide. TDDFT calculations are also done on the same level of theory and a theoretical UV-vis spectrum of title molecules are also drawn. HOMO-LUMO analysis has been done to describe the way the molecule interacts with other species. Natural bond orbitals (NBO) analysis has been carried out to inspect the intra- and inter- molecular hydrogen-bonding, conjugative and hyper conjugative interactions and their second order stabilization energy. Nonlinear optical (NLO) analysis has been performed to study the non-linear optical properties of the molecule by computing the first hyperpolarizability. The variation of thermodynamic properties with temperature has been studied. QATIM analysis shows that hydrogen bonding occurs in 4HBH, isomer II and III respectively. [ABSTRACT FROM AUTHOR]

Three organoselenium and organotellurium compounds containing ortho substitutents, namely, bis(2‐nitrophenyl) selenide, C12H8N2O4Se, 2, bis(2‐aminophenyl) selenide, C12H12N2Se, 3, and bis(2‐aminophenyl) telluride, C12H12N2Te, 7, have been investigated by both structural and theoretical methods. In the structures of all three compounds, there are intramolecular contacts between both Se and Te with the ortho substituents. In the case of 2, this is achieved by rotation of the nitro group from the arene plane. For 3, both amino groups exhibit pyramidal geometry and are involved in intramolecular N—H...Se interactions, with one also participating in intermolecular N—H...N hydrogen bonding. While 3 and 7 are structurally similar, there are some significant differences. In addition to both intramolecular N—H...Te interactions and intermolecular N—H...N hydrogen bonding, 7 also exhibits intramolecular N—H...N hydrogen bonding. In the packing of these molecules, for 2, there are weak intermolecular C—H...O contacts and these, along with the O...N interactions mentioned above, link the molecules into a three‐dimensional array. For 3, in addition to the N—H...N and N—H...Se interactions, there are also weak intermolecular C—H...Se interactions, which also link the molecules into a three‐dimensional array. On the other hand, 7 shows intermolecular N—H...N interactions linking the molecules into R22(16) centrosymmetric dimers. In the theoretical studies, for compound 2, AIM (atoms in molecules) analysis revealed critical points in the Se...O interactions with values of 0.017 and 0.026 a.u. These values are suggestive of weak interactions present between Se and O atoms. For 3 and 7, the molecular structures displayed intramolecular, as well as intermolecular, hydrogen‐bond interactions of the N—H...N type. The strength of this hydrogen‐bond interaction was calculated by AIM analysis. Here, the intermolecular (N—H...N) hydrogen bond is stronger than the intramolecular hydrogen bond. This was confirmed by the electron densities for 3 and 7 [ρ(r) = 0.015 and 0.011, respectively]. [ABSTRACT FROM AUTHOR]

Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.

In this study, cyclic peptide (CP) with cyclooctaglycine model and gold nanoparticles (AuNP) with Au6 cluster model were used to examin the function of penicillamine (PCA) drug on ten different configurations of cyclic peptide-gold nanoparticles (CPAuNP). Binding energies, quantum molecular descriptors such as electrophilicity power (?), global hardness (?), and solubility energies were studied in aqueous solution and gas phase at the M06-2X density functional level. The binding energy analysis was performed on (CPAuNP/PCA1-10) structures to determine the most stable structure. The obtained values for solvation energies indicate that CPAuNPs can have an effective performance when used along with PCA drug, which is a major factor in drug delivery. The quantum molecular descriptors reveal that the reactivity of cyclic peptide (CP) and PCA drug increases in (CPAuNP/PCA1- 10) structures. AIM calculations for all structures show that intermolecular hydrogen bonding and Au-L (L = H, O, S, C, N) interactions play an important role for this drug delivery system. When the PCA drug is parallel to the CPAuNP carrier, interacting simultaneously with CP and AuNP, the structure is more stable than the structures in which the drug has interactions only with the CP or AuNP. [ABSTRACT FROM AUTHOR]

