Vibrations of a molecule in an external force field

Abstract

The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

Lateral manipulation of single iron adatoms by means of combined atomic force and scanning tunneling microscopy using CO-terminated tips

“…By using a sinusoidal model potential, this translates into a lateral force needed to overcome these barriers of 65 ± 20 pN and 84.4 pN, respectively. Emmrich et al 38 proposed a lowering of the potential barrier by 50% due to the presence of the AFM tip in lateral manipulation experiments of single CO molecules on Cu(111) and recent experiments report a bond weakening between CO and Cu(111) induced by the presence of the tip 45 . In our experiments with single iron adatoms on Cu(111), the lowering of the potential barrier is up to 70% with respect to the theoretical value of 28.5 meV 32 , and, hence, even higher.…”

Controlling an SN2 Reaction by Electronic and Vibrational Excitation: Tip‐Induced Ether Cleavage on Si(001)

“…S N 2 reactions are textbook examples for how to control solution‐based chemical reactions by means of steric hindrance or the choice of solvent. On the other hand, scanning probe microscopy has proven to be a powerful tool to induce and manipulate reactions on the single‐molecule level . Herein, we show for ether cleavage on silicon, which is a surface analogue of an S N 2 reaction, that the reaction cannot only be induced by tip‐induced excitation of the system but that the type of the final products can be controlled by selectively addressing different excitation mechanisms.…”

Quantitative prediction model for affinity of drug–target interactions based on molecular vibrations and overall system of ligand-receptor

“…Moreover, molecular vibrations are affected by various factors such as conjugation effect, induction effect, spatial effect, hydrogen bonding, vibrational coupling effect, etc. Therefore, molecular vibrations can reflect drug molecular structure and physicochemical properties of drugs to a certain extent [ 37 ]. It should be remembered that seven physicochemical properties are particularly relevant to molecular vibrations, including electronegativity, π-atomic charge, total charge, and bond polarity [ 38 ].…”