Ellipsometry from infrared to vacuum ultraviolet: Structural properties of thin anisotropic guanine films on silicon

Abstract

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-

Structural and Optical Properties of DNA Layers Covalently Attached to Diamond Surfaces

“…adenine, thymine, guanine, and cytosine). 45 This decrease in intensity and frequency shifts upon base pairing has 14 also been observed by other authors. 57,60 However, additional studies are necessary in order to relate the IR intensities of the single DNA bases to those of DNA molecules.…”

“…The optical response of the DNA layers on UNCD substrate has been described by a uniaxial anisotropic layer model consisting of two sets of Lorentz functions corresponding to the inplane (xy) and out-of-plane (z) directions of the film, as has been employed previously for pure guanine films on silicon. 40,45 The optical response of the measured substrate has been used in the ellipsometric modeling. The model has the advantage of taking into account the roughness of the UNCD substrate before introduction of DNA (see AFM result in Fig.…”

“…42,43 DNA molecules are particularly interesting to be studied with SE in the UV range, because they contain transition dipole moments oriented along two well-defined directions: in the plane of the bases and, perpendicular to this, along the backbone of the strands. 44,45 SE has already been applied to study films of single bases on silicon, 40,45 but to our knowledge this is the first report on its application to study the average tilt angle of integral DNA molecules on CVD diamond surfaces. Although the analysis of SE measurements is more straightforward for atomically flat substrates, the roughness of NCD and especially UNCD films is low and regular enough to correct for by introducing an additional layer in the optical model, with intermediate optical properties.…”

Diamond‐based DNA sensors: surface functionalization and read‐out strategies

“…Whereas ellipsometry using a fixed excitation wavelength is mainly used for determining layer thicknesses, SE allows for the calculation of more parameters, such as the optical constants (refractive index n and extinction coefficient k), the roughness and orientation of molecules [88]. We applied SE in the infrared (IR) and vacuum UV range to investigate the orientation of DNA layers on (U)NCD surfaces.…”

Detection of ultrathin biological films using vacuum ultraviolet spectroscopic ellipsometry

“…guanine, adenine, cytosine, and thymine in the energy range from near-IR to UV have been investigated using VUV-SE. The imaginary part of the dielectric properties ε 2 of the DNA base films was compared to the electronic transitions of single molecules calculated using time dependent density function theory [24], [25] and [26]. The photophysical and photochemical behavior of the organic molecules such as phenylsilane on silicon was also studied by VUV-SE [27].…”