Molecular Mechanochemistry Understood at the Nanoscale: Thiolate

Apr 16, 2009 - Slovak University of Technology. , ‡. Slovak Academy of Sciences. , §. Ruhr-Universität Bochum. Cite this:J. Phys. Chem. C 113, 20,...
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J. Phys. Chem. C 2009, 113, 8878–8887

Molecular Mechanochemistry Understood at the Nanoscale: Thiolate Interfaces and Junctions with Copper Surfaces and Clusters Martin Konoˆpka,*,† Robert Turansky´,‡ Matu´sˇ Dubecky´,†,‡ Dominik Marx,§ and Ivan Sˇtich*,‡ Center for Computational Materials Science (CCMS), SloVak UniVersity of Technology (FEI STU), IlkoVicˇoVa 3, 81219, BratislaVa, SloVakia, Institute of Physics, SloVak Academy of Sciences, 84511 BratislaVa, SloVakia, and Lehrstuhl fu¨r Theoretische Chemie, Ruhr-UniVersita¨t Bochum, 44780 Bochum, Germany ReceiVed: February 24, 2009

Two very different approaches to activate chemical bonds, nanoscale mechanochemistry and the ubiquitous thermochemistry, are studied and compared for a range of different thiolate/copper interfaces and junctions using self-assembled monolayers (SAMs) on perfect surfaces as well as single molecules anchored at steps and on clusters. In nanoscale mechanochemistry the activation proceeds by supplying locally pure mechanical energy to the desired atom(s) and/or bond(s). Using both dynamic and static electronic structure methods we predict vastly different reaction pathways and product classes for the two types of activation. These differences can be understood in terms of directional mechanical manipulation of coordination numbers and system fluctuations in the process of mechanical activation which affect the coupling of the thiolate molecular orbitals to the metal part of the molecule/metal junction or interface. The observed conceptual differences are huge in size and general in nature. 1. Introduction Chemical reactions often require activation in order to overcome reaction barriers on meaningful time scales. Many different ways of activating chemical reactions are known such as thermochemistry, electrochemistry, or photochemistry. They differ not only in the nature of the energy supplied for activation, that is heat, electricity, or light, but often reaction pathways, and, most importantly, reaction products turn out to be different. However, in addition to these rather well-known “chemistries” chemical reaction may also be induced by a purely mechanical type of activation, namely by mechanochemistry (see ref 1 for an excellent recent review). Despite the fact that the concept of mechanochemistry is over a century old2 and notwithstanding the fact that even industrial applications are operational,3 understanding molecular mechanochemistry at the nanoscale is almost completely missing apart from some interesting glimpses taken.4–13 Yet, current experimental setups such as atomic force or scanning tunneling microscopy (AFM/STM)14 or mechanically controllable break junctions15,16 (MCBJ) provide a broad set of nanoengineering techniques to trigger and control chemical reactions by applying purely mechanical forces in order to activate chemical bonds. In these approaches a single molecule is anchored to metallic tips or surfaces via so-called “alligator clips” before manipulating them mechanically. The prototypical system here is a single organic molecule attached to gold tips via a covalent thiolate bond.17–19 Apart from paving the pathway for mechanical activation of chemical reactions these particular molecule-metal junctions also generate technological interest in areas such as molecular electronics.20,21 * To whom correspondence should be addressed. [email protected] (M.K.); [email protected] (I.S.). † Slovak University of Technology. ‡ Slovak Academy of Sciences. § Ruhr-Universita¨t Bochum.


In order to shed light on fundamental aspects of mechanochemistry at the nanoscale, we study, using electronic structure methods, short-chain thiolates chemisorbed on different copper complexes, including self-assembled monolayers (SAMs) on perfect surfaces, stepped surfaces, and small clusters as model systems for molecule-metal nanojunctions. In order to detect and to understand the peculiarities of mechanical activation we compare the mechanochemistry of those systems to the most common type of chemical activation, namely thermochemistry. These systems, at sufficiently high temperatures, will start to decompose by desorbing molecules from the surface as a result of increasingly strong thermal fluctuations, which can be measured by thermal desorption spectroscopy (TDS) techniques. We pose now a simple but general question: If that very same system is strained at low temperatures in an AFM, STM, or MCBJ apparatus by pulling individual molecules off the surface along its normal will the result match the results obtained by just heating the system until molecules desorb? In order words, does mechanical desorption lead to the same outcome as thermal desorption? It is noted in passing that, in this spirit, force spectroscopy14 could also be called “mechanical desorption spectroscopy” (MDS) in analogy to TDS. Second, what happens if both heat and mechanical strain are used simultaneously for activation? The reason why we study these systems is that compared to the widely studied gold counterparts22–26 such thiolate-copper contacts are known to display a rich disintegration behavior including even cleavage of covalent bonds of the anchored organic molecules themselves.27–35 Indeed we recently found pronounced phenomenological differences in both reaction pathways and products between mechanochemical and thermochemical disintegration of thiolate-copper interfaces and junctions.35 While thermal activation leads to C-S bond rupture within the thiolate molecule as also experimentally observed,27–29,31,32 mechanical activation strengthens the very same bond significantly, and, for sufficiently large extensions along the surface normal, the

10.1021/jp9017025 CCC: $40.75  2009 American Chemical Society Published on Web 04/16/2009

