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Reaction mechanisms for on-surface synthesis of covalent nanostructures
This content has been downloaded from IOPscience. Please scroll down to see the full text. 2016 J. Phys.: Condens. Matter 28 083002 (http://iopscience.iop.org/0953-8984/28/8/083002) View the table of contents for this issue, or go to the journal homepage for more
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Journal of Physics: Condensed Matter J. Phys.: Condens. Matter 28 (2016) 083002 (15pp)
doi:10.1088/0953-8984/28/8/083002
Topical Review
Reaction mechanisms for on-surface synthesis of covalent nanostructures J Björk Department of Physics, Chemistry and Biology, IFM, Linköping University, Sweden E-mail: [email protected] Received 15 May 2015, revised 8 January 2016 Accepted for publication 14 January 2016 Published 2 February 2016 Abstract
In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms. Keywords: surface chemistry, density functional theory, transition state theory (Some figures may appear in colour only in the online journal)
1. Introduction
how a molecule will react on a surface. Therefore, we often rely on trial-and-error, coupled to insight from organic synthesis, and finding new covalent materials has become a quite time- consuming activity. To improve this research field into a direction where we can make, from a blueprint of a covalent material, rational choices of the appropriate molecules and surfaces for creating a material, there is a need for a greater understanding of the underlying mechanisms of relevant on-surface reactions. The ultimate goal would be to comprehend how the these mech anisms are governed by the selection of molecules and surfaces. To reach this ambition, there is a great need for theoretical input into mechanisms of on-surface reactions. The objective of this topical review is to sum up the theoretical work that has been done so far, and identify some of the research questions that theory should focus on during the forthcoming years, for advancing the propitious field of on-surface synthesis. The topical review is structured the following way: first I will give a brief introduction of how reactions on surfaces can be studied by electronic structure theory. This is followed by sections devoted to separate on-surface reactions, each summarizing key experimental studies followed by a more indepth discussion of the efforts from theoretical modeling. I will particularly be addressing on-surface Ullmann coupling,
On-surface synthesis has great prospects for manufacturing covalent nanostructures with atomic precision. In contrast to the vast field of heterogeneous catalysis, which has primarily focused on the chemical transformation of rather small organic molecules, the central research target is the synthesis of covalent materials extended in either one or two dimensions. By coupling molecular building blocks, aided by the reactivity on a metal surface under ultra-high vacuum (UHV) conditions, covalent structures can be formed following a bottom-up strategy. This has resulted in the synthesis of various covalent materials, such as graphene nanoribbons [1], extended graphdiyne wires [2], porous graphene [3], and single-chirality carbon nanotubes [4]. In principle, the dimensions of a formed structure could be controlled on the sole basis of molecular building blocks and the type of reaction triggered between the molecules. Thus, by equipping right molecular building block with proper reacting groups, any imaginable type of covalent material should be within reach. However, the reality is not that simple, and mastering the onsurface reactions has shown to be a severely complicated task. Since the insight into the mechanisms of the reactions relevant for on-surface synthesis is rather limited, it is difficult to foresee 0953-8984/16/083002+15$33.00
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© 2016 IOP Publishing Ltd Printed in the UK
Topical Review
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surface chemistry of terminal alkynes, and cyclodehydrogenation reactions; for which the most extensive theoretical invest igations have been made; but will briefly cover other types of on-surface reactions. The topical review is concluded by an outlook.
state theory, in which it is assumed that a reaction can be characterized by an initial state (IS), a transition state (TS) and a final state (FS) and the rate of crossing the transition state at a temperature T is given by the Arrhenius equation ν = A exp(−Ea /kBT ), (2)
where the activation energy Ea is defined as the energy difference between the TS and FS, and kB is Boltzmann’s constant. The prefactor A may be approximated from the vibrational frequencies at the TS and IS, but is normally assigned the rule-of-thumb value of 1013 s−1. The IS and FS are local minima on the potential energy surface, obtained by conventional structural optimization by minimizing the forces in the calculations. The TS of a reaction is, however, less trivial to determine as it is characterized by a saddle point on the potential energy landscape. There are several methods for finding saddle points in DFT. The most commonly applied way for finding saddle points in on-surface synthesis is with the Nudged Elastic Band (NEB) method. In this method several images (states) are connected to trace a path between the IS and the FS. The reaction path is then found by minimizing the forces acting perpendicular to the tangents of the path (nudging). To ensure that images are equally distributed along the path, spring-forces acting parallel to the tangent of the path are introduced (elastic bands). From the NEB method, typically none of the images are found at, or even close to, the TS and the TS energy is estimated by interpolation. This led to the development of climbing image NEB (CI-NEB) [15]. The only difference from regular NEB is that the spring force acting on the highest energy is replaced with the negative of the force parallell to the tangent of the path [15]. This way the highest energy image, referred to as the climbing image, moves up the energy surface along the elastic band, towards the transition state of the path. Importantly, the path determined by the NEB methods depends on the initial interpolation between IS and FS. Therefore, depending on the type of reaction, one may need to compare the outcome of several initial guesses of the path. With some vigilance, NEB and CI-NEB present reliable ways of studying reaction paths. Particularly they find the number of barriers separating initial and final states. However, as they rely on accurate tangent description of the reaction path (obtained by finite differences between images), they require an adequate number of images for converging the path. This makes the methods numerically expensive as we need individual DFT calculations for the separate images. Minimum mode following methods, exemplified by the Dimer method [16, 17], are numerically cheaper since they focus on the optimization of a transition state, omitting the information about the complete reaction path. The Dimer method is based on using three images (or states): the central image and the two images constituting the dimer. The dimer images are slightly displaced from each other by a fixed distance with the central image in the middle. The TS search algorithm involves two steps. In the first step the vector defined by the dimer is rotated into the lowest curvature mode of the potential energy at the central image.
2. Density functional theory description of on-surface reactions Here, density functional theory (DFT) will be introduced, including a brief discussion of how well DFT describes molecules on surface (in particular, the treatment of van der Waals interactions). Then it will be described how DFT together with transition state theory can be used to study reactions, outlining different methods for computing reaction pathways and transition states. In density functional theory, the total energy of a system is obtained as a functional of the ground state electron density, n ≡ n(r) [5] 1 E [n] = Ts [n] + ∫ dr v(r)n(r) + 2
∫ drdr′
n(r)n(r ′) + Exc [n] , r − r′
(1) where the first term is the kinetic energy of non-interacting electrons, the second and third terms give the electron-nuclei and electron-electron Coloumb energy, respectively, and the final term is the so-called exchange-correlation (XC) energy. All these terms can be determined exactly, within the numer ical accuracy of the calculations, except for the XC energy, which has to be approximated. 2.1. Treating van der Waals interactions
An important, and highly timely, aspect of modeling the adsorption of molecules on surfaces is how to treat so-called van der Waals (vdW), or London dispersion, forces. By construction, conventionally used generalized gradient approx imation (GGA) and local density approximation (LDA) fail to include these interactions, why adsorption heights are generally overestimated for weakly adsorbed systems, or molecules with a π-conjugated core, and the reactivity of a molecule on a surface may not be described correctly. Two schools of thought for treating vdW interactions in DFT have been established. The first is based on semi-empirical corrections, known as dispersion-corrected DFT [6], while the other solves the problem by introducing a non-local density functional commonly denoted as the van der Waals density functional (vdWDF) [7]. Without going into detail, it has been illustrated that with their respective most recent developments, molecular adsorption heights are now described with a precision of 0.1 Å both by dispersion-corrected DFT [8, 9] and vdWDF [10–14]. 2.2. Studying reaction mechanisms
The approach for studying reaction paths of reactions related to on-surface synthesis has exclusively been transition 2
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Then, the central image and the dimer are translated a certain step length, moving the central image towards the TS. The TS is found by iterating the algorithm until the forces on the central image are converged, under the condition that the curvature of the potential energy at the central images in the direction of the dimer is negative. The method explores transition states either by moving the dimer in different directions from the IS (even without knowledge of the FS), or by making use of the output from a NEB calculation as initial guess of the TS. For complex multidimensional reactions, often encountered in on-surface synthesis, the last alternative is most appealing, since we have the full trajectory between initial and final state from NEB, thereby knowing the number of barriers separating the FS from the IS and, for example, the Dimer method is used to refine the TS found from NEB.
two processes: radical diffusion and radical-radical coupling. The coupling step is considered as a more or less irreversible process, resulting in that self-healing, inherent to supramolecular self-assembly, is generally missing (although this problem may be solved by the formation of metal-organic intermediates [36]). Bieri et al [18] demonstrated that this adds some restriction on the diffusion and coupling step, for the formation of ordered covalent 2D materials. They defined a coupling probability between two adjacent radicals as νcouple P= , (3) νcouple + νdiff
where νcouple is the rate of coupling and νdiff is the rate of diffusion. Small values of P indicates that the diffusion is much faster than the coupling (a coupling limited process), while values close to 1 indicates that the coupling is much faster than the diffusion (a diffusion limited process). Figure 2 illustrates kinetic Monte Carlo (kMC) simulations of the nucleation of surface-stabilized radicals for different values of P. For P values close to 1, fractal-like networks are formed, while smaller values of P give more ordered 2D networks. The results of Bieri et al [18] illustrates the requirement of a coupling-limited process for the formation of ordered 2D materials with the on-surface Ullmann coupling, and any other method requiring a recombination step between surfacestabilized radicals.
3. On-surface Ullmann coupling The on-surface Ullmann coupling is without doubt the most commonly applied strategy for creating covalent materials through on-surface synthesis. The approach is reminiscent of the Ullmann coupling in wet chemistry, in which aryl halides comprise the molecular building blocks. The halogens of these molecules are thermally abstracted more easily than other atoms, making it possible to generate surface-stabilized radicals [18], which can then couple into patterns of covalently bonded molecules. By controlling the number of halogens, and their positions within the molecules, one can in principle control the dimensions of the formed nanostructures. The basic concept is illustrated in figure 1 for two model systems based on benzene substituted with different number of halogen atoms. The on-surface Ullmann coupling was demonstrated already 1992 for the synthesis of biphenyl from iodobenzene on Cu(1 1 1) [19], but was not demonstrated for the formation of covalent nanostructures until 15 years later [20]. In a pioneering study by Grill et al it was illustrated how porphyrins equipped with bromine can couple into larger molecules (0D), chains (1D) or clusters (2D) depending on the number of bromine atoms in the molecules [20]. The method has since then been used numerous times [1, 3, 18, 21–31]. For example, it can be used to form graphene nanoribbons, either complemented by a cyclodehydrogenation reaction [1], or as the sole reaction step [31]. In several cases metal-organic intermediate structures have been observed [32–36], in which the dehalogenated molecules coordinate to metal adatoms thermally generated from the substrate. The exact role of these adatoms in the overall process is not yet clear, as the theoretical work so far has focused on reactions on atomically flat surfaces, as will be described here.
