83 pages, 8 figures, 5 tables, to be published in a Thematic Issue "Astrochemistry" in Chem. Reviews (December 2013). This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Chemical Reviews, copyright (c) American Chemical Society after peer review
This comprehensive review summarizes our current understanding of the evolution of gas, solids and molecular ices in protoplanetary disks. Key findings related to disk physics and chemistry, both observationally and theoretically, are highlighted. We discuss which molecular probes are used to derive gas temperature, density, ionization state, kinematics, deuterium fractionation, and study organic matter in protoplanetary disks.
The composition of a protoplanetary disk is set by a combination of interstellar inheritance and gas and grain surface chemical reactions within the disk. The survival of inherited molecules, as well as the disk in situ chemistry depends on the local temperature, density and irradiation environment, which can change over time due to stellar and disk evolution, as well as transport in the disk. We address one aspect of this coupling between the physical and chemical evolution in disks by following accretion streamlines of gas and small grains in the disk midplane, while simultaneously taking th…
The origin of the reservoirs of water on Earth is debated. The Earth's crust may contain at least three times more water than the oceans. This crust water is found in the form of phyllosilicates, whose origin probably differs from that of the oceans. We test the possibility to form phyllosilicates in protoplanetary disks, which can be the building blocks of terrestrial planets. We developed an exploratory rate-based warm surface chemistry model where water from the gas-phase can chemisorb on dust grain surfaces and subsequently diffuse into the silicate cores. We apply the phyllosilicate forma…
We investigate the effects of magnetic field configurations on the ionization rate by cosmic rays in protoplanetary disks. First, we consider cosmic-ray propagation from the interstellar medium (ISM) to the protoplanetary disks and showed that the cosmic-ray density around the disk should be 2 times lower than the ISM value. Then, we compute the attenuation of cosmic rays in protoplanetary disks. The magnetic fields in the disk are stretched to the azimuthal directions, and cosmic rays need to detour while propagating to the midplane. Our results show that the detouring effectively enhances th…
The effect of H$_2$ ro-vibrational excitation on the chemistry of protoplanetary disks is studied using a framework that solves for the disk physical and chemical structure and includes a detailed calculation of H$_2$ level populations. Chemistry with ro-vibrationally excited H$_2$ is found to be important for the formation of several commonly observed species in disks and this work demonstrates the need to accurately treat PDR chemistry in disks if we are to make inferences on the chemical state of the disk during planet formation epochs. This is found to be even more critical for molecules l…
We study the effects of grain surface reactions on the chemistry of protoplanetary disks where gas, ice surface layers and icy mantles of dust grains are considered as three distinct phases. Gas phase and grain surface chemistry is found to be mainly driven by photo-reactions and dust temperature gradients. The icy disk interior has three distinct chemical regions: (i) the inner midplane with low FUV fluxes and warm dust ($\gtrsim 15$K) that lead to the formation of complex organic molecules, (ii) the outer midplane with higher FUV from the ISM and cold dust where hydrogenation reactions domin…
Context. Several sulfur-bearing molecules are observed in the interstellar medium and in comets, in strong contrast to protoplanetary disks where only CS, H$_2$CS and SO have been detected so far. Aims. We combine observations and chemical models to constrain the sulfur abundances and their sensitivity to physical and chemical conditions in the DM Tau protoplanetary disk. Methods. We obtained $0.5^{"}$ ALMA observations of DM Tau in Bands 4 and 6 in lines of CS, SO, SO$_2$, OCS, CCS, H$_2$CS and H$_2$S, achieving a $\sim 5$ mJy sensitivity. Using the non-LTE radiative transfer code RADEX and t…
We use two-dimensional Fourier transformation to measure the pitch angle ($φ$) of the dominant spiral Fourier mode of well-defined spiral arms in 13 protoplanetary disks, making use of near-infrared scattered-light images of AB Aur, SAO 206462, MWC 758, V1247 Ori, HD 142527, DZ Cha, LkH$α$ 330, and HD 100453, and ALMA millimeter continuum images of Elias 2-27, IM Lup, AS 205, and HT Lup. We find that the measured pitch angle correlates strongly with disk mass ($M_{D}$), such that more massive protoplanetary disks have smaller pitch angles, following $|φ| = -(7.8\pm1.7)\log(M_{D}/M_{\odot})+(2.…
