Topological analysis (BCP) of vibrational spectroscopic studies, docking, RDG, DSSC, Fukui functions and chemical reactivity of 2-methylphenylacetic acid

Prediction of vibrational spectrum and thermodynamic properties for phosphorus mononitride

In this work, an accurate potential energy curve (PEC) for the ground electronic state of phosphorus mononitride (PN) molecule has been determined from a variationally improved Hulburt-Hirschfelder (VIHH) oscillator model in conjunction with the experimental spectral constants (De,ωe,ωexe,Be,αe,re). We have numerically solved the Schrödinger equation for the VIHH potential using the LEVEL program, obtaining the pure vibrational spectrum that converges to the dissociation limit. In addition, the partition functions of PN molecule are calculated using the full rovibrational energies. Ultimately, thermodynamic properties like molar heat capacity, entropy, enthalpy, and Gibbs free energy were calculated for the PN molecule and show good agreement with those data from the NIST (National Institute of Standards and Technology) database.

Regioselective Direct C-H Bond Heteroarylation of Thiazoles Enabled by an Iminopyridine-Based α-Diimine Nickel(II) Complex Evaluated by DFT Studies

Direct C-H bond arylation is a highly effective method for synthesizing arylated heteroaromatics. This method reduces the number of synthetic steps and minimizes the formation of impurities. We report an air- and moisture-stable iminopyridine-based α-diimine nickel(II) complex for direct C5-H bond arylation of thiazole derivatives. Under a low catalyst loading and performing the reactions at lower temperatures (80 °C) under aerobic conditions, we produced mono- and diarylated thiazole units. Competition experiments and density functional theory calculations revealed that the mechanism of C-H activation in 4-methylthiazole involves an electrophilic aromatic substitution.

Synthesis, molecular structure and urease inhibitory activity of novel bis-Schiff bases of benzyl phenyl ketone: A combined theoretical and experimental approach

Background

Urease belongs to the family of amid hydrolases with two nickel atoms in their core structure. On the basis of literature survey, this research work is mainly focused on the study of bis-Schiff base derivatives of benzyl phenyl ketone nucleus.

Objective

Synthesis of benzyl phenyl ketone based bis-Schiff bases in search of potent urease inhibitors.

Method

In the current work, bis-Schiff bases were synthesized through two steps reaction by reacting benzyl phenyl ketone with excess of hydrazine hydrate in ethanol solvent in the first step to get the desired hydrazone. In last, different substituted aromatic aldehydes were refluxed in catalytic amount of acetic acid with the desired hydrazone to obtain bis-Schiff base derivatives in tremendous yields. Using various spectroscopic techniques including FTIR, HR-ESI-MS, and ¹H NMR spectroscopy were used to clarify the structures of the created bis-Schiff base derivatives.

Results

The prepared compounds were finally screened for their in-vitro urease inhibition activity. All the synthesized derivatives (3-9) showed excellent to less inhibitory activity when compared with standard thiourea (IC₅₀ = 21.15 ± 0.32 µM). Compounds 3 (IC₅₀ = 22.21 ± 0.42 µM), 4 (IC₅₀ = 26.11 ± 0.22 µM) and 6 (IC₅₀ = 28.11 ± 0.22 µM) were found the most active urease inhibitors near to standard thiourea among the synthesized series. Similarly, compound 5 having IC₅₀ value of 34.32 ± 0.65 µM showed significant inhibitory activity against urease enzyme. Furthermore, three compounds 7, 8, and 9 exhibited less activity with IC₅₀ values of 45.91 ± 0.14, 47.91 ± 0.14, and 48.33 ± 0.72 µM respectively. DFT used to calculate frontier molecular orbitals including; HOMO and LUMO to indicate the charge transfer from molecule to biological transfer, and MEP map to indicate the chemically reactive zone suitable for drug action. The electron localization function (ELF), non-bonding orbitals, AIM charges are also calculated. The docking study contributed to the analysis of urease protein binding.

Synthesis, crystal structure, Hirshfeld surface analysis, energy frameworks and computational studies of Schiff base derivative

The compound (E)-ethyl 3-(2-(2,4-dinitrophenyl)hydrazono)butanoate (3) was synthesised and crystallized using ethanol as a solvent. The compound was characterized by ¹H NMR, and single crystal X-ray diffraction. The compound crystallizes in the monoclinic crystal system with the space group P2₁/c. The intermolecular interactions and the interaction energies responsible for the stabilization of the molecules were determined by Hirshfeld surface analysis and energy framework calculations. The structure of the compound was optimized by Density Functional Theory calculations and HOMO–LUMO energy gap was calculated. The non–covalent interactions were revealed by reduced density gradient analysis. The Mulliken atomic charges and natural atomic charges were calculated by density functional theory calculations. The reactive sites present in the molecule are shown by molecular electrostatic potential map. The inter and intra molecular charge transfer were investigated by NBO analysis.

