Chemical Processes in Protoplanetary Disks II. On the importance of photochemistry and X-ray ionization

6 MB·English

by  Catherine Walsh

Draftversion January13,2012
PreprinttypesetusingLATEXstyleemulateapjv.5/2/11
CHEMICAL PROCESSES IN PROTOPLANETARY DISKS. II.
ON THE IMPORTANCE OF PHOTOCHEMISTRY AND X-RAY IONIZATION
Catherine Walsh1, Hideko Nomura2, T. J. Millar1 and Yuri Aikawa3
Draft version January 13, 2012
ABSTRACT
We investigate the impact of photochemistry and X-ray ionization on the molecular composition
2
of, and ionization fraction in, a protoplanetary disk surrounding a typical T Tauri star. We use a
1
sophisticated physical model, which includes a robust treatment of the radiative transfer of UV and
0
X-rayradiation,andcalculatethetime-dependentchemicalstructureusingacomprehensivechemical
2
network. Inpreviouswork,weapproximatedthephotochemistryandX-rayionization,here,werecal-

n culate the photoreactionrates using the explicit UV wavelengthspectrum andwavelength-dependent
a reaction cross sections. We recalculate the X-ray ionization rate using our explicit elemental compo-
J
sition and X-ray energy spectrum. We find photochemistry has a larger influence on the molecular

2 composition than X-ray ionization. Observable molecules sensitive to the photorates include OH,
1 HCO+, N H+, H O, CO and CH OH. The only molecule significantly affected by the X-ray ion-
2 2 2 3
ization is N2H+ indicating it is safe to adopt existing approximations of the X-ray ionization rate in
]
A 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
G
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 and C+/C ratios. The disk ionization frac-
h 2
tion is not significantly affected by the methods adopted to calculate the photochemistry and X-ray
p
ionization. We determine there is a probable ‘dead zone’ where accretion is suppressed, present in a
-
o layer, Z/R . 0.1 - 0.2, in the disk midplane, within R ≈ 200 AU.
r Subject headings: astrochemistry – protoplanetary disks – stars:formation – ISM:molecules
t
s
a
[ 1. INTRODUCTION ern disk models, wavelength-dependent radiative trans-
fer is preferred (van Zadelhoff et al. 2003) as is the
1 Protoplanetary disks have several vital functions in
inclusion of UV excess radiation (Bergin et al. 2003;
v star and planet formation: they (1) aid the dissipation
3 of angular momentum away from the protostellar sys- Nomura & Millar 2005) and X-rays (Glassgold et al.
1 tem, (2) allow the efficient accretion of matter from the 1997; Aikawa & Herbst 1999). Along with cosmic-rays,
6 constituent cloud material onto the central star, and (3) the X-ray and UV radiationcontrols the ionization frac-
2 contain the material which may eventually form an ac- tion in the disk which has consequences on the disk
. accretion rate and the location and extent of ‘dead
1 companying planetary system.
zones’, regions where accretion is potentially suppressed
0 Protoplanetary disks are physically and thus, chemi-
(Balbus & Hawley 1991; Gammie 1996). The varying
2 cally,complexobjects(seee.g.,Bergin et al.2007). They
radiation field will also have a direct effect on the disk
1 are heavily irradiated by UV radiation from their par-
chemical structure, controlling the abundance and dis-
: ent T Tauri star and are permeated by X-rays and ex-
v tribution of atoms, ions and molecules through pho-
cess UV photons thought to arise from an accretion
i tochemistry and influencing the molecular composition
X shock generated as disk material impinges upon the
of the icy grain mantle via non-thermal desorption
stellar surface (Herbig & Goodrich 1986; Kastner et al.
r
and this has been demonstrated in many works (see
a 1997). Beyond a radius r & 100 AU, the UV radi-
e.g., van Zadelhoff et al. 2003; Aikawa & Nomura 2006;
ation field originating from the parent star decreases
Walsh et al. 2010; Kamp et al. 2010; Vasyunin et al.
in strength due to a combination of absorption of UV
2011). For these reasons, the treatment of photo pro-
photons by the intervening disk material and geomet-
cesses in protoplanetary disks should be thoroughly in-
rical dilution. Here, irradiation by UV photons orig-
vestigated, in order to aid the interpretation of obser-
inating from the interstellar radiation field (ISRF) in-
vational data, especially with the impending completion
creases in importance and, as a result, the wavelength
of the Atacama Large Millimeter Array (ALMA) which,
dependence (or shape) of the radiation field varies as
for the first time, will enable the observation of molecu-
a function of disk radius and height (Aikawa & Herbst
laremissionfromnearby(∼140pc)protoplanetarydisks
1999; Willacy & Langer 2000). As a result, in mod-
onaroundsub-milli-arcsecondscaleswithunprecedented
[email protected] spectral resolution.
1Astrophysics Research Centre, School of Mathematics and A plethora of molecules have been detected in proto-
Physics, Queen’s University Belfast, University Road, Belfast, planetarydisks vialine emissionin the (sub)mm andin-
NorthernIreland,UK,BT71NN
2DepartmentofAstronomy,GraduateSchoolofScience,Ky- fraredregionsoftheelectromagneticspectrum. Earlyob-
otoUniversity,Kyoto606-8502,Japan servationsat(sub)mm wavelengthswere made using the
3DepartmentofEarthandPlanetarySciences, KobeUniver- JamesClerkMaxwellTelescope(JCMT)andIRAM30m
sity,1-1Rokkodai-cho, Nada,Kobe657-8501, Japan
2 Walsh et al.
radio telescope (e.g., Kastner et al. 1997; Dutrey et al. cal model. In Section 2.2 we describe our chemical net-
1997; van Zadelhoff et al. 2001; Thi et al. 2004), with work and processes we include in our calculation of the
more recent detections using the Submillimeter Array chemical structure with a thorough description of the
(SMA) (e.g., Qi et al. 2006, 2008; O¨berg et al. 2010). methods used to compute the photochemical and X-ray
Mostmoleculesobservedinthisspectralregionaresmall, ionization rates (Sections 2.2.1 and 2.2.2, respectively).
simple, abundant molecules, molecular ions and radicals InSection2.3,wedescribethetheorybehindtheidentifi-
(e.g., CO, CN, CS, HCO+, N H+, HCN) and associated cationofregionsofourdiskinwhichangularmomentum
2
isotopologues (e.g., 13CO, DCO+, and C34S). A recent transport and thus, accretion, may be suppressed. The
survey of disks around T Tauri and Herbig Ae stars has resultsofourcalculationsarepresentedinSection3with
led to the first successful detection of SO in a circum- a summary given in Section 4.
stellar disk (Fuente et al. 2010), with the authors also
reporting a tentative detection of H S. Due to the limi- 2. PROTOPLANETARYDISKMODEL
2
tations of existing telescopes and the small angular size 2.1. Physical Model
of disks, the most complex molecule observed to date is
The physical model of a protoplanetary disk we use is
formaldehyde, H CO (Dutrey et al. 1997; Aikawa et al.
