Gisbert Winnewisser, emeritus Professor of Physics at the University of Köln, passed away in March 2011 after a long illness. His dedication to molecular spectroscopy in the laboratory and in the interstellar medium, coupled with his very influential voice for molecular science will be extremely difficult to replace.

Over the last 20 years, we have discovered that we live in a molecular Universe: A Universe with a rich and varied organic inventory; A Universe where molecules are abundant and widespread; A Universe where molecules play a central role in key processes that dominate the structure and evolution of galaxies; A Universe where molecules provide convenient thermometers and barometers to probe local physical conditions; A Universe where molecules can work together to form such complex species as you and me. Understanding the origin and evolution of interstellar and circumstellar molecules is thus key to understanding the Universe around us and our place in it and has become a fundamental goal of modern astrophysics. This review focuses on the organic inventory and the chemical processes that may play a role in stablishing molecular complexity in regions of planet formation.

Stars like our Sun and planets like our Earth form in dense regions within interstellar molecular clouds, called pre-stellar cores (PSCs). PSCs provide the initial conditions in the process of star and planet formation. In the past 15 years, detailed observations of (low-mass) PSCs in nearby molecular cloud complexes have allowed us to find that they are cold (T < 10K) and quiescent (molecular line widths are close to thermal), with a chemistry profoundly affected by molecular freeze-out onto dust grains. In these conditions, deuterated molecules flourish, becoming the best tools to unveil the PSC physical and chemical structure. Despite their apparent simplicity, PSCs still offer puzzles to solve and they are far from being completely understood. For example, what is happening to the gas and dust in their nuclei (the future stellar cradles) is still a mystery that awaits for ALMA. Other important questions are: how do different environments and external conditions affect the PSC physical/chemical structure? Are PSCs in high-mass star forming regions similar to the well-known low-mass PSCs? Here I review observational and theoretical work on PSCs in nearby molecular cloud complexes and the ongoing search and study of massive PSCs embedded in infrared dark clouds (IRDCs), which host the initial conditions for stellar cluster and high-mass star formation.

We investigate the molecular evolution in star forming cores from dense cloud cores (nH ~ 104 cm−3, T ~ 10 K) to protostellar cores. A detailed gas-grain reaction network is solved in infalling fluid parcels in 1-D radiation hydrodynamic model. Large organic molecules are mainly formed via grain-surface reaction at T ~ several 10 K and sublimated to the gas-phase at ~ 100 K, while carbon-chain species are formed at a few 10 K after the sublimation of CH4 ice. The former accounts for the high abundance of large organic molecules in hot corinos such as IRAS16293, and the latter accounts for the carbon chain species observed toward L1527. The relative abundance of carbon chain species and large organic species would depend on the collapse time scale and/or temperature in the dense core stage. The large organic molecules and carbon chains in the protostellar cores are heavily deuterated; although they are formed in the warm temperatures, their ingredients have high D/H ratios, which are set in the cold core phase and isothermal collapse phase. HCOOH is formed by the gas-phase reaction of OH with the sublimated H2CO, and is further enriched in Deuterium due to the exothermic exchange reaction of OH + D → OD + H.

In the fluid parcels of the 1-D collapse model, warm temperature T. ~ several 10 K lasts for only ~ 104 yr, and the fluid parcels fall to the central star in ~ 100 yr after the temperature of the parcel rises to T ≥ 100 K. These timescales are determined by the size of the warm region and infall (~ free-fall) velocity: rwarm/tff. In reality, circum stellar disk is formed, in which fluid parcels stay for a longer timescale than the infall timescale. We investigate the molecular evolution in the disk by simply assuming that a fluid parcel stays at a constant temperature and density (i.e. a fixed disk radius) for 104 − 105 yrs. We found that some organic species which are underestimated in our 1-D collapse model, such as CH3OCH3 and HCOOCH3, become abundant in the disk. We also found that these disk species have very high D/H ratio as well, since their ingredients are highly deuterated.

Finally we investigate molecular evolution in a 3D hydrodynamic simulation of star forming core. We found CH3OH are abundant in the vicinity of the first core. The abundances of large organic species are determined mainly by the local temperature (sublimation), because of the short lifetime of the first core and the efficient mass accretion via angular momentum transfer.

Low-mass star forming regions are rich inventories of complex organic molecules. Furthermore, they show significant chemical diversity even among sources in a similar physical evolutionary stage (i.e. Class 0 sources). One distinct case is the hot corino chemistry characterized by rich existence of saturated complex organic molecules such as HCOOCH3 and C2H5CN, whereas the other is the warm carbon-chain chemistry (WCCC) characterized by extraordinary richness of unsaturated complex organic molecules such as carbon-chain molecules. We here summarize these observational achievements during the last decade, and present a unified picture of carbon chemistry in low-mass protostellar cores. The chemical diversity most likely originates from the source-to-source difference in chemical compositions of grain mantles. In particular, the gas-phase abundance of CH4 evaporated from grain mantles is thought to be a key factor for appearance of WCCC. The origin of the diversity and its evolution to protopranetary disks are discussed.

