Free energy perturbation and molecular dynamics calculations of copper binding to azurin

Free energy perturbation/molecular dynamics simulations have been carried out on copper/azurin systems calculating the binding affinities of copper (II) ion to azurin either in the native or in the unfolded state. In order to test the validity of the strategy adopted for the calculations and to establish what force field is suitable for these kinds of calculations, three different force fields, AMBER, CVFF, and CFF, have been alternatively used for the calculations and the results have been compared with experimental data obtained by spectroscopic titrations of copper (II)/azurin solutions and denaturation experiments. Our findings have pointed out that only CFF gives satisfactory results, thus providing a reliable tool for copper binding simulations in copper protein.     

Synthesis and spectroscopic and structural characterization of two novel photoactivatable Ca2+ compounds

Two novel photoactivatable Ca(2+) compounds were synthesized to achieve a fast concentration jump of calcium ions in solution; this is of paramount importance for investigating the physiological cellular response. The light-sensitive ligands 4-(2-nitrophenyl)-3,6-dioxaoctane dioic acid (H2L1) and 4-(4,5-dimethoxy-2-nitrophenyl)-3,6-dioxaoctane dioic acid (H2L2) were generated by multistep syntheses, and the corresponding calcium complexes, Ca1 and Ca2, were isolated and characterized. The solution equilibria of H2L1 and H2L2 with Ca2+ were investigated; for both ligands, the formation of a 1:2 Ca2+/ligand species is detected and the complete characterization is presented. The crystal structures of Ca1 and Ca2 were determined. In Ca1 the solid state assembly is attained by a polymeric association of [(CaL1(H2O))2(mu-OH2)] dimeric units. Each calcium ion coordinates four oxygen atoms of one ligand (two ethereal, one carboxylic, and one bridging carboxylic oxygen atom), one water molecule, one bridging water molecule, and a carboxylate group of the other ligand within the dimer. The octacoordination of the metal is completed by an interaction with the adjacent dimeric unit. The crystal structure of the complex Ca2 does not show a polymeric nature, but it is a centrosymmetric dimer. The coordination number of the metal ion is still 8:4 oxygen atoms of the ligand; 3 water molecules; 1 bridging carboxylate group. A preliminary study of the photochemical features of the complexes Ca1 and Ca2 is reported: photoexcitation by a nanosecond pulsed UV laser induces the cleavage of the ligand. This drastically reduces the affinity of the ligand toward Ca2+, which is then released in solution.     

Control of the Intermolecular Coupling of Dibromotetracene on Cu(110) by the Sequential Activation of CBr and CH Bonds

Dibromotetracene molecules are deposited on the Cu(110) surface at room temperature. The complex evolution of this system has been monitored at different temperatures (i.e., 298, 523, 673, and 723 K) by means of a variety of complementary techniques that range from STM and temperature‐programmed desorption (TPD) to high‐resolution X‐ray spectroscopy (XPS) and near‐edge X‐ray absorption fine structure spectroscopy (NEXAFS). State‐of‐the‐art density‐functional calculations were used to determine the chemical processes that take place on the surface. After deposition at room temperature, the organic molecules are transformed into organometallic monomers through debromination and carbon‐radical binding to copper adatoms. Organometallic dimers, trimers, or small oligomers, which present copper‐bridged molecules, are formed by increasing the temperature. Surprisingly, further heating to 673 K causes the formation of elongated chains along the Cu(110) close‐packed rows as a consequence of radical‐site migration to the thermodynamically more stable molecule heads. Finally, massive dehydrogenation occurs at the highest temperature followed by ring condensation to nanographenic patches. This study is a paradigmatic example of how intermolecular coupling can be modulated by the stepwise control of a simple parameter, such as temperature, through a sequence of domino reactions.     

Ocimum campechianum Mill. from Amazonian Ecuador: Chemical Composition and Biological Activities of Extracts and Their Main Constituents (Eugenol and Rosmarinic Acid)

