# MINDS. JWST-MIRI Reveals a Dynamic Gas-Rich Inner Disk Inside the Cavity of
SY Cha

Kamber R. Schwarz Max-Planck-Institut für Astronomie (MPIA), Königstuhl 17,
69117 Heidelberg, Germany  Thomas Henning Max-Planck-Institut für Astronomie
(MPIA), Königstuhl 17, 69117 Heidelberg, Germany  Valentin Christiaens STAR
Institute, Université de Liège, Allée du Six Août 19c, 4000 Liège, Belgium
Danny Gasman Institute of Astronomy, KU Leuven, Celestijnenlaan 200D, 3001
Leuven, Belgium  Matthias Samland Max-Planck-Institut für Astronomie (MPIA),
Königstuhl 17, 69117 Heidelberg, Germany  Giulia Perotti Max-Planck-Institut
für Astronomie (MPIA), Königstuhl 17, 69117 Heidelberg, Germany  Hyerin Jang
Department of Astrophysics/IMAPP, Radboud University, PO Box 9010, 6500 GL
Nijmegen, The Netherlands  Sierra L. Grant Max-Planck Institut für
Extraterrestrische Physik (MPE), Giessenbachstr. 1, 85748, Garching, Germany
Benoît Tabone  Université Paris-Saclay, CNRS, Institut d’Astrophysique
Spatiale, 91405, Orsay, France  Maria Morales-Calderón Centro de Astrobiología
(CAB), CSIC-INTA, ESAC Campus, Camino Bajo del Castillo s/n, 28692 Villanueva
de la Cañada, Madrid, Spain  Inga Kamp Kapteyn Astronomical Institute,
Rijksuniversiteit Groningen, Postbus 800, 9700AV Groningen, The Netherlands
Ewine F. van Dishoeck Leiden Observatory, Leiden University, 2300 RA Leiden,
the Netherlands  Max-Planck Institut für Extraterrestrische Physik (MPE),
Giessenbachstr. 1, 85748, Garching, Germany  Manuel Güdel Dept. of
Astrophysics, University of Vienna, Türkenschanzstr. 17, A-1180 Vienna,
Austria  Max-Planck-Institut für Astronomie (MPIA), Königstuhl 17, 69117
Heidelberg, Germany  ETH Zürich, Institute for Particle Physics and
Astrophysics, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland  Pierre-Olivier
Lagage  Université Paris-Saclay, Université Paris Cité, CEA, CNRS, AIM,
F-91191 Gif-sur-Yvette, France  David Barrado Centro de Astrobiología (CAB),
CSIC-INTA, ESAC Campus, Camino Bajo del Castillo s/n, 28692 Villanueva de la
Cañada, Madrid, Spain  Alessio Caratti o Garatti INAF – Osservatorio
Astronomico di Capodimonte, Salita Moiariello 16, 80131 Napoli, Italy  Dublin
Institute for Advanced Studies, 31 Fitzwilliam Place, D02 XF86 Dublin, Ireland
Adrian M. Glauser ETH Zürich, Institute for Particle Physics and Astrophysics,
Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland  Tom P. Ray Dublin Institute
for Advanced Studies, 31 Fitzwilliam Place, D02 XF86 Dublin, Ireland  Bart
Vandenbussche Institute of Astronomy, KU Leuven, Celestijnenlaan 200D, 3001
Leuven, Belgium  L. B. F. M. Waters Department of Astrophysics/IMAPP, Radboud
University, PO Box 9010, 6500 GL Nijmegen, The Netherlands  SRON Netherlands
Institute for Space Research, Niels Bohrweg 4, NL-2333 CA Leiden, the
Netherlands  Aditya M. Arabhavi Kapteyn Astronomical Institute,
Rijksuniversiteit Groningen, Postbus 800, 9700AV Groningen, The Netherlands
Jayatee Kanwar Kapteyn Astronomical Institute, Rijksuniversiteit Groningen,
Postbus 800, 9700AV Groningen, The Netherlands  Space Research Institute,
Austrian Academy of Sciences, Schmiedlstr. 6, A-8042, Graz, Austria  TU Graz,
Fakultät für Mathematik, Physik und Geodäsie, Petersgasse 16 8010 Graz,
Austria  Göran Olofsson Department of Astronomy, Stockholm University,
AlbaNova University Center, 10691 Stockholm, Sweden  Donna Rodgers-Lee Dublin
Institute for Advanced Studies, 31 Fitzwilliam Place, D02 XF86 Dublin, Ireland
Jürgen Schreiber  Max-Planck-Institut für Astronomie (MPIA), Königstuhl 17,
69117 Heidelberg, Germany  Milou Temmink Leiden Observatory, Leiden
University, 2300 RA Leiden, the Netherlands

