Developing correlation-consistent numeric atom-centered orbital basis sets for krypton: Applications in RPA-based correlated calculations.

Localized atomic orbitals are the preferred basis set choice for large-scale explicit correlated calculations, and high-quality hierarchical correlation-consistent basis sets are a prerequisite for correlated methods to deliver numerically reliable results. At present, numeric atom-centered orbital (NAO) basis sets with valence correlation consistency (VCC), designated as NAO-VCC-nZ, are only available for light elements from hydrogen (H) to argon (Ar) [Zhang et al., New J. Phys. 15, 123033 (2013)]. In this work, we extend this series by developing NAO-VCC-nZ basis sets for krypton (Kr), a prototypical element in the fourth row of the periodic table. We demonstrate that NAO-VCC-nZ basis sets facilitate the convergence of electronic total-energy calculations using the Random Phase Approximation (RPA), which can be used together with a two-point extrapolation scheme to approach the complete basis set limit. Notably, the Basis Set Superposition Error (BSSE) associated with the newly generated NAO basis sets is minimal, making them suitable for applications where BSSE correction is either cumbersome or impractical to do. After confirming the reliability of NAO basis sets for Kr, we proceed to calculate the Helmholtz free energy for Kr crystal at the theoretical level of RPA plus renormalized single excitation correction. From this, we derive the pressure-volume (P-V) diagram, which shows excellent agreement with the latest experimental data. Our work demonstrates the capability of correlation-consistent NAO basis sets for heavy elements, paving the way toward numerically reliable correlated calculations for bulk materials.

Basis-Set-Error-Free Random-Phase Approximation Correlation Energies for Atoms Based on the Sternheimer Equation.

The finite basis set errors for all-electron random-phase approximation (RPA) correlation energy calculations are analyzed for isolated atomic systems. We show that, within the resolution-of-identity (RI) RPA framework, the major source of the basis set errors is the incompleteness of the single-particle atomic orbitals used to expand the Kohn-Sham eigenstates, instead of the auxiliary basis set (ABS) to represent the density response function χ0 and the bare Coulomb operator v. By solving the Sternheimer equation for the first-order wave function on a dense radial grid, we are able to eliminate the major error─the incompleteness error of the single-particle atomic basis set─for atomic RPA calculations. The error stemming from a finite ABS can be readily rendered vanishingly small by increasing the size of the ABS, or by iteratively determining the eigenmodes of the χ0v operator. The variational property of the RI-RPA correlation energy can be further exploited to optimize the ABS in order to achieve fast convergence of the RI-RPA correlation energy. These numerical techniques enable us to obtain basis-set-error-free RPA correlation energies for atoms, and in this work, such energies for atoms from H to Kr are presented. The implications of the numerical techniques developed in the present work for addressing the basis set issue for molecules and solids are discussed.

Implementation of the meta-GGA exchange-correlation functional in numerical atomic orbital basis: With systematic testing on SCAN, rSCAN, and r2SCAN functionals.

Kohn-Sham density functional theory (DFT) is nowadays widely used for electronic structure theory simulations, and the accuracy and efficiency of DFT rely on approximations of the exchange-correlation functional. By including the kinetic energy density τ, the meta-generalized-gradient approximation (meta-GGA) family of functionals achieves better accuracy and flexibility while retaining the efficiency of semi-local functionals. For example, the strongly constrained and appropriately normed (SCAN) meta-GGA functional has been proven to yield accurate results for solid and molecular systems. We implement meta-GGA functionals with both numerical atomic orbitals and plane wave bases in the ABACUS package. Apart from the exchange-correlation potential, we also discuss the evaluation of force and stress. To validate our implementation, we perform finite-difference tests and convergence tests with the SCAN, rSCAN, and r2SCAN meta-GGA functionals. We further test water hexamers, weakly interacting molecules from the S22 dataset, as well as 13 semiconductors using the three functionals. The results show satisfactory agreement with previous calculations and available experimental values.

Tunable Interband Transitions in Twisted h-BN/Graphene Heterostructures.

