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DOE OSTI2024

Investigating the impact of donor atoms of single-source precursors on f-element nanomaterial formation and mechanisms of initial bond cleavage

Nanotechnology is advancing exponentially, with novel discoveries and applications emerging every day across various fields, including environmental remediation, biomedicine, electronics, and textiles. Nanoparticles (NPs) are defined as particles with sizes ranging from 1 to 100 nm, and their properties are influenced by factors such as composition, phase, size, and shape. Single-source precursors (SSPs) offer a promising method for controlling the synthesis of phase-pure nanoparticles with the desired stoichiometry and have been successfully applied to prepare transition metal and lanthanide NPs. SSPs are molecular compounds that contain all the necessary components to form the final nanomaterial and decompose under mild conditions, such as heating, to create the solid-state product. The objective of this work was to garner a mechanistic understanding of cerium oxide NP formation from cerium SSPs. To achieve these goals, first, ligands with oxygen and sulfur donor atoms were synthesized; among the array of ligands synthesized, some were novel. These ligands were then chelated to cerium ions to synthesize cerium precursors. Initially, known cerium alkoxide precursors were synthesized. Subsequently, these basic cerium complexes were further manipulated through acid-base protonolysis reactions to install a diverse set of ligands. Within this body of work, 10 novel cerium precursors were successfully synthesized. The ligands and the SSPs were analyzed using nuclear magnetic resonance (NMR) and thermogravimetric analysis coupled with differential scanning calorimetry (TGA-DSC). These SSPs were then introduced to a collision-induced dissociation mass spectrometer (CID-MS), and their dissociation pathways were studied.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗

DOE OSTI2020

Catalytic consequences of hydrogen addition events and solvent-adsorbate interactions during guaiacol-H 2 reactions at the H 2 O-Ru(0 0 0 1) interface

Catalytic reactions of biomass-derived phenolics and H 2 occur on transition metal surfaces via competitive C–O cleavage and ring saturation pathways, with both requiring multiple hydrogen addition events before forming their respective rate limiting transition states. These events are markedly affected by solvent chemical identity, with polar protic solvents ionizing hydrogen adatoms (H*) to interfacial protons (H + ) and opening up new catalytic routes. Here, we establish the reaction coordinate space for guaiacol-H 2 reactions on Ru(0 0 0 1) using density functional theory and describe the atomic-scale effect of a polar protic solvent, H 2 O. Coupled H + and H* attack leads to quasi-equilibrated enol and keto intermediates as the precursors for C–O cleavage and ring saturation, respectively. For C–O cleavage, H 2 O solvent enables a lower energy pathway via concomitant transfer of the hydroxyl H + to the methoxy oxygen during C–OCH 3 cleavage, forming a charge separated [Ru(s)–(C 6 H 5 O – )…(H + )…OCH 3 ] transition state and reducing the barrier by up to 0.8 eV as compared to unassisted C–OCH 3 cleavage. For ring saturation, H* attack onto an unsaturated meta carbon is rate limiting with no direct solvent participation, suggesting that protic polar solvents selectively promote the C–O cleavage pathway. Taken together, we show that activating guaiacol for either C–O bond cleavage or ring saturation product formation depends on the reactive hydrogen identity (H* or H + ), enol/keto isomerization equilibrium, and accessibility of the proton assisted Car–OCH 3 cleavage transition state. Here, all such factors are tunable via changes to the solvent or metal identity.

09 BIOMASS FUELS↗

DOE OSTI2024

Data Analytics for Catalysis Predictions: Are We Ready Yet?

Catalysis informatics has received tremendous attention in recent years as a tool to design catalysts and discover unique descriptors that capture the relationships between chemical properties and catalytic performance. One of the stop-gaps in understanding catalytic effects, which is often ignored and limits the deployment of data science tools, relates to the lack of uniform data. The catalytic cleavage of C–X (X= H, C, N, and O) bonds is relevant to many fundamental catalytic processes. In this Perspective, we performed data analytics on four groups of C–X cleavage reactions that are common in production, upcycling, or reactive separation: the C–C cleavage in cyclopropyl alcohol, the C–H cleavage in hydroacylation reactions, the C–O cleavage in β-O-4 linkages, and the C–N cleavage in amides, using experimental data collected from the literature to understand their underlying correlations. Experimental variables of high impact are identified for each reaction by dimensionality reduction methods. We highlight the urgent need for experimental data sets that include full details on the reaction conditions, such as reagent concentration, reaction temperature, or time in machine-readable forms. We discuss the potential improvement of the data of these reactions and promising approaches such as autonomous experiments to fill the gaps in unbiased experimental data. Finally, we also address the early stage consideration of separation aspects in the experimental design of efficient catalytic systems for these fundamental examples of chemical reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Emergence of catalytic function in prebiotic information-coding polymers

Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10 2 –10 3 , a factor consistent with the existing experiments. The evolutionary pressure leads to a further increase in catalytic efficiency. The presented mechanism provides an escape route from a relatively simple pairwise replication of oligomers toward a more complex behavior involving catalytic function. This provides a bridge between the information-first origin of life scenarios and the paradigm of autocatalytic sets and hypercycles, albeit based on cleavage rather than synthesis of reactants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Emergence of catalytic function in prebiotic information-coding polymers

Tkachenko, Alexei V. (ORCID:000000031291243X)↗

DOE OSTI2023

Mechanistic insights to drive catalytic hydrogenation of formamide intermediates to methanol via deaminative hydrogenation

Amine-promoted hydrogenation of CO 2 to methanol typically proceeds via a formamide intermediate when amines are used as additives or if the hydrogenation is performed in carbon capture solvents. The catalysts used for the hydrogenation of the formamide intermediate dictate the selectivity of the products formed: 1) Deoxygenative hydrogenation (C–O bond cleavage) resulting in N-methylation of amine and deactivation of the solvent, 2) Deaminative hydrogenation (C–N bond cleavage) resulting in formation of methanol and regeneration of the solvent. To date, catalytic reductions of CO 2 with amine promoters suffer from poor selectively for methanol which we attribute to the limiting formamide intermediate, though to date, the conditions that favor C–N cleavage have yet to be fully understood. To better understand the reactivity of the formamide intermediates, a range of heterogenous catalysts were used to study the hydrogenation of formamide. Well-known gas phase CO 2 hydrogenation catalysts catalyze the hydrogenation of formamide to N-methyl product via C–O bond cleavage. However, the selectivity can be readily shifted to selective C–N bond cleavage by addition of an additive with sufficient basicity for both homogenous and heterogeneous catalytic systems. The base additive shifts the selectivity by deprotonating a hemiaminal intermediate formed in situ during the formamide hydrogenation. This prevents dehydration process leading to N-methylated product, which is a key capture solvent deactivation pathway that hinders amine use in carbon capture, utilization, and storage (CCUS). The findings from this study provide a roadmap on how to improve the selectivity of known heterogenous catalysts, enabling catalytic reduction of captured CO 2 to methanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Insights into the mechanism of SARS-CoV-2 main protease autocatalytic maturation from model precursors

A critical step for SARS-CoV-2 assembly and maturation involves the autoactivation of the main protease (MPro WT ) from precursor polyproteins. Upon expression, a model precursor of MPro WT mediates its own release at its termini rapidly to yield a mature dimer. A construct with an E290A mutation within MPro exhibits time dependent autoprocessing of the accumulated precursor at the N-terminal nsp4/nsp5 site followed by the C-terminal nsp5/nsp6 cleavage. In contrast, a precursor containing E290A and R298A mutations (MPro M ) displays cleavage only at the nsp4/nsp5 site to yield an intermediate monomeric product, which is cleaved at the nsp5/nsp6 site only by MPro WT . MPro M and the catalytic domain (MPro 1-199 ) fused to the truncated nsp4 region also show time-dependent conversion in vitro to produce MPro M and MPro 1-199 , respectively. The reactions follow first-order kinetics indicating that the nsp4/nsp5 cleavage occurs via an intramolecular mechanism. These results support a mechanism involving an N-terminal intramolecular cleavage leading to an increase in the dimer population and followed by an intermolecular cleavage at the C-terminus. Thus, targeting the predominantly monomeric MPro precursor for inhibition may lead to the identification of potent drugs for treatment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases

White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic monomericcompounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into ß-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.

dioxygenase↗

DOE OSTI2022

Steric and Lewis Basicity Influence of the Second Coordination Sphere on Electrocatalytic CO 2 Reduction by Manganese Bipyridyl Complexes

