First-principles modeling of oligo(ethylene glycol)-terminated and amide group containing alkanethiolates

Recently, self-assemblies of HS(CH2)15CONH(CH2CH2O)6H were found to undergo a reversible temperature-driven conformational transition from the helical to all-trans state [R. Valiokas, M. Östblom, S. Svedhem, S.C.T. Svensson, B. Liedberg 104 (2000) 7565]. The transition reveals distinctive signatures in the reflection-absorption (RA) spectrum associated with different conformations of the OEG portion of the SAM [R. Valiokas, M. Östblom, S. Svedhem, S.C.T. Svensson, B. Liedberg 104 (2000) 7565]. Here we report an extensive ab initio modeling of infrared RA spectra of molecular constituents of OEG-terminated amide-containing SAMs. The model spectra for this type of molecules (with large OEG and alkyl portions) are obtained, for the first time, by using DFT methods with gradient corrections. The position and relative intensities of all characteristic bands, observed in the fingerprint region of the SAM RA spectrum, are shown to be well reproduced by the single-molecule model spectrum calculated for a certain relative orientation of the alkyl- and OEG portions and the amide bridge. This provides us additional information about actual structure, particularly, molecular orientation within the OEG-containing SAMs in focus.