Intramolecular Hydroamination of Selenoalkynes to 2-Selenylindoles in the Absence of Catalyst.

In this work, a series of 2-chalcogenylindoles was synthesized by an efficient methodology, starting from chalcogenoalkynes, including a previously unreported tellurium indole derivative. For the first time, these 2-substituted chalcogenylindoles were obtained in the absence of metal catalyst or base, under thermal conditions only. In addition, the results described herein represent a methodology with inverse regioselectivity for the chalcogen functionalization of indoles.

Proton transfer in fluorescent secondary amines: synthesis, photophysics, theoretical calculation and preparation of photoactive phosphatidylcholine-based liposomes.

In this article, new fluorescent lipophilic based benzazoles were synthesized from the reaction between photoactive formyl derivatives and aliphatic amines followed by NaBH4 reduction with good yields. The photophysics of the benzazoles was investigated experimentally and theoretically. These compounds present absorption maxima in the UV region (∼339 nm) and fluorescence emission maxima in the cyan to green region with a large Stokes shift (∼175 nm) due to a proton transfer process in the excited state. Two fluorophores were successfully used as a proof of concept to produce stable photoactive liposomes prepared from phosphatidylcholine (PC) and were characterized by zeta potential, small angle X-ray scattering (SAXS), FTIR and UV-Vis experiments (turbidity). The scattering data indicate that the presence of compounds 20 and 23 reduces the overall surface charge of the PC vesicles, possibly due to the partial neutralization of phosphatidic acid and/or phosphatidylinositol phosphate by the amine groups, and they also modify the structural features of the assemblies, leading, in particular, to a reduction in the thickness of the hydrophobic inner segment (tt) of the liposomes. DFT and TD-DFT calculations were performed with the ωB97XD functional. Geometric analyses show that the 2-(2'-hydroxyphenyl)benzazolic planar portion allows an effective ππ* electronic transition. Additionally, the calculations indicate a small energy barrier to proton transfer. The results of the absorption and emission maxima show a slight solvent influence on the wavelengths.

CASPT2, CASSCF and non-adiabatic molecular dynamics (NAMD) studies on the low-lying electronic states of 1H-1,2,3-triazole photolysis.

The photolysis mechanisms of 1H-1,2,3-triazole and 1H-1,2,3-benzotriazole were elucidated by employing multiconfigurational methods (CASSCF and CASPT2). The potential energy curves and crossing points for the low-lying excited states were analyzed. In addition to the static electronic structure calculations, non-adiabatic molecular dynamics (NAMD) was propagated at the CASSCF level using SHARC (Surface Hopping including ARbitrary Couplings) dynamics in order to verify the proposed static picture, thereby understanding the possible reaction paths and the time scale of the photo-induced events. The S1 state for 1H-1,2,3-triazole reached a conical intersection between the S0 and S1 surfaces on a time scale of 100 fs. The emerging picture of the reaction presented here is the rupture of the triazole ring in the S1 state and the relaxation through a conical intersection to the S0 state. On the S0 surface, the triazoles easily extrude N2 and then undergo the hetero-Wolff rearrangement forming ethanimine.

Synthesis of Amino Acid-Derived 1,2,3-Triazoles: Development of a Nontrivial Fluorescent Sensor in Solution for the Enantioselective Sensing of a Carbohydrate and Bovine Serum Albumin Interaction.

A series of amino acid-derived 1,2,3-triazoles presenting the amino acid and the aromatic moieties connected by a triazole-4-carboxylate spacer is discussed in this work. These compounds were achieved in good yields by organocatalytic enamine-azide [3 + 2] cycloadditions. One of the molecules obtained, bearing a 7-chloroquinoline moiety, was photoactive in the UV-violet region and was successfully employed as a probe for substrate-specific enantiomeric sensing using d-(-)-arabinose and l-(+)-arabinose. The potential application as a fluorescent probe to detect protein in phosphate buffer solution was also explored using as model bovine serum albumin (BSA). The studied compounds presented both suppression and association behavior in the presence of BSA. In addition, theoretical calculations were performed at levels ωB97XD/cc-pVDZ and PBE1PBE/6-311+G(d,p) together with the polarizable continuum model to understand the interaction of the molecules with the enantiomers.

A three-state model for the photo-Fries rearrangement.

A three-state model for the photo-Fries rearrangement (PFR) is proposed based on multiconfigurational calculations. It provides a comprehensive mechanistic picture of all steps of the reaction, from the photoabsorption to the final tautomerization. The three states participating in the PFR are an aromatic 1ππ*, which absorbs the radiation; a pre-dissociative 1nπ*, which transfers the energy to the dissociative region; and a 1πσ*, along which dissociation occurs. The transfer from 1ππ* to 1nπ* involves pyramidalization of the carbonyl carbon, while transfer from 1nπ* to 1πσ* takes place through CO stretching. Different products are available after a conical intersection with the ground state. Among them is a recombined radical intermediate, which can yield ortho-PFR products after an intramolecular 1,3-H tunneling. The three-state model is developed for phenyl acetate, the basic prototype for the PFR, and it reconciles the theory with a series of observations from time-resolved spectroscopy. It also delivers a rational way to optimize PFR yields, since, as shown for four different systems, diverse substituents can change the energetic order of the 1ππ* and 1nπ* states, preventing or enhancing the PFR.

A DFT study on the insertion of CO2 into styrene oxide catalyzed by 1-butyl-3-methyl-Imidazolium bromide ionic liquid.

