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DOE OSTI2021

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC 50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for M pro -ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M pro . Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2026

Hydrogen Adsorption over Transition Metals in Water

The adsorption free energy of atomic hydrogen on Pt(111), Pd(111), Ni(111), Ru(0001), Cu(111), and Rh(111) in liquid water was computed using a quantum mechanical/molecular mechanical free-energy perturbation scheme. The Pt(111) computations indicate that the solvent effect on H adsorption on atop sites (+0.20 eV) is almost twice that on fcc (+0.12 eV), showing it is less likely to find adsorbed hydrogen in atop position in the presence of water than in the gas phase. The solvent effect for the fcc site, which is the most favorable site for adsorbed H on Pt(111), agrees qualitatively with experimental work by Lercher et al., who reported an effect of +0.2 eV. Overall, an endergonic solvent effect for hydrogen adsorption is observed for all metals, indicating a lower hydrogen coverage relative to free site coverage at metal-water interfaces compared to metal-gas interfaces, even when hydrogen transport effects through the fluid phase are negligible; a result with important implications for (de)hydrogenation catalysis.

Zare, Mehdi↗

DOE OSTI2026

Metal–bicarbonate ion pairing in alkaline aqueous solutions from multilevel embedded correlated wavefunction theory and molecular dynamics

In this work, we examine ion-pairing mechanisms of bicarbonates in alkaline aqueous solutions with the divalent metal ions most abundantly present in seawater, namely, Ca 2+ and Mg 2+ . We employ a rare-event enhanced sampling approach within first-principles molecular dynamics to explore regions of phase space spanning solvent-shared to contact ion pairs. Second-order Møller–Plesset perturbation theory (MP2) corrections are subsequently applied in an embedding framework (EMB) to refine the electronic structure of stationary states and associated reaction barriers along the free-energy profiles while retaining the extended solvent effects at the density functional theory (DFT) level. Ca 2+ –HCO 3 − was previously hypothesized to exist in a solvent-shared ion pair (SSHIP) by DFT studies with an endergonic contact ion pair (CIP) formation; however, our EMB-MP2 refinement of the DFT ion-pairing pathways reveals that Ca 2+ and HCO 3 − form a virtually barrier-free CIP in alkaline solutions, with even more energetic ease than the widely studied Ca–CO 3 ion pair. We find qualitative agreement between DFT and EMB-MP2 for Mg 2+ —unlike Ca 2+ , Mg 2+ refuses to shed its strong hydration shell, thereby preferring a SSHIP state with a significant activation barrier to crossover to the CIP forms—a trait reminiscent of ion pairing in Mg–CO 3 and closely related to the kinetic limitations underlying the famous subject of the dolomite problem. Our study highlights the importance of improved electronic structure descriptions of liquids, modeled as a condensed phase of matter lacking in long-range crystalline order. It also strongly suggests that Ca 2+ –HCO 3 − CIPs are likely precursors involved in prenucleation of CaCO 3 mineral formation in seawater.

Sharma, Vidushi [Princeton Plasma Physics Laborato↗

DOE OSTI2025

Perturbative Stability and Error-Correction Thresholds of Quantum Codes

Topologically ordered phases are stable to local perturbations, and topological quantum error-correcting codes enjoy thresholds to local errors. We connect the two notions of stability by constructing classical statistical mechanics models for decoding general Calderbank-Shor-Steane codes and classical linear codes. Our construction encodes correction success probabilities under uncorrelated bit-flip and phase-flip errors, and simultaneously describes a generalized ℤ 2 lattice-gauge theory with quenched disorder. We observe that the clean limit of the latter is precisely the discretized imaginary-time path integral of the corresponding quantum code Hamiltonian when the errors are turned into a perturbative 𝑋 or 𝑍 magnetic field. Motivated by error-correction considerations, we define general order parameters for all such generalized ℤ 2 lattice-gauge theories, and show that they are generally lower bounded by success probabilities of error correction. For CSS codes satisfying the low-density parity-check condition and with a sufficiently large code distance, we prove the existence of a low-temperature ordered phase of the corresponding lattice-gauge theories, particularly for those lacking Euclidean spatial locality and/or when there is a nonzero code rate. We further argue that these results provide evidence for stable phases in the corresponding perturbed quantum Hamiltonians, obtained in the limit of continuous imaginary time. To do so, we distinguish space- and timelike defects in the lattice-gauge theory. A high free-energy cost of spacelike defects corresponds to a successful “memory experiment” and suppresses the energy splitting among the ground states, while a high free-energy cost of timelike defects corresponds to a successful “stability experiment” and points to a nonzero gap to local excitations.

quantum error correction↗

DOE OSTI2022

Correlating Thermodynamic and Kinetic Hydricities of Rhenium Hydrides

The kinetics of hydride transfer from Re( R bpy)(CO) 3 H (bpy = 4,4'-R-2,2'-bipyridine; R = OMe, t Bu, Me, H, Br, COOMe, CF 3 ) to CO 2 and seven different cationic N-heterocycles were determined. Additionally, the thermodynamic hydricities of complexes of the type Re( R bpy)(CO) 3 H were established primarily using computational methods. Linear free-energy relationships (LFERs) derived by correlating thermodynamic and kinetic hydricities indicate that, in general, the rate of hydride transfer increases as the thermodynamic driving force for the reaction increases. Kinetic isotope effects range from inverse for hydride transfer reactions with a small driving force to normal for reactions with a large driving force. Hammett analysis indicates that hydride transfer reactions with greater thermodynamic driving force are less sensitive to changes in the electronic properties of the metal hydride, presumably because there is less buildup of charge in the increasingly early transition state. Bronsted α values were obtained for a range of hydride transfer reactions and along with DFT calculations suggest the reactions are concerted, which enables the use of Marcus theory to analyze hydride transfer reactions involving transition metal hydrides. It is notable, however, that even slight perturbations in the steric properties of the Re hydride or the hydride acceptor result in large deviations in the predicted rate of hydride transfer based on thermodynamic driving forces. This indicates that thermodynamic considerations alone cannot be used to predict the rate of hydride transfer, which has implications for catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