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Understanding the reactivity of carbon surfaces is crucial for the development of advanced functional materials. In this study, we systematically investigate the reactivity of graphene surfaces with the Stone-Wales (SW) defect using Density Functional Theory calculations. We explore the atomic adsorption of various elements, including rows 1-3 of the Periodic Table, potassium, calcium, and selected transition metals. Our results demonstrate that the SW defect enhances binding with the studied adsorbates when compared to pristine graphene, with carbon and silicon showing the most significant differences. Additionally, we examine the effects of mechanical deformation on the lattice by constraining the system with the SW defect to the pristine graphene cell. Interestingly, these constraints lead to even stronger binding interactions. Furthermore, for carbon, nitrogen, and oxygen adsorbates, we observe that mechanical deformation triggers the incorporation of adatoms into the carbon bond network, leading to the reorganization of the SW defect structure. This work establishes a foundation for future studies in the defect and strain engineering of graphene, opening avenues for developing advanced materials and catalysts with enhanced reactivity and performance., Comment: 19 pages, 6517 words, 10 figures, 4 tables, 49 references; includes supplementary information on 6 pages with 7 figures

Graphene is thought to be a promising materials for many applications. However, pristine graphene is not suitable for most electrochemical devices, where defect engineering is crucial for its performance. We demonstrate how boron doping of graphene can alter its reactivity, electrical conductivity and potential application for sodium and aluminium storage, with the emphasis on novel metal-ion batteries. Using DFT calculations, we investigate both the influence of boron concentration and the oxidation of the material, on the mentioned properties. It is demonstrated that the presence of boron in graphene increases its reactivity towards atomic hydrogen and oxygen-containing species, in other words, it makes B-doped graphene more prone to oxidation. Additionally, the presence of these surface functional groups significantly alters the type and strength of the interaction of Na and Al with the given materials. Boron-doping and oxidation of graphene is found to increase Na storage capacity of graphene by the factor of up to 4., Comment: 22 pages, 2 of which are supplementary information. 10 figures, 2 tables

Single-atom catalysts (SACs) are rapidly developing in various application areas, including electrocatalysis of different reactions, usually taking place under harsh pH-electrode potential conditions. Thus, a full atomic-level understanding of the nature of the active sites under realistic electrochemical conditions is needed, having in mind that the state of SACs active centers could be altered by the adsorption of spectating species. In this contribution, Density Functional Theory is employed to conduct thermodynamic analysis of SACs with metal atoms (Mn, Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, or Au) embedded into N4 moiety in graphene. Various surface electrochemical processes on such SACs are considered, their Pourbaix plots are constructed, and their activity, selectivity, and stability under operating conditions are discussed. It is demonstrated how adsorption of H, O and OH can cause blockage and restructuring of the active sites and alter the electronic structure. Furthermore, when one deals with metals with lower d-band filling, it is shown that metal center oxidation is preferred over the oxidation of carbon lattice. The effect of the state of the metal center on the reactivity of the carbon lattice is discussed in the case of Fe@N4-graphene. Finally, a possible strategy for confirming the changes in the architecture of the SACs' active site by analyzing their vibration spectra is suggested., Comment: 23 pages, 73 references, 9 figures, 3 tables

Graphene oxide finds applications in different fields of science, including energy conversion. Electrochemical reduction of graphene oxide (GO) significantly improves its conductivity. However, the kinetics of this process depends on the solvent, supporting electrolyte, pH, and numerous other factors. Most studies report the macroscopic views and ex-situ properties of reduced GO. To expand the knowledge about GO reduction, in this study, we used cyclic voltammetry (CV), simultaneous 2 points and 4 points resistance measurement (s24), conductive atomic force microscopy (AFM), and theoretical calculations. Using CV, we demonstrated that the choice of supporting electrolyte (KCl or LiCl) influences the potential range in which electrochemical GO reduction occurs. The activation energy of this process was estimated to be below 30 kJ mol-1 in both electrolytes, being significantly lower than that required for thermal reduction of GO. Simultaneous in situ s24 resistance measurements suggest that GO films reach a highly conductive state at deep negative potentials, with an abrupt, irreversible switch from non-conductive to the conductive state. However, conductive AFM presents a more exact picture of this process: the reduction of GO films starts locally while the formed conductive islands grow during the reduction. This mechanism was confirmed by theoretical calculations indicating that the reduction starts on isolated oxygen-functional groups over the GO basal plane, while clustered OH groups are more difficult to reduce. The presented results can help in tailoring reduced GO for a particular electrochemical application by precisely controlling the reduction degree and percentage of the conductive area of the reduced GO films., Comment: 27 page, 6 figures

