The Case for a Defect Genome Initiative.

The Materials Genome Initiative (MGI) has streamlined the materials discovery effort by leveraging generic traits of materials, with focus largely on perfect solids. Defects such as impurities and perturbations, however, drive many attractive functional properties of materials. The rich tapestry of charge, spin, and bonding states hosted by defects are not accessible to elements and perfect crystals, and defects can thus be viewed as another class of "elements" that lie beyond the periodic table. Accordingly, a Defect Genome Initiative (DGI) to accelerate functional defect discovery for energy, quantum information, and other applications is proposed. First, major advances made under the MGI are highlighted, followed by a delineation of pathways for accelerating the discovery and design of functional defects under the DGI. Near-term goals for the DGI are suggested. The construction of open defect platforms and design of data-driven functional defects, along with approaches for fabrication and characterization of defects, are discussed. The associated challenges and opportunities are considered and recent advances towards controlled introduction of functional defects at the atomic scale are reviewed. It is hoped this perspective will spur a community-wide interest in undertaking a DGI effort in recognition of the importance of defects in enabling unique functionalities in materials.

Capturing dynamical correlations using implicit neural representations.

Understanding the nature and origin of collective excitations in materials is of fundamental importance for unraveling the underlying physics of a many-body system. Excitation spectra are usually obtained by measuring the dynamical structure factor, S(Q, ω), using inelastic neutron or x-ray scattering techniques and are analyzed by comparing the experimental results against calculated predictions. We introduce a data-driven analysis tool which leverages 'neural implicit representations' that are specifically tailored for handling spectrographic measurements and are able to efficiently obtain unknown parameters from experimental data via automatic differentiation. In this work, we employ linear spin wave theory simulations to train a machine learning platform, enabling precise exchange parameter extraction from inelastic neutron scattering data on the square-lattice spin-1 antiferromagnet La2NiO4, showcasing a viable pathway towards automatic refinement of advanced models for ordered magnetic systems.

Computational Methods for Charge Density Waves in 2D Materials.

Two-dimensional (2D) materials that exhibit charge density waves (CDWs)-spontaneous reorganization of their electrons into a periodic modulation-have generated many research endeavors in the hopes of employing their exotic properties for various quantum-based technologies. Early investigations surrounding CDWs were mostly focused on bulk materials. However, applications for quantum devices require few-layer materials to fully utilize the emergent phenomena. The CDW field has greatly expanded over the decades, warranting a focus on the computational efforts surrounding them specifically in 2D materials. In this review, we cover ground in the following relevant theory-driven subtopics for TaS2 and TaSe2: summary of general computational techniques and methods, resulting atomic structures, the effect of electron-phonon interaction of the Raman scattering modes, the effects of confinement and dimensionality on the CDW, and we end with a future outlook. Through understanding how the computational methods have enabled incredible advancements in quantum materials, one may anticipate the ever-expanding directions available for continued pursuit as the field brings us through the 21st century.

Examining Experimental Raman Mode Behavior in Mono- and Bilayer 2H-TaSe2 via Density Functional Theory: Implications for Quantum Information Science.

Tantalum diselenide (TaSe2) is a metallic transition metal dichalcogenide whose structure and vibrational behavior strongly depend on temperature and thickness, and this behavior includes the emergence of charge density wave (CDW) states at very low temperatures. In this work, observed Raman modes for mono- and bilayer are described across several spectral regions and compared to those seen in the bulk case. These modes, which include an experimentally observed forbidden Raman mode and low-frequency CDWs, are then matched to corresponding vibrations predicted by density functional theory (DFT). The reported match between experimental and computational results supports the presented vibrational visualizations of these modes. Support is also provided by experimental phonons observed in additional Raman spectra as a function of temperature and thickness. These results highlight the importance of understanding CDWs since they are likely to play a fundamental role in the future realization of solid-state quantum information platforms based on nonequilibrium phenomena.

Phonon origin and lattice evolution in charge density wave states.

Metallic transition metal dichalcogenides, such as tantalum diselenide (TaSe2), display quantum correlated phenomena of superconductivity and charge density waves (CDW) at low temperatures. Here, the photophysics of 2H-TaSe2 during CDW transitions is revealed by combining temperature-dependent, low-frequency Raman spectroscopy and density functional theory (DFT). The spectra contain amplitude, phase, and zone-folded modes that are assigned to specific phonons and lattice restructuring predicted by DFT calculations with superb agreement. The non-invasive and efficient optical methodology detailed here demonstrates an essential link between atomic-scale and microscopic quantum phenomena.

Computational screening of high-performance optoelectronic materials using OptB88vdW and TB-mBJ formalisms.

We perform high-throughput density functional theory (DFT) calculations for optoelectronic properties (electronic bandgap and frequency dependent dielectric function) using the OptB88vdW functional (OPT) and the Tran-Blaha modified Becke Johnson potential (MBJ). This data is distributed publicly through JARVIS-DFT database. We used this data to evaluate the differences between these two formalisms and quantify their accuracy, comparing to experimental data whenever applicable. At present, we have 17,805 OPT and 7,358 MBJ bandgaps and dielectric functions. MBJ is found to predict better bandgaps and dielectric functions than OPT, so it can be used to improve the well-known bandgap problem of DFT in a relatively inexpensive way. The peak positions in dielectric functions obtained with OPT and MBJ are in comparable agreement with experiments. The data is available on our websites http://www.ctcms.nist.gov/~knc6/JVASP.html and https://jarvis.nist.gov.

Probing the dielectric response of the interfacial buffer layer in epitaxial graphene via optical spectroscopy.

