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DOE OSTI2018

An In Situ Surface-Enhanced Infrared Absorption Spectroscopy Study of Electrochemical CO 2 Reduction: Selectivity Dependence on Surface C-Bound and O-Bound Reaction Intermediates

The CO2 electroreduction reaction (CO2RR) is a promising avenue to convert greenhouse gases into high-value fuels and chemicals, in addition to being an attractive method for storing intermittent renewable energy. Although polycrystalline Cu surfaces have long been known to be unique in their capabilities of catalyzing the conversion of CO2 to higher-order C1 and C2 fuels, such as hydrocarbons (CH4, C2H4, etc.) and alcohols (CH3OH, C2H5OH), product selectivity remains a challenge. Rational design of more selective catalysts would greatly benefit from a mechanistic understanding of the complex, multiproton, and multielectron conversion of CO2. In this study, we select three metal catalysts (Pt, Au, Cu) and apply in situ surface enhanced infrared absorption spectroscopy (SEIRAS) and ambient-pressure X-ray photoelectron spectroscopy (APXPS), coupled to density-functional theory (DFT) calculations, to get insight into the reaction pathway for the CO2RR. We present a comprehensive reaction mechanism for the CO2RR and show that the preferential reaction pathway can be rationalized in terms of metal–carbon (M–C) and metal–oxygen (M–O) affinity. We show that the final products are determined by the configuration of the initial intermediates, C-bound and O-bound, which can be obtained from CO2 and (H)CO3, respectively. C1 hydrocarbons are produced via OCH3,ad intermediates obtained from O-bound CO3,ad and require a catalyst with relatively high affinity for O-bound intermediates. Additionally, C2 hydrocarbon formation is suggested to result from the C–C coupling between C-bound COad and (H)COad, which requires an optimal affinity for the C-bound species, so that (H)COad can be further reduced without poisoning the catalyst surface. It is suggested that the formation of C1 alcohols (CH3OH) is the most challenging process to optimize, as stabilization of the O-bound species would both accelerate the formation of key intermediates (OCH3,ad) but also simultaneously inhibit their desorption from the catalyst surface. Our findings pave the way toward a design strategy for CO2RR catalysts with improved selectivity, based on the experimental/theoretical reaction mechanisms that have been identified. These results also suggest that designing the electronic structure of the catalyst is not the sole determining factor to achieve highly selective CO2RR catalysis; rather, tuning additional experimental reaction conditions such as electrolyte–intermediate interactions also become critical.

Katayama, Yu↗

DOE OSTI2016

Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy

Chemical transformations at the interface between solid/liquid or solid/gaseous phases of matter lie at the heart of key industrial-scale manufacturing processes. A comprehensive study of the molecular energetics and conformational dynamics that underlie these transformations is often limited to ensemble-averaging analytical techniques. In this paper we report the detailed investigation of a surface-catalysed cross-coupling and sequential cyclization cascade of 1,2-bis(2-ethynyl phenyl)ethyne on Ag(100). Using non-contact atomic force microscopy, we imaged the single-bond-resolved chemical structure of transient metastable intermediates. Theoretical simulations indicate that the kinetic stabilization of experimentally observable intermediates is determined not only by the potential-energy landscape, but also by selective energy dissipation to the substrate and entropic changes associated with key transformations along the reaction pathway. Finally, the microscopic insights gained here pave the way for the rational design and control of complex organic reactions at the surface of heterogeneous catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Revisiting Understanding of Electrochemical CO 2 Reduction on Cu(111): Competing Proton-Coupled Electron Transfer Reaction Mechanisms Revealed by Embedded Correlated Wavefunction Theory

Copper (Cu) electrodes, as the most efficacious of CO 2 reduction reaction (CO 2 RR) electrocatalysts, serve as prototypes for determining and validating reaction mechanisms associated with electrochemical CO 2 reduction to hydrocarbons. As in situ electrochemical mechanism determination by experiments is still out of reach, such mechanistic analysis typically is conducted using density functional theory (DFT). The semilocal exchange-correlation (XC) approximations most often used to model such catalysis unfortunately engender a basic error: predicting the wrong adsorption site for CO (a key CO 2 RR intermediate) on the most ubiquitous facet of Cu, namely, Cu(111). This longstanding inconsistency casts lingering doubt on previous DFT predictions of the attendant CO 2 RR kinetics. Here, we apply embedded correlated wavefunction (ECW) theory, which corrects XC functional error, to study the CO 2 RR on Cu(111) via both surface hydride (*H) transfer and proton-coupled electron transfer (PCET). We predict that adsorbed CO (*CO) reduces almost equally to two intermediates, namely, hydroxymethylidyne (*COH) and formyl (*CHO) at –0.9 V vs the RHE. In contrast, semilocal DFT approximations predict a strong preference for *COH. With increasing applied potential, the dominance of *COH (formed via potential-independent surface *H transfer) diminishes, switching to the competitive formation of both *CHO and *COH (both formed via potential-dependent PCET). Furthermore, our results also demonstrate the importance of including explicitly modeled solvent molecules in predicting electron-transfer barriers and reveal the pitfalls of overreliance on simple surface *H transfer models of reduction reactions.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2018

