Publications

Abstract In spite of recent advances towards understanding the mechanism of firefly bioluminescence, there is no consensus about which oxyluciferin (OxyLH(2)) species are the red and yellow-green emitters. The crystal structure of Luciola cruciata luciferase (LcLuc) revealed different conformations for the various steps of the bioluminescence reaction, with different degrees of polarity and rigidity of the active-site microenvironment. In this study, these different conformations of luciferase (Luc) are simulated and their effects on the different chemical equilibria of OxyLH(2) are investigated as a function of pH by means of density functional theory with the PBE0 functional. In particular, the thermodynamic properties and the absorption spectra of each species, as well as their relative stabilities in the ground and excited states, were computed in the different conformations of Luc. From the calculations it is possible to derive the acid dissociation and tautomeric constants, and the corresponding distribution diagrams. It is observed that the anionic keto form of OxyLH(2) is both the red and the yellow-green emitter. Consequently, the effect of Luc conformations on the structural and electronic properties of the Keto-(-1) form are studied. Finally, insights into the Luc-catalyzed light-emitting reaction are derived from the calculations. The multicolor bioluminescence can be explained by interactions of the emitter with active-site molecules, the effects of which on light emission are modulated by the internal dielectric constant of the different conformations. These interactions can suffer also from rearrangement due to entry of external solvent and changes in the protonation state of some amino acid residues and adenosine monophosphate (AMP).

Abstract Firefly luciferase exhibits a color-tuning mechanism based on pH-induced changes in the structure of the active site. These changes increase the polarity of the active site, and thus modulate the intermolecular interactions between the light emitter and active site molecules. In this study, the effects exerted by adenosine monophosphate (AMP), water molecules, and amino acids of Luciola cruciata luciferase active site on the emission wavelength of oxyluciferin were assessed by TD-DFT calculations. The redshift results mainly from decreased interaction of oxyluciferin with AMP and increased interaction of the emitter with a water molecule and Phe249. Breaking of a hydrogen bond between the benzothiazole oxygen atom with formation of a similar bond to the thiazolone oxygen atom is also instrumental.

Abstract Gold nanowire networks (AuNWNs) with average widths of 17.74 nm (AuNWN1) or 23.54 nm (AuNWN2) were synthesized by direct reduction of HAuCl4 with sodium borohydride powder in deep eutectic solvents, such as ethaline or reline, at 40 degrees C. Their width and length were dependent on the type of solvent and the NaBH4/HAuCl4 molar ratio (32 in ethaline and 5.2 in reline). High resolution transmission electron microscopy (HR-TEM) analysis of the gold nanowire networks showed clear lattice fringes of polycrystalline nanopowder of d = 2.36, 2.04, 1.44, and 1.23 angstrom corresponding to the (111), (200), (220), or (311) crystallographic planes of face centered cubic gold. The purified AuNWNs were used as catalysts for the chemical reduction of p-nitroaniline to diaminophenylene with sodium borohydride in aqueous solution. The reaction was monitored in real time by UV-vis spectroscopy. The results show that the reduction process is six times faster in the presence of gold nanowire networks stabilized by urea from the reline (AuNWN2) than in the presence of gold nanowire networks stabilized by ethylene glycol from ethaline (AuNWN1). This is due to a higher number of corners and edges on the gold nanowires synthesized in reline than on those synthesized in ethaline as proven by X-ray diffraction (XRD) patterns recorded for both types of gold nanowire networks. Nevertheless, both types of nanomaterials determined short times of reaction and high conversion of p-nitroaniline to diaminophenylene. These gold nanomaterials represent a new addition to a new generation of catalysts: gold based catalysts.

Abstract A series of molecular dynamics (MD) simulations of different pregelification mixtures representing intermediate stages of the sol gel process were set up to gain insight into the molecular imprinting process in xerogels, namely, to assess the template gel affinity and template self-aggregation. The physical plausibility of the parametrization was checked, confirming the reliability of the simulations. The simulated mixtures differed in the water/methanol ratio (1:3, 5:3, and 5:1) and in the absence/presence of an organic functional group (phenylaminopropyl-) in the silicate species. The simulation results, expressed mainly by the radial distribution functions and respective coordination numbers, showed that the affinity of the template molecule, damascenone (a hydrophobic species), for the gel backbone would not be attained without the tested functional group, phenylaminopropyl-. The affinity, related to the capability to trap the template within the gel network, was derived mostly from the hydrophobic interaction. It was also inferred from MD simulations that lower water contents (methanol-richer mixtures) would facilitate a better dispersion of both the functional group and the template within the final gel, therefore favoring the imprinting process. From the experimental counterparts of the simulated mixtures, a series of imprinted and nonimprinted xerogels were obtained. There was only one xerogel exhibiting the imprinting effect, namely, the one containing the organic group obtained at the lower water/methanol ratio (1:3), in agreement with predictions from the MD simulations. Such congruence demonstrates the ability of MD simulations to provide information regarding the fine aspects of molecular interactions in pregelification mixtures for imprinting.

Abstract Aromaticity is of continuing interest to the organic chemical community. We recently presented a model for the aromaticity of carbocyclic and heterocyclic derivatives of indane and indene, i.e. species defined as benzenes fused to 5-membered rings. The current note extends this model to related derivatives of tetralin and naphthalene, benzenes fused to 6-membered rings. Explicit species discussed herein are: benzopyran, both alpha- and beta-tetralone, coumarin and quinoline.

