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DOE OSTI2019

Electronic structures and binding motifs of sodium polysulfide clusters NaSn- (n = 5-9): a joint negative ion photoelectron spectroscopy and computational investigation

Motivated by the significant biological functions of polysulfides in life processes and important applications of sodium polysulfides in battery sciences, herein we report a joint experimental and computational study on the electronic and geometric structures of a series of NaSn- (n = 5-9) clusters. The cryogenic, size-selective, negative ion photoelectron spectroscopy (NIPES) is employed to obtain their photoelectron spectra, in which distinctive spectral features with electron binding energy (EBE) up to 6.4 eV are unraveled. The EBE of the first peak in each spectrum for NaSn- (n =5-9), assigned to the transition from the ground state of anion to the ground state of each neutral radical, is observed to increase with cluster size. The vertical detachment energies (VDEs), determined from the first peak maximum, are 3.43 ± 0.02, 3.57 ± 0.02, 3.82 ± 0.03, 3.86 ± 0.02, and 4.00 ± 0.02 eV and the adiabatic detachment energies (ADEs), determined by the onset of the first peak, are 3.27 ± 0.05, 3.44 ± 0.05, 3.65 ± 0.05, 3.75 ± 0.05, and 3.93 ± 0.05 eV, for n = 5-9, respectively. A plural of low-lying isomers of anions are screened and identified with density functional theory calculations, showing that all featuring preference for a chain-like polysulfide moiety electrostatically interacted with a sodium cation. The calculated VDEs and ADEs using the high-level CCSD(T)/aug-cc-pVTZ method are in excellent agreement with experimental results, further confirming the identified isomers as most stable ones. Further analyses based on the excited-state transition, molecular orbitals and natural population charge are performed to assign all observed spectral bands along the binding energy axis, suggesting that the electron detachment process and observed excitations mainly derived from the polysulfide chain of NaSn- clusters. This work provides a fundamental understanding of the intrinsic molecular properties of sodium polysulfide systems, which widely exist in life science and sodium-sulfur cells.

Li, Zhipeng↗

DOE OSTI2020

Computational modeling of charge hopping dynamics along a disordered one-dimensional wire with energy gradients in quantum environments

This computational study investigates the effects of energy gradients on charge hopping dynamics along a one-dimensional chain of discrete sites coupled to quantum bath, which is modeled at the level of Pauli master equation (PME). This study also assesses the performance of different approximations for the hopping rates. Three different methods for solving the PME, a fourth order Runge–Kutta method, numerical diagonalization of the rate matrix followed by analytic propagation, and kinetic Monte Carlo simulation method, are tested and confirmed to produce virtually identical values of time dependent mean square displacement, diffusion constant, and mobility. Five different rate expressions, exact numerical evaluation of Fermi’s Golden Rule (FGR) rate, stationary phase interpolation (SPI) approximation, semiclassical approximation, classical Marcus rate, and Miller–Abrahams rate, are tested to help understand the effects of approximations in representing quantum environments in the presence of energy gradients. The results based on direct numerical evaluation of FGR rate exhibit transition from diffusive to non-diffusive behavior with the increase in the gradient and show that the charge transport in the quantum bath is more sensitive to the magnitude of the gradient and the disorder than in the classical bath. Among all the four approximations for the hopping rates, the SPI approximation is confirmed to work best overall. A comparison of two different methods to calculate the mobility identifies drift motion of the population distribution as the major source of non-diffusive behavior and provides more reliable information on the contribution of quantum bath.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Ultrafast hole transfer from monolayer ReS 2 to thin-film F 8 ZnPc

We report a combined experimental and computational study on the charge transfer properties of heterostructures formed by monolayer 1T’-ReS 2 and fluorinated zinc phthalocyanine, F 8 ZnPc. Two-dimensional (2D) ReS 2 monolayer flakes were exfoliated from bulk crystals, and a F 8 ZnPc film with a thickness of 4 nm was thermally deposited on ReS 2 . Density functional theory shows that the two materials form a type-II band alignment. In transient absorption measurements, photocarriers are selectively excited in ReS 2 and monitored in F 8 ZnPc. Here, we found that holes in ReS 2 can transfer to F 8 ZnPc on a time scale shorter than 0.35 ps. The transferred holes have a long lifetime in F 8 ZnPc on the order of 1 ns, confirming the lack of electron transfer. The efficient charge transfer from a 1T’ transition metal dichalcogenide monolayer to an organic semiconductor illustrates the feasibility of developing 2D/organic heterostructures with in-plane anisotropic electronic and optoelectronic properties.