Trapping intermediates in metal transfer reactions of the CusCBAF export pump of Escherichia coli

Escherichia coli CusCBAF represents an important class of bacterial efflux pump exhibiting selectivity towards Cu(I) and Ag(I). The complex is comprised of three proteins: the CusA transmembrane pump, the CusB soluble adaptor protein, and the CusC outer-membrane pore, and additionally requires the periplasmic metallochaperone CusF. Here we used spectroscopic and kinetic tools to probe the mechanism of copper transfer between CusF and CusB using selenomethionine labeling of the metal-binding Met residues coupled to RFQ-XAS at the Se and Cu edges. The results indicate fast formation of a protein–protein complex followed by slower intra-complex metal transfer. An intermediate coordinated by ligands from each protein forms in 100 ms. Stopped-flow fluorescence of the capping CusF-W44 tryptophan that is quenched by metal transfer also supports this mechanism. The rate constants validate a process in which shared-ligand complex formation assists protein association, providing a driving force that raises the rate into the diffusion-limited regime.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Multiphysics modeling of accelerators through code integration

This work aims to improve the ability of particle accelerator researchers to develop high-performance accelerator cavity designs by creating an overall multiphysics framework that integrates and couples existing application codes. This framework will allow accelerator researchers to build multiphysics models that will optimize cavity design, improve understanding of whole-device performance, and reduce the development and fabrication costs of accelerator research. We utilize the open-source VizSchema data standard as an intermediate data structure interface layer to standardize interfaces between individual application codes. VizScema is extensively documented online, and plugins for VizSchema are available for popular visualization packages, including VisIt and ParaView. Currently, the work focuses on coupling the EM field solver COMSOL and the electron gun code MICHELLE to allow COMSOL field-solve results to be seamlessly used by MICHELLE for particle-solve. Later work will extend this integration to include other fields, particles, and thermodynamics simulation codes.

43 PARTICLE ACCELERATORS↗

DOE OSTI2016

Photocatalytic Conversion of Nitrobenzene to Aniline through Sequential Proton-Coupled One-Electron Transfers from a Cadmium Sulfide Quantum Dot

This paper describes the use of cadmium sulfide quantum dots (CdS QDs) as visible-light photocatalysts for the reduction of nitrobenzene to aniline through six sequential photoinduced, proton-coupled electron transfers. At pH 3.6–4.3, the internal quantum yield of photons-to-reducing electrons is 37.1% over 54 h of illumination, with no apparent decrease in catalyst activity. Monitoring of the QD exciton by transient absorption reveals that, for each step in the catalytic cycle, the sacrificial reductant, 3-mercaptopropionic acid, scavenges the excitonic hole in ~5 ps to form QD •– ; electron transfer to nitrobenzene or the intermediates nitrosobenzene and phenylhydroxylamine then occurs on the nanosecond time scale. The rate constants for the single-electron transfer reactions are correlated with the driving forces for the corresponding proton-coupled electron transfers. This result suggests, but does not prove, that electron transfer, not proton transfer, is rate-limiting for these reactions. Furthermore, nuclear magnetic resonance analysis of the QD–molecule systems shows that the photoproduct aniline, left unprotonated, serves as a poison for the QD catalyst by adsorbing to its surface. Performing the reaction at an acidic pH not only encourages aniline to desorb but also increases the probability of protonated intermediates; the latter effect probably ensures that recruitment of protons is not rate-limiting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Quantum dynamical investigation of the simplest Criegee intermediate CH{sub 2}OO and its O–O photodissociation channels