3.2. Recombination mechanisms
Theoretical calculations of reaction mechanisms together with experimental observations corroborated the prediction that a coupling-limited process is a prerequisite for the formation of ordered 2D materials. Figure 3 illustrates calculated recombination mechanisms of cyclohexa-m-phenylene radicals (CHPR) on Cu(1 1 1) and Ag(1 1 1) [18]. CHPR is chemically bonded via its six radical sites to the metal atoms and the calculated reaction sequence is similar for both surfaces: Two carbon radicals (one from each molecule) are bonded to adjacent surface atoms in the initial state (denoted II). The reactions are initiated by a multi-barrier diffusion step, leading to the intermediate states IM2, where the two molecules are chemically bonded with a carbon radical to the same surface atom. On Cu(1 1 1), the coupling-step is barrier-free (IM2 to IM3), while the final step in the simulated path is simply a diffusion step for one half of the dimer. On Ag(1 1 1), the coupling is a two-step process between IM2 and FI, with a barrier larger than that for diffusion. These results indicate that the recombination process of CHPR is diffusion limited on Cu(1 1 1) (compare the diffusion barrier of 2.2 eV to the spontaneous coupling reaction), while it is coupling limited on Ag(1 1 1) (diffusion barrier of 0.8 eV and coupling barrier of 1.8 eV). Thus, from the discussion around equation (3) one would expect that CHPR more likely forms ordered 2D materials on Ag(1 1 1) than on Cu(1 1 1). Notably, experiments have shown exactly this: On Ag(1 1 1) a porous graphene structure with relatively low
3.1. Ideal conditions for creating ordered 2D-materials
An important step for the on-surface Ullmann coupling is the recombination of surface-stabilized radicals. The recombination is, in a simplified picture, associated with 3
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Figure 1. Basic principle of the on-surface Ullmann coupling for the formation of (a) 1D and (b) 2D materials, by controlling the number of halogens of the molecular precursors.
Figure 2. Kinetic Monte Carlo simulations for the recombination process between surface-stabilized radicals for different coupling probabilities P, defined by equation (3). The smaller values of P, the smaller number of defects are found in the resulting 2D networks. Reprinted with permission from [18]. Copyright (2010) American Chemical Society.
defect density was observed, resembling the simulated structure obtained for a small coupling probability in figure 2(c). Contrarily, branches of a single molecule width were found on Cu(1 1 1) [3]. In the same study, experiments found networks of intermediate quality on Au(1 1 1), suggesting it has properties somewhere between Ag(1 1 1) and Cu(1 1 1) in terms of promoting a coupling or a diffusion limited process. However, there are no theoretical studies for the recombination of two
CHPRs on this surface, which certainly would be of great interest. 3.3. The formation of biphenyl
Before discussing the complete reaction sequence to form biphenyl with on-surface Ullmann coupling presented in [37] it is important to have in mind that Nguyen et al were the first 4
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Figure 3. Calculated recombination pathways of CHPR on Cu(1 1 1) and Ag(1 1 1), as indicated. The chemical structure of CHPR is shown in the inset. Reprinted with permission from [18]. Copyright (2010) American Chemical Society.
surface. The picture is very similar on all the three surfaces for both bromo- and iodobenzene. An important point is the chemical state of the resulting radicals. In the FS the phenyl radical is chemisorbed on the surface, resulting in the un-paired spin being quenched, why in literature one frequently use the notation ‘surface-stabilized radical’ [18]. Often, the term radical is used quite loosely, but as a general rule, for these type of radicals the un-paired spin is most likely quenched, and the notation that we have a surface-stabilized radical is more appropriate. In figure 4(c) the energy barriers (activation energies) and reaction energies are shown for the six dehalogenation reactions. Given that both reactions are highly endothermic in gas phase, with reaction energies of 3.85 eV and 3.33 eV for bromobenzene and iodobenzene, respectively, it is clear that all three surfaces have catalytic effects on dehalogenation. For bromobenzene, the barriers range from 1.02 eV on Au to 0.66 eV on Cu(1 1 1). A similar trend, shifted by roughly −0.3 eV is found for iodobenzene, with barriers of 0.71 eV on Au(1 1 1) and 0.40 eV on Cu(1 1 1) [37]. Notably, the reaction energies follow a quite different trend, with largest difference between the two molecules for Au(1 1 1) and a rather small difference for Cu(1 1 1).
to study the particular case of recombining phenyl radicals on Cu(1 1 1) [38]. Both these studies [37, 38] gave the same conclusion regarding the diffusion and coupling on Cu(1 1 1), and for simplicity, the discussion herein is based on the results presented in [37]. To date, the only study of the complete procedure for a synthesis protocol making use of the on-surface Ullmann coupling investigated the formation of biphenyl from bromo- and iodobenzene on Cu(1 1 1), Ag(1 1 1) and Au(1 1 1) [37]. The overall process is initiated by dehalogenation, followed by the recombination (diffusion and coupling) of the surface-stabilized phenyl radicals, resulting in biphenyl. We will begin by discussing the dehalogenation of bromobenzene and iodobenzene on the three surfaces. A typical energy profile is shown in figure 4(a) and IS, TS and FS of the dehalogenation is exemplified for bromobenzene on Au(1 1 1) in figure 4(b). In the IS, the molecule is physisorbed on the surface, while in the TS a chemical bond has begun to form between the halogenated carbon atom and the surface as the same time as the carbon-halogen bond is elongated. Ultimately, in the FS the C-Br bond is completely dissociated, with the resulting phenyl radical and bromine chemisorbed to the 5
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they are chemisorbed to the same surface atom, defined as IS of the coupling reaction. The pathways for coupling are depicted in figure 6. In the TS the two radicals are still chemisorbed to the surface atoms, and only differs from the IS in that the two radical carbon atoms are closer to each other. The energies of the states are defined with respect of having the two molecules well separated. The activation energy for coupling was defined as the energy of the TS rather than the energy difference between TS and IS. The activation energy for coupling is smallest for Cu(1 1 1) and largest for Ag(1 1 1), while an intermediate value was found for Au(1 1 1). For all surfaces the coupling is highly exothermic, manifesting the irreversibility of the covalent bond formation [37]. Following the argumentation that the slide diffusion is more relevant than the flip diffusion, it gives that the phenyl radical has the same trend as CHPR, in which the recombination is diffusion limited on Cu(1 1 1) and coupling limited on Ag(1 1 1). For Au(1 1 1), the recombination is considered being neither diffusion nor coupling limited, as the barrier of diffusion is similar to that of the coupling. 4. Surface chemistry of terminal alkynes Molecules functionalized with terminal alkynes participate in another group of on-surface reactions. In particular, homocoupling between terminal alkynes has gained a lot of interest since it was first reported on a surface in 2012 [39]. This method has enabled thermal coupling of acetylene functional groups, creating butadiyne (diacetylene) bridges between adjacent molecules, and is highly relevant for the realization of materials related to graphdiyne, a carbon allotrope in which benzene rings are interlinked by butadiyne bridges. For example, extended graphdiyne wires have been synthesized on a silver surface [2]. The surface chemistry of terminal alkynes has proven to be extremely versatile, and several reactions have been reported [40–46]. Maybe most intriguingly, a cyclotrimerization reaction has been observed in a few studies [41–45]. For example, Zhou et al demonstrated how a linear molecular building blocks undergo a [2+2+2] cyclotrimerization on Au(1 1 1) [43]. In another example [44], 1,3,5-tris-(4-ethynylphenyl)benzene (Ext-TEB) molecules were observed to cyclotrimerize on Au(1 1 1). Notably, the Ext-TEB molecule was also used in the first report of the homo-coupling [39], but on Ag(1 1 1). The two types of reaction products obtained for Ext-TEB on Ag(1 1 1) and Au(1 1 1), together with the basic principles of the homo-coupling and cyclotrimerization, are compared in figure 7. Furthermore, if instead deposited on Cu(1 1 1), Ext-TEB dehydrogenates and forms an unusual deprotonated alkynyl hydrogen bonding network, inhibiting the coupling between molecules [46]. The Ext-TEB molecule gives an excellent example of the versatile surface chemistry of terminal alkynes, where the chemoselectivity can be tuned by changing the reactivity of the surface. The versatile surface chemistry of terminal alkynes have been observed in several other studies. For example, the linear 4,4”-diethynyl- 1,1’:4’,1”-terphenyl molecule gives a multitude
Figure 4. (a) Typical potential energy profile for dehalogenation reactions, such as (b) the dissociation of bromobenzene on Au(1 1 1). (c) Ebarrier (left) and E react (right) for the dissociation of bromobenzene and iodobenzene on the (1 1 1) facets of Au, Ag, and Cu. Reprinted with permission from [37]. Copyright (2013) American Chemical Society.
The next step of the reaction is the recombination of two phenyl radicals into biphenyl. The overall recombination is associated with two processes, namely diffusion and the coupling between surface-stabilized radicals. As illustrated in figure 5 the phenyl can follow two types of diffusion. The slide diffusion, in which the orientation of the phenyl ring is the same in the IS and the FS, and a flip diffusion in which the phenyl ring flips between two sites such that its orientation changes. On all surface, except for Au(1 1 1) for which the two diffusion modes have the same TS, the flip diffusion has the lowest barrier. However, the flip diffusion is probably only possible for molecules of similar size as phenyl, as it has a TS or intermediate state where the molecule is standing upright on the surface [37]. Such a configuration would not be possible for a larger molecule due to the cost of breaking vdW interactions, and definitely not for a molecule with more than one radical site, as it would require the scission of chemical bonds. When the molecules have diffused over the surface, they will eventually come in the near proximity to another molecule such that they can react. In the case of phenyl radicals, the closest two molecules can be without reacting is when 6
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Figure 5. Energy diagrams for (a) sliding diffusion and (b) flipping diffusion of phenyl on Au(1 1 1), Ag(1 1 1), and Au(1 1 1), where the top and side views of the paths are depicted in the top panel for (a) Ag(1 1 1) and (b) Au(1 1 1). In both processes, phenyl diffuses between two adjacent surface atoms rendered darker than other surface atoms. On Au(1 1 1), the flipping and sliding diffusions have identical TSs and differ only by the relative orientation of the molecule in the IS and FS. The flipping diffusion (b) is a two-step process on Cu(1 1 1) and Ag(1 1 1). Reprinted with permission from [37]. Copyright (2013) American Chemical Society.
