Context. Protoplanetary disks are vital objects in star and planet formation, possessing all the material, gas and dust, which may form a planetary system orbiting the new star. Small, simple molecules have traditionally been detected in protoplanetary disks; however, in the ALMA era, we expect the molecular inventory of protoplanetary disks to significantly increase. Aims. We investigate the synthesis of complex organic molecules (COMs) in protoplanetary disks to put constraints on the achievable chemical complexity and to predict species and transitions which may be observable with ALMA. Methods. We have coupled a 2D steady-state physical model of a protoplanetary disk around a typical T Tauri star with a large gas-grain chemical network including COMs. We compare the resulting column densities with those derived from observations and perform ray-tracing calculations to predict line spectra. We compare the synthesised line intensities with current observations and determine those COMs which may be observable in nearby objects. We also compare the predicted grain-surface abundances with those derived from cometary comae observations. Results. We find COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances ∼10 −6 -10 −4 that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, ∼10 −12 -10 −7 . Including the irradiation of grain mantle material helps build further complexity in the ice through the replenishment of grain-surface radicals which take part in further grain-surface reactions. There is reasonable agreement with several line transitions of H 2 CO observed towards T Tauri star-disk systems. There is poor agreement with HC 3 N lines observed towards LkCa 15 and GO Tau and we discuss possible explanations for these discrepancies. The synthesised line intensities for CH 3 OH are consistent with upper limits determined towards all sources. Our models suggest CH 3 OH should be readily observable in nearby protoplanetary disks with ALMA; however, detection of more complex species may prove challenging, even with ALMA "Full Science" capabilities. Our grain-surface abundances are consistent with those derived from cometary comae observations providing additional evidence for the hypothesis that comets (and other planetesimals) formed via the coagulation of icy grains in the Sun's natal disk.

Context. Near-to mid-infrared observations of molecular emission from protoplanetary disks show that the inner regions are rich in small organic volatiles (e.g., C 2 H 2 and HCN). Trends in the data suggest that disks around cooler stars (T eff ≈ 3000 K) are potentially (i) more carbon-rich; and (ii) more molecule-rich than their hotter counterparts (T eff > ∼ 4000 K). Aims. We explore the chemical composition of the planet-forming region (<10 AU) of protoplanetary disks around stars over a range of spectral types (from M dwarf to Herbig Ae) and compare with the observed trends. Methods. Self-consistent models of the physical structure of a protoplanetary disk around stars of different spectral types are coupled with a comprehensive gas-grain chemical network to map the molecular abundances in the planet-forming zone. The effects of (i) N 2 self shielding; (ii) X-ray-induced chemistry; and (iii) initial abundances, are investigated. The chemical composition in the "observable" atmosphere is compared with that in the disk midplane where the bulk of the planet-building reservoir resides. Results. M dwarf disk atmospheres are relatively more molecule rich than those for T Tauri or Herbig Ae disks. The weak far-UV flux helps retain this complexity which is enhanced by X-ray-induced ion-molecule chemistry. N 2 self shielding has only a small effect in the disk molecular layer and does not explain the higher C 2 H 2 /HCN ratios observed towards cooler stars. The models underproduce the OH/H 2 O column density ratios constrained in Herbig Ae disks, despite reproducing (within an order of magnitude) the absolute value for OH: the inclusion of self shielding for H 2 O photodissociation only increases this discrepancy. One possible explanation is the adopted disk structure. Alternatively, the "hot" H 2 O (T > ∼ 300 K) chemistry may be more complex than assumed. The results for the atmosphere are independent of the assumed initial abundances; however, the composition of the disk midplane is sensitive to the initial main elemental reservoirs. The models show that the gas in the inner disk is generally more carbon rich than the midplane ices. This effect is most significant for disks around cooler stars. Furthermore, the atmospheric C/O ratio appears larger than it actually is when calculated using observable tracers only. This is because gas-phase O 2 is predicted to be a significant reservoir of atmospheric oxygen.Conclusions. The models suggest that the gas in the inner regions of disks around cooler stars is more carbon rich; however, calculations of the molecular emission are necessary to definitively confirm whether the chemical trends reproduce the observed trends.

Detailed models for the density and temperature profiles of gas and dust in protoplanetary disks are constructed by taking into account X-ray and ultraviolet (UV) irradiation from a central T Tauri star, as well as dust size growth and settling toward the disk midplane. The spatial and size distributions of dust grains in the disks are numerically computed by solving the coagulation equation for settling dust particles, with the result that the mass and total surface area of dust grains per unit volume of the gas in protoplanetary disks are very small, except at the disk midplane. The level populations and line emission of molecular hydrogen are calculated using the derived physical structure of the disks. X-ray irradiation is the dominant heating source of the gas in the inner disk region and in the surface layer, while the far UV heating dominates otherwise. If the central star has strong X-ray and weak UV radiation, the level populations of molecular hydrogen are controlled by X-ray pumping, and the X-ray induced transition lines could be observable. If the UV irradiation is strong, the level populations are controlled by thermal collisions or UV pumping, depending on the properties of the dust grains in the disks. As the dust particles evolve in the disks, the gas temperature at the disk surface drops because the grain photoelectric heating becomes less efficient, while the UV radiation fields become stronger due to the decrease of grain opacity. This makes the level populations of molecular hydrogen change from local thermodynamic equilibrium (LTE) to non-LTE distributions, which results in changes to the line ratios of molecular hydrogen emission. Our results suggest that dust evolution in protoplanetary disks could be observable through the line ratios of molecular hydrogen. The emission lines are strong from disks irradiated by strong UV and X-rays and possessing small dust grains; such disks will be good targets in which to observe molecular hydrogen emission.

