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SAM structure modelling

First principal modeling of SAM structure and IR RA spectra (Visby program)

In the theoretical part of the Visby project (now ended), we used ab initio modeling of molecules of the type S-(CH2) nCNOH-EGmR , R = CH3, H.

Calculations of geometry, vibration frequencies, and transition dipole moments of SAM molecular constituents are performed on the basis of density functional theory (DFT) with non-local gradient corrections and elaborated basis sets. The main focus of this modeling is on the microscopic interpretation of experimental data on reflection-absorption spectra of ( oligo )ethylene glycol (OEG) terminated SAMs.


The results of calculations are rationalized in terms of three sets of Euler angles shown in the figure and provide the most complete information about molecular orientation within the SAM respective to the substrate surface and relative orientation of alkane , amide, and OEG moieties. These data are crucial for the understanding of OEG-terminated SAMs functionalities and their modification in a desirable way. For example, it was shown that in highly ordered SAMs , OEG axis is substantially tilted by more than 20o that gives a new platform for the basic understanding for SAM-surface Physics and Chemistry. By improving our computing facilities and calculation routine, we are trying to make a qualitatively new step: modeling of self-assemblies with full account to intermolecular interactions at ab initio level. Although this will be done within a somewhat restricting framework of periodic boundary conditions, the results are expected to give an informative insight into the interior of self-assemblies of OEG-terminated amide bridged alkane­thiolates . In particular, we hope to visualize the network of lateral hydrogen bonding and to refine our knowledge about precise positioning of SAM molecular constituents, especially, regarding the orientation of terminus head group R. In the future work, we plan to investigate the role of disorder, adsorption and penetration of water molecules into SAMs and other aspects closely connected with current experimental research.

Figure1: Euler angles Ø(A ,E,N) (tilt) and y(A,E,N) (rotation) for alkyl (A), OEG (E) and amide (N) group. Axes ( xA ,yA,zA ), ( xE,yE,zE ) and ( xN,yN,zN ) correspond to alkyl segment, OEG helix, and amide group. Azimuthal angle jA denotes rotation with respect to the surface normal.

Further reading:

1. R . Valiokas , L . Malysheva , A . Onipko , Hung - Hsun Lee , Ž. Ru ž el ė, S . Svedhem , S . C . T . Svensson , U . Gelius , and B . Liedberg . On the quality and structural characteristics of oligo ( ethylene glycol) assemblies on gold: An experimental and theoretical study. J. of Electron Spectroscopy and Related Phenomena, 172, Issues 1-3, pp. 9-20 .

2. Hung-Hsun Lee , Ž. Ruželė , L . Malysheva , A . Onipko , A . Guts , F . Bj o refors , R . Valiokas and B . Liedberg . Long-chain alkylthiol assemblies containing buried in-plane stabilizing architectures. Langmuir, 2009, DOI: 10.1021/la901668u

(In collaboration with Lyuba Malysheva and Alexander Onipko, Bogolyubov Institute for Theoretical Physics, Kiev , 03143, Ukraine.)

Responsible for this page: Erik Martinsson
Last updated: 01/13/15