A quantum chemical perspective of 31 structures contains electron acceptors: ASCl3 (arsenic trichloride), PCl3 (phosphorous trichloride) and NCl3 (nitrogen trichloride); forming non-covalent bond with various nitrogen-based electron donors that resulted in pnicogen bonds, AS...N, P...N and N...N were calculated at M062X/def2-QZVP level of theory. Besides the above method, MP2/def2-QZVP and CCSD(T)/def2-QZVP level of theories have also been analysed to have in depth knowledge about the bonds formed. The nature of the bonds was assumed from the electrostatic potential evaluated for all the monomers, where σ hole is positive for all the monomers. The strongest pnicogen bonds are ASCl3–NF2H, PCl3–NCH3CH3CH3 and NCl3–NCH3CH3CH3 having interaction energies as −4.15, −11.58 and −3.25 kcal/mol, respectively, at MP2/def2-QZVP level of theory. Further at CCSD(T)/def2-QZVP level of theory, ASCl3–NF2H and NCl3–NCH3CH3CH3 are found to be the most stable with interaction energies as −3.53 and −2.45 kcal/mol, respectively. The potential energy surface scan was performed for all the stable complexes in order to confirm the existences of energies are true minima. Moreover to confirm the halogen and pnicogen bonds, AIM analysis was carried out. The results from the above factors of pnicogen bond will help crystal growth, material science and engineering community to explore novel materials, which abide for modernization. [ABSTRACT FROM AUTHOR]

Surge for the advancement of sensor that accurately and selectively detect toxic materials particularly cyanides and fluorides, is expanding every day. Herein, we analyze the sensing ability of carbon nitride (C 6 N 8) monolayer for precise detection of hydrogen cyanide (HCN) and hydrogen fluoride (HF) using DFT approach. Interaction energy analysis reveals that HF binds strongly to C 6 N 8 monolayer which is probably due to chemical bond formation whereas, HCN adsorbed to the surface by weak van der Waals forces. The atom in molecules (AIM), the density of states (DOS), non-covalent interaction (NCI), molecular electrostatic potential (MEP), electron localization function (ELF), frontier molecular orbitals (FMO), and Q NBO were used to gain a thorough understanding of the complexation of HCN and HF with monolayer. HCN and HF analytes with C 6 N 8 monolayer exhibit slight variations in band gap energy in FMO analysis (4.206 to 4.267 eV) indicating weak NCIs. Furthermore, MEP map demonstrate that more charge transfer is occurred from the C 6 N 8 monolayer towards HF@C 6 N 8 resulting in a strong ionic bonding. In addition, the existence of non-covalent interactions among complexes confirmed by NCI-RDG and QTAIM analysis. A short recovery period for HCN@C 6 N 8 (1.677 × 10−7 s) makes desorption process simpler. Appreciable selectivity of monolayer towards analytes and prospects of all findings will provide an experimentalist with practical suggestions to build highly sensitive sensors for HCN and HF using C 6 N 8 monolayer. DFT calculations were carried out to study the interactions between HCN and HF on C 6 N 8 and new dimension of carbon nitride usage as sensor for poisonous gases was investigated. [Display omitted] • DFT study of adsorption of analytes on C 6 N 8 monolayer were studied. • QTAIM, DOS, NCI, MEP, ELF, FMO, and Q NBO demonstrate the nature of interaction between analytes and C 6 N 8 monolayer. • HCN and HF analytes with C 6 N 8 monolayer exhibit slight variations in band gap energy in FMO analysis indicating weak NCIs. • Short recovery time of C 6 N 8 monolayer at 300 K, suggesting that it works as a sensing material for HCN and HF analytes. [ABSTRACT FROM AUTHOR]

