Molecular Dynamics Simulations of the Self-Assembly of

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Molecular Dynamics Simulations of the Self-Assembly of Tetraphenylporphyrin-Based Monolayers and Bilayers at a Silver Interface Vincenzo Barone,† Maurizio Casarin,‡ Daniel Forrer,‡ Susanna Monti,*,§ and Giacomo Prampolini† †

Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy Dipartimento di Scienze Chimiche, Univerisit
a di Padova, via Marzolo 1, I-35131 Padova, Italy § CNR
Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UoS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy ‡

bS Supporting Information ABSTRACT: A theoretical study of the adsorption and dynamics of tetraphenylporphyrins on a Ag(111) substrate and the subsequent aggregation of the formed monolayers with fullerene molecules is reported. Classical molecular dynamics simulations were able to reveal the various phases of monolayer and bilayer formation and succeeded in identifying all the interactions responsible for self-assembling and surface binding. Possible supramolecular configurations extracted from the molecular dynamics trajectories were classified and characterized in detail and revealed to be in satisfactory agreement with experimental data.

’ INTRODUCTION During the past few years, the growing interest in designing artificially decorated surfaces predisposed to control specific optical and electronic responses of nanomolecular devices1
4 has led the scientific community to conduct intensive experimental and theoretical research in the field of supramolecular chemistry.5
7 Big efforts have been put into the modification of a large variety of functional organic molecules, such as DNA, polypeptides, polyphenols, porphyrins, fullerenes, and other systems in order to create multicomponent assemblies of definite size and shape (namely, spheres, toroids, helices, two-dimensional porous networks, etc.) on a surface with highly adhesive motifs and tuned properties.8
16 In many cases, the exact interfacial distribution of the molecules, the geometry of the molecular network, and the quantity of effectively interacting species have been characterized experimentally by using various techniques, which include scanning probe methods.8,17
19 When these techniques are used in combination with quantum mechanical calculations on model structures, a deeper insight into the molecular and atomic-level conformations upon binding can be obtained.18,20
24 However, due to the complexity of the systems, the majority of these quantum computational investigations have dealt with medium-sized molecular clusters and small model substrates.18,25
27 Even though the use of periodic boundary conditions has allowed theoreticians to simulate r 2011 American Chemical Society

infinite molecular networks, these systems are just dependent replicas of the chosen simulation box and, as such, represent an ordered molecular phase where the molecules perform concerted movements. There is a need to define and characterize the various stages that occur when an initially disordered molecular arrangement changes into an ordered configuration where the molecules conform to certain patterns. This is required to identify the most effective moieties and to suggest appropriate design strategies to obtain specific surface decorations. To define a disordered phase, bigger models should be created, which would imply the use of larger simulation boxes containing a sufficient number of molecular species. In light of these considerations, it is evident that quantum mechanical calculations become prohibitively expensive and practically unfeasible. One way of approaching this problem could be to define appropriate simulation strategies based on a classical or semiclassical description of the systems. These methods have been shown to be efficient and reliable techniques to study both conformation and dynamics of adsorbed multicomponents on metal/metal alloy substrates.28
30 The idea dates back to the 1980s, and a great variety of representations have been proposed to date.31
39 Recently, Received: May 17, 2011 Revised: August 11, 2011 Published: August 11, 2011 18434

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The Journal of Physical Chemistry C more sophisticated metal models have been defined and tuned to simulate the adsorption properties of small and large molecular structures, such as proteins, nucleic acids, and their complexes.23,40
46 During the implementation of more efficient computational models, a careful parametrization is mandatory in order to obtain trustworthy results. In fact, the prediction of the self-aggregation dynamics of molecular species on a supporting substrate needs a clear understanding of all intermolecular interactions that come into play. These consist essentially of the selective and directional adsorbate
adsorbate noncovalent interactions, which determine the spontaneous organization of the molecules into structurally well-defined architectures, and adsorbate
surface interactions, which control not only molecular mobility, diffusivity, and surface patterning but also the conformation adopted by the molecules upon adsorption.47 For example, in the case of porphyrins, the interaction of the molecule with the substrate could preserve the planarity of the porphyrin core but induce significant deformation of the molecular conformation and, as a consequence, affect supramolecular self-assembly.47 The present computational work has been focused on the dynamics and self-assembly characteristics of tetraphenylporphyrins (in particular, 5,10,15,20-tetraphenylporphyrin (TPP) and 5,15-bis(4-aminophenyl)-10,20-diphenylporphyrin (TPP(NH2)2)) on the Ag(111) surface and on their interactions with C60 molecules deposited on the assembled layer. TPPs and fullerenes are very interesting systems because of their tunable photophysical and electrochemical properties, which depend on the incorporated metal ions and substituent groups. Porphyrins self-assemble, adsorb on metals, and spontaneously attract C60 molecules through dispersion and donor
acceptor interactions.10,48 The formation of molecular patterns of self-assembled monolayers (SAMs) of TPPs on Ag(111), their intramolecular conformation, and supramolecular ordering have been characterized in detail from an experimental point of view in numerous studies (see, for example, refs 47 and 49 and references therein), and various mechanisms responsible for self-assembly have been explained. In a recent article by Buchner and coworkers,49 a complete description of the aggregation process and the conformational arrangement of the metalated and nonmetalated molecules on Ag(111), at room temperature, have been reported. The authors, through a systematic scanning tunneling microscopy (STM) investigation, concluded that (1) the interaction of the porphyrin core with the substrate induced specific TPP orientations epitaxially related to the surface but did not determine the supramolecular organization of the TPPs, which was instead stabilized by T-type interactions between the phenyl substituents; (2) TPPs could nucleate into chiral mirror domains that could be interlocked through zipper-like configurations of the boundary molecules; and (3) the intramolecular conformation of TPPs upon binding to the surface was bent and deviated strongly from the planar geometry when a metal ion was inserted in the porphyrin core. Another related experimental/theoretical study by Rojas and co-workers18 supports this general view and extends the examination of TPP behavior upon adsorption on metal surfaces to different substrates, namely, Cu(111) and Au(111). In this investigation, the authors found that, on Ag(111), at very low TPP coverage, the molecules were located at the substrate stepedges and, only after a total occupation of step-edges, they nucleated into clusters on terraces. Ordered bidimensional networks, consisting of tetragonal unit cells, 13.8 Å in length, with a

