Publications

Abstract The therapeutic effects of drugs are well known to result from their interaction with multiple intracellular targets. Accordingly, the pharma industry is currently moving from a reductionist approach based on a 'one-target fixation' to a holistic multitarget approach. However, many drug discovery practices are still procedural abstractions resulting from the attempt to understand and address the action of biologically active compounds while preventing adverse effects. Here, we discuss how drug discovery can benefit from the principles of evolutionary biology and report two real-life case studies. We do so by focusing on the desirability principle, and its many features and applications, such as machine learning-based multicriteria virtual screening.

Abstract Methylation at the C2 position of 1,3-disubstituted imidazolium-based ionic liquids (ILs) is one of the structural features that has gained attention due to its drastic impact on thermophysical and transport properties. Several hypotheses have been proposed to explain this effect but there is still much discrepancy. Aiming for the rationalization of the effects of these structural features on the properties of imidazolium ILs, we present a thermodynamic and computational study of two methylated ILs at the C2 position of imidazolium, [C-1(4) C-2(1) (3)C(1)im][NTf2] and [C-1(3) C-2(1) (3)C(1)im][NTf2]. The phase behaviour (glass transition and vaporization equilibrium) and computational studies of the anion rotation around the cation and ion pair interaction energies for both ILs were explored. The results have shown that C2-methylation has no impact on the enthalpy of vaporization. However, it decreases the entropy of vaporization, which is a consequence of the change in the ion pair dynamics that affects both the liquid and gas phases. In addition, the more hindered dynamics of the ion pair are also reflected in the increase in the glass transition temperature, Tg. The entropic contribution of anion-around-cation rotation in the imidazolium [NTf2] ILs was quantified experimentally by the comparative analysis of the entropy of vaporization, and computationally by the calculation of the entropies of hindered internal rotation. The global results exclude the existence of significant H-bonding in the C2-protonated (non-methylated) ILs and explain the C2-methylation effect in terms of reduced entropy of the ion pair in the liquid and gas phases. In light of these results, the C2-methylation effect is intrinsically entropic and originates from the more hindered anion-around-cation rotation as a consequence of the substitution of the -H with a bulkier -CH3 group.

Abstract The molecular and supramolecular structure and energetics of tetracene and rubrene were investigated by a combined experimental and theoretical study. Accurate equilibrium vapour pressures at various temperatures were measured for both compounds. For rubrene the energetic analysis evidences lower crystal packing efficiency, strong molecular destabilization and confirms the non-planar twisted equilibrium structure in the gas phase. The results also indicate that phenyl internal rotation in rubrene is highly hindered. The intra- and intermolecular interactions in crystal tetracene and rubrene were evaluated by computational methods. The representative stacked dimer of the tetracene...tetracene interaction in rubrene has lower ionization energy than the one modelling the same interaction in tetracene, due to stronger cation...pi interactions in the cation-radical of rubrene. Charge distribution in the cation dimer is symmetrical in rubrene, whereas in tetracene it is largely localized on the C-H center dot center dot center dot pi donor partner of the herringbone dimer. These findings highlight the impact of cation...pi interactions on the semiconducting properties of OSCs.

Abstract A comprehensive thermodynamic study of the whole ortho-polyphenylbenzenes series from biphenyl (n = 1) to hexaphenylbenzene (n = 6) is presented. Combustion calorimetry and phase equilibria measurements for 1,2,3,4-tetraphenylbenzene (n = 4) and pentaphenylbenzene (n = 5) together with literature data were used to understand and quantify the constraint effect of ortho-substitution on the molecular energetics and phase stability of polyaromatic compounds. All of the derived thermodynamic properties (enthalpy of sublimation, entropy of sublimation, and gas phase molecular energetics) show a marked trend shift at n = 4 to 5, which is related to the change of the degree of molecular flexibility after 1,2,3,4-tetraphenylbenzene (n = 4). The greater intramolecular constraint in the more crowded members of the series (n = 5 and 6) leads to a significant change in the molecular properties and cohesive energy. The trend shift in the molecular properties is related with the decrease in molecular flexibility, which leads to lower molecular entropy and destabilization of the intramolecular interaction potential due to the increased hindrance in a confined molecular space.