With the advances in high angular resolution (sub)millimeter observations of low-mass protostars, windows of opportunities are opening up for very detailed studies of the molecular structure of star forming regions on wide range of spatial scales. Deeply embedded protostars provide an important laboratory to study the chemistry of star formation – providing the link between dense regions in molecular clouds from which stars are formed, i.e., the initial conditions and the end product in terms of, e.g., disk and planet formation. High angular resolution observations at (sub)millimeter wavelengths provide an important tool for studying the chemical composition of such low-mass protostars. They for example constrain the spatial molecular abundance variations – and can thereby identify which species are useful tracers of different components of the protostars at different evolutionary stages. In this review I discuss the possibilities and limitations of using high angular resolution (sub)millimeter interferometric observations for studying the chemical evolution of low-mass protostars – with a particular keen eye toward near-future ALMA observations.

Icy grain mantles are commonly observed through infrared spectroscopy toward dense clouds, cloud cores, protostellar envelopes and protoplanetary disks. Up to 80% of the available oxygen, carbon and nitrogen are found in such ices; the most common ice constituents – H2O, CO2 and CO – are second in abundance only to H2 in many star forming regions. In addition to being a molecular reservoir, ice chemistry is responsible for much of the chemical evolution from H2O to complex, prebiotic molecules. Combining the exisiting ISO, Spitzer, VLT and Keck ice data results in a large sample of ice sources (~80) that span all stages of star formation and a large range of protostellar luminosities (<0.1–105 L⊙). Here we summarize the different techniques that have been applied to mine this ice data set on information on typical ice compositions in different environments and what this implies about how ices form and evolve during star and planet formation. The focus is on how to maximize the use of empirical constraints from ice observations, followed by the application of information from experiments and models. This strategy is used to identify ice bands and to constrain which ices form early during cloud formation, which form later in the prestellar core and which require protostellar heat and/or UV radiation to form. The utility of statistical tests, survival analysis and ice maps is highlighted; the latter directly reveals that the prestellar ice formation takes place in two phases, associated with H2O and CO ice formation, respectively, and that most protostellar ice variation can be explained by differences in the prestellar CO ice formation stage. Finally, special attention is paid to the difficulty of observing complex ices directly and how gas observations, experiments and models help in constraining this ice chemistry stage.

Recent models of hot cores have incorporated previously-uninvestigated chemical pathways that lead to the formation of complex organic molecules (COMs; i.e. species containing six or more atoms). In addition to the gas-phase ion-molecule reactions long thought to dominate the organic chemistry in these regions, these models now include photodissociation-driven grain surface reaction pathways that can also lead to COMs. Here, simple grain surface ice species photodissociate to form small radicals such as OH, CH3, CH2OH, CH3O, HCO, and NH2. These species become mobile at temperatures above 30 K during the warm-up phase of star formation. Radical-radical addition reactions on grain surfaces can then form an array of COMs that are ejected into the gas phase at higher temperatures. Photodissociation experiments on pure and mixed ices also show that these complex molecules can indeed form from simple species. The molecules predicted to form from this type of chemistry reasonably match the organic inventory observed in high mass hot cores such as Sgr B2(N) and Orion-KL. However, the relative abundances of the observed molecules differ from the predicted values, and also differ between sources. Given this disparity, it remains unclear whether grain surface chemistry governed by photodissociation is the dominant mechanism for the formation of COMs, or whether other unexplored gas-phase reaction pathways could also contribute significantly to their formation. The influence that the physical conditions of the source have on the chemical inventory also remains unclear. Here we overview the chemical pathways for COM formation in hot cores. We also present new modeling results that begin to narrow down the possible routes for production of COMs based on the observed relative abundances of methyl formate (HCOOCH3) and its C2H4O2 structural isomers.

Bipolar outflows constitute some of the best laboratories to study shock chemistry in the interstellar medium. A number of molecular species have their abundance enhanced by several orders of magnitude in the outflow gas, likely as a combined result of dust mantle disruption and high temperature gas chemistry, and therefore become sensitive indicators of the physical changes taking place in the shock. Identifying these species and understanding their chemical behavior is therefore of high interest both to chemical studies and to our understanding of the star-formation process. Here we review some of the recent progress in the study of the molecular composition of bipolar outflows, with emphasis in the tracers most relevant for shock chemistry. As we discuss, there has been rapid progress both in characterizing the molecular composition of certain outflows as well as in modeling the chemical processes likely involved. However, a number of limitations still affect our understanding of outflow chemistry. These include a very limited statistical approach in the observations and a dependence of the models on plane-parallel shocks, which cannot reproduce the observed wing morphology of the lines. We finish our contribution by discussing the chemistry of the so-called extremely high velocity component, which seems different from the rest of the outflow and may originate in the wind from the very vicinity of the protostar.

