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Core binding energy difference between bridging and nonbridging oxygen atoms in silicate chain of pyroxenes, using X ray photoelectron spectra
Transition metal based materials containing Fe have drawn great attention as oxygen evolution reaction (OER) catalysts. The nature of the electrocatalytic active species remains under debate due to the ambiguous physicochemical properties of the catalyst materials, such as the oxidation states and crystal structures. Here, in order to address this issue, transition metal Prussian blue analogues (TM-PBA, Na(TM)(Fe)(CN) 6 , TM = V, Fe, Co, and Ni) with an isomorphous structure are investigated for OER catalysis. Our combined experimental measurements and density functional theory (DFT) calculations reveal that TM-PBAs exhibit volcano-like OER activity with Ni-PBA located near the top of the volcano. Such a volcano-like activity profile can be attributed to the distinctive binding energy difference between *O and *OH on different TM-PBAs surfaces. This research demonstrates that TM-PBAs can be used as platform materials for understanding structure-property-activity relationships in OER catalysts.
We have designed, built, and tested a gas gap heat switch that works passively, without the need for a separate, thermally activated getter. This switch uses He-3 condensed as a thin film on alternating plates of copper. The switch is thermally conductive at temperatures above about 0.2 K, and is insulating if either end of the switch is below about 0.15 K. The "on" conductance (7 mW/K at 0.25K) is limited by the surface area and gap between the copper leaves, the saturated vapor pressure of the He-3, and the Kapitza boundary resistance between the He-3 and the copper. The "off" conductance is determined by the helium containment shell which physically supports the two conductive ends. We have also designed and are building passive gas gap heat switches which will passively turn off near 1 K and 4 K. For these switches we rely on the rapidly changing vapor pressure of He-4 above neon or copper substrates, respectively, when the coverage is less than one monolayer. The different binding energies of the He-4 to the neon or copper give rise to the different temperatures where the switches transition between the on and off states.
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.
Recent studies of La 3 Ni 2 O 7 have identified a bilayer (2222) structure and an unexpected alternating monolayer-trilayer (1313) structure, both of which feature signatures of superconductivity near 80 K under high pressures. Using angle-resolved photoemission spectroscopy, we measure the electronic structure of 1313 samples. In contrast to the previously studied 2222 structure, we find that the 1313 structure hosts a flat band with a markedly different binding energy, as well as an additional electron pocket and band splittings. By comparison to local-density approximation calculations, we find renormalizations of the Ni-d z 2 and Ni-d x 2 -y 2 derived bands to be about 5 to 7 and about 4 respectively, suggesting strong correlation effects. These results reveal important differences in the electronic structure brought about by the distinct structural motifs with the same stoichiometry. Such differences may be relevant to the putative high temperature superconductivity.
Here, we present a high-precision mass measurement of the proton-rich nucleus 23 Si, performed with the LEBIT Penning trap at the Facility for Rare Isotope Beams (FRIB) utilizing the time-of-flight ion cyclotron resonance (TOF-ICR) technique. We determined a mass excess of 23362.9(5.8) keV, which agrees with a recent storage-ring measurement from the experimental Cooler-Storage Ring (CSRe) in Lanzhou but has a factor of 20 improved precision 23 Si is hence the nucleus with the most precisely known mass among all nuclei with an isospin projection of 𝑇 𝑧 = −5/2. We performed shell-model calculations with the USDC and USDCm Hamiltonians to study binding energy differences and Thomas-Ehrmann shifts in mirror systems with an isospin up to 𝑇 = 5/2. Our experimental result and other recently reported masses of neutron-deficient sd-shell nuclei agree well with the theoretical predictions, demonstrating that isospin symmetry breaking in sd-shell nuclei—even at high isospin values—is well described by modern shell-model calculations.
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RG n –Co + (H 2 O) cation complexes (RG = Ar, Ne, He) are generated in a supersonic expansion by pulsed laser vaporization. Here, complexes are mass-selected using a time-of-flight spectrometer and studied with infrared laser photodissociation spectroscopy, measuring the respective mass channels corresponding to the elimination of the rare gas “tag” atom. Spectral patterns and theory indicate that the structures of the ions with a single rare gas atom have this bound to the cobalt cation opposite the water moiety in a near-C 2v arrangement. The O–H stretch vibrations of the complex are shifted compared to those of water because of the metal cation charge-transfer interaction; these frequencies also vary systematically with the rare gas atom attached. The efficiencies of photodissociation also vary with the rare gas atoms because of their widely different binding energies to the cobalt cation. The spectrum of the argon complex could only be measured when at least three argon atoms were attached. In the case of the helium complex, the low binding energy allows the spectra to be measured for the low-frequency H–O–H scissors bending mode and for the O–D stretches of the deuterated analog. The partially resolved rotational structure for the antisymmetric O–H and O–D stretches reveals the temperature of these complexes (6 K) and establishes the electronic ground state. The helium complex has the same 3 B 1 ground state as the tag-free complex studied previously by Metz and co-workers (2013), but the A rotational constant is contaminated by vibrational averaging from the bending motion of the helium.
