Coexistence of Homochiral and Heterochiral Adenine Domains at the

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Coexistence of Homochiral and Heterochiral Adenine Domains at the Liquid/Solid Interface Wael Mamdouh,*,† Mingdong Dong,† Ross E. A. Kelly,‡,£ Lev N. Kantorovich,‡ and Flemming Besenbacher*,† Interdisciplinary Nanoscience Center (iNANO), and Centre for DNA Nanotechnology (CDNA), and Department of Physics and Astronomy, UniVersity of Aarhus, DK-8000 Arhus C, Denmark, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London, U.K., WC2R 2LS ReceiVed: August 17, 2007; In Final Form: September 19, 2007

In this work, the self-assembly of the DNA base molecule adenine (A) is imaged with high-resolution scanning tunneling microscopy (STM) at the liquid (1-octanol)/solid (HOPG) interface at room temperature. Rather surprisingly, the STM results reveal, for the first time, the spontaneous formation of two coexisting distinct (homo- and heterochiral) domains of adenine, which are formed at the liquid/solid interface without changing any experimental conditions. Ab initio density functional theory (DFT) calculations support our STM findings and suggest the existence of various A networks of nearly similar stability that all are constructed from the most stable A dimer.

1. Introduction The expression of two-dimensional 2D molecular chirality of chiral or prochiral building blocks upon adsorption on surfaces has been a topic of extensive research in recent years,1 with considerable impact on biology and medicine.2 In particular, many biological species have characteristic chiral properties which make them suitable candidates for targeting specific drugs with high precision,3 in addition to their unique properties in enantioselective heterogeneous catalysis4 or nonlinear optics.5 Scanning tunneling microscopy (STM) offers a unique capability to recognize the chiral properties of individual adsorbed molecules on solid supports,6 and also, the nucleation and growth of crystalline chiral phases can be followed in great detail with atomic resolution.1,7 Generally, molecular adsorption on a surface always leads to a certain preferable orientation of the molecules with respect to the symmetry of the surface lattice, and8 therefore, surfaces can induce chirality in otherwise achiral molecules,9 resulting in the formation of distinct homochiral species, for example, 1D arrangements,10 2D extended domains,11 and 3D clusters,1,12,13 In this context, the adsorption of nucleic acid-base molecules, the basic building blocks of DNA, has recently been studied extensively experimentally as well as theoretically,14-18 leading to a wide variety of supramolecular structures. Moreover, it is of great importance to investigate the expression of molecular chirality of DNA bases on 2D surfaces since this may lead to the formation of supramolecular complex patterns and * To whom correspondence should be addressed. E-mail: [email protected] (W.M.); [email protected] (F.B.). † University of Aarhus. ‡ King’s College London. £ Present address: Department of Physics and Astronomy, University College London, Gower Street, London, U.K., WC1E 6BT.

10.1021/jp076623h CCC: $37.00

nanoscale structures that may have applications in a variety of fields such as directed drug design and the design of bioactive surfaces. 2. Experimental and Computational Section The STM experiments were performed at the liquid (1octanol)/solid (highly oriented pyrolytic graphite (HOPG)) interface under ambient conditions at room temperature using a Multimode SPM system with a Nanoscope IIIa controller (Veeco Instruments Inc., Santa Barbara, CA). STM tips were mechanically cut from a 0.25 mm Pt/Ir (80/20%) wire and tested on freshly cleaved HOPG surfaces (HOPG, grades ZYA and ZYB, Advanced Ceramics Inc., Cleveland, OH and NT-MDT, respectively). Prior to imaging, adenine (Sigma Aldrich, 99% purity) was dissolved in 1-octanol (Sigma Aldrich 99%) at a concentration of 0.7 mg/1gr, and a drop of the solution was applied onto a freshly cleaved surface of HOPG. The STM tip was immersed in the solution, and images were recorded at the 1-octanol/graphite interface. HOPG is used as the convenient substrate for adsorbing A molecules, because it is chemically inert, has a smooth and flat surface, and its cleaning and cleaving procedures are rather easily performed as compared to those for other surfaces.19 Several tips and HOPG samples were used to ensure that reproducible results were obtained and to avoid any artifacts related to the STM imaging. The STM images were recorded in constant height mode. For a proper unit cell calibration of the adenine STM recorded structures, the molecular STM images were subsequently followed by imaging the underlying graphite substrate under the same experimental conditions by lowering the bias voltage. The STM images were analyzed using the Scanning Probe Image Processor (SPIP) software program (Image Metrology ApS, Lyngby, Denmark),20 and the STM images were corrected for any drift using the recorded graphite © 2007 American Chemical Society