[Display omitted] • 3,5-disubstituted isoxazole exhibits excellent antitrypanosomal activity compared to drug reference, pentamidine. • Molecular docking shows seven hydrogen interactions and low binding energy for 3,5-disubstituted isoxazole. • 3,5-disubstituted isoxazole shows considerable stability during MD simulation compared to drug reference, pentamidine. • Quantum Theory of Atoms in Molecules (AIM) and Non-Covalent Interaction (NCI) analysis corroborate molecular docking and MD simulation findings revealing the strength of H-bonds found. • Cycloaddition [3 + 2] follows reverse electron demand, and dechloromethane has a significant impact on the regioselectivity. The antitrypanosomal activity of 3,5-disubstituted isoxazole has been investigated through molecular docking, revealing its binding to Plasmodium falciparum through seven hydrogen interactions demonstrating high affinity, supported by Molecular Dynamics Simulations. Followed by the Quantum Theory of Atoms in Molecules (AIM) studies, confirming the strength of hydrogen bonds and an acceptable ADMET profile has been found. The chemical reactivity of the cycloaddition [3 + 2] has been explored using Density Functional Theory (DFT). Results revealed a reverse electron demand, which was confirmed by global reactivity indices. Electron displacement was investigated based on Fukui functions, Methyl Cation Affinity (MCA), Methyl Anion Affinity (MAA), and Molecular Electrostatic Potential (MEP). The regioselectivity of the reaction was explored in the gas phase first and in dichloromethane secondarily to assess their impact on the reaction using the Integral Equation Formalism Polarizable Continuum (IEFPCM) model. Finally, additional bioactive compounds with 3,5-disubstituted isoxazole properties have been found using screening methods. [ABSTRACT FROM AUTHOR]

X-ray structures of a number of silatranes with Si ← N dative bonds of various lengths were analyzed using the AIM analysis method. The features of the effect of substituents at the silicon atom and in the silatranyl core on the length of the Si ← N dative bond have been established. The relationship between optimazed in the crystal length of the Si ← N dative bond and its calculated energy with a high correlation coefficient is obtained. A similar dependence was obtained for the electron density at the bond critical point of the Si ← N dative contact. The calculated value of the positive charge on silicon atoms is determined by the electronegative properties of the axial substituent. [ABSTRACT FROM AUTHOR]

The supramolecular frameworks of two metal complexes with 1,3-diamino-2-hydroxypropanetetraacetic acid (H 4 Hpdta) have been explored in the context of crystal engineering, and the noncovalent interactions are further characterized by Bader's quantum theory of "atoms-in-molecules" (QTAIM), Noncovalent Interaction (NCI) plot index and Scatter plot. [Display omitted] A new 1,3-diamino-2-hydroxypropanetetraacetate copper complex (1) [{Cu(Hpdta)}{Cu(H 2 O) 6 }] has been synthesized and structurally characterized by single crystal X-ray diffraction and compared with a similar cobalt complex (2) of H 4 Hpdta (H 4 Hpdta = 1,3-diamino-2-hydroxypropanetetraacetic acid) retrieved from CSD (CSD ref code: TELBAN) with a detailed analysis of intermolecular interactions. X-ray crystallography reveals that both complexes are stabilized through C−H⋯O and O−H⋯O interactions generating different supramolecular networks. Detailed analysis of Hirshfeld surfaces and 2D fingerprint plot has been carried out for the title complexes to quantify the intermolecular interactions. Further, the noncovalent interactions are characterized through the Bader's theory of 'Atoms in Molecules' (AIM) and noncovalent interaction (NCI) plot index. At the bond critical point (BCP), the electron density (ρ BCP) and the Laplacian of electron density ( ∇ 2 (ρ BCP)) differ significantly for strong and weak noncovalent interactions. The dissociation energies are evaluated for validating the intermolecular interactions required to stabilize the complexes. The analysis of topological parameters extracted from AIM calculation characterized the interactions as closed-shell interactions. [ABSTRACT FROM AUTHOR]

