Modulating Morphology of Thiol-Based Monolayers in Honeycomb

Article pubs.acs.org/JPCC

Modulating Morphology of Thiol-Based Monolayers in Honeycomb Hydrogen-Bonded Nanoporous Templates on the Au(111) Surface: Simulations with the Modified Force Field Jin Wen and Jing Ma* Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China S Supporting Information *

ABSTRACT: The difference in monolayer morphology caused by different functional thiols (ASH, BP3SH, and C12SH) within the surface-supported porous network of naphthalene tetracarboxylic di-imide (NDI) and melamine (MEL) molecules has been investigated by molecular dynamics simulations with the modified force field. The hydrogen-bonded bimolecular network is taken as the template when different thiols are deposited on the Au(111) surface. Force field parameters of intermolecular (NDI−NDI, MEL−MEL, NDI−MEL, and thiol−thiol) and interfacial (Au···S) interactions are modified to reproduce MP2 potential energy curves and the adsorption height. Interfacial interactions between the network and the Au(111) surface support the NDI−MEL bimolecular template, lying flat in an ordered hexagonal pattern on the substrate. The packing morphology of the triple hydrogen-bonded network obtained from molecular dynamics simulations and quantum chemical calculations matches the image from the scanning tunneling microscope. The backbone flexibility, which varies with the length and shape of thiol chains, is demonstrated to affect the monolayer morphology. The packing arrangement tends to be more ordered with the increase of the coverage for alkane thiols. The subsequently deposited thiols also disturb the bicomponent nanopore to a different extent, originating from the subtle balance between the thiol−thiol, thiol−template, and the intratemplate hydrogen-bonding interactions. It is demonstrated that the aromatic rings in BP3SH add a chance to perturb the host network through the π···π stacking in low coverage. The understanding of nanotemplate effect on the thiol-based monolayer growth is helpful for fabricating novel surface-supported host−guest hybrid nanodevices at the single molecular level.

1. INTRODUCTION Self-assembled porous networks with highly ordered packing conformations have aroused considerable attention due to the potential applications to molecular electronics, photonics, and optical devices.1−9 Many hexagonal close-packed architectures have been demonstrated by using various building blocks,8−20 such as 3,4,9,10-perylene-tetracarboxylic-3,4,9,10-dianhydride (PTCDA), perylene tetracarboxylic di-imine (PTCDI), naphthalene tetracarboxylic di-imide (NDI), and melamine (MEL) molecules. The highly ordered packing structures make them widely used as templates to control molecular deposition when other guest molecules are further deposited on surfaces.14,21−25 When the guest molecules are deposited on surfaces, they may modify the porous nanonetwork precisely. Various alkane thiols with different chain size, terminal aromatic moieties, and flexibility have been used as the encapsulated molecules on preconfined surfaces to tune the guest selectivity.22,26−32 Achieving a precise control over the surface-based supramolecular self-assembly patterns requires an understanding of the factor that governs the morphology and electronic property of these packing systems. However, it is still unclear how the terminal of the guest thiols affects the morphology of the © 2012 American Chemical Society

self-assembled monolayers (SAMs) and the network structure of the surface-supported host. It is hence necessary to elucidate the mutual influence of the deposited thiols on the intermolecular and interfacial interactions between the host−guest system through a systematic theoretical study. In the present work, three kinds of guest thiol molecules, adamantane thiol (ASH), ω-(4′-methylbiphenyl-4-yl)propane thiol (BP3SH), and dodecane thiol (C12SH), are selected in terms of different flexibility and aromatic properties (Scheme 1). Comparing to BP3SH and C12SH molecules, the shorter chain ASH is more rigid and rather “inert”, with weaker intermolecular interactions.33,34 The BP3SH molecule is featured by its two aromatic rings, which are bonded to an alkyl connector on the surface. In this work, we will demonstrate that the aromatic rings in BP3SH add a chance to disturb the host network through the π···π stacking. The alkane chain C12SH is more flexible than BP3SH when they are deposited in the porous network. We attempt to study the Received: November 21, 2011 Revised: February 26, 2012 Published: March 23, 2012 8523

dx.doi.org/10.1021/jp211206n | J. Phys. Chem. C 2012, 116, 8523−8534

The Journal of Physical Chemistry C

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Scheme 1. NDI−MEL Bicomponent Porous Network and SAM/Network Hybrid Structures on the Au(111) Surface

Figure 1. Binding energy curves calculated by MP2, modified CVFF, and default CVFF methods, respectively, for (a) intermolecular interactions between NDI−NDI, MEL−MEL, and NDI−MEL dimers and (b) interthiol interactions between the deposited ASH, BP3SH, and C12SH molecules.