The development of new electrochromic materials and devices, like smart windows, has an enormous impact on the energy efficiency of modern society. One of the crucial materials in this technology is nickel-oxide. Ni-deficient NiO shows anodic electrochromism whose mechanism is still under debate. Using DFT+U calculations, we show that Ni vacancy generation results in the formation of hole polarons localised at the two oxygens next to the vacancy. Upon Li insertion or injection of an extra electron into Ni-deficient NiO, one hole gets filled, and the hole bipolaron is converted into a hole polaron well-localized at one O atom. Furthermore, the calculated absorption coefficients demonstrate that Li insertion/extraction or rather the addition/removal of an extra electron into Ni-deficient NiO can lead to switching between the oxidized (colored) and the reduced (bleached) states. Hence, our results suggest a new mechanism of Ni-deficient NiO electrochromism not related to the Ni2+/Ni3+ transition but based on the formation and annihilation of hole polarons in oxygen p-states., Comment: main text (19 pages, 6 figures, 1 table, 44 references) and supplementary information (4 pages, 4 figures)

Pristine graphene interacts relatively weakly with Al, which is a specie of importance for novel generations of metal-ion batteries. We employ DFT calculations to explore the possibility of enhancing Al interaction with graphene. We investigate non-doped and N-doped graphene nanoribbons, address the impact of the edge sites, which are always present to some extent in real samples, and N-containing defects on the material's reactivity towards Al. The results are compared to that of pristine graphene. We show that introduction of edges does not affect the energetics of Al adsorption significantly by itself. On the other hand, N-doping of graphene nanoribbons is found to affect the adsorption energy of Al to the extent that strongly depends on the type of N-containing defect. While graphitic and pyrrolic N induce minimal changes, the introduction of edge NO group and doping with in plane pyridinic N result in Al adsorption nearly twice as strong as on pristine graphene. The obtained results could guide the further design of advanced materials for Al-ion rechargeable batteries., Comment: 20 pages in total, 2 of which are supplementary information

Single atom catalysts (SACs) present the ultimate level of catalyst utilization, which puts them in the focus of current research. For this reason, their understanding is crucial for the development of new efficient catalytic systems. Using Density Functional Theory calculations, model SACs consisted of nine metals (Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt and Au) on four different supports (pristine graphene, N- and B-doped graphene and graphene with single vacancy) were analyzed. Among them, only graphene with a single vacancy enables the formation of SACs, which are stable in terms of aggregation and dissolution under harsh conditions of electrocatalysis. Reactivity of models SACs was probed using atomic (hydrogen and A = C, N, O and S) and molecular adsorbates (AHx, x = 1, 2, 3 or 4, depending on A), giving nearly 600 different systems included in this study. Scaling relations between adsorption energies of A and AHx on model SACs were confirmed. However, the scaling is broken for the case of CH3. There is also an evident scaling between adsorption energies of atomic and molecular adsorbates on metals SAs supported by pristine, N-doped and B-doped graphene, which originates from similar electronic structures of SAs on these supports. Using the obtained data, we have analyzed the hydrogen evolution on the model SACs. Only M@graphene vacancy systems (excluding Ag and Au) are stable under hydrogen evolution conditions in highly acidic solutions. Additional interfacial effects are discussed and the need for proper theoretical treatment when studying SACs interactions with molecular species., Comment: This is the pre-peer reviewed version of the following article: Jovanovi\'c et al., Adv. Mater. Interfaces 2020, 2001814, which has been published in final form at https://doi.org/10.1002/admi.202001814. The main text and supplementary information, 23 figures, 8 tables, 46 references, 41 pages in total