Figure 6. Coupling reaction of two phenyls into biphenyl on Au(1 1 1), Ag(1 1 1) and Cu(1 1 1), depicted for Ag(1 1 1) in the top panel. Energies are given with respect to having the two phenyl well separated from each other on respective surface. Reprinted with permission from [37]. Copyright (2013) American Chemical Society.
of side reactions on Ag(1 1 1), with coupling motifs of up to five monomers, while a high chemoselectivity towards the homo coupling is obtained when depositing it with a delicately tuned coverage on the stepped Ag(877) surface [2]. The deposition of 1,4-diethynylbenzene on Cu(1 1 1) gives rise to a multitude of reactions, such as homo-coupling and cyclotrimerization [42], but does not result in the deprotonated alkynyl hydrogen bonding network reported for Ext-TEB on Cu(1 1 1) [46].
It should be further noted that while the Au(1 1 1) surface has been observed to activate mainly cyclotrimerization reactions in a couple of examples [43, 44], other molecules on this surface have resulted in the homo-coupling among with other reaction products [41]. Thus, the chemoselectivity toward homo-coupling versus cyclotrimerization is not simply controlled by the choice of surface, but rather the molecule-surface combination is important. 7
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does not have time to thermally equilibrate after the highly exothermic coupling step. As a consequence, the energy gained in the coupling is reinvested into the dehydrogenation steps, reminiscent of hot adsorbates that can form in dissociative adsorption [50]. An alternative path for initiating the homo-coupling would be to directly dehydrogenate the terminal alkyne prior to the coupling. However, calculations have shown that the barrier is twice that to initially couple two TEB molecules [48]. A similar barrier was found for dehydrogenating ethynyl-benzene on Ag(1 1 1), while it is slightly lowered to 1.64 eV on Au(1 1 1) [49]. In other words, initially coupling of terminal alkynes is significantly more probable than dehydrogenating the molecules followed by the coupling. Figure 7. The prefered reaction path of the Ext-TEB molecule depends on the underlying surface: on Ag(1 1 1) the homocoupling reaction is obtained [39], while the molecules undergo a cyclotrimerization reaction on Au(1 1 1) [44].
4.2. Considerations of the cyclotrimerization mechanism
Zhou et al provided insight into the cyclotrimerization between terminal alkynes by studying the formation of benzene from three acetylene molecules [43], as shown in figure 10. The reaction was considered to be non-concerted, where two acetylene first couple, followed by the reaction with the third molecule, resulting in benzene. The first step is smaller than the second one (compare 1.54 eV to 1.72 eV), suggesting that the intermediate (INT), in which only two alkynes have coupled, should be observable. Indeed, such intermediate state has been observed in STM experiments [43]. One needs to bear in mind that these calculations were done by using a planar cluster of 14 Au atoms representing the surface [43], which will be significantly more reactive than the real Au(1 1 1) surface. Furthermore, the pathway’s intermediate state (denoted INT) resembles the cis intermediate state (IntS1cis) for the homo-coupling, which is a result of using acetylene as model molecule, for which it is not possible to differentiate the initial step of cyclotrimerization and homo-coupling. This aspect is demonstrated in figure 11, which compares the respective mechanisms of homo-coupling and cyclotrimerization. The study by Zhou et al still provides valuable insights into the cyclotrimerization between alkynes, despite that investigations on realistic surfaces and more representative molecules are needed for a full appreciation of the reaction.
For a more extensive account of the work devoted to the surface chemistry of terminal alkynes see the recent review in [47]. Hereon I will focus on the theoretical efforts made for understanding the underlying mechanisms of their multifaceted surface chemistry. 4.1. Mechanism of homo-coupling
Two independent theoretical studies of the homo-coupling have been presented [48, 49], both reaching the conclusion that the coupling of the terminal alkynes precedes the release of hydrogen atoms. I will center the discussion around the dimerization between 1,3,5-triethynyl-benzene (TEB) molecules on Ag(1 1 1), one of the systems used to initially demonstrate the homo-coupling [39], and reflect on how it relates to other molecules and surfaces. The initial coupling step between two TEB molecules is illustrated in figure 8. The barrier of coupling the two molecules (going from IS to IntS1trans) is 0.90 eV [48], which is the same barrier found for ethynyl-benzene on Ag(1 1 1), while a slightly smaller barrier (0.79 eV) was found for Au(1 1 1) [49]. Following the initial coupling, the formed TEB dimer can exist in a trans (IntS1trans) and cis state (IntS1cis). In IntS1trans one of the carbon atoms is under-coordinated and it has been made quite clear that the molecule will exist in the more stable IntS1cis configuration at some point before continuing the reaction [48]. The homo-coupling between two TEB monomers is finalized by two subsequent dehydrogenation steps, with barriers of 1.27 eV and 1.53 eV, respectively, as shown in figure 9. Particularly the second barrier is considerable having in mind that the reaction takes place at 300 K in experiments [39]. Several explanations for this anomaly between theory and experiments have been proposed. For example, the calcul ations give the potential energy landscape at 0 K and it was shown that temperature effects, in terms of vibrational enthalpy and entropy, indeed reduce the dehydrogenation barrier [48]. Another possibility might be that the system
5. Surface-assisted cyclodehydrogenation Cyclodehydrogenation is a category of intramolecular ringclosure reactions in which a carbon-carbon bond is formed simultaneously with the release of two hydrogen atoms (bonded to the carbon atoms in the reactant). In figure 12 a cyclodehydrogenation reaction is demonstrated for an illustrative model system. Surface-assisted cyclodehydrogenation has been used together with on-surface Ullmann coupling for the on-surface synthesis of different types of graphene nanoribbons on Au(1 1 1) and Ag(1 1 1), such as the transformation of a polyanthrylene intermediate into a seven carbon atoms wide ribbon [1]. It has also been employed to form large polycyclic 8
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Figure 8. The homo-coupling between two TEB molecules is initiated by a coupling step, with the hydrogen remaining on the molecules. The coupled transition state can exist in a trans- and cis-isomer, where the latter is the more stable one. The two hydrogen atoms taking part in the coupling were rendered red for clarity. Reprinted with permission from [48]. Copyright (2014) American Chemical Society.
Figure 9. Following the initial coupling of two TEB molecules (figure 8), the resulting dimer undergoes two subsequent dehydrogenation steps, which finalizes the overall homo-coupling. The two hydrogen atoms being split-off were rendered in red for clarity. Reprinted with permission from [48]. Copyright (2014) American Chemical Society.
Figure 10. Mechanism of the formation of benzene from three acetylene molecules through cyclotrimerization on Au(1 1 1). Reprinted
with permission from [43]. Copyright (2014) American Chemical Society. 9
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Figure 11. Comparison between the mechanism of (a) homo-coupling and (b) cyclotrimerization between terminal alkynes, with the
metal surface indicated as Me. If using acetylene as a model compound, in which the group R is represented by a hydrogen atom, the first intermediate state of the homo-coupling and the intermediate state of the cyclotrimerization are identical.
bianthryl units couple into polyanthrylene following an on-surface Ullmann coupling procedure. This is followed by the cyclodehydrogenation step, yielding the graphene nanoribbons. A staggering amount of work has been devoted to the seven atoms wide armchair graphene nanoribbons initially demonstrated by Cai et al [1]. However, only a couple of theoretical studies have been devoted to the mechanism of the cyclodehydrogenation reaction [52, 53]. Blankenburg et al studied the mechanism on Ag(1 1 1), and backed up their theoretical results by STM experiments [53]. Their reaction pathway is illustrated in figure 15. In short, they found that the reaction is initiated by the coupling between two carbon atoms (S0 to S1), followed by the abstraction of a hydrogen atom (S1 to S2). Then a hydrogen is tautomerized, in other words migrated between two carbon atoms (S2 to S3) followed by an additional carbon-carbon coupling step (S3 to S4), which is succeeded by the tautomerization of an additional hydrogen atom (S4 to S5) and the abstraction of two hydrogen atoms (S5 to S6). The reaction then procedes stepwise in a similar fashion. For a more detailed view of the mechanism see [53]. An interesting aspect of the mechanism presented by Blankenburg et al is that the cyclotrimerization between two carbon atoms has a reducing effect on the barrier of cyclotrimerization between the adjecent anthracene units (at the same side of the nanoribbon). This was in fact also observed STM experiments, in which it was possible to activate the cyclotrimerization in one side of the polyanthrylene, while keeping the other side unreacted [53]. Another study reported a theor etical investigation of the cyclotrimerization on Au(1 1 1) [52], and came to the same conclusion that the cyclotrimerization proceeds in a domino-like fashion, where the cyclodehydrogenation between two pairs of anthracene units enable the coupling between the next units. However, in this study is was concluded that both sides of the polymer is cyclodehydrogenated before moving to the next units and not the side-wise activation that was found on Ag(1 1 1) [53]. It is not clear whether this is a difference between Ag(1 1 1) and Au(1 1 1), or if the
Figure 12. In cyclodehydrogenation two carbon atoms couple
simultaneously as detaching their hydrogen atoms, effectively resulting in a ring-closure.
aromatics hydrocarbons (PAHs), so called nanographenes, from cyclohexa-o-p-o-p-o-p-phenylene (CHP) on Cu(1 1 1) [51]. 5.1. Nanographenes
Treier et al performed a rigorous theoretical investigation of the reaction mechanism of the cyclodehydrogenation of CHP into a nanographene [51], the main results of which are illustrated in figure 13. The overall reaction procedes in a six-step process, via the formation of three supplementary carbon-carbon bonds and abstraction of six hydrogen atoms. The reaction is initiated by a dehydrogenation step (state 1 to 2), followed by a carbon-carbon coupling and concomitant dehydrogenation (state 2 to 3). This is accompanied by a third dehydrogenation (state 3 to 4) and carbon-carbon coupling (state 4 to 5). The reaction is finalized by a combined carboncarbon coupling and dehydrogenation (state 5 to 6), ultimately leading to the release of a hydrogen molecule (state 6 to 7). It is quite interesting to note that two of the intermediate states were observed in STM experiments [51], namely state 3 and 6. These states are followed by two of the rate-limiting steps of the overall reaction and it is intriguing how well this is captured by the computed pathway. 5.2. Graphene nanoribbons
The formation of graphene nanoribbons is probably the most famous, and well-studied, example of on-surface synthesis. The overall reaction is shown in figure 14. Firstly, brominated 10
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Figure 13. Calculated reaction mechanism for the triple cyclodehydrogenation of CHP into a nanographene on the Cu(1 1 1) surface.