2 fromNomura & Millar(2005)withtheadditionofX-ray
2003).
heatingasdescribedinNomura et al.(2007). Thedegree
Use of the Infrared Spectrograph (IRS) on the
of ionization in the disk depends on the disk parameters
Spitzer Space Telescope increased the inventory of
adopted and the resulting surface density distribution.
gas-phase molecules detected in disks to include OH,
The theoretical foundation of our model comes from the
H O, CO and C H (Lahuis et al. 2006; Carr & Najita
2 2 2 2 standard accretion disk model of Lynden-Bell & Pringle
2008; Salyk et al. 2008; Pontoppidan et al. 2010). Ex-
(1974) and Pringle (1981) which defines a surface den-
isting (sub)mm observations probe the colder, outer
sity distribution for the disk given the central star’s
disk material whereas infrared observations probe
mass and radius and a disk accretion rate, M˙ . The
the warmer gas in the inner disk surface in the
kinematic viscosity in the disk is parameterised accord-
so-called ‘planet-forming’ region. There have also
ing to the work of Shakura & Sunyaev (1973), the so-
been detections of water ice absorption features in
called, α-prescription. We consider an axisymmetric
‘edge-on’ T Tauri systems (Creech-Eakman 2002;
disk surrounding a typical T Tauri star with mass,
Terada et al. 2007; Schegerer & Wolf 2010). More re-
cently, Hogerheijde et al. (2011) report the first detec- M∗ = 0.5 M⊙, radius, R∗ = 2 R⊙ and effective tem-
tionoftheground-staterotationalemissionlinesofboth perature, T∗ = 4000 K. We adopt a viscous parameter,
spinisomerstatesofwaterinaprotoplanetarydiskusing α=0.01andamassaccretionrate,M˙ =10−8 M⊙ yr−1.
the Heterodyne Instrument for the Far-Infrared (HIFI) We use a model X-ray spectrum created by fitting the
mounted on the Herschel Space Observatory. These sets observedXMM-NewtonspectrumoftheclassicalTTauri
of observations, of both gas and ice, give us a reason- star, TW Hydrae (Kastner et al. 2002) with a two-
ably sufficient benchmark with which we can compare temperaturethinthermalplasmamodel(MEKALmodel
our results. see e.g., Liedahl et al. (1995)). The derived best-fit pa-
In Walsh et al. (2010), henceforth referred to as Pa- rametersfortheplasmatemperaturesarekT1 = 0.8keV
per I, we used the physical disk model described in and kT2 = 0.2 keV and for the foreground interstellar
Nomura & Millar (2005) and Nomura et al. (2007) to hydrogen column density, NH = 2.7 × 1020 cm−2. For
compute the chemical structure of a typical protoplan- the X-ray extinction, we include attenuation due to ion-
etary disk on small scales (sub-milli-arcsecond in the ization of all elements and Compton scattering by hy-
inner disk for an object at the distance of Taurus, drogen. The X-ray luminosity is LX ∼ 1030 erg s−1 and
∼ 140 pc), investigating the effects of the addition of the resulting high-resolution X-ray spectrum is given in
non-thermaldesorptionmechanisms(cosmic-ray-induced Figure 1 of Nomura et al. (2007) assuming a distance to
desorption, photodesorption and X-ray desorption) and source of 56 pc, and is reproduced in binned form here
grain-surface chemistry on the disk chemical structure. in the right-hand panel of Figure 1.
In that work,we presentedresults frommodels in which The UV radiation field in disks has two sources, the
we approximated the photoreaction rates by scaling the star and the interstellar medium. In this disk model,
rates from the UMIST Database for Astrochemistry or the radiation field due to the T Tauri star has three
UDfA (Woodall et al.2007), whichassumethe interstel- components: black-body emission at the star’s effective
lar radiation field (ISRF), by the wavelength integrated temperature, optically thin hydrogenic bremsstrahlung
UV flux at each point in the disk (see Section 2.2.1 for emission and strong Lyman-α line emission. For the
further details). Here, we report results from models in UV extinction, we include absorption and scattering by
which we explicitly calculate the photodissociation and dust grains. We assume the dust and gas in the disk
photoionization rates taking into consideration the UV is well mixed and adopt a dust-size distribution model
spectrum at each point and the wavelength-dependent which reproduces the observational extinction curve of
absorptioncrosssectionfor eachphotoreaction. In addi- dense clouds (Weingartner & Draine 2001). The calcu-
tion,werecalculatetheX-rayionizationrateeverywhere lation of the dust opacity in the disk is described in
in the disk accounting for the elemental composition of Appendix D of Nomura & Millar (2005) with the result-
the gas and include the direct X-ray ionization of ele- ing wavelength-dependent absorption coefficient shown
ments, in both cases, using the X-ray energy spectrum in Figure D.1. The total FUV luminosity in our model
at each point. is LUV ∼ 1031 erg s−1 with the calculation of the radia-
In Section 2.1, we give a brief overview of our physi- tionfieldinthediskdescribedindetailinAppendixCof
Nomura & Millar (2005). We display the resulting stel-
Photochemistry in Protoplanetary Disks 3
lar flux density in the disk surface at a radius of 1 AU,
including each individual component, in the left-hand TABLE 1
Photodesorption Yields
panelofFigure1. ThemainsourceofUVphotonsshort-
wardof2000˚Aisdue toBrehmsstrahlungandLyman-α Species Yield(molecules photon−1) Reference
radiationwiththeLyman-αlinecontributingaround103
timestheUVcontinuumphotonfluxat≈1216˚Aoveran CO 2.7×10−3 1
assumedFWHMof≈2˚A(seee.g.,Herczeg et al.2002). NCO22 12..83××1100−−43 12
The resulting disk physical structure is given in Fig- H2O 1.3×10−3 2
ures 1 and 13 in Paper I and we refer readers to the Allother species 3.0×10−3 3
Appendix of that publication for a thorough discussion.
References. —(1)O¨bergetal.(2009a),(2)O¨bergetal.