hydrogen-bonding network. In this work, we chose NDI and MEL molecules as building blocks in bimolecular networks, which are different from the extensively studied PTCDI− MEL-based system.14,21,22,26,35 Since NDI (with a naphthalene

difference in monolayer morphology caused by these three kinds of thiols. It is well recognized that both the NDI−MEL7 and PTCDI− MEL14,21,22,26,35 nanotemplates are assembled by the triple 8524



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group) is shorter than PTCDI (with a perylene group) in the long molecular axis, the present NDI−MEL system is expected to be smaller than the PTCDI−MEL template in the pore size. The behavior of thiol molecules in such a smaller porous template arouses our attention. On the basis of some model systems, the intermolecular interactions in the bicomponent template as well as the interfacial interactions between the molecule and substrate have been addressed by using functional-modified density functional theory (DFT), second-order Møller−Plesset perturbation theory (MP2), and multireference perturbation theory (CASPT2) calculations.2,3,19,24,35−38 To the best of our knowledge, few attempts have been made on the theoretical study of the selected SAM-network/Au(111) complex systems.18,39−41 On going from the model systems to the really complicated SAM-network/Au(111) system, the computationally economic force field method is desired in combination with the sophisticated MP2 and DFT calculations. The good performance of the force field lies in the wellbehaved parameters. The NDI−MEL network has been shown to be clearly adsorbed on the Au(111) surface physically due to the nonbonded interfacial interaction, contrasting to the specific Au···S interaction between Au(111) and thiol molecules.42−44 Therefore, the challenge in our theoretical simulation is to set up suitable force field parameters to reasonably describe the different intermolecular and interfacial interactions in the SAM-network/Au(111) system. Here, force field parameters for both the intermolecular (NDI−NDI, MEL−MEL, NDI−MEL, and thiol−thiol) and interfacial (Au···S) interactions are modified to reproduce MP2 binding energies and experimental packing arrangement. The classical Lennard-Jones potential with the newly fitted parameters is used to treat the nonbonded interfacial interaction, and the Morse potential is used to describe the Au···S binding. The MD simulations with the modified force field are then carried out on the host−guest systems with three different thiol guests. It will be demonstrated that the morphology of guests varies with terminal in thiol chains, which are confined by the network. On the other hand, templates are also distorted by the guests to a different extent, due to the intermolecular guest−template interactions. The systematic theoretical results may motivate further experimental works toward the controllable construction of the hybrid molecular devices the on surface.

Figure 2. Binding energy curves calculated by MP2, modified CVFF, and default CVFF methods, respectively, for interfacial interactions between the deposited thiols (a) AS, (b) BP3S, and (c) C12S on the Au13 cluster models at hcp hollow sites.

2.1. Parameters for Intermolecular Interactions. For the hydrogen-bonded hexagonal NDI−MEL nanopore, we laid emphasis on two types of hydrogen bonds, O···H−N and N−H···N, in both homodimers (NDI−NDI, MEL−MEL) and the heterodimer (NDI−MEL), as shown in Figure 1a. The interthiol interactions are also tested in two typical packing conformations (face-to-face, noted as ff, and side-by-side, noted as ss), cf., Figure 1b. These hydrogen-bonding and interthiol interactions are treated in a van der Waals form with the new parameters Aij and Bij fitted from MP2 potential curves (Figure 1).

2. MODIFIED FORCE FIELD AND COMPUTATIONAL DETAILS The selection of proper force field is the key to successful application of the molecular mechanism to the studied SAMnetwork/Au(111) system. The consistent valence force field (CVFF)45 has been widely applied in molecular aggregates in solutions,46 as a solid state,47 and on surfaces.48−50 However, the usage of default parameters in the CVFF failed to reproduce the MP2 intermolecular energy curves of the present guest− host systems. Both intermolecular (NDI−NDI, MEL−MEL, and NDI−MEL as shown in Figure 1a) and interfacial (Au···S) interactions (Figure 2) are underestimated by the original CVFF, but interthiol (BP3SH−BP3SH) (shown in Figure 1b) and NDI−Au and MEL−Au interfacial interactions (Figure 3) are overestimated. Therefore, we need to modify the force field parameters with respect to the nonbonded interaction in both the interfacial and intermolecular interactions.