###### Abstract

SY Cha is a T Tauri star surrounded by a protoplanetary disk with a large
cavity seen in the millimeter continuum but has the spectral energy
distribution (SED) of a full disk. Here we report the first results from
_JWST_ -MIRI Medium Resolution Spectrometer (MRS) observations taken as part
of the MIRI mid-INfrared Disk Survey (MINDS) GTO Program. The much improved
resolution and sensitivity of MIRI-MRS compared to _Spitzer_ enables a robust
analysis of the previously detected H2O, CO, HCN, and CO2 emission as well as
a marginal detection of C2H2. We also report the first robust detection of
mid-infrared OH and ro-vibrational CO emission in this source. The derived
molecular column densities reveal the inner disk of SY Cha to be rich in both
oxygen and carbon bearing molecules. This is in contrast to PDS 70, another
protoplanetary disk with a large cavity observed with _JWST_ , which displays
much weaker line emission. In the SY Cha disk, the continuum, and potentially
the line, flux varies substantially between the new _JWST_ observations and
archival _Spitzer_ observations, indicative of a highly dynamic inner disk.

††software: emcee (Foreman-Mackey et al., 2013), matplotlib (Hunter, 2007),
numpy (van der Walt et al., 2011), spectres (Carnall, 2017), VIP (Gomez
Gonzalez et al., 2017; Christiaens et al., 2023)

##  1 Introduction

SY Cha is a $1-2$ million year old protoplanetary disk in the Chamaeleon I
star-forming region at a distance of 180.7 pc (Gaia Collaboration et al.,
2021; Galli et al., 2021). Recent ALMA observations revealed a large cavity
with a radius 70 au in the millimeter continuum emission(Orihara et al.,
2023). Such cavities are a hallmark of transtion disks. Transition disks were
first identified as a sub-class of protoplanetary disks based on the
comparatively small excess of emission relative to a stellar blackbody in the
near infrared (Strom et al., 1989). This was interpreted as due to a
deficiency of dust in the inner regions of the disk, which was later confirmed
by imaging in the sub-millimeter (Calvet et al., 2002; Hughes et al., 2007).
During the _Spitzer_ era, the term pre-transitional disks was coined to
describe disks with a deficit of emission from 5-20 $\mathrm{\mu}$m while
still displaying excess emission in the 2-5 $\mathrm{\mu}$m range, interpreted
as arising from an optically thick inner disk (Brown et al., 2007; Espaillat
et al., 2007).

Many transition disks have now been identified, both from SEDs and imaging
(Andrews et al., 2011; Espaillat et al., 2014; Ercolano & Pascucci, 2017;
Francis & van der Marel, 2020). While the term ‘transition disk’ was first
coined based on SEDs, here we use the more general definition of any
protoplanetary disk with a large dust cavity, regardless of whether a system
would be classified as transitional or pre-transitional based on its SED alone
(e.g., Espaillat et al., 2014; van der Marel, 2023). The mismatch between SED
and millimeter imaging can be due to, e.g., a misaligned inner disk or a
millimeter grain poor cavity which still contains micron-sized grains (van der
Marel et al., 2018; Villenave et al., 2019). The mechanisms through which the
inner disk is cleared of millimeter grains remain unclear. Potential
explanations include clearing by photoevaporative winds, inward drift of large
grains, and gap clearing by a low-mass companion (Lin & Papaloizou, 1979;
Birnstiel et al., 2012; Alexander et al., 2014; Bae et al., 2023; Pascucci et
al., 2023).

The median accretion rate for stars with transition disks is comparable to
that of full protoplanetary disks, i.e., those without large inner dust
cavities, indicating gas is still present at small radii (Sicilia-Aguilar et
al., 2010). Photoevaporative winds are disfavored as the cavity forming
mechanism for disks with large accretion rates (van der Marel et al., 2018).
Many transition disks have gas cavities which are smaller than the associated
dust cavity, which is expected in the planet-disk scenario (e.g., Carmona et
al., 2014, 2017). Two such disks, PDS 70 and HD 169142, have been conclusively
shown to host planets in their dust cavites (Müller et al., 2018; Keppler et
al., 2018; Haffert et al., 2019; Gratton et al., 2019; Hammond et al., 2023).
Tentative evidence for planets within the inner cavity of transition disks
exists for several additional systems (e.g., Long et al., 2022; Currie et al.,
2022; Stadler et al., 2023). Whether all transition disks are formed by planet
clearing or multiple mechanisms are at play remains unclear.

