Results for “complexity analysis” — Page 42

DOE OSTI2023

Machine Learning for Prediction of Thermodynamic Descriptors

Our objective is to apply machine learning (ML) algorithms for the prediction of molecular catalysis descriptors from geometric properties derived from experimental crystallographic databases. Catalysis is often considered a “low-data” discipline that is poorly suited for ML methods. An exception is the extensive structural information that is available for molecular catalysts through the Cambridge Structural Database (CSD), which contains atomically precise molecular structures from X-ray diffraction analysis for >600K metal complexes. As a proof-of-principle, we targeted the prediction of hydricity, a thermodynamic property that provides understanding and control of catalytic hydride transfer. We built a training set composed of ~100 molecular complexes with a known hydricity and structural information from the CSD. This data set was converted into a machine-readable format using the smooth overlap of atomic positions (SOAP) representation and further labeled with simple electronic descriptors for the metal centers. Multiple different neural networks were trained on this data set, and the accuracy of the hydricity predictions ranged from < 2 kcal/mol to 20 kcal/mol. The accuracy of each model was highly sensitive to which compounds were in the train versus test set, underscoring the challenges associated with small and chemically diverse data sets. Finally, to further augment the data set, we attempted to experimentally measure several new hydricity values, however these experiments were unsuccessful due to undesired chemical reactivity of the selected complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis

Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.

09 BIOMASS FUELS↗

DOE OSTI2026

Determining Optimal Magnetometer Configuration on MAGIS-100

Long-baseline atom interferometers such as the Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) require stringent control and continuous characterization of background magnetic fields and spatial gradients to prevent systemic phase shifts that mimic ultralight dark matter or gravitational wave signatures. Because direct sensor placement within the ultra-high vacuum beam pipe is infeasible, in-situ magnetic field monitoring relies on external sensor arrays situated in the surrounding annular region. This work demonstrates a field reconstruction framework for a 5.3-meter MAGIS-100 modular section using finite-element Opera simulations. Transverse magnetic fields are expanded using a cylindrical multipole framework as informed by Fermilab’s Muon g-2 experiment, with magnetometer array configurations optimized via Fisher information matrix D-optimality. Inverting external sensor readings through a Gauss-Newton scheme recovers interior tube fields across distinct axial positions. In the discontinuity-averse uniform region (slice pair P4), the model achieves sub-noise-floor performance with a cross-validated root-mean-square error (RMSE) of $6.7227 \times 10^{-4}\text{ A/m}$ ($0.845\times$ sensor noise floor) and an interior field coefficient of variation of $1.71\%$. An elbow criterion in the Fisher bounds establishes $n_{\text{max}} = 2$ as the optimal multipole truncation order to prevent noise amplification from over-parameterization, with $n_{\text{max}} = 3$ (sextupole) order chosen for analysis to demonstrate further complexity and cross-pair comparison. Furthermore, analytical differentiation of the fitted multipole coefficients yields dense spatial maps of the transverse Jacobian gradient matrix $\nabla \mathbf{H}$ along with propagated $1\sigma$ uncertainty bounds across the beam region ($r \le 2.75\text{ in}$). This operational framework confirms that external magnetometer arrays can reliably monitor magnetic field uniformity and spatial gradients along the 100-meter flight path given appropriate sampling for any complexity order.