• Molecular docking presented 3D models for binding of 2, 6-diamine-7H-purine. • NBO analysis elucidates the effect of hyperconjugation and rehybridization. • The DFT study on the HOMO-LUMO, spectroscopic profiles and density surface maps were analyzed. • The cytotoxic importance of anticancer activity against inhuman thyroid cancer cells was perceived by MTT assay. • Molecular descriptors were clarified with the aid of global and local relativities. The molecular structure of 6-diamine-7H-purine (DAP) was optimized by the DFT/B3LYP method with 6-311++G(d,p) level of theory using the Gaussian 09 W package. The structural elucidation of the title compound was performed by FT-IR/Raman, 1H and 13C NMR spectral analyses. The complete theoretically calculated and experimentally observed vibrational frequencies were assigned on the basis of potential energy distribution (PED) calculations using the VEDA 4.0 program. The HOMO-LUMO analysis, topological AIM approaches and atomic charge density analysis of the title compound were also investigated. In addition, the result of the docking score was found to play an important role in bioactivity, which can be supported by the cytotoxic analysis (MTT assay) of the title compound. [ABSTRACT FROM AUTHOR]

Two new triorganotin(IV) complexes of Schiff base, Bu 3 SnL (1) and Ph 3 SnL (2) (where, L is the monoanion of Schiff base (HL= (E)-4-amino-3-(2-(2-hydroxybenzylidene) hydrazinyl)-1H-1,2,4-triazole-5(4H)-thione)) have been synthesized and thoroughly characterized by elemental analysis, IR, NMR (1H, 13C, 119Sn), ESI-MS and UV–Vis studies. The spectroscopic evidences suggest that both complexes adopt distorted trigonal bipyramidal geometry around tin atom with O phenolic and two organic groups in equatorial plane and the N azomethine and the third organic group in axial position in which Schiff base ligand acts as monoanionic bidentate coordinating through the O phenolic and N azomethine. DFT based quantum chemical calculation have been performed at B3LYP/6-31G(d,p)/Def2-SVP(Sn) level of theory, in order to get optimized geometry and electronic structure of the studied complexes. A comparative analysis of the experimental vibrational frequencies and simulated harmonic frequencies indicates good correlation between them. The assignment and the nature of the electronic transitions observed in the UV–visible spectra were analysed using time-dependent (TD-DFT) calculations. NBO analysis has also been performed to analyse the intra and inter-molecular interactions that leads stabilization in the studied systems. The topological and energetic properties of the electron density distribution for the tin-ligand interaction in studied system have been calculated in terms of atoms-in-molecules (AIM) theory using AIMAll. The synthesized complexes were screened for their in vitro antifungal activity against chosen fungal strains. The studied complexes were exhibited significant antifungal activity against all the chosen strains. In silico , docking experiment has also been carried out on the active site of the cytochrome P450 14-α-demethylase (CYP-51). Image 1 • Triorganotin(IV) complexes of schiff base have been synthesized by sodium salt method. • Structural characterization of the studied complexes has been performed by various spectroscopic techniques. • Geometrical parameters, frontier MO's, NBO and AIM have been explained. • Antifungal activity of the synthesized complexes has been investigated. • Bioactivity results have been explained through molecular docking studies. [ABSTRACT FROM AUTHOR]

1,5‐Bis([1,1′‐biphenyl]‐4‐yl)‐5‐hydroxy‐3‐methylheptane‐1,6‐dione, C32H30O3, was investigated by X‐ray analysis, quantum chemical calculations and AIM (atoms in molecules) analysis. It was shown that four intramolecular C—H...π forces are established between the two biphenyl fragments. C—H...π interactions lead to a bending of the biphenyl part. The energy of the intramolecular interactions was estimated and the exclusive role of the moment of force was established. [ABSTRACT FROM AUTHOR]

