The next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics
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Lappala, Anna (ORCID:0000000199262972)↗
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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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Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6
Not provided.
Biochemistry & Molecular Biology↗
Development of a PBPK model of thiocyanate in rats with an extrapolation to humans: A computational study to quantify the mechanism of action of thiocyanate kinetics in thyroid
Thyroid homeostasis can be disturbed due to thiocyanate exposure from the diet or tobacco smoke. Thiocyanate inhibits both thyroidal uptake of iodide, via the sodium-iodide symporter (NIS), and thyroid hormone (TH) synthesis in the thyroid, via thyroid peroxidase (TPO), but the mode of action of thiocyanate is poorly quantified in the literature. The characterization of the link between intra-thyroidal thiocyanate concentrations and dose of exposure is crucial for assessing the risk of thyroid perturbations due to thiocyanate exposure. We developed a PBPK model for thiocyanate that describes its kinetics in the whole-body up to daily doses of 0.15 mmol/kg, with a mechanistic description of the thyroidal kinetics including NIS, passive diffusion, and TPO. The model was calibrated in a Bayesian framework using published studies in rats. Goodness-of-fit was satisfactory, especially for intra-thyroidal thiocyanate concentrations. Thiocyanate kinetic processes were quantified in vivo, including the metabolic clearance by TPO. The passive diffusion rate was found to be greater than NIS-mediated uptake rate. The model captured the dose-dependent kinetics of thiocyanate after acute and chronic exposures. Model behavior was evaluated using a Morris screening test. The distribution of thiocyanate into the thyroid was found to be determined primarily by the partition coefficient, followed by NIS and passive diffusion; the impact of the latter two mechanisms appears to increase at very low doses. Extrapolation to humans resulted in good predictions of thiocyanate kinetics during chronic exposure. The developed PBPK model can be used in risk assessment to quantify dose-response effects of thiocyanate on TH. - Highlights: • A PBPK model of thiocyanate (SCN{sup −}) was calibrated in rats in a Bayesian framework. • The intra-thyroidal kinetics of thiocyanate including NIS and TPO was modeled. • Passive diffusion rate for SCN{sup −} seemed to be greater than the NIS-mediated uptake. • The dose-dependent kinetics of SCN{sup −} was captured after an acute and chronic exposure. • The PBPK model of thiocyanate was successfully extrapolated to humans.
54 ENVIRONMENTAL SCIENCES↗
Cloud computing and rural globalization: Evidence for the U.S. nonfarm economy
Not provided.
Communication↗
Integrating computation and experiment to investigate photoelectrodes for solar water splitting at the microscopic scale.
CONSPECTUS: Photoelectrochemical water-splitting is a promising and sustainable way to store the energy of the sun in chemical bonds and use it to produce hydrogen gas, a clean fuel. The key components in photoelectrochemical cells (PECs) are photoelectrodes, including a photocathode that reduces water to hydrogen gas and a photoanode that oxidizes water to oxygen gas. Materials used in photoelectrodes for PECs must effectively absorb sunlight, yield photogenerated carriers, and exhibit electronic properties that enable the efficient shuttling of carriers to the surface to participate in relevant water-splitting reactions. Discovering and understanding the key characteristics of optimal photoelectrode materials is paramount to the realization of PEC technologies. Oxide-based photoelectrodes can satisfy many of these materials requirements, including stability in aqueous environments, band edges with reasonable alignment with the redox potentials for water splitting, and ease of synthesis. However, oxide photoelectrodes generally suffer from poor charge transport properties and considerable bulk electron-hole separation, and they have relatively large band gaps. Numerous strategies have been proposed to improve these aspects and understand how these improvements are reflected in the photoelectrochemical performance. Unfortunately, the structural and compositional complexity of multinary oxides accompanied by the inherent complexity of photoelectrochemical processes makes it challenging to understand the individual effects of composition, structure, and defects in the bulk and on the surface on a material's photoelectrochemical properties. The integration of experiment and theory has great potential to increase our atomic-level understanding of structure-composition-property relationships in oxide photoelectrodes. In this Account, we describe how integrating experiment and theory is beneficial for achieving scientific insights at the microscopic scale. We highlight studies focused on understanding the role of (i) bulk composition via solid-state solutions, intercalation, and comparison with isoelectronic compounds, (ii) dopants for both the anion and cation and their interactions with oxygen vacancies, and (iii) surface/interface structure in the photocurrent generation and photoelectrochemical performance in oxide photoelectrodes. In each instance, we outline strategies and considerations for integrating experiment and theory and describe how this integration led to valuable insights and new directions in uncovering structure-composition-property relationships. Our aim is to demonstrate the unique value of combining experiment and theory in studying photoelectrodes and to encourage the continued effort to bring experiment and theory in closer step with each other.