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entire molecule is pulled off the surface before a metal-metal bond breaks. It is noted in passing that breaking the S-metal bond by mechanical force is not observed. The differences between the two reaction pathways are explained in terms of presence (in thermal activation) or absence (in mechanical pulling) of fluctuations which may cause transient overcoordination of sulfur and weakening the C-S bond in the thermally activated system. Contrary to the thermal case, the mechanical pulling force reduces the fluctuations, tends to decrease sulfurto-copper coordination, and consequently strengthens the very same C-S bond. As the strength of the C-S bond strongly depends on the size of the metal complex,33 this scenario is verified for various system setups, i.e., flat and stepped surfaces as well as finite clusters of different sizes. 2. Models and Methods All electronic structure calculations were done in the framework of the density-functional theory (DFT) using the Perdew-Burke-Ernzerhof (PBE) functional36 and the CPMD code.37,38 Several different types of ab initio simulations have been performed: (i) structure relaxation, (ii) mechanochemical pulling at T ) 0 K, (iii) mechanochemical pulling at T ) 300 K, and (iv) standard ab initio molecular dynamics (AIMD);38,39 suitable constraints or restraints were applied as discussed in the text. For optimizations and AIMD we used ultrasoft pseudopotentials40 for all species with a 25 Ry plane wave cutoff, and the structural relaxation was performed using standard optimization methods such as LBFGS.41 All AIMD simulations are performed using the Car-Parrinello algorithm with a time step of 6 or 7 au together with Nose´-Hoover-chain thermostats attached to both ions and orbitals.38,39 Kohn-Sham diagonalizations needed to calculate the local densities of states (LDOS) as well as charge densities have been done with an identical setup except for use of norm-conserving dual-space Goedecker pseudopotentials42 with a 100 Ry plane wave cutoff. The validity of our basic computational approach has been carefully checked earlier against quantum-chemical data and all-electron calculations with localized basis sets.33 Using this set of simulation methods three different thiolatecopper systems have been simulated: (a) a thiolate SAM on a perfect Cu(111) surface, (b) a single thiolate molecule chemisorbed at the Cu(221) step, and (c) a single thiolate molecule chemisorbed at small Cun clusters as visualized in Figure 1 from right to left. (a) A SAM on a flat copper surface (molecule-metal interface slab model) is represented33–35 by a periodically repeated sixlayer thick slab using a c(4 × 4) supercell of Cu(111) with four chemisorbed ethylthiolate molecules, CH3CH2S, according to the upper right panel of Figure 1. The slab consists of 6 × 16 ) 96 Cu atoms where the atoms in the bottom Cu layer are kept fixed at their optimized bulk positions. The bulk lattice parameter used was 3.61 Å.33,35 We use a large (24 ÷ 30 Å) length of the supercell normal to the surface to decouple the two faces of the slab. Smaller (larger) lengths are applied for smaller (larger) mechanical extensions in pulling simulations, and similarly we increase cell size for higher temperatures in the AIMD simulations. (b) A thiolated step on a copper surface (molecule-metal junction slab model) was modeled using the Cu(221) vicinal surface which can be thought of as Cu(111) surface with a periodically repeated monatomic step on it. The same model was used earlier to study a thiolated stepped gold surface.7 We used a supercell consisting of 59 Cu atoms, the bottom subset of atoms was again fixed, and a single ethylthiolate molecule was chemisorbed at the step; see center panel of Figure 1.

Figure 1. The upper three panels depict models of the studied systems: an ethylthiolated Cu9 cluster, a single thiolate at a (stepped) Cu(221) surface, and a full SAM on the Cu(111) surface from left to right. Note that these systems feature different coordination numbers nS-Cu of sulfur by copper: nS-Cu ) 2 for the thiolated cluster and the stepped surface whereas nS-Cu ) 3 for the SAM on Cu(111) surface. A simplified sketch of a mechanochemistry experiment is shown in the lower half. The pulling force applied to the aliphatic chain, emulated in simulations by constraining and pulling the terminal C-atom of CH3CH2S, can be due to an AFM or STM tip using “alligator clips” or it may be exerted by moving apart the two leads of an MCBJ device. Atomic structures on this and other figures have been visualized using VMD.43,44

(c) Thiolated copper clusters (molecule-metal junction cluster model)8,33 were considered by studying the CH3CH2S-Cun molecule-metal adducts with n ) 1,3,5,7, and 9 (see left panel of Figure 1 for the n ) 9 case); n was chosen so as to form closed-shell systems. The structures were optimized but may not necessarily correspond to global minima of the adducts, in particular when larger clusters are used to chemisorb the ethylthiolate. However, the adduct structures have been optimized to local minima based on representative cluster structures.33 While these setups are standard models to study thermochemistry they clearly introduce a simplification of any real AFM/STM/MCBJ pulling process; see lower panel of Figure 1. In particular, one tip or counterelectrode is emulated implicitly by applying axial strain in terms of a holonomic distance constraint acting on the C atom of the terminal methyl group whereas the other tip is represented by an explicit metal surface or cluster, parts of which are fixed in space. Our previous work has shown that this setup indeed leads to useful predictions of mechanochemical manipulations of molecule-metal junctions and interfaces.7,8,35 In particular, such a model allows one to focus on mechanical effects of the tip depending only on the most important characteristics, which is the extension of the junction from equilibrium and the corresponding exerted force. The mechanical pulling is either (quasi)static in terms of constrained structure relaxation at T ) 0 K or dynamical via constrained AIMD at T ) 300 K (see below); note that in both cases the extension of the junction is imposed. In the static surface calculations the effect of uniaxial pulling force perpendicular to the surface is modeled by moving the C atom of the methyl group in small steps of 0.2 ÷ 0.8 Å perpendicularly away from the surface with the lowest-layer copper atoms kept fixed at their optimized bulk positions. Similarly, in static cluster calculations only one “bottom” copper atom in the cluster is fixed and the pulling steps are fixed to 0.2 Å in this case, with few steps for the CH3CH2S-Cu7 system made larger because the specific geometry of this system allows for this; see below.