Monolayer epitaxial graphene (EG) is a suitable candidate for a variety of electronic applications. One advantage of EG growth on the Si face of SiC is that it develops as a single crystal, as does the layer below, referred to as the interfacial buffer layer (IBL), whose properties include an electronic band gap. Though much research has been conducted to learn about the electrical properties of the IBL, not nearly as much work has been reported on the optical properties of the IBL. In this work, we combine measurements from Mueller matrix ellipsometry, differential reflectance contrast, atomic force microscopy, and Raman spectroscopy, as well as calculations from Kramers-Kronig analyses and density functional theory (DFT), to determine the dielectric function of the IBL within the energy range of 1 eV to 8.5 eV.

Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum.

BACKGROUND: Rhodospirillum centenum is a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic N2-fixing environment. It is emerging as a genetically amenable model organism for molecular genetic analysis of cyst formation, photosynthesis, phototaxis, and cellular development. Here, we present an analysis of the genome of this bacterium. RESULTS: R. centenum contains a singular circular chromosome of 4,355,548 base pairs in size harboring 4,105 genes. It has an intact Calvin cycle with two forms of Rubisco, as well as a gene encoding phosphoenolpyruvate carboxylase (PEPC) for mixotrophic CO2 fixation. This dual carbon-fixation system may be required for regulating internal carbon flux to facilitate bacterial nitrogen assimilation. Enzymatic reactions associated with arsenate and mercuric detoxification are rare or unique compared to other purple bacteria. Among numerous newly identified signal transduction proteins, of particular interest is a putative bacteriophytochrome that is phylogenetically distinct from a previously characterized R. centenum phytochrome, Ppr. Genes encoding proteins involved in chemotaxis as well as a sophisticated dual flagellar system have also been mapped. CONCLUSIONS: Remarkable metabolic versatility and a superior capability for photoautotrophic carbon assimilation is evident in R. centenum.

Mechanistic investigation of the hydrogenation of O(2) by a transfer hydrogenation catalyst.

The mechanistic details of the hydrogenation of molecular oxygen by the 18e amino-hydride Cp*IrH(TsDPEN) (1H(H)) complex to give Cp*Ir(TsDPEN-H) (1) and 1 equiv of H(2)O were investigated by means of hybrid density functional calculations (B3LYP). To comprehensively describe the overall catalytic cycle of the hydrogenation of dioxygen using H(2) catalyzed by the Ir complex 1, the potential energy surfaces for the hydrogenation process of both the catalyst 1 and the corresponding unsaturated iridium(III) amine cation ([1H](+)) were explored at the same level of theory. The results of our computations, in agreement with experimental findings, confirm that the addition of H(2) to the 16e diamido complexes 1 is favorable but is slow and is accelerated by the presence of Bronsted acids, such as HOTf, which convert 1 into the corresponding amine cation [1H](+). By deprotonation of the subsequently hydrogenated [1H(H(2))](+) complex the amine hydride catalyst 1H(H) is generated, which is able to reduce molecular oxygen. Calculations corroborate that the O(2) reduction goes through formation of an intermediate iridium hydroperoxo complex that reacts with 1H(H) to eliminate water, restore 1, and restart the catalytic cycle. From the outcomes of our computational analysis it results that the slow step of the overall O(2) hydrogenation process is the O(2) insertion into the Ir-H bond, and the highest calculated barrier along this pathway to give the hydroperoxo product shows a good agreement with the experimentally estimated value. As a consequence, unreacted 1H(H) approaches 1H(OOH) to give 1H(OH) and water according to the experimentally observed second-order kinetics with respect to [1H(H)]. Calculations were carried out to explore the possibility that H(2)O(2) is released from the hydroperoxo intermediate together with catalyst 1, and the subsequent water elimination reaction occurs by reduction of produced H(2)O(2) with 1H(H) to regenerate catalyst 1. Preliminary results concerning the O(2) reduction in acidic conditions show that the reaction proceeds by intermediate production of H(2)O(2), which reacts with 1H(H) to eliminate water, restore [1H](+), and restart the catalytic cycle. The energetics of the process appear to be definitely more favorable with respect the analogous pathways in neutral conditions.

Theoretical Investigation of the Mechanism of Acid-Catalyzed Oxygenation of a Pd(II)-Hydride To Produce a Pd(II)-Hydroperoxide.

Density Functional Theory (DFT) has been applied to a comprehensive mechanistic study of the conversion reaction of the Pd(II)-hydride complex, (IMe)2(RCO2)PdH (R=CH3, Ph, and p-O2NC6H4), to the corresponding Pd(II)-hydroperoxide in the presence of molecular oxygen. The calculations have evaluated the two mechanistic proposed alternatives, that are both considered viable on the basis of current data, of slow RCO2H reductive elimination followed by oxygenation (Path A) and direct O2 insertion (Path B). Results suggest that the mechanism of direct insertion of molecular oxygen into the Pd-H bond of the initial complex is energetically preferred. The activation energy relative to the rate-determining step of Path A, indeed, is calculated to be lower than the activation energy of the rate determining step of the alternative Path B, whatever ligand (CH3CO2, Ph, CO2, p-O2NC6H4CO2) is coordinated to the Pd center. The calculated free activation energy of the rate-determining hydrogen abstraction step (ΔG* = 24.8 kcal/mol) in the case of the oxygenation reaction of the benzoate-ligated Pd(II)-hydride complex is in very good agreement with the experimentally determined value of 24.4 kcal/mol. In addition, according to the experimentally detected enhancement of the reaction rate due to the presence of a nitro group on the benzoate ligand, our calculations show that the transition state for the hydrogen atom abstraction by molecular oxygen along the pathway for the oxygenation reaction of (IMe)2(p-O2NC6H4CO2)PdH lies lower in energy with respect to the analogous transition state calculated for R=Ph.