Benzo-bis(imidazole) self-assembled monolayers molecular junctions in meta or para conformation: effects of protonation on the electrical and thermal conductances

This study demonstrates that protonation of benzo-bis(imidazole) self-assembled monolayers reversibly enhances thermal conductance while reducing electrical conductance specifically in meta-connected molecular junctions, a phenomenon attributed to protonation-induced structural reorganization at the molecule-electrode interfaces rather than changes in molecular orbital energy levels.

The Gist

Imagine you have a tiny, microscopic bridge made of a single layer of molecules. This bridge connects two metal "islands" (electrodes). Scientists are trying to figure out how well this bridge lets two things pass through: electricity (like traffic) and heat (like warmth from a fire).

This paper is about testing two different designs for these molecular bridges and seeing what happens when you "turn on a switch" by adding a little bit of acid (protonation).

Here is the breakdown in simple terms:

1. The Two Bridge Designs: "The Highway" vs. "The Maze"

The researchers built bridges using special molecules called benzo-bis(imidazole). The key difference was how they attached the molecule to the metal islands.

• The "Para" Design (The Highway): Imagine a straight, open highway. The molecule is attached at the very ends, creating a direct, straight path.
• The "Meta" Design (The Maze): Imagine a winding road or a maze where the molecule is attached in a way that forces the path to twist and turn.

The Finding:

• Electricity: As expected, the straight "Highway" (Para) lets electricity flow easily. The "Maze" (Meta) is much worse at it because the electrons get confused by the twists (a phenomenon called destructive quantum interference). It's like trying to run a race on a straight track versus a track with sudden U-turns; the runner on the U-turn track is much slower.
• Heat: Surprisingly, the "Maze" (Meta) also blocks heat much better than the "Highway." It's like a maze that not only confuses runners but also stops warm air from flowing through it easily. This confirms a theory that twisting the path stops heat vibrations (phonons) from traveling efficiently.

2. The Magic Switch: Adding Acid (Protonation)

The molecules have a special "switch" in their middle. When the scientists exposed the bridges to acid vapors (protonation), they added a tiny positive charge to the molecules.

What happened to the "Highway" (Para)?

• Electricity: It acted differently depending on the specific molecule. Sometimes it got faster, sometimes slower.
• Heat: It didn't really care. The heat flow stayed the same. The highway was too rigid and straight to change its shape much.

What happened to the "Maze" (Meta)?

• Electricity: It got slower. The traffic jam got worse.
• Heat: It got faster (about 50% faster)! This was the big surprise.

3. The Secret Reason: The "Dancing Crowd"

Why did the "Maze" get better at conducting heat when the switch was flipped?

Imagine the molecules in the "Maze" (Meta) are like a crowd of people standing on a dance floor, but they are all leaning heavily to the side (tilted) and bumping into each other awkwardly. This makes it hard for heat to pass from one person to the next.

When the scientists added the acid (protonation):

1. The molecules stood up straighter, like people in the crowd suddenly standing up and lining up neatly.
2. Because they stood up, the "hands" of the molecules (the sulfur anchors) touched the metal islands more firmly.
3. This created a better handshake between the molecule and the metal.

The Analogy:
Think of heat transfer like passing a bucket of water down a line of people.

• Before (Tilted): The people are leaning over, struggling to pass the bucket. A lot of water spills (heat is lost).
• After (Upright): The acid made them stand up straight. Now they can pass the bucket smoothly and quickly. The "handshake" is tighter, so the heat flows better.

4. Why Does This Matter?

This research is a big deal for two reasons:

1. Proof of Theory: It proves that twisting a molecule (Meta) really does block heat, which helps engineers design better materials.
2. Smart Materials: It shows that we can build tiny switches that control heat and electricity just by changing the chemistry (adding acid). This could lead to super-small computers or sensors that can turn heat flow on and off like a light switch.

In a nutshell:
The scientists found that a "twisted" molecular bridge blocks heat better than a straight one. But, when they added acid, the twisted bridge stood up straight, improved its grip on the metal, and suddenly became much better at conducting heat. It's like a messy room that, when you tidy it up, suddenly lets the air circulate perfectly.

Technical Summary

1. Problem Statement

Molecular junctions (MJs) exhibit distinct electron transport properties depending on the connectivity of the molecule to the electrodes (para vs. meta). It is well-established that meta-connected molecules suffer from Destructive Quantum Interference (DQI), resulting in significantly lower electrical conductance compared to their para-connected counterparts. While the impact of connectivity on electrical transport and thermoelectric properties (Seebeck coefficient) is documented, the effect on thermal conductance remains less explored experimentally.

Furthermore, there is a need to understand how stimuli-responsive (switchable) molecular junctions behave under external triggers (such as pH changes/protonation) regarding both electrical and thermal transport. Specifically, it is unclear whether protonation affects thermal conductance similarly to electrical conductance, and if the structural reorganization of the monolayer upon protonation influences heat transfer at the molecule-electrode interfaces.

