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

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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Zymogen and activated protein C have similar structural architecture

Activated protein C is a trypsin-like protease with anticoagulant and cytoprotective properties that is generated by thrombin from the zymogen precursor protein C in a reaction greatly accelerated by the cofactor thrombomodulin. The molecular details of this activation remain elusive due to the lack of structural information. We now fill this gap by providing information on the overall structural organization of these proteins using single molecule Förster resonance energy transfer and small angle X-ray scattering. Under physiological conditions, both zymogen and protease adopt a conformation with all domains vertically aligned along an axis 76 Å long and maximal particle size of 120 Å. This conformation is stabilized by binding of Ca 2+ to the Gla domain and is affected minimally by interaction with thrombin. Hence, the zymogen protein C likely interacts with the thrombin-thrombomodulin complex through a rigid body association that produces a protease with essentially the same structural architecture. This scenario stands in contrast to an analogous reaction in the coagulation cascade where conversion of the zymogen prothrombin to the protease meizothrombin by the prothrombinase complex is linked to a large conformational transition of the entire protein. The presence of rigid EGF domains in protein C as opposed to kringles in prothrombin likely accounts for the different conformational plasticity of the two zymogens. The new structural features reported here for protein C have general relevance to vitamin K-dependent clotting factors containing EGF domains, such as factors VII, IX, and X.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Wavelength- and irradiance-dependent changes in intracellular nitric oxide level

Photobiomodulation (PBM) refers to beneficial effects of low energy light absorption. Although there is a large and growing body of literature describing down-stream physiological benefits of PBM, there is limited understanding of the molecular mechanisms that initiate and mediate these effects at the level of photon absorption. At present, the leading hypothesis is that light absorption induces release of nitric oxide (NO) from the active site of cytochrome c oxidase (COX), allowing it to bind O 2 instead. This is believed to increase mitochondrial respiration, and result in greater overall health of the cell due to increased ATP production. Aim: Although NO itself is a powerful signaling molecule involved in a host of biological responses, less attention has been devoted to the mechanisms of NO release and subsequent effects on cell signaling. The purpose of this work is to investigate wavelength-specific effects on intracellular NO release in living cells. Approach: We have conducted in depth dosimetry analyses of NO production and function in an in vitro retinal model in response to low energy exposure to one or more wavelengths of laser light. Results: We found statistically significant wavelength-dependent elevations (10-30%) in intracellular NO levels following laser exposures at 447, 532, 635 or 808 nm. Sequential or simultaneous exposures to light at two different wavelengths enhanced the NO modulation up to 50% of unexposed controls. Additionally, the immediate increases in cellular NO levels were independent of the function of nitric oxide synthase, depended greatly on the substrate source of electrons entering the electron transport chain, and did not result in increased levels of cGMP. Conclusions: This study concludes the simple model of light-mediated release of NO from COX is unlikely to explain the wide variety of PBM effects reported in the literature. Our multi-wavelength method provides a novel tool for studying immediate and early mechanisms of PBM, as well as exploring intracellular NO signaling networks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nondispersing Wave Packets in Lattice Floquet Systems

We show that in a one-dimensional translationally invariant tight binding chain, nondispersing wave packets can in general be realized as Floquet eigenstates—or linear combinations thereof—using a spatially inhomogeneous drive, which can be as simple as modulation on a single site. The recurrence time of these wave packets (their “round-trip” time) locks in at rational ratios sT/r of the driving period T, where s, r are coprime integers. Wave packets of different s / r can coexist under the same drive, yet travel at different speeds. They retain their spatial compactness either infinitely (s/r = 1) or over a long time (s/r ≠ 1). Discrete time translation symmetry is manifestly broken for s ≠ 1, reminiscent of integer and fractional Floquet time crystals. We further demonstrate how to reverse engineer a drive protocol to reproduce a target Floquet micromotion, such as the free propagation of a wave packet, as if coming from a strictly linear energy spectrum. The variety of control schemes open up a new avenue for Floquet engineering in quantum information sciences.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Improved naive Bayesian probability classifier in predictions of nuclear mass