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phenyl CH-π spacing of about 3.9 Å, were formed, and TPPs were organized in three characteristic domains oriented according to the substrate symmetry. The characteristics of fullerene monolayers on metal surfaces have been intensively studied as well, due to the great variety of interaction between the two species that can confer specific properties to the assembled hybrid materials. STM, photoemission spectroscopy (PES), X-ray photoelectron diffraction (XPD), low-energy electron diffraction (LEED), and density functional theory calculations (DFT) have been used to investigate the surface, the electronic structure of the fullerene films, and the bonding nature of the C60/Ag(111) complexes.50
57 These studies found that twodimensional fullerene monolayers with a close-packed arrangement could form and adopt a mixture of orientations on the surface at a nearest-neighbor separation of about 10 Å. The bonding of the adsorbates at the interface was prevalently covalent, but a small ionic contribution was also observed. Apart from their ability to adsorb on different types of metal substrates and decorate them, fullerenes have also shown a tendency to interact effectively with other molecular species having a concave structure, which is complementary to their convex conformation. In this context, calixarenes,58 cyclothiophenes,59 corannulenes,60 and porphyrins61,48,62
64 are of special interest. Fullerene
porphyrin association was proposed to be ubiquitous and to occur in solution.62 Moreover, experimental and theoretical data suggested that the interactions were prevalently of π
π type and could be perturbed by weak electrostatic and charge-transfer effects.48,60 As far as the complexation of fullerenes with TPPs assembled on silver is concerned, STM investigations were able to characterize both the mobility and the adsorption behavior of C60 molecules. They revealed that the host molecules were weakly adsorbed and could form long chains, move from one site to another, and accommodate into the pores of the underlying network without disrupting its structure.61,65 From a computational point of view, as already mentioned at the beginning of the Introduction, numerous studies have dealt with the conformational flexibility of TPPs and the adsorption, organization, and self-assembly of TPPs and C60 on metal substrates. These studies have used both relatively demanding approaches, such as periodic DFT calculations, eventually corrected for dispersion contributions, and less expensive techniques, such as simulations based on preparametrized force fields. The results were promising and in line with the experimental findings. On the basis of this premise, this research has employed classical molecular dynamics simulations to investigate the structural and orientational changes of these systems at a silver interface. In agreement with the experimental observations, it has been demonstrated that the dynamic behavior of the layers is mainly associated with phenyl
surface and phenyl
phenyl interactions, whereas the orientation of the aggregates is induced by the morphology of the substrate. Various supramolecular structures at different molecular concentrations have been identified and described in detail and comparison with experimental data has been reported. Finally, the fullerene adsorption on the preformed porphyrin layers has been scrutinized. The classical MD simulations carried out in this work are essentially based on a modified version of GolP,45,46 which has been reparametrized to reproduce the adsorption energy of selected molecular fragments on the Ag(111) surface. The description of the metal has taken into account recent developments of classical parameters for face-centered cubic 18435

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The Journal of Physical Chemistry C lattices, which have employed highly tuned Lennard-Jones potentials compatible with the different widely used force fields (AMBER,66 OPLS,67 etc.) and have proven to give a sound and precise picture of the adsorption of various organic compounds.45,46,68
72 Following the procedure of Corni and co-workers,73,45 the electronic metal polarization has been reproduced classically by placing dipole vectors on the metal centers. These vectors were able to reorient themselves when interacting with an adsorbed molecule and could adopt preferential alignments energetically convenient. Such an approach has been extensively tested and turned out to be an efficient and practical methodology to describe the interaction of many classes of molecular systems with the metal surface. The introduction of Lennard-Jones (LJ) virtual sites in the hollow regions of the surface guaranteed a correct location of the adsorbed species, in agreement with the experiments.45 Indeed, as already commented by Corni and co-workers in ref 45, when only virtual sites were used, benzene adsorbed in the hollow position (preferred configuration74), whereas when LJ parameters were assigned to the real surface metal atoms, the preferred orientation was not obtained. The rationale of the method has been welldocumented;46,75,76,73 the model is fast and efficient from a computational point of view and thus appropriate for this study.