Reprinted by permission from Macmillan Publishers Ltd: Nature Chem. [51], copyright (2011).
model system used for studying the cyclodehydrogenation on Au(1 1 1) did not capture all aspects of the reaction, and constitutes an open question still awaiting an answer. 6. Other types of on-surface reactions Ullmann coupling, coupling between terminal alkynes and cyclodehydrogenation are probably the three most thoroughly studied on-surface reactions from theory, although a lot of work remains to fully comprehend them. Here I will highlight some of the work that has been performed to elucidate mech anisms for other types of reactions. Throughout this topical review different types of cyclization reactions have been accounted for. In fact, several additional examples of cyclization on surfaces exist. For example,
Figure 14. Schematics of the formation of graphene nanoribbons.
In a first step, brominated bianthryl units form polyanthrylene through on-surface Ullmann coupling. Then the polymer cyclodehydrogenates, resulting in the graphene nanoribbon [1].
11
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Figure 15. Calculated reaction mechanism for the cyclodehydrogenation of poly-anthracene into a graphene nanoribbon on the Ag(1 1 1)
surface. Reprinted with permission from [53]. Copyright (2012) American Chemical Society.
Yang et al demonstrated how acetyl-functionalized molecules couple either in a dimerization or a cyclotrimerization reaction [54]. Theoretical considerations of the reaction pathway of the initial dimerization between two molecules concluded that the reaction is initiated by the dehydrogenation of the methyl in an acetyl group, illustrated in figure 16(a). From this point there are two competing pathways: either the dehydrogenated molecule reacts with an intact molecule (figure 16(b)), or two dehydrogenated molecules react (figure 16(c)). The latter alternative requires a sufficient concentration of dehydrogenated molecules, but since the initial dehydrogenation is significantly larger than coupling two molecules, it was concluded that the coupling between an intact and a dehydrogenated molecule is more likely [54]. The initial coupling is followed by subsequent dehydroxylation and dehydrogenation steps,
and the abstraction of oxygen was supported by XPS experiments [54]. In another study, an azide-alkyne cycloaddition (figure 17) was observed on Au(1 1 1) [55]. Two reaction pathways were considered by DFT calculations, one occurring at an atomically flat Au(1 1 1) surface, and another in the presence of an Au adatom, as shown in figure 18. Both pathways have a barrier of around 0.7 eV, which was also found for the reaction in gas phase, concluding that the Au surface has an insignificant chemical impact on the reaction [55]. This gives an excellent, but rare, example where the surface instead of catalyzing the reaction, provides a support that enables the reaction by lowering the degrees of freedom of the molecular building blocks into two dimensions. Further examples of cyclization reactions have been reported. For example, Bergman cyclization 12
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Figure 16. Comparison of different reaction pathways involving acetyls. (a) Dehydrogenation of the acetyl’s methyl group, (b) coupling
between an intact and a dehydrogenated molecule, and (c) coupling between two dehydrogenated molecules. Valence bond structures have been included for reactants, intermediates and products for the different pathways, with the metal surface denoted as Me. Note that in (b) IntS2 and FS have the same chemical structure and differ only by the adsorption site of the abstracted OH-group. Adapted with permission from [54]. Copyright (2015) American Chemical Society.
The experimentally observed behavior was explained by theoretical modeling, which concluded that the activation energy for splitting of a hydrogen from the meta-carbon has a significantly smaller barrier compared to splitting-off hydrogen from other carbon atoms. Figure 17. Schematics of the azide-alkyne cycloaddition.
was demonstrated on Cu(1 1 0) [56], but for which no reaction pathways have been considered from theory. As a final example, Sun et al studied reactions between quaterphenyl molecules on Cu(1 1 0) in STM experiments, observing that the molecules couple via a selective C-H activation of the meta-carbon site of the terminal phenyl group [57].
7. Outlook In this topical review I have outlined some of the theoretical work that has been performed to understand reactions responsible for the formation of covalent nanostructures on surfaces, with particular focus on the on-surface Ullmann coupling, 13
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Figure 18. Calculations of azide-alkyne cycloaddition on Au(1 1 1) for an atomically flat surface ((A)–(C)) and aided by an Au adatom
((D)–(F)). Reprinted with permission from [55]. Copyright (2013) American Chemical Society.
surface-chemistry of terminal alkynes and surface-assisted cyclodehydrogenation. Regarding the on-surface Ullmann coupling, theoretical modeling has successfully modeled the pathways for specific systems. However, the predictive power of the current knowledge is rather limited, and we need to put our forthcoming efforts in systematic studies of on-surface reactions. A part icularly important milestone would the development of a theory that could predict whether a specific molecule-surface combination gives rise to a coupling-limited or a diffusionlimited recombination process. This would specifically guide the formation of ordered covalent 2D materials, for which a coupling limited process is a prerequisite. Furthermore, to date, theoretical studies have exclusively considered processes on atomically flat surfaces. However, as seen numerous of times in experiments, metal-organic intermediate structures can play an important role, possibly enabling self-healing protocols. Insight into the exact role of metal adatoms would therefore be of immediate interest. Molecules functionalized with terminal alkynes have demonstrated a highly versatile surface chemistry. Although there are some aspects that remain to be unraveled about the homocoupling reaction, the most immense theoretical effort will be to comprehend other possible types of reactions terminal alkynes can undergo. In particular, we need a more sophisticated understanding of the cyclotrimerization, and the next years theory is expected to make important contributions in this regard. In the long-term perspective, theoretical modeling should aim at finding general design rules governing the chemoselectivity of the surface chemistry of terminal alkynes. Cyclodehydrogenation is probably the most studied, and well-understood, on-surface reaction from theory. Although there are some issues to unravel about how the reaction differs
between various surfaces, the on-surface synthesis field is in a more urgent need for theoretical studies about other reactions. Here we have focused on the work where theory has provided input into on-surface reaction mechanisms. However, for the majority of the reported reactions, information of mechanisms is missing. It is only the last years that the comp uter resources have become sufficient to study on-surface reactions in a more routinely and systematic manner. During the next years it is anticipated that theoretical insights, and with this our appreciation, of on-surface synthesis will grow with a spiralling rate.
References [1] Cai J et al 2010 Nature 466 470 [2] Cirera B, Zhang Y Q, Björk J, Klyatskaya S, Chen Z, Ruben M, Barth J V and Klappenberger F 2014 Nano Lett. 14 1891 [3] Bieri M et al 2009 Chem. Commun. 6919 [4] Sanchez-Valencia J R, Dienel T, Gröning O, Shorubalko I, Mueller A, Jansen M, Amsharov K, Ruffieux P and Fasel R 2014 Nature 512 61 [5] Kohn W and Sham L 1965 Phys. Rev. 140 A1133 [6] Grimme S 2006 J. Comput. Chem. 27 1787 [7] Dion M, Rydberg H, Schröder E, Langreth D C and Lundqvist B I 2004 Phys. Rev. Lett. 92 246401 [8] Ruiz V, Liu W, Zojer E, Scheffler M and Tkatchenko A 2012 Phys. Rev. Lett. 108 146103 [9] Bürker C, Ferri N, Tkatchenko A, Gerlach A, Niederhausen J, Hosokai T, Duhm S, Zegenhagen J, Koch N and Schreiber F 2013 Phys. Rev. B 87 165443 [10] Klimeš J, Bowler D R and Michaelides A 2010 J. Phys.: Condens. Matter 22 022201 [11] Mittendorfer F, Garhofer A, Redinger J, Klimeš J, Harl J and Kresse G 2011 Phys. Rev. B 84 201401 14
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[36] Eichhorn J, Strunskus T, Rastgoo-Lahrood A, Samanta D, Schmittel M and Lackinger M 2014 Chem. Commun. 50 7680 [37] Björk J, Hanke F and Stafström S 2013 J. Am. Chem. Soc. 135 5768 [38] Nguyen M T, Pignedoli C A and Passerone D 2011 Phys. Chem. Chem. Phys. 13 154 [39] Zhang Y Q et al 2012 Nat. Commun. 3 1286 [40] Cirera B, Zhang Y Q, Klyatskaya S, Ruben M, Klappenberger F and Barth J V 2013 ChemCatChem 5 3281 [41] Gao H Y, Wagner H, Zhong D, Franke J H, Studer A and Fuchs H 2013 Angew. Chem. Int. Ed. 52 4024 [42] Eichhorn J, Heckl W M and Lackinger M 2013 Chem. Commun. 49 2900 [43] Zhou H, Liu J, Du S, Zhang L, Li G, Zhang Y, Tang B Z and Gao H J 2014 J. Am. Chem. Soc. 136 5567 [44] Liu J, Ruffieux P, Feng X, Müllen K and Fasel R 2014 Chem. Commun. 50 11200 [45] Riss A et al 2014 Nano Lett. 14 2251 [46] Zhang Y Q et al 2015 J. Phys. Chem. C 119 9669 [47] Klappenberger F, Zhang Y Q, Björk J, Klyatskaya S, Ruben M and Barth J V 2015 Acc. Chem. Res. 48 2140 [48] Björk J, Zhang Y Q, Klappenberger F, Barth J V and Stafström S 2014 J. Phys. Chem. C 118 3181 [49] Gao H Y, Franke J, Wagner H, Zhong D, Held P A, Studer A and Fuchs H 2013 J. Phys. Chem. C 117 18595 [50] Meyer J and Reuter K 2014 Angew. Chem. Int. Ed. 53 4721 [51] Treier M, Pignedoli C A, Laino T, Rieger R, Müllen K, Passerone D and Fasel R 2011 Nat. Chem. 3 61 [52] Björk J, Stafström S and Hanke F 2011 J. Am. Chem. Soc. 133 14884 [53] Blankenburg S, Cai J, Ruffieux P, Jaafar R, Passerone D, Feng X, Fasel R and Pignedoli C A 2012 ACS Nano 6 2020 [54] Yang B, Björk J, Lin H, Zhang X, Zhang H, Li Y, Fan J, Li Q and Chi L 2015 J. Am. Chem. Soc. 137 4904 [55] Díaz Arado O, Mönig H, Wagner H, Franke J H, Langewisch G, Held P A, Studer A and Fuchs H 2013 ACS Nano 7 8509 [56] Sun Q, Zhang C, Li Z, Kong H, Tan Q, Hu A and Xu W 2013 J. Am. Chem. Soc. 135 8448 [57] Sun Q, Zhang C, Kong H, Tan Q and Xu W 2014 Chem. Commun. 50 11825
