Directed Assembly of End-Functionalized Single Wall Carbon

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Directed assembly of end-functionalized single wall carbon nanotube segments Erika Penzo, Matteo Palma, Risheng Wang, Haogang Cai, Ming Zheng, and Shalom J. Wind Nano Lett., Just Accepted Manuscript • DOI: 10.1021/acs.nanolett.5b02220 • Publication Date (Web): 04 Sep 2015 Downloaded from http://pubs.acs.org on September 8, 2015

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Directed assembly of end-functionalized single wall carbon nanotube segments Erika Penzo1, Matteo Palma1,†, Risheng Wang2,†, Haogang Cai3, Ming Zheng4, and Shalom J. Wind1* 1

Department of Applied Physics and Applied Mathematics, Columbia University, New York,

NY, USA; 2Department of Chemistry, Columbia University, New York, NY, USA; †Present address: Department of Chemistry & Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK; ††Present address: Department of Chemistry, Missouri University of Science & Technology, Rolla, MO, USA; 2Department of Mechanical Engineering, Columbia University, New York, NY, USA; 4National Institute of Standards and Technology, Gaithersburgh, MD, USA. *Corresponding Author: [email protected] KEYWORDS: carbon nanotubes; directed assembly; DNA assembly; multivalent binding.

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ABSTRACT: A key impediment to the implementation of a nanoelectronics technology based on single wall carbon nanotubes (SWCNTs) is the inability to arrange them in a manner suitable for integration into complex circuits. As a step toward addressing this problem, we explore the binding of fixed-length, end-functionalized SWCNT segments to lithographically-defined nanoscale anchors, such that individual SWCNTs can be placed with control over position and orientation. Both monovalent and bivalent binding are explored using covalent and non-covalent binding chemistries. Placement efficiency is assessed in terms of overall yield of SWCNT binding, as well as binding specificity and the degree of non-specific binding. Placement yields as high as 93% and 79% are achieved, respectively, for covalent binding and for binding through DNA hybridization. Orientational control of the SWCNT segments is achieved with 95% and 51% efficiency for monovalent and bivalent binding respectively. This represents a new approach that could pave the way toward complex SWCNT devices and circuits.


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Single wall carbon nanotubes (SWCNTs) have long been recognized for their outstanding electronic properties. Within only a few short years of the first demonstrations of electronic switching in SWCNTs,1, 2 examples of high transconductance transistors3-6 proved the potential of SWCNTs for high performance nanoelectronics, with even relatively crude SWCNT field effect transistors outperforming advanced devices built in silicon.5, 7, 8 Since that time, however, little progress has been made in the creation of complex SWCNT circuits, although, notably, all the critical elements of a SWCNT-based computer have been demonstrated9, which provides strong motivation for seeking ways to advance the development of such circuits. The obstacles to building complex SWCNT circuits are well known, chief among them being difficulties in obtaining purely semiconducting tubes of a given diameter and the inability thus far to arrange SWCNTs into circuit-amenable topologies on surfaces, such that they can be wired into circuits. To be sure, there has been great progress in purifying SWCNTs by type, diameter and even individual chirality by such means as density-gradient ultracentrifugation,10 column chromatorgraphy,11 and recently, aqueous two-phase (ATP) extraction.12-15 Some of these methods are capable of achieving up to 99.9% pure semiconductor or metallic SWCNT solutions.11 It is expected that improvements will continue to be realized until the required 0.0001% purity7 is attained. Progress on SWCNT patterning has not been quite as impressive. Whilst aligned growth of SWCNTs on mis-cut quartz16-19 and sapphire20, 21 substrates, along with transfer onto oxidized silicon substrates,22, 23 may provide a viable route to circuit creation if sufficient density can be achieved7 (indeed, the work by Shulaker et al.9 employed precisely that technique), however this places severe constraints on circuit layout, and, as pointed out above, complex circuit topologies have yet to be demonstrated with this method. Previous directed assembly techniques24-27 have


