Ab initio Hartree–Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 7-acetoxy-6-(2,3-dibromopropyl)-4,8-dimethylcoumarin molecule

Unusual Ni⋯Ni interaction in Ni(ii) complexes as potential inhibitors for the development of new anti-SARS-CoV-2 Omicron drugs

Two nickel(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) of a tetradentate Schiff base ligand (H2L) derived from 2-hydroxy-1-naphthaldehyde with ethylenediamine were synthesized, designed, and characterized via spectroscopic and single crystal XRD analyses. Both nickel(ii) complexes exhibited unusual Ni⋯Ni interactions and were fully characterized via single-crystal X-ray crystallography. Nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) crystallize in monoclinic and triclinic crystal systems with P21/c and P1̄ space groups, respectively, and revealed square planar geometry around each Ni(ii) ion. The structure of both the complexes have established the existence of a new kind of metal system containing nickel(ii)-nickel(ii) interactions with a square planar-like geometry about the nickel(ii) atoms. Both square planar Ni(ii) complexes were often stacked with relatively short Ni⋯Ni distances. The non-bonded Ni-Ni distance (Ni⋯Ni separation) seems to be 3.356 Å and 3.214 Å from the nickel atoms of [Ni(L)]2(1) and [Ni(L)]n(2), respectively. These distances are shorter than the sum of their van der Waals radii (4.80 Å) but longer than the sum of their covalent radii (2.50 Å), indicating that there is a Ni⋯Ni interaction but not a Ni-Ni bond. The discrete molecules are π-stacked and connected via weak intermolecular interactions (C-H⋯O and C-H⋯N). Cyclic voltammetry measurements were obtained for both the complexes, and their pharmacokinetic and chemoinformatics properties were also explored. Detailed structural analysis and non-covalent supramolecular interactions were investigated using single-crystal structure analysis and computational approaches. Both the unique structures show good inhibition performance for the Omicron spike proteins of the SARS CoV-2 virus. To gain insights into potential SARS-CoV-2 Omicron drugs and find inhibitors against the Omicron variants of SARS-CoV-2, we examined the molecular docking of the nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron spike protein (PDB ID: 7WK2 and 7WVO). A strong binding was predicted between Ni(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron variant receptor protein through the negative value of binding affinity. Molecular docking of Nil(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with a DNA duplex (PDB ID: 7D3T) and RNA (PDB ID: 7TDC) binding protein was also studied. Overall, this study suggests that Ni(ii) complexes can be considered as drug candidates against the Omicron variants of SARS-CoV-2.

Exploration of nonlinear optical properties of 4-methyl-4H-1,2,4-triazol-3-yl)thio)-N-phenylpropanamide based derivatives: experimental and DFT approach

Triazoles, nitrogen-containing heterocycles, have gained attention for their applications in medicinal chemistry, drug discovery, agrochemicals, and material sciences. In the current study, we synthesized novel derivatives of N-substituted 2-((5-(3-bromophenyl)-4-methyl-4H-1,2,4-triazol-3-yl)thio)-N-phenylpropanamide and conducted a comprehensive investigation using density functional theory (DFT). These novel structural hybrids of 1,2,4-triazole were synthesized through the multi-step chemical modifications of 3-bromobenzoic acid (1). Initially, compound 1 was converted into its methyl-3-bromobenzoate (2) which was then transformed into 3-bromobenzohydrazide (3). The final step involved the cyclization of compound 3, producing its 1,2,4-triazole derivative (4). This intermediate was then coupled with different electrophiles, resulting in the formation of the final derivatives (7a-7c). Additionally, the characterization of these triazole-based compounds (7a, 7b, and 7c) were carried out using techniques such as IR, HNMR, and UV-visible spectroscopy to understand their structural and spectroscopic properties. The DFT study utilized M06/6-311G(d,p) functional to investigate geometrical parameters, HOMO-LUMO energies, natural bond orbital analyses, transition density matrix (TDM), density of states, and nonlinear optical (NLO) properties. The FMO analysis revealed that compound 7c exhibited the lowest band gap value (4.618 eV). Notably, compound 7c exhibited significant linear polarizability (4.195 >  × 10-23) and first and second hyperpolarizabilities (6.317 >  × 10-30, 4.314 × 10-35), signifying its potential for nonlinear optical applications. These NLO characteristics imply that each of our compounds, especially 7c, plays a crucial part in fabricating materials showing promising NLO properties for optoelectronic applications.

Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine

Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.

Synthesis, Cytotoxic Activity and In Silico Study of Novel Dihydropyridine Carboxylic Acids Derivatives

To aid the possible prevention of multidrug resistance in tumors and cause lower toxicity, a set of sixteen novel dihydropyridine carboxylic acids derivatives 3a-p were produced; thus, the activation of various ynones with triflic anhydride was performed, involving a nucleophilic addition of several bis(trimethylsilyl) ketene acetals, achieving good yields requiring easy workup. The target molecules were unequivocally characterized by common spectroscopic methods. In addition, two of the tested compounds (3a, and 3b) were selected to perform in silico studies due to the highest cytotoxic activity towards the HCT-15 cell line (7.94 ± 1.6 μM and 9.24 ± 0.9 μM, respectively). Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) showed that the molecular parameters correlate adequately with the experimental results. In contrast, predictions employing Osiris Property Explorer showed that compounds 3a and 3b present physicochemical characteristics that would likely make it an orally active drug. Moreover, the performance of Docking studies with proteins related to the apoptosis pathway allowed a proposal of which compounds could interact with PARP-1 protein. Pondering the obtained results (synthesis, in silico, and cytotoxic activity) of the target compounds, they can be judged as suitable antineoplastic agent candidates.

Synthesis, Empirical and Theoretical Investigations on New Histaminium Bis(Trioxonitrate) Compound

In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C₅H₁₁N₃)(NO₃)₂, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this compound after it was made using a slow evaporation method at room temperature. This compound was elaborated and crystallized to the monoclinic system with space group P2₁/c, and the lattice parameters obtained were: a = 10.4807 (16)Å, b = 11.8747 (15)Å, c = 16.194 (2)Å, β = 95.095 (6)°, V = 2007.4 (5)ų and Z = 8. The title compound's atomic structure couldbe modeled as a three-dimensional network. Organic cations and nitrate anions were connected via N-H...O and C-H...O hydrogen bonds in the HTN structure. The intermolecular interactions responsible for the formation of crystal packing were evaluated using Hirshfeld surfaces and two-dimensional fingerprint plots. The compound's infrared spectrum, which ranged from 4000 to 400 cm^-1, confirmed the presence of the principal bands attributed to the internal modes of the organic cation and nitrate anions. Additionally, spectrofluorimetry and the ultraviolet-visible spectrum was used to investigate this compound. DFT calculations were used to evaluate the composition and properties of HTN. The energy gap, chemical reactivity and crystal stability of HTN were quantified by performing HOMO-LUMO frontier orbitals analysis. Topological analysis (AIM), Reduced Density Gradient (RDG), molecular electrostatic potential surface (MEPS) and Mulliken population were processed to determine the types of non-covalent interactions, atomic charges and molecular polarity in detail.

Research on the Electron Structure and Antimicrobial Properties of Mandelic Acid and Its Alkali Metal Salts

This article investigated the structure, and the spectroscopic and antimicrobial properties of mandelic acid and its alkali metal salts. The electron charge distribution and aromaticity in the analyzed molecules were investigated using molecular spectroscopy methods (FT-IR, FT-Raman, ¹H NMR, and ¹³C NMR) and theoretical calculations (structure, NBO, HOMO, LUMO, energy descriptors, and theoretical IR and NMR spectra). The B3LYP/6-311++G(d,p) method was used in the calculations. The antimicrobial activities of mandelic acid and its salt were tested against six bacteria: Gram-positive Listeria monocytogenes ATCC 13932, Staphylococcus aureus ATCC 25923, Bacillus subtilis ATCC 6633, and Loigolactobacillus backii KKP 3566; Gram-negative Escherichia coli ATCC 25922 and Salmonella Typhimurium ATCC 14028, as well as two yeast species, Rhodotorulla mucilaginosa KKP 3560 and Candida albicans ATCC 10231.

