Efficient pseudopotentials for plane-wave calculations. II. Operators for fast iterative diagonalization

Ethane under pressure revisited using x-ray diffraction, Raman spectroscopy, infrared absorption, and ab initio calculations up to 150 GPa

Ethane (C2H6) is anticipated to be the most stable compound within the carbon-hydrogen system under the 100 GPa pressure range. Nevertheless, the properties of ethane under pressure are still poorly documented. Here, we present a comprehensive study of the structural and vibrational properties of C2H6 in a diamond anvil cell at pressures up to 150 GPa. To obtain detailed data, ethane single-crystal was grown in a helium pressure-transmitting medium. Utilizing single-crystal x-ray diffraction, the distortion mechanism between the tetragonal and monoclinic phases, occurring over the 3.2-5.2 GPa pressure range, is disclosed. Subsequently, no phase transition is observed up to 150 GPa. The accurately measured compression curve is compared to various computational approximations. The vibrational modes measured by Raman spectroscopy and infrared absorption are well identified, and their evolution is well reproduced by ab initio calculations. In particular, an unusual anticrossing phenomenon occurs near 40 GPa between a rocking and a stretching mode, likely attributable to intermolecular interactions through hydrogen bonding.

Mechanistic study of the atomic layer deposition of cobalt: a combined mass spectrometric and computational approach

Cobaltcarbonyl-tert-butylacetylene (CCTBA) is a conventional precursor for the selective atomic layer deposition of Co onto silicon surfaces. However, a limited understanding of the deposition mechanism of such cobalt precursors curbs rational improvements on their design for increased efficiency and tuneable selectivity. The impact of using a less reactive internal alkyne instead of a terminal alkyne was investigated using experimental and computational methods. Using electrospray-ionization mass spectrometry, the formation of CCTBA analogs and their gas phase decomposition pathways were studied. Decomposition experiments show very similar decomposition pathways between the two complexes. The internal alkyne dissociates from the Co complex at slightly lower energies than the terminal alkyne, suggesting that an internal alkynyl ligand may be more suited to low temperature ALD. In addition, transition state calculations using the nudged elastic band method confirm an increased reaction barrier between the internal alkyne and the Si-H surface bonds on Si(111). These results suggests that using a less reactive internal alkyne will result in fewer embedded carbon impurities during deposition onto Si wafers. DFT calculations using the PBE functional and periodic boundary conditions also predict increased surface binding with the metal centers of the internal alkynyl complex.

RNA targeting and cleavage by the type III-Dv CRISPR effector complex

CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction1-5. Target RNA cleavage at regular intervals is characteristic of type III effector complexes6-8. Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors9,10, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2'-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.

Optoelectronic Readout of Single Er Adatom's Electronic States Adsorbed on the Si(100) Surface at Low Temperature (9 K)

Integrating nanoscale optoelectronic functions is vital for applications such as optical emitters, detectors, and quantum information. Lanthanide atoms show great potential in this endeavor due to their intrinsic transitions. Here, we investigate Er adatoms on Si(100)-2×1 at 9 K using a scanning tunneling microscope (STM) coupled to a tunable laser. Er adatoms display two main adsorption configurations that are optically excited between 800 and 1200 nm while the STM reads the resulting photocurrents. Our spectroscopic method reveals that various photocurrent signals stem from the bare silicon surface or Er adatoms. Additional photocurrent peaks appear as the signature of the Er adatom relaxation, triggering efficient dissociation of nearby trapped excitons. Calculations using density functional theory with spin-orbit coupling correction highlight the origin of the observed photocurrent peaks as specific 4f→4f or 4f→5d transitions. This spectroscopic technique can facilitate optoelectronic analysis of atomic and molecular assemblies by offering insight into their intrinsic quantum properties.

Electrical tuning of quantum light emitters in hBN for free space and telecom optical bands

Quantum light emitters (also known as single photon emitters) are known to be the heart of quantum information technologies. Irrespective of possessing ideal single photon emitter properties, quantum emitters in 2-D hBN defect structures, exhibit constrained quantum light emission within the 300-700 nm range. However, this emission range cannot fully satisfy the needs of an efficient quantum communication applications such as quantum key distribution (QKD), which demands the quantum light emission in fiber optic telecom wavelength bands (from 1260 to 1625 nm) and the free space optical (FSO) (UV-C-solar blind band-100 to 280 nm) wavelength ranges. Hence, there is a necessity to tune the quantum light emission into these two bands. However, the most promising technique to tune the quantum light emitters in hBN here, is still a matter of debate and till date there is no experimental and theoretical assurances. Hence, this work will focus on one of the most promising simple techniques known as Stark electrical tuning of the quantum light emission of hBN defect structures (NBVN, VB, CB, CBVN, CBCN, CBCNCBCN complex, and VBO2). These hBN defects are designed and sandwiched as metal/graphene/hBN defect structure/graphene/metal heterostructure and electrically tuned towards FSO and fiber optic bands (tuning range from UV-C to O-band IR region) region, using constrained DFT computations. The external electric field predicted to yield an atomic bond angle tilt associated with this point defect structure creates out-of-plane dipole moments, enabling the tuning of quantum emission. This electrical tuning technique leads to a simple passive photonic component which enables easier compatibility with quantum circuits and it is found to be one of the perfect alternative solutions, which does not require much external hardware setup to implement as compared to earlier published strain induced tuning experiments.

