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Results for “small molecule activation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Polymerized small molecular acceptor based all-polymer solar cells with an efficiency of 16.16% via tuning polymer blend morphology by molecular design

All-polymer solar cells (all-PSCs) based on polymerized small molecular acceptors (PSMAs) have made significant progress recently. Here, we synthesize two A-DA’D-A small molecule acceptor based PSMAs of PS-Se with benzo[c][1,2,5]thiadiazole A’-core and PN-Se with benzotriazole A’-core, for the studies of the effect of molecular structure on the photovoltaic performance of the PSMAs. The two PSMAs possess broad absorption with PN-Se showing more red-shifted absorption than PS-Se and suitable electronic energy levels for the application as polymer acceptors in the all-PSCs with PBDB-T as polymer donor. Cryogenic transmission electron microscopy visualizes the aggregation behavior of the PBDB-T donor and the PSMA in their solutions. In addition, a bicontinuous-interpenetrating network in the PBDB-T:PN-Se blend film with aggregation size of 10~20 nm is clearly observed by the photoinduced force microscopy. The desirable morphology of the PBDB-T:PN-Se active layer leads its all-PSC showing higher power conversion efficiency of 16.16%.

14 SOLAR ENERGY↗
DOE OSTI2022

The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in-situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations

This research will provide new methods to determine the structures and compositions of heterogeneous catalysts as they exist in reaction conditions. The new tools will make it possible to understand how extremely small material structures—ones in a size range spanning from single atoms to larger polyatomic clusters—make it possible to carry out highly selective chemical transformations required to synthesize useful materials as well as for efficient energy production and utilization. The tools will make it possible to see how the atomic structures of catalytic materials evolve over time under the conditions of their use, and in this way provide understandings to guide the design of new energy-efficient catalysts. The work will make it possible to answer long standing questions that include the following. How does catalyst structure help guide molecules along specific reaction pathways? What are the important intermediates involved in these transformations? How do the structures and reactivity of catalytic materials, as well as the chemistry of their interfaces, vary with reaction conditions? Is it possible to develop new catalytic materials using new knowledge of the active structures and reaction mechanisms? The work will provide heretofore unavailable experimental tools that can be applied in advanced programs of research addressing such questions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Depletion of the Protein Hydration Shell with Increasing Temperature Observed by Small-Angle X-ray Scattering and Molecular Simulations

The hydration shell is an integral part of proteins since it plays key roles in conformational transitions, molecular recognition, and enzymatic activity. While the dynamics of the hydration shell have been described by spectroscopic techniques, the structure of the hydration shell remains less understood due to the lack of hydration shell-sensitive structural probes with high spatial resolution. We combined temperature-ramp small-angle X-ray scattering (T-ramp SAXS) from 255 to 335 K with molecular simulations to demonstrate that the hydration shells of the IgG-binding domain of Protein G (GB3) and the villin headpiece are remarkably temperature-sensitive. For proteins in the folded state, T-ramp SAXS data and explicit-solvent SAXS predictions consistently demonstrate decays of protein contrasts and radii of gyration with increasing temperature, which are shown to reflect predominantly temperature-sensitive, depleting hydration shells. The depletion is caused not merely by enhanced disorder within the hydration shells but also by partial displacements of surface-coordinated water molecules. Together, T-ramp SAXS and explicit-solvent SAXS calculations provide a novel structural view of the protein hydration shell, which underlies temperature-dependent processes such as cold denaturation, thermophoresis, or biomolecular phase separation.

electron density↗
DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sequentially regular polymer acceptors featuring flexible spacers for high-performance and mechanically robust all-polymer solar cells

Developing high-performance and mechanically robust polymer solar cells (PSCs) is crucial for realizing wearable power sources. While efficient all-polymer solar cells (all-PSCs) can be fabricated from polymerized small-molecule acceptors (PSMAs) with high optical absorption and electron mobilities, they still show limited mechanical robustness. Here, we achieve highly efficient and mechanically robust all-PSCs by designing a PSMA (PYFS-Reg) containing sequence-regular flexible spacers (FSs). The regular incorporation of the FS units into PSMAs is essential in simultaneously improving the electrical and mechanical properties of blend films. As a result, all-PSCs featuring PYFS-Reg achieve a high power conversion efficiency (PCE = 16.1%) and stretchability (crack onset strain (COS) = 22.4%), outperforming PSMAs without FSs (i.e., PYBDT, PCE = 12.6% and COS = 11.7%) or with randomly distributed FSs (i.e., PYFS-Ran, PCE = 12.2% and COS = 18.1%). Importantly, these all-PSCs are fabricated by an environmentally benign, non-halogenated solvent process. To further demonstrate their feasible applications in wearable devices, we construct intrinsically stretchable (IS) all-PSCs by using PYFS-Reg-based active layers, which exhibit a high PCE (10.6%) and excellent device stretchability (strain at PCE 80% = 36.7%).

