Crystal structure analysis,Hirshfeld surface analysis,spectral investigations (FT-IR,FT-R), DFT calculations,ADMET studies and molecular docking of 3H-Methyl-1H-pyrazole-1-carboxamide (3MPC)

On 3H-Methyl-1H-pyrazole-1-carboxamide (3MPC), Single crystal XRD, Fourier Transform Infrared Spectroscopy, Fourier Transform Raman Spectroscopy, Molecular Electrostatic Potential, Density function theoretical analysis and Molecular docking analysis are conducted. The target protein docking experiments revealed that the small molecule (MET) is a good molecule that docks well with several Nav channel 1 targets. Molecular Electrostatic Potential (MEP) aids in the optimization of protein-ligand electrostatic interactions. The molecular surface and hydrogen bonding interactions in the 3MPC crystal structure were located and analyzed using a fingerprint plot and Hirshfeld Surfaces. DFT–B3LYP calculations with the 6-31G (d,p) basis set are used to establish the optimised structure of the MET molecule, and the measured vibrational frequencies are compared to experimental values. The parameters of absorption, distribution, metabolism, excretion (ADME) and toxic (Tox) were assessed using the online server preADMET.     

Synthesis,crystal structure,vibrational, optical properties,and a theoretical study of a new Pb(II) complex with bis(1-methylpiperazine-1,4-diium): [C5H14N2]2PbCl6·3H2O

An investigation of the solid-state X-ray structure of the new organic–inorganic compound [C₅H₁₄N₂]₂PbCl₆·3H₂O shows a layered organization of the (PbCl₆)^4– anions, with (R₂NH₂)⁺ groups and water molecules developed in the [001 A. Hu, H.L. Ngo, W. Lin. J. Am. Chem. Soc., 125, 11490 (2003).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]] plane at x = (2n?+?1)/4. The crystal structure is stabilized by N???H···Cl, N???H···O, O???H···Cl, O???H···O, and C???H···Cl hydrogen bonds. The powder X-ray diffraction and X-ray photoelectron spectroscopic (XPS) analyses confirm the phase purity of the crystal sample. The intermolecular contacts are quantified using the Hirshfeld surfaces computational method. The major inter-contacts contributing to the Hirshfeld surfaces are H…Cl, H…H, and O…H. The vibrational modes were identified and assigned by IR and Raman spectroscopies. The optical properties were investigated by UV–visible and photoluminescence spectroscopic studies. The compound was characterized by thermal analysis to determine its thermal behavior with respect to the temperature. Finally, X-ray photoelectron spectroscopy analysis is reported for analyzing the surface chemistry of [C₅H₁₄N₂]₂PbCl₆·3H₂O.     

Synthesis,crystal structure,vibrational spectra,optical properties and theoretical investigation of a two-dimensional self-assembled organic-inorganic hybrid material

Organic–inorganic hybrid material of formula (C₄H₃SC₂H₄NH₃)₂[PbI₄] was synthesized and studied by X-ray diffraction, Infrared absorption, Raman scattering, UV–Visible absorption and photoluminescence measurements. The molecule crystallizes as an organic–inorganic two-dimensional (2D) structure built up from infinite PbI₆ octahedra surrounded by organic cations. Such a structure may be regarded as quantum wells system in which the inorganic layers act as semiconductor wells and the organic cations act as insulator barriers. Room temperature IR and Raman spectra were recorded in the 520–3500 and 10–3500 cm⁻¹ frequency range, respectively. Optical absorption measurements performed on thin films of (C₄H₃SC₂H₄NH₃)₂[PbI₄] revealed three distinct bands at 2.4, 2.66 and 3.25 eV. We also report DFT calculations of the electric dipole moments (μ), polarizability (α), the static first hyperpolarizability (β) and HOMO–LUMO analysis of the title compound investigated by GAUSSIAN 09 package. The calculated static first Hyperpolarizability is equal to 11.46 × 10⁻³¹ esu.     

Crystal structure,vibrational studies,optical properties,and Hirshfeld surface analysis of (C5H6N5)2[Cr2O7]

Single crystals of a new organic–inorganic compound, (C₅H₆N₅)₂Cr₂O₇ (1), adeninium dichromate, were grown by the slow evaporation technique and characterized by X-ray diffraction, infrared absorption, and the optical properties were also investigated by UV-vis absorption spectroscopy. The compound crystallizes in the triclinic system and P-1 space group with a = 11.6850(2) Å, b = 11.7531(5) Å, c = 14.5603(7) Å, α = 83.956(3)°, β = 70.481(4)°, γ = 61.863(2)°, V = 1658.70(12) Å³. The structure of the compound consists of four adeninium, (C₅H₅N₂)⁺, cations, and two dichromate dianions with all the atoms situated in general positions. Each dichromate anion is formed by two tetrahedral CrO₄ joined through shared O atoms and are linked to the cations with several weak hydrogen bonding interactions resulting in an extended network. 3-D Hirshfeld surface analysis and 2-D fingerprint plots indicate that the packing is dominated by H?O/O?H and H?N/N?H contacts.     

