Design and Fabrication of Plasmonic Nanomaterials Based on Gold

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Design and Fabrication of Plasmonic Nanomaterials based on Gold Nanorod Supercrystals Leonardo Scarabelli, Cyrille Hamon, and Luis M. Liz-Marzán Chem. Mater., Just Accepted Manuscript • DOI: 10.1021/acs.chemmater.6b02439 • Publication Date (Web): 08 Sep 2016 Downloaded from http://pubs.acs.org on September 9, 2016

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Chemistry of Materials

Design and Fabrication of Plasmonic Nanomaterials based on Gold Nanorod Supercrystals Leonardo Scarabellia, Cyrille Hamona,b, Luis M. Liz-Marzána,c,d a

Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia -

San Sebastián, Spain b

Matiére et Systèmes Complexes, Université Paris Diderot & CNRS (UMR 7057), 75205 Paris

Cedex 13, France c

Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain

d

CIBER de Bioingeniería, Biomateriales y Nanomedicina, Ciber-BBN, 20009 Donostia - San Sebastián, Spain Introduction Nanotechnology might represent the biggest technology leap in modern human history, as it is expected to provide solutions to various challenges that threaten our future; it promises faster computers, improved security, longer healthier lives and a cleaner Earth.1 Many recent review articles deal with the impact of nanotechnology in a variety of different fields: medicine,2,3 solar harvesting,4,5 photochemistry,6 sensing,7,8 or photodynamics,3,9 to name a few. At the cornerstone of nanotechnology resides the concept of “less is different”, meaning that decreasing the size of an object may lead to completely new phenomena. This is true for particles of very different compositions, and generates the need for a new level of description as compared to the bulk material.1 The research activity of our lab deals with making and understanding the growth of noble metal nanoparticles with controlled composition, size and morphology, as well as their self-assembly into ordered structures, with the ambition of engineering their optical properties, i.e. fine tuning the associated surface plasmon resonances throughout the visible and near-IR spectral ranges.10 We ultimately aim at the application of nanoparticles and nanostructures in the biomedical field. In this point-of-view article we describe our approach towards the rational development of functional nanomaterials (or nanodevices). In particular, we focus on a current “study case” that we believe represents a good example. Practical and technical details will play a central role in 1 ACS Paragon Plus Environment


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the manuscript, but the reader will be referred to the original publications for a complete description of methods and materials characterization. In our view, this example comprises methodologies and experimental pros and cons that can be applied to other projects.

Toward a plasmonic nanodevice Generally speaking, we can identify four distinct stages involved in the development of a nanodevice (Scheme 1), but they are all strongly interconnected: the output of one stage is used as input for the next one. -

Formulation/refining of a starting idea or hypothesis, which requires devising a specific system;

-

Fabrication of the different components and their assembly into the desired structure;

-

Systematic and detailed characterization of the produced materials;

-

Interpretation of the experimental data on the basis of existing or new theory.

As can be seen in Scheme 1, these four stages can be organized in a cycle, where each “round” represents a step forward towards the design of a new functional material. We feel the need to particularly emphasize on the importance of comprehensive characterization, which is capital toward the correct interpretation of the results, the best possible input for modeling and the identification of directions for improvement. Indeed, the development of nanosystems with increased complexity often requires new strategies and improved instrumentation, so it is not a coincidence that this field is growing in tandem with the development of new characterization techniques such as electron tomography,11 environmental electron microscopy,12,13 electron energy loss spectroscopy,14,15 cathodoluminescence,16,17 or micro-Raman spectroscopy,18–22 to name a few. Research toward the development of a new nanomaterial can in practice start from any of the four phases listed above; nonetheless it is conceptually more appropriate to start from the definition of a scientific problem and then identifying the issues that need to be tackled. This strategy is helpful for the organization of the experimental work and subsequently for preparing a scientific publication or a patent application.23,24

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Scheme 1. Schematic representation of an “improvement loop” that leads to the development of a new material/device.