TTauri disks located in nearby star-forming regions (e.g. Taurus-Auriga at 140 pc) are thought to be the site of planet formation, since proto-planetary disks orbiting around active (still accreting) TTauri stars should contain, in many cases, enough gas to form giant gaseous planets. As such, circumstellar disks are ideal laboratories to study planet formation, provided the gas and dust observations have enough sensitivity and resolving power. I will focus in these proceedings, on recent results of molecular observations which unveil the physical conditions of gas disks and reveal the weakness of our current understanding and modeling.

In this paper we review recent progress in our understanding of the chemical evolution of protoplanetary disks. Current observational constraints and theoretical modeling on the chemical composition of gas and dust in these systems are presented. Strong variations of temperature, density, high-energy radiation intensities in these disks, both radially and vertically, result in a peculiar disk chemical structure, where a variety of processes are active. In hot, dilute and heavily irradiated atmosphere only the most photostable simple radicals and atoms and atomic ions exist, formed by gas-phase processes. Beneath the atmosphere a partly UV-shielded, warm molecular layer is located, where high-energy radiation drives rich ion-molecule and radical-radical chemistry, both in the gas phase and on dust surfaces. In a cold, dense, dark disk midplane many molecules are frozen out, forming thick icy mantles where surface chemistry is active and where complex polyatomic (organic) species are synthesized. Dynamical processes affect disk chemical composition by enriching it in abundances of complex species produced via slow surface processes, which will become detectable with ALMA.

There remain many fundamental unanswered questions about protoplanetary disks, including how (and if?) they form planets, how mass is transferred through the disk and onto the star, and how they ultimately disperse. Also, a major goal of protoplanetary disk studies is to understand the relationship between disk properties and the physical and chemical properties of planetary systems. IR molecular spectroscopy is a particularly powerful tool for probing the conditions and physical process in protoplanetary disks, which are too small and close to their parent stars to be imaged with ease. I will discuss the suite of infrared molecular transitions observed to date, which highlight the following three techniques of IR spectroscopy. Firstly, line shapes and strengths can be used as tracers of disk physics, including volatile condensation/evaporation, photo-processes, grain growth and turbulence. Secondly, observations of multiple molecular abundances provide constraints for disk chemical models, which may ultimately help explain the great diversity of planetary bodies. Finally, resolved line shapes and spectro-astrometry provide a means to study disk structure on extremely small size scales. Because IR observations are typically sensitive to radii of a few AU or smaller, the processes and structures being probed are relevant to the birth and growth of terrestrial and giant planets. Recent results that I will highlight include the discovery of a multitude of molecules in disks around sun-like stars (including H2O, OH, HCN, C2H2 and CO2), with detection rates that depend on stellar mass, constraints on gas mass and location in transitional disks, detection and characterization of ‘snow lines’, measurements of inner disk rims, and detections of inner disk asymmetries. I will also discuss how IR spectroscopy will remain relevant even with the emergence of facilities such as ALMA, as it allows us to connect the conditions in terrestrial-planet-forming regions with those in the cold outer reaches of disks, and to better construct a comprehensive understanding of the nature of protoplanetary disks.

The chemical composition of a protoplanetary disk is determined not only by in situ chemical processes during the disk phase, but also by the history of the gas and dust before it accreted from the natal envelope. In order to understand the disk's chemical composition at the time of planet formation, especially in the midplane, one has to go back in time and retrace the chemistry to the molecular cloud that collapsed to form the disk and the central star. Here we present a new astrochemical model that aims to do just that. The model follows the core collapse and disk formation in two dimensions, which turns out to be a critical upgrade over older collapse models. We predict chemical stratification in the disk due to different physical conditions encountered along different streamlines. We argue that the disk-envelope accretion shock does not play a significant role for the material in the disk at the end of the collapse phase. Finally, our model suggests that complex organic species are formed on the grain surfaces at temperatures of 20 to 40 K, rather than in the gas phase in the T > 100 K hot corino.

The infrared spectra of many galactic and extragalactic objects are dominated by emission features at 3.3, 6.2, 7.7, 8.6 and 11.2 μm. The carriers of these features remained a mystery for almost a decade, hence the bands were dubbed the unidentified infrared (UIR) bands. Since the mid-80's, the UIR bands are generally attributed to the IR fluorescence of Polycyclic Aromatic Hydrocarbon molecules (PAHs) upon absorption of UV photons – the PAH hypothesis. Here we review the progress made over the past 25 years in understanding the UIR bands and their carriers.