X-ray diffraction, DFT theoretical, and IR polarized spectroscopic studies of the crystal-like E-mesophase of 4′-hexyloxy-isothiocyanatotolane (6OTOLT)

The dynamics of 6OTOLT molecules was analyzed based on IR absorption spectra and DFT calculations. Of particular interest was the mode ascribed to the ν_as(NCS) vibrations, the transition dipole moment of which is directed along the long axes of the molecules. Polarized IR spectra in the region of this mode allowed a characterization of the ordering of molecules in the analyzed phases. In a case of the smectic E phase, a random distribution of molecules aligned laterally in two-dimensional space between KRS-5 windows was found. The crystals of 6OTOLT were successfully grown and are characterized by an interesting Pc space group. The molecules are parallely arranged in layers and cross the adjoining ones underneath at an angle of 86.04°. The distance between the ring planes is 3.48 Å. The packing of molecules indicates a tendency to maintain short contacts between NCS groups and alkyl chains. The crystals grown do not correspond to the ordering of the smectic E phase and thus to the solid state obtained after cooling the smectic phase. Calculations of the interaction energy for three possible arrangements of dimeric species show a predominance of the core-to-core units. It was also shown that in this case an increase in ν_as(NCS) frequency should be expected, in good agreement with experimental data.     

A Hirshfeld surface analysis,crystal structure,and physicochemical studies of a new Cu(II) complex with the 1,10-phenanthroline ligand

Abstract

The new coordination compound, [Cu(H₂PO₄)₂(C₁₂N₂H₈)H₂O]·2H₂O, was prepared and characterized by physico-chemical studies. In this monomeric complex, the central Cu(II) atom is in a square pyramidal environment and chelated by two nitrogen atoms of 1,10-phenanthroline, two dihydrogeno-monophosphate oxygen atoms and one water oxygen atom. Intermolecular interactions were investigated by Hirshfeld surfaces. The ³¹P NMR spectrum of this paramagnetic complex displays a relatively sharp peak at 2,070?ppm. The vibrational absorption bands were identified by infrared spectroscopy. Electronic properties such as HOMO and LUMO energies were derived.     

Synthesis,Experimental and Theoretical Study of Azidochromones

A series of 2-(haloalkyl)-3-azidomethyl and 6-azido chromones has been synthetized, characterized and studied by theoretical (DFT calculations) and spectroscopic methods (UV-Vis, NMR). The crystal structure of 3-azidomethyl-2-difluoromethyl chromone, determined by X-ray diffraction methods, shows a planar framework due to extended π-bond delocalization. Its molecular packing is stabilized by F···H, N···H and O···H hydrogen bonds, π···π stacking and C–O···π intermolecular interactions. Moreover, AIM, NCI and Hirshfeld analysis evidenced that azido moiety has a significant role in the stabilization of crystal packing through weak intermolecular interactions, where analysis of electronic density suggested closed-shell (CS) interatomic interactions.     

A new trans-dioxorhenium(V) complex with 4-aminopyridine: synthesis,structure, electrochemical aspects,DFT, and TD-DFT calculations

The reaction of 1?:?4.4?M proportion of cis-[ReO₂I(PPh₃)₂] and 4-aminopyridine (ampy) in acetone–water gives trans-[ReO₂(ampy)₄]I·2H₂O (1a) in 85% yield. 1a has been characterized by C, H, and N microanalyses, FT-IR, UV–vis, ¹H NMR spectroscopy, and molar conductivity. The X-ray crystal structure of 1a reveals an octahedral trans dioxorhenium(V) complex with a “N₄O₂” coordination for rhenium. 1a has an orthorhombic space group C2221 with a?=?17.576(4), b?=?19.370(4), c?=?15.730(4) Å, V?=?5355(2) ų, and Z?=?8. Geometry optimization of the trans-O,O complex, 1a and its cis-O,O analog, 1b performed at the level of density functional theory reveal that 1a is more stable than 1b by 25?kcal M^–1 in the gas phase. The electronic spectrum of 1a was also analyzed at the level of time-dependent density functional theory. Excitation of 1a in methanol at 450?nm leads to a fluorescent emission at 505?nm with a quantum yield (Ф) of 0.04. Electrochemical studies of 1a in acetonitrile show a quasi-reversible Re(V) to Re(VI) oxidation at 0.618?V versus Ag/AgCl. This redox potential matches with the calculated redox potential of 0.621?V versus Ag/AgCl.     

