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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid–amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Effect of point and grain boundary defects on the mechanical behavior of monolayer MoS{sub 2} under tension via atomistic simulations

Atomistic simulation is used to study the structure and energy of defects in monolayer MoS{sub 2} and the role of defects on the mechanical properties of monolayer MoS{sub 2}. First, energy minimization is used to study the structure and energy of monosulfur vacancies positioned within the bottom S layer of the MoS{sub 2} lattice, and 60° symmetric tilt grain boundaries along the zigzag and armchair directions, with comparison to experimental observations and density functional theory calculations. Second, molecular dynamics simulations are used to subject suspended defect-containing MoS{sub 2} membranes to a state of multiaxial tension. A phase transformation is observed in the defect-containing membranes, similar to prior work in the literature. For monolayer MoS{sub 2} membranes with point defects, groups of monosulfur vacancies promote stress-concentration points, allowing failure to initiate away from the center of the membrane. For monolayer MoS{sub 2} membranes with grain boundaries, failure initiates at the grain boundary and it is found that the breaking force for the membrane is independent of grain boundary energy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

A first principle study for the comparison of phonon dispersion of armchair carbon and silicon nanotubes

Using first principles density functional theoretical calculations, the present paper reports a systematic study of phonon dispersion curves in pristine carbon (CNT) and silicon nanotubes (SiNT) having chirality (6,6) in the armchair configuration. Some of the phonon modes are found to have negative frequencies which leads to instability of the systems under study. The number of phonon branches has been found to be thrice as much as the number of atoms. The frequency of the higher optical bands varies from 1690 to 1957 cm{sup −1} for CNT(6,6) while it is 596 to 658 cm{sup −1} for SiNT.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Adsorption and self-assembled structures of sexithiophene on the Si(111)-√(3)×√(3)-Ag surface

The adsorption and self-assembled structures of α-sexithiophene (α-6T) have been investigated on a Si(111)-Ag surface using scanning tunneling microscopy (STM), low-energy electron diffraction, and density functional theory calculations. The adsorbed α-6T molecules are arranged into unidirectional molecular rows with a side-by-side orientation. The molecular rows reveal three kinds of appearances in the filled-state STM images, which reflect the distinct adsorption sites. From tunneling spectroscopy, we find that the filled-state STM images of α-6T should be influenced by the surface states of Si(111)-Ag. At one monolayer coverage, sequentially ordering of the triple molecular rows results in the close-packed arrangement of the α-6T overlayer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Well‐Dispersed Nickel‐ and Zinc‐Tailored Electronic Structure of a Transition Metal Oxide for Highly Active Alkaline Hydrogen Evolution Reaction

Abstract The practical scale‐up of renewable energy technologies will require catalysts that are more efficient and durable than present ones. This is, however, a formidable challenge that will demand a new capability to tailor the electronic structure. Here, an original electronic structure tailoring of CoO by Ni and Zn dual doping is reported. This changes it from an inert material into one that is highly active for the hydrogen evolution reaction (HER). Based on combined density functional theory calculations and cutting‐edge characterizations, it is shown that dual Ni and Zn doping is responsible for a highly significant increase in HER activity of the host oxide. That is, the Ni dopants cluster around surface oxygen vacancy of the host oxide and provide an ideal electronic surface structure for hydrogen intermediate binding, while the Zn dopants distribute inside the host oxide and modulate the bulk electronic structure to boost electrical conduction. As a result, the dual‐doped Ni, Zn CoO nanorods achieve current densities of 10 and 20 mA cm −2 at overpotentials of, respectively, 53 and 79 mV. This outperforms reported state‐of‐the‐art metal oxide, metal oxide/metal, metal sulfide, and metal phosphide catalysts.

