On-Surface Isomerization of Indigo within 1D Coordination Polymers.

Natural products are attractive components to tailor environmentally friendly advanced new materials. We present surface-confined metallosupramolecular engineering of coordination polymers using natural dyes as molecular building blocks: indigo and the related Tyrian purple. Both building blocks yield identical, well-defined coordination polymers composed of (1 dehydroindigo : 1 Fe) repeat units on two different silver single crystal surfaces. These polymers are characterized atomically by submolecular resolution scanning tunnelling microscopy, bond-resolving atomic force microscopy and X-ray photoelectron spectroscopy. On Ag(100) and on Ag(111), the trans configuration of dehydroindigo results in N,O-chelation in the polymer chains. On the more inert Ag(111) surface, the molecules additionally undergo thermally induced isomerization from the trans to the cis configuration and afford N,N- plus O,O-chelation. Density functional theory calculations confirm that the coordination polymers of the cis-isomers on Ag(111) and of the trans-isomers on Ag(100) are energetically favoured. Our results demonstrate post-synthetic linker isomerization in interfacial metal-organic nanosystems.

Descriptors and graphical construction for in silico design of efficient and selective single atom catalysts for the eNRR.

The electrochemical nitrogen reduction reaction (eNRR) offers the possibility of ammonia synthesis under mild conditions; however, it suffers from low yields, a competing hydrogen evolution reaction pathway, and hydrogen poisoning. We present a systematic approach toward screening single atom catalysts (SACs) for the eNRR, by focusing on key parameters computed from density functional theory and relationships between them. We illustrate this by application to 66 model catalysts of the types, TM-Pc, TM-N X C Y , and TM-N3, where TM is a 3d transition metal or molybdenum. We identified the best SACs as Sc-Pc, Cr-N4, Mn-Pc, and Fe-N2C2; these show eNRR selectivity over the HER and no hydrogen poisoning. The catalysts are identified through multi-parameter optimization which includes the condition of hydrogen poisoning. We propose a new electronic descriptor Oval, the valence electron occupancy of the metal center that exhibits a volcano-type relationship with eNRR overpotential. Our multi-parameter optimization approach can be mapped onto a simple graphical construction to find the best catalyst for the eNRR over the HER and hydrogen poisoning.

Identification and Manipulation of Defects in Black Phosphorus.

We identify and manipulate commonly occurring defects in black phosphorus, combining scanning tunneling microscopy experiments with density functional theory calculations. A ubiquitous defect, imaged at negative bias as a bright dumbbell extending over several nanometers, is shown to arise from a substitutional Sn impurity in the second sublayer. Another frequently observed defect type is identified as arising from an interstitial Sn atom; this defect can be switched to a more stable configuration consisting of a Sn substitutional defect + P adatom, by application of an electrical pulse via the STM tip. DFT calculations show that this pulse-induced structural transition switches the system from a non-magnetic configuration to a magnetic one. We introduce States Projected Onto Individual Layers (SPOIL) quantities which provide information about atom-wise and orbital-wise contributions to bias-dependent features observed in STM images.

Blue and black phosphorene on metal substrates: a density functional theory study.

We have performed density functional theory calculations to study blue phosphorene and black phosphorene on metal substrates. The substrates considered are the (111) and (110) surfaces of Al, Cu, Ag, Ir, Pd, Pt and Au and the (0001) and (101¯0) surfaces of Zr and Sc. The formation energyEFis negative (energetically favorable) for all 36 combinations of overlayer and substrate. By comparing values of ΔΩ, the change in free energy per unit area, as well as the overlayer-substrate binding energyEb, we identify that Ag(111), Al(110), Cu(111), Cu(110) and possibly Au(110) may be especially suitable substrates for the synthesis and subsequent exfoliation of blue phosphorene, and the Ag(110) and Al(111) substrates for the synthesis of black phosphorene. However, these conclusions are drawn assuming the source of P atoms is bulk phosphorus, and can alter upon changing synthesis conditions (chemical potential of phosphorus). Thus, when the source of phosphorus atoms is P4, blue phosphorene is favored only over Pt(111). We find that for all combinations of overlayer and substrate, the charge transfer per bond can be captured by the universal descriptorD=Δχ/ΔR, where ΔχandΔRare, respectively, the differences in electronegativity and atomic size between phosphorus and the substrate metal.

