Reactivity of amino acids and short peptide sequences: identifying bioactive compounds via DFT calculations.

Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds.

Nickel(II)-Catalyzed Formal [3+2] Cycloadditions between Indoles and Donor-Acceptor Cyclopropanes.

This article describes the development of a nickel-catalyzed regio- and diastereoselective formal [3+2] cycloaddition between N-substituted indoles and donor-acceptor cyclopropanes to synthesize cyclopenta[b]indoles. Optimized reaction conditions provide the desired nitrogen-containing cycloadducts in up to 93% yield and dr 8.6:1 with complete regioselectivity. The substrate scope showed high tolerance to various substituted indoles and cyclopropanes, resulting in the synthesis of six new cyclopenta[b]indoles and the isolation of five derivatives previously reported in the literature. In addition, a mechanistic proposal for the reaction was studied through online reaction monitoring by ESI-MS, allowing for the identification of the reactive intermediates in the Ni(II) catalyzed process. X-ray crystallography confirmed the structure and relative endo stereochemistry of the products. This method enables the fast and efficient construction of fused indolines from readily accessible starting materials.

Shedding Light on Highly Emissive 1,4-Dihydropyrrolo[3,2-b]pyrrole Derivatives: Synthesis and Aggregate-Dependent Emission.

Three tetraaryl-1,4-dihydropyrrolo[3,2-b]pyrrole derivatives containing different number of long alkoxy chains (2, 4 and 6) were synthesized, characterized and applied in Organic Light Emitting Diodes (OLEDs). The compounds showed good emission properties with Photoluminescence Quantum Yields (PLQYs) higher than 80 % in solution and 50 % in solid state (thin film). The solvatochromism results revealed a pronounced vibronic emission in methylcyclohexane and toluene, characterized by two distinct sharp emission peaks and a small redshift in the following order: methylcyclohexane>toluene>dichloromethane>tetrahydrofuran>acetonitrile. Also, the compounds formed aggregates with redshifted emission, which can be attributed to excimer formation. This phenomenon was observed in solutions containing 90 % water and with the concentration variation in methylcyclohexane (MCH). Compounds with a greater number of peripheral chains showed the capacity to keep hexagonal columnar organization in films after fast cooling from liquid state. OLEDs fabricated with these compounds showed turn-on voltages lower than 4.0 V, with luminance higher than 1400 cd m-2 , electroluminescence spectra with Full Width at Half Maximum lower than 70 nm and maximum External Quantum Efficiency between 7.2 % and 4.3 %. Overall, this shows that the 1,4-dihydropyrrolo[3,2-b]pyrrole moiety is promising for applications where luminescence is paramount, as in organic light-emitting devices.

To Prevent Oxidative Stress, What about Protoporphyrin IX, Biliverdin, and Bilirubin?

The pigments responsible for eggshell color and patterning in birds are protoporphyrin IX (PP) and biliverdin (BV). Both are involved in the catalytic degradation of the hemo group. Bilirubin (BR), another pigment, is produced when BV is broken down. PP, BV, and BR are free radical scavengers. In this study, we theoretically investigated the antioxidant capacities of these three biological meaningful molecules using Density Functional Theory calculations. First, two antioxidant mechanisms were analyzed for PP, BV, and BR: electron transfer and Hydrogen Atom Transfer. Second, since PP and BV interact with the calcium carbonate matrix of the eggshell, we analyzed the interaction of these pigments with Ca2+ and investigated their chelate compounds. Third, we explored the pro-oxidant properties of PP and BV, which have been proposed for PP when photoactivated to the triplet state, but not for BV. Our results show that PP, BV, and BR are just as good antiradical as other important natural pigments (carotenoids). Neither the antiradical properties of PP and BV nor the UV-visible spectra change due to the presence of calcium, suggesting that the signaling function of these pigments is not affected by the link with Ca2+. Finally, we found that both PP and BV (alone and when linked to Ca2+) can transfer energy from its triplet state to molecular-oxygen-producing singlet oxygen, indicating their pro-oxidant capacity. This investigation answers important questions about the function of these pigments, which may help to understand their influence on the reproductive success of birds.