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not demonstrated the ability of organizing SWCNTs into ordered arrays with single nanotube control. In this work we explore a new approach to the rational organization of individual SWCNTs on surfaces with precise control over location and orientation. Ultrahigh resolution lithographic patterning is combined with selective chemical and biochemical functionalization, enabling the assembly of SWCNTs by means of molecular and/or biomolecular recognition. DNA-wrapped, fixed-length28 SWCNT segments are selectively functionalized at their ends to bind to molecular-scale, chemically functionalized metallic anchors created by nanoimprint lithography with self-aligned pattern transfer.29 This technique is based, in part, upon the approach demonstrated in our earlier work with a one-dimensional DNA rod30 (when applied to SWCNTs, however, additional factors, such as end-functionalization chemistry, SWCNT segment length and solution chemistry must be considered, as will be described below). Here, two binding schemes are considered, yielding different degrees of control over the position and the orientation of the SWCNT segments. In one scheme, referred to here as “monovalent binding,” the SWCNTs are bound at one end to the anchor sites. Capillary force drying yields arrays of SWCNTs all oriented in the same direction (Figure 1). A second scheme, termed “bivalent binding,” is also explored. In this scheme, molecular-scale binding sites are patterned in pairs (dimers), with the intra-dimer distance designed to match the average length of the SWCNT segments, so as to maximize the probability of attaching the two functionalized ends of each SWCNT segment to the two binding sites in the dimer, resulting in the control of the orientation of each SWCNT segment on a substrate on an individual basis (Figures 2 and 3). This approach can facilitate the organization of SWCNTs in a variety of topologies (i.e., the position and orientation of each SWCNT segment can be independently determined). The effects of different


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binding chemistries are studied, and we find that a covalent binding chemistry is best suited for monovalent binding, whereas bivalent binding is increased when DNA hybridization, a weaker linking chemistry, is employed. Silicon substrates with thermally grown oxide are patterned with arrays of metallic nanodots (AuPd alloy, Au 60%, Pd 40%) made by nanoimprint lithography with self-aligned pattern transfer29. The nanodots are spherical (due to a high temperature annealing step in the fabrication process) with a diameter of ~ 2 to 10 nm (Figure S1 in the Supporting Information shows a histogram of the nanodot size distribution). They can be arranged as close as 15 - 20 nm with a typical positional error in the nanometer regime. Thiol chemistry allows for the selective functionalization of the AuPd nanodots30. Patterned substrates are first treated with a 1.5 hours old piranha solution and with UV–ozone, and then immersed in a solution of thiol-amine (10 µM) or thiol-DNA (1 µM) for 18 hours (overnight). Amine molecules or DNA molecules bind to the nanodots through a thiol linkage while the SiO2 substrate remains free of molecules (as verified by epifluorescence microscopy30). Zheng et al. found that DNA wrapping promotes efficient solvation of SWCNT in water 31 and enables the purification of SWCNT segments with uniform length32 and chirality33. For this work, length sorted SWCNT segments are used, with a ssDNA wrapping sequence (GT)20. Importantly, the process to cut and solubilize SWCNT in DI water by ssDNA wrapping produces SWCNT segments with oxidized ends presenting carboxyl groups34, 35. These carboxyl groups are available for reaction with amine groups to form covalent amide bonds36, 37. Upon activation in 0.1 M MES buffer with 2 mM EDC and 5 mM sulfo-NHS, these can be covalently bound to amine functionalized nanodots on the substrate (Figures 1a and 2a). The selective binding to amine molecules on a surface has been confirmed with a control experiment, detailed in the