Abstract In spite of recent advances in understanding the mechanism of coelenterate bioluminescence, there is no consensus about which coelenteramide specie and/or state are the light emitter. In this study, a systematic investigation of the geometries and spectra of all possible light emitters has been performed at the TD omega B97XD/6-31+ G(d) level of theory, including various fluorescent and chemiluminescent states in vacuum, in a hydrophobic environment and in aqueous solution. To deduce the most probable form of the fluorescent and chemiluminescent coelenteramide emitter, the equilibrium constants for the fluorescent and chemiluminescent states connecting the various species have been calculated. wB97XD gives a qualitatively good description of fluorescent and chemiluminescent structures. Coelenteramide is formed in a "dark" chemiluminescent state and must evolve to a bright fluorescent state. Moreover, the photoacidity of the phenol group is significantly higher in the fluorescent state than in the chemiluminescent state, which allows the formation of phenolate coelenteramide and clarifies its role as the bioluminescent emitter.

Abstract This work presents a comprehensive evaluation of the phase behaviour and cohesive enthalpy of protic ionic liquids (PILs) composed of 1,5-diazabicyclo[4.3.0]non-5-ene (DBN) or 1,8-diazabicyclo[5.4.0] undec-7- ene (DBU) organic superbases with short-chain length (acetic, propionic and butyric) carboxylic acids. Glass transition temperatures, T-g, and enthalpies of vaporization, Delta H-vap, were measured for six [BH][A] (1 : 1) PILs (B = DBN, DBU; A = MeCOO, EtCOO, nPrCOO), revealing more significant changes upon increasing the number of -CH2- groups in the base than in the acid. The magnitude of Delta H-vap evidences that liquid PILs have a high proportion of ions, although the results also indicate that in DBN PILs the concentration of neutral species is not negligible. In the gas phase, these PILs exist as a distribution of ion pairs and isolated neutral species, with speciation being dependent on the temperature and pressure conditions at high temperatures and low pressures the separated neutral species dominate. The higher T-g and Delta H-vap of the DBU PILs are explained by the stronger basicity of DBU (as supported by NMR and computational calculations), which increases the extent of proton exchange and the ionic character of the corresponding PILs, resulting in stronger intermolecular interactions in condensed phases.

Abstract Steady-state and time-resolved optical spectroscopy techniques were employed to study the photo physics and photochemistry of 4- (4HC) and 3-hydroxycoumarin (3HC). We found that the p K-a of 4HC in aqueous solutions is about 7.5 and the p K-a* is only 4.5. We also found that the nonradiative rate of 4-hydroxycoumarin is high and the excited state proton transfer (ESPT) rate to water is rather slow and so an ESPT process is not observed. Quantum mechanical calculations confirm that the ESPT rate should be slow and the intersystem crossing rate St -> 4 T is large. An ESPT process was also not observed for 3HC, but it might still take place and not being observed as the fluorescence quantum yield of the anion is two orders of magnitude smaller than that of the protonated form. The nonradiative decay of protonated 3HC is explained with an H-atom abstraction mechanism, leading to the formation of a radical species.

Abstract Coelenterazine, a member of the imidazopyrazinone class of chemiluminescent substrates, presents significant potential as a dynamic probe of reactive oxygen species in a biological environment, such as a superoxide anion, in which these species are important in cellular biology and pathology. The objective of the current study was to understand in what way the efficiency of singlet and triplet chemiexcitation could be modulated, towards a more efficient use of imidazopyrazinone-based compounds as dynamic chemiluminescent probes. To this end the thermolysis of imidazopyrazinone dioxetanone, substituted at the C-8-position with electron-donating or electron-withdrawing groups, was characterized with a theoretical approach based on density functional theory. Substituents with different electron-donating/withdrawing characters have only a limited effect on the singlet chemiexcitation of anionic dioxetanone. For neutral dioxetanone, both electron-withdrawing and weak electron-donating substituents increase singlet chemiexcitation, to the contrary of strong electron-donating groups. During their thermolysis reaction, all molecules presented regions of degeneracy with triplet states, thereby indicating the possibility of triplet chemiexcitation.