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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Distinct Kinetic Signatures of Photodesorption from Metal Nanoparticles

Visible photon fluxes can influence the rate and selectivity of heterogeneously catalyzed reactions on metal nanoparticle surfaces. Models describing the influence of photon fluxes have typically introduced photon flux dependent apparent thermal kinetic parameters (reaction orders, activation energies, binding energies, etc.). This has relied on empirical fitting of reaction rate data, making mechanistic interpretations of how photon fluxes influence elementary step rates challenging and inconsistent with fundamental descriptions of photochemistry on metal surfaces developed from surface science studies. Using the CO adsorption–desorption quasi-equilibrium reaction on Pt/Al 2 O 3 catalysts as a model system, we measured steady state adsorbed CO (CO*) coverages under isothermal and isobaric (1 mbar CO) conditions as a function of temperature (473–573 K) and of 440 nm photon flux ((0.1–5.2) × 10 3 # hv Pt site –1 s –1 ) using in situ IR spectroscopy. Steady state CO* coverage on Pt was photon flux dependent with increasing photon flux causing decreasing coverage, consistent with photons driving CO* desorption rates faster than thermal CO* desorption rates. However, photon flux dependent CO* coverages were essentially temperature independent, inconsistent with models that describe photon effects using perturbations to apparent thermal kinetic parameters. Instead, 120 steady state CO* coverages as a function of temperature and photon flux are quantitatively described by a kinetic model in which the overall desorption rate is a summation of independent thermal and photon induced CO* desorption rates. Site-resolved analysis reveals distinct kinetic parameters for photon driven desorption of CO* from well-coordinated, under-coordinated, and highly under-coordinated Pt sites, with temperature-dependent apparent quantum efficiencies (AQE) consistent with temperature dependence of vibrational quanta distribution of adsorbed CO. The rigorous kinetic rate laws for independent photon and thermal driven pathways allow for predictive modeling of the influence of photon fluxes on the rates of CO* desorption under catalytic conditions. Further, the analysis provides evidence that steady state continuous wave photon fluxes can drive desorption/adsorption reactions on metal surfaces out of thermal equilibrium, reconciling surface science observations of molecular photodesorption with applied catalysis. The work establishes a general kinetic framework to be considered for photon driven processes on metals, and defines catalyst, reaction, and photon flux characteristic design principles for breaking Sabatier limitations.

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

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.

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

Mechanistic insight into the effects of A-site doping in perovskite nanorods on interfacial Li-ion and Na-ion transport in polymer–perovskite composite electrolytes

Composite polymer electrolytes (CPEs) offer a promising pathway to safer and higher energy density electrochemical energy storage yet optimizing interfacial ion transport remains a critical challenge due to high resistances and a lack of understanding of the complex interfacial electrostatic interactions. This work investigates the mechanistic origins of the interfacial ion transport enhancement in single-ion conducting (SIC) polymer electrolytes filled with A-site disordered perovskite LaxMyTiOz (LMTO) (M = Li, Na, K) nanorods. By integrating Density Functional Theory (DFT) with broadband dielectric spectroscopy (BDS) and pulsed-field-gradient NMR (PFG-NMR), we analyze the ion transport behavior in Li-based and Na-based SIC systems containing compositionally distinct LMTO fillers (LMTO800 and LMTO900). Specifically, we introduce the site-to-site energy difference (ΔE) descriptor, which extends beyond single-site descriptors such as adsorption energy and ion binding energies. We demonstrate that ΔE together with ion binding energies provide a more comprehensive picture of the energy landscape at the polymer–ceramic interface. The combined DFT and experimental results show that A-site doping in the ceramic filler can effectively modulate ΔE and ion binding energies, creating a favorable potential energy landscape that promotes enhanced ion transport along the interface. This comprehensive study illustrates the impact of ceramic compositional tuning on interfacial ion transport and provides materials design rules towards real-world applications.

