Nano-protrusions in intercalated graphite: understanding the structural and electronic effects through DFT.

Complex phenomena characterize the intercalation of ions inside stratified crystals. Their comprehension is crucial in view of exploiting the intercalation mechanism to change the transport properties of the crystal or obtaining a fine control of crystal delamination. In particular, the relationship between the concentration and nature of intercalated ions and surface structural modifications of the host stratified crystal is still under debate. Here, we discuss a theoretical effort to provide a rationale for some structural changes observed on the highly oriented pyrolytic graphite (HOPG) surface after electrochemical treatment in perchloric and sulphuric acid solutions. The formation of the so-called nano-protrusions on the basal plane of intercalated graphite was previously observed with scanning tunneling microscopy (STM). In this work, we employed both STM and density functional theory (DFT) simulations to elucidate the physical and chemical mechanisms driving the emergence of these nano-protrusions. The DFT results show that, in a bilayer graphene system, the presence of a single ion can generate a nano-protrusion with 2.49 Å height and 21.27 Å width. In the deformed area, the C-C bond length is stretched by about 2.5% more than the normal graphene bond. These values are of the same dimensional scale as those reported in previous STM experimental results.25 However, the simulated STM images obtained by increasing the amount of intercalated ions per area suggest that the presence of more than one ion is needed for the deformation of the uppermost graphite layer during the early stages of intercalation. In contrast, in a multilayer graphene system, no significant surface deformation is detected when ions are intercalated between the third and fourth layers. Charge analysis indicates an altered distribution of the charges as a consequence of the intercalation. The charge transfer from graphene layers to the intercalated ions results in a surface layer more prone to oxidation.

Atomistic investigation of surface characteristics and electronic features at high-purity FeSi(110) presenting interfacial metallicity.

Iron silicide (FeSi) is a fascinating material that has attracted extensive research efforts for decades, notably revealing unusual temperature-dependent electronic and magnetic characteristics, as well as a close resemblance to the Kondo insulators whereby a coherent picture of intrinsic properties and underlying physics remains to be fully developed. For a better understanding of this narrow-gap semiconductor, we prepared and examined FeSi(110) single-crystal surfaces of high quality. Combined insights from low-temperature scanning tunneling microscopy and density functional theory calculations (DFT) indicate an unreconstructed surface termination presenting rows of Fe-Si pairs. Using high-resolution tunneling spectroscopy (STS), we identify a distinct asymmetric electronic gap in the sub-10 K regime on defect-free terraces. Moreover, the STS data reveal a residual density of states in the gap regime whereby two in-gap states are recognized. The principal origin of these features is rationalized with the help of the DFT-calculated band structure. The computational modeling of a (110)-oriented slab notably evidences the existence of interfacial intragap bands accounting for a markedly increased density of states around the Fermi level. These findings support and provide further insight into the emergence of surface metallicity in the low-temperature regime.

The Winner Takes It All: Carbon Supersedes Hexagonal Boron Nitride with Graphene on Transition Metals at High Temperatures.

The production of high-quality hexagonal boron nitride (h-BN) is essential for the ultimate performance of 2D materials-based devices, since it is the key 2D encapsulation material. Here, a decisive guideline is reported for fabricating high-quality h-BN on transition metals. It is crucial to exclude carbon from the h-BN related process, otherwise carbon prevails over boron and nitrogen due to its larger binding energy, thereupon forming graphene on metals after high-temperature annealing. The surface reaction-assisted conversion from h-BN to graphene with high-temperature treatments is demonstrated. The pyrolysis temperature Tp is an important quality indicator for h-BN/metals. When the temperature is lower than Tp , the quality of the h-BN layer is improved upon annealing. While the annealing temperature is above Tp , in case of carbon-free conditions, the h-BN disintegrates and nitrogen desorbs from the surface more easily than boron, eventually leading to clean metal surfaces. However, once the h-BN layer is exposed to carbon, graphene forms on Pt(111) in the high-temperature regime. This not only provides an indispensable principle (avoid carbon) for fabricating high-quality h-BN materials on transition metals, but also offers a straightforward method for the surface reaction-assisted conversion from h-BN to graphene on Pt(111).

N-Heterocyclic Carbenes: Molecular Porters of Surface Mounted Ru-Porphyrins.

