First-principle DFT modeling of IR spectra
of oriented helical HS(CH
2
CH
2
O)
n
CH
3
molecules
Lyuba Malysheva
£
and Alexander Onipko
†
£
Bogolyubov Institute for Theoretical Physics, Kiev, 03143, Ukraine
†
Division of Physics, Luleå University of Technology, S-971 87 Luleå, Sweden
Abstract. Only very recently have chemically defined, highly ordered self-assembled monolayers
(SAMs) of HS(CH
2
CH
2
O)
n
CH
3
, n
5
6, become accessible for systematic infrared spectroscopy
analysis [1]. Here we report the results of the first ab initio modeling of reflection-absorption (RA)
spectraofspecificallyorientednon-interactingmoleculeswhichrepresent these SAM constituents.
1
The RA spectra of HS(CH
2
CH
2
O)
5
6
CH
3
, 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 CH
2
-stretching
region of experimental SAM spectra. Arguments which show that the observed band (which earlier
was attributed to symmetric CH
3
-stretching vibrations) has a distinctively different character are
presented.
INTRODUCTION
Oligo(ethylene glycol) (OEG) terminated SAMs are attracting much attention as biomi-
matic materials, principally (but not only) because of their unique protein selective sur-
face properties due to exposed OEG-segments, see [1, 2] and references therein. Infor-
mation about the structure of the surface and SAM molecular constituents is mostly
inferred from infrared RA and IR–visible sum frequency vibrational spectra [3, 4]. In
this type of analysis, the availability of reliable reference spectra is crucially important.
The well-established spectral data for ethylene-glycol polymers are not quite suitable
and therefore, often insufficient for the purpose of comparison. Additionally, the OEG-
containing SAMs studied so far include a large a lkyl portion whose contribution to the
observed spectrum makes the identification of the OEG bands difficult and uncertain.
For these reasons for a long time one of the most characteristic features in the RA spec-
tra of self-assembled OEG-terminated alkanethiolates was misassigned and identified as
the symmetric CH
2
-stretching vibration of the OEG in the helical conformation [5].
Very recently, highly ordered self-assemblies of OEGs with thiol and methyl ter-
mini [HS(CH
2
CH
2
O)
n
CH
3
, n
5
6] have been obtained and characterized by RA
spectroscopy and other methods [1, 2]. This suggests that we have a possibility of
straightforward comparison of the first-principle calculations of the OEG structure and
1
The authors thank Dr. D.J. Vanderah for his data files of the reflection-absorption SAM spectra.
© 2003 American Institute of Physics 0-7354-0154-3/03/$20.00
Electronic Properties of Novel Materials,
edited by H. Kuzmany, J. Fink, M. Mehring, and S. Roth
CP685,
Molecular Nanostructures: XVII Int'l. Winterschool/Euroconference on
486