Wang, Wennie↗
Computational Exploration of the Li-Electrode|Electrolyte Interface in the Presence of a Nanometer Thick Solid-Electrolyte Interphase Layer [Computational exploration of the Li-electrode|electrolyte interface complicated by a nanometer thin solid-electrolyte interphase (SEI) layer]
A nanometer thick passivation layer will spontaneously form on Li-metal in battery applications due to electrolyte reduction reactions. This passivation layer in rechargeable batteries must have “selective” transport properties: blocking electrons from attacking the electrolytes, while allowing Li + ion to pass through so the electrochemical reactions can continue. The classical description of the electrochemical reaction, Li + + e → Li 0 , occurring at the Li-metal|electrolyte interface is now complicated by the passivation layer and will reply on the coupling of electronic and ionic degrees of freedom in the layer. We consider the passivation layer, called “solid electrolyte interphase (SEI)”, as “the most important but the least understood in rechargeable Li-ion batteries,” partly due to the lack of understanding of its structure–property relationship. In predictive modeling, starting from the ab initio level, we find that it is an important tool to understand the nanoscale processes and materials properties governing the interfacial charge transfer reaction at the Li-metal|SEI|electrolyte interface. Here, we demonstrate pristine Li-metal surfaces indeed dissolve in organic carbonate electrolytes without the SEI layer. Based on joint modeling and experimental results, we point out that the well-known two-layer structure of SEI also exhibits two different Li + ion transport mechanisms. The SEI has a porous (organic) outer layer permeable to both Li + and anions (dissolved in electrolyte), and a dense (inorganic) inner layer facilitate only Li + transport. This two-layer/two-mechanism diffusion model suggests only the dense inorganic layer is effective at protecting Li-metal in electrolytes. This model suggests a strategy to deconvolute the structure–property relationships of the SEI by analyzing an idealized SEI composed of major components, such as Li 2 CO 3 , LiF, Li 2 O, and their mixtures. After sorting out the Li+ ion diffusion carriers and their diffusion pathways, we design methods to accelerate the Li + ion conductivity by doping and by using heterogonous structure designs. We will predict the electron tunneling barriers and connect them with measurable first cycle irreversible capacity loss. We note that the SEI not only affects Li + and e – transport, but it can also impose a potential drop near the Li-metal|SEI interface. Our challenge is to fully describe the electrochemical reactions at the Li - metal|SEI|electrolyte interface. This will be the subject of ongoing efforts.