Understanding the reactions in M-O2 cells (M = Li or Na) is of great importance for further advancement of this promising technology. Computational modelling can be helpful along this way, but an adequate approach is needed to model such complex systems. We propose a new scheme for modelling processes in M-O2 cells, where reference energies are obtained from high-level theory, CCSD(T), while the interactions of reaction intermediates with catalyst surfaces are extracted from computationally less expensive DFT. The approach is demonstrated for the case of graphene-based surfaces as model catalysts in Li-O2 and Na-O2 cells using the minimum viable mechanism. B-doped graphene was identified as the best catalyst among considered surfaces, while pristine graphene performs poorly. Moreover, we show that the inclusion of dispersion corrections for DFT has a significant impact on calculated discharge and charge potentials and suggests that long-range dispersion interactions should always be considered when graphene-based materials are modelled as electrocatalysts. Finally, we offer general guidelines for designing new ORR catalysts for M-O2 cells in terms of the optimization of the interactions of catalyst surface with reaction intermediates., Comment: 27 pages, including supplementary information, 7 figures in the main text, 1 table, 66 references, 5 figures in supplementary information

For carbon-based materials, in contrast to metal surfaces, the relationship between strain and reactivity is not yet established, even though there are literature reports on strained graphene. Knowledge of such relationships would be extremely beneficial for understanding the reactivity of graphene-based surfaces and finding optimisation strategies which would make these materials more suitable for targeted applications. Here we investigate the effects of compressive and tensile strain (up to +/-5%) on the structure, electronic properties and the reactivity of pure, N-doped and P-doped graphene, using DFT calculations. We demonstrate the possibility of tuning the topology of the graphene surface by strain, as well as by the choice of the dopant atom. The reactivity of (doped) strained graphene is probed using H and Na as simple adsorbates of great practical importance. Strain can both enhance and weaken H and Na adsorption on (doped) graphene. In case of Na adsorption, a linear relationship is observed between the Na adsorption energy on P-doped graphene and the phosphorus charge. A linear relationship between the Na adsorption energy on flat graphene surfaces and strain is found. Based on the adsorption energies and electrical conductivity, potentially good candidates for hydrogen storage and sodium-ion battery electrodes are discussed., Comment: Manuscript: 22 pages, 11 figures; supplementary information: 1 page, 1 figure and 1 table

Oxide materials offer a wide range of interesting physical and chemical properties. Even more versatile behavior of oxides is seen at the nanoscale, qualifying these materials for a number of applications. In this study we used DFT calculations to investigate the physical and chemical properties of small hexagonal MgO nanotubes of different length. We analyzed the effect of Li, B, C, N, and F doping on the properties of the nanotubes. We find that all dopants favor the edge positions when, incorporated into the nanotubes. Doping results in the net magnetization whose value depends on the type of the impurity. Using the CO molecule as a probe, we studied the adsorption properties of pristine and doped MgO nanotubes. Our results show that the dopant sites are also the centers of significantly altered chemical reactivity. While pristine MgO nanotubes adsorb CO weakly, very strong adsorption at the dopant sites (B-, C-, and N-doped nanotubes) or neighboring edge atoms (F- and Li-doped nanotubes) is observed. Our results suggest that impurity engineering in oxide materials can be a promising strategy for the development of novel materials with possible use as selective adsorbents or catalysts., Comment: 23 pages, 8 figures, 3 tables, 45 references, included Supplementary Information (8 pages, 2 figures, 12 tables); submitted to Applied Surface Science

Due to its unique physical and chemical properties, graphene is being considered as a promising material for energy conversion and storage applications. Introduction of functional groups and dopants on/in graphene is a useful strategy for tuning its properties. In order to fully exploit its potential, atomic-level understanding of its interaction with species of importance for such applications is required. We present a DFT study of the interaction of sodium atoms with epoxy-graphene and analyze how this interaction is affected upon doping with boron and nitrogen. We demonstrate how the dopants, combined with oxygen-containing groups alter the reactivity of graphene towards Na. Dopants act as attractors of epoxy groups, enhancing the sodium adsorption on doped oxygen-functionalized graphene when compared to the case of non-doped epoxy-graphene. Furthermore, by considering thermodynamics of the Na interaction with doped epoxy-graphene it has been concluded that such materials are good candidates for Na storage applications. Therefore, we suggest that controlled oxidation of doped carbon materials could lead to the development of advanced anode materials for rechargeable Na-ion batteries., Comment: 16 pages, 6 figures

