Model Of Electronic Structure Research Articles

Optical properties of two-dimensional materials with tilted anisotropic Dirac cones: theoretical modeling with application to doped 8-Pmmn borophene

The optical reflection, transmission and absorption properties of borophene, a newly discovered two-dimensional material with tilted anisotropic Dirac cones, are explored within a simple electronic band structure model of 8-Pmmn borophene, proposed by Zabolotskiy and Lozovik (2016 Phys. Rev. B 94 165403). It is assumed that the borophene layer is deposited on a dielectric substrate, such as Al2O3, and that the borophene’s electron density is controlled by an external gate voltage. The reflectance, transmittance and absorbance of the borophene layer, the conduction band of which is filled with electrons up to the Fermi level, are calculated against the frequency of the incident radiation, as well as on the angle of its incidence on the layer. Considered are the two principal cases of the incident radiation polarization either parallel to or normal to the plane of incidence. We reveal that the optical characteristics of 8-Pmmn borophene are distinctly different for the above two cases at all angles of radiation incidence, excepting the grazing incidence, for which the borophene layer is found to behave like a mirror regardless of the wave polarization. The results obtained indicate the possibility of visualizing the borophene layer deposited on a dielectric substrate by observing the minimum reflectivity of this layer at a certain angle incidence (called the quasi-Brewster angle) of the p-polarized radiation, which may differ by a value of about ten degrees from the Brewster angle of the substrate.

Mutual miscibility of diethyl sulfoxide and acetonitrile: Fundamental origin

Diethyl sulfoxide (DESO) is an environmentally friendly liquid that has prospective applications in the accomplishment of robust freezing/thawing of biological entities. DESO possesses one polar and two symmetric non-polar moieties thus exhibiting a mixed solvation behavior. Understanding the intermolecular interactions of DESO with other common liquids is a cornerstone of fostering its efficient usage. Herein, we report global- and local-minimum molecular configurations of a few DESO/acetonitrile (ACN) mixtures using a comprehensive electronic-structure modeling of the potential energy surface. We discuss energetics, distributions functions, structure descriptors, and vibrational spectra of the mixture components. The presented results provide a clear understanding of the DESO/ACN miscibility origin and unambiguously rationalize the previously reported experimental results on these liquid systems.

(Invited) Development and Understanding of Advanced Materials for Hydrogen Storage and Delivery

Continued efforts to advance hydrogen storage and delivery require development and validation of efficient materials platforms coupled with mechanistic understanding of storage and conversion of hydrogen or its carriers. The Hydrogen Materials Advanced Research Consortium (HyMARC) is working with the research community to provide cutting-edge materials development advanced characterization, and theoretical modeling in support of these efforts, leveraging multiple U.S. Department of Energy national labs and their user facilities. Within this program, Berkeley Lab is developing stable and efficient solutions to hydrogen storage involving nanoscale encapsulation, and boosts to the conversion efficiency for liquid organic carriers through the development of single-atom catalyst platforms. The Molecular Foundry and The Advanced Light Source at Berkeley Lab provide deep insight into our materials advances through first-principles modeling of atomic and electronic structure, and X-ray spectroscopy of evolving materials systems at high temperatures and pressures.

Highly efficient modelling of electronic structure

Highly efficient modelling of electronic structure

Modeling of electronic structure for dome-shaped quantum dots

A Hamiltonian operator in assessing the energy levels and wavefunctions of quantum dots (QDs) was proposed. The finite element method was used to solve the numerical Schrödinger equation for envelope function in the effective mass approximation. Within this model, we have investigated QDs with different geometries (cone, lens and dome-shaped dot). While it is easy to attain stability for conical QDs, it is difficult with lens QDs. Strain and mole-fraction effects are also studied. Our results coincide with the experimental one.