30 DIRECT ENERGY CONVERSION↗
Computational and Experimental Investigations of Na-Ion Conduction in Cubic Na[subscript 3]PSe[subscript 4]
Abstract not provided
Bo, Shou-Hang↗
X-ray Crystal Structure of Thorium Tetrahydroborate, Th(BH 4 ) 4 , and Computational Studies of An(BH 4 ) 4 (An = Th, U)
Here the crystal structure of Th(BH 4 ) 4 is described. Two of the four BH 4 – ions are terminal and tridentate (κ 3 ), whereas the other two bridge between neighboring Th IV centers in a κ 2 ,κ 2 (i.e., bis-bidentate) fashion. Thus, each thorium center is bound to six BH 4 – groups by 14 Th–H bonds. The six boron atoms describe a distorted octahedron in which the κ 3 -BH 4 – ions are mutually cis; the 14 ligating hydrogen atoms define a highly distorted bicapped hexagonal antiprism. The thorium centers are linked into a polymer consisting of interconnected helical chains wound about 4-fold screw axes. The structures of An(BH 4 ) 4 (An = Th, U) were also investigated by DFT. The geometries of [An(BH 4 ) 6 ] 2– , [An3(BH 4 ) 16 ] 4– , and [An 5 (BH 4 ) 26 ] 6– fragments of the polymeric structures were optimized at the B3LYP and/or PBE levels. Most calculated geometries are 14-coordinate and agree with the experimental structures, but isolated [Th(BH 4 ) 6 ] 2– units are predicted to feature 16-coordinate Th IV centers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Spectroscopic and Computational Evaluation of Uranyl Oxo Engagement with Transition Metal Cations
Here, we report the synthesis and characterization of five novel Cd 2+ /UO 2 2+ heterometallic complexes that feature Cd-oxo distances ranging from 78 to 171% of the sum of the van der Waals radii for these atoms. This work marks an extension of our previously reported Pb 2+ /UO 2 2+ and Ag + /UO 2 2+ complexes, yet with much more pronounced structural and spectroscopic effects resulting from Cd-oxo interactions. We observe a major shift in the U═O symmetric stretch and significant uranyl bond length asymmetry. The ρbcp values calculated using Quantum Theory of Atoms in Molecules (QTAIM) support the asymmetry displayed in the structural data and indicate a decrease in covalent character in U═O bonds with close Cd-oxo contacts, more so than in related compounds containing Pb 2+ and Ag + . Second-order perturbation theory (SOPT) analysis reveals that O sp x → Cd s is the most significant orbital overlap and U═O bonding and antibonding orbitals also contribute to the interaction (U═O σ/π → Cd d and Cd s → U═O σ/π*). The overall stabilization energies for these interactions were lower than those in previously reported Pb 2+ cations, yet larger than related Ag + compounds. Analysis of the equatorial coordination sphere of the Cd 2+ /UO 2 2+ compounds (along with Pb 2+ /UO 2 2+ complexes) reveals that 7-coordinate uranium favors closer, stronger M n+ -oxo contacts. These results indicate that U═O bond strength tuning is possible with judicious choice of metal cations for oxo interactions and equatorial ligand coordination.
cations↗
Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II
In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment–protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (–CH 3 ) on one of its pyrrole rings, while Chl b has a formyl group (–CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a . It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type ( a or b ) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b . The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a -binding sites. Finally, it is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.
chemical calculations↗
Computational Investigation of the Catalytic Hydrodeoxygenation of Propanoic Acid over a Cu(111) Surface
Cu-based alloy catalysts have recently been investigated experimentally for the hydrodeoxygenation (HDO) of biomass-derived organic acids. Here, the HDO of propanoic acid (PAc) has been studied over Cu(111) by mean-field microkinetic modeling based on parameters obtained from first-principles calculations. Models were developed for the gas- and liquid-phase HDO in condensed water and 1,4-dioxane. In agreement with experimental observations, the gas-phase PAc conversion rate is low at 573 K and increases in liquid water by 1 order of magnitude. In all reaction environments, the decarboxylation mechanism is dominant at low hydrogen partial pressures less than 0.1 bar, and the C–COO bond dissociation is the rate-controlling elementary step. This observation contrasts with the rate-controlling step identified over most group VIII metal surfaces, which is the C–OH bond dissociation in the decarbonylation mechanism. At high hydrogen (H 2 ) partial pressures greater than 10 bar, the HDO of PAc produces propionaldehyde that can readsorb and further react through decarbonylation to produce C 2 alkane products, which is conceptually different from the low H 2 partial pressure scenario. At high H 2 partial pressures, the initial hydrogenation at the carbonyl carbon of PAc becomes the rate-controlling elementary step.