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Crystal structure was confirmed by X-ray diffraction analysis and the atomic coordinates were optimized by DFT calculations.

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Hirshfeld surface analysis and energy frameworks calculations were carried out.

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HOMO - LUMO frontier molecular orbitals and molecular electrostatic potential were studied.

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Reduced density gradient (RDG), and topology analyses were performed.

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Natural bond orbital analysis was performed to study intramolecular charge transfer.

New benzyltriethylammonium/urea deep eutectic solvent: Quantum calculation and application to hyrdoxylethylcellulose modification

In this paper, a new deep eutectic solvent (DES) has been successfully synthesized that is based on benzyltriethylammonium bromide as a hydrogen bond acceptor (HBA) and urea as a hydrogen bond donor (HBD). However, its usability in modifying cellulose derivatives, especially acylating hydroxyethylcellulose (HEC) was investigated. The chemical modification (acetylation) of HEC was carried out in BTEAB/urea DES system without any additional conventional solvent or catalyst. However, the proposed structure of acetylated HEC (HECA) was confirmed according to the structural spectra analyses FTIR-ATR, ¹H, ¹³C, and APT-NMR. The crystalline behavior of acetylated and unmodified HEC in the DES system has been evaluated using XRD patterns, where the thermal stability was evaluated basing on the TD-TGA thermograms. Hence, SEM images and EDX spectra were recorded to prove the changes that are expected at the morphological level and elemental profile. Yet, the nanometric sheets aspect was observed. The Functional Density Theory (DFT) was investigated as a useful computational tool to understand mechanism and donor-acceptor interactions. The topological parameters (electron density Laplacian, kinetic energy density, potential energy density, and energy density) at the bond critical points (BCP), between TBEAB and urea, are deducted according to Quantum Bader's theory, and Atoms-in-molecules (AIM). The non-covalent interactions and steric effect in the DES system were studied using the reduced density gradient isosurface (RDG). Theoretical and computational calculations revealed that the H-bonds and the electrostatic coexist, as predominant interactions in the BTEAB-based DES resulting chemical structure, and mechanism formation. The physical interactions between the component entities of DES lead to a new equilibrium that is more stable than that of HBA and HBD in their separate states.

The study on the interactions of two 1,2,3-triazoles with several biological macromolecules by multiple spectroscopic methodologies and molecular docking

1-(4-chlorophenyl)-5-phenyl-1H-1,2,3-triazole (CPTC) and 5-(3-chlorophenyl) -1-phenyl-1H-1,2,3-triazole (PCTA) are two new derivatives of 1,2,3-triazole. Their structural and spectral properties were characterized by density functional theory calculations (DFT). The binding properties of CPTC or PCTA with several typical biomacromolecules such as human serum albumin (HSA), bovine hemoglobin (BHb), human immunoglobulin (HIgG) or DNA were investigated by molecular docking and multiple spectroscopic methodologies. The different parameters including binding constants and thermodynamic parameters for CPTC/PCTA-HSA/BHb/HIgG/DNA systems were obtained based on various fluorescence enhancement or quenching mechanisms. The results of binding constants indicated that there were the strong interactions between two triazoles and four biological macromolecules due to the higher order of magnitude between 10³ and 10⁵. The values of thermodynamic parameters revealed that the binding forces for these systems are mainly hydrophobic interactions, electrostatic force, or hydrogen bond, respectively, which are in agreement with the results of molecular docking to a certain extent. Moreover, the information from synchronous, 3D fluorescence and UV-Vis spectroscopies proved that two compounds CPTC and PCTA could affect the microenvironment of amino acids residues of three kinds of proteins. Based on the above experimental results, a comparison of the interaction mechanisms for CPTC/PCTA-proteins/DNA systems have been performed in view of their different molecular structures, which is beneficial for the further research in order to design them as the novel drugs.

