Abstract. In this paper, we present mean gas and dust opacities relevant to the physical conditions typical of protoplanetary discs. As the principal absorber for temperatures below ∼1500 K, we consider spherical and aggregate dust particles of various sizes, chemical structure, and porosity, consisting of ice, organics, troilite, silicates, and iron. For higher temperatures, ions, atoms, molecules, and electrons are included as the main opacity sources. Rosseland and Planck mean opacities are calculated for temperatures between 5 K and 10 000 K and gas densities ranging from 10 −18 g cm −3 to 10 −7 g cm −3 . The dependence on the adopted model of dust grains is investigated. We compare our results with recent opacity tables and show how different opacity models affect the calculated hydrodynamical structure of accretion discs.

We calculate the ionisation fraction in protostellar disk models using a number of different chemical reaction networks, including gas-phase and gas-grain reaction schemes. The disk models we consider are conventional α-disks, which include viscous heating and radiative cooling. The primary source of ionisation is assumed to be X-ray irradiation from the central star. For most calculations we adopt a specific disk model (with accretion rateṀ = 10 −7 M yr −1 and α = 10 −2 ), and examine the predictions made by the chemical networks concerning the ionisation fraction, magnetic Reynolds number, and spatial extent of magnetically active regions. This is to aid comparison between the different chemical models.We consider a number of gas-phase chemical networks. The simplest is the five species model proposed by Oppenheimer & Dalgarno (1974). We construct more complex models by extracting species and reactions from the UMIST data base. In general we find that the simple models predict higher fractional ionisation levels and more extensive active zones than the more complex models. When heavy metal atoms are included the simple models predict that the disk is magnetically active throughout. The complex models predict that extensive regions of the disk remain magnetically uncoupled ("dead") even when the fractional abundance of magnesium x Mg = 10 −8 . This is because of the large number of molecular ions that are formed, which continue to dominate the recombination with free electrons in the presence of magnesium. The addition of submicron sized grains with a concentration of x gr = 10 −12 causes the size of the "dead zone" to increase dramatically for all kinetic models considered, as the grains are highly efficient at sweeping up the free electrons. We find that the simple and complex gas-grain reaction schemes agree on the size and structure of the resulting "dead zone", as the grains play a dominant role in determining the ionisation fraction. We examine the effects of depleting the concentration of small grains as a crude means of modeling the growth of grains during planet formation. We find that a depletion factor of 10 −4 causes the gas-grain chemistry to converge to the gas-phase chemistry when heavy metals are absent. When magnesium is included a depletion factor of 10 −8 is required to reproduce the gas-phase ionisation fraction. This suggests that efficient grain growth and settling will be required in protoplanetary disks, before a substantial fraction of the disk mass in the planet forming zone between 1-10 AU becomes magnetically active and turbulent. Only after this has occurred can gas-phase chemical models be used to predict reliably the ionisation degree in protoplanetary disks.

Abstract. The distributions of molecules in the inner regions of a protostellar disk are presented. These were calculated using an uncoupled chemical/dynamical model, with a numerical integration of the vertical disk structure. A comparison between models with and without the effects of X-ray ionisation is made, and molecules are identified which are good tracers of the ionisation level in this part of the disk, notably CN and C2H. In the region considered in this paper (r ≤ 10 AU), the chemistry is dominated by the thermal desorption of species from grains. This shows that a critically important detail in this region of the disk, as far as molecular distributions are concerned, is the temperature profile. We find that not all of the gaseous material is frozen onto grain surfaces at 10 AU, and we identify species, including some organic molecules, which should exist in observable quantities in the inner regions of protostellar disks.

We calculate the ionisation fraction in protostellar disk models using two different gas-phase chemical networks, and examine the effect of turbulent mixing by modelling the diffusion of chemical species vertically through the disk. The aim is to determine in which regions of the disk gas can couple to a magnetic field and sustain MHD turbulence. The disk models are conventional α-disks, and the primary source of ionisation is X-ray irradiation from the central star. We assume that the vertical mixing arises because of turbulent diffusion, and accordingly equate the vertical diffusion coefficient, D, with the kinematic viscosity, ν. We find that the effect of diffusion depends crucially on the elemental abundance of heavy metals (magnesium) included in the chemical model. In the absence of heavy metals, diffusion has essentially no effect on the ionisation structure of the disks, as the recombination time scale is much shorter than the turbulent diffusion time scale. When metals are included with an elemental abundance above a threshold value, the diffusion can dramatically reduce the size of the magnetically decoupled region ("dead zone"), or even remove it altogther. This arises when recombination is dominated by metal ions, and the recombination time exceeds the vertical diffusion time scale. For a complex chemistry the elemental abundance of magnesium required to remove the dead zone is x Mg = 10 −10 -10 −8 . We also find that diffusion can modify the reaction pathways, giving rise to dominant species when diffusion is switched on that are minor species when diffusion is absent. This suggests that there may be chemical signatures of diffusive mixing that could be used to indirectly detect turbulent activity in protoplanetary disks. We find examples of models in which the dead zone in the outer disk region is rendered deeper when diffusion is switched on. This is caused by turbulent mixing diluting the electron fraction in regions where the ionisation degree is marginally above that required for good coupling. Overall these results suggest that global MHD turbulence in protoplanetary disks may be self-sustaining under favourable circumstances, as turbulent mixing can help maintain the ionisation fraction above that necessary to ensure good coupling between the gas and magnetic field.

Abstract.We study the influence of mass transport processes on the chemical evolution in a protoplanetary accretion disk. Local transport processes by advection as well as global transport processes by diffusion are taken into account. Concerning the multi-component system only diffusion in the vertical direction was taken into account. Depending on the transport properties, different schemes are explored to couple/decouple the physical and chemical evolution. Our model is based on a simplified description of hydrodynamics in terms of a steady 1+1-D-α-disk model and includes the kinetics of an extended chemical network of about 250 species. We restrict our calculations to the inner planet formation zone within a distance to the central star of 10 AU. Vertical mixing does change the global chemical evolution as it is demonstrated in detail through a discussion of the chemistry of sulphur-bearing molecules. In addition, the influence of the local disk structure on the chemical evolution is analysed. Our results demonstrate that the chemical evolution is influenced globally by mass transport processes. However, in addition to mass transport processes, information about the local conditions, which determine the kinetics, is still needed in order to analyze the chemical evolution.