Plasma polymers are synthesized from hexamethyldisiloxane by capacitively coupled glow discharge. The effect of current density and monomer flow rate on the polymer structure is investigated by FTIR spectroscopy. The influence of the same parameters on the NO2 sensing properties of the polymers is studied by a quartz crystal microbalance.

One of the pre ferred con for ma tions of gua nine-rich nu cleic ac ids in aque ous so lu tions is a four-stranded G-mo tif. Both oligonucleotides and monomeric guanosine mono phos phates can form G-quadruplex struc ture at cer tain ex per i men tal con di tions. At lower con cen tra tions they rep re sent an iso tro pic so lu tion of four-stranded sys tems. How ever, above cer tain con cen tra tion these struc tures can self-as so ci ate and form liq uid crys tal line phases. De pend ing on the con cen tra tion two types of as sem blies can be dis tin guished, cholesteric and hex ag o nal. The op ti cal be hav iour of these supra mo lecu lar sys tems can be most con ve niently mon i tored in the in fra red re gion by vi bra tional cir cu lar dichroism (VCD) spec tros copy. An ab nor mally high VCD in ten sity was ob served for both liq uid crys tal line phases com pared to the iso tro pic so lu tion. The di rec tion of the he li cal twist was ob tained for guadruplexes as well as for their supra mo lecu lar ag gre gates.

This paper deals with the optical properties of thin As2S3–In2S3 films. The thin layers were deposited by thermal co-evaporation of As2S3 and In2S3. The composition of the coatings was controlled by x-ray microanalysis; it was found to be close to the expected one. The refractive index n and optical band gap were calculated from the transmittance and reflectance spectra. The results showed that the refractive index of thin As–S films is not affected by the addition of 1 at% indium and it increases from 2.46 to 2.58 for thin film with 13 at% In. A decrease in the changes in the refractive index, Δn, after exposure to light or annealing with addition of indium in arsenic sulfide is observed. To explain the influence of the indium on the photoinduced changes in the optical properties of thin As–S–In films, the glass structure was investigated by infrared spectroscopy. The calculated values of the optical constants were compared with those obtained from ellipsometric measurements.

A set of newly synthesized aryl-substituted amides of 16-mercaptohexadecanoic acid (R = 4-OH; 3,5-di-OH) are self-assembled on Au(111) substrate. Self assembled monolayers (SAMs) formed by these molecules are studied by ellipsometry from infrared to visible spectral range. Best fit calculations based on the three-phase optical model are employed in order to determine the average tilt angle of the hydrocarbon chains. The data revealed that the SAMs reside in a crystalline-like environment as the long methylene chains predominantly exist in all-trans conformation. The calculated tilt angle of the hydrocarbon chain is decreased by approximately 12° in comparison with the one for the correspondent long-chain n-alkyl thiols. Strong hydrogen bonded networks were detected between the amide proton and the carbonyl oxygen as well as between hydroxyl groups in the end aryl substituents. The transition dipole moments of the C=O, N-H and O-H modes are oriented almost parallel to the gold surface.

The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.

Infrared spectroscopic ellipsometry was used for determination of molecular orientation and for lateral homogeneity studies of organic monolayers on GaAs and Au, the organic layer being either octanedithiol or hexadecanethiol (HDT). The laterally resolved measurements were performed with the infrared mapping ellipsometer at the synchrotron storage ring BESSY II. The molecular orientation within the monolayers was determined by optical model simulations of the measured ellipsometric spectra. Different tilt angles were obtained for the monolayers of HDT and octanedithiol on GaAs: 19 degrees and >30 degrees , respectively. The tilt angle of the methylene chains for HDT on Au substrate (22 degrees ) is similar to the 19 degrees tilt which was obtained for the HDT monolayers on GaAs, thus suggesting similar molecular ordering of the thiolates on both substrates.

Amorphous AsxSe100-x, thin films with different compositions (28 <= x <= 60) were deposited onto Si wafers and optical glass substrates BK-7 by thermal evaporation. The changes in the optical properties and structure of thin films as a function of the composition, film thickness and conditions of thermal evaporation and exposure to light were studied. Optical constants (refractive index, n, and absorption coefficient, alpha) and thickness, d, as well as the optical band gap, E-g, were determined using a method similar to Swanepoel's envelope method and two triple - TRfRm and TRbRm methods (for very thin films). Applying the Wemple and Di Domenico model, the dispersion energy, E-d, sing le-oscillator energy, E-o, and effective coordination number per cation, N-c, for the studied films were estimated. It was shown that the calculated values of n, k and E-g do not depend on the evaporation rate (0.2-25 nm/s), film thickness (50-1000nm) and other conditions of evaporation. The maximum value of n was found to be in thin As40Se60 films. After exposure to light, an increase in n and decrease in thin film's thickness and optical band gap was observed. We have found that E-o and N-c increase with increasing the Se-content. Non-linear parameters obtained by different formulae for prediction of non-linear absorption and refractive index were compared. A correlation between the non-linear refractive index and linear optical properties of As-Se thin films was demonstrated. The results of photo-induced changes in the infrared spectra of thermally deposited As-Se were interpreted in terms of the changes in the film structure due to the photopolymerization of As4Se4 molecular units and selenium chains into an As2Se3 glassy network. The great changes in n after exposure to light of As-rich films suggest an opportunity for applying the films examined as inorganic photoresists, in multi-layered structures and for producing Bragg gratings.

