Bio-molecular films of the DNA base guanine were characterized by ellipsometry from the Infrared (IR) to Vacuum Ultraviolet (VUV) spectral range, X-ray diffraction (XRD) and atomic force microscopy (AFM). In this study we in particular focus on the contact-less and reference-free characterization of thin anisotropic bio-molecular films by ellipsometry. Ellipsometric spectra in the IR as well as in the UV -VUV spectral range are molecule specific and the absorption bands could be used to identify molecules deposited on a substrate, since both the vibrational and electronic excitations are molecule specific. Especially we demonstrate that the measured pseudo-dielectric function in the mid infrared (MIR) spectral range can be used as a characteristic "fingerprint" for DNA base molecules and their orientation in a thin film. Moreover an interpretation of the ellipsometric spectra in an optical model delivers the dielectric function and could give information about the molecular structure, orientation and conductivity. The determination of average molecular orientations from IR and UV/VUV ellipsometry spectra is discussed. General remarksBio-molecules are of increasing interest in particular in the field of nanotechnology and the development of new materials. For the DNA base molecules guanine it turned out that aggregates could be used as conducting nanomaterials [1,2]. Modifications of solid surfaces by organic films are of high technological interest in diverse fields such as development of bio-sensors or new types of electronic and optoelectronic devices [3,4]. A central issue for designing such organic hybrid devices is the determination of structural, electronic and optical properties of organic films and how they are bonded to the substrate. In the present article we show that spectroscopic ellipsometry in the infrared and UV-VUV spectral range is a powerful technique to address such type of questions. Ellipsometry can be, on the one hand, extremely sensitive to ultra thin layers and, on the other hand, deliver quantitative information related to their structure and thickness. In the recent decades several studies on the vibrational and electronic properties of guanine molecules have been performed with different methods [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. In our study a deeper insight into the properties of a bio-molecular film was achieved by a combination of XRD, AFM and ellipsometry. Guanine molecules were deposited under ultra-high vacuum (UHV) conditions on hydrogen passivated Si(111) surfaces in order to ensure well defined preparation conditions. Hydrogen pas-
This work is reporting the dielectric functions of DNA base films, i.e. guanine, adenine, cytosine, and thymine in the energy range from near-infrared to ultra-violet. Spectroscopic ellipsometry using synchrotron radiation was employed in situ on DNA base films grown on hydrogen terminated Si(111) surfaces under ultra-high vacuum conditions. The optical response of adenine and guanine films is described by a uniaxial model while in the case of thymine and cytosine films an isotropic model was employed. The imaginary part of the dielectric functions ε 2 of the DNA base films is compared with the electronic transitions of single molecules calculated using time-dependent density functional theory.
The vibrational properties of single-layer PTCDA (perylene-3,4,9,10-tetracarboxylic dianhydride) and H 2 Pc (metal-free phthalocyanine) thin films and PTCDA-H 2 Pc double-layer heterostructures are studied by Raman scattering. The evidence of crystallinity of the single-layer films can be supported by the existence of phonons, as well as polarization dependence. Resonance enhancement Raman scattering has been used to selectively measure the individual layer properties in double-layer H 2 Pc/PTCDA and PTCDA/H 2 Pc heterostructures. When H 2 Pc is grown on PTCDA, its structure departs from the herringbone arrangement characteristic of unstrained H 2 Pc films, as demonstrated by the different peak intensities in the Raman spectra. Well-defined phonons and the polarization dependence in the H 2 Pc top layer are characteristic of long-range order, indicating that the H 2 Pc molecular planes in the templated structure are crystalline. No evidence for a new structure was observed for PTCDA deposited on top of a H 2 Pc first layer. Here, the relative intensity of the phonons in the PTCDA top layer demonstrates that the PTCDA forms microcrystallites due to strain at the molecular heterojunction, before relaxing to its bulk crystalline form.
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