The SIESTA method; developments and applicability

Unusual Transport Properties of CNT-Nickelocene-Based Circuits: Role of Structural Symmetry

At the nano- or molecular scale, electron transport is often governed by quantum effects, for which the symmetry of the system could become a key factor. In this work, by state-of-the-art first-principles modeling and simulation, we show that the structural symmetry plays a unique role in properties of electronic circuits made of CNT (5,5) electrodes and nickelocene (NiCp2) molecules, resulting in unusual transport phenomena beyond the classical circuit theories. For a single NiCp2 molecule sandwiched between two CNT (5,5) electrodes, we find that the symmetry change caused by the rotation of one CNT electrode greatly affects the conductance of the device, which may have important implications for understanding the performances of CNT-based quantum devices. We further show that when two NiCp2 molecular resistors are connected in series, the conductance of the resulting series-NiCp2 circuit can be significantly higher than the single-NiCp2 device at certain biases, in which the structural symmetry of the circuit plays a critical role. These results provide new opportunities for the future design of molecular devices with novel functions.

Topological Superconductivity in Heavily Doped Single-Layer Graphene

The existence of superconductivity (SC) appears to be established in both twisted and nontwisted graphene multilayers. However, whether their building block, single-layer graphene (SLG), can also host SC remains an open question. Earlier theoretical works predicted that SLG could become a chiral d-wave superconductor driven by electronic interactions when doped to its van Hove singularity, but questions such as whether the d-wave SC survives the strong band renormalizations seen in experiments, its robustness against the source of doping, or if it will occur at any reasonable critical temperature (Tc) have remained difficult to answer, in part due to uncertainties in model parameters. Furthermore, doping of graphene beyond its van Hove singularity remained experimentally challenging and was not demonstrated until recently. In this study, we n dope SLG past the van Hove singularity by employing Tb intercalation and derive structural models from angle-resolved photoemission spectroscopy measurements. We adopt a reliable numerical framework based on a random-phase approximation technique to investigate the emergence of unconventional SC in the heavily doped monolayer. We predict that robust d + id topological SC could arise in SLG doped by Tb, with a Tc up to 600 mK. We also employ first-principles calculations to investigate the possibility of realizing d-wave SC with other dopants, such as Li or Cs. We find that dopants that change the lattice symmetry of SLG are detrimental to the d-wave state. The stability of the d-wave SC predicted here in Tb-doped SLG could provide a valuable insight for guiding future experimental efforts aimed at exploring topological superconductivity in monolayer graphene.

The effect of the oxygen dangling on the thermoelectric properties of organic Thienoisoindigo single-molecule junction

CONTEXT

Theoretical investigation for thermoelectric characteristics of organic Thienoisoindigo single-molecule is carried out using the first-principles calculations based on the density functional theory. It reveals that modifying the position or removing oxygen atoms significantly alters the thermoelectric properties. Transmission coefficient calculations show that the lowest unoccupied molecular orbital (LUMO) dominates across all molecular configurations. Repositioning oxygen atoms increases the bandgap from 1.14 to 1.53 eV, while the complete removal of oxygen further increases to 1.8 eV. This change leads to the disruption of constructive quantum interference, which is replaced by destructive one. The electrical conductance is similarly affected by changes in oxygen atom positioning, with values shifting from - 1.06 to - 1.63. Molecules without oxygen atoms exhibit lower conductance compared to those with dangling oxygen, resulting in reduced semiconductor-like behavior and enhanced insulating properties. The Seebeck coefficient remains stable at - 2.99 μ V/K when oxygen atoms are repositioned. However, the removal of one oxygen atom changes the coefficient to a positive value (290.14 μ V/K), causing the molecule to transition from n-type to p-type behavior. The complete absence of oxygen atoms returns the Seebeck coefficient to a negative value ( - 256.08 μ V/K), switching the molecule back to n-type conduction.

METHODS

This investigation was achieved by applying the SIESTA software through density functional theory (DFT) computations. To account for exchange and correlation effects, we use a double-zeta polarized (DZP) basis set in conjunction with the generalized gradient approximation (GGA-PBE) to determine the ideal ground-state atomic locations. By combining the Hamiltonian of each system with the quantum transport code GOLLUM, we can calculate the transmission coefficient, projected density of states, electrical conductance, and Seebeck coefficient to examine the thermoelectric characteristics of the molecular junction.

Effect of graphene electrode functionalization on machine learning-aided single nucleotide classification

Solid-state nanogap-based DNA sequencing with a quantum tunneling approach has emerged as a promising avenue due to its potential to deliver swift and precise sequencing outcomes. Nevertheless, despite significant progress, experimentally achieving single base resolution with a high signal-to-noise ratio remains a daunting challenge. In this work, we have utilized a machine learning (ML) framework coupled with the quantum transport method to assess and compare the nucleotide identification performance of graphene nanogaps functionalized with four different edge-saturating entities (C, H, N, and OH). The optimized ML model, especially the random forest classifier (RFC), demonstrates high accuracy (>90%) in classifying unlabeled nucleotides from their transmission readouts with the four functionalized graphene nanogaps. Additionally, the minor variance in the accuracy of nucleotide classification across the nanogaps highlights that RFC can capture the role of electrode-nucleotide coupling dynamics in their transmission function. Moreover, we have also conducted conductance sensitivity (%) and current-voltage (I-V) analyses of each functionalized nanogap. Among the edge-saturating entities, the nitrogen atom terminated graphene nanogap (NGN) is found to be the most sensitive for distinguishing DNA nucleotides. Our quantum transport combined ML study provides a useful perspective by conducting a comparative analysis of the role of edge-saturating entities in single-molecule DNA sequencing.