Development of novel materials may often require a rational use of high price components, like noble metals, in combination with the possibility to tune their properties in a desirable way. Here we present a theoretical DFT study of Au and Pd single atoms supported by doped MgO(001). By introducing B, C and N impurities into the MgO(001) surface, the interaction between the surface and the supported metal adatoms can be adjusted. Impurity atoms act as strong binding sites for Au and Pd adatoms and can help to produce highly dispersed metal particles. The reactivity of metal atoms supported by doped MgO(001), as probed by CO, is altered compared to their counterparts on pristine MgO(001). We find that Pd atoms on doped MgO(001) are less reactive than on perfect MgO(001). In contrast, Au adatoms bind CO much stronger when placed on doped MgO(001). In the case of Au on N-doped MgO(001) we find that charge redistribution between the metal atom and impurity takes place even when not in direct contact, which enhances the interaction of Au with CO. The presented results suggest possible ways for optimizing the reactivity of oxide supported metal catalysts through impurity engineering., Comment: 26 pages, 8 figures, 4 tables, 65 references, submitted to Physical Chemistry Chemical Physics

Vacancies in graphene present sites of altered chemical reactivity and open possibilities to tune graphene properties by defect engineering. The understanding of chemical reactivity of such defects is essential for successful implementation of carbon materials in advanced technologies. We report the results of a systematic DFT study of atomic adsorption on graphene with a single vacancy for the elements of rows 1 to 6 of the Periodic Table of Elements (PTE), excluding lanthanides. The calculations have been performed using PBE, long-range dispersion interaction-corrected PBE (PBE+D2 and PBE+D3) and non-local vdW-DF2 functional. We find that most elements strongly bind to the vacancy, except for the elements of groups 11 and 12, and noble gases, for which the contribution of dispersion interaction to bonding is most significant. The strength of the interaction with the vacancy correlates with the cohesive energy of the elements in their stable phases: the higher the cohesive energy is the stronger bonding to the vacancy can be expected. As most atoms can be trapped at the SV site we have calculated the potentials of dissolution and found that in most cases the metals adsorbed at the vacancy are more "noble" than they are in their corresponding stable phases., Comment: 22 pages, 10 figures, Supplementary Information included, Submitted to Physical Chemistry Chemical Physics

Increasing demand and high prices of advanced catalysts motivate a constant search for novel active materials with reduced content of noble metals. The development of thin films and core-shell catalysts seem to be a promising strategy along this path. Using Density Functional Theory we have analyzed a number of surface properties of supported bimetallic thin films with composition A3B (where A = Pt, Pd, B = Cu, Ag, Au). We focus on surface segregation, dissolution stability and surface electronic structure. We also address the chemisorption properties of Pd3Au thin films supported by different substrates, by probing the surface reactivity with CO. We find a strong influence of the support in the case of mono- and bilayers, while the surface strain seems to be the predominant factor in determining the surface properties of supported trilayers and thicker films. In particular, we show that the studied properties of the supported trilayers can be predicted from the lattice mismatch between the overlayer and the support. Namely, if the strain dependence of the corresponding quantities for pure strained surfaces is known, the properties of strained supported trilayers can be reliably estimated. The obtained results can be used in the design of novel catalysts and predictions of the surface properties of supported ultrathin catalyst layers., Comment: 23 pages, 5 figures, Supplementary Information included, submitted to Physical Chemistry Chemical Physics

The understanding of atomic adsorption on graphene is of high importance for many advanced technologies. Here we present a complete database of the atomic adsorption energies for the elements of the Periodic Table up to the atomic number 86 (excluding lanthanides) on pristine graphene. The energies have been calculated using the projector augmented wave (PAW) method with PBE, long-range dispersion interaction corrected PBE (PBE+D2, PBE+D3) as well as non-local vdW-DF2 approach. The inclusion of dispersion interactions leads to an exothermic adsorption for all the investigated elements. Dispersion interactions are found to be of particular importance for the adsorption of low atomic weight earth alkaline metals, coinage and s-metals (11th and 12th groups), high atomic weight p-elements and noble gases. We discuss the observed adsorption trends along the groups and rows of the Periodic Table as well some computational aspects of modelling atomic adsorption on graphene., Comment: 27 pages, 7 figures, submitted to Applied Surface Science

Molybdenum supported thin films of ScN, MgO and NaF with a Cu adatom have been studied in the framework of density functional theory. We have observed a charge transfer from the metal/film interface to the Cu atom and investigated its relation to surface and interface deformations. We find that a weak interaction between the metal and the film is a promising prerequisite for adatom charging. The detailed study of Cu/NaF/Mo and NaF/Mo indicates that the distortion of the NaF film caused by the Cu adsorption has essentially anharmonic character, as it is coupled to a strong charge redistribution in the system.

KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily extended and customized by the user to allow for the development of complex custom KMC models for specific systems without having to modify the core functionality of the program. Analysis modules and on-the-fly elementary step diffusion rate calculations can be implemented as plugins following a well-defined API. The plugin modules are loosely coupled to the core KMCLib program via the Python scripting language. KMCLib is written as a Python module with a backend C++ library. After initial compilation of the backend library KMCLib is used as a Python module; input to the program is given as a Python script executed using a standard Python interpreter. We give a detailed description of the features and implementation of the code and demonstrate its scaling behavior and parallel performance with a simple one-dimensional A-B-C lattice KMC model and a more complex three-dimensional lattice KMC model of oxygen-vacancy diffusion in a fluorite structured metal oxide. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids.

The present density functional theory study addresses the question whether the presence of H2O influences the catalytic activity of small gold clusters, Au1-4/MgO(100), towards the oxidation of carbon monoxide. To this end, we studied the (co-)adsorption of H2O and CO/O2 on these gold clusters. The ground state structures in the presence of all three molecular species, that we found, are Au1O2/MgO and Au2-4CO/MgO with H2O adsorbed on the surface in the proximity of the clusters-molecule complex. In this configuration the catalytic activity of Au1-4/MgO is indifferent to the presence of H2O. We also found that a stable, highly activated hydroperoxyl-hydroxyl complex, O2H\dot\dot OH, can be formed on Au1,3/MgO. For the catalytic active system Au8/MgO, it has been predicted that this complex opens an alternative catalytic reaction pathway towards CO oxidation. Our results suggest that this water mediated catalytic cycle is unlikely to occur on Au1,3/MgO. In the case of Au1/MgO the cycle is interrupted by the dissociation of the remaining (OH)2 complex after forming the first CO2 molecule. On Au3 /MgO the O2 H\dot\dot OH complex is likely to decompose upon the impact of a CO molecule, since three of its bond dissociation energies are comparable to the reaction barrier of the CO to CO2 oxidation.

We performed a systematic density functional study of the adsorption of copper, silver, and gold adatoms on graphene, especially accounting for van der Waals interactions by the vdW-DF and the PBE+D2 methods. In particular, we analyze the preferred adsorption site (among top, bridge, and hollow positions) together with the corresponding distortion of the graphene sheet and identify diffusion paths. Both vdW schemes show that the coinage metal atoms do bind to the graphene sheet and that in some cases the buckling of the graphene can be significant. The results for silver are at variance with those obtained with GGA, which gives no binding in this case. However, we observe some quantitative differences between the vdW-DF and the PBE+D2 methods. For instance the adsorption energies calculated with the PBE+D2 method are systematically higher than the ones obtained with vdW-DF. Moreover, the equilibrium distances computed with PBE+D2 are shorter than those calculated with the vdW-DF method.

Motivated by the experimentally observed high mobility of gold atoms on graphene and their tendency to form nanometer-sized clusters, we present a density functional theory study of the ground state structures of small gold clusters on graphene, their mobility and clustering. Our detailed analysis of the electronic structures identifies the opportunity to form strong gold-gold bonds and the graphene mediated interaction of the pre-adsorbed fragments as the driving forces behind gold's tendency to aggregate on graphene. While clusters containing up to three gold atoms have one unambiguous ground state structure, both gas phase isomers of a cluster with four gold atoms can be found on graphene. In the gas phase the diamond shaped Au$_{4}^{D}$ cluster is the ground state structure, whereas the Y shaped Au$_{4}^{Y}$ becomes the actual ground state when adsorbed on graphene. As we show, both clusters can be produced on graphene by two distinct clustering processes. We also studied in detail the stepwise formation of a gold dimer out of two pre-adsorbed adatoms, as well as the formation of Au$_{3}$. All reactions are exothermic and no further activation barriers, apart from the diffusion barriers, were found. The diffusion barriers of all studied clusters range from 4 to 36 meV, only, and are substantially exceeded by the adsorption energies of -0.1 to -0.59 eV. This explains the high mobility of Au$_{1-4}$ on graphene along the C-C bonds., Comment: 10 pages, 12 figures