Ru-porphyrins act as convenient pedestals for the assembly of N-heterocyclic carbenes (NHCs) on solid surfaces. Upon deposition of a simple NHC ligand on a close packed Ru-porphyrin monolayer, an extraordinary phenomenon can be observed: Ru-porphyrin molecules are transferred from the silver surface to the next molecular layer. We have investigated the structural features and dynamics of this portering process and analysed the associated binding strengths and work function changes. A rearrangement of the molecular layer is induced by the NHC uptake: the NHC selective binding to the Ru causes the ejection of whole porphyrin molecules from the molecular layer on silver to the layer on top. This reorganisation can be reversed by thermally induced desorption of the NHC ligand. We anticipate that the understanding of such mass transport processes will have crucial implications for the functionalisation of surfaces with carbenes.

Assembly and Manipulation of a Prototypical N-Heterocyclic Carbene with a Metalloporphyrin Pedestal on a Solid Surface.

The controlled arrangement of N-heterocyclic carbenes (NHCs) on solid surfaces is a current challenge of surface functionalization. We introduce a strategy of using Ru porphyrins in order to control both the orientation and lateral arrangement of NHCs on a planar surface. The coupling of the NHC to the Ru porphyrin is a facile process which takes place on the interface: we apply NHCs as functional, robust pillars on well-defined, preassembled Ru porphyrin monolayers on silver and characterize these interfaces with atomic precision via a battery of experimental techniques and theoretical considerations. The NHCs assemble at room temperature modularly and reversibly on the Ru porphyrin arrays. We demonstrate a selective and complete functionalization of the Ru centers. With its binding, the NHC modifies the interaction of the Ru porphyrin with the Ag surface, displacing the Ru atom by 1 Å away from the surface. This arrangement of NHCs allows us to address individual ligands by controlled manipulation with the tip of a scanning tunneling microscope, creating patterned structures on the nanometer scale.

Conformational Control of Chemical Reactivity for Surface-Confined Ru-Porphyrins.

We assess the crucial role of tetrapyrrole flexibility in the CO ligation to distinct Ru-porphyrins supported on an atomistically well-defined Ag(111) substrate. Our systematic real-space visualisation and manipulation experiments with scanning tunnelling microscopy directly probe the ligation, while bond-resolving atomic force microscopy and X-ray standing-wave measurements characterise the geometry, X-ray and ultraviolet photoelectron spectroscopy the electronic structure, and temperature-programmed desorption the binding strength. Density-functional-theory calculations provide additional insight into the functional interface. We unambiguously demonstrate that the substituents regulate the interfacial conformational adaptability, either promoting or obstructing the uptake of axial CO adducts.

Proton disorder in cubic ice: Effect on the electronic and optical properties.

The proton disorder in ice has a key role in several properties such as the growth mode, thermodynamical properties, and ferroelectricity. While structural phase transitions from proton disordered to proton ordered ices have been extensively studied, much less is known about their electronic and optical properties. Here, we present ab initio many body perturbation theory-based calculations of the electronic and optical properties of cubic ice at different levels of proton disorder. We compare our results with those from liquid water, that acts as an example of a fully (proton- and oxygen-)disordered system. We find that by increasing the proton disorder, a shrinking of the electronic gap occurs in ice, and it is smallest in the liquid water. Simultaneously, the excitonic binding energy decreases, so that the final optical gaps result to be almost independent on the degree of proton disorder. We explain these findings as an interplay between the local dipolar disorder and the electronic correlation.

Chemical Reactions on Metal-supported Hexagonal Boron Nitride Investigated with Density Functional Theory.

Nanotechnology, in order to become ultimately efficient, requires achieving the construction of elemental structures at the atomistic precision. One way toward this goal is using templated surfaces as support for directed synthesis. The nanomesh, a single-atom thick layer of hexagonal boron nitride on Rh(111) [Corso et al., Science 2004, 303, 217], has appeared as one candidate that provides a periodically corrugated structure on the nanometre scale. We present density functional theory studies where we investigate various properties of the nanomesh, ranging from intrinsic defects to covalent functionalisation with hydroxyl radicals. Further we study selective dehalogenation of an organic molecule (I6-CHP) on the nanomesh. This molecule adsorbs at particular sites of the template and has been activated for C-C coupling in recent experiments via dissociation of its halogen ligands. In all cases we find explicit templating effects, either in full agreement with experimental studies or predicting novel phenomena. The studies are evidence for the predictive power of modern electronic structure simulations and the insight that can be gained when used together with experiments on complex chemical structures.

