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

Large prebiotic molecules in space: photo-physics of acetic acid and its isomers

An increasing number of large molecules have been positively identified in space. Many of these molecules are of biological interest and thus provide insight into prebiotic organic chemistry in the protoplanetary nebula. Among these molecules, acetic acid is of particular importance due to its structural proximity to glycine, the simplest amino acid. We compute electronic and vibrational properties of acetic acid and its isomers, methyl formate and glycolaldehyde, using density functional theory. From computed photo-absorption cross-sections, we obtain the corresponding photo-absorption rates for solar radiation at 1 AU and find them in good agreement with previous estimates. We also discuss glycolaldehyde diffuse emission in Sgr B2(N), as opposite to emissions from methyl formate and acetic acid that appear to be concentrate in the compact region Sgr B2(N-LMH).Comment: 8 pages, 5 figure

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&

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

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

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

Perturbed structural dynamics underlie inhibition and altered efflux of the multidrug resistance pump AcrB

Resistance–nodulation–division efflux pumps play a key role in inherent and evolved multidrug resistance in bacteria. AcrB, a prototypical member of this protein family, extrudes a wide range of antimicrobial agents out of bacteria. Although high-resolution structures exist for AcrB, its conformational fluctuations and their putative role in function are largely unknown. Here, we determine these structural dynamics in the presence of substrates using hydrogen/deuterium exchange mass spectrometry, complemented by molecular dynamics simulations, and bacterial susceptibility studies. We show that an efflux pump inhibitor potentiates antibiotic activity by restraining drug-binding pocket dynamics, rather than preventing antibiotic binding. We also reveal that a drug-binding pocket substitution discovered within a multidrug resistant clinical isolate modifies the plasticity of the transport pathway, which could explain its altered substrate efflux. Our results provide insight into the molecular mechanism of drug export and inhibition of a major multidrug efflux pump and the directive role of its dynamics