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Molecular orbital interpretation of thymine/graphite nc‐AFM images
Author(s) -
Komiyama Masaharu,
Uchihashi Takayuki,
Sugawara Yasuhiro,
Morita Seizo
Publication year - 2001
Publication title -
surface and interface analysis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.52
H-Index - 90
eISSN - 1096-9918
pISSN - 0142-2421
DOI - 10.1002/sia.1004
Subject(s) - thymine , highly oriented pyrolytic graphite , adsorption , crystallography , chemistry , graphite , molecule , hydrogen bond , dimer , substrate (aquarium) , chemical physics , materials science , dna , organic chemistry , biochemistry , oceanography , geology
Recent non‐contact atomic force microscopy (nc‐AFM) images of a deoxyribonucleic acid (DNA) base thymine (2,4‐dioxy‐5‐methylpyrimidine) vacuum‐deposited on a highly oriented pyrolytic graphite (HOPG) surface are interpreted by means of theoretical adsorption simulations, and the molecular geometry and the energetics of the adsorption system are estimated. The lowest‐energy dimer configuration was found to be the one in which the respective hydrogen on N1 and the oxygen on C6 of two thymine molecules hydrogen bond to each other. A surface unit cell structure was reproduced. Adsorption energy for the thymine pair on HOPG is rather small, amounting to only ∼1 kcal mol −1 , with small variations depending on the molecular orientation with respect to the substrate surface. The possibility of having a mirrored adsorption configuration in adjacent domains also is suggested. Copyright © 2001 John Wiley & Sons, Ltd.