RCARM: Reaction classification using automated reaction mapping

Detailed chemical kinetic modeling of gas‐phase reactions can result in automatically generated mechanisms that contain thousands of reactions. In this paper, we describe the development of a rule‐based expert system tool that organizes these reactions into classes such as hydrogen abstraction and beta scission. We have developed 29 simple classification rules, 20 complex (well‐skipping) classification rules, and four second‐stage classification rules. This greatly simplifies the task of the chemical kineticist who wishes to verify, analyze, and gain insights into the reactions comprising the mechanism. This system, which is based on the automated identification of the bonds that break and form in a chemical reaction (the reaction mapping problem), is used to classify reactions in three different mechanisms. © 2012 Wiley Periodicals, Inc. Int J Chem Kinet 45: 125–139, 2013     

Synthesis and thin‐film orientation of poly(styrene‐block‐trimethylsilylisoprene)

The successful synthesis, characterization, and directed self‐assembly of a silicon‐containing block copolymer, poly(styrene‐block‐trimethylsilylisoprene) (P(S‐b‐TMSI)), which has much higher oxygen etch contrast than the de facto standard, poly(styrene‐block‐methyl methacrylate) is reported. A Sakurai, Grignard‐type coupling reaction provided the key monomer in good yield. Living anionic polymerization was employed to prepare the block copolymer, which has very low polydispersity. P(S‐b‐TMSI) was successfully ordered and oriented by directed self‐assembly. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

On‐bead combinatorial synthesis and imaging of europium(III)‐based paraCEST agents aids in identification of chemical features that enhance CEST sensitivity

The rate of water exchange between the inner sphere of a paramagnetic ion and bulk water is an important parameter in determining the magnitude of the chemical exchange saturation transfer signal from paramagnetic CEST agents (paraCEST). This is governed by various geometric, steric and ligand field factors created by macrocyclic ligands surrounding the paramagnetic metal ion. Our previous on‐bead combinatorial studies of di‐peptoid–europium(III)–1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA)–tetraamide complexes revealed that negatively charged groups in the immediate vicinity of the metal center strongly enhances the CEST signal. Here, we report a solid phase synthesis and on‐bead imaging of 76 new DOTA derivatives that are developed by coupling with a single residue onto each of the three arms of a DOTA–tetraamide scaffold attached to resin beads. This single residue predominantly carries negatively charged groups blended with various physico‐chemical characteristics. We found that non‐bulky negatively charged groups are best suited at the immediate vicinity of the metal ion, while positive, bulky and halogen containing moieties suppress the CEST signal. Copyright © 2017 John Wiley & Sons, Ltd.     

A Reactivity-Driven Approach to the Discovery and Development of Gold-Catalyzed Organic Reactions

Approaches to research in organic chemistry are as numerous as the reactions they describe. In this account, we describe our reactivity-based approach. Using our work in the area of gold-catalysis as a background, we discuss how a focus on reaction mechanism and reactivity paradigms can lead to the rapid discovery of new synthetic tools.     

Stereospecificity of acetylene reduction catalyzed by nitrogenase.

In addition to catalyzing the reduction of dinitrogen to ammonia, the metalloenzyme nitrogenase catalyzes the reduction of a number of alternative substrates, including acetylene (C(2)H(2)) to ethylene (C(2)H(4)) and, in certain cases, to ethane (C(2)H(6)). The stereochemistry of proton addition for C(2)D(2) reduction to C(2)D(2)H(2) catalyzed by the Mo-dependent nitrogenase has been used to probe substrate binding and proton addition mechanisms. In the present work, the C(2)D(2) reduction stereospecificity of altered MoFe proteins having amino acid substitutions within the active site FeMo-cofactor environment was examined by Fourier transform infrared (FTIR) spectroscopy. Altered MoFe proteins examined included those having the alpha-subunit 96(Arg) residue substituted by Gln, Leu, or Ala, the alpha-subunit 69(Gly) residue substituted by Ser, and the alpha-subunit 195(His) residue substituted by Asn. The stereochemistry of proton addition to C(2)D(2) does not correlate with the measured K(m) values for C(2)H(2) reduction, or with the ability of the enzyme to reduce C(2)H(2) by four electrons to yield C(2)H(6). Instead, the electron flux through nitrogenase was observed to significantly influence the ratio of cis- to trans-1,2-C(2)H(2)D(2) formed. Finally, the product distribution observed for reduction of C(2)H(2) in D(2)O is not consistent with an earlier proposed enzyme-bound intermediate. An alternative model that accounts for the stereochemistry of C(2)H(2) reduction by nitrogenase based on a branched reaction pathway and an enzyme-bound eta(2)-vinyl intermediate is proposed.     

Evaluation of pI Marker Sources for cIEF Characterization of a Therapeutic Antibody

Isoelectric point markers from five sources have been compared and evaluated to replace the Bio-Rad brand markers (pI 6.2 and 7.5) used for pI determination of the charge isoforms of a therapeutic monoclonal cancer antibody (pI range of 6.3–7.2) in a capillary isoelectric focusing (cIEF) identity assay. Two of the five sources were found to be optimal replacement markers for the antibody molecule. Isoelectric point markers manufactured by Fluka (pI 5.5 and 7.6) and synthetic peptide markers prepared in-house (pI 5.91 and 7.27) produced antibody cIEF profiles, pI values, and percent corrected peak areas most comparable to the Bio-Rad marker results. Marker robustness was demonstrated by evaluating the markers using different CE instruments, marker lots, and capillary lots, as well as evaluating the markers at multiple Amgen sites.     

Studies on the drift properties and spatial resolution using a microMEGAS-equipped time projection chamber

R&D studies on the performance as well as on the gas properties of the microMEGAS-based time projection chamber with standard readout were carried out in June 2005 using 4 GeV/c pion beam in a magnetic field from 0 to 1 T at the proton synchrotron beam line at KEK, Japan. Analysis of the electron drift velocity, diffusion constant and point resolution of padrow measurement for MicroMEGAS TPC filled with 95% argon and 5% isobutane gas are presented. The underlying physical mechanism which determines the optimal TPC performance are briefly discussed. Preliminary measurements of gas properties and spatial resolution in close agreement with the analytical calculation and MAGBOLTZ simulation are summarized and presented in this paper.