In twisted h-BN/graphene heterostructures, the complex electronic properties of the fast-traveling electron gas in graphene are usually considered to be fully revealed. However, the randomly twisted heterostructures may also have unexpected transition behaviors, which may influence the device performance. Here, we study the twist-angle-dependent coupling effects of h-BN/graphene heterostructures using monochromatic electron energy loss spectroscopy. We find that the moiré potentials alter the band structure of graphene, resulting in a redshift of the intralayer transition at the M point, which becomes more pronounced up to 0.22 eV with increasing twist angle. Furthermore, the twisting of the Brillouin zone of h-BN relative to the graphene M point leads to tunable vertical transition energies in the range of 5.1-5.6 eV. Our findings indicate that twist-coupling effects of van der Waals heterostructures should be carefully considered in device fabrications, and the continuously tunable interband transitions through the twist angle can serve as a new degree of freedom to design optoelectrical devices.

Preferential decomposition of the major anion in a dual-salt electrolyte facilitates the formation of organic-inorganic composite solid electrolyte interphase.

The performance of a lithium metal battery (LMB) with liquid electrolytes depends on the realization of a stable solid electrolyte interphase (SEI) on the Li anode surface. According to a recent experiment, a high-concentrated (HC) dual-salt electrolyte is effective in modulating the SEI formation and improving the battery performance. However, the underlying reaction mechanism between this HC dual-salt electrolyte and the lithium metal anode surface remains unknown. To understand the SEI formation mechanism, we first performed 95 ps ab initio Molecular Dynamics (AIMD) simulation and then extend this AIMD simulation to another 1 ns by using Hybrid ab Initio and Reactive Molecular Dynamics (HAIR) to investigate the deep reactions of such dual-salt electrolytes consists of lithium difluorophosphate and lithium bis(trifluoromethanesulfonyl)imide in dimethoxyethane (DME) solvent at lithium metal anode surface. We observed the detailed reductive decomposition processes of DFP- and TFSI-, which include the formation pathway of CF3 fragments, LiF, and LixPOFy, the three main SEI components observed experimentally. Furthermore, after extending the simulation to 1.1 ns via the HAIR scheme, the decomposition reactions of DME solvent molecules were also observed, producing LiOCH3, C2H4, and precursors of organic oligomers. These microscopic insights provide important guidance in designing the advanced dual-salt electrolytes for developing high-performance LMB.

Vertex effects in describing the ionization energies of the first-row transition-metal monoxide molecules.

The GW approximation is considered to be the simplest approximation within Hedin's formulation of many-body perturbation theory. It is expected that some of the deficiencies of the GW approximation can be overcome by adding the so-called vertex corrections. In this work, the recently implemented G0W0Γ0 (1) scheme, which incorporates the vertex effects by adding the full second-order self-energy correction to the GW self-energy, is applied to a set of first-row transition-metal monoxide (TMO) anions. Benchmark calculations show that results obtained by G0W0Γ0 (1) on top of the B3LYP hybrid functional starting point (SP) are in good agreement with experiment data, giving a mean absolute error of 0.13 eV for a testset comprising the ionization energies (IEs) of 27 outer valence molecular orbitals (MOs) from nine TMO anions. A systematic SP-dependence investigation by varying the ratio of the exact exchange (EXX) component in the PBE0-type SP reveals that, for G0W0Γ0 (1), the best accuracy is achieved with 20% EXX. Further error analysis in terms of the orbital symmetry characteristics (i.e., σ, π, or δ) in the testset indicates the best amount of EXX in the SP for G0W0Γ0 (1) calculations is independent of MO types, and this is in contrast with the situation in G0W0 calculations, where the best EXX ratio varies for different classes of MOs. Despite its success in describing the absolute IE values, we, however, found that G0W0Γ0 (1) faces difficulties in describing the energy separations between certain states of interest, worsening the already underestimated G0W0 predictions.

Localized Resolution of Identity Approach to the Analytical Gradients of Random-Phase Approximation Ground-State Energy: Algorithm and Benchmarks.