The work we describe here has been carried out by many group members at CIC biomaGUNE and collaborators at the University of Vigo, in the framework of an ambitious research program,25 toward the development of nanostructured plasmonic materials based on crystalline assemblies of anisotropic nanoparticles, to be used as optical enhancers for the surface enhanced Raman scattering (SERS) detection of small signaling molecules in bacteria colonies.26,27 The objective already sets the most important and/or critical steps that need be taken into consideration when designing the material. - The choice of SERS spectroscopy as the detection tool calls for the implementation of a plasmonic component. SERS is a vibrational spectroscopy technique furnishing chemical fingerprint-like information about the substance of interest, which can be detected with high sensitivity ONLY when in the near proximity to plasmonic nanostructures.22 As a consequence, our synthetic efforts focus on gold and silver: whereas silver is plasmonically more efficient than gold and therefore higher Raman enhancement is to be expected (thereby lowering the limit of detection of the device), gold is chemically more inert and robust, while offering a wider range of synthetic possibilities. - A detection method requires high sensitivity and reproducibility, i.e. all the produced devices must render reproducible signals as well as sensitivity and selectivity for the selected analyte. In the context of SERS, this is mainly related to hot-spot engineering,28 i.e. the ability to control and 3 ACS Paragon Plus Environment


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organize interparticle gaps. In particular, a homogenous distribution of hot spots at a high density ensures reproducibility and sensitivity, respectively. - Stability represents another important concern. We ultimately need to carry out measurements in situ from living bacterial colonies, even during biofilm formation, meaning that our nanodevices will have to stand high ionic strength conditions (potential aggregation issues),29 in the presence of living organisms (nanoparticle internalization),30,31 proteins (protein-corona formation, changes in surface chemistry),32–35 enzymes (oxidation/degradation),36 etc. Taking all this into account, we decided to orient our work towards a solid state plasmonic material, which can minimize aggregation and internalization issues. We selected a bottom-up approach instead of a more mainstream lithography-based method, which provides high surface to volume ratio, possibility of working in three dimensions, and improved plasmonic performance. Tunability of the resulting plasmonic properties can be obtained by working at three different levels, namely synthesis of the nanoparticle building blocks (size, shape, composition and crystallinity), directed self-assembly (organization, plasmon coupling) and posttreatment (surface chemistry, coating). On top of this, a reproducible 3D assembly of plasmonic building blocks would present broad plasmonic features that can capture multiple excitation wavelengths for SERS, as well as a dense array of hotspots. This suggests the possibility of ultrasensitive and quantitative detection by SERS with no need for statistical and multivariate analysis.

Self-assembly of gold nanorods into vertical superlattices: a brief review Once we have identified the general features, we proceed with the identification of the most suitable nanoparticle building blocks. Among a wide variety of available morphologies, gold nanorods were selected because they display efficient plasmonic response that can be tuned across a broad spectral range, by simple variations of a well established synthesis method that can be readily scaled up.37–40 Importantly, directed self-assembly of gold nanorods into highly organized superlattices has been demonstrated,41–43 as well as their use for SERS detection of a variety of analytes,44,45 including scrambled prions46 and food contaminants.47,48 In particular, organization of nanorods into densely packed, standing vertical arrays, maximize hotspot density in the focal volume of the laser, and it has been proven to outperform many other SERS


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substrates. Interestingly, the homogeneous hot-spot distribution within ordered supercrystals is crucial for quantitative analysis. Generally speaking, self-assembly is a dissipative process triggered by different types of interactions between the building blocks, which can be either encoded in the building blocks themselves, induced by external fields,49,50 or directed by a template.51,52 Among many different approaches, evaporation induced self-assembly (EISA) has proven a simple and convenient way to obtain a variety of nanoparticle assemblies.49,51,52 In the case of EISA the organization is achieved using entropic forces alone, which can be described as phenomenological forces resulting from the entire system's statistical tendency to increase its entropy.53,54 The concept of organization obtained as a result of entropy increase may sound counter-intuitive and deserves a better description. The gradual evaporation of the solvent leads to an increase in the rod-rod interactions, until a critical concentration is reached, inducing a phase transition into an ordered state. The driving force is the maximization of the free volume available for surfactant micelles and other small solutes, in order to increase the overall entropy of the system;13 simply put: the entropy loss due to nanoparticles organization is counter-balanced by an increment in the entropy of other components in the system.53,55 This is well understood both theoretically, from the pioneering work of Onsager56 and later by others,53,55,57,58 and experimentally on different systems like rod-shaped viruses59,60 and semiconductor nanorods.61–63 Since a number of different procedures have been described regarding the organization of gold nanorods by EISA, an overview of the field is necessary toward discussing important parameters that are often not taken into consideration. Importantly, the choice of the nanorod aspect ratio and concentration in the starting solution is crucial toward obtaining controlled self-assembly and optimizing the design of the device. Additional parameters are involved in EISA, such as the surface chemistry of the nanoparticles, which can be adjusted to optimize the long range order in the system. In Table 1 we tried to summarize the experimental parameters considered in selected works from the literature, where vertical superlattices of gold nanorods were obtained by EISA. The different length × diameter (L×D) values in the first column suggest that the gold nanorod volume is not a critical parameter to obtain vertical superlattices. However, no systematic studies have been reported on the organization of larger nanorods (L>100 nm) into vertical superlattices, presumably due to sedimentation issues. On the contrary, gold nanorod aspect ratios (L/D) are consistently comprised between 2 and 5, suggesting that the formation of vertical superlattices is 5 ACS Paragon Plus Environment


