Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms by ab initio molecular dynamics

The electrophilic N‐trifluoromethylation of MeCN with a hypervalent iodine reagent to form a nitrilium ion, that is rapidly trapped by an azole nucleophile, is thought to occur via reductive elimination (RE). A recent study showed that, depending on the solvent representation, the S_N2 is favoured to a different extent over the RE. However, there is a discriminative solvent effect present, which calls for a statistical mechanics approach to fully account for the entropic contributions. In this study, we perform metadynamic simulations for two trifluoromethylation reactions (with N‐ and S‐nucleophiles), showing that the RE mechanism is always favoured in MeCN solution. These computations also indicate that a radical mechanism (single electron transfer) may play an important role. The computational protocol based on accelerated molecular dynamics for the exploration of the free energy surface is transferable and will be applied to similar reactions to investigate other electrophiles on the reagent. Based on the activation parameters determined, this approach also gives insight into the mechanistic details of the trifluoromethylation and shows that these commonly known mechanisms mark the limits within which the reaction proceeds. © 2015 Wiley Periodicals, Inc.     

XPS and AFM characterization of the enzyme glucose oxidase immobilized on SiO(2) surfaces

A process to immobilize the enzyme glucose oxidase on SiO2 surfaces for the realization of integrated microbiosensors was developed. The sample characterization was performed by monitoring, step by step, oxide activation, silanization, linker molecule (glutaraldehyde) deposition, and enzyme immobilization by means of XPS, AFM, and contact angle measurements. The control of the environment during the procedure, to prevent silane polymerization, and the use of oxide activation to obtain a uniform enzyme layer are issues of crucial importance. The correct protocol application gives a uniform layer of the linker molecule and the maximum sample surface coverage. This result is fundamental for maximizing the enzyme bonding sites on the sample surface and achieving the maximum surface coverage. Thin SiO2 layers thermally grown on a Si substrate were used. The XPS Si 2p signal of the substrate was monitored during immobilization. Such a signal is not completely shielded by the thin oxide layer and it is fully suppressed after the completion of the whole protocol. A power spectral density analysis on the AFM measurements showed the crucial role of both the oxide activation and the intermediate steps (silanization and linker molecule deposition) to obtain uniform immobilized enzyme coverage. Finally, enzymatic activity measurements confirmed the suitability of the optimized protocol.     

Naphthochromenones: Organic Bimodal Photocatalysts Engaging in Both Oxidative and Reductive Quenching Processes

Twelve naphthochromenone photocatalysts (PCs) were synthesized on gram scale. They absorb across the UV/Vis range and feature an extremely wide redox window (up to 3.22 eV) that is accessible using simple visible light irradiation sources (CFL or LED). Their excited‐state redox potentials, PC*/PC^.? (up to 1.65 V) and PC^.+/PC* (up to ?1.77 V vs. SCE), are such that these novel PCs can engage in both oxidative and reductive quenching mechanisms with strong thermodynamic requirements. The potential of these bimodal PCs was benchmarked in synthetically relevant photocatalytic processes with extreme thermodynamic requirements. Their ability to efficiently catalyze mechanistically opposite oxidative/reductive photoreactions is a unique feature of these organic photocatalysts, thus representing a decisive advance towards generality, sustainability, and cost efficiency in photocatalysis.     

Comparison of Penta and Tetra-pyridyl Cobalt-based Catalysts for Water Reduction: H2 Production Cycle,Solvent Response and Reduction Free Energy

Understanding water reduction towards H₂ generation is crucial to overcome today's renewable energy obstacles. Previous studies have shown the superior H₂ production performances of Cobalt based penta-pyridyl (CoaPPy) and tetra-pyridyl (CoaTPy) complexes in solution. We investigate H₂ production cycles of CoaPPy and CoaTPy complexes immersed in water solution by means of Ab-initio Molecular Dynamics and Density Functional Theory. We monitor dynamic properties of the systems, solvent response and structural changes occurring in the catalysts, by simulating all intermediate steps of the H₂ production cycle. Reduction free energies and reorganization energies are calculated. Our results show that, following the first electron injection, H₂ production proceeds with the singlet spin state. Following the first electron insertion, we observe a significant rearrangement of the hydrogen bonding network in the first solvation shell. The cobalt center turns out to be more accessible for the surrounding water molecules in the case of CoaTPy at all the intermediate steps, which explains its higher catalytic performance over CoaPPy. Following the first reduction reaction, a larger gain in reduction free energy is estimated for CoaTPy with respect to CoaPPy, with a difference of 0.14 eV, in line with the experiments. For the second reduction, instead, CoaPPy shows more negative reduction potential, by 0.41 eV.     