In this work, we extend the damped Zaremba-Kohn model (dZK) for long-range dispersion interaction between a molecule and a planar surface to molecules adsorbed on a curved cylindrical surface, and employ this extended model as an additive correction to the semilocal density functionals PBE (Perdew-Burke-Ernzerhof) and SCAN (strongly constrained and appropriately normed). The resulting PBE+vdW (van der Waals)-dZK and SCAN+vdW-dZK are applied to two systems, NH3 and NO2 molecules adsorbed on a single-wall carbon nanotube (CNT), for calculations of binding energies and equilibrium distances. For comparison, the results from vdW nonlocal functionals, such as SCAN+rVV10 and PBE+rVV10, are also presented. The binding energies from PBE+rVV10 (Vydrov and Van Voorhis), SCAN+rVV10, PBE+vdW-dZK, and SCAN+vdW-dZK are about 70–115 meV for the system of CNT + NH 3 and 300–500 meV for the system of CNT + NO 2 . The results from PBE+vdW-dZK and SCAN+vdW-dZK are closer to each other than those from PBE+rVV10 and SCAN+rVV10 are. The relatively closer results from PBE+vdW-dZK and SCAN+vdW-dZK indicate the consistency of our developed vdW–dZK model for cylindrical surfaces. All methods, including PBE, SCAN, PBE+rVV10, SCAN+rVV10, PBE+vdW-dZK, and SCAN+vdW-dZK, give approximately the same binding energy differences between two adsorption configurations (types I and II) for the two systems. This implies that the two adsorption sites have approximately the same adsorption stability. The exponent of the vdW interaction power law from our vdW-dZK model for the two systems is about 0 at short distance, largely due to the damping factor, and tends slowly to –4 to –4.5 at distances D about 20–50 Å. At even larger distances, the vdW power-law exponent approaches –5. This feature is very similar to the one calculated with random-phase approximation and renormalization group approaches, supporting the applicability of our methods. Our developed vdW-dZK method provides a highly efficient and reliable method for large systems with cylindrical surfaces, such as vdW interactions with nanotubes.
Collision probabilities between identical binaries of three different binding energies are computed for binaries in the cores of globular clusters. The more tightly bound a binary is, the smaller the chance is that it suffers a collision. It is found that a given binary in a globular cluster core probably does not suffer more than a very few collisions. If it is not broken up into single stars, it will become so tightly bound that collisions involving it are very rare. Since it is found that head-on collisions are so rare, the collisions which are probably more important in affecting the evolution of the cluster core are the long-range (large impact parameter) encounters.
We examine the many-body expansion (MBE) for alkaline earth metal clusters, Be n , Mg n , Ca n ( n = 4, 5, 6), at the Møller–Plesset second order perturbation theory, coupled-cluster singles and doubles with perturbative triples, multi-reference perturbation theory, and multi-reference configuration interaction levels of theory. The magnitude of each term in the MBE is evaluated for several geometrical configurations. We find that the behavior of the MBE for these clusters depends strongly on the geometrical arrangement and, to a lesser extent, on the level of theory used. Another factor that affects the MBE is the in situ (ground or excited) electronic state of the individual atoms in the cluster. For most geometries, the three-body term is the largest, followed by a steady decrease in absolute energy for subsequent terms. Though these systems exhibit non-negligible multi-reference effects, there was little qualitative difference in the MBE when employing single vs multi-reference methods. Useful insights into the connectivity and stability of these clusters have been drawn from the respective potential energy surfaces and quasi-atomic orbitals for the various dimers, trimers, and tetramers. Through these analyses, we investigate the similarities and differences in the binding energies of different-sized clusters for these metals.
