We report orientation angles for the alkyl chain, amide group, and oligo(ethylene glycol) (OEG) portion within self-assembled monolayers (SAMs) of OEG-terminated and amide containing alkanethiolates which, depending on the OEG length and substrate temperature, display unique conformations - all-trans or helical. Optimized geometries of the molecular constituents, characteristic vibration frequencies and transition dipole moments are obtained by using DFT methods with gradient corrections. These ab initio data are subsequently used to simulate infrared reflection-absorption (RA) spectra associated with different conformations and orientations. The obtained results have generated a deeper knowledge of the internal SAM structure, which is crucial for understanding phase and folding characteristics, interaction with water and ultimately the protein repellent properties of OEG-containing SAMs.

First-principle modeling is used to obtain a comprehensive understanding of infrared reflection absorption (RA) spectra of helical oligo(ethylene glycol) (OEG) containing self-assembled monolayers (SAMs). Highly ordered SAMs of methyl-terminated 1-thiaoligo(ethylene glycols) [HS(CH2CH2O)(n)CH3, n = 5, 6] on gold recently became accessible for systematic infrared analyses [Vanderah et al., Langmuir, 2003, 19, 3752]. We utilized the quoted experimental data to validate the first-principle modeling of infrared RA spectra of HS(CH2CH2O)(5,6)CH3 obtained by (i) DFT methods with gradient corrections (using different basis sets, including 6-311++G) and (ii) HF method followed by a Moller-Plesset (MP2) correlation energy correction. In focus are fundamental modes in the fingerprint and CH-stretching regions. The frequencies and relative intensities in the calculated spectra for a single molecule are unambiguously identified with the bands observed in the experimental RA spectra of the corresponding SAMs. In addition to confirming our earlier assignment of the dominating peak in the CH-stretching region to CH2 asymmetric stretching vibrations, all other spectral features observed in that region have received an interpretation consistent (but not in all cases coinciding) with previous investigations. The obtained results provide an improved understanding of the orientation and conformation of the molecular building blocks within OEG-containing assemblies, which, in our opinion, is crucial for being able to predict the folding and phase characteristics and interaction of OEG-SAMs with water and proteins

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

The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH2)15CONH(CH2CH2O)6H 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.

The density functional theory methods are used to calculate the equilibrium molecular structures and vibrational spectra of helical H(CH2CH2O)nH (OEG) oligomers (n = 4-7) at a level of precision that has not been accomplished before. The largest deviation between experimentally observed frequencies, obtained from infrared reflection-absorption spectra of OEG-monolayers on gold, and calculated, single molecule frequencies (unscaled), is slightly above 2%. Moreover, the most intense peak in the CH2-stretching region at about 2890 cm-1, commonly regarded as a trademark of the OEG helical conformation, is reassigned in this study to the asymmetric CH2-stretching mode.

Only very recently have chemically defined, highly ordered self-assembled monolayers (SAMs) of HS(CH2CH2O)nCH3, n = 5, 6, become accessible for systematic infrared spectroscopy analysis. Here we report the results of the first ab initio modeling of reflection-absorption (RA) spectra of specifically oriented non-interacting molecules which represent these SAM constituents. The RA spectra of HS(CH2CH2O)5,6CH3, are obtained by DFT methods with gradient corrections and using a variety of basis sets, including 6-311++G**. Positioning and relative intensities of all model spectra are unambiguously identified in all but one intense band in the CH2-stretching region of experimental SAM spectra. Arguments which show that the observed band (which earlier was attributed to symmetric CH3-stretching vibrations) has a distinctively different character are presented.

In the single-band approximation, an explicit expression of the exponential factor, that governs tunneling through a thin crystal subjected to a constant electric field, is derived. The basic features of Wannier-Stark, Airy, and intermediate type of quantization, as they are displayed in the transmission spectrum and hence in tunneling current, are thus described analytically.