Signature of pressure-induced topological phase transition in ZrTe5

The layered van der Waals material ZrTe5 is known as a candidate topological insulator (TI), however its topological phase and the relation with other properties such as an apparent Dirac semimetallic state is still a subject of debate. We employ a semiclassical multicarrier transport (MCT) model to analyze the magnetotransport of ZrTe5 nanodevices at hydrostatic pressures up to 2 GPa. The temperature dependence of the MCT results between 10 and 300 K is assessed in the context of thermal activation, and we obtain the positions of conduction and valence band edges in the vicinity of the chemical potential. We find evidence of the closing and re-opening of the band gap with increasing pressure, which is consistent with a phase transition from weak to strong TI. This matches expectations from ab initio band structure calculations, as well as previous observations that CVT-grown ZrTe5 is a weak TI in ambient conditions.

Pressure and temperature diagram of C60 from atomistic simulations

Although widely studied experimentally in the 1990s, the structure and properties of low-dimensional or high-pressure phases of fullerenes have recently been re-examined. Remarkably, recent experiments have shown that transparent, nearly pure amorphous sp3-bonded carbon phases can be obtained by heating a C60 molecular crystal at a high pressure. With the additional aim of testing the ability of three classical carbon potentials reactive empirical bond order, environment-dependent interatomic potential, and reactive force-field to reproduce these results, we investigate the details of the structural transformations undergone by fullerene crystals over a wide range of pressures and temperatures. All the potentials tested show that the initial polymerization of fullerenes is accompanied by negative thermal expansion, albeit in slightly different ranges. However, more significant differences in structural and mechanical properties are observed in the amorphous phases, in particular the sp3 carbon fraction and the existence of layered amorphous carbon. Overall, these results indicate to which extent classical reactive potentials can be used to explore phase transitions over a wide range of pressures and temperatures.

DFT-based finite element analysis of compressive response in armchair phosphorene nanotubes

In this paper, the finite element method is utilized to evaluate the behavior of the armchair phosphorene nanotubes under the compressive loading. The energy equations of the molecular and structural mechanics are used to obtain the elemental properties. The critical compressive forces of various armchair phosphorene nanotubes are computed with clamped-clamped and clamped-free boundary conditions. Results show that the stability of armchair phosphorene nanotubes increases with increasing nanotube aspect ratio, particularly under clamped-clamped boundary conditions. Finally, the buckling mode shapes of armchair phosphorene nanotubes under different boundary conditions are compared. Our work offers valuable insights into how these nanotubes respond to mechanical stress, helps determine elemental properties, and investigates the effects of nanotube geometry and different boundary conditions on their stability. This knowledge has broad applications in fields like nanotechnology, materials science, and nanomechanics, advancing the understanding of nanoscale materials and their potential for various practical uses.

Investigation of thermoelectric properties of cadmium selenide CdnSen (n= 7, 11, 13) molecular junctions: a DFT study

CONTEXT

The thermoelectric properties of cadmium selenide (CdnSen) molecular junctions (n = 7, 11, 13) were investigated before and after adding hydrogen atoms. The effects of hydrogen passivation on the transmission and thermopower curves were analyzed. CdSe-diamantane (Cd7Se7) and CdSe-tetramantane (Cd11Se11) junctions exhibited the best thermoelectric performance due to their low surface reconstruction energy, which is attributed to the number of dangling and unsaturated bonds. This study guides the design of new molecular junctions with desired thermoelectric properties.

METHOD

The electrical and thermal properties of cadmium selenide (CdnSen) molecular junctions (n = 7, 11, 13) were investigated using a ballistic quantum transport method based on the non-equilibrium Green's function (NEGF) approach. Thermoelectric properties were calculated for the molecular junctions with different structures before and after hydrogen passivation. Density functional theory (DFT) calculations were performed at the B3LYP level with the 3-21G basis set for the Cd atoms and the 6-31G** basis set for the Se atoms. The SIESTA and GOLLUM codes were used to study the effect of changing the shape and size of each structure on its electrical and thermal characteristics.

Finite Difference Interpolation for Reduction of Grid-Related Errors in Real-Space Pseudopotential Density Functional Theory

The real-space pseudopotential approach is a well-known method for large-scale density functional theory (DFT) calculations. One of its main limitations, however, is the introduction of errors associated with the positioning of the underlying real-space grid, a phenomenon usually known as the "egg-box" effect. The effect can be controlled by using a finer grid, but this raises the cost of the calculations or even undermines their feasibility altogether. Therefore, there is ongoing interest in the reduction of the effect per a given real-space grid. Here, we present a finite difference interpolation of electron orbitals as a means of exploiting the high resolution of the pseudopotential to reduce egg-box effects systematically. We implement the method in PARSEC, a finite difference real-space pseudopotential DFT code, and demonstrate error mitigation and improved convergence at a low additional computational cost.

Quantum Interference and Contact Effects in the Thermoelectric Performance of Anthracene-Based Molecules

We report on the single-molecule electronic and thermoelectric properties of strategically chosen anthracene-based molecules with anchor groups capable of binding to noble metal substrates, such as gold and platinum. Specifically, we study the effect of different anchor groups, as well as quantum interference, on the electric conductance and the thermopower of gold/single-molecule/gold junctions and generally find good agreement between theory and experiments. All molecular junctions display transport characteristics consistent with coherent transport and a Fermi alignment approximately in the middle of the highest occupied molecular orbital/lowest unoccupied molecular orbital gap. Single-molecule results are in agreement with previously reported thin-film data, further supporting the notion that molecular design considerations may be translated from the single- to many-molecule devices. For combinations of anchor groups where one binds significantly more strongly to the electrodes than the other, the stronger anchor group appears to dominate the thermoelectric behavior of the molecular junction. For other combinations, the choice of electrode material can determine the sign and magnitude of the thermopower. This finding has important implications for the design of thermoelectric generator devices, where both n- and p-type conductors are required for thermoelectric current generation.