B shepard, Lauren [Pennsylvania State University]↗
DOE OSTI2025

Effect of heteroatom incorporation on electronic communication in metal chalcogenide nanoclusters

Metal chalcogenide nanoclusters (NC), specifically of type TM 6 E 8 (L) 6 (TM = transition metal, E = chalcogen, L = ligand) have garnered attention in recent years as promising catalysts and biosensors due to their remarkable electronic and magnetic properties, as well as their ability to undergo supramolecular assembly into 2D materials. Furthermore, the undercoordinated metal chalcogenide NCs have shown distinct surface reactivity, which is strongly dependent on the composition of the TM core. The differences in the reactivity of the undercoordinated species have been attributed to differences in ligand binding energies. Although ligand binding energies in homometallic NCs have been extensively studied, little is known about the effect of heteroatoms in the core on the strength of ligand binding in metal chalcogenide NCs. In this work, we provide new insights into this topic by examining the relative stability of [Co 6−x Fe x S 8 (PEt 3 ) 6 ] + (x = 0–6) NCs towards fragmentation using collision energy-resolved collision-induced dissociation (CID) experiments. We observe that the ligand binding energy gradually decreases until four Fe atoms are incorporated into the cluster core and then gradually increases until all the Co atoms are replaced with Fe. This experimental trend was compared with the results of density functional theory (DFT) calculations, which indicate drastic differences in the electronic communication between Co and Fe atoms in the TM core. By understanding the effect of heteroatom incorporation on ligand binding energy to the NC core, our work provides important insights into the effect of atom-by-atom substitution on the functional properties of tunable nanostructures.

Havenridge, Shana [Argonne National Laboratory (AN↗
DOE OSTI2020

On the importance of np-pairs in the isovector pairing model

Abstract It is shown that the isovector np-pair number operator can be realized in the O (5) quasi-spin basis. The computation of the isovector np-pair number is demonstrated for even-even and odd-odd ds -shell nuclei described by the charge-independent mean field plus isovector pairing model restricted within the O (5) seniority-zero subspace, thereby binding energies and low-lying excited states of these ds -shell nuclei are fit, along with estimates for the isovector neutron-proton pairing contributions. For reasonable neutron-proton pairing strengths the isovector np-pairing energy contribution to the total binding energy in odd-odd N = Z nuclei is systematically larger than that in the even-even nuclei. In sum, the results suggest that the isovector np-pairing mode is favored in odd-odd N = Z nuclei; and additionally, a decrease in the double binding-energy difference for odd-odd nuclei is primarily due to the symmetry and Wigner energy contributions to the binding energy.

Physics↗
DOE OSTI2021

Carbon complexes in highly C-doped GaN

We investigate the properties of heavily C-doped GaN grown by hydride vapor phase epitaxy using both optical experiments and hybrid density functional theory calculations. Previous work has established that carbon acceptors (C N ) give rise to a yellow luminescence band near 2.2 eV along with a blue luminescence band near 2.9 eV. Photoluminescence measurements show the yellow band shifting as a function of carbon concentration, suggesting a change in the behavior of carbon species as carbon content increases. With hybrid density functional theory we calculate the electrical and optical behavior of carbon centers containing multiple carbon impurities, which may arise in heavily doped material. We compare the behavior of these complexes to the isolated centers, and find that the dicarbon donor-acceptor (C Ga –C N ) complex is a candidate to explain the shift in the yellow luminescence peak. Tricarbon complexes have high formation energies and modest binding energies, and also give rise to optical transitions that are inconsistent with the observed spectra. We also identify the split dicarbon interstitial on the gallium site as a low-energy species with a large binding energy that may act to compensate carbon acceptors. Here, local vibrational modes are calculated for carbon impurity centers, and we compare these results to recent experiments. Dicarbon and tricarbon complexes involving C Ga and C N exhibit modes that are only slightly higher than the isolated species, while carbon interstitials and related complexes give rise to vibrational modes much higher than C Ga and C N .

36 MATERIALS SCIENCE↗
DOE OSTI2025

Further steps toward the next generation of covariant energy density functionals

The present study aims at further development of covariant energy density functionals (CEDFs) towards more accurate description of binding energies across the nuclear chart. Infinite basis corrections to binding energies in the fermionic and bosonic sectors of the covariant density functional theory are taken into account in the fitting protocol within the covariant density functional theory. In addition, total electron binding energies are used in the conversion of atomic binding energies into nuclear ones. Their dependence on neutron excess is investigated across the nuclear chart within the atomic approach. Furthermore, these factors were disregarded in the previous generation of covariant energy density functionals, but their omission leads to substantial global calculation errors for physical quantities of interest. For example, these errors for binding energies are of the order of 0.8 MeV or higher for the three major classes of covariant energy density functionals.

