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In this study, the electronic transport properties of 11-Cis and Trans retinal, components of rhodopsin, were investigated as optical molecular switches using the nonequilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT). These isomers, which can be reversibly converted into each other, were examined in detail. The structural and spectroscopic properties, including infrared (IR), Raman, nuclear magnetic resonance (NMR), and ultraviolet (UV) spectra, were analyzed using the hybrid B3LYP/6-311 + + G** level of theory. Complete vibrational assignments were performed for both forms utilizing the scaled quantum mechanical force field (SQMFF) methodology. To evaluate the conductivity of these molecules, we utilized current-voltage (I-V) characteristics, transmission spectra, molecular projected self-consistent Hamiltonian (MPSH), HOMO-LUMO gap, and second-order interaction energies (E2). The trendline extrapolation of the current-voltage plots confirmed our findings. We investigated the effect of different electrodes (Ag, Au, Pt) and various connection sites (hollow, top, bridge) on conductivity. The Ag electrode with the hollow site exhibited the highest efficiency. Our results indicate that the Cis form has higher conductivity than the Trans form.

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A potential new drug to treat SARS-CoV-2 infections and chloroquine analogue, 5-((1H-imidazol-1-yl)methyl)quinolin-8-ol (DD1) has been here synthesized and characterized by FT-IR, 1H-NMR, 13C-NMR, ultraviolet-visible, ESI-MS and single-crystal X-ray diffraction. DD1 was optimized in gas phase, aqueous and DMSO solutions using hybrid B3LYP/6-311++G(d,p) method. Comparisons between experimental and theoretical infrared spectra, 1H and 13C NMR chemical shifts and electronic spectrum in DMSO solution evidence good concordances. Higher solvation energy was observed in aqueous solution than in DMSO, showing in aqueous solution a higher value than antiviral brincidofovir and chloroquine. on Bond orders, atomic charges and topological studies suggest that imidazole ring play a very important role in the properties of DD1. NBO and AIM analyses support the intra-molecular O15-H16•••N17 bonds of DD1 in the three media. Low gap value supports the higher reactivity of DD1 than chloroquine justified by the higher electrophilicity and low nucleophilicity. Complete vibrational assignments of DD1 in gas phase and aqueous solution are reported together with the scaled force constants. In addition, better intermolecular interactions were observed by Hirshfeld surface analysis. Finally, the molecular docking mechanism between DD1 ligand and COVID-19/6WCF and COVID-19/6Y84 receptors were studied to explore the binding modes of these compounds at the active sites. Molecular docking results have shown that the DD1 molecule can be considered as a potential agent against COVID-19/6Y84-6WCF receptors.

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In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G(∗) basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated (1)H NMR and (13)C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations.

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In this study 3,3',4,4'-tetrachloroazobenzene (TCAB) was prepared and then characterized by infrared, Raman, multidimensional nuclear magnetic resonance (NMR) and ultraviolet-visible spectroscopies. The density functional theory (DFT) together with the 6-31G(*) and 6-311++G(**) basis sets were used to study the structures and vibrational properties of the two cis and trans isomers of TCAB. The harmonic vibrational wavenumbers for the optimized geometries were calculated at the same theory levels. A complete assignment of all the observed bands in the vibrational spectra of TCAB was performed combining the DFT calculations with the scaled quantum mechanical force field (SQMFF) methodology. The molecular electrostatic potentials, atomic charges, bond orders and frontier orbitals for the two isomers of TCAB were compared and analyzed. The comparison of the theoretical ultraviolet-visible spectrum with the corresponding experimental demonstrates a good concordance while the calculated (1)H and (13)C chemicals shifts are in good conformity with the corresponding experimental NMR spectra of TCAB in solution. The npp(*) transitions for both forms were studied by natural bond orbital (NBO) while the topological properties were calculated by employing Bader's Atoms in the Molecules (AIM) theory. This study shows that the cis and trans isomers exhibit different structural and vibrational properties and absorption bands.

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We have studied and characterized the structural and vibrational properties of 2R-(-)-6-hydroxytremetone, isolated from Xenophyllum poposum (Phil.) by infrared and Raman spectroscopy in the solid phase. The density functional theory (DFT) method together with Pople's basis set show that two stable molecules for the compound have been theoretically determined in the gas phase and that both conformations are present in the solid phase, as was experimentally observed. The harmonic vibrational wavenumbers for the optimized geometry were calculated at B3LYP/6-31G*and B3LYP/6-311++G** levels. For a complete assignment of the vibrational spectra, DFT calculations were combined with Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical wavenumber values to the experimental ones. Then, a complete assignment of all the observed bands in the infrared spectrum for the compound was performed. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two structures, while the corresponding topological properties of electronic charge density are analyzed by employing Bader's Atoms in the Molecules theory (AIM).

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We have studied L-ascorbic acid and characterized it by infrared spectroscopy in solid and aqueous solution phases. The density functional theory (DFT) method together with Pople's basis set show that three stable molecules for the compound have been theoretically determined in the gas phase, and that an average of only two more stable conformations are present in the solid phase, as it was experimentally observed. The harmonic vibrational wavenumbers for the optimized geometries of both structures were calculated at B3LYP/6-31G*and B3LYP/6-311++G** levels at the proximity of the isolated molecule. For a complete assignment of the vibrational spectra in the compound solid and aqueous solution phases, DFT calculations were combined with Pulay's scaled quantum mechanics force field methodology in order to fit the theoretical wavenumber values to the experimental ones. In this way, a complete assignment of all the observed bands in the infrared spectrum for l-ascorbic acid was performed. The natural bond orbital study reveals the characteristics of the electronic delocalization of the three structures while the corresponding topological properties of electronic charge density are analyzed by employing Bader's atoms-in-molecules theory.

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The molecular structure of trimethylgermane has been determined by gas electron diffraction experiments. Infrared spectra for the gaseous, liquid, and solid phases were also recorded. Parallel and perpendicular polarized Raman spectra for the liquid were measured to obtain depolarization values. The experimental studies were supported by a series of computational calculations using HF, B3LYP, and MP2 methods and a variety of basis sets. The force fields obtained from density functional theory using both B3LYP/6-31G* and B3LYP/6-311+G** were scaled with both Pulay's SQM methodology and Yoshida's WLS procedure to simulate the vibrational spectra and assist in the assignment of fundamental bands. The Raman intensities were obtained from polarizability derivatives. The vibrational spectra of trimethylgermane were completely assigned on the basis of the experimental data and the theoretical prediction of vibrational frequencies and intensities.

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The geometry of iodotrimethylgermane has been determined by experimental and computational methods. Fourier transform infrared spectra have been recorded over a range of temperatures along with the Raman spectrum to obtain comprehensive vibrational data for the fundamental modes. The stretching, rocking, and deformation bands of the methyl groups have been resolved into their components with the aid of low-temperature infrared spectroscopy using Fourier self-deconvolution and curve-fitting methods. The optimized geometries and vibrational harmonic frequencies were calculated by density functional theory methods employing Pople-type basis sets, as well as those with descriptions for an effective core potential describing both germanium and iodine atoms. A scaled quantum mechanical analysis was carried out to yield the best set of harmonic force constants and obtain a transferable set of scale factors that can be applied to the (CH3)(3-)GeX (X = H, Cl, Br, I) series.

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