Dehydrogenated polycyclic aromatic hydrocarbons and UV bump

Recent calculations have shown that the UV bump at about 217.5 nm in the extinction curve can be explained by a complex mixture of PAHs in several charge states. Other studies proposed that the carriers are a restricted population made of neutral and singly-ionised dehydrogenated coronene molecules (C24Hn, n less than 3), in line with models of the hydrogenation state of interstellar PAHs predicting that medium-sized species are highly dehydrogenated. To assess the observational consequences of the latter hypothesis we have undertaken a systematic study of the electronic spectra of dehydrogenated PAHs. We use our first results to see whether such spectra show strong general trends upon dehydrogenation. We used state-of-the-art techniques in the framework of the density functional theory (DFT) to obtain the electronic ground-state geometries, and of the time- dependent DFT to evaluate the electronic excited-state properties. We computed the absorption cross-section of the species C24Hn (n=12,10,8,6,4,2,0) in their neutral and cationic charge-states. Similar calculations were performed for other PAHs and their fullydehydrogenated counterparts. pi electron energies are always found to be strongly affected by dehydrogenation. In all cases we examined, progressive dehydrogenation translates into a correspondingly progressive blue shift of the main electronic transitions. In particular, the pi-pi* collective resonance becomes broader and bluer with dehydrogenation. Its calculated energy position is therefore predicted to fall in the gap between the UV bump and the far-UV rise of the extinction curve. Since this effect appears to be systematic, it poses a tight observational limit on the column density of strongly dehydrogenated medium-sized PAHs.Comment: 5 pages, 7 figures, Astronomy & Astrophysics, in pres

The role of the charge state of PAHs in ultraviolet extinction

Aims: We explore the relation between charge state of polycyclic aromatic hydrocarbons (PAHs) and extinction curve morphology. Methods: We fit extinction curves with a dust model including core-mantle spherical particles of mixed chemical composition (silicate core, $sp^2$ and $sp^3$ carbonaceous layers), and an additional molecular component. We use exact methods to calculate the extinction due to classical particles and accurate computed absorption spectra of PAHs in different charge states, for the contribution due to the molecular component, along a sample of five rather different lines of sight. Results: A combination of classical dust particles and mixtures of real PAHs satisfactorily matches the observed interstellar extinction curves. Variations of the spectral properties of PAHs in different charge states produce changes consistent with the varying relative strengths of the bump and non-linear far-UV rise.Comment: 5 pages, 3 figures, Astronomy & Astrophysics Letters, in pres

On-line database of the spectral properties of polycyclic aromatic hydrocarbons

We present an on-line database of computed molecular properties for a large sample of polycyclic aromatic hydrocarbons (PAHs) in four charge states: -1, 0, +1, and +2. At present our database includes 40 molecules ranging in size from naphthalene and azulene (C10H8) up to circumovalene (C66H20). We performed our calculations in the framework of the density functional theory (DFT) and the time-dependent DFT to obtain the most relevant molecular parameters needed for astrophysical applications. For each molecule in the sample, our database presents in a uniform way the energetic, rotational, vibrational, and electronic properties. It is freely accessible on the web at http://astrochemistry.ca.astro.it/database/ and http://www.cesr.fr/~joblin/database/.Comment: Accepted for pubblication in Chem. Phys. (01/01/07

Estimated IR and phosphorescence emission fluxes for specific Polycyclic Aromatic Hydrocarbons in the Red Rectangle

Following the tentative identification of the blue luminescence in the Red Rectangle by Vijh et al. (2005), we compute absolute fluxes for the vibrational IR emission and phosphorescence bands of three small polycyclic aromatic hydrocarbons. The calculated IR spectra are compared with available ISO observations. A subset of the emission bands are predicted to be observable using presently available facilities, and can be used for an immediate, independent, discriminating test on their alleged presence in this well-known astronomical object.Comment: accepted for publication on A&

Time-Dependent Density Functional Theory Investigation on the Electronic and Optical Properties of Poly-C,Si,Ge-acenes

We report a comparative computational investigation on the first six members of linear poly-C,Si,Ge-acenes (X4n+2H2n+4, X = C,Si,Ge; n = 1, 2, 3, 4, 5, 6). We performed density functional theory (DFT) and time-dependent DFT calculations to compare morphological, electronic, and optical properties. While C-acenes are planar, Si-and Ge-acenes assume a buckled configuration. Electronic properties show similar trends as a function of size for all families. In particular, differently from C-based compounds, in the case of both Si-and Ge-acenes, the excitation energies of the strongest low-lying electronic transition (β peaks) span the visible region of the spectrum, demonstrating their size tunability. For all families, we assessed the plasmonic character of this transition and found a linear relationship for the wavelength-dependence of the β peaks as a function of the number of rings. A similar slope of about 56 nm is observed for Si-and Ge-acenes, although the peak positions of the former are located at lower wavelengths. Outcomes of this study are compared with existing theoretical results for 2D lattices and nanoribbons, and experiments where available