Green systems able to capture or fix CO(2) are becoming more important specially to reduce environmental impacts. In this work, the mechanism of insertion of CO(2) into styrene oxide (STYO) both in the absence and presence of the catalyst 1-butyl-3-methyl-imidazolium bromide (BMIm Br) was investigated through calculations based on density functional theory in the ωB97X-D level. Two different routes were considered and it was shown they are energetically available and compete against each other. For both routes, the rate-determinant step is the ring opening of STYO resulting from the nucleophilic attack of the Br(-) on the C atom from STYO and is associated mainly to the participation of the cation and the anion from the catalyst in the reaction. Reactive indices and noncovalent interaction analysis were used as a tool to investigate this reason. This work allowed a better comprehension of the underlying mechanism and the supplied data provide valuable support for the design of new more efficient ionic liquid catalyst.

Effective enantioselective recognition by steady-state fluorescence spectroscopy: Towards a paradigm shift to optical sensors with unusual chemical architecture.

A series of amino acid-derived 1,2,3-triazoles presenting the amino acid residue and the benzazole fluorophore connected by a triazole-4-carboxylate spacer was studied for enantioselective recognition using only steady-state fluorescence spectroscopy in solution. In this investigation, the optical sensing was performed with D-(-) and L-(+)-Arabinose and (R)-(-) and (S)-(+)-Mandelic acid as chiral analytes. The optical sensors showed specific interactions with each pair of enantiomers, allowing photophysical responses, which were used for their enantioselective recognition. DFT calculations confirm the specific interaction between the fluorophores and the analytes corroborating the observed high enantioselectivity of these compounds with the studied enantiomers. Finally, this study investigated nontrivial sensors for chiral molecules by a mechanism different than turn-on fluorescence and has the potential to broad chiral compounds with fluorophoric units as optical sensors for enantioselective sensing.

Synthesis, characterization, and spectroscopic investigation of benzoxazole conjugated Schiff bases.

Two Schiff bases were synthesized by reaction of 2-(4'-aminophenyl)benzoxazole derivatives with 4-N,N-diethylaminobenzaldehyde. UV-visible (UV-vis) and steady-state fluorescence in solution were applied in order to characterize its photophysical behavior. The Schiff bases present absorption in the UV region with fluorescence emission in the blue-green region, with a large Stokes' shift. The UV-vis data indicates that each dye behaves as two different chromophores in solution in the ground state. The fluorescence emission spectra of the dye 5a show that an intramolecular proton transfer (ESIPT) mechanism takes place in the excited state, whereas a twisted internal charge transfer (TICT) state is observed for the dye 5b. Theoretical calculations were performed in order to study the conformation and polarity of the molecules at their ground and excited electronic states. Using density functional theory (DFT) methods at theoretical levels BLYP/Aug-SV(P) for geometry optimizations and B3LYP/6-311++G(2d,p) for single-point energy evaluations, the calculations indicate that the lowest energy conformations are in all cases nonplanar and that the dipole moments of the excited state relaxed structures are much larger than those of the ground state structures, which corroborates the experimental UV-vis absorption results.

Self-assembly and structural characterization of Echinococcus granulosus antigen B recombinant subunit oligomers.

Echinococcus granulosus antigen B is an oligomeric protein of 120-160 kDa composed by 8-kDa (AgB8) subunits. Here, we demonstrated that the AgB8 recombinant subunits AgB8/1, AgB8/2 and AgB8/3 are able to self-associate into high order homo-oligomers, showing similar properties to that of parasite-produced AgB, making them valuable tools to study AgB structure. Dynamic light scattering, size exclusion chromatography and cross-linking assays revealed approximately 120- to 160-kDa recombinant oligomers, with a tendency to form populations with different aggregation states. Recombinant oligomers showed helical circular dichroism spectra and thermostability similar to those of purified AgB. Cross-linking and limited proteolysis experiments indicated different degrees of stability and compactness between the recombinant oligomers, with the AgB8/3 one showing a more stable and compact structure. We have also built AgB8 subunit structural models in order to predict the surfaces possibly involved in electrostatic and hydrophobic interactions during oligomerization.

Correction: Dipolar vinyl sulfur fluorescent dyes. Synthesis and photophysics of sulfide, sulfoxide and sulfone based D-π-A compounds.

[This corrects the article DOI: 10.1039/C6RA27989A.].

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation.

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.

Free energy of solvation from molecular dynamics simulations for low dielectric solvents.

Using molecular dynamics simulation, we present new results for the free energy of solvation for solvents with low dielectric constants (CCl(4), CHCl(3), benzene). The solvation free energy is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent repulsion and dispersion interactions, and the electrostatic solvation of the solute. The cavitational contribution has been obtained from the Claverie-Pierotti model applied to excluded volumes obtained from distances for nearest neighbor configurations between the solute's atoms and a spherical solvent description. An electrostatic continuum model has been adapted for the computation of the electrostatic free energy of solvation, whereas the van der Waals contribution has been calculated directly from the intermolecular interactions defined by the force fields applied to the simulations. For each solvent, a large set of solute molecules containing most of the chemically interesting functionalities has been treated. The simulated solvation free energies are in very good agreement with experimental data, although a small systematical overestimation of the free energy of solvation indicates a failure of the spherical approach to the solvent molecules in the case of benzene.

New approach to free energy of solvation applying continuum models to molecular dynamics simulation.

A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.