β-l-Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining β-l-Arabinofuranosidases

GH127 and GH146 microorganismal retaining β-l-arabinofuranosidases, expressed by human gut microbiomes, feature an atypical catalytic domain and an unusual mechanism of action. We recently reported that both Bacteroides thetaiotaomicron BtGH146 and Bifidobacterium longum HypBA1 are inhibited by β-l-arabinofuranosyl cyclophellitol epoxide, supporting the action of a zinc-coordinated cysteine as a catalytic nucleophile, where in most retaining GH families, an aspartate or glutamate is employed. This work presents a panel of β-l-arabinofuranosyl cyclophellitol epoxides and aziridines as mechanism-based BtGH146/HypBA1 inhibitors and activity-based probes. The β-l-arabinofuranosyl cyclophellitol aziridines both inhibit and label β-l-arabinofuranosidase efficiently (however with different activities), whereas the epoxide-derived probes favor BtGH146 over HypBA1. These findings are accompanied by X-ray structural analysis of the unmodified β-l-arabinofuranosyl cyclophellitol aziridine in complex with both isozymes, which were shown to react by nucleophilic opening of the aziridine, at the pseudoanomeric carbon, by the active site cysteine nucleophile to form a stable thioether bond. Altogether, our activity-based probes may serve as chemical tools for the detection and identification of low-abundance β-l-arabinofuranosidases in complex biological samples.

Valley filters using graphene blister defects from first principles

Valleytronics, which makes use of the two valleys in graphenes, attracts considerable attention and a valley filter is expected to be the central component in valleytronics. We propose the application of the graphene valley filter using blister defects to the investigation of the valley-dependent transport properties of the Stone-Wales and blister defects of graphenes by density functional theory calculations. It is found that the intervalley transition from theKvalley to theK'valleys is completely suppressed in some defects. Using a large bipartite honeycomb cell (BHC) including several carbon atoms in a cell and replacing atomic orbitals with molecular orbitals in the tight-binding model, we demonstrate analytically and numerically that the symmetry between the A and B sites of the BHC contributes to the suppression of the intervalley transition. In addition, the universal rule for the atomic structures of the blisters suppressing the intervalley transition is derived. Furthermore, by introducing additional carbon atoms to graphenes to form blister defects, we can split the energies of the states at which resonant scattering occurs on theKandK'channel electrons. Because of this split, the fully valley-polarized current will be achieved by the local application of a gate voltage.

Ion trap and release dynamics enables nonintrusive tactile augmentation in monolithic sensory neuron

An iontronic-based artificial tactile nerve is a promising technology for emulating the tactile recognition and learning of human skin with low power consumption. However, its weak tactile memory and complex integration structure remain challenging. We present an ion trap and release dynamics (iTRD)-driven, neuro-inspired monolithic artificial tactile neuron (NeuroMAT) that can achieve tactile perception and memory consolidation in a single device. Through the tactile-driven release of ions initially trapped within iTRD-iongel, NeuroMAT only generates nonintrusive synaptic memory signals when mechanical stress is applied under voltage stimulation. The induced tactile memory is augmented by auxiliary voltage pulses independent of tactile sensing signals. We integrate NeuroMAT with an anthropomorphic robotic hand system to imitate memory-based human motion; the robust tactile memory of NeuroMAT enables the hand to consistently perform reliable gripping motion.

Rational Design of Photocontrolled Rectifier Switches in Single-Molecule Junctions Based on Diarylethene

The construction of multifunctional, single-molecule nanocircuits to achieve the miniaturization of active electronic devices is a challenging goal in molecular electronics. In this paper, we present an effective strategy for enhancing the multifunctionality and switching performance of diarylethene-based molecular devices, which exhibit photoswitchable rectification properties. Through a molecular engineering design, we systematically investigate a series of electron donor/acceptor-substituted diarylethene molecules to modulate the electronic properties and investigate the transport behaviors of the molecular junctions using the non-equilibrium Green's function combined with the density functional theory. Our results demonstrate that the asymmetric configuration, substituted by both the donor and acceptor on the diarylethene molecule, exhibits the highest switching ratio and rectification ratio. Importantly, this rectification function can be switched on/off through the photoisomerization of the diarylethene unit. These modulations in the transport properties of these molecular junctions with different substituents were obtained with molecule-projected self-consistent Hamiltonian and bias-dependent transmission spectra. Furthermore, the current-voltage characteristics of these molecular junctions can be explained by the molecular energy level structure, showing the significance of energy level regulation. These findings have practical implications for constructing high-performance, multifunctional molecular-integrated circuits.