Effect of Dodecyl Trimethyl Ammonium Bromide on the Migration of Water Molecules in the Pores of Lignite: An Experimental and Molecular Simulation Study

Molecular dynamics simulations and experiments were used to study the influence of dodecyl trimethyl ammonium bromide (DTAB) on the migration of water molecules in the pores of lignite. To simulate the accuracy, 13C NMR was used to confirm the structure of Shengli lignite. It was found through adsorption experiments that DTAB reduces the specific surface area and pore volume of lignite. Molecular simulations indicate that the lignite and water molecules are primarily connected by hydrogen bonding. DTAB impedes the movement of water molecules in the pores of lignite and the storage space of compressed water molecules. Water molecules are mainly present in the pores of lignite in a posture parallel to the XOY plane, which facilitates the formation of hydrogen-bonding networks. However, this also leads to a decrease in the mobility of water molecules. Experimental and simulation results show that DTAB can enter lignite pores, reducing the water absorption in lignite. This is highly significant for the processing and utilization of lignite.

Interaction and selectivity of 14-crown-4 derivatives with Li+, Na+, and Mg2+ metal ions

The interactions between crown ether ligands (14-crown-4, 14C4; 4,4,5,5-tetramethylbenzo-14-crown-4, BC₄H₁₂-14C4; 4,4,5,5,9,9,10,10-octamethyl-14-crown-4, C₈H₂₄-14C4; dibenzo-14-crown ether-4, DB14C4) and alkaline and alkaline earth metal ions (Li⁺, Na⁺, Mg²⁺) were investigated using density functional theory modeling at the M062X/def2SVP and def2TZVP level. The condensed softness analysis of crown ethers, a condensed Fukui function, a condensed dual descriptor, and frontier molecular orbital theory were used to analyze the reactivities of the complexes. The complex stability was analyzed in terms of the binding energies, standard Gibbs free energy of formation, and energy decomposition of the interaction in aqueous solution. The results show that the active sites were mainly located at the carbon atoms of the benzene ring and oxygen atoms. The reactivities of DB14C4 and BC₄H₁₂-14C4 are higher than those of 14C4 and C₈H₂₄-14C4. The electrostatic interaction is the principal factor determining the stability of the complexes. The complexes containing Li⁺ has the greatest stability in aqueous solution among the complexes containing Li⁺, Na⁺, and Mg²⁺. BC₄H₁₂-14C4 shows selective adsorption toward Li⁺ in a mixed solution of Li⁺, Na⁺, and Mg²⁺. To evaluate the stability of complexes containing Mg²⁺, the solvent effect must be accurately described. An energy decomposition analysis was used to evaluate the stability of complexes containing Li⁺, Na⁺, and Mg²⁺, and the solvent effects were considered.

DFT and Thermal Decomposition Studies on Gemcitabine

Geometry optimization of gemcitabine was carried out by DFT with B3LYP/6-311++G(d,p) level in the gas phase. Chemical activity (electronegativity, electrophilicity, hardness, chemical softness and chemical potential) was predicted with the help of HOMO-LUMO energy values. Experimental FT-IR was recorded and computed values are also analyzed using the same level of DFT. A complete vibrational spectrum was made to analyze the potential energy distribution (PED). Stability of the molecule arising from the hyper-conjugative interaction was analyzed by the natural bond orbital (NBO). The molecular electrostatic potential map was used to detect the possible electrophilic and nucleophilic sites in the molecule. Nonisothermal decomposition of gemcitabine was carried out in an air atmosphere. The two decomposition steps of the molecule were analyzed kinetically by linear and nonlinear methods for elucidation of the kinetic triplet (Ea , ln A and f(α)) of the decomposition processes. Powder X-ray diffraction indicated that gemcitabine crystallizes in the monoclinic system (SG P2/m). Molecular docking studies were also described.

Synthesis and Characterization of a Molecularly Imprinted Polymer of Spermidine and the Exploration of Its Molecular Recognition Properties

Spermidine is a functional ingredient that can extend the lifespan of many foods and indicate meat safety. However, its synthesis and enrichment is expensive and complex. To develop an effective separation material that can offer highly selective recognition of spermidine, we first applied non-covalent molecular imprinting technology using methacrylic acid as a functional monomer, azobisisobutyronitrile as an initiator, and ethylene glycol dimethacrylate as a cross-linker. The adsorption properties of the polymers were analyzed using the Scatchard equation, the Lagergren kinetic equation, and the static distribution coefficient. The optimal polymerization molar ratio of the template molecule spermidine to the functional monomer was 1:4, the maximum adsorption amount was 97.75 μmol/g, and the adsorption equilibrium time was 300 min. The selective experiment showed that the interfering substances tyramine and histamine had selectivity factor α values of 2.01 and 1.78, respectively, indicating that the prepared polymer had good spermidine recognition ability. The density function theory calculations showed that the hydrogen bond strength, steric effect, and product energy caused adsorption and separation differences among the different imprinted polymer complexes.