X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges.

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode.

A spectroscopic study of self-assembled monolayer of porphyrin-functionalized oligo(phenyleneethynylene)s on gold: the influence of the anchor moiety.

Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for molecular electronics applications. Three such molecules (1-3) with the common structure P-OPE-AG (P and AG are a porphyrin and anchor group, respectively) and different anchor groups, viz. an acetyl protected thiol, -S-COCH3 (1), an acetyl protected thiol with methylene linker, -CH2-S-COCH3 (2), and a trimethylsilylethynyl group, -C(triple bond)C-Si(CH3)3 (3) have been synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have been prepared.

Is X-ray absorption spectroscopy sensitive to the amino acid composition of functional proteins?

We report, compare, and analyze near-edge X-ray absorption fine structure (NEXAFS) spectra of powder samples of four different functional proteins, namely, lysozyme, ovalbumin, bovine serum albumin, and type-I collagen, at all relevant absorption edges. The spectra of all of the above proteins were found to be quite similar and to exhibit minor differences only. Nevertheless, despite the general similarity, the spectra of the individual proteins are distinguishable, and some of the respective differences clearly correlate with their amino acid compositions.

NEXAFS spectroscopy of homopolypeptides at all relevant absorption edges: polyisoleucine, polytyrosine, and polyhistidine.

Carefully calibrated high-resolution low-noise near-edge X-ray absorption fine structure spectra of three homopolypetides, viz., polyisoleucine, polytyrosine, and polyhistidine at the C, N, and O K-edges, are compared with the respective spectra of parent amino acids and glycine-derived cyclic dipeptide, 2,5-diketopiperazine. An assignment of the spectral features related to the nitrogen and oxygen atoms constituting the peptide bond is suggested on the basis of a comparative analysis of the experimental spectra as well as theoretical calculations for 2,5-diketopiperazine within the real-space multiple-scattering formalism.

Characterization of self-assembled monolayers of oligo(phenyleneethynylene) derivatives of varying shapes on gold: effect of laterally extended pi-systems.

Fully conjugated organic molecules, such as the oligo(phenyleneethynylene) (OPE) systems, are of growing interest within the field of molecular electronics, as is the self-assembly of well-defined molecular thin films with predefined functions. The structure and function of such films are intimately related and governed by the structures of their molecular constituents, through the intermolecular interactions and the interactions between the molecules and the substrate, onto which the film is assembled. Here we report on the synthesis of a series of three OPE derivatives, with the general structure phenylethynylene-aryl-ethynylenephenylene-headgroup, and the structural investigation of the self-assembled monolayers (SAMs) formed from them on Au(111) surfaces.

Monomolecular films of phthalocyanines: formation, characterization, and expelling by alkanethiols.

Adsorption of aluminum-2,3-naphthalocyanine (Al-PC) onto gold (111) substrate from the pure and mixed (with alkanethiols) solutions of the target molecules in ethanol was studied. The resulting films were characterized by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The adsorption from the pure solution resulted in formation of an Al-PC monolayer composed of the strongly inclined molecules.

Self-assembled monolayers of ferrocene-substituted biphenyl ethynyl thiols on gold.

Homogeneous and mixed [with biphenylthiol (BPT)] self-assembled monolayers (SAMs) of ferrocene-substituted biphenyl ethynyl thiols (Fc) were prepared on Au(111) substrates and characterized by several complementary spectroscopic techniques. The mixed films were fabricated either by subsequent immersion of the substrates into the BPT and Fc solutions or by immersion of the substrate into a mixed solution of BPT and Fc. The first procedure resulted in the preparation of high-quality mixed SAMs, in which the Fc molecules were stochastically distributed in the BPT matrix and well-separated from each other.

Effect of irradiation dose in making an insulator from a self-assembled monolayer.

A combination of functionalization and irradiation-induced cross-linking allows fabrication of stable metal film on top of an aromatic self-assembled monolayer, [1,1';4',1' '-terphenyl]-4,4' '-dimethanethiol (TPDMT) on Au. Using X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and ion-scattering spectroscopy the optimal irradiation dose for producing a stable metal overlayer was estimated to be 40-45 mC/cm2. This dose is necessary for complete 2D-polymerization and closure of transient channels, which would otherwise allow metal penetration into the SAM.

Innershell absorption spectroscopy of amino acids at all relevant absorption edges.

The C, N, and O K-edge near-edge X-ray absorption fine structure spectra of the 22 most common proteinogenic alpha-amino acids in the zwitterionic form collected from solvent-free polycrystalline powder films in the partial electron yield mode are reported. Spectral features common to all amino acids, as well as distinctive fingerprints of specific subgroups of these compounds, are presented and discussed.

Novel tripod ligands for prickly self-assembled monolayers.

The new tridentate thioether ligands PhSi(CH2SMe)3 (1) and Ph-p-C6H4Si(CH2SMe)3 (2) have been synthesised and used for the preparation of the chelates fac-[W(kappa3-1)(CO)3] and fac-[W(kappa3-2)(CO)3], which were characterised by single-crystal X-ray diffraction. 1 and 2 were used as tripodal adsorbate molecules for the fabrication of self-assembled monolayers (SAMs) on gold. Film formation from solution was investigated in situ by second harmonic generation (SHG) and ellipsometry, which revealed a two-stepped process (fast adsorption, followed by slow film ordering).

Molecular self-assembly at bare semiconductor surfaces: preparation and characterization of highly organized octadecanethiolate monolayers on GaAs(001).

Through rigorous control of preparation conditions, organized monolayers with a highly reproducible structure can be formed by solution self-assembly of octadecanethiol on GaAs (001) at ambient temperature. A combination of characterization probes reveal a structure with conformationally ordered alkyl chains tilted on average at 14 +/- 1 degrees from the surface normal with a 43 +/- 5 degrees twist, a highly oleophobic and hydrophobic ambient surface, and direct S-GaAs attachment. Analysis of the tilt angle and film thickness data shows a significant mismatch of the average adsorbate molecule spacings with the spacings of an intrinsic GaAs(001) surface lattice.

Self-assembled monolayers from biphenyldithiol derivatives: optimization of the deprotection procedure and effect of the molecular conformation.

A series of biphenyl-derived dithiol (BDDT) compounds with terminal acetyl-protected sulfur groups and different structural arrangements of both phenyl rings have been synthesized and fully characterized. The different arrangements were achieved by introducing hydrocarbon substituents in the 2 and 2' positions of the biphenyl backbone. The presented model compounds enable the investigation of the correlation between the intramolecular conformation and other physical properties of interest, like, e.

Solid-state near-edge X-ray absorption fine structure spectra of glycine in various charge states.

The experimental solid-state near-edge X-ray absorption fine structure spectra for a series of glycine-related samples including alpha-glycine, beta-glycine, glycinium chloride, glycinium trifluoroacetate, and sodium glycinate at the C, N, and O K-edges measured under identical conditions are reported and compared. An assignment of spectral features for alpha-glycine is proposed on the basis of extended theoretical simulations of polarization-dependent spectra performed within the real-space multiple-scattering formalism explicitly taking into account the intermolecular environment of a glycine molecule in a crystal.