InFigure2,wedisplaythe gasanddusttemperaturesin
(2009b),(3)Westleyetal.(1995)
K(topright),thegasnumberdensityincm−3 (topleft),
the wavelength-integratedUV flux (bottom left) and X-
ray flux (bottom right) both in units of erg cm−2 s−1,
TABLE 2
asa function ofdiskradius andheight(scaledby the ra- Molecular Binding Energies
dius). Inthetemperatureplot,thecolourmaprepresents
the gas temperature whereas the contours represent the Species BindingEnergy(K) Reference
dust temperature. As expected, the disk surface closest
CO 855 1
to the parentstaris subjectedtothe largestflux ofboth
N2 790 1
UVandX-rayradiation. Thediskmidplaneiseffectively CO2 2990 2
completelyshieldedfromUVphotonsoverthe radialex- C2S 5320 2
tentofourdiskmodel. ThehigherenergyX-rayphotons, H2O 4800 3
SO2 5330 2
althoughresulting inalowerflux inthe disksurface,are NH3 2790 3
able to penetrate the disk more effectively leading to a CH4 1090 4
small, yet appreciable, X-ray flux in the disk midplane HCOOH 5000 5
beyond ≈ 10 AU. CH3OH 4930 3
CH3CHO 3800 5
2.2. Chemical Model C2H6 2300 5
HCOOCH3 4000 5
As in Paper I, our gas-phase chemistry is ex- CH3OCH3 3300 5
tracted from the latest release of the UMIST C2H5OH 5200 5
Database for Astrochemistry or ‘Rate06’, available at References. — (1) O¨bergetal. (2005), (2)
http://www.udfa.net (Woodall et al. 2007). We use Edridge(2010),(3)Brown&Bolina(2007),(4)
almost the entire Rate06 network removing only those Herreroetal.(2010),(5)O¨bergetal.(2009c)
reactions involving fluorine- and phosphorus-containing
species. Here, we also include the subset of three- forsimplicity,however,theyshouldbeinvestigatedinfu-
body reactions from Rate06, since these may play a sig- ture models.
nificant role in the densest regions of our disk model In Paper I, we used a constant photodesorption yield
(n ∼ 1015 cm−3). of 3×10−3 photon−1 as determined for pure water ice
We allow gas-grain interactions i.e., the accretion of by Westley et al. (1995). To take into consideration the
gas-phase species onto dust grains with removal of the composition of the grain mantle we now determine the
grainmantleviathermaldesorption,cosmic-ray-induced photodesorption rate for a specific species according to
desorption (L´eger et al. 1985; Hasegawa & Herbst 1993)
and photodesorption (Westley et al. 1995; O¨berg et al. kpid =GUVYUiVσdxdxis s−1, (1)
2007; Willacy 2007). In Paper I we provided a thor-
where G is the radiation field in units of photons
ough description of the methods used to determine our cm−2 s−1U,VYi photon−1 is the specific desorption yield
accretion and desorption rates. We also include the UV
of species i, as listed in Table 1, xi = ni/ntot is the
grain-surface network from Hasegawa et al. (1992) and s s s
fractional abundance of species i on the dust grains and
Hasegawa & Herbst (1993).
σ and x are the dust-grain geometrical cross section
Here, we calculate our photodesorption rates taking d d
andfractionalabundance, respectively. We have also re-
intoaccountthemolecularcompositionofthegrainman-
viewedoursetofmoleculardesorptionenergiesinlightof
tle. Experiments into the photodesorption of UV ir-
recent experimental results and in Table 2 we list those
radiated ices conducted by O¨berg et al. (2009a,b) sug-
species for which the binding energies, E , have been
d
gest that the photodesorption yields are dependent on
updated.
the ice composition with pure CO, N , CO and H O
2 2 2 Our initial fractional abundances are the result of
ices giving different desorptionyields (listed in Table 1).
a dark cloud model run with typical molecular cloud
The picture is further complicated by evidence of codes- parameters i.e., T = 10 K, n(H ) = 104 cm−3 and
2
orption in mixed ices, with the photodesorption yield of
A =10magusingthesetofoxygen-richlow-metallicity
v
N increasing when present in a 1:1 N /CO ice mixture
2 2 elemental abundances from Graedel et al. (1982) as
(O¨berg et al. 2007). More recent work suggests that in listed in Table 8 of Woodall et al. (2007). In the gen-
organic ices, irradiation by UV photons initiates chem- eration of our initial abundances we allow for freeze out
istrywithphotodesorptionproductsdetectedotherthan and thermal desorption and we extract abundances at a
those present in the original ice mixture (O¨berg et al. time of 105 years which is thought to be the age of dark
2009c). Theselattereffectsarenotincludedinthismodel clouds on the brink of star formation.
4 Walsh et al.
1015 10-1
Stellar UV Spectrum at 1 AU Total Stellar X-ray Spectrum
1−1 Å)1014 BremBslastcrka hBLlyuo−ndagy -1eV) 10-2
−2−s cm s1013 Ly−a -2-1m s k 1100--43
n c
hoto1012 ons 10-5
UV Flux Density (p11001101 X-ray Flux (phot 111000---876
109 10-9
103 104 0.1 1 10
Wavelength (Å) Energy (keV)
Fig.1.—StellarUVfluxdensityinthedisksurfaceat1AUinphotons cm−2 s−1 ˚A−1 (left)andbinnedX-rayfluxdensityinphotons
cm−2 s−1 keV−1 (right). Thelatterassumesadistancetosourceof56pc.
0.8 104 0.8 1015
0.7 Temperature 0.7 Density 1014
(K) (cm-3) 1013
0.6 0.6
2300 KK 103 1012
0.5 50 K 0.5 1011
70 K
Z/R 0.4 150000 KK Z/R 0.4 1010
0.3 0.3 109
102 108
0.2 0.2
107
0.1 0.1 106
0 101 0 105
0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU)
0.8 107 0.8 107
UV Flux 106 X-ray Flux 106
0.7 105 0.7 105
(erg cm-2 s-1) 104 (erg cm-2 s-1) 104
0.6 103 0.6 103
0.5 102 0.5 102
101 101
Z/R 0.4 1100-01 Z/R 0.4 1100-01
0.3 10-2 0.3 10-2
10-3 10-3
0.2 10-4 0.2 10-4
0.1 10-5 0.1 10-5
10-6 10-6
0 10-7 0 10-7
0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU)
Fig.2.—Temperature(top left),numberdensity(top right),UVflux(bottom left)andX-rayflux(bottom right)asafunctionofdisk
radius,R,andheight(scaledbytheradiusi.e.,Z/R). Onthetemperaturepanel,thecolourmaprepresentsthegastemperaturewhereas
thecontours representthedusttemperature.
2.2.1. Photochemistry 2000˚A
point, GUV(r,z)= ˚ Gλ(r,z)dλ i.e.,
912A
R
The photoreaction rates in Rate06 are calculated as- G
suming the UV radiation field is given by the Draine kph = UVk0 s−1 (2)
G
field (Draine 1978), an adequate assumption for the 0
unshielded ISRF. For use in chemical models, these where G is the unshielded interstellar UV flux and
0
ratesaresubsequentlyparameterisedaccordingtooptical k is the rate calculated for the unshielded interstellar
0
depth or A . In Paper I, we approximated our photore- medium. Note, G (r,z)includes boththe stellarandin-
v λ
action rates in the disk, k , by scaling the rates from terstellarcomponentsoftheradiationfield. Thisapprox-
ph
Rate06 using the wavelength-integratedUV flux at each imation is unsuitable for use in protoplanetary disks as
Photochemistry in Protoplanetary Disks 5
these objects are irradiated by UV radiation with three ratio of CO /H O changes from ≈ 0.045 in model UV-
2 2
components: the central star, UV excess due to accre- old to ≈ 1.90 in model UV-new at 100 AU. We discuss
tion and the interstellar radiation field. Hence, the UV thepossibleeffectsofincludingLyman-αradiationinthe
spectrum at each point in the disk will not only vary calculation of the photorates in Section 3.6.