Sepiolite as a novel polysulfide trapper for energy applications: an electrochemical, X-ray spectroscopic and DFT study

Capacity retention is a critical property to enhance in electrochemical storage systems applied to renewable energy. In lithium-sulfur (Li-S) batteries, the capacity fade resulting from the shuttle effect of polysulfides is a major obstacle to their practical application. Sepiolite, an eco-friendly earth-abundant clay with suitable surface chemistry for anchoring and retaining various molecules and structures, was studied as a cathode additive to mitigate the shuttle effect using experimental and theoretical approaches. Electrochemical measurements, spectroscopy, and ab initio calculations were performed to describe the mechanism and interfaces involved in polysulfide retention using 2 wt% of sepiolite as an additive in Li-S batteries. The results showed that the addition of sepiolite significantly improved the capacity retention during battery cycling. Spectroscopic analysis revealed that the effective sepiolite-polysulfide interface was governed by oxidized sulfur species. Additionally, ab initio studies showed a highly exothermic adsorption both inside and outside the sepiolite pore. This study demonstrates the potential use of eco-friendly, low-cost, non-toxic, natural, and abundant materials as additives to increase capacity retention.

Creation of Single Vacancies in hBN with Electron Irradiation

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of 2D materials. The displacement cross sections of monolayer hexagonal boron nitride (hBN) are measured using aberration-corrected scanning transmission electron microscopy in near ultra-high vacuum at primary beam energies between 50 and 90 keV. Damage rates below 80 keV are up to three orders of magnitude lower than previously measured at edges under poorer residual vacuum conditions, where chemical etching appears to dominate. Notably, it is possible to create single vacancies in hBN using electron irradiation, with boron almost twice as likely as nitrogen to be ejected below 80 keV. Moreover, any damage at such low energies cannot be explained by elastic knock-on, even when accounting for the vibrations of the atoms. A theoretical description is developed to account for the lowering of the displacement threshold due to valence ionization resulting from inelastic scattering of probe electrons, modeled using charge-constrained density functional theory molecular dynamics. Although significant reductions are found depending on the constrained charge, quantitative predictions for realistic ionization states are currently not possible. Nonetheless, there is potential for defect-engineering of hBN at the level of single vacancies using electron irradiation.

Evolution of Mn1-xGexBi2Te4 Electronic Structure under Variation of Ge Content

One of the approaches to manipulate MnBi2Te4 properties is the magnetic dilution, which inevitably affects the interplay of magnetism and band topology in the system. In this work, we carried out angle-resolved photoemission spectroscopy (ARPES) measurements and density functional theory (DFT) calculations for analysing changes in the electronic structure of Mn1-xGexBi2Te4 that occur under parameter x variation. We consider two ways of Mn/Ge substitution: (i) bulk doping of the whole system; (ii) surface doping of the first septuple layer. For the case (i), the experimental results reveal a decrease in the value of the bulk band gap, which should be reversed by an increase when the Ge concentration reaches a certain value. Ab-initio calculations show that at Ge concentrations above 50%, there is an absence of the bulk band inversion of the Te pz and Bi pz contributions at the Γ-point with significant spatial redistribution of the states at the band gap edges into the bulk, suggesting topological phase transition in the system. For case (ii) of the vertical heterostructure Mn1-xGexBi2Te4/MnBi2Te4, it was shown that an increase of Ge concentration in the first septuple layer leads to effective modulation of the Dirac gap in the absence of significant topological surface states of spatial redistribution. The results obtained indicate that surface doping compares favorably compared to bulk doping as a method for the Dirac gap value modulation.

Polarization Doping in a GaN-InN System-Ab Initio Simulation

Polarization doping in a GaN-InN system with a graded composition layer was studied using ab initio simulations. The electric charge volume density in the graded concentration part was determined by spatial potential dependence. The emerging graded polarization charge was determined to show that it could be obtained from a polarization difference and the concentration slope. It was shown that the GaN-InN polarization difference is changed by piezoelectric effects. The polarization difference is in agreement with the earlier obtained data despite the relatively narrow bandgap for the simulated system. The hole generation may be applied in the design of blue and green laser and light-emitting diodes.

Enhancement in photocatalytic water splitting using van der Waals heterostructure materials based on penta-layers

Recently, van der Waals heterostructures (vdWHs) have been used to improve the performance of 2D materials, enabling more applications. By using first-principles calculations, we have studied the electronic and optical properties of vdWHs composed of penta-siligraphene and other penta-layers (p-Si2C4/p-X; X = Si₂N₄, ZnO₂, Ge₂C₄ or SiGeC₄). The stability of the vdWHs is verified by computing their binding energy, vibrational phonon spectra and ab initio molecular dynamics simulations. By assessing the electronic properties, we have found that the p-Si2C4/p-ZnO2, p-Si2C4/p-Ge2C4 and p-Si2C4/p-SiGeC4 vdWHs are semiconductors with an indirect band gap characterized by type-I band alignment. Meanwhile, the p-Si2C4/p-Si2N4 vdWH is a quasi-direct band gap semiconductor characterized by type-II band alignment. Bader charge analysis and charge density of p-Si2C4/p-Si2N4 vdWHs showed that photogenerated electrons move from the p-Si2N4 monolayer to the p-Si2C4 monolayer limiting the recombination of photogenerated charges and improving the photocatalytic efficiency. Furthermore, the p-Si2C4/p-Si2N4 vdWH exhibits suitable band edge positions compared to isolated monolayers suggesting its potential applicability in photocatalytic water splitting. The calculated optical absorption revealed that the p-Si2N4 monolayer exhibits substantial optical absorption in the ultraviolet (UV) range, while the p-Si2C4 monolayer and the p-Si2C4/p-Si2N4 vdWH show outstanding optical absorption on the order of 10⁵ cm^-1 in the visible and UV ranges. More importantly, the p-Si2C4/p-Si2N4 vdWH can greatly improve the optical absorption in these regions, which leads to high-efficiency usage of solar energy. Our study provides a route to design new vdWHs based on pentagonal monolayers, as well as an efficient photocatalyst for photocatalytic water splitting and optical devices.

