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At least 1,081 records · Page 60

Visible Light Sensitized CO 2 Activation by the Tetraaza [Co II N 4 H(MeCN)] 2+ Complex Investigated by FT-IR Spectroscopy and DFT Calculations

In situ FT-IR measurements and electronic structure calculations are reported for the reduction of CO 2 catalyzed by the macrocyclic complex [Co II N 4 H] 2+ (N 4 H = 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]-heptadeca-1(17),2,11,13,15-pentaene). Beginning from the [Co II N 4 H] 2+ resting state of the complex in wet acetonitrile solution, two different visible light sensitizers with substantially different reducing power are employed to access reduced states. Accessing reduced states of the complex with a [Ru(bpy) 3 ] 2+ sensitizer yields an infrared band at 1670 cm -1 attributed to carboxylate, which is also observed for an authentic sample of the one-electron reduced complex [CoN 4 H(MeCN)] + in CO 2 saturated acetonitrile solution. The results are interpreted based on calculations using the pure BP86 functional that correctly reproduces experimental geometries. Continuum solvation effects are also included. The calculations show that Co is reduced to CoIin the first reduction, which is consistent with experimental d-d spectra of square Co(I) macrocycle complexes. The energy of the CO 2 adduct of the one-electron reduced catalyst complex is essentially the same as for [CoN 4 H(MeCN)] + , which implies that only a fraction of the latter forms an adduct with CO 2 . By contrast, the calculations indicate a crucial role for redox noninnocence of the macrocyclic ligand in the doubly reduced state, [Co I (N 4 H) -• ], and show that [Co I (N 4 H) -• ] binds partially reduced CO 2 fairly strongly. Experimentally accessing [Co I (N 4 H)-•] with an Ir(bpy) 3 sensitizer with greater reducing power closes the catalytic cycle as FT-IR spectroscopy shows CO production. Use of isotopically substituted C 18 O 2 also shows clear evidence for 18 O-substituted byproducts from CO 2 reduction to CO.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strengthening of Calcite Assemblages Through Chemical Complexation Reactions

Abstract Utilization of subsurface reservoirs, including fluid extraction/injection, can induce stress changes and modify in‐situ chemical equilibrium causing subcritical fracturing and deformation. Here, we show that chemical complexation reactions at the newly created fracture surfaces within the crack tip limit fracturing during consolidation of granular calcite assemblages. Previously, we showed that analogous chemical complexation reactions can increase in‐situ fracture toughness in pre‐fractured single crystal calcite. To test the chemical complexation effect under subsurface conditions, we consolidated samples under increasing hydrostatic pressure to induce widespread intergranular fracturing in the presence of fluid containing common anions. Measured consolidation, acoustic emissions, and microfracturing demonstrate that deformation correlates with complexation affinity for calcium in calcite and aqueous anions. We observed that deformation is lowest in the presence of strongly complexing anions (e.g., sulphate), provided sufficient anion diffusion rates. This understanding is important for predicting reservoir effective strength in the presence of complex aqueous fluids.

Choens, R. C.↗

Selecting Appropriate Model Complexity: An Example of Tracer Inversion for Thermal Prediction in Enhanced Geothermal Systems

Abstract A major challenge in the inversion of subsurface parameters is the ill‐posedness issue caused by the inherent subsurface complexities and the generally spatially sparse data. Appropriate simplifications of inversion models are thus necessary to make the inversion process tractable and meanwhile preserve the predictive ability of the inversion results. In this study, we investigate the effect of model complexity on fracture aperture inversion and thermal performance prediction in a field‐scale EGS model. Principal component analysis was used to map the aperture field to a low‐dimensional latent space. The complexity of the inversion model was quantitatively represented by the percentage of total variance in the original aperture fields preserved by the latent space. Tracer, pressure and flow rate data were used to invert for fracture aperture through an ensemble‐based inversion method, and the inferred aperture field was used to predict thermal performance. With an over‐simplified aperture model, ensemble collapse occurred. The inverted aperture models failed to resolve necessary flow and transport features, leading to a biased thermal performance prediction. A complex aperture model involved excessive features and was prone to overinterpreting the inversion data. Both the tracer/pressure/flow rate data reproduction and thermal prediction showed significant uncertainties, making it difficult to properly estimate long‐term thermal performance. Fortunately, our results indicate that there exists an appropriate model complexity which can simultaneously match inversion data and predict thermal performance with an acceptable uncertainty. The quality of the fit of tracer data appears to be a useful indicator of such an appropriate model complexity.

