Enzymatically synthesized polyaniline film deposition studied by simultaneous open circuit potential and electrochemical quartz crystal microbalance measurements

The chemical and enzymatic deposition of polyaniline (PANI) films by in situ polymerization was studied and the resulting films were characterized. The film formation and polymerization processes were simultaneously monitored by the evolution of the open circuit potential and quartz-crystal microbalance measurements. Different substrates, such as Indium-Tin oxide electrodes and gold-coated quartz-crystal electrodes were used as substrates for PANI deposition. Electroactive PANI films were successfully deposited by in situ enzymatic polymerization at low oxidation potential. The electrogravimetric response of the enzymatically deposited PANI film was studied by cyclic voltammetry in monomer-free acidic medium. The morphology of the films was observed by scanning electron microscopy, revealing a granular structure in enzymatically deposited PANI. The PANI films were also characterized by thermogravimetric analysis, electrochemical impedance spectroscopy, and X-ray photoelectron and Fourier-transformed infrared spectroscopy. The simultaneous use of quartz crystal microbalance and open circuit potential is presented as a very useful technique to monitor enzymatic reactions involving oxidoreductases.     

Surfactant (bi)layers on gold nanorods

Gold nanorods in aqueous solution are generally surrounded by surfactants or capping agents. This is crucial for anisotropic growth during synthesis and for their final stability in solution. When CTAB is used, a bilayer has been evidenced from analytical methods even though no direct morphological characterization of the precise thickness and compactness has been reported. The type of surfactant layer is also relevant to understand the marked difference in further self-assembling properties of gold nanorods as experienced using 16-EO(1)-16 gemini surfactant instead of CTAB. To obtain a direct measure of the thickness of the surfactant layer on gold nanorods synthesized by the seeded growth method, we coupled TEM, SAXS, and SANS experiments for the two different cases, CTAB and gemini 16-EO(1)-16. Despite the strong residual signal from micelles in excess, it can be concluded that the thickness is imposed by the chain length of the surfactant and corresponds to a bilayer with partial interdigitation.     

Thermoresponsive hydrogels from symmetrical triblock copolymers poly(styrene-block-(methoxy diethylene glycol acrylate)-block-styrene)

A series of symmetrical, thermo-responsive triblock copolymers was prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization, and studied in aqueous solution with respect to their ability to form hydrogels. Triblock copolymers were composed of two identical, permanently hydrophobic outer blocks, made of low molar mass polystyrene, and of a hydrophilic inner block of variable length, consisting of poly(methoxy diethylene glycol acrylate) PMDEGA. The polymers exhibited a LCST-type phase transition in the range of 20-40 °C, which markedly depended on molar mass and concentration. Accordingly, the triblock copolymers behaved as amphiphiles at low temperatures, but became water-insoluble at high temperatures. The temperature dependent self-assembly of the amphiphilic block copolymers in aqueous solution was studied by turbidimetry and rheology at concentrations up to 30 wt %, to elucidate the impact of the inner thermoresponsive block on the gel properties. Additionally, small-angle X-ray scattering (SAXS) was performed to access the structural changes in the gel with temperature. For all polymers a gel phase was obtained at low temperatures, which underwent a gel-sol transition at intermediate temperatures, well below the cloud point where phase separation occurred. With increasing length of the PMDEGA inner block, the gel-sol transition shifts to markedly lower concentrations, as well as to higher transition temperatures. For the longest PMDEGA block studied (DP(n) about 450), gels had already formed at 3.5 wt % at low temperatures. The gel-sol transition of the hydrogels and the LCST-type phase transition of the hydrophilic inner block were found to be independent of each other.     

On-chip electrochemical detection of CdS quantum dots using normal and multiple recycling flow through modes

A flexible hybrid polydimethylsiloxane (PDMS)-polycarbonate (PC) microfluidic chip with integrated screen printed electrodes (SPE) was fabricated and applied for electrochemical quantum dots (QDs) detection. The developed device combines the advantages of flexible microfluidic chips, such as their low cost, the possibility to be disposable and amenable to mass production, with the advantages of electrochemistry for its facility of integration and the possibility to miniaturize the analytical device. Due to the interest in biosensing applications in general and particularly the great demand for labelling alternatives in affinity biosensors, the electrochemistry of cadmium sulfide quantum dots (CdS QDs) is evaluated. Square wave anodic stripping voltammetry (SWASV) is the technique used due to its sensitivity and low detection limits that can be achieved. The electrochemical as well as the microfluidic parameters of the developed system are optimized. The detection of CdS QDs in the range between 50 to 8000 ng mL(-1) with a sensitivity of 0.0009 μA/(ng mL(-1)) has been achieved. In addition to the single in-chip flow through measurements, the design of a recirculation system with the aim of achieving lower detection limits using reduced volumes (25 μL) of sample was proposed as a proof-of-concept.     

Arylsulfonylacetylenes as alkynylating reagents of Csp2-H bonds activated with lithium bases

Chameleon: a new strategy for the synthesis of a wide variety of alkynyl derivatives by the reaction of substituted arylsulfonylacetylenes with organolithium species is described. The high yields, the simplicity of the experimental procedure, the broad scope of this reaction, and the formation of C(sp)-C(sp2) bonds without using transition metals are the main features of this methodology.     