Metastable Polymorphic Phases in Monolayer TaTe2

Polymorphic phases and collective phenomena-such as charge density waves (CDWs)-in transition metal dichalcogenides (TMDs) dictate the physical and electronic properties of the material. Most TMDs naturally occur in a single given phase, but the fine-tuning of growth conditions via methods such as molecular beam epitaxy (MBE) allows to unlock otherwise inaccessible polymorphic structures. Exploring and understanding the morphological and electronic properties of new phases of TMDs is an essential step to enable their exploitation in technological applications. Here, scanning tunneling microscopy (STM) is used to map MBE-grown monolayer (ML) TaTe₂ . This work reports the first observation of the 1H polymorphic phase, coexisting with the 1T, and demonstrates that their relative coverage can be controlled by adjusting synthesis parameters. Several superperiodic structures, compatible with CDWs, are observed to coexist on the 1T phase. Finally, this work provides theoretical insight on the delicate balance between Te…Te and Ta-Ta interactions that dictates the stability of the different phases. The findings demonstrate that TaTe₂ is an ideal platform to investigate competing interactions, and indicate that accurate tuning of growth conditions is key to accessing metastable states in TMDs.

Mixed-Valence Conductors from Ni Bis(diselenolene) Complexes with a Thiazoline Backbone

Highly conducting, mixed-valence, multi-component nickel bis(diselenolene) salts were obtained by electrocrystallization of the monoanionic species [Ni(Me-thiazds)₂]^-1 (Me-thiazds: N-methyl-1,3-thiazoline-2-thione-4,5-diselenolate), with 1:2 and 1:3 stoichiometries depending of the counter ion used (Et₄N⁺ and nBu₄N⁺ vs Ph₄P⁺, respectively). This behavior strongly differs from that of the corresponding monoanionic dithiolene complexes whose oxidation afforded the single component neutral species. This provides additional rare examples of mixed-valence conducting salts of nickel diselenolene complexes, only known in two examples with the dsit (1,3-dithiole-2-thione-4,5-diselenolate) and dsise (1,3-dithiole-2-selone-4,5-diselenolate) ligands. The mixed-valence salts form highly dimerized or trimerized bi- and trimetallic units, rarely seen with such nickel complexes. Transport measurements under a high pressure (up to 10 GPa) and band structure calculations confirm the semiconducting character of [Ph₄P][Ni(Me-thiazds)₂]₃ and the quasi metallic character of [Et₄N][Ni(Me-thiazds)₂]₂ and [NBu₄]_x[Ni(Me-thiazds)₂]₂ salts (0 < x < 1).

Bis(Vinylenedithio)-Tetrathiafulvalene-Based Coordination Networks

Novel coordination polymers embedding electroactive moieties present a high interest in the development of porous conducting materials. While tetrathiafulvalene (TTF) based metal-organic frameworks were reported to yield through-space conducting frameworks, the use of S-enriched scaffolds remains elusive in this field. Herein is reported the employment of bis(vinylenedithio)-tetrathiafulvalene (BVDT-TTF) functionalized with pyridine coordinating moieties in coordination polymers. Its combination with various transition metals yielded four isostructural networks, whose conductivity increased upon chemical oxidation with iodine. The oxidation was confirmed in a single-crystal to single-crystal X-ray diffraction experiment for the Cd(II) coordination polymer. Raman spectroscopy measurements and DFT calculations confirmed the oxidation state of the bulk materials, and band structure calculations assessed the ground state as an electronically localized antiferromagnetic state, while the conduction occurs in a 2D manner. These results are shedding light to comprehend how to improve through-space conductivity thanks to sulfur enriched ligands.

Plasmonic Ag/Cu/PEG nanofluids prepared when solids meet liquids in the gas phase

Since the time of Faraday's experiments, the optical response of plasmonic nanofluids has been tailored by the shape, size, concentration, and material of nanoparticles (NPs), or by mixing different types of NPs. To date, water-based liquids have been the most extensively investigated host media, while polymers, such as poly(ethylene glycol) (PEG), have frequently been added to introduce repulsive steric interactions and protect NPs from agglomeration. Here, we introduce an inverse system of non-aqueous nanofluids, in which Ag and Cu NPs are dispersed in PEG (400 g mol^-1), with no solvents or chemicals involved. Our single-step approach comprises the synthesis of metal NPs in the gas phase using sputtering-based gas aggregation cluster sources, gas flow transport of NPs, and their deposition (optionally simultaneous) on the PEG surface. Using computational fluid dynamics simulations, we show that NPs diffuse into PEG at an average velocity of the diffusion front of the order of μm s^-1, which is sufficient for efficient loading of the entire polymer bulk. We synthesize yellow Ag/PEG, green Cu/PEG, and blue Ag/Cu/PEG nanofluids, in which the color is given by the position of the plasmon resonance. NPs are prone to partial agglomeration and sedimentation, with a slower kinetics for Cu. Density functional theory calculations combined with UV-vis data and zeta-potential measurements prove that the surface oxidation to Cu₂O and stronger electrostatic repulsion are responsible for the higher stability of Cu NPs. Adopting the De Gennes formalism, we estimate that PEG molecules adsorb on the NP surface in mushroom coordination, with the thickness of the adsorbed layer L < 1.4 nm, grafting density σ < 0.20, and the average distance between the grafted chains D > 0.8 nm. Such values provide sufficient steric barriers to retard, but not completely prevent, agglomeration. Overall, our approach offers an excellent platform for fundamental research on non-aqueous nanofluids, with metal-polymer and metal-metal interactions unperturbed by the presence of solvents or chemical residues.

