Search

In the present work, the structural, topological and vibrational properties of five members of the series C8H13N3O5POR (RH, (CH2)3OCH2CH3, (CH2)3O(CH2)7CH3, (CH2)3O(CH2)13CH3 and (CH2)3O(CH2)15CH3), where the first and the latter members are the two potential antiviral agents, cidofovir and brincidofovir, respectively, were studied by using density functional theory (DFT), natural bond orbital (NBO), atoms in molecules theory (AIM), frontier orbitals and molecular electrostatic potential (MEP) calculations and the hybrid B3LYP/6-31G∗ method. Here, the changes in the properties were followed modifying the side chain from cidofovir to brincidofovir. This study reveals clearly the differences in the properties when they change the longitude of the side chain. The high dipole moment value of brincidofovir together with the large side chain could explain the ability of brincidofovir to traverse biological membranes more rapidly than cidofovir while the low bond order that presents the POR bond in brincidofovir probably supports the quick removal of its side chain inside the cell. The frontier orbitals predicted a high reactivity and a higher electrophilicity index for brincidofovir, as compared with cidofovir. The complete assignment of the 90 vibration modes of cidofovir was proposed. Keywords: Brincidofovir, Vibrational spectra, Molecular structure, Force field, DFT calculations

In this study, three anhydrous species of trehalose and their dihydrated form were studied using the Fourier Transform Infrared (FTIR) and Raman spectroscopy combined with theoretical calculations derived from the theory of the functional of the density (DFT). Here, the structural and vibrational properties were predicted using the hybrid B3LYP/6-31G∗ method. The complete vibrational assignments were performed using the scaled mechanical force fields (SQMFF) methodology and their internal normal coordinates. The natural bond orbital (NBO) and atoms in molecules (AIM) calculations predicted high stabilities for the dihydrated species in gas and aqueous solution phases. The little variation observed in the dipole moment for the dihydrated species in solution could be related to a small perturbation of water hydration shell and short hydrogen bonds, as revealed by NBO and AIM studies. The lower volume expansion, low solvation energy and the higher nucleophilicity index observed for trehalose species in solution, in relation to maltose and sucrose could probably explain that different water molecules are around of trehalose/water mixtures generating higher “rigidity” in trehalose, as was experimentally reported in the literature. On the other hand, the low f(νO–H)H2O force constant value for trehalose, as compared with maltose and lactose could justify the very fragile character from the trehalose/water system to the temperature and concentration changes, as was experimentally observed from viscosity and Raman scattering studies. Keywords: Trehalose, Molecular structure, Vibrational spectra, DFT calculations, Force field

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, 1H 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. The infrared, 1H NMR, 13C NMR and UV-visible spectra are in reasonable concordance with those experimental available in the literature. The vibrational analysis of sodium picosulphate was performed considering C3V symmetries for both SO42− groups and the complete assignments of the 126 vibration modes were reported in gas phase and aqueous solution together with their corresponding force fields. In addition, the reactivities of sodium picosulfate increase in solution due to their ionic characteristic which probably justifies their behaviour as a stimulant cathartic and their easy metabolic conversion, as reported in the literature.

Cyclo[4n+2]carbons are sp-bonded carbon rings in which Hückel rule predicts a fully symmetric structure that is, however, in competition with the second order Jahn–Teller (Peierls) distortion. This picture, however, neglects the crucial role played by nuclear quantum effects. Here we investigate the magnitude of nuclear quantum effects on the stability, vibrational and optical properties of cyclo[4n+2]carbons (n=1,2,3,4) in vacuum. The quantum structural minimization reduces the energy separation between the different isomers and determines that the most stable C14 isomer is the cumulenic one, setting the transition from the polyyenic to the cumulenic form at n=3 (at odd with the classical structural optimization setting the transition at n=2). Moreover, the quantum anharmonic effects generate very large frequency shifts, linewidth broadenings and satellites in the phonon spectral weight hindering any possible interpretation based on the non-interacting harmonic spectrum. The optical absorbance is completely reshaped by quantum anharmonic vibrations with redshifts ranging from 0.4 to 1.0 eV in the first excitonic absorption with respect to the static ionic picture. Finally, we also determine the crystal structure of C18 on a NaCl bilayer to be a buckled polyynic phase in agreement with recent experimental findings. Our work outlines the crucial role of nuclear quantum effects in the understanding of carbon molecular systems.