Unconventional Band Structure via Combined Molecular Orbital and Lattice Symmetries in a Surface-Confined Metallated Graphdiyne Sheet.

Graphyne (GY) and graphdiyne (GDY)-based monolayers represent the next generation 2D carbon-rich materials with tunable structures and properties surpassing those of graphene. However, the detection of band formation in atomically thin GY/GDY analogues has been challenging, as both long-range order and atomic precision have to be fulfilled in the system. The present work reports direct evidence of band formation in on-surface synthesized metallated Ag-GDY sheets with mesoscopic (≈1 µm) regularity. Employing scanning tunneling and angle-resolved photoemission spectroscopies, energy-dependent transitions of real-space electronic states above the Fermi level and formation of the valence band are respectively observed. Furthermore, density functional theory (DFT) calculations corroborate the observations and reveal that doubly degenerate frontier molecular orbitals on a honeycomb lattice give rise to flat, Dirac and Kagome bands close to the Fermi level. DFT modeling also indicates an intrinsic band gap for the pristine sheet material, which is retained for a bilayer with h-BN, whereas adsorption-induced in-gap electronic states evolve at the synthesis platform with Ag-GDY decorating the (111) facet of silver. These results illustrate the tremendous potential for engineering novel band structures via molecular orbital and lattice symmetries in atomically precise 2D carbon materials.

Transmetalation in Surface-Confined Single-Layer Organometallic Networks with Alkynyl-Metal-Alkynyl Linkages.

Transmetalation represents an appealing strategy toward fabricating and tuning functional metal-organic polymers and frameworks for diverse applications. In particular, building two-dimensional metal-organic and organometallic networks affords versatile nanoarchitectures of potential interest for nanodevices and quantum technology. The controlled replacement of embedded metal centers holds promise for exploring versatile material varieties by serial modification and different functionalization. Herein, we introduce a protocol for the modification of a single-layer carbon-metal-based organometallic network via transmetalation. By integrating external Cu atoms into the alkynyl-Ag organometallic network constructed with 1,3,5-triethynylbenzene precursors, we successfully realized in situ its highly regular alkynyl-Cu counterpart on the Ag(111) surface. While maintaining a similar lattice periodicity and pore morphology to the original alkynyl-Ag sheet, the Cu-based network exhibits increased thermal stability, guaranteeing improved robustness for practical implementation.

Hidden polymorphs drive vitrification in B2O3.

Understanding the conditions that favour crystallization or vitrification of liquids has been a long-standing scientific problem. Another connected, and not yet well understood question is the relationship between the glassy and the various possible crystalline forms a system may adopt. In this context, B(2)O(3) represents a puzzling case. It is one of the best glass-forming systems despite an apparent lack of low-pressure polymorphism. Furthermore, the system vitrifies in a glassy form abnormally different from the only known crystalline phase at ambient pressure. Last but not least, it never crystallizes from the melt unless pressure is applied, an intriguing behaviour known as the crystallization anomaly. Here, by means of ab initio calculations, we discover the existence of previously unknown B(2)O(3) crystalline polymorphs with structural properties similar to the glass and formation energies comparable to the known ambient crystal. The energy degeneracy of the crystals, which is high at ambient pressure and suppressed under pressure, provides a framework to understand the system's ability to vitrify and the origin of the crystallization anomaly. This work reconciles the behaviour of B(2)O(3) with that from other glassy systems and reaffirms the role played by polymorphism in a system's ability to vitrify. Some of the predicted crystals are cage-like materials entirely made of three-fold rings, opening new perspectives for the synthesis of boron-based nanoporous materials.

Growing sp2 materials on transition metals: calculated atomic adsorption energies of hydrogen, boron, carbon, nitrogen, and oxygen atoms, C2 and BN dimers, C6 and (BN)3 hexamers, graphene and h-BN with and without atomic vacancies.