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more favorable in this specific range. A similar situation is observed regarding the initial concentration of gold nanorods, which usually ranges between nanomolar and micromolar.64,65

Table 1. Summary of experimental parameters used in the literature to form vertical superlattices (vertical SL) of gold nanorods. OD refers to optical density: it can be easily determined by mean of a UV/Vis spectrometer, using an approprieate dilution to bring the OD of the specimen below 2 (i.e. 99% of the light absorbed by the specimen). Unless otherwise indicated, CTAB was used as surfactant. In all cases the SLs were prepared by drop casting, exept for ref.

66

where they are preared by drop coating. All synthesis used a seed mediated technique (exept for ref. 41,

where a seedless method is employed) and ascorbic acid as a reductant in the growth stage. Additionaly, ref. 67 used salicylic acid as co-reducing agent that may influence the self assembling process (ref.

68

) but the colloidal

suspension was washed and the chemical environement of the rods was modified with MUDOL before use.

Ligand

AR (L/D)

(LxD) (nm)

[GNR]

[Surfactant]

Assembly

Drying

Ref.

CTAB

2.7

92 × 34

≈nM

2.5 mM +0.01 M NaCl

vertical SLs

≈12h

47

CTAB

3.0

75 × 25

nM

≈ 1 mM

vertical SLs

24h

46

CTAB

3.5

59 × 17

33 nM

2.5 mM

vertical SLs

4h

69

CTAB

4.4

75 × 17

20 nM

3 mM

horizontal SLs

in air 65

CTAB

3.8

42 × 11

20 nM

3 mM

vertical & horizontal SLs

Gemini

3.1

34 × 10

10-1000 nM

1 mM (Gemini)

vertical SLs

in air

Gemini

4.1

42 × 10

1 mM (Gemini)

vertical SLs

in air

ODS (in CHCL3)

4.5

29 × 6.5

OD=25

-

vertical SLs

in air

70

TOAB (in C6H5Cl)

2.3

54 × 23

1.4-14 nM

-

vertical SLs

20 min

71

MUDOL

3.1

22 × 7

1-1000 nM

(Tween 20) 0.1 mM

vertical SLs

6h

41

MUDOL

3.2

55 × 17

1-1000 nM

(CTAB) 0.5 mM + (MUDOL) 0.1 mM

vertical SLs

6h

67

MUDOL

3.5

60 × 17

in 50% H2O

72

18h

73

43

5 nM

horizontal SLs MUDOL 1.5 mM

15-35 nM MUDOL

3.6

58 × 16

in air

15 nM

vertical SLs MUDOL 0.1 mM

vertical SLs


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S-A11-E6-CO2H

3.0

45 × 15

9 nM

0,05% Tween 20, 0.5 M NaCl in 20 mM PbS.