Controlling anisotropic properties by manipulating the orientation of chiral small molecules

Chiral π-conjugated molecules bring new functionality to technological applications and represent an exciting, rapidly expanding area of research. Their functional properties, such as the absorption and emission of circularly polarized light or the transport of spin-polarized electrons, are highly anisotropic. As a result, the orientation of chiral molecules critically determines the functionality and efficiency of chiral devices. Here we present a strategy to control the orientation of a small chiral molecule (2,2'-dicyano[6]helicene) by the use of organic and inorganic templating layers. Such templating layers can either force 2,2'-dicyano[6]helicene to adopt a face-on orientation and self-assemble into upright supramolecular columns oriented with their helical axis perpendicular to the substrate, or an edge-on orientation with parallel-lying supramolecular columns. Through such control, we show that low- and high-energy chiroptical responses can be independently 'turned on' or 'turned off'. The templating methodologies described here provide a simple way to engineer orientational control and, by association, anisotropic functional properties of chiral molecular systems for a range of emerging technologies.

Observation of competing, correlated ground states in the flat band of rhombohedral graphite

In crystalline solids, the interactions of charge and spin can result in a variety of emergent quantum ground states, especially in partially filled, topological flat bands such as Landau levels or in "magic angle" graphene layers. Much less explored is rhombohedral graphite (RG), perhaps the simplest and structurally most perfect condensed matter system to host a flat band protected by symmetry. By scanning tunneling microscopy, we map the flat band charge density of 8, 10, 14, and 17 layers and identify a domain structure emerging from a competition between a sublattice antiferromagnetic insulator and a gapless correlated paramagnet. Our density matrix renormalization group calculations explain the observed features and demonstrate that the correlations are fundamentally different from graphene-based magnetism identified until now, forming the ground state of a quantum magnet. Our work establishes RG as a platform to study many-body interactions beyond the mean-field approach, where quantum fluctuations and entanglement dominate.

Accelerated Deep Learning Dynamics for Atomic Layer Deposition of Al(Me)3 and Water on OH/Si(111)

Knowledge of the detailed mechanism behind the atomic layer deposition (ALD) can greatly facilitate the optimization of the manufacturing process. Computational modeling can potentially foster the understanding; however, the presently available capabilities of the accurate ab initio computational techniques preclude their application to modeling surface processes occurring on a long time scale, such as ALD. Although the situation can be greatly improved using machine learning (ML), this technique requires an enormous amount of data for training datasets. Here, we propose an iterative protocol for optimizing ML training datasets and apply ML-assisted ab initio calculations to model surface reactions occurring during the Al(Me)₃/H₂O ALD process on the OH-terminated Si (111) surface. The protocol uses a recently developed low-dimensional projection technique (TDUS), greatly reducing the amount of information required to achieve high accuracy (ca. 1 kcal/mol or less) of the developed ML models. The resulting free energy landscapes reveal fine details of various aspects of the target ALD process, such as the surface proton transfer, zwitterionic surface configurations, elimination-addition/addition-elimination, and S_N2 reactions as well as the role of the surface entropic and temperature effects. Simulations of adsorption dynamics predict that the maximum physisorption rate of ca. 70% is achieved at the incidence velocity u_rms of the reactants in the range of 15-20 Å/ps. Hence, the proposed protocol furnishes a very effective tool to study complex chemical reaction dynamics at a much reduced computational cost.

Electronic Properties and Structure of Silicene on Cu and Ni Substrates

Silicene, together with copper or nickel, is the main component of electrodes for solar cells, lithium-ion batteries (LIB) and new-generation supercapacitors. The aim of this work was to study the electronic properties and geometric structure of “silicene–Ni” and “silicene–Cu” systems intended for use as LIB electrodes. The densities of electronic states, band structures, adhesion energies and interatomic distances in the silicene–(Cu, Ni) systems were determined by ab initio calculations. Silicene on a copper substrate exhibited temperature stability in the temperature range from 200 to 800 K, while on a nickel substrate, the structure of silicene was rearranged. Adsorption energies and bond lengths in the “silicene–Cu” system were calculated in the range of Li/Si ratios from 0.125 to 0.5. The formation of the Li₂ isomer during the adsorption of lithium in a ratio to silicon of 0.375 and 0.5 was observed. Silicene was found to remain stable when placed on a copper substrate coated with a single layer of nickel. The charge redistribution caused by the addition of a nickel intermediate layer between silicene and a copper substrate was studied.

Multi-component self-assembled molecular-electronic films: towards new high-performance thermoelectric systems

The thermoelectric properties of parallel arrays of organic molecules on a surface offer the potential for large-area, flexible, solution processed, energy harvesting thin-films, whose room-temperature transport properties are controlled by quantum interference (QI). Recently, it has been demonstrated that constructive QI (CQI) can be translated from single molecules to self-assembled monolayers (SAMs), boosting both electrical conductivities and Seebeck coefficients. However, these CQI-enhanced systems are limited by rigid coupling of the component molecules to metallic electrodes, preventing the introduction of additional layers which would be advantageous for their further development. These rigid couplings also limit our ability to suppress the transport of phonons through these systems, which could act to boost their thermoelectric output, without comprising on their impressive electronic features. Here, through a combined experimental and theoretical study, we show that cross-plane thermoelectricity in SAMs can be enhanced by incorporating extra molecular layers. We utilize a bottom-up approach to assemble multi-component thin-films that combine a rigid, highly conductive 'sticky'-linker, formed from alkynyl-functionalised anthracenes, and a 'slippery'-linker consisting of a functionalized metalloporphyrin. Starting from an anthracene-based SAM, we demonstrate that subsequent addition of either a porphyrin layer or a graphene layer increases the Seebeck coefficient, and addition of both porphyrin and graphene leads to a further boost in their Seebeck coefficients. This demonstration of Seebeck-enhanced multi-component SAMs is the first of its kind and presents a new strategy towards the design of thin-film thermoelectric materials.