Synthesis, crystallization, XRD, Hirshfeld surface, vibrational spectra, and quantum chemical studies and Computational investigation of Caffeinium bisulfate: a new noncentrosymmetric form

Crystals of caffienium bisulfate were grown by solution growth technique. The vibrational spectra were scaled by adopting FT-IR and FT-Raman spectroscopy with the wide range, between 4000-400 cm^-1. X-ray diffraction study exhibited that the functional group such as N-H….O hydrogen bonds played an effective role in generating hydrogen-bonded crystal packing, pre-dominant. The examined molecules showed an interconnection of anions, by the O-H…O hydrogen bonds, establishing a chain C (4) motif, extending along the b-axis of the unit cell. Further, anions have shown interaction with cations, through N-H…O hydrogen bond, resulting from a ring R₁² (4) motif. The formed ring and chain motifs manifested an alternate hydrophilic stratum at z = ¼ and ¾. Geometrical optimization of tester molecule was done with Density Functional Theory (DFT) employing B3LYP function along with Hartree-Fock (HF) using 6-311++G(d,p) level basis set. Optimum molecular geometry and calculated database on the vibrational spectra were critically analyzed by comparing with experimental findings, resulting in a good correlating exhibited among them. Natural Bond Orbital (NBO) study revealed that hyper conjugation affinities and intermolecular charge transfer (ICT). An advanced technique such as HOMO-LUMO plot was performed to understand the chemical hardness, electro negativity and chemical efficacy of the tested molecules. The results showed that the occurrence of lower band gap value in the frontier orbital was responsible for the possible biological activities of the study materials. Bioinformatics analysis is applied for analyzing the biological activity of CAFSUL against Alzheimer's disease through computational methods.Communicated by Ramaswamy H. Sarma.

Preparation, DFT calculations, docking studies, antioxidant, and anticancer properties of new pyrazole and pyridine derivatives

Seven novel pyrazole derivatives (4a-g) and four novel starting compounds incorporating substituted pyridine moieties were synthesized successfully. Cell viability assay for the tested compounds was performed, and the inhibitory concentrationlogarithmic 50 (LogIC₅₀ ) values of the compounds were calculated after a 24-h treatment. Four of the examined compounds (3d, 3g, 4f, and 4g) showed comparable cytotoxic activity against CaCo-2 compared to the standard drug docetaxel at 0.1 and 1 μM concentrations. Although the LogIC₅₀  of docetaxel was -0.678 μM for CaCo-2 cells at 24 h, the LogIC₅₀ values of compounds were -0.794, -0.567, -0.657, and -0.498 μM, respectively. Five of the compounds (2d, 2g, 3d, 3g, and 4e) showed comparable cytotoxic activity against MCF-7 at 0.1 μM concentration compared to docetaxel (p < 0.05). Docking studies revealed the compounds have a good affinity to the active site of the human topoisomerase II β enzyme. The antioxidant capacities of all compounds were determined using both 1,1-diphenyl-2-picrylhydrazyl and metal chelation methods. Although the compounds did not show significant antioxidant activity, relatively effective are compounds 3c, 3d, and 3g, which are hydrazine derivatives with approximately 50% antioxidant activity of standard antioxidants at concentrations of 62.5 and 125 μg/ml.

A Theoretical Study on the Medicinal Properties and Eletronic Structures of Platinum(IV) Anticancer Agents With Cl Substituents

In this paper, we selected Pt(en)Cl4, Pt(dach)Cl4, and Pt(bipy)Cl4 with gradually increasing ligands to explore the ligand effect on the properties of platinum(IV) anticancer drugs. The electronic structures and multiple drug properties of these three complexes were studied at the LSDA/SDD level using the density functional theory (DFT) method. By comparing the gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), electron affinity, atomic charge population, and natural bond orbital (NBO), we found that the order of reducibility is Pt(bipy)Cl4 > Pt(en)Cl4 > Pt(dach)Cl4. Our research can provide the theoretical basis for the development of anticancer drugs.

