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.

Vibrational assignments of cyclic dimers and inter-monomers of adenine relating FT-IR, FT-Raman and UV spectra with SQMFF and DFT calculations.

In this work, three different cyclic dimers and a tetramer of adenine taken from the experimental structure determined by X-ray diffraction have been studied by combination of experimental FT-IR, FT-Raman and UV-Visible spectra with hybrid B3LYP/6-311++G** and scaled quantum mechanical force field (SQMFF) calculations in order to perform the complete assignments of bands observed in the vibrational spectra. The characteristics of different N-H···N interactions of those three cyclic structures together with the group of IR bands observed between 2865 and 2599 cm have been elucidated considering the tetrameric structure. The cyclic dimers and the tetramer of adenine confirm that the bands observed between 2865 and 2599 cm are not due to N-H···N interactions but to bands of combination, as was previously suggested.

Structural and vibrational characterization of di-hydrated hydrochloride tacrine combining DFT with SQMFF approach.

This research is a continuation of previously reported article on anhydrous freebase, cationic and hydrochloride tacrine. Here, structures and properties of di-hydrated species of cholinesterase inhibitor tacrine have been studied in gas phase and aqueous solution by using B3LYP/6-311G* and wB97XD/6-311G* levels of theory. Both methods show strong changes in the positions of two water molecules and similar solvation energies (-192.

Structural, harmonic force field and vibrational studies of cholinesterase inhibitor tacrine used for treatment of Alzheimer's disease.

Different structures of free base (FB), two cationic forms (CA) and three hydrochloride forms (HCl) of cholinesterase inhibitor tacrine used for treatment of Alzheimer 's disease was evaluated using hybrid B3LYP calculations in order to perform their complete vibrational assignments using the scaled harmonic force fields. Structures of anhydrous form of tacrine have been optimized in gas phase and in aqueous solution. The structure of form III HCl is in agreement with the experimental determined by X-ray diffraction while the predicted IR, Raman, H- C NMR and UV spectra show good correlations with the corresponding experimental ones.

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.

A combined study on structures and vibrational spectra of the antiviral rimantadine using SQMFF and DFT calculations.

In this research, a combined study on structures and vibrational spectra of antiviral rimantadine have been performed using hybrid B3LYP/6-311++G∗∗ calculations and the scaled quantum force field (SQMFF) procedure. Harmonic force fields and scaled force constants of Free Base (FB), Cationic (CA) and Hydrochloride (HCl) species derived from the antiviral rimantadine have been calculated in gas phase and in aqueous solution using normal internal coordinates and scaling factors. Good correlations were acquired comparing the theoretical IR, Raman, H- C-NMR and UV spectra of three species with the analogous experimental ones, suggesting probably, the presence of all them in both phases.

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.

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.

5-((1H-imidazol-1-yl)methyl)quinolin-8-ol as potential antiviral SARS-CoV-2 candidate: Synthesis, crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies.

A potential new drug to treat SARS-CoV-2 infections and chloroquine analogue, 5-((1H-imidazol-1-yl)methyl)quinolin-8-ol () has been here synthesized and characterized by FT-IR, H-NMR, C-NMR, ultraviolet-visible, ESI-MS and single-crystal X-ray diffraction. 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, H and C NMR chemical shifts and electronic spectrum in DMSO solution evidence good concordances.

Searching potential antiviral candidates for the treatment of the 2019 novel coronavirus based on DFT calculations and molecular docking.

In the present work, the succinic acid (SA), L-pyroglutamic acid (L-PGA), N-phenyl-thioacetamide (N-NPTA), 2-amino-5-chloropyridine hydrogen succinate (ACPS), epigallocatechine Gallate (EGCG) or KDH and, selenomethionine (SeM) compounds have been proposed as potential antiviral candidates to treatment of COVID-19 based on B3LYP/6-311++G∗∗ calculations and molecular docking. Solvation energies, stabilization energies, topological properties have been evaluated as function of acceptors and donors groups present in their structures. ACPS presents the higher reactivity in solution possibly because has the higher nucleophilicity and elecrophilicity indexes while KDH evidence the higher solvation energy probably due to the higher quantity of donors and acceptors groups.

Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities.

Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies.

Experimental isolation and spectroscopic characterization of squamocin acetogenin combining FT-IR, FT-Raman and UV-Vis spectra with DFT calculations.

Squamocin, an annonaceous acetogenin has been experimentally isolated and characterized in the solid state using the FT-IR and FT-Raman spectra and in methanol solution by UV-visible spectrum. The main bands observed were assigned combining the IR and Raman spectra with hybrid functional B3LYP/6-31G∗ calculations. Structural, electronic and topological properties were predicted at the same level of theory for the most stable conformer of squamocin in gas phase and methanol solution.

Exploring properties of potassium 6-X-2-isonicotinoyltrifluoroborate (X=H, F, Cl, Br) salts and their anions by using ab initio calculations.

The structural, electronic, and topological properties of a series of four members of potassium 6-X-2-isonicotinoyltrifluoroborate (X=H, F, Cl, Br) salts have been explored by using ab initio calculations with the hybrid B3LYP/6-311++G** method. According to the potential energy surface only the properties for the most stable conformer of each member of the series and their anions were analyzed in function of electronegativity and atomic radius of X. The results show that when X=H, the salt and its anion have symmetry C while the symmetry change to C for the halogenated F, Cl, and Br derivatives and their anions.

