High-pressure polymorphism in pyridine

Investigation of the molecular structure of CHBP, biological activities and SARS-CoV-2 protein binding interaction by molecular and biomolecular spectroscopy approaches

The objective of this investigation is to learn more about the structural, electrical, spectroscopic, and physiochemical characteristics of biologically active cyano-4'-hydroxybiphenyl (CHBP). The title molecule's optimized conformational analysis was computed using the DFT/B3LYP/6-311++G (d, p) level of theory. The observed wavenumbers were compared with theoretical FT-IR and FT-Raman spectra. 1H and 13C NMR experimental spectra in CDCl3 solution (solvent phase) were recorded and the chemical shift was calculated. NBO analysis was used to examine the transfer of charge as well as the intermolecular and intramolecular bonding of orbitals. The TD-DFT (time-dependent DFT) approach was used to estimate theoretical values for both the gas and solvent (ethanol) in the corresponding transitional research, which was conducted using UV-Vis's spectra. Energy gap (Eg = 0.26764 eV) implies that the strong potential for charge transfer, and the stability of the CHBP compound. CHBP compound's has bioactive nature, its drug-likeness and biological properties were evaluated. The predicted topological polar surface area of 44.02 \AA2 for the molecule falls within the permissible range of < 140 \AA2. Based on the docking results, the most stable docking score value is -6.84 kcal/mol. In that interaction, MET 165 affects both phenyl rings in a pi-sulphur fashion and a single bond hydrogen with protein moieties GLN 192. This suggests that the pi-alkyl in PRO 168 is a hydroxyl substitutional ring. Our findings demonstrate the CHBP compound is a good inhibitor against the SAR COVID-19 viral protein.

Quantum chemical, spectroscopic and molecular docking studies on methyl 2-chloro-6-methyl pyridine-4-carboxylate: A potential inhibitor for irritable bowel syndrome

The methyl 2-chloro-6-methyl pyridine-4-carboxylate (MCMP) was studied using quantum chemical density functional theory (DFT) approach. The DFT/B3LYP method with cc-pVTZ basis set was employed to obtain the optimized stable structure and vibrational frequencies. The potential energy distribution (PED) calculations were used to assign the vibrational bands. The ¹³C NMR spectrum of MCMP molecule was simulated by the Gauge-Invariant-atomic orbital (GIAO) method using DMSO solution and the corresponding chemical shift values were calculated and observed. The maximum absorption wavelength was obtained using TD-DFT method and were compared with the experimental values. The bioactive nature of the MCMP compound was identified using the FMO analysis. The possible sites of electrophilic and nucleophilic attack were predicted using the MEP analysis and local descriptor analysis. The pharmaceutical activity of the MCMP molecule is validated through the NBO analysis. The molecular docking analysis confirms that the MCMP molecule can be used in the drug designing for the treatment of irritable bowel syndrome (IBS).

Photochemically Mediated Polymerization of Molecular Furan and Pyridine: Synthesis of Nanothreads at Reduced Pressures

Nanothreads are emerging one-dimensional sp³-hybridized materials with high predicted tensile strength and a tunable band gap. They can be synthesized by compressing aromatic or nonaromatic small molecules to pressures ranging from 15-30 GPa. Recently, new avenues are being sought that reduce the pressure required to afford nanothreads; the focus has been placed on the polymerization of molecules with reduced aromaticity, favorable stacking, and/or the use of higher reaction temperatures. Herein, we report the photochemically mediated polymerization of pyridine and furan aromatic precursors, which achieves nanothread formation at reduced pressures. In the case of pyridine, it was found that a combination of slow compression/decompression with broadband UV light exposure yielded a crystalline product featuring a six-fold diffraction pattern with similar interplanar spacings to previously synthesized pyridine-derived nanothreads at a reduced pressure. When furan is compressed to 8 GPa and exposed to broadband UV light, a crystalline solid is recovered that similarly demonstrates X-ray diffraction with an interplanar spacing akin to that of the high-pressure synthesized furan-derived nanothreads. Our method realizes a 1.9-fold reduction in the maximum pressure required to afford furan-derived nanothreads and a 1.4-fold reduction in pressure required for pyridine-derived nanothreads. Density functional theory and multiconfigurational wavefunction-based computations were used to understand the photochemical activation of furan and subsequent cascade thermal cycloadditions. The reduction of the onset pressure is caused by an initial [4+4] cycloaddition followed by increasingly facile thermal [4+2]-cycloadditions during polymerization.