The singlet electronic potential energy surfaces for the simplest Criegee intermediate CH{sub 2}OO are computed over a two-dimensional reduced subspace of coordinates, and utilized to simulate the photo-initiated dynamics on the S{sub 2} (B) state leading to dissociation on multiple coupled excited electronic states. The adiabatic electronic potentials are evaluated using dynamically weighted state-averaged complete active space self-consistent field theory. Quasi-diabatic states are constructed from the adiabatic states by maximizing the charge separation between the states. The dissociation dynamics are then simulated on the diabatically coupled excited electronic states. The B ← X electronic transition with large oscillator strength was used to initiate dynamics on the S{sub 2} (B) excited singlet state. Diabatic coupling of the B state with other dissociative singlet states results in about 5% of the population evolving to the lowest spin-allowed asymptote, generating H{sub 2}CO (X {sup 1}A{sub 1}) and O ({sup 1}D) fragments. The remaining ∼95% of the population remains on repulsive B state and dissociates to H{sub 2}CO (a {sup 3}A″) and O ({sup 3}P) products associated with a higher asymptotic limit. Due to the dissociative nature of the B state, the simulated electronic absorption spectrum is found to be broad and devoid of any vibrational structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1980

Excitation of the b 3 Sigma u + state of H2 by electron impact - Semiclassical exchange potentials at intermediate energies

Integrated and differential cross sections for the excitation of the b 3 Sigma u + state of H2, from the ground state, by electron impact, are presented. The energy range of interest is 10.5 to 40.0 eV. The close-coupling equations for this process are solved in five different exchange approximations: exact two-electron exchange terms, no orthogonality; exact two-electron exchange terms, orthogonality; semiclassical exchange terms, no orthogonality, with barrier term; semiclassical exchange terms, no orthogonality, no barrier term; and semiclassical exchange terms, orthogonality, with barrier term. The purpose is to judge the reliability of the semiclassical exchange approximation for electronic excitation of molecules by electron impact at intermediate energies. The results are compared with recent theoretical estimates for the same process.

Weatherford, C. A.↗

DOE OSTI2022

Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations

The mechanism of rotatory catalysis in ATPhydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V 1 -type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using Xray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P i ) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V 1 -ATPase to be the rate-limiting step of motor action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Hydrogen Evolution Mediated by Cobalt Diimine‐Dioxime Complexes: Insights into the Role of the Ligand Acid/Base Functionalities.

Abstract The benchmarking of the performance for H 2 evolution of cobalt diimine‐dioxime catalysts is provided based on a comprehensive study of their catalytic mechanism. The latter follows an ECE'CC pathway with intermediate formation of a Co(II)‐hydride intermediate and second protonation possibly at a basic site of the ligand, acting as a proton relay. This suggests an intramolecular coupling between the hydride and protonated ligand as the proton concentration‐independent rate‐determining step controlling the turnover frequency for H 2 evolution.

Sun, Dongyue↗

DOE OSTI2022

Crystallographic dependence of CO 2 hydrogenation pathways over HCP-Co and FCC-Co catalysts

We report efficient conversion of CO 2 is of great significance for sustainable supply of chemicals and fuels. While Co-based catalysts are known to be effective for CO hydrogenation in Fischer-Tropsch synthesis, they work very differently in CO 2 hydrogenation. This study reveals a crystallographic dependence of reaction pathways for CO 2 hydrogenation on Co catalyst showing a new type of structure sensitivity and structure-activity-selectivity relationship for CO 2 conversion to chemicals and fuels. The experimental work on CO 2 conversion including steady-state isotopic transient kinetic analysis (SSITKA) using 13 C-labeled CO 2 shows a preferential CH 4 formation over HCP-Co but dominant CO formation over FCC-Co. The density functional theory calculations indicate that CO 2 does dissociate directly into chemisorbed CO * and O * on both HCP-Co and FCC-Co, but the CO * intermediates on HCP-Co prefer to be hydrogenated to form CH 4 whereas the CO* on FCC-Co preferentially desorb to form CO. The significantly altered adsorption strength of CO * due to the presence of chemisorbed O * and CO 2 * species on the catalyst surface is responsible for the mechanistic disconnection in product selectivity between the CO 2 and CO hydrogenation over Co catalysts. This study also shows that the addition of K to Co diminishes the direct impact of Co crystal structure, but improves the selectivity to C 2 + hydrocarbons along with higher CO 2 conversion. This seems to result from another pathway originating from HCOO* intermediate from bonding interaction of surface Co atoms with carbon in CO 2 , leading to the formation of CH x * whose coupling subsequently give rises to C 2 + products. The present study sheds new light into the crystallographic structural sensitivity of CO 2 hydrogenation towards the rational design of more selective catalysts for CO 2 conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Direct Conversion of Methane to Ethylene and Acetylene over an Iron-Based Metal–Organic Framework

