Biogeochemical fate of ferrihydrite-model organic compound complexes during anaerobic microbial reduction
Abstract not provided
Wordofa, Dawit N.↗
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Results for “COMPLEXITY”
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Addition of Si-H and B-H bonds and redox reactivity involving low-coordinate nitrido-vanadium complexes
Abstract not provided
Thompson, Rick↗
Structural Diversities in Heterometallic Mn–Ca Cluster Chemistry from the Use of Salicylhydroxamic Acid: {Mn III 4 Ca 2 }, {Mn II/III 6 Ca 2 }, {Mn III/IV 8 Ca}, and {Mn III 8 Ca 2 } Complexes with Relevance to Both High- and Low-Valent States of the Oxygen-Evolving Complex
We report that one-pot reactions between the [Mn 3 O(O 2 CPh) 6 (py) x ] +/o triangular precursors and either CaBr 2 ·xH 2 O or CaCl 2 ·6H 2 O, in the presence of salicylhydroxamic acid (shaH 2 ), have afforded the heterometallic complexes [MnIII 4 Ca 2 (O 2 CPh) 4 (shi) 4 (H 2 O) 3 (Me 2 CO)] ( 1 ) and (pyH)[Mn II 2 Mn III 4 Ca 2 Cl 2 (O 2 CPh) 7 (shi) 4 (py) 4 ] ( 2 ), respectively, in good yields. Further reactions but using a more flexible synthetic scheme comprising the Mn(NO 3 ) 2 · 4 H 2 O/Ca(NO 3 ) 2 · 4 H 2 O and Mn(O 2 CPh) 2 · 2 H 2 O/Ca(ClO 4 ) 2 · 4 H 2 O "metal blends" and shaH 2 , in the presence of external base NEt 3 , led to the new complexes (NHEt 3 ) 2 [Mn III 4 Mn IV 4 Ca(OEt) 2 (shi) 10 (EtOH) 2 ] ( 3 ) and (NHEt 3 ) 4 [Mn III 8 Ca 2 (CO 3 ) 4 (shi) 8 ] ( 4 ), respectively. In all reported compounds, the anion of the tetradentate (N,O,O,O)-chelating/bridging ligand salicylhydroxime (shi 3- ), resulting from the in situ metal-ion-assisted amide-iminol tautomerism of shaH 2 , was found to bridge both Mn and Ca atoms. Complexes 1-4 exhibit a variety of different structures, metal stoichiometries, and Mn oxidation-state descriptions; 1 possesses an overall octahedral metal arrangement, 2 can be described as a Mn 4 Ca 2 octahedron bound to an additional Mn 2 unit, 3 consists of a Mn 8 "ring" surrounding a Ca II atom, and 4 adopts a rectangular cuboidal motif of eight Mn atoms accommodating two CaIIatoms. Solid-state direct-current magnetic susceptibility studies revealed the presence of predominant antiferromagnetic exchange interactions between the Mn centers, leading to S = 0 spin ground-state values for all complexes. Lastly, from a bioinorganic chemistry perspective, the reported compounds may demonstrate some relevance to both high-valent scheme ( 3 ) and lower-oxidation-level species ( 1, 2, and 4 ) of the catalytic cycle of the oxygen-evolving complex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
M IV /Co –I (M = Zr, Hf) Bis(phosphinoamide) Complexes with η 6 - and η 4 -Arenes
Despite their relevance to catalysis, low-/subvalent cobalt complexes are difficult to synthesize and isolate. Consequently, very few “cobaltate” complexes are known and there is a lack of architectural diversity in this field. Lewis acidic d 0 group IV metals have been demonstrated to stabilize Co –I centers via metal–metal bonds. Herein, we report the synthesis of bis(phosphinoamide) heterobimetallic M IV /Co –I arene complexes (M = Zr, Hf). The driving force to maintain the aromaticity of the arenes dictates the hapticity of the Co-bound arene ligands and influences the binding arrangement of the phosphinoamide ligands. Benzene and toluene were observed to bind η 6 to the Co –I center, forcing dissociation of one of the phosphinoamide ligands, whereas η 4 -coordination of anthracene allows both phosphinoamide ligands to remain bound to the Co center. The identity of both the arene and the group IV metal ion starkly influence the lability of the arene. For instance, the Co-bound benzene ligand in the Zr IV /Co –I benzene complex rapidly exchanges with C 6 D 6 in solution, whereas toluene/C 6 D 6 exchange is much slower and appreciable C 6 H 6 /C 6 D 6 exchange is not observed for the Hf analogue. The Zr IV /Co –I benzene complex loses benzene upon repeated exposure to vacuum to form an arene-free tetrametallic dimer.