’ MOLECULAR STRUCTURES AND COMPUTATIONAL METHODOLOGY Silver Substrate. The anhydrous Ag(111) slab models used in this investigation are composed of five atomic silver layers arranged on planes parallel to the xy plane of the simulation box. A small square surface (area ≈ 400 Å2), containing 56 Ag atoms (the slab was composed of 280 Ag atoms in all), was built and employed to parametrize the interactions of various molecular building blocks, whereas a bigger supercell with a dimension of ≈60  84 Å2 (total number of Ag atoms = 3480), containing 696 silver atoms (in each layer), was constructed in order to study the dynamics of the adsorbed porphyrin monolayer as a function of surface coverage. As already mentioned in the Introduction, the calculations were based on a modified version of the GolP model.45,46 The silver atoms in the upper layer, which were replaced with dipoles (two equal and opposite charges at fixed distance), were flanked by virtual atoms with appropriate LJ parameters. These new virtual centers, located in the hollow sites, were effective in inducing the adsorbed molecule to adopt the correct binding position compatible with experimental observations. The interactions between nitrogen and silver atoms were reparametrized to reproduce chemical bonds with the substrates,18,77 and the Lennard-Jones parameters of ring carbons were refitted to simulate the interactions between the π orbitals of the molecules and the d orbitals of the metal.78 The initial values of the Lennard-Jones atom
atom pair potentials for the nonbonded interactions of the virtual sites were taken from Heinz et al.43 and readjusted to reproduce quantum mechanical calculations and experimental data when available. All the parameters were determined, through curve-fitting procedures, starting from reasonable values.41 In some cases, only minor corrections were introduced. Although polarization effects at the metal interface are important,46 very often they made a modest contribution to the total interaction energy between the molecule and the surface79
81 and thus were implicitly included in the van der

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Waals parameters assigned to the surface centers.43 However, recently, a new computational approach was developed by Heinz and co-workers82 in order to evaluate the influence that induced charges on even Au surfaces had on the interfacial structure and adsorption of water, amino acids, and peptides. Polarization was quantified, and the authors concluded that, on metal surfaces, such as Au(111), the net contribution of polarization to biomolecular adsorption was small, whereas on surfaces where the epitaxial attraction was weak and a water layer was present between the surface and the biomolecule, such as the Au(100) surface, the net contribution of induced charges to the adsorption of the molecule was significant or even dominant. Even though appropriate LJ parameters could have been sufficient to describe polarization effects in the present investigation, the polarizability of the silver surface was introduced in the simulations according to the protocol proposed in ref 73, and the surface dipole charges were balanced consequently. The positions of all the slab atoms were frozen during the whole simulation time, and thus minor or major surface deformations could not be observed.

’ AROMATIC ADSORBATES AND PORPHYRIN SIDE CHAINS: FORCE FIELD PARAMETER DERIVATION In this section, the definition of the phenyl ring parameters (i.e., benzene/aniline surface interactions and phenyl torsional profiles) will be reported in detail. As observed in other theoretical and experimental works,1,2,18,23,49 these moieties are responsible for the high mobility of the molecules at the surface, their characteristic self-assembling behavior, and their reciprocal orientation. Therefore, instead of using general descriptors, available in the literature,23 new coefficients for the cosine series expansion defining the torsional potential were carefully determined. All parameters employed in the present calculations are reported in the Supporting Information. From both an experimental and a theoretical point of view, it has been evidenced that the molecular conformation of porphyrins on Au, Ag, and Cu surfaces is quite different from the one adopted by the molecule in the bulk phase23,47,49,83,84 and the motion and adsorption characteristics of the molecules, namely, orientation, packing, and diffusion, are mainly due to the interactions of their side chains (for example, phenyl and pyridyl moieties) with the interface.2,18,47,49,61,85
87 On the contrary, the porphyrin core seems less influenced by mutual interactions of the molecules and by the presence of the metal layer. The only deformations appear to be a slight bending of this portion that, on the whole, adsorbs flat on the surface. The potential parameters describing the interaction between benzene/aniline and the Ag atoms were derived by calculating the free energy profiles of both molecules as a function of their distance to the Ag interface. As already done in previous investigations,88,89 MD simulations and the potential of mean constraint force (PMF) method were employed. To identify the optimal parameters, a trial-and-error approach was used and consisted essentially of repeating the whole PMF procedure, after readjustment of the data, until a satisfactory match with the theoretical/experimental observations was found (almost 10 times for each molecule). The vertical distance between the top plane of the silver surface and the center of the ring was chosen as the reaction coordinate (z direction). About 20 molecular dynamics simulations, where the vertical separation of the molecule was constrained to a different value in each run, 18436

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Figure 1. PMF free energy profile for the adsorption of benzene and aniline, at the anhydrous Ag(111) slab model, as a function of the distance between the adsorbate center of mass and the interface.

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were identified in line with experimental and theoretical results (Figure 1). Bond, angle, and torsion parameters of the porphyrin core were described using data in the literature,93 whereas the torsion angle defining the orientation of the phenyl ring was appropriately parametrized through density functional theory calculations, at the M062X/6-31+G(d,p) level, on a reduced model system, where all of the phenyl substituents, except one, were replaced with hydrogen atoms. The M062X functional, which belongs to the new M06 suite of functionals developed in 2006 by Truhlar and co-workers,94 was chosen because, differently from B3LYP, which is unable to accurately describe medium-range exchange correlation energies, has improved performance for main group thermochemistry, barrier heights, and noncovalent interactions. The torsion profile and the dihedral parameters can be found in the Supporting Information. As it can be observed, the preferential orientation of the phenyl group corresponds to an arrangement with a torsional angle of about 64°, which agrees very well with the value obtained by other authors.20,23,95 As far as the fullerene parametrization is concerned, in order to maintain a coherent and balanced description of the various components of the system, C60 atoms were defined as aromatic carbons and the force field parameters of the molecule were extracted from the general amber force field.96 No partial charges were assigned to the atoms of this molecule.97,98 However, studies by Fasel and co-workers60 revealed that such a representation produced C60 host
guest systems on a copper surface, in line with the experimental data. Partial charges for both of the porphyrin molecules were obtained from DFT-M062X/6-31+G(d,p) calculations and the RESP99,100 procedure. The LJ interaction parameters between different atoms were calculated by the standard Lorentz
Berthelot combination rules, and nonspecific interactions were described with the OPLS-AA force field.67

