The structure and chemistry of protoplanetary disks depends strongly on the nature of the central star around which it has formed. The dust temperature is mainly set by the stellar luminosity, while the chemistry of the upper disk layers depends on the amount of intercepted UV and X-ray flux. We discuss here the differences in chemistry, thermal structure and line emission around Herbig Ae/Be, T Tauri stars and low-mass M dwarfs. Predictions will be made for future observations with SOFIA and Herschel.

Disks surrounding young stars play a fundamental role in the formation of stars and planets. Accretion through disks is believed to be responsible for the build up of stellar masses, and the gas and dust in disks is a reservoir for the potential formation of planets. As a result, one of the motivations for observing the inner regions of disks (i.e., the region within 10 AU) is to obtain clues to the processes that govern how stars and planets form. Significant progress has been made over the last decade in probing the inner regions of gaseous disks through the use of infrared molecular transitions. I discuss the observational tools that are currently available to study the gaseous component. These tools can be used to explore the evolution of gas in the inner disk and thereby help us to understand the processes of giant and terrestrial planet formation. These same tools may also be used to place constraints on the physical mechanisms that drive the disk accretion process.

In this paper I describe some of the recent advances made in the modelling of chemistry of protoplanetary disks, and in particular, of the inner regions where $r<100$ AU. These advances include the treatment of mass-transport processes, the interaction of radiation with chemistry, the augmentation of chemical networks to include isotopic species and their fractionation, and the attempt to connect disk chemistry with solar system bodies like comets. In the spirit of the title of this volume, I also briefly describe what in my opinion are the current challenges facing models of disk chemistry. These include the unification of chemistry, radiation and dynamics, the treatment of gas-grain interaction and the usefulness of observations to discriminate the different models in the literature.

As a prerequisite to returning their molecular inventory to the gas phase, icy grain mantles must desorb from the refractory core material of the grain. This desorption process can be instigated through interactions with photons or cosmic rays but can equally well be thermally driven. In this invited paper, the application of thermal desorption techniques borrowed from ultrahigh vacuum surface science to problems of astronomical interest will be discussed. The experimental methods employed by surface scientists to probe thermal desorption processes will be described and the analysis of the resulting empirical data outlined. The results of recent laboratory measurements from a number of groups will be highlighted.

A series of experiments on the surface reactions of hydrogen and deuterium atoms with solid CO, formaldehyde (H2CO), and methanol (CH3OH) has been performed. Successive hydrogenation of CO on surfaces at $\sim $10 K was found to proceed efficiently via tunneling to produce H2CO and CH3OH on dust grains under the typical conditions of molecular clouds. Formation rates are strongly dependent on the surface temperature and composition. The role of surface reactions in the formation of deuterated formaldehyde and methanol was investigated. The deuterium fractionation of methanol observed in molecular clouds was reproduced experimentally via H-D substitution in solid methanol at an accreting atomic D/H ratio of 0.05-0.1. This is the first evidence that grain-surface reactions can be responsible for fractionation. We have determined several effective rate constants for hydrogenation, deuteration, and H-D substitution to construct the surface reaction network for CO, H2CO, CH3OH, deuterated formaldehyde, and deuterated methanol.

The classical trajectory methodology for studying scattering of ions, atoms, or molecules from ice surfaces, and photodissociation of water at or in the surface of ice, is presented. The forces between the collider and the water molecules, or between the fragments of a dissociating molecule and the surrounding water molecules, are based on pair potentials taken either from ab initio calculations or derived empirically. Dynamical observables like sticking probabilities and kinetic energy distributions of desorbing photo-fragments are computed by solving Newton's equations of motion, starting from representative initial conditions. Four studies with relevance to astrochemistry are considered: the sticking of H atoms to ice Ih, the sticking of CO to ice Ih and ice Ia, the sticking of protons to ice Ih, and the photodissociation of water in ice Ih and ice Ia, also with a view to the subsequent chemistry of the H-and OH-products with co-adsorbed molecules. Where possible, the theoretical results are compared with experiments.

