Structural analysis of HS(CD(2))(12)(O-CH(2)-CH(2))(6)OCH(3) monolayers on gold by means of polarization modulation infrared reflection absorption spectroscopy. progress of the reaction with bromine

A self-assembled monolayer (SAM) on gold was formed with specifically perdeuterated hexaethylene glycol-terminated alkanethiol HS(CD(2))(12)(O-CH(2)-CH(2))(6)OCH(3) (D-OEG). The structure of the d-alkane and the oligoethylene glycol (OEG) parts of the molecule in a SAM was studied by means of polarization modulation infrared reflection absorption spectroscopy. The D-OEG monolayers are highly ordered and exist in a crystalline phase. The d-alkane chain adopts an all-trans conformation. Both, the d-alkane chain and long axis of the OEG part make an angle of 26.0 degrees +/- 1.5 degrees with respect to the surface normal, a value characteristic for the tilt of solid n-alkane thiols in the SAMs on Au. The positions of nu(as)(COC) and CH(2) wagging and rocking modes indicate a helical arrangement of the OEG chains. The D-OEG SAMs were exposed to 25 muM Br(2) in two ways: (i) by immersion into the Br(2) solution and (ii) in the galvanic cell Au|D-OEG SAM|25 muM Br(2) + 0.1 M Na(2)SO(4)|| 50 muM KBr + 0.1 M Na(2)SO(4)|Au. In the galvanic cell, the oxidant (Br(2)) is scavenged by a heterogeneous electron transfer reaction, slowing the reaction of D-OEG with Br(2). The slow progress of the reaction with Br(2) allowed us to draw conclusions about molecular rearrangements taking place during this reaction. The reaction with Br(2) starts on boundaries and/or defects present in the SAM. First, at the defect place, the alpha-C atom of the OEG chain reacts with Br(2) and the OEG part of the molecule is removed from the monolayer. In consequence an increase in disorder in the OEG part of the SAM is observed. The same mechanism of the reaction with Br(2) is applied for the d-dodecane alkanethiol part of the molecule. This reaction is slow, thus the order and the tilt of the hydrocarbon chain changes only a little during the reaction time.