Strain tunable quantum emission from atomic defects in hexagonal boron nitride for telecom-bands

This study presents extending the tunability of 2D hBN Quantum emitters towards telecom (C-band - 1530 to 1560 nm) and UV-C (solar blind - 100 to 280 nm) optical bands using external strain inducements, for long- and short-range quantum communication (Quantum key distribution (QKD)) applications, respectively. Quantum emitters are the basic building blocks of this QKD (quantum communication or information) technologies, which need to emit single photons over room temperature and capable of tuning the emission wavelength to the above necessary range. Recent literature revealed that quantum emitters in 2D hBN only has the ability to withstand at elevated temperatures and aggressive annealing treatments, but density functional theory (DFT) predictions stated that hBN can only emit the single photons from around 290 to 900 nm (UV to near-IR regions) range. So, there is a need to engineer and further tune the emission wavelength of hBN quantum emitters to the above said bands (necessary for efficient QKD implementation). One of the solutions to tune the emission wavelength is by inducing external strain. In this work, we examine the tunability of quantum emission in hBN with point defects by inducing three different normal strains using DFT computations. We obtained the tunability range up to 255 nm and 1589.5 nm, for the point defects viz boron mono vacancies (V_B) and boron mono vacancies with oxygen atoms (V_BO₂) respectively, which can enhance the successful implementation of the efficient QKD. We also examine the tunability of the other defects viz. nitrogen mono vacancies, nitrogen mono vacancy with self-interstitials, nitrogen mono vacancy with carbon interstitials, carbon dimers and boron dangling bonds, which revealed the tunable quantum emission in the visible, other UV and IR spectrum ranges and such customized quantum emission can enhance the birth of other quantum photonic devices.

Unravelling the binding affinity and selectivity of molybdenum(II) phenanthroline complexes with DNA G-quadruplexes by using linear-scaling DFT studies. The important role of ancillary ligands

We have used near linear-scaling density functional theory (LS-DFT) methods including dispersion, for the first time, to study the interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η³-C₃H₅)Br(CO)₂(phen)] metal complex with the DNA G-quadruplexes (GQ) to gain insight into its cytotoxicity. The LMKLL/DZDP level of calculation, which includes van der Waals contributions, with the SIESTA software was used to treat by means of first-principles computations the whole biological studied model system with ∼1000 atoms. Computed formation energies point to systems containing the Ax isomer as the most stable although the nearest system in energy containing the Eq isomer is only 7.5 kcal mol^-1 above. On the other hand, the energy decomposition analysis (EDA) favours interaction energies for the systems containing the Eq isomer. However, when solvent effects are taken into account the systems containing the Ax isomer are again the most stable. This Ax isomer was found interacting by means of end-stacking with the GQ and surprisingly totally inside the non-canonical secondary structure, where all the ligands of the metal complex produce several weak interactions with the DNA structure. On the other hand, the Eq isomer prefers to interact from outside by means of intercalation in which the ancillary ligands also have some role in the interaction. Such features and comparison with the results regarding the interaction of the [Mo(η³-C₃H₅)Br(CO)₂(phen)] metal complex with duplex DNA suggest that the [Mo(η³-C₃H₅)Br(CO)₂(phen)] would have a higher affinity and eventual selectivity for non-canonical DNA GQ structures.

Geometries of hydrogen bonds in water-ethanol mixtures from ab initio molecular dynamics simulations

We outline a simple procedure to determine the geometry of hydrogen bonds between different molecular species in binary mixtures from ab initio molecular dynamics (AIMD) trajectories. Here we determine the geometry of the hydrogen bonds arising from intermolecular OH⋯O interactions between different H-bonded pairs, water-water, ethanol-ethanol and water-ethanol in water-alcohol mixtures at different compositions by plotting the intermolecular non-bonded OH⋯O and O⋯O distances, and the ∠HO⋯O (θ) angles for each of the possible pairs in the ensemble. Two regions separate out in each of the scatter-plots; the one with short OH⋯O and O⋯O intermolecular distances and almost linear ∠HO⋯O angles may be identified as the region where the intermolecular OH⋯O geometry would be favorable for hydrogen bonding. Using the different geometric criteria for each of the three possible H-bonded pairs we estimate the average number of water and ethanol molecules that are hydrogen bonded to a water molecule, and to an ethanol molecule, respectively, at different mole fractions of the mixture. We validate the results from values of the chemical shift of the two OH resonances (water and ethanol) in the proton NMR spectra of the mixtures at different concentrations as these values are known to be sensitive to the local chemical environment of the resonating nuclei.