aromatic compounds↗
Reversible Heterolytic Cleavage of the H-H Bond by Molybdenum Complexes: Controlling the Dynamics of Exchange Between Proton and Hydride
Controlling the heterolytic cleavage of the H-H bond of dihydrogen is critically important in catalytic hydrogenations and in the catalytic oxidation of H2. We show how the rate of reversible heterolytic cleavage of H2 can be controlled over nearly four orders of magnitude at 25 °C, from 2.1 × 103 s-1 to ≥107 s-1. Bifunctional Mo complexes, [CpMo(CO)(κ3-P2N2)]+ (P2N2 = 1,5-diaza-3,7-diphosphacyclooctane with alkyl/aryl groups on N and P), have been developed for heterolytic cleavage of H2 into a proton and a hydride, akin to Frustrated Lewis Pairs. The H-H bond cleavage is enabled by the basic amine in the second coordination sphere. The products of heterolytic cleavage of H2, Mo hydride complexes bearing protonated amines, [CpMo(H)(CO)(P2N2H)]+, were characterized by spectroscopic studies and by X-ray crystallography. Variable temperature 1H, 15N and 2-D 1H-1H ROESY NMR spectra indicated rapid exchange of the proton and hydride. The exchange rates are in the order [CpMo(H)(CO)(PPh2NPh2H)]+ > [CpMo(H)(CO)(PtBu2NPh2H)]+ > [CpMo(H)(CO)(PPh2NBn2H)]+ > [CpMo(H)(CO)(PtBu2NBn2H)]+ > [CpMo(H)(CO)(PtBu2NtBu2H)]+. The pKa values determined in acetonitrile range from 9.3 to 17.7, and show a linear correlation with the logarithm of the exchange rates. Thus the exchange dynamics are controlled through the relative acidity of the [CpMo(H)(CO)(P2N2H)]+ and [CpMo(H2)(CO)(P2N2)]+ isomers, providing a design principle for controlling heterolytic cleavage of H2.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures
We examine how the catalytic domain of a glycoside hydrolase family 7 endoglucanase catalytic domain (Cel7B CD) facilitates complexation of cellulose chains from a crystal surface. With direct relevance to the science of biofuel production, this problem also represents a model system of biopolymer processing by proteins in Nature. Interactions of Cel7B CD with a cellulose microfibril along different paths of complexation are characterized by mapping the atomistic fluctuations recorded in free-energy simulations onto the parameters of a coarse-grain model. The resulting patterns of protein-biopolymer couplings also uncover the sequence signatures of the enzyme in peeling off glucan chains from the microfibril substrate. We show that the semiopen active site of Cel7B CD exhibits similar barriers and free energies of complexation over two distinct routes; namely, scooping of a chain into the active-site cleft and threading from the chain end into the channel. On the other hand, the complexation energetics strongly depends on the surface packing of the targeted chain and the resulting interaction sites with the enzyme. A revealed principle is that Cel7B CD facilitates cellulose deconstruction via adaptive coupling to the emergent substrate. The flexible, peripheral segments of the protein outside of the active-site cleft are able to accommodate the varying features of cellulose along the simulated paths of complexation. The general strategy of linking physics-based molecular interactions to protein sequence could also be helpful in elucidating how other protein machines process biopolymers.