vertical SLs

66

12h

Regardless of the selected conditions, successful supercrystal assembly requires using monodisperse building blocks. We therefore optimized the synthesis of single crystal gold nanorods using a double reducing agent (ascorbic and salicylic acid) seeded growth method.38 The main advantage of this synthetic protocol is represented by the possibility of tuning the aspect ratio of the final product acting on a single parameter, the pre-reduction of the gold precursor by salicylic acid, keeping the shape-yield above 90% and a size distribution well below 10%. Importantly, batch-to-batch reproducibility and scale-up are also improved by using this method. The practical details involved in the synthesis of high quality gold nanorods have been thoroughly described in a recent publication by our group.40 During the work presented here, we optimized the synthetic protocol to prepare gold nanorods displaying a longitudinal LSPR around 790 nm (in water), corresponding to average dimensions of 58(±5) × 17(±2) nm and an average aspect ratio of 3.4(±0.4); the nanorods were synthesized in batches of either 1 L or 2 L, which were sufficient for the preparation of 50 to 100 substrates starting from the very same colloidal suspension, so as to guarantee consistency between different preparations. Apart from the morphology, the surface chemistry of the building blocks also plays an important role: self-assembly by EISA is observed only when energy-driven interaction between the building blocks can be considered negligible;74,75 however, the high positive charge created by the CTAB double layer induces a strong short-range repulsion between neighboring particles, which must be overcome to allow packing of gold nanorods into vertical superlattices. Different strategies have been proposed in this respect, e.g. gold nanorod assemblies are observed when CTAB concentration is above its critical micellar concentration (1mM), so that additional attractive depletion forces are present during the self-assembly process.65,76,77 In another approach, the range of electrostatic forces (the so-called Debye length) is shortened by the addition of electrolyte solution or using buffers.47,66 Other strategies rely on ligand exchange to cover the gold nanorods with uncharged ligands in water or to transfer them into non-polar solvents. We decided to apply a ligand exchange reaction, replacing CTAB with (1mercaptoundec-11-yl)hexa(ethyleneglycol), also known as MUDOL, which is soluble in water, uncharged and has been reported to induce the formation of gold nanorod superlattices through 7 ACS Paragon Plus Environment


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EISA.41,72 The evaporation rate is another critical parameter, so that long range structures were obtained when carrying out the evaporation inside a controlled atmosphere chamber,46,78 even though homemade (cheaper) setups can achieve similar results, by increasing the drying time up to 12 hours (Figure 1A).67,68 Finally, one should also take into consideration the physical and chemical properties of the substrates,63,73,79 such as wettability, which can drastically influence the surface area onto which the nanorods will be deposited: more hydrophobic surfaces (higher contact angle) will reduce the contact area between the drop and the surface, more hydrophilic ones (lower contact angle) will increase it. A detailed discussion on the topic is beyond the scope on this article, and thus we refer interested readers to recent reviews.80,81 In a typical experiment, 1L of pre-washed CTAB coated gold nanorod solution (i.e. [CTAB] ≈ 0.5 mM and [Au0] = 0.5 mM, corresponding to an absorbance of 1.2 at 400 nm)40 is mixed with 10 mL of a 10 mM MUDOL solution (Figure 1B) and stored undisturbed overnight. Finally, the gold nanorod concentration was adjusted by centrifugation (up to a factor of 104) to induce supercrystal formation.

Our approach toward vertical gold nanorod superlattices Now that the building blocks have been chosen and prepared, we aimed at obtaining a model system that could be used to understand the collective plasmonic properties of these assemblies, so that we could refine our final design. We thus assembled nanorods by simple drop casting of a 10 µL drop of colloidal dispersion on a clean glass surface, using a homemade setup to increase the evaporation time up to 6 hours (Figure 1A). Before carrying on with more complex investigation, optical observation of the prepared sample was carried out as a convenient and rapid check. We used dark field optical microscopy to confirm that MUDOL drives the formation of supercrystals with circular shapes (Figure 1C), whereas CTAB rods formed more extended and less organized films instead (data not shown).82,83 A typical phenomena related to drying upon drop casting is the so-called coffee ring effect, which induces the accumulation of colloidal particles at the edge of the drying solvent.49,84,85 As a result, supercrystals close to the dried edge typically contain a larger number of nanorods and stacked layers, whereas supercrystals in the center were composed of fewer building blocks and eventually comprised single monolayers of standing nanorods. Most research groups would try to avoid this effect, so as to obtain more homogeneous substrates;73,86 on the contrary, in this 8 ACS Paragon Plus Environment

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context we exploited it, using dark field microscopy to identify convenient areas containing abundant supercrystals, which were selected at different distances from the dried edge, so that they were composed of different numbers of layers. It should be stressed that all analyzed supercrystals were made of standing gold nanorod arrays, as could be confirmed by atomic force microscopy (AFM, see Figure 2A). Subsequently, we used various electron microscopy techniques (HR-SEM, STEM, electron tomography) to gain information about the intra- and inter-layer reciprocal organization of the building blocks: the top view confirmed the vertical orientation of the nanorods, imaging their organization into an hexagonal lattice, while the formation of Moiré patterns suggests an ABA type of interlamellar organization (Figure 1D), which is further confirmed by the 3D reconstruction of an entire bilayer supercrystal (Figure 1E).