Quantum neural networks force fields generation

Accurate molecular force fields are of paramount importance for the efficient implementation of molecular dynamics techniques at large scales. In the last decade, machine learning (ML) methods have demonstrated impressive performances in predicting accurate values for energy and forces when trained on finite size ensembles generated with ab initio techniques. At the same time, quantum computers have recently started to offer new viable computational paradigms to tackle such problems. On the one hand, quantum algorithms may notably be used to extend the reach of electronic structure calculations. On the other hand, quantum ML is also emerging as an alternative and promising path to quantum advantage. Here we follow this second route and establish a direct connection between classical and quantum solutions for learning neural network (NN) potentials. To this end, we design a quantum NN architecture and apply it successfully to different molecules of growing complexity. The quantum models exhibit larger effective dimension with respect to classical counterparts and can reach competitive performances, thus pointing towards potential quantum advantages in natural science applications via quantum ML.

Pentavalent Uranium Incorporated in the Structure of Proterozoic Hematite

Characterizing the chemical state and physical disposition of uranium that has persisted over geologic time scales is key for modeling the long-term geologic sequestration of nuclear waste, accurate uranium-lead dating, and the use of uranium isotopes as paleo redox proxies. X-ray absorption spectroscopy coupled with molecular dynamics modeling demonstrated that pentavalent uranium is incorporated in the structure of 1.6 billion year old hematite (α-Fe₂O₃), attesting to the robustness of Fe oxides as waste forms and revealing the reason for the great success in using hematite for petrogenic dating. The extreme antiquity of this specimen suggests that the pentavalent state of uranium, considered a transient, is stable when incorporated into hematite, a ubiquitous phase that spans the crustal continuum. Thus, it would appear overly simplistic to assume that only the tetravalent and hexavalent states are relevant when interpreting the uranium isotopic record from ancient crust and contained ore systems.

Structural, dynamical, and electronic properties of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide

We provide a microscopic insight, both structural and electronic, into the multifold interactions occurring in the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [EMIM][TFSI] currently targeted for applications in next-generation low-power electronics and optoelectronic devices. To date, practical applications have remained hampered by the lack of fundamental understanding of the interactions occurring both inside the IL and at the interface with the substrate. Our first principles dynamical simulations provide accurate insights into the nature of bonding and non-bonding interactions, dynamical conformational changes and induced dipole moments, along with their statistical distributions, of this ionic liquid, that have so far not been completely unraveled. The mobilities of the two ionic species are obtained by long-lasting dynamical simulations at finite temperature, allowing simultaneous monitoring and quantification of the isomerization occurring in the IL. Moreover, a thorough analysis of the electronic structure and partial charge distributions characterizing the two components, the cation and anion, allow rationalization of the nature of the electrostatic interactions, hydrogen bonding properties of the two ionic counterparts, and the infra-red and dielectric response of the system, especially in the low frequency range, for the full characterization of the IL.

Janus 2H-VSSe monolayer: two-dimensional valleytronic semiconductor with nonvolatile valley polarization

Valleytronic as a hot topic in recent years focuses on electrons' valley degree of freedom as a quantum information carrier. Here, by combining two-bandk.pmodel with high-throughput density functional theory (DFT) calculations, the valley states of Janus 2H-VSSe monolayer are studied which have spontaneous polarization. Nonvolatile valley polarization state is mainly arises from intrinsic ferromagnetism contributed by V-3d electronic configuration and not the spontaneous out-of-plane dipole moment of VSSe monolayer. The effective Hamiltonian model and DFT calculations both showed that the valley splitting mainly originates from the smaller spin splitting coming from the spin-orbit coupling effect rather than the spin splitting of magnetic exchange field. By using the effective Dirac Hamiltonian and Kubo formula, we further calculated the longitudinal and transversal conductivities and absorption spectra of VSSe monolayer which exhibits an anomalous valley Hall effect and clear valley-selective circular dichroism. Our calculations indicate that the modification of valley and spin splitting related to Berry curvature by applying an external strain is more noticeable than by the change of the magnetic moment orientation and electric field. We found that carriers accumulation with particular spin and valley label can be manipulated by tuning effective Hamiltonian parameters. The coexistence of robust in-plane magnetic ordering and spontaneous valley polarization of 2H-VSSe monolayer supports the possibility of applications in spintronics, valleytronics and optoelectronics devices.