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However, as the molecule-cluster junctions are expected to be more flexible compared to surfaces, the C atom of the methyl group is allowed to move in a plane perpendicular to the pulling direction during the pulling process as introduced in ref 8. In the pulling simulations the extension D is defined as the vertical distance of the C atom from its equilibrium position, i.e., the relaxed position without any pulling force applied. At each extension all allowed degrees of freedom are optimized until the maximum force on any nonconstrained atom drops to ≈10-4 au (corresponding to ≈0.008 nN). For the sake of analyses, the following quantities, in addition to various structural parameters, are recorded during the simulations. In the mechanochemical simulations the pulling force and the total energy variation are monitored as a function of D. The S-Cu bond in both mechanical and thermal decomposition simulations is characterized in addition to its length by the sulfur-to-copper coordination number, nS-Cu, defined as the number of S/Cu contacts that are within a sphere of radius 2.75 Å around the sulfur atom. The so-called “vertical frag is defined for a given configuration fragmentation energy”EC-S A-B that connects two fragments A and B via a chemical interaction as frag EA-B ) E(A) + E(B) - E(A-B)

without allowing any structural relaxation of the A and B fragments, which are simply frozen according to an instantaneous configuration (as generated by static optimization or as sampled from an AIMD simulation at finite temperature). Insights into chemical bonding were obtained with the aid of local density of states (LDOS) calculated using the Kohn-Sham orbitals {φi} and energies {εi} as usual, which have been subsequently integrated over properly chosen regions of space,


r 2δ(E - εi) ∫region d 3r∑ |φi(b)| i

where the spatial region is defined here specifically as a sphere centered at the midpoint of thiolate C-S bond and with a diameter equal to the C-S bond length dC-S. Note that the C-S bond length does change throughout the mechanochemical and thermochemical activation scenarios and so does also the spherical integration region applied. 3. Results 3.1. Thermochemical Decomposition. To set the stage, we start by discussing the thermochemical decomposition of the thiolate-copper systems. In particular, the SAM/Cu(111) and the cluster system are used here to analyze the mechanism of the thermal decomposition. Thermal decomposition of SAMs of thiolates on copper show experimentally a rich desorption behavior depending on the applied temperature, hydrocarbon chain lengths, and to a lesser extent on the surface plane.27–32 However, one universal feature can be identified, namely that at sufficiently elevated temperatures starting already below room temperatures the C-S bond undergoes thermal cleavage leaving sulfur behind on the surface.27 At temperatures 400 ÷ 500 K the process ultimately forms sulfur monolayers on copper with all hydrocarbons desorbed.31,32 Thermal decomposition of these systems was studied by AIMD simulations35 starting from a fully relaxed SAM of CH3CH2S on the Cu(111) surface. However, the experimental processes of thermal decomposition occur at time scales of the order of seconds or minutes which are not accessible to the AIMD simulations. Therefore, in order to increase the thermal reaction rates, we first thermalized the fully

Figure 2. Interatomic distances from AIMD simulation of thermal decomposition of a thiolate interface and junction via cleavage of the C-S bond. Results for the ethylthiolate SAM on the Cu(111) surface and a single ethylthiolate molecule anchored on a Cu9 cluster are shown in the upper and lower panels, respectively. The distance djS-Cu represents the time evolution of the average of the five (for the surface) or three (for the cluster) shortest S-Cu distances. The regions I, II, and III marked by the shaded areas correspond to the three essential stages of the C-S bond cleavage process by thermal decomposition; see text.

relaxed SAM/Cu(111) at 500 K before gradually increasing the temperature typically in steps of 100 K of duration ≈ 1 ps from 500 K until the first bond scission was observed. At T ≈ 1800 K, i.e., after about 8 ps of AIMD simulation, we observed the first bond breakage event. The relatively high temperature simulations, although not allowing for quantitatively precise reproduction of the ≈500 K desorption dynamics, allow us to identify interactions and processes leading to it. Let us now analyze only the last picosecond, just before the thermal decomposition takes place, i.e., before C-S bond scission is observed. The results in the upper panel of Figure 2 show that heating up the system leads to thermally induced cleavage of one of the four covalent C-S bonds in the c(4 × 4) superstructure. This result reproduces qualitatively the experimental findings29,32 of sulfur layer formation upon thermal degradation of such SAMs. Detailed analysis shows that thermal decomposition is a complex, multistep process where several subprocesses have to happen simultaneously. Three key stages, as indicated in Figure 2, can be identified. In stage I, the sulfur coordination increases because of thermal fluctuations from the equilibrium value of nS-Cu ) 3 to 5. The root-mean-square fluctuations obtained from the C-S bond-length dynamics roughly correspond to Lindemann’s criterion for melting.45 This, though, is not sufficient, as similar coordination fluctuations occurred several times during the simulation without breaking

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TABLE 1: Vertical Fragmentation Energies (see text) for Breaking a C-S Bond in the SAM/Cu(111) Interface and in the Molecule/Cu9 Junctiona SAM/Cu(111) t/ps nS-Cu dC-S/Å frag EC-S /eV

6.82 1 2.31 1.12 (1.18)

7.45 5 2.31 0.25 (0.79)

molecule/Cu9 7.51 2 1.60 0.12 (0.88)

9.54 1 2.18 1.33 (2.01)

9.67 3 2.18 0.40 (N/A)

a In both cases results are shown first for two configurations sampled from the AIMD runs with identical C-S bond lengths of dC-S ) 2.31 and 2.18 Å, respectively, but differing in the sulfur-to-copper coordination number nS-Cu; for completeness the particular C-S distances and S-Cu coordination numbers are also included. Corresponding fragmentation energies after eliminating the hydrogen/sulfur repulsive interactions by constrained structural relaxation (see text) are reported in parentheses. The third column of SAM block lists results for another configuration which is specifically strongly affected by sulfur/hydrogen repulsion (see text); again data in parentheses report the results after relaxing the hydrogens. The indicated times t correspond to the simulation times when the configurations were sampled from the respective trajectories according to Figure 2.