Binding energy & masses↗
DOE OSTI2020

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling many of the practical aspects regarding the preparation of the different thermodynamic end states of complex molecular systems and the numerous processing scripts often remains a burden for successful applications. Here, we present CHARMM-GUI Free Energy Calculator (http://www.charmm-gui.org/input/fec) that provides various alchemical free energy perturbation molecular dynamics (FEP/MD) systems with input and post-processing scripts for NAMD and GENESIS. Four submodules are available: Absolute Ligand Binder (for absolute ligand binding FEP/MD), Relative Ligand Binder (for relative ligand binding FEP/MD), Absolute Ligand Solvator (for absolute ligand solvation FEP/MD), and Relative Ligand Solvator (for relative ligand solvation FEP/MD). Each module is designed to build multiple systems of a set of selected ligands at once for high-throughput FEP/MD simulations. The capability of Free Energy Calculator is illustrated by absolute and relative solvation FEP/MD of a set of ligands and absolute and relative binding FEP/MD of a set of ligands for T4-lysozyme in solution and the adenosine A 2A receptor in a membrane. The calculated free energy values are overall consistent with the experimental and published free energy results (within ~1 kcal/mol). We hope that Free Energy Calculator is useful to carry out high-throughput FEP/MD simulations in the field of biomolecular sciences and drug discovery.

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

The role of precursor decomposition in the formation of samarium doped ceria nanoparticles via solid-state microwave synthesis

The impact on the final morphology of ceria (CeO 2 ) nanoparticles made from different precursors (commercial: cerium acetate/nitrate) and in house: cerium tri(methylsilyl)amide (Ce-TMSA)) via a microwave solid state reaction has been determined. In all instances, powder X-ray diffraction indicated that the cubic fluorite CeO 2 phase (PDF# 04–004-9150, with the space group Fm-3 m) had formed. Scanning electron microscopy (SEM) images revealed spherical nanoparticles were produced from the Ce-TMSA precursor. The commercial acetate and nitrate precursors produced particles with irregular morphology. The roles of the precursor decomposition and binding energy in the synthesis of the nanocrystals with various morphologies, as well as a possible growth mechanism, were evaluated based on experimental and computational data. The formation of spherical shaped nanoparticles was determined to be due to the preferential single-step decomposition of the Ce-TMSA as well as the low activation energy to overcome decomposition. Due to the complicated decomposition of the commercial precursors and high activation energy the resulting particles adopted an irregular morphology. Highly uniform samarium doped ceria (Sm x Ce 1-x O 2-δ ) nanospheres were also synthesized from Ce-TMSA and samarium tri(methylsilyl)amide (Sm-TMSA). The effects of reaction time and temperature, on the final morphology were observed through SEM. The rapid single-step decomposition of TMSA-based precursors as observed through thermogravimetric analysis (TGA) and confirmed through the calculation of potential energy surfaces and binding energies from density functional theory (DFT) calculations, indicated that nanoparticle formation follows LaMer’s classical nucleation theory.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the lambda-exchange of free energy perturbation (FEP). Further, two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/lambda-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.

