Chalcogen bond-assisted syn-locked scaffolds: DFT analysis and biological implications of novel tubulin inhibitors

A series of new tubulin inhibitors containing chalcogen bonds have been discovered. Density functional theory (DFT) analysis of the O-C-C-S torsion profile shows a preference of 0.8 kcal/mol for the syn-conformer over the anti-conformer. Besides, the O-S natural bond orbital (NBO) analysis reveals that the O_LP ∼ C-S_BD∗ energy potential is 0.62 kcal/mol. Further pharmacochemical screening of several series of (4-arylthiophen-2-yl)(3,4,5-trimethoxyphenyl)methanones identified IPO-10 as a highly effective tubulin inhibitor with an IC₅₀ of 23 nm for MCF-7.

Quantum chemical insight into molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-19 molecule 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluorophenyl)acetamide - dimer

Novel antiviral active molecule 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl)acetamide has been synthesised and characterized by FT-IR and FT-Raman spectra. The equilibrium geometry, natural bond orbital calculations and vibrational assignments have been carried out using density functional B3LYP method with the 6-311G++(d,p) basis set. The complete vibrational assignments for all the vibrational modes have been supported by normal coordinate analysis, force constants and potential energy distributions. A detailed analysis of the intermolecular interactions has been performed based on the Hirshfeld surfaces. Drug likeness has been carried out based on Lipinski's rule and the absorption, distribution, metabolism, excretion and toxicity of the title molecule has been calculated. Antiviral potency of 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro-phenyl) acetamide has been investigated by docking against SARS-CoV-2 protein. The optimized geometry shows near-planarity between the phenyl ring and the pyrimidine ring. Differences in the geometries due to the substitution of the most electronegative fluorine atom and intermolecular contacts due to amino pyrimidine were analyzed. NBO analysis reveals the formation of two strong stable hydrogen bonded N-H···N intermolecular interactions and weak intramolecular interactions C-H···O and N-H···O. The Hirshfeld surfaces and consequently the 2D-fingerprint confirm the nature of intermolecular interactions and their quantitative contributions towards the crystal packing. The red shift in N-H stretching frequency exposed from IR substantiate the formation of N-H···N intermolecular hydrogen bond. Drug likeness and absorption, distribution, metabolism, excretion and toxicity properties analysis gives an idea about the pharmacokinetic properties of the title molecule. The binding energy -8.7 kcal/mol of the nonbonding interaction present a clear view that 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl) acetamide can irreversibly interact with SARS-CoV-2 protease.

Discovering the stacking landscape of a pyridine-pyridine system

Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the interaction energies of the particular systems-one can learn how the pyridine dimer stability changes along with various geometrical parameters. Other calculations such as natural bond orbital and energy decomposition have also been applied. The interplay of two significant factors, electrostatic forces and electron correlation effects, have been evaluated. The role of π···π interactions in the stacked pyridine systems has also been confirmed, and surprisingly, this happened to be true even for the geometries where the formation of C-H···π interactions might be proposed instead. The combination of many different methods has revealed the complexity of the stacking interactions. Apart from providing a "literal new look" into pyridine interaction patterns another picture has emerged. A stacking interaction in a pyridine dimer system is perceived as a combination of many different sources of the interaction energy, including orbital ones, and this is true for many different geometries.

Z-Isomers of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH. Conformational properties, electronic structure and aqueous solvent effects

Procyanidins are highly hydroxylated polymers known as antioxidant compounds, thereby exhibiting beneficial effects. These compounds are protective agents against oxidative stress and the damage induced by free radicals in membranes and nucleic acids. This paper describes a study of the conformational space of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH as part of a larger study of similar structures with different substitutions. The relationships between aqueous solution-vacuum variations of some properties were studied, as well as the stabilization and reactivity of (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=H, R'=H, R=OH, R'=R=OH, and (+)-catechin. The variations in geometric parameters and electronic properties due to conformational changes, as well as the effects of substituents and polar solvents, were evaluated and analyzed. Bader's theory of atoms in molecules was applied to characterize intramolecular interactions, along with a natural bond orbital analysis for each conformer described. The molecular electrostatic potential was rationalized by charge delocalization mechanisms and interatomic intramolecular interactions, relating them to the structural changes and topological properties of the electron charge density. Molecular polarizability and permanent electric dipole moment values were estimated. The results show the importance of a knowledge of the conformational space, and values for each conformer. Based on our previous results, we showed the existence of electron charge delocalization mechanisms acting cooperatively as "delocalization routes", showing interactions between different rings not even sharing the same plane. These "delocalization routes" were more effective for (4α→6″, 2α→O→1″)-phenylflavan substituted with R'=R=OH than for (+)-catechin, and are proposed as adding insight into the structure-antioxidant activity relationship of flavans.

FT-IR and Raman spectroscopic and DFT studies of anti-cancer active molecule N-{(meta-ferrocenyl) Benzoyl} - l-alanine - glycine ethyl ester

FT-Raman and FT-IR spectra of N-{(meta-ferrocenyl) Benzoyl} - l-alanine - glycine ethyl ester were recorded in solid phase. The optimized molecular geometry, the vibrational wavenumbers, the infrared intensities and the Raman scattering intensities were calculated by using density functional method(B3LYP) with 6-31G(d, p) basis set. Vibrational assignment of the molecule was done by using potential energy distribution analysis. Natural bond orbital analysis, Mulliken charge analysis and HOMO-LUMO energy were used to elucidate the reasons for intra molecular charge transfer. Docking studies were conducted to predict its anticancer activity.