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J. Phys. Chem. B, Vol. 111, No. 42, 2007 12049

calibration images, which allowed us to determine the unit cells accurately. Furthermore, the correlation averaging method20,21 was used for the more-detailed image analysis and for the display of the high-resolution STM images. We always investigated very thoroughly that this method did not affect the unit cell parameters. The imaging parameters (the tunneling current, Itunn, and the sample bias voltage, Vbias) are stated in the Figure captions. The ab initio DFT SIESTA method22 was used to calculate numerous A networks, which were considered in the gas phase. Briefly, the code uses a localized numerical atomic orbital basis set, periodic boundary conditions, and pseudopotentials. In all calculations, the DZP (double-ζ plus polarization orbitals) basis set was used, with the energy cutoff of 10 meV. We found that the large size of the basis set is essential in order to obtain realistic bonding between molecules. The Perdew, Becke, and Ernzerhof (PBE)23 density functional method was used for the exchange and correlation energies. Atomic relaxation was performed until the forces on each atom were not larger than 0.05 eV/Å. Only one (gamma) k point was required for these calculations. As in previous theoretical studies,14,15 we find that the basis set superposition error (BSSE) corrections are essential to obtain reliable energetics in the localized basis set calculations. These corrections have been calculated by the standard Boys-Bernardi counterpoise correction method.24 This ab initio technique has been extensively tested for DNA and RNA homopairs15 and a large selection of heteropairs25 involving DNA and RNA bases by comparing with high-level quantum chemistry (QC) calculations.26 The stability of various A networks, all formed using the very stable A dimer as the fundamental building block (AA1, stabilization energy -0.86 eV, shown in Figure 1),15a has been calculated theoretically and compared with experimentally observed structures. All proposed structural models have space group symmetry p2, except for model B, which has p2gg. Note that these structural models were proposed previously but relaxed using semiclassical methods,14d which we consider to be less accurate. Models A and B have been reported previously by several groups as the most stable possible structural A network models, which could explain the molecular arrangements of adenine observed on a variety of different surfaces.14,16

Figure 1. Top panel: the structure of the AA1 dimer and its mirrorimage; the mirror symmetry plane is indicated by a dashed vertical line. High-resolution correlation averaged STM images of physisorbed adlayers of adenine at the 1-octanol/graphite interface: (A) and (C) large-scale STM images with zoom-in areas each indicated by white squares with the letters B and D, respectively, which are shown at higher resolution in the right panel. The tunneling parameters are Itunn) 1.58 nA, Vbias) -804.0 mV (A,B) and Itunn) 1.58 nA, Vbias) -981.6 mV (C,D). The main graphite axes are illustrated by red arrows superimposed on (A). Adenine dimers of either chirality are shown by solid (dashed) ovals (see the definitions in the top panel), with the corresponding arrows inside of the ovals indicating individual molecules. The mirror-images chains and domains are indicated by solid (dashed) white arrows, respectively. The unit cells are indicated in red. Molecular models are superimposed on the STM images in (B) and (D).

3. Results and Discussion In this report, the self-assembly of the DNA base molecule adenine (A) is imaged with high-resolution STM at the liquid (1-octanol)/solid (HOPG) interface at room temperature. Rather surprisingly, the STM images in Figure 1 reveal, for the first time, the spontaneous formation of two coexisting distinct (homo- and heterochiral) domains of A structures at the liquid/ solid interface. Figure 1A and C depicts large-scale STM images in which the coexisting homochiral and heterochiral domains, respectively, are clearly distinguishable. Each structure appears with different orientations due to the commensurability of the domains with respect to the graphite lattice axes (indicated by red arrows superimposed in Figure 1A). High-resolution STM images of the depicted white square regions are shown in Figure 1B and D, respectively. The STM images in Figure 1A and B show a molecular packing corresponding to model A of Figure 2A, whereas Figure 1C and D shows a molecular packing that is similar to that of model B in Figure 2B. The corresponding molecular models are superimposed on the STM images, the unit cells are indicated in red, and AA1 dimers are illustrated with ovals for convenience. The structure of the AA1 dimer and its mirror-image are shown in the top panel in Figure 1. Each AA1 dimer is illustrated

