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Raugei, Simone

Publications and source records attributed to Raugei, Simone.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2024

Importance of Electron Correlation on the Geometry and Electronic Structure of [2Fe–2S] Systems: A Benchmark Study of the [Fe 2 S 2 (SCH 3 ) 4 ] 2–,3–,4– , [Fe 2 S 2 (SCys) 4 ] 2– , [Fe 2 S 2 (S- p -tol) 4 ] 2– , and [Fe 2 S 2 (S- o -xyl) 4 ] 2– Complexes

Iron–sulfur clusters are crucial for biological electron transport and catalysis. Obtaining accurate geometries, energetics, manifolds of their excited electronic states, and reduction energies is important to understand their role in these processes. Here, using a [2Fe–2S] model complex with Fe II and Fe III oxidation states, which leads to different charges, i.e., [Fe 2 S 2 (SMe) 4 ] 2–,3–,4– , we benchmarked a variety of computational methodologies ranging from density functional theory (DFT) to post-Hartree–Fock methods, including complete active space self-consistent field (CASSCF), multireference configuration interaction, the second-order N-electron valence state perturbation theory (NEVPT2), and the linearized integrand approximation of adiabatic connection (AC0) approaches. Additionally, we studied three experimentally well-characterized complexes, [Fe 2 S 2 (SCys) 4 ] 2– , [Fe 2 S 2 (S-o-tol) 4 ] 2– , and [Fe 2 S 2 (S-o-xyl) 4 ] 2– , via DFT methods. We conclude that the dynamic electron correlation is important for accurately predicting the geometry of these complexes. Broken symmetry (BS) DFT correctly predicts experimental geometries of low-spin multiplicity, while CASSCF does not. However, BS-DFT significantly overestimates the difference between the low- and high-spin electronic states for a given oxidation state. At the same time, CASSCF underestimates it but provides relative energies closer to the reference NEVPT2 results. Finally, AC0 provides energetics of NEVPT2 quality with the additional advantage of being able to use large CASSCF sizes. NEVPT2 gives the best estimates of the Fe III /Fe III → Fe II /Fe III (4.27 eV) and Fe II /F III → Fe II /F II (7.72 eV) reduction energies. The results provide insight into the electronic structure of these complexes and assist in the understanding of their physical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Dynamic Activation of Single-Atom Catalysts by Reaction Intermediates: Conversion of Formic Acid on Rh/Fe 3 O 4 (001)

The stability and activity of supported single-atom catalysts (SACs) represent critical yet opposing factors limiting our ability to explore and exploit their unique properties. Here, this study demonstrates the operation of a switchable catalyst that is activated in the presence of surface intermediates and reverts back to a stable but inactive form when the reaction is completed. We employ atomically defined Rh-Fe 3 O 4 (001) catalysts to demonstrate how structurally stable Rh, bound in surface octahedral Fe sites, gets destabilized to form highly active Rh adatoms and small clusters. Conversion of formic acid, leading initially to surface formate and hydroxyl species, is employed as a model reaction to probe the dynamics of such processes. We find that surface hydroxyl recombination to water through the Mars van Krevelen mechanism reduces Rh coordination, triggering its conversion to active Rh adatoms. Since such lattice oxygen exchange is observed in many acid-base and redox chemistries, the process can be broadly applicable to controlling the activation of the range of SACs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Ni 2 P active site ensembles tune electrocatalytic nitrate reduction selectivity

Here, we demonstrate that active site ensembles on transition metal phosphides tune the selectivity of the nitrate reduction reaction. Using Ni 2 P nanocrystals as a case study, we report a mechanism involving competitive co-adsorption of H* and NO x * intermediates. A near 100% faradaic efficiency for nitrate reduction over hydrogen evolution is observed at -0.4 V, while NH 3 selectivity is maximized at -0.2 V vs. RHE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1