Rotation in an Enantiospecific Self-Assembled Array of Molecular Raffle Wheels.

Tailored nano-spaces can control enantioselective adsorption and molecular motion. We report on the spontaneous assembly of a dynamic system-a rigid kagome network with each pore occupied by a guest molecule-employing solely 2,6-bis(1H-pyrazol-1-yl)pyridine-4-carboxylic acid on Ag(111). The network cavity snugly hosts the chemically modified guest, bestows enantiomorphic adsorption and allows selective rotational motions. Temperature-dependent scanning tunnelling microscopy studies revealed distinct anchoring orientations of the guest unit switching with a 0.95 eV thermal barrier. H-bonding between the guest and the host transiently stabilises the rotating guest, as the flapper on a raffle wheel. Density functional theory investigations unravel the detailed molecular pirouette of the guest and how the energy landscape is determined by H-bond formation and breakage. The origin of the guest's enantiodirected, dynamic anchoring lies in the specific interplay of the kagome network and the silver surface.

Adsorption of methane on single metal atoms supported on graphene: Role of electron back-donation in binding and activation.

We consider single metal atoms supported on graphene as possible candidate systems for on-board vehicular storage of methane or for methane activation. We use density functional theory to study the adsorption of one and two molecules of methane on such graphene-supported single atoms, where the metal atom M is a 3d-transition metal (Sc to Zn). Our results suggest that M = Sc, Ti, and V are the best candidates for gas storage applications, while Ni and Co seem particularly promising with respect to activation of the C-H bond in methane. We find a strong and linear correlation between the adsorption energy of methane and the degree of back-donation of electrons from occupied metal d-states to antibonding methane states. A similar correlation is found between the elongation of C-H bonds and electron back-donation. An important role is played by the graphene substrate in enhancing the binding of methane on metal atoms, compared to the negligible binding observed on isolated metal atoms.

Direct Observation of the Reduction of a Molecule on Nitrogen Pairs in Doped Graphene.

Incorporating functional atomic sites in graphene is essential for realizing advanced two-dimensional materials. Doping graphene with nitrogen offers the opportunity to tune its chemical activity with significant charge redistribution occurring between molecules and substrate. The necessary atomic scale understanding of how this depends on the spatial distribution of dopants, as well as their positions relative to the molecule, can be provided by scanning tunneling microscopy. Here we show that a noncovalently bonded molecule such as CoPc undergoes a variable charge transfer when placed on N-doped graphene; on a nitrogen pair, it undergoes a redox reaction with an integral charge transfer whereas a lower fractional charge transfer occurs over a single nitrogen. Thus, the charge state of molecules can be tuned by suitably tailoring the conformation of dopant atoms.

Support work function as a descriptor and predictor for the charge and morphology of deposited Au nanoparticles.

We show, using density functional theory calculations, that the charge, magnetic moment, and morphology of deposited Au nanoclusters can be tuned widely by doping the oxide support with aliovalent cations and anions. As model systems, we have considered Aun (n = 1, 2, or 20) deposited on doped MgO and MgO/Mo supports. The supports have been substitutionally doped with varying concentrations θ of F, Al, N, Na, or Li. At θ = 2.78%, by varying the dopant species, we are able to tune the charge of the Au monomer between -0.84e and +0.21e, the Au dimer between -0.87e and -0.16e, and, most interestingly, Au20 between -3.97e and +0.49e. These ranges can be further extended by varying θ. These changes in charge are correlated with changes in adsorption and/or cluster geometry and magnetic moment. We find that the work function Φ of the bare support is a good predictor and descriptor of both the geometry and charge of the deposited Au cluster; it can, therefore, be used to quickly estimate which dopant species and concentration can result in a desired cluster morphology and charge state. This is of interest as these parameters are known to significantly impact cluster reactivity, with positively or negatively charged clusters being preferred as catalysts for different chemical reactions. It is particularly noteworthy that the Na-doped and Li-doped supports succeed in making Au20 positively charged, given the high electronegativity of Au.

