Optical properties and exciton transfer between N-heterocyclic carbene iridium(III) complexes for blue light-emitting diode applications from first principles.

N-heterocyclic carbene (NHC) iridium(III) complexes are considered as promising candidates for blue emitters in organic light-emitting diodes. They can play the roles of the emitter as well as of electron and hole transporters in the same emission layer. We investigate optical transitions in such complexes with account of geometry and electronic structure changes upon excitation or charging and exciton transfer between the complexes from first principles. It is shown that excitation of NHC iridium complexes is accompanied by a large reorganization energy ∼0.7 eV and a significant loss in the oscillator strength, which should lead to low exciton diffusion. Calculations with account of spin-orbit coupling reveal a small singlet-triplet splitting ∼0.1 eV, whereas the oscillator strength for triplet excitations is found to be an order of magnitude smaller than for the singlet ones. The contributions of the Förster and Dexter mechanisms are analyzed via the explicit integration of transition densities. It is shown that for typical distances between emitter complexes in the emission layer, the contribution of the Dexter mechanism should be negligible compared to the Förster mechanism. At the same time, the ideal dipole approximation, although giving the correct order of the exciton coupling, fails to reproduce the result taking into account spatial distribution of the transition density. For charged NHC complexes, we find a number of optical transitions close to the emission peak of the blue emitter with high exciton transfer rates that can be responsible for exciton-polaron quenching. The nature of these transitions is analyzed.

Precise graphene cutting using a catalyst at a probe tip under an electron beam.

The method of precise cutting of 2D materials by simultaneous action of a catalyst at the tip of the scanning microscope probe and an electron beam in a high-resolution transmission electron microscope is proposed and studied using atomistic simulations by the example of graphene and a nickel catalyst. Reactive molecular dynamics simulations within the Compu-TEM approach for the description of electron impact effects show that the combination of the nickel catalyst and electron irradiation is crucial for graphene cutting. Cuts with straight edges with widths of about 1-1.5 nm can be obtained. The detailed atomistic mechanism of graphene cutting is investigated via the analysis of statistics on atom ejection and bond reorganization reactions induced by the irradiation. The principal and secondary channels of atom ejection which lead to propagation of the cut are shown to be ejection of two-coordinated atoms at the cut edges bonded to the nickel tip and three-coordinated atoms from the defective graphene structure near the tip. At the same time, the ejection of two-coordinated atoms not bonded to the tip and atoms in chains at the cut edges favors smoothing of free cut edges behind the tip. A considerable difference from the atomistic mechanism of cutting a carbon nanotube via the simultaneous action of electron irradiation and nickel catalyst is discussed. The ab initio calculations performed show a decrease of the binding energy of two-coordinated carbon atoms bonded to the nickel cluster in comparison with the same cut edge in the absence of the cluster confirming that the principal channel of atom ejection is related to the cut propagation.

Formation of carbon propeller-like molecules from starphenes under electron irradiation.

Formation of carbon propeller-like molecules (CPLMs) from starphenes on a graphene substrate under electron irradiation with about 100% yield is observed in molecular dynamics simulations using the REBO-1990EVC_CH potential and CompuTEM algorithm. A CPLM consists of three carbon atomic chains connected to the central hexagon and is formed as a result of the spontaneous breaking of bonds between zigzag atomic rows in starphene arms after hydrogen removal by electron impacts. In the absence of the substrate, the CPLM yield is slightly decreased due to sticking between forming chains, while the formation time is increased threefold. The increase of the kinetic electron energy from 45 to 80 keV has no effect on the CPLM formation. Density functional theory (DFT) calculations performed show the stability of CPLMs with respect to the formation of new bonds between carbon atoms in the chains. DFT calculations using the accurate hybrid B3LYP functional provide an insight into the electronic structure of these new molecules.

Transformation of a graphene nanoribbon into a hybrid 1D nanoobject with alternating double chains and polycyclic regions.