were performed in each case. After the initial equilibration phase, 500 ps long, the production sampled a span of 2 ns, which resulted in a total simulation time of about 40 ns for each curve (thus, a total time of about 800 ns). The GROMACS pull code90 was used, and the resulting average constraint force, λ, was integrated over all values of z. The position-dependent PMF of the free energy change, F(z), was obtained as Z ð1Þ FðzÞ ¼ z dz

’ SUPRAMOLECULAR MODELS AND MOLECULAR DYNAMICS SETUP

Benzene adsorption on Ag(111) has been extensively investigated both experimentally and theoretically (see, for example, ref 91 and cited articles therein), and all the studies have shown that the interaction of the molecule with the silver substrate is weak and the preferential adsorption mode sees the molecule in a flat configuration on a three-coordinated hollow site. The binding energy and the distance from the surface were found in the ranges of 9
13 kcal/mol and 2.4
3.2 Å, respectively.41 As far as aniline is concerned, adsorption energy and position on the molecule were compared with the data reported in refs 41 and 92, which predicted a binding energy of about 17 kcal/mol and a geometry of adsorption where nitrogen and the benzene ring were directly above the third row of Ag atoms (3-fold fcc hollow site). The potential models derived here satisfactorily reproduce the structure and energetics of the molecules while keeping the same description for the carbon atoms of both rings (aromatic carbons). These potentials were evaluated against experimental binding energies and location of the molecules with respect to the hollow or on top positions. Satisfactory agreement was obtained, and the most favorable arrangements

Preliminary Checks and Procedure Calibration. Before performing the MD simulations of adsorbed molecular clusters, short explorative MD runs (500
1000 ps, T = 298 K) of each single component of the investigated systems and of the porphyrin
C60 complexes were carried out in order to define the most appropriate simulation conditions, check the validity of the developed method/parameters, and obtain a first estimate of the interaction/adsorption energy of the different molecular species. From these calculations, the average interaction energy (at T = 298 K) of TPP, TPP-(NH2)2, and C60 with the substrate turned out to be 70, 75, and 24 kcal/mol on average, respectively (with a standard deviation of about 4 kcal/mol), whereas the complex of the porphyrin molecules with fullerene, which was stably located on top of the porphyrin core for the whole exploratory run, gave an average attractive interaction energy of about 20 kcal/mol. This energy became more favorable when the complex was energy minimized, and a more compact structure was obtained (about 24 kcal/mol). However, this is a local minimum and better values could be obtained through a more exhaustive conformational search. 18437

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Figure 2. Initial configurations with 20 (A, B, D, E) and 24 (C, F) TPP (A, B, C) and TPP-(NH2)2 (D, E, F) molecules positioned on the anhydrous Ag(111) surface. (B, E) Configurations of the hybrid bilayer made of porphyrin and C60 molecules after energy minimization.

The force field parametrization of C60
porphyrin association was checked against DFT-M062X/6-31G(p,d) single-point calculations (in order to be coherent with the parametrization of the dihedral angle of the phenyl) on the frozen geometries extracted from the production dynamics, and the association resulted to be in agreement (≈20 kcal/mol) with the classical description. Even though the estimated interaction energies cannot be compared directly with the experimental binding energies reported in the literature, they reproduce adequately the relative trend found by other authors. For example, in ref 41, an average adsorption energy of 29 kcal/mol for C60 was predicted, whereas TPP-C60 association energies were found in the range of 18
31 kcal/mol.62,101 It has been shown that the most important component of the association energy between porphyrins and fullerenes is the dispersive contribution. This is included explicitly (van der Waal’s terms) in the empirical force fields that succeeded in reproducing the results of ab initio correlated calculations.48,62,101 Instead, no experimental reference was found for the interaction energy between the TPPs and the Ag(111) surface. A theoretical estimate was given by Rojas and co-workers,18 who performed DFT calculations with the HCTH functional. As the authors stated, even though binding values obtained for model systems underestimated the interactions, they reproduced qualitatively the general trend and thus could be used to describe their systems. Our interaction energy seems overestimated in comparison to their description, but reasonable when compared to the data found for other close-packed (111) metal surfaces.23,85 To obtain more accurate binding free energies of large systems, such as TPP and C60, to the Ag(111) surface, large-scale simulations would be necessary. Different potential of mean force techniques could be employed, choosing various reaction coordinates and sampling exhaustively the configurational space. However, this was beyond the aim of the present work, which was focused on self-assembly and dynamics of the adsorbates on the substrate. A caveat to be introduced here is the fact that all the parameters have been defined considering small fragments, which are the constituent units of the molecular species under study, in the general philosophy of force field development. As such, they are not highly specific for each single system but are