the C-S bond; see Figure 2. Only the combination of such overcoordination periods with energy transfer of strongly repulsive hydrogen vibrations from the methylene CH2 group leads to C-S bond cleavage as observed in stage III (Figure 2). In simple terms, in stage II one of the hydrogens gets too close and thus incurs repulsive contact with sulfur (cf. dS-H ≈ 2 Å), which is already overcoordinated, and delivers the energy that can finally break the C-S bond. To put the arguments on a more quantitative basis, we characterize the C-S bond strength by the vertical fragmentation energies Efrag C-S as defined in section 2. We recall the major factors frag responsible for particular values of EC-S . Although the length of the C-S bond has some influence, the most interesting impact frag from a chemical point of view is related to the S-Cu on EC-S coordination number nS-Cu. The bond integrity is also affected by the sulfur-hydrogen fluctuations and by possible interactions of the methylene group with copper surface atoms. In order to quantify the effects of coordination and hydrogen fluctuations frag and to disentangle them from the obvious effect of the on EC-S C-S bond length, we analyze several representative configurations that were generated in the course of the AIMD simulation. frag changes due to S-Cu First, to make an estimate of EC-S overcoordination, we compare two configurations, one with nS-Cu ) 5 (sampled at t ≈ 7.45 ps) and another one with nS-Cu ) 1 (at t ≈ 6.82 ps) (see upper panel of Figure 2), which both have the same bond length dC-S ) 2.31 Å. Since these two configurations may still differ in the effect of sulfur-hydrogen repulsion, we relax the two hydrogens of the CH2 group to their equilibrium positions (keeping all other atoms fixed). The frag calculated EC-S are shown in Table 1 both for the case of the hydrogens in their original positions and for the relaxed hydrogens (numbers in parentheses). One can quantify the effect of S-Cu coordination by calculating the energy difference frag frag (nS-Cu ) 1) - EC-S (nS-Cu ) 5) considering the energies EC-S of configurations with relaxed hydrogens; see numbers in parentheses in Table 1. This yields about 0.4 eV as a drop of the fragmentation energy upon increasing the coordination number from one to five. The effect of repulsive hydrogen-sulfur interactions is even stronger and accounts for another 0.79 0.25 ≈ 0.5 eV destabilization in addition. This latter effect, if it occurs concurrently with S-Cu overcoordination (as observed in stage II), has the potential to reduce the fragmentation barrier

to a value comparable to thermal energies (kBT ≈ 0.15 eV at 1800 K). Another snapshot from stage II (at t ≈ 7.51 ps), representing a configuration with one hydrogen very close (1.94 Å) to the sulfur atom, is considered as well and shows even larger impact of the S-H repulsive interaction; see the difference 0.88 - 0.12 ) 0.76 eV in Table 1. In summary, while the increased (over)coordination of the sulfur atom helps to reduce the fragmentation barrier, energy transfer due to hydrogen vibration provides the kinetic energy required to push the system over the reaction barrier. Thermal decomposition of thiolated Cu clusters was simulated in addition to the surface scenario by considering an ethylthiolatecopper adduct, CH3CH2S-Cu9. The system was gradually heated to 1800 K as well, when the first bond cleavage was observed; see lower panel of Figure 2. However, in contrast to the SAM/surface case we observed not only cleavage of the C-S bond but also fragmentation of the Cu9 cluster at very similar temperatures in different AIMD runs. Analysis of the thermal C-S bond scission reveals otherwise qualitatively the same multistep process with the key steps being identical to those found also in the case of the SAM/surface system. On the level of quantitative analyses there are two differences due to the different geometry: (a) the maximum sulfur coordination is nS-Cu ) 3 instead of 5, and (b) because of the more flexible structure of the molecule/Cu9 adduct there is now the entire CH2 methylene group close to the cluster itself, thus occasionally interacting with it which can additionally lead to a less stable C-S bond; see Figure 2. A quantitative measure of the effect of the different steps of the process may again be obtained from the calculated vertical frag for two configurations differing in fragmentation energies EC-S nS-Cu but having identical dC-S now found as 2.181 Å as sampled from AIMD shown in Table 1. The fragmentation energy difference between the two differently coordinated structures is now 0.93 eV, similar to that for the surface case. However, it is now more difficult to disentangle the contributions frag from the different bonds/contacts because of multiple to EC-S interactions of the methylene group with the cluster. Hence, frag was calculated by rotating the molecule so as to break EC-S only the C-S bond while leaving the other contact(s) with the metal cluster intact. In this situation we did not attempt to determine the effect of the other interactions on the fragmentation energies, such as those formed by interaction of the methylene group with the copper cluster, but one expects such effects to further reduce the barriers. We will complete the treatment of the C-S bond thermal activation by analysis of its electronic structure in terms of LDOS as defined in section 2. This will be conveniently done in section 3.3 together with similar exploration of structures occurring in the mechanochemistry simulations. 3.2. Mechanochemical Fragmentation. From the analysis of the thermochemical decompositions of both surface and cluster systems it should by now be clear that C-S bond scission is triggered by concurrent effects of S-Cu overcoordination and H-S repulsion, all due to random thermal fluctuations. Molecule-metal coordination can experimentally be controlled also mechanically by either pulling a thiolate molecule out of the SAM or vice versa by pushing it onto the surface. In either case, the mechanical activation will also limit thermal fluctuations, or at least constrain them anisotropically, in addition to stretching bonds. The former process as a means for modification of the sulfur coordination nS-Cu is intuitively expected to provide more control over the sulfur chemistry than the reverse compressive process.


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Figure 3. Mechanochemical decomposition (see text) of the SAM/ Cu(111) interface and of the molecule-metal junction at the Cu(221) surface where one ethylthiolate is anchored close to the step. Shown are total energy variations (red lines), C-S fragmentation energies (black lines with circles), and pulling forces (black lines without circles). The insets show representative configurations at extensions D[Cu(111)] ∈ {1.6,4.6,5.8} Å and D[Cu(221)] ∈ {0.0,2.6,5.4} Å in the upper and lower panel, respectively. Important atoms and bonds are highlighted using thicker balls and sticks. The varying sulfur-to-copper coordination number nS-Cu, reported inside the circles, are highlighted also by differently shaded areas.