Recently, novel statistical methods such as neural networks and Bayesian learning methods are implemented to describe the nuclear masses. Based on previous studies, an improved naive Bayesian probability (iNBP) classifier is proposed to study the nuclear masses by refining the results of sophisticated nuclear models. In the iNBP method, the prediction for nuclear masses is treated as a classification problem. The residuals are classified into several groups to generate prior and conditional probabilities, and the posterior probabilities are further determined by the Bayesian formula. We choose the expectation with maximum probability as the final prediction. Reliability of the iNBP method is assessed by analyzing the global optimizations and the extrapolating capabilities. Here, the iNBP method exhibits impressive improvements on global descriptions for different mass models. Moreover, the method shows robust extrapolating capabilities. Results demonstrate the iNBP method can be applied to predict the nuclear masses of unknown regions. Considering the local mass relations, the iNBP method can offer considerable fine-tuning of the mass descriptions from nuclear models. The methodology proposed in this paper can also be applied to other model-based extrapolations of nuclear observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Cohesion and excitations of diamond-structure silicon by quantum Monte Carlo: Benchmarks and control of systematic biases

We have carried out quantum Monte Carlo (QMC) calculations of silicon crystal focusing on the accuracy and systematic biases that affect the electronic structure characteristics. The results show that 64 and 216 atom supercells provide an excellent consistency for extrapolated energies per atom in the thermodynamic limit for ground, excited, and ionized states. We have calculated the ground state cohesion energy with both systematic and statistical errors below ≈ 0.05 eV. The ground state exhibits a fixed-node error of only 1.3(2)% of the correlation energy, suggesting an unusually high accuracy of the corresponding single-reference trial wave function. We obtain a very good agreement between optical and quasiparticle gaps that affirms the marginal impact of excitonic effects. Our most accurate results for band gaps differ from the experiments by about 0.2 eV. This difference is assigned to a combination of residual finite-size and fixed-node errors. In conclusion, we have estimated the crystal Fermi level referenced to vacuum that enabled us to calculate the edges of valence and conduction bands in agreement with experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Complex Adsorption Behavior of Neodymium and Ytterbium on Structurally-Distinct Alumina Surfaces

New sources of rare earth elements (REEs) are needed to support a green energy transition. REEs adsorbed to aluminum-rich clays in weathering deposits represent important resources but the mechanisms responsible for their retention and ease of extraction are unresolved. Disordered coordination and co-occurrence of multiple species pose challenges to investigating REE adsorption processes via established spectroscopic methods. In this study, we applied element-specific surface crystallography methods to obtain a new perspective on the complexity of REE adsorption mechanisms and affinities. Alumina (001) and (012) crystal surfaces were utilized to evaluate surface-specific controls on Nd(III) and Yb(III) adsorption behavior. The REEs displayed similar total adsorption to alumina (001) as a mixture of inner- and outer-sphere complexes, but Nd displayed a greater proportion of inner-sphere binding. Adsorption of ordered inner- and outer-sphere REE species was substantially lower on alumina (012). These distinct behaviors reflect differences in the surface functional group charging and topography of the two surfaces. However, alumina (012) also hosted a substantial population of disordered adsorbed species, especially for Nd, potentially associated with Al vacancy surface defects. Here, the accumulation of light versus heavy REEs via adsorption in weathering deposits likely results from multiple, competing reactions affected by clay particle morphology. Leaching procedures for resource recovery should account for differential rates of desorption by coexisting inner- and outer-sphere REE surface complexes.

58 GEOSCIENCES↗
DOE OSTI2024

Using data-science approaches to unravel insights for enhanced transport of lithium ions in single-ion conducting polymer electrolyte