On the Donor: Acceptor Features for Poly(3-hexylthiophene): TiO2 Quantum Dots Hybrid Materials Obtained via Water Vapor Flow Assisted Sol-Gel Growth.

Here, we present a novel methodology for the preparation of P3HT:TiO2 quantum dots hybrid materials via water vapor flow-assisted sol-gel growth focusing on the structural, optical and electrical property characterization complemented with first-principles calculations as a promising donor-acceptor system for polymer and hybrid solar cells. X-ray diffraction and UV-Vis spectroscopy analyses suggest that the increasing concentration of TiO2 quantum dots leads to the formation of higher amounts of amorphous regions while the crystalline regions exhibited interesting aspect ratio modifications for the P3HT polymer. Raman spectra evidenced the formation of charge carriers in the P3HT with increasing TiO2 quantum dots content and the P3HT:TiO2 50:50 weight ratio resulted in the best composition for optimizing the bulk electronic conductivity, as evidenced by impedance spectroscopy studies. Our DFT calculations performed for a simplified model of the P3HT:TiO2 interface revealed that there is an important contribution of the thiophene carbon atoms states in the conduction band at the Fermi level. Finally, our DFT calculations also reveal an evident gain of electron density at the TiO2 (101) surface while the thiophene rings showed a loss of the electron density, thus confirming that the P3HT:TiO2 junction acts as a good donor-acceptor system. In our opinion, these results not only present a novel methodology for the preparation of P3HT:TiO2 quantum dots hybrid materials but also reveal some key aspects to guide the more rational design of polymer and hybrid solar cells.

Photoinduced Intervalence Charge Transfers: Spectroscopic Tools to Study Fundamental Phenomena and Applications.

The exploitation of excited state chemistry for solar energy conversion or photocatalysis has been continuously increasing, and the needs of a transition to a sustainable human development indicate this trend will continue. In this scenario, the study of mixed valence systems in the excited state offers a unique opportunity to explore excited state electron transfer reactivity, and, in a broader sense, excited state chemistry. This Concept article analyzes recent contributions in the field of photoinduced mixed valence systems, i. e. those where the mixed valence core is absent in the ground state but created upon light absorption. The focus is on the utilization of photoinduced intervalence charge transfer bands, detected via transient absorption spectroscopy, as key tools to study fundamental phenomena like donor/acceptor inversion, hole delocalization, coexistence of excited states and excited state nature, together with applications in molecular electronics.

Global and local charge transfer in electron donor-acceptor complexes.

The formation of electron donor-acceptor complexes is studied with global and local charge transfer partitionings. The 1-parabola model is applied to the bromination reaction of alkenes and the correlations found between the global and local charge transferred with the transition energy of the charge transfer bands and the kinetic rate constants indicate that the nucleophilic attack of alkenes to bromine is the electronic process controlling the reactivity in the formation of the electron donor-acceptor complexes in this reaction. The 2-parabolas model is used in studying the nitrosation of aromatic compounds where colorful electron donor-acceptor complexes are formed. In this case, and like previous applications of the 2-parabolas model, the consistent usage of the model mandates the explicit consideration of reaction conditions in preparing the reactants to have a direction of electron transfer that is consistent with the chemical potential differences. For the nitrosation reaction this implies considering the nitrosonium cation as the charge acceptor. Both applications support that the charge transferred predicted from chemical reactivity models can be used as a scale to measure the nucleophilicity in reactivity trends. Graphical Abstract ᅟ.

PANI Branches onto Donor-Acceptor Copolymers: Synthesis, Characterization and Electroluminescent Properties of New 2D-Materials.