Figure 1. A: Photograph and schematic representation of a home-made setup for slow drying of nanoparticle colloids. B: Normalized UV-vis-NIR spectra of gold nanorods coated with CTAB (black) and MUDOL (red). C: Dark field microscopy image of supercrystals obtained by drop casting of a concentrated nanorod dispersion. D: HAADF-STEM image of a bilayer with a small angular misorientation between neighboring gold nanorod layers, as indicated by Moiré patterns. E: Electron tomography reconstruction of a complete gold nanorod bilayer. Adapted with permission from: B - C:



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Ref. 67; D - E: Ref. 82.

Optimization of the sensing substrate requires a detailed understanding of the plasmonic performance of the supercrystals, as well as the influence of the number of nanorod monolayers. Previous works conducted on similar nanostructures suggested a direct correlation between the number of layers and the field enhancement at the top surface of the supercrystal, which would indicate that larger supercrystals would be more efficient.46,73 We carried out a correlated structural and optical characterization on selected supercrystals (Figure 2A). AFM was used to measure height profiles, as a convenient way to determine the number of layers in the different assemblies, while SEM imaging confirmed the hexagonal order of standing nanorods within the supercrystal. Additionally, micro-Raman spectroscopy was used to analyze the SERS performance as a direct measurement of the sensing performance of each selected self-assembled structure. From an experimental point of view, a few considerations should be made before proceeding with the measurements. First of all, AFM and SEM could possibly damage the surface of the assemblies, thereby affecting their SERS performance. Therefore, SERS measurements were performed first, followed by SEM and AFM (Figure 2A). Additionally, it is important to remove residual surfactant from the surface of the supercrystals, which would likely hinder the diffusion of analyte molecules toward the SERS-active surface (Figure 2B). Plasma etching is a common surface cleaning technique, which however requires careful optimization of the conditions, so as to achieve the highest SERS signal while preserving structural integrity (Figure 2E). Interestingly, Argon plasma was found to be favorable for supercrystals obtained by drop casting because both oxygen plasma and UV/Ozone cleaning originated cracks in the supercrystals, as well as welding of adjacent nanorods (Figure 2C). In the former case, X-ray photoelectron spectroscopy (XPS) studies showed that even though the carbon content decreases significantly after cleaning, the oxygen amount significantly increased, suggesting a change in the surface chemistry of the crystals (Table 2); ideally, the best situation is represented by the maximum reduction in the carbon content, avoiding a corresponding increase in oxygen and modification of the sample morphology.

Table 2. XPS surface analysis on samples prepared by drop casting on a ITO substrate (30 nm on a glass slide) and cleaned by different procedures. Conditions for oxygen plasma: 0.4 mbar O2, 200 W for 2 min 10 ACS Paragon Plus Environment

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(PICO, Diener Electronic). Conditions for UV: >2h (UV Ozone Cleaner – ProCleaner™ Plus (BIOFORCE)). Conditions for argon plasma: 30 min at 4 W, 24 mbar Ar. (Aja magnetron sputtering system (ATC 2200)). Sample

Si (at.%)

Au (at.%)

O (at.%)

C (at.%)

No cleaning

29.2

0.3

25.9

44.7

O2 Plasma

28.0

0.2

56.8

14.8

O2 Plasma and UV/O3 cleaning

30.5

0.4

64.4

4.6

Argon plasma

23.6

0.6

49.0

26.8

Argon plasma and UV/O3 cleaning

30.2

0.8

63.5

5.3

XPS experiments were performed in a SPECS Sage HR 100 spectrometer with a non monochromatic X ray source (Magnesium Kα line of 1253.6 eV energy and 250 W and calibrated using the 3d5/2 line of Ag with a full width at half maximum of 1.1 eV). The selected resolution for spectra was 15 eV of Pass Energy and 0.15 eV/step. All measurements were made in an ultra high vacuum chamber at a pressure around 8·108 mbar.

It is worth mentioning here that, in the context of using templates made of polydimethylsiloxane (PDMS) to direct gold nanorod EISA (see below), a combined treatment with oxygen plasma and UV cleaning yielded the best results, most likely because residual PDMS was left on the supercrystals, requiring a more aggressive treatment. We also explored the use of a chemical treatment for ligand desorption based on hydrides, but the use of an aqueous solution resulted in partial redispersion of the supercrystals (Figure 2D).87 In this context, alternative treatments with hydrochloric acid (0.1 M in ethanol or another immiscible solvent, 10 min) could be promising when more sophisticated surface cleaning equipment is not available, even though such treatments usually require longer times.