withdisk radiusandheight,but willalsobearno resem- We include the self-shielding of H using the approx-
2
blance to the interstellar radiation field (see Figure 4 in imation from Federman et al. (1979) in the generation
Nomura & Millar(2005)). Forthesereasons,wehavein- of our physical model giving us the initial conditions
vestigated a recalculation of the photorates in the disk in our disk, however, we do not explicitly include the
takingintoconsiderationtheUVspectrumateachpoint self- and mutual shielding of H and CO in our calcula-
2
(van Dishoeck 1987; van Dishoeck et al. 2006). tion of the subsequent chemical structure. We find the
The photodissociation rate due to continuous absorp- dominant component of the radiation field in the disk
tion, kc , is calculated using surface is the radial component which is the direct stel-
ph
lar radiation (the vertical component consists of both
kc = λmaxσ(λ)I(λ) dλs−1, (3) the contribution from the interstellar radiationfield and
ph Z scattered stellar radiation). In addition, throughout the
λmin majorityofthedisk,thestellarradiationdominatesover
where, λ is the wavelength, σ(λ) is the cross sectionand the interstellar radiation. Hence, we argue against the
I(λ) is the mean intensity of UV radiation. The rate for validity of adopting the usual plane-parallel approxima-
photoionization, kpi, is calculated using the same equa- tion for the calculation of the self-shielding factors and
tion. For indirect photodissociation via absorption into the application of shielding factors computed for irra-
a bound upper state, u, from a lower state, l, the rate is diated interstellar clouds, to protoplanetary disks. To
πe2 correctlyinclude the effects ofself- andmutualshielding
kl = λ2 f µ I(λ)s−1, (4) in disks, a self-consistent two-dimensional treatment is
ph mc2 ul ul u
needed which takes into consideration the time-varying
where, λul is the wavelength of the line transition, ful H2 and CO abundances throughout the disk, the col-
is the oscillator strength of the transition and µul is umn densities in the radial and vertical direction and
an efficiency factor. The parameters, e, c and m are the two-dimensionalphysicalstructure ofthe disk which
the electron charge, the speed of light and the atomic will effect the line widths and line strengths and hence,
or molecular mass, respectively. The total photodis- shielding factors. We discuss this issue further in Sec-
sociation rate is found by summing over all possible tion 3.5.
channels. The photoreaction cross sections, σ(λ), are
those adopted in van Zadelhoff et al. (2003) which 2.2.2. X-ray Ionization
originate from calculations by van Dishoeck (1988), up-
The model of Nomura et al. (2007) calculates an over-
datedbyJansen et al.(1995a,b)andvan Dishoeck et al.
allX-rayionizationrateateachpointinthediskaccord-
(2006). The photo cross sections are downloadable from
http://www.strw.leidenuniv.nl/∼ewine/photo/. ing to the theory of Maloney et al. (1996). The rate at
eachpoint is calculated assuming a power-lawfit for the
For species which do not havea calculatedcrosssection,
X-ray absorption cross section dependent on X-ray en-
we use the rate for a similar type of molecule.
ergy and it is these approximate rates that are used in
We should note here we include Lyman-α radiation
ourchemicalcalculationsinPaperI.Inthiswork,were-
in the calculation of the wavelength-integrated UV flux
calculatetheX-rayionizationrateeverywhereinthedisk
(Equation 2) which accounts for approximately 85% of
taking into account the X-ray energy spectrum, F (E),
the total flux (see e.g., Bergin et al. 2003), however, we X
at each point and the explicit elemental composition of
ignore it in the calculation of the wavelength-dependent
the gas (Glassgold et al. 1997). The overall X-ray ion-
UVradiationfieldandsubsequentphotorates(seeEqua-
izationrate, ζ , is givenby summing overallelements,
tions 3 and 4). The exclusion of Lyman-α is primar- XR
ily due to the difficulties in treating the scattering of Emax E−E
Lyman-αphotonsfromthesurfaceintothedisk(seee.g., ζ = x σ (E)F (E) k dE s−1,
XR k k X
Bergin et al.2003). Lyman-αscatteringdiffersfromthat Xk ZEk (cid:20) ∆ǫ (cid:21)
of the background UV photons since the scattering oc- (5)
curs predominantly by H atoms rather than dust grains. where,foreachelement,k,E istheionizationpotential,
k
Indeed, Lyman-α radiation has been historically ne- σ (E) is the cross section and x is the fractional abun-
k k
glected in protoplanetary disk models and has only very dancewithrespecttoHnucleidensity. Inthisexpression,
recentlybeenaddressedintheworkbyBethell & Bergin thenumberofsecondaryionizationsperunitenergypro-
(2011). However, the photorates calculated according duced by primary photoelectrons, N , is given by the
sec
to Equations 3 and 4 are more accurate than those de- expression, (E −E )/∆ǫ, where ∆ǫ is the mean energy
k
termined using Equation 2 since the shape of the back- requiredtomakeanionpair(≈37eV).Onlythenumber
groundradiationfieldisincludedinthecalculation. The ofsecondaryionizationsneedsto be consideredasthis is
photoratescalculated using Equation2 include the total generally much larger than the number of primary ion-
flux of UV photons (background plus Lyman-α) heav- izationevents. Typically,eachkeVofsecondaryelectron
ily overestimating the strength of the UV field at wave- energyproducesanaverageof1000/37≈ 27ionpairs so
lengthsotherthantheLyman-αwavelength(≈1216˚A). that N ≫ N . Note that X-rays interact only with
sec pri
Theeffectofincludingthewavelength-dependenceinthe atoms, regardless of whether an atom is bound within a
photoratesisapparentindifferencesintherelativeabun- molecule or free (Glassgold et al. 1997).
dancesofmolecules(seeTable3)e.g.,thecolumndensity We have also added the direct X-ray ionization of ele-
6 Walsh et al.
ments, the rate for which is given by
TABLE 3
ColumnDensities Emax
ζ = σ (E)F (E)dE s−1. (6)
k k X
Z
Species UV-old XR+UV-old UV-new XR+UV-new Ek
using the ionization cross sections for each element, k,
0.1AU from Verner et al. (1993).
