Substrate distortion and the catalytic reaction mechanism of 5-carboxyvanillate decarboxylase

5-Carboxyvanillate decarboxylase (LigW) catalyzes the conversion of 5-carboxyvanillate to vanillate in the biochemical pathway for the degradation of lignin. This enzyme was shown to require Mn2+ for catalytic activity and the kinetic constants for the decarboxylation of 5-carboxyvanillate by the enzymes from Sphingomonas paucimobilis SYK-6 (kcat = 2.2 s–1 and kcat/Km = 4.0 × 104 M–1 s–1) and Novosphingobium aromaticivorans (kcat = 27 s–1 and kcat/Km = 1.1 × 105 M–1 s–1) were determined. The three-dimensional structures of both enzymes were determined in the presence and absence of ligands bound in the active site. The structure of LigW from N. aromaticivorans, bound with the substrate analogue, 5-nitrovanillate (Kd = 5.0 nM), was determined to a resolution of 1.07 Å. The structure of this complex shows a remarkable enzyme-induced distortion of the nitro-substituent out of the plane of the phenyl ring by approximately 23°. A chemical reaction mechanism for the decarboxylation of 5-carboxyvanillate by LigW was proposed on the basis of the high resolution X-ray structures determined in the presence ligands bound in the active site, mutation of active site residues, and the magnitude of the product isotope effect determined in a mixture of H2O and D2O. In the proposed reaction mechanism the enzyme facilitates the transfer of a proton to C5 of the substrate prior to the decarboxylation step

Catalyst composition and impurity-dependent kinetics of nanowire heteroepitaxy.

The mechanisms and kinetics of axial Ge-Si nanowire heteroepitaxial growth based on the tailoring of the Au catalyst composition via Ga alloying are studied by environmental transmission electron microscopy combined with systematic ex situ CVD calibrations. The morphology of the Ge-Si heterojunction, in particular, the extent of a local, asymmetric increase in nanowire diameter, is found to depend on the Ga composition of the catalyst, on the TMGa precursor exposure temperature, and on the presence of dopants. To rationalize the findings, a general nucleation-based model for nanowire heteroepitaxy is established which is anticipated to be relevant to a wide range of material systems and device-enabling heterostructures.S.H. acknowledges funding from ERC grant InsituNANO (No. 279342). A.D.G. acknowledges funding from the Marshall Aid Commemoration Commission and the National Science Foundation. C.D. acknowledges funding from the Royal Society. A portion of the research was also performed using EMSL, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. DOE under Contract DE-AC05-76RL01830. We gratefully acknowledge the use of facilities within the LeRoy Eyring Center for Solid State Science at Arizona State University. This work was performed in part at CINT, a U.S. DOE, Office of Science User Facility. The research was funded in part by the Laboratory Directed Research and Development Program at LANL, an affirmative action equal opportunity employer operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the U.S. DOE under Contract DE-AC52-06NA25396.This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Nano, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/nn402208p. Gamalski AD, Perea DE, Yoo J, Li N, Olszta MJ, Colby R, Schreiber DK, Ducati C, Picraux ST, Hofmann S, ACS Nano 2013, 7 (9), 7689–7697, doi:10.1021/nn402208

Periodically Changing Morphology of the Growth Interface in Si, Ge, and GaP Nanowires

Nanowire growth in the standard \u3c 111 \u3e direction is assumed to occur at a planar catalyst-nanowire interface, but recent reports contradict this picture. Here we show that a nonplanar growth interface is, in fact, a general phenomenon. Both III-V and group IV nanowires show a distinct region at the trijunction with a different orientation whose size oscillates during growth, synchronized with step flow. We develop an explicit model for this structure that agrees well with experiment and shows that the oscillations provide a direct visualization of catalyst supersaturation. We discuss the implications for wire growth and structure

Atomic-Scale Variability and Control of III-V Nanowire Growth Kinetics

In the growth of nanoscale device structures, the ultimate goal is atomic-level precision. By growing III-V nanowires in a transmission electron microscope, we measured the local kinetics in situ as each atomic plane was added at the catalyst-nanowire growth interface by the vapor-liquid-solid process. During growth of gallium phosphide nanowires at typical V/III ratios, we found surprising fluctuations in growth rate, even under steady growth conditions. We correlated these fluctuations with the formation of twin defects in the nanowire, and found that these variations can be suppressed by switching to growth conditions with a low V/III ratio. We derive a growth model showing that this unexpected variation in local growth kinetics reflects the very different supply pathways of the V and III species. The model explains under which conditions the growth rate can be controlled precisely at the atomic level