[12] Hamada I 2014 Phys. Rev. B 89 121103 [13] Björk J and Stafström S 2014 ChemPhysChem 15 2851 [14] Matena M, Björk J, Wahl M, Lee T L, Zegenhagen J, Gade L H, Jung T A, Persson M and Stöhr M 2014 Phys. Rev. B 90 125408 [15] Henkelman G, Uberuaga B P and Jónsson H 2000 J. Chem. Phys. 113 9901 [16] Henkelman G and Jónsson H 1999 J. Chem. Phys. 111 7010 [17] Kästner J and Sherwood P 2008 J. Chem. Phys. 128 014106 [18] Bieri M et al 2010 J. Am. Chem. Soc. 132 16669 [19] Xi M and Bent B E 1992 Surf. Sci. 278 19 [20] Grill L, Dyer M, Lafferentz L, Persson M, Peters M V and Hecht S 2007 Nat. Nanotechnol. 2 687 [21] Lafferentz L, Eberhardt V, Dri C, Africh C, Comelli G, Esch F, Hecht S and Grill L 2012 Nat. Chem. 4 215 [22] Fan Q, Wang C, Han Y, Zhu J, Hieringer W, Kuttner J, Hilt G and Gottfried J M 2013 Angew. Chem. Int. Ed. 52 4668 [23] Chen M, Xiao J and Steinruck H 2014 J. Phys. Chem. C 118 6820 [24] Rastgoo-Lahrood A, Björk J, Heckl W M and Lackinger M 2015 Chem. Commun. 51 13301 [25] Basagni A, Sedona F, Pignedoli C A, Cattelan M, Nicolas L, Casarin M and Sambi M 2015 J. Am. Chem. Soc. 137 1802 [26] Fan Q, Wang T, Liu L, Zhao J, Zhu J and Gottfried J M 2015 J. Chem. Phys. 142 101906 [27] Morchutt C, Björk J, Krotzky S, Gutzler R and Kern K 2015 Chem. Commun. 51 2440 [28] Simonov K A 2015 ACS Nano 9 8997 [29] Smykalla L, Shukrynau P, Korb M, Lang H and Hietschold M 2015 Nanoscale 7 4234 [30] Beggan J P, Boyle N M, Pryce M T and Cafolla A A 2015 Nanotechnology 26 365602 [31] Zhang H et al 2015 J. Am. Chem. Soc. 137 4022 [32] Wang W, Shi X, Wang S, Van Hove M A and Lin N 2011 J. Am. Chem. Soc. 133 13264 [33] Di Giovannantonio M et al 2013 ACS Nano 7 8190 [34] Gutzler R et al 2014 Nanoscale 6 2660 [35] Eichhorn J, Nieckarz D, Ochs O, Samanta D, Schmittel M, Szabelski P J and Lackinger M 2014 ACS Nano 8 7880
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Reaction mechanisms for on-surface synthesis of covalent nanostructures
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Journal of Physics: Condensed Matter J. Phys.: Condens. Matter 28 (2016) 083002 (15pp)
doi:10.1088/0953-8984/28/8/083002
Topical Review
Reaction mechanisms for on-surface synthesis of covalent nanostructures J Björk Department of Physics, Chemistry and Biology, IFM, Linköping University, Sweden E-mail: [email protected] Received 15 May 2015, revised 8 January 2016 Accepted for publication 14 January 2016 Published 2 February 2016 Abstract
In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms. Keywords: surface chemistry, density functional theory, transition state theory (Some figures may appear in colour only in the online journal)
1. Introduction
how a molecule will react on a surface. Therefore, we often rely on trial-and-error, coupled to insight from organic synthesis, and finding new covalent materials has become a quite time- consuming activity. To improve this research field into a direction where we can make, from a blueprint of a covalent material, rational choices of the appropriate molecules and surfaces for creating a material, there is a need for a greater understanding of the underlying mechanisms of relevant on-surface reactions. The ultimate goal would be to comprehend how the these mech anisms are governed by the selection of molecules and surfaces. To reach this ambition, there is a great need for theoretical input into mechanisms of on-surface reactions. The objective of this topical review is to sum up the theoretical work that has been done so far, and identify some of the research questions that theory should focus on during the forthcoming years, for advancing the propitious field of on-surface synthesis. The topical review is structured the following way: first I will give a brief introduction of how reactions on surfaces can be studied by electronic structure theory. This is followed by sections devoted to separate on-surface reactions, each summarizing key experimental studies followed by a more indepth discussion of the efforts from theoretical modeling. I will particularly be addressing on-surface Ullmann coupling,
On-surface synthesis has great prospects for manufacturing covalent nanostructures with atomic precision. In contrast to the vast field of heterogeneous catalysis, which has primarily focused on the chemical transformation of rather small organic molecules, the central research target is the synthesis of covalent materials extended in either one or two dimensions. By coupling molecular building blocks, aided by the reactivity on a metal surface under ultra-high vacuum (UHV) conditions, covalent structures can be formed following a bottom-up strategy. This has resulted in the synthesis of various covalent materials, such as graphene nanoribbons [1], extended graphdiyne wires [2], porous graphene [3], and single-chirality carbon nanotubes [4]. In principle, the dimensions of a formed structure could be controlled on the sole basis of molecular building blocks and the type of reaction triggered between the molecules. Thus, by equipping right molecular building block with proper reacting groups, any imaginable type of covalent material should be within reach. However, the reality is not that simple, and mastering the onsurface reactions has shown to be a severely complicated task. Since the insight into the mechanisms of the reactions relevant for on-surface synthesis is rather limited, it is difficult to foresee 0953-8984/16/083002+15$33.00
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surface chemistry of terminal alkynes, and cyclodehydrogenation reactions; for which the most extensive theoretical invest igations have been made; but will briefly cover other types of on-surface reactions. The topical review is concluded by an outlook.
state theory, in which it is assumed that a reaction can be characterized by an initial state (IS), a transition state (TS) and a final state (FS) and the rate of crossing the transition state at a temperature T is given by the Arrhenius equation ν = A exp(−Ea /kBT ), (2)
where the activation energy Ea is defined as the energy difference between the TS and FS, and kB is Boltzmann’s constant. The prefactor A may be approximated from the vibrational frequencies at the TS and IS, but is normally assigned the rule-of-thumb value of 1013 s−1. The IS and FS are local minima on the potential energy surface, obtained by conventional structural optimization by minimizing the forces in the calculations. The TS of a reaction is, however, less trivial to determine as it is characterized by a saddle point on the potential energy landscape. There are several methods for finding saddle points in DFT. The most commonly applied way for finding saddle points in on-surface synthesis is with the Nudged Elastic Band (NEB) method. In this method several images (states) are connected to trace a path between the IS and the FS. The reaction path is then found by minimizing the forces acting perpendicular to the tangents of the path (nudging). To ensure that images are equally distributed along the path, spring-forces acting parallel to the tangent of the path are introduced (elastic bands). From the NEB method, typically none of the images are found at, or even close to, the TS and the TS energy is estimated by interpolation. This led to the development of climbing image NEB (CI-NEB) [15]. The only difference from regular NEB is that the spring force acting on the highest energy is replaced with the negative of the force parallell to the tangent of the path [15]. This way the highest energy image, referred to as the climbing image, moves up the energy surface along the elastic band, towards the transition state of the path. Importantly, the path determined by the NEB methods depends on the initial interpolation between IS and FS. Therefore, depending on the type of reaction, one may need to compare the outcome of several initial guesses of the path. With some vigilance, NEB and CI-NEB present reliable ways of studying reaction paths. Particularly they find the number of barriers separating initial and final states. However, as they rely on accurate tangent description of the reaction path (obtained by finite differences between images), they require an adequate number of images for converging the path. This makes the methods numerically expensive as we need individual DFT calculations for the separate images. Minimum mode following methods, exemplified by the Dimer method [16, 17], are numerically cheaper since they focus on the optimization of a transition state, omitting the information about the complete reaction path. The Dimer method is based on using three images (or states): the central image and the two images constituting the dimer. The dimer images are slightly displaced from each other by a fixed distance with the central image in the middle. The TS search algorithm involves two steps. In the first step the vector defined by the dimer is rotated into the lowest curvature mode of the potential energy at the central image.