Ling, Tao↗
DOE OSTI2019

Understanding Structure–Property Relationships of MoO 3 -Promoted Rh Catalysts for Syngas Conversion to Alcohols

Rh-based catalysts have shown promise for the direct conversion of syngas to higher oxygenates. Although improvements in higher oxygenate yield have been achieved by combining Rh with metal oxide promoters, details of the structure of the promoted catalyst and the role of the promoter in enhancing catalytic performance are not well understood. In this work, we show that MoO 3 -promoted Rh nanoparticles form a novel catalyst structure in which Mo substitutes into the Rh surface, leading to both a 66-fold increase in turnover frequency and an enhancement in oxygenate yield. By applying a combination of atomically controlled synthesis, in situ characterization, and theoretical calculations, we gain an understanding of the promoter-Rh interactions that govern catalytic performance for MoO 3 -promoted Rh. We use atomic layer deposition to modify Rh nanoparticles with monolayer-precise amounts of MoO 3 , with a high degree of control over the structure of the catalyst. Through in situ X-ray absorption spectroscopy, we find that the atomic structure of the catalytic surface under reaction conditions consists of Mo–OH species substituted into the surface of the Rh nanoparticles. Furthermore, using density functional theory calculations, we identify two roles of MoO 3 : first, the presence of Mo–OH in the catalyst surface enhances CO dissociation and also stabilizes a methanol synthesis pathway not present in the unpromoted catalyst; and second, hydrogen spillover from Mo–OH sites to adsorbed species on the Rh surface enhances hydrogenation rates of reaction intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

In-situ probing of coupled atomic restructuring and metallicity of oxide heterointerfaces induced by polar adsorbates

Microscopic understanding of the surface-controlled conductivity of the two dimensional electron gas at complex oxide interfaces is crucial for developing functional interfaces. We observe conductivity and structural modification using in-situ synchrotron surface x-ray diffraction as the surface of a model LaAlO 3 /SrTiO 3 (001) heterostructure is changed by polar adsorbates. We find that polar adsorbate-induced interfacial metallicity reduces polar distortions in the LaAlO 3 layer. First-principles density functional theory calculations show that surface dipoles introduced by polar adsorbates lead to additional charge transfer and the reduction of polar displacements in the LaAlO 3 layer, consistent with the experimental observations. Our study supports that internal structural deformations controlling functionalities can be driven without the application of direct electrical or thermal bias and offers a route to tuning interfacial properties. Furthermore, these results also highlight the important role of in-situ x-ray scattering with atomic resolution in capturing and exploring structural distortions and charge density changes caused by external perturbations such as chemical adsorption, redox reaction, and generation and/or annihilation of surface defects.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Canted antiferromagnetic order and spin dynamics in the honeycomb-lattice compound Tb 2 Ir 3 Ga 9

Here, single-crystal neutron diffraction, inelastic neutron scattering, bulk magnetization measurements, and first-principles calculations are used to investigate the magnetic properties of the honeycomb lattice Tb 2 Ir 3 Ga 9 . While the R ln 2 magnetic contribution to the low-temperature entropy indicates a J eff = 1 / 2 moment for the lowest-energy crystal-field doublet, the Tb 3 + ions form a canted antiferromagnetic structure below 12.5 K. Due to the Dzyaloshinskii-Moriya interactions, the Tb moments in the a b plane are slightly canted towards b with a canted moment of 1.22 μ B per formula unit. A minimal x x z spin Hamiltonian is used to simultaneously fit the spin-wave frequencies along the high-symmetry directions and the field dependence of the magnetization along the three crystallographic axes. Long-range magnetic interactions for both in-plane and out-of-plane couplings up to the second nearest neighbors are needed to account for the observed static and dynamic properties. The z component of the exchange interactions between Tb moments is larger than the x and y components. This compound also exhibits bond-dependent exchange with negligible nearest-neighbor exchange coupling between moments parallel and perpendicular to the 4 f orbitals. Despite the J eff = 1 / 2 moments, the spin Hamiltonian is denominated by a large in-plane anisotropy K z ~ – 1 meV . DFT calculations confirm the antiferromagnetic ground state and the substantial interplane coupling at larger Tb-Tb distances.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Diverse and tunable electronic structures of single-layer metal phosphorus trichalcogenides for photocatalytic water splitting