Abstract.We have modeled self-consistently the density and temperature profiles of gas and dust in protoplanetary disks, taking into account irradiation from a central star. Making use of this physical structure, we have calculated the level populations of molecular hydrogen and the line emission from the disks. As a result, we can reproduce the observed strong line spectra of molecular hydrogen from protoplanetary disks, both in the ultraviolet (UV) and the near-infrared, but only if the central star has a strong UV excess radiation.

We have developed a high-resolution combined physical and chemical model of a protoplanetary disk surrounding a typical T Tauri star. Our aims were to use our model to calculate the chemical structure of disks on small scales (submilliarcsecond in the inner disk for objects at the distance of Taurus, ∼140 pc) to investigate the various chemical processes thought to be important in disks and to determine potential molecular tracers of each process. Our gas-phase network was extracted from the UMIST Database for Astrochemistry to which we added gas-grain interactions including freezeout and thermal and non-thermal desorption (cosmic-ray-induced desorption, photodesorption, and X-ray desorption), and a grain-surface network. We find that cosmic-ray-induced desorption has the least effect on our disk chemical structure while photodesorption has a significant effect, enhancing the abundances of most gas-phase molecules throughout the disk and affecting the abundances and distribution of HCN, CN, and CS, in particular. In the outer disk, we also see enhancements in the abundances of H 2 O and CO 2. X-ray desorption is a potentially powerful mechanism in disks, acting to homogenize the fractional abundances of gas-phase species across the depth and increasing the column densities of most molecules, although there remain significant uncertainties in the rates adopted for this process. The addition of grain-surface chemistry enhances the fractional abundances of several small complex organic molecules including CH 3 OH, HCOOCH 3 , and CH 3 OCH 3 to potentially observable values (i.e., a fractional abundance of 10 −11).

We investigate the impact of photochemistry and X-ray ionization on the molecular composition of, and ionization fraction in, a protoplanetary disk surrounding a typical T Tauri star. We use a sophisticated physical model, which includes a robust treatment of the radiative transfer of UV and X-ray radiation, and calculate the time-dependent chemical structure using a comprehensive chemical network. In previous work, we approximated the photochemistry and X-ray ionization, here, we recalculate the photoreaction rates using the explicit UV wavelength spectrum and wavelength-dependent reaction cross sections. We recalculate the X-ray ionization rate using our explicit elemental composition and X-ray energy spectrum. We find photochemistry has a larger influence on the molecular composition than X-ray ionization. Observable molecules sensitive to the photorates include OH, HCO + , N 2 H + , H 2 O, CO 2 and CH 3 OH. The only molecule significantly affected by the X-ray ionization is N 2 H + indicating it is safe to adopt existing approximations of the X-ray ionization rate in typical T Tauri star-disk systems. The recalculation of the photorates increases the abundances of neutral molecules in the outer disk, highlighting the importance of taking into account the shape of the UV spectrum in protoplanetary disks. A recalculation of the photoreaction rates also affects the gas-phase chemistry due to the adjustment of the H/H 2 and C + /C ratios. The disk ionization fraction is not significantly affected by the methods adopted to calculate the photochemistry and X-ray ionization. We determine there is a probable 'dead zone' where accretion is suppressed, present in a layer, Z/R 0.1 -0.2, in the disk midplane, within R ≈ 200 AU.

The first detection of gas-phase methanol in a protoplanetary disk (TW Hya) is presented. In addition to being one of the largest molecules detected in disks to date, methanol is also the first disk organic molecule with an unambiguous ice chemistry origin. The stacked methanol emission, as observed with ALMA, is spectrally resolved and detected across six velocity channels (> 3σ), reaching a peak signal-to-noise of 5.5σ, with the kinematic pattern expected for TW Hya. Using an appropriate disk model, a fractional abundance of 3 × 10 −12 − 4 × 10 −11 (with respect to H 2 ) reproduces the stacked line profile and channel maps, with the favoured abundance dependent upon the assumed vertical location (midplane versus molecular layer). The peak emission is offset from the source position suggesting that the methanol emission has a ring-like morphology: the analysis here suggests it peaks at ≈ 30 AU reaching a column density ≈ 3−6×10 12 cm −2 . In the case of TW Hya, the larger (up to mm-sized) grains, residing in the inner 50 AU, may thus host the bulk of the disk ice reservoir. The successful detection of cold gas-phase methanol in a protoplanetary disk implies that the products of ice chemistry can be explored in disks, opening a window to studying complex organic chemistry during planetary system formation.

We apply the theory of radiative torque (RAT) alignment for studying protoplanetary disks around a T-Tauri star and perform 3D radiative transfer calculations to provide the expected maps of polarized radiation to be compared with observations, such as with ALMA. We revisit the issue of grain alignment for large grains expected in the protoplanetary disks and find that mm-sized grains at midplane do not align with magnetic field as the Larmor precession timescale for such large grains becomes longer than the gaseous damping timescale. Hence, for these grains the RAT theory predicts that the alignment axis is determined by the grain precession with respect to the radiative flux. As a result, we expect that the polarization will be in the azimuthal direction for a face-on disk. It is also shown that if dust grains have superparamagnetic inclusions, magnetic field alignment is possible for (sub-)micron grains at the surface layer of disks, and this can be tested by mid-infrared polarimetric observations.