Experimental electron‐density studies based on high‐resolution diffraction experiments allow halogen bonds between heavy halogens to be classified. The topological properties of the electron density in Cl...Cl contacts vary smoothly as a function of the interaction distance. The situation is less straightforward for halogen bonds between iodine and small electronegative nucleophiles, such as nitrogen or oxygen, where the electron density in the bond critical point does not simply increase for shorter distances. The number of successful charge–density studies involving iodine is small, but at least individual examples for three cases have been observed. (a) Very short halogen bonds between electron‐rich nucleophiles and heavy halogen atoms resemble three‐centre–four‐electron bonds, with a rather symmetric heavy halogen and without an appreciable σ hole. (b) For a narrow intermediate range of halogen bonds, the asymmetric electronic situation for the heavy halogen with a pronounced σ hole leads to rather low electron density in the (3,−1) critical point of the halogen bond; the properties of this bond critical point cannot fully describe the nature of the associated interaction. (c) For longer and presumably weaker contacts, the electron density in the halogen bond critical point is only to a minor extent reduced by the presence of the σ hole and hence may be higher than in the aforementioned case. In addition to the electron density and its derived properties, the halogen–carbon bond distance opposite to the σ hole and the Raman frequency for the associated vibration emerge as alternative criteria to gauge the halogen‐bond strength. We find exceptionally long C—I distances for tetrafluorodiiodobenzene molecules in cocrystals with short halogen bonds and a significant red shift for their Raman vibrations. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Functionalization of iron oxide nanoparticles with cytarabine anticancer drug were studied. • The solvation and binding energies are energetically suitable. • Iron oxide nanoparticles can act as a favorable system for cytarabine drug delivery. • Hydrogen bonding plays an important role in noncovalent functionalization. • Covalent functionalization can occur through CH 2 OH functional group. Abstract Noncovalent functionalization of iron oxide nanoparticles (ION) with cytarabine anticancer drug (CYT) has been studied at B3LYP and M06-2X functionals using seven different configurations (ION/CYT1-7) and Fe 6 (OH) 18 (H 2 O) 6 cluster model for ION. The energetic stability of seven noncovalent structures was determined by the calculation of adsorption energies. The AIM studies demonstrated that the noncovalent functionalization mainly occurs through intermolecular hydrogen bonds. The reaction between ION and CYT may produce seven different products (IONCYT1-7/H 2 O). The high barrier of IONCYT2/H 2 O (via CH 2 OH) product is lower than that of IONCYT3/H 2 O (via OH) product and therefore is the preferred pathway for covalent functionalization. [ABSTRACT FROM AUTHOR]

[Display omitted] • Intermolecular hydrogen bonding due to O 1 -H 1B ...Cl 1 (2.266 Å), N 1 -H 1A ...Cl 1 (2.102 Å) and C 9 -H 9A ...F 3B (2.655 Å) • Electrons were resonated on the aromatic ring systems. • Surface view of FDC with SARS-CoV-2 main protease shows that FDC is well accommodated within in the binding pocket. • Radius of gyration signifies the ligands binding compel the proteins to become more compact and less flexible. A detailed vibrational analysis of flupentixol dihydrochloride (FDC) is performed by Density Functional Theory (DFT) calculations. Wavefunction reactivity properties and Atoms In Molecules (AIM) analysis are also performed. There is enormous O 1 -H 1B ...Cl 1 , N 1 -H 1A ...Cl 1 and C 9 -H 9A ...F 3B intermolecular hydrogen bonding in FDC. Electrons were resonated on the aromatic rings without any interference with aliphatic moiety of both highest occupied molecular orbital (HOMO) and in least unoccupied molecular orbital (LUMO) which is due to participation of fluorine atom intermolecular hydrogen bonding with adjacent C–H. The electron localization function (ELF) shows under populated N-C single bonds of ring A owing to the strong electron withdrawing effect of nitrogen atoms. SARS-CoV-2 main protease with FDC had energy −80 kcal/mol. With the help of molecular dynamics (MD), radial distribution functions (RDF) are calculated to identify the most critical interaction with water molecules. [ABSTRACT FROM AUTHOR]