The interstellar medium constitutes a physically and chemically complex component of galaxies and is important in the cycle of matter and the evolution of stars. From various spectroscopic clues we now know that the interstellar medium is rich in organic compounds. However, identifying the exact nature of all these components remains a challenge. In particular the identification of the so-called diffuse band carriers has been alluding astronomers for almost a century.

In recent decades, observational, experimental and theoretical advances have rapidly lead to renewed interest in the diffuse interstellar bands (DIBs). This has been instigated partly by their perceived relation to the infrared aromatic emission bands, the UV extinction bump and far-UV rise, and the growing number of (small) organic molecules identified in space.

This chapter gives an overview of the observational properties and behaviour of the DIBs, and their presence throughout the Universe. I will highlight recent progress in identifying their carriers and discuss their potential as tracers and probes of (extra)-Galactic ISM conditions.

An overview of the important thermal and chemical processes in “photon-dominated regions” or “photo-dissociation regions” (PDRs) and “X-ray dominated regions” (XDRs) is presented. Applications of the models are shown to observations of the ultra-luminous infrared galaxy Mrk 231, and the starburst galaxy M 82.

The diffuse interstellar medium (ISM) hosts the first steps of interstellar chemistry and the seeds of dense structures. Since its turbulent pressure by far exceeds its thermal pressure, turbulence must play a prominent role in its evolution. Fed at galactic scales, turbulent energy cascades down to the dissipation scales, but as in both laboratory and atmospheric turbulence, it does so in an intermittent way : only a tiny fraction of the small-scales is fed by the turbulent cascade, so that dissipation occurs in bursts. In diffuse molecular clouds, where they can be observed, the signatures of intermittency are: (1) the non-Gaussian statistics of velocity increments, and (2) the existence of coherent structures of intense velocity-shear that appear to channel the large-scale turbulent energy down to milliparsec scales. Attempts at modelling the warm chemistry triggered in the diffuse ISM by bursts of turbulent dissipation are promising : in this framework, the so far unexplained molecular richness observed in this medium is naturally understood, in particular its CH+, HCO+ and CO abundances. Turbulent dissipation is also likely at the origin of the H2 rotational line emission of the diffuse ISM and of a significant fraction of its [C II] emission.

The late stages of stellar evolution from the Asymptotic Giant Branch (AGB) to planetary nebulae represent the most active phase of molecular synthesis in a star's life. Over 60 molecular species, including inorganics, organics, radicals, chains, rings, and molecular ions have been detected in the circumstellar envelopes of evolved stars. Most interestingly, complex organic compounds of aromatic and aliphatic structures are synthesized over very short time intervals after the end of the AGB. Also appeared during the post-AGB evolution are the unidentified 21 and 30 μm emission features, which are believed to originate from carbonaceous compounds.

The circumstellar environment is an ideal laboratory for the testing of theories of chemical synthesis. The distinct spectral behavior among AGB stars, proto-planetary nebulae (PPN), and planetary nebulae (PN) and the short evolutionary time scales that separate these stages pose severe constraints on models. In this paper, we will present an observational summary of the chemical synthesis in the late stages of stellar evolution, discuss chemical and physical processes at work, and speculate on the possible effects these chemical products have on the Galaxy and the Solar System.

We recently identified several emission bands in the Spitzer-IRS spectrum of the unusual planetary nebula Tc 1 with the infrared active vibrational modes of the neutral fullerene species C60 and C70. Since then, the fullerene bands have been detected in a variety of sources representing circumstellar and interstellar environments. Abundance estimates suggest that C60 represents ~0.1%–1.5% of the available carbon in those sources. The observed relative band intensities in various sources are not fully compatible with single-photon heating and fluorescent cooling, and are better reproduced by a thermal distribution at least in some sources. The observational data suggests that fullerenes form in the circumstellar environments of evolved stars, and survive in the interstellar medium. Precisely how they form is still a matter of debate.

The first molecules detected at infrared wavelengths in the ejecta of a Type II supernova, namely SN1987A, consisted of CO and SiO. Since then, confirmation of the formation of these two species in several other supernovae a few hundred days after explosion has been obtained. However, supernova environments appear to hamper the synthesis of large, complex species due to the lack of microscopically-mixed hydrogen deep in supernova cores. Because these environments also form carbon and silicate dust, it is of importance to understand the role played by molecules in the depletion of elements and how chemical species get incorporated into dust grains. In the present paper, we review our current knowledge of the molecular component of supernova ejecta, and present new trends and results on the synthesis of molecules in these harsh, explosive events.