2. Density functional theory description of on-surface reactions Here, density functional theory (DFT) will be introduced, including a brief discussion of how well DFT describes molecules on surface (in particular, the treatment of van der Waals interactions). Then it will be described how DFT together with transition state theory can be used to study reactions, outlining different methods for computing reaction pathways and transition states. In density functional theory, the total energy of a system is obtained as a functional of the ground state electron density, n ≡ n(r) [5] 1 E [n] = Ts [n] + ∫ dr v(r)n(r) + 2
∫ drdr′
n(r)n(r ′) + Exc [n] , r − r′
(1) where the first term is the kinetic energy of non-interacting electrons, the second and third terms give the electron-nuclei and electron-electron Coloumb energy, respectively, and the final term is the so-called exchange-correlation (XC) energy. All these terms can be determined exactly, within the numer ical accuracy of the calculations, except for the XC energy, which has to be approximated. 2.1. Treating van der Waals interactions
An important, and highly timely, aspect of modeling the adsorption of molecules on surfaces is how to treat so-called van der Waals (vdW), or London dispersion, forces. By construction, conventionally used generalized gradient approx imation (GGA) and local density approximation (LDA) fail to include these interactions, why adsorption heights are generally overestimated for weakly adsorbed systems, or molecules with a π-conjugated core, and the reactivity of a molecule on a surface may not be described correctly. Two schools of thought for treating vdW interactions in DFT have been established. The first is based on semi-empirical corrections, known as dispersion-corrected DFT [6], while the other solves the problem by introducing a non-local density functional commonly denoted as the van der Waals density functional (vdWDF) [7]. Without going into detail, it has been illustrated that with their respective most recent developments, molecular adsorption heights are now described with a precision of 0.1 Å both by dispersion-corrected DFT [8, 9] and vdWDF [10–14]. 2.2. Studying reaction mechanisms
The approach for studying reaction paths of reactions related to on-surface synthesis has exclusively been transition 2
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Then, the central image and the dimer are translated a certain step length, moving the central image towards the TS. The TS is found by iterating the algorithm until the forces on the central image are converged, under the condition that the curvature of the potential energy at the central images in the direction of the dimer is negative. The method explores transition states either by moving the dimer in different directions from the IS (even without knowledge of the FS), or by making use of the output from a NEB calculation as initial guess of the TS. For complex multidimensional reactions, often encountered in on-surface synthesis, the last alternative is most appealing, since we have the full trajectory between initial and final state from NEB, thereby knowing the number of barriers separating the FS from the IS and, for example, the Dimer method is used to refine the TS found from NEB.
two processes: radical diffusion and radical-radical coupling. The coupling step is considered as a more or less irreversible process, resulting in that self-healing, inherent to supramolecular self-assembly, is generally missing (although this problem may be solved by the formation of metal-organic intermediates [36]). Bieri et al [18] demonstrated that this adds some restriction on the diffusion and coupling step, for the formation of ordered covalent 2D materials. They defined a coupling probability between two adjacent radicals as νcouple P= , (3) νcouple + νdiff
where νcouple is the rate of coupling and νdiff is the rate of diffusion. Small values of P indicates that the diffusion is much faster than the coupling (a coupling limited process), while values close to 1 indicates that the coupling is much faster than the diffusion (a diffusion limited process). Figure 2 illustrates kinetic Monte Carlo (kMC) simulations of the nucleation of surface-stabilized radicals for different values of P. For P values close to 1, fractal-like networks are formed, while smaller values of P give more ordered 2D networks. The results of Bieri et al [18] illustrates the requirement of a coupling-limited process for the formation of ordered 2D materials with the on-surface Ullmann coupling, and any other method requiring a recombination step between surfacestabilized radicals.
3. On-surface Ullmann coupling The on-surface Ullmann coupling is without doubt the most commonly applied strategy for creating covalent materials through on-surface synthesis. The approach is reminiscent of the Ullmann coupling in wet chemistry, in which aryl halides comprise the molecular building blocks. The halogens of these molecules are thermally abstracted more easily than other atoms, making it possible to generate surface-stabilized radicals [18], which can then couple into patterns of covalently bonded molecules. By controlling the number of halogens, and their positions within the molecules, one can in principle control the dimensions of the formed nanostructures. The basic concept is illustrated in figure 1 for two model systems based on benzene substituted with different number of halogen atoms. The on-surface Ullmann coupling was demonstrated already 1992 for the synthesis of biphenyl from iodobenzene on Cu(1 1 1) [19], but was not demonstrated for the formation of covalent nanostructures until 15 years later [20]. In a pioneering study by Grill et al it was illustrated how porphyrins equipped with bromine can couple into larger molecules (0D), chains (1D) or clusters (2D) depending on the number of bromine atoms in the molecules [20]. The method has since then been used numerous times [1, 3, 18, 21–31]. For example, it can be used to form graphene nanoribbons, either complemented by a cyclodehydrogenation reaction [1], or as the sole reaction step [31]. In several cases metal-organic intermediate structures have been observed [32–36], in which the dehalogenated molecules coordinate to metal adatoms thermally generated from the substrate. The exact role of these adatoms in the overall process is not yet clear, as the theoretical work so far has focused on reactions on atomically flat surfaces, as will be described here.
3.2. Recombination mechanisms
Theoretical calculations of reaction mechanisms together with experimental observations corroborated the prediction that a coupling-limited process is a prerequisite for the formation of ordered 2D materials. Figure 3 illustrates calculated recombination mechanisms of cyclohexa-m-phenylene radicals (CHPR) on Cu(1 1 1) and Ag(1 1 1) [18]. CHPR is chemically bonded via its six radical sites to the metal atoms and the calculated reaction sequence is similar for both surfaces: Two carbon radicals (one from each molecule) are bonded to adjacent surface atoms in the initial state (denoted II). The reactions are initiated by a multi-barrier diffusion step, leading to the intermediate states IM2, where the two molecules are chemically bonded with a carbon radical to the same surface atom. On Cu(1 1 1), the coupling-step is barrier-free (IM2 to IM3), while the final step in the simulated path is simply a diffusion step for one half of the dimer. On Ag(1 1 1), the coupling is a two-step process between IM2 and FI, with a barrier larger than that for diffusion. These results indicate that the recombination process of CHPR is diffusion limited on Cu(1 1 1) (compare the diffusion barrier of 2.2 eV to the spontaneous coupling reaction), while it is coupling limited on Ag(1 1 1) (diffusion barrier of 0.8 eV and coupling barrier of 1.8 eV). Thus, from the discussion around equation (3) one would expect that CHPR more likely forms ordered 2D materials on Ag(1 1 1) than on Cu(1 1 1). Notably, experiments have shown exactly this: On Ag(1 1 1) a porous graphene structure with relatively low
3.1. Ideal conditions for creating ordered 2D-materials
An important step for the on-surface Ullmann coupling is the recombination of surface-stabilized radicals. The recombination is, in a simplified picture, associated with 3
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Figure 1. Basic principle of the on-surface Ullmann coupling for the formation of (a) 1D and (b) 2D materials, by controlling the number of halogens of the molecular precursors.
Figure 2. Kinetic Monte Carlo simulations for the recombination process between surface-stabilized radicals for different coupling probabilities P, defined by equation (3). The smaller values of P, the smaller number of defects are found in the resulting 2D networks. Reprinted with permission from [18]. Copyright (2010) American Chemical Society.
defect density was observed, resembling the simulated structure obtained for a small coupling probability in figure 2(c). Contrarily, branches of a single molecule width were found on Cu(1 1 1) [3]. In the same study, experiments found networks of intermediate quality on Au(1 1 1), suggesting it has properties somewhere between Ag(1 1 1) and Cu(1 1 1) in terms of promoting a coupling or a diffusion limited process. However, there are no theoretical studies for the recombination of two
CHPRs on this surface, which certainly would be of great interest. 3.3. The formation of biphenyl
Before discussing the complete reaction sequence to form biphenyl with on-surface Ullmann coupling presented in [37] it is important to have in mind that Nguyen et al were the first 4
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Figure 3. Calculated recombination pathways of CHPR on Cu(1 1 1) and Ag(1 1 1), as indicated. The chemical structure of CHPR is shown in the inset. Reprinted with permission from [18]. Copyright (2010) American Chemical Society.
surface. The picture is very similar on all the three surfaces for both bromo- and iodobenzene. An important point is the chemical state of the resulting radicals. In the FS the phenyl radical is chemisorbed on the surface, resulting in the un-paired spin being quenched, why in literature one frequently use the notation ‘surface-stabilized radical’ [18]. Often, the term radical is used quite loosely, but as a general rule, for these type of radicals the un-paired spin is most likely quenched, and the notation that we have a surface-stabilized radical is more appropriate. In figure 4(c) the energy barriers (activation energies) and reaction energies are shown for the six dehalogenation reactions. Given that both reactions are highly endothermic in gas phase, with reaction energies of 3.85 eV and 3.33 eV for bromobenzene and iodobenzene, respectively, it is clear that all three surfaces have catalytic effects on dehalogenation. For bromobenzene, the barriers range from 1.02 eV on Au to 0.66 eV on Cu(1 1 1). A similar trend, shifted by roughly −0.3 eV is found for iodobenzene, with barriers of 0.71 eV on Au(1 1 1) and 0.40 eV on Cu(1 1 1) [37]. Notably, the reaction energies follow a quite different trend, with largest difference between the two molecules for Au(1 1 1) and a rather small difference for Cu(1 1 1).