Appleby, Darwin [William Rainey Harper Coll.] (ORC↗

DOE OSTI2026

Determining Optimal Magnetometer Configuration on MAGIS-100

Long-baseline atom interferometers such as the Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) require stringent control and continuous characterization of background magnetic fields and spatial gradients to prevent systemic phase shifts that mimic ultralight dark matter or gravitational wave signatures. Because direct sensor placement within the ultra-high vacuum beam pipe is infeasible, in-situ magnetic field monitoring relies on external sensor arrays situated in the surrounding annular region. This work demonstrates a field reconstruction framework for a 5.3-meter MAGIS-100 modular section using finite-element Opera simulations. Transverse magnetic fields are expanded using a cylindrical multipole framework as informed by Fermilab’s Muon g-2 experiment, with magnetometer array configurations optimized via Fisher information matrix D-optimality. Inverting external sensor readings through a Gauss-Newton scheme recovers interior tube fields across distinct axial positions. In the discontinuity-averse uniform region (slice pair P4), the model achieves sub-noise-floor performance with a cross-validated root-mean-square error (RMSE) of $6.7227 \times 10^{-4}\text{ A/m}$ ($0.845\times$ sensor noise floor) and an interior field coefficient of variation of $1.71\%$. An elbow criterion in the Fisher bounds establishes $n_{\text{max}} = 2$ as the optimal multipole truncation order to prevent noise amplification from over-parameterization, with $n_{\text{max}} = 3$ (sextupole) order chosen for analysis to demonstrate further complexity and cross-pair comparison. Furthermore, analytical differentiation of the fitted multipole coefficients yields dense spatial maps of the transverse Jacobian gradient matrix $\nabla \mathbf{H}$ along with propagated $1\sigma$ uncertainty bounds across the beam region ($r \le 2.75\text{ in}$). This operational framework confirms that external magnetometer arrays can reliably monitor magnetic field uniformity and spatial gradients along the 100-meter flight path given appropriate sampling for any complexity order.

Appleby, Darwin [William Rainey Harper Coll.] (ORC↗

DOE OSTI2020

Characterization of Extreme Wave Conditions for Wave Energy Converter Design and Project Risk Assessment

Best practices and international standards for determining n-year return period extreme wave (sea states) conditions allow wave energy converter designers and project developers the option to apply simple univariate or more complex bivariate extreme value analysis methods. The present study compares extreme sea state estimates derived from univariate and bivariate methods and investigates the performance of spectral wave models for predicting extreme sea states at buoy locations within several regional wave climates along the US East and West Coasts. Two common third-generation spectral wave models are evaluated, a WAVEWATCH III® model with a grid resolution of 4 arc-minutes (6–7 km), and a Simulating WAves Nearshore model, with a coastal resolution of 200–300 m. Both models are used to generate multi-year hindcasts, from which extreme sea state statistics used for wave conditions characterization can be derived and compared to those based on in-situ observations at National Data Buoy Center stations. Comparison of results using different univariate and bivariate methods from the same data source indicates reasonable agreement on average. Discrepancies are predominantly random. Large discrepancies are common and increase with return period. There is a systematic underbias for extreme significant wave heights derived from model hindcasts compared to those derived from buoy measurements. This underbias is dependent on model spatial resolution. However, simple linear corrections can effectively compensate for this bias. A similar approach is not possible for correcting model-derived environmental contours, but other methods, e.g., machine learning, should be explored.

16 TIDAL AND WAVE POWER↗

DOE OSTI2020

Bistable dynamics and Hopf bifurcation in a refined model of early stage HIV infection

Recent clinical studies have shown that HIV disease pathogenesis can depend strongly on many factors at the time of transmission, including the strength of the initial viral load and the local availability of CD4+ T-cells. In this article, a new within-host model of HIV infection that incorporates the homeostatic proliferation of T-cells is formulated and analyzed. Due to the effects of this biological process, the influence of initial conditions on the proliferation of HIV infection is further elucidated. The identifiability of parameters within the model is investigated and a local stability analysis, which displays additional complexity in comparison to previous models, is conducted. The current study extends previous theoretical and computational work on the early stages of the disease and leads to interesting nonlinear dynamics, including a parameter region featuring bistability of infectious and viral clearance equilibria and the appearance of a Hopf bifurcation within biologically relevant parameter regimes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Estimating the state of a geophysical system with sparse observations: time delay methods to achieve accurate initial states for prediction

The problem of forecasting the behavior of a complex dynamical system through analysis of observational time-series data becomes difficult when the system expresses chaotic behavior and the measurements are sparse, in both space and/or time. Despite the fact that this situation is quite typical across many fields, including numerical weather prediction, the issue of whether the available observations are "sufficient" for generating successful forecasts is still not well understood. An analysis by Whartenby et al. (2013) found that in the context of the nonlinear shallow water equations on a β plane, standard nudging techniques require observing approximately 70 % of the full set of state variables. Here we examine the same system using a method introduced by Rey et al. (2014a), which generalizes standard nudging methods to utilize time delayed measurements. Here, we show that in certain circumstances, it provides a sizable reduction in the number of observations required to construct accurate estimates and high-quality predictions. In particular, we find that this estimate of 70 % can be reduced to about 33 % using time delays, and even further if Lagrangian drifter locations are also used as measurements.