A new set of aryl-substituted amides of 16-mercaptohexadecanoic acid (R = 4-OCH3; 3,5-di-OCH3) are synthesized using a simple and general procedure. Self-assembled monolayers of these molecules on Au(111) are studied by infrared and visible ellipsometry and contact angle measurements. Model calculations are employed to determine the molecular tilt angle. The SAM methylene chains exist in prevailing all-trans conformation and the tilt of the CCC plane is decreased by approximately 15 degrees in comparison with the correspondent value for n-alkanethiols. Strong hydrogen bonds between the amide proton and the carbonyl oxygen are detected with C=O and N-H dipoles oriented parallel to the gold surface. The wetting of the outermost film surface reveals predominantly OCH3 groups exposed.

The electrochemical deposition of polypyrrole (PPy) on p-Si(1 0 0) electrodes was investigated. The electrodeposition was performed in aqueous electrolyte solutions utilising cyclic voltammetry. Thin, adhesive, uniform PPy films were successfully deposited on p-Si(1 0 0) electrodes. The Si/PPy interface was characterised with infrared spectroscopic ellipsometry (IR-SE) and photoluminescence (PL) measurements to obtain information of a possible oxidation of the Si interface and charge carrier recombination at the interface, respectively. Very small amounts of interfacial silicon oxides have been found at the Si/PPy interface. PL measurements lead to the assumption that electrodeposition of PPy onto the Si electrodes generated only very few additional non-radiative recombination-active (nr) defects. Hence, polypyrrole is an excellent passivation of nr defects at the silicon surface.

Monolayers from para-substituted benzyl esters of 16-mercaptohexadecanoic acid (R = -Cl; -OCH 3 ) self-assembled on (111)-textured gold films have been studied in detail with infrared and visible spectroscopic ellipsometry and contact angles measurements. The experimental data testify that these monolayers on gold tend to adopt tilt angles smaller than typical for n-alkanethiols, while the orientation of the phenyl rings is almost perpendicular to the surface. The same precursor molecules self-assembled on silver showed arrangement of the aliphatic chains characteristic for long-chain alkanethiols but differently tilted orientation of the terminal phenyl rings. An attempt was made to explain that different behavior with the different surface energetics of gold and silver substrates.

Transition moment directions of the vibrational states of nitro and carbonyl groups of p-nitrobenzyl-16-mercaptohexadecanoate are evaluated by infrared linear dichroism (IR LD) to be further exploited as film orientation markers in self-assembled monolayers (SAMs) that the respective compound forms on metal surfaces. DFT calculations followed by a complete normal coordinate analysis were employed to assist in the vibrational bands assignments. The analysis of the experimental IR LD spectra in conjunction with the step-wise reduction procedure of Thulstrup–Eggers indicated that the transition moment directions of the antisymmetric NO2 stretching and the carbonyl stretching modes are collinear, and confirmed previous results that those of the symmetric and the antisymmetric NO2 stretching vibrations are not exactly mutually perpendicular.

Results from investigations on multi-component vacuum evaporated thin As40S60-xSex. (0 < x < 60) films are presented. The compositional dependence of the refractive index n and the absorption coefficient, alpha, have been studied. Linear dependences of n and the optical band gap, E-g, on the Se-content have been observed. In addition, in order to clarify the structure and to determine the interactions between the separate structural units, we have applied the single-oscillator model, proposed by Wemple and Di Domenico. Thus, the dispersion energy, E-d, single-oscillator energy, E-0, and effective coordination number per cation, N-c, have been calculated. In agreement with other publications, we have observed E-d and N-c increasing with Se-content. The influence of light on the dispersion parameters has been demonstrated. Some conclusions on the photo-induced changes in the optical properties and the structure of As-S-Se films have been drawn from IR spectra.

Self-assembled monolayers (SAM) from para-substituted benzyl-16-mercaptohexadecanoates (R=–Cl; –OCH3; –NO2; –CN) were prepared using standard deposition procedures on silver substrates. The substituents were attached to the terminal benzyl group of the SAM precursor molecules in order to modify the properties of the outer film surface and to probe their influence on the organizational order of the monolayers. The SAMs were characterized by infrared spectroscopic ellipsometry and contact angle measurements. The carbonyl stretching as well as the methylene symmetric and antisymmetric stretching vibrations were employed to determine the tilt angle of the methylene chains. The water advancing contact angles implied that the wetting of the film's outermost surface is substantially different from that expected for more polar groups like NO2, CN and OCH3 and is much closer to that reported for aryl terminated SAMs. The flexible methylene linkage can facilitate the free rotation around C–Ph bond that leads to a specific orientation of the terminal phenyl rings in which they are closely exposed to the interface. An attempt was made to qualitatively characterize the phenyl ring orientations of the different SAMs using the IR spectroscopic ellipsometry data and IR absorption spectra of the same molecules.