Cooperative particle rearrangements facilitate the self-organized growth of colloidal crystal arrays on strain-relief patterns.

Strain-relief pattern formation in heteroepitaxy is well understood for particles with long-range attraction and is a routinely exploited organizational principle for atoms and molecules. However, for particles with short-range attraction such as colloids and nanoparticles, which form brittle assemblies, the mechanism(s) of strain-relief is not known. Here, we found that for colloids with short-range attraction, monolayer films on substrates with square symmetry could accommodate large compressive misfit strains through locally dewetted hexagonally ordered stripes. Unexpectedly, over a window of compressive strains, cooperative particle rearrangements first resulted in a periodic strain-relief pattern, which then guided the growth of laterally ordered defect-free colloidal crystals. Particle-resolved imaging of monomer dynamics on strained substrates also helped uncover cooperative kinetic pathways for surface transport. These processes, which substantially influenced the film morphology, have remained unobserved in atomic heteroepitaxy studies hitherto. Leaning on our findings, we developed a heteroepitaxy approach for fabricating hierarchically ordered surface structures.

Size-selective Pt siderophores based on redox active azo-aromatic ligands.

We demonstrate a strategy inspired by natural siderophores for the dissolution of platinum nanoparticles that could enable their size-selective synthesis, toxicological assessment, and the recycling of this precious metal. From the fabrication of electronics to biomedical diagnosis and therapy, PtNPs find increasing use. Mitigating concerns over potential human toxicity and the need to recover precious metal from industrial debris motivates the study of bio-friendly reagents to replace traditional harsh etchants. Herein, we report a family of redox-active siderophore-viz. π-acceptor azo aromatic ligands (L) that spontaneously ionize and chelate Pt atoms selectively from nanoparticles of size ≤6 nm. The reaction produces a monometallic diradical complex, PtII(L˙-)2, isolated as a pure crystalline compound. Density functional theory provides fundamental insights on the size dependent PtNP chemical reactivity. The reported findings reveal a generalized platform for designing π-acceptor ligands to adjust the size threshold for dissolution of Pt or other noble metals NPs. Our approach may, for example, be used for the generation of Pt-based therapeutics or for reclamation of Pt nano debris formed in catalytic converters or electronic fabrication industries.

Diffusion barriers, growth pathways, and scaling relations for small supported metal clusters.

Sintering is one of the main causes of degradation of nanocatalysts. With a view to studying the process of sintering, and its relative likelihood across elements, we have used ab initio density functional theory to compute the pathways and energy barriers Ed for the diffusion of small clusters Ptn on MgO(001), n = 1-4. We compare with the corresponding results for Aun, Agn, and Pdn. In general, diffusion barriers, but also sintering energies, are highest for Pt, resulting in opposing trends from kinetics and thermodynamics. We find smooth and positive correlations between Ed and Eb, Eb and Ecoh, Ecoh and Tm, and thus, between Ed and Tm, where Eb is the binding energy of the cluster on MgO, and Ecoh and Tm are the cohesive energy and melting temperature, respectively, of the corresponding bulk metal. These trends are present for diffusion of the monomers, trimers, and tetramers, but not the dimers; this can be explained by the topography of the energy landscape separating the global minimum from the transition state. The temperature T0 at which metal clusters on a given support become mobile is given by α + ßTm, where α and ß are constants that depend on the support. We also present similar results for self-diffusion of monomers of the four metals on the (111) surfaces. Such scaling relations could be used to rapidly estimate diffusion barriers, and hence the growth and sintering behavior, of potential catalytic metal clusters.