58 GEOSCIENCES↗

DOE OSTI2020

PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.

Swenson, Nicolas↗

DOE OSTI2026

In-Situ Magnetic Field Reconstruction in the MAGIS-100 Experiment

Long-baseline atom interferometers such as the Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) require stringent control and continuous characterization of background magnetic fields and spatial gradients to prevent systemic phase shifts that mimic ultralight dark matter or gravitational wave signatures. Because direct sensor placement within the ultra-high vacuum beam pipe is infeasible, in-situ magnetic field monitoring relies on external sensor arrays situated in the surrounding annular region. This work demonstrates a field reconstruction framework for a 5.3-meter MAGIS-100 modular section using finite-element Opera simulations. Transverse magnetic fields are expanded using a cylindrical multipole framework as informed by Fermilab’s Muon g-2 experiment, with magnetometer array configurations optimized via Fisher information matrix D-optimality. Inverting external sensor readings through a Gauss-Newton scheme recovers interior tube fields across distinct axial positions. In the discontinuity-averse uniform region (slice pair P4), the model achieves sub-noise-floor performance with a cross-validated root-mean-square error (RMSE) of $6.7227 \times 10^{-4}\text{ A/m}$ ($0.845\times$ sensor noise floor) and an interior field coefficient of variation of $1.71\%$. An elbow criterion in the Fisher bounds establishes $n_{\text{max}} = 2$ as the optimal multipole truncation order to prevent noise amplification from over-parameterization, with $n_{\text{max}} = 3$ (sextupole) order chosen for analysis to demonstrate further complexity and cross-pair comparison. Furthermore, analytical differentiation of the fitted multipole coefficients yields dense spatial maps of the transverse Jacobian gradient matrix $\nabla \mathbf{H}$ along with propagated $1\sigma$ uncertainty bounds across the beam region ($r \le 2.75\text{ in}$). This operational framework confirms that external magnetometer arrays can reliably monitor magnetic field uniformity and spatial gradients along the 100-meter flight path given appropriate sampling for any complexity order.

Appleby, Darwin [William Rainey Harper Coll.; Ferm↗

DOE OSTI2017

Four thiophene-pyridyl-amide-based Zn{sup II}/Cd{sup II} coordination polymers: Assembly, structures, photocatalytic properties and fluorescent recognition for Fe{sup 3+}

By tuning metal ions and combining with different dicarboxylates, four new semi-rigid thiophene-bis-pyridyl-bis-amide-based coordination polymers, namely, [Zn(3-bptpa)(1,3-BDC)]·DMA·2H{sub 2}O (1), [Zn(3-bptpa)(5-MIP)] (2), [Cd(3-bptpa)(1,3-BDC)]·2H{sub 2}O (3) and [Cd(3-bptpa)(5-MIP)]·4H{sub 2}O (4) (3-bptpa=N,N′-bis(pyridine-3-yl)thiophene-2,5-dicarboxamide, 1,3-H{sub 2}BDC=1,3-benzenedicarboxylic acid, 5-H{sub 2}MIP=5-methylisophthalic acid, DMA=N,N-dimethylacetamide), were solvothermally/hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction analyses, IR spectra, UV–vis diffuse-reflectance spectra (DRS), powder X-ray diffraction (PXRD) and thermal gravimetric analyses (TG). The structural analysis reveals that Zn-complexes 1 and 2 are similar 2D networks. While Cd-complexes 3 and 4 exhibit similar 2-fold interpenetrating 3D α-Po frameworks with the (4{sup 12}·6{sup 3}) topology. The photocatalytic properties for the degradation of methylene blue (MB) under ultraviolet light irradiation of the title complexes have been investigated in detail. Furthermore, the luminescent sensing behaviors for metal cations of 1–4 have been studied, the results indicate that 3 is an excellent fluorescent probe, with high sensitivity, selectivity, and simple regeneration, for environmentally relevant Fe{sup 3+} ions. - Graphical abstract: Four Zn{sup II}/Cd{sup II} coordination polymers with a thiophene-pyridyl-amide ligand have been prepared. The photocatalytic activities and fluorescent sensing properties for metal ions of the title complexes have been investigated. - Highlights: • Four coordination polymers with thiophene-pyridyl-amide ligands have been obtained. • The central metal ions play an important role in the formation of the frameworks. • The photoluminescent sensing and the photocatalytic properties have been investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Confocal Raman Microscopy for Measuring In Situ Temperature-Dependent Structural Changes in Poly(Ethylene Oxide) Thin Films

