Photophysics of Phenylpyrrole Derivatives and Their Acetonitrile Clusters in the Gas Phase and in Argon Matrixes: Simulations of Structure and Reactivity

Recent expts. on the dual fluorescence of phenylpyrrole (PP) and pyrrolobenzonitrile (PBN) in supersonic jets and in cryogenic matrixes are analyzed. The structures of the 1:1 clusters are calcd. using ab initio, d. functional theory (DFT) and mol. mechanics (MM) methods. In these calcns., the structures of PP and PBN in the ground state and in two possible min. on the charge-transfer excited state are taken from a recent theor. anal. The structures of PP and PBN clusters with a larger no. of acetonitrile mols. are also calcd. using the mol. mechanics method. It is shown that the fact that small PP:AN and PBN:AN clusters do not exhibit any charge-transfer (CT) type emission, whereas for PBN:ANn clusters (n >= 4) CT emission is obsd., can be understood on the basis of the calcd. structures. The trapping of PP and of PBN in an argon matrix (neat and doped with acetonitrile) is simulated by a mol. dynamics procedure. The observation of locally excited (LE) fluorescence only from PP in neat argon, whereas from argon-trapped PBN both CT and LE emission bands are obsd., is readily understood on the basis of these simulations. Moreover, the appearance of CT emission from PP-doped argon matrixes when acetonitrile is added is also explained, as well as the relatively small spectral shift obsd. upon addn. of acetonitrile to PBN-doped argon matrixes

Charge-Transfer-Type Fluorescence of 4-(1H-Pyrrol-1-yl)benzonitrile (PBN) and N-Phenylpyrrole (PP) in Cryogenic Matrixes: Evidence for Direct Excitation of the CT Band

The fluorescence spectrum of PBN in a neat argon matrix is excitation-wavelength-dependent: at short excitation wavelengths, it consists of dual emission assigned to a charge-transfer (CT) state and a much weaker band assigned to the locally excited (LE) state. The CT emission is broad and almost completely devoid of vibrational structure, whereas the LE band is characterized by vibrationally resolved emission. At long excitation wavelengths, only CT emission is obsd., indicating that the CT state is populated directly by light absorption and not via the LE state. Comparison with jet-cooled spectra of the bare mol. allows the unambiguous assignment of the LE spectrum and the location of the 0,0 band. The matrix LE emission spectrum is blue-shifted with respect to that of the gas phase, showing that the dipole moment of the LE state is smaller than that of the ground state. The fluorescence spectrum of PBN in an argon matrix does not change appreciably when acetonitrile (AN) is added to the matrix, in contrast to the case of N-phenylpyrrol (PP) (Schweke, D.; Haas, Y. J. Phys. Chem. A 2003, 107, 9554), for which addn. of AN results in the appearance of two well sepd. emission bands. The different photophys. behaviors of PP and PBN in an argon matrix (and in supersonic jets) are analyzed by a simple model that considers the restriction of large-amplitude motions in the matrix. The implications of these low-temp. studies for understanding the properties of these systems in liq. soln. are discussed

Soil carbon is only higher in the surface soil under minimum tillage in Vertosols and Chromosols of New South Wales North-West Slopes and Plains, Australia

Reduced carbon stock levels in Australian soil due to cropping provide a significant opportunity for carbon sequestration, and the recent initiative to consider soil carbon in domestic emissions trading requires a scientific assessment of soil carbon levels under a range of cropping soil management practices. Some of the previous research in southern and western New South Wales (NSW) showed that the rate of carbon decline in cropping soils is slowed under minimum tillage when the stubble is also retained. However, such comparison is rare in the NSW North-West Slopes and Plains region, particularly on the red soils (Chromosols) which are one of the major soil types in the region. We surveyed 50 dryland Chromosols, 72 dryland Vertosols, and 25 irrigated Vertosols on commercial farms across this region to examine the effects of conventional tillage, minimum tillage, and irrigation on total soil organic carbon. Samples of 0.1 m segments to 0.3 m depth were analysed for total organic carbon and other soil properties. Mid-infrared scans were used to predict the particulate, humus, and resistant soil organic carbon fractions. Bulk density was used to calculate total organic carbon stock for each segment, and equivalent soil mass (ESM) for 0–0.3 m. In Vertosols, for 0–0.3 m ESM, total organic carbon and particulate organic carbon were not different between management practices, whereas humic organic carbon and resistant organic carbon were consistently lower under conventional tillage. However, in 0–0.1 m, total organic carbon was greater under minimum tillage (15.2 Mg ha–1 ) than conventional tillage (11.9 Mg ha–1 ) or irrigation (12.0 Mg ha–1 ), reflecting less soil surface disturbance under minimum tillage. In Chromosols, only total organic carbon was higher under minimum tillage than conventional tillage in the 0–0.3 m ESM (39.8 v. 33.5 Mg ha–1 ) and in 0–0.1 m (19.7 v. 16.9 Mg ha–1 ). The strong influences of rainfall, temperature, bulk density, texture, and management history on soil carbon stocks suggested that these environmental and management factors require further consideration when gauging soil carbon sequestration potential under current and novel tillage practices in key regional locations

CC+: A Searchable Database of Validated Coiled Coils in PDB Structures and AlphaFold2 Models

α‐Helical coiled coils are common tertiary and quaternary elements of protein structure. In coiled coils, two or more α helices wrap around each other to form bundles. This apparently simple structural motif can generate many architectures and topologies. Coiled coil‐forming sequences can be predicted from heptad repeats of hydrophobic and polar residues, hpphppp , although this is not always reliable. Alternatively, coiled‐coil structures can be identified using the program SOCKET, which finds knobs‐into‐holes (KIH) packing between side chains of neighboring helices. SOCKET also classifies coiled‐coil architecture and topology, thus allowing sequence‐to‐structure relationships to be garnered. In 2009, we used SOCKET to create a relational database of coiled‐coil structures, CC + , from the RCSB Protein Data Bank (PDB). Here, we report an update of CC + following an update of SOCKET (to Socket2) and the recent explosion of structural data and the success of AlphaFold2 in predicting protein structures from genome sequences. With the most‐stringent SOCKET parameters, CC + contains ≈12,000 coiled‐coil assemblies from experimentally determined structures, and ≈120,000 potential coiled‐coil structures within single‐chain models predicted by AlphaFold2 across 48 proteomes. CC + allows these and other less‐stringently defined coiled coils to be searched at various levels of structure, sequence, and side‐chain interactions. The identified coiled coils can be viewed directly from CC + using the Socket2 application, and their associated data can be downloaded for further analyses. CC + is available freely at http://coiledcoils.chm.bris.ac.uk/CCPlus/Home.html . It will be updated automatically. We envisage that CC+ could be used to understand coiled‐coil assemblies and their sequence‐to‐structure relationships, and to aid protein design and engineering.</p

An atlas of protein homo-oligomerization across domains of life

Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes

MAPPING ECONOMIC DEVELOPMENT POLICY CHANGE IN THE AMERICAN STATES -super-1

This article explores an interesting question. Why, despite compelling evidence arguing against their effectiveness, do ever-larger incentive packages continue to be offered by the states to attract firms&quest; Copyright 2002 by The Policy Studies Organization.