Thiolated flat and stepped surfaces, Cu(111) and Cu(221), have been statically pulled in the spirit of the sketch provided in Figure 1; see Figure 3. At variance with the thermochemical decomposition, the universal result of these purely mechanical pulling simulations is fragmentation of the system such that the sulfur coordination number nS-Cu is reduced and a single Cu atom is finally pulled out of the surface. During the fragmentation process, the surface is observed to undergo a series of stressreleasing elastic and plastic deformations. In both cases the C-S bond stabilizes during the pulling process with dC-S varying in a narrow interval of only 1.85 ÷ 1.95 Å. This interesting effect can be appreciated from the calculated vertical fragmentation frag , see Figure 3, which quantify the bond stability. energies EC-S frag The bond strengthening, as measured by EC-S , is truly significant: 2 eV [1.5 eV] for the Cu(111) [Cu(221)] surface! The vertical fragmentation energies are clearly correlated with the sulfur coordination both in terms of the initial coordination as well as with the transient changes in nS-Cu; see Figure 3. Thus, the observed mechanochemical fragmentation pattern including both reaction pathways and products is completely different from both our theoretical and the experimental27–29,31,32 results obtained for thermochemical decomposition of alike systems. From the argument above, one has to expect the compressive strain to have a destabilizing effect on the C-S bond. It must be kept in mind that experimental application of compressive strain to molecular junctions will be more difficult than application of dilating strain. Nevertheless, in order to check the consistency of our arguments and to demonstrate the effect explicitly, we have performed calculations of fragmentation frag , under compressive strain by energies of the C-S bond, EC-S moving rigidly one of the thiolate molecules from its equilibrium position toward the Cu(111) surface atoms, which have been fixed for the purpose of this exercise. In detail, displacing the molecule by amounts {0.0, - 0.2, - 0.4} Å results in frag-

Figure 4. Mechanochemical decomposition of the CH3CH2S-Cun adducts for n ) 1, 3, 5, 7, and 9; for labeling and legend, see Figure 3. The insets show representative configurations at extensions D[Cu1] ∈ {0.0, 1.2, 3.0} Å, D[Cu3] ∈ {0.0, 1.6, 3.8, 6.0} Å, D[Cu5] ∈ {0.0, 2.7, 3.1, 4.7, 7.1} Å, D[Cu7] ∈ {0.0, 3.0, 6.2, 7.2, 9.2} Å, and D[Cu9] ∈ {0.0, 2.0, 4.0, 5.0, 7.0} Å. frag of {1.17, 1.03, 0.97} eV, respectively. mentation energies EC-S The calculated fragmentation energies show most clearly, as anticipated, the effect of C-S bond weakening upon compressiVe strain to be indeed operational. Mechanical responses of the CH3CH2S-Cun adducts were studied using various cluster sizes, n ) 1, 3, 5, 7, 9, similar to what was done for the two thiolate-surface systems as depicted in Figure 4. As on the surfaces, the final result of the mechanical activation is breaking a copper-copper bond and not the S-Cu bond, except of course for the limiting case n ) 1. Still, there is an important difference in the structure of the S-Cu junctions. In the case of n > 1 clusters, the initial coordination number is nS-Cu ) 2, and for sizes n g 5, this coordination is conserved

Molecular Mechanochemistry during the pulling process. Similarly as for the surfaces, the C-S bond length is almost constant along the pulling trajectory as observed earlier using the surface setups. Because of the frag to be conserved S-Cu coordination one can expect the EC-S approximately constant as well, which is confirmed by calculations compiled in Figure 4. The copper part of the adducts again undergoes a series of elastic/plastic deformations upon pulling the system apart, and the respective isomerization processes are clearly detectable from the corresponding force-distance curves. The maxima represent the highest sustainable force in which the given shape of the Cun cluster is still stable, just before relaxing into another isomeric structure upon further strain. These processes eventually transform the compact Cun clusters into high-energy structures. It is noted in passing that the required “isomerization energies” are provided by the mechanical work done on the adduct as a result of the mechanical stretching, and as such it is “stored” as “chemical energy”,8 apart from the kinetic energy that would be released in bond breakage events. The jumps in the force-distance curves after the maxima represent structural rearrangements within the Cun clusters leading to formation of energetically more favorable structures. The unique result in all cases, except obviously for n ) 1, is the creation of a Cu2 dimer and a CH3CH2S-Cun-2 adduct after stretching CH3CH2S-Cun adducts until fragmentation. An interesting observation is that the larger clusters reduce their dimensionality before fragmentation from three-dimensional to planar for n ) 9 and 7, or from planar to quasi-one-dimensional for n ) 5 and 3. The thiolate-Cu7 adduct represents a particularly interesting exception in the series in that its equilibrium structure hosts the methyl group relatively close to the copper atoms. This frag (D ) 0) and that pulling feature causes a lower value of EC-S can be extended up to about D ≈ 9 Å, which is approximately 2 Å longer than that found for the analogous n ) 9 adduct. There is also a 3d f 2d transition occurring at about D ) 4 ÷ frag . Lowering 5 Å accompanied by a noticeable increase in EC-S the dimensionality of the cluster partially decreases coupling of the thiolate to the cluster in the sense that there are less Cu atoms that can closely interact with sulfur. For this reason reducing the dimensionality of the copper subsystem is seen to have a qualitatively similar although not so strong impact on C-S bond stabilities as lowering the coordination number nS-Cu. Finally, quite differently from the surface systems, the larger clusters (n ) 5, 7, 9) do not change their sulfur-to-copper coordination number during the pulling process keeping this quantity constantly at nS-Cu ) 2. It can then readily be understood that the value of Efrag C-S for these cluster systems varies only weakly. The observed variations can be understood as consequences of dimensionality changes of particular clusters, apart from the obvious effect of the slightly varying C-S bond length occurring in the course of the mechanical pulling processes; see Figure 4 for details. 3.3. Electronic Structure and C-S Bond Strength. The striking impact of sulfur-to-copper coordination on the stability of the thiolate C-S bond is a true chemical effect and is expected to be reflected in the electronic structure of the bond. It has been shown that bonding of thiolates to copper causes charge transfer from the metal to the molecule.33 Because of coupling to copper there is another charge redistribution causing drainage of charge from the C-S bond. Detailed inspection shows, however, that the total electronic density in the C-S bond region varies only weakly because of changes of the S-Cu coordination. The electronic structure processes responsible for the C-S bond strength can, however, be inspected and