Crystallization from the melt is a critical process governing the properties of semi-crystalline polymeric materials. While structural analyses of melting and crystallization transitions in bulk polymers have been widely reported, in contrast, those in thin polymer films on solid supports have been underexplored. Herein, in situ Raman microscopy and self-modeling curve resolution (SMCR) analysis are applied to investigate the temperature-dependent structural changes in poly(ethylene oxide) (PEO) films during melting and crystallization phase transitions. By resolving complex overlapping sets of spectra, SMCR analysis reveals that the thermal transitions of 50 µm thick PEO films comprise two structural phases: an ordered crystalline phase and a disordered amorphous phase. The ordered structure of the crystalline PEO film entirely disappears as the polymer is heated; conversely, the disordered structure of the amorphous PEO film reverts to the ordered structure as the polymer is cooled. Broadening of the Raman bands was observed in PEO films above the melting temperature (67 °C), while sharpening of bands was observed below the crystallization temperature (45 °C). The temperatures at which these spectral changes occurred were in good agreement with differential scanning calorimetry (DSC) measurements, especially during the melting transition. The results illustrate that in situ Raman microscopy coupled with SMCR analysis is a powerful approach for unraveling complex structural changes in thin polymer films during melting and crystallization processes. Furthermore, we show that confocal Raman microscopy opens opportunities to apply the methodology to interrogate the structural features of PEO or other surface-supported polymer films as thin as 2 µm, a thickness regime beyond the reach of conventional thermal analysis techniques.

Koh, Miharu [Department of Chemistry, University o↗

DOE OSTI2017

High-resolution mass spectrometric analysis of biomass pyrolysis vapors

Vapors generated from the pyrolysis of lignocellulosic biomass are made up of a complex mixture of oxygenated compounds. Direct analysis of these vapors provides insight into the mechanisms of depolymerization of cellulose, hemicellulose, and lignin as well as insight into reactions that may occur during condensation of pyrolysis vapors into bio-oil. Studies utilizing pyrolysis molecular beam mass spectrometry have provided valuable information regarding the chemical composition of pyrolysis vapors. Mass spectrometers generally employed with these instruments have low mass resolution of approximately a mass unit. The presence of chemical species with identical unit mass but differing elemental formulas cannot be resolved with these instruments and are therefore detected as a single ion. In this study we analyzed the pyrolysis vapors of several biomass sources using a high-resolution double focusing mass spectrometer. High-resolution analysis of pyrolysis vapors allowed for speciation of several compounds that would be detected as a single ion with unit mass resolution. Lastly, these data not only provide greater detail into the composition of pyrolysis vapors but also highlight differences between vapors generated from multiple biomass feedstocks.

09 BIOMASS FUELS↗

DOE OSTI2023

A data analysis method to rapidly characterize gallium concentration in plutonium matrices using LIBS

The processing of actinide samples is a complex and costly endeavor that requires compositional analysis at various stages. Laser-induced breakdown spectroscopy (LIBS) has been used to analyze actinide-containing samples in many nuclear applications including waste management, fuel processing and forensics. The LIBS spectrum obtained from actinide materials are generally extremely complex, exhibiting many thousands of strong emission lines. This makes it difficult to identify other elements within the sample of interest, given the rich and dominant actinide spectrum. Here, in this article, we describe a recent effort to identify and quantify impurities and alloying constituents in plutonium matrices using a hand-held LIBS instrument that is used to rapidly and efficiently measure an emission spectrum from a material sample. We tabulate the emission line positions and intensities of plutonium. We report the development of machine-learning software that can identify gallium and quantify its concentration in plutonium matrices. This work has the potential to provide a rapid and nearly non-destructive technique that allows more confidence in characterizing the composition of materials that are present within complex actinide associated targets. We describe how our LIBS measurements and data analysis methods have successfully quantified the gallium concentration in a variety of samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Three-dimensional imaging of grain boundaries via quantitative fluorescence X-ray tomography analysis