(P-Bis(pentafluorophenyl) substituted) PCP-pincer Ru(II) complexes: A theoretical study of the molecular structure and electronic properties

The differences between the molecular structures of the PCP-pincer complex [RuCl{C₆H₃(CH₂P(C₆H₅)₂)₂-2,6}(PPh₃)] ([RuCl(PCP^H)(PPh₃)], 1) and its tetrakis-pentafluorophenyl substituted analogue [RuCl{C₆H₃(CH₂P(C₆F₅)₂)₂-2,6}(PPh₃)] ([RuCl(PCP^F20)(PPh₃)], 2) have been rationalised by performing calculations on the cations [Ru(PCP^H)(PPh₃)]⁺ (1cat) and [Ru(PCP^F20)(PPh₃)]⁺ (2cat). The molecular interactions between the chloride ligand and the axial rings, as found in 1 and 2, respectively, have been studied computationally in the model systems [(C₆X₅PH₂)₂Cl⁻] (X = H, F). The calculations on 2cat show that in 2 it is most likely the attractive electrostatic interaction between the chloride ligand and the fluorinated phenyl rings that forces the C_ipso atom to occupy an axial position rather than an equatorial one in the observed (X-ray of 2) square pyramidal arrangement. In 1, however, repulsive steric hindrance forces the PPh₃ ligand to take the apical position. The applicability of the TD-DFT method for the calculation of the electronic spectra of the PCP-pincer compounds 1 and 2 has been tested. The results indicate that the excitation energies calculated for both complexes are in a reasonable agreement with the experimental absorption maxima. However, for 1, all the calculated transition energies are underestimated.     

Separation of oligonucleotides and DNA fragments by capillary electrophoresis in dynamically and permanently coated capillaries,using a copolymer of acrylamide and β-D-glucopyranoside as a new low viscosity matrix with high sieving capacity

New copolymers of acrylamide and β-D -glucopyranoside were synthesized and characterized. The different reactivity of the two monomers towards radical polymerization meant we could control the growth of the polymer chains whose length was inversely related to the number of glucose residues incorporated in the copolymers. The properties of these polymers were investigated in the separation of oligonucleotides and double-stranded DNA by capillary electrophoresis (CE) in coated and uncoated capillaries. The new copolymers were a suitable matrix for CE due to their high-resolving capacity and low viscosity. We also looked into the advantages of a new method of dynamic suppression of electroosmotic flow based on the addition of small amounts (0.03–0.05%) of dimethylacrylamide to the sieving and to the running buffer. A complete test was run on the reproducibility and efficiency of separations carried out in a permanently and dynamically coated capillary, and the advantages and disadvantages of the two methods were compared.     

Efficient organic monoliths prepared by γ-radiation induced polymerization in the evaluation of histone deacetylase inhibitors by capillary(nano)-high performance liquid chromatography and ion trap mass spectrometry

New monolithic HPLC columns were prepared by γ-radiation-triggered polymerization of hexyl methacrylate and ethylene glycol dimethacrylate monomers in the presence of porogenic solvents. Polymerization was carried out directly within capillary (250-200 μm I.D.) and nano (100-75 μm I.D.) fused-silica tubes yielding highly efficient columns for cap(nano)-LC applications. The columns were applied in the complete separation of core (H2A, H2B, H3, and H4) and linker (H1) histones under gradient elution with UV and/or electrospray ionization (ESI) ion trap mass spectrometry (MS) detections. Large selectivity towards H1, H2A-1, H2A-2, H2B, H3-1, H3-2 and H4 histones and complete separation were obtained within 8 min time windows, using fast gradients and very high linear flow velocities, up to 11 mm/s for high throughput applications. The method developed was the basis of a simple and efficient protocol for the evaluation of post-translational modifications (PTMs) of histones from NCI-H460 human non-small-cell lung cancer (NSCLC) and HCT-116 human colorectal carcinoma cells. The study was extended to monitoring the level of histone acetylation after inhibition of Histone DeACetylase (HDAC) enzymes with suberoylanilide hydroxamic acid (SAHA), the first HDAC inhibitor approved by the FDA for cancer therapy. Attractive features of our cap(nano)-LC/MS approach are the short analysis time, the minute amount of sample required to complete the whole procedure and the stability of the polymethacrylate-based columns. A lab-made software package ClustMass was ad hoc developed and used to elaborate deconvoluted mass spectral data (aligning, averaging, clustering) and calculate the potency of HDAC inhibitors, expressed through a Relative half maximal Inhibitory Concentration parameter, namely R_IC(50) and an averaged acetylation degree.     