SUCROSE-NON-FERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), a central plant metabolic sensor kinase, phosphorylates its target proteins, triggering a global shift from anabolism to catabolism. Molecular modeling revealed that upon binding of KIN10 to GEMINIVIRUS REP-INTERACTING KINASE1 (GRIK1), KIN10’s activation T-loop reorients into GRIK1’s active site, enabling its phosphorylation and activation. Trehalose 6-phosphate (T6P) is a proxy for cellular sugar status and a potent inhibitor of SnRK1. T6P binds to KIN10, a SnRK1 catalytic subunit, weakening its affinity for GRIK1. Here, we investigate the molecular details of T6P inhibition of KIN10. Molecular dynamics simulations and in vitro phosphorylation assays identified and validated the T6P binding site on KIN10. Under high-sugar conditions, T6P binds to KIN10, blocking the reorientation of its activation loop and preventing its phosphorylation and activation by GRIK1. Under these conditions, SnRK1 maintains only basal activity levels, minimizing phosphorylation of its target proteins, thereby facilitating a general shift from catabolism to anabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Homologous acetone carboxylases select Fe(II) or Mn(II) as the catalytic cofactor

The Irving-Williams series refers to the predicted stabilities of transition metal complexes where the observed general stability for divalent first-row transition metal complexes increase across the row. Acetone carboxylases (ACs) use a coordinated divalent metal at their active site in the catalytic conversion of bicarbonate and acetone to form acetoacetate. Highly homologous ACs discriminate among different divalent metals at their active sites such that variations of the enzyme prefer Mn(II) over Fe(II), defying Irving-Williams-predicted behavior. Defining the determinants that promote metal discrimination within the first-row transition metals is of broad fundamental importance in understanding metal-mediated catalysis and metal catalyst design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner

The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.

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

Bioinspired Catalyst Design Principles: Progress in Emulating Properties of Enzymes in Synthetic Catalysts

Catalysis enables many aspects of modern life, including fuels, products, plastics, and medicines. Recent advances in catalysis have enabled us to realize higher efficiencies and new processes. Ideally, we seek to achieve high rates of selective conversions using catalysts derived from abundantly available elements and operating under mild conditions, specifically lower reaction temperatures and pressures. Such catalysts could enable decentralized, on-demand synthesis of chemicals and energy carriers. Nature has demonstrated the feasibility of this approach with enzymes, which showcase catalytic processes at low temperatures and pressures with nonprecious metals. Current thinking holds that in addition to the active site, the complexity of the enzyme structure, specifically the protein scaffold, is also critical to achieving this performance. Recreating this environment has been a long-standing scientific goal. However, we still understand the functions of enzymes better than we understand the de novo design of catalysts that mimic enzymes features, while also retaining their activity and selectivity under more demanding conditions. Here, in this Perspective, we will critically examine four key areas of catalyst design that incorporate the chemical and structural properties of enzymes into synthetic catalysts: (i) the use of confinement to enhance catalytic activity, (ii) tailoring the environment around the active site, (iii) proton transport, and (iv) bifunctionality and cooperativity.

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

A conformational equilibrium in the nitrogenase MoFe protein with an α-V70I amino acid substitution illuminates the mechanism of H 2 formation

