Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold:  Results of ab Initio Modeling

Abstract

The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH(2))(15)CONH(CH(2)CH(2)O)(6)H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.

Surface functionalization of germanium ATR devices for use in FTIR-biosensors

“…2. The peaks found at 2956 cm −1 (w, CH 3 st as), 2923 cm −1 (s, CH 2 st as) and 2853 cm −1 (m, CH 3 st sy) are in moderate agreement with previous theoretical works devoted to PEG-SAMs on gold and experimental measurement by infrared reflection-absorption (RA) spectroscopy [34][35][36][37][38]. Sample Si-PEG 2b showed similar features in the 2800-3000 cm −1 region; the carbamate NH stretching was also visible (broad peak at 3330 cm −1 ).…”

“…region, a broad band centered at 1110 cm −1 (C-O-C asymmetric stretching) was visible. In the spectrum of Ge-PEG 2b, the signals due to the N-(3-silyloxypropyl)-carbamate moiety superposed partially on the (EO)n pattern [34][35][36][37][38]. Main signals attribution of Ge-PEG 2b are given in Table 3.…”

“…3). Ge-PEG 1a sample showed broad bands at 2938 cm −1 and 2871 cm −1 (CH 2 asymmetric and symmetric stretching, respectively), more typical of disordered ethylene oxide (EO) methylene groups than oriented SAMs of (EO) n [34][35][36][37][38]. In the fingerprint Fig.…”

Structural and kinetic properties of laterally stabilized, oligo(ethylene glycol)-containing alkylthiolates on gold: A modular approach

“…Note, that we used a three-layer optical model treating the SAM as a transparent isotropic material with the refractive index n = 1.5, which certainly is an oversimplification. Nevertheless, the chosen model gives a thickness that is in excellent agreement with values obtained by superimposing the thickness for an oriented SAM of EG 6 , 39.8± 1.7 Å, 28 and that of a HS͑CH 2 ͒ 15 CH 3 ͑hereafter SC 16 …”

“…The results are compared with recent observations obtained for a related system of OEGs, 16,17 where the OEG portion pins directly to gold via the thiol group and forms a crystalline support for a highly ordered outermost layer of the alkyl chains. Our experimental findings are also compared with data obtained for simple alkylthiols and an analogous set of OEG derivatives without the extended alkyl chain, as well as with results from recent theoretical studies 28,29 in order to reveal the influence of the competing intra-and intermolecular interactions on the phase behavior and overall stability of the SAM. Finally, we demonstrate a potential application of such highly ordered alkyl-terminated OEG SAMs for the fabrication of microarrays based on confined hydrophilic and disordered "hydrogel-like" domains.…”