This study aims to provide a greater insight into the balance between steric (bpy vs (Ph) 2 bpy vs mes 2 bpy ligands) and Lewis basic ((Ph) 2 bpy vs (MeOPh) 2 bpy vs (MeSPh) 2 bpy ligands) influence on the efficiencies of the protonation-first vs reduction-first CO 2 reduction mechanisms with [Mn I (R 2 bpy)(CO) 3 (CH 3 CN)] + precatalysts, and on their respective transition-state geometries/energies for rate-determining C–OH bond cleavage toward CO evolution. The presence of only modest steric bulk at the 6,6'-diphenyl-2,2'-bipyridyl ((Ph) 2 bpy) ligand has here allowed unique insight into the mechanism of catalyst activation and CO 2 binding by navigating a perfect medium between the nonsterically encumbered bpy-based and the highly sterically encumbered mes2bpy-based precatalysts. Cyclic voltammetry conducted in CO 2 -saturated electrolyte for the (Ph) 2 bpy-based precatalyst [2-CH 3 CN] + confirms that CO 2 binding occurs at the two-electron-reduced activated catalyst [2] – in the absence of an excess proton source, in contrast to prior assumptions that all manganese catalysts require a strong acid for CO 2 binding. This observation is supported by computed free energies of the parent–child reaction for [Mn–Mn] o dimer formation, where increased steric hindrance relative to the bpy-based precatalyst correlates with favorable CO 2 binding. A critical balance must be adhered to, however, as the absence of steric bulk in the bpy-based precatalyst [1-CH 3 CN] + maintains a lower overpotential than [2-CH 3 CN] + at the protonation-first pathway with comparable kinetic performance, whereas an ~2-fold greater TOF max is observed at its reduction-first pathway with an almost identical overpotential as [2-CH 3 CN] + . Notably, excessive steric bulk in the mes2bpy-based precatalyst [3-CH 3 CN] + results in increased activation free energies of the C–OH bond cleavage transition states for both the protonation-first and the reduction-first pathways relative to both [1-CH 3 CN] + and [2-CH 3 CN] + . In fact, [3-CH 3 CN] + requires a 1 V window beyond its onset potential to reach its peak catalytic current, which is in contrast to the narrower (<0.30 V) potential response window of the remaining catalysts here studied. Furthermore, voltammetry recorded under 1 atm of CO 2 with 2.8 M (5%) H 2 O establishes [2-CH 3 CN] + to have the lowest overpotential (η = 0.75 V) in the series here studied, attributed to its ability to lie “on the fence” when providing sufficient steric bulk to hinder (but not prevent) [Mn–Mn] o dimerization, while simultaneously having a limited steric impact on the free energy of activation for the rate-determining C–OH bond cleavage transition state. While the methoxyphenyl bpy-based precatalyst [4-CH 3 CN] + possesses an increased steric presence relative to [2-CH 3 CN] + , this is offset by its capacity to stabilize the C–OH bond cleavage transition states of both the protonation-first and the reduction-first pathways by facilitating second coordination sphere H-bonding stabilization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Theoretical Investigation of Solvent Effects on the Hydrodeoxygenation of Propionic Acid over a Ni(111) Catalyst Model

The effect of two solvents, liquid water and 1,4-dioxane, has been studied from first principles on the hydrodeoxygenation of propionic acid over a Ni (111) catalyst surface model. A mean-field microkinetic model was developed to investigate these effects at a temperature of 473 K. Under all reaction conditions, a decarbonylation mechanism is favored significantly over a decarboxylation pathway. Although no significant solvent effects were observed on the decarbonylation rate, a substantial solvent stabilization of two key surface intermediates in the decarboxylation mechanism, CH 3 CCOO and CH 3 CHCOO, lead to a notable increase of the decarboxylation rate by two orders of magnitude in liquid water and by one order of magnitude in liquid 1,4-dioxane. Furthermore, a significant solvent stabilization of the transition state of C-H bond cleavage of the α-carbon of CH 3 CHCO, relative to the stabilization of the C-C bond cleavage of the α-carbon of CH 3 CHCO, leads to a change in dominant pathway in the liquid phase environments. Finally, a sensitivity analysis shows that the C-OH bond cleavage of propionic acid and C-C bond cleavage of the α-carbon of CH 3 CHCO are the most rate controlling states in the gas phase. In contrast, in solvents the dehydrogenation of CH 3 CHCO becomes the most influential step. This shift in rate controlling state is attributed to the solvent effect on the dehydrogenation of CH 3 CHCO, which is facilitated in aqueous phase. Altogether, it is likely that the investigated (111) facet of Ni is not active for the hydrodeoxygenation of propionic acid in neither the gas nor liquid phase and other Ni facets or phases must be responsible for the experimentally observed kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Insights into Spontaneous Solid Electrolyte Interphase Formation at Magnesium Metal Anode Surface from Ab Initio Molecular Dynamics Simulations