Importance of Epitaxial Strain at a Spin-Crossover Molecule-Metal Interface.

Spin-crossover molecules are very appealing for use in multifunctional spintronic devices because of their ability to switch between high-spin and low-spin states with external stimuli such as voltage and light. In actual devices, the molecules are deposited on a substrate, which can modify their properties. However, surprisingly little is known about such molecule-substrate effects. Here we show for the first time, by grazing incidence X-ray diffraction, that an FeII spin-crossover molecular layer displays a well-defined epitaxial relationship with a metal substrate. Then we show, by both density functional calculations and a mechanoelastic model, that the resulting epitaxial strain and the related internal pressure can induce a partial spin conversion at low temperatures, which has indeed been observed experimentally. Our results emphasize the importance of substrate-induced spin state transitions and raise the possibility of exploiting them.

Using first principles calculations to interpret XANES experiments: extracting the size-dependence of the (p , T) phase diagram of sub-nanometer Cu clusters in an O2 environment.

We have used ab initio density functional theory together with ab initio atomistic thermodynamics, and in situ x-ray absorption near edge spectroscopy (XANES) experiments, to study the oxidation of sub-nanometer clusters of Cu n O x supported on a hydroxylated amorphous alumina substrate in an O2-rich environment. We obtain (p , T) phase diagrams: these differ notably for the nanoclusters compared to the bulk. Both the theory and experiment suggest that in the presence of oxygen, the cluster will oxidize from its elemental state to the oxidized state as the temperature decreases. We obtain a clear trend for the transition of Cu n → Cu n O n/2: we see that the smaller the cluster, the greater is the tendency toward oxidation. However, we do not see a monotonic size-dependent trend for the transition of Cu n O n/2 → Cu n O n . We suggest that theoretically computed Bader charges constitute a simple yet quantitative way to align experimental measures of XANES edges with theoretical calculations, so as to yield oxidation states for nanoclusters. Our results have important implications for the use of small clusters in fields such as nanocatalysis and nanomedicine.

Inducing wetting morphologies and increased reactivities of small Au clusters on doped oxide supports.

Au nanoparticles are promising catalysts for industrially important reactions. Their catalytic activity is known to depend on their charge state and morphology. Using density functional theory calculations, we have studied how the induced charge and dimensionality of small Au clusters can be tuned by doping the oxide support that they are deposited on. We have investigated Au n clusters of sizes n = 1, 2, 3, and 20 on Al-doped MgO and Mo-doped CaO. We show that substitutionally doping the oxide support with an electron donor changes the cluster morphology from an upright and/or three-dimensional geometry to a flat geometry. This structural wetting transition results in an increase in the negative charge induced on the cluster and a consequent lowering in the dissociation barrier for the O2 atoms adsorbed on the cluster. We find that the nature of Mo and Al dopants differs: only for the former is it true that the charge state of the dopant atoms depends on the presence or absence of Au nanoparticles and their size.

Substrate doping: A strategy for enhancing reactivity on gold nanocatalysts by tuning sp bands.

We suggest that the reactivity of Au nanocatalysts can be greatly increased by doping the oxide substrate on which they are placed with an electron donor. To demonstrate this, we perform density functional theory calculations on a model system consisting of a 20-atom gold cluster placed on a MgO substrate doped with Al atoms. We show that not only does such substrate doping switch the morphology of the nanoparticles from the three-dimensional tetrahedral form to the two-dimensional planar form, but it also significantly lowers the barrier for oxygen dissociation by an amount proportional to the dopant concentration. At a doping level of 2.78%, the dissociation barrier is reduced by more than half, which corresponds to a speeding up of the oxygen dissociation rate by five orders of magnitude at room temperature. This arises from a lowering in energy of the s and p states of Au. The d states are also lowered in energy, however, this by itself would have tended to reduce reactivity. We propose that a suitable measure of the reactivity of Au nanoparticles is the difference in energy of sp and d states.