E = A ij /r12 − Bij /r 6

(1)

where A ij =

Ai ·Aj

(2)

Bij =

Bi ·Bj

(3)

Ai (Bi) and Aj (Bj) are parameters of atoms i and j, respectively. The new parameters are given in Table 1. In comparison with the original default parameters, the parameter for dispersion energy (Bi) was increased in hydrogen-bonded pairs; however, in the inter thiol (BP3SH−BP3SH) pair, dispersion energy is decreased, and repulsion energy (Ai) is increased slightly. 8525



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described by Esurf and Eadsorbate, respectively. A more negative value in Ebind means stronger interfacial interaction. Interfacial interaction between the NDI−MEL network and the Au(111) surface is stronger than that between thiols and the Au(111) surface; thus, these two kinds of interfacial interactions were treated differently in our modified force field parameters. NDI−Au and MEL−Au interfacial interactions were still described by the van der Waals interaction with the modified parameters, Ai and Bi, of C, N, and Au atoms listed in Table 1. Particularly, the Morse potential was used to model the specific interaction between the Au(111) surface and thiols, which is described as EAu···S = D·{1 − exp[ −α·(r − r0)]}2

where the force constants D and α and equilibrium bond length r0 are also listed in Table 1. The other parameters, charges, and geometries adopt the default values of the CVFF45 (Figure S1 and S2, Supporting Information). 2.3. Validations of the Modified Force Field. It is wellknown that the current ab initio quantum mechanism methods are only affordable for the medium-sized metal clusters. Several one- and two-layer Au cluster models were selected to test the influence of Au cluster size on the binding energies with all Au atoms fixed at their crystal structures, as shown in Tables 2 and 3. To test the behavior of different density functionals of DFT, a C12S molecule was set on the top side of the Au7 cluster as shown in Figure S3 (Supporting Information). It could be found that the B3LYP functional underestimated interfacial interaction between Au7 and C12S compared with the MP2 method. The binding energy obtained from the M06 density functional51 was in a good agreement with MP2 calculation results (Figure S3, Supporting Information). Furthermore, DFT/M06 calculations were performed for larger cluster models (Au13, Au18, Au28, and Au31), in comparison with MP2 results (Tables 2 and 3). It could be found that DFT/ M06 underestimated the binding energies in a larger cluster model but gave a reasonable adsorption height. The truncated Au18 and Au28 cluster models were selected to calculate interfacial interactions (NDI−Au and MEL−Au), as shown in Figure S4 (Supporting Information) and Table 2. The adsorption of NDI and MEL molecules was studied at three adsorption sites (top, bridge, and hcp) on the Au28 model by both DFT/M06 and MP methods. Little preference was found among these binding sites, thus the MP2 result for the bridge site was selected as a benchmark to get the modified force field parameters. The other two cluster models, Au13 and Au31, were chosen for Au···S interaction calculations (Figure S5, Supporting Information, and Table 3). It has been demonstrated that the difference in interaction energy between the top and hollow sites is significant but negligible between hcp and fcc hollow sites for thiol alkane molecules.43 Here, the Au13 cluster was considered for both top and hcp hollow adsorption sites with 7 and 6 atoms in the upper layer, respectively. In Table 3, our calculation results on both Au13 and Au31 clusters also suggested that the adsorption on the hcp hollow site was more favorable than others. Given the similarity of the binding energy curves by the M06 functional between the different cluster models, the network− surface and thiol−surface interactions show little size dependence in surface models. Thus, Au18 and Au13 cluster molecules were chosen in the force field parametrization.

Figure 3. Binding energy curves calculated by MP2, modified CVFF, and default CVFF methods, respectively, for interfacial interactions between the deposited NDI (a) and MEL (b) on the Au18 cluster models at bridge sites.

Table 1. Modified Force Field Parameters (1) vdW for thiol−thiol E = Aij/r12 − Bij/r6 where Aij = (Ai·Aj)1/2, Bij = (Bi·Bj)1/2 Ai

atom type

Bi

cg (BP3SH-BP3SH)a 25790340.7240 (2) vdW for NDI−Au and MEL−Au Ai

atom type b

n c′c Au

8.48190 Bi

2266872.4000 2968753.3590 4603936.5046 (3) Morse potential for Au···S

2545.90000 1767.14000 6376.69000

E = D·{1 − exp[−α·(r − r0)]}2 bond type

r0

D

α

Au−sh (AS) Au−sh (BP3S) Au−sh (C12S)

1.6000 1.9000 1.8000

100.9500 125.9500 123.9500

0.5653 0.3653 0.4653

d

a

C atom in the benzene group of BP3SH. bN atom of NDI. cC atom in the acyl group of NDI. dS atom in thiols.

