Mathias Rapacioli

Analysis of the emission of very small dust particles from Spitzer spectro-imagery data using blind signal separation methods

Context: This work was conducted as part of the SPECPDR program, dedicated to the study of very small particles and astrochemistry, in Photo-Dissociation Regions (PDRs). Aims: We present the analysis of the mid-IR spectro-imagery observations of Ced 201, NCG 7023 East and North-West and ? Ophiuchi West filament. Methods: Using the data from all four modules of the InfraRed Spectrograph onboard the Spitzer Space Telescope, we produced a spectral cube ranging from 5 to 35 ?m, for each one of the observed PDRs. The resulting cubes were analysed using Blind Signal Separation methods (NMF and FastICA). Results: For Ced 201, ? Ophiuchi West filament and NGC 7023 East, we find that two signals can be extracted from the original data cubes, which are 5 to 35 ?m spectra. The main features of the first spectrum are a strong continuum emission at long wavelengths, and a broad 7.8 ?m band. On the contrary, the second spectrum exhibits the classical Aromatic Infrared Bands (AIBs) and no continuum. The reconstructed spatial distribution maps show that the latter spectrum is mainly present at the cloud surface, close to the star whereas the first one is located slightly deeper inside the PDR. The study of the spectral energy distribution of Ced 201 up to 100 ?m suggests that, in cool PDRs, the 5-25 ?m continuum is carried by Very Small Grains (VSGs). The AIB spectra in the observed objects can be interpreted as the contribution of neutral and positively-charged Polycyclic Aromatic Hydrocarbons (PAHs). Conclusions: We extracted the 5 to 25 ?m emission spectrum of VSGs in cool PDRs, these grains being most likely carbonaceous. We show that the variations of the mid-IR (5-35 ?m) spectra of PDRs can be explained by the photo-chemical processing of these VSGs and PAHs, VSGs being the progenitors of free PAHs. This work is based on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA. Spectra are only available in electronic form (FITS files) at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/469/575

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Modeling Charge Resonance in Cationic Molecular Clusters: Combining DFT-Tight Binding with Configuration Interaction

In order to investigate charge resonance situations in molecular complexes, Wu et al. (J. Chem. Phys. 2007, 127, 164119) recently proposed a configuration interaction method with a valence bond-like multiconfigurational basis obtained from constrained DFT calculations. We adapt this method to the Self-Consistent Charge Density-Functional-based Tight Binding (SCC-DFTB) approach and provide expressions for the gradients of the energy with respect to the nuclear coordinates. It is shown that the method corrects the wrong SCC-DFTB behavior of the potential energy surface in the dissociation regions. This scheme is applied to determine the structural and stability properties of positively charged molecular dimers with full structural optimization, namely, the benzene dimer cation and the water dimer cation. The method yields binding energies in good agreement with experimental data and high-level reference calculations.

Molecular Dynamics Simulations of Anharmonic Infrared Spectra of [SiPAH]+π-Complexes

This paper presents an investigation of anharmonic effects in the IR spectra of [SiPAH](+) complexes by using Born-Oppenheimer molecular dynamics for a variety of PAHs ranging from naphthalene (C(10)H(8)) to ovalene (C(32)H(14)). The potential energy surfaces are calculated with the self-consistent charge density functional-based tight binding approach (DFTB). The DFTB parameters are modified to reproduce potential energy surfaces and the harmonic infrared spectra of the studied complexes with respect to DFT calculations. For bare PAHs, we find that the evolution of the vibrational frequencies of the C-H out-of-plane bending and C-C stretching modes as a function of temperature follows a linear law in quantitative agreement with experimental data. For cationic PAHs, the anharmonicity of the bands in terms of position shifts is found to be enhanced with respect to that of neutrals. As compared with bare cationic PAHs, the coordination of Si induces (i) larger broadenings, (ii) a slightly larger shift of the C-C stretching mode, and (iii) a smaller shift of the C-H out-of-plane bending modes. We discuss the implications of the work and the spectroscopic constraints for the detection of [SiPAH](+) in the interstellar medium.

Molecular dynamics simulations on [FePAH]+ π-complexes of astrophysical interest: anharmonic infrared spectroscopy

In this article, classical Born-Oppenheimer molecular dynamics (MD) simulations in the microcanonical ensemble are performed on neutral and cationic polycyclic aromatic hydrocarbon (PAH) species, focusing on [FePAH](+)π-complexes. Their anharmonic mid-infrared (mid-IR) spectra in the classical approximation are derived. This approach allows us to describe the influence of the energy of a system on its IR spectrum in terms of band-shifts and broadenings. The MD simulations are performed on a potential energy surface (PES) described at the self-consistent-charge density functional tight-binding level of theory. The PES is benchmarked on DFT calculations, showing the validity of the approach for complexes of Fe(+) with PAHs larger than coronene (C(24)H(12)) that are of astrophysical interest. MD simulations at high temperature show the occurrence of the diffusion of the Fe cation on the surface of the PAH. It proceeds through the edge of the carbon skeleton which is the lowest energy pathway presenting barriers smaller than 1 eV. Although only qualitative information on the band broadenings can be obtained, we show that the dependence of the computed positions of the main bands of [C(24)H(12)](0/+)and [FeC(24)H(12)](+)π-complexes on temperature can be fit by linear laws. The spectral trends determined for [FeC(24)H(12)](+) are compared to those of N-substituted [C(23)NH(12)](+)and [SiC(24)H(12)](+)π-complexes of astrophysical interest.

