Well over 100 molecules, many of them organic, have been identified in interstellar gas. The clumps and cores in molecular clouds out of which stars form have densities ranging from 104 cm-3 to 108 cm-3 and low temperatures. In this state, cold gas chemistry can account for the formation of simple molecules (CO, N2, O2, C2H2, C2H4, and HCN). The surfaces of dust grains play host to the formation of more complex organic molecules, which include nitriles, aldehydes, alcohols, acids, ethers, ketones, amines, amides, and long-chain hydrocarbons.
For decades, our knowledge of the chemistry in the solar nebula was based on studies of planetary atmospheres, meteorites, and comets. Current observations allow us to study directly the chemistry of disks around other stars. This work reveals that active chemistry occurs near the surface regions of protoplanetary disks. This chemistry is in disequilibrium and is similar observationally to that found in dense regions directly exposed to ultraviolet and X-ray irradiation (Bergin et al., 2006).
Chemistry and reaction rates in protoplanetary disks depend on the local gas density, temperature, and radiation field. Disks are not flat but are instead observed to be flared. Their surfaces, therefore, are exposed to radiation from the central star. The vertical structure of disks arises from the fact that the pressure gradient of the gas at any radius and scale height in the disk supports the weight of the material above it. The force that must be balanced is the vertical component of the gravitational field of the central star (e.g., Dubruelle et al. (2006)).
Self-consistent calculations show that the heating of such flaring disks is due primarily to the ultraviolet radiation from the central star that is absorbed by dust grains in such surface layers (Chiang and Goldreich, 1997; D'Alessio et al., 1998). The dust in the disk envelope then reradiates this energy in the form of infrared and submillimetre photons - about half of which escape vertically away from the disk,
while the remainder radiate downwards towards the disk midplane. These infrared photons are then absorbed by the deeper lying dust and ultimately radiate out of the disk. The gas is heated by collisions with the warm dust and cools by radiating this energy in the form of molecular vibration-rotation emission lines that can be observed. This overall process produces a disk that is hottest near the surface layers and cooler towards the midplane. By balancing all of these heating and cooling rates, one can determine the local disk temperature distribution and hence the disk's SED. The prediction that the temperature should scale as T a r-0 5 is close to that observed.
The vertical structure of disks at disk radii beyond 100 AU consists of three layers; the radiation-dominated surface layer or 'photon-dominated region' (PDR), which consists mainly of atomic and ionized species, a molecular layer at greater depth beyond which most ultraviolet radiation has been absorbed by the grains, and the cold midplane layer noted above. This midplane region turns out to be so cold (around 20 K) that most heavy species, such as CO, freeze out on the dust grains. Figure 4.2 shows a schematic of the disk. It is the molecular layer that is of primary interest for the synthesis of complex organic molecules.
Observations of molecules so far are still limited by the sensitivity of telescopes as the emission is so weak. By far, the most abundant molecule is molecular hydrogen, H2, but it is generally hard to detect. The most abundant species that have been observed to date in disks include HCO+, CN, CS, HCN, H2CO, and DCO+ (e.g., Dutrey et al. (1997), van Zadelhoff et al. (2001)). Silicates such as Mg2SiO4 (forsterite) have been detected in the hot surface layers of the inner regions of the disk (r < 1-10 AU). This is important because the shape and strength of silicate features in disk spectra allow one to track the evolution and growth of dust grains in disks with time. Ices of H2O, CO2, and CO are observed in the outer regions of the disks, where temperatures drop to less than 100 K. The most abundant organic molecules observed are the polycyclic aromatic hydrocarbons, or PAHs. Their abundance per H atom is of the order of 10-7. Up to 50% of carbon may be locked up in such carbonaceous solids. They are important for disk chemistry because they absorb ultraviolet radiation and act as potential sites for H2 formation.
Dust grains that are coated with simple icy mantles warm up as they are mixed and transported to dense, active protostellar regions. This can occur in regions such as the so-called hot cores that are hosts to massive star formation or the innermost regions of protoplanetary disks. These regions are particularly rich in organic molecules. Ultraviolet irradiation, or perhaps X-ray bombardment, then breaks bonds, and allows reactions that can produce organic molecules. However, evaporation of these simple dust grain surfaces can drive gas phase production of organics.
It is now well established that organic molecules of extra terrestrial origin are found in carbonaceous chondrite meteorites. The best-studied of these is the Murchison meteorite, in which 8 of the 20 biological amino acids have been found (Engel and Nagy, 1982). Meteorites also contain many other organic molecules that are relevant in astrobiology (Sephton, 2002), including lipids that have been shown to be capable of membrane formation (see Chapter 5). The organic molecules in meteorites may have originally arisen on dust grains, which were then incorporated into comets and meteorites. The possibility that dust grains with icy mantles are a site for amino acid synthesis has been investigated experimentally. Bernstein et al. (2002) and Munoz-Caro et al. (2002) have shown that amino acids such as glycine, alanine, and serine may result from the exposure of icy mantles consisting of HCN, ammonia (NH3), and formaldehyde (H2CO) to ultraviolet radiation.
Alternatively, it has been proposed that amino acids such as glycine and alanine, and the base adenine can form during the gravitational collapse of a core. Chakrabarti and Chakrabarti (2000) added reactions that make amino acids (e.g., by the Strecker process - wherein an aldehyde starting material combines with HCN in ammonia to form the corresponding aminonitrile, which upon hydrolysis forms the amino acid) to the existing UMIST database of chemical reactions in molecular clouds. This created a reaction network involving 421 molecular species. As an example, they found that the glycine that was formed had a mass fraction of order 10-12. It peaks at a radius of approximately 100 AU and a time of a million years after the initiation of the collapse. The astronomical detection of interstellar amino acids, such as glycine, would strengthen the link between the chemistry of disks and observed amino acids in meteorites. A spectroscopic survey for amino acids in clouds and disks will be possible with ALMA.
Organic molecules contained in comets and meteorites are delivered to Earth when impact events occur, and it is known that impacts were frequent in the early history of the Solar System. Impacts release huge amounts of energy which might cause thermal degradation of macromolecules. However, Pierazzo and Chyba (1999) predicted that molecules such as amino acids can survive such impacts and that the rate of delivery of biomolecules from space could exceed the rate of synthesis on Earth.
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