We develop and implement a formalism which enables calculating the analytical gradients of particle-hole random-phase approximation (RPA) ground-state energy with respect to the atomic positions within the atomic orbital basis set framework. Our approach is based on a localized resolution of identity (LRI) approximation for evaluating the two-electron Coulomb integrals and their derivatives, and the density functional perturbation theory for computing the first-order derivatives of the Kohn-Sham (KS) orbitals and orbital energies. Our implementation allows one to relax molecular structures at the RPA level using both Gaussian-type orbitals (GTOs) and numerical atomic orbitals (NAOs). Benchmark calculations against previous implementations show that our approach delivers adequate numerical precision, highlighting the usefulness of LRI in the context of RPA gradient evaluations. A careful assessment of the quality of RPA geometries for small molecules reveals that post-KS RPA systematically overestimates the bond lengths. We furthermore optimized the geometries of the four low-lying water hexamers-cage, prism, cyclic, and book isomers, and determined the energy hierarchy of these four isomers using RPA. The obtained RPA energy ordering is in good agreement with that yielded by the coupled cluster method with single, double and perturbative triple excitations, despite that the dissociation energies themselves are appreciably underestimated. The underestimation of the dissociation energies by RPA is well corrected by the renormalized single excitation correction.

Reproducibility of Hybrid Density Functional Calculations for Equation-of-State Properties and Band Gaps.

Hybrid density functional (HDF) approximations usually deliver higher accuracy than local and semilocal approximations to the exchange-correlation functional, but this comes with drastically increased computational cost. Practical implementations of HDFs inevitably involve numerical approximations─even more so than their local and semilocal counterparts due to the additional numerical complexity arising from treating the exact-exchange component. This raises the question regarding the reproducibility of the HDF results yielded by different implementations. In this work, we benchmark the numerical precision of four independent implementations of the popular Heyd-Scuseria-Ernzerhof (HSE) range-separated HDF on describing key materials' properties, including both properties derived from equations of state (EOS) and band gaps of 20 crystalline solids. We find that the energy band gaps obtained by the four codes agree with each other rather satisfactorily. However, for lattice constants and bulk moduli, the deviations between the results computed by different codes are of the same order of magnitude as the deviations between the computational and experimental results. On the one hand, this means that the HSE functional is rather accurate for describing the cohesive properties of simple insulating solids. On the other hand, this also suggests that the numerical precision achieved with current major HSE implementations is not sufficiently high to unambiguously assess the physical accuracy of HDFs. It is found that the pseudopotential treatment of the core electrons is a major factor that contributes to this uncertainty.

Density Functional Theory Plus Dynamical Mean Field Theory within the Framework of Linear Combination of Numerical Atomic Orbitals: Formulation and Benchmarks.

The combination of density functional theory with dynamical mean-field theory (DFT+DMFT) has become a powerful first-principles approach to tackle strongly correlated materials in condensed matter physics. The wide use of this approach relies on robust and easy-to-use implementations, and its implementation in various numerical frameworks will increase its applicability on the one hand and help crosscheck the validity of the obtained results on the other. In this work, we develop a formalism within the linear combination of numerical atomic orbital (NAO) basis set framework, which allows for merging of NAO-based DFT codes with DMFT quantum impurity solvers. The formalism is implemented by interfacing two NAO-based DFT codes with three DMFT impurity solvers, and its validity is testified by benchmark calculations for a wide range of strongly correlated materials, including 3d transition metal compounds, lanthanides, and actinides. Our work not only enables DFT+DMFT calculations using popular and rapidly developing NAO-based DFT code packages but also facilitates the combination of more advanced beyond-DFT methodologies available in these codes with the DMFT machinery.

DFT+U within the framework of linear combination of numerical atomic orbitals.

We present a formulation and implementation of the density functional theory (DFT)+U method within the framework of linear combination of numerical atomic orbitals (NAO). Our implementation not only enables single-point total energy and electronic-structure calculations but also provides access to atomic forces and cell stresses, hence allowing for full structure relaxations of periodic systems. Furthermore, our implementation allows one to deal with non-collinear spin texture, with the spin-orbit coupling (SOC) effect treated self-consistently. The key aspect behind our implementation is a suitable definition of the correlated subspace when multiple atomic orbitals with the same angular momentum are used, and this is addressed via the "Mulliken charge projector" constructed in terms of the first (most localized) atomic orbital within the d/f angular momentum channel. The important Hubbard U and Hund J parameters can be estimated from a screened Coulomb potential of the Yukawa type, with the screening parameter either chosen semi-empirically or determined from the Thomas-Fermi screening model. Benchmark calculations are performed for four late transition metal monoxide bulk systems, i.e., MnO, FeO, CoO, and NiO, and for the 5d-electron compounds IrO2. For the former type of systems, we check the performance of our DFT+U implementation for calculating bandgaps, magnetic moments, electronic band structures, as well as forces and stresses; for the latter, the efficacy of our DFT+U+SOC implementation is assessed. Systematic comparisons with available experimental results, especially with the results from other implementation schemes, are carried out, which demonstrate the validity of our NAO-based DFT+U formalism and implementation.