14 SOLAR ENERGY↗
DOE OSTI2024

The HHV-6B U20 glycoprotein binds ULBP1, masking it from recognition by NKG2D and interfering with natural killer cell activation

Human Herpesvirus 6B (HHV-6B) impedes host immune responses by downregulating class I MHC molecules (MHC-I), hindering antigen presentation to CD8+ T cells. Downregulation of MHC-I disengages inhibitory receptors on natural killer (NK) cells, resulting in activation and killing of the target cell if NK cell activating receptors such as NKG2D have engaged stress ligands upregulated on the target cells. Previous work has shown that HHV-6B downregulates three MHC-like stress ligands MICB, ULBP1, and ULBP3, which are recognized by NKG2D. The U20 glycoprotein of the related virus HHV-6A has been implicated in the downregulation of ULBP1, but the precise mechanism remains undetermined. We set out to investigate the role of HHV-6B U20 in modulating NK cell activity. We used HHV-6B U20 expressed as a recombinant protein or transduced into target cells, as well as HHV-6B infection, to investigate binding interactions with NK cell ligands and receptors and to assess effects on NK cell activation. Small-angle X-ray scattering was used to align molecular models derived from machine-learning approaches. We demonstrate that U20 binds directly to ULBP1 with sub-micromolar affinity. Transduction of U20 decreases NKG2D binding to ULBP1 at the cell surface but does not decrease ULBP1 protein levels, either at the cell surface or in toto. HHV-6B infection and soluble U20 have the same effect. Transduction of U20 blocks NK cell activation in response to cell-surface ULBP1. Structural modeling of the U20 – ULBP1 complex indicates some similarities to the m152-RAE1γ complex.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

microRNAs (miR 9, 124, 155 and 224) transdifferentiate mouse macrophages to neurons

Highlights: • miR 9, miR 124 and miR155 could reprogramme macrophages to mature neurons. • miR-induced neuronal reprogramming involves stem cell-like intermediate phenotype. • miR 9, miR 124 and miR155 could also reprogramme CD133+ stem cells to mature neurons. Development is an irreversible process of differentiating the undifferentiated cells to functional cells. Brain development involves generation of cells with varied phenotype and functions, which is limited during adulthood, stress, damage/degeneration. Cellular reprogramming makes differentiation reversible process with reprogramming somatic/stem cells to alternative fate with/without stem cells. Exogenously expressed transcription factors or small molecule inhibitors have driven reprogramming of stem/somatic cells to neurons providing alternative approach for pre-clinical/clinical testing and therapeutics. Here in, we report a novel approach of microRNA (miR)- induced trans-differentiation of macrophages (CD11b high) to induced neuronal cells (iNCs) (neuronal markershigh- Nestin, Nurr1, Map2, NSE, Tubb3 and Mash1) without exogenous use of transcription factors. miR 9, 124, 155 and 224 successfully transdifferentiated macrophages to neurons with transient stem cell-like phenotype. We report trans differentiation efficacy 18% and 21% with miR 124 and miR 155. in silico(String 10.0, miR gator, mESAdb, TargetScan 7.0) and experimental analysis indicate that the reprogramming involves alteration of pluripotencygenes like Oct4, Sox2, Klf4, Nanog and pluripotency miR, miR 302. iNCs also shifted to G0 phase indicating manipulation of cell cycle by these miRs. Further, CD133+ intermediate cells obtained during current protocol could be differentiated to iNCs using miRs. The syanpsin{sup +} neurons were functionally active and displayed intracellular Ca{sup +2} evoke on activation. miRs could also transdifferentiate bone marrow-derived macrophages and peripheral blood mononuclear cells to neuronal cells. The current protocol could be employed for direct in vivo reprogramming of macrophages to neurons without teratoma formation for transplantation and clinical studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals