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Figure 5. LDOS in the C-S bond region for the thiolated stepped Cu(221) surface at different extensions D of the junction as indicated. The position of the most important σss and σpp MOs of the C-S bond are highlighted by gray shadings. The horizontal gray areas at the bottom mark the ranges of Cu(4s) (discrete) and Cu(3d) (quasicontinuum) states exhibiting significant LDOS around the copper atoms directly in contact to sulfur in the fully relaxed ethylthiolate/Cu(221) equilibrium structure. All chemical potentials have been aligned to E ) 0.

understood in terms of the local density of states (LDOS) and molecular orbitals (MOs). LDOS (see section 2) is a tool that allows one to observe how changes in any close or remote part of the system are reflected, if at all, in the electronic structure at a chosen point or region of space. In the present context we will focus this type of analysis onto the C-S bond region. Let us discuss first this topic for the case of mechanical pulling of ethylthiolate from one of the copper surfaces, specifically from the stepped surface, see sections 2 and 3.2. The LDOS integrated over the C-S bond spherical regions were calculated for many extensions, but only a representative subset of them is presented in Figure 5. We can clearly see that for the largest extension D, which is characterized by an essentially isolated CH3CH2S-Cu1 adduct above the Cu surface (see lower panel of Figure 3), the peaks of the LDOS are very sharp as they should be for any small isolated molecule. Indeed, comparison of the D ) 5.4 Å plot of Figure 5 with the LDOS calculated for truly a isolated CH3CH2S-Cu1 molecule with the same structure clearly shows that the two LDOSs are quantitatively almost identical (data not shown). In stark contrast to this scenario found at significant stretching, the system at equilibrium (i.e., at extension D ) 0) features substantially split and broadened states due to the interaction with the copper surface. The most striking feature is the complete disappearance of the peak at E ≈ -3.78 eV for the molecule in full interaction with the surface. More detailed analyses of LDOS calculated for other regions (data not shown) indicate that the -3.78 eV peak for D ) 5.4 Å represents a MO which displays σpp properties on the C-S bond and extends also over part of the copper cluster, in particular over the Cu atom which is nearest to sulfur. The complete “dissolving” of the σpp orbital, responsible for a significant part of the C-S bond stability, due to interaction with the copper surface in the molecule-surface system at small D’s is consistent with the significant weakening frag . of the C-S bond as quantified earlier in terms of EC-S In addition to investigating the surface, we have performed an analogous LDOS exploration also for the T ) 0 pulling simulation of the ethylthiolate-Cu9 adduct; see Figure 4 for


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Figure 6. LDOS at the C-S bond region for the CH3CH2S-Cu9 adduct at extensions D of the system as indicated. For labeling and legend, see Figure 5.

the basic characteristics of this process. The respective LDOSs in the C-S bond region are plotted in Figure 6 again for several system extensions D. Compared to the surface case, cf. Figure 5, the peaks are now much sharper as expected for such a relatively small isolated adduct. What is most important is that the LDOS pattern does not change much upon increasing the extension. This behavior is consistent with the conserved 2-fold S-Cu coordination staying constant during the entire pulling process and consequently with more or less invariant C-S bond fragmentation energies as a function of D. Finally we focus on the impact of thermal fluctuations on S-Cu coordination and on their effect on electronic properties of the C-S bond. For this purpose we take the two CH3CH2S-Cu9 configurations from the thermochemical AIMD bond cleavage simulations which exhibit low (nC-S ) 1) and high (nC-S ) 3) S-Cu coordinations, namely the structures described in Table 1 occurring at times 9.54 and 9.67 ps in the simulation; see also lower panel of Figure 2. The corresponding LDOS for these configurations, calculated again around their C-S bonds, are plotted in Figure 7. Differences between the two spectra are significant. Their interpretation is less obvious since the configurations are affected by the random thermal fluctuations. Detailed inspection of the peaks and spatial profiles of the corresponding MOs unveils which MOs, apart from the core-electron ones, have significant bonding character around the C-S interconnection. They are all highlighted by the vertical shadings in Figure 7. For the singly coordinated configuration (black line), we can observe the strong σss-like MO and two MOs reminiscent of the σpp bond. The 3-fold coordinated configuration (red line) shows that the other σss-like MO contributes more to C-S, and there is only one significant σpplike MO present in this case. Considering the C-S bond stability in terms of its electronic structure for the two configurations, it thus turns out that the higher number of MOs with significant bonding character on the C-S bond determines the strength of that bond. 3.4. Combining Mechanical Fragmentation with Thermal Decomposition. In the previous section we have studied mechanoactivation of chemical bonds by constrained structure optimization methods in the absence of any thermal fluctuation effects, i.e., at T ) 0 K. A more realistic experimental situation corresponds to a setup where an AFM tip is used to activate the system at a finite temperature, whereby the system is

Konoˆpka et al.

Figure 7. LDOS in the C-S bond region for the two specific CH3CH2S-Cu9 configurations occurring in the AIMD simulation and strongly differing in their S-Cu coordinations. The key peaks which correspond to molecular orbitals with significant bonding character on the C-S interconnection are highlighted. The gray shaded boxes at the bottom indicate the ranges with significant LDOS on those Cu atoms which form contacts to sulfur. The undercoordinated (nS-Cu ) 1, black line) and overcoordinated (nS-Cu ) 3, red line) structures have been introduced in section 3.1 and are included in Table 1 at times t ) 9.54 and 9.67 ps, respectively, and analyzed also in the lower panel of Figure 2. See also Figure 6, lowest (D ) 0) plot, where the LDOS for the same system but in its optimized geometry is shown.