Abstract Three-dimensional visualization of material composition within multiple grains and across complex networks of grain boundaries at nanoscales can provide new insight into the structure evolution and emerging functional properties of the material for diverse applications. Here, using nanoscale scanning X-ray fluorescence tomography, coupled with an advanced self-absorption correction algorithm developed in this work, we analyze the three-dimensional gain distributions and compositions in a Ce 0.8 Gd 0.2 O 2-δ -CoFe 2 O 4 mixed ionic-electronic conductor system with high accuracy and statistical significance. Our systematic investigation reveals an additional emergent phase and uncovers highly intriguing composition stability ranges for the multiple material phases within this system. The presented visualization of composition variations across complex interfaces, supported by our quantitative composition analysis, discloses mechanistic pathways of the diverse phase transformations occurring in the material synthesis, providing insights for the optimization of transport properties in the mixed ionic-electronic conductor system.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Thylakoid-integrated recombinant Hcf106 participates in the chloroplast twin arginine transport system

The chloroplast twin arginine transport (cpTat) system distinguishes itself as a protein transport pathway by translocating fully folded proteins, using the proton-motive force (PMF) as the sole source of energy. The cpTat pathway is evolutionarily conserved with the Tat pathway found in the plasma membrane of many prokaryotes. The cpTat (Escherichia coli) system uses three proteins, Tha4 (TatA),Hcf106 (TatB), and cpTatC (TatC), to form a transient translocase allowing the pas-sage of precursor proteins. Briefly, cpTatC and Hcf106, with Tha4, form the initial receptor complex responsible for precursor protein recognition and binding in an energy-independent manner, while a separate pool of Tha4 assembles with the pre-cursor-bound receptor complex in the presence the PMF. Analysis by blue-native polyacrylamide gel electrophoresis (BN-PAGE) shows that the receptor complex, in the absence of precursor, migrates near 700 kDa and contains cpTatC and Hcf106with little Tha4 remaining after detergent solubilization. To investigate the role thatHcf106 may play in receptor complex oligomerization and/or stability, systematic cysteine substitutions were made in positions from the N-terminal transmembrane domain to the end of the predicted amphipathic helix of the protein. BN-PAGE analysis allowed us to identify the locations of amino acids in Hcf106 that were critical for interacting with cpTatC. Oxidative cross-linking allowed us to map interactions of the transmembrane domain and amphipathic helix region of Hcf106. In addition, we showed that in vitro expressed, integrated Hcf106 can interact with the precursor signal peptide domain and imported cpTatC, strongly suggesting that a subpopulation of the integrated Hcf106 is participating in competent cpTat complexes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Computational Spectroscopy of the Cr–Cr Bond in Coordination Complexes

In this work, we report the accurate computational vibrational analysis of the Cr–Cr bond in dichromium complexes using second-order multireference complete active space methods (CASPT2), allowing direct comparison with experimental spectroscopic data both to facilitate interpreting the low-energy region of the spectra and to provide insights into the nature of the bonds themselves. Recent technological development by the authors has realized such computation for the first time. Accurate simulation of the vibrational structure of these compounds has been hampered by their notorious multiconfigurational electronic structure that yields bond distances that do not correlate with bond order. Some measured Cr–Cr vibrational stretching modes, ν(Cr 2 ), have suggested weaker bonding, even for so-called ultrashort Cr–Cr bonds, while others are in line with the bond distance. Here, we optimize geometries and compute ν(Cr 2 ) with CASPT2 for three well-characterized complexes, Cr 2 (O 2 CCH 3 ) 4 (H 2 O) 2 , Cr 2 (mhp) 4 , and Cr 2 (dmp) 4 . We obtain CASPT2 harmonic ν(Cr 2 ) modes in good agreement with experiment at 282 cm –1 for Cr 2 (mhp) 4 and 353 cm –1 for Cr 2 (dmp) 4 , compute 50 Cr and 54 Cr isotope shifts, and demonstrate that the use of the so-called IPEA shift leads to improved Cr–Cr distances. Additionally, normal mode sampling was used to estimate anharmonicity along ν(Cr 2 ), leading to an anharmonic mode of 272 cm –1 for Cr 2 (mhp) 4 and 333 cm –1 for Cr 2 (dmp) 4 .