Boceprevir is an HCV NSP3 inhibitor that was explored as a repurposed drug for COVID-19. It inhibits the SARS-CoV-2 main protease (M Pro ) and contains an α-ketoamide warhead, a P1 β-cyclobutylalanyl moiety, a P2 dimethylcyclopropylproline, a P3 tert-butylglycine, and a P4 N-terminal tert-butylcarbamide. By introducing modifications at all four positions, we synthesized 20 boceprevir-based M Pro inhibitors including PF-07321332 and characterized their M Pro inhibition potency in test tubes (in vitro) and 293T cells (in cellulo). Crystal structures of M Pro bound with 10 inhibitors and cytotoxicity and antiviral potency of 4 inhibitors were characterized as well. Replacing the P1 site with a β-(S-2-oxopyrrolidin-3-yl)-alanyl (Opal) residue and the warhead with an aldehyde leads to high in vitro potency. The original moieties at P2, P3 and the P4 N-terminal cap positions in boceprevir are better than other tested chemical moieties for high in vitro potency. In crystal structures, all inhibitors form a covalent adduct with the M Pro active site cysteine. Here, the P1 Opal residue, P2 dimethylcyclopropylproline and P4 N-terminal tert-butylcarbamide make strong hydrophobic interactions with M Pro , explaining high in vitro potency of inhibitors that contain these moieties. A unique observation was made with an inhibitor that contains a P4 N-terminal isovaleramide. In its M Pro complex structure, the P4 N-terminal isovaleramide is tucked deep in a small pocket of M Pro that originally recognizes a P4 alanine side chain in a substrate. Although all inhibitors show high in vitro potency, they have drastically different in cellulo potency to inhibit ectopically expressed M Pro in human 293T cells. In general, inhibitors with a P4 N-terminal carbamide or amide have low in cellulo potency. This trend is reversed when the P4 N-terminal cap is changed to a carbamate. The installation of a P3 O-tert-butyl-threonine improves in cellulo potency. Three molecules that contain a P4 N-terminal carbamate were advanced to cytotoxicity tests on 293T cells and antiviral potency tests on three SARS-CoV-2 variants. They all have relatively low cytotoxicity and high antiviral potency with EC 50 values around 1 μM. A control compound with a nitrile warhead and a P4 N-terminal amide has undetectable antiviral potency. Based on all observations, we conclude that a P4 N-terminal carbamate in a boceprevir derivative is key for high antiviral potency against SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure of the human dopamine transporter and mechanisms of inhibition

Abstract The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement 1 . Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, the human dopamine transporter (hDAT) and mechanisms by which it is inhibited by small molecules and Zn 2+ are without a high-resolution structural context. Here we determine the structure of hDAT in a tripartite complex with the competitive inhibitor and cocaine analogue, (–)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane 2 (β-CFT), the non-competitive inhibitor MRS7292 3 and Zn 2 + (ref. 4 ). We show how β-CFT occupies the central site, approximately halfway across the membrane, stabilizing the transporter in an outward-open conformation. MRS7292 binds to a structurally uncharacterized allosteric site, adjacent to the extracellular vestibule, sequestered underneath the extracellular loop 4 (EL4) and adjacent to transmembrane helix 1b (TM1b), acting as a wedge, precluding movement of TM1b and closure of the extracellular gate. A Zn 2+ ion further stabilizes the outward-facing conformation by coupling EL4 to EL2, TM7 and TM8, thus providing specific insights into how Zn 2+ restrains the movement of EL4 relative to EL2 and inhibits transport activity.

Science & Technology - Other Topics↗
DOE OSTI2023

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Insights into regulatory T-cell and type-I interferon roles in determining abacavir-induced hypersensitivity or immune tolerance