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

Fundamental optical transitions in hexagonal boron nitride epilayers

Fundamental optical transitions in hexagonal boron nitride (h-BN) epilayers grown on sapphire by metal–organic chemical vapor deposition (MOCVD) using triethylboron as the boron precursor have been probed by photoluminescence (PL) emission spectroscopy. The low temperature (10 K) PL spectrum exhibits two groups of emission lines. The first group includes the direct observation of the free exciton and impurity bound exciton (BX) transitions and phonon replicas of the BX transition, whereas the second group is attributed to the direct observation of the band-to-band transition and its associated phonon replicas. The observations of zero-phonon lines of the band-to-band and exciton transitions, which are supposedly forbidden or “dark” in perfect h-BN crystals, result from a relaxed requirement of momentum conservation due to symmetry-breaking in the presence of high concentrations of impurities/defects and strain, which in turn provided more deterministic values of the energy bandgap (E g ), exciton binding energy (E x ), and binding energy of impurity bound excitons (E BX ) in h-BN epilayers. Excitonic parameters of h-BN epilayers grown by MOCVD, carbon-free chemical vapor deposition, and high purity h-BN bulk materials are compared and discussed. The present results, together with available information in the literature, represent a significant improvement in the understanding of the fundamental optical properties and excitonic parameters of h-BN ultrawide bandgap semiconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Rigorous constraints on three-nucleon forces in chiral effective field theory from fast and accurate calculations of few-body observables

We explore the constraints on the three-nucleon force (3NF) of chiral effective field theory (χ EFT) that are provided by bound-state observables in the A = 3 and A = 4 sectors. Our statistically rigorous analysis incorporates experimental error, computational method uncertainty, and the uncertainty due to truncation of the χ EFT expansion at next-to-next-to-leading order. A consistent solution for the 3 H binding energy, the 4 He binding energy and radius, and the 3 H β-decay rate can only be obtained if χ EFT truncation errors are included in the analysis. Here, the β-decay rate is the only one of these that yields a nondegenerate constraint on the 3NF low-energy constants, which makes it crucial for the parameter estimation. We use eigenvector continuation for fast and accurate emulation of no-core shell model calculations of the few-nucleon observables. This facilitates sampling of the posterior probability distribution, allowing us to also determine the distributions of the parameters that quantify the truncation error. We find a χ EFT expansion parameter of Q = 0.33 ± 0.06 for these observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

DFT-based investigation of solvation of Nd(III)/Yb(III) cations in room-temperature ionic-liquid

We report a DFT study on the solvation of bare rare-earth (RE) cations [Nd(III) and Yb(III)] in the room-temperature ionic-liquid (RTIL) based on 1,3-dimethyl-imidazolium + , PF 6 - , [MMI][PF 6 ]. In the present article, we aim to investigate whether the chosen RTIL can preferentially solvate any of the RE cations under study. First, the RTIL binding to the RE cation is studied in the gas phase, and then explored with continuum solvation model employing RTIL parameters. First, we considered the formation of the first solvation shell, where the PF 6 - anions directly bond with the Ln(III) cation. We then further surrounded the first solvation shell with [MMI]+ cations to form the second solvation shell. The stability of PF 6 - coordinated complexes is studied by calculating the binding energy values. The number of PF 6 - anions for both Ln(III) cations starts with three ligands and goes until the maximum binding energy in the RTIL medium is reached. The coordination number and binding modes of PF 6 - depend on the size of the RE cation. Comparing the binding energy values between the RE cations for the first solvation shell complexes, it is noticed that Yb-complexes have relatively greater binding energy than Nd-complexes. We have further performed a Boltzmann population analysis to find out the most dominant conformer among each category of PF 6 - coordinated complexes. A study using Natural Population Analysis shows that after complexation with PF 6 - the charge on the Yb-centers lower to a greater extent than Nd-centers, implying stronger bonding between Yb and PF 6 - , which is in harmony with the binding energy analysis. Overall, the computational investigation provides an in-depth understanding of the complexation phenomena of RE cations in RTIL, which can be useful for the practical separation of RE cations using RTIL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Global optimization of harmonic oscillator basis in covariant density functional theory

The present investigation focuses on the improvement of the accuracy of the description of binding energies within moderately sized fermionic basis. Using the solutions corresponding to infinite fermionic basis it was shown that in the case of meson exchange (ME) covariant energy density functionals (CEDFs) the global accuracy of the description of binding energies in the finite $N_F$ = 16 - 20 bases can be drastically (by a factor ranging from ~3 up to ~9 dependent on the functional and $N_F$) improved by a global optimization of oscillator frequency of the basis. This is a consequence of the unique feature of the ME functionals in which with increasing fermionic basis size fermionic and mesonic energies approach the exact (infinite basis) solution from above and below, respectively. As a consequence, an optimal oscillator frequency $\hbar\omega_0$ of the basis can be defined which provides an accurate reproduction of exact total binding energies by the ones calculated in truncated basis. This leads to a very high accuracy of the calculations in moderately sized $N_F=20$ basis when mass dependent oscillator frequency is used: global rms differences $\delta B_{rms}$ between the binding energies calculated in infinite and truncated bases are only 0.025 MeV and 0.031 MeV for the NL5(Z) and DD-MEZ functionals, respectively. Optimized values of the oscillator frequency $\hbar\omega_0$ are provided for three major classes of CEDFs, i.e. for density dependent meson exchange functionals, nonlinear meson exchange ones and point coupling functionals.