Environmental Molecular Sciences Laboratory↗
Ephemeral collision complexes mediate chemically termolecular transformations that affect system chemistry [Ephemeral collision complexes induce chemically termolecular transformations that affect global chemistry]
Termolecular association reactions involve ephemeral collision complexes—formed from the collision of two molecules—that collide with a third and chemically inert ‘bath gas’ molecule that simply transfers energy to/from the complex. These collision complexes are generally not thought to react chemically on collision with a third molecule in the gas-phase systems of combustion and planetary atmospheres. Such ‘chemically termolecular’ reactions, in which all three molecules are involved in bond making and/or breaking, were hypothesized long ago in studies establishing radical chain branching mechanisms, but were later concluded to be unimportant. Here, with data from ab initio master equation and kinetic-transport simulations, we reveal that reactions of H+O 2 collision complexes with other radicals constitute major kinetic pathways under common combustion situations. These reactions are also found to influence flame propagation speeds, a common measure of global reactivity. As a result, analogous chemically termolecular reactions mediated by ephemeral collision complexes are probably of significance in various combustion and planetary environments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Evaluation of Attractive Interactions in the Second Coordination Sphere of Iron Complexes Containing Pendant Amines
The interactions between pendant amines in the second coordination sphere and ligands in the first coordination sphere are important for understanding the structures and reactivity of complexes containing PR2NR'2 ligands, which have been shown to be highly active H2 oxidation/production catalysts. A series of [Fe(PPh2NBn2)2(X)(Y)]n+ complexes have been prepared and structurally characterized. These complexes have two different ligands with which the pendant amines of the diphosphine ligand can interact. The solid state structure of cis-Fe(PPh2NBn2)2Cl2 reveals that the six-membered rings adjacent to the P atoms are in a boat confirmation, resulting in close N•••P distances that suggests the P atoms have a greater affinity for the lone pair of electrons on the N atom than chloride ligands. Similarly, boat conformations are observed for both rings adjacent to the hydride ligands of trans-[HFe(PPh2NBn2)2(CH3CN)]+ and trans-HFe(PPh2NBn2)2Cl, resulting in short N•••H distances. Spectroscopic and computational studies of trans-[HFe(PPh2NBn2)2(CO)]+, trans-[HFe(PPh2NBn2)(PPh2NBn2H)(CO)]2+, and trans-[HFe(PPh2NBn2)2(H2)]+ indicate the complexes are more stable when the pendant amines in boat conformations are adjacent to the hydride ligand. These data suggest an attractor ordering of H- > CO > H2 > PR3 > Cl- ~ CH3CN. This work was supported by the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for the U.S. DOE. Computations were performed using the Cascade supercomputer at the Environmental Molecular Sciences Laboratory, a National Scientific User Facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL.
Liao, Qian↗
Molecular counting by photobleaching in protein complexes with many subunits: best practices and application to the cellulose synthesis complex
The constituents of large, multisubunit protein complexes dictate their functions in cells, but determining their precise molecular makeup in vivo is challenging. One example of such a complex is the cellulose synthesis complex (CSC), which in plants synthesizes cellulose, the most abundant biopolymer on Earth. In growing plant cells, CSCs exist in the plasma membrane as six-lobed rosettes that contain at least three different cellulose synthase (CESA) isoforms, but the number and stoichiometry of CESAs in each CSC are unknown. To begin to address this question, we performed quantitative photobleaching of GFP-tagged AtCESA3-containing particles in living Arabidopsis thaliana cells using variable-angle epifluorescence microscopy and developed a set of information-based step detection procedures to estimate the number of GFP molecules in each particle. The step detection algorithms account for changes in signal variance due to changing numbers of fluorophores, and the subsequent analysis avoids common problems associated with fitting multiple Gaussian functions to binned histogram data. The analysis indicates that at least 10 GFP-AtCESA3 molecules can exist in each particle. In conclusion, these procedures can be applied to photobleaching data for any protein complex with large numbers of fluorescently tagged subunits, providing a new analytical tool with which to probe complex composition and stoichiometry.