2D materials↗

DOE OSTI2022

Energy, angle, and temperature dependencies of the sticking of D atoms on Li surfaces

Detailed experimental and computational information on the response of lithium surfaces to irradiation by slow hydrogenic particles (ions, atoms, molecules) is sparse and mainly speculative. In this work, we present a computational study of the reflection and retention of deuterium (D) atoms at crystalline and amorphous lithium surfaces at 300 and 500 K, where the D atoms have an impact energy in the range of 0.025–5 eV and incident angles of 0° (perpendicular incidence) or 85° (near-grazing incidence). Classical molecular dynamics simulations are performed with the reactive bond-order force field (ReaxFF) potentials. This study provides quantitative information on the deuterium sticking probability and recycling coefficient for lithium surfaces. Further, our results support the ongoing work at the Lithium Tokamak eXperiment-β fusion experiment as well as relevant experiments in the laboratory setting.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

How generic is iodide-tagging photoelectron spectroscopy: An extended investigation on the Gly· X - (Gly = glycine, X = Cl or Br) complexes

We report a joint negative ion photoelectron spectroscopy (NIPES) and quantum chemical computational study on glycine-chloride/bromide complexes (denoted Gly·X - , X = Cl/Br) in close comparison to the previously studied Gly·I - cluster ion. Combining experimental NIPE spectra and theoretical calculations, various Gly·X - complexes were found to adopt the same types of low-lying isomers, albeit with different relative energies. Despite more congested spectral profiles for Gly·Cl - and Gly·Br - , spectral assignments were accomplished with the guidance of the knowledge learned from Gly·I - , where a larger spin–orbit splitting of iodine afforded well-resolved, recognizable spectral peaks. Three canonical plus one zwitterionic isomer for Gly·Cl - and four canonical conformers for Gly·Br - were experimentally identified and characterized in contrast to the five canonical ones observed for Gly·I - under similar experimental conditions. Taken together, this study investigates both genericity and variations in binding patterns for the complexes composed of glycine and various halides, demonstrating that iodide-tagging is an effective spectroscopic means to unravel diverse ion-molecule binding motifs for cluster anions with congested spectral bands by substituting the respective ion with iodide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Neutral gas pressure dependence of ion–ion mutual neutralization rate constants using Landau–Zener theory coupled with trajectory simulations

In this computational study, we describe a self-consistent trajectory simulation approach to capture the effect of neutral gas pressure on ion–ion mutual neutralization (MN) reactions. The electron transfer probability estimated using Landau–Zener (LZ) transition state theory is incorporated into classical trajectory simulations to elicit predictions of MN cross sections in vacuum and rate constants at finite neutral gas pressures. Electronic structure calculations with multireference configuration interaction and large correlation consistent basis sets are used to derive inputs to the LZ theory. The key advance of our trajectory simulation approach is the inclusion of the effect of ion-neutral interactions on MN using a Langevin representation of the effect of background gas on ion transport. For H + – H – and Li + – H(D) – , our approach quantitatively agrees with measured speed-dependent cross sections for up to ~10 5 m/s. For the ion pair Ne + – Cl – , our predictions of the MN rate constant at ~1 Torr are a factor of ~2 to 3 higher than the experimentally measured value. Similarly, for Xe + – F – in the pressure range of ~20 000–80 000 Pa, our predictions of the MN rate constant are ~20% lower but are in excellent qualitative agreement with experimental data. Here, the paradigm of using trajectory simulations to self-consistently capture the effect of gas pressure on MN reactions advanced here provides avenues for the inclusion of additional nonclassical effects in future work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Learning the stable and metastable phase diagram to accelerate the discovery of metastable phases of boron