Introduction Clinical use of several small molecule drugs may lead to severe T-cell-mediated idiosyncratic drug hypersensitivity reactions (iDHR) linked to HLA alleles, including abacavir (ABC) with HLA-B*57:01. Due to study limitations in humans, pathogenic networks in iDHR remain elusive. HLA transgenic murine models have been proposed to bridge knowledge gaps in tolerance and susceptibility to drugs. Methods Mice expressing HLA-B*57:01 and Foxp3-DTR/EGFP were generated to selectively deplete regulatory T-cells (Treg) with diphtheria toxin. ABC was administered for 8 days alone or together with cell- and cytokine-depleting antibodies. Cellular and transcriptomic responses were analyzed by RNA, flow cytometry and fluorescence methods. Results While CD8 + T-cell responses to ABC require HLA presentation, ABC also triggered mitochondrial stress in macrophagesin vitro, independently of HLA.In vivo, Treg were the primary mechanism of drug tolerance controlling HLA presentation and costimulation by antigen presenting cells. Treg ablation uncovered immune adverse events linked to activation and proliferation of both drug-specific and bystander CD8 + T-cells through CD28-mediated pathways with support from CD4 + non-Treg. Type-I interferon (IFN-I) and cellular-stress pathways influenced the fate of lymph node cells responding to ABC, implicating innate immune cells such as macrophages and plasmacytoid dendritic cells in the development of T-cell responses against the drug. IFN-I and IL-2 were necessary for CD8 + T-cell differentiation and ABC-induced adverse reactions. Conclusions This study unveils novel immune mechanisms driven by drug and host-related factors required forin vivoreactions and sheds light on potential biomarker and therapeutic targets for managing and preventing severe and life-threatening iDHR.

Immunology↗
DOE OSTI2020

Pt–Co truncated octahedral nanocrystals: a class of highly active and durable catalysts toward oxygen reduction

We report a facile and scalable synthesis of Pt–Co truncated octahedral nanocrystals (TONs) by employing Pt(acac) 2 and Co(acac) 2 as precursors, together with CO molecules and Mn atoms derived from the decomposition of Mn 2 (CO) 10 as a reductant and a {111} facet-directing agent, respectively. Both the composition and yield of the Pt–Co TONs could be varied through the introduction of CHCl 3 . When tested at 80 °C using membrane electrode assembly (MEA), the 4 nm Pt 2.6 Co TONs gave a mass activity of 294 A g Pt –1 at beginning-of-life (BOL) and it increased to 384 A g Pt –1 during recovery cycles. The mass activity at BOL only dropped by 24% after 30 000 voltage cycles at end-of-life (EOL) in a metal dissolution accelerated stress test. The Pt 2.6 Co/C catalyst outperformed the commercial TKK Pt 3 Co/C (230 A g Pt –1 at BOL and 40% loss after 30 000 cycles at EOL) in terms of both activity and durability. Our systematic analysis suggested that the enhancement in activity can be attributed to the combination of small, uniform size and well-defined {111} facets. This new class of catalysts holds promise for applications in proton-exchange membrane fuel cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The Chemical Inventory of the Planet-hosting Disk PDS 70

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS 70 disk and report the first chemical inventory of the system. With a spatial resolution of 0."4–0."5 (~50 au), 12 species are detected, including CO isotopologs and formaldehyde, small hydrocarbons, HCN and HCO{sup +} isotopologs, and S-bearing molecules. SO and CH{sub 3}OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub)millimeter continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature, and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the nondetections. Excitation temperature is obtained for H{sub 2}CO. Deuteration and nitrogen fractionation profiles from the hydrocyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon-to-oxygen ratio C/O > 1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Single-Atom Doping at the Molecule–Metal Interface: How Rh Affects Surface Explosion Kinetics

Controlling chemical reactions at interfaces is central to many fields, including atmospheric, environmental, and biological chemistry as well as catalysis and corrosion. We performed a fundamental study of how catalytically active Rh atoms placed at and above a molecule-metal interface influence the surface reaction kinetics of tartaric acid (TA) decomposition. Specifically, TA decomposition on Cu(100) exhibits autocatalytic decomposition kinetics involving a slow initiation step followed by fast decomposition of the molecular layer. These so-called “surface explosions” are extremely sensitive to initial conditions, making it fundamentally interesting to study how the placement of reactive atoms affects the reaction rate. Temperature-programmed reaction (TPR) experiments reveal that Rh atoms embedded in the Cu(100) surface beneath TA (TA/Rh/Cu) or atop the TA layer (Rh/TA/Cu) reduce the decomposition temperature and modify the reaction rate constants. Isothermal TPR analysis reveals that Rh enhances both the initiation rate constant, k i , and the explosion rate constant, k e , facilitating explosive decomposition at lower temperatures. This result provides evidence that both the initiation and explosion steps occur at the metal-molecule interface and are accelerated by the presence of Rh at this interface. This study illustrates how small amounts of reactive elements may be used to control nonlinear kinetic processes at interfaces.