The investigation of polarized light of protoplanetary disks is key for constraining the dust properties, disk morphology and embedded magnetic fields. However, different polarization mechanisms and the diversity of dust grain shapes and compositions lead to ambiguities in the polarization pattern. The so-called "self-scattering" of thermal, re-emitted radiation in the infrared and mm/submm is discussed as a major polarization mechanism. If the net flux of the radiation field is in radial direction, it is commonly assumed that the polarization pattern produced by scattering in a protoplanetary…
Measurements of the gas mass are necessary to determine the planet formation potential of protoplanetary disks. Observations of rare CO isotopologues are typically used to determine disk gas masses; however, if the line emission is optically thick this will result in an underestimated disk mass. With ALMA we have detected the rarest stable CO isotopologue, 13C17O, in a protoplanetary disk for the first time. We compare our observations with the existing detections of 12CO, 13CO, C18O and C17O in the HD163296 disk. Radiative transfer modelling using a previously benchmarked model, and assuming …
It has recently been established that the evolution of protoplanetary disks is primarily driven by magnetized disk winds, requiring large-scale magnetic flux threading the disks. The size of such disks is expected to shrink in time, as opposed to the conventional scenario of viscous expansion. We present the first global 2D non-ideal magnetohydrodynamic (MHD) simulations of protoplanetary disks that are truncated in the outer radius, aiming to understand the interaction of the disk with the interstellar environment, as well as global evolution of the disk and magnetic flux. We find that as the…
We assess the ionising effect of low energy protostellar cosmic rays in protoplanetary disks around a young solar mass star for a wide range of disk parameters. We assume a source of low energy cosmic rays located close to the young star which travel diffusively through the protoplanetary disk. We use observationally inferred values from nearby star-forming regions for the total disk mass and the radial density profile. We investigate the influence of varying the disk mass within the observed scatter for a solar mass star. We find that for a large range of disk masses and density profiles that…
The nature and abundance of sulfur chemistry in protoplanetary disks (PPDs) may impact the sulfur inventory on young planets and therefore their habitability. PPDs also present an interesting test bed for sulfur chemistry models, since each disk present a diverse set of environments. In this context, we present new sulfur molecule observations in PPDs, and new S-disk chemistry models. With ALMA we observed the CS 5-4 rotational transition toward five PPDs (DM Tau, DO Tau, CI Tau, LkCa 15, MWC 480), and the CS 6-5 transition toward three PPDs (LkCa 15, MWC 480 and V4046 Sgr). Across this sample…
The volatile contents of protoplanetary disks both set the potential for planetary chemistry and provide valuable probes of defining disk system characteristics such as stellar mass, gas mass, ionization, and temperature structure. Current disk molecular inventories are fragmented, however, giving an incomplete picture: unbiased spectral line surveys are needed to assess the volatile content. We present here an overview of such a survey of the protoplanetary disks around the Herbig Ae star MWC 480 and the T Tauri star LkCa 15 in ALMA Band 7, spanning $\sim$36 GHz from 275--317 GHz and represen…
Grain surface chemistry is key to the composition of protoplanetary disks around young stars. The temperature of grains depends on their size. We evaluate the impact of this temperature dependence on the disk chemistry. We model a moderately massive disk with 16 different grain sizes. We use POLARIS to calculate the dust grain temperatures and the local UV flux. We model the chemistry using the 3-phase astrochemical code NAUTILUS. Photoprocesses are handled using frequency-dependent cross-sections, and a new method to account for self and mutual shielding. The multi-grain model outputs are com…
The formation of asteroids, comets and planets occurs in the interior of protoplanetary disks during the early phase of star formation. Consequently, the chemical composition of the disk might shape the properties of the emerging planetary system. In this context, it is crucial to understand whether and what organic molecules are synthesized in the disk. In this Letter, we report the first detection of formic acid (HCOOH) towards the TW Hydrae protoplanetary disk. The observations of the trans-HCOOH 6$_{(1,6)-5(1,5)}$ transition were carried out at 129~GHz with ALMA. We measured a disk-average…