H 1.4(21) 1.4(21) 4.5(20) 4.2(20)
H2 1.1(26) 1.1(26) 1.1(26) 1.1(26) 2.3. Disk Ionization Fraction
CO 9.7(21) 9.5(21) 9.5(21) 9.6(21)
HCO+ 2.1(14) 2.5(14) 3.2(12) 1.7(12) In addition to investigating the importance of photo-
HCN 5.2(19) 5.0(19) 5.4(19) 4.9(19) chemistry and X-ray chemistry in protoplanetary disks,
CN 8.2(13) 6.9(13) 4.3(13) 6.5(13) we have determined the location and extent of potential
CS 1.3(17) 1.5(17) 1.5(17) 1.5(17)
dead zones where accretion may be inhibited. Angular
C2H 1.0(15) 9.9(14) 9.6(14) 9.8(14)
H2CO 6.9(15) 8.2(15) 6.5(15) 8.3(15) momentum transport in disks is thought to arise from
N2H+ 3.7(09) 8.7(08) 2.0(11) 9.2(10) turbulence initiated by a weak-field magnetorotational
OH 6.0(16) 6.0(16) 6.1(15) 5.1(15) instability or MRI (Balbus & Hawley 1991), hence, ac-
H2O 2.8(22) 2.8(22) 2.8(22) 2.8(22) cretionmaybeinefficientinregionswheretheinstability
CO2 3.8(18) 5.4(18) 3.7(18) 5.5(18) is suppressed. The turbulence generated by the insta-
C2H2 6.1(18) 9.6(18) 9.3(18) 9.1(18)
CH3OH 2.3(18) 2.4(18) 2.3(18) 2.4(18) bility can sustain a disordered magnetic field to which
the gas is coupled. The degree of the coupling, in turn,
1AU depends on the ionization fraction in the disk.
H 1.1(21) 1.1(21) 8.8(20) 8.3(20) Following Gammie (1996), we can define a magnetic
H2 1.9(25) 1.9(25) 1.9(25) 1.9(25) Reynolds number, Re , everywhere,
CO 1.9(21) 1.9(21) 1.9(21) 1.9(21) M
HCO+ 1.7(14) 1.9(14) 9.4(13) 6.5(13) V H
A
HCN 2.0(18) 2.0(18) 2.0(18) 2.0(18) Re = , (7)
M
CN 2.7(14) 2.7(14) 1.0(14) 1.3(14) η
CS 8.7(12) 8.4(12) 6.2(12) 6.3(12)
C2H 4.1(14) 4.4(14) 9.1(13) 1.5(14) where VA ≈ α1/2cs is the Alfv´en speed, a function of α,
NH22CHO+ 53..21((1130)) 93..31((1039)) 23..72((1132)) 53..11((1131)) tthhee saccaclrientgiopnardaimsketmerodfoerltohfeSvhiasckousriaty&(νSu=nyαacesvH()1f9r7o3m)
OH 1.7(16) 1.8(16) 2.4(16) 2.2(16)
and c , the sound speed in the disk. H is the disk scale
H2O 2.2(21) 2.2(21) 2.2(21) 2.2(21) s
CO2 7.7(20) 7.7(20) 7.7(20) 7.7(20) height given by H = cs/Ω, where Ω is the Keplerian
C2H2 1.6(14) 1.9(14) 1.5(14) 1.8(14) velocity at a particular radius, R, and η is the magnetic
CH3OH 1.0(15) 1.0(15) 1.0(15) 1.0(15) resistivity which is related to the electron fraction, χ ≡
n /n by
10AU e H
η =(6.5×103)χ−1 cm2s−1, (8)
H 7.3(20 7.2(20) 6.1(20) 5.7(20)
H2 2.6(24) 2.6(24) 2.6(24) 2.6(24) (see Gammie (1996) for further details). Accretion is
CO 2.0(20) 2.0(20) 2.0(20) 2.0(20)
HCO+ 4.8(13) 4.5(13) 1.4(14) 1.6(14) likelysuppressedinregionswherethemagneticReynolds
HCN 8.0(14) 2.1(15) 4.5(14) 6.9(14) number, ReM, falls below a critical value, RecMrit. This
CN 7.3(13) 8.1(13) 3.0(14) 3.4(14) parameter determines the degree to which the ionized
CS 4.7(13) 4.4(13) 4.3(13) 5.5(13)
gas is effectively coupled to the magnetic field. Recent
C2H 5.4(13) 6.7(13) 1.1(14) 1.6(14) MHD simulations suggest Recrit ∼ 100 (Sano & Stone
H2CO 2.0(12) 2.0(12) 1.2(12) 8.1(11) M
N2H+ 2.0(10) 5.7(09) 2.8(11) 9.2(10) 2002; Ilgner & Nelson 2006) which corresponds roughly
OH 8.9(15) 9.4(15) 2.1(16) 2.3(16) to an electron fraction, χ ∼ 10−12, although the exact
H2O 5.4(15) 5.9(15) 8.5(16) 9.2(16) value is dependent on the disk model adopted. Using
CO2 2.8(16) 3.7(16) 2.7(17) 6.5(17)
ourchemicalmodelresults, we calculatethe value of the
C2H2 7.5(13) 3.2(13) 7.9(13) 3.7(13)
CH3OH 1.0(08) 9.1(07) 5.3(09) 5.2(09) magnetic Reynolds number, ReM, everywhere and iden-
tify possible dead zones where Re .100.
M
100AU Chiang & Murray-Clay(2007)arguethatasecondcri-
H 3.3(19) 1.7(19) 3.2(19) 1.5(19) terion, taking into account the influence of ambipolar
H2 2.0(23) 2.0(23) 2.0(23) 2.0(23) diffusion in suppressing the MRI, must be applied for
CO 9.1(18) 9.7(18) 8.9(18) 9.3(18)
protoplanetary disks. They define a dimensionless pa-
HCO+ 3.9(13) 3.6(13) 5.8(13) 4.3(13)
HCN 4.8(14) 2.5(14) 2.3(14) 2.1(14) rameter, Am, which describes the degree to which neu-
CN 2.4(14) 2.6(14) 5.0(14) 4.1(14) tral H molecules (which make up the bulk of the gas),
2
CS 3.1(13) 3.7(13) 1.8(13) 1.7(13) are coupled to the accreting plasma. In order for neu-
C2H 1.0(14) 1.2(14) 7.7(13) 5.4(13) tral gas to be unstable, a H molecule must collide with
H2CO 4.4(12) 3.7(12) 8.2(12) 2.9(12) 2
N2H+ 1.9(11) 8.8(10) 1.5(12) 5.5(11) enough ions within the e-folding time of the instability,
OH 9.0(14) 3.0(14) 6.3(15) 3.3(15) 1/Ω, where Ω is the Keplerian velocity of the gas.