2. Methodology

The study employed a combination of chemical synthesis, self-assembly, and advanced nanoscale characterization techniques:

• Molecular Design & Synthesis:
  • Four benzo-bis(imidazole) derivatives were synthesized: 1-para, 1-meta, 2-para, and 2-meta.
  • Molecules 1 lack side groups, while molecules 2 possess phenylamine side groups.
  • All molecules feature thiol anchoring groups protected by (trimethylsilyl)ethane, allowing for Self-Assembled Monolayer (SAM) formation on gold.
• Junction Fabrication:
  • SAMs were formed on ultra-flat template-stripped gold (TSAu) substrates.
  • The thiol protecting groups were removed in situ using tetrabutylammonium fluoride (NBu4F) in a DMSO:ethanol solution.
• Characterization Techniques:
  • Conductive Atomic Force Microscopy (C-AFM): Used to measure current-voltage (I-V) characteristics and determine electrical conductance.
  • Scanning Thermal Microscopy (SThM): Specifically Null-Point SThM (NP-SThM) was used to measure thermal conductance. This differential method eliminates parasitic heat contributions (e.g., air conduction) by measuring the temperature jump ($T_{NC} - T_C$) when the tip contacts the sample.
  • Ellipsometry: Used to measure SAM thickness and infer molecular tilt angles.
• Stimuli Application:
  • Protonation was achieved by exposing SAMs to HCl vapors; deprotonation was achieved using NEt$_3$ vapors.
  • Measurements were taken in three states: Pristine, Protonated, and Deprotonated.
• Data Analysis:
  • Electrical data was fitted using the Single Energy Level (SEL) model to extract HOMO energy levels ($\epsilon_H$) and molecule-electrode coupling energies ($\Gamma$).
  • Thermal data was analyzed using the Dryden model to decouple the SAM's thermal conductance from the underlying gold substrate.

3. Key Contributions

• Experimental Verification of Phonon Interference: The study provides experimental evidence that meta-connected molecular junctions exhibit lower thermal conductance than para-connected ones, confirming theoretical predictions regarding phonon destructive interference.
• Decoupling Electrical and Thermal Switching Mechanisms: The research demonstrates that protonation affects electrical and thermal conductances differently depending on the connectivity (meta vs. para).
• Structural Reorganization as a Control Mechanism: The authors establish that the switching behavior in meta-connected junctions is driven primarily by structural reorganization (changes in molecular tilt and packing density) rather than intrinsic changes in molecular orbital energy levels.

4. Key Results

A. Electrical Conductance

• Connectivity Effect: As expected, meta-connected junctions showed lower electrical conductance than para-connected ones due to DQI.
  • Meta: $\approx 10^{-9}$ to $4.1 \times 10^{-9}$ S.
  • Para: $\approx 4.2 \times 10^{-9}$ to $2.4 \times 10^{-8}$ S.
• Protonation Effect:
  • Meta-connected: Electrical conductance decreased reversibly upon protonation (by factors of $\approx 2$ for 1-meta and $\approx 15$ for 2-meta).
  • Para-connected: Behavior was mixed; 1-para conductance increased, while 2-para decreased.
• Mechanism: The SEL model analysis revealed that the HOMO energy level ($\epsilon_H$) remained largely unchanged upon protonation. The decrease in conductance for meta-junctions was attributed to a reduction in the electronic coupling energy ($\Gamma$) caused by the increase in SAM thickness (molecules straightening up) and changes in the contact geometry.

B. Thermal Conductance

• Connectivity Effect: Meta-connected SAMs exhibited significantly lower thermal conductance than para-connected SAMs, consistent with phonon interference theory.
  • Para (Pristine): $\approx 37 - 40$ nW/K.
  • Meta (Pristine): $\approx 16 - 29$ nW/K.
• Protonation Effect (The Novel Finding):
  • Meta-connected: Thermal conductance increased significantly (by $\approx 50\%$) upon protonation and returned to baseline upon deprotonation.
  • Para-connected: Thermal conductance remained unchanged upon protonation/deprotonation.
• Mechanism: The increase in thermal conductance for meta-junctions is attributed to structural reorganization:
  1. Tilt Angle Change: In the pristine state, meta-molecules are highly tilted ($\approx 66^\circ$). Upon protonation, they straighten ($\approx 45^\circ$), increasing SAM thickness.
  2. Interface Modification: The straightening exposes more thiol (S) groups at the top surface, allowing the SThM tip to form a chemisorbed (-C-S-Pd) contact rather than a weak mechanical contact with the molecular backbone. This improves the interfacial thermal conductance (Kapitza resistance reduction).
  3. Para Stability: Para-molecules are already nearly perpendicular; thus, protonation does not significantly alter their packing or interface quality.

5. Significance

• Fundamental Physics: This work bridges the gap between theoretical predictions of phonon interference in molecular junctions and experimental reality, confirming that meta-connectivity suppresses thermal transport just as it suppresses electrical transport.
• Thermal Switching: It demonstrates that thermal conductance in molecular junctions can be reversibly switched (tuned) via chemical stimuli (pH), but this switching is highly dependent on the molecular connectivity and the resulting structural dynamics of the monolayer.
• Design Principles: The study highlights that for responsive molecular devices, the interface quality (chemisorbed vs. physisorbed) and molecular packing are critical determinants of thermal transport, often outweighing intrinsic molecular properties. This provides a new design rule for molecular thermoelectrics and thermal management at the nanoscale.
• Differentiation of Transport Modes: It clarifies that electrical and thermal transport in these systems are not always coupled in the same way; a stimulus can increase thermal conductance while decreasing electrical conductance, depending on the structural changes induced.