Conversion of methane (CH 4 ) to ethylene (C 2 H 4 ) and/or acetylene (C 2 H 2 ) enables routes to a wide range of products directly from natural gas. However, high reaction temperatures and pressures are often required to activate and convert CH 4 controllably, and separating C 2+ products from unreacted CH 4 can be challenging. Here, we report the direct conversion of CH 4 to C 2 H 4 and C 2 H 2 driven by non-thermal plasma under ambient (25 °C and 1 atm) and flow conditions over a metal–organic framework material, MFM-300(Fe). The selectivity for the formation of C 2 H 4 and C 2 H 2 reaches 96% with a high time yield of 334 μmol g cat –1 h –1 . At a conversion of 10%, the selectivity to C 2+ hydrocarbons and time yield exceed 98% and 2056 μmol g cat –1 h –1 , respectively, representing a new benchmark for conversion of CH 4 . In situ neutron powder diffraction, inelastic neutron scattering and solid-state nuclear magnetic resonance, electron paramagnetic resonance (EPR), and diffuse reflectance infrared Fourier transform spectroscopies, coupled with modeling studies, reveal the crucial role of Fe–O(H)–Fe sites in activating CH 4 and stabilizing reaction intermediates via the formation of an Fe–O(CH 3 )–Fe adduct. In addition, a cascade fixed-bed system has been developed to achieve online separation of C 2 H 4 and C 2 H 2 from unreacted CH 4 for direct use. Integrating the processes of CH 4 activation, conversion, and product separation within one system opens a new avenue for natural gas utility, bridging the gap between fundamental studies and practical applications in this area.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Control of zeolite microenvironment for propene synthesis from methanol

Optimising the balance between propene selectivity, propene/ethene ratio and catalytic stability and unravelling the explicit mechanism on formation of the first carbon–carbon bond are challenging goals of great importance in state-of-the-art methanol-to-olefin (MTO) research. We report a strategy to finely control the nature of active sites within the pores of commercial MFI-zeolites by incorporating tantalum(V) and aluminium(III) centres into the framework. The resultant TaAlS-1 zeolite exhibits simultaneously remarkable propene selectivity (51%), propene/ethene ratio (8.3) and catalytic stability (>50 h) at full methanol conversion. In situ synchrotron X-ray powder diffraction, X-ray absorption spectroscopy and inelastic neutron scattering coupled with DFT calculations reveal that the first carbon–carbon bond is formed between an activated methanol molecule and a trimethyloxonium intermediate. The unprecedented cooperativity between tantalum(V) and Brønsted acid sites creates an optimal microenvironment for efficient conversion of methanol and thus greatly promotes the application of zeolites in the sustainable manufacturing of light olefins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Three interaction energy scales in the single-layer high-$T_c$ cuprate HgBa 2 CuO 4+δ

The lamellar cuprate superconductors exhibit the highest ambient-pressure superconducting transition temperatures ($T_c$), and after more than three decades of extraordinary research activity, continue to pose formidable scientific challenges. A major experimental obstacle has been to distinguish universal phenomena from materials- or technique-dependent ones. Angle-resolved photoemission spectroscopy (ARPES) measures momentum-dependent single-particle electronic excitations and has been invaluable in the endeavor to determine the anisotropic momentum-space properties of the cuprates. HgBa 2 CuO 4+δ (Hg1201) is a single-CuO 2 -layer cuprate with a particularly high optimal Tc and a simple crystal structure, yet there exists little information from ARPES about the electronic properties of this model system. In this paper we present an ARPES study of doping-, temperature-, and momentum-dependent systematics of near-nodal dispersion anomalies in Hg1201. The data reveal a hierarchy of three distinct energy scales: a subgap low-energy kink, an intermediate-energy kink near 55 meV, and a peak-dip-hump structure. The first two features are attributed to the coupling of electrons to Ba-derived optical phonons and in-plane bond-stretching phonons, respectively. The nodal peak-dip-hump structure appears to have a common doping dependence in several single-layer cuprates and is interpreted as a manifestation of pseudogap physics at the node. These results establish several universal phenomena, both in terms of connecting multiple experimental techniques for a single material and in terms of connecting comparable spectral features in multiple structurally similar cuprates.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Luther-Emery liquid and dominant singlet superconductivity in the hole-doped Haldane spin-1 chain