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balanced values that, as shown by the simulation results reported in this paper, correctly describe adsorption, complex formation, self-assembly, and dynamics of the various molecular species. Porphyrin Self-Assembled Monolayers and Bilayers. The porphyrin molecules, in their energy-minimized conformation, were placed over the surface quite close to each other in an almost ordered alignment (Figure 2). Three dimensional periodic boundary conditions were applied in all directions. The vacuum zone separating the slabs was about 70 Å, which is large enough for the fictitious interactions between the slabs to be negligible. The system resulted to be an infinite slab in the xy plane. Once created, each molecular assembly was energyminimized without constraints, using the steepest descent method, for 2000 steps, followed by 3000 steps of conjugate gradient optimization. Starting from these energy-minimized complexes, molecular dynamics simulations were then performed in the NVT canonical ensemble (T = 298 K) with the Nose
Hoover thermostat coupling scheme.102,103 Nonbonded Lennard-Jones interactions were cut off at 12 Å, and electrostatic interactions were treated through the particle mesh Ewald (PME) method104 with a real-space cutoff of 12 Å. After an initial equilibration phase, 500 ps long, all the simulations were run for 20 ns and the system configurations were saved every 0.5 ps. Four independent simulations were performed to study and compare dynamics and self-assembly of TPP and TPP-(NH2)2 monolayers at different coverages (≈60% and ≈75%). To explore the possible configurations adopted by porphyrin/ C60 hybrid bilayers and the ability of the porphyrin monolayers (both TPP and TPP-(NH2)2) to host the fullerene guests in a low-concentration regime, six C60 units were positioned randomly on the already decorated surfaces where the molecular layers were only partially self-organized. These monolayer configurations were extracted from the MD trajectories (one for each system) at 60% coverage, during the first nanoseconds of the production runs. Before adding the new guest molecules, however, the two snapshots were superimposed, modified by repositioning some of the porphyrins of both models, and energyminimized to remove unfavorable steric interactions with the aim of creating two very similar networks. The six fullerene molecules were then inserted in each simulation cell sufficiently far from both the porphyrin core and the silver surface (at an initial separation of about 6 Å). After energy minimization, the deposited units migrated toward suitable locations. They lodged directly above the porphyrin molecules and on top of the Ag surface, but the resulting arrangements of the two systems were quite different (Figure 2B,E). Afterward, the configurations were equilibrated for about 1 ns and then the simulation time was extended to 20 ns for conformational sampling.

’ RESULTS AND DISCUSSION The influence of the silver interface on the porphyrin selfassembling process is mainly determined by the preferred adsorption positions, namely, top, bridge, and hollow of the molecular core, whereas the location of the phenyl groups plays only a minor role because of the limited number of possible orientations they can adopt, which do not correspond to the preferential surface binding configurations identified for the isolated fragments. As already evidenced by the torsional profile of the free molecule, displayed in Figure SI1 of the Supporting Information, these side chains can rotate independently and explore quite a large range of equally populated conformations. 18438

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Figure 3. Snapshot at t = 2 ns extracted from preliminary MD simulations where the dynamics and self-assembling properties of TPP at low surface coverage were investigated. Starting from a disordered arrangement, the molecules self-assemble in ordered nanostructures (pentagonal and tetragonal shapes, colored dotted lines and stripes). The simulation cell and the first periodic images in x and y directions are shown to evidence island formations and possible connections. For clarity, only the silver atoms of the top layer are displayed.

However, because of the presence of the substrate, these rotations are presumably substantially hindered. In all the conformations adopted by the molecules, the phenyl hydrogens are close to the surface but, because they are not involved in the adsorption process, their contribution to the location of the molecule is essentially connected with porphyrin
porphyrin intermolecular interactions and thus self-assembly. Before discussing the results obtained through MD simulations at relatively high coverage (60
75%), additional features, observed in the preparatory studies at low surface coverage (≈35%), deserve to be mentioned. Preliminary Observations. During the initial exploratory stage, which was necessary to define the simulation protocols, short MD simulations (≈2 ns) of the motion of 12 TPP molecules (≈35% coverage), randomly positioned on the Ag surface far from each other, were carried out and the results were compared with the experimental data obtained by Buchner and co-workers49 at a similar coverage (about 40%). Analysis of the trajectory revealed that the molecules gathered together and originated ordered islands (see Figure 3, where the final configuration obtained after a 2 ns dynamics run is shown) where a central unit appeared surrounded by five or even six structures. However, through a more careful examination of the location of each molecule with respect to the others, it was noticed that four TPPs formed a square unit cell with a lattice constant of 13.4 ( 0.1 Å (green lines in Figure 3), which is comparable to the tetragonal phase, identified by Rojas and co-workers,18 where the unit cell had a length of about 13.8 Å. As can be clearly seen, the other TPP molecules joined to this central aggregate and nucleated into clusters organized as irregular pentagons, which, as suggested by the position of the molecules surrounding the central unit, could be the precursors to the formation of larger hexagonal arrangements. The domains, identified experimentally,18,49 were aligned along the substrate high symmetry directions and could be rotated by multiple of 120°. Our computational findings agree fairly well with this picture. The closest distance between the center of mass of the porphyrin cores was about 13.4 Å (base of the pentagon, units P1 and P2). Units P3 and P5 were located at the same distance from the base

Figure 4. Final snapshot of the 20 ns MD simulations of TPP (a, b) and TPP-(NH2)2 (c, d) molecules adsorbed on the anhydrous Ag(111) surface at low (a, c) and high (b, d) surface coverage.