Solid polymer electrolytes have yet to achieve the an ionic conductivity > 1 mS/cm at room temperature for realistic applications. This target implies the need to reduce the effective energy barriers of ion transport in polymer electrolytes to around 20 kJ/mol. In this work, we combine information extracted from existing experimental results with theoretical calculations to provide insights into ion transport in single-ion conductors (SICs) with a focus on lithium ion SICs. Through the analysis of temperature-dependent ionic conductivity data obtained from the literature, we evaluate different methods of extracting energy barriers for lithium transport. The traditional Arrhenius fit to the temperature-dependent ionic conductivity data indicates that the Meyer-Neldel rule holds for SICs. However, the values of the fitting parameters remain unphysical. Our modified approach based on recent work (Macromolecules, 56, 15, 6051(2023)), which incorporates a fixed pre-exponential factor, reveals that the energy barriers exhibit temperature dependence over a wide range of temperatures. Using this approach, we identify a series of anions leading to the energy barriers less than 30 kJ/mol, which include trifluoromethane sulfonimide (TFSI), fluoromethane sulfonimide (FSI), and boron-based organic anions. In our efforts to design the next generation of anions, which can exhibit the energy barriers less than 20 kJ/mol, we focused on boron-containing SICs, and performed density functional theory (DFT) based calculations to connect the chemical structures via the binding energy of cation (lithium)-anion pairs with the experimentally derived effective energy barriers for ion transport. Not only have we identified a correlation between the binding energy and the energy barriers, but we also propose a strategy to design new boron-based anions by using the correlation. This combined approach involving experiments and theoretical calculations is capable of facilitating the identification of promising new anions, which can exhibit ionic conductivity $> 1$ mS/cm near room temperature, thereby expediting the development of novel superionic single-ion conducting polymer electrolytes. The published datasets include all the temperature-dependent ionic conductivity collected from the literature with literature DOIs, DFT calculated binding energies, and python scripts to analyze data, construct statistical models, and generate plots.

36 MATERIALS SCIENCE↗
NASA NTRS1996

Electronic Characterization of Defects in Narrow Gap Semiconductors-Comparison of Electronic Energy Levels and Formation Energies in Mercury Cadmium Telluride, Mercury Zinc Telluride, and Mercury Zinc Selenide

We have used a Green's function technique to calculate the energy levels and formation energy of deep defects in the narrow gap semiconductors mercury cadmium telluride (MCT), mercury zinc telluride (MZT) and mercury zinc selenide (MZS). The formation energy is calculated from the difference between the total energy with an impurity cluster and the total energy for the perfect crystal. Substitutional (including antisite), interstitial (self and foreign), and vacancy deep defects are considered. Relaxation effects are calculated (with molecular dynamics). By use of a pseudopotential, we generalize the ideal vacancy model so as to be able to consider relaxation for vacancies. Different charge states are considered and the charged state energy shift (as computed by a modified Haldane-Anderson model) can be twice that due to relaxation. Different charged states for vacancies were not calculated to have much effect on the formation energy. For all cases we find deep defects in the energy gap only for cation site s-like orbitals or anion site p-like orbitals, and for the substitutional case only the latter are appreciably effected by relaxation. For most cases for MCT, MZT, MZS, we consider x (the concentration of Cd or Zn) in the range appropriate for a band gap of 0.1 eV. For defect energy levels, the absolute accuracy of our results is limited, but the precision is good, and hence chemical trends are accurately predicted. For the same reason, defect formation energies are more accurately predicted than energy level position. We attempt, in Appendix B, to calculate vacancy formation energies using relatively simple chemical bonding ideas due to Harrison. However, these results are only marginally accurate for estimating vacancy binding energies. Appendix C lists all written reports and publications produced for the grant. We include abstracts and a complete paper that summarizes our work which is not yet available.

Patterson, James D.↗
DOE OSTI2021

Solvent Effects on Catalytic Reactions and Related Phenomena at Liquid-Solid Interfaces

Catalytic reactions involve the direct interaction of reactants, intermediates and products with the catalyst surface. We not only need to control the atomic structure and electronic properties of the active site, but also explore the multiple molecular interactions that occur beyond the active site; they play an essential role in altering the binding and reactivity of surface species. In liquid-phase catalysis, solvents provide additional degrees of freedom in the design of the catalytic process for desirable activity and selectivity. Here, the multi-faceted effects of solvents have a profound impact on the catalyst performance by restricting the mass transfer to the site, tuning the chemical potential of the surface species, competing for active sites, stabilizing the initial and transition states, and causing mechanistic changes by participating in the kinetically relevant elementary steps. This review addresses the different aspects of solvent effects, using a few prototype solid-liquid interfaces to illustrate these fundamental features. Recent experimental and computational studies that provide new insight at the molecular level are examined. Solvent structures in the proximity of the catalyst surface are discussed along with their influence in molecular binding and reaction at the solid-liquid interfaces. Furthermore, opportunities to alter such a solid-liquid interaction by tuning the wettability of the catalyst surfaces are explored.