Car-Parrinello treatment for an approximate density-functional theory method

The authors formulate a Car-Parrinello treatment for the density-functional-based tight-binding method with and without self-consistent charge corrections. This method avoids the numerical solution of the secular equations, the principal drawback for large systems if the linear combination of atomic orbital ansatz is used. The formalism is applicable to finite systems and for supercells using periodic boundary conditions within the Gamma-point approximation. They show that the methodology allows the application of modern computational techniques such as sparse matrix storage and massive parallelization in a straightforward way. All present bottlenecks concerning computer time and consumption of memory and memory bandwidth can be removed. They illustrate the performance of the method by direct comparison with Born-Oppenheimer molecular dynamics calculations. Water molecules, benzene, the C(60) fullerene, and liquid water have been selected as benchmark systems.

Benchmarking Density Functional Based Tight-Binding for Silver and Gold Materials: From Small Clusters to Bulk

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size AgN and AuN clusters (N from 2 to 13), medium-size clusters with N = 20 and 55, and finally larger nanoparticles with N = 147, 309, and 561. For bulk materials, structural, energetics and elastic properties are discussed. We show that SCC-DFTB is quite satisfactory in reproducing essential differences between silver and gold aggregates, in particular their 2D-3D structural transitions, and their dependency upon cluster charge. SCC-DFTB is also in agreement with DFT and experiments in the medium-size regime regarding the energetic ordering of the different low-energy isomers and allows for an overall satisfactory treatment of bulk properties. A consistent convergence between the cohesive energies of the largest investigated nanoparticles and the bulks is obtained. On the basis of our results for nanoparticles of increasing size, a two-parameter analytical extrapolation of the cohesive energy is proposed. This formula takes into account the reduction of the cohesive energy for undercoordinated surface sites and converges properly to the bulk cohesive energy. Values for the surface sites cohesive energies are also proposed.

Cationic Methylene-Pyrene Isomers and Isomerization Pathways: Finite Temperature Theoretical Studies.

This paper provides spectral characterizations of the two isomers of the 1-methylenepyrene cation, namely, the 1-pyrenemethylium and a pyrene-like isomer owing a tropylium cycle. Both are possible photodissociation products of the 1-methylpyrene cation and were proposed as potential contributors to the diffuse interstellar bands. In that respect, vibrational and electronic spectra are computed for the optimized structures at the density functional theory (DFT) and time-dependent (TD-)DFT levels. Finite temperature effects on these spectra are estimated from molecular dynamics simulations within the density functional-based tight-binding (DFTB) and TD-DFTB frameworks, these methods being first benchmarked against DFT and TD-DFT calculations. The computed spectra allow discrimination of the two isomers. When the temperature increases, bands are observed to redshift and merge. The isomerization mechanism is investigated with the metadynamics technique, a biased dynamics scheme allowing to probe reaction mechanisms with high energy barriers by investigating the free energy surface at various temperatures. Four pathways with similar barrier heights (3.5-4 eV) are found, showing that the interconversion process would only occur in interstellar clouds under photoactivation. The present study opens the way to simulations on larger methyl- and methylenePAHs of astrophysical interest and their experimental investigation.

A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C6H6)+/0Arn clusters

We propose in the present paper a SCC-DFTB/FF (Self-Consistent-Charge Density Functional based Tight Binding/Force-Field) scheme adapted to the investigation of molecules trapped in rare gas environments. With respect to usual FF descriptions, the model involves the interaction of quantum electrons in a molecule with rare gas atoms in an anisotropic scheme. It includes polarization and dispersion contributions and can be used for both neutral and charged species. Parameters for this model are determined for hydrocarbon-argon complexes and the model is validated for small hydrocarbons. With the future aim of studying polycyclic aromatic hydrocarbons in Ar matrices, extensive benchmark calculations are performed on (C6H6)(+/0)Arn clusters against DFT and CCSD(T) calculations for the smaller sizes, and more generally against other experimental and theoretical data. Results on the structures and energetics (isomer ordering and energy separation, cohesion energy per Ar atom) are presented in detail for n = 1-8, 13, 20, 27, and 30, for both neutrals and cations. We confirm that the clustering of Ar atoms leads to a monotonous decrease of the ionization potential of benzene for n ⩽ 20, in line with previous experimental and FF data.

A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.We present an algorithm and its parallel implementation for solving a self consistent problem as encountered in Hartree Fock or Density Functional Theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density functional based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines (ii) calculations involving intermediate size systems (1 000–100 000 atoms) are also strongly accelerated and can run efficiently on standard servers (iii) the error on the total energy due to the use of a cut-off in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.