Label-Free Dynamic Detection of Single-Molecule Nucleophilic-Substitution Reactions

Abstract

The mechanisms of chemical reactions, including the transformation pathways of the electronic and geometric structures of molecules, are crucial for comprehending the essence and developing new chemistry. However, it is extremely difficult to realize at the single-molecule level. Here, we report a single-molecule approach capable of electrically probing stochastic fluctuations under equilibrium conditions and elucidating time trajectories of single species in non-equilibrated systems. Through molecular engineering, a single molecular wire containing a functional center of 9-phenyl-9-fluorenol was covalently wired into nanogapped graphene electrodes to form stable single-molecule junctions. Both experimental and theoretical studies consistently demonstrate and interpret the direct measurement of the formation dynamics of individual carbocation intermediates with a strong solvent dependence in a nucleophilic-substitution reaction. We also show the kinetic process of competitive transitions between acetate and bromide species, which is inevitable through a carbocation intermediate, confirming the classical mechanism. This unique method creates plenty of opportunities for carrying out single-molecule dynamics or biophysics investigations in broad fields beyond reaction chemistry through molecular design and engineering.

Side-group chemical gating via reversible optical and electric control in a single molecule transistor

“…The B3LYP hybrid functional and the 6-31G basis set were taken in the Gaussian calculation. The electric potential energy under finite biases and the charge transport properties of the two-probe structures were obtained by carrying out the DFT within the NEGF formalism, as implemented in the quantum transport package Nanodcal 47,48 . Double-zeta polarised atomic orbital basis set was used in the NEGF–DFT calculation, and exchange-correlation was treated at the PBE-GGA level.…”

Electric field–catalyzed single-molecule Diels-Alder reaction dynamics

“…The present work used an electrical monitoring platform based on graphene-molecule-graphene single-molecule junctions (GMG-SMJs) (21,22) to show that (i) a single-molecule connection can be directly characterized by photoelectric integration, (ii) stable covalent anchoring and determined interface coupling are suitable for complex reaction conditions, (iii) the fixed single-molecule system can provide in situ monitoring of reactions, and (iv) label-free highspeed electrical sampling of the molecular conductance provides high temporal resolution and faithful synchronization to the chemical reaction. Previous studies detecting intermolecular interactions (23,24) and chemical reactions (25,26) are extended here to offer the most complete description of single-molecule Diels-Alder reaction dynamic.…”

Single molecule electronic devices with carbon-based materials: status and opportunity

“…Gu et al developed a method to use single-molecule junctions (SMJs) as an electrical platform to measure a reversible unimolecular nucleophilic substitution (S N 1) reaction at the single-molecule level. 31 Stable graphene-molecule-graphene single-molecule junctions (GMG-SMJs) were formed via covalent attachment of a single molecular wire comprised of a functional center of 9-phenyl-9-fluorenol into graphene nanogapped electrodes (Fig. 5).…”