2.2. Parameters for Interfacial Interactions. The substrate plays an important role in the further deposition of SAMs in the surface-supported hexagonal template. The binding energy, also known as the interfacial interaction, is defined as Ebind = E tot − Esurf − Eadsorbate

(5)

(4)

where Etot is the total energy of the packing system, and the energies of the isolated Au(111) surface and adsorbate are 8526



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Table 2. Binding Energies (in kcal/mol) between NDI/MEL and Aun Cluster Models and Adsorption Height (Shown in Parentheses in Å) Calculated by MP2 and DFT/M06 Methodsa

NDI/Aun site

a

top

MEL/Aun

bridge

MP2 DFT/M06

− −

−44.5 (3.2) −16.5 (3.4)

DFT/M06

−16.3 (3.4)

−17.7 (3.4)

hcp Au18 cluster − − Au28 cluster −14.9 (3.4)

top

bridge

hcp

− −

−27.5 (2.9) −18.0 (3.2)

− −

−19.0 (3.2)

−19.0 (3.2)

−15.8 (3.1)

The 6-31G(d) basis sets are used for H, C, N, and O atoms and LANL2DZ basis sets for Au atoms.

Table 3. Binding Energies (in kcal/mol) between Thiols and Aun Cluster Models and Adsorption Height (Shown in Parentheses in Å) Calculated by MP2 and DFT/M06 Methodsa

AS/Aun site

top

MP2 DFT/ M06

−5.7 (2.4) −1.1 (2.6)

DFT/ M06

3.1 (2.5)

a

bridge

BP3S/Aun hcp

top

bridge

− −

−41.1 (1.8) −28.0 (1.9)

−21.3 (2.3) −8.7 (2.5)

Au13 − −

−14.8 (2.1)

−21.3 (1.9)

−10.8 (2.5)

Au31 −12.3 (2.3)

C12S/Aun hcp

top

−26.5 (2.0) −18.2 (2.2)

−7.4 (2.4) −1.4 (2.6)

−16.9 (2.1)

0.9 (2.5)

bridge

hcp

− −

−31.1 (1.9) −22.0 (2.0)

−13.8 (2.1)

−13.8 (2.0)

The 6-31G(d) basis sets are used for H, C, and S atoms and LANL2DZ basis sets for Au atoms.

length (from methane thiol to C12S thiol) using the BLYP functional on the Au(111) surface.43 The DFT calculation result revealed that all alkane thiol interaction with the Au(111) surface at the hollow site is much stronger than that at the top site. In our work, we also found thiols (AS, BP3S, and C12S) preferred to bind at hollow sites, and this will be further addressed in Subsection 3.2.1. The Discover module in the Material Studio software package53 was used for MD simulations. The canonical NVT ensemble with constant moles (N), volume (V), and temperature (T) was used in MD simulations. An annealing process was carried out to overcome the local barriers in different conformations. A higher temperature, 350 K, was used in the 100 ps pre-equilibrium process. Then the temperature was gradually decreased to 298 K and controlled by an Andersen thermostat.54 The trajectories were collected every 50 fs during the 1 ns simulations with a 1 fs time step. To reveal the substituent effects of guest thiols on the SAM morphology and the nanoporous templates, the statistic analysis was carried out for the SAMs thickness, orientation, and distortion of pore size from MD trajectories.

For all these calculations on interfacial and intermolecular interaction potentials, we used 6-31G(d) basis sets for H, C, N, O, and S atoms and LANL2DZ basis sets for Au atoms using the Gaussian 09 software package.52 The counterpoise correction was used to reduce the basis set superposition error in the single-point MP2 calculations. To achieve a compromise between computational costs and accuracy, the tight SCF convergence 10−8 was used in smaller Au13 and Au18 cluster models, and looser SCF convergence 10−5 was used in larger Au28 and Au31 cluster models. 2.4. Molecular Dynamics Simulations. The modified force field was used to simulate the packing arrangement of the bimolecular network on the Au(111) surface in MD simulations. The Au(111) surface was modeled as a trilayer slab of Au atoms without consideration of surface reconstruction. The periodical boundary condition was applied, and the slab is about 57.68 Å × 49.95 Å × 40.00 Å for 12 NDI and 8 MEL molecules adsorbed on the Au(111) surface. A different number of thiols was put into the nanopore, with S atoms randomly located at the hollow site on the Au(111) surface. The binding energies were studied as a function of alkane chain 8527