Atomically Sharp Lateral Superlattice Heterojunctions Built-In Nitrogen-Doped Nanoporous Graphene

Nanometer scale lateral heterostructures with atomically sharp band discontinuities can be conceived as the 2D analogues of vertical Van der Waals heterostructures, where pristine properties of each component coexist with interfacial phenomena that result in a variety of exotic quantum phenomena. However, despite considerable advances in the fabrication of lateral heterostructures, controlling their covalent interfaces and band discontinuities with atomic precision, scaling down components and producing periodic, lattice-coherent superlattices still represent major challenges. Here, a synthetic strategy to fabricate nanometer scale, coherent lateral superlattice heterojunctions with atomically sharp band discontinuity is reported. By merging interdigitated arrays of different types of graphene nanoribbons by means of a novel on-surface reaction, superlattices of 1D, and chemically heterogeneous nanoporous junctions are obtained. The latter host subnanometer quantum dipoles and tunneling in-gap states, altogether expected to promote interfacial phenomena such as interribbon excitons or selective photocatalysis.

Metal-Organic Frameworks for NOx Adsorption and Their Applications in Separation, Sensing, Catalysis, and Biology

Nitrogen oxide (NO_x ) is a family of poisonous and highly reactive gases formed when fuel is burned at high temperatures during anthropogenic behavior. It is a strong oxidizing agent that significantly contributes to the ozone and smog in the atmosphere. Thus, NO_x removal is important for the ecological environment upon which the civilization depends. In recent decades, metal-organic frameworks (MOFs) have been regarded as ideal candidates to address these issues because they form a reticular structure between proper inorganic and organic constituents with ultrahigh porosity and high internal surface area. These characteristics render them chemically adaptable for NO_x adsorption, separation, sensing, and catalysis. In additional, MOFs enable potential nitric oxide (NO) delivery for the signaling of molecular NO in the human body. Herein, the different advantages of MOFs for coping with current environmental burdens and improving the habitable environment of humans on the basis of NO_x adsorption are reviewed.

X-ray Induced Fragmentation of Protonated Cystine

We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur L-edge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.

Strain modulating electronic band gaps and SQ efficiencies of semiconductor 2D PdQ2 (Q = S, Se) monolayer

We studied the physical, electronic transport and optical properties of a unique pentagonal PdQ2 (Q = S, Se) monolayers. The dynamic stability of 2Dwrinkle like-PdQ2 is proven by positive phonon frequencies in the phonon dispersion curve. The optimized structural parameters of wrinkled pentagonal PdQ2 are in good agreement with the available experimental results. The ultimate tensile strength (UTHS) was calculated and found that, penta-PdS2 monolayer can withstand up to 16% (18%) strain along x (y) direction with 3.44 GPa (3.43 GPa). While, penta-PdSe2 monolayer can withstand up to 17% (19%) strain along x (y) dirrection with 3.46 GPa (3.40 GPa). It is found that, the penta-PdQ2 monolayers has the semiconducting behavior with indirect band gap of 0.94 and 1.26 eV for 2D-PdS2 and 2D-PdSe2, respectively. More interestingly, at room temperacture, the hole mobilty (electron mobility) obtained for 2D-PdS2 and PdSe2 are 67.43 (258.06) cm2 V-1 s-1 and 1518.81 (442.49) cm2 V-1 s-1, respectively. In addition, I-V characteristics of PdSe2 monolayer show strong negative differential conductance (NDC) region near the 3.57 V. The Shockly-Queisser (SQ) effeciency prameters of PdQ2 monolayers are also explored and the highest SQ efficeinciy obtained for PdS2 is 33.93% at -5% strain and for PdSe2 is 33.94% at -2% strain. The penta-PdQ2 exhibits high optical absorption intensity in the UV region, up to 4.04 × 105 (for PdS2) and 5.28 × 105 (for PdSe2), which is suitable for applications in optoelectronic devices. Thus, the ultrathin PdQ2 monolayers could be potential material for next-generation solar-cell applications and high performance nanodevices.

Computational Methods for Charge Density Waves in 2D Materials

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

Molecular Modelling of Optical Biosensor Phosphorene-Thioguanine for Optimal Drug Delivery in Leukemia Treatment

Thioguanine is an anti-cancer drug used for the treatment of leukemia. However, thioguanine has weak aqueous solubility and low biocompatibility, which limits its performance in the treatment of cancer. In the present work, these inadequacies were targeted using density functional theory-based simulations. Three stable configurations were obtained for the adsorption of thioguanine molecules on the phosphorene surface, with adsorption energies in the range of -76.99 to -38.69 kJ/mol, indicating physisorption of the drug on the phosphorene surface. The calculated bandgap energies of the individual and combined geometries of phosphorene and thioguanine were 0.97 eV, 2.81 eV and 0.91 eV, respectively. Owing to the physisorption of the drug molecule on the phosphorene surface, the bandgap energy of the material had a direct impact on optical conductivity, which was significantly altered. All parameters that determine the potential ability for drug delivery were calculated, such as the dipole moment, chemical hardness, chemical softness, chemical potential, and electrophilicity index. The higher dipole moment (1.74 D) of the phosphorene-thioguanine complex reflects its higher biodegradability, with no adverse physiological effects.

From Zero- to One-Dimensional, Opportunities and Caveats of Hybrid Iodobismuthates for Optoelectronic Applications

The association of the electron acceptor 4,4'-amino-bipyridinium (AmV²⁺) dication and BiI₃ in an acidic solution affords three organic-inorganic hybrid materials, (AmV)₃(BiI₆)₂ (1), (AmV)₂(Bi₄I₁₆) (2), and (AmV)BiI₅ (3), whose structures are based on isolated BiI₆^3- and Bi₄I₁₆^4- anion clusters in 1 and 2, respectively, and on a one-dimensional (1D) chain of trans-connected corner-sharing octahedra in 3. In contrast with known methylviologen-based hybrids, these compounds are more soluble in polar solvents, allowing thin film formation by spin-coating. (AmV)BiI₅ exhibits a broad absorption band in the visible region leading to an optical bandgap of 1.54 eV and shows a PV effect as demonstrated by a significant open-circuit voltage close to 500 mV. The electronic structure of the three compounds has been investigated using first-principles calculations based on density functional theory (DFT). Unexpectedly, despite the trans-connected corner-shared octahedra, for (AmV)BiI₅, the valence state shows no coupling along the wire direction, leading to a high effective mass for holes, while in contrast, the strong coupling between Bi 6p_x orbitals in the same direction at the conduction band minimum suggests excellent electron transport properties. This contributes to the low current output leading to the low efficiency of perovskite solar cells based on (AmV)BiI₅. Further insight is provided for trans- and cis-MI₅ 1D model structures (M = Bi or Pb) based on DFT investigations.