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Figure 2. A: Overview of the characterization of gold nanorod supercrystals, involving SERS mapping, SEM and AFM morphological imaging. B: SEM image of a supercrystal before cleaning. C: Example of partially molten supercrystal. D: Supercrystal partially redispersed after immersion in a NaBH4 aqueous solution. E: Representative SEM image of a supercrystal after Ar plasma cleaning, ready for SERS measurements. Adapted with permission from Ref. 82.

Investigation of the optical properties of nanorod supercrystals After a suitable cleaning procedure has been selected, the plasmonic efficiency of selected supercrystals with different number of layers was evaluated by drop casting a model analyte (Crystal Violet) on the surface of the supercrystal and then recording the SERS signal of the analyte. A solution of CV in ethanol was used because immersion of the supercrystals in aqueous solutions was found to lead to partial resuspension of the assemblies. Unexpectedly, no obvious increase in the average SERS intensity was obtained from different supercrystals, regardless of the number of layers (Figure 2A), indicating that the effect of the number of layers is more complicated than previously hypothesized by other groups. We thus decided to carry out detailed simulations of the expected enhancement. Although several computational methods are available, most of them are restricted to relatively simple morphologies and a small number of nanoparticles. However, our colleagues at the University of Vigo and University of Extremadura recently implemented a full-wave boundary-element-based method of moments (MoM) that can be applied to much larger systems, comprising even thousands of nanoparticles, in a single 12 ACS Paragon Plus Environment

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computational run. MoM provides a key advantage in nanoplasmonics:88–91 since the field singularities and hotspots arising with LSPRs are analytically addressed, the method does not suffer from numerical dispersion or instability due to rapid field variations. We could additionally exploit the repetition pattern in our supercrystals, i.e. the fact that the building blocks are periodically repeated throughout the structure, in order to reduce the computational demand (for both runtime and memory), which usually leads to the need for supercomputers to deal with such overly-populated meshes. In this way we were able to simulate structures having dimensions close to the real systems, i.e. composed of up to 15,000 plasmonic nanocrystals. The results of the simulations allowed deriving important conclusions (Figure 3). First of all, the periodic nanorods arrangement was observed to originate standing waves, which were distributed at different resonant depths according to the number of layers composing the supercrystals, thereby creating a dense array of intense hotspots inside the supercrystal structure (Figure3A).82 On the other hand, a high degree of order was essential, since similar calculations indicated that light would not penetrate longer than a few tens of nm inside a film of randomly assembled gold nanorods.91 These results were important to dictate the experimental design and reassured us to build up highly ordered three dimensional gold nanorod supercrystals for plasmon enhanced applications. Finally, the simulations confirmed that the relationship between the number of layers and the enhancement of the SERS signal empirically presented in the literature is not that simple: the enhancement from a specific superstructure strongly depends on the selected laser excitation wavelength and on the ability of the analyte to penetrate inside the structure itself, so that the high density of hot-spots can be fully exploited (Figure3B).

Figure 3. A: Cross sectional view of the hotspot distribution (SERS performance, calculated as |E (633 nm)|4) of gold nanorod supercrystals with different numbers of layers. The formation of standing waves can be appreciated. B: Calculated maximum SERS intensity at the upper surface of a supercrystal, as a



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function of the excitation wavelength. Adapted with permission from Ref. 82.

Optimizing the sensitivity of the plasmonic nanodevice The information collected from this thorough characterization was subsequently used to improve the design of the sensing material (Scheme 1). Even though we exploited the coffeering effect to find a suitable area to study the plasmonic properties of supercrystals, the free evaporation of the solvent and associated flows during drying lead to poor reproducibility in terms of supercrystal morphology. Our first improvement was therefore to realize a multiscale (hierarchical) organization of gold nanoparticles over large areas (centimeters squared), with high signal reproducibility and control over the collective plasmonic properties of the system. We additionally aimed at obtaining supercrystals with dimensions that could be easily identified with an optical microscope, while controlling their size, shape, height and long range distribution on the substrate. We tackled this issue by means of micropatterned templates, which would confine the drying of the nanorod dispersion within specific areas with pre-determined shape and size. Polydimethylsiloxane (PDMS) was selected as the a suitable material because it is inexpensive, easy-to-handle and well-documented,92 compatible with our nanoparticles and can be readily modified by chemical methods if needed (Scheme 2A). In a typical experiment, 2 µL of a MUDOL coated gold nanorod solution with an Au0 concentration of 375 mM was drop casted and confined between a silicon (Si/SiO2) substrate and the microtextured PDMS template (Scheme 2A). Even though the quality and versatility of the obtained hierarchical substrates was fully satisfying, we know from the simulations that the analyte must penetrate inside the supercrystals, so that the sensing performance is optimal (Figure 3A). Additionally, the structural integrity of the supercrystals and the selectivity of the detection may be important issues once the device is introduced in a real cell or bacteria culture media. In fact, the detachment of entire supercrystals from the substrate was occasionally observed after several days of immersion in Milli-Q water (Figure 4F). As a consequence, we explored the use of mesoporous silica as a protective coating for the supercrystals, which could prevent redispersion while avoiding direct contact with the bacteria. The silica films were formed by hydrolysis of tetraethyl orthosilicate (TEOS) in the presence of cetyltrimethylammonium bromide (CTAB) micelles in a 3:1 water:ethanol solution, with a pH between 9 and 10 (adjusted by the addition of NH4OH, Scheme 2B). The substrates 14 ACS Paragon Plus Environment

