Unravelling the Structure of Peroxides with Antiparasitic Activity: The Relative Impact of a Trioxolane or a Tetraoxane Pharmacophore on the Overall Molecular Structure.

Plasmodium falciparum artemisinin-resistance boosted the quest for novel plasmodial "fast killers," uncovering antimalarial candidates OZ439 and E209, whose peroxide precursors are 1,2,4-trioxolane (1) and 1,2,4,5-tetraoxane (2), differing solely in the pharmacophore (trioxolane or tetraoxane). Combining X-ray crystallography and vibrational spectroscopy, along with Hirshfeld surface analysis and calculations (CE-B3LYP/6-31G(d,p)) of pairwise interaction energies of intermolecular contacts existing in the crystal structure, may deepen the understanding of relative reactivity and properties of these endoperoxides classes. In the crystal, the tetraoxane ring in 2 and the trioxolane-adamantyl fragment in 1 are disordered, with molecules 1 and 2 existing as two distinct, stable conformations. Whereas the dominant C-H⋅⋅⋅O H-bonds in 1 connect an adamantyl C-H and O1 or O2 of the trioxolane ring, in 2 they involve the carbonyl oxygen, acting as a double acceptor from phenyl ring C-H groups. C-H⋅⋅⋅O and C-H⋅⋅⋅π H-bonds define the molecular packing of 2, while C-H⋅⋅⋅H-C van der Waals interactions determine the packing of 1. The dispersive component dominates the interaction energies calculated for the most representative molecular pairs.

UV-Induced Photochemistry of 1,3-Benzoxazole, 2-Isocyanophenol, and 2-Cyanophenol Isolated in Low-Temperature Ar Matrixes.

The monomers of 1,3-benzoxazole isolated in a cryogenic argon matrix were characterized by infrared spectroscopy. The photochemistry of matrix-isolated 1,3-benzoxazole, induced by excitation with a frequency-tunable narrowband UV light, was investigated. Irradiation at 233 nm resulted in a nearly quantitative conversion of 1,3-benzoxazole into 2-isocyanophenol. The individual photochemical behavior of the in situ produced 2-isocyanophenol was studied upon excitations at 290 nm, where 1,3-benzoxazole does not react. The photochemistry of isomeric matrix-isolated 2-cyanophenol was also studied. The photoreactions of 2-substituted (cyano- or isocyano-) phenols were found to have many similarities: (i) OH bond cleavage, yielding a 2-substituted (cyano- or isocyano-) phenoxyl radical and an H-atom, (ii) recombination of the detached H-atom, resulting in an oxo tautomer, and (iii) decomposition leading to fulvenone, together with HCN and HNC. In another photoprocess, 2-cyanophenol undergoes a [1,5] H-shift from the hydroxyl group to the cyano group yielding isomeric ketenimine. The analogous [1,5] H-shift from the hydroxyl group to the isocyano group must have also occurred in 2-isocyanophenol; however, the resulting nitrile ylide isomer is kinetically unstable and collapses to benzoxazole. All photoproducts were characterized by comparing their observed infrared spectra with those computed at the B3LYP/6-311++G(d,p) level. The mechanistic analysis of the photochemistry occurring in the family of the title compounds is presented.

Conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution.

This work presents an investigation on the conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution. Eighty-one systematically selected structures were studied at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level, giving rise to 40 unique conformers. The 19 lower energy structures and some selected other were further re-optimized at the B3LYP/6-311++G(d,p) level. The main factors accounting for the conformer's stability were pointed out and discussed. NBO and QTAIM analyses were performed in some selected conformers in order to address the anomeric and exo-anomeric effects as well as intramolecular hydrogen bonding. The effect of solvent water on the relative stability of the conformers was accounted for by applying the conductor-like polarizable continuum model, CPCM.

Structure of isolated 1,4-butanediol: combination of MP2 calculations, NBO analysis, and matrix-isolation infrared spectroscopy.

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.

Hydration of cyclohexylamines: CPCM calculation of hydration Gibbs energy of the conformers.

This work presents a theoretical study on the hydration of cyclohexylamine and isomers of cyclohexyldiamine. All possible conformers were fully optimized in solution using the conductor-like polarizable continuum model (CPCM) and density functional theory. Values of the Gibbs energy of solvation, its respective contributions (electrostatic, nonelectrostatic and conformational change), and the relative Gibbs energy of the conformers in aqueous solution and gas phase are reported. From these values and the Boltzmann populations of the conformers in both phases, the weighted mean values of DeltaG(solv) for the compounds are calculated. Three structural features were found to be important for the hydration of these compounds: the distance between the two NH2 groups (proximity disfavors hydration), their position relative to the ring (equatorial is preferred over axial), and the orientation of the nitrogen lone-pairs (gauche is more favorable to hydration than trans). In the particular case of vicinal cyclohexyldiamines, in addition to these two factors, the relative orientation of one group to the other should also be taken into account.