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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Reactivity descriptors in acid catalysis: acid strength, proton affinity and host–guest interactions

Brønsted acids mediate chemical transformations via proton transfer to bound species and interactions between the conjugate anion and bound cationic intermediates and transition states that are also stabilized by van der Waals forces within voids of molecular dimensions in inorganic hosts. This Feature Article describes the relevant descriptors of reactivity in terms of the properties of acids and molecules that determine their ability to donate and accept protons and to reorganize their respective charges to optimize their interactions at bound states. The deprotonation energy (DPE) of the acids and the protonation energy (Eprot) of the gaseous analogs of bound intermediates and transition states reflect their respective properties as species present at non-interacting distances. These properties accurately describe the reactivity of acids of a given type, such as polyoxometalates (POM) with a given type of addenda atom but different central atoms and heterosilicates, for different families of reactions. They do not fully capture, however, differences among acid types (e.g., Mo and W POM, heterosilicates, mineral acids) for diverse types of chemical transformations (e.g., elimination, isomerization, dimerization, condensation). The incompleteness of such descriptors reflects their inability to describe how protonated molecular species and conjugate anions restructure their respective charges when present as a binding pair at interacting distances. Such interaction energies represent electrostatic forces that depend on charge distributions in the cations and anions and the ability to reorganize the distributions to maximize the interactions. In the case of deprotonation, the electrostatic and charge reorganization components of DPE for various acids solely reflect the ability of the conjugate anion to accept and distribute the negative charge, a characteristic unique of each type of solid acid and specifically of the composition of its extended conjugate anion framework. The energy required to accept and rearrange the positive charge in bound intermediates and transition states reflects, in turn, their respective ability to recover the ionic and covalent components of DPE, the energy required to detach proton from conjugate anions. The DPE components and the recovery fractions together lead to a modified DPE, which captures only the part of DPE that remains unrecovered by the ion-pair interactions at bound intermediates and transition states, as the unifying descriptor for broad families of acids and reactions. The electrostatic and charge reorganization energies involved in these general descriptors are placed in historical context by assessing their connections to the heuristics of hard–soft acid–base displacements. Further development of these concepts requires benchmarking and extension of electrostatic and reorganization components of energies for a more diverse set of reaction types and acid families and advancement of methods for more efficient calculations of electrostatic interactions. Reactivity descriptors must also account for dispersive interactions between host cavities and guest molecules, requiring a framework analogous to the one described here for ion-pair interactions; these dispersive interactions depend on the fit between their shapes and sizes as well as their ‘‘structural stiffness’’ that determines the ability to modify the shapes of molecules and voids to minimize free energy. Entropy considerations and estimates of their dependence on properties of catalysts and molecules are also required for accurately determining Gibbs free energies that ultimately determine reaction rates.

Deshlahra, Prashant↗
DOE OSTI2023

Probing Complex Chemical Processes at the Molecular Level with Vibrational Spectroscopy and X-ray Tools

Understanding the origins of structure and bonding at the molecular level in complex chemical systems spanning magnitudes in length and time is of paramount interest in physical chemistry. Here, we have coupled vibrational spectroscopy and X-ray based techniques with a series of microreactors and aerosol beams to tease out intricate and sometimes subtle interactions, such as hydrogen bonding, proton transfer, and noncovalent interactions. This allows for unraveling the self-assembly of arginine-oleic acid complexes in an aqueous solution and growth processes in a metal–organic framework. Terahertz and infrared spectroscopy provide an intimate view of the hydrogen-bond network and associated phase changes with temperature in neopentyl glycol. The hydrogen-bond network in aqueous glycerol aerosols and levels of protonation of nicotine in aqueous aerosols are visualized. Future directions in probing the hydrogen-bond networks in deep eutectic solvents and organic frameworks are described, and we suggest how X-ray scattering coupled to X-ray spectroscopy can offer insight into the reactivity of organic aerosols.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1999

Computer Simulation Studies of Ion Channel Gating: Characteristics of the M2 Channel of Influenza-A Virus in a Phospholipid Bilayer

The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.