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

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer

Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

First observation of 28 O

Subjecting a physical system to extreme conditions is one of the means often used to obtain a better understanding and deeper insight into its organization and structure. In the case of the atomic nucleus, one such approach is to investigate isotopes that have very different neutron-to-proton ($N/Z$) ratios than in stable nuclei. Light, neutron-rich isotopes exhibit the most asymmetric $N/Z$ ratios and those lying beyond the limits of binding, which undergo spontaneous neutron emission and exist only as very short-lived resonances (about 10 -21 s), provide the most stringent tests of modern nuclear-structure theories. Here we report on the first observation of 28 O and 27 O through their decay into 24 O and four and three neutrons, respectively. The 28 O nucleus is of particular interest as, with the $Z$ = 8 and $N$ = 20 magic numbers, it is expected in the standard shell-model picture of nuclear structure to be one of a relatively small number of so-called ‘doubly magic’ nuclei. Furthermore, both 27 O and 28 O were found to exist as narrow, low-lying resonances and their decay energies are compared here to the results of sophisticated theoretical modelling, including a large-scale shell-model calculation and a newly developed statistical approach. In both cases, the underlying nuclear interactions were derived from effective field theories of quantum chromodynamics. Finally, it is shown that the cross-section for the production of 28 O from a 29 F beam is consistent with it not exhibiting a closed $N$ = 20 shell structure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Anomalous two-photon Compton scattering

Abstract X-ray free-electron lasers can generate radiation pulses with extreme peak intensities at short wavelengths. This enables the investigation of laser–matter interactions in a regime of high fields, yet at a non-relativistic ponderomotive potential, where ordinary rules of light–matter interaction may no longer apply and nonlinear processes are starting to become observable. Despite small cross-sections, first nonlinear effects in the hard x-ray regime have recently been observed in solid targets, including x-ray-optical sum-frequency generation (XSFG), x-ray second harmonic generation (XSHG) and two-photon Compton scattering (2PCS). Nonlinear interactions of bound electrons in the x-ray range are fundamentally different from those dominating at optical frequencies. Whereas in the optical regime nonlinearities are predominantly caused by anharmonicities of the atomic potential in the chemical bonds, x-ray nonlinearities far above atomic resonances are expected to be due to nonlinear oscillations of quasi-free electrons, including inner-shell atomic electrons. While the quasi-free-electron model agrees reasonably well with the experimental data for XSFG and XSHG, 2PCS measurements have led to unexpected results: the energy of the nonlinearly scattered photons from non-relativistic electrons shows a substantial unexpected red shift in addition to the Compton shift that is well beyond that predicted by a nonlinear quantum electrodynamics model for free electrons. A potential explanation for the spectral broadening is based on a previously unexplored scattering process that involves the whole atom rather than just quasi-free electrons. A first simulation that includes the atomic binding potential was successful in describing a broadening of the spectrum of the nonlinearly scattered photons to longer wavelengths for soft x-rays. However, the same model does not show any broadening at hard x-ray wavelengths, which is in agreement with other simulation approaches. To this point no calculation has been able to reproduce the experimentally observed broadening. Here we present further experimental data of 2PCS for an extended parameter range using additional diagnostics. In particular, we present measurements of the electron momentum distribution during the interaction that strongly suggest that the spectral broadening is not caused by an increased plasma temperature. We extend our measurement of the magnitude of the red shift in beryllium to > 1.9 k e V in addition to the Compton shift expected for free electrons and expand the measurement of the angular distribution to include forward scattering angles. We also present first measurements of 2PCS from diamond.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Excitons in two-dimensional metal-halide perovskites