Real-Time, Time-Dependent Density Functional Theory Study on Photoinduced Isomerizations of Azobenzene Under a Light Field.

The trans to cis photoisomerization of azobenzene and its reverse (i.e., the cis to trans) processes are studied using real-time propagation time-dependent density functional theory combined with molecular dynamics for ions. We show that the wavelength of the applied laser may significantly affect the transition process. The simulations also show that the photon-excited electrons play essential roles in the isomerization processes, in which the hot electrons couple to phonon modes that drive the transitions.

Effect of depression and suicidal behavior on neuropeptide Y (NPY) and its receptors in the adult human brain: A postmortem study.

Neuropeptides are small proteinaceous molecules (3-100 amino acids) that are secreted by neurons and act on both neuronal and non-neuronal cells. Neuropeptide Y (NPY), a highly conserved and expressed neuropeptide in the central nervous system of mammals, plays a major role in stress response and resilience. Increasing evidence suggests that NPY and its receptors are altered in depression and suicide, pointing to their antidepressant-like nature. The objective of this study was to examine the role of NPY system in depression and suicidal behavior. Expression of NPY and its four receptors, NPY1R, NPY2R, NPY4R, and NPY5R was studied at the transcriptional and translational levels in the prefrontal cortex (PFC) and hippocampus regions of the postmortem brain of normal control (NC) (n = 24) and depressed suicide (DS) (n = 24) subjects. We observed a significant decrease in NPY mRNA and upregulation in NPY1R and NPY2R mRNA in both brain regions of DS subjects compared with NC subjects. We also observed a significant decrease in NPY protein expression in the PFC of subjects with DS. This study provides the first detailed evidence of alterations in the NPY system and the associated stress response in depression and suicidal behavior in humans. The outcomes of this study could be applied in the development of novel NPY system-targeted approaches for the treatment of depression.

Inflammation, depressive symptoms, and emotion perception in adolescence.

BACKGROUND: Individuals with depression often demonstrate an altered peripheral inflammatory profile, as well as emotion perception difficulties. However, correlations of inflammation with overall depression severity are inconsistent and inflammation may only contribute to specific symptoms. Moreover, measurement of the association between inflammation and emotion perception is sparse in adolescence, despite representing a formative window of emotional development and high-risk period for depression onset. METHODS: Serum interleukin (IL)-6, tumor necrosis factor (TNF)-α, and IL-1ß were measured in 34 adolescents aged 12-17 with DSM-IV depressive disorders (DEP) and 29 healthy controls (HC). Participants were evaluated using the Children's Depression Rating Scale-Revised (CDRS-R) and symptom subscales were extracted based on factor analysis. Participants also completed a performance-based measure of emotion perception, the Facial Emotion Perception Test (FEPT), which assesses the accuracy of categorizing angry, fearful, sad, happy, and neutral facial emotions. RESULTS: IL-6 and TNF-α correlated with reported depressed mood and somatic symptoms, respectively, but not total CDRS-R score, anhedonia or observed mood, across both DEP and HC. DEP demonstrated lower accuracy for identifying angry facial expressions. Higher IL-6 was inversely related to accuracy and discrimination of angry and neutral faces across all participants. IL-1ß was associated with reduced discrimination of fearful faces. CONCLUSIONS: Inflammatory markers were sensitive to affective and somatic symptoms of depression and processing of emotional threat in adolescents. In particular, IL-6 was elevated in depressed adolescents and therefore may represent a specific target for modulating depressive symptoms and emotion processing.