Transition metal-based compounds have shown promising uses as therapeutic agents. Among their unique characteristics, these compounds are suitable for interaction with specific biological targets, making them important potential drugs to treat various diseases. Copper compounds, of which Casiopeinas® are an excellent example, have shown promising results as alternatives to current cancer therapies, in part because of their intercalative properties with DNA. Vanadium compounds have been extensively studied for their pharmacological properties and application, mostly in diabetes, although recently, there is a growing interest in testing their activity as anti-cancer agents. In the present work, two compounds, [Cu(Metf)(bipy)Cl]Cl·2H2O and [Cu(Impy)(Gly)(H2O)]VO3, were obtained and characterized by visible and FTIR spectroscopies, single-crystal X-ray diffraction, and theoretical methods. The structural and electronic properties of the compounds were calculated through the density functional theory (DFT) using the Austin–Frisch–Petersson functional with dispersion APFD, and the 6-311 + G(2d,p) basis set. Non-covalent interactions were analyzed using Hirshfeld surface analysis (HSA) and atom in molecules analysis (AIM). Additionally, docking analysis to test DNA/RNA interactions with the Casiopeina-like complexes were carried out. The compounds provide metals that can interact with critical biological targets. In addition, they show interesting non-covalent interactions that are responsible for their supramolecular arrangements.

In this study at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of quantum-mechanical theory it was explored conformational variety of the isolated quercetin molecule due to the mirror-symmetrical hindered turnings of the O3H, O5H and O7H hydroxyl groups, belonging to the A and C rings, around the exocyclic C−O bonds. These dipole active conformational transformations proceed through the 72 transition states (TSs; C1 point symmetry) with non-orthogonal orientation of the hydroxyl groups relatively the plane of the A or C rings of the molecule (HO7C7C8/HO7C7C6 = ±(89.9−93.3), HO5C5C10 = ±(108.9−114.4) and HO3C3C4 = ±(113.6−118.8 degrees) (here and below signs ‘±’ corresponds to the enantiomers)) with Gibbs free energy barrier of activation ΔΔGTS in the range 3.51−16.17 kcal·mol−1 under the standard conditions (T = 298.1 K and pressure 1 atm): ΔΔGTSO7H (3.51−4.27) < ΔΔGTSO3H (9.04−11.26) < ΔΔGTSO5H (12.34−16.17 kcal mol−1). Conformational dynamics of the O3H and O5H groups is partially controlled by the intramolecular specific interactions O3H…O4, C2′/C6′H…O3, O3H…C2′/C6′, O5H…O4 and O4…O5, which are flexible and cooperative. Dipole-active interconversions of the enantiomers of the non-planar conformers of the quercetin molecule (C1 point symmetry) is realized via the 24 TSs with C1 point symmetry (HO3C3C2C1 = ±(11.0−19.1), HC2′/C6′C1′C2 = ±(0.6−2.9) and C3C2C1′C2′/C3C2C1′C6′ = ±(1.7−9.1) degree; ΔΔGTS = 1.65−5.59 kcal·mol−1), which are stabilized by the participation of the intramolecular C2′/C6′H…O1 and O3H…HC2′/C6′ H-bonds. Investigated conformational rearrangements are rather quick processes, since the time, which is necessary to acquire thermal equilibrium does not exceed 6.5 ns.

An unsymmetrical tridentate Schiff base 4-((E)-(2-amino-5-nitrophenylimino)methyl)-5-(hydroxymethyl)- 2-methylpyridin-3-ol is newly synthesized and characterized experimentally. Its geometrical parameters, the assignment of IR bands and NMR chemical shifts are also computed by the density functional theory (DFT) method. In addition, the atoms in molecules (AIM) analysisis employed to investigate its geometry. Only one of the diamine-NH2 groups undergoes the condensation reaction. In the structure of the synthesized Schiff base, the remaining aminogroup lies in the para position with respect to the nitro group (isomer 1). In both gas and solution phases, isomer 1 is more stable than isomer 2 with the meta orientation of the amino and nitro groups. The NMR chemical shifts and the AIM analysis show that isomer 1 is a more favorite structure for the synthesized Schiff base. It has no planar structure. The phenolic proton is engaged in the intramolecular hydrogen bond with the azomethine nitrogen atom. The experimental results are in good agreement with the theoretical ones, confirming the validity of the optimized geometry. [ABSTRACT FROM AUTHOR]