The essential oil (EO), the methanolic (MeOH), and the 70% ethanolic (70% EtOH) extracts obtained from the aerial parts of Ocimum campechianum Mill. (Ecuador) were chemically characterized through gas-chromatography coupled to mass spectrometry detector (GC-MS), high-performance liquid chromatography coupled to diode array-mass spectrometry detectors (HPLC-DAD-MS) and studied for their in vitro biological activity. The radical scavenger activity, performed by spectrophotometric 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assays, highlighted significant IC₅₀ values for the EO, extracts and their main constituents (eugenol and rosmarinic acid). EO (and eugenol) showed noteworthy activity against Pseudomonas syringae pv. syringae and a moderate effect against clinical Candida strains, with possible synergism in association to fluconazole against the latter microorganisms. The extracts and pure molecules exhibited weak cytotoxic activity against the HaCat cell line and no mutagenicity against Salmonella typhimurium TA98 and TA100 strains, giving indication of safety. Instead, EO showed a weak activity against adenocarcinomic human alveolar basal epithelial cells (A549). The above-mentioned evidence leads us to suggest a potential use of the crude drug, extracts, and EO in cosmetic formulation and food supplements as antioxidant agents. In addition, EO may also have a possible application in plant protection and anti-Candida formulations.     

New perspectives in hydrogenase direct electrochemistry

Electrochemical studies of hydrogenases, the biological catalysts of H₂ oxidation and production, have proven wrong the old saying that enzymes do not easily transfer electrons to electrodes in the absence of mediators. Many distinct hydrogenases have actually been directly connected to electrodes or particles, for studying their catalytic mechanism or for designing solar-fuels catalysts. In this review, we list the electrodes that have proved successful for direct electron transfer to hydrogenases, and we discuss recent results which illustrate new directions in this research field: the study of the biosynthesis of FeFe hydrogenase, the electrochemical characterization of non-standard NiFe or FeFe hydrogenases, the general discussion of what makes a catalyst better in one particular direction of the reaction, and the elucidation of the molecular mechanisms of hydrogenase catalysis by combining electrochemistry and theoretical chemistry, spectroscopy or photochemistry. The electrochemical methods described herein will probably prove useful for studying or using other redox enzymes.     

Benzyl Mono-P-Fluorophosphonate and Benzyl Penta-P-Fluorophosphate Anions Are Physiologically Stable Phosphotyrosine Mimetics and Inhibitors of Protein Tyrosine Phosphatases

α,α-Difluoro-benzyl phosphonates are currently the most popular class of phosphotyrosine mimetics. Structurally derived from the natural substrate phosphotyrosine, they constitute classical bioisosteres and have enabled the development of potent inhibitors of protein tyrosine phosphatases (PTP) and phosphotyrosine recognition sites such as SH2 domains. Being dianions bearing two negative charges, phosphonates, however, do not permeate membranes and thus are often inactive in cells and have not been a successful starting point toward therapeutics, yet. In this work, benzyl phosphonates were modified by replacing phosphorus-bound oxygen atoms with phosphorus-bound fluorine atoms. Surprisingly, mono-P-fluorophosphonates were fully stable under physiological conditions, thus enabling the investigation of their mode of action toward PTP. Three alternative scenarios were tested and mono-P-fluorophosphonates were identified as stable reversible PTP1B inhibitors, despite of the loss of one negative charge and the replacement of one oxygen atom as an H-bond donor by fluorine. In extending this replacement strategy, α,α-difluorobenzyl penta-P-fluorophosphates were synthesized and found to be novel phosphotyrosine mimetics with improved affinity to the phosphotyrosine binding site of PTP1B.     

Pushing Up the Size Limit of Boron-doped peri-Acenes: Modular Synthesis and Characterizations

Heteroatom-doped peri-acenes (PAs) have recently attracted considerable attention considering their fascinating physical properties and chemical stability. However, the precise sole addition of boron atoms along the zigzag edges of PAs remains challenging, primarily due to the limited synthetic approach. Herein, we present a novel one-pot modular synthetic strategy toward unprecedented boron-doped PAs (B-PAs), including B-[4,2]PA ( 1 a-2 ), B-[4,3]PA ( 1 b-2 ) and B-[7,2]PA ( 1 c-3 ) derivatives, through efficient intramolecular electrophilic borylation. Their chemical structures are unequivocally confirmed with a combination of mass spectrometry, NMR, and single-crystal X-ray diffraction analysis. Notably, 1 b-2 exhibits an almost planar geometry, whereas 1 a-2 displays a distinctive bowl-like distortion. Furthermore, the optoelectronic properties of this series of B-PAs are thoroughly investigated by UV/Vis absorption and fluorescence spectroscopy combined with DFT calculation. Compared with their parent all-carbon analogs, the obtained B-PAs exhibit high stability, wide energy gaps, and high photoluminescence quantum yields of up to 84 %. This study reveals the exceptional ability of boron doping to finely tune the physicochemical properties of PAs, showcasing their potential applications in optoelectronics.