by an oval (solid or dashed) with two opposite arrows inside of each oval representing each A molecule. The direction of each arrow inside of an oval is drawn from the six-membered ring to the five-membered ring of the corresponding A molecule. Note that the AA1 dimers possess C2 symmetry due to the 180° rotational axis, which is perpendicular to the AA1 dimer plane and is passing through its center. The dashed ovals (lines) represent the enantiomer (mirror-image) geometry of the AA1 dimer. Upon adsorption of the A molecules on a surface, they adopt a certain orientation mediated by a subtle balance between the A-A and A-substrate interactions. Several domains can clearly be distinguished in the large-scale STM images in Figure 1A and C, from which the registry of the adenine molecules with the substrate underneath can be revealed. When all AA1 dimers adopt the same orientation on the surface, a homochiral domain is formed. Note that the unit cell consists of one dimer (see Figure 1B). However, each domain is equally possible, as illustrated in Figure 1A and B where the domains are seen to pack beside each other. However, heterochiral domains also form, as shown in Figure 1C and D, and their orientation can also be clearly distinguished, as indicated by the solid/dashed white arrows. Figure 1C shows two mirror-image heterochiral domains.

12050 J. Phys. Chem. B, Vol. 111, No. 42, 2007

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Figure 2. Left panels: structural models A, B, C, and D corresponding to ab initio DFT fully relaxed A networks with the unit cells and the corresponding lattice vectors a and b indicated in red. Right panels: schematic representation of the calculated models shown. It is seen that the four presented A networks have different unit cells. Characteristics of each monolayer are given in Table 1.

We would like to stress that the observed A network structures depicted in Figure 1 do not result from any STM tip effects or from any change in the scan angle, as has been reported previously.27 Indeed, the scan angle was not altered during scanning to avoid any influence on the A molecular network. Ab initio DFT calculations suggest the existence of various A networks of very similar stability that all are constructed from A dimers, which are found to be the most stable building block. Note that a total of 21 possible adenine dimers have been reported previously.15a If A networks in which A molecules form the basic building block are considered, over a thousand gasphase A networks can be generated.14a However, if we only

consider the most-favorable A dimer (AA1 shown in Figure 1) as the fundamental building block for constructing A networks, then a much smaller number exists. By considering various chiral arrangements of the A dimers within the supramolecular networks and different numbers of A dimers in the unit cell, it is possible to construct systematically various homo- and heterochiral molecular networks. In Figure 2, the results of the ab initio DFT calculations (using SIESTA)22 of the four possible structures considered here (structural models A, B, C, and D) corresponding to unit cells containing up to four AA1 dimers are depicted. The ab initio DFT results reveal, surprisingly, that all of these A networks have extremely similar stabilities and lattice vectors and thus are very likely to coexist (See in Table 1). In model A (Figures 1A,B and 2A), all AA1 dimers have the same organizational chirality on the surface as that in a homochiral domain. However, in models B (Figures 1C,D and 2B) and C (Figure 2C), the adenine enantiomers pack alternatively inside of a 2D A network and coexist in the same domains as in heterochiral domains. In model D in Figure 2D, only one dimer in the four-dimer unit cell has the mirror-image symmetry of the rest of the dimers in the same unit cell. Although the number of A molecules per unit cell in each of the four proposed models is different (except in models B and C), these structural models have extremely similar stabilities and lattice parameters (see Table 1). We therefore conclude that based on the ab initio DFT calculations, it is very likely that these structures coexist, as observed experimentally. The lattice parameters determined from the STM images are found to be a ) 1.0 ( 0.1 nm, b ) 0.9 ( 0.2 nm, and γ ) 69 ( 2° for model A and a ) 2.2 ( 0.2 nm, b ) 0.8 ( 0.1 nm, and γ ) 76 ( 2.3° for model B, as shown in Table 1. The former structure (Figures 1B and 2A) corresponds to the unit cell of the smallest. The four A networks presented in Figure 2 were superimposed on the STM images, and it was found that, in particular, models A and B fit perfectly to the STM images. However, due to the limitation of the STM technique and the insufficient contrast in the rest of the STM images, models C and D in Figure 2 have not yet been uniquely identified. However, it should be pointed out that any AA1 dimer chosen randomly in any of the four A networks can have a different orientation without affecting its hydrogen bonding “abilities” with respect to the four neighboring A dimers. For instance, by comparing the molecular models in Figure 2A and D, a single AA1 dimer with a different orientation is still “connected” to each of its four neighbors by two N-H-N bonds of similar stability. Such defects can be formed anywhere in either of the periodic networks, leading to a completely disordered adenine monolayer in which every A dimer is still connected to four adjacent A dimers via highly stable hydrogen bonds, and average distances between A dimers are not strongly effected. From these simple arguments, we conclude that a wide variety of molecular