to study the particular case of recombining phenyl radicals on Cu(1 1 1) [38]. Both these studies [37, 38] gave the same conclusion regarding the diffusion and coupling on Cu(1 1 1), and for simplicity, the discussion herein is based on the results presented in [37]. To date, the only study of the complete procedure for a synthesis protocol making use of the on-surface Ullmann coupling investigated the formation of biphenyl from bromo- and iodobenzene on Cu(1 1 1), Ag(1 1 1) and Au(1 1 1) [37]. The overall process is initiated by dehalogenation, followed by the recombination (diffusion and coupling) of the surface-stabilized phenyl radicals, resulting in biphenyl. We will begin by discussing the dehalogenation of bromobenzene and iodobenzene on the three surfaces. A typical energy profile is shown in figure 4(a) and IS, TS and FS of the dehalogenation is exemplified for bromobenzene on Au(1 1 1) in figure 4(b). In the IS, the molecule is physisorbed on the surface, while in the TS a chemical bond has begun to form between the halogenated carbon atom and the surface as the same time as the carbon-halogen bond is elongated. Ultimately, in the FS the C-Br bond is completely dissociated, with the resulting phenyl radical and bromine chemisorbed to the 5
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they are chemisorbed to the same surface atom, defined as IS of the coupling reaction. The pathways for coupling are depicted in figure 6. In the TS the two radicals are still chemisorbed to the surface atoms, and only differs from the IS in that the two radical carbon atoms are closer to each other. The energies of the states are defined with respect of having the two molecules well separated. The activation energy for coupling was defined as the energy of the TS rather than the energy difference between TS and IS. The activation energy for coupling is smallest for Cu(1 1 1) and largest for Ag(1 1 1), while an intermediate value was found for Au(1 1 1). For all surfaces the coupling is highly exothermic, manifesting the irreversibility of the covalent bond formation [37]. Following the argumentation that the slide diffusion is more relevant than the flip diffusion, it gives that the phenyl radical has the same trend as CHPR, in which the recombination is diffusion limited on Cu(1 1 1) and coupling limited on Ag(1 1 1). For Au(1 1 1), the recombination is considered being neither diffusion nor coupling limited, as the barrier of diffusion is similar to that of the coupling. 4. Surface chemistry of terminal alkynes Molecules functionalized with terminal alkynes participate in another group of on-surface reactions. In particular, homocoupling between terminal alkynes has gained a lot of interest since it was first reported on a surface in 2012 [39]. This method has enabled thermal coupling of acetylene functional groups, creating butadiyne (diacetylene) bridges between adjacent molecules, and is highly relevant for the realization of materials related to graphdiyne, a carbon allotrope in which benzene rings are interlinked by butadiyne bridges. For example, extended graphdiyne wires have been synthesized on a silver surface [2]. The surface chemistry of terminal alkynes has proven to be extremely versatile, and several reactions have been reported [40–46]. Maybe most intriguingly, a cyclotrimerization reaction has been observed in a few studies [41–45]. For example, Zhou et al demonstrated how a linear molecular building blocks undergo a [2+2+2] cyclotrimerization on Au(1 1 1) [43]. In another example [44], 1,3,5-tris-(4-ethynylphenyl)benzene (Ext-TEB) molecules were observed to cyclotrimerize on Au(1 1 1). Notably, the Ext-TEB molecule was also used in the first report of the homo-coupling [39], but on Ag(1 1 1). The two types of reaction products obtained for Ext-TEB on Ag(1 1 1) and Au(1 1 1), together with the basic principles of the homo-coupling and cyclotrimerization, are compared in figure 7. Furthermore, if instead deposited on Cu(1 1 1), Ext-TEB dehydrogenates and forms an unusual deprotonated alkynyl hydrogen bonding network, inhibiting the coupling between molecules [46]. The Ext-TEB molecule gives an excellent example of the versatile surface chemistry of terminal alkynes, where the chemoselectivity can be tuned by changing the reactivity of the surface. The versatile surface chemistry of terminal alkynes have been observed in several other studies. For example, the linear 4,4”-diethynyl- 1,1’:4’,1”-terphenyl molecule gives a multitude
Figure 4. (a) Typical potential energy profile for dehalogenation reactions, such as (b) the dissociation of bromobenzene on Au(1 1 1). (c) Ebarrier (left) and E react (right) for the dissociation of bromobenzene and iodobenzene on the (1 1 1) facets of Au, Ag, and Cu. Reprinted with permission from [37]. Copyright (2013) American Chemical Society.
The next step of the reaction is the recombination of two phenyl radicals into biphenyl. The overall recombination is associated with two processes, namely diffusion and the coupling between surface-stabilized radicals. As illustrated in figure 5 the phenyl can follow two types of diffusion. The slide diffusion, in which the orientation of the phenyl ring is the same in the IS and the FS, and a flip diffusion in which the phenyl ring flips between two sites such that its orientation changes. On all surface, except for Au(1 1 1) for which the two diffusion modes have the same TS, the flip diffusion has the lowest barrier. However, the flip diffusion is probably only possible for molecules of similar size as phenyl, as it has a TS or intermediate state where the molecule is standing upright on the surface [37]. Such a configuration would not be possible for a larger molecule due to the cost of breaking vdW interactions, and definitely not for a molecule with more than one radical site, as it would require the scission of chemical bonds. When the molecules have diffused over the surface, they will eventually come in the near proximity to another molecule such that they can react. In the case of phenyl radicals, the closest two molecules can be without reacting is when 6
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Figure 5. Energy diagrams for (a) sliding diffusion and (b) flipping diffusion of phenyl on Au(1 1 1), Ag(1 1 1), and Au(1 1 1), where the top and side views of the paths are depicted in the top panel for (a) Ag(1 1 1) and (b) Au(1 1 1). In both processes, phenyl diffuses between two adjacent surface atoms rendered darker than other surface atoms. On Au(1 1 1), the flipping and sliding diffusions have identical TSs and differ only by the relative orientation of the molecule in the IS and FS. The flipping diffusion (b) is a two-step process on Cu(1 1 1) and Ag(1 1 1). Reprinted with permission from [37]. Copyright (2013) American Chemical Society.
Figure 6. Coupling reaction of two phenyls into biphenyl on Au(1 1 1), Ag(1 1 1) and Cu(1 1 1), depicted for Ag(1 1 1) in the top panel. Energies are given with respect to having the two phenyl well separated from each other on respective surface. Reprinted with permission from [37]. Copyright (2013) American Chemical Society.
of side reactions on Ag(1 1 1), with coupling motifs of up to five monomers, while a high chemoselectivity towards the homo coupling is obtained when depositing it with a delicately tuned coverage on the stepped Ag(877) surface [2]. The deposition of 1,4-diethynylbenzene on Cu(1 1 1) gives rise to a multitude of reactions, such as homo-coupling and cyclotrimerization [42], but does not result in the deprotonated alkynyl hydrogen bonding network reported for Ext-TEB on Cu(1 1 1) [46].
It should be further noted that while the Au(1 1 1) surface has been observed to activate mainly cyclotrimerization reactions in a couple of examples [43, 44], other molecules on this surface have resulted in the homo-coupling among with other reaction products [41]. Thus, the chemoselectivity toward homo-coupling versus cyclotrimerization is not simply controlled by the choice of surface, but rather the molecule-surface combination is important. 7
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does not have time to thermally equilibrate after the highly exothermic coupling step. As a consequence, the energy gained in the coupling is reinvested into the dehydrogenation steps, reminiscent of hot adsorbates that can form in dissociative adsorption [50]. An alternative path for initiating the homo-coupling would be to directly dehydrogenate the terminal alkyne prior to the coupling. However, calculations have shown that the barrier is twice that to initially couple two TEB molecules [48]. A similar barrier was found for dehydrogenating ethynyl-benzene on Ag(1 1 1), while it is slightly lowered to 1.64 eV on Au(1 1 1) [49]. In other words, initially coupling of terminal alkynes is significantly more probable than dehydrogenating the molecules followed by the coupling. Figure 7. The prefered reaction path of the Ext-TEB molecule depends on the underlying surface: on Ag(1 1 1) the homocoupling reaction is obtained [39], while the molecules undergo a cyclotrimerization reaction on Au(1 1 1) [44].
4.2. Considerations of the cyclotrimerization mechanism
Zhou et al provided insight into the cyclotrimerization between terminal alkynes by studying the formation of benzene from three acetylene molecules [43], as shown in figure 10. The reaction was considered to be non-concerted, where two acetylene first couple, followed by the reaction with the third molecule, resulting in benzene. The first step is smaller than the second one (compare 1.54 eV to 1.72 eV), suggesting that the intermediate (INT), in which only two alkynes have coupled, should be observable. Indeed, such intermediate state has been observed in STM experiments [43]. One needs to bear in mind that these calculations were done by using a planar cluster of 14 Au atoms representing the surface [43], which will be significantly more reactive than the real Au(1 1 1) surface. Furthermore, the pathway’s intermediate state (denoted INT) resembles the cis intermediate state (IntS1cis) for the homo-coupling, which is a result of using acetylene as model molecule, for which it is not possible to differentiate the initial step of cyclotrimerization and homo-coupling. This aspect is demonstrated in figure 11, which compares the respective mechanisms of homo-coupling and cyclotrimerization. The study by Zhou et al still provides valuable insights into the cyclotrimerization between alkynes, despite that investigations on realistic surfaces and more representative molecules are needed for a full appreciation of the reaction.
For a more extensive account of the work devoted to the surface chemistry of terminal alkynes see the recent review in [47]. Hereon I will focus on the theoretical efforts made for understanding the underlying mechanisms of their multifaceted surface chemistry. 4.1. Mechanism of homo-coupling
Two independent theoretical studies of the homo-coupling have been presented [48, 49], both reaching the conclusion that the coupling of the terminal alkynes precedes the release of hydrogen atoms. I will center the discussion around the dimerization between 1,3,5-triethynyl-benzene (TEB) molecules on Ag(1 1 1), one of the systems used to initially demonstrate the homo-coupling [39], and reflect on how it relates to other molecules and surfaces. The initial coupling step between two TEB molecules is illustrated in figure 8. The barrier of coupling the two molecules (going from IS to IntS1trans) is 0.90 eV [48], which is the same barrier found for ethynyl-benzene on Ag(1 1 1), while a slightly smaller barrier (0.79 eV) was found for Au(1 1 1) [49]. Following the initial coupling, the formed TEB dimer can exist in a trans (IntS1trans) and cis state (IntS1cis). In IntS1trans one of the carbon atoms is under-coordinated and it has been made quite clear that the molecule will exist in the more stable IntS1cis configuration at some point before continuing the reaction [48]. The homo-coupling between two TEB monomers is finalized by two subsequent dehydrogenation steps, with barriers of 1.27 eV and 1.53 eV, respectively, as shown in figure 9. Particularly the second barrier is considerable having in mind that the reaction takes place at 300 K in experiments [39]. Several explanations for this anomaly between theory and experiments have been proposed. For example, the calcul ations give the potential energy landscape at 0 K and it was shown that temperature effects, in terms of vibrational enthalpy and entropy, indeed reduce the dehydrogenation barrier [48]. Another possibility might be that the system
5. Surface-assisted cyclodehydrogenation Cyclodehydrogenation is a category of intramolecular ringclosure reactions in which a carbon-carbon bond is formed simultaneously with the release of two hydrogen atoms (bonded to the carbon atoms in the reactant). In figure 12 a cyclodehydrogenation reaction is demonstrated for an illustrative model system. Surface-assisted cyclodehydrogenation has been used together with on-surface Ullmann coupling for the on-surface synthesis of different types of graphene nanoribbons on Au(1 1 1) and Ag(1 1 1), such as the transformation of a polyanthrylene intermediate into a seven carbon atoms wide ribbon [1]. It has also been employed to form large polycyclic 8
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Figure 8. The homo-coupling between two TEB molecules is initiated by a coupling step, with the hydrogen remaining on the molecules. The coupled transition state can exist in a trans- and cis-isomer, where the latter is the more stable one. The two hydrogen atoms taking part in the coupling were rendered red for clarity. Reprinted with permission from [48]. Copyright (2014) American Chemical Society.
Figure 9. Following the initial coupling of two TEB molecules (figure 8), the resulting dimer undergoes two subsequent dehydrogenation steps, which finalizes the overall homo-coupling. The two hydrogen atoms being split-off were rendered in red for clarity. Reprinted with permission from [48]. Copyright (2014) American Chemical Society.