H2O 4.9(16) 2.5(16) 3.1(16) 1.4(16)
CO2 2.2(15) 2.1(15) 5.9(16) 8.8(16) Am= xenβ >Amcrit (9)
C2H2 3.0(13) 3.1(13) 2.4(13) 1.6(13) Ω
CH3OH 4.1(10) 4.0(11) 7.9(10) 2.1(11)
Here, x is the disk ionization fraction, n is the number
Note. —a(b)meansa×10b densityeoftheneutralgasandβ ≈2.0×10−9 cm3 s−1 is
Photochemistry in Protoplanetary Disks 7
theratecoefficientforion-neutralcollisions. EarlyMHD 2006). Inourdiskmodel,wefindinthemidplanethegas
simulations by (Hawley & Stone 1998) suggested that temperature reaches values higher than this only within
sufficient turbulence and angular momentum transport aradiusofafew tenthsofanAU,nevertheless,itshould
is achieved when the ‘ambipolar diffusion parameter’, looked at in future models since, due to this source of
Am, exceeds a criticalvalue, Amcrit ≈ 100. More recent ionization,the gas maybe magnetorotationallyunstable
simulations by Bai & Stone (2011) suggest that in very close to the star.
weakly ionized media where the ‘strong coupling’ limit
3. RESULTS
holds,suchasprotoplanetarydisks,the criticalvalue for
Amis≈1. The‘strongcoupling’limitisdefinedaswhen We calculate the chemical abundances in the disk as
theioninertiaisnegligibleandtherecombinationtimeis a function of radius, height and time. The results dis-
muchshorterthantheorbitaltime(Bai2011). Weadopt played in this section are those extracted at a time of
this latter criterionin our determinationof the suscepti- 106 years, the typical age of visible T Tauri stars with
bilityofthedisktosuppressionoftheMRIbyambipolar accompanying protoplanetary disks. Throughout this
diffusion. The results are reported in Section 3. section, fractional abundance refers to the abundance of
Note, the extent and location of a dead zone is also each species with respect to total particle number den-
dependent on the treatment of gas-grain interactions sity. As in Paper I, we ran several different models with
and the size distribution of grains (Sano et al. 2000; differing chemical ingredients in order to determine the
Ilgner & Nelson 2006). Sano et al. (2000) calculated influence ofeachchemicalprocessandthese arelisted in
that, for a fixed gas-to-dust mass ratio, the dead zone Table 4. Here, model UV-old, is our ‘fiducial’ model in
shrinks as the grain size increases, assuming all grains whichweusethesamemethodasinPaperI tocalculate
have the same radius. As the grains increase in size the photochemicalratesand we use the X-rayionization
(likelyduetocoagulation)theiondensityincreasessince ratesascalculatedinNomura et al.(2007). Wecompare
the total surface area of grains decreases. This subse- the results from model UV-old with those from mod-
quently decreases the recombination rate of gas-phase els which include a recalculation of the photochemical
cations on grain surfaces. They also determine that in rates only (model UV-new), the X-ray ionization rates
the midplane, grains are the dominant charged species only (model XR+UV-old) and both processes (model
(with charge ±e). XR+UV-new). All models include freeze out, thermal
It has also been postulated that gravitational grain desorption,cosmic-ray-induceddesorption,photodesorp-
settling (or sedimentation) towards the disk mid- tion and grain-surface chemistry.
plane influences the protoplanetary disk physical and
3.1. Column Densities
chemical structure and thus, ionization fraction, the
persistence of the MRI and the subsequent loca- In Figure 3, we present the radial column density
tion and extent of dead zones (see e.g., Chiang et al. (cm−2) of molecules detected or searched for in pro-
2001;Dullemond & Dominik2004;D’Alessio et al.2006; toplanetary disks at both (sub)mm and infrared wave-
Nomura et al. 2007; Fogel et al. 2011; Vasyunin et al. lengths. The solid lines and dashed lines are the gas-
2011). Since the dust is the dominant source of opac- phase and grain-surface column densities, respectively.
ity in disks, grain settling allows deeper penetration of Molecules whose column densities are relatively unaf-
stellar and interstellar UV radiation potentially ionizing fectedbythe methodemployedtocalculatethephotore-
alargerproportionofthegaseouscomponentofthedisk. action rates and the X-ray ionization rate include CO,
Inparticular,D’Alessio et al.(2006)findthatanabsence CN, CS, C H, C H , H CO, HCN, OH, CH and SO.
2 2 2 2 4
ofsmallgrainsintheupperdisklayer,duetosedimenta- Over the radial extent of the disk, the column densities
tion,enhancesthe ionizationinthe disksurfaceandalso of the listed species vary, at most, by a factor of a few
decreases the temperature of the gas in the disk mid- between chemical models. The gas-phase column den-
planesincethereisadecreaseintheamountofradiation sities of H O and CH OH are affected only beyond a
2 3
processed by grains and directed towards the midplane. radius of ≈ 1 AU with that of CO altered beyond a ra-
2
In reality, disk ionization, turbulence by MRI and dust dius of ≈ 10 AU. In all three cases we see a rise in the
settling are coupled and thus, ideally should be solved column density of each species when the photorates are
self-consistently (see e.g., Fromang & Papaloizou 2006; recalculated. For the molecular ions, HCO+ and N H+,
2
Ciesla 2007; Turner et al. 2010). we see a different behaviour with the column density of
Inthis work,for ourgas-graininteractions,we assume the former species affected significantly within a radius
a constant grainradius of 0.1 µm and a fixed dust-grain ofapproximately1AUonly. Forthelattermolecule,the
fractionalabundanceof2.2×10−12. Weassumethatall column density is affected throughout the radial extent
grains are negatively charged and allow the recombina- of the disk. For all molecules which possess an appre-
tion of cations on grain surfaces. This is valid assump- ciable grain-surface column density, the values are rel-
tion since negatively-chargedgrains dominate in regions atively unaffected by the method used to compute the
where the number density, n, is . 1012 cm−3 and this photochemical rates and the X-ray ionization rate.
holds throughout most of our disk model. We intend Overall, the recalculation of the photoreaction rates
to investigate the effects of adding neutral grains and a has a much bigger effect on the column densities than
variable dust-grain size distribution caused by coagula- that of the X-ray ionization rate with models UV-old
tion and settling in future models. and XR+UV-old, on the whole, producing similar val-
We havealsoneglectedthethermalionizationofalkali ues and behaviour. This is also true for models UV-
metals,suchasNa+ andK+,whichbecomesasignificant newandXR+UV-new. ExceptionstothisincludeN H+
2
source of ionization when the gas temperature is greater (throughoutthedisk)andOH(intheouterdiskbeyonda
than ≈ 103 K (Fromang et al. 2002; Ilgner & Nelson radiusof≈50AU).Afurthergeneralobservationisthat
8 Walsh et al.
TABLE 4
ChemicalModels
ChemicalProcess UV-old UV-new XR+UV-old XR+UV-new
Thermaldesorption X X X X
Cosmic-ray-induceddesorption X X X X
Photodesorption X X X X
Grain-surfacechemistry X X X X
Photochemistry X X
X-rayionization X X
the recalculation of the photorates affects each molecule The molecular column densities, although useful for
in a different manner. The spectrum-dependent pho- tracingthegeneralradialstructureandidentifyingthose
torates do not only directly affect the abundance and molecules significantly affected by the inclusion or omis-
distribution of atoms and molecules which can undergo sion of each process, provide little information on the
photoionization and photodissociation, they also indi- spatial distribution and abundance. This ultimately af-
rectlyaffectthe subsequentgas-phasechemistry,leading fectsthestrengthofthelineemissionfromthedisksince
to enhancements/depletions of molecules which are not thisisinfluencedbythephysicalconditionsintheregion
directly formed or destroyed via a photochemical route, where each molecule is most abundant. In the following
e.g., HCO+. Section, we look more closely at the effects on the two-
Weseeaninterestingstructureinthecolumndensities dimensional molecular structure of the disk due to the
of the sulphur-bearing species, CS and SO. Both show a recalculation of the photoreaction and X-ray ionization
peak between ≈ 2 AU and ∼ 10 AU. In the outer disk, rates.