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Supporting Information. In this experiment, the activated SWCNT solution is brought to interact with substrates patterned with Au features that were previously functionalized with amine molecules, and with substrates patterned with Au features that were not functionalized with amine molecules. Scanning electron microscopy (SEM) finds that SWCNTs bind to the Au features only if they are functionalized with amine molecules, confirming the existence of carboxyl groups on the SWCNT segments and their interaction with surface bound amines (Figure S3, Supporting Information). When substrates with amine functionalized nanodots are incubated with the activated SWCNT solution, the nanotubes bind to the nanodots, with an average binding yield of 93%, (i.e. 93% of the nanodots on a substrate have at least one SWCNT segment attached, Table 1) as measured by atomic force microscopy (AFM). Notably, 100% of the binding occurs at the SWCNT ends, as seen in Figures 1b and 2b, and non-specific binding to the SiO2 substrate is rarely observed (as seen in Table 1, on average ~ 0.4 physisorbed nanotubes are found in a µm2). Figure 1b shows a substrate in which SWCNT segments are covalently bound monovalently to linear arrays of nandots; they are aligned in the same direction. This alignment is achieved by directional blow-drying of the samples after washing in DI water and ethanol, following incubation in the activated SWCNT solution. For this process the binding yield is found to be 91% (i.e. 91% of the nanodots have at least one SWCNT segment attached). The alignment yield is quite high as well. When only a single SWCNT segment per nanodot is considered, 93% of them are oriented along the same direction, within ± 2.5 °. (When multiple tube segments are attached, steric effects or, possibly, electrostatic repulsion cause some spreading; nonetheless, 95% of the SWCNT segments are within ± 10°.) The distance between the aligned SWCNT segments is 70 nm, corresponding to the spacing of the nanodots pattern. (As a comparison, Figure S4 in the Supporting Information shows an array of nanodots with


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SWCNT segments attached through a covalent bond when no directional blow-drying is applied. No preferential alignment direction is observed.) Patterning substrates with nanodot dimers, with the inter-dot distance matching the average length of the SWCNT segments38, should support the bivalent binding of the SWCNTs, where interactions with the nanodots must occur at both ends of the SWCNTs. As observed in Figure 2b and in Table 1, the covalent binding scheme produces successful bivalent binding for ~ 22% of the SWCNT segments on the substrate. This relatively low yield is consistent with our previous results on bivalent binding of a one-dimensional DNA nanostructure, where we found that bivalent binding is not thermodynamically favorable when produced by bonds involving large changes in Gibbs free energy30. These results, together with our previous thermodynamic analysis, suggest that a higher yield of bivalent binding could be achieved by reducing the monovalent binding affinity. DNA hybridization is based on multiple hydrogen bonds rather than covalent bonds, enabling the modulation of the interaction strength between the SWCNTs and the nanodot binding sites. In this scheme, the change of Gibbs free energy upon binding can be modulated by varying the length of the complementary DNA strands. In order to test this, the ends of the SWCNT segments are functionalized with DNA oligomers. They are first activated for 30 minutes at room temperature in a 0.1 M MES buffer solution with 2 mM EDC and 5 mM sulfo-NHS followed by adding a DPBS solution of amine-functionalized DNA (final concentration 167 nM). The DNA strand consists of a 10 base pair double stranded portion, with an amine group on the 3’ side, and a single stranded poly-adenine portion on the opposite side. The double stranded portion serves as a spacer, separating the ssDNA sticky-end from the SWCNT, in order to prevent unwanted interactions with the DNA on the sidewalls of the nanotube. After overnight


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reaction at room temperature, unreacted DNA strands are removed by centrifugation (Millipore Amicon 100K). The residual concentration of unreacted DNA after purification is estimated to be less than 0.5 nM. Substrates with nanodots arranged in arrays of dimers are functionalized with the complementary ssDNA (poly-thymines) of different length. The functionalized substrates are incubated overnight with the purified ssDNA end-functionalized SWCNT solution in 1X DPBS with ~ 15 mM MgCl2 to promote hybridization. SWCNT binding through DNA hybridization achieves an overall binding yield of 79% (i.e. 79% of the dots have at least one SWCNT segment attached, either monovalently or bivalently, Figure 3b and Table 1). 100% of the binding is at the SWCNT ends, showing negligible interaction between the ssDNA wrapping around the tubes and the DNA on the nanodots. As in the previous case, non-specific binding to the SiO2 substrate is rare, with incidence as low as 0.1 physisorbed SWCNTs per µm2. The bivalent binding yield is evaluated as a function of the length of the hybridizing ssDNA, as well as the nanodot spacing. Nanodot dimers are patterned with inter-dot spacings of 70 nm, 100 nm, 150 nm and 200 nm. Substrates are functionalized with poly-thymines (poly-T) of different length: 3T, 10T, 19T and 30T. SWCNT segments are functionalized with poly-adenines (poly-A) of different length: 10A and 30A. The highest yield of bivalent binding is observed for 30A functionalized SWCNT hybridizing to 10T functionalized nanodots spaced 150 nm apart (matching the average length of 148 ± 93 nm, evaluated by AFM imaging and software analysis, see Figure S2 in the Supporting Information). AFM images reveal a yield of bivalent binding as high as 51% for nanodot dimers in an isolated configuration (Figure 3b) and 35% when the dots are patterned in linear arrays with the same interdot spacing39 (see Table 1 and Figure S5 in the Supporting Information). For nanodot dimer spacings of 200 nm, 100 nm and 70 nm, bivalent