Covalently Linked Porphyrins as One-Dimensional Conductors

We apply first-principles calculations to address the problem of the formation and characterization of covalently linked porphyrin-like structures. We show that upon pressure a rehybridization process takes place which leads to one-dimensional compounds resembling nanothreads, in which carbon atoms are all 4-fold coordinated. We also show that the resulting nanostructures have metallic character and possess remarkable mechanical properties. Moreover, in the case of porphyrin-metal complexes, we find that the covalently linked structures may be a platform for the stabilization of straight metallic wires.

Approaching the basis set limit in Gaussian-orbital-based periodic calculations with transferability: Performance of pure density functionals for simple semiconductors

Simulating solids with quantum chemistry methods and Gaussian-type orbitals (GTOs) has been gaining popularity. Nonetheless, there are few systematic studies that assess the basis set incompleteness error (BSIE) in these GTO-based simulations over a variety of solids. In this work, we report a GTO-based implementation for solids and apply it to address the basis set convergence issue. We employ a simple strategy to generate large uncontracted (unc) GTO basis sets that we call the unc-def2-GTH sets. These basis sets exhibit systematic improvement toward the basis set limit as well as good transferability based on application to a total of 43 simple semiconductors. Most notably, we found the BSIE of unc-def2-QZVP-GTH to be smaller than 0.7 mEh per atom in total energies and 20 meV in bandgaps for all systems considered here. Using unc-def2-QZVP-GTH, we report bandgap benchmarks of a combinatorially designed meta-generalized gradient approximation (mGGA) functional, B97M-rV, and show that B97M-rV performs similarly (a root-mean-square-deviation of 1.18 eV) to other modern mGGA functionals, M06-L (1.26 eV), MN15-L (1.29 eV), and Strongly Constrained and Appropriately Normed (SCAN) (1.20 eV). This represents a clear improvement over older pure functionals such as local density approximation (1.71 eV) and Perdew-Burke-Ernzerhof (PBE) (1.49 eV), although all these mGGAs are still far from being quantitatively accurate. We also provide several cautionary notes on the use of our uncontracted bases and on future research on GTO basis set development for solids.

Basic aspects of the charge density wave instability of transition metal trichalcogenides NbSe3and monoclinic-TaS3

NbSe₃and monoclinic-TaS₃(m-TaS₃) are quasi-1D metals containing three different types of chains and undergoing two different charge density wave Peierls transitions atTP1andTP2associated with type III and type I chains, respectively. The nature of these transitions is discussed on the basis of first-principles DFT calculation of their Fermi surface (FS) and electron-hole response function. Because of the stronger inter-chain interactions, the FS and electron-hole response function are considerably more complex for NbSe₃thanm-TaS₃; however a common scenario can be put forward to rationalize the results. The intra-chain inter-band nesting processes dominate the strongest response for both type I and type III chains of the two compounds. Two well-defined maxima of the electron-hole response for NbSe₃are found with the (0a^*, 0c^*) and (1/2a^*, 1/2c^*) transverse components atTP1andTP2, respectively, whereas the second maximum is not observed form-TaS₃atTP2. Analysis of the different inter-chain coupling mechanisms leads to the conclusion that FS nesting effects are only relevant to set the transversea^*components in NbSe₃. The strongest inter-chain Coulomb coupling mechanism must be taken into account for the transverse coupling alongc^*in NbSe₃and along botha^*andc^*form-TaS₃. Phonon spectrum calculations reveal the formation of a giant 2k_FKohn anomaly form-TaS₃. All these results support a weak coupling scenario for the Peierls transition of transition metal trichalcogenides.

Interplay between structural deformations and flat band phenomenology in twisted bilayer antimonene

In this work we apply first principles calculations to investigate the flat band phenomenology in twisted antimonene bilayer. We show that the relatively strong interlayer interactions which characterize this compound have profound effects in the emergence and properties of the flat bands. Specifically, when the moiré length becomes large enough to create well defined stacking patterns along the structure, out-of-plane displacements take place and are stabilized in the regions dominated by the AB stacking, leading to the emergence of flat bands. The interplay between structural and electronic properties allows for detection of flat bands in higher twist angles comparable to other two-dimensional materials. We also show that their energy position may be modulated by noncovalent functionalization with electron acceptor molecules.

Insights into the growth of nanoparticles in liquid polyol by thermal annealing

We report on the growth of metal- and metal-oxide based nanoparticles (NPs) in heated polyol solutions. For this purpose, NPs are produced by the sputtering of a silver, gold, or a copper target to produce either silver, gold, or copper oxide NPs in pentaerythritol ethoxylate (PEEL) which has been annealed up to 200 °C. The objective of the annealing step is the fine modulation of their size. Thus, the evolution of the NP size and shape after thermal annealing is explained according to collision/coalescence kinetics and the affinity between the metal-/metal-oxide and PEEL molecule. Moreover, highlights of few phenomena arising from the annealing step are described such as (i) the reduction of copper oxide into copper by the polyol process and (ii) the effective formation of carbon dots after annealing at 200 °C.

Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study

We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.