Glyphosate and glufosinate ammonium, herbicides commonly used on genetically modified crops, and their interaction with microplastics: Ecotoxicity in anuran tadpoles

The effects of glyphosate (GLY)-based and glufosinate ammonium (GA)-based herbicides (GBH and GABH, respectively) and polyethylene microplastic particles (PEMPs) on Scinax squalirostris tadpoles were assessed. Tadpoles were exposed to nominal concentrations of both herbicides (from 1.56 to 100 mg L-1) and PEMPs (60 mg L-1), either alone or in combination, and toxicity evaluated at 48 h. Acetylcholinesterase (AChE), carboxylesterase (CbE), and glutathione-S-transferase (GST) activities were analyzed at the three lowest concentrations (1.56, 3.12 and 6.25 mg L-1, survival rates >85%) of both herbicides alone and with PEMPs. Additionally, the thermochemistry of the interactions between the herbicides and polyethylene (PE) was analyzed by Density Functional Theory (DFT). The median-lethal concentration (LC50) was 43.53 mg L-1 for GBH, 38.56 mg L-1 for GBH + PEMPs, 7.69 for GABH, and 6.25 mg L-1 for GABH+PEMPs. The PEMP treatment increased GST but decreased CbE activity, whereas GBH and GABH treatments increased GST but decreased AChE activity. In general, the mixture of herbicides with PEMPs increased the effect observed in the individual treatments: the highest concentration of GBH + PEMPs increased GST activity, whereas GABH+PEMP treatments decreased both AChE and CbE activities. DFT analysis revealed spontaneous interactions between the herbicides and PE, leading to the formation of bonds at the herbicide-PE interface, significantly stronger for GA than for GLY. The experimental and theoretical findings of our study indicate that these interactions may lead to an increase in toxicity when pollutants are together, meaning potential environmental risk of these combinations, especially in the case of GA.

Strain- and electric field-enhanced optical properties of the penta-siligraphene monolayer

The effect of biaxial strain and an external electric field on the optical properties of the penta-siligraphene monolayer are reported.

Metal ions impact on the isostructurality and properties of 2D coordination polymers

Two new 2,6-diacetylpyridine bis(nicotinoylhydrazone) coordination polymers with general formula {[MIIL]∙xsolvent}n, in which MII=Fe, Co, were prepared solvothermally and characterized by various methods. Both compounds exhibit isostructurality with different solvents with...

Semi-empirical and Linear-Scaling DFT Methods to Characterize duplex DNA and G-quadruplexes in Presence of Interacting Small Molecules

The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of...

Efficient electrocatalytic water splitting by bimetallic cobalt iron boride nanoparticles with controlled electronic structure

Developing an efficient bifunctional catalyst for Hydrogen Evolution Reaction (HER) and Oxygen Evolution Reaction (OER) in water splitting technology is very attractive for clean energy. Here, a new Co-Fe-B ternary catalyst with improved crystallinity is successfully synthesized by combining the chemical reduction and subsequent solid-state reaction method. Synchrotron-based X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) indicate the electronic structure redistribution is favor for the improved performance. The overpotential is only 129 mV and 280 mV for hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) in alkaline condition, the corresponding Tafel slope is 67.3 mV dec^-1 and 38.9 mV dec^-1. Density functional theory calculations distinguish that the ternary crystalline Co-Fe-B catalysts are thermodynamically favorable for HER and OER. The actual active species of the ternary catalyst in OER is the CoOOH and FeOOH as indicated in ex situ Raman spectra. The present work may introduce promising crystallinity borides material for the anode and cathode of water splitting device.

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.

Requirements for an accurate dispersion-corrected density functional

Post-self-consistent dispersion corrections are now the norm when applying density-functional theory to systems where non-covalent interactions play an important role. However, there is a wide range of base functionals and dispersion corrections available from which to choose. In this work, we opine on the most desirable requirements to ensure that both the base functional and dispersion correction, individually, are as accurate as possible for non-bonded repulsion and dispersion attraction. The base functional should be dispersionless, numerically stable, and involve minimal delocalization error. Simultaneously, the dispersion correction should include finite damping, higher-order pairwise dispersion terms, and electronic many-body effects. These criteria are essential for avoiding reliance on error cancellation and obtaining correct results from correct physics.

Coupled deep-mantle carbon-water cycle: Evidence from lower-mantle diamonds

Diamonds form in a variety of environments between subducted crust, lithospheric and deep mantle. Recently, deep source diamonds with inclusions of the high-pressure H₂O-phase ice-VII were discovered. By correlating the pressures of ice-VII inclusions with those of other high-pressure inclusions, we assess quantitatively the pressures and temperatures of their entrapment. We show that the ice-VII-bearing diamonds formed at depths down to 800 ± 60 km but at temperatures 200–500 K below average mantle temperature that match the pressure-temperature conditions of decomposing dense hydrous mantle silicates. Our work presents strong evidence for coupled recycling of water and carbon in the deep mantle based on natural samples.