(P1P5 = P2P3 = 15.5 Å), and also the vertex (P4) was at about 18.4 Å from both P3 and P5 molecules, respectively. Notwithstanding, TPP macrocycles were flatly adsorbed on the surface, with the pyrrole rings preferentially situated on top of the hollow sites and the nonprotonated nitrogens slightly bent toward the surface atoms. Great mobility was imparted to the molecules by the frequent rotations of the phenyl rings (tilting and twisting47), and the units could leave or reach the agglomerated islands (twodimensional condensation105). Self-organization in regular rows was also evident. Various molecular alignments (highlighted by colored dotted lines in Figure 3) could be identified, and the tendency to further aggregations could be deduced from the molecular chain almost connecting the two clusters. Although the sampled time was not sufficient to characterize the numerous aspects of the aggregation mechanism of all the units inserted in the simulation box, the analysis of the data suggested that the formed islands increased their size through collection of the free molecules, which, due to the Brownian motion, slowly migrated toward the initial nucleation centers. These results, in line with experimental data,10,105 suggest that stabilizing effects on the molecular matrices could be enhanced by a higher surface coverage. Indeed, as this study will indicate, a progressive increase in the surface coverage can lead to the formation of ordered molecular networks through the expansion of localized molecular patches. We could speculate that, once formed, the macrostructures reorganize themselves, by means of concerted movements of the constituting units, in order to get to stable patterns. This preliminary analysis and speculation agree satisfactorily with the experimental observations.49 Self-Assembly Monolayers of Porphyrin Structures: Orientation and Dynamics. The final configurations of the four systems obtained after 20 ns of molecular dynamics are displayed in Figure 4. From the comparison with the starting structures, shown in Figure 2, it is evident that neither the initial orientations nor the arrangements of the molecules close to them were suitable stable alignments of such a system, and consequently, 18439

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Figure 6. Molecular dynamics snapshot of TPP-(NH2)2 molecules adsorbed on the Ag(111) surface (high coverage) displaying the characteristic positions of the phenyl rings that determine self-aggregation (T-shaped arrangement, highlighted by yellow lines). Only a portion of the whole configuration is displayed. The angle of each molecular axis, connecting two opposite rings (magenta segment), with respect to the lattice vector of the unit cell (green square) is about 30°. The Ag(111) substrate has been undisplayed for clarity.

Figure 5. Density maps. In the background, Ag surface atoms are represented by gray empty circles. The motion of the pyrrole nitrogen atoms is rendered by means of contour plots colored using fading tones of blue (nonprotonated nitrogens) and fading tones of cyan (protonated nitrogens). The axes of the simulation box are also displayed. The analysis has been performed during the last 10 ns of the simulations. TPP (A, B) and TPP-(NH2)2 (C, D). Low (B, D) and high (A, C) surface coverage.

the molecules performed substantial rototranslational movements upon the surface, at least during the first 10 ns of the whole simulation time, in order to find the most favorable mutual orientations and compact assemblages. At high surface coverage, the final complexes appear organized in two equivalent architectures consisting of regular long stripes, two porphyrin molecules in width, rotated by about 20°, at most, with respect to the y axis of the simulation cell (Figure 5). The closest core
core average separation in the stripes is about 13.4 Å, which compares well with tetragonal unit cell parameters found in the literature18,49,106 (long-range ordered square assembly). Twodimensional surface density maps shown in Figure 5, representing, by means of colored areas, the high probability regions where the pyrrole nitrogens can be found during the last 10 ns of the simulations, reveal that the molecules have reached, within 20 ns, a quite stable self-organization. The motion of their core is confined within the boundary of the silver hexagonal cell, and their orientation is induced mainly by the characteristic symmetry of the underlying substrate. Indeed, stably adsorbed molecules orient the NN (nonprotonated pyrrole nitrogens, dark blue areas of the density maps) vectors toward specific directions, forming angles of about 62° (σ = 3°) and 90° (σ = 5°) with the

y axis of the simulation cell (Figure 5), but configurations belonging to the 90° domain are less-populated (≈20%). However, the overall mobility of the system is restrained by the closeness of the various components and prevalently concerted movements have been observed. When the density maps at low surface coverage are examined, a slightly different picture emerges. The systems are less uniform, presenting irregular pores that alternate with densely populated regions. In these areas, most of the molecules arrange in ordered phases, forming tetragonal bidimensional patterns. The units are aligned to the silver substrate, but they show a higher degree of mobility, in relation to the high coverage case, as confirmed by the wider ranges of orientations of the NN vectors (≈30°) and by the increase in the percentage population of the perpendicular alignments (40%). Adjacent molecules, which are located at distances of about 13.4 Å and are arranged as a square unit cell (Figure 6), form stable complexes due to their phenyl moieties that are engaged in T-shaped interactions. Both stacking and T-type interactions were observed during porphyrin assembling, and both of them were equally important in defining stable supramolecular organizations. However, T-shaped motifs are decidedly predominant when the final compact packing is adopted (in agreement with refs 23 and 49). Indeed, as it can be observed in Figure 6, the involvement of each phenyl ring, at the center of the square cell, in T-type interactions with the rings of both of the two adjacent molecules originates a closely knit configuration where attractive forces are maximized.47 Besides, the centers of mass of the carbon rings are at an average distance of 5.2 Å (in the case of TPP), which is very close to the optimal intermonomer separation found in benzene dimers.47,107
109 Instead, when the NH2 substituent was present, this separation became 5.5 Å, but one of the hydrogen atoms of the NH2 group was involved in a hydrogen-bond interaction with the π density of the adjacent ring (the distance between the hydrogen and the center of mass of the ring was about 2.2 Å). This is a typical stable alignment of 18440

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Figure 7. Distribution of the phenyl torsion angles: TPP (A, B) and TPP-(NH2)2 (C, D). Low (A, C) and high (B, D) surface coverages.