Environmentally hazardous gas sensing ability of MoS2-nanotubes: an insight from the electronic structure and transport properties

Herein we have investigated the ability of the (6,6) MoS₂-nanotube (NT) to sense environmentally hazardous electrophilic and nucleophilic gases using density functional theory (DFT). CO, CO₂, H₂O and NH₃ gases were chosen for adsorption on the (6,6) MoS₂-NT and different adsorption parameters such as adsorption energy, projected density of states (PDOS), band structure and structural changes after adsorption were evaluated. Nucleophilic gases NH₃ and H₂O showed a fairly high amount of electron density transfer from gas molecules to the NT while the opposite trend was realized for electrophilic gases CO and CO₂. Among the four gases, H₂O has the highest amount of adsorption energy (-1.74 eV) and a moderately high amount of charge transfer from H₂O to the NT. Gas sensing behaviour was further rationalized from the enhanced I-V characteristics of gas adsorbed nanotubes compared to pristine ones. Analysis of results revealed that the (6,6) MoS₂-NT showed a decent level of gas sensing properties towards CO, CO₂, H₂O and NH₃ gases, and high selectivity for H₂O makes the MoS₂-NT superior to previously reported MoS₂-monolayer in this matter. These results suggest the possibility of fabrication of highly efficient MoS₂-NT based gas sensors for environmentally hazardous gases.

Enhanced reliability of phase-change memory via modulation of local structure and chemical bonding by incorporating carbon in Ge2Sb2Te5

In this study, we investigated the effect of phase-change characteristics on the device performance of carbon-incorporated Ge₂Sb₂Te₅ (CGST) to understand the origin of the enhanced reliability and stabilization of the device. Macroscopic and microscopic measurements confirmed that the structural stability significantly increased with the incorporation of as much as 10% carbon. After the completion of bond formation between C and Ge, the excess C (>5 atomic%) engages in bonding with Sb in localized regions because of the difference in formation energy. These bonds of C with Ge and Sb induce non-uniform local charge density of the short-range order. Finally, because the strong bonds between Ge and C shorten the short Ge-Te bonds, the high thermal stability of CGST relative to that of GST can be attributed to intensified Peierls distortion. The formation of strong bonds successfully underpins the local structures and reduces the stochastic effect. Moreover, extension of the C bonding to Sb enhances the structural reliability, resulting in highly stable CGST in the amorphous phase. Finally, the device stability of CGST in the reset state of the amorphous structure during the device switching process was significantly improved.

Influence of polyethylene glycol plasticizer on the structural and electronic properties of PEO-NaI complex: a density functional study

Ab initio study has been carried out to investigate the influence of low molecular weight polyethylene glycol (PEG) plasticizer on structural and electronic properties of the polyethylene oxide-sodium iodide (PEO-NaI) polymer-metal complex. DOS and PDOS analysis provided a quantitative explanation of the electronic bandgap of the PEO-NaI and PEO-PEG-NaI system. Hirshfeld population charge analysis (HPA) explains better dissociation of NaI in presence of polyethylene glycol, based on the Hard Soft Acid Base Principle. Also, an increase in amorphic content of polymer system is observed with the addition of PEG, evident from the increment in the strength of anti-bonding orbitals in COOP plot. Bond strength of the polymeric system is also found to be affected with the addition of plasticizer. The findings provide an avenue that the present polymer system [PEO-PEG-NaI] is a potential candidate to be used as an electrolyte for next-generation energy storage technology.

Metallic Diluted Dimerization in VO2 Tweeds

The observation of electronic phase separation textures in vanadium dioxide, a prototypical electron-correlated oxide, has recently added new perspectives on the long standing debate about its metal-insulator transition and its applications. Yet, the lack of atomically resolved information on phases accompanying such complex patterns still hinders a comprehensive understanding of the transition and its implementation in practical devices. In this work, atomic resolution imaging and spectroscopy unveils the existence of ferroelastic tweed structures on ≈5 nm length scales, well below the resolution limit of currently used spectroscopic imaging techniques. Moreover, density functional theory calculations show that this pretransitional fine-scale tweed, which on average looks and behaves like the standard metallic rutile phase, is in fact weaved by semi-dimerized chains of vanadium in a new monoclinic phase that represents a structural bridge to the monoclinic insulating ground state. These observations provide a multiscale perspective for the interpretation of existing data, whereby phase coexistence and structural intermixing can occur all the way down to the atomic scale.

In silico design of a new Zn-triazole based metal-organic framework for CO2 and H2O adsorption

In search for future good adsorbents for CO₂ capture, a nitrogen-rich triazole-type Metal-Organic Framework (MOF) is proposed based on the rational design and theoretical molecular simulations. The structure of the proposed MOF, named Zinc Triazolate based Framework (ZTF), is obtained by replacing the amine-organic linker of MAF-66 by a triazole, and its structural parameters are deduced. We used grand-canonical Monte Carlo (GCMC) simulations based on generic classical force fields to correctly predict the adsorption isotherms of CO₂ and H₂O. For water adsorption in MAF-66 and ZTF, simulations revealed that the strong hydrogen bonding interactions of water with the N atoms of triazole rings of the frameworks are the main driving forces for the high adsorption uptake of water. We also show that the proposed ZTF porous material exhibits exceptional high CO₂ uptake capacity at low pressure, better than MAF-66. Moreover, the nature of the interactions between CO₂ and the MAF-66 and ZTF surface cavities was examined at the microscopic level. Computations show that the interactions occur at two different sites, consisting of Lewis acid-Lewis base interactions and hydrogen bonding, together with obvious electrostatic interactions. In addition, we investigated the influence of the presence of H₂O molecules on the CO₂ adsorption on the ZTF MOF. GCMC simulations reveal that the addition of H₂O molecules leads to an enhancement of the CO₂ adsorption at very low pressures but a reduction of this CO₂ adsorption at higher pressures.