An unsymmetrical tridentate Schiff base 4-((E)-(2-amino-5-nitrophenylimino)methyl)-5-(hydroxymethyl)- 2-methylpyridin-3-ol is newly synthesized and characterized experimentally. Its geometrical parameters, the assignment of IR bands and NMR chemical shifts are also computed by the density functional theory (DFT) method. In addition, the atoms in molecules (AIM) analysisis employed to investigate its geometry. Only one of the diamine-NH2 groups undergoes the condensation reaction. In the structure of the synthesized Schiff base, the remaining aminogroup lies in the para position with respect to the nitro group (isomer 1). In both gas and solution phases, isomer 1 is more stable than isomer 2 with the meta orientation of the amino and nitro groups. The NMR chemical shifts and the AIM analysis show that isomer 1 is a more favorite structure for the synthesized Schiff base. It has no planar structure. The phenolic proton is engaged in the intramolecular hydrogen bond with the azomethine nitrogen atom. The experimental results are in good agreement with the theoretical ones, confirming the validity of the optimized geometry. [ABSTRACT FROM AUTHOR]

In order to characterize various interactions in the G-quadruplex ⋯ M n+ (G-Q ⋯ M n+ ) complexes, the individual H-bond (E HB ) and metal ion-ligand interaction (E MO ) energies have been estimated using the electron charge densities (ρs) calculated at the X ⋯ H (X = N and O) and M n+ ⋯ O (M n+ is an alkaline, alkaline earth and transition metal ion) bond critical points (BCPs) obtained from the atoms in molecules (AIM) analysis. The estimated values of E MO and E HB were evaluated using the structural parameters, results of natural bond orbital analysis (NBO), aromaticity indexes and atomic charges. The E MO value increase with the ratio of ionic charge to radius, e/r, where a linear correlation is observed between E MO and e/r (R = 0.97). Meaningful relationships are also observed between E MO and indexes used for aromaticity estimation. The E NH value is higher than E OH in the complexes; this is in complete agreement with the trend of N⋯H N and O⋯H N angles, the E (2) value of n N → σ* NH and n O → σ* NH interactions and the difference between the natural charges on the H-bonded atom and the hydrogen atom of guanine (Δq). In general, the O 1 MO 2 angle becomes closer to 109.5° with the increase in E MO and decrease in E HB in the presence of metal ion. [ABSTRACT FROM AUTHOR]

Designing and introducing novel wheel-shaped supramolecular as host complexes with new magnetic properties is the theme of the day. So in this study, new eight binuclear chromium (III) complexes, as models of real chromium-wheel host complexes, were designed based on changing of bridged-ligands and exchange coupling constants (J) of them were calculated using the broken symmetry density functional theory approach. Substitution of fluorine ligand in fluoro-bridged model [Cr2F(tBuCO2)2(H2O)2(OH)4]−1 by halogen anions (Cl−, Br− and I− ) decreased the antiferromagnetic exchange coupling between Cr(III) centres such that by going from F− to I− the J values became more positive. In the case of hydroxo-bridged model [Cr2OH(tBuCO2)2(H2O)2(OH)4]−1, replacement of hydroxyl by methoxy anion (OMe−) strengthened the antiferromagnetic property of the complex but substitution by sulfanide (SH−) and amide (NH2−) anions weakened it and changed the nature of complexes to ferromagnetic. Because of their different magnetic properties, these new investigated complexes can be suggested as interesting synthetic targets. Also, the J value changes due to ligand substitution were evaluated and it was found that the Cr-X bond strength and partial charges of involved atoms were the most effective factors on it. [ABSTRACT FROM AUTHOR]