Synthesis,molecular structure,vibrational studies,optical properties and electrical conduction mechanism of the new hybrid compound based on selenate

The new hybrid material tetrapropylammonium hydrogen selenate bis (selenic acid), N(C₃H₇)₄[HSeO₄][H₂SeO₄]₂ (hereafter abbreviated TPSe) has been synthesized by slow evaporation technique at room temperature. Crystal structure, DTA-TGA measurements, Raman, Infrared spectroscopy, nuclear magnetic resonance (NMR) electrical properties, and optical properties were provided to characterize the TPSe. This crystal structure contains one organic cation [N(C₃H₇)₄]⁺, one [HSeO₄]⁻ tetrahedra, and two neutral selenic acids H₂SeO₄. The inorganic [HSeO₄]⁻ and H₂SeO₄ species consist of infinite two-dimensional inter-linkers via strong hydrogen bonds (O-H⋯O), giving birth to trimmers [(H₂SeO₄)₂ HSeO₄]_nⁿ⁻. The IR and Raman spectra of the compound recorded at room temperature were studied in regard to the literature data, and on the basis of theoretical group analysis. The theoretical calculations using the density functional theory DFT at the B3LYP/6-31G(d) level, are made to study the optimized molecular structure, the vibrational spectra, and the optical properties of TPSe compound. Good agreements were found between the theoretical results and the experimental Raman, IR spectra and the molecular structure. The polarizability α, the hyperpolarizability β, and the electric dipole μ calculated using DFT/B3LYP-31G(d) exhibit the non-zero hyperpolarizability β of the TPSe, indicating that this material could be used in certain NLO applications. The thermal DTA-TGA analyses did not show any phase transition in the 333–500 K temperature domain. The complex impedance spectroscopy is measured and discussed in the temperature (290–363 K) and frequency (1 kHz−13 MHz) domains to study the electrical propreties of the compound.     

Crystal structure and solid state computational (DFT/Hirshfeld surface) study for probing a new efficient and recyclable oxidation reagent, 1,2-ethandiylbis(triphenylphosphonium) peroxodisulfate dihydrate

A new, efficient and recyclable reagent, 1,2-Ethandiylbis(triphenylphosphonium) peroxodisulfate dihydrate, for the oxidation of benzylic alcohols has been synthesized and characterized by IR, NMR spectroscopy, and single crystal X-ray crystallography. Using the title compound, the results indicate that the oxidation reactions are rapid, take place under mild reaction conditions, easily to work-up and high yielding. The Hirshfeld surface and associated finger print plots were derived from the X-ray structure to visualize the significant nonclassical C-H ??? O/π interactions in the crystal packing. The geometry, vibrational spectroscopy and electronic properties of the bis(triphenylphosphonium) dication have also been investigated by various DFT computational methods.     

A structural study of new tetrakis(1H-pyrazol-1-yl)methanes

Tetrakis(1H-pyrazol-1-yl)methanes are very rare compounds of which only two are known: the unsubstituted 1 obtained classically by Hückel in 1937 from carbon tetrachloride and prepared again several times and the 3,5-dimethyl substituted 2 obtained serendipitously by Pombeiro in 2009. We have now extended this group to include four new derivatives 8, 9, 11 and 12 bearing methyl groups. The X-ray crystal structure of the four compounds has been determined. They have been studied by NMR both in solution (¹H, ¹³C, ¹⁵N) and in the solid state (¹³C and ¹⁵N). DFT calculations of the six compounds (geometries, energies and absolute shieldings) have been used to discuss the experimental observations.     