Boron, an element of captivating chemical intricacy, has been surrounded by controversies ever since its discovery in 1808. The complexities of boron stem from its unique position between metals and insulators in the Periodic Table. Recent computational studies have shed light on some of the stable boron allotropes. However, the demand for multifunctionality necessitates the need to go beyond the stable phases into the realm of metastability and explore the potentially vast but elusive metastable phases of boron. Traditional search for stable phases of materials has focused on identifying materials with the lowest enthalpy. Here, we introduce a workflow that uses reinforcement learning coupled with decision trees, such as Monte Carlo tree search, to search for stable and metastable boron phases, with enthalpy as the objective. We discover new boron metastable phases and construct a phase diagram that locates their phase space (T, P) at different levels of metastability (ΔG) from the ground state and provides useful information on the domains of relative stability of the various stable and metastable boron phases.

42 ENGINEERING↗

DOE OSTI2024

Deprotonated sulfamic acid and its homodimers: Does sulfamic acid adopt zwitterion during cluster growth?

Here we present a joint experimental and computational study on the geometric and electronic structures of deprotonated sulfamic acid (SA) clusters [(SA) n –H] – (n = 1, 2) employing negative ion photoelectron spectroscopy and high-level ab initio calculations. The photoelectron spectra provide the vertical/adiabatic detachment energy (VDE/ADE) of the sulfamate anion (SM – ) H 2 N•SO 3 – at 4.85 ± 0.05 and 4.58 ± 0.08 eV, respectively, and the VDE and ADE of the SM – •SA dimer at 6.41 ± 0.05 and 5.87 ± 0.08 eV, respectively. The significantly increased electron binding energies of the dimer confirm the enhanced electronic stability upon the addition of one SA molecule. The CCSD(T)-predicted VDEs/ADEs agree excellently with the experimental data, confirming the identified structures as the most stable ones. Two types of dimer isomers possessing different hydrogen bonding (HB) motifs are identified, corresponding to SM – binding to a zwitterionic SA (SM – •SA z ) and a canonical SA (SM – •SA c ), respectively. Two N–H$\cdots$O HBs and one superior O–H$\cdots$O HB are formed in the lowest-lying SM – •SA c , while SM – •SA z has three moderate N–H$\cdots$O HBs, with the former being 4.71 kcal/mol more stable. Further theoretical analyses reveal that the binding strength advantage of SM – •SA c over SM – •SA z arises from its significant contributions of orbital interactions between fragments, illustrating that sulfamate strongly interacts with its parent SA acid and preferably chooses the canonical SA in the subsequent cluster formations. Given the prominent presence of SA, this study provides the first evidence that the canonical dimer model of sulfamic acid should exist as a superior configuration during cluster growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Compositionally complex carbide ceramics: A perspective on irradiation damage

Extensive experimental and computational studies have demonstrated outstanding physical and chemical properties of the novel materials of compositionally complex carbides (CCCs), enabling their promising applications in advanced fission and fusion energy systems. This perspective provides a comprehensive overview of radiation damage behavior reported in the literature to understand the fundamental mechanisms related to the impact of multi-principal metal components on phase stability, irradiation-induced defect clusters, irradiation hardening, and thermal conductivity of compositionally complex carbides. Several future research directions are recommended to critically evaluate the feasibility of designing and developing new ceramic materials for extreme environments using the transformative “multi-principal component” concept. Compared to the existing materials for nuclear applications including stainless steels, nickel alloys, ZrC, SiC, and potentially high-entropy alloys, as well as certain other compositionally complex ceramic families. CCCs appear to be more resistant to amorphization, growth of irradiation defect clusters, and void swelling.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Calculation of ion–ion mutual neutralization rate constants using Landau–Zener theory coupled with trajectory simulations for Ar + –Cl − , Br − , I −