36 MATERIALS SCIENCE↗

DOE OSTI2022

Electronically-coupled redox centers in trimetallic cobalt complexes

Synthesis and isolation of molecular building blocks of metal–organic frameworks (MOFs) can provide unique opportunities for characterization that would otherwise be inaccessible due to the heterogeneous nature of MOFs. Herein, we report a series of trinuclear cobalt complexes incorporating dithiolene ligands, triphenylene-2,3,6,7,10,11-hexathiolate (THT) (1 3+ ), and benzene hexathiolate (BHT) (2 3+ ), with 1,1,1,-tris(diphenylphosphinomethyl)ethane (triphos) employed as the capping ligand. Single crystal X-ray analyses of 1 3+ and 2 3+ display three five-coordinate cobalt centers bound to the triphos and dithiolene ligands in a distorted square pyramidal geometry. Cyclic voltammetry studies of 1 3+ and 2 3+ reveal three redox features associated with the formation of mixed valence states due to the sequential reduction of the redox-active metal centers (Co III/II ). Using this electrochemical data, the comproportionality values were determined for 1 and 2 (log K c = 1.4 and 1.5 for 1, and 4.7 and 5.8 for 2), suggesting strong resonance-stabilized coupling of the metal centers, with stronger electronic coupling observed for complex 2 compared to that for complex 1. Cyclic voltammetry studies were also performed in solvents of varying polarity, whereupon the difference in the standard potentials (ΔE 1/2 ) for 1 and 2 was found to shift as a function of the polarity of the solvent, indicating a negative correlation between the dielectric constant of the electrochemical medium and the stability of the mixed valence species. Spectroelectrochemical studies of in situ generated multi-valent (MV) states of complexes 1 and 2 display characteristic NIR intervalence charge transfer (IVCT) bands, and analysis of the IVCT transitions for complex 2 suggests a weakly coupled class II multi-valent species and relatively large electronic coupling factors (1700 cm –1 for the first multi-valent state of 2 2+ , and 1400 and 4000 cm –1 for the second multi-valent state of 2 + ). Here, density functional theory (DFT) calculations indicate a significant deviation in relative energies of the frontier orbitals of complexes 1 3+ , 2 3+ , and 3 + that contrasts those calculated for the analogous trinuclear cobalt dithiolene complexes employing pentamethylcyclopentadienyl (Cp*) as the capping ligand (Co 3 Cp* 3 THT and Co 3 Cp* 3 BHT, respectively), and may be a result of the cationic nature of complexes 1 3+ , 2 3+ , and 3 + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Structural and functional characterization of KEOPS dimerization by Pcc1 and its role in t 6 A biosynthesis

KEOPS is an ancient protein complex required for the biosynthesis of N6-threonylcarbamoyladenosine (t 6 A), a universally conserved tRNA modification found on all ANN-codon recognizing tRNAs. KEOPS consist minimally of four essential subunits, namely the proteins Kae1, Bud32, Cgi121 and Pcc1, with yeast possessing the fifth essential subunit Gon7. Bud32, Cgi121, Pcc1 and Gon7 appear to have evolved to regulate the central t6A biosynthesis function of Kae1, but their precise function and mechanism of action remains unclear. Pcc1, in particular, binds directly to Kae1 and by virtue of its ability to form dimers in solution and in crystals, Pcc1 was inferred to function as a dimerization module for Kae1 and therefore KEOPS. We now present a 3.4 Å crystal structure of a dimeric Kae1–Pcc1 complex providing direct evidence that Pcc1 can bind and dimerize Kae1. Further biophysical analysis of a complete archaeal KEOPS complex reveals that Pcc1 facilitates KEOPS dimerization in vitro. Interestingly, while Pcc1-mediated dimerization of KEOPS is required to support the growth of yeast, it is dispensable for t 6 A biosynthesis by archaeal KEOPS in vitro, raising the question of how precisely Pcc1-mediated dimerization impacts cellular biology.

59 BASIC BIOLOGICAL SCIENCES↗