Abstract One of the major mysteries regarding firefly bioluminescence is its pH-dependent multicolor variation. At basic pH, the emission is on the yellow-green region, whereas at acid pH, the light emission is observed on the red region of the visible spectrum. Theoretical calculations using density functional theory, molecular mechanics, and semiempirical methods were made to investigate the effect exerted by intermolecular forces on light emission, and their modulation by polarity, and the differences in the conformation of the active site at basic and acid pH. Red emission is achieved by the weakening of the interactions of the emitter with ionic and hydrophobic molecules, by the polarization of the benzothiazole microenvironment, by ionization of the enzyme-emitter complex and by changes of the hydrogen bond network. Arg220, Glu346, Ala350, Leu344 and adenosine-5'-monophosphate have blue-shifting effects, while His247, Phe249, Gly341, Thr253, and Ile288 exert a redshifting one. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2654-2663, 2011

Abstract In this paper, the first, second and mean (N-O) bond dissociation enthalpies (BDEs) were derived from the standard (p degrees = 0.1 MPa) molar enthalpies of formation, in the gaseous phase, Delta H-r degrees(m)(g), at T = 298.15 K, of 2,2'-dipyridil N-oxide and 2,2'-dipyridil N,N'-dioxide. These values were calculated from experimental thermodynamic parameters, namely from the standard (p degrees = 0.1 MPa) molar enthalpies of formation, in the crystalline phase, Delta H-f degrees(m)(cr), at T = 298.15 K, obtained from the standard molar enthalpies of combustion, Delta H-c degrees(m), measured by static bomb combustion calorimetry, and from the standard molar enthalpies of sublimation, at T = 298.15 K, determined from Knudsen mass-loss effusion method.

Abstract A study on the molecular structure and energetics of 10,11-dihydro-5H-dibenzo[a,d]cycloheptene (dibenzosuberane) was performed combining experimental calorimetric techniques and high level computational calculations. In the experimental work, the solid phase standard (p degrees = 0.1 MPa) molar enthalpy of formation of 10,11-dihydro-5H-dibenzo[a,d]cycloheptene was derived from its standard massic energy of combustion, at T = 298.15 K, measured by static bomb combustion calorimetry, in oxygen. The respective standard molar enthalpy of sublimation, at T = 298.15 K, was measured by Calvet microcalorimetry enabling the calculation of the standard molar enthalpy of formation (161.4 +/- 3.7) kJ . mol(-1), in the gaseous phase, at T = 298.15 K. In addition, computational calculations were performed using the density functional theory with the B3LYP hybrid functional and extended basis sets in order to obtain the molecular structure of 10,11-dihydro-5H-dibenzo[a,d]cycloheptene and that of related molecules. Estimates of the standard molar enthalpy of formation, in the gaseous phase, at T = 298.15 K, for 10,11-dihydro-5H-dibenzo[a,d]cycloheptene were performed using three different methods: G3(MP2)//B3LYP, MC3BB, and MC3MPW and appropriate homodesmic reactions. Computational estimates are in very good agreement with the experimental value.

Abstract The present work reports an experimental and computational study of the energetics of 1,2-benzisothiazol-3(2H)-one and 1,4-benzothiazin-3(2H, 4H)-one. The standard (p degrees = 0.1 MPa) massic energy of combustion, at T = 298.15K, of each compound was measured by rotating bomb combustion calorimetry, in oxygen that allowed the calculation of the respective standard molar enthalpy of formation, in the condensed phase, at T = 298.15 K. The standard molar enthalpies of sublimation, at T = 298.15 K, were measured by high-temperature Calvet microcalorimetry. From the combination of data obtained by both techniques we have calculated the standard molar enthalpies of formation, in the gaseous phase, at T =298.15 K. In addition, computational calculations were carried using the density functional theory with the B3LYP functional and the 6-31G* basis set and some correlations between structure and energetics were obtained for the keto and enol forms of both compounds. Using the G3(MP2)//B3LYP composite method and various appropriate reactions, the standard molar enthalpies of formation of 1,2-benzisothiazol-3(2H)-one and 1,4-benzothiazin-3(2H, 4H)-one, at T = 298.15 K. were computationally derived and compared with the experimental data. The aromaticity of 1,2-benzisothiazol-3(2H)-one, 1,4-benzothiazin-3(2H, 4H)-one and that of some related species was evaluated by analysis of nucleus independent chemical shifts (NICS).

Abstract In this work, we have determined the experimental standard (p degrees = 0.1 MPa) molar enthalpies of formation, in the gas phase, of 2,6-dimethy1-4-pyrone -(261.5 +/- 2.6) kJ . mol(-1) and 2-ethy1-3-hydroxy-4-pyrone -(420.9 +/- 2.8) kJ . mol(-1). These values were obtained by combining the standard molar enthalpy of formation in the condensed phase, derived from combustion experiments in oxygen, at T = 298.15 K, in a static bomb calorimeter, with the standard molar enthalpy of sublimation, at T = 298.15 K, obtained by Calvet microcalorimetry. Additionally, high-level density functional theory calculations using the B3LYP hybrid exchange-correlation energy functional with extended basis sets have been performed for these two compounds. Good agreement was obtained between the experimental and computational results. Using the same methodology, we calculated the standard molar enthalpy of formation of gaseous 2-methyl-3-hydroxy-4-pyrone.