Figure 8. Density maps. In the background, Ag surface atoms are represented by gray empty circles. The motion of the pyrrole nitrogen atoms is rendered by means of contour plots colored using fading tones of blue (nonprotonated nitrogens) and fading tones of cyan (protonated nitrogens). The position of C60 molecules is represented by yellow areas. The axes of the simulation box are also displayed. The analysis has been performed during the last 10 ns of the simulations. TPP/C60 (A) and TPP-(NH2)2/C60 (B).

aniline
benzene dimers that was identified through spectroscopic methods.110 The comparison of the numerous square cell configurations has shown that the T-shaped groups are almost perpendicular to

each other, but their centers of mass are shifted by about 2 Å in order to improve the mutual location of the various units. The analysis of Figure 6 demonstrates fairly high correlations with the high-resolution STM images displayed in ref 49. Indeed, in both experimental and theoretical resulting arrangements, the molecular axes are rotated out of the unit cell by about 30° and each phenyl ring inside the square is involved in two T-type interactions with the neighboring molecules. Furthermore, a relatively optimal setting of the interacting groups is guaranteed by the continuous exploration of different arrangements, which is achieved through the frequent tilting of these moieties. This finding has been confirmed by checking the distribution of the four dihedral angles τ1
4 (defining the position of the rings) shown in Figure 7 and by a detailed analysis of the angular values as a function of the simulation time. All distributions have narrow peaks centered at about 60 and 120°, which correspond to the minima in the torsional energy profile (see Figure SI1, Supporting Information). Even though the rotational barrier separating the two minima is low and can be easily overcome at T = 298 K, the width of the peaks indicates that, in the examined cases, the rotation is limited and the angular range explored by the phenyl legs is reduced (about 20°). Despite the restraint to the phenyl rotation introduced by the presence of a substrate, switching of the rings (from one orientation to the other) has been observed. This rotation is very fast (at times lower than 0.5 ps), and its frequency, which is 0.0042 and 0.0035 ps
1 at low and high coverages, respectively, seems connected with surface coverage and packing of the structures. The trends of 18441

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Figure 9. Final snapshots of the 20 ns MD simulations of TPP/C60 (a) and TPP- (NH2)2/C60 (b) hybrid systems.

the torsional distributions (different heights at low and high coverages) reflect this behavior. Indeed, inspection of the trajectories has revealed that the frequency of jumps decreases by 7% when the surface is more populated. Bilayer Supramolecular Aggregates: Porphyrins and C60. From the examination of the results of the MD simulations of the hybrid systems, it emerged that C60 units have the tendency to adopt preferential arrangements on the surface, which determine the formation of linear chains. Comparison of the data with the previous findings suggests that the appearance of such hybrid ordered nanostructures, made of lines of fullerenes and stripes of porphyrins, could be largely ascribed to the substrate crystallography, to the concentration of the species (expressed as surface coverage), to the rotational and translational movements, and to the strength of their intermolecular interactions. These factors are all equally important for obtaining specific decorative motifs. The analysis of the dihedral angle distributions of the phenyl rings of all porphyrin species has showed trends almost identical to those found in the monolayer simulations. Also, both the evolution of the torsion angles and the jump frequency are in line with the previous data, confirming that, at this concentration of C60, the small concerted movements of the porphyrin units are not affected by the presence of the guest molecules. Inspection of the density maps corresponding to the last 10 ns of the simulations (Figure 8), which should give an idea of location and mobility of the various molecular modules, has shown that the orientations of both TPP and TPP-(NH2)2 (blue and cyan areas) fall in the two domains already identified in the absence of C60 and both regions seemed equally populated. The structures are quite stably adsorbed on the surface, as confirmed by the very limited motion of their cores, and in a few cases (four for TPP and three for TPP-(NH2)2), they surround the fullerene guests. The small size of the yellow areas, identifying the position of C60's, evidence a scarce mobility of these units, which were located both on the surface and on top of the porphyrin cores (Figure 9). However, the most important stabilization of fullerene on the surface appeares to be obtained when it is in direct contact with the Ag(111) slab and practically entrapped within

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Figure 10. Final snapshots of the 20 ns MD simulations of TPP/C60 (a) and TPP- (NH2)2/C60 (b) hybrid systems. Zoomed sections extracted from Figure 9.

the porphyrin network (Figure 10). As can be observed in Figure 10, each adsorbed guest is enveloped by at least three porphyrin molecules (four in the best cases), which slightly reorient their aromatic moieties and engage stacking interactions with the fullerene faces (stacking arrangements). As a matter of fact, the phenyl legs become also arms that embrace the C60 and keep it, through a multianchoring mode, close to the silver interface. In this configuration, the guest is almost static. On the contrary, weaker adsorption is obtained when fullerenes reside on top of the porphyrin cores, as confirmed by the frequent displacements evidenced by the wide areas visible in the density maps. These findings suggest that, at this concentration of the various species, migration of the C60 units from their host toward the available pores of the surface could take place.