A non-empirical intermolecular force-field for trinitrobenzene and its application in crystal structure prediction

An anisotropic atom-atom distributed intermolecular force-field (DIFF) for rigid trinitrobenzene (TNB) is developed using distributed multipole moments, dipolar polarizabilities, and dispersion coefficients derived from the charge density of the isolated molecule. The short-range parameters of the force-field are fitted to first- and second-order symmetry-adapted perturbation theory dimer interaction energy calculations using the distributed density-overlap model to guide the parameterization of the short-range anisotropy. The second-order calculations are used for fitting the damping coefficients of the long-range dispersion and polarization and also for relaxing the isotropic short-range coefficients in the final model, DIFF-srL2(rel). We assess the accuracy of the unrelaxed model, DIFF-srL2(norel), and its equivalent without short-range anisotropy, DIFF-srL0(norel), as these models are easier to derive. The model potentials are contrasted with empirical models for the repulsion-dispersion fitted to organic crystal structures with multipoles of iterated stockholder atoms (ISAs), FIT(ISA,L4), and with Gaussian Distributed Analysis (GDMA) multipoles, FIT(GDMA,L4), commonly used in modeling organic crystals. The potentials are tested for their ability to model the solid state of TNB. The non-empirical models provide more reasonable relative lattice energies of the three polymorphs of TNB and propose more sensible hypothetical structures than the empirical force-field (FIT). The DIFF-srL2(rel) model successfully has the most stable structure as one of the many structures that match the coordination sphere of form III. The neglect of the conformational flexibility of the nitro-groups is a significant approximation. This methodology provides a step toward force-fields capable of representing all phases of a molecule in molecular dynamics simulations.

Alloxan under pressure-squeezing an extremely dense molecular crystal structure

The crystal structure of the small organic molecule, alloxan, has been explored using high-pressure neutron diffraction; its already efficiently-packed structure provides a 'chemical head-start' on the pressure experiment. At the highest pressure measured, alloxan reaches a density of 2.36 g cm-3-unprecedented for a C, H(D), N, O-containing organic material of appreciable molecular weight. Its crystal structure is stable until ca. 6.5 GPa above which the sample starts to undergo amorphisation.

Modulating the H-bond strength by varying the temperature for the high pressure synthesis of nitrogen rich carbon nanothreads

Carbon nanothreads are among the most attractive new materials produced under high pressure conditions. Their synthesis can be achieved by compressing the crystals of aromatic molecules exploiting both the anisotropic stress produced by the unidirectional applied force and that intrinsic to the crystal arrangement. We explored here the transformation of pyridine into a nitrogen rich carbon nanothread crystal by varying the pressure and temperature conditions with the twofold purpose of disclosing the microscopic mechanism of transformation and optimizing the yield and quality of the produced crystalline nanothreads. The best conditions for the synthesis were identified in the 14-18 GPa range at temperatures between 400 and 500 K with a product yield greater than 30%. The comparison of experiments performed under different P-T conditions allowed us to understand the role of high temperature, which is necessary to weaken or even destroy the complex H-bond network characterizing the pyridine crystal and preventing the correct approach of the aromatic rings for nanothread formation. X-ray diffraction data confirm the excellent 2D hexagonal packing of the nanothreads over several tens of microns, whereas the sharp absorption lines observed in the IR spectrum strongly support a substantial order along the threads. Diffraction results suggest a polytwistane structure of the threads derived from a Diels-Alder [4 + 2] polymerization involving molecules arranged in a slipped parallel configuration along the pyridine crystal a and b axes. Electron microscopy evidences an arrangement of the nanothreads in bundles of tens of nanometers.

A Short Review of Current Computational Concepts for High-Pressure Phase Transition Studies in Molecular Crystals

High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. The interconnection of experimental and computational methods is highlighted, showing the importance of energy calculations in this field. Based on our deep understanding of methods’ limitations, we suggested the most convenient scheme for the computational study of high-pressure crystal structure changes. Finally, challenges and possible ways for progress in high-pressure phase transitions research of organic compounds are briefly discussed.