S(-) and R(+) species derived from antihistaminic promethazine agent: structural and vibrational studies.

Structural and vibrational properties of free base, cationic and hydrochloride species derived from both S(-) and R(+) enantiomers of antihistaminic promethazine (PTZ) agent have been theoretically evaluated in gas phase and in aqueous solution by using the hybrid B3LYP/6-31G* calculations. The initial structures of S(-) and R(+) enantiomers of hydrochloride PTZ were those polymorphic forms 1 and 2 experimentally determined by X-ray diffraction. Here, all structures in aqueous solution were optimized at the same level of theory by using the polarized continuum (PCM) and the universal solvation model.

Influence of atomic bonds on the properties of the laxative drug sodium picosulphate.

In this work, the influence of the different S═O, S-O, N⋯H, O⋯H, Na⋯O bonds present in the structures of the powerful laxative drug, sodium picosulphate in gas and aqueous solution phases were studied combining the density functional theory (DFT) calculations with the experimental available infrared, H NMR and UV-visible spectra. The structural, topological, electronic and vibrational properties were investigated in both media by using the hybrid B3LYP/6-31G* method and the integral equation formalism variant polarised continuum model (IEFPCM). Here, the characteristics of the S═O, S-O, N⋯H, O⋯H, Na⋯O bonds were completely revealed by using atomic charges, natural bond orbital (NBO) and atoms in molecules (AIM) studies.

FTIR, HATR and FT-Raman studies on the anhydrous and monohydrate species of maltose in aqueous solution.

The structures of α- and β-maltose anhydrous and their corresponding monohydrated species were studied combining the FT-IR, FT-Raman and HATR spectra with DFT calculations. The four structures were optimized in gas and aqueous solution by using the hybrid B3LYP/6-31G* method. The self-consistent force field (SCRF) calculations together with the polarized continuum (PCM) model were used to study the systems in solution while the solvation energies were computed using the solvation model (SM).

Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology.

Spectroscopic and structural studies on lactose species in aqueous solution combining the HATR and Raman spectra with SCRF calculations.

In this work, the α and β isomers, the α-lactose monohydrate and dihydrate and the dimeric species of lactose were studied from the spectroscopic point of view in gas and aqueous solution phases combining the infrared, Horizontal Attenuated Total Reflectance (HATR) and Raman spectra with the density functional theory (DFT) calculations. Aqueous saturated solutions of α-lactose monohydrate and solutions at different molar concentrations of α-lactose monohydrate in water were completely characterized by infrared, HATR and Raman spectroscopies. For all the species in solution, the solvent effects were studied using the solvation polarizable continuum (PCM) and solvation (SM) models and, then, their corresponding solvation energies were predicted.

FT-IR, FT-Raman, UV-visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol.

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.

A complete vibrational study on a potential environmental toxicant agent, the 3,3',4,4'-tetrachloroazobenzene combining the FTIR, FTRaman, UV-Visible and NMR spectroscopies with DFT calculations.

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 the vibrational spectra of sucrose in aqueous medium based on the SQM methodology and SCRF calculations.

In the present study, a complete assignment of the vibrational spectra of sucrose in aqueous medium was performed combining Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology with self-consistent reaction field (SCRF) calculations. Aqueous saturated solutions of sucrose and solutions at different molar concentrations of sucrose in water were completely characterized by infrared, HATR, and Raman spectroscopies. In accordance with reported data of the literature for sucrose, the theoretical structures of sucrose penta and sucrose dihydrate were also optimized in gas and aqueous solution phases by using the density functional theory (DFT) calculations.

A complete assignment of the vibrational spectra of 2-furoic acid based on the structures of the more stable monomer and dimer.

The structural and vibrational properties of cyclic dimer of 2-furoic acid (2FA) were predicted by combining the available experimental infrared and Raman spectra in the solid phase and ab initio calculations based on density functional theory (DFT) with Pople's basis sets. The calculations show that there are two cyclic dimers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, cis conformer, is present in the solid phase. The complete assignment of the 66 normal vibrational modes for the cis cyclic dimer was performed using the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology.

Molecular structure of 4-hidroxy-3-(3-methyl-2-butenyl) acetophenone, a plant antifungal, by X-ray diffraction, DFT calculation, and NMR and FTIR spectroscopy.

The molecular structure of two mixed and closely related conformers of the title compound, C13H16O2, found in the solid with unequal occupancies has been determined by X-ray diffraction methods. The substance crystallizes in the monoclinic Pca2(1) space group with a=17.279(2), b=5.

A complete characterization of the vibrational spectra of sucrose.

We combined experimental vibrational spectroscopy (FTIR-Raman) and ab-initio calculations based on density functional theory (DFT) to predict the structural and vibrational properties of sucrose in solid phase. The structural properties of sucrose, such as the bond order, possible charge-transfer, and the topological properties of the glucopyran and glucofuran rings were studied by means of the Natural Bond Orbital (NBO) and Atoms in Molecules theory (AIM) investigation. For a complete assignment of the infrared and Raman spectra, the density functional theory (DFT) calculations were combined with Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical frequency values to the experimental ones.

Structural study, coordinated normal analysis and vibrational spectra of 4-hydroxy-3-(3-methyl-2-butenyl)acetophenone.

Structural and vibrational properties of 4-hydroxy-3-(3-methyl-2-butenyl)acetophenone, isolated from Senecio nutans Sch. Bip. (Asteraceae) were studied by infrared and Raman spectroscopies in solid phase.