In this computational study, we self-consistently calculate the rate constants of mutual neutralization reactions by incorporating the electron transfer probability, using Landau–Zener state transition theory with inputs derived from ab initio quantum chemistry calculations, into classical trajectory simulations. Electronic structure calculations are done using correlation consistent basis sets with multi-reference configuration interaction to map all the molecular electronic states below the ion-dissociation limit as a function of the distance between the reacting species. Our electronic structure calculations have been significantly improved from our previous work through improved selection of molecular electronic configurations maintaining a fine grid of 1a 0 over a wide range of bond lengths and accurate treatment of spin–orbit couplings. Non-adiabatic coupling matrix elements are calculated with the three-point central difference method near each avoided crossing to estimate the exact crossing point R x and coupling parameter H if , which are inputs to the multi-channel Landau–Zener theory to calculate the electron transition probability. Our approach is applied to estimate the mutual neutralization rate constants for the following ion pairs: Ar + –Cl − , Ar + –Br − , Ar + –I − at ∼133 Pa. Furthermore, our predictions are compared against the experimental data reported. It is seen that the improvement in the electronic structure calculation results in excellent agreement between the simulation results and the available experimental data to within a factor of ∼2 or ∼±50%.

Complete-active space self-consistent field↗

DOE OSTI2025

Effect of nozzle translation on a bounded vortex flow

A bounded vortex flow is generated by a nozzle that combines azimuthally tilted downward jets in a circular array and a central suction port. When the nozzle is directed toward a bottom surface (called the impingement surface), the flow develops a strong intake vortex spanning from the impingement surface to the suction port, which acts to generate strong shear stress on the impingement surface. This strong shear stress can aid in removing particles attached to the impingement surface or in enhancement of heat or mass transfer, where in typical applications, the nozzle would be translated along the impingement surface. This paper reports on a computational study of the effect of nozzle translation on the bounded vortex flow field. The nozzle translation induces a bending of the bounded vortex in the downstream flow direction, which becomes larger with increase in the nozzle translation speed. We identify an interesting oscillatory phenomenon by which the bounded vortex can resist the bending induced by the translational flow and rotate about a mean position downstream of the suction port. At sufficiently high translation speeds, the oscillatory process can no longer resist the downwash effect from nozzle translation and the vortex eventually detaches from the impingement surface, limiting the effectiveness of this flow device.

42 ENGINEERING↗

DOE OSTI2014

Copper-sulfenate complex from oxidation of a cavity mutant of Pseudomonas aeruginosa azurin

Metal–sulfenate centers are known to play important roles in biology and yet only limited examples are known due to their instability and high reactivity. Herein we report a copper–sulfenate complex characterized in a protein environment, formed at the active site of a cavity mutant of an electron transfer protein, type 1 blue copper azurin. Reaction of hydrogen peroxide with Cu(I)–M121G azurin resulted in a species with strong visible absorptions at 350 and 452 nm and a relatively low electron paramagnetic resonance g z value of 2.169 in comparison with other normal type 2 copper centers. The presence of a side-on copper–sulfenate species is supported by resonance Raman spectroscopy, electrospray mass spectrometry using isotopically enriched hydrogen peroxide, and density functional theory calculations correlated to the experimental data. In contrast, the reaction with Cu(II)–M121G or Zn(II)–M121G azurin under the same conditions did not result in Cys oxidation or copper–sulfenate formation. Structural and computational studies strongly suggest that the secondary coordination sphere noncovalent interactions are critical in stabilizing this highly reactive species, which can further react with oxygen to form a sulfinate and then a sulfonate species, as demonstrated by mass spectrometry. Engineering the electron transfer protein azurin into an active copper enzyme that forms a copper–sulfenate center and demonstrating the importance of noncovalent secondary sphere interactions in stabilizing it constitute important contributions toward the understanding of metal–sulfenate species in biological systems.