The family of bulk metal phosphorus trichalcogenides (APX{sub 3}, A = M{sup II}, M{sub 0.5}{sup I}M{sub 0.5}{sup III}; X = S, Se; M{sup I}, M{sup II}, and M{sup III} represent Group-I, Group-II, and Group-III metals, respectively) has attracted great attentions because such materials not only own magnetic and ferroelectric properties, but also exhibit excellent properties in hydrogen storage and lithium battery because of the layered structures. Many layered materials have been exfoliated into two-dimensional (2D) materials, and they show distinct electronic properties compared with their bulks. Here we present a systematical study of single-layer metal phosphorus trichalcogenides by density functional theory calculations. The results show that the single layer metal phosphorus trichalcogenides have very low formation energies, which indicates that the exfoliation of single layer APX{sub 3} should not be difficult. The family of single layer metal phosphorus trichalcogenides exhibits a large range of band gaps from 1.77 to 3.94 eV, and the electronic structures are greatly affected by the metal or the chalcogenide atoms. The calculated band edges of metal phosphorus trichalcogenides further reveal that single-layer ZnPSe{sub 3}, CdPSe{sub 3}, Ag{sub 0.5}Sc{sub 0.5}PSe{sub 3}, and Ag{sub 0.5}In{sub 0.5}PX{sub 3} (X = S and Se) have both suitable band gaps for visible-light driving and sufficient over-potentials for water splitting. More fascinatingly, single-layer Ag{sub 0.5}Sc{sub 0.5}PSe{sub 3} is a direct band gap semiconductor, and the calculated optical absorption further convinces that such materials own outstanding properties for light absorption. Such results demonstrate that the single layer metal phosphorus trichalcogenides own high stability, versatile electronic properties, and high optical absorption, thus such materials have great chances to be high efficient photocatalysts for water-splitting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Co(salen)-Catalyzed Oxidation of Lignin Models to Form Benzoquinones and Benzaldehydes: A Computational and Experimental Study

Lignin is a highly abundant polyphenolic polymer that imparts mechanical strength to plant biomass. Transition-metal complexes can catalyze lignin oxidation to produce value-added products, but low catalytic efficiency has hampered their use in industry. Identifying the chemical and structural factors that govern catalytic activity is a prerequisite to rational design of catalysts with improved activity. In this study, we combine computational and experimental approaches to investigate the mechanism of Co(salen)-catalyzed oxidation of the monomeric lignin models syringyl (S), vanillyl (G), and 4-hydroxybenzyl alcohol (H) to produce benzoquinone and benzaldehyde products. Experimentally, S oxidation to form dimethoxybenzoquinone proceeded efficiently with a Co(salen) catalyst coordinated by a pyridine ligand, but G and H did not undergo oxidation. Density functional theory calculations reveal that catalyst regeneration is energetically unfavorable in the presence of H, which prevents oxidation. In contrast, S readily facilitates catalyst regeneration. Formation of methoxybenzoquinone from G was achieved experimentally by adding bulky, noncoordinating bases. These findings provide a fundamental baseline for enhancing the activity of Co-Schiff base catalysts toward lignin-like molecules by adding sterically hindered nitrogenous bases or potentially by including a cocatalyst that promotes catalyst regeneration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Effect of oxygen incorporation on the structure and elasticity of Ti-Al-O-N coatings synthesized by cathodic arc and high power pulsed magnetron sputtering

Ti-Al-O-N coatings were synthesized by cathodic arc and high power pulsed magnetron sputtering. The chemical composition of the coatings was determined by means of elastic recoil detection analysis and energy dispersive X-ray spectroscopy. The effect of oxygen incorporation on the stress-free lattice parameters and Young's moduli of Ti-Al-O-N coatings was investigated by X-ray diffraction and nanoindentation, respectively. As nitrogen is substituted by oxygen, implications for the charge balance may be expected. A reduction in equilibrium volume with increasing O concentration is identified by X-ray diffraction and density functional theory calculations of Ti-Al-O-N supercells reveal the concomitant formation of metal vacancies. Hence, the oxygen incorporation-induced formation of metal vacancies enables charge balancing. Furthermore, nanoindentation experiments reveal a decrease in elastic modulus with increasing O concentration. Based on ab initio data, two causes can be identified for this: First, the metal vacancy-induced reduction in elasticity; and second, the formation of, compared to the corresponding metal nitride bonds, relatively weak Ti-O and Al-O bonds.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Experimental and theoretical comparison of Sb, As, and P diffusion mechanisms and doping in CdTe