desorption↗
DOE OSTI2022

Antioxidant-induced transformations of a metal-acid hydrocracking catalyst in the deconstruction of polyethylene waste

Plastics are ideal for numerous applications, as driven by the development of complex formulations containing various additives to improve performance and processability. Unfortunately, chemical valorization strategies (e.g., catalytic deconstruction) often can be challenged by the presence of small-molecule additives, and quantification of the impact of these molecular constituents on upcycling processes remains elusive. Here, this dearth of information restricts catalyst design efforts to combine the robustness and performance necessary to improve plastics circularity. In this communication, we describe a systematic study of common plastics additives—phenolic antioxidants, and we quantify the relationship between additive content and deconstruction yields of high-density polyethylene (HDPE) over a platinum on tungstated zirconium (Pt/WO 3 /ZrO 2 ) hydrocracking catalyst. In the simplest case of a base (antioxidant- and slip agent-containing) HDPE resin versus a pure (additive-stripped) HDPE polymer, a two-fold decrease in the yield of gas and liquid products is noted for base HDPE resin. Furthermore, both antioxidant chemistry and concentration strongly impact conversion and individual product selectivities. Using infrared spectroscopy, we determine that antioxidants change the effective ratio of metal to acid sites (i.e., metal-acid balance) through reactions of phenols and/or other functional groups (e.g., acids, esters) with catalyst active sites. Overall, this work demonstrates the impact of one common set of additives on plastics deconstruction, and the analysis herein provides a blueprint for quantitatively assessing the effects of additives on plastics deconstruction processes and for evaluating the development of more robust catalytic strategies or more tolerable additive formulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO – , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. Finally, these features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise tens of billions of compounds due to advances in combinatorial chemistry. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have the major drawback that they require exceptional computing capabilities for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently-proposed learning paradigm that represents data with high-dimension binary vectors; this allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encodings of a commonly-used molecular representation, the extended connectivity fingerprint (ECFP). We show that HDC-based inference methods are as much as 91 times more efficient than traditional machine learning methods, and achieve an acceleration of nearly nine orders of magnitude compared to molecular docking. Our results show that HDC accelerated methods retain competitive accuracy on a number of well-studied tasks such as molecular property predictions using the MoleculeNet dataset, and bind/no-bind activity classification using the DUD-E and LIT-PCBA datasets. Our work thus motivates further investigation into molecular representation learning to develop ultraefficient pre-screening tools.

Jones, William↗
DOE OSTI2025

A Cocatalytic System for Electrooxidation of Primary, Secondary, and Benzyl Alcohols Based on a Triruthenium Oxo-Centered Cluster and NHPI

Increasing interest in alternative methods for fuel generation and chemical synthesis has resulted in an increased focus on the development of electrocatalysts for energy relevant small molecule transformations, such as the oxidation of methanol. Partial methanol oxidation is a crucial step in the generation of the commodity chemical formaldehyde, and its complete oxidation to carbon dioxide can also serve as the anodic reaction in direct methanol fuel cells. We report a coelectrocatalytic system comprised of an oxo-centered triruthenium cluster (Ru 3 O) as the catalyst, with the electro-generated N-phthalimido-N-oxyl (PINO) radical species acting as a redox mediator. Only a mild Brønsted base, 2,6-lutidine, is required to achieve an electrocatalytic response. The cocatalytic system demonstrates remarkable cooperativity, shifting the oxidation potential of MeOH (Ep) less positive by ca. 0.5 V compared to the intrinsic response of the Ru 3 O complex. Controlled potential electrolysis on a model substrate, 4-trifluoromethylbenzyl alcohol, demonstrates selective production of the two-electron, two-proton aldehyde product with a Faradaic efficiency of 79 ± 11% at a rate of 3.14 s –1 . The rate of cocatalysis is 50-fold greater than the intrinsic activity of Ru3O and 26-fold greater than that of PINO alone under otherwise identical conditions. Mechanistic studies reveal the oxidation of a Ru 3 O–alkoxide species as the potential-determining step, while two possible rate-determining steps are identified depending on the substrate. A preference for sterically uninhibited electron-rich benzyl alcohol substrates suggests that a H atom transfer from the Ru 3 O–alkoxide adduct to PINO is rate-determining, while the lack of an observed kinetic isotope effect using deuterated MeOH suggests the oxidation of the Ru 3 O–alkoxide species is both rate- and potential-determining for cocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