The growth of graphene and hexagonal boron nitride on hot transition metal surfaces involves the adsorption of precursor molecules, and their dissociation and assembly into two-dimensional honeycomb lattices. In a recent account it was found that h-BN may be distilled on a rhodium metal surface, which yields higher quality h-BN [Cun et al., ACS Nano, 2020, 15, 1351]. In this context, we calculated in a systematic approach the adsorption energies and sites of hydrogen, boron, carbon, nitrogen, and oxygen atoms and from the site dependence the activation energy for diffusion. Existing computed values of the solvation energy into the bulk were compared to the present ones with our calculation scheme and found to be in good agreement. For the distinction of different systems we introduce the concepts of epiphilicity and epiphobicity. The adsorption energies and stabilities of the C2 and BN dimers, the C6 and (BN)3 ring-hexamers and the graphene and h-BN monolayers allow the prediction of the performance of different substrates in chemical vapor deposition (CVD) processes for the growth of graphene and h-BN. Finally, vacancy creation energies were calculated as a criterion for the stability of graphene and h-BN on metallic substrates.

Stress fluctuations and adiabatic speed of sound in liquids: a simple way to estimate it from ab initio simulations.

One of the fundamental quantities in dynamics of the liquid state, the adiabatic speed of sound [Formula: see text], is extremely difficult to predict from computer simulations, especially in ab initio simulations. Here we derive an expression for the instantaneous correlator of fluctuations of longitudinal component of stress tensor, which contains [Formula: see text] along with others quantities easy accessible via classical and ab initio computer simulations. We show that the proposed methodology works well in the case of Lennard-Jones and soft-sphere simple fluids, Kr-Ar liquid mixture in connection with simulations with effective pair interactions as well as for liquid Sb, fluid Hg and molten NaCl from ab initio simulations.

Nature of the attractive interaction between proton acceptors and organic ring systems.

Systematic ab initio calculations are combined with a deconvolution of electrostatic contributions to analyze the interplay between potential hydrogen bond acceptors and organic rings with C(sp(2))-H groups (benzene, pyridine and cyclopentadiene). A distinct anisotropic interaction between the ring systems and the electron lone pairs of cyanide, water and other acceptor species is revealed that favors the in-plane orientation of the proton acceptor group. In the attractive regime this interaction carries a pronounced electrostatic signature. By decomposing the electrostatic contribution into parts attributed to different subunits of the ring systems we demonstrate that a major proportion of the interaction energy gain is originating from the non-adjacent moieties, that are not in close contact with. This behavior holds equally for homocyclic, heterocyclic and non-aromatic rings but contrasts that of the ethyne molecule, taken as reference for a weak hydrogen bond donor clearly exhibiting the expected localized character. The ring interaction requires the presence of π-electron clouds and typically results in an interaction energy gain of 40 to 80 meV. Our findings suggest the proton acceptor-ring interaction as a new category of intermolecular non-covalent interactions.

Interaction of cyclosporin A molecules with alkali and transition metal atoms on Cu(111).

The structure of a cyclic peptide with important biological functionalities, cyclosporin A (CsA), is investigated at the single molecule level. Its adsorption on Cu(111) under ultra-high vacuum is characterised with scanning tunnelling microscopy (STM) and density functional theory. With STM investigations, we demonstrate element specific on-surface coordination schemes of CsA with coadsorbed K, Co and Fe atoms. Thus, clear insights emerge in the behaviour of cyclic peptides at interfaces and their interactions with different metal atoms, providing control of the adsorption structure and assembly and paving the way for the integration of cyclic peptides in functional metal-organic nanostructures on surfaces.

Electron spectroscopies of 3-hydroxyflavone and 7-hydroxyflavone in MCM-41 silica nanoparticles and in acetonitrile solutions. Experimental data and DFT/TD-DFT calculations.

The data presented here concern the photophysical characterization of luminescent MCM-41 nanoparticles doped with 3-hydroxyflavone and 7-hydroxyflavone, two fluorescent flavonoids. UV-Vis and fluorescence spectra obtained on freshly-prepared samples and aged (2 months exposed to air) samples are shown. The effect of light exposure is also studied. In parallel, experiments have been carried out in acetonitrile solutions of the two flavonoids as a term of comparison. Time-dependent density functional theory calculations have also been used to simulate UV-Vis and emission spectra of different species for both flavonoids (neutral molecule, tautomers, cationic and anionic forms), taking into account the effect of the surrounding medium (solvent). Density functional theory calculations of vibrational spectra (IR, Raman) of neutral and tautomeric species of 3HF and 7HF are also provided.

Dynamic response of chlorine atoms on a RuO(2)(110) model catalyst surface.