’ CONCLUSIONS The results of the present computational study agree very satisfactorily with the experimental findings, support their view, and confirm the interpretation of the data, by means of a detailed analysis of the configurations sampled during long MD simulation runs. It has been shown that there is a clear epitaxial relationship between TPPs and the Ag(111) surface, which determines the observed long-range order. Indeed, the formation and mobility of the organized networks depend, on the one hand, on the substrate morphology, which drives the alignment of the molecules, and on the strength of the interactions between the interface and the adsorbed species, which is mainly responsible for the mobility of the whole structure, and, on the other hand, on the ability of the molecular modules to self-interact effectively, which determines both the stability of specific shapes and the amplitude of the local regulating relocations. T-type intermolecular interactions between the phenyl rings of the adjacent TPPs are mainly responsible for the stabilization of the ordered networks and guide the self-assembling process. The phenomena observed during the monolayer formation (porphyrin phase) have also been found embedded in the wider frame of reference represented by the hybrid bilayer dynamics (porphyrin and C60 18442

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The Journal of Physical Chemistry C phase). The identification of characteristic traits common to the two phases (that is, porphyrin phase and porphyrin + C60 phase) suggests possible explanations of the reasons for specific assembly arrangements of C60 with respect to the porphyrin layer, which turn out to be controlled by the underlaying configurations of the SAM.

’ ASSOCIATED CONTENT

bS

Supporting Information. Torsional profile of the phenyl ring and topology files. This material is available free of charge via the Internet at http://pubs.acs.org.

’ AUTHOR INFORMATION Corresponding Author

*Phone: +39-050-3152552. Fax +39-050-3152555. E-mail: smonti@ iccom.cnr.it or [email protected].

’ ACKNOWLEDGMENT This work was financially supported by MIUR (PRIN 2008: prot. 2008MXZEAS). S.M. thanks Stefano Corni for granting her the use of GolP and for useful discussions. The authors gratefully acknowledge the computing facilities of CASPUR (Inter-University Consortium for the Application of Super-Computing for Universities and Research, Rome). ’ REFERENCES (1) Barth, J. V. Annu. Rev. Phys. Chem. 2007, 58, 58. (2) Barth, J. V.; Costantini, G.; Kern, K. Nature 2005, 437, 671. (3) De Feyter, S.; deSchryver, F. C. Chem. Soc. Rev. 2003, 32, 139. (4) Whitesides, G.; Mathias, J.; Seto, C. Science 1991, 254, 1312. (5) Verbiest, T.; Elshocht, S. V.; Kauranen, M.; Hellemans, L.; Snauwaert, J.; Nuckolls, C.; Katz, T. J.; Persoons, A. Science 1998, 282, 913. (6) Ray, K.; Ananthavel, S. P.; Waldeck, D. H.; Naaman, R. Science 1999, 283, 814. (7) Lehn, J. M. Science 1998, 260, 1762. (8) Bonifazi, D.; Mohnani, S.; Llanes-Pallas, A. Chem.—Eur. J. 2009, 15, 7004. (9) Spillmann, H.; Kiebele, A.; St€ohr, M.; Jung, T. A.; Bonifazi, D.; Cheng, F.; Diederich, F. Adv. Mater. 2006, 18, 275. (10) Bonifazi, D.; Kiebele, A.; St€ohr, M.; Cheng, F.; Jung, T. A.; Diederich, F.; Spillmann, H. Adv. Funct. Mater. 2007, 17, 1051. (11) Pitchiaya, S.; Krishnan, Y. Chem. Soc. Rev. 2006, 35, 1111. (12) Rothemund, R. Nature 2006, 440, 297. (13) Larken, E.; DuPont, J. A.; Gratton, S.; DeSimone, J. Chem. Soc. Rev. 2006, 35, 1095. (14) Gothelf, K. V.; LaBean, T. H. Org. Biomol. Chem. 2005, 3, 4023. (15) Liu, Y.; Ke, Y.; Yan, H. J. Am. Chem. Soc. 2005, 127, 17140. (16) He, Y.; Chen, Y.; Liu, H.; Ribbe, A. E.; Mao, C. J. Am. Chem. Soc. 2005, 127, 12202. (17) Mohnani, S.; Bonifazi, D. Coord. Chem. Rev. 2010, 254, 2342. (18) Rojas, G.; Chen, X.; Bravo, C.; Kim, J.-H.; Kim, J.-S.; Xiao, J.; Dowben, P. A.; Gao, Y.; Zeng, X. C.; Choe, W.; Enders, A. J. Phys. Chem. C 2010, 114, 9408. (19) Resta, A.; Felici, R.; Kumar, M.; Pedio, M. J. Non-Cryst. Solids 2010, 356, 1951. (20) Yokoyama, T.; Yokoyama, S.; Kamikado, T.; Mashiko, S. J. Chem. Phys. 2001, 115, 3814. (21) Moresco, F.; Meyer, G.; Rieder, K.-H. Phys. Rev. Lett. 2001, 86, 672. (22) Moresco, F.; Meyer, G.; Rieder, K.-H.; Tang, H.; Gourdon, A.; Joachim, C. Appl. Phys. Lett. 2001, 78, 306.

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