Density functional study of trans,trans,trans-[Pt(N3)2(OH)2(Py)2] on molecular structure and vibrational spectroscopy

This study records the selection of the best combination of geometric optimization and frequency calculation methods of the trans,trans,trans-[Pt(N₃)₂(OH)₂(py)₂](FM-190) by using different density functional calculation methods and basis sets. The results show that the CAM-B3LYP/SDD method has the best fit to the experimental data for geometric optimization, while the LSDA/SDD method has better performance in frequency calculation, and the infrared vibration peak is assigned. In addition, the calculated HOMO and LUMO show the energy gap and the internal charge transfer of this complex. The hyperconjugation of the pyridine ring have been explained by NBO analysis.

Induced Nematic Phase of New Synthesized Laterally Fluorinated Azo/Ester Derivatives

A new series of laterally fluorinated mesomorphic compounds, namely 2-fluoro-4-((4-(alkyloxy)phenyl)diazenyl)phenyl 4-substitutedbenzoate (Inx) were prepared and evaluated for their mesophase behavior. The synthesized series constitutes five members that possess different terminally attached polar groups (X). Their molecular structures were confirmed by elemental analyses and both FT-IR and NMR spectroscopy. Examination of the prepared derivatives was conducted via experimental and theoretical tools. Mesomorphic investigations were carried by polarized optical microscopy (POM) and differential scanning calorimetry (DSC). DSC and POM measurements indicated that except for the un-substituted analogue, all other derivatives were purely nematogenic, possessing their nematic (N) mesophase enantiotropically. This is to say that insertions of terminal polar substituents on their mesogenic structures induced the N phase. In addition, the location of lateral and terminal polar moieties played a considerable role in achieving good thermal N stability. Computational calculations were investigated to determine the deduced optimized molecular structures. Theoretical data indicated that both size and polarity of the terminal substituent (X) have essential impact on the thermal parameters and optical properties of possible geometries.

Synthesis, Optical and DFT Characterizations of Laterally Fluorinated Phenyl Cinnamate Liquid Crystal Non-Symmetric System

A new laterally fluorinated unsymmetric liquid crystalline homologous series, based on cinnamate linkage, named 2-fluoro-4-(4-(alkoxy)phenyl)diazenyl)phenyl cinnamate (In), was synthesized and evaluated via different experimental and computational tools. The series had different terminal alkoxy-chain lengths with a lateral F atom in the meta position with respect to the azo moiety. The experimental mesomorphic and optical investigations were carried out using differential scanning calorimetry (DSC) and polarized optical microscopy (POM). Theoretical calculations and geometrical parameter predictions were conducted using the DFT program method at B3LYP/6-311G** level of theory. The results revealed that all the designed compounds exhibited the nematic (N) mesophase enantiotropically. The nematic stability and temperature range were impacted by the terminal alkoxy chain length. Compounds with the shortest chains (I6 and I8) showed a monotropic smectic A (SmA) phase, while the longest chain derivative, I16, possessed enantiotropic Sm A phase. Theoretical density functional theory (DFT) predictions were correlated with the practically observed data from the mesomorphic investigations. Data revealed that the terminal alkoxy and lateral F groups had an essential impact on the total energy of possible geometrical structures and their physical and thermal parameters.

Growth, spectral, optical, electrical and computational analysis of sodium oxalate single crystals

Single crystals of Sodium Oxalate (SO) were grown by adopting the slow evaporation solution growth approach from aqueous solution. The prominent functional groups seen in the SO crystal were distinctly detected with Fourier transform infrared and FT-Raman spectral analysis. The cut-off wavelength of 230 nm was measured using Ultraviolet -visible spectral analysis. Theoretical quantum chemical computations were done by DFT using Gaussian software package. The different properties such as structural, vibrational and electronic properties of SO was studied at the B3LYP/LanL2DZ level. The chemical activity of SO molecule was revealed by HOMO-LUMO energies. From Topology analysis the chemical significance of the molecules has been enunciated. The electron density centered on local reactivity descriptors like Mulliken atomic charges and Fukui function were calculated to describe the chemical reactivity of the SO compound. The mechanical property of the grown crystal was disclosed from Vicker's micro hardness test carried out on the grown SO crystals and the test confirms the soft nature of the crystal. The dielectric behavior of SO crystal was completely investigated for different temperatures and the activation energies were calculated for different frequencies.

Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2

Currently, Covid-19 pandemic infects staggering number of people around the globe and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(pyridin-3-ylmethyl) amino]-2H-chromen-2-one) (LTA) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between LTA and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that LTA crystallizes in a monoclinic system with P2 1  space group. The reactivity descriptors such as nucleophilic index confirm that LTA is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-LTA complex and the calculated inhibition constant using docking simulation showed that the active LTA molecule has the ability to inhibit SARS-CoV-2.

Single crystal, Hirshfeld surface and theoretical analysis of methyl 4-hydroxybenzoate, a common cosmetic, drug and food preservative-Experiment versus theory

Methyl 4-hydroxybenzoate, commonly known as methyl paraben, is an anti-microbial agent used in cosmetics and personal-care products, and as a food preservative. In this study, the single crystal X-ray structure of methyl 4-hydroxybenzoate was determined at 120 K. The crystal structure comprises three methyl 4-hydroxybenzoate molecules condensed to a 3D framework via extensive intermolecular hydrogen bonding. Hirshfeld surface analysis was performed to determine the intermolecular interactions and the crystal packing. In addition, computational calculations of methyl 4-hydroxybenzoate were obtained using the Gaussian 09W program, and by quantum mechanical methods, Hartree Fock (HF) and Density Functional Theory (DFT) with the 6–311G(d,p) basis set. The experimental FT-IR spectrum strongly correlated with the computed vibrational spectra (R² = 0.995). The energies of the frontier orbitals, HOMO and LUMO, were used to calculate the chemical quantum parameters. The lower band gap value (ΔE) indicates the molecular determinants underlying the known pharmaceutical activity of the molecule.

N-{2-[(2-chlorothieno[3,2-d]pyrimidin-4-yl)amino]ethyl}-3-methoxybenzamide: design, synthesis, crystal structure, antiproliferative activity, DFT, Hirshfeld surface analysis and molecular docking study

The compound N-{2-[(2-chlorothieno[3,2-d]pyrimidin-4-yl)amino]ethyl}-3-methoxybenzamide (8) was synthesized by the condensation of 3-methoxybenzoic acid (7) with N¹-(2-chlorothieno[3,2-d]pyrimidin-4-yl)ethane-1,2-diamine (6). This intermediate was prepared from methyl 3-aminothiophene-2-carboxylate (1) by the condensation with urea, chlorination with phosphorus oxychloride and then condensation with ethane-1,2-diamine. The crystal structure of the title compound was determined and the crystal of the title compound belongs to the tetragonal system, space group P4(3) with a = 9.4694(10) Å, b = 9.4694(10) Å, c = 18.886(3) Å, α = 90°, β = 90°, γ = 90°. The optimized geometric bond lengths and bond angles obtained by using density functional theory (DFT) have been compared with X-ray diffraction values. The calculated HOMO and LUMO energies showed the character of the title compound. The molecular electrostatic potential (MEP) surface map of the related molecule was investigated with theoretical calculations at the B3LYP/6-311 + G(d,p) levels. A quantitative analysis of the intermolecular interactions in the crystal structures has been performed using Hirshfeld surface analysis. In addition, the title compound possesses marked inhibition against the proliferation of human colon cancer cell line HT-29 (IC₅₀ = 1.76 μM), human lung adenocarcinoma cell line A549 (IC₅₀ = 1.98 μM) and human gastric cancer cell line MKN45 (IC₅₀ = 2.32 μM), displaying promising anticancer activitiy. The molecular docking studies revealed that the title compound may exhibit activity inhibiting PDB:3D15.Communicated by Ramaswamy H. Sarma.