We investigate the pairing tendencies in the hole-doped Haldane spin-1 chain. To allow for doping, we extend the original spin chain Hamiltonian into a fermionic model involving a two-orbital Hubbard chain at intermediate or strong repulsive interaction strengths U and for degenerate orbitals. At half filling and large U, the ferromagnetic Hund's coupling, J H , generates effective spin-1 moments, with antiferromagnetic correlations between sites. Using large-scale density matrix renormalization group calculations, we accurately study the system's behavior under light hole-doping. For U = 1.6 in units of the noninteracting bandwidth and for J H /U ≳ 0.275, we find that singlet pairing dominates the long-distance physics, establishing this system as a promising platform for repulsively mediated superconductivity. We provide concrete examples of materials that could realize the physics described here. We also provide evidence that the system approaches a Luther-Emery liquid state at large system sizes, reminiscent of the behavior of doped one-orbital two-leg ladders at weak coupling, which also have superconducting tendencies. The numerically calculated central charge approaches one in the thermodynamic limit, indicating a single gapless mode as is expected for the Luther-Emery state. Exponents characterizing the power-law decays of singlet pair-pair and charge density-density correlations are determined, and found to approximately satisfy the Luther-Emery identity.

1-dimensional systems↗

DOE OSTI2015

SU-D-210-03: Limited-View Multi-Source Quantitative Photoacoustic Tomography

Purpose: This work is to investigate a novel limited-view multi-source acquisition scheme for the direct and simultaneous reconstruction of optical coefficients in quantitative photoacoustic tomography (QPAT), which has potentially improved signal-to-noise ratio and reduced data acquisition time. Methods: Conventional QPAT is often considered in two steps: first to reconstruct the initial acoustic pressure from the full-view ultrasonic data after each optical illumination, and then to quantitatively reconstruct optical coefficients (e.g., absorption and scattering coefficients) from the initial acoustic pressure, using multi-source or multi-wavelength scheme.Based on a novel limited-view multi-source scheme here, We have to consider the direct reconstruction of optical coefficients from the ultrasonic data, since the initial acoustic pressure can no longer be reconstructed as an intermediate variable due to the incomplete acoustic data in the proposed limited-view scheme. In this work, based on a coupled photo-acoustic forward model combining diffusion approximation and wave equation, we develop a limited-memory Quasi-Newton method (LBFGS) for image reconstruction that utilizes the adjoint forward problem for fast computation of gradients. Furthermore, the tensor framelet sparsity is utilized to improve the image reconstruction which is solved by Alternative Direction Method of Multipliers (ADMM). Results: The simulation was performed on a modified Shepp-Logan phantom to validate the feasibility of the proposed limited-view scheme and its corresponding image reconstruction algorithms. Conclusion: A limited-view multi-source QPAT scheme is proposed, i.e., the partial-view acoustic data acquisition accompanying each optical illumination, and then the simultaneous rotations of both optical sources and ultrasonic detectors for next optical illumination. Moreover, LBFGS and ADMM algorithms are developed for the direct reconstruction of optical coefficients from the acoustic data. Jing Feng and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

CO electroreduction on single-atom copper

Electroreduction of carbon dioxide (CO 2 ) or carbon monoxide (CO) toward C 2+ hydrocarbons such as ethylene, ethanol, acetate and propanol represents a promising approach toward carbon-negative electrosynthesis of chemicals. Fundamental understanding of the carbon–carbon (C-C) coupling mechanisms in these electrocatalytic processes is the key to the design and development of electrochemical systems at high energy and carbon conversion efficiencies. Here, we report the investigation of CO electreduction on single-atom copper (Cu) electrocatalysts. Atomically dispersed Cu is coordinated on a carbon nitride substrate to form high-density copper–nitrogen moieties. Chemisorption, electrocatalytic, and computational studies are combined to probe the catalytic mechanisms. Unlike the Langmuir-Hinshelwood mechanism known for copper metal surfaces, the confinement of CO adsorption on the single-copper-atom sites enables an Eley-Rideal type of C-C coupling between adsorbed (*CO) and gaseous [CO(g)] carbon moxide molecules. The isolated Cu sites also selectively stabilize the key reaction intermediates determining the bifurcation of reaction pathways toward different C 2+ products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX

Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity.

59 BASIC BIOLOGICAL SCIENCES↗