Innate immunity receptors in depression and suicide: upregulated NOD-like receptors containing pyrin (NLRPs) and hyperactive inflammasomes in the postmortem brains of people who were depressed and died by suicide.

BACKGROUND: Abnormalities of inflammation have been implicated in the pathophysiology of depression and suicide, based on observations of increased levels of proinflammatory cytokines in the serum of people who were depressed and died by suicide. More recently, abnormalities in cytokines and innate immunity receptors such as toll-like receptors have also been observed in the postmortem brains of people who were depressed and died by suicide. In addition to toll-like receptors, another subfamily of innate immunity receptors known as NOD-like receptors containing pyrin (NLRPs) are the most widely present NOD-like receptors in the central nervous system. NLRPs also form inflammasomes that play an important role in brain function. We studied the role of NLRPs in depression and suicide. METHODS: We determined the protein and mRNA expression of NLRP1, NLRP3 and NLRP6 and the components of their inflammasomes (i.e., adaptor molecule apoptosis-associated speck-like protein [ASC], caspase1, caspase3, interleukin [IL]-1ß and IL-18) postmortem in the prefrontal cortex of people who were depressed and died by suicide, and in healthy controls. We determined mRNA levels using quantitative polymerase chain reaction, and we determined protein expression using Western blot immunolabelling. RESULTS: We found that the protein and mRNA expression levels of NLRP1, NLRP3, NLRP6, caspase3 and ASC were significantly increased in people who were depressed and died by suicide compared to healthy controls. LIMITATIONS: Some people who were depressed and died by suicide were taking antidepressant medication at the time of their death. CONCLUSION: Similar to toll-like receptors, NLRP and its inflammasomes were upregulated in people who were depressed and died by suicide compared to healthy controls. Innate immunity receptors in general - and NLRPs and inflammasomes in particular - may play an important role in the pathophysiology of depression and suicide.

Assessing the G0W0Γ0(1) Approach: Beyond G0W0 with Hedin's Full Second-Order Self-Energy Contribution.

We present and benchmark a self-energy approach for quasiparticle energy calculations that goes beyond Hedin's GW approximation by adding the full second-order self-energy (FSOS-W) contribution. The FSOS-W diagram involves two screened Coulomb interaction (W) lines, and adding the FSOS-W to the GW self-energy can be interpreted as first-order vertex correction to GW (GWΓ(1)). Our FSOS-W implementation is based on the resolution-of-identity technique and exhibits better than O(N5) scaling with system size for small- to medium-sized molecules. We then present one-shot GWΓ(1) (G0W0Γ0(1)) benchmarks for the GW100 test set and a set of 24 acceptor molecules. For semilocal or hybrid density functional theory starting points, G0W0Γ0(1) systematically outperforms G0W0 for the first vertical ionization potentials and electron affinities of both test sets. Finally, we demonstrate that a static FSOS-W self-energy significantly underestimates the quasiparticle energies.

First-principles study of benzo[a]pyrene-7,8-dione and DNA adducts.

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in environments, and some of them are causative agents of human cancer. Previous studies concluded that benzo[a]pyrene-7,8-dione (BPQ), which is one kind of carcinogenic PAH metabolites, forms covalently bonded adducts with DNA, and the major adduct formed is a deoxyguanosine adduct. In this work, we investigate the interactions between BPQ and DNA molecules via first-principles calculations. We identify six possible DNA adducts with BPQ. In addition to the four adducts forming covalent bonds, there are two adducts bound purely by van der Waals (vdW) interactions. Remarkably, the two vdW-bound adducts have comparable, if not larger, binding energies as the covalent adducts. The results may help us gain more understanding of the interactions between PAH metabolites and DNA.

Real-time GW-BSE investigations on spin-valley exciton dynamics in monolayer transition metal dichalcogenide.

We develop an ab initio nonadiabatic molecular dynamics (NAMD) method based on GW plus real-time Bethe-Salpeter equation (GW + rtBSE-NAMD) for the spin-resolved exciton dynamics. From investigations on MoS2, we provide a comprehensive picture of spin-valley exciton dynamics where the electron-phonon (e-ph) scattering, spin-orbit interaction (SOI), and electron-hole (e-h) interactions come into play collectively. In particular, we provide a direct evidence that e-h exchange interaction plays a dominant role in the fast valley depolarization within a few picoseconds, which is in excellent agreement with experiments. Moreover, there are bright-to-dark exciton transitions induced by e-ph scattering and SOI. Our study proves that e-h many-body effects are essential to understand the spin-valley exciton dynamics in transition metal dichalcogenides and the newly developed GW + rtBSE-NAMD method provides a powerful tool for exciton dynamics in extended systems with time, space, momentum, energy, and spin resolution.

