Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules

We present a method to automatically plan a robotic process to mix individual combinations of reactants in individual reaction vessels (vials or wells in a multiwell plate), mixing any number of reactants in any desired stoichiometry, and ordering the mixing steps according to an arbitrarily complex treelike assembly protocol. This process enables the combinatorial generation of complete or partial product libraries in individual reaction vessels from intermediates formed in the presence of different sets of reactants. It can produce either libraries of chimeric genes constructed by ligation of fragments from different parent genes or libraries of chemical compounds constructed by convergent synthesis. Given concentrations of the input reactants and desired amounts or volumes of the products, our algorithm, RoboMix, computes the required reactant volumes and the resulting product concentrations, along with volumes and concentrations for all intermediate combinations. It outputs a sequence of robotic liquid transfer steps that ensures that each combination is correctly mixed even when individualized stoichiometries are employed and with any fractional yield for a product. It can also account for waste in robotic liquid handling and residual volume needed to ensure accurate aspiration. We demonstrate the effectiveness of the method in a test mixing dyes with different UV-vis absorption spectra, verifying the desired combinations spectroscopically.     

Understanding the flowing atmospheric-pressure afterglow (FAPA) ambient ionization source through optical means

The advent of ambient desorption/ionization mass spectrometry (ADI-MS) has led to the development of a large number of atmospheric-pressure ionization sources. The largest group of such sources is based on electrical discharges; yet, the desorption and ionization processes that they employ remain largely uncharacterized. Here, the atmospheric-pressure glow discharge (APGD) and afterglow of a helium flowing atmospheric-pressure afterglow (FAPA) ionization source were examined by optical emission spectroscopy. Spatial emission profiles of species created in the APGD and afterglow were recorded under a variety of operating conditions, including discharge current, electrode polarity, and plasma-gas flow rate. From these studies, it was found that an appreciable amount of atmospheric H₂O vapor, N₂, and O₂ diffuses through the hole in the plate electrode into the discharge to become a major source of reagent ions in ADI-MS analyses. Spatially resolved plasma parameters, such as OH rotational temperature (T_rot) and electron number density (n_e), were also measured in the APGD. Maximum values for T_rot and n_e were found to be ~1100 K and ~4 × 10¹⁹ m^–3, respectively, and were both located at the pin cathode. In the afterglow, rotational temperatures from OH and N₂⁺ yielded drastically different values, with OH temperatures matching those obtained from infrared thermography measurements. The higher N₂⁺ temperature is believed to be caused by charge-transfer ionization of N₂ by He₂⁺. These findings are discussed in the context of previously reported ADI-MS analyses with the FAPA source.     

Synthesis, spectroscopy, and reactivity of meso-unsubstituted azuliporphyrins and their heteroanalogues. Oxidative ring contractions to carba-, oxacarba-, thiacarba-, and selenacarbaporphyrins

This paper reports the first detailed study on meso-unsubstituted azuliporphyrins, an important family of porphyrin-like molecules where one of the usual pyrrole rings has been replaced by an azulene subunit. Although the azulene moiety introduces an element of cross-conjugation, zwitterionic resonance contributors with tropylium and carbaporphyrin substructures give azuliporphyrins diatropic character that falls midway between true carbaporphyrins and nonaromatic benziporphyrins. Protonation affords an aromatic dication where this type of resonance interaction is favored due to the associated charge delocalization. Two different "3 + 1" syntheses of meso-unsubstituted azuliporphyrins have been developed. Acid-catalyzed reaction of readily available tripyrrane dicarboxylic acids with 1,3-azulenedicarbaldehyde, followed by oxidation with DDQ or FeCl(3), affords good yields of azuliporphyrins. Alternatively, azulene reacted with acetoxymethylpyrroles (2 equiv) in refluxing acetic acid/2-propanol to give tripyrrane analogues, and following a deprotection step, condensation with a pyrrole dialdehyde in TFA-CH(2)Cl(2) gave the azuliporphyrin system. The latter approach was also used to prepare 23-thia- and 23-selenaazuliporphyrins. However, reaction of the azulitripyrrane with 2,5-furandicarbaldehyde produced a mixture of three oxacarbaporphyrins in moderate yield. The free base forms of thia- and selenaazuliporphyrins both showed intermediary aromatic character that was considerably enhanced upon protonation. The UV-vis spectra for azuliporphyrins and their heteroanalogues showed four bands between 350 and 500 nm and broad absorptions at higher wavelengths. Addition of TFA gave dications that showed porphyrin-like spectra with Soret bands between 460 and 500 nm. In the presence of pyrrolidine, azuliporphyrins and their heteroanalogues undergo nucleophilic attack on the seven-membered ring to give carbaporphyrin adducts. These systems also undergo oxidative rearrangements under basic conditions with t-BuOOH to give benzocarbaporphyrins. The selenaazuliporphyrin afforded two benzoselenacarbaporphyrins, a previously unknown core-modified carbaporphyrin system. The proton NMR spectra for these compounds showed strong diatropic ring currents with the internal CH resonance upfield above -5 ppm, while the meso-protons resonated downfield near 10 ppm. The UV-vis spectra were also porphyrin-like and gave strong Soret bands at ca. 440 nm.     

Experimental and theoretical study of the surface-controlled dissolution of cylindrical particles. Application to solubilization of potassium hydrogen carbonate in hot dimethylformamide

In this paper we present a mathematical model for the surface-controlled dissolution of cylindrical solid particles. This is employed to interpret experimental data published previously for the dissolution of potassium bicarbonate in dimethylformamide at elevated temperatures. Significant kinetic differences in assuming cylindrical rather than spherical shapes are reported with the former representing a closer approximation to the true shape of the particles as revealed by scanning electron microscopy. From the fits of experimental data to the cylindrical model for the surface-controlled dissolution, the dissolution rate constant, k, for the dissolution of KHCO(3) in DMF was found to be (9.6 +/- 1.6) x 10(-9) mol cm(-2) s(-1) at 100 degrees C, and the activation energy for the dissolution was 34.5 kJ mol(-1) over the temperature range of 60-100 degrees C. Comparison between cylindrical and spherical dissolution theory highlights the importance of considering the particle shapes for realistic modeling of surface-controlled dissolution kinetics.     

Creating a Low‐Potential Redox Polymer for Efficient Electroenzymatic CO2 Reduction

Increasing greenhouse gas emissions have resulted in greater motivation to find novel carbon dioxide (CO₂) reduction technologies, where the reduction of CO₂ to valuable chemical commodities is desirable. Molybdenum‐dependent formate dehydrogenase (Mo‐FDH) from Escherichia coli is a metalloenzyme that is able to interconvert formate and CO₂. We describe a low‐potential redox polymer, synthesized by a facile method, that contains cobaltocene (grafted to poly(allylamine), Cc‐PAA) to simultaneously mediate electrons to Mo‐FDH and immobilize Mo‐FDH at the surface of a carbon electrode. The resulting bioelectrode reduces CO₂ to formate with a high Faradaic efficiency of 99±5 % at a mild applied potential of ?0.66 V vs. SHE.     

(+)-Myristinin A, a naturally occurring DNA polymerase beta inhibitor and potent DNA-damaging agent

The first stereoselective total synthesis of the naturally occurring flavan myristinin A has been accomplished, as well as its biochemical evaluation. This synthesis verified the structural assignment and allowed for the determination of the absolute stereochemistry. Myristinin A exhibits biochemical activity both as a potent DNA-damaging agent and DNA polymerase beta inhibitor. Relaxation of supercoiled plasmid DNA was observed at picomolar concentrations, in addition to inhibition of polymerase beta at low micromolar concentrations.