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3. RESULTS AND DISCUSSIONS 3.1. Bimolecular Network on the Au(111) Surface. 3.1.1. Hydrogen Bonding between NDI and MEL: QM Calculations. The directional intermolecular interactions are linkages for the complex networks. The control of hydrogen-bonded interactions is hence crucial to assemble the network morphology. Evaluation of the strength of the hydrogen bonding interaction is still an interesting but challenging topic for theoretical chemists. The counterpoise-corrected binding energy decreases with the increase of distance, R, between the hydrogen bonding donor and acceptor, as shown in Figure 1a. Since default parameters in CVFF underestimate hydrogen-bonding interactions, both homodimer and heterodimer parameters in the van der Waals part are modified. As presented by both our modified CVFF and MP2 calculations, the interaction energy between NDI and MEL molecules is about −15.0 kcal/mol. The triple hydrogen bondings in NDI−MEL make the heterodimer interaction 5.0 kcal/mol stronger than that in homodimers NDI−NDI and MEL−MEL. It suggests that the formation of the NDI−MEL network is more favorable rather than independent NDI and MEL networks on surfaces. It is also interesting to estimate the individual hydrogen-bond strength in triple hydrogen bonding dimers (NDI−NDI, MEL−MEL, and NDI−MEL). A simple atom-replacement approach55 was adopted to estimate the relative strength of each hydrogen bond. In that method, the H−N part was replaced by the O atom as shown in Figure S6 (Supporting Information), and several subsystems are then built. Each hydrogen bonding interaction was calculated by summing the interaction energy of each subsystem (eq S1) in Figure S6 (Supporting Information).55 By using such an atom-replacement method, the individual hydrogen bonding strengths are calculated at the MP2/6-311++G(d,p)//M06/6-311++G(d,p) level with the results depicted in Figure 4a. It can be found that the individual O···H−N hydrogen-bond strength is about 4.0 kcal/mol in these triple hydrogen bonding pairs, and the N−H···N hydrogen bonding interaction (8.0−10.0 kcal/mol) is almost double that of the O···H−N type. The summation in triple hydrogen bonds in NDI−MEL gives the total intermolecular interaction of −17.7 kcal/mol, consistent with previous DFT calculation results of −17.7 kcal/mol (−0.768 eV)7 in Palma et al.’s work. In addition, the natural bond orbital (NBO) analysis56 was carried out to understand the nature of O···H−N and N−H···N hydrogen bondings in both hetero- and homodimers. In Figure 4a, NBO analysis shows that the p type lone pair orbitals of O and N atoms (nO and nN with sp2 hybridization) in O···H−N and N−H···N contacts play the role of electron donors, and the antibonding orbitals σNH* are acceptors. The stabilization energy, E2, in nN → σNH* (NDI−MEL: 30.83 kcal/mol; MEL− MEL: 14.0 kcal/mol) is much larger than that in nO → σNH* (NDI−MEL: 8.09 kcal/mol; NDI−NDI: 7.0−10.0 kcal/mol). In all, both individual hydrogen bond strength and NBO analysis calculations demonstrate that the N−H···N hydrogen bonding is stronger than O···H−N in these triple hydrogen bonding dimers. That is in good agreement with previous binding energy calculations at the cc-pVTZ(-f)/LMP2 level.57 Now, we are going to the higher molecular aggregation, containing six pairs of MEL−NDI dimer. However, the conventional MP2 method is prohibited for such a big hexagonal supramolecule with 2754 basis functions at the

level of 6-31G(d). A more economic method is hence desired. The generalized energy-based fragmentation (GEBF) approach58−60 in the Lower Scaling Quantum Chemistry (LSQC) package61 has been adopted in both geometry optimization (at M06/6-31G(d) level) and binding energy calculations (at MP2/6-31G(d) level). The basic idea underlying the GEBF method is to decompose the large system into smaller fragments, and the total electron energy is then assembled from all the fragment energies that are obtained from individual energy calculations on each subunit. In each calculation on fragment energy, the working subunit is embedded in the background point charges that centered on the atoms in other fragments, to consider the electrostatic interactions between the distant fragments.58,62 The optimized geometry of MEL−NDI pairs does show a hexagonal pattern. The hydrogen bond lengths of O···H−N and N−H···N are 1.95 and 1.88 Å, respectively, close to those (1.96 and 1.86 Å) in the MEL−NDI dimer. The pore size is about 27.1 Å in diameter and 17.0 Å for an arm (Figure 4b). The counterpoisecorrected binding energy is predicted to be −297.8 kcal/mol in the hexagonal model by GEBF-MP2/6-31G(d) calculation. It can be conceived that the optimal surface-supported hexagonal packing structure is directed by hydrogen bonding between NDI−MEL pairs. With these MP2 results at hand, it is also a good chance to test the performance of force fields in this hexagonal pore. The modified CVFF optimization also gives a local minimum with a nearly hexagon structure. As mentioned in Subsection 2.1, the hydrogen bonding interaction is underestimated by the force field: the hydrogen bonds of O···H−N (2.05 Å) and N−H···N (1.99 Å) are longer than those obtained by QM calculations. The CVFF pore size, 28.4 Å in diameter and 17.5 Å of arm length, is also larger than the QM results. To our encouragement, the binding energy calculated from the modified force field parameters gives a good match with MP2. In the following part, we employ the new parameters to simulate the more complicated surface-supported nanopores. 3.1.2. Morphology of the Surface-Supported Network. We have already shown in Figure 1 that the default CVFF overestimates the interfacial interactions (NDI−Au and MEL−Au). Again, our modified CVFF reproduces MP2 results for both the optimal adsorption height of ∼3.0 Å and interfacial binding interactions −45 kcal/mol (NDI−Au) and −28 kcal/mol (MEL−Au). Although our modified CVFF gives better performance than the original parameters in description for NDI−Au interactions, it is still difficult to reproduce the MP2 binding energy accurately. Further works are desired to improve the NDI−Au interfacial parameters. When the bimolecular networks are adsorbed on the surface, the intermolecular interaction competes with interfacial interaction, determining the packing arrangement of the networks on the substrate. To study the preference of packing orientations of the NDI and MEL molecules on the surface, the rotation barrier is calculated with the adsorption height fixed at 3.0 Å and rotates around the [11̅0] axis of the Au(111) surface. DFT/M06 calculations show that the rotation energy surface is quite flat with an energy barrier less than 5.0 kcal/mol using the Au28 cluster model (Figure S7, Supporting Information). It agrees well with the potential surface that was obtained by vdW-DF calculations on the MEL/Au(111) system.63 The influence of interfacial interaction on the PTCDI−MEL bimolecular electronic density has also been reported on the Ag(111) surface.35 Interestingly, the intermolecular interaction 8528



