A. Dutrey (Laboratoire d'Astrophysique de Bordeaux, Floirac Cedex, France),
D. Semenov (MPIA, Germany),
E. Chapillon (ASIAA, Taiwan),
U. Gorti (NASA Ames, United States),
F. Gueth (IRAM, France),
S. Guilloteau (Laboratoire d'Astrophysique de Bordeaux, France),
F. Hersant (Laboratoire d'Astrophysique de Bordeaux, France),
M. Hogerheijde (Leiden Univ., Netherlands),
M. Hughes (Wesleyan University, Astronomy Department, United States),
H. Nomura (Kyoto Univ., Japan),
V. Pietu (IRAM, France),
C. Qi (Harvard-Smithsonian Center for Astrophysics, United States),
V. Wakelam (Laboratoire d'Astrophysique de Bordeaux, France),
G. Meeus (Universidad Autonoma de Madrid)

Protoplanetary disks composed of dust and gas are ubiquitous around young stars. Their lifetime, appearance, and structure are determined by an interplay between stellar radiation, gravity, thermal pressure, magnetic field, gas viscosity, turbulence, and rotation. Molecules and dust serve as major heating and cooling agents in disks. Dust grains dominate the disk opacities, reprocess most of the stellar radiation, and shield molecules from ionizing UV/X-ray photons. In turn, the ratio of ions to neutral molecules determines the level of turbulence and redistribution of the angular momentum. Therefore, the evolution of the gas and dust is a key element that regulates the efficiency and timescale of planet formation. The situation is complicated by the fact that the dust and gas physically and chemically interact. The dust and gas are initially dynamically well coupled because of the very small sizes of the dust particles, but later grains evolve differently because of significant growth in the disks, up to cm size and larger. Grain growth is more pronounced in very dense, inner disk regions. After large dust grains become dynamically decoupled from the gas, they gravitationally settle towards the disk midplane, and spiral inwards very fast or experience mutual collisions and get destroyed. Collisionallygenerated small grains are either collected by larger grains locally or swept up by turbulence into the disk atmosphere. Dust settling and turbulent stirring radially and vertically change the dust-to-gas ratio and average dust sizes. All these processes affect the disk thermal and density structure, and, as such, control its chemical composition. In the dense disk midplane the thermal equilibrium between gas and dust is achieved, with dust transferring heat to gas by rapid gas-grain collisions. The disk midplane is well shielded from stellar radiation and thus is "dark", with low ionization degree and low turbulence velocities. The outer disk midplane is so cold that many molecules severely freeze out onto dust grains there, leading to the production of complex ices. Above the midplane a more dilute region is located, where gas-grain collisional coupling is no longer efficient, and dust and gas temperatures start to depart from each other, with the latter being usually hotter. The upper surface disk layer is warmer than the midplane since the heating photons that come from the star are absorbed there by small dust grains or PAHs. This layer is more ionized and dynamically active, with rich gas-phase and gas-grain chemistry, leading to the synthesis of numerous gaseous species. Finally, in heavily irradiated, ionized, hot and dilute atmosphere only simple atoms, ions, photostable radicals and PAHs are able to survive. The above picture is far more complicated as disks dynamically evolve and build up planetary systems, changing drastically disk gas and dust density structures. Detailed studies of protoplanetary disks remain an observationally challenging task because disks are compact low-mass objects which appear optically thick at visual and infrared wavelengths. One uses millimeter/sub-millimeter observations to peer through their structure. Since observations of the most dominant species in disks, H2, are impossible (except of the warm upper layers via its weak quadrupole IR transitions), other molecules are employed to trace disk kinematics, temperature, density, and chemical structure. Apart from a handful of molecules, like CO, HCO+, CS, CN and HCN, the molecular content of protoplanetary disks remains largely unknown. The spatial distribution of molecular abundances is still poorly determined, hampering a detailed comparison with existing chemical models. Due to the complexity of the molecular line excitation, unambiguous interpretation of the observational results also necessitates advanced modeling of the disk physical structure and evolution, chemical history, and radiative transfer. Over the past decade significant progress has been achieved in our understanding of disk chemical composition. Since PPV, major breakthroughs have been reached. Upgraded and new mm/submm facilities (IRAM, SMA, Herschel and ALMA) have permitted the detection of new molecular species (DCN, H2O, HC3N...) at better spatial and frequency resolution, while disk models have benefited from improvements in astrochemistry databases (like KIDA and UDFA’06), development of coupled thermochemical disk physical models, line radiative transfer codes, and better analysis tools. This review will present and discuss the impact of such improvements on our understanding of the disk physical structure and chemical composition.

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