A new series of two-dimensional statistical conjugated polymers based on aniline and 9,9-dihexylfluorene as donor units and benzo- or naphtho-quinoxaline/thiadiazole derivatives as acceptor moieties, possessing PANI segments as side chains, were designed and synthesized. To investigate the effects of the perpendicular PANI branches on the properties of the main chain, the optical, electrochemical, morphological and electroluminescence properties were studied. The 2D materials tend to possess lower molecular weights and to absorb and to emit light red-shifted compared to the trunk 1D-polymers, in the yellow-red region of the visible spectrum. The 1D- and 2D-conjugated polymers present optical band gaps ranging from 2.15⁻2.55 eV, HOMO energy levels between -5.37 and -5.60 eV and LUMO energy levels between -3.02 and -3.29 eV. OLED devices based on these copolymers were fabricated. Although the performances were far from optimal due to the high turn-on voltages for which electroluminescence phenomena occur, a maximum luminescence of 55,100 cd/m² together with a current density of 65 mA/cm² at 18.5 V were recorded for a 2D-copolymer, PAFC6TBQ-PANI.

Small Molecules Derived from Thieno[3,4-c]pyrrole-4,6-dione (TPD) and Their Use in Solution Processed Organic Solar Cells.

In this work, microwave synthesis, chemical, optical and electrochemical characterization of three small organic molecules, TPA-TPD, TPA-PT-TPD and TPA-TT-TPD with donor-acceptor structure and their use in organic photovoltaic cells are reported. For the synthesis, 5-(2-ethylhexyl)-4H-thieno[3,4-c]pyrrole-4,6(5H)-dione was used as electron withdrawing fragment while the triphenylamine was used as electron donating fragment. Molecular electronic geometry and electronic distribution density were established by density functional theory (DFT) calculations and confirmed by optical and chemical characterization. These molecules were employed as electron-donors in the active layer for manufacturing bulk heterojunction organic solar cells, where [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) was used as electron-acceptor. As cathode, Field's metal (FM), an eutectic alloy (Bi/In/Sn: 32.5%, 51%, and 16.5%, respectively) with a melting point above 62 °C, was easily deposited by drop casting under vacuum-free process and at air atmosphere. Prepared devices based on TPA-TPD:PC71BM (1:4 w/w ratio) presented a large VOC = 0.97 V, with JSC = 7.9 mA/cm², a FF = 0.34, then, a power conversion efficiency (PCE) of 2.6%.

Thermally induced anchoring of fullerene in copolymers with Si-bridging atom: Spectroscopic evidences.

We use X-ray photoelectron spectroscopy (XPS), Near-edge X-ray absorption fine structure (NEXAFS), resonant Auger spectroscopy (RAS), Attenuation Total Reflection Infrared (ATR-IR) and Atomic Force Microscopy (AFM) to study the blend between the copolymer poly[2,7-(9,9-bis(2-ethylhexyl)-dibenzosilole)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole] (PSiF-DBT) and the fullerene derivative PC71BM submitted to different annealing temperatures. Those measurements indicate that there is an incidental anchoring of a fullerene derivative to the Si-bridging atoms of a copolymer induced by thermal annealing of the film. Insights about the physical properties of one possible PSiF-DBT/PC71BM anchored structure are obtained using Density Functional Theory calculations. Since the performance of organic photovoltaic based on polymer-fullerene blends depends on the chemical structure of the blend components, the anchoring effect might affect the photovoltaic properties of those devices.

Structural aspects of two α-dihydrazones displaying a complete survey of intermolecular interactions.

The compounds (2'E,2'E)-2,2'-(propane-1,2-diylidene)bis[1-(2-nitrophenyl)hydrazine], C15H14N6O4, (I), and (2Z,3Z)-ethyl 3-[2-(2-nitrophenyl)hydrazinylidene]-2-[2-(4-nitrophenyl)hydrazinylidene]butanoate tetrahydrofuran hemisolvate, C18H18N6O6·0.5C4H8O, (II), are puzzling outliers deviating from a general synthetic route aimed at the preparation of substituted pyrazoles. Possible reasons for this outcome, which is exceptional in an otherwise firmly established synthetic procedure, are analyzed. Compound (I) is unsolvated, while compound (II) crystallizes with a tetrahydrofuran solvent molecule lying on an inversion centre. The ethoxycarbonyl chain of (II), in turn, appears disordered into two equally populated (50%) moieties. In both structures, a plethora of different commonly occurring weak intermolecular interactions [viz. π(phenyl)...π(phenyl), π(C=N)...π(C=N), π(phenyl)...π(C=N), N-H...O and C-H...O] appear responsible for the crystal stability. Much less common are the short O(nitro)...O(nitro) contacts which are observed in the structure of (I), an example of unusual `electron donor-acceptor' (EDA) interactions.