The studies of electronic structure, mechanical properties and ideal fracture behavior of U3Si1.75Al0.25: first-principle investigations

As one of the accident-tolerance nuclear fuels with potential application prospects, U3Si2 shows its merits of high melting point, high thermal conductivity and high uranium density. However, the mechanical brittleness is one major problem for its practical applications. The strategy of Al-alloying could effectively improve the ductility of U3Si2, yet the intrinsic mechanism is not clear. In this work, the mechanisms for the ductility enhancement of U3Si2 via substituting Al into Si site (i.e. U3Si1.75Al0.25) is studied from two aspects: 1) the interatomic bonding characteristics that are responsible for the ductility enhancement are analyzed in detail; 2) the tensile-shear tests of U3Si1.75Al0.25 are carried out via first-principle calculations, and then the ductility-enhancing mechanism is analyzed. It is found that the increasing number of bonding electrons in U–U layer results in the enhancement of the d-σ interactions between U–Si and U–Si–Al six-membered rings, while the decreasing number of bonding electrons within U–Si layer corresponds to the weakening of the d-s interactions. Finally, one electronic structure model is proposed to picture the interactions of bonding electrons during the tensile-shear tests; providing a novel and inspiration logic of mechanical property modification for alloying-U3Si2.

Strategies for solving the excited-state self-consistent-field problem for highly excited and multiply ionized states

The dynamics of molecules exposed to intense x-ray radiation involve a large number of multiply ionized and highly excited electronic configurations. To model these dynamics a reliable and efficient electronic structure model is imperative. Employing the Hartree-Fock-Slater electronic structure model in combination with the maximum overlap method, we quantify the associated convergence failures when calculating electronic states of carbon monoxide with multiple vacancies in the core and valence levels. We characterize these cases and describe strategies to overcome the convergence problems. The described techniques not only eliminate all convergence issues for CO but also result in a significant reduction of convergence failures for simulations of the x-ray-induced multiple ionization dynamics of the phenol molecule.

Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase.

The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.

Metamagnetism of few-layer topological antiferromagnets

MnBi$_2$Te$_4$ (MBT) is a promising antiferromagnetic topological insulator whose films provide access to novel and technologically important topological phases, including quantum anomalous Hall states and axion insulators. MBT device behavior is expected to be sensitive to the various collinear and non-collinear magnetic phases that are accessible in applied magnetic fields. Here, we use classical Monte Carlo simulations and electronic structure models to calculate the ground state magnetic phase diagram as well as topological and optical properties for few layer films with thicknesses up to six septuple layers. Using magnetic interaction parameters appropriate for MBT, we find that it is possible to prepare a variety of different magnetic stacking sequences, some of which have sufficient symmetry to disallow non-reciprocal optical response and Hall transport coefficients. Other stacking arrangements do yield large Faraday and Kerr signals, even when the ground state Chern number vanishes.

Magnetic constitution of topologically trivial thermoelectric PbTe:Cr

In this paper we report on detailed temperature and magnetic field dependence of magnetization of IV-VI semiconductor PbTe doped with mixed valence transition metal Cr2+/3+. The material is studied solely by a SQUID magnetometer in order to quantitatively determine the contribution of single substitutional Cr2+/3+ as well as of various Cr-Te magnetic nanocrystals, including their identification. The applied experimental procedure reveals the presence of about 1019 cm−3 paramagnetic Cr ions, of which 2/3 are the Cr3+ ions formed via self-ionization of Cr2+ resonant donors. These are known to improve the thermoelectric figure of merit parameter zT of this semiconductor. The magnetic finding agrees with previous Hall effect studies thus providing a new experimental support for the proposed electronic structure model of PbTe:Cr system with resonant Cr2+/3+ state located (at low temperatures) about 100 meV above the bottom of the conduction band. Below room temperature a ferromagnetic-like signal points to the presence of Cr-rich nanocrystalline precipitates. Two most likely candidates, namely: Cr2Te3 and Cr5Te8 are identified upon dedicated temperature cycling of the sample at the remnant state. As an ensemble, the nanocrystals exhibit (blocked) superparamagnetic properties. The magnetic susceptibility of both n- and p-type PbTe in the temperature range 100<T<400 K has been established. These magnitudes are essential to properly account for the high temperature magnetic susceptibility of PbTe:Cr.