Spontaneous chemical reactivity at multivalent (Mg, Ca, Zn, Al) electrode surfaces is critical to solid electrolyte interphase (SEI) formation, and hence, directly affects the longevity of batteries. Here, we report an investigation of the reactivity of 0.5 M Mg(TFSI)2 in 1,2-dimethoxyethane (DME) solvent at a Mg(0001) surface using ab initio molecular dynamics (AIMD) simulations and detailed Bader charge analysis. Based on the simulations, the initial degradation reactions of the electrolyte strongly depend on the structure of the Mg(TFSI)2 species near the anode surface. At the surface, the dissociation of Mg(TFSI)2 species occurs via cleavage of the N-S bond for the solvent separated ion pair (SSIP) and via cleavage of the C-S bond for the contact ion pair (CIP) configuration. In the case of the CIP, both TFSI anions undergo spontaneous bond dissociation reactions to form atomic O, C, S, F, and N species adsorbed on the surface of the Mg anode. These products indicate that the initial SEI layer formed on the surface of the pristine Mg anode consists of a complex mixture of multiple components such as oxides, carbides, sulfides, fluorides, and nitrides. We believe that the atomic level insights gained from these simulations will lay the groundwork for the rational design of tailored and functional interphases that are critical for the success of multivalent battery technology.

Agarwal, Garvit↗

DOE OSTI2022

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI

Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein–DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Density functional theory calculation of helium segregation and decohesion effect in W110/Ni111 interphase boundary

Density functional theory (DFT) is employed to study the preferential distribution and decohesion effect of He in a W-NiFe composite consisting of W particles embedded in an Ni-based solid solution matrix. A slab containing {110}<100>W//{111}<110>Ni interface is employed as a surrogate model for the W-NiFe system. Firstly, the fracture energy of the W/Ni interphase boundary (IB) (4.37 J/m 2 ) is higher than the cleavage energy of Ni{111} (3.82 J/m^2) and lower than the cleavage energy of W{110} (6.60 J/m 2 ). The comparison shows that the cohesion of the IB is stronger than the Ni{111} planes that are away from the IB. However, the cohesion between the Ni{111} planes adjacent to the IB is found to be the weakest in this system, with a cleavage energy of 3.11 J/m 2 . Subsequently, formation energy of He is calculated in the Ni slab, W slab, and various interstitial sites in the IB. The DFT calculations show that He is significantly more stable in Ni than in W, by about 1.75 eV. Interestingly, He does not prefer to segregate at the IB as compared to bulk Ni. Nevertheless, it prefers to segregate to the region between the Ni{111} planes adjacent to the IB, and decreases the cohesion of the already weakest region. Based on an estimated amount of He gas production in 5 years under first wall neutron irradiation (neutron flux of 1.04x10 15 n/cm 2 /s), the He will decrease the cleavage energy of the weakest region by 21.2%, 15.4%, and 12.2% at 800, 1000, and 1200 C, respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair

Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Computational Investigations of the Reactivity of Metalloporphyrins for Ammonia Oxidation

Density functional theory and molecular dynamics simulations were used to assess the ability of tetraphenylporphyrin (TPP)M complexes (where M = Cr, Mn, Fe, Co, Ni, Mo, Ru, W, and Os) to coordinate and weaken the N-H bonds of ammonia, as well as their reactivity towards N-N bond formation for N 2 generation. Compared to other metalloporphyrins, bis-ammonia complexes (TPP)Mo(NH 3 ) 2 and (TPP)W(NH 3 ) 2 exhibit low and level N-H BDFEs due to a stabilized (TPP)M(NH 3 )(NH) intermediate by multiple metal-ligand bonding. These results resemble those previously obtained for polypyridyl metal complexes, suggesting that broad trends in reactivity towards N-H bond cleavage are more metal-dependent rather than ligand-dependent for a metal in a nitrogen pseudo-octahedral environment. We investigated N-N bond formation via NH 3 nucleophilic attack on M-NH and M-N intermediates, compared to bimolecular coupling of M-NH x intermediates. We evaluated the reactivity of (TPP)Fe(NH 3 ) 2 towards N-N bond formation via a hydrazine pathway, and found amide-amide coupling to form a bridged hydrazido complex to be the most favorable pathway for N-N bond formation. Further investigation of possible N-N bond formation pathways by reaction with NH 3 led us to identify a possible Fe III -•NH species with significant aminyl character that bypasses the nucleophilic attack of NH 3 and that promotes homolytic N-H bond cleavage of ammonia. This reaction forms a Fe-NH 2 moiety and a transient •NH 2 radical that subsequently forms an N-N bond with the Fe-NH 2 moiety to form a (TPP)Fe(NH 3 )(N 2 H 4 ) species. Furthermore, these results indicate the need to evaluate the radical character of imido species and their reactivity towards N-H bond cleavage of ammonia.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Towards understanding the formation of internal fragments generated by collisionally activated dissociation for top-down mass spectrometry

