Microscopic Visualization of Porous Nanographenes Synthesized through a Combination of Solution and On-Surface Chemistry
March 4th, 2021
A combination of solution and surface assisted synthesis opens new directions in the atomically precise synthesis of nanostructures. Scanning tunneling microscopy (STM) supplemented by non-contact atomic force microscopy (nc-AFM) enables detailed characterization of newly designed and generated carbon-based nano-objects.
Combination of solution and on-surface chemistry brings novel carbon-based materials into our lives. Modern imaging techniques like scanning tunneling microscopy, or atomic force microscopy provide detailed insight into the structure, composition, and properties of newly designed and synthesized compounds down to single atoms. Begin with rinsing the gold monocrystal by completely submerging it in the laboratory beaker filled with acetone and cover the glass beaker with Parafilm.
Subsequently, clean the sample in the ultrasonic scrubber for five minutes. Mount the gold monocrystal on the sample holder and vent the load lock. Transfer the sample to the UHV system to heat it to above 100 degrees Celsius for several hours.
Anneal the sample at 450 degrees Celsius using the resisted heater mounted in the preparation chamber for 15 minutes. Controlling the temperature with the thermocouple type K.After calibrating the gun with phosphor, orient the sample and adjust the distance between the gun and the sample to within 50 millimeters. During annealing sputter the sample with argon ions.
Do not forget to switch off the ion pump and sublimation pump before opening the gas valve. Perform sample sputtering using the ion gun oriented at an angle of 45 degrees with respect to the sample surface with the gas pressure set at five by 10 rays to the power minus seven millibar. After completing cleaning cycles, check the quality of the gold 111 sample with STM.
Move back the Knudsen cell, and close the valve between the Knudsen cell and the preparation chamber before venting the Knudsen cell. Fill the dedicated quartz crucible with around one milligram of the molecular powder and properly place the crucible inside the Knudsen cell. After mounting the Knudsen cell onto the valve at the preparation chamber, pump it down with the external vacuum pump.
Do not open the valve between the preparation chamber and the Knudsen cell until it is pumped down to avoid contamination of the preparation chamber. Transfer the clean gold sample from the microscope chamber into the preparation chamber. Then set the sample directly in line with the Knudsen cell and adjust the distance between the sample and the evaporator to be within 50 to 100 millimeters.
Keep the sample facing away from the Knudsen cell to avoid uncontrolled deposition of the molecular material. Switch on the Knudsen cell and set the temperature calibrated previously with a quartz microbalance for molecule evaporation. Deposit the molecules by rotating the sample to face the Knudsen cell, and keep the sample in this position for four minutes.
Then rotate the sample to face away from the Knudsen cell and switch off the Knudsen cell to stop evaporation. Anneal the sample with molecules at 320 degrees Celsius for 15 minutes, and then to 370 degrees Celsius for 15 minutes. After each annealing step, measure the sample by LTSTM coupled with AFM to investigate the current stage of the experiment and verify the presence and type of generated objects.
When lock-in is off, approach the sample surface with the STM tip. First, perform the course approach using the Z drive. During the approach, observe the STM tip and its mirror image using a camera.
Further approach the sample into the tunneling distance with the use of the microscope software. Then retract the tip two to three steps from the surface. Turn on the lock-in, and set the lock-in parameters such as frequency, amplitude, and time constant.
Monitor the IT signal. By changing the phase of the lock-in amplifier, minimize the IT signal around zero. Approach to the surface.
Then calibrate the DIDV on a clean gold 111 surface by looking for the position and shape of the Shockley surface state. For DIDV mapping, set the low value of the scan speed. After cooling the sample in the microscope, open the valve for 1.5 minutes and set the carbon monoxide pressure at five by 10 raised to the power minus eight millibars.
Check the sample under STM. When the tip is metallic, the carbon monoxide molecules on the gold surface exhibit a specific contrast. To pick up a single molecule, place the tip above the carbon monoxide molecule and retract the tip by at least 0.3 nanometers.
Ramp the voltage to three volts before returning the tip to the predefined position. The abrupt change in the I value indicates the carbon monoxide pickup manipulation process. Check if the STM contrast of the CO molecule changed.
The image shows the typical appearance recorded at 0.5 volts and 15 picoamperes. After performing the STM scan, choose the separated single molecule for NC-AFM measurements. Find a proper Z plane parallel to the molecule plane.
Retract the tip from the surface by approximately 0.7 nanometers, and turn off the STM loop. The microscope is ready to start NC-AFM measurements. The first step of cyclo-dehydrogenation is achieved by annealing molecular precursors at 320 degrees Celsius, resulting in isolated molecular propellers.
The non-planar conformation of the molecules can be inferred from their STM appearance with three discernible bright lobes. The final cyclo-dehydrogenation yields aniline pores, and is achieved when the sample is heated up to 370 degrees Celsius, resulting in a molecular mixture with single entities containing one, two, or three embedded pores. The detailed structural characterization is obtained by bond-resolved NC-AFM measurements, which display the presence of the trigonal porous nanographene.
The central phenyl ring is located closer to the gold surface. The appearance of the nanographene suggests that the structure adopts a non-planar conformation, due to the steric interactions between hydrogen atoms inside the aniline pores. The single point STS and spatial STS mapping provide unprecedented insight into the properties of the nanoscale objects with submolecular resolution.
The resonance recorded at minus 1.06 volts could be linked with the highest occupied molecular orbital, while the one acquired at 1.61 volts is dominated by the lowest unoccupied molecular orbital. The on-surface synthesis paves the way to our low-dimensional anatomically precise systems, like nanometric molecules, graphene aniline bonds, and new carbon allotropes. It also inspires the development of carbon-based magnetism or new functional devices.
