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.

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. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (µ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings.

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. The solvent effects for the three studied species were analyzed using the solvation PCM/SMD model and, then, their corresponding solvation energies were predicted. The presence of pure water, sucrose penta-hydrate, and sucrose dihydrate was confirmed by using theoretical calculations based on the hybrid B3LYP/6-31G(∗) method and the experimental vibrational spectra. The existence of both sucrose hydrate complexes in aqueous solution is evidenced in the IR and HATR spectra by means of the characteristic bands at 3388, 3337, 3132, 1648, 1375, 1241, 1163, 1141, 1001, 870, 851, 732, and 668cm(-1) while in the Raman spectrum, the groups of bands in the regions 3159-3053cm(-1), 2980, 2954, and 1749-1496cm(-1) characterize the vibration modes of those complexes. The inter and intra-molecular H bond formations in aqueous solution were studied by Natural Bond Orbital (NBO) and Atoms in Molecules theory (AIM) investigation.

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=5.1716(7), c=12.549(2)Å, and Z=4 molecules per unit cell. The structure was solved from 1314 reflections with I>2σI and refined to an agreement R1-factor of 0.049. The minor conformer (34.7%) is nearly mirror-related to and extensively overlapped with the major one. The skeleton of the 4-hydroxyacetophenone molecular fragment and the prenyl group, (CH2)(CH)C(CH3)2, pendant arm attached to it are both planar and perpendicular to each other. A strong intermolecular O-H⋯O bond links neighboring molecules in the lattice to produce a polymeric structure. The conformational structures of the compound in the gas phase have been calculated by the DFT method and the geometrical results have been compared with the X-ray data. These data allow a complete assignment of vibration modes in the solid state FTIR and Raman spectra. The calculated 1H and 13C chemicals shifts are in good agreement with the corresponding experimental NMR spectra of the compound in solution.

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. An agreement between theoretical and available experimental results was found. A complete assignment of the 129 normal vibration modes for sucrose was performed. Five very intense characteristic bands in the infrared spectrum of sucrose at 3391, 3339, 1069, 1053, and 991 cm(-1) were assigned, the first two to the OH stretching modes while the other ones to C-O stretching modes.

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. The Density Functional Theory (DFT) method together with Pople's basis set show seven stable conformers for the compound in the gas phase and that only two conformations are probably present in the solid phase. 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 vibrational spectra was performed. The natural bond orbital (NBO) study reveals the characteristics of the electronic delocalization of the two stable structures, while the corresponding topological properties of electronic charge density were analyzed by employing Bader's Atoms in the Molecules theory (AIM).

Experimental and theoretical vibrational investigation on the saccharinate ion in aqueous solution.

We combined experimental vibrational spectroscopy (FTIR-Raman) and ab-initio calculations based on the density functional theory (DFT) to predict the structural and vibrational properties of sodium saccharinate in the solid and aqueous solution phases. The structural properties for the saccharinate ion and its dimer, such as the bond order, possible charge-transfer and the topological properties for both rings in the two media were studied by means of the Natural Bond Orbital (NBO) and the Atoms in Molecules theory (AIM) investigation. For a complete assignment of the IR and Raman spectra, the density functional theory 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. An agreement between theoretical and available experimental results was found. Four intense bands in the infrared spectrum characteristic of the dimeric species of the compound were detected.

Structural analysis, vibrational spectra and coordinated normal of 2R-(-)-6-hydroxytremetone.

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).

Phytotoxic activities of (2R)-6-hydroxytremetone.

Benzofurans are bioactive compounds isolated from the Asteraceae family. Benzofuran derivatives have been extensively studied because of their toxic effects on humans and animals. The phytotoxic activity of the benzofuran derivative (2R)-6-hydroxytremetone was studied on germination, seedling development, and cytotoxic and genotoxic effects on monocotyledoneous (onion and wheat) and dicotyledoneous (lettuce and tomato) species. Results of these assays demonstrated that (2R)-6-hydroxytremetone is a potent germination inhibitor of onion, lettuce, and tomato seeds. Germination reductions of approximately 80% were measured when seeds were exposed to 100 mg l(-1) of the compound, and showed considerably effects on the posterior development of the sprouts, including rootlets and hypocotyl elongations. Moreover, this benzofuran derivative also significantly reduced the root length and mitotic division of Allium cepa bulbs, although DNA damages were not observed. Our findings suggest that a mechanism of mitosis inhibition may play a role in the phytotoxic effects of plants producing these compounds.