Sieracki, Nathan A.↗

DOE OSTI2016

Enhanced limonene production in cyanobacteria reveals photosynthesis limitations

Terpenes are the major secondary metabolites produced by plants, and have diverse industrial applications as pharmaceuticals, fragrance, solvents, and biofuels. Cyanobacteria are equipped with efficient carbon fixation mechanism, and are ideal cell factories to produce various fuel and chemical products. Past efforts to produce terpenes in photosynthetic organisms have gained only limited success. Here we engineered the cyanobacterium Synechococcus elongatus PCC 7942 to efficiently produce limonene through modeling guided study. Computational modeling of limonene flux in response to photosynthetic output has revealed the downstream terpene synthase as a key metabolic flux-controlling node in the MEP (2- C -methyl-d-erythritol 4-phosphate) pathway-derived terpene biosynthesis. By enhancing the downstream limonene carbon sink, we achieved over 100-fold increase in limonene productivity, in contrast to the marginal increase achieved through stepwise metabolic engineering. The establishment of a strong limonene flux revealed potential synergy between photosynthate output and terpene biosynthesis, leading to enhanced carbon flux into the MEP pathway. Moreover, we show that enhanced limonene flux would lead to NADPH accumulation, and slow down photosynthesis electron flow. In conclusion, fine-tuning ATP/NADPH toward terpene biosynthesis could be a key parameter to adapt photosynthesis to support biofuel/bioproduct production in cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Potential high- T c superconducting lanthanum and yttrium hydrides at high pressure

Significance Theoretical predictions and subsequent experimental observations of high-temperature superconductivity in dense hydrogen-rich compounds have reinvigorated the field of superconductivity. A systematic computational study of the hydrides of lanthanum and yttrium over a wide composition range reveals hydrogen-rich structures with intriguing electronic properties under pressure. Electron–phonon coupling calculations predict the existence of new superconducting phases, some exhibiting superconductivity in the range of room temperature. Moreover, the calculated stabilities indicate the materials could be synthesized at pressures that are currently accessible in the laboratory. The results open the prospect for the design, synthesis, and recovery of new high-temperature superconductors with potential practical applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor

Neurotransmitter:sodium symporters (NSSs) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. Results from many structural, functional, and computational studies on LeuT, a bacterial NSS homolog, have provided critical insight into the mechanism of sodium-coupled transport, but the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of molecular dynamics simulations, single-molecule fluorescence resonance energy transfer (smFRET) imaging, and measurements of Na + binding and substrate transport that reveals an allosteric substrate specificity mechanism. In this mechanism, residues F259 and I359 in the substrate binding pocket couple the binding of substrate to Na + release from the Na2 site by allosterically modulating the stability of a partially open, inward-facing state. We propose a model for transport selectivity in which residues F259 and I359 act as a volumetric sensor that inhibits the transport of bulky amino acids.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

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

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

bioenergetics↗

DOE OSTI2021

Combining pressure and electrochemistry to synthesize superhydrides

Significance Superhydrides are a materials system where near–room-temperature superconductivity has been achieved but only at very high (megabar) pressures. This work proposes an approach that combines pressure and electrochemistry to stabilize superhydrides at moderate pressures. Through a computational study of the palladium–hydrogen system, we construct electrochemical phase diagrams and show that electrochemically synthesizing superhydrides may be possible when combined with moderate pressures. We generalize this to other binary metal superhydrides of interest for superconductivity, including La, Y, and Mg hydrides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Hydrogen ejection from hydrocarbons: Characterization and relevance in soot formation and interstellar chemistry

Polycyclic aromatic hydrocarbons (PAHs) play a major role in the chemistry of combustion, pyrolysis, and the interstellar medium. Production (or activation) of radical PAHs and propagation of their resulting reactions require efficient dehydrogenation, but the preferred method of hydrogen loss is not well understood. Unimolecular hydrogen ejection (i.e., direct C─H bond fission) and bimolecular radical abstraction are two main candidate pathways. We performed a computational study to characterize the role of H ejection, particularly as a driver for radical-centric hydrocarbon-growth mechanisms and particle formation. Electronic structure calculations establish that C─H bond strengths span a broad range of energies, which can be weaker than 30 kcal/mol in some C 9 and C 13 PAH radicals. At T > 1200 K, calculated thermal rates for hydrogen ejection from weak C─H bonds at zigzag sites on PAH radicals are significantly larger than typical H-abstraction rates. These results are highly relevant in the context of chain reactions of radical species and soot inception under fuel-rich combustion conditions. Furthermore, calculated microcanonical rates that include the additional internal energy released by bond formation (e.g., ring closure to yield C 9 H 9 ) yield significantly higher rates than those associated with full thermalization. These microcanonical considerations are relevant to the astrochemical processes associated with hydrocarbon growth and processing in the low-density interstellar environment.

08 HYDROGEN↗