Theoretical study on the structure, spectroscopic, and current-voltage behavior of 11-Cis and Trans retinal isomers in rhodopsin.

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.

Tautomerism of pyridinylbutane-1,3-diones: An NMR and DFT study.

The three possible 1-(n-pyridinyl)butane-1,3-diones (nPM) have been synthesized. Structures, tautomerism, and conformations are investigated by means of DFT calculations. 1 H and 13 C NMR spectra are assigned, and deuterium isotope effects on 13 C chemical shifts have been measured. Analysis of the isotope effects leads to the equilibrium constants of the keto-enol tautomers. Some interesting differences are seen between the three compounds and the phenyl analogs. The isotope effects can also rank the hydrogen bonds of the compounds, with the one with nitrogen in the three positions of the pyridine ring as the weakest. Structures, conformers, energies, and NMR nuclear shieldings are calculated using DFT calculations at the B3LYP/6-311++G(d,p) level.

Electronic transport on the two state "ON-OFF" of 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran as a light-driven molecular optical switch: A first-principle study.

Here, the electronic transport characteristics of the 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran were studied by using NEGF and DFT methods. By being exposed to UV or visible light, this molecule can change from its MC to SP states. The titled structure was optimized at B3LYP/6-311++G(d,p) level of theory. To obtain conductivity results, the electrons of metal and organic atoms were approached by the single-plus polarization (SZP) for single-zeta and double-plus polarization (DZP) for double zeta basis sets, respectively. We examined some factors in this study, including various molecule geometries, the type of surface materials (Platinum, gold, and silver), the switching ratio, the gap between HOMO and LUMO levels, and the transmission spectra, at different bias voltages. The outcomes show that conductivity transforms from an off-state (high resistance) to an on-state as the molecule switches from MC to SP form (low resistance).

Structural and vibrational investigation of Cis-Trans isomers of potent insecticide allethrin.

In this research, the optimised structural and vibrational properties of cis-trans isomers of powerful insecticide allethrin were theoretically studied in gas phase and in aqueous and ethanol solutions by using hybrid B3LYP/6-311 + + g(d,p) level of theory. The results revealed that the permittivity of solvent has influence on the properties of both isomers, thus, higher dipole moments and solvation energies are observed in water, a solvent of higher permittivity (78.355) than ethanol. Complete vibrational assignments of both isomers were done by combining the experimental IR spectrum of allethrin with the scaled quantum mechanical force field (SQMFF) methodology and the determination of corresponding scaled force constants in gas phase and aqueous solution are reported. Different signs of dihedral O2C10C6C4 angles of both isomers (negative in cis and positive in trans) support the differences in the vibrational assignments. Natural bond orbital (NBO) calculations suggest that both isomers are highly stable in gas phase and aqueous solution and that the side chains and five member's rings are involved in the n → σ* interactions. However, atoms in molecules (AIM) studies reveal a higher stability of form cis in both media than the trans one. Merz-Kollman (MK), Mulliken and natural population atomic (NPA) charges for both isomers support the higher hydration of trans isomer in aqueous media and, hence, the higher solvation energy in water (ΔGC/ZPVE = - 80.29 kJ/mol). Changes in the bond orders of O and C atoms of side chain are observed in water as a consequence of hydration. The higher stability of the cis form in the above solutions could be explained by the lower solvation energy in water, as supported by AIM calculations. The studies of frontier orbital reveal that the cis form in both media is sligthly more reactive than the trans form.

Behaviours of antiviral Oseltamivir in different media: DFT and SQMFF calculations.

The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6-311 + + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH2 group and NH group reveals lower solvation energy compared with other antiviral agents with an NH2 group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH2 groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities.

Validation of potential energy distribution by VEDA in vibrational assignment some of ß-diketones; comparison of theoretical predictions and experimental vibration shifts upon deutration.

The harmonic vibrational frequencies of the cis-enol forms of some of ß-diketones with different substitution in beta position, vis. H, CH3, and Ph ring, as the symmetric and asymmetric molecules, were calculated using density functional theory (DFT) at the B3LYP/6-311++G(d,p) level of theory. The results of DFT calculations were used to obtain the potential energy distribution (PED) by VEDA software. The PED results compared with the Gauss View animation, as our reassignments, and the experimental IR shifts upon deuteration of hydrogen in the OH and CHα. According to our study, the PED contributions, Gauss View animation and observed shifts show similar results for most of the bands which are not coupled with the OH and/or CHα bending, such as asymmetric and symmetric CH3 stretching and in-plane deformations, CH3 rocking vibrations and 8a, 19b, 9a, 15, 18a, and 12 motions of the phenyl ring. The largest discrepancies were observed in the 1700-1000 cm-1 region, likely due to the coupling with the OH and CHα in-plane bending vibrations, such as νaC = C-C = Ο, νsC = C-C = Ο and δOH. Furthermore, the calculated PED contributions by VEDA software do not well define the vibrational contributions to those groups in the molecule that are directly involved in the intramolecular hydrogen bond and the observed failure of the VEDA procedure is possibly due to inappropriateness of the default options.