09 BIOMASS FUELS↗
Nuclear three-body problem in the complex energy plane: Complex-scaling Slater method
The physics of open quantum systems is an interdisciplinary area of research. The nuclear “openness” manifests itself through the presence of the many-body continuum representing various decay, scattering, and reaction channels. As the radioactive nuclear beam experimentation extends the known nuclear landscape toward the particle drip lines, the coupling to the continuum space becomes exceedingly more important. Of particular interest are weakly bound and unbound nuclear states appearing around particle thresholds. Theories of such nuclei must take into account their open quantum nature. To describe open quantum systems, we introduce a complex-scaling (CS) approach in the Slater basis. We benchmark it with the complex-energy Gamow shell model (GSM) by studying energies and wave functions of the bound and unbound states of the two-neutron halo nucleus 6 He viewed as an $α + n + n$ cluster system. Both CS and GSM approaches are applied to a translationally invariant Hamiltonian with the two-body interaction approximated by the finite-range central Minnesota force. In the CS approach, we use the Slater basis, which exhibits the correct asymptotic behavior at large distances. To extract particle densities from the back-rotated CS solutions, we apply the Tikhonov regularization procedure, which minimizes the ultraviolet numerical noise. In this paper, we show that the CS-Slater method is both accurate and efficient. Its equivalence to the GSM approach has been demonstrated numerically for both energies and wave functions of 6 He. One important technical aspect of our calculation was to fully retrieve the correct asymptotic behavior of a resonance state from the complex-scaled (square-integrable) wave function. While standard applications of the inverse complex transformation to the complex-rotated solution provide unstable results, the stabilization method fully reproduces the GSM benchmark. We also propose a method to determine the smoothing parameter of the Tikhonov regularization. The combined suite of CS-Slater and GSM techniques has many attractive features when applied to nuclear problems involving weakly bound and unbound states. While both methods can describe energies, total widths, and wave functions of nuclear states, the CS-Slater method—if it can be applied—can provide additional information about partial energy widths associated with individual thresholds.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form
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99 GENERAL AND MISCELLANEOUS↗
Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes
The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.
Hargittai, M.↗
Perimetric Complexity of Binary Digital Images: Notes on Calculation and Relation to Visual Complexity
Perimetric complexity is a measure of the complexity of binary pictures. It is defined as the sum of inside and outside perimeters of the foreground, squared, divided by the foreground area, divided by 4p . Difficulties arise when this definition is applied to digital images composed of binary pixels. In this paper we identify these problems and propose solutions. Perimetric complexity is often used as a measure of visual complexity, in which case it should take into account the limited resolution of the visual system. We propose a measure of visual perimetric complexity that meets this requirement.