Based on over two decades of experimental, observational, and theoretical studies by scientists around the world, it is now widely accepted that the composite emission of mixtures of vibrationally-excited PAHs and PAH ions can accommodate the general pattern of band positions, intensities, and profiles observed in the discrete IR emission features of carbon-rich interstellar dust, as well as the variations in those characteristics. These variations provide insight into the detailed nature of the emitting PAH population and reflect conditions within the emitting regions giving this population enormous potential as probes of astrophysical environments. Moreover, the ubiquity and abundance of this material has impacts that extend well beyond the IR.

In this paper we will examine recent, combined experimental, theoretical, and observational studies that indicate that nitrogen-substituted PAHs represent an important component of the interstellar dust population, and we will go on to explore some of the ramifications of this result. We will also explore the results of recent experimental studies of the strong, low-lying electronic transitions of ionized PAH ions in the near-IR (0.7–2.5 $\mu$m) and explore the role that these transitions might play in pumping the PAH IR emission in regions of low excitation.

Pure rotational spectra of three polycyclic aromatic hydrocarbons – acenaphthene, acenaphthylene and fluorene – have been obtained by Fourier transform microwave spectroscopy of a molecular beam and subsequently by millimeter wave absorption spectroscopy for acenaphthene and fluorene. The data presented here will be useful for deep radio astronomical searches for PAHs employing large radio telecopes.

In this paper, we will review recent progress made in the understanding of cosmic silicates and the experimental characterization of relevant analogue materials. We will introduce the main structural properties of silicates. Then we will discuss recent infrared observations with a special emphasis on protoplanetary disks and AGNs. In the experimental section we will describe the optical properties of silicate grains. Here we will concentrate on fundamental optical data and the dependence of the optical behavior on particle shape and temperature.

Comets are among the most primitive bodies of the solar system, and their chemical composition is rich in information on the protosolar nebula and its possible connection with interstellar cloud chemistry. Comets are also a source of light atoms and, possibly, prebiotic organic molecules for the early Earth. We know better and better the abundances of cometary volatiles through spectroscopy, mainly at infrared and radio wavelengths. Another crucial component of cometary matter – organic refractories – is still poorly characterized, however.

We summarize here the $\sim$30 abundances and $\sim$20 upper limits obtained on cometary volatiles and highlight a few species and problems: ethylene glycol, NS, HNC/HCN, $^{14}$N/$^{15}$N, the origin of CN, CS$_{2}$, PAHs, and H$_{2}$O. Comet-to-comet variations and comet internal heliocentric variations can now be studied, and cometary comas can be mapped with a variety of techniques. We list a number of temperature indicators, for they can help understand the relation between IS and cometary matters, which present both a global similarity but also marked differences, such as the high ethylene glycol content of comets.

We conclude by outlining a few key problems to be addressed by future ground-based and space instruments or by cometary sample analysis. For many species, we stress that laboratory data are missing on spectroscopy, photodissociation and collisions with H$_{2}$O.

With the notable exception of those originating on the Moon and Mars, all known meteorites are pieces of objects in the asteroid belt. As such, they have recorded a succession of chemical processes, starting from reactions in the interstellar medium (ISM), followed by reactions that accompanied the formation and evolution of the early solar system, and culminated with reactions during aqueous alteration in the meteorite parent bodies. One of the challenges in meteorite research is to decipher this record and to learn about interstellar formation processes as well as to conditions in the early solar system. The rare class of carbonaceous chondrites contains up to 5% by weight of organic carbon, most of which is locked in an insoluble macromolecular material and only about 20% of it is in the form of distinct organic compound classes. The molecular and isotopic data of these organic compounds clearly show an interstellar heritage, but a fraction of these precursors were later modified. For example, the amino acids were probably formed inside the meteorite parent body during the aqueous alteration period from simple molecules such as HCN, NH3 and carbonyl compounds. However, the CI type carbonaceous chondrites contain a significantly distinct amino acid composition, indicating that there may be other synthetic processes involved. Polycyclic aromatic hydrocarbons (PAHs) are probably the most abundant form of organic carbon in the gas phase in the ISM. PAHs are among the most abundant organic compounds in carbonaceous meteorites, and they have been shown to have a presolar origin. A fraction of these PAHs are present in an extractable form, while the rest is part of the insoluble macromolecular matter. Progress is being made in the understanding of the evolution of this material in relation to aqueous alteration and oxidation. Although the potential of cometary meteorites cannot be ruled out, no such macro-meteorite has been recognized in the meteorite collections. Therefore, the organic composition of comets has been inferred mostly from astronomical observations. Future in-situ investigation of comets with spacecraft such as Rosetta will deliver new data on their organic composition, in particular the non-volatile fraction. However, in order to understand the contributions of different formation processes in primitive solar system objects, the analysis of the organic composition of meteorites remains essential.