Fundamental material doping challenges have limited CdTe electro-optical applications. In this work, the As atomistic diffusion mechanisms in CdTe are examined by spatially resolving dopant incorporation in both single-crystalline and polycrystalline CdTe over a range of experimental conditions. Density-functional theory calculations predict experimental activation energies and indicate As diffuses slowly through the Te sublattice and quickly along GBs similar to Sb. Because of its atomic size and associated defect chemistry, As does not have a fast interstitial diffusion component similar to P. Experiments to incorporate and activate P, As, and Sb in polycrystalline CdTe are conducted to examine if ex-situ Group V doping can overcome historic polycrystalline doping limits. The distinct P, As, and Sb diffusion characteristics create different strategies for increasing hole density. Because fast interstitial diffusion is prominent for P, less aggressive diffusion conditions followed by Cd overpressure to relocate the Group V element to the Te lattice site is effective. For larger atoms, slower diffusion through the Te sublattice requires more aggressive diffusion, however further activation is not always necessary. Based on the new physical understanding, we have obtained greater than 10^16 cm^-3 hole density in polycrystalline CdTe films by As and P diffusion.

14 SOLAR ENERGY↗
DOE OSTI2014

Phonon Spectrum of SrFe2As2 determined by multizone phonon refinement

The ferropnictidesuperconductors exhibit a sensitive interplay between the lattice and magnetic degrees of freedom, including a number of phonon modes that are much softer than predicted by nonmagnetic calculations using density functional theory (DFT). However, it is not known what effect, if any, the long-range magnetic order has on phonon frequencies above 23 meV, where several phonon branches are very closely spaced in energy and it is challenging to isolate them from each other. We measured these phonons using inelastic time-of-flight neutron scattering in 40 Brillouin zones, and developed a technique to determine their frequencies. We find this method capable of determining phonon energies to 0.1 meV accuracy, and that the DFT calculations using the experimental structure yield qualitatively correct energies and eigenvectors. We do not find any effect of the magnetic transition on these phonons.

Parshall, D↗
DOE OSTI2023

Two-dimensional Dirac semimetal based on the alkaline earth metal CaP 3

Using an evolutionary algorithm in combination with first-principles density-functional theory calculations, we identify a two-dimensional (2D) CaP 3 monolayer as a new Dirac semimetal due to inversion and nonsymmorphic spatial symmetries of the structure. This new topological material, composed of light elements, exhibits high structural stability (higher than the phase known in the literature), which is confirmed by thermodynamic and kinetic stability analysis. Moreover, it satisfies the electron filling criteria, so that its Dirac state is located near the Fermi level. The existence of the Dirac state predicted by the theoretical symmetry analysis is also confirmed by first-principles electronic band structure calculations. We find that the energy position of the Dirac state can be tuned by strain, while the Dirac state is unstable against an external electric field since it breaks the spatial inversion symmetry. In conclusion, our findings should be instrumental in the development of 2D Dirac fermions based on light elements for their application in nanoelectronic devices and topological electronics.

2-dimensional systems↗
DOE OSTI2015

Towards a predictive route for selection of doping elements for the thermoelectric compound PbTe from first-principles

Striving for improvements of the thermoelectric (TE) properties of the technologically important lead telluride (PbTe) compound, we investigate the influence of different doping elements on the thermal conductivity, Seebeck coefficient, and electrical conductivity applying density functional theory calculations. Our approach combines total-energy calculations yielding lattice vibrational properties with the Boltzmann transport theory to obtain electronic transport properties. We find that doping with elements from the 1st and 3rd columns of the periodic table reduces the sound velocity and, consequently, the lattice thermal conductivity, while 2nd column dopants have no such influence. Furthermore, 1.6 at. % doping with 4th and 5th column elements provides the highest reduction of lattice thermal conductivity. Out of this group, Hf doping results in maximum reduction of the sound velocity from 2030 m s{sup −1} for pure PbTe to 1370 m s{sup −1}, which is equivalent to ca. 32% reduction of lattice thermal conductivity. The highest power factor values calculated for 1.6 at. % doping range between 40 and 56 μW cm{sup −1} K{sup −2}, and are obtained for substitution with dopants having the same valence as Pb or Te, such as those located at the 2nd, 14th, and 16th columns of the periodic table. We demonstrate how this method may be generalized for dopant-selection-oriented materials design aimed at improving TE performance of other compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Chemical and phase evolution of amorphous molybdenum sulfide catalysts for electrochemical hydrogen production [Chemical and phase evolution of amorphous molybdenum sulfide catalysts for electrochemical hydrogen production directly observed using environmental transmission electron microscopy]