Watson, Andrew B.↗
Stabilization of dinitrosyl iron complexes under matrix isolation conditions: solvent and polymer effects on the synthesis of composites based on poly(methyl methacrylate) and iron complexes [Fe{sub 2}(μ-NCS-R){sub 2}(NO){sub 4}]
Homogeneous composites based on poly(methyl methacrylate) and its copolymers with methacrylic acid and on the nitrosyl iron complexes with 2-mercaptobenzimidazole and 2-mercaptobenzthiazole were synthesized. An analysis of the experimental data obtained by the methods of small-angle X-ray diffraction and SQUID magnetometry in combination with the results of quantum chemical calculations showed that the nitrosyl complexes did not retain their initial binuclear structure under the matrix isolation conditions: some complexes decompose to mononuclear ones. The percentage ratio of the dimers and monomers depends on the fraction of the methacrylic acid copolymer in the polymeric matrix and is almost independent of the type of thiol ligand in the iron complex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex
Manganese oxidation is an important biogeochemical process that is largely regulated by bacteria through enzymatic reactions. However, the detailed mechanism is poorly understood due to challenges in isolating and characterizing these unknown enzymes. A manganese oxidase, Mnx, from Bacillus sp. PL-12 has been successfully overexpressed in active form as a protein complex with a molecular mass of 211 kDa. We have recently used surface induced dissociation (SID) and ion mobility-mass spectrometry (IM-MS) to release and detect folded subcomplexes for determining subunit connectivity and quaternary structure. The data from the native mass spectrometry experiments led to a plausible structural model of this multicopper oxidase, which has been difficult to study by conventional structural biology methods. It was also revealed that each Mnx subunit binds a variable number of copper ions. Becasue of the heterogeneity of the protein and limited mass resolution, ambiguities in assigning some of the observed peaks remained as a barrier to fully understanding the role of metals and potential unknown ligands in Mnx. In this study, we performed SID in a modified Fourier transform-ion cyclotron resonance (FTICR) mass spectrometer. The high mass accuracy and resolution offered by FTICR unveiled unexpected artificial modifications on the protein that had been previously thought to be iron bound species based on lower resolution spectra. Additionally, isotopically resolved spectra of the released subcomplexes revealed the metal binding stoichiometry at different structural levels. This method holds great potential for in-depth characterization of metalloproteins and protein–ligand complexes. .
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Cryo-EM structures of engineered active bc 1- cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes
Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc 1 (Complex III, CIII 2 ), and may have specific cbb 3 -type cyt c oxidases (Complex IV, CIV) instead of the canonical aa 3 -type CIV. Electron transfer between these complexes is mediated by soluble ( c 2 ) and membrane-anchored ( c y ) cyts. Here, we report the structure of an engineered bc 1 - cbb 3 type SC (CIII 2 CIV, 5.2Å resolution) and three conformers of native CIII 2 (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c y and the assembly factor CcoH. The cyt c y is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c 2 . The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.
42 ENGINEERING↗
Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules
The soil microbiome is an invaluable component of the biosphere and critical for ecosystem functions, including biogeochemical cycling, soil-atmosphere gas exchange, degradation of toxic compounds, and promotion of plant growth and stress resistance/resilience. An improved understanding of the soil microbiome will help with predicting how these processes respond to external perturbations, and with harnessing beneficial aspects of the soil microbiome for agronomic applications such as crop amendments. However, the extensive taxonomic and functional diversity inherent within the soil microbiome hinders efficient analysis of this system. Microbial biodiversity in soils is orders of magnitude greater than other commonly studied systems such as the human gut microbiome (Blum, Zechmeister-Boltenstern, and Keiblinger 2019; Berendsen, Pieterse, and Bakker 2012). Thousands of microbial taxa may be found in a single gram of soil (Roesch et al. 2007), and high rates of gene flow and mutation further promote microbial diversification (Sergaki et al. 2018). Concomitantly, functional diversity in soil is similarly extensive. Soil is a heterogeneous mixture of microenvironments with defined physical and chemical attributes (Bach et al. 2018), within which numerous microbial guilds of distinct life-strategies and metabolic capacities can be found (Perez-Garcia, Lear, and Singhal 2016; H.-S. Song et al. 2014). Furthermore, the soil microbiome harbors a significant fraction of rare and/or quiescent members (Blagodatskaya and Kuzyakov 2013) that exist below the threshold of detection of current technologies. Such rare taxa may make significant contributions to process rates (Shade and Gilbert 2015; Dawson et al. 2017), but their scarcity complicates their identification and analysis. Finally, the vast amounts of information generated through holistic analyses of soil communities represent an intense computational burden (Scholz, Lo, and Chain 2012; Prosser 2015) that precludes assessment of the complete functional and taxonomic diversity contained in this ecosystem.
Naylor, Dan T.↗