On 4 July 2005 at 5:52 UT the Deep Impact mission successfully completed its goal to hit the nucleus of 9P/Tempel 1 with an impactor, forming a crater on the nucleus and ejecting material into the coma of the comet (A'Hearn et al. 2005). The 370 kg impactor collided with the sunlit side of the nucleus with a relative velocity of 10.2 km s$^{-1}$. NASA's Submillimeter Wave Astronomy Satellite (SWAS) observed the $1_{10}-1_{01}$ ortho-water ground-state rotational transition in comet 9P/Tempel 1 before, during, and after the impact. No excess emission from the impact was detected by SWAS. However, the water production rate of the comet showed large natural variations of more than a factor of three during the weeks before the impact.

Over 150 extrasolar planets are known to orbit sun-like stars. A growing number of them (9 to date) are transiting “hot Jupiters” whose physical characteristics can be measured. Atmospheres of two of these planets have already been detected. We summarize the atmosphere detections and useful upper limits, focusing on the MOST albedo upper limit and II exosphere detection for IID 209458b as the most relevant for photochemical models. We describe our photochemical model for hot Jupiters and present a summary explanation of the main results: a low gas-phase abundance of hydrocarbons; an absence of hydrocarbon hazes; and a large reservoir of II atoms in the upper atmospheres of hot Jupiters. We conclude by relating these model results to the relevant observational data.

In this review the present status of molecules in circumstellar envelopes of AGB stars is presented. Emphasis is put on the determination of abundances, and estimates of their uncertainties, from an observational point of view. Despite an impressive number of circumstellar species detected, about 60, there remains much work before general conclusions can be drawn. In particular, sophisticated radiative transfer modelling of circumstellar line emission must be done. This requires a detailed knowledge of the stellar and circumstellar properties, as well as basic molecular physics/chemistry data.

A mid-infrared high-resolution spectral survey of the source IRC+10216 (CW Leo) has been carried out between 11 and 14 $\mu$m. A large number of lines of C$_2$H$_2$ and HCN and their most abundant isotopologues, have been identified. Lines involving high-energy ro-vibrational levels allow an accurate derivation of the physical and chemical conditions in the innermost envelope. We have developed a radiative transfer model capable of fitting the observed lines satisfactorily. The fit of more than 200 ro-vibrational lines allowed us to get the kinetic, vibrational and rotational temperatures and the abundances of the C$_2$H$_2$ and HCN between 1 and 300 R$_*$.

We report the discovery of broad mid-infrared resonances in the outer regions of the Red Rectangle outflow (Markwick-Kemper et al. 2005). The peak position and the strength of the resonances vary spatially, but the full width at half maximum, as well as the shape of the feature, appears remarkably constant. While emission due to polycyclic aromatic hydrocarbons (PAHs) is also present at these locations, we show that PAHs cannot be the carriers of these new components. Instead, we argue that these resonances are caused by solid state components, perhaps simple Mg-Fe-oxides. The presence of such O-rich species in the otherwise C-rich outflows further complicates the picture of the formation and chemistry of the Red Rectangle nebula.

A summary is given of the presentations delivered at IAU Symposium 231.

An account of a free-ranging Panel Discussion held during the Symposium.