Atomic-Resolution Kinked Structure of an ... - ACS Publications

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Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite Yiing Chin,† Dwi Panduwinata,† Maxine Sintic,† Tze Jing Sum,† Noel S. Hush,†,‡ Maxwell J. Crossley,† and Jeffrey R. Reimers*,† †

School of Chemistry, The University of Sydney, NSW 2006, Australia, and ‡School of Biomolecular Sciences, The University of Sydney, NSW 2006, Australia

ABSTRACT The atomic structure of the chains of an alkyl porphyrin (5,10,15,20tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for porphyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible. A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and, of the many possible atomic structures modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains. SECTION Surfaces, Interfaces, Catalysis elf-assembled monolayers (SAMs) may be useful in next-generation electronic devices, as ordered organic layers tailor surface properties and template the growth of nanostructured materials.1-8 Porphyrins are readily suited to device applications owing to their stability, synthetic flexibility, low-lying energy levels, and strong optical absorption, and a variety of porphyrin SAMs have been assembled on highly ordered pyrolytic graphite (HOPG), gold, and other substrates. Many substituents, including aromatic rings and alkyl chains, as well as pyrrolic-ring annulation are introduced to the basic porphyrin skeleton to enhance porphyrinsurface interactions. High-resolution scanning tunneling microscopy (STM) images for systems involving alkyl chains typically reveal little more than the chain direction.8-20 To tailor porphyrins for specific purposes, however, greater details of the surface packing are required, features that can be readily observed in other systems.1,2,21-32 We present high-resolution STM images for 5,10,15,20tetranonadecylporphyrin (Chart 1) at the solid/liquid interface of HOPG and 1-phenyloctane, obtaining atomic resolution for the alkyl chains which, when combined with extensive calculations of the monolayer structure and STM image, allows for the first time the determination of the full atomic structure of an alkyl porphyrin monolayer. 5,10,15,20-Tetranonadecylporphyrin was synthesized in gram amounts by the method of Crossley et al.33 Three droplets of a 4 mM solution in distilled 1-phenyloctane were deposited on freshly cleaved HOPG (SPI Supplies) using a pipet, and STM measurements were conducted in constantcurrent mode under ambient conditions using a PicoPlus STM (Agilent Technologies), with the STM tips prepared from

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r 2010 American Chemical Society

Chart 1. 5,10,15,20-Tetranonadecylporphyrin

mechanically cut Pt/Ir (80:20) wire of diameter 0.2 mm (SPI Supplies). STM image simulations were performed using density functional theory (DFT) and the Tersoff-Hamann approximation34 at a bias voltage of 0.8 V. The VASP package35,36 was used for this purpose, employing the PW91 density functional,37 ultrasoft pseudopotentials38,39 with plane-wave cutoff set to the standard value for N, 287 eV, two atomic layers of carbon in a cell of height 25 Å, and k-point sampling at only the Γ point. Optimized coordinates for the monolayer were determined considering a wide range of possible alternative conformations for the porphyrin chains. A control program called GAUSSIAN-0940 to evaluate the intramolecular energy and forces using the ONIOM method41 in which the porphyrin macrocycle and first 7 CH2 units of each alkyl chain are treated at the B3LYP/6-31G* level42,43 while the remaining atoms are treated using the AMBER force field.44 This intramolecular term is then added to intermolecular contributions Received Date: November 11, 2010 Accepted Date: December 13, 2010 Published on Web Date: December 22, 2010

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DOI: 10.1021/jz101529t |J. Phys. Chem. Lett. 2011, 2, 62–66