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were let undisturbed in the reaction mixture for 3 days and subsequently washed with HCl (0.1 M in ethanol) and heated at 130°C for 2 hours. The mesochannels in the resulting silica layer were expected to allow diffusion of the analyte toward the plasmonic nanoparticle surfaces, but also to act as molecular sieves preventing the contamination of the sensing surface with proteins and other large (bio)molecules.93 To our advantage, silica was found not only to cover the supercrystals but also to infiltrate between gold nanorod layers, thereby increasing the interlamellar distance without drastically affecting the internal organization of each monolayer (Figure 4G).

Scheme 2. A: Schematic representation of templated EISA. The inset shows an optical microscopy image of the PDMS mould. B: Schematic representation of the silica growing process. The substrates were immersed in a growth solution containing TEOS, ammonia and CTAB, in a 3:1 mixture of ethanol and water at 60 ºC for 3 days. Adapted with permission from Refs. 67,94.

This templated EISA approach indeed allowed us to prepare centimeter squared areas, uniformly covered by gold nanorod supercrystals (see inset in Scheme 2A).67 Additionally, by simply varying the nanorod concentration in the starting colloidal dispersion, the height of the obtained nanostructures could be tuned, up to 4 microns, corresponding to millions of nanorods within each supercrystal (Figure 4A). However, the increased complexity related to the larger size of these supercrystals required additional characterization of the internal structure, i.e. an 15 ACS Paragon Plus Environment


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AFM height profile would not be sufficient. In collaboration with A. Chuvilin at CIC nanoGUNE, we used a slice and view approach by successively cutting thin slices with a focused ion beam (FIB), which could then be imaged by SEM (Figure 4B).94 A 3D reconstruction of the supercrystal was then obtained by combining all slices together (Figure 4C). Subsequently, the orientation of every building block was identified by image analysis (Figure 4D), which allowed us to quantitatively show that the majority of the nanorods were aligned perpendicular to the substrate, with an average angle of 92(±8)º (Figure 4E). A similar characterization was repeated after silica infiltration, which demonstrated an internal organization of alternating gold nanorods and silica layers (Figure 4G - H). The porosity of the silica layers and accessibility to the internanorod areas was demonstrated by two separate experiments in which the silica-coated supercrystals were incubated with either a solution of uranyl acetate or dilute aqua regia. In the first case we were able to detect uranium at multiple spots inside the supercrystal by EDX analysis (Figure 4I), while incubation in aqua regia resulted in complete dissolution of the gold nanorods composing the supercrystals, leaving empty silica boxes (Figure 4J).


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Figure 4. A: SEM image of a supercrystal obtained with a starting Au concentration of 375 mM (ca. 800 fold more concentrated than the initial nanorod dispersion). B: Schematic representation of the Slice&View technique used for the 3D reconstruction of the gold nanorods organization within the supercrystals. C: 3D reconstruction of a box within the supercrystal, with a volume of 1.3 µm3, showing smectic order. D: Identification of the orientation of every building block inside the reconstructed volume shown in C. E: Orientation scattering maps obtained from D, revealing the distribution of nanorod orientations. F: SEM images of gold nanorod supercrystals after immersion in a water/ethanol mixture (3:1) for one week. The white arrows indicate supercrystals that have detached from the substrate. G: SEM image of a gold nanorod-silica hybrid supercrystal cross section. H: Orientation scattering maps obtained from Slice&View analysis, revealing the distribution of nanorod orientations in the hybrid. I: SEM image of a gold-silica supercrystal cross section after incubation with a 1.5% uranyl acetate solution overnight. Green and red spots indicate positive or negative EDX detection of uranium, respectively. J: SEM image of a substrate after incubation with aqua regia, showing complete dissolution of gold nanorods. Adapted with permission from Ref. 94. 17 ACS Paragon Plus Environment