Molecular dynamics simulations show that a graphene nanoribbon with alternating regions which are one and three hexagons wide can transform into a hybrid 1D nanoobject with alternating double chains and polycyclic regions under electron irradiation in HRTEM. A scheme of synthesis of such a nanoribbon using Ullmann coupling and dehydrogenation reactions is proposed. The reactive REBO-1990EVC potential is adapted for simulations of carbon-hydrogen systems and is used in combination with the CompuTEM algorithm for modeling of electron irradiation effects. The atomistic mechanism of formation of the new hybrid 1D nanoobject is found to be the following. Firstly hydrogen is removed by electron impacts. Then spontaneous breaking of bonds between carbon atoms leads to the decomposition of narrow regions of the graphene nanoribbon into double chains. Simultaneously, thermally activated growth of polycyclic regions occurs. Density functional theory calculations give barriers along the growth path of polycyclic regions consistent with this mechanism. The electronic properties of the new 1D nanoobject are shown to be strongly affected by the edge magnetism and make this nanostructure promising for nanoelectronic and spintronic applications. The synthesis of the 1D nanoobject proposed here can be considered as an example of the general three-stage strategy of production of nanoobjects and macromolecules: (1) precursors are synthesized using a traditional chemical method, (2) precursors are placed in HRTEM with the electron energy that is sufficient only to remove hydrogen atoms, and (3) as a result of hydrogen removal, the precursors become unstable or metastable and transform into new nanoobjects or macromolecules.

Two Phases with Different Domain Wall Networks and a Reentrant Phase Transition in Bilayer Graphene under Strain.

The analytical two-chain Frenkel-Kontorova model is used to describe domain wall networks in bilayer graphene upon biaxial stretching of one of the layers. We show that the commensurate-incommensurate phase transition leading to formation of a regular triangular domain wall network at the relative biaxial elongation of 3.0×10^{-3} is followed by the transition to another incommensurate phase with a striped network at the elongation of 3.7×10^{-3}. The reentrant transition to the phase with a triangular domain wall network is predicted for the elongation ∼10^{-2}.

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems.

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

The CECAM electronic structure library and the modular software development paradigm.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.

Formation of Nickel Clusters Wrapped in Carbon Cages: Toward New Endohedral Metallofullerene Synthesis.

Despite the high potential of endohedral metallofullerenes (EMFs) for application in biology, medicine and molecular electronics, and recent efforts in EMF synthesis, the variety of EMFs accessible by conventional synthetic methods remains limited and does not include, for example, EMFs of late transition metals. We propose a method in which EMF formation is initiated by electron irradiation in aberration-corrected high-resolution transmission electron spectroscopy (AC-HRTEM) of a metal cluster surrounded by amorphous carbon inside a carbon nanotube serving as a nanoreactor and apply this method for synthesis of nickel EMFs. The use of AC-HRTEM makes it possible not only to synthesize new, previously unattainable nanoobjects but also to study in situ the mechanism of structural transformations. Molecular dynamics simulations using the state-of-the-art approach for modeling the effect of electron irradiation are performed to rationalize the experimental observations and to link the observed processes with conditions of bulk EMF synthesis.

Energetics of atomic scale structure changes in graphene.

The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required.

Ab initio study of edge effect on relative motion of walls in carbon nanotubes.

Interwall interaction energies of double-walled nanotubes with long inner and short outer walls are calculated as functions of coordinates describing relative rotation and displacement of the walls using van der Waals corrected density functional theory. The magnitude of corrugation and the shape of the potential energy relief are found to be very sensitive to changes of the shorter wall length at subnanometer scale and atomic structure of the edges if at least one of the walls is chiral. Threshold forces required to start relative motion of the short walls and temperatures at which the transition between diffusive and free motion of the short walls takes place are estimated. The edges are also shown to provide a considerable contribution to the barrier to relative rotation of commensurate nonchiral walls. For such walls, temperatures of orientational melting, i.e., the crossover from rotational diffusion to free relative rotation, are estimated. The possibility to produce nanotube-based bolt∕nut pairs and nanobearings is discussed.