15 GEOTHERMAL ENERGY↗

Chirality-selected phase behaviour in ionic polypeptide complexes

In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with a β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.

36 MATERIALS SCIENCE↗

Atomic structure of the Y complex of the nuclear pore

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Munc18 and Munc13 serve as a functional template to orchestrate neuronal SNARE complex assembly

The transition of the Munc18-1/syntaxin-1 complex to the SNARE complex, a key step involved in exocytosis, is regulated by Munc13-1, SNAP-25 and synaptobrevin-2, but the underlying mechanism remains elusive. Here, we identify an interaction between Munc13-1 and the membrane-proximal linker region of synaptobrevin-2, and reveal its essential role in transition and exocytosis. Upon this interaction, Munc13-1 not only recruits synaptobrevin-2-embedded vesicles to the target membrane but also renders the synaptobrevin-2 SNARE motif more accessible to the Munc18-1/syntaxin-1 complex. Afterward, the entry of SNAP-25 leads to a half-zippered SNARE assembly, which eventually dissociates the Munc18-1/syntaxin-1 complex to complete SNARE complex formation. Furthermore, our data suggest that Munc18-1 and Munc13-1 together serve as a functional template to orchestrate SNARE complex assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Atomically precise control of rotational dynamics in charged rare-earth complexes on a metal surface

Abstract Complexes containing rare-earth ions attract great attention for their technological applications ranging from spintronic devices to quantum information science. While charged rare-earth coordination complexes are ubiquitous in solution, they are challenging to form on materials surfaces that would allow investigations for potential solid-state applications. Here we report formation and atomically precise manipulation of rare-earth complexes on a gold surface. Although they are composed of multiple units held together by electrostatic interactions, the entire complex rotates as a single unit when electrical energy is supplied from a scanning tunneling microscope tip. Despite the hexagonal symmetry of the gold surface, a counterion at the side of the complex guides precise three-fold rotations and 100% control of their rotational directions is achieved using a negative electric field from the scanning probe tip. This work demonstrates that counterions can be used to control dynamics of rare-earth complexes on materials surfaces for quantum and nanomechanical applications.

36 MATERIALS SCIENCE↗

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

The synthesis and characterization of an iron(VII) nitrido complex

Abstract Complexes of iron in high oxidation states are captivating research subjects due to their pivotal role as active intermediates in numerous catalytic processes. Structural and spectroscopic studies of well-defined model complexes often provide evidence of these intermediates. In addition to the fundamental molecular and electronic structure insights gained by these complexes, their reactivity also affects our understanding of catalytic reaction mechanisms for small molecule and bond-activation chemistry. Here, we report the synthesis, structural and spectroscopic characterization of a stable, octahedral Fe(VI) nitrido complex and an authenticated, unique Fe(VII) species, prepared by one-electron oxidation. The super-oxidized Fe(VII) nitride rearranges to an Fe(V) imide through an intramolecular amination mechanism and ligand exchange, which is characterized spectroscopically and computationally. This enables combined reactivity and stability studies on a single molecular system of a rare high-valent complex redox pair. Quantum chemical calculations complement the spectroscopic parameters and provide evidence for a diamagnetic ( S = 0) d 2 Fe(VI) and a genuine S = 1/2, d 1 Fe(VII) configuration of these super-oxidized nitrido complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here, in this work, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

Structures of the TMC-1 complex illuminate mechanosensory transduction

The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid–protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.

