Deposited Transition Metal‐Centered Porphyrin and Phthalocyanine Molecules: Influence of the Substrates on the Magnetic Properties

The field of molecular spintronics has gained much attention since molecules withmagnetic centers form natural magnetic units, which do not suffer from the size limitations of conventional electronics, opening a new path towards miniaturization. To fabricate devices, the molecules have to be deposited on a substrate. The key questions are the interaction of the molecules with the substrate and the control of the magnetic properties. Considering molecule‐substrate hybrid interfaces as building blocks for spintronic devices, a deep understanding of the electronic structure and the coupling mechanisms is central to future applications. The orientation and reconstruction of the substrates can strongly affect the electronic and magnetic characteristics of the adsorbed molecule and drastically change the properties of the free molecules. In this chapter, we will discuss the interaction of transition metal‐centered porphyrins and phthalocyanines with different types of substrates, for example, ferromagnetic transition metals or graphene sheets, in the framework of state‐of‐the‐art density functional theory methods plus insights gained from X‐ray absorption/X‐ray magnetic circular dichroism experiments. The goal is to give an insight into the relevant processes on the atomic scale and to present possible routes to tailor magnetic properties in molecule‐substrate hybrid structures

Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform

DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently available for the analysis of DNA methylation. However, accurate and reproducible quantification of DNA methylation remains challenging. In this report, we describe Bio-COBRA (combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform), as a novel approach to quantitative DNA methylation analysis. The combination of a well-established method, COBRA, which interrogates DNA methylation via the restriction enzyme analysis of PCR-amplified bisulfite treated DNAs, with the Bioanalyzer platform allows for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. The sensitivity and reproducibility of Bio-COBRA make it a valuable tool for the analysis of DNA methylation in clinical samples, which could aid in the development of diagnostic and prognostic parameters with respect to disease detection and management

m-MTDATA on Au(111): Spectroscopic Evidence of Molecule-Substrate Interactions

The starburst π-conjugated molecule based on triphenylamine (TPA) building blocks, 4,4′,4″-tris(N-3-ethylphenyl-N-phenylamino)triphenylamine (C57H48N4, m-MTDATA), is widely used in optoelectronic devices due to its electron-donating properties. The electronic structure of m-MTDATA adsorbed on an Au(111) surface was investigated by means of photoelectron spectroscopy (PES) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The results were further compared to gas-phase measurements and DFT calculations. Our results clearly indicate a significant molecule-substrate interaction that induces considerable modifications on the electronic structure of the adsorbate compared to the isolated molecule. The energy level alignment analysis shows that the HOMO-LUMO gap is filled by new interface states

Atomic contributions to the valence band photoelectron spectra of metal-free, iron and manganese phthalocyanines

The present work reports a photoelectron spectroscopy study of the low-energy region of the valence band of metal-free phthalocyanine (H2Pc) compared with those of iron phthalocyanine (FePc) and manganese phthalocyanine (MnPc). Density Functional Theory calculations have been used to resolve the atomic orbital composition of the valence spectra of all the phthalocyanines (Pcs) analyzed in this study. Moreover we show how the atomic character of the Highest Occupied Molecular Orbital (HOMO) is reflected on the outermost valence band binding energy region. The intensity related to the C 2p contributions, resulting in the HOMO for H2Pc and FePc and in the HOMO-1 for MnPc as described by the theoretical predictions is in very good agreement with the experimental results. The DFT simulations, discerning the atomic contribution to the density of states, indicate how the central metal atom interacts with the C and N atoms of the molecule, giving rise to different partial and total density of states for these three different Pc molecules

Elucidating the 3d Electronic Configuration in Manganese Phthalocyanine

To shed light on the metal 3d electronic structure of manganese phthalocyanine, so far controversial, we performed photoelectron measurements both in the gas phase and as thin film. With the purpose of explaining the experimental results, three different electronic configurations close in energy to one another were studied by means of density functional theory. The comparison between the calculated valence band density of states and the measured spectra revealed that in the gas phase the molecules exhibit a mixed electronic configuration, while in the thin film, manganese phthalocyanine finds itself in the theoretically computed ground state, namely, the b12ge3ga1gb01g electronic configuration

Global methylation profiling of lung cancer identifies novel methylated genes

Epigenetic changes, including DNA methylation, are a common finding in cancer. In lung cancers methylation of cytosine residues may affect tumor initiation and progression in several ways, including the silencing of tumor suppressor genes through promoter methylation and by providing the targets for adduct formation of polycyclic aromatic hydrocarbons present in combustion products of cigarette smoke. Although the importance of aberrant DNA methylation is well established, the extent of DNA methylation in lung cancers has never been determined. Restriction landmark genomic scanning (RLGS) is a highly reproducible two-dimensional gel electrophoresis that allows the determination of the methylation status of up to 2000 promoter sequences in a single gel. We selected 1184 CpG islands for RLGS analysis and determined their methylation status in 16 primary non-small cell lung cancers. Some tumors did not show methylation whereas others showed up to 5.3% methylation in all CpG islands of the profile. Cloning of 21 methylated loci identified 11 genes and 6 ESTs. We demonstrate that methylation is part of the silencing process of BMP3B in primary tumors and lung cancer cell lines

Variability in organ-specific EGFR mutational spectra in tumour epithelium and stroma may be the biological basis for differential responses to tyrosine kinase inhibitors

Organ-specific differences in epidermal growth factor receptor (EGFR) mutational spectra and frequencies were found in lung cancer and sporadic and BRCA1/2-related breast cancers. Additionally, we found a high frequency of EGFR mutations in the tumour stroma of these invasive breast carcinomas. Those organ-specific mutational spectra and potential targets in the cancer-associated stroma might influence the efficacy of TKI therapy