Schweighofer, Karl J.↗
DOE OSTI2026

Understanding Adsorption and Reactions at Aqueous Oxide Interfaces with Neural Network Potential Molecular Dynamics

Chemical processes at metal oxide−water interfaces are of central importance in geochemistry, biology, and energy technologies. A better understanding of these processes would allow us to make a significant step toward optimizing and controlling them, which could in turn lead to broader impacts. Computational modeling is indispensable to accomplishing this task because complexity and disorder often make it difficult to extract atomistic information from experiments. Balancing computational cost and accuracy, simulation schemes based on efficient machine learning representations of the potential energy surface (PES) predicted by ab initio calculations have become increasingly popular over the past decade. In particular, several studies have demonstrated the ability of machine learning models to accurately reproduce the complex ab initio PESs of aqueous oxide interfaces, allowing simulations of systems and processes that are not accessible with ab initio methods. In this Account, we review our recent efforts to understand adsorption processes and reactions at aqueous oxide interfaces using deep potential molecular dynamics (DPMD), a simulation scheme employing deep neural networks (DNNs), which has proven to be quite successful in accurately describing many different systems in the condensed phase. After summarizing the DPMD methodology, we first review our work on the acid−base chemistry of oxide surfaces in contact with water, a fundamental characteristic that controls proton transfer and surface charge at the interface. We focus on the aqueous interface of rutile IrO 2 , an oxide material thus far considered the best catalyst for the oxygen evolution reaction (OER). We show that this interface is characterized by a large fraction of dissociated water and a strong Brønsted acidity of the surface sites, in good agreement with the experimentally measured value of the point of zero proton charge. In our second example, we investigate how the adsorption of organic species from ambient air or water affects the structure and wettability of the aqueous interfaces of TiO 2 , a prototypical photocatalytic material. This is a question that is relevant to understanding the UV-induced hydrophilicity of TiO 2 surfaces, a property at the basis of self-cleaning windows and related applications. Specifically focusing on formic and acetic acids, the two most common atmospheric organic acids, our simulations reveal that these acids control the wettability of TiO 2 largely through acid−base chemistry at the interface rather than chemisorption on the oxide surface, a finding that could help improve the design of self-cleaning surfaces and photocatalytic devices. Finally, we review our recent study of methanol at TiO 2 −water interfaces, a system whose interest is largely motivated by the role of methanol in enhancing photocatalytic hydrogen evolution on TiO 2 . Our simulations provide mechanistic insights into the coupled roles of the organic adsorbate and water at the TiO 2 interface, with implications for how methanol enhances the activity of H 2 evolution.

adsorption↗
NASA NTRS2004

Ionic Liquids and New Proton Exchange Membranes for Fuel Cells

There is currently a great surge of activity in fuel cell research as laboratories across the world seek to take advantage of the high energy capacity provided by &el cells relative to those of other portable electrochemical power systems. Much of this activity is aimed at high temperature fie1 cells, and a vital component of such &el cells must be the availability of a high temperature stable proton-permeable membrane. NASA Glenn Research Center is greatly involved in developing this technology. Other approaches to the high temperature fuel cell involve the use of single- component or almost-single-component electrolytes that provide a path for protons through the cell. A heavily researched case is the phosphoric acid fuel cell, in which the electrolyte is almost pure phosphoric acid and the cathode reaction produces water directly. The phosphoric acid fie1 cell delivers an open circuit voltage of 0.9 V falling to about 0.7 V under operating conditions at 170 C. The proton transport mechanism is mainly vehicular in character according to the viscosity/conductance relation. Here we describe some Proton Transfer Ionic Liquids (PTILs) with low vapor pressure and high temperature stability that have conductivities of unprecedented magnitude for non-aqueous systems. The first requirement of an ionic liquid is that, contrary to experience with most liquids consisting of ions, it must have a melting point that is not much above room temperature. The limit commonly suggested is 100 C. PTILs constitute an interesting class of non-corrosive proton-exchange electrolyte, which can serve well in high temperature (T = 100 - 250 C) fuel cell applications. We will present cell performance data showing that the open circuit voltage output, and the performance of a simple H2(g)Pt/PTIL/Pt/O2(g) fuel cell may be superior to those of the equivalent phosphoric acid electrolyte fuel cell both at ambient temperature and temperatures up to and above 200 C. My work at NASA Glenn Research Center during this summer is to develop and characterize proton exchange membranes doped with ionic liquids. The main techniques used to characterize these materials are: Impedance Spectroscopy, NMR, DSC, TGA, DMA, IR, and SEM ...