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Figure 4. (a) Individual hydrogen bond strength and NBO analysis and (b) BSSE-corrected binding energies, obtained from GEBF-MP2//M06 calculations with the 6-31G(d) basis set (left) and modified CVFF and original CVFF (right) methods for hexagonal NDI/MEL networks, respectively.

A primitive unit cell with three NDI and two MEL molecules presents a molecular pattern of the hexagonal network. It can be clearly seen that the unit cell parameters, |a| = |b| = 28.0 ± 0.4 Å, averaged from the MD trajectories, are in good agreement with the experimental measurements of 28.0 ± 0.2 Å for vectors a and b.7 The angle γ between vectors a and b is 60 ± 5°, corresponding well to the experimental data of 58 ± 3°.7 Indeed, populations of the interatomic distance of RO···H and RH···N have peaks around 2.0 Å (Figure 5b). Typical

affected the tetrapyridylporphyrin arrangement on the Cu(111) surface, showing the increased diffusivity in the dimer.64 In comparison with these progresses, little is known about the details of the NDI−MEL nanopores adsorbed on the Au(111) surface. To further test the changes of NDI−MEL packing structures on the Au(111) surface, MD simulations were carried out on the NDI−MEL/Au(111) system. A snapshot of the packing conformation of the bicomponent nanopore on the Au(111) surface is shown in Figure 5a in a 2 × 2 super cell pattern. 8529



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Figure 5. Simulation results of the honeycomb porous NDI−MEL network on the Au(111) surface. The calculated unit cell vectors a and b and the angle γ are compared with the experimental results (shown in parentheses, ref 7). The statistic populations of the atomic distances and bond angles are shown in (b) and (c).

prevent the loss of assembly on the Au(111) surface. The hexagonal network is clearly seen when the thiols are further deposited into the surface-supported pores. The thiol molecules bend over and move horizontally in the porous structure of the networks. Both MP2 and modified CVFF calculations show that the interthiol strength increases in the order of AS (4.0 kcal/mol), BP3S (6.0 kcal/mol), and C12S (8.0 kcal/mol) in Figure 1b. MD simulations show that thiol chains tend to change from lying-down to standing-up orientations with the increase of chain coverage, shown in Figure 6. With the same number of thiols (n = 11/pore), AS is much more ordered than BP3S and C12S. When number of chains, n, increases, the thiol monolayer tends to stand up with much ordered orientation in BP3S and C12S SAMs. It can be featured from Figure 6 that the tilt angle, ω, which is defined as the angle between vectors S−Cend and the [111] axis, varies for the different thiol monolayers. In this way, the tilt angle changes between 0∼90° and −90∼0°, since it can bend to right- or left-hand sides, as shown from the side view in Figure 6. Especially, two typical orientations (standing-up and lying-down) of BP3S/C12S are also depicted in the side view of the snapshots, being ascribed to the intermolecular interaction between the aromatic rings/ alkane chain and π-conjugated template (discussed later in the next subsection). It shows that at lower coverage the tilt angle of thiols, ω, is distributed more widely than that at higher coverage (Figure 6 and Figure S8, Supporting Information). It was reported that the potential energy curve as a function of thiol alkane chain length on the Au(111) surface was flat at the same adsorption site.43 Therefore, it is interesting to survey how the flexibility of thiol molecules affects the packing structures in SAM-network/ Au(111) systems. Taking the “natural” chain length, L, as a reference, we define the flexibility index, δ, as