Laboratory studies of CHF2CF2CH2OH and CF3CF2CH2OH: UV and IR absorption cross sections and OH rate coefficients between 263 and 358 K

Fluorinated alcohols, such as 2,2,3,3-tetrafluoropropanol (TFPO, CHF(2)CF(2)CH(2)OH) and 2,2,3,3,3-pentafluoropropanol (PFPO, CF(3)CF(2)CH(2)OH), can be potential replacements of hydrofluorocarbons with large global warming potentials, GWPs. IR absorption cross sections for TFPO and PFPO were determined between 4000 and 500 cm(-1) at 298 K. Integrated absorption cross sections (S(int), base e) in the 4000-600 cm(-1) range are (1.92 ± 0.34) × 10(-16) cm(2) molecule(-1) cm(-1) and (2.05 ± 0.50) × 10(-16) cm(2) molecule(-1) cm(-1) for TFPO and PFPO, respectively. Uncertainties are at a 95% confidence level. Ultraviolet absorption spectra were also recorded between 195 and 360 nm at 298 K. In the actinic region (λ > 290 nm), an upper limit of 10(-23) cm(2) molecule(-1) for the absorption cross sections (σ(λ)) was reported. Photolysis in the troposphere is therefore expected to be a negligible loss for these fluoropropanols. In addition, absolute rate coefficients for the reaction of OH radicals with CHF(2)CF(2)CH(2)OH (k(1)) and CF(3)CF(2)CH(2)OH (k(2)) were determined as a function of temperature (T = 263-358 K) by the pulsed laser photolysis/laser induced fluorescence (PLP-LIF) technique. At room temperature, the average values obtained were k(1) = (1.85 ± 0.07) × 10(-13) cm(3) molecule(-1) s(-1) and k(2) = (1.19 ± 0.03) × 10(-13) cm(3) molecule(-1) s(-1). The observed temperature dependence of k(1)(T) and k(2)(T) is described by the following expressions: (1.35 ± 0.23) × 10(-12) exp{-(605 ± 54)/T} and (1.36 ± 0.19) × 10(-12) exp{-(730 ± 43)/T} cm(3) molecule(-1) s(-1), respectively. Since photolysis of TFPO and PFPO in the actinic region is negligible, the tropospheric lifetime (τ) of these species can be approximated by the lifetime due to the homogeneous reaction with OH radicals. Global values of τ(OH) were estimated to be of 3 and 4 months for TFPO and PFPO, respectively. GWPs relative to CO(2) at a time horizon of 500 years were calculated to be 8 and 12 for TFPO and PFPO, respectively. Despite the higher GWP relative to CO(2), these species are not expected to significantly contribute to the greenhouse effect in the next decades since they are short-lived species and will not accumulate in the troposphere even as their emissions grow up.     

Potent Antimalarial 1,2,4‐Trioxanes through Perhydrolysis of Epoxides

Perhydrolysis of a sterically congested multifunctional epoxide was achieved in ethereal H₂O₂ with the aid of a recently developed Mo catalyst. The resulting hydroperoxide cyclized to give a 1,2,4‐trioxane, which could be readily elaborated into qinghaosu and a range of novel analogues. Some of the compounds with two such trioxane moieties showed in vitro antimalarial activity comparable to or even better than that of artesunate or chloroquine.     

Three‐Dimensional Architectures Incorporating Stereoregular Donor–Acceptor Stacks

We report the synthesis of two [2]catenane‐containing struts that are composed of a tetracationic cyclophane (TC⁴⁺) encircling a 1,5‐dioxynaphthalene (DNP)‐based crown ether, which bears two terphenylene arms. The TC⁴⁺ rings comprise either 1) two bipyridinium (BIPY²⁺) units or 2) a BIPY²⁺ and a diazapyrenium (DAP²⁺) unit. These degenerate and nondegenerate catenanes were reacted in the presence of Cu(NO₃)₂?2.5 H₂O to yield Cu‐paddlewheel‐based MOF‐1050 and MOF‐1051. The solid‐state structures of these MOFs reveal that the metal clusters serve to join the heptaphenylene struts into grid‐like 2D networks. These 2D sheets are then held together by infinite donor–acceptor stacks involving the [2]catenanes to produce interpenetrated 3D architectures. As a consequence of the planar chirality associated with both the DNP and hydroquinone (HQ) units present in the crown ether, each catenane can exist as four stereoisomers. In the case of the nondegenerate (bistable) catenane, the situation is further complicated by the presence of translational isomers. Upon crystallization, however, only two of the four possible stereoisomers—namely, the enantiomeric RR and SS forms—are observed in the crystals. An additional element of co‐conformational selectivity is present in MOF‐1051 as a consequence of the substitution of one of the BIPY²⁺ units by a DAP²⁺ unit: only the translational isomer in which the DAP²⁺ unit is encircled by the crown ether is observed. The overall topologies of MOF‐1050 and MOF‐1051, and the selective formation of stereoisomers and translational isomers during the kinetically driven crystallization, provide evidence that weak noncovalent bonding interactions play a significant role in the assembly of these extended (super)structures.     

Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.