AA stacking, tribological and electronic properties of double-layer graphene with krypton spacer.

Structural, energetic, and tribological characteristics of double-layer graphene with commensurate and incommensurate krypton spacers of nearly monolayer coverage are studied within the van der Waals-corrected density functional theory. It is shown that when the spacer is in the commensurate phase, the graphene layers have the AA stacking. For this phase, the barriers to relative in-plane translational and rotational motion and the shear mode frequency of the graphene layers are calculated. For the incommensurate phase, both of the barriers are found to be negligibly small. A considerable change of tunneling conductance between the graphene layers separated by the commensurate krypton spacer at their relative subangstrom displacement is revealed by the use of the Bardeen method. The possibility of nanoelectromechanical systems based on the studied tribological and electronic properties of the considered heterostructures is discussed.

Modular implementation of the linear- and cubic-scaling orbital minimization methods in electronic structure codes using atomic orbitals.

We present a code modularization approach to design efficient and massively parallel cubic- and linear-scaling solvers for electronic structure calculations using atomic orbitals. The modular implementation of the orbital minimization method, in which linear algebra and parallelization issues are handled via external libraries, is demonstrated in the SIESTA code. The distributed block compressed sparse row (DBCSR) and scalable linear algebra package (ScaLAPACK) libraries are used for algebraic operations with sparse and dense matrices, respectively. The MatrixSwitch and libOMM libraries, recently developed within the Electronic Structure Library, facilitate switching between different matrix formats and implement the energy minimization. We show results comparing the performance of several cubic-scaling algorithms, and also demonstrate the parallel performance of the linear-scaling solvers, and their supremacy over the cubic-scaling solvers for insulating systems with sizes of several hundreds of atoms.

Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies.

Human monoclonal antibodies (mAbs) that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been isolated from convalescent individuals and developed into therapeutics for SARS-CoV-2 infection. However, therapeutic mAbs for SARS-CoV-2 have been rendered obsolete by the emergence of mAb-resistant virus variants. Here we report the generation of a set of six human mAbs that bind the human angiotensin-converting enzyme-2 (hACE2) receptor, rather than the SARS-CoV-2 spike protein. We show that these antibodies block infection by all hACE2 binding sarbecoviruses tested, including SARS-CoV-2 ancestral, Delta and Omicron variants at concentrations of ~7-100 ng ml-1. These antibodies target an hACE2 epitope that binds to the SARS-CoV-2 spike, but they do not inhibit hACE2 enzymatic activity nor do they induce cell-surface depletion of hACE2. They have favourable pharmacology, protect hACE2 knock-in mice against SARS-CoV-2 infection and should present a high genetic barrier to the acquisition of resistance. These antibodies should be useful prophylactic and treatment agents against any current or future SARS-CoV-2 variants and might be useful to treat infection with any hACE2-binding sarbecoviruses that emerge in the future.

Reconstruction of Zigzag Graphene Edges: Energetics, Kinetics, and Residual Defects.

Ab initio calculations are performed to study consecutive reconstruction of a zigzag graphene edge. According to the obtained energy profile along the reaction pathway, the first reconstruction step, formation of the first pentagon-heptagon pair, is the slowest one, while the growth of an already nucleated reconstructed edge domain should occur steadily at a much higher rate. Domains merge into one only in 1/4 of cases when they get in contact, while in the rest of the cases, residual defects are left. Structure, energy, and magnetic properties of these defects are studied. It is found that spontaneous formation of pairs of residual defects (i.e., spontaneous domain nucleation) in the fully reconstructed edge is unlikely at temperatures below 1000 K. Using a kinetic model, we show that the average domain length is several micrometers at room temperature and it decreases exponentially upon increasing the temperature at which the reconstruction takes place.

Interlayer interaction and relative vibrations of bilayer graphene.