Graphene oxide as an optimal candidate material for methane storage.

Methane, the primary constituent of natural gas, binds too weakly to nanostructured carbons to meet the targets set for on-board vehicular storage to be viable. We show, using density functional theory calculations, that replacing graphene by graphene oxide increases the adsorption energy of methane by 50%. This enhancement is sufficient to achieve the optimal binding strength. In order to gain insight into the sources of this increased binding, that could also be used to formulate design principles for novel storage materials, we consider a sequence of model systems that progressively take us from graphene to graphene oxide. A careful analysis of the various contributions to the weak binding between the methane molecule and the graphene oxide shows that the enhancement has important contributions from London dispersion interactions as well as electrostatic interactions such as Debye interactions, aided by geometric curvature induced primarily by the presence of epoxy groups.

Physical origins of weak H2 binding on carbon nanostructures: insight from ab initio studies of chemically functionalized graphene nanoribbons.

We have performed ab initio density functional theory calculations, incorporating London dispersion corrections, to study the absorption of molecular hydrogen on zigzag graphene nanoribbons whose edges have been functionalized by OH, NH2, COOH, NO2, or H2PO3. We find that hydrogen molecules always preferentially bind at or near the functionalized edge, and display induced dipole moments. Binding is generally enhanced by the presence of polar functional groups. The largest gains are observed for groups with oxygen lone pairs that can facilitate local charge reorganization, with the biggest single enhancement in adsorption energy found for "strong functionalization" by H2PO3 (115 meV/H2 versus 52 meV/H2 on bare graphene). We show that for binding on the "outer edge" near the functional group, the presence of the group can introduce appreciable contributions from Debye interactions and higher-order multipole electrostatic terms, in addition to the dominant London dispersion interactions. For those functional groups that contain the OH moiety, the adsorption energy is linearly proportional to the number of lone pairs on oxygen atoms. Mixed functionalization with two different functional groups on a graphene edge can also have a synergistic effect, particularly when electron-donating and electron-withdrawing groups are combined. For binding on the "inner edge" somewhat farther from the functional group, most of the binding again arises from London interactions; however, there is also significant charge redistribution in the π manifold, which directly reflects the electron donating or withdrawing capacity of the functional group. Our results offer insight into the specific origins of weak binding of gas molecules on graphene, and suggest that edge functionalization could perhaps be used in combination with other strategies to increase the uptake of hydrogen in graphene. They also have relevance for the storage of hydrogen in porous carbon materials, such as activated carbons.

Tuning spin transport properties and molecular magnetoresistance through contact geometry.

Molecular spintronics seeks to unite the advantages of using organic molecules as nanoelectronic components, with the benefits of using spin as an additional degree of freedom. For technological applications, an important quantity is the molecular magnetoresistance. In this work, we show that this parameter is very sensitive to the contact geometry. To demonstrate this, we perform ab initio calculations, combining the non-equilibrium Green's function method with density functional theory, on a dithienylethene molecule placed between spin-polarized nickel leads of varying geometries. We find that, in general, the magnetoresistance is significantly higher when the contact is made to sharp tips than to flat surfaces. Interestingly, this holds true for both resonant and tunneling conduction regimes, i.e., when the molecule is in its "closed" and "open" conformations, respectively. We find that changing the lead geometry can increase the magnetoresistance by up to a factor of ∼5. We also introduce a simple model that, despite requiring minimal computational time, can recapture our ab initio results for the behavior of magnetoresistance as a function of bias voltage. This model requires as its input only the density of states on the anchoring atoms, at zero bias voltage. We also find that the non-resonant conductance in the open conformation of the molecule is significantly impacted by the lead geometry. As a result, the ratio of the current in the closed and open conformations can also be tuned by varying the geometry of the leads, and increased by ∼400%.