Amorphous MoS x is a highly active, earth-abundant catalyst for the electrochemical hydrogen evolution reaction. Previous studies have revealed that this material initially has a composition of MoS 3 , but after electrochemical activation, the surface is reduced to form an active phase resembling MoS 2 in composition and chemical state. However, structural changes in the Mo Sx catalyst and the mechanism of the activation process remain poorly understood. In this study, we employ transmission electron microscopy (TEM) to image amorphous MoS x catalysts activated under two hydrogen-rich conditions: ex situ in an electrochemical cell and in situ in an environmental TEM. For the first time, we directly observe the formation of crystalline domains in the MoS x catalyst after both activation procedures as well as spatially localized changes in the chemical state detected via electron energy loss spectroscopy. Using density functional theory calculations, we investigate the mechanisms for this phase transformation and find that the presence of hydrogen is critical for enabling the restructuring process. Our results suggest that the surface of the amorphous MoS x catalyst is dynamic: while the initial catalyst activation forms the primary active surface of amorphous MoS 2 , continued transformation to the crystalline phase during electrochemical operation could contribute to catalyst deactivation. Finally, these results have important implications for the application of this highly active electrocatalyst for sustainable H 2 generation.

36 MATERIALS SCIENCE↗
DOE OSTI2014

First-principles study of carrier-induced ferromagnetism in bilayer and multilayer zigzag graphene nanoribbons

We studied magnetism in bilayer and multilayer zigzag graphene nanoribbons (ZGNRs) through first-principles density functional theory calculations. We found that the magnetic ground state of bilayer ZGNRs is the C-type antiferromagnetic (AFM) state, which is the AFM order between intraplane-edge carbon atoms and ferromagnetic (FM) order between interplane edge carbon atoms. In the cases of infinitely stacked multilayer ZGNRs, i.e., zigzag graphite nanoribbons, the C-type AFM state is also the most stable. By carrier doping, we found that the magnetic ground state changed from the C-AFM state to the FM state and, thus, realized two-dimensional FM surface (edge) states of graphite with a metallic conductivity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Relationships between the surface electronic and chemical properties of doped 4d and 5d late transition metal dioxides

Density functional theory calculations were performed to elucidate the underlying physics describing the adsorption energies on doped late transition metal dioxide rutiles. Adsorption energies of atomic oxygen on doped rutiles M{sup D}-M{sup H}O{sub 2}, where transition metal M{sup D} is doped into M{sup H}O{sub 2}, were expressed in terms of a contribution from adsorption on the pure oxide of the dopant M{sup D} and perturbations to this adsorption energy caused by changing its neighboring metal cations and lattice parameters to that of the host oxide M{sup H}O{sub 2}, which we call the ligand and strain effects, respectively. Our analysis of atom projected density of states revealed that the t{sub 2g}-band center had the strongest correlation with adsorption energies. We show that charge transfer mediated shifts to the t{sub 2g}-band center describe the ligand effect, and the radii of the atomic orbitals of metal cations can predict the magnitude and direction of this charge transfer. Strain produces systematic shifts to all features of the atom projected density of states, but correlations between the strain effect and the electronic structure were dependent on the chemical identity of the metal cation. The slope of these correlations can be related to the idealized d-band filling. This work elucidates the underlying physics describing adsorption on doped late transition metal oxides and establishes a foundation for models that use known chemical properties for the prediction of reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