Binding energy & masses↗
DOE OSTI2025

First-Principles-Based Study of the Decomposition of Phenol and Hydroquinone on Pt(111) Combined with Quantitative Information from XPS Spectra to Address the Impact of Coverage and Number of Hydroxyl Functional Groups

A combined first-principles-based and experimental X-ray photoelectron spectroscopy approach was used to investigate the thermal decomposition of two model biofuel compounds, phenol and hydroquinone, on Pt(111) at both low and high coverages. The DFT-based approach yields adsorption geometries and energies, activation barriers and core-level binding energy shifts for C 1s and O 1s. Increasing the coverage in the theoretical model leads to slight shifts in core-level binding energies─toward higher values for C 1s and lower values for O 1s. It also alters the energy profiles of the decomposition reaction pathway, resulting in weaker adsorption energies and changes in both reaction and activation barriers. At low temperatures, we observe a multilayer for phenol and hydroquinone upon adsorption, with desorption occurring at 200 and 270 K, respectively. Following desorption of the multilayer, decomposition proceeds via initial O–H bond scission, followed by two parallel pathways involving either C–H or C–C bond scission, whereby in the case of phenol C–H bond scission occurs first. Here, we further provide characteristic core level binding energies by theoretical calculations that are subsequently used in experimental analyses, establishing a reference database for key spectra of phenolic functionalities applicable to a range of catalytic reactions.

09 BIOMASS FUELS↗
DOE OSTI2024

The charge and mass symmetry breaking in the KK K¯ system

Abstract In the framework of the Faddeev equations in configuration space, we investigate theK(1460) meson as a resonant state of the KK K ¯ kaonic system. We perform calculations for the particle configurationsK 0 K + K − and K 0 K + K 0 ¯ within two models: theABCmodel, in which all three particles are distinguishable, and theAACmodel when two particles are identical. The models differ in their treatment of the kaon mass difference and the attractive Coulomb force between theK + K − pair. We found that the Coulomb shift adds over 1 MeV to the three-body binding energy. The expected correction to the binding energy due to mass redistribution fromAAtoABis found to be negligible, up to a maximum of 6% of the relative mass correction. At the same time, the symmetry of the wave function is distorted depending on the mass ratio value. We found that the repulsiveKKinteraction plays an essential role in the binding energy of the KK K ¯ system and reports the mass of 1461.8 or 1464.1 MeV for the neutralK 0 (1460) and 1466.5 or 1468.8 MeV for the chargedK + (1460) resonances, respectively, depending on the parameter sets forKKand K K ¯ interactions.

Physics↗
DOE OSTI2020

Stability of heterogeneous single-atom catalysts: a scaling law mapping thermodynamics to kinetics

Heterogeneous single-atom catalysts (SACs) hold the promise of combining high catalytic performance with maximum utilization of often precious metals. We extend the current thermodynamic view of SAC stability in terms of the binding energy (E bind ) of single-metal atoms on a support to a kinetic (transport) one by considering the activation barrier for metal atom diffusion. A rapid computational screening approach allows predicting diffusion barriers for metal–support pairs based on E bind of a metal atom to the support and the cohesive energy of the bulk metal (E c ). Metal–support combinations relevant to contemporary catalysis are explored by density functional theory. Assisted by machine-learning methods, we find that the diffusion activation barrier correlates with (E bind ) 2 /E c in the physical descriptor space. This diffusion scaling-law provides a simple model for screening thermodynamics to kinetics of metal adatom on a support.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