Paper Citing NAMD - Abstract
Tagami, K.; Tsukada, M.
Simulated non-contact AFM images of an alcohol molecule in an alkanethiol self-assembled monolayer
NANOTECHNOLOGY, 18 Art. No. 084005, FEB 28 2007
Based on all-atom empirical force field calculations, non-contact atomic force microscopy ( nc- AFM) images are simulated of a self- assembled monolayer ( SAM) of 1- hexanethiol ( C-6) in which a single 4- mercapto- 1- butanol ( C4OH) molecule is inserted. The tip is modelled by a carbon nanocone apex and the temperature is assumed to be 0 K. It is found that the C6 molecules can be recognized individually in the topographic, frequency shift and energy dissipation images. In addition, the position of a H2O molecule, which is adsorbed by forming a hydrogen bond with the hydroxyl head group of the C4OH molecule, is observed more clearly in the energy dissipation image than in the topographic image. Furthermore, this H2O molecule is observed to be higher than the surrounding C-6 matrix in the topographic image, although the former is slightly lower than the latter. This can be explained by the enhancement of the normal force by an attractive electrostatic interaction between the water molecule and the tip apex.