hydrogen bonding angles are also shown in Figure 5c by the high population of angles θO···H−N and θN−H···N around 170°. As expected, the pore size of the NDI−MEL hexagon, 28.0 Å in diameter, is smaller than that of the PTCDI−MEL template (34.6−34.7 Å).35 Is it possible to form an ordered monolayer in those smaller NDI−MEL pores? We will answer this question as follows. 3.2. Various Thiols on the Template/Au(111) Surface. 3.2.1. Au···S Interactions between Thiols and the Surface. When the SAM is grown in the NDI−MEL nanoporous networks, the interfacial interaction between the Au(111) surface and the thiol molecule is involved. On the basis of the Au31 cluster model, it is found that the Au···S interaction on the hcp site is much stronger than the top and bridge sites for AS and BP3S thiols (Figure S5b, Supporting Information), while the binding energies are almost the same on hcp and bridge sites for C12S. According to MP2 calculations, the adsorption height of the thiol molecules is about 1.9 Å on the hcp hollow site of the Au13 cluster model, shorter than those of about 2.5 Å on the top site. It has been reported from Tielens and Santons’ DFT/PBE calculations that a binding energy is about −31.1 kca/mol (−1.35 eV) in the Au···S chemsorption, and the adsorption length is 2.45 Å.32 It is also revealed from DFT/BLYP calculations that the interfacial interactions between S(CH2)11CH3 and the Au(111) surface are different on top and hcp (fcc) sites, with a Au···S bond length around 2.59 Å.43 As introduced in Section 2, the Morse function is adopted in this work to reproduce the shorter MP2 adsorption height of the thiol molecule on Au(111). In comparison with MP2 results, our modified CVFF gives a good description of both adsorption height and binding energy for thiol molecules on the Au(111) surface, as shown in Figure 2. 3.2.2. Morphology of SAMs. The fact that the network persists in the hexagonal structure indicates that triple hydrogen-bonding interactions between the NDI−MEL pair

δ = l /L 8530

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Figure 6. Snapshots of (a) AS, (b) BP3S, and (c) C12S molecules deposited in the NDI−MEL nanopores on the Au(111) surface. The tilt angle, ω, is the angle between the vector S−Cend and the [111] axis on the Au(111) surface, whose distributions are also given as a function of the surface coverage.

where l is the end-to-end length between S and ended C atoms in the deposited chain, and L is the natural S−Cend length before deposition. The statistic distributions of δ are shown in Figure 7, representing the different extents of bending and

stretching of thiols. The end-to-end length, l, in both BP3S and C12S molecules varies broadly, in contrast to a sharp peak at 4.8 Å in the S−Cend bond length distribution of the AS molecule in Figure S9 (Supporting Information). In other words, C12S and BP3S are more flexible than AS when they are deposited on the network/Au(111) surface. The value of δ in BP3S and C12S mostly distributes in the range 0.9−1.0, shorter than that in AS, indicating AS has been stretched more than BP3S and C12S. A close look at the geometry change in the terminal cage of AS (the height of cage, hcage, as shown in Figure S10, Supporting Information) displays that the hollow cages are horizontally squeezed by the closely packed neighboring thiols and the template. This may result in a slight vertical stretching of the AS cage from original 4.7 Å (before the attachment) to 4.8 Å (after being planted into the surface-supported nanopores). 3.2.3. Perturbations of Thiols on Template Geometry. As mentioned above, two packing conformations, standing-up and lying-down, of BP3S and C12S make them different from the stretched AS molecule at low coverage. Unlike the C12S thiol, there is a π···π stacking interaction between the benzene rings of BP3S and the aromatic rings of the template. Interactions between thiols (BP3S or C12S) and template (NDI or MEL) for these two orientations are calculated by our modified CVFF method. Furthermore, the interaction energies, sampled from the 1 ns snapshots of BP3S-networks and C12S-networks, are decomposed into vdW interactions, including dispersion (Edisp.(vdw)) and repulsion (Erep.(vdw)), electrostatic (Eelec.), and internal interactions (Ebond.), respectively. To make it easier to

Figure 7. Distributions of the flexibility of thiols, defined as the ratio between end-to-end, l, and “natural” molecular lengths, L (inset). 8531