Georgia Tech School of Chemistry and Biochemistry Special Summer Seminar Series, Prof Carlos Silva; While polarons --- charges bound to a lattice deformation induced by electron-phonon coupling --- are primary photoexcitations at room temperature in bulk metal-halide hybrid organic-inorganic perovskites (HOIP), excitons --- Coulomb-bound electron-hole pairs --- are the stable quasi-particles in their two-dimensional (2D) analogues. Here we address the fundamental question: are polaronic effects consequential for excitons in 2D-HIOPs? Based on our recent work, we argue that polaronic effects are manifested intrinsically in the exciton spectral structure, which is comprised of multiple non-degenerate resonances with constant inter-peak energy spacing. We highlight measurements of population and dephasing dynamics that point to the apparently deterministic role of polaronic effects in excitonic properties. We contend that an interplay of long-range and short-range exciton-lattice couplings give rise to exciton polarons, a character that fundamentally establishes their effective mass and radius, and consequently, their quantum dynamics. Given this complexity, a fundamentally far-reaching issue is how Coulomb-mediated many-body interactions---elastic scattering such as excitation-induced dephasing, inelastic exciton bimolecular scattering, and multi-exciton binding---depend upon the specific exciton-lattice coupling within the structured excitation lineshape. We measure the intrinsic and density-dependent exciton dephasing rates of the multiple excitons and their dependence on temperature by means of two-dimensional coherent excitation spectroscopy. We find that diverse excitons display distinct intrinsic dephasing rates mediated by phonon scattering involving different effective phonons, and contrasting rates of exciton-exciton elastic scattering. These findings establish specifically the consequence of distinct lattice dressing on exciton many-body quantum dynamics, which critically define fundamental optical properties that underpin photonics and quantum optoelectronics.

solar cells, metal-halide perovskites, excitons, p↗
NASA NTRS2022

The Influence of surface binding energy on sputtering in models of the sodium exosphere of Mercury

We have simulated the sodium (Na) exosphere of Mercury to show how the exosphere is affected by the assumed surface binding energy (SBE) of Na in the sputtered component. We constrained ion precipitation onto the surface using distributions for the cusp regions that are consistent with measurements by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging Fast Imaging Plasma Spectrometer instrument. We have simulated sputtering with SBEs of 0.27, 2.6, 4.4, and 7.9 eV, with the lowest value commonly used in exosphere models and the highest from recent molecular dynamics calculations for the Na-bearing feldspar end-member, albite. A gradual change in the exosphere is seen as the yield decreases and the ejecta energy increases with increasing SBE. We describe the corresponding exosphere source functions for ion sputtering (IS), as well as for the previously studied processes of micrometeoroid impact vaporization and photon-stimulated desorption (PSD), along with their release energy distributions and spatial distributions. We have summed the contributions of the various source processes to explain how and when the different sources can be distinguished by observations. The modeled exosphere scale heights range from 72 km for PSD to over 1000 km for IS using a SBE of 7.9 eV. We find that the processes responsible for generating Mercury's Na exosphere are separable by measuring line-of-sight column densities tangent to the planet at various altitudes and positions around the planet. Our initial results are consistent with the Na being sputtered from a high-SBE material such as feldspar, which has been predicted to be abundant on the Mercury's surface.

Rosemary M. Killen↗
DOE OSTI2023

Magnetic bulk photovoltaic effect: Strong and weak field

Shift current and ballistic current have been proposed to explain the bulk photovoltaic effect (BPVE), and there have been experiments designed to separate the two mechanisms. These experiments are based on the assumption that under magnetic field, ballistic current can have a Hall effect while the shift current cannot, which is from some energy-scale arguments and has never been proven. A recent work [D. Hornung and R. von Baltz, Phys. Rev. B 103, 195203 (2021)] using quantum transport formalism achieves a conclusion that shift current indeed has a Hall current, seemingly contradicting the previous assumption and making the situation more confusing. Moreover, the behavior of BPVE under strong magnetic field is still unexplored. In this Letter, using a minimal two-dimensional tight-binding model, we carry out a systematic numerical study of the BPVE under weak and strong magnetic field by treating the field in a nonperturbative way. Further, our model clearly shows the appearance of the magnetically induced ballistic current along the transverse direction, which agrees with the previous predictions, and interestingly a sizable longitudinal response of the shift current is also observed, a phenomenon that is not captured by any existing theories where the magnetic field is treated perturbatively. More surprisingly, drastically different shift current is found in the strong-field regime, and the evolution from weak to strong field resembles a phase transition. We hope that our work could resolve the debate over the behavior of BPVE under magnetic field, and the strong-field behavior of shift current is expected to inspire more studies on the relation between nonlinear optics and quantum geometry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Bulk electronic structure of lanthanum hexaboride (LaB 6 ) by hard x-ray angle-resolved photoelectron spectroscopy

