Calculating free energies of organic molecules on insulating substrates

Beilstein Journal of Nanotechnology

关键词: entropy;    free energy;    molecular dynamics;    organic molecules;    potential of mean force;    thermodynamic integration surface step;   

DOI  :  10.3762/bjnano.8.71

学科分类：地球科学(综合)

来源: Beilstein - Institut zur Foerderung der Chemischen Wissenschaften

【 摘 要 】

The challenges and limitations in calculating free energies and entropies of adsorption and interaction of organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free energy profiles and entropy changes were calculated for step adhesion and dimer formation of these molecules. However, converging these calculations is nontrivial and comes at large computational cost. We illustrate the difficulties as well as the possibilities of applying these methods towards understanding dynamic processes of organic molecules on insulating substrates.

【 授权许可】

CC BY