beyond ∼ 10 AU, sulphur exists primarily in the disk
midplaneasH Siceonthegrainmantle. Within10AU, 3.2. Photochemistry
2
the disk midplane is warm enough for H S to evaporate
2 In Figure 4 we display the fractional abundance of
from the grain mantle replenishing the gas with sulphur HCO+, OH, H O, CO and N H+ as a function of disk
which forms SO and CS. Within ≈ 2 AU, SO takes 2 2 2
2 radius and height (scaled by the radius) for models UV-
overfromSOasthedominantgas-phasesulphur-bearing
old (left column) and UV-new (right column). These
species. CSincreasesinabundanceagainwithin∼1AU
molecules are those we have identified as being most af-
in the very warm, dense midplane.
fected by the recalculation of the photorates.
The radial column densities, N, of a selection of In the plots for HCO+, it is clearly seen that within a
molecules are listed in Table 3 at radii of 0.1, 1, 10 and radius of ≈ 1 AU, the fractional abundance of HCO+ in
100 AU. Molecules whose column densities are affected
the‘molecularlayer’inthisregion,locatedatZ/R=0.1,
by more than one order of magnitude are highlighted
is around two orders of magnitude lower in model UV-
in bold text. The general trend we see (with several
new than in model UV-old. Also clearly visible is the
exceptions discussed below) is a reduction in molecular
reason for the larger column density calculated beyond
column densities in the inner disk (within 1 AU) and this radius, the depth of the layer of HCO+ in model
an increase in the outer disk (beyond 1 AU) in models
UV-new is much larger than that in model UV-old al-
UV-new andXR+UV-new relativeto modelUV-old. At
though the maximum fractional abundance attained in
0.1 AU, N(HCO+) is reduced by two orders of magni- both models is similar (x(HCO+) ∼ 10−6). The abun-
tude with N(OH) reduced by one order of magnitude, dance of HCO+ is controlled by ion-molecule chemistry
when the photochemistry is recalculated. The column
andthus depends onthe abundance of ionic andneutral
densityofN H+ isaffectedbybothX-rayionizationand
2 precursors. An exampleofanion-moleculegas-phasere-
photochemistrywith the formerincreasingthe value rel- action which leads to the production of HCO+ is
ative to model UV-old and the latter reducing it. At
1 AU, only N(N H+) is significantly affected where it is CO+H+−→HCO++H .
2 3 2
enhancedbyalmosttwoordersofmagnitudebytherecal-
In model UV-new, where we see an increase in HCO+,
culation of the photochemistry and reduced by a factor
we see a corresponding increase in CO and H +. CO is
ofafewbytherecalculationoftheX-rayionizationrate. 3
directlyinfluencedbythe photochemistrysinceitcanbe
At10AU,themoleculesaffectedareH O,CO ,CH OH
2 2 3 photodissociatedtoproduceCandO.H +,onthe other
and N H+. The column density of H O and CO are 3
2 2 2 hand, is primarily formed via the reaction of H with
both enhanced by over an order of magnitude in models 2
H + and destroyed via electron recombination. The en-
UV-newandXR+UV-new. Asat1AU,X-rayionization 2
hancement in HCO+ in model UV-new also corresponds
reduces N(N H+), whereas photochemistry enhances it.
2 to where we see a slight decrease in electron abundance
It is a similar storyfor methanol,however,X-rayioniza-
(seeFigure7). Relatingthisbacktothephotochemistry,
tion has a much smaller effect than photochemistry. At
thisindicatesanoverestimationinthisregioninboththe
the final radius we consider here, 100 AU, again, N H+
2 photodissociationofCOandphotoionization(ingeneral)
andCH OHareaffectedinasimilarmannerasat10AU.
3 in our fiducial model (model UV-old).
We also find the column density of OH increased sig-
ThedepthofthemolecularlayerwhereOHreachesits
nificantly in model UV-new with that for CO also en-
2 maximum fractional abundance (x(OH) ∼ 10−4) within
hanced in models UV-new and XR+UV-new. The only
1 AU is smaller in model UV-old than in model UV-
molecules for which X-ray ionizationsignificantly affects
new, whereas, beyond this radius, the depth is larger.
the column density are N H+ and CH OH.
2 3 This accounts for the smaller column density in model
Photochemistry in Protoplanetary Disks 9
1022 1018 1018
1021 1017 1017
CO CN CS
-2m)1020 -2m)1016 -2m)1016
Density (c11001189 Density (c11001145 Density (c11001145
mn 1017 mn 1013 mn 1013
Colu1016 Colu1012 Colu1012
UV-old UV-old UV-old
1015 XURV+-nUeVw-old 1011 XURV+-nUeVw-old 1011 XURV+-nUeVw-old
1014 XR+UV-new 1010 XR+UV-new 1010 XR+UV-new
0.1 1 10 100 0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU) Radius (AU)
1018 1015 1018
1017 1014 1017
-2m)1016 HCO+ -2m)1013 N2H+ -2m)1016 C2H
Density (c11001145 Density (c11001112 Density (c11001145
mn 1013 mn 1010 mn 1013
Colu1012 Colu 109 Colu1012
UV-old UV-old UV-old
1011 XURV+-nUeVw-old 108 XURV+-nUeVw-old 1011 XURV+-nUeVw-old
1010 XR+UV-new 107 XR+UV-new 1010 XR+UV-new
0.1 1 10 100 0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU) Radius (AU)
1022 1020 1023
1021 1019 1022
-2m)1020 CO2 -2m)1018 C2H2 -2m)1021 H2O
mn Density (c111000111789 UXURVV-+-onUledVw-old mn Density (c111000111567 XUXURRVV+-+-noUUeldVVw--onledw mn Density (c111000112890 UXUXRRVV-+-+onUUledVVw--onledw
Colu1016 XR+UV-new Colu1014 Colu1017
1015 1013 1016
1014 1012 1015
0.1 1 10 100 0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU) Radius (AU)
1018 1021 1020
UV-old
1017 1020 XR+UV-old 1019
-2m)1016 H2CO -2m)1019 UXRV-+nUeVw-new HCN -2m)1018 OH
Density (c11001145 Density (c11001178 Density (c11001167
mn 1013 mn 1016 mn 1015
Colu1012 Colu1015 Colu1014
UV-old UV-old
1011 XURV+-nUeVw-old 1014 1013 XURVU-nVe-wold
1010 XR+UV-new 1013 1012 XR+UV-new
0.1 1 10 100 0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU) Radius (AU)
1022 1019 1018
-2Column Density (cm)111111000000111122678901 CH4 -2Column Density (cm)111111111000000000111111111012345678 CH3OH XUXURRVV+-+-noUUeldVVw--onledw -2Column Density (cm)111111000000111111234567 SO
1015 XUURVV+--noUeldVw-old 110089 1011 UXURVV-+-onUledVw-old
1014 XR+UV-new 107 1010 XR+UV-new
0.1 1 10 100 0.1 1 10 100 0.1 1 10 100
Radius (AU) Radius (AU) Radius (AU)
Fig.3.— Column density (cm−2) as a function of radius, R, for a range of molecules detected or searched for inprotoplanetary disks.