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binding is still observed, but the yield is lower. This is consistent with the mean length of the SWCNT segments: 147.7 ± 92.8 nm. Similar results are obtained for nanodots functionalized with 10T and SWCNT segments functionalized with 10A (see Table S2 and Figure S5 in the Supporting Information). When substrates are functionalized with 3, 19 or 30 thymines, binding is observed, but with an overall lower yield (as shown in Table S2 and in Figure S5 in the Supporting Information). As reported in previous thermodynamics studies30, the highest probability of bivalent binding is realized for binding energies below a certain threshold, corresponding to a system for which bivalent binding results in a stable and irreversible binding configuration, while monovalent binding is unstable and reversible. When the energy of a single binding event is sufficiently high, the probability of monovalent binding increases, binding sites are thus occupied by monovalently attached tubes, reducing the probability of bivalent binding. This appears to be the case for nanodots functionalized with 19T and 30T, while for 3T less overall binding is observed, whether monovalent or bivalent, because of the lower binding affinity of the shorter strands. Applying thermodynamic calculations30 to our system supports these observations (see Supporting Information for details and Table 2 for a summary of the calculated dissociation constants). The dissociation constants for monovalent binding of 3 or 10 A-Ts indicate that stable bonds are not thermodynamically allowed (kd-mono ~ 103 M and 10-3 M respectively). When monovalent binding is given by the hybridization of 19 or 30 A-Ts the binding is thermodynamically favorable and stable (kd-mono ~ 10-10 M and 10-19 M respectively). In the case of bivalent binding, the hybridization of 3 A-Ts, as in the monovalent case, does not result in stable binding (kd-bi ~ 104 M), whereas the hybridization of 10 A-Ts yields a thermodynamically favorable and stable system (kd-bi ~ 10-8 M). Bivalent binding given by the hybridization of 19 or 30 A-Ts is thermodynamically favorable and stable, similar to the


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(kd-bi ~ 10-22 M and 10-39 M respectively). The calculated values of the

dissociation constant for the different experimental conditions are summarized in Table 2. The calculated dissociation constants do not show a pronounced difference between nanotubes functionalized with 10 adenines or with 30 adenines, but experimentally an overall lower binding yield is observed for SWCNT segments functionalized with 10 adenines. This may be attributable to secondary effects not considered in the simple thermodynamic model (e.g., the poly-A strands are less accessible for binding to the poly-Ts on the nanodots due to electrostatic repulsion between the nanotube sidewalls and the substrate). In this work we present a directed assembly technique to create ordered arrays of individual SWCNT segments on a surface. The approach is relatively simple, low cost, and high throughput, because all the steps of the process (nanodot patterning, nanodot functionalization and nanostructures assembly) are parallel. It can also generate large arrays (up to centimeters) with nanometer resolution and complete flexibility over the patterning layout (the limit being the minimum distance between the patterned nanodots, which is currently about 20 nm). Nonetheless, the binding yields we achieve still fall short of the requirements for high performance nanoelectronics7. There are various steps that can be taken to improve the yield. First is controlling the nanodot size. We have already noted that the small dimension of the nanodots results in the binding of a limited number of SWCNT segments. More specifically, the average number of nanostructures bound to each nanodot depends on the nanodot size and on the chemistry of binding. In the cases of covalent binding and of binding through hybridization of 30A to 10T, only one or two SWCNT segments are observed to bind to each nanodot when the nanodot diameter is 5 nm or less (see Table S3 and Figure S7). Nanodots smaller than 5 nm preferentially bind only a single nanotube. Uniform arrays of nanodots of a given size would