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evaluated using the AMBER force field with periodic imaging combined with a specific HOPG-alkane potential45 that gives results similar to related models.21,46-50 An observed STM image is shown in Figure 1. During this scan, the bias voltage was changed51 so that different vertical regions of the image reveal both the underlying HOPG and the SAM. A graphite lattice is then overlaid and fitted to the graphite section and extended over the entire image, allowing ^ between the x and y the scan x-length, y-length, and angle xOy axes to be determined based on the known graphite-lattice vector length of 2.46 Å and angle of 120°. Another set of lattice vectors are then fitted to the porphyrin lattice and the lattice-parameters extracted using the deduced scan x-length,

y-length, and angle. No indication of nonlinearity in the scans was detected, allowing the entire scan area to be effectively used to determine the lattice parameters. The results are given in Table 1, including error bars determined by averaging over 35 different measurements. While the internal calibration procedure corrects for drift of the STM tip, results are also presented averaged over scans in both the up and down directions and found to be in good agreement. In Table 1 the lattice parameters are expressed in terms of the vector lengths a and b, the angle θ between these vectors, and the angle R between the b vector and the graphite [110] lattice vector, as defined in Figure 1. Spots are observed covering the regions away from the porphyrin macrocycle that form in a pattern similar to that expected for the graphite substrate. While indeed scans can be obtained in which the

^ = 84°) topography Figure 1. Observed STM (88 Å 81 Å, xOy image of 5,10,15,20-tetranonadecylporphyrin on HOPG at a setpoint current of 36 pA and alternating bias voltages during topdown scanning from -450 mV (top part) to 50 mV (middle part) to -451 mV (bottom part). Superimposed lattice vectors for the HOPG (doubled, yellow) and porphyrin (red) are then fitted to the image.

^ = 84°) topography Figure 2. Observed STM (88 Å 81 Å, xOy image of 5,10,15,20-tetranonadecylporphyrin on HOPG at a setpoint current of 8 pA and a bias voltages of -683 mV. Superimposed is the fitted adsorbate lattice vectors (yellow).

Table 1. Observed, Best-Fit Graphite, and Calculated Lattice Parameters for 5,10,15,20-Tetranonadecylporphyrin on HOPGa a

method

b

θ

R

area

ΔE

obs. 17 down scans

21.9 ( 0.5

33.6 ( 0.4

49.2 ( 1.9

10.3 ( 0.3

557 ( 9

-

obs. 18 up scans

21.4 ( 0.4

34.0 ( 0.7

49.6 ( 1.8

10.2 ( 0.7

552 ( 9

-

obs. total

21.7 ( 0.5

33.8 ( 0.6

49.4 ( 1.8

10.2 ( 0.6

554 ( 9

-

flat udd/udd

20.7

33.3

52.6

9.6

549

-195

flat udd/udd (obs)b flat udd/udd (gr)c

21.9 22.1

33.6 33.8

49.2 49.1

8.9 10.9

551 564

-191 -184

flat uud/udd

19.7

33.7

57.1

9.3

558

-187

flat udd/ddd

20.7

33.5

53.6

11.4

559

-174

upright uud/uud

16.6

31.9

79.3

17.1

521

-187

upright uud/uuu

18.4

32.7

57.5

9.6

509

-175

-1 b

Lattice vector lengths a and b in Å, area in Å , angle θ and alignment angle R in degrees, binding energy ΔE in kcal mol . At observed structure from down scans. c At a graphite-commensurate structure for STM image simulation. a

2


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Figure 4. Calculated configurations of the turns from the lowenergy structures optimized for 5,10,15,20-tetranonylporphyrin on HOPG. The second, third, and fourth C atoms of each alkyl chain are highlighted in green, while the last 11 (horizontally oriented) CH2 units of each chain are not shown for clarity.