The vibrational circular dichroism (VCD) and infrared absorption (IR) spectra of the mismatched octamer oligonucleotides d(CGTGCGCG)(2) (CGT) and d(CGCGTGCG)(2) (CGC) and their complexes with the antitumor drug daunomycin were measured in D(2)O, interpreted, and compared to the octamer d(CGCGCGCG)(2) (CG). The IR spectra of the mismatched octamers in the carbonyl-stretching region are similar to those of the parent CG, whereas the VCD spectra differ in several respects between each other. The main VCD feature due to carbonyl stretching is informative for the mismatches and CG. Vibrational modes in the sugar-phosphate region remain essentially unchanged especially for PO(2) (-) symmetric stretching. Differences between the free and complexed mismatch octamers occurred mainly in the carbonyl-stretching region (1,700-1,600 cm(-1)). The absorption intensity of the C==O peak of G is more prominent for CGC than CGT and resembles CG in this respect. The detailed composition of this doublet is clearly visible, indicating the geometric rearrangement of the base pairs in the presence of the mismatch and upon forming the daunomycin complex.

The vibrational characteristics of the nitro group (-NO 2 ) in long-chain organic molecules, deposited as oriented thin films on metallic or semiconductor surfaces, are discussed. The dependence of the ellipsometric spectra on the average orientation of the vibrational transition moments of the -NO 2 group in the aligned organic films is addressed. As illustrative examples, the ellipsometric spectra of a 60 nm thick Langmuir-Blodgett film of 2-[4-(N-dodecanoyl-amino)phenyl]-5-(4-nitrophenyl)-l,3,4-oxadiazole either on gold or on silicon, as well as a 2.5 nm thick self-assembled monolayer (SAM) of 4-nitrobenzyl-16-mercaptohexadecanoate on silver, are presented. The -NO 2 resonance frequencies, oscillator strengths and damping constants determined for the Langmuir-Blodgett film on gold were used to evaluate the change in the tilt angle after the film had been annealed at 130°C. The same values were further employed to reveal the orientation of such a film on silicon and to analyze the self-assembled monolayer on silver.

Hexamethyldisiloxane polymer layers obtained at low frequency glow discharge were post-treated by ammonia vapours under the same plasma conditions. Infrared spectroscopic ellipsometry and atomic force microscopy studies were carried out with the aim to elucidate the structural and morphological changes accompanying this modification. The infrared ellipsometry combined with best-fit calculations was used to evaluate the optical constants of the polymer film before and after the treatment, and thus to provide data for the vibrational band analysis. No additional modified layer due to the plasma treatment was detected, but a newly emerged weak band at 1562 cm(-1) was observed in the ellipsometric spectra of the ammonia-treated sample, which was ascribed to N-H deformation in amines.The surface morphology was imaged by atomic force microscopy. The data revealed that the NH3 treatment had caused distinct microstructural modification on the top layer surface. The size of the nodule aggregates was largely reduced and this contributed to-a much better developed top surface. (c) 2004 Elsevier B.V. All rights reserved.

The four-stranded intercalated DNA structure exemplified by the oligonucleotide 5′-d(CCCCCCCCCCCC) (d(C)12) was studied at acidic pH by infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopy and compared with spectra of the same oligonucleotide at neutral pH to establish distinct VCD markers for the intercalation motif. The most striking feature is a new absorption at 1694 cm−1 and its corresponding VCD couplet with reversed sign. These are unique for the intercalated structure and have not been observed for other parallel stranded duplexes. Significant characteristic features resulting from the spatial arrangement of the sugar-phosphate backbone are also clearly present for d(C)12 at acidic pH. An extensive network of CH…O bonds twists the backbone such that multiple through-space vibrational coupling occurs among neighbouring sugar-phosphate residues resulting in unusual VCD signals.

New 4-substituted benzyl esters of 16-mercaptohexadecanoic acid were prepared by developing a practicable synthetic procedure and using readily available staring materials. The compounds synthesized have been characterized by NMR, MS, IR spectra and elemental analysis. The mercapto derivatives are precursors for the formation of self-assembled monolayers on metal substrates.

The vibrational characteristics of the nitro group (-NO 2 ) in long-chain organic molecules, deposited as oriented thin films on metallic or semiconductor surfaces, are discussed. The dependence of the ellipsometric spectra on the average orientation of the vibrational transition moments of the -NO 2 group in the aligned organic films is addressed. As illustrative examples, the ellipsometric spectra of a 60 nm thick Langmuir-Blodgett film of 2-[4-(N-dodecanoyl-amino)phenyl]-5-(4-nitrophenyl)-l,3,4-oxadiazole either on gold or on silicon, as well as a 2.5 nm thick self-assembled monolayer (SAM) of 4-nitrobenzyl-16-mercaptohexadecanoate on silver, are presented. The -NO 2 resonance frequencies, oscillator strengths and damping constants determined for the Langmuir-Blodgett film on gold were used to evaluate the change in the tilt angle after the film had been annealed at 130°C. The same values were further employed to reveal the orientation of such a film on silicon and to analyze the self-assembled monolayer on silver.