simultaneously affected by two concurrent effects: the thermal fluctuations can cause a transient sulfur overcoordination and thus weaken the C-S bond, while the applied pulling force will simultaneously counteract by tending to reduce the S-Cu coordination and consequently by strengthening the very same C-S bond. What would be the net effect on fragmentation/ decomposition? Before addressing this question in more detail, an important practical issue is the maximum simulation time accessible by MD in general and by AIMD in particular. For sufficiently long observation times we expect either scenario to occur, depending on the magnitude of the applied pulling force versus temperature; note that even in the absence of pulling there is a certain (but vanishingly small) Boltzmann probability for spontaneous decomposition even at very low temperatures. Time scales accessible by both MD and AIMD simulation are many orders of magnitude shorter than the typical experimental time scales; hence, the rare event overcoordination processes are unlikely to be observed in the simulations at least at low temperatures. However, what our study can tell us is how the pulling process is affected by entropy changes, which will shed light onto the qualitative impact of thermal fluctuations in the presence of mechanical strain. In order to provide a broad but affordable database for such analysis we have studied the CH3CH2S-Cun adducts for n ) 5, 7, and 9 at T ) 300 K in the presence of an externally applied mechanical pulling force. The simulations started from the respective lowest-energy isomers, see Figure 4, and the finite temperature T ) 300 K pulling simulations were mimicked by a stepwise stretching using ≈3 ps of Nose´-Hoover-chain thermostatted Car-Parrinello AIMD simulation37–39 for each pulling increment.7 The average extension forces exerted on the fixed Cu atom, i.e., the constraint force, were used for thermodynamic integration from which the Helmholtz free energy profiles relative to the reactant well were calculated along the reaction coordinate z from

Molecular Mechanochemistry

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Figure 8. Mechanochemical decomposition of the CH3CH2S-Cun adducts for n ) 5, 7, and 9 at finite temperature T ) 300 K; see Figure 4 for results at T ) 0 K. Shown are time-averaged pulling forces (black lines) and the entropy contributions T∆S (green lines) as a function of extension D of the junctions; for other labeling and the legend, see Figure 3. The insets show representative configurations at extensions D[Cu5] ∈ {4.4, 7.7, 8.3} Å, D[Cu7] ∈ {2.9, 5.7, 8.3} Å, and D[Cu9] ∈ {3.2, 4.4, 6.8} Å.

A(zi) - A(z0) ) -

∫zz dz〈F(z)〉, i


where 〈F(z)〉 is the mean extension force (obtained by averaging the Lagrange parameter due to the constraint for each canonical AIMD simulation increment) as a function of the reaction coordinate and A(z) is the relative free energy, i.e., the free energy profile as a function of the reaction coordinate. The entropy contribution ∆S along z at fixed temperature T was calculated from T∆S ) ∆E - ∆A, with E being the mean total energy (averaged for each canonical AIMD simulation increment at temperature T ) 300 K). As strain reduces the configurational freedom, we can a priori expect the entropic contribution to be a decreasing function of the applied strain, except when the rigidity of the system is changed because of the applied strain, e.g., in the sense of the aforementioned plastic/elastic transformations. First of all, even at T ) 300 K we generally see a fragmentation behavior very similar to that observed earlier at T ) 0 K including identical reaction products and similar fragmentation pathways, except for the n ) 5 case; see Figure 8. For this cluster size, the fragmentation behavior of that system at finite temperature is qualitatively different in that, unlike at T ) 0 K, the sulfur coordination number reduces from nS-Cu ) 2 to 1. This change of nS-Cu seems to be a specific feature of the n ) 5 system since we have not found it for both n ) 7 and 9. Hence, for n ) 5 there is a d ) 2 f d ) 1 transformation thus reducing the dimensionality, whereby a compact Cu5 cluster is transformed to a monatomic wire before finally a Cu2 dimer is detached from the Cu5 cluster. Thus, despite the slightly different pathway, the final reaction product at 300 K is the same as that found in

the purely mechanical limit at T ) 0. Although the entropy fluctuations are substantially smaller compared to free energy variations (≈5 times, data not shown), significant structural modifications such as reduction of sulfur coordination by copper or cluster dimensionality share clear entropic fingerprints according to Figure 8. 3.5. Insights: Constraining Coordination. From the various analyses of the decomposition processes it is the sulfur coordination by copper, nS-Cu, that emerged to be the key chemical factor affecting the fragmentation scenario. Here we directly test that hypothesis by performing simulations with artificially enforced coordinations as imposed by appropriate constraints. The idea is to change or to restrict the preferred course of fragmentation by enforced under/overcoordination. This amounts to examining whether the enforced low coordination helps to prevent the thermochemical C-S bond breaking and whether enforced higher coordinations promote its cleavage in mechanochemistry setups. In the first set of these simulations we consider thermal activation with enforced single S-Cu coordination, i.e., nS-Cu ) 1, using the CH3CH2S-Cu9 system. The concept of coordination constraints has already been used in the past.46 However, the definition of the coordination number introduced in ref 46 is not appropriate for our purposes, as this implementation does not increase the coordination but rather shortens the existing bond lengths. In order to keep the coordination fixed at the required value of nS-Cu ) 1 we instead use an additional restraining potential from which we calculate the restraining forces which we add to the usual forces from DFT. The additional potential has both repulsive and attractive parts in order to keep the selected Cu atom close to S and to repel the other Cu atoms at the same time. The details of this approach are presented in the Supporting Information. The restraints were applied to the otherwise unconstrained ethylthiolate-Cu9 system, and its temperature has been gradually increased up to 1800 ÷ 2000 K, i.e., a regime in which we normally have observed thermal C-S cleavage. As expected, under the enforced low S-Cu coordination nS-Cu ) 1 we found no evidence for C-S bond breaking, whereas unconstrained thermochemical activation led to bond scission on the same picosecond time scale at 1800 K. Clearly, this lends strong support to the picture that increasing the sulfur-to-copper coordination number is a prerequisite for C-S bond cleavage and thus to thermal decomposition of thiolate/copper interfaces and junctions. Next, the reverse choice is now realized within the mechanochemical scenario by simulations that enforce 3-fold S-Cu coordination, i.e., nS-Cu ) 3, using the very same ethylthiolate-Cu9 adduct but subject to an external pulling force. This adduct normally prefers to keep 2-fold S-Cu coordination during stretching, and only the dimensionality of the Cu cluster is reduced from three-dimensional to planar, both for static and room temperature pulling processes; see Figures 4 and 8. Hence, the initial thiolate-cluster system must be properly prepared in the case of the enforced nS-Cu ) 3 coordination, i.e., we determined an isomer with such a coordination and initiated the pulling process from it. The constant 3-fold coordination in this constrained pulling setup is maintained using hard constraints on the S-Cu3 subsystem. In one such case we perform quasistatic, i.e., essentially zero temperature, AIMD pulling simulations.47 In addition we also consider a dynamical setup at finite temperature, again at T ) 300 K. The results of the quasistatic pulling simulations with the enforced 3-fold coordination are shown in the lower panel of Figure 9 (red line with circles) and compared to the case of unconstrained coordination