Self-Interaction-Corrected Random Phase Approximation.

The short-range correlation energy of the random phase approximation (RPA) is too negative and is often corrected by local or nonlocal methods. These beyond-RPA corrections usually lead to a mixed performance for thermodynamics and dissociation properties. RPA+ is an additive correction based on density functional approximations that often gives realistic total energies for atoms or solids. RPA+ adds a moderate correction to the ionization energies/electron affinities of RPA but does not yield an improvement beyond RPA for atomization energies of molecules. This incompleteness results in severely underestimated atomization energies just like in RPA. Exchange-correlation kernels within the Dyson equation could simultaneously improve atomization, ionization energies, and electron affinities, but their implementation is computationally less feasible in localized basis set codes. In preceding work ( Phys. Rev. A 100, 2019022515), two of the authors proposed a computationally efficient generalized RPA+ (gRPA+) that changes RPA+ only for spin-polarized systems by making gRPA+ exact for all one-electron densities. gRPA+ was found to yield a large improvement of ionization energies and electron affinities of light atoms over RPA, and a smaller improvement over RPA+. Within this work, we investigate to what extent this improvement transfers to atomization energies, ionization energies, and electron affinities of molecules, using a modified gRPA+ (mgRPA+) method that can be applied in codes with localized basis functions. We thereby aim to understand the applicability of beyond-RPA corrections based on density functional approximations.

Beryllium and Magnesium Metal Clusters: New Globally Stable Structures and G0W0 Calculations.

We study the structural and electronic properties of beryllium (Be) and magnesium (Mg) clusters for sizes 2-20 using a two-step approach. In the first step, a global search of the stable and low-lying metastable isomer structures is carried out on the basis of first-principles potential energy surfaces at the level of the generalized gradient approximation (GGA) of density functional theory (DFT). In the second step, vertical ionization potentials (VIPs) and energy gaps between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are determined using the G0W0 methods for up to the fourth-lowest-energy isomers. Novel globally lowest-energy isomer structures are identified for Be14, Mg14, and Mg16 clusters. The van der Waals interactions are found to have a stronger influence on Mg clusters than on Be clusters. A second-difference analysis for both the binding energies and HOMO-LUMO gaps reveals a close relationship between the structural stability and chemical hardness for both types of clusters.

Dysregulation of Protein Kinase C in Adult Depression and Suicide: Evidence From Postmortem Brain Studies.

BACKGROUND: Several lines of evidence suggest the abnormalities of protein kinase C (PKC) signaling system in mood disorders and suicide based primarily on the studies of PKC and its isozymes in the platelets and postmortem brain of depressed and suicidal subjects. In this study, we examined the role of PKC isozymes in depression and suicide. METHODS: We determined the protein and mRNA expression of various PKC isozymes in the prefrontal cortical region (Brodmann area 9) in 24 normal control subjects, 24 depressed suicide (DS) subjects, and 12 depressed nonsuicide (DNS) subjects. The levels of mRNA in the prefrontal cortex were determined by quantitative real-time reverse transcription PCR, and the protein expression was determined by western blotting. RESULTS: We observed a significant decrease in mRNA expression of PKCα, PKCßI, PKCδ, and PKCε and decreased protein expression in either the membrane or the cytosol fraction of PKC isozymes PKCα, PKCßI, PKCßII, and PKCδ in DS and DNS subjects compared with normal control subjects. CONCLUSIONS: The current study provides detailed evidence of specific dysregulation of certain PKC isozymes in the postmortem brain of DS and DNS subjects and further supports earlier evidence for the role of PKC in the platelets and brain of the adult and teenage depressed and suicidal population. This comprehensive study may lead to further knowledge of the involvement of PKC in the pathophysiology of depression and suicide.