Overview
This article demonstrates the on-surface synthesis of non-planar nanographenes using a combination of solution chemistry and sequential surface-assisted processes. The protocol details the preparation of gold substrates, deposition of molecular precursors, and stepwise annealing, followed by advanced characterization using scanning tunneling microscopy (STM) and non-contact atomic force microscopy (NC-AFM). The approach enables atomic-scale insight into the structure and electronic properties of novel carbon-based nanostructures.
Key Study Components
Area of Science
- Surface chemistry
- Nanoscale materials science
- Scanning probe microscopy
Background
- On-surface synthesis is a promising method for creating new molecular structures, including graphene nanoribbons and nanographenes.
- This approach combines solution-phase preparation of molecular precursors with ultra-high vacuum (UHV) surface-assisted transformations.
- Advanced imaging techniques such as STM and AFM allow for atomic-scale characterization of synthesized nanostructures.
- Challenges include reliance on metallic surfaces and limited yield, motivating efforts to expand the method's applicability and productivity.
Purpose of Study
- To demonstrate the synthesis of non-planar nanographenes via on-surface methods.
- To combine solution chemistry with sequential surface-assisted reactions for precise nanostructure fabrication.
- To achieve detailed atomic-scale characterization of the resulting nanographenes.
Methods Used
- Preparation and cleaning of gold (111) monocrystal substrates using acetone, ultrasonic cleaning, annealing, and argon ion sputtering.
- Deposition of molecular precursors onto the gold surface via a Knudsen cell under UHV conditions.
- Stepwise annealing of the sample at 320°C and 370°C to induce cyclo-dehydrogenation and nanographene formation.
- Characterization using low-temperature STM, NC-AFM, and scanning tunneling spectroscopy (STS) for structural and electronic analysis.
Main Results
- Successful synthesis of non-planar nanographenes with trigonal porous structures on gold surfaces.
- STM images revealed isolated molecular propellers and the formation of aniline pores after sequential annealing steps.
- NC-AFM provided bond-resolved images confirming the non-planar conformation and detailed structure of the nanographenes.
- STS measurements identified electronic resonances corresponding to the highest occupied and lowest unoccupied molecular orbitals.
Conclusions
- On-surface synthesis enables the creation of atomically precise, low-dimensional carbon nanostructures.
- The combination of solution and surface chemistry, along with advanced microscopy, provides unprecedented insight into nanoscale materials.
- This approach paves the way for new carbon allotropes and functional devices, including potential applications in carbon-based magnetism.
Frequently Asked Questions
Executive Industry Relevance
Atomic-scale visualization and synthesis of porous nanographenes via combined solution and on-surface chemistry provide a platform for precise molecular engineering in early discovery. This approach enables detailed structural and electronic characterization, supporting mechanistic de-risking and predictive confidence in nanoscale material development. The methodology is strategically positioned to inform R&D decisions in advanced materials and device prototyping pipelines.
Strategic Applications in Biopharma R&D
Early Discovery & Target Validation
- Enables atomic-level interrogation of carbon-based nanostructures for functional property assessment.
- Supports mechanistic de-risking by revealing structure-property relationships in novel materials.
- Facilitates predictive confidence in the design of next-generation nanomaterials for biomedical interfaces.
Screening & Assay Development
- Provides validated nanoscale systems for downstream functionalization and screening workflows.
- Delivers reproducible, quantitative imaging outputs for comparative analysis of molecular architectures.
- Enables platform standardization for high-resolution material characterization.
Translational & Preclinical Research
- Aligns atomic-scale material insights with translational research on device and sensor interfaces.
- Supports continuity from discovery to preclinical validation of nanomaterial-enabled technologies.
- Informs risk-adjusted advancement of carbon-based platforms for biomedical applications.
Pipeline & Workflow Integration
This method integrates at the interface of early discovery and advanced material screening, bridging solution-phase synthesis with atomic-resolution surface analysis.
- Discovery Biology: Enables hypothesis testing on structure-function relationships in engineered nanographenes.
- Screening: Provides reproducible, quantitative STM and NC-AFM outputs for material comparison.
- Analytics: Delivers electronic and structural readouts supporting cross-condition analysis.
- Translational Research: Connects atomic-scale findings to preclinical device and sensor development when relevant.
- Enterprise Reuse: Establishes a reusable workflow for precision nanomaterial synthesis and characterization.
Operational & Enterprise Impact
- Scientific Value: Increases predictive confidence and reduces ambiguity in nanomaterial design.
- Operational Value: Standardizes high-resolution imaging and synthesis protocols for reproducibility.
- Strategic Value: Informs go/no-go decisions for advanced material platforms in R&D portfolios.
- Portfolio Impact: Supports risk-adjusted prioritization of nanomaterial-enabled technologies.
Implementation Considerations
- Requires expertise in surface chemistry, scanning probe microscopy, and UHV instrumentation.
- Demands access to advanced imaging infrastructure and precise thermal control systems.
- Necessitates rigorous cross-team standardization for reproducible synthesis and analysis.
- Adaptation to non-metallic substrates may require further methodological development.
- Yield and scalability limitations should be considered for broader application.
Biopharma FAQs
Chapters in this video
0:00
Introduction
0:24
Preparation of the Atomically Clean Gold Surface
1:53
Deposition of the Nanographene Precursor on the Gold Crystal
2:32
On-Surface Preparation of the Nanographenes
3:52
dI/dV Measurements
4:55
NC-AFM Sensor Functionalization and NC-AFM with Carbon Monoxide Measurements
6:19
Results: Characterization of Nanographenes by Scanning Probe Microscopy Methods
7:58
Conclusion