Coordination chemistry of di-2-pyridylketone. Synthesis, spectroscopic investigations, X-ray studies and DFT calculations of Re(III) and Re(V) complexes

The paper presents a combined experimental and computational study of Re(III) and Re(V) complexes containing di-2-pyridylketone and its gem-diol form – [ReCl₃(dpk-N,O)(PPh₃)] (1), [ReCl₃(dpk-N,N′)(OPPh₃)] (2) and [ReOBr₃(dpk-OH)]·2(dpkH⁺Br⁻) (3). All the complexes have been characterized spectroscopically and structurally (by single-crystal X-ray diffraction). The complex 2 has been additionally studied by magnetic measurement. The magnetic behavior of 2 is characteristic of mononuclear octahedral Re(III) complex with d⁴ low-spin (³T_1g ground state) and arise because of the large spin–orbit coupling (ζ = 2500 cm⁻¹), which gives diamagnetic ground state. DFT and time-dependent (TD)DFT calculations have been carried out for [ReCl₃(dpk-N,N′)(OPPh₃)] and [ReOBr₃(dpk-OH), and their UV–vis spectra have been discussed on this basis.     

Synthesis,spectroscopic studies,and single-crystal structures of two 3-D supramolecular zinc(II) and nickel(II) complexes containing thiazole ring: Antimicrobial assays,time-dependent density functional theory calculations,and Hirshfeld surface analysis

Two novel complexes [Zn( L )₂·(NO₃)₂] ( 1 ) and [Ni( L )₂·2H₂O]·2CH₃OH·(NO₃)₂ ( 2 ) ( L = 2-(2-thiazolyl)-4-methyl-1,2-dihydroquinazoline-N³-oxide) were synthesized successfully and characterized by elemental analysis, as well as various spectroscopic techniques. Specifically, the photoluminescence behavior of complex 1 was explored in different solvents. The structural characterization of both complexes has been determined single-crystal X-ray diffraction. It revealed that the metals in 1 and 2 are chelated by two L ligands in centro-symmetrically fashion and the complexes are counterbalanced by nitrate ions which act as coordinating species in 1 , while two water molecules complete the Ni coordination sphere in 2 . In the crystal structures, the adjacent molecules of complex 1 disclosed a ladder-like 2-D network and 3-D supramolecular self-assembly. Simultaneously, an infinite 1-D chain, 2-D layered skeleton, and even meter-shaped 3-D network of 2 was governed by molecular interactions (H–bonds, C–H⋯π). Most strikingly, the research of antibacterial activity proved that two complexes had good activity against two standard bacteria strains. To ascertain deeply the optimum geometric configurations and detect the frontier molecular orbital energy gaps, density functional theory (DFT) calculations were also investigated. Additionally, analyses of Hirshfeld surfaces (HS) and electrostatic potential (ESP) were also performed to quantify the presence of diverse noncovalent interactions.     

A hirshfeld surface analysis,crystal structure and physicochemical characterization of 1-ethylpiperazinium trichlorocadmate(II)

A novel organic–inorganic hybrid material, C₆H₁₅N₂CdCl₃.H₂O, was synthesized, and its structure was determined at room temperature in the monoclinic space group P2₁/n with the following parameters: a = 10.3829 (17), b = 7.7459 (12), c = 14.905 (2) Å, β = 98.801 (15), and Z = 4. Its crystal structure is characterized by one-dimensional polymeric chains of edge-sharing CdCl₅N distorted octahedra. These chains are linked to the water molecules via OH … Cl hydrogen bonds to form layers parallel to the (b, a + c) plane. The crystal structure was stabilized by an extensive network of NH … Cl, OH … Cl and NH … O hydrogen bonds. The differential scanning calorimetry (DSC) reveals that the title compound is stable until 101.6 °C.The optimized geometry parameters, normal mode frequencies, and corresponding vibrational assignments of the present compound were theoretically examined by DFT/B3LYP method with the Lanl2dz basis set. The FT-IR spectrum of the polycrystalline sample was examined and compared to the calculated spectrum. The calculated results showed that the optimized geometry could well reproduce the crystal structure and that the theoretical vibrational frequency values were in good agreement with their experimental counterparts.     

Crystal structures,theoretical calculations,spectroscopic and electrochemical properties of Cr(III) complexes with dipicolinic acid and 1,10-phenantroline

The crystal structures of compounds Na[Cr(dipic)₂] · 2H₂O (1) and [Cr(dipic)(phen)Cl] · 1/2H₂O (2), dipic = dipicolinate, phen = 1,10-phenantroline, were determined. In both complexes, Cr(III) is in a distorted octahedral environment. In complex (1), the metal is coordinated to two nearly perpendicular dipic anions acting as tridentate ligands through one oxygen of each carboxylate group and the pyridinic nitrogen atom. In complex (2), Cr(III) ion is similarly coordinated to a dipic anion, defining a ligand equatorial plane. The phen molecule bridges the remaining equatorial coordination site and one of the axial positions through its N-atoms. The other axial position is occupied by a chloride ion.     