Solvent effects on the complexation of 1-alkanols by parent and modified cyclodextrins. Calorimetric studies at 298 K

The formation of complexes of parent and alkylated cyclodextrins (CDs) with 1-heptanol and 1-octanol has been studied calorimetrically at 298 K in water and in concentrated aqueous solutions of urea. The forces involved in the association process are discussed in the light of the signs and values of the thermodynamic parameters obtained: association enthalpy, binding constant, Gibbs free energy, and entropy. It was inferred that: (i) in water, the formation of complexes for parent and substituted α-cyclodextrins (αCDs) is determined by enthalpy. For parent and substituted β-cyclodextrins (βCDs), instead, hydrophobic interactions are the prevailing forces determining complexation, as indicated by the small and negative or positive enthalpies and by the high and positive entropies. (ii) In urea, hydrophilic interactions are attenuated. The formation of complexes with alkylated CDs does not occur. (iii) The analysis of the thermodynamic properties confirms that inclusion is a process dominated by hydration phenomena. Modifications experienced by the solvent water in the hydration shells of the interacting substances upon association determine the formation of the complexes.     

New heterocyclic structures. [1,3]Thiazino[3,2-a]purine and [1,2,3]triazolo[4,5-d][1,3]thiazino[3,2-a]pyrimidine

Derivatives of two new molecular structures, namely, [1,3]thiazino[3,2-a]purine and [1,2,3]triazolo[4,5-d]-[1,3]thiazino[3,2-a]pyrimidine, were synthesized together with other heterocyclic compounds. Retrosynthetic analysis of their molecular skeletons suggested a simple way of obtaining 3,4-dihydro-7,8-diamino-2H,6H-pyrimido[2,1-b][1,3]thiazin-6-one, which is a useful intermediate for their synthesis. This intermediate and the thiazole homologue were obtained directly by reaction of 5,6-diamino-2,3-dihydro-2-thioxo-4(lH)-pyrimidi-none with 1,3- or 1,2-dibromoalkane, respectively.     

Diorganoruthenium complexes incorporating noninnocent [C(6)H(2)(CH(2)ER(2))(2)-3,5](2)(2-) (E = N, P) bis-pincer bridging ligands: synthesis, spectroelectrochemistry, and DFT studies

The dinuclear complex [(tpy)RuII(PCP-PCP)RuII(tpy)]Cl2 (bridging PCP-PCP = 3,3',5,5'-tetrakis(diphenylphosphinomethyl)biphenyl, [C6H2(CH2PPh2)2-3,5]22-) was prepared via a transcyclometalation reaction of the bis-pincer ligand [PC(H)P-PC(H)P] and the Ru(II) precursor [Ru(NCN)(tpy)]Cl (NCN = [C6H3(CH2NMe2)2-2,6]-) followed by a reaction with 2,2':6',2' '-terpyridine (tpy). Electrochemical and spectroscopic properties of [(tpy)RuII(PCP-PCP)RuII(tpy)]Cl2 are compared with those of the closely related [(tpy)RuII(NCN-NCN)RuII(tpy)](PF6)2 (NCN-NCN = [C6H2(CH2NMe2)2-3,5]22-) obtained by two-electron reduction of [(tpy)RuIII(NCN-NCN)RuIII(tpy)](PF6)4. The molecular structure of the latter complex has been determined by single-crystal X-ray structure determination. One-electron reduction of [(tpy)RuIII(NCN-NCN)RuIII(tpy)](PF6)4 and one-electron oxidation of [(tpy)RuII(PCP-PCP)RuII(tpy)]Cl2 yielded the mixed-valence species [(tpy)RuIII(NCN-NCN)RuII(tpy)]3+ and [(tpy)RuIII(PCP-PCP)RuII(tpy)]3+, respectively. The comproportionation equilibrium constants Kc (900 and 748 for [(tpy)RuIII(NCN-NCN)RuIII(tpy)]4+ and [(tpy)RuII(PCP-PCP)RuII(tpy)]2+, respectively) determined from cyclic voltammetric data reveal comparable stability of the [RuIII-RuII] state of both complexes. Spectroelectrochemical measurements and near-infrared (NIR) spectroscopy were employed to further characterize the different redox states with special focus on the mixed-valence species and their NIR bands. Analysis of these bands in the framework of Hush theory indicates that the mixed-valence complexes [(tpy)RuIII(PCP-PCP)RuII(tpy)]3+ and [(tpy)RuIII(NCN-NCN)RuII(tpy)]3+ belong to strongly coupled borderline Class II/Class III and intrinsically coupled Class III systems, respectively. Preliminary DFT calculations suggest that extensive delocalization of the spin density over the metal centers and the bridging ligand exists. TD-DFT calculations then suggested a substantial MLCT character of the NIR electronic transitions. The results obtained in this study point to a decreased metal-metal electronic interaction accommodated by the double-cyclometalated bis-pincer bridge when strong sigma-donor NMe2 groups are replaced by weak sigma-donor, pi-acceptor PPh2 groups.