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Figure 9. Evolution of C-S distances as a function of the system extension D for pulling simulations of the CH3CH2S-Cu9 adduct under two different S-Cu coordination regimes and for both (quasi)static47 pulling (lower panel) and the analogous situation at T ) 300 K (upper panel). The black curves show the results of pulling without applying any constraints on nS-Cu whereas the red curves show the results of pulling with the artificially constrained coordination number, nS-Cu ) 3. The insets show the starting and final structures (D ) 0.0 and 7.8 Å) for the nS-Cu ) 3 constrained quasistatic pulling.

(black line with squares). The softening of the C-S bond due to the overcoordination is evident. Despite this observation, however, increasing the sulfur-to-copper coordination from two to nS-Cu ) 3 was not sufficient to modify the reaction pathway and to affect the products. Can thermal fluctuations at 300 K, and thus additional activation, change the outcome? The answer is provided in the upper panel of Figure 9 where the timeaverage of dC-S and its rms fluctuations are shown for both nS-Cu ) 3 (red, upper curve) and the unconstrained case of section 3.4 (black, lower curve) as a function of the extension. All statistical averages have been carried out using 1.5 ps sampling intervals, omitting the first 0.5 ps of each trajectory to allow for equilibration. The first observation is that djS-C(t) for the artificially overcoordinated sulfur is larger than in the case of the unconstrained pulling. Both djC-S of the nS-Cu ) 3 plot and its fluctuations indeed increase for mild extensions, D ≈ 1.25 ÷ 2.25 Å, to values comparable to the Lindemann’s criterion.45 Still, cleavage of the C-S bond is not observed on the AIMD time scale. However, in line with our findings on thermal activation, it is likely that breaking of the clearly weakened C-S bond could be observed on experimental time scales even for quite small extensions of the junction. 4. Conclusions and Outlook We have presented an extensive computational study of mechanical and thermal activation of thiolates chemisorbed on copper surfaces and clusters. Two completely different reaction pathways and product classes were observed for the two types of chemistries. In thermal activation cleavage of the covalent

Konoˆpka et al. C-S bond in the thiolate molecule and desorption of hydrocarbons is observed in agreement with thermal desorption experiments,27–29,31,32 while mechanical “desorption” stabilizes selectively and significantly the very same bond. These differences mainly stem from totally opposite effects of thermal fluctuations and mechanical uniaxial stress on sulfur-to-copper coordination. While the fluctuations can transiently overcoordinate the sulfur atom, the pulling force tends to reduce the very same coordination number systematically. Different sulfurto-copper coordination patterns, however, are reflected in differences of the local electronic structure that governs the C-S bond such that higher coordination leads to less stable C-S bonds and vice versa. By a selective use of the two activation scenarios it is possible to manipulate the vertical fragmentation energy of the C-S bond on a scale of ≈3 eV! Combining the two types chemistries at ambient temperature does not change our findings qualitatively in this case. Although obtained using specific model systems the uncovered conceptual differences that rule mechanochemical versus thermochemical processes are of a much more general nature. For example, the much studied archetypal thiolate/gold system exhibits desorption of entire thiolates26 and thus breaking of S-Au bonds upon thermochemical activation. In stark contrast, the formation of monatomic gold wires and a subsequent breaking of an Au-Au bond within such a wire, while keeping the S-Au bond intact, is predicted as a result of mechanochemical activation7,8 using for instance AFM or MCBJ type setups. Here, the thermal fluctuations do not break the C-S bond, which is less weakened because of the interaction with the metal in the thiolate/gold system compared to thiolate/ copper,33 but rather cleave the weaker S-Au bond in this case. Application of mechanical energy during the pulling process reduces again the coordination number fluctuations, strengthens the S-Au bond and, hence, leads to fragmentation of one of the metal-metal bonds in the Au-wire. Finally, we note that the force-induced activation protocols studied here could be converted into a design or operation principle to strengthen or to weaken specific covalent bonds by purely mechanical means, e.g., to counteract thermal degradation or to introduce “yield points” at the molecular level, respectively. Acknowledgment. We are grateful to Harald Fuchs and Joachim Reichert for stimulating discussions. Financial support from Volkswagen-Stiftung (Stressmol), APVT (20-019202), DFG (Reinhart Koselleck Grant to D.M.), and FCI as well as computer resources from SSC Karlsruhe, [email protected] and Rechnerverbund-NRW are gratefully acknowledged. M. Dubecky´ was supported by the Konto Orange, n.f. project Sˇanca pre talenty. Supporting Information Available: The additional interatomic potential used to constrain the S-Cu coordination number in the AIMD simulations discussed in section 3.5 and the Cartesian coordinates of all structures discussed in the article. This material is available free of charge via the Internet at http:// References and Notes (1) Beyer, M. K.; Clausen-Schaumann, H. Chem. ReV. 2005, 105, 2921. (2) Carey Lea, M. Philos. Mag. 1892, 34, 46. (3) See, for instance, Fumio, S. Mater. Life 1999, 11, 152. (4) Grandbois, M.; Beyer, M.; Rief, M.; Clausen-Schaumann, H.; Gaub, H. E. Science 1999, 283, 1727. (5) Marco Saitta, A.; Soper, P. D.; Wasserman, E.; Klein, M. L. Nature (London) 1999, 399, 46.

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