The van der Waals corrected first-principles approach (DFT-D) is for the first time applied for investigation of interlayer interaction and relative motion of graphene layers. A methodological study of the influence of parameters of calculations with the dispersion corrected and original PBE functionals on characteristics of the potential relief of the interlayer interaction energy is performed. Based on the DFT-D calculations, a new classical potential for interaction between graphene layers is developed. Molecular dynamics simulations of relative translational vibrations of graphene layers demonstrate that the choice of the classical potential considerably affects dynamic characteristics of graphene-based systems. The calculated low values of the Q-factor for these vibrations Q≈ 10-100 show that graphene should be perfect for the use in fast-responding nanorelays and nanoelectromechanical memory cells.

Diffusion and drift of graphene flake on graphite surface.

Diffusion and drift of a graphene flake on a graphite surface are analyzed. A potential energy relief of the graphene flake is computed using ab initio and empirical calculations. Based on the analysis of this relief, different mechanisms of diffusion and drift of the graphene flake on the graphite surface are considered. A new mechanism of diffusion and drift of the flake is proposed. According to the proposed mechanism, rotational transition of the flake from commensurate to incommensurate state takes place with subsequent simultaneous rotation and translational motion until a commensurate state is reached again, and so on. Analytic expressions for the diffusion coefficient and mobility of the flake corresponding to different mechanisms are derived in wide ranges of temperatures and sizes of the flake. The molecular dynamics simulations and estimates based on ab initio and empirical calculations demonstrate that the proposed mechanism can be dominant under certain conditions. The influence of structural defects on the diffusion of the flake is examined on the basis of calculations of the potential energy relief and molecular dynamics simulations. The methods of control over the diffusion and drift of graphene components in nanoelectromechanical systems are discussed. The possibility to experimentally determine the barriers to relative motion of graphene layers based on the study of diffusion of a graphene flake is considered. The results obtained can also be applied to polycyclic aromatic molecules on graphene and should be qualitatively valid for a set of commensurate adsorbate-adsorbent systems.

Autocrine regulation of mda-7/IL-24 mediates cancer-specific apoptosis.

A noteworthy aspect of melanoma differentiation-associated gene-7/interleukin-24 (mda-7/IL-24) as a cancer therapeutic is its ability to selectively kill cancer cells without harming normal cells. Intracellular MDA-7/IL-24 protein, generated from an adenovirus expressing mda-7/IL-24 (Ad.mda-7), induces cancer-specific apoptosis by inducing an endoplasmic reticulum (ER) stress response. Secreted MDA-7/IL-24 protein, generated from cells infected with Ad.mda-7, induces growth inhibition and apoptosis in surrounding noninfected cancer cells but not in normal cells, thus exerting an anti-tumor "bystander" effect. The present studies reveal a provocative finding that recombinant MDA-7/IL-24 protein can robustly induce expression of endogenous mda-7/IL-24, which generates the signaling events necessary for bystander killing. To evaluate the mechanism underlying this positive autocrine feedback loop, we show that MDA-7/IL-24 protein induces stabilization of its own mRNA without activating its promoter. Furthermore, this posttranscriptional effect depends on de novo protein synthesis. As a consequence of this autocrine feedback loop MDA-7/IL-24 protein induces sustained ER stress as evidenced by expression of ER stress markers (BiP/GRP78, GRP94, GADD153, and phospho-eIF2alpha) and reactive oxygen species production, indicating that both intracellular and secreted proteins activate similar signaling pathways to induce apoptosis. Thus, our results clarify the molecular mechanism by which secreted MDA-7/IL-24 protein (generated from Ad.mda-7-infected cells) exerts cancer-specific killing.

Precision genetic cellular models identify therapies protective against ER stress.