Pythonic Black-box Electronic Structure Tool (PyBEST). An open-source Python platform for electronic structure calculations at the interface between chemistry and physics

Pythonic Black-box Electronic Structure Tool (PyBEST) represents a fully-fledged modern electronic structure software package developed at Nicolaus Copernicus University in Toruń. The package provides an efficient and reliable platform for electronic structure calculations at the interface between chemistry and physics using unique electronic structure methods, analysis tools, and visualization. Examples are the (orbital-optimized) pCCD-based models for ground- and excited-states electronic structure calculations as well as the quantum entanglement analysis framework based on the single-orbital entropy and orbital-pair mutual information. PyBEST is written primarily in the Python programming language with additional parts written in C＋＋, which are interfaced using Pybind11, a lightweight header-only library. By construction, PyBEST is easy to use, to code, and to interface with other software packages. Moreover, its modularity allows us to conveniently host additional Python packages and software libraries in future releases to enhance its performance. The electronic structure methods available in PyBEST are tested for the half-filled 1-D model Hamiltonian. The capability of PyBEST to perform large-scale electronic structure calculations is demonstrated for the model vitamin B12 compound. The investigated molecule is composed of 190 electrons and 777 orbitals for which an orbital optimization within pCCD and an orbital entanglement and correlation analysis are performed for the first time. Program summaryProgram title: PyBESTCPC Library link to program files:https://doi.org/10.17632/xf9kb7yfwr.1Developer’s repository link:https://zenodo.org/record/3925278#.X5KAZS8Rq6sLicensing provisions: GNU General Public License 3Programming language:Python, C＋＋Nature of problem: Efficient and reliable modeling of electronic structures featuring both weakly- and strongly-correlated electrons. Small- and large-scale quantum-mechanical problems at the interface between chemistry and physics comprising both quantum chemical and model Hamiltonians. Specifically, modeling potential energy surfaces of complex electronic structures including bond breaking/formation, elucidating complex electronic structures through the picture of interacting orbitals, describing noncovalent interactions, ultra-cold trapped quantum gases, and a variety of applications in interdisciplinary quantum mechanical-based problems.Solution method: Modular implementation of a series of unconventional (and conventional) electronic structure models based on the pCCD ansatz to solve the electronic Schrödinger equation. These include the description of both ground- and excited-states, the determination of interaction energies, and the analysis and interpretation of electronic wavefunctions. All modules are implemented in the modern Python programming language, where bottleneck operations are handled by C＋＋ code interfaced by the Pybind11 header-only library. The implemented (wavefunction) modules and modular code structure make PyBEST a very efficient alternative to existing electronic structure packages.Additional comments including restrictions and unusual features:PyBEST features unconventional electronic structure methods (pCCD and post-pCCD methods) that are not available in any other quantum chemistry/physics software package. It also includes a general orbital entanglement and correlation module that supports both pCCD and selected post-pCCD methods. PyBEST is designed to be easy to use and code in. Due to its modularity (for instance of the tensor contraction engine), new Python modules and features can be straightforwardly imported and exploited without changing any wavefunction modules directly.

Multiscale simulations of the electronic structure of III-nitride quantum wells with varied indium content: Connecting atomistic and continuum-based models

Carrier localization effects in III-N heterostructures are often studied in the frame of modified continuum-based models utilizing a single-band effective mass approximation. However, there exists no comparison between the results of a modified continuum model and atomistic calculations on the same underlying disordered energy landscape. We present a theoretical framework that establishes a connection between atomistic tight-binding theory and continuum-based electronic structure models, here a single-band effective mass approximation, and provide such a comparison for the electronic structure of (In,Ga)N quantum wells. In our approach, in principle, the effective masses are the only adjustable parameters since the confinement energy landscape is directly obtained from tight-binding theory. We find that the electronic structure calculated within effective mass approximation and the tight-binding model differ noticeably. However, at least in terms of energy eigenvalues, an improved agreement between the two methods can be achieved by adjusting the band offsets in the continuum model, enabling, therefore, a recipe for constructing a modified continuum model that gives a reasonable approximation of the tight-binding energies. Carrier localization characteristics for energetically low lying, strongly localized states differ, however, significantly from those obtained using the tight-binding model. For energetically higher lying, more delocalized states, good agreement may be achieved. Therefore, the atomistically motivated continuum-based single-band effective mass model established provides a good, computationally efficient alternative to fully atomistic investigations, at least at when targeting questions related to higher temperatures and carrier densities in (In,Ga)N systems.