Top-down mass spectrometry (TD-MS) generates fragment ions that returns information on the polypeptide amino acid sequence. In addition to terminal fragments, internal fragments that result from multiple cleavage events can also be formed. Traditionally, internal fragments are largely ignored due to a lack of available software to reliably assign them, mainly caused by a poor understanding of their formation mechanism. To accurately assign internal fragments, their formation process needs to be better understood. Here we applied a statistical method to compare fragmentation patterns of internal and terminal fragments of peptides and proteins generated by collisionally activated dissociation (CAD). Internal fragments share similar fragmentation propensities with terminal fragments (e.g., enhanced cleavages N-terminal to proline and C-terminal to acidic residues), suggesting that their formation follows conventional CAD pathways. Internal fragments should be generated by subsequent cleavages of terminal fragments and their formation can be explained by the well-known mobile proton model. Additionally, internal fragments can be coupled with terminal fragments to form complementary product ions that span the entire protein sequence. These enhance our understanding of internal fragment formation and can help improve sequencing algorithms to accurately assign internal fragments, which will ultimately lead to more efficient and comprehensive TD-MS analysis of proteins and proteoforms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Hydrogenation and C-S bond activation pathways in thiophene and tetrahydrothiophene reactions on sulfur-passivated surfaces of Ru, Pt, and Re nanoparticles

Thiophene-H2 reactions proceed via sulfur removal and hydrogenation routes on dispersed metal nanoparticles that become decorated by refractory S-adlayers during catalysis. The identity and kinetic relevance of the required elementary steps are described here based on rates measured at S-chemical potentials set by H2S/H2 ratios similar to those prevalent during practical catalysis on Re, ReSx, Ru, and Pt catalysts. Free energies for S adatom formation (from H2S decomposition and H2 evolution) are strongly exothermic (< -50 kJ mol-1 on Pt(111) and < -150 kJ mol-1 on Re and Ru(0001)), but strong repulsions between S adatoms cause adsorption free energies to increase significantly with coverage on all three surfaces, preventing complete monolayer formation. These adlayers, composed of unreactive S-atoms (S') that cover 1/3–2/3 ML leave residual interstitial spaces (*) that bind S-atoms (S*), intermediates, and transition states reversibly, as required for catalytic turnovers. The number and binding properties of these interstices depend on the identity and chemical state of the nanoparticle bulk phase, which influences S'-binding and coverages and cause large differences in direct desulfurization and hydrogenation turnover rates (per exposed metal atom) on dispersed Re, ReSx, Ru, and Pt. The identity and kinetic relevance of elementary steps for desulfurization (to C4¬ hydrocarbons) and hydrogenation (to tetrahydrothiophene; THT) are similar among these catalysts; they involve the kinetically-relevant formation of a thiophene-derived intermediate (monohydrothiophene on Re and ReSx; dihydrothiophene on Ru and Pt) that either cleaves its C-S bond or “over-hydrogenates” to THT in one surface sojourn. THT then undergoes C-S bond cleavage in secondary reactions that correct such over-hydrogenation to form the more unsaturated species that cleave C-S bonds. THT/C4 product ratios are insensitive to H2S/H2 ratios and thiophene pressure, even though active interstitial spaces are covered by kinetically-detectable coverages of S* and thiophene; therefore, primary and secondary reactions must involve the same active surfaces. The observed increase in THT/C4 ratios with H2 pressure shows that THT formation transition states involve a larger number of H-atoms than for C-S cleavage. The requirement for bound species with intermediate unsaturation (between THT and thiophene) for C-S bond cleavage is reminiscent of the H-shuttling required in C-C and C-O hydrogenolysis, reactions that involve the partial dehydrogenation of alkanes and alkanols, respectively, to weaken such bonds and to increase the formation entropy of the relevant transition states via the evolution of H2(g). These mechanistic details challenge prevalent paradigms about different site requirements for hydrogenation and desulfurization pathways and about how metal-sulfur bond energies act as descriptors of reactivity; in fact, such binding energies merely act to define the refractory S-adlayers that enable the formation of weakly-binding interstices that reversibly bind intermediates and transition states, thus allowing catalytic turnovers.

Yik, Edwin↗