Rare monogenic disorders often share molecular etiologies involved in the pathogenesis of common diseases. Congenital disorders of glycosylation (CDG) and deglycosylation (CDDG) are rare pediatric disorders with symptoms that range from mild to life threatening. A biological mechanism shared among CDG and CDDG as well as more common neurodegenerative diseases such as Alzheimer's disease and amyotrophic lateral sclerosis, is endoplasmic reticulum (ER) stress. We developed isogenic human cellular models of two types of CDG and the only known CDDG to discover drugs that can alleviate ER stress. Systematic phenotyping confirmed ER stress and identified elevated autophagy among other phenotypes in each model. We screened 1049 compounds and scored their ability to correct aberrant morphology in each model using an agnostic cell-painting assay based on >300 cellular features. This primary screen identified multiple compounds able to correct morphological phenotypes. Independent validation shows they also correct cellular phenotypes and alleviate each of the ER stress markers identified in each model. Many of the active compounds are associated with microtubule dynamics, which points to new therapeutic opportunities for both rare and more common disorders presenting with ER stress, such as Alzheimer's disease and amyotrophic lateral sclerosis.

MDA-7/IL-24 as a cancer therapeutic: from bench to bedside.

The novel cytokine melanoma differentiation associated gene-7 (mda-7) was identified by subtractive hybridization in the mid-1990s as a protein whose expression increased during the induction of terminal differentiation, and that was either not expressed or was present at low levels in tumor cells compared with non-transformed cells. On the basis of conserved structure, chromosomal location and cytokine-like properties, MDA-7, has now been classified as a member of the expanding interleukin (IL)-10 gene family and designated as MDA-7/IL-24. Multiple studies have shown that the expression of MDA-7/IL-24 in a wide variety of tumor cell types, but not in the corresponding equivalent non-transformed cells, causes their growth arrest and ultimately cell death. In addition, MDA-7/IL-24 has been noted to be a radiosensitizing cytokine, which is partly because of the generation of reactive oxygen species and ceramide that cause endoplasmic reticulum stress. Phase I clinical trial data has shown that a recombinant adenovirus expressing MDA-7/IL-24 [Ad.mda-7 (INGN-241)] was safe and had measurable tumoricidal effects in over 40% of patients, which strongly argues that MDA-7/IL-24 may have significant therapeutic value. This review describes what is known about the impact of MDA-7/IL-24 on tumor cell biology and its potential therapeutic applications.

Eradication of therapy-resistant human prostate tumors using a cancer terminator virus.

Terminal prostate cancer is refractory to conventional anticancer treatments because of frequent overexpression of antiapoptotic proteins Bcl-2 and/or Bcl-x(L). Adenovirus-mediated delivery of melanoma differentiation associated gene-7/interleukin-24 (mda-7/IL-24), a secreted cytokine having cancer-selective apoptosis-inducing properties, profoundly inhibits prostate cancer cell growth. However, forced overexpression of Bcl-2 or Bcl-x(L) renders prostate cancer cells resistant to Ad.mda-7. We constructed a conditionally replication-competent adenovirus in which expression of the adenoviral E1A gene, necessary for replication, is driven by the cancer-specific promoter of progression elevated gene-3 (PEG-3) and which simultaneously expresses mda-7/IL-24 in the E3 region of the adenovirus (Ad.PEG-E1A-mda-7), a cancer terminator virus (CTV). This CTV generates large quantities of MDA-7/IL-24 as a function of adenovirus replication uniquely in cancer cells. Infection of Ad.PEG-E1A-mda-7 (CTV) in normal prostate epithelial cells and parental and Bcl-2- or Bcl-x(L)-overexpressing prostate cancer cells confirmed cancer cell-selective adenoviral replication, mda-7/IL-24 expression, growth inhibition, and apoptosis induction. Injecting Ad.PEG-E1A-mda-7 (CTV) into xenografts derived from DU-145-Bcl-x(L) cells in athymic nude mice completely eradicated not only primary tumors but also distant tumors (established in the opposite flank), thereby implementing a cure. These provocative findings advocate potential therapeutic applications of this novel virus for advanced prostate cancer patients with metastatic disease.