In the last decade rare-earth hexaborides have been investigated for their fundamental importance in condensed matter, and for their applications in advanced technological fields. Among these compounds, LaB 6 has a special place, being a traditional d-band metal without additional f- bands. In order to understand the bulk electronic structure of the more complex rare-earth hexaborides, in this paper we investigate the bulk electronic structure of LaB 6 using tender/hard x-ray photoemission spectroscopy, measuring both core-level and angle-resolved valence-band spectra. Furthermore, we compare the La 3d core level spectrum to cluster model calculations in order to understand the bulk-like core-hole screening effects. The results show that the La 3d well-screened peak is at a lower binding energy compared to the main poorly-screened peak; the relative intensity between these peaks depends on how strong the hybridization is between La and B atoms. Here, we show that the recoil effect, negligible in the soft x-ray regime, becomes prominent at higher kinetic energies for lighter elements, such as boron, but is still negligible for heavy elements, such as lanthanum. In addition, we report the bulk-like band structure of LaB6 determined by tender/hard x-ray angle-resolved photoemission spectroscopy (HARPES). We compare HARPES experimental results to the free-electron final-state calculations and to the more precise one-step photoemission theory including matrix element and phonon excitation effects. The agreement between the features present in the experimental ARPES data and the theoretical calculations is very good. In addition, we consider the nature and the magnitude of phonon excitations in order to interpret HARPES experimental data measured at different temperatures and excitation energies. We demonstrate that one step theory of photoemission and HARPES experiments provide, at present, the only approach capable of probing, both experimentally and theoretically, true “bulk-like” electronic band structure of rare-earth hexaborides and strongly correlated materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors

The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MPro WT ) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373), and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is ~400-fold weaker corresponding to 3.5 kcal/mol and 13.3 °C decrease in free energy (ΔG) and thermal stability (T m ), respectively, relative to MPro WT . The H41A mutation results in a 20-fold increase in the dissociation constant (K d ), and 1.7 kcal/mol and 1.4 °C decreases in ΔG and T m , respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MPro H41A , whereas no significant change is observed in binding to MPro WT . Structures of the four inhibitor complexes with MPro 1-304/C145A show that the active site geometries of the complexes are nearly identical to that of MPro WT with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MPro WT that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MPro C145A also results in a significant, but smaller, increase in K d and decrease in ΔG and T m , relative to NMV.

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

Mechanisms Underlying Plastocyanin-Cytochrome f Electron Transfer Investigated via Site-Specific Linear and Two-dimensional Infrared Spectroscopy

The goal of this research is to further our understanding of biological electron transfer in photosynthesis through the development and application of new methods for studying proteins with high spatial and temporal detail. Biological electron transfer occurs between metal sites imbedded in proteins where the environment and its motions can be very different from those of normal bulk liquids. Moreover, electron transfer between two proteins typically involves short-lived binding interactions within a highly mobile complex. We have directed our studies at photosynthetic electron transfer proteins plastocyanin and cytochrome f. We have labeled two key ligands to the copper ion of plastocyanin with carbon deuterium probe vibrations that enable their selective analysis by infrared spectroscopy. This analysis has shown that association of plastocyanin with cytochrome f leads to large changes in the bonding between the copper ion and ligands. In addition, the probes have been used to assess the contribution of the protein scaffold of plastocyanin in dictating the copper coordination geometry. We also have made progress to extend our experiments from equilibrium to non-equilibrium studies. The studies help to illuminate how proteins are tuned to control biological electron transfer. A better understanding of electron transfer reactions in natural photosynthesis will bolster efforts to develop artificial systems for energy production.

59 BASIC BIOLOGICAL SCIENCES↗