Observations of transition disks with the _Spitzer_ InfraRed Spectrograph
(IRS) reveal that mid-IR variability on timescales of several years is common,
with two general types of variability (Espaillat et al., 2011). The first is
when emission at short and long wavelengths varies inversely in a “seesaw”
behavior. Such variability could be caused by unseen planets warping the inner
disk (Muzerolle et al., 2009). A more uniform intensity shift at all mid-IR
wavelengths has also been observed in transition disks, and is likely due to a
change in incident flux from the central star (Espaillat et al., 2011).

Spectral indices, a measure of the ratio of the flux density for two
wavelength ranges, denoted $n$, are used to characterize the SEDs of
protoplanetary disks (e.g., Kessler-Silacci, 2006; Furlan et al., 2006).
Pontoppidan et al. (2010) found that the five systems classified as transition
disks in their _Spitzer_ sample, based on their infrared spectral index,
$n_{13-30}$, did not exhibit molecular line emission other than H2 down to the
1% line-to-continuum level. Subsequent work by Banzatti et al. (2020) found an
inverse correlation between the outer radius of the millimeter dust disk as
observed by ALMA and the luminosity of H2O lines in the mid-IR. They further
speculated that disks with large inner cavities may have weaker H2O lines
compared to other large disks, since icy pebbles are prevented from drifting
inward. However, they note additional data is needed to confirm this
hypothesis. It has also been suggested that even when pebbles are stopped from
moving inward, micron-size particles well coupled to the gas can transport
water inward (Potapov et al., 2018; Perotti et al., 2023).

Here we report our findings on the inner disk of SY Cha, based on JWST
observations. SY Cha was observed as part of the as part of the MIRI mid-
INfrared Disk Survey (MINDS) GTO Program (PID: 1282, PI: T. Henning). Previous
results from the MINDS program include the first detection of 13CO2 in a
protoplanetary disk (Grant et al., 2023), rich hydrocarbon chemistry in a disk
around a very low-mass star (Tabone et al., 2023), abundant water but a sub-
stellar C/O ratio in a full protoplanetary disk (Gasman et al., 2023), and
water in the inner disk of a transition disk known to host planets in its
cavity (Perotti et al., 2023). An overview of the full MINDS sample is given
by Kamp et al. (2023) and Henning et al. (in prep).

SY Cha would not be classified as a transition disk based on its infrared
spectral index of $n_{13-30}=-0.17$ (Banzatti et al., 2020). However, recent
ALMA observations reveal a ring of continuum emission centered at
$0\farcs{559}$ (101 au) with a FWHM of $0\farcs{22}$ (40 au), an inner gap,
and unresolved emission centered on the star with a radius no larger than
$0\farcs{025}$ (2.3 au, Orihara et al., 2023). This small scale component
could be due to an inner disk, free-free emission, or an ionized wind (Francis
& van der Marel, 2020). Other source properties are listed in Table 1. The
$\mathrm{{}^{13}CO}$ and C18O $J=2-1$ emission also appears to be ring like,
though with an inner radius smaller than that of the dust ring. Additionally,
near the central star the 12CO emission displays a deviation from Keplerian
rotation, which Orihara et al. (2023) posit could be due to either a warped
inner disk or a radial flow such as a wind. Interestingly, the CO ro-
vibrational lines at 4.7 $\mathrm{\mu}$m, which often include a disk wind
component, were not detected toward SY Cha using the high spectral resolution
CRIRES instrument on the VLT (Brown et al., 2013). Either a highly inclined
inner disk or the presence of gas (and thus also small dust grains coupled to
the gas) inside the millimeter cavity would explain why SY Cha’s SED does not
include the classic signature of a transition disk. Orihara et al. (2023)
found models with a highly inclined inner disk to be consistent with their
ALMA observations, though more modeling work is needed to provide a definitive
result. _Spitzer_ detected mid-infrared emission originating from the inner
disk for H2O, HCN, C2H2, and CO2, while only upper limits for OH were reported
(Salyk et al., 2011b; Banzatti et al., 2020). The much improved sensitivity
and spectral resolution of MIRI-MRS compared to _Spitzer_ -IRS enables a more
detailed analysis of the mid-IR line emission, particularly in the 5-10
$\mathrm{\mu}$m range, which was not covered by _Spitzer_ -IRS’s high
resolution mode.