Microcrystal Electron Diffraction for Molecular Design of Functional Non-Fullerene Acceptor Structures.

Understanding the relationship between molecular structure and solid-state arrangement informs about the design of new organic semiconductor (OSC) materials with improved optoelectronic properties. However, determining their atomic structure remains challenging. Here, we report the lattice organization of two non-fullerene acceptors (NFAs) determined using microcrystal electron diffraction (MicroED) from crystals not traceable by X-ray crystallography. The MicroED structure of o-IDTBR was determined from a powder without crystallization, and a new polymorph of ITIC-Th is identified with the most distorted backbone of any NFA. Electronic structure calculations elucidate the relationships between molecular structures, lattice arrangements, and charge-transport properties for a number of NFA lattices. The high dimensionality of the connectivity of the 3D wire mesh topology is the best for robust charge transport within NFA crystals. However, some examples suffer from uneven electronic coupling. MicroED combined with advanced electronic structure modeling is a powerful new approach for structure determination, exploring polymorphism and guiding the design of new OSCs and NFAs.

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models.

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

Effect of charge-transfer enhancement on the efficiency and rotary mechanism of an oxindole-based molecular motor.

Harvesting energy and converting it into mechanical motion forms the basis for both natural and artificial molecular motors. Overcrowded alkene-based light-driven rotary motors are powered through sequential photochemical and thermal steps. The thermal helix inversion steps are well characterised and can be manipulated through adjustment of the chemical structure, however, the insights into the photochemical isomerisation steps still remain elusive. Here we report a novel oxindole-based molecular motor featuring pronounced electronic push–pull character and a four-fold increase of the photoisomerization quantum yield in comparison to previous motors of its class. A multidisciplinary approach including synthesis, steady-state and transient absorption spectroscopies, and electronic structure modelling was implemented to elucidate the excited state dynamics and rotary mechanism. We conclude that the charge-transfer character of the excited state diminishes the degree of pyramidalisation at the alkene bond during isomerisation, such that the rotational properties of this oxindole-based motor stand in between the precessional motion of fluorene-based molecular motors and the axial motion of biomimetic photoswitches.

Electronic structure modelling of the edge-functionalisation of graphene by MnxOy particles.

The use of graphenic carbon is attractive as a basal or intermediate support for catalytic particles in advanced catalytic electrodes. This popularity is motivated by its excellent electrical properties and ability to form foliated conformal coatings of exceptional surface area and flexibility. Surface- and edge-functionalisation of graphene sheets affords diverse routes to the covalent attachment of candidate catalytic species. Of particular interest to advanced water oxidation is the possibility of covalent attachment of MnxOy species partially recapitulating the chemistry of the Mn4O5Ca active site of Photosystem II (PSII), which achieves the four-electron oxidation of water under physiological conditions. Here, we report aperiodic density functional theory (DFT) investigations of candidate attachment geometries for a variety of manganese oxide particles to graphene sheets. We find that the flexibility of graphene sheets as well as the conformational degrees of freedom of candidate edge functionalisation permits a large variety of realistic attachment geometries that can act as attachment sites for molecular manganese-oxide species or nuclei for the growth of periodic manganese oxides. We find that substantially simplified models of graphene attachment afford an excellent compromise between computational efficiency, tractability, and accuracy, and characterise the accuracy of these models in detail.

Influence of Electronic Structure Modeling and Junction Structure on First-Principles Chiral Induced Spin Selectivity.