Belieres, Jean-Philippe↗
NASA NTRS1993

The protonation of N2O reexamined - A case study on the reliability of various electron correlation methods for minima and transition states

The protonation of N2O and the intramolecular proton transfer in N2OH(+) are studied using various basis sets and a variety of methods, including second-order many-body perturbation theory (MP2), singles and doubles coupled cluster (CCSD), the augmented coupled cluster (CCSD/T/), and complete active space self-consistent field (CASSCF) methods. For geometries, MP2 leads to serious errors even for HNNO(+); for the transition state, only CCSD/T/ produces a reliable geometry due to serious nondynamical correlation effects. The proton affinity at 298.15 K is estimated at 137.6 kcal/mol, in close agreement with recent experimental determinations of 137.3 +/- 1 kcal/mol.

Martin, J. M. L.↗
DOE OSTI2025

Constructing Water‐Stable Porous Organic Salts via Suppressed Proton Integration Using Fluorinated Tetrazole Tectons

Porous organic salts (POSs) are an emerging class of materials with ordered ionic architectures, offering excellent proton transfer and water uptake properties. However, conventional POS synthesis via strong acid–base neutralization (e.g., ─SO₃H and ─NH₂) leads to extensive hydrogen bonding with water, compromising stability in aqueous and water-lean environments. Here, we address this challenge by designing POSs with hydrophobic porous channels and minimal hydrogen bonding formation. Our key innovation is the use of fluorinated tetrazole as a weak acid tecton and a tetra-substituted imidazole precursor devoid of active protons as the base. Single-crystal analysis and computational modeling reveal that the structural integrity of the synthesized POSs arises primarily from cation–anion interactions, with water confined as clusters in the pores, independent of hydrogen bonding with the scaffold. Robustness of the POS structure under aqueous and water-lean conditions is confirmed by X-ray and neutron scattering, as well as computational modeling, confirming preserved packing and crystal structures. The stability of POS is further demonstrated in aqueous iodine capture, with imidazolium cations and C–F functionalizations serving as strong adsorption sites. As a result, the approach developed herein further pushes the boundary of POS materials to withstand both aqueous and water-lean conditions.

Fluorinated tecton↗
DOE OSTI2025

Observation of three-proton-decaying resonant states in 21 Al

The structure of the proton-unbound nucleus 21 Al has been studied via proton transfer from a 9 Be target to a 20 Mg beam at E/A = 103 MeV. Three resonant states in 21 Al are identified by the invariant-mass reconstruction of 18 Ne + 3p events. The decay-energy spectra for the two subsystems of 21 Al , i.e. 18 Ne+ 1 p and 18 Ne+ 2 p , indicate that the observed resonant state with the lowest energy has decay branches consisting of three sequential steps of one-proton decay. Based on the ab initio and the distorted-wave Born approximation (DWBA) calculations, this resonant state at Ε ⁎ = 6.09(11) MeV likely has a spin-parity of (1/2 + - 7/2 + ). Meanwhile, the possibility that the observed resonant peak represents an admixture of several states cannot be ruled out. The good isospin-symmetry of the low-lying states with d 5/2 , d 3/2 configurations in the 21 Al- 21 O pair and the ab initio calculations indicate weak configuration mixing between the s - and d -orbital components. The systematics of experimental energy differences between the 5/2 + ground state and lowest-lying 3/2 + excited state for isotopes (isotones) of Z(N) = 13 suggest a likely semimagic nature of 21 Al.

21Al↗
DOE OSTI2021

Transition Path Sampling Study of the Feruloyl Esterase Mechanism

Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine–histidine–aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the “moving histidine” mechanism, thus calling into question the “ring flip” mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s –1 . Altogether, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.