The dynamic behavior of surface accommodated chlorine atoms on RuO(2)(110) was studied by a variety of experimental methods including high resolution core level shift, thermal desorption-, and in situ infrared spectroscopy as well as in situ surface X-ray diffraction in combination with state-of-the-art density functional theory calculations. On the chlorinated RuO(2)(110) surface the undercoordinated oxygen atoms have been selectively replaced by chlorine. These strongly bound surface chlorine atoms shift from bridging to on-top sites when the sample is annealed in oxygen, while the reverse shift of Cl from on-top into bridge positions is observed during CO exposure; the vacant bridge position is then occupied by either chlorine or CO. For the CO oxidation reaction over chlorinated RuO(2)(110), the reactant induced site switching of chlorine causes a site-blocking of the catalytically active one-fold coordinatively unsaturated (1f-cus) Ru sites. This site blocking reduces the number of active sites and, even more important, on-top Cl blocks the free migration of the adsorbed reactants along the one-dimensional 1f-cus Ru rows, thus leading to a loss of catalytic activity.

Understanding the Superior Stability of Single-Molecule Magnets on an Oxide Film.

The stability of magnetic information stored in surface adsorbed single-molecule magnets is of critical interest for applications in nanoscale data storage or quantum computing. The present study combines X-ray magnetic circular dichroism, density functional theory and magnetization dynamics calculations to gain deep insight into the substrate dependent relevant magnetization relaxation mechanisms. X-ray magnetic circular dichroism reveals the opening of a butterfly-shaped magnetic hysteresis of DyPc2 molecules on magnesium oxide and a closed loop on the bare silver substrate, while density functional theory shows that the molecules are only weakly adsorbed in both cases of magnesium oxide and silver. The enhanced magnetic stability of DyPc2 on the oxide film, in conjunction with previous experiments on the TbPc2 analogue, points to a general validity of the magnesium oxide induced stabilization effect. Magnetization dynamics calculations reveal that the enhanced magnetic stability of DyPc2 and TbPc2 on the oxide film is due to the suppression of two-phonon Raman relaxation processes. The results suggest that substrates with low phonon density of states are beneficial for the design of spintronics devices based on single-molecule magnets.

Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy.

There are currently no experimental techniques that combine atomic-resolution imaging with elemental sensitivity and chemical fingerprinting on single molecules. The advent of using molecular-modified tips in noncontact atomic force microscopy (nc-AFM) has made it possible to image (planar) molecules with atomic resolution. However, the mechanisms responsible for elemental contrast with passivated tips are not fully understood. Here, we investigate elemental contrast by carrying out both nc-AFM and Kelvin probe force microscopy (KPFM) experiments on epitaxial monolayer hexagonal boron nitride (hBN) on Ir(111). The hBN overlayer is inert, and the in-plane bonds connecting nearest-neighbor boron and nitrogen atoms possess strong covalent character and a bond length of only ∼1.45 Å. Nevertheless, constant-height maps of both the frequency shift Δ f and the local contact potential difference exhibit striking sublattice asymmetry. We match the different atomic sites with the observed contrast by comparison with nc-AFM image simulations based on the density functional theory optimized hBN/Ir(111) geometry, which yields detailed information on the origin of the atomic-scale contrast.

Epitaxy-Induced Assembly and Enantiomeric Switching of an On-Surface Formed Dinuclear Organocobalt Complex.

We report on the surface-guided synthesis of a dinuclear organocobalt complex, its self-assembly into a complex nanoarchitecture, and a single-molecule level investigation of its switching behavior. Initially, an organic layer is prepared by depositing hexakis((trimethylsilyl)ethynyl)-benzene under ultrahigh-vacuum conditions onto Ag(111). After Co dosage at 200 K, low-temperature scanning tunneling microscopy (STM) reveals an epitaxy-mediated organization mechanism of molecules and on-surface formed organometallic complexes. The dinuclear complexes contain two bis(η2-alkynyl) π-tweezer motifs, each stabilizing a single Co atom and express two enantiomers due to a conformation twist. The chirality is transferred to the two-dimensional architecture, whereby its Co adatoms are located at the corners of a 3.4.6.4 rhombitrihexagonal tessellation due to the systematic arrangement and anchoring of the complexes. Extensive density functional theory simulations support our interpretation of an epitaxy-guided surface tessellation and its chiral character. Additionally, STM tip-assisted manipulation experiments on isolated dinuclear complexes reveal controlled and reversible switching between the enantiomeric states via inelastic electron processes. After activation by bias pulses, structurally modified complexes display a distinctive Kondo feature attributed to metastable Co configurations.