We have carried out a comprehensive study of the influence of electronic structure modeling and junction structure description on the first-principles calculation of the spin polarization in molecular junctions caused by the chiral induced spin selectivity (CISS) effect. We explore the limits and the sensitivity to modeling decisions of a Landauer/Green's function/two-component density functional theory approach to CISS. We find that although the CISS effect is entirely attributed in the literature to molecular spin filtering, spin-orbit coupling being partially inherited from the metal electrodes plays an important role in our calculations on ideal carbon helices, even though this effect cannot explain the experimental conductance results. Its magnitude depends considerably on the shape, size, and material of the metal clusters modeling the electrodes. Also, a pronounced dependence on the specific description of exchange interaction and spin-orbit coupling is manifest in our approach. This is important because the interplay between exchange effects and spin-orbit coupling may play an important role in the description of the junction magnetic response. Our calculations are relevant for the whole field of spin-polarized electron transport and electron transfer, because there is still an open discussion in the literature about the detailed underlying mechanism and the magnitude of physical parameters that need to be included to achieve a consistent description of the CISS effect: seemingly good quantitative agreement between simulation and the experiment can be caused by error compensation, because spin polarization as contained in a Landauer/Green's function/two-component density functional theory approach depends strongly on computational and structural parameters.

Locality of interatomic forces in tight binding models for insulators

The tight binding model is a minimalistic electronic structure model for predicting properties of materials and molecules. For insulators at zero Fermi-temperature we show that the potential energy surface of this model can be decomposed into exponentially localised site energy contributions, thus providing qualitatively sharp estimates on the interatomic interaction range which justifies a range of multi-scale models. For insulators at finite Fermi-temperature we obtain locality estimates that are uniform in the zero-temperature limit. A particular feature of all our results is that they depend only weakly on the point spectrum. Numerical tests confirm our analytical results. This work extends Chen and Ortner [Multiscale Model. Simul. 14 (2016) 232–264] and Chen et al. [Arch. Ration. Mech. Anal. 230 (2018) 701–733] to the case of zero Fermi-temperature as well as strengthening the results proved therein.

Interplay of electron correlations, spin-orbit couplings, and structural effects for Cu centers in the quasi-two-dimensional magnet InCu2/3V1/3O3

Less common ligand coordination of transition-metal centers is often associated with peculiar valence-shell electron configurations and outstanding physical properties. One example is the Fe$^+$ ion with linear coordination, actively investigated in the research area of single-molecule magnetism. Here we address the nature of 3$d^9$ states for Cu$^{2+}$ ions sitting in the center of trigonal bipyramidal ligand cages in the quasi-two-dimensional honeycomb compound InCu$_{2/3}$V$_{1/3}$O$_3$, whose unusual magnetic properties were intensively studied in the recent past. In particular, we discuss the interplay of structural effects, electron correlations, and spin-orbit couplings in this material. A relevant computational finding is a different sequence of the Cu ($xz$, $yz$) and ($xy$, $x^2\!-\!y^2$) levels as compared to existing electronic-structure models, which has implications for the interpretation of various excitation spectra. Spin-orbit interactions, both first- and second-order, turn out to be stronger than previously assumed, suggesting that rather rich single-ion magnetic properties can be in principle achieved also for the 3$d^9$ configuration by properly adjusting the sequence of crystal-field states for such less usual ligand coordination.

Theory-Guided Machine Learning Finds Geometric Structure-Property Relationships for Chemisorption on Subsurface Alloys

Summary Developing physically transparent and quantitatively accurate models that relate the chemical interaction (chemisorption strength) between an adsorbate and a solid surface to the adsorption site's geometry is critical for our understanding of catalysis, corrosion, and electrochemistry. We develop a theory-guided machine-learning (ML) approach, which uses an interpretable class of ML models called generalized additive models (iGAM models), to discover predictive structure-property models that can quantify and explain the link between the geometric structure of an adsorption site and the chemisorption strength. We demonstrate the approach through several case studies, where we analyze the chemisorption strength of chemically distinct adsorbates (O, OH, S, and Cl) on subsurface metal alloy surfaces subjected to various strain- and ligand-induced changes in the local geometric structure. By comparing the ML-derived chemisorption models to previously established electronic-structure models, we clarify the critical physical parameters that control the chemisorption process on metal surfaces.