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

Modeling the Solvation and Acidity of Carboxylic Acids Using an Ab Initio Deep Neural Network Potential

Formic and acetic acid constitute the simplest of carboxylic acids, yet they exhibit fascinating chemistry in the condensed phase such as proton transfer and dimerization. The go-to method of choice for modeling these rare events have been accurate but expensive ab-initio molecular dynamics simulations. Here, we present a deep neural network potential trained using accurate ab-initio data that can be used in tandem with enhanced-sampling methods to perform an efficient exploration of the free-energy surface of aqueous solutions of weak carboxylic acids. In particular, we show that our model captures proton dissociation and provides a good estimate of the pK a , as well as the dimerization of formic and acetic acid. This provides a suitable starting point for applications in different research areas where computational efficiency coupled with the accuracy of ab-initio methods is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Nanoarchitectonic Semiconductor–Bio Hybrid Systems with Enhanced Charge Transfer for Hydrogen Peroxide Production

Nanoarchitectonics offers a systematic approach to creating an artificial framework by integrating different multiscale components such as semiconductor lattices and biological substances. However, most nanoarchitectonic abiotic-biotic hybrid systems have intrinsic limitations in imparting nonequilibrium biological features into semiconductor lattices at the nanoscale. Here, in this study, we report a new nanoarchitectonic system integrating bismuth oxychloride (BiOCl) nanosheets with purple membrane (PM) patches. PM is an archaeal subcellular fraction capable of unidirectionally transferring photogenerated charge carriers to its surroundings at the nanoscale independent of archaeal metabolism and retaining this dynamic functionality after isolation from living archaea. Microscopy, spectroscopy, electrochemical, and synchrotron X-ray scattering analyses verify that the nanoarchitectonic hybridization between BiOCl and PM generates a vertical heterostructure, thereby enhancing photogenerated charge-carrier dynamics and enabling the associated photocatalytic capacity. The resulting PM-BiOCl hybrid nanosheets efficiently convert dioxygen into hydrogen peroxide through a two-electron and two-proton transfer process under ambient conditions while simultaneously converting ethylene glycol into value-added chemicals. This study presents a nanoarchitectonic approach that leverages the photogenerated charge-carrier dynamics of the archaeal subcellular fractions to modulate the optoelectronic and catalytic capacity limitations of semiconductors.

catalysis↗
DOE OSTI2021

Aqueous TiO 2 Nanoparticles React by Proton-Coupled Electron Transfer

Redox reactions of aqueous colloidal TiO 2 4 nm nanoparticles (NPs) have been examined, including both citratecapped and uncapped NPs (c-TiO 2 and uc-TiO 2 ). Photoreduction gave stable blue colloidal c-TiO 2 R NPs with 10–60 electrons per particle. Equilibration of these reduced NPs with soluble redox reagents such as methylviologen (MV 2+ ) provided measurements of the colloid reduction potential as a function of pH. The potentials of c-TiO 2 from pH 2–9 varied linearly with pH, with a slope of –60 ± 5 mV/pH. Estimates of the potential at pH 12 were consistent with extrapolating that line to high pH. The reduction potentials did not correlate with the zeta potentials (ζ) or the surface charge of the NPs across this pH range. Similar reduction potentials were observed for c- and uc-TiO 2 at low pH even though they have quite different ζ potentials. These results show that the common surface-charging explanation of the pH dependence is not tenable in these systems. Oxidation of reduced c-TiO 2 R with the electron-transfer oxidant potassium triiodide (KI 3 ) occurred with a significant drop in pH, showing that protons were released when the electrons were removed from the NPs. Smaller pH drops were observed for the proton-coupled electron transfer (PCET) reagents O 2 (air) and 4-MeO-TEMPO (4-methoxy-2,2,6,6-tetramethylpiperine-1-oxy radical). The difference in the number of protons released with KI 3 vs O 2 and 4-MeO-TEMPO was roughly one proton per electron removed. Thus, the thermodynamically preferred reactivity of these colloidal TiO 2 NPs is PCET over the pH 2–13 range studied. The measured redox potentials refer to the chemical process TiO 2 + H + + e – → TiO 2 ·e – ,H + ; and therefore they do not correspond with an electronic energy such as a conduction band edge or flat band potential. The 1e – /1H + stoichiometry means that the TiO 2 reduction potentials correspond to a TiO 2 –H bond dissociation free energy (BDFE), determined to be 49 ± 2 kcal mol –1 . The PCET description is consistent with the pH dependence of E(TiO 2 /TiO 2 ·e – ,H + ), the release of protons upon oxidation, the lack of correlation with ζ potentials, the similarity of capped and uncapped NPs, and the small change in the potential and BDFE from the first to the last electron/proton pair (H atom) removed. Furthermore, this behavior is suggested to be the norm for redox-active oxide/water interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Incorporation of Ion Transport Chains into Multivariate MOF for Improved Water Oxidation