Study of α-V70I-substituted nitrogenase MoFe protein identified Fe6 of FeMo-cofactor (Fe 7 S 9 MoC-homocitrate) as a critical N 2 binding/reduction site. Freeze-trapping this enzyme during Ar turnover captured the key catalytic intermediate in high occupancy, denoted E 4 (4H), which has accumulated 4[e — /H + ] as two bridging hydrides, Fe2–H–Fe6 and Fe3–H–Fe7, and protons bound to two sulfurs. E 4 (4H) is poised to bind/reduce N 2 as driven by mechanistically-coupled H 2 reductive-elimination of the hydrides. This process must compete with ongoing hydride protonation (HP), which releases H 2 as the enzyme relaxes to state E 2 (2H), containing 2[e — /H + ] as a hydride and sulfur-bound proton; accumulation of E 4 (4H) in α-V70I is enhanced by HP suppression. EPR and 95 Mo ENDOR spectroscopies now show that resting-state α-V70I enzyme exists in two conformational states, both in solution and as crystallized, one with wild type (WT)-like FeMo-co and one with perturbed FeMo-co. These reflect two conformations of the Ile residue, as visualized in a reanalysis of the X-ray diffraction data of α-V70I and confirmed by computations. EPR measurements show delivery of 2[e — /H + ] to the E 0 state of the WT MoFe protein and to both α-V70I conformations generating E 2 (2H) that contains the Fe3–H–Fe7 bridging hydride; accumulation of another 2[e — /H + ] generates E 4 (4H) with Fe2–H–Fe6 as the second hydride. E 4 (4H) in WT enzyme and a minority α-V70I E 4 (4H) conformation as visualized by QM/MM computations relax to resting-state through two HP steps that reverse the formation process: HP of Fe2–H–Fe6 followed by slower HP of Fe3–H–Fe7, which leads to transient accumulation of E 2 (2H) containing Fe3–H–Fe7. In the dominant α-V70I E 4 (4H) conformation, HP of Fe2–H–Fe6 is passively suppressed by the positioning of the Ile sidechain; slow HP of Fe3–H–Fe7 occurs first and the resulting E 2 (2H) contains Fe2–H–Fe6. Importantly, it is this HP suppression in E 4 (4H) that enables α-V70I MoFe to accumulate E 4 (4H) in high occupancy. In addition, HP suppression in α-V70I E 4 (4H) kinetically unmasks hydride reductive-elimination without N 2 -binding, a process that is precluded in WT enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Modeling Absolute Redox Potentials of Ferrocene in the Condensed Phase

Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis beyond the relative scales typically employed. In principle, theoretical methods can provide such quantification but are often hindered by the innate complexity of strong electron correlation and dynamic relaxation of solvent environments. Here, we present and validate a protocol for calculating the redox potentials of ferrocene/ferrocenium redox pair in the acetonitrile. Equation-of-motion ionization potential coupled-cluster single-double (EOM-IP-CCSD) and effective fragment potential (EFP) methods are used to characterize the adiabatic and vertical ionization potentials (IP) as well as the electron affinity processes. We benchmark molecular mechanics against the EFP model to show the differences in ferrocene electronic polarizability in two redox states. Our best estimate of the redox potential (4.94 eV) agrees well with the experimental value (4.93 eV). This demonstrated the ability of modern computational methods to predict absolute redox potentials quantitatively and, more critically, quantify the correlation of dynamic effects, which underlie their origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

13 C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe 6 Core Is a Stabilizing “Heart of Steel”

Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe–9S–C–Mo–homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe 6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13 C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe–C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. Here this report compares 13 CFe 6 ENDOR measurements for (i) the wild-type protein resting state (E 0 ; α-Val 70 ) to those of (ii) α-Ile 70 , (iii) α-Ala 70 -substituted proteins; (iv) crystallographically characterized CO-inhibited “hi-CO” state; (v) E 4 (4H) Janus intermediate, activated for N 2 binding/reduction by accumulation of 4[ e– /H + ]; (vi) E 4 (2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13 C isotropic hyperfine coupling constants, $^Ca$ = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe 6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe–C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe–C bonding of the CFe 6 core indicate that it does not provide a functionally dynamic (hemilabile) “beating heart”-instead it acts as “a heart of steel”, stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Hydrogen Atom Abstraction from an Os II (NH 3 ) 2 Complex Generates an Os IV (NH 2 ) 2 Complex: Experimental and Computational Analysis of the N–H Bond Dissociation Free Energies and Reactivity