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With the complete design in place, we are ready to test the SERS performance of the supercrystals, both before and after deposition of the mesoporous silica coating. Crystal Violet was again used as a model analyte, exploiting the resonance of the molecule with the exciting wavelength (633nm) to maximize the signals. A remarkable and important observation is that, even though each supercrystal grows independently inside a cavity of the PDMS template, the SERS signals recorded from supercrystals in different areas were found to display similar intensity levels (Figure 5A-B), which is promising toward potential quantitative analysis. We were also very pleased to see that, as expected, the enhancement factor of the supercrystals after coating with mesoporous silica was determined to be ca. 7-fold higher than that of uncoated supercrystals (2.7×106). This is not only confirming that the analyte molecules can diffuse inside the supercrystals, but also that the porosity of infiltrated silica makes it possible to fully exploit the high density of hot-spots that is characteristic of these assemblies (Figure 5C).

Figure 5. A: Optical microscopy images (left column) of gold nanorod supercrystals and the corresponding SERS mappings (right column) obtained by recording the intensity of the crystal violet CC stretch vibrational peak integrated over 1618-1632 cm-1 (shaded area in C). The scale bars on all images are 10 µm. B: SERS mappings of differently shaped gold nanorod supercrystals coated with silica, overimposed on the corresponding optical microscopy images. C: SERS spectra (averaged over ca. 5 measurements on different spots) of gold supercrystals before (black line) and after (red line) coating with mesoporous silica.


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OUTLOOK In conclusion, we presented here a “case of study” in which we developed a nanodevice, ultimately designed for real time sensing of Quorum Sensing (QS) signaling molecules (small diffusible signals secreted by bacteria) in a living bacteria colony. Ideally, we would like to apply our substrates both for detection and as a scientific tool for improved understanding of a biological process. In particular, we currently focus our research on biofilms of Pseudomonas aeruginosa (P. aeruginosa); these bacteria are one of the leading causes of nosocomial infections in hospitals, where prosthetics and catheters represent an ideal substrate for biofilm growth, being related to 8-10% of all healthcare-associated infections;95–97 In about 13% of these cases, multidrug-resistant strains were observed and an increasing number of pan-drug-resistant specimens have been reported, which can lead to severe complications, like cystic fibrosis or the rejection of an implant.98,99 Furthermore, the precise biochemical mechanism involved in the development of such biofilms is still a grey box, particularly for the earlier stages of the process. Detection of small diffusible molecules involved in Quorum Sensing pathways (i.e. a cell-to-cell communication mechanism) is one of the most promising approaches that could allow the detection and monitoring of the formation of biofilms at an early stage, when a targeted antibacterial therapy can still be effective.100–102 However, most of the available techniques for the analysis of QS are either based on invasive approaches by means of genetically modified bacteria103,104 or non-invasive but in its planktonic form (i.e. no biofilm).105,106 In this scenario, the performance of our SERS substrate could not only detect Quorum Sensing at a very early stage of biofilm formation and monitor its production in situ, thereby leading to a better understanding of this form of bacterial communication. Additionally, one of the main advantages of our design is the filtering effect of the mesoporous silica layer, which can prevent the contamination of the plasmonic surface by larger biomolecules such as lipids and proteins, as only small analytes (< 2.5 nm) can diffuse trough the porous network.107 As a final point, we would like to spend a few words on what we consider a fundamental ingredient of “good science”; a friendly lab environment, fertile for the creation of good networking, where the different backgrounds of each component can be shared and fused together into smart solutions, is crucial for the successful development of a complex research project. The same argument holds true on a wider scale: a major part of the results presented here were only possible thanks to external collaborations; only exploiting the complementary 19 ACS Paragon Plus Environment


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expertise inside our laboratory and with our collaborators we were able to realize what was initially established as the final goal. Therefore, we acknowledge all the scientists who contributed to the realization of this ambitious project.

ACKNOWLEDGEMENTS The authors acknowledge financial support from the European Research Council (ERC Advanced Grant # 267867, PLASMAQUO). REFERENCES (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) (12)

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