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The hydrogen-bonding interactions in the hexagonal template are not significantly disrupted by the codeposition of thiol molecules. Since the Au−thiol interfacial and thiol− thiol interactions have not caused the significant reconstruction of the hexagonal porous network, the NDI−MEL is a good template for the guest-induced monolayer growth. Shown in Figure 9, however, there are still some perturbations on the porous network with the appearance of four typical pore sizes, I−IV, caused by guest molecular deposition. The network is nearly unchanged in hexagonal structure (type I), upon the AS thiols encapsulated. The displacement of the hexagonal framework is observed for BP3S deposition due to the π-stacking interaction. An asymmetry hexagonal pore (type III) observed

compare the contributions with each other, the absolute values in energy difference (more than 10 kcal/mol) are shown in Figure 8. For example, the difference in the dispersion energy between two conformations for BP3S packing on NDI is 37.8 kcal/mol, much larger than the difference (15.4 kcal/mol) in the repulsion part. Other contributions such as electrostatic and bonded terms are almost unchanged upon the configuration change from lying-down to standing-up. The BP3S monolayer tends to bend over the Au(111) surface with two benzene rings parallel to the surface due to the π-stacking interaction between the hexagonal network and BP3S molecules. Such a π-packing effect may be used in fabricating charge transfer for functional monolayers on the pore-templated surface.

Figure 8. Interaction energy between the packed BP3S/C12S molecule on NDI and MEL template molecules with the lying-down and standing-up conformations, respectively. The decomposition of total interaction energy into the vdW (dispersion and repulsion), electrostatic, and bonded interactions is also given.

Figure 9. Distortion of NDI−MEL nanopore structures induced by the thiol deposition. The size and proportion of the observed pore types I−IV are shown in the inset table. 8532



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network and binding energy using the generalized energy-based fragmentation (GEBF) approach in the Lower Scaling Quantum Chemistry (LSQC) package and two referees for their good suggestions. This work was supported by the National Basic Research Program (No. 2011CB808604), the National Natural Science Foundation of China (No. 20825312), and the Specialized Research Fund for the Doctoral Program of Higher Education of China (20100091110024). The authors gratefully thank the High Performance Computing Center of Nanjing University for providing the IBM Blade cluster system and Dr. Debra H. Biasca for her scientific writing course at the University of Colorado.

for the template after the BP3S and C12S deposition was probably caused by a dispersion interaction between thiols and the template. When the coverage increases to n = 23/pore for C12S, the framework of the hexagonal structure tends to expand with the hexagon arm increased from 17.5 to 18.0 Å (as in type IV) by the intermolecular interaction between the template and the “crowd” guest thiols.

4. CONCLUSIONS The NDI−MEL bimolecular network is used as the template when other guest molecules are adsorbed on the Au(111) surface. The interfacial interactions on the Au(111) surface and intermolecular interactions are investigated by using both quantum mechanics and molecular mechanics calculations. Force field parameters of intermolecular and interfacial interactions are modified to reproduce the MP2 adsorption height and binding energies within the CVFF framework. Hydrogen-bonding interaction between NDI and MEL molecules is crucial in the formation of a stable honeycomb template. It was shown that the N−H···N interaction is much stronger than the O···H−N contact. The arrangement of the NDI−MEL bimolecular network is displayed by the modified force field in MD simulations. The simulation morphology is in good agreement with the experimental results. The deposition of guest thiols into the pore template is affected by the chain flexibility and coverage. The vdW interaction (especially the dispersion part) between the guests and π-conjugated template results in two typical (standing-up and lying-down) orientations of BP3S and C12S SAMs. Conversely, thiol-based SAMs also disturb the arrangement of the porous network. The understanding of the intermolecular and interfacial interactions is helpful to control the template-based molecular building blocks on the surface in electro-optics technology.

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ASSOCIATED CONTENT

S Supporting Information *

Figure S1 gives atomic type of force field and partial charges in NDI and MEL molecules, and Figure S2 presents the optimized structures of NDI, MEL, and thiol molecules. Figures S3−S5 show binding energy curves between NDI/MEL/thiols and different Au cluster (Au7, Au13, Au18, Au23, and Au31) models by MP2 and DFT methods. Figure S6 shows NDI−NDI, MEL− MEL, and NDI−MEL pairs and the model systems constructed for estimating the strength of O···H−N and N−H···N hydrogen bonds, respectively. Figure S7 displays the rotation barrier of the NDI and MEL molecules on the Au28 cluster model by DFT/M06. Snapshots for BP3S and C12S at different coverages are illustrated in Figure S8. Distribution of end-toend length, l, for thiols is shown in Figure S9. The statistic analysis of the terminal cage height, hcage, and the attached bond length, S−Cend, is shown in Figure S10. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We sincerely thank Dr. Shugui Hua and Professor Shuhua Li for their help in obtaining the optimized hexagonal NDI/MEL 8533



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Modulating Morphology of Thiol-Based Monolayers in Honeycomb

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