59 BASIC BIOLOGICAL SCIENCES↗

Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

Molecular dynamics studies showed that LDH and GAPDH tetramers can form a complex which can breakdown when the enzymes are saturated with NADH molecules. The interaction sites are conserved between LDH isozymes from heart and muscle cells, and between GAPDH molecules from rabbit and yeast cells. Positive electric fields between the NAD(H) binding sites showed that NAD(H) channeling within LDH-GAPDH complex can be an extension of NAD(H) channeling between the adjacent subunits within LDH and GAPDH tetramers. Analytical ultracentrifugation and enzyme kinetics studies indicated that LDH and GAPDH molecules can form a transient channeling complex. The transient complex can support the channeled and the diffusive paths in parallel, the relative contribution from each path depends on the off-rates for (GAPDH-NADH)-LDH complex and GAPDH-NADH complex. Negative cooperativity in NADH binding to different subunits in GAPDH tetramers can provide allosteric regulation of NADH channeling from GAPDH to LDH.

INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMI↗

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Deep learning methods that achieved great success in predicting intrachain residue-residue contacts have been applied to predict interchain contacts between proteins. However, these methods require multiple sequence alignments (MSAs) of a pair of interacting proteins (dimers) as input, which are often difficult to obtain because there are not many known protein complexes available to generate MSAs of sufficient depth for a pair of proteins. In recognizing that multiple sequence alignments of a monomer that forms homomultimers contain the co-evolutionary signals of both intrachain and interchain residue pairs in contact, we applied DNCON2 (a deep learning-based protein intrachain residue-residue contact predictor) to predict both intrachain and interchain contacts for homomultimers using multiple sequence alignment (MSA) and other co-evolutionary features of a single monomer followed by discrimination of interchain and intrachain contacts according to the tertiary structure of the monomer. We name this tool DNCON2_Inter. Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of 22.9% for homodimers and 17.0% for higher-order homomultimers. In some instances, especially where interchain contact densities are high, DNCON2_Inter predicted interchain contacts with 100% precision. We also developed Con_Complex, a complex structure reconstruction tool that uses predicted contacts to produce the structure of the complex. Using Con_Complex, we show that the predicted contacts can be used to accurately construct the structure of some complexes. Our experiment demonstrates that monomeric multiple sequence alignments can be used with deep learning to predict interchain contacts of homomeric proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Fluorescence-excitation and Emission Spectroscopy on Single FMO Complexes

In green-sulfur bacteria sunlight is absorbed by antenna structures termed chlorosomes, and transferred to the RC via the Fenna-Matthews-Olson (FMO) complex. FMO consists of three monomers arranged in C 3 symmetry where each monomer accommodates eight Bacteriochlorophyll a (BChl a) molecules. It was the first pigment-protein complex for which the structure has been determined with high resolution and since then this complex has been the subject of numerous studies both experimentally and theoretically. Here we report about fluorescence-excitation spectroscopy as well as emission spectroscopy from individual FMO complexes at low temperatures. The individual FMO complexes are subjected to very fast spectral fluctuations smearing out any possible different information from the ensemble data that were recorded under the same experimental conditions. In other words, on the time scales that are experimentally accessible by single-molecule techniques, the FMO complex exhibits ergodic behaviour.

59 BASIC BIOLOGICAL SCIENCES↗

A molecular view of the role of chirality in charge-driven polypeptide complexation

Polyelectrolyte molecules of opposite charge are known to form stable complexes in solution. Depending on the system conditions, such complexes can be solid or liquid. The latter are known as complex coacervates, and they appear as a second liquid phase in equilibrium with a polymer-dilute aqueous phase. This work considers the complexation between poly(glutamic acid) and poly(lysine), which is of particular interest because it enables examination of the role of chirality in ionic complexation, without changes to the overall chemical composition. Systematic atomic-level simulations are carried out for chains of poly(glutamic acid) and poly(lysine) with varying combinations of chirality along the backbone. Achiral chains form unstructured complexes. In contrast, homochiral chains lead to formation of stable beta-sheets between molecules of opposite charge, and experiments indicate that beta-sheet formation is correlated with the formation of solid precipitates. Changes in chirality along the peptide backbone are found to cause "kinks" in the beta-sheets. These are energetically unfavorable and result in irregular structures that are more difficult to pack together. Taken together, these results provide new insights that may be of use for the development of simple yet strong bioinspired materials consisting of beta-rich domains and amorphous regions.