Theoretical studies on the dissolution of chitosan in 1-butyl-3-methylimidazolium acetate ionic liquid

In this work, the dissolution mechanism of chitosan in imidazolium acetic-based ionic liquid (IL) 1-butyl-3-methylimidazolium acetate was investigated by density functional theory (DFT). Chitobiose is considered to symbolize chitosan during the DFT calculations. [Bmim]OAc is supposed to be the best suitable IL among the investigated ILs for the dissolution of chitosan since the complex formed between [Bmim]OAc and chitobiose has the lowest energy. The hydrogen bonds formed by IL and chitobiose were studied by discussing the geometric parameter variations and the vibration mode analyses. Four strong hydrogen-bond patterns C1-H1 ⋯ O16, C2-H2 ⋯ O16, O38-H39 ⋯ O1 and O40-H41 ⋯ O2 were found, which means the existence of strong interaction between chitosan and [Bmim]OAc. In addition, natural bond orbital (NBO) analysis was used to study the second order perturbation stabilization energies (E(2)) that denotes the intensity of the interactions between chitobiose with H2O and ILs. The E(2) of chitobiose with [Bmim]OAc is larger than that of chitobiose with other ILs and solvents studied, which proves that chitobiose can be dissolved in [Bmim]OAc but cannot in water and other solvents. Atom in molecules (AIM) theory shows that hydrogen bonds between chitobiose and [Bmim]OAc are stronger than that between chitobiose and other solvents. It means that the interactions between [Bmim]OAc and chitobiose interrupt the initial hydrogen bonds in the chitobiose due to the formation of new hydrogen bonds in the complexes. The calculation data provide the interaction mechanism of the dissolution of chitosan in [Bmim]OAc.

Theoretical and experimental study of a novel psolaren derivate: (E)-9-(3,4-dimethylpent-2-enyloxy)-7H-furo[3,2-g]chromen-7-one

A new psolaren derivate, (E)-9-(3,4-dimethylpent-2-enyloxy)-7H-furo[3,2-g]chromen-7-one, has been isolated and characterized by experimental and theoretical methodologies. The solid state molecular structure has been determined by X-ray diffraction methods. The substance crystallizes in the monoclinic P21/c space group with a=4.2389(5), b=26.090(3), c=12.482(1)Å, β=96.990(9)°, and Z=4 molecules per unit cell. The crystal structure shows the molecule fused phenyl and hetero-cycle rings to be coplanar with each other. Ab initio(MP2) and DFT methods have been used to predict the molecular structure in the isolated molecule approximation and the results compared with the experimental data. The MP2/6-311G(d,p) calculations are in good agreement with the X-ray results. The calculated HOMO-LUMO energy gap shows that the intra-molecular charge transfer could easily occur, a prediction closely related to the observed bioactivity of this new compound. In addition, the infrared absorption and Raman dispersion spectra were recorded and an assignment of the observed spectral features to molecular vibrations was made. The vibrational study was assisted by quantum chemistry calculations at the MP2 and DFT level, which provided theoretical mode frequencies. The study was completed by natural bond orbital (NBO) analysis.

Layered crystal structure, conformational and vibrational properties of 2,2,2-trichloroethoxysulfonamide: an experimental and theoretical study

The molecular structure of 2,2,2-trichloroethoxysulfonamide, CCl3CH2OSO2NH2, has been determined in the solid state by X-ray diffraction data and in the gas phase by ab initio (MP2) and DFT calculations. The substance crystallizes in the monoclinic P21/c space group with a = 9.969(3)Å, b = 22.914(6)Å, c = 7.349(2)Å, β = 91.06(3)°, and Z = 8 molecules per unit cell. There are two independent, but closely related molecular conformers in the crystal asymmetric unit. They only differ in the angular orientation of the sulfonamide (SO2NH2) group. The conformers are arranged in the lattice as center-symmetric NH · · · O(sulf)-bonded dimers. Neighboring dimers are linked through further NH · · · O(sulf) bonds giving rise to a crystal layered structure. The solid state infrared and Raman spectra have been recorded and the observed bands assigned to the molecular vibration modes. Also, the thermal behavior of the substance was investigated by TG-DT analysis. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond (NBO) analysis.

Molecular structure, intramolecular hydrogen bonding and vibrational spectral investigation of 2-fluoro benzamide--a DFT approach

The FTIR and FT-Raman spectra of 2-fluoro benzamide (2FBA) have been recorded in the region 4000-400 and 4000-100 cm(-1), respectively. The structuralanalysis, hydrogen bonding, optimized geometry, frequency and intensity of the vibrational bands of 2FBA were obtained by the density functional theory (DFT) with complete relaxation in the potential energy surface using 6-31G** basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The (13)C NMR spectra have been recorded and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method and their respective linear correlations were obtained. The electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. The Mulliken charges, the values of electric dipole moment (μ) of the molecule were computed using DFT calculations. The change in electron density (ED) in the σ* antibonding orbitals and stabilization energies E(2) have been calculated by natural bond (NBO) analysis to give clear evidence of stabilization originating in the hyper conjugation of hydrogen-bonded interactions.