Efectos cooperaiivos en heterotetrámeros (etanol)3-auua / Cooperatve effeccts in (ethanol)3-water heterotetramers / Efeitos cooperativos em heterotetrámeros (etanol)3-água

La teoría de funcionales de la densidad (DFT: B3LYP/6-31+G(d)) fue empleada para la optimización de agregados estables sobre la superficie de energía potencial de los heterotetrámeros (etanol)3-agua. Las energías de tetramerización pueden llegar a valores hasta de -21,00 kcal/mol. Esta energía no se puede obtener considerando solo contribuciones de interacciones entre dos moléculas del agregado, lo cual sugiere la presencia de efectos cooperativos globales (positivos). Tales efectos son reflejados en distancias menores de los puentes de hidrógeno y distancias menores oxígeno-oxígeno, lo mismo que en elongaciones mayores del enlace O-Hen la molécula dadora de protón con un corrimiento hacia el rojo mayor en los heterotetrámeros, comparado con los heterodímeros de etanol-agua y el dímero de etanol. La mayor cooperatividad fue observada en los cuatro puentes de hidrógeno dispuestos en el patrón geométrico cíclico más grande posible, actuando todas las moléculas como aceptoras y dadoras de protón simultáneamente. Un análisis similar al de la caracterización de heterotetrámeros de (etanol)3-agua se llevó a cabo para los heterotetrámeros (metanol)3-agua y tetrámeros de etanol y metanol. La comparación de estos valores mostró que existe una gran similitud entre todos los parámetros analizados para agregados con el mismo patrón geométrico.

Density Functional Theory (DFT: B3LYP/6-31 + G(d)) was used for the optimization of clusters on the potential energy surface of (ethanol)3-water heterotetramers. The tetramerization energies can reach values up to -21.00 kcal/ mol. This energy can not be obtained by just considering the contributions from interactions between two cluster molecules, which suggests of the presence of global cooperative effects (positive). These effects are reflected in smaller hydrogen bond distances and smaller oxygen-oxygen distances, as well as in greater elongations of the O-H proton donor bond with a stronger "red-shift" in the heterotetramers compared to the ethanol-water heterodimers and the ethanol dimer. The largest cooperativity effect was observed in the four hydrogen bonds arranged in the largest possible cyclic geometric pattern, where all the molecules act as proton acceptor and donor simultaneously. A similar analysis to the characterization of (ethanol)3-water heterotetramers was carried out on (methanol)3-water heterotetramers, and ethanol and methanol tetramers, whose comparison showed a great similarity between all evaluated parameters for the clusters with equal geometric pattern.

A teoria de funcionais de densidade (DFT: B3LYP/6-31+G(d)) foi empregada para a otimização de agregados sobre a superfície de energia potencial dos heterotetrâmeros (etanol)3-água. As energias de tetramerização podem alcançar valores de até -21.00 kcal/mol. Esta energia não pode ser obtida por apenas considerando as contribuições das interações entre agregados de duas moléculas, o que sugere a presença global dos cooperativos efeitos (positivos). Tais efeitos são refletidos em menores comprimentos das pontes de hidrogênio e distâncias oxigênio-oxigênio, e também em maiores alongamentos da ligação O-H na molécula doadora de prótons, com um maior "red-shift" associado nos heterotetrâmeros do que nos heterodímeros de etanol-água e no dímero de etanol. A mais alta cooperatividade foi observada com as quatro pontes de hidrogênio dispostas no maior padrão geométrico cíclico possível, atuando simultaneamente todas as moléculas como aceptoras e doadoras de prótons. Uma análise similar ao da caracterização de heterotetrâmeros de (eta-nol)3-água se levou a cabo sobre heterotetrâmeros de (metanol)3-água e metanol, cuja comparação mostrou uma grande similaridade entre todos os parâmetros analisados para agregados com igual padrão geométrico.