Figure 10. Mechanism of the formation of benzene from three acetylene molecules through cyclotrimerization on Au(1 1 1). Reprinted
with permission from [43]. Copyright (2014) American Chemical Society. 9
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Figure 11. Comparison between the mechanism of (a) homo-coupling and (b) cyclotrimerization between terminal alkynes, with the
metal surface indicated as Me. If using acetylene as a model compound, in which the group R is represented by a hydrogen atom, the first intermediate state of the homo-coupling and the intermediate state of the cyclotrimerization are identical.
bianthryl units couple into polyanthrylene following an on-surface Ullmann coupling procedure. This is followed by the cyclodehydrogenation step, yielding the graphene nanoribbons. A staggering amount of work has been devoted to the seven atoms wide armchair graphene nanoribbons initially demonstrated by Cai et al [1]. However, only a couple of theoretical studies have been devoted to the mechanism of the cyclodehydrogenation reaction [52, 53]. Blankenburg et al studied the mechanism on Ag(1 1 1), and backed up their theoretical results by STM experiments [53]. Their reaction pathway is illustrated in figure 15. In short, they found that the reaction is initiated by the coupling between two carbon atoms (S0 to S1), followed by the abstraction of a hydrogen atom (S1 to S2). Then a hydrogen is tautomerized, in other words migrated between two carbon atoms (S2 to S3) followed by an additional carbon-carbon coupling step (S3 to S4), which is succeeded by the tautomerization of an additional hydrogen atom (S4 to S5) and the abstraction of two hydrogen atoms (S5 to S6). The reaction then procedes stepwise in a similar fashion. For a more detailed view of the mechanism see [53]. An interesting aspect of the mechanism presented by Blankenburg et al is that the cyclotrimerization between two carbon atoms has a reducing effect on the barrier of cyclotrimerization between the adjecent anthracene units (at the same side of the nanoribbon). This was in fact also observed STM experiments, in which it was possible to activate the cyclotrimerization in one side of the polyanthrylene, while keeping the other side unreacted [53]. Another study reported a theor etical investigation of the cyclotrimerization on Au(1 1 1) [52], and came to the same conclusion that the cyclotrimerization proceeds in a domino-like fashion, where the cyclodehydrogenation between two pairs of anthracene units enable the coupling between the next units. However, in this study is was concluded that both sides of the polymer is cyclodehydrogenated before moving to the next units and not the side-wise activation that was found on Ag(1 1 1) [53]. It is not clear whether this is a difference between Ag(1 1 1) and Au(1 1 1), or if the
Figure 12. In cyclodehydrogenation two carbon atoms couple
simultaneously as detaching their hydrogen atoms, effectively resulting in a ring-closure.
aromatics hydrocarbons (PAHs), so called nanographenes, from cyclohexa-o-p-o-p-o-p-phenylene (CHP) on Cu(1 1 1) [51]. 5.1. Nanographenes
Treier et al performed a rigorous theoretical investigation of the reaction mechanism of the cyclodehydrogenation of CHP into a nanographene [51], the main results of which are illustrated in figure 13. The overall reaction procedes in a six-step process, via the formation of three supplementary carbon-carbon bonds and abstraction of six hydrogen atoms. The reaction is initiated by a dehydrogenation step (state 1 to 2), followed by a carbon-carbon coupling and concomitant dehydrogenation (state 2 to 3). This is accompanied by a third dehydrogenation (state 3 to 4) and carbon-carbon coupling (state 4 to 5). The reaction is finalized by a combined carboncarbon coupling and dehydrogenation (state 5 to 6), ultimately leading to the release of a hydrogen molecule (state 6 to 7). It is quite interesting to note that two of the intermediate states were observed in STM experiments [51], namely state 3 and 6. These states are followed by two of the rate-limiting steps of the overall reaction and it is intriguing how well this is captured by the computed pathway. 5.2. Graphene nanoribbons
The formation of graphene nanoribbons is probably the most famous, and well-studied, example of on-surface synthesis. The overall reaction is shown in figure 14. Firstly, brominated 10
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Figure 13. Calculated reaction mechanism for the triple cyclodehydrogenation of CHP into a nanographene on the Cu(1 1 1) surface.
Reprinted by permission from Macmillan Publishers Ltd: Nature Chem. [51], copyright (2011).
model system used for studying the cyclodehydrogenation on Au(1 1 1) did not capture all aspects of the reaction, and constitutes an open question still awaiting an answer. 6. Other types of on-surface reactions Ullmann coupling, coupling between terminal alkynes and cyclodehydrogenation are probably the three most thoroughly studied on-surface reactions from theory, although a lot of work remains to fully comprehend them. Here I will highlight some of the work that has been performed to elucidate mech anisms for other types of reactions. Throughout this topical review different types of cyclization reactions have been accounted for. In fact, several additional examples of cyclization on surfaces exist. For example,
Figure 14. Schematics of the formation of graphene nanoribbons.
In a first step, brominated bianthryl units form polyanthrylene through on-surface Ullmann coupling. Then the polymer cyclodehydrogenates, resulting in the graphene nanoribbon [1].
11
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Figure 15. Calculated reaction mechanism for the cyclodehydrogenation of poly-anthracene into a graphene nanoribbon on the Ag(1 1 1)
surface. Reprinted with permission from [53]. Copyright (2012) American Chemical Society.
Yang et al demonstrated how acetyl-functionalized molecules couple either in a dimerization or a cyclotrimerization reaction [54]. Theoretical considerations of the reaction pathway of the initial dimerization between two molecules concluded that the reaction is initiated by the dehydrogenation of the methyl in an acetyl group, illustrated in figure 16(a). From this point there are two competing pathways: either the dehydrogenated molecule reacts with an intact molecule (figure 16(b)), or two dehydrogenated molecules react (figure 16(c)). The latter alternative requires a sufficient concentration of dehydrogenated molecules, but since the initial dehydrogenation is significantly larger than coupling two molecules, it was concluded that the coupling between an intact and a dehydrogenated molecule is more likely [54]. The initial coupling is followed by subsequent dehydroxylation and dehydrogenation steps,
and the abstraction of oxygen was supported by XPS experiments [54]. In another study, an azide-alkyne cycloaddition (figure 17) was observed on Au(1 1 1) [55]. Two reaction pathways were considered by DFT calculations, one occurring at an atomically flat Au(1 1 1) surface, and another in the presence of an Au adatom, as shown in figure 18. Both pathways have a barrier of around 0.7 eV, which was also found for the reaction in gas phase, concluding that the Au surface has an insignificant chemical impact on the reaction [55]. This gives an excellent, but rare, example where the surface instead of catalyzing the reaction, provides a support that enables the reaction by lowering the degrees of freedom of the molecular building blocks into two dimensions. Further examples of cyclization reactions have been reported. For example, Bergman cyclization 12
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Figure 16. Comparison of different reaction pathways involving acetyls. (a) Dehydrogenation of the acetyl’s methyl group, (b) coupling
between an intact and a dehydrogenated molecule, and (c) coupling between two dehydrogenated molecules. Valence bond structures have been included for reactants, intermediates and products for the different pathways, with the metal surface denoted as Me. Note that in (b) IntS2 and FS have the same chemical structure and differ only by the adsorption site of the abstracted OH-group. Adapted with permission from [54]. Copyright (2015) American Chemical Society.
The experimentally observed behavior was explained by theoretical modeling, which concluded that the activation energy for splitting of a hydrogen from the meta-carbon has a significantly smaller barrier compared to splitting-off hydrogen from other carbon atoms. Figure 17. Schematics of the azide-alkyne cycloaddition.
was demonstrated on Cu(1 1 0) [56], but for which no reaction pathways have been considered from theory. As a final example, Sun et al studied reactions between quaterphenyl molecules on Cu(1 1 0) in STM experiments, observing that the molecules couple via a selective C-H activation of the meta-carbon site of the terminal phenyl group [57].
7. Outlook In this topical review I have outlined some of the theoretical work that has been performed to understand reactions responsible for the formation of covalent nanostructures on surfaces, with particular focus on the on-surface Ullmann coupling, 13
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Figure 18. Calculations of azide-alkyne cycloaddition on Au(1 1 1) for an atomically flat surface ((A)–(C)) and aided by an Au adatom
((D)–(F)). Reprinted with permission from [55]. Copyright (2013) American Chemical Society.
surface-chemistry of terminal alkynes and surface-assisted cyclodehydrogenation. Regarding the on-surface Ullmann coupling, theoretical modeling has successfully modeled the pathways for specific systems. However, the predictive power of the current knowledge is rather limited, and we need to put our forthcoming efforts in systematic studies of on-surface reactions. A part icularly important milestone would the development of a theory that could predict whether a specific molecule-surface combination gives rise to a coupling-limited or a diffusionlimited recombination process. This would specifically guide the formation of ordered covalent 2D materials, for which a coupling limited process is a prerequisite. Furthermore, to date, theoretical studies have exclusively considered processes on atomically flat surfaces. However, as seen numerous of times in experiments, metal-organic intermediate structures can play an important role, possibly enabling self-healing protocols. Insight into the exact role of metal adatoms would therefore be of immediate interest. Molecules functionalized with terminal alkynes have demonstrated a highly versatile surface chemistry. Although there are some aspects that remain to be unraveled about the homocoupling reaction, the most immense theoretical effort will be to comprehend other possible types of reactions terminal alkynes can undergo. In particular, we need a more sophisticated understanding of the cyclotrimerization, and the next years theory is expected to make important contributions in this regard. In the long-term perspective, theoretical modeling should aim at finding general design rules governing the chemoselectivity of the surface chemistry of terminal alkynes. Cyclodehydrogenation is probably the most studied, and well-understood, on-surface reaction from theory. Although there are some issues to unravel about how the reaction differs
between various surfaces, the on-surface synthesis field is in a more urgent need for theoretical studies about other reactions. Here we have focused on the work where theory has provided input into on-surface reaction mechanisms. However, for the majority of the reported reactions, information of mechanisms is missing. It is only the last years that the comp uter resources have become sufficient to study on-surface reactions in a more routinely and systematic manner. During the next years it is anticipated that theoretical insights, and with this our appreciation, of on-surface synthesis will grow with a spiralling rate.
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