The climate crisis demands clean energy technologies to cut CO 2 emissions from fossil fuels. Hydrogen fuel cells and solar-driven CO 2 reduction are promising, but both rely on efficient water oxidation. Polypyridyl ruthenium complexes are active catalysts for water oxidation; however, they exhibit poor stability and recyclability. Our group improved performance by embedding these complexes into metal−organic frameworks (MOFs). As water oxidation is pH-dependent, proton management further enhances reactivity. To address the issue, we introduced proton transfer pathways into the MOF structure. Specifically, we incorporated −SO 3 H groups onto the biphenyl linkers of UiO-67 loaded with [Ru(tpy)(dcbpy)OH 2 ]PF 6 catalyst (where tpy = 2,2′:6′,2″-terpyridine; dcbpy = 5,5-dicarboxy-2,2′- bipyridine). The sulfonated MOF exhibited a 2.5-fold increase in oxygen evolution compared to the nonsulfonated analogue. After 1 h of electrolysis, the sulfonated MOF exhibited a turnover number of 25 for oxygen evolution reaction compared to 10 for the native MOF, demonstrating the benefits of built-in proton management.

Catalysts↗
DOE OSTI2022

Covalent Organic Frameworks with Irreversible Linkages via Reductive Cyclization of Imines

Covalent organic frameworks (COFs) show great potential for many advanced applications on account of their structural uniqueness. To address the synthetic challenges, facile chemical routes to engineer the porosity, crystallinity, and functionality of COFs are highly sought after. Herein, we report a synthetic approach that employs the Cadogan reaction to introduce nitrogen-containing heterocycles as the linkages in the framework. Irreversible indazole and benzimidazolylidene (BIY) linkages are introduced into COFs for the first time via phosphine-induced reductive cyclization of the common imine linkages following either stepwise or one-pot reaction protocols. Further, the successful linkage transformation introduces new functionalities, as demonstrated in the case of BIY-COF, which displays excellent intrinsic proton conductivity without the need of impregnation with external proton transfer reagents. Such a general strategy will open the window to a broader class of functional porous crystalline materials.

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

Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site

Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo 3 ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o 3 , and Cu B ), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71 I . In both structures, residue H98 I occupies two conformations. In conformation 1, H98 I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 I has flipped to form a hydrogen bond with E14 I at the N-terminal end of TM0. We propose that H98 I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98 I .

bioenergetics↗
DOE OSTI2020

Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: insights into enzyme mechanism and drug design

The emergence of the novel coronavirus SARS-CoV-2 has resulted in a worldwide pandemic not seen in generations. Creating treatments and vaccines to battle COVID-19, the disease caused by the virus, is of paramount importance in order to stop its spread and save lives. The viral main protease, 3CL M pro , is indispensable for the replication of SARS-CoV-2 and is therefore an important target for the design of specific protease inhibitors. Detailed knowledge of the structure and function of 3CL M pro is crucial to guide structure-aided and computational drug-design efforts. Here, the oxidation and reactivity of the cysteine residues of the protease are reported using room-temperature X-ray crystallography, revealing that the catalytic Cys145 can be trapped in the peroxysulfenic acid oxidation state at physiological pH, while the other surface cysteines remain reduced. Only Cys145 and Cys156 react with the alkylating agent N -ethylmaleimide. It is suggested that the zwitterionic Cys145–His45 catalytic dyad is the reactive species that initiates catalysis, rather than Cys145-to-His41 proton transfer via the general acid–base mechanism upon substrate binding. The structures also provide insight into the design of improved 3CL M pro inhibitors.

3CL Mpro↗
DOE OSTI2026

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.

Drago, Victoria N. [Oak Ridge National Laboratory ↗
DOE OSTI2021

Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications

Here, we present an update and revision to our 2010 review on the topic of proton- coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XHn in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H 2 ), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H 2 ) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