Catalysts↗
Surface Interactions and Confinement of Methane: A High Pressure Magic Angle Spinning NMR and Computational Chemistry Study
Characterization and modeling of the molecular-level behavior of simple hydrocarbon gases, such as methane, in the presence of both nonporous and nano-porous mineral matrices allows for predictive understanding of important processes in engineered and natural systems. In this study, changes in local electromagnetic environments of the carbon atoms in methane under conditions of high pressure (up to 130 bar) and moderate temperature (up to 346 K) were observed with 13C magic-angle spinning (MAS) NMR spectroscopy while the methane gas was mixed with two model solid substrates: a fumed non-porous, 12 nm particle size silica and a mesoporous silica with 200 nm particle size and 4 nm average pore diameter. Examination of the interactions between methane and the silica systems over temperatures and pressures that include the supercritical regime was allowed by a novel high pressure MAS sample containment system, which provided high resolution spectra collected under in situ conditions. For pure methane, no significant thermal effects were found for the observed 13C chemical shifts at all pressures studied here (28.2 bar, 32.6 bar, 56.4 bar, 65.1 bar, 112.7 bar, and 130.3 bar). However, the 13C chemical shifts of resonances arising from confined methane changed slightly with changes in temperature in mixtures with mesoporous silica. The chemical shift values of 13C nuclides in methane change measurably as a function of pressure both in the pure state and in mixtures with both silica matrices, with a more pronounced shift when meso-porous silica is present. Molecular-level simulations utilizing GCMC, MD and DFT confirm qualitatively that the experimentally measured changes are attributed to interactions of methane with the hydroxylated silica surfaces as well as densification of methane within nanopores and on pore surfaces.
confinement↗
Computational Investigation of the Bonding in [(η 5 –Cp′) 3 (η 1 –Cp′)M] 1– (M = Pu, U, Ce)
Despite the similar ionic radii for Ce 3+ , U 3+ , and Pu 3+ , [(η 5 –Cp′) 3 (η 1 –Cp′)Ce] 1– (Cp′ = C 5 H 4 SiMe 3 , 1-Ce) displays a significantly longer η 1 –Cp′ distance in the solid state compared to the U 3+ and Pu 3+ analogues. To better understand this observation, a theoretical investigation was undertaken to examine the differences in bonding between the actinides 1-Pu and 1-U and how they compare with 1-Ce. The results show that although the bonding is largely ionic and dominated by ligand (2p)–metal (6d/5d) interactions, the polarization of 5f orbitals plays a significant role for 1-Pu and 1-U compared to the 4f-orbitals of 1-Ce. The lack of Ce(4f) interactions is compensated for by increased participation of the Ce(5d) orbitals relative to the actinide 6d orbitals, particularly for the σ-bound η 1 –Cp′ ligand. Furthermore, the use of multiple theoretical approaches including topological, localization, and energy decomposition approaches shows that 1-Pu and 1-U are very similar in covalent character compared to 1-Ce, though the composition and energy of the different interactions suggest that 1-U presents the strongest overall interactions.
Actinides↗
Computational and Experimental Mechanistic Insights into the Ethanol-to-Butanol Upgrading Reaction over MgO
The mechanism of ethanol upgrading to higher products is still under debate, especially regarding intermediate species and hydrogenation and dehydrogenation steps. In this work, we conducted a combined theoretical and experimental approach to contribute to this discussion. For such, detailed electronic structure density functional theory calculations (aiming at probing density of states, infrared spectra, geometric parameters, charge densities, and reaction energetics) and diffuse reflectance infrared Fourier transform spectroscopy experiments were carried out revealing the relevance of an appropriate combination of reactive surface sites to support the formation of several intermediates that are formed in the C-C coupling over MgO. The roles of Mg and O sites were also studied under an electronic perspective and different geometrical arrangements. We found that a kink configuration was the most adequate for ethanol to 1-butanol upgrading. Our calculations also gave us arguments to propose distinct reaction routes, whose mutual predominance would depend upon reaction temperature. At temperatures up to 573 K, the so-called β-route, which goes through scission of a Cβ-H bond and formation of an oxametallacycle-like intermediate, would dominate the coupling, whereas at higher temperatures, up to 673 K, a more usual Guerbet mechanism, via an aldol coupling step and then consecutive hydrogenations, would be expected. Here, the theoretical conclusions were followed by a careful experimental strategy using sequential experimental planning techniques in order to estimate accurate parameters with the lowest possible experimental load. Information from these different sources were coupled to develop a mathematical model for the rate of the ethanol upgrading reaction, using a Langmuir-Hinshelwood-Hougen-Watson approach. The developed and statistically validated model adequately described the experimental data at 673 K and 1.1 bar total pressure for ethanol partial pressures in the range from 0 to 20 kPa.
09 BIOMASS FUELS↗