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likely result in the binding of a predictable number of SWCNT segments with a narrow distribution. Second, and perhaps more important, is achieving better control over the nanotube length. While the SWCNT solution is considered monodisperse, as can be seen in Figure S2, by some standards the distribution can be considered rather broad. We believe that the yield of bivalent binding can be significantly improved by more precisely matching the SWCNT segment length to the distance between nanodots. Other factors, such as the type and concentration of salts in the buffer solution, may also be optimized to produce higher binding yields. Proximity to the substrate may also affect the binding. It is possible to etch the substrate back somewhat to mitigate any such effects. While we do expect that these changes would result in an overall improvement in the binding yield, it is not clear that it would reach the level required for high performance circuits. It would, however, very likely be sufficient for other applications, such as SWCNT sensors and transducers, which can tolerate a higher level of defects. In conclusion, we have demonstrated a simple technique to organize SWCNT segments from solution to ordered arrays on a surface. Covalent chemistry and directional drying produce arrays of aligned SWCNT segments as close as 70 nm. This distance can be reduced to 20 nm (and possibly below) by extending the nanodot fabrication process to smaller spacings. DNA hybridization allows the implementation of a bivalent binding scheme that is capable of controlling the binding position and orientation of each SWCNT segment individually. A bivalent binding yield as high as 51% is achieved, a result that should improve with the availability of SWCNT segments with narrower length distribution. This technique opens new possibilities for the utilization of SWCNT in the production of nanoelectronic devices and circuits.


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Supporting Information. Substrate patterning; chemical and biochemical functionalization; covalent binding of SWCNT segments; binding of SWCNT segments through DNA hybridization; binding yields; parameters for thermodynamic calculations of dissociation constants; control experiments; length distribution of SWCNT segments; bivalent binding via DNA hybridization. This material is available free of charge via the Internet at http://pubs.acs.org.

ACKNOWLEDGMENT The authors thank Profs. C. Nuckolls, J. Hone and M. Sheetz for resource support, as well as the staff and facilities of the Columbia University CEPSR cleanroom, where much of the fabrication work was performed. The authors also gratefully acknowledge financial support from the Office of Naval Research under Award No. N00014-09-1-1117.


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27. Wang, Y.; Maspoch, D.; Zou, S.; Schatz, G. C.; Smalley, R. E.; Mirkin, C. A. Proc Natl Acad Sci U S A 2006, 103, (7), 2026-31. 28. See the histogram of the SWCNT segments length distribution in Figure S2 in the Supporting Information. 29. Schvartzman, M.; Wind, S. Nano Lett 2009, 9, (10), 3629-3634. 30. Wang, R. S.; Palma, M.; Penzo, E.; Wind, S. J. Nano Research 2013, 6, (6), 409-417. 31. Zheng, M.; Jagota, A.; Semke, E.; Diner, B.; McLean, R.; Lustig, S.; Richardson, R.; Tassi, N. Nature materials 2003, 2, (5), 338-342. 32. Huang, X.; McLean, R.; Zheng, M. Anal Chem 2005, 77, (19), 6225-6228. 33. Tu, X.; Manohar, S.; Jagota, A.; Zheng, M. Nature 2009, 460, (7252), 250-253. 34. Kaempgen, M.; Lebert, M.; Haluska, M.; Nicoloso, N.; Roth, S. Adv Mater 2008, 20. 35. Riesz, P.; Kondo, T. Free radical biology & medicine 1992, 13, (3), 247-270. 36. Palma, M.; Wang, W.; Penzo, E.; Brathwaite, J.; Zheng, M.; Hone, J.; Nuckolls, C.; Wind, S. J. Journal of the American Chemical Society 2013, 135, (23), 8440-8443. 37. Weizmann, Y.; Chenoweth, D. M.; Swager, T. M. J Am Chem Soc 2010, 132, (40), 14009-14011. 38. The length sorting process based on size exclusion chromatography yields solutions of SWCNT segments with a relatively narrow length distribution. One example is provided in the Supporting Information. 39. We believe the difference between binding yields for the linear nanodot arrays vs. the isolated dimers may be attributable to the reduced probability of binding two SWCNT segments to a single nanodot anchor.