Hoffmann, K. Q.↗

First-principles molecular dynamics simulation of the Ca 2 UO 2 (CO 3 ) 3 complex in water

Recent experiments have shown that the neutral Ca 2 UO 2 (CO 3 ) 3 complex is the dominant species of uranium in many uranyl-containing streams. However, the structure and solvation of such a species in water has not been investigated from first principles. Herein we present a first principles molecular dynamics perspective of the Ca 2 UO 2 (CO 3 ) 3 complex in water based on density functional theory and Born–Oppenheimer approximation. We find that the Ca 2 UO 2 (CO 3 ) 3 complex is very stable in our simulation timeframe for three different concentrations considered and that the key distances from our simulation are in good agreement with the experimental data from extended X-ray absorption fine structure (EXAFS) spectroscopy. More important, we find that the two Ca ions bind differently in the complex, as a result of the hydrogen-bonding network around the whole complex. Furthermore, this finding invites confirmation from time-resolved EXAFS and has implications in understanding the dissociative equilibrium of the Ca 2 UO 2 (CO 3 ) 3 complex in water.

74 ATOMIC AND MOLECULAR PHYSICS↗

Screening of metal complexes and organic solvents using the COSMOSAC-LANL model to enhance the energy density in a non-aqueous redox flow cell: an insight into the solubility

In this paper, we have proposed a first-principles methodology to screen transition metal complexes against a particular organic solvent and organic solvents against a particular transition metal complex based on their solubility information without the knowledge of heat of fusion and melting temperature. The energy density of a non-aqueous redox flow cell directly depends on the solubility of the redox active species in the non-aqueous medium. Here, we have used the “COSMOSAC-LANL” activity coefficient model which is based on first-principles COSMO calculations where the microscopic information is passed to the macroscopic world via a dielectric continuum solvation model, followed by a post-statistical thermodynamic treatment of the self-consistent properties of the solute particle to calculate the solubility. To model the activity coefficient at infinite dilution for the binary mixtures, a 3-suffix Margules (3sM) function is introduced for the quantitative estimation of the asymmetric interactions and, for the combinatorial term, the Staverman–Guggenheim (SG) form is used. The new activity coefficient model is separately called the “LANL” activity coefficient model. The metal complex and the organic solvent have been treated as a simple binary mixture. The present model has been applied to a set of 14 different organic solvents and 16 different transition metal complexes. Using the new LANL activity coefficient model in combination with the ADF-COSMOSAC-2013 model, we have shown how one can improve the solubility of a transition metal complex in an organic solvent. We applied our model to screen 84 binary mixtures to predict the compatible pair of redox active species and organic solvent to increase the energy density. The solvation mechanism of the transition metal complexes in the organic solvents was obtained using the new model. The results have been compared with the experimental and theoretical results where they are available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CASPT2 molecular geometries of Fe( II ) spin-crossover complexes

Using fully internally contracted (FIC)-CASPT2 analytical gradients, geometry optimizations of spin-crossover complexes are reported. This approach is tested on a series of Fe(II) complexes with different sizes, ranging from 13 to 61 atoms. A combination of active space and basis set choices are employed to investigate their role in determining reliable molecular geometries. The reported strategy demonstrates that a wave function-based level of theory can be used to optimize the geometries of metal complexes in reasonable times and enables one to treat the molecular geometry and electronic structure of the complexes using the same level of theory. For a series of smaller Fe(II) SCO complexes, strong field ligands in the LS state result in geometries with the largest differences between DFT and CASPT2; however, good agreement overall is observed between DFT and CASPT2. For the larger complexes, moderate sized basis sets yield geometries that compare well with DFT and available experimental data. Here we recommend using the (10e,12o) active space since convergence to a minimum structure was more efficient than with truncated active spaces despite having similar Fe–ligand bond distances.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