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A novel approach was developed to assess the pressure-temperature conditions of entrapment of inclusions in diamonds

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The viscoelastic relaxation of diamond has a significant effect on the evolution of pressure and temperature

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Ice-VII-bearing diamonds have formed in wet, cool environments at depths down to 800 km

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The coupled recycling of water and carbon is present in the deep mantle

On the adsorption mechanism of caffeine on MAPbI3 perovskite surfaces: a combined UMC-DFT study

Recently, it was experimentally shown that the performance and thermal stability of the perovskite MAPbI₃ were improved upon the adsorption of a molecular layer of caffeine. In this work, we used a hybrid methodology that combines uncoupled monte carlo (UMC) and density functional theory (DFT) simulations to carry out a detailed and comprehensive study of the adsorption mechanism of a caffeine molecule on the surface of MAPbI₃. Our results showed that the adsorption distance and energy of a caffeine molecule on the MAPbI₃ surface are 2.0 Å and -0.3 eV, respectively. The caffeine/MAPbI₃ complex presents a direct bandgap of 2.38 eV with two flat intragap bands distanced 1.15 and 2.18 eV from the top of valence bands. Although the energy band levels are not significantly shifted by the presence of caffeine, the interaction MAPbI₃/perovskite is enough to affect the bands' dispersion, particularly the conduction bands.

Lattice dynamics in the conformational environment of multilayered hexagonal boron nitride (h-BN) results in peculiar infrared optical responses

Stacking mismatches in hexagonal boron nitride (h-BN) nanostructures affect their photonic, mechanical, and thermal properties. To access information about the stacked configuration of layered ensembles, highly sophisticated techniques like X-ray photoemission spectroscopy or electron microscopy are necessary. Here, instead, by taking advantage of the geometrical and chemical nature of h-BN, we show how simple structural models, based on shortened interplanar distances, can produce effective charge densities. Accounting these in the non-analytical part of the lattice dynamical description makes it possible to access information about the composition of differently stacked variants in experimental samples characterized by infrared spectroscopy. The results are obtained by density functional theory and confirmed by various functionals and pseudopotential approximations. Even though the method is shown using h-BN, the conclusions are more general and show how effective dielectric models can be considered as valuable theoretical pathways for the vibrational structure of any layered material.

Formation of large low shear velocity provinces through the decomposition of oxidized mantle

Large Low Shear Velocity Provinces (LLSVPs) in the lowermost mantle are key to understanding the chemical composition and thermal structure of the deep Earth, but their origins have long been debated. Bridgmanite, the most abundant lower-mantle mineral, can incorporate extensive amounts of iron (Fe) with effects on various geophysical properties. Here our high-pressure experiments and ab initio calculations reveal that a ferric-iron-rich bridgmanite coexists with an Fe-poor bridgmanite in the 90 mol% MgSiO₃-10 mol% Fe₂O₃ system, rather than forming a homogeneous single phase. The Fe³⁺-rich bridgmanite has substantially lower velocities and a higher V_P/V_S ratio than MgSiO₃ bridgmanite under lowermost-mantle conditions. Our modeling shows that the enrichment of Fe³⁺-rich bridgmanite in a pyrolitic composition can explain the observed features of the LLSVPs. The presence of Fe³⁺-rich materials within LLSVPs may have profound effects on the deep reservoirs of redox-sensitive elements and their isotopes.

Nitrogen Dissolution in Liquid Ga and Fe: Comprehensive Ab Initio Analysis, Relevance for Crystallization of GaN

The dissolution of molecular nitrogen in Ga and Fe was investigated by ab initio calculations and some complementary experiments. It was found that the N bonding inside these solvents is fundamentally different. For Ga, it is between Ga4s and Ga4p and N2p states whereas for Fe this is by N2p to Fe4s, Fe4p and Fe3d states. Accordingly, the energy of dissolution of N2 for arbitrarily chosen starting atomic configurations was 0.535 eV/mol and -0.299 eV/mol for Ga and Fe, respectively. For configurations optimized with molecular dynamics, the difference between the corresponding energy values, 1.107 eV/mol and 0.003 eV/mol, was similarly large. Full thermodynamic analysis of chemical potential was made employing entropy-derived terms in a Debye picture. The entropy-dependent terms were obtained via a normal conditions path to avoid singularity of ideal gas entropy at zero K. Nitrogen solubility as a function of temperature and N2 pressure was evaluated, being much higher for Fe than for Ga. For T=1800 K and p=104 bar, the N concentration in Ga was 3×10-3 at. fr. whereas for Fe, it was 9×10-2 at. fr. in very good agreement with experimental data. It indicates that liquid Fe could be a prospective solvent for GaN crystallization from metallic solutions.

Molecular Transistor Controlled through Proton Transfer

The potential of proton transfer reactions as a fundamental mechanism to realize a nanoscale molecular transistor is investigated. Employing density functional theory and the nonequilibrium Green's function formalism, we identify molecule-graphene nanojunctions, which exhibit high- and low-conducting states depending on the specific location of protons in the molecular bridge. In addition, we show that an electrostatic gate field can control the proton transfer process and thus allow specific conductance states to be selected. In this way, the current in the junction can be switched on and off as in a field-effect transistor. The underlying mechanism is analyzed in detail.

Crystal reorientation and plastic deformation of single-layer MoS2 and MoSe2 under uniaxial stress

We investigate theoretically, through of first-principles calculations, the effect of the application of large in-plane uniaxial stress on single-layer of MoS2, MoSe2, and MoSSe alloys. For stress applied along the zigzag (zz) direction, we predict an anomalous behavior near the point fracture. This behavior is characterized by the reorientation of the MoS2 structure along the applied stress from zz to armchair due to the formation of transient square-lattice regions in the crystal, with an apparent crystal rotation of 30 degrees. After reorientation, a large plastic deformation [Formula: see text] remains after the stress is removed. This behavior is also observed in MoSe2 and in MoSSe alloys. This phenomenon is observed both in stress-constrained geometry optimizations and in ab initio molecular dynamics simulations at finite temperature and applied stress.