Diagnostics for specific PAHs in the far-IR: searching neutral naphthalene and anthracene in the Red Rectangle

Context. In the framework of the interstellar polycyclic aromatic hydrocarbons (PAHs) hypothesis, far-IR skeletal bands are expected to be a fingerprint of single species in this class. Aims. We address the question of detectability of low energy PAH vibrational bands, with respect to spectral contrast and intensity ratio with ``classical'' Aromatic Infrared Bands (AIBs). Methods. We extend our extablished Monte-Carlo model of the photophysics of specific PAHs in astronomical environments, to include rotational and anharmonic band structure. The required molecular parameters were calculated in the framework of the Density Functional Theory. Results. We calculate the detailed spectral profiles of three low-energy vibrational bands of neutral naphthalene, and four low-energy vibrational bands of neutral anthracene. They are used to establish detectability constraints based on intensity ratios with ``classical'' AIBs. A general procedure is suggested to select promising diagnostics, and tested on available Infrared Space Observatory data for the Red Rectangle nebula. Conclusions. The search for single, specific PAHs in the far-IR is a challenging, but promising task, especially in view of the forthcoming launch of the Herschel Space Observatory.Comment: 13 pages, 13 figures, accepted for publication in A&

Electronic and optical properties of families of polycyclic aromatic hydrocarbons: a systematic (time-dependent) density functional theory study

Homologous classes of Polycyclic Aromatic Hydrocarbons (PAHs) in their crystalline state are among the most promising materials for organic opto-electronics. Following previous works on oligoacenes we present a systematic comparative study of the electronic, optical, and transport properties of oligoacenes, phenacenes, circumacenes, and oligorylenes. Using density functional theory (DFT) and time-dependent DFT we computed: (i) electron affinities and first ionization energies; (ii) quasiparticle correction to the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap; (iii) molecular reorganization energies; (iv) electronic absorption spectra of neutral and $\pm1$ charged systems. The excitonic effects are estimated by comparing the optical gap and the quasiparticle corrected HOMO-LUMO energy gap. For each molecular property computed, general trends as a function of molecular size and charge state are discussed. Overall, we find that circumacenes have the best transport properties, displaying a steeper decrease of the molecular reorganization energy at increasing sizes, while oligorylenes are much more efficient in absorbing low-energy photons in comparison to the other classes.Comment: 26 pages, 9 figures, 4 tables, accepted for pubblication in Chemical Physics (14/04/2011

Extracellular Vesicles: Mechanisms in Human Health and Disease

SIGNIFICANCE: Secreted extracellular vesicles (EVs) are now considered veritable entities for diagnosis, prognosis, and therapeutics. These structures are able to interact with target cells and modify their phenotype and function. Recent Advances: Since composition of EVs depends on the cell type of origin and the stimulation that leads to their release, the analysis of EV content remains an important input to understand the potential effects of EVs on target cells. CRITICAL ISSUES: Here, we review recent data related to the mechanisms involved in the formation of EVs and the methods allowing specific EV isolation and identification. Also, we analyze the potential use of EVs as biomarkers in different pathologies such as diabetes, obesity, atherosclerosis, neurodegenerative diseases, and cancer. Besides, their role in these diseases is discussed. Finally, we consider EVs enriched in microRNA or drugs as potential therapeutic cargo able to deliver desirable information to target cells/tissues. FUTURE DIRECTIONS: We underline the importance of the homogenization of the parameters of isolation of EVs and their characterization, which allow considering EVs as excellent biomarkers for diagnosis and prognosis

Molecular interactions of carbapenem antibiotics with the multidrug efflux transporter acrb of escherichia coli

The drug/proton antiporter AcrB, engine of the major efflux pump AcrAB(Z)-TolC of Escherichia coli and other bacteria, is characterized by its impressive ability to transport chemically diverse compounds, conferring a multi-drug resistance (MDR) phenotype. Although hundreds of small molecules are known to be AcrB substrates, only a few co-crystal structures are available to date. Computational methods have been therefore intensively employed to provide structural and dynamical fingerprints related to transport and inhibition of AcrB. In this work, we performed a systematic computational investigation to study the interaction between representative carbapenem antibiotics and AcrB. We focused on the interaction of carbapenems with the so-called distal pocket, a region known for its importance in binding inhibitors and substrates of AcrB. Our findings reveal how the different physico-chemical nature of these antibiotics is reflected on their binding preference for AcrB. The molecular-level information provided here could help design new antibiotics less susceptible to the efflux mechanism