All four alkyl chains lie on the surface, in contrast to the only results observed for an analogous system, 5,10,15,20tetradodecylporphyrin on HOPG, in which two of the chains are not detected and are presumed to orientate into the solution;15 consequently, the observed molecular area of 554 ( 9 Å2 is 50% larger than would be expected based on this other structure. The high-resolution image shown in Figure 2 indicates that each adsorbate molecule has C2 symmetry. It is, however, unclear as to which porphyrin macrocycle each alkyl chain is attached, and it is also unclear as to why the images of the macrocyle cores do not show 4-fold symmetry. Gas-phase B3LYP/6-31G* optimized structures of the porphyrin indicate that the alkyl chains are not coplanar with the porphyrin but instead head away, producing a table-like structure or its variants. Kinks involving gauche chain conformations are thus required to produce the observed SAMs, and a wide range of possible structures were considered computationally. These are categorized as to whether the second, third, and fourth atoms in the chain are up located above the porphyrin plane (u) or down in it (d). Further, as the porphyrins have C2 symmetry, two different types of kinks may simultaneously be involved. Results for the 5 lowest-energy structures identified are presented in Table 1 while the kink patterns for four of these structures are shown in Figure 4. Figure 5 illustrates the observed and calculated surface-cell lattices. The lowest-energy structure optimized in the calculations has lattice parameters in good agreement with the experimental data, and it is this structure that is overlaid upon the experimental image in Figure 3; its kinks are both of “udd” type, meaning that the second carbon is located above the porphyrin plane with the next two atoms starting the flat-lying region. Its simulated STM image is also shown in Figure 3 and is in excellent agreement with the observed image. Compared to the lowest-energy “flat udd/udd” structure, the “flat uud/udd” structure reported in Table 1 and Figures 3-5 has its chains connected to different porphyrins. However, the

Figure 3. An extract of the observed STM image of 5,10,15,20tetranonylporphyrin on HOPG from Figure 2, after conversion to orthogonal coordinates is compared to three DFT-calculated STM images for optimized structures with graphite-commensurate lattices. The molecular structures are overlaid on the calculated images, with the “Flat uud/uud” structure also overlaid on the observed image.

porphyrin macrocycle and the substrate are simultaneously imaged, the overlays on Figure 1 indicate that this pattern is subtly different and arises instead from the alkyl chains. These chains clearly align in the [110] direction, as reported for similar SAMs,15 with an average spacing (in the orthogonal [112] direction) between the chains of 4.66 ( 0.11 Å. This value is typical of that for flat-lying alkyl chains and is much larger than that typical for upright chains (ca. 4.1-4.2 Å);47,50 the appearance of two parallel sets of spots per chain, highlighted in the higher resolution image shown in Figure 2, is also usually taken as being an indication of flat alignment. Calculated STM images for chains with both upright and flat alignment are shown in Figure 3, along with an appropriately orthogonalized and aligned extract from the observed image in Figure 2, with superimposed molecular structures. The hydrogen atoms, not the carbon atoms, are shown to act as the tunneling-current conduit,52,53 with two sets of spots produced for both upright and flat alignment. However, quantitative differences in the patterns indicate that indeed the chains lie flat on the surface.


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Figure 5. The observed graphite lattice (black lines, 2.46 Å spacing) and 5,10,15,20-tetranonadecylporphyrin lattice (circles indicating uncertainty) are compared with the calculated lattice vectors for the flat udd/udd lattice (blue), flat uud/udd lattice (green), flat udd/ddd lattice (red), upright uud/uud lattice (magenta), and upright uud/uuu lattice (brown).

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optimized lattice parameters are inconsistent with the observed ones, its simulated STM image does not match, and its calculated energy is 8 kcal mol-1 higher. The “flat udd/ddd” structure, with just one set of kinks, has realistic lattice parameters, but its energy is 21 kcal mol-1 higher than “flat udd/ udd”, and its simulated STM image does not match. The “upright uud/uud” and “upright uud/uuu” SAMs are much more densely packed and so have inconsistent lattice parameters; also their calculated energies are 8-20 kcal mol-1 higher, and their calculated STM images are inconsistent with experiment. In summary, high-resolution STM imaging, including detailed instrument calibration and error determinations, when combined with high-level structural and image simulations, indicate that only one atomic structure of the alkyl chains is viable, the one calculated to be of lowest energy. Hence, for the first time, the atomic structure of an alkylporphyrin SAM is determined.

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SUPPORTING INFORMATION AVAILABLE Descriptions of the synthesis and characterization of 5,10,15,20-tetranonadecylporphyrin and the calculated coordinates for the SAMs described in Table 1. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION Corresponding Author:

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*Authors to whom correspondence should be sent. Author e-mail address: [email protected]. (17)

ACKNOWLEDGMENT We thank the Australian Research Council for funding this work and the Australia Partnership for Advanced Computing (APAC) for computational resources.

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