Interactions between negatively charged aluminosilicate species and positively charged metal cations are critical to many important engineering processes and applications, including sustainable cements and aluminosilicate glasses. In an effort to probe these interactions, here we have calculated the pair-wise interaction energies (i.e., binding energies) between aluminosilicate dimer/trimer and 17 different metal cations M n+ (M n+ = Li + , Na + , K + , Cu + , Cu 2+ , Co 2+ , Zn 2+ , Ni 2+ , Mg 2+ , Ca 2+ , Ti 2+ , Fe 2+ , Fe 3+ , Co 3+ , Cr 3+ , Ti 4+ and Cr 6+ ) using a density functional theory (DFT) approach. Analysis of the DFT-optimized structural representations for the clusters (dimer/trimer + M n+ ) shows that their structural attributes (e.g., interatomic distances) are generally consistent with literature observations on aluminosilicate glasses. The DFT-derived binding energies are seen to vary considerably depending on the type of cations (i.e., charge and ionic radii) and aluminosilicate species (i.e., dimer or trimer). A survey of the literature reveals that the difference in the calculated binding energies between different M n+ can be used to explain many literature observations associated with the impact of metal cations on materials properties (e.g., glass corrosion, mineral dissolution, and ionic transport). Analysis of all the DFT-derived binding energies reveals that the correlation between these energy values and the ionic potential and field strength of the metal cations are well captured by 2nd order polynomial functions ( R 2 values of 0.99–1.00 are achieved for regressions). Given that the ionic potential and field strength of a given metal cation can be readily estimated using well-tabulated ionic radii available in the literature, these simple polynomial functions would enable rapid estimation of the binding energies of a much wider range of cations with the aluminosilicate dimer/trimer, providing guidance on the design and optimization of sustainable cements and aluminosilicate glasses and their associated applications. Finally, the limitations associated with using these simple model systems to model complex interactions are also discussed.
Diffusion in bcc uranium and U–Mo alloys is of great interest because fission gas and other fission products impact the performance of nuclear fuels. We investigate the mobility of xenon and molybdenum in bcc uranium ($γ$-U) and metallic U–Mo alloys by calculating the migration energies of xenon and molybdenum for various local compositions using density functional theory. We also calculate the solute–vacancy binding energies of different solutes to vacancies in bcc uranium. We find that the solute–vacancy binding energy in bcc uranium is significantly higher than it is in other bcc metals (e.g., Fe and W). We also find that the migration energy of molybdenum is substantially higher than the migration energy of xenon, indicating that xenon is much more mobile than molybdenum in bcc uranium. The presence of molybdenum in the nearest-neighbor shell around a xenon atom typically increases the migration energy of xenon, which indicates a reduction of xenon mobility in U–Mo alloys compared to pure bcc uranium.
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.
Developing an understanding of the response of mineral/water interfaces to applied electric fields is central to detecting and interpreting signatures of interfacial processes in the subsurface. Here we focus density functional theory calculations on understanding K + cation binding and diffusion across the (001) surface of orthoclase feldspar under various applied electric fields with and without surface hydration. The calculations reveal how water ligands labilize surface K + cations for diffusion while also increasing their sensitivity to electric field effects on the binding energy at different surface sites. The calculations also show how the direction and strength of the electric field systematically affect surface cation mobility, sorption, and hydration behavior. Specifically, electric fields directed toward the surface increase the potassium binding energies, facilitate K + diffusion across multiple binding sites, and increase the propensity of surface K + ions to lose their hydration shells. Furthermore, the findings help fill a major knowledge gap into the impact of electric fields on mineral/water interface structure and dynamics more generally, featuring in this case a commonly found type of feldspar involved in a multitude of atmospheric and geochemical processes.
Quantifying adsorption behaviors is crucial for various applications such as catalysis, separation, and sensing, yet it is generally challenging to access in solution. Here, we report a combined experimental and computational study of the adsorption behaviors of alkyl-trimethylammonium bromides (xTAB), a class of ligands important for colloidal nanoparticle stabilization and shape control, with various alkyl chain lengths x on Au nanoparticles. We use density functional theory (DFT) to calculate xTAB binding energies on Au{111} and Au{110} surfaces with standing-up and lying-down configurations, which provides insights into the adsorption affinity and cooperativity differences of xTAB on these two facets. We demonstrate the key role of van der Waals interactions in determining the xTAB adsorption behavior. These computational results predict and explain the experimental discovery of xTAB’s adsorption behavior switch from stronger affinity, negative cooperativity to weaker affinity, positive cooperativity when the concentration of xTAB increases in solution. We also show that in the standing-up configuration, bilayer adsorption may occur on both facets, which can lead to different differential binding energies and consequently adsorption crossover between the two facets when the ligand concentration increases. Our combined experimental and computational approaches demonstrate a paradigm for gaining molecular-scale insights into adsorbate–surface interactions.
Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln 3+ ) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln 3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln 3+ coordinated to ligands in water and embedded in metal–organic frameworks (MOFs), and ΔΔE for Ln 3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln 3+ in the periodic table. Static DFT calculations with a full Ln 3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. Finally, we also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.
Abstract RNA modifications shape gene expression through a variety of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.