Benzophenones ( BP s) of the type 2-R-BP and 2,2′-R-BP , carrying silicon- or germanium-containing substituents R (R = EY 2 X; E = Si, Ge; Y = H, Me, F, Cl; X = H, F, Cl, OTf) at one or at two ortho -positions of the arene rings, were theoretically designed. Among 26 compounds considered, only 10 mono-substituted 2-R-BP and 5 bis-substituted 2,2′-R-BP (in hexane and DMSO solutions) belong to the first examples of hypervalent benzophenones. In these “true” chelates, the length of the O→E dative contact (which has a covalent component, according to the AIM analysis) is in the range of 2.0–2.4 Å, and the degree of pentacoordination of E is higher than 40%. In these compounds, a significant planarization of the benzophenone part occurs, compared to the initial BP . The TD-DFT calculations suggest the UV spectral properties of the hypervalent BP s to differ fundamentally from those of BP . For the “true” chelates 2-R-BP and 2,2′-R-BP , there is a well pronounced trend of a change of the coordination O→E contact strength along with the difference between the wavelengths of their first high-intensity band and the ππ* band of the unsubstituted BP . [ABSTRACT FROM AUTHOR]

The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S. . .Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S. . .π in 3a,b, S. . .S in 3c, and S. . .O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a-;d: S. . .π (3a: 2.4%; 3b: 2.4%), S. . .S (3c: less 1%), S. . .O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader's theory (AIM method), confirm the presence of intra-/intermolecular BCB S. . .Cl/S. . .S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature. [ABSTRACT FROM AUTHOR]

The theoretical study was carried out on the nickel (II) complexes with the bidentatethiosemicarbazone ligands; aromatic and aliphatic presented in square planar geometries. The calculations were performed using the density functional theory (DFT) at the PW91/TZP level. The nature of the nickel-ligand bonding in these low-spin complexes and ofthegeneral formulaNi [L n ] 2 (n = 1–9), was analyzed. The contributions of electrostatic and covalent interactions to the Ni-L n bonds are estimated by analyzing the energy decomposition. The covalent bond follows the Dewar-Chatt-Ducanson model; the explanation is provided by the orbital pattern highlighting the electronic donation-retrodonation. The AIM analysis, by means of the electronic density values, confirms the presence of weak intramolecular hydrogen interactions. The absence of the biological activity in the two complexes, Ni [L 5 ] 2 and Ni [L 9 ] 2 , can be correlated to a geometric descriptor quantified by the topological distortion. [ABSTRACT FROM AUTHOR]

A range of novel 1,1,2-trichloro-2-[2-chloro-2-(organylsulfanyl)ethenyl]cyclopropanes 2a-f were synthesized by reaction of (2-chloroprop-1-en-3-yl)sulfides with dichlorocarbene generated from CHCl 3 . The process apparently proceeds via carbenylation of sulfur atom followed by 2,3-sigmatropic rearrangement with subsequent dehydrochloration and cyclopropanation of the terminal double bond. The resulted trichlorocyclopropane derivatives were studied by 1 H and 13 C NMR spectroscopy as well as X-ray single-crystal analysis that revealed intramolecular CH-π interaction and the formation of intermolecular halogen bonds. [ABSTRACT FROM AUTHOR]

In the recent work, NMR study and the stability of the Z- and the E- isomers were undertaken for the two rotational isomers of phosphorus ylides involving 2-hydroxybenzimidazole [namely dimethyl-2-(2-hydroxybenzimidazole-n-yl)-3-(triphenylphosp hanylidene) succinate] by natural population analysis (NPA) and atoms in molecules (AIM) methods. Quantum mechanical calculation was clarified how the ylides exist in solution as a mixture of the two geometrical isomers (Z- and E-) as a minor or major form. In addition, Kinetic studies were performed for the reaction between triphenylphosphine and dialkyl acetylenedicarboxilate in the presence of NH– heterocyclic compound, such as 2-hydroxybenzimidazole. To determine the kinetic parameters of the reaction, it was monitored by UV spectrophotometry. Useful information was obtained from studies of the effect of solvent and concentration of reactants on the rate of reaction. Proposed mechanism was confirmed according to the obtained results and steady state approximation and first step (k2) and third step of reaction were recognized as a rate determining step and fast step, respectively on the basis of experimental data.