TABLE 1: Lattice Parameters and Stabilization Energies of the A Network Possibilities

a

monolayer

number of molecules in unit cell

Aa

2

Ba

4

Ca D

4 8

a (nm)

lattice parameters b (nm)

γ (°)

1.14 (1.0 ( 0.1)b 2.38 (2.2 ( 0.2)b 1.18 2.41

0.86 (0.9 ( 0.2)b 0.85 (0.8 ( 0.1)b 1.74 1.72

73.7 (69 ( 2°)b 69.0 (76 ( 2.3°)b 68.4 66.3

These monolayers have been considered earlier.14c

b

The values obtained from the STM images.

stabilization energy (eV) per eight molecules -7.04 -7.42 -6.78 -7.02

Letters structures, all having similar geometrical parameters, may coexist on the surface without affecting the overall molecular network stability. Chiral phase transition has recently been shown to exist where homochiral phases are present exclusively until a critical coverage is reached and the transition to the new heterochiral phase is completed within a very narrow coverage range.28 In another study, it has been reported that nitronaphthalene molecules form 1D homochiral double chains at low surface coverage, while by increasing the coverage, a racemate structure where the homochiral and heterochiral phases coexist gradually develops.10g Furthermore, 2D lattice structures formed by racemic tartaric acid on a single crystalline Cu(110) surface have been studied and compared with the enantiopure lattices. At low coverage, the doubly deprotonated bitartrate species is separated into 2D conglomerates showing opposite enantiomorphism. At higher coverage, however, a singly deprotonated monotartrate species forms a heterochiral, racemic crystal lattice.29 Moreover, DFT calculations have previously been used to examine dense adlayers of glycine and alanine adsorbed on two flat Cu surfaces. Cu(110) and Cu(100) presented a fascinating view of the diverse phenomena that can occur when amino acids are deposited on metal surfaces; glycine adopts a single adlayer structure on Cu(110), but two distinct glycine structures will coexist on Cu(100). These calculations also allowed predicting of the fate of racemic mixtures of adsorbed alanine in terms of the local chirality of the resulting adlayers.30 However, in our case, the coexistence of adenine homochiral and heterochiral domains is observed spontaneously at the liquid/ solid interface, without changing any experimental parameters. Note that the homochiral network has also been observed on Ag-terminated Si(111),14c whereas the heterochiral network has been observed on HOPG in air16d,16f,27 and Cu(111).16a,16b The present liquid/solid interface offers a great possibility for observing the 2D molecular chirality of adenine, where all A molecules achieve optimum stability, both thermodynamically and kinetically, upon adsorption onto the HOPG substrate. Indeed, the A molecules can move freely around in the liquid, allowing some of the AA1 dimers to adopt a certain chiral orientation on the surface, while other AA1 dimers adopt a different orientation (mirror-image) inside of the same 2D molecular network structure. This may explain the spontaneous coexistence of the homochiral and heterochiral A network domains which could be formed and imaged on HOPG at the liquid/solid interface. 4. Conclusions In summary, we have observed by high-resolution STM the coexistence of two distinct homo- and heterochiral domains of adenine adlayers that spontaneously form upon adsorption from 1-octanol solution onto a graphite surface at the liquid/solid interface. Ab initio DFT calculations support our STM findings and suggest the existence of various A networks of nearly similar stability that all are constructed from A dimers, which are found to be the most stable building block. The spontaneous selfassembly of coexisting homochiral and heterochiral domains of adenine molecules in 2D assemblies opens new ways to explore molecular design and surface architecture in a bottomup approach, which may lead to the design of novel 2D supramolecular nanostructures, for applications in enantioselective heterogeneous catalysis, chiral separation, chiral recognition, biocompatibility, and bioactive surfaces. Acknowledgment. The authors acknowledge financial support from the Danish Ministry for Science, Technology, and

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