Thedashedlinesrepresentgrain-surface(ice)columndensities.
10 Walsh et al.
UV-new at 1 AU and the larger at 10 and 100 AU. The CO when the fractional abundance of ionic carbon be-
2
distribution of OH is also somewhat different in model gins to increase relative to atomiccarbon. Note, CO is
2
UV-newreachinganorderofmagnitudehigherfractional destroyedviareactionwithC+ toformCO+ andCO.In
abundance in the disk surface throughout the radial ex- model UV-new, the boundary where C+/C ∼ 1 is much
tent. The abundance of OH is directly controlled by the higher in the disk than in model UV-old (at a height of
photochemistry since OH is one of the products of the ≈5AUand≈2AU,respectively,ataradiusof10AU).
photodissociationof H O andcanitself be photodissoci- Thus in model UV-new, gas-phase CO can evaporate
2 2
atedtoformOandH.We seeinthecorrespondingplots from the grain surface and remain intact in this layer
forwaterinFigure4thatitsfractionalabundanceisalso due to the lack of sufficient gas-phase destruction mech-
slightly higher in the disk surface in model UV-new rel- anisms. Wedisplaythe photodissociationrateofCO as
2
ativeto modelUV-old. We alsofindthat the abundance a function of disk height (scaled by the radius) at radii
of free oxygen atoms decreases in this region, indicating of 1 AU, 10 AU and 100 AU in Figure 5. As in the case
in model UV-new, more atomic oxygen is locked up in for OH and H O, we see an decrease of around an order
2
oxygen-bearing molecules than in model UV-old. of magnitude in model UV-new compared with UV-old.
Lookingatthedistributionofwater,weseealargeen- ThisaccountsfortheincreaseintheabundanceofCO in
2
hancement in the fractional abundance in the molecular the upper disk layers in model UV-new. Note, in model
layer beyond a radius of ≈ 1 AU, going from a value of UV-old, the dissociation rates for CO are consistently
2
∼ 10−6 in model UV-old to ∼ 10−4 in model UV-new. largerthan that ofH O andOH, reflecting the the rates
2
Not only is the maximum fractional abundance reached calculatedfortheunshieldedinterstellarmedium(14,5.9
much higher, the extent over which water exists with a and 3.5 × 10−10 s−1, respectively). However, in model
value & 10−9 in model UV-new is also much larger. We UV-new, the H O photodissociation has the largest rate
2
conclude that the abundance of gas-phase water is very at each radius, with OH also having a larger rate than
sensitive to the method employed to calculate the pho- CO at100AU.Thisdemonstrateshowtherelativepho-
2
torates. torates are sensitive to the shape of the radiation field
Both OH and H2O can be formed via neutral-neutral due to the specific variationin the photo crosssectionof
gas-phase reactions in warm regions of the disk where each species.
T & 200 K (Glassgold et al. 2009). Whenthephotochemistryisrecalculated,weseeadra-
maticincreaseintheregionoverwhichN H+ reachesits
H +O−→OH+H 2
2 maximumfractionalabundance,nowresidinginamolec-
H +OH−→H O+H ular layer which permeates the entire disk. The most
2 2
dramatic increase is seen in the inner disk (< 100 AU)
Since we see an increase in the fractional abundance of wherex(N H+)jumpsfromamaximumvalueof∼10−12
2
H2 in model UV-new relative to UV-old over the region in model UV-old to ∼ 10−9 in model UV-new. Similar
where both OH and H2O are increased, this gas-phase to HCO+, the abundance of N H+ is controlled by ion-
production route for both species is more important in 2
molecule chemistry, it is formed via the reaction of N
model UV-new than in model UV-old. Hence, the en- with H + and is destroyed effectively by reaction with2
hancement seen in the abundances of OH and H O in 3
2 CO and electron recombination. Looking at Figure 7
model UV-new is a combination of increased gas-phase
which displays the electron fractional abundance for all
productionanddecreasedphotodestruction. InFigure5,
four models as a function of disk radius and height, we
wedisplaythephotodissociationratesofOHandH2Oas see in the layer where N H+ is significantly enhanced,
a function of disk height (scaled by the radius) at radii 2
there is a respective decrease in the electron fraction in
of 1 AU, 10 AU and 100 AU. A decrease of around an model UV-new. N H+ and HCO+ show different be-
orderofmagnitudeinthephotodissociationratesofboth haviours since the a2bundance of N H+ is more sensitive
species is clearly seen in the upper disk layers account- totheabundanceofH +thanHCO2+. HCO+hasvarious
ing for the increase in abundance of both species in this 3
alternative routes to formation other than the reaction
region. The gross overestimation of the the photodisso- of CO and H +, e.g., C+ + H O, whereas N H+ forms
ciation rates in model UV-old is due to the inclusion of mainly via th3e reaction of N2 with H +. W2 e discuss
Lyman-α photons in the calculation of the wavelength- N H+ chemistry further in Sec2tion 3.3.3
integratedUVphotonflux(seeSection2.2.1). Also,note 2
In Figure 6, we present the fractional abundances of
that the dissociation rates vary differently as a function
several atoms and ions at a radius of 1 (top panel) and
of height in model UV-new versus UV-old since in the 10 AU (bottom panel). We display the results for C+
former model, the wavelength dependence of both the
also since the ionization potential for carbon is much
photo cross sections and UV field are included.
lower than that for oxygen and nitrogen. In model UV-
Gas-phaseCO isaffectedmainlyintheouterdiskbe-
2 new, there is a significant depletion of free O atoms and
yondaradiusof≈10AU.WeseethatCO2inthisregion C+ ions in the region where we see an increase in the
existsinalayerlowerthanthatofwater(duetoitslower
fractional abundance of OH, H O and the main carbon
binding energy to dust grains) and is enhanced in the 2
species, C. Note that the atomic carbon abundance in
outer disk from a fractionalabundance ∼ 10−6 in model
thedisksurfaceislargerinmodelUV-newthaninmodel
UV-old to ∼ 10−4 in model UV-new. In model UV-
UV-old, however,here free carbon exists mainly in ionic
new, in this region, it possesses a comparable fractional form as C+. In this region, we also see an enhance-
abundancetotheothermainoxygen-bearingspecies,CO
ment inthe fractionalabundances of the molecularions,
and O2. As in the case for water, the extent over which HCO+ and N H+. Hence, in model UV-new, in the
x(CO ) has a value & 10−9 is muchlargerinmodel UV- 2
2 molecular layer where molecules reach their maximum
new than in model UV-old. We see an enhancement in