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Figure 1. a) Schematics of monovalent binding between SWCNT segments presenting carboxyl groups at the ends, and amine functionalized nanodots on a surface. The binding chemistry is detailed in the inset. b) AFM image of an array of SWCNT segments covalently attached to amine functionalized nanodots. The SWCNT segments are all aligned along a direction due to capillary force drying. The closest distance between nanodots is 70 nm; the diameter varies between 7 nm and 2 nm. 91% of the nanodots have at least one SWCNT segment attached; 95% of the SWCNT segments attached to the nanodots lay within a 20˚ angle around the direction of alignment.


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Figure 2. a) Schematics of bivalent binding between SWCNT segments presenting carboxyl groups at the ends, and amine functionalized nanodots on a surface. The binding chemistry is detailed in the inset. b) AFM image of SWCNT segments covalently attached to a square grid of amine functionalized nanodots. The distance between nanodots is 200 nm, matching the average length of the SWCNT segments. The diameter varies between 7 nm and 2 nm. 93% of the nanodots have at least one SWCNT segment attached; the yield of bivalent binding is 22%.


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Figure 3. a) Schematics of bivalent binding between SWCNT segments presenting 30 adenines (30A) at the ends, and nanodots on a surface functionalized functionalized with 10 thymines (10T). The binding is due to DNA hybridization, as detailed in the inset. b) AFM image of 30A functionalized SWCNT segments attached to 10T functionalized nanodots. The nanodots are arranged in pairs with 150 nm distance, matching the average length of the SWCNT segments. The diameter varies between 10 nm and 3 nm. 80% of the nanodots have at least one SWCNT segment attached; the yield of bivalent binding is 51%.


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Nano Letters

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Table 1. Binding yields. Binding chemistry:

Binding yield (monovalent binding)

Yield of aligned SWCNT

Binding yield (bivalent binding)

Non-specific binding (tubes/µm2)

Covalent

93%

-

22%

0.4

Covalent with directional drying

91%

95%

-

0.5

DNA hybridization

79%

-

35% - 51%*

0.08

Table 1. Yield of monovalent and bivalent binding between SWCNT segments and functionalized nanodots, when attachment is through a covalent bond or through DNA hybridization. Yield of SWCNT segments aligned along a direction determined by the drying process (SWCNT segments are considered misaligned when they lay at an angle greater or equal than 20˚ from the alignment direction). Incidence of non-specific binding, expressed as number of physisorbed SWCNT segments per unit area. Data for covalent binding (non directional) are taken from two AFM images (area = 18 µm2). Data for covalent binding (with directional drying) are taken from five AFM images (area = 45 µm2). Data for binding through DNA hybridization are taken from four AFM images (area = 34 µm2). * The first value comes from two AFM images in which the nanodots are patterned in lines with spacing 150 nm. The second value comes from AFM images in which the nanodots are patterned in isolated dimers with separation 150 nm. See Table S1 in the Supporting Information for the number of binding sites counted in each case.


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Table 2. Dissociation constants. DNA on SWCNTs

DNA on nanodots

kd-mono (M)

kd-bi (M)

30A

3T

4.52×103

3.51×104

10A

10T

9.21×10-3

5.74×10-8

30A

10T

6.89×10-3

8.15×10-8

30A

19T

4.16×10-10

2.98×10-22

30A

30T

8.79×10-19

1.33×10-39

Table 2. Dissociation constants for monovalent binding (kd-mono) and bivalent binding (kd-bi) for different lengths of the DNA strands on the SWCNT segments and on the nanodots. Calculations are made following the thermodynamic model in30 (See Supporting Information for details).


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Nano Letters

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TOC Graphic:

Synopsis: Approaches are explored for the precise placement of individual single wall carbon nanotube segments via directed assembly onto a nanodot breadboard.


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Directed Assembly of End-Functionalized Single Wall Carbon

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