Table 1: Properties of SY Cha

Parameter | Value
---|---
Stellar mass | 0.70 M⊙
Stellar luminosity | 0.55 L⊙
Effective temperature | 4030 K
Accretion luminosity | 7.39${}\times 10^{-3}$ L⊙ yr-1
Mass accretion rate | 6.6${}\times 10^{-10}$ M⊙ yr-1
Spectral type | K5Ve
Distance | 180.7 pc
Disk inclination | 51.1∘

Note. — Spectral type classification from Frasca et al. (2015). Disk
inclination from Orihara et al. (2023). All other values are from Manara et
al. (2023), using updated data from Gaia Collaboration et al. (2021) and
stellar models from Feiden (2016).

##  2 Data Reduction & Analysis

###  2.1 Observations and Data Reduction

SY Cha was observed with the Mid-InfraRed Instrument (MIRI)111Rieke et al.
(2015); Wright et al. (2015) in Medium Resolution Spectroscopy (MRS)222Wells
et al. (2015) mode on 8 August, 2022 as part of the MINDS GTO Program (PID:
1282, PI: T. Henning). The total exposure time was 3696 seconds using a four-
point dither pattern in the positive direction.

The data were processed using version 1.9.4 of the _JWST_ pipeline (Bushouse
et al., 2023). Bespoke routines based on the VIP package were used for
background subtraction, bad pixel correction after stage 2, and spectrum
extraction (Gomez Gonzalez et al., 2017; Christiaens et al., 2023). At the
Spec2 stage the standard flat fielding and fringe correction from the _JWST_
pipeline were used. The background was then created using the minimum values
among the four dither positions and smoothed with a median filter. Spectra
were extracted from the final cubes using apertures twice the full width half
max in size centered on the source centroid, identified with a 2D Gaussian
fit. After extraction, residual fringe correction was carried out for each
wavelength band. The final spectrum is presented in Figure 1.

Figure 1: Top: _JWST_ -MIRI MRS spectrum of SY Cha. Coloring designates the
short, medium, and long sub-bands in the four integral field units. Major
atomic and H2 lines, as well as dust features, are labeled. Bottom: Mid-IR
spectrum of SY Cha as observed by _Spitzer_ -IRS in high resolution and low
resolution mode compared to _JWST_ -MIRI MRS. _Spitzer_ observations taken
from CASSIS (Lebouteiller et al., 2011, 2015).

Visual inspection of the data cubes reveals the H2 and [NeII] emission to be
extended, while the rest of the line emission and the continuum is spatially
unresolved. The above data reduction was not optimized for extended emission.
Analysis of the extended H2 emission, likely indicating the molecular
component of a wind, will be presented in a separate work and is not discussed
further here.

###  2.2 Continuum Emission

The overall spectrum shows stronger emission than observed by _Spitzer_ in
either low-resolution or high-resolution mode, with the _Spitzer_ high
resolution observations (2004-08-31 and 2008-05-01) sitting between the low
resolution (2009-04-09) and MIRI observations (2022-08-08, see Figure 1). The
largest differences are seen between the new MIRI observations and the low
resolution _Spitzer_ observations from 2009, with the MIRI spectrum roughly
10% stronger at 6 $\mathrm{\mu}$m, 40% at 10 $\mathrm{\mu}$m, and 30% at 20
$\mathrm{\mu}$m. The spectro-photometric accuracy is 2-10% for the _Spitzer_
IRS and $5.6\pm 0.7\%$ for the _JWST_ -MIRI MRS (Furlan et al., 2006; Watson
et al., 2009; Argyriou et al., 2023). The increased spatial resolution of
_JWST_ lessens the chance of contaminating emission from other objects. Such
contamination in the _Spitzer_ data would result in a higher flux relative to
_JWST_ , the opposite of what we observe. While the difference in flux at
short wavelengths is within the calibration uncertainty, the difference beyond
10 $\mathrm{\mu}$m is not.

Transition disks are known to be variable in the IR. The level of variability
seen between the _Spitzer_ and _JWST_ observations of SY Cha is similar to the
variability of transition and pre-transition disks observed over multiple
epochs with _Spitzer_ by Espaillat et al. (2011). That the variability is
greater at longer wavelengths points to changes in the inner disk geometry as
the source of the variability in SY Cha. A more nuanced understanding of the
cause of the mid-IR variability in SY Cha requires detailed radiative transfer
modeling, which will be presented in subsequent work.