We report double hydrogen atom abstraction from (TMP)Os II (NH 3 ) 2 (TMP = tetramesitylporphyrin) with phenoxyl or nitroxyl radicals leads to (TMP)Os IV (NH 2 ) 2 . This unusual bis(amide) complex is diamagnetic and displays an N-H resonance at 12.0 ppm in its 1 H NMR spectrum. 1 H- 15 N correlation experiments identified a 15 N NMR spectroscopic resonance at –267 ppm. Experimental reactivity studies and density functional theory calculations support relatively weak N-H bonds of 73.3 kcal/mol for (TMP)Os II (NH 3 ) 2 and 74.2 kcal/mol for (TMP)Os III (NH 3 )(NH 2 ). Cyclic voltammetry experiments provide an estimate of the pK a of [(TMP)Os III (NH 3 ) 2 ] + . In the presence of Barton’s base, a current enhancement is observed at the Os(III/II) couple, consistent with an ECE event. Spectroscopic experiments confirmed (TMP)Os IV (NH 2 ) 2 as the product of bulk electrolysis. Double hydrogen atom abstraction is influenced by π donation from the amides of (TMP)Os IV (NH 2 ) 2 into the d orbitals of the Os center, favoring the formation of (TMP)Os IV (NH 2 ) 2 over N-N coupling. This π donation leads to a Jahn-Teller distortion that splits the energy levels of the d xz and d yz orbitals of Os, results in a low spin electron configuration, and leads to minimal aminyl character on the N atoms, rendering (TMP)Os IV (NH 2 ) 2 unreactive towards amide-amide coupling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multilevel Computational Studies Reveal the Importance of Axial Ligand for Oxygen Reduction Reaction on Fe–N–C Materials

The systematic improvement of Fe–N–C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel computational approach, which combines ab initio molecular dynamics simulations and constant potential density functional theory calculations, is used to assess proton-coupled electron transfer (PCET) processes and adsorption thermodynamics of key ORR intermediates. These calculations indicate that the potential-limiting step for ORR on Fe–N–C materials is the formation of the Fe III –OOH intermediate. They also show that an active site model with a water molecule axially ligated to the iron center throughout the catalytic cycle produces results that are consistent with the experimental measurements. In particular, reliable prediction of the ORR onset potential and the Fe(III/II) redox potential associated with the conversion of Fe III –OH to Fe II and desorbed H 2 O requires an axial H 2 O co-adsorbed to the iron center. The observation of a five-coordinate rather than four-coordinate active site has significant implications for the thermodynamics and mechanism of ORR. Importantly, these findings highlight the importance of solvent–substrate interactions and surface charge effects for understanding the PCET reaction mechanisms and transition-metal redox couples under realistic electrochemical conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Weakening the N–H Bonds of NH 3 Ligands: Triple Hydrogen-Atom Abstraction to Form a Chromium(V) Nitride

Weakening and cleaving N-H bonds is crucial for improving molecular ammonia oxidation catalysts. In this work, we report the synthesis and hydrogen atom abstraction chemistry of bis(ammonia) Cr porphyrin complexes Cr(TPP)(NH 3 ) 2 and Cr(TMP)(NH 3 ) 2 (TPP = 5,10,15,20-tetraphenyl-meso-porphyrin and TMP = 5,10,15,20-tetramesityl-meso-porphyrin) using bulky aryloxyl radicals. The triple hydrogen atom abstraction reaction results in the formation of Cr V (por)(≡N), with the nitride deriving from ammonia, as indicated by UV-Vis and FT-IR spectroscopy, and a single crystal structural determination of Cr(TPP)(≡N). Subsequent oxidation of this chromium(V)-nitrido complex results in the formation of Cr III (por), with scission of the Cr≡N bond. A computational analysis illustrates the progression from Cr II to Cr V and evaluates the energetics of abstracting hydrogen atoms from Cr II -NH 3 to generate Cr V ≡N. The formation and isolation of Cr V (por)(≡N) illustrates the stability of these species and the need to chemically activate the nitride moiety for atom transfer or N-N coupling reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines

Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on Earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as “P 2 N 2 ” ligands, have profound effects on the reactivity of many catalysts. The resulting [Ni(P R 2 N R ´ 2 ) 2 ] 2+ complexes are electrocatalysts for both the oxidation and production of H 2 . Achieving the optimal benefit of the pendant amine requires that it has suitable basicity and is properly positioned relative to the metal center. In addition to the catalytic efficacy demonstrated with [Ni(P R 2 N R ´ 2 )2] 2+ complexes for the oxidation and production of H2, catalysts with diphosphine ligands containing pendant amines have also be demonstrated for a variety of metals for many different reactions, both in solution and immobilized on surfaces. Here, the impact of pendant amines in catalyst design has been demonstrated and continues to expand.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