Synthesis, spectroscopic characterization, X-ray structure and DFT calculations of rhenium(III) complex with bis(3,5-dimethylpyrazol-1-yl)methane

[ReCl₃(MeCN)(PPh₃)₂] reacts with bis(3,5-dimethypyrazol-1-yl)methane (bdmpzm) in acetone to give [ReCl₃(bdmpzm)(PPh₃)]. The compound has been studied by IR, UV–Vis spectroscopy and X-ray crystallography. The molecular orbital diagram of [ReCl₃(bdmpzm)(PPh₃)] has been calculated with the density functional theory (DFT) method.     

Two dinuclear copper (II) and nickel (II) complexes based on 4‐(diethylamino)salicylaldehyde: X‐ray structures,spectroscopic, electrochemical,antibacterial, Hirshfeld surfaces analyses,and time‐dependent density functional theory calculations

The quinazoline‐type ligand 2‐(4‐diethylamino‐2‐hydroxyphenyl)‐4‐methyl‐1,2‐dihydroquinazoline 3‐oxide ( HL ¹ ; H is the deprotonatable hydrogen) was prepared. Two 2‐D supramolecular complexes [Cu₂( L ² )₂(NO₃)₂] ( 1 ) and [Ni₂( L ² )₂(CH₃COO)₂] ( 2 ) ( L ² = 1‐(2‐{[(E)‐(4‐diethylamino‐2‐hydroxybenzylidene]amino} phenyl)ethanone oxime) were synthesized using HL ¹ and characterized by elemental analysis, spectroscopic methods, and single‐crystal X‐ray diffraction studies. It revealed that 1 had coordinated two nitrate ions whereas 2 had acetate ions. In the crystal structures, six‐coordinated Cu (II) complex 1 formed an infinite 2‐D and X‐shaped 3‐D supramolecular frameworks. Simultaneously, Ni (II) complex 2 assembled into wavy 2‐D networks. Furthermore, electrochemical properties and antimicrobial activities of all compounds were as well investigated. Afterwards, the electrophilic and nucleophilic attack sites identified by electrostatic potential (ESP) calculations confirmed that hydrogen bonds were observed in the optimized structure of the crystal, and the closest contact between the active atoms of both complexes was confirmed through Hirshfeld surface analysis and time‐dependent density functional theory (TD‐DFT) calculations.     

Synthesis,structural and theoretical investigations on 3-diethyl 2-({4-[3-ethoxy-2-(ethoxycarbonyl)-3-oxo-2-phenylpropyl]-2,5-dimethylphenyl}methyl)-2-phenylpropanedioate

Because bioactive ester derivatives are important pharmacophores, the current study focuses on the synthesis and evaluation of their pharmacological activity. In this case, novel 1,3-diethyl 2-(4-[3-ethoxy-2-(ethoxycarbonyl)-3-oxo-2-phenylpropyl]-2,5-dimethylphenylmethyl)-2-phenylpropanedioate (C₃₆H₄₂O₈) was synthesized in good yield. Elemental analysis, mass spectroscopy, FT-IR and NMR spectroscopy are used to analyse the compound. The X-ray diffraction examination of a single crystal indicates that the molecular structure crystallises in the monoclinic space group P21/n, with half of the molecule being crystallographically unique (Z' = 0.5) with Z = 2. Surprisingly, the inversion centre is located at the centre of the methyl-substituted benzene ring, which generates the entire molecule via symmetry operation. Crystallographic and computational chemistry technologies are used to examine the nature and strength of intermolecular interactions amongst inversion-related dimers (Hirshfeld surface, energy framework, QTAIM and NCI analysis). Koopman's approximation was used to calculate the frontier molecular orbitals, HOMO-LUMO energy gap, and associated reactive parameters. Furthermore, molecular docking experiments demonstrated the compound with Antieczematic proteins as well as protein-ligand interactions, hydrogen bond interactions are delibrated.     

Experimental and theoretical study of the conformational analysis of hydrochlorothiazide

Hydrochlorothiazide was characterized in order to determine the possible structural modifications at different temperatures due to its importance as a drug to control heart diseases and a diuretic. This compound could present conformers due to the rotation of the NH₂ group, which was studied by using different techniques such as Thermal Analysis, IR spectroscopy, X-Ray Diffraction and complemented by theoretical calculations. The theoretical and experimental results point to the conclusion that no polymorphic forms are present in the compound under study. The calculations confirm the apparent difference in values between theory and experiment for the vibration frequencies explained by the hydrogen bonds between near molecules.