Nickel isotopic evidence for late-stage accretion of Mercury-like differentiated planetary embryos

Earth's habitability is closely tied to its late-stage accretion, during which impactors delivered the majority of life-essential volatiles. However, the nature of these final building blocks remains poorly constrained. Nickel (Ni) can be a useful tracer in characterizing this accretion as most Ni in the bulk silicate Earth (BSE) comes from the late-stage impactors. Here, we apply Ni stable isotope analysis to a large number of meteorites and terrestrial rocks, and find that the BSE has a lighter Ni isotopic composition compared to chondrites. Using first-principles calculations based on density functional theory, we show that core-mantle differentiation cannot produce the observed light Ni isotopic composition of the BSE. Rather, the sub-chondritic Ni isotopic signature was established during Earth's late-stage accretion, probably through the Moon-forming giant impact. We propose that a highly reduced sulfide-rich, Mercury-like body, whose mantle is characterized by light Ni isotopic composition, collided with and merged into the proto-Earth during the Moon-forming giant impact, producing the sub-chondritic Ni isotopic signature of the BSE, while delivering sulfur and probably other volatiles to the Earth.

Computational study of the staircase molecular conductivity of polyoxovanadates adsorbed on Au(111)

This computational study presents the molecular conduction properties of polyoxovanadates V₆O₁₉ (Lindqvist-type) and V₁₈O₄₂, as possible successors of the materials currently in use in complementary metal–oxide semiconductor (CMOS) technology.

Effect of interfacial defects on the electronic properties of MoS2 based lateral T–H heterophase junctions

Our systematic study shows significant improvement in transport properties of MoS2-based lateral T–H heterophase junctions when interfacial defects are present.

Short range order and network connectivity in amorphous AsTe3: a first principles, machine learning, and XRD study

The atomic scale structure of amorphous AsTe₃ is investigated through X-ray diffraction, first-principles molecular dynamics (FPMD), and machine learning interatomic potentials (ML-GAP) obtained by exploiting the ab initio data. We obtain good agreement between the measured and modelled diffraction patterns. Our FPMD results show that As and Te obey the 8-N rule with average coordination numbers of 3 and 2, respectively. We find that small fractions of under and over coordinated As and Te atoms are present in the amorphous phase with about 6% (FPMD), and 13% (ML-GAP) of 3-fold Te. As is found at the center of pyramidal structures predominantly linked through Te_n chains rather than rings. Despite the low As concentration in AsTe₃, its local environment features a very high chemical disorder that manifests through the occurrence of homopolar bonds including at least 57% of As atoms.

Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics

CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum-classical molecular dynamics (MD) and free energy methods are used to disclose the two-metal-dependent mechanism of phosphodiester bond cleavage in CRISPR-Cas9. Ab initio MD reveals a conformational rearrangement of the Mg2+-bound RuvC active site, which entails the relocation of H983 to act as a general base. Then, the DNA cleavage proceeds through a concerted associative pathway fundamentally assisted by the joint dynamics of the two Mg2+ ions. This clarifies previous controversial experimental evidence, which could not fully establish the catalytic role of the conserved H983 and the metal cluster conformation. The comparison with other two-metal-dependent enzymes supports the identified mechanism and suggests a common catalytic strategy for genome editing and recombination. Overall, the non-target DNA cleavage catalysis described here resolves a fundamental open question in the CRISPR-Cas9 biology and provides valuable insights for improving the catalytic efficiency and the metal-dependent function of the Cas9 enzyme, which are at the basis of the development of genome editing tools.

Molecular Conformation and Hydrogen Bond Formation in Liquid Ethylene Glycol

The ethylene glycol (EG) molecule, HOCH₂CH₂OH, adopts a conformation where the central OCCO dihedral is exclusively gauche in the gaseous and crystalline states, but in the liquid state, for close to 20% of the molecules, the central OCCO adopts the energetically unfavorable trans conformation. Here we report calculations, based on ab initio molecular dynamics simulations, on the thermodynamics associated with hydrogen bond formation in the liquid state of EG between donor-acceptor pairs with different molecular conformations. We establish an operational, geometric definition of hydrogen bonds in liquid EG from an analysis of the proton NMR data and show that the key feature, irrespective of the conformation, is marked directionality with almost linear ∠HO···O angles. The free energy for hydrogen bond formation estimated as the potential of mean force for the reversible work associated with the passage from a hypothetical state where hydrogen bonding is absent and donor-acceptor pairs are randomly oriented to the hydrogen-bonded state where the pairs are oriented showed comparable magnitudes irrespective of the molecular conformation of either the donor or acceptor. The results suggest that the presence of the trans conformer in liquid EG would require an understanding of its role in the extended hydrogen-bonded network of the liquid.