Co-sputtering of gold and copper onto liquids: a route towards the production of porous gold nanoparticles

Effective methods for the synthesis of high-purity nanoparticles (NPs) have been extensively studied for a few decades. Among others, cold plasma-based sputtering metals onto a liquid substrate appears to be a very promising technique for the synthesis of high-purity NPs. The process enables the production of very small NPs without using any toxic reagents and complex chemical synthesis routes, and enables the synthesis of alloy NPs which can be the first step towards the formation of porous NPs. In this paper, the synthesis of gold-copper alloy NPs has been performed by co-sputtering gold and copper targets over pentaerythritol ethoxylate. The resulting solutions contain a mixture of gold, copper oxide, and alloy NPs having a radius of few angstroms. The annealing of these NPs, inside the solution, has been performed in order to increase their size and further induce the dealloying of the Au-Cu NPs. The resulting NPs exhibit either a nanoporous structure or are self-organized in an agglomerate of small NPs.

KIMERA: A Kinetic Montecarlo Code for Mineral Dissolution

KIMERA is a scientific tool for the study of mineral dissolution. It implements a reversible Kinetic Monte Carlo (KMC) method to study the time evolution of a dissolving system, obtaining the dissolution rate and information about the atomic scale dissolution mechanisms. KIMERA allows to define the dissolution process in multiple ways, using a wide diversity of event types to mimic the dissolution reactions, and define the mineral structure in great detail, including topographic defects, dislocations, and point defects. Therefore, KIMERA ensures to perform numerous studies with great versatility. In addition, it offers a good performance thanks to its parallelization and efficient algorithms within the KMC method. In this manuscript, we present the code features and show some examples of its capabilities. KIMERA is controllable via user commands, it is written in object-oriented C++, and it is distributed as open-source software.

A DFT-based finite element approach for studying elastic properties, buckling and vibration of the arsenene

A finite element model is developed to modeli the arsenene nanosheet. To obtain the element properties, which are used to represent As-As bonds in the structure of the arsenene, first principle calculation is used. The developed model is then used to compute Young's modulus, critical compressive force and the fundamental frequency of the arsenene nanosheet with different geometrical parameters. It is seen that the employed finite element model can be efficiently used to predict surface Young's modulus of the arsenene. Furthermore, larger arsenene nanosheets have larger surface Young's modulus. In the next step, the critical compressive forces of the arsenene nanosheet under different boundary conditions are computed. It is seen that the influence of the boundary conditions has higher impact on the bunking force of the smaller arsenenes nanosheets. Finally, investigating the vibrational characteristics of the arsenene nanosheets revealed that increasing the horizontal side length at a constant vertical side length leads to a reduction in the fundamental natural frequency.

Symmetry Dictated Grain Boundary State in a Two-Dimensional Topological Insulator

Grain boundaries (GBs) are ubiquitous in solids and have been of central importance in understanding the nature of polycrystals. In addition to their classical roles, topological insulators (TIs) offer a chance to realize GBs hosting distinct topological states that can be controlled by their crystal symmetries. However, such roles of crystalline symmetry in two-dimensional (2D) TIs have not been definitively measured yet. Here, we present the first direct evidence of a symmetry-enforced metallic state along a GB in 1T'-MoTe₂, a prototypical 2D TI. Using scanning tunneling microscopy, we show a metallic state along a GB with nonsymmorphic lattice symmetry and its absence along another boundary with symmorphic symmetry. Our atomistic simulations demonstrate in-gap Weyl semimetallic states for the former, whereas they demonstrate gapped states for the latter, explaining our observation well. The observed metallic state, tightly linked to its crystal symmetry, can be used to create a stable conducting nanowire inside TIs.

New insights into the structural properties of κ-(BEDT-TTF)2Ag2(CN)3 spin liquid

Here, the first accurate study is presented of the room-temperature and 100 K structures of one of the first organic spin liquids, κ-(BEDT-TTF)₂Ag₂(CN)₃. It is shown that the monoclinic structure determined previously is only the average one. It is shown that the exact structure presents triclinic symmetry with two non-equivalent dimers in the unit cell. But surprisingly this does not lead to a sizeable charge disproportionation between dimers. The difference from the analogue compound κ-(BEDT-TTF)₂Cu₂(CN)₃ which also presents a spin liquid phase is discussed in detail. The data provided here show the importance of the anionic layer and in particular the transition metal position in the process of symmetry breaking. The possible impact of the symmetry breaking, albeit weak, on the spin-liquid mechanism and the influence of various disorders on the physical properties of this system is also discussed.

XO-PBC: An Accurate and Efficient Method for Molecular Crystals

In this work, we propose the XO-PBC method, which combines the eXtended ONIOM method (XO) with the periodic boundary condition (PBC) for the description of molecular crystals. XO-PBC tries to embed a finite cluster cut out from the solid into the periodic environment, making it feasible to employ advanced molecular quantum chemistry methods, which are usually prohibitively expensive for direct PBC calculations. In particular, XO-PBC utilizes the results from force calculations to design the scheme to fragment the molecule when crystals are made of large molecules and to select cluster model systems automatically consisting of dimer up to tetramer interactions for embedding. By applying an appropriate theory to each model, a satisfactory accuracy for the system under study is ensured, while a high efficiency is achieved with massively parallel computing by distributing model systems onto different processors. A comparison of the XO-PBC calculations with the conventional direct PBC calculations at the B3LYP level demonstrates its accuracy at substantially low cost for the description of molecular crystals. The usefulness of the XO-PBC method is further exemplified, showing that XO-PBC is able to predict the lattice energies of various types of molecular crystals within chemical accuracy (<4 kJ/mol) when the doubly hybrid density functional XYG3 is used as the target high level and the periodic PBE as the basic low level. The XO-PBC method provides a general protocol that brings the great predictive power of advanced electronic structure methods from molecular systems to the extended solids.