###  2.3 Fitting Atomic Emission

The strongest atomic line features are shown in Figure 2. To determine the
total flux from each transition, we fit a Gaussian line profile using the
Markov Chain Monte Carlo package emcee (Foreman-Mackey et al., 2013). Because
many of the atomic lines overlap with nearby transitions, a two component
Gaussian is used. Only the Gaussian fit to the atomic transition is used when
integrating to get the total flux. Each Gaussian fit is integrated over the
respective wavelength range shown in Figure 2. For subtraction purposes, the
continuum is defined by selecting apparently line-free pixels (See App. A) and
then interpolating with a spline fit. The spline fit to these points is then
subtracted from the spectrum. The rms noise, $\sigma$, of the continuum
subtracted spectrum is calculated by taking the standard deviation in a line-
free wavelength range. Values for $\sigma$ are given in Table 2. Best-fit
models are identified using a modified reduced $\chi^{2}$ fitting:

$\chi^{2}=\frac{1}{N}\sum_{i=1}^{N}\frac{(F_{obs,i}-F_{mod,i})^{2}}{\sigma^{2}}$
(1)

where $N$ is the number of data points used in the fitting, $F_{obs}$ and
$F_{mod}$ are the observed and model line flux, respectively, and $\sigma$ is
the root mean squared noise calculated in a nearby line-free region.

Figure 2: Zoom in of continuum subtracted spectra at the brightest atomic lines. Grey dots denote wavelengths used for continuum subtraction. Yellow line shows the best-fit Gaussian for the atomic line. When applicable, red and dark blue lines show the additional Gaussian fit to overlapping lines and the combined fit respectively. Table 2: Integrated flux for Gaussian fits to atomic lines Transition | Line Center | $\mathrm{\sigma}$ | Integrated Flux | Continuum | rms | $\mathrm{\chi^{2}}$
---|---|---|---|---|---|---
| ($\mathrm{\mu}$m) | 10-3($\mathrm{\mu}$m) | 10-15(erg s-1 cm-2) | ($\mathrm{\mu}$m) |  $10^{-27}$(erg s-1 cm-2 Hz-1) |
HI 10-6 | 5.129 | 1.2 | 1.98 | 5.096-5.102 | 1.52 | 25.5
HI 12-7 | 6.772 | 1.3 | 1.62 | 6.777-6.782 | 0.46 | 26.9
HI 6-5 | 7.460 | 4.3 | 8.17 | 7.49-7.4954 | 2.65 | 20.3
HI 8-6 | 7.503 | 4.2 | 1.58 | 7.49-7.4954 | 2.65 | 1.24
HI 11-7 | 7.508 | 1.1 | 0.48 | 7.49-7.4954 | 2.65 | 1.24

###  2.4 Fitting Molecular Emission

We characterize the observed molecular emission by fitting local thermodynamic
equilibrium (LTE) 0D slab models, as presented by Tabone et al. (2023), to the
individual sub-bands. Each model is a slab of gas with a uniform temperature
and density and no implicit spatial information. The LTE assumption is valid
when all energy levels of a given species are well characterized by a single
excitation temperature. Continuum subtraction and noise estimation is carried
out in the same way as for the atomic emission (Section 2.3). The points used
for continuum subtraction are listed in App. A. The wavelength range used to
calculate the noise and the resulting values are shown in Figures 3 & 4.

When generating the slab models, the intrinsic line profile is assumed to be a
Gaussian. We include mutual shielding from closely spaced transitions of the
same molecule following the method described by Tabone et al. (2023):

$\tau(\lambda)=\sum_{i}\tau_{0,i}e^{-(\lambda-\lambda_{0,i})^{2}/2\sigma_{\lambda}^{2}},$
(2)

where $\lambda_{0,i}$ is the rest wavelength of a given line $i$,
$\sigma_{\lambda}$ is the intrinsic broadening of the line in microns, assumed
to be equivalent to $\sigma_{\lambda}=2$ km s-1 (Salyk et al., 2011a) and
$\Delta V=4.7$ km s-1, and $\tau_{0,i}$ is the optical depth at line center:

$\tau_{0}=\sqrt{\frac{\ln 2}{\pi}}\frac{A_{ul}N\lambda_{0}^{3}}{4\pi\Delta
V}(x_{l}\frac{g_{u}}{g_{l}}-x_{u}).$ (3)

Here, $x_{u}$ and $x_{l}$ are the level population of the upper and lower
states respectively, $g_{u}$ and $g_{l}$ are their respective statistical
weights, $A_{ul}$ is the Einstein A coefficient, giving the rate of
spontaneous emission, and $N$ is the total column density of the molecule.

To find the best-fit for each molecule a grid of models is generated with
three free parameters: column density $N$ (grid spacing $\Delta\log N=0.2$
dex), excitation temperature $T$ ($\Delta T=50$ K), and emitting area $\pi
R^{2}$ ($\Delta\log R=0.003$ dex):

$F(\lambda)=\pi\left(\frac{R}{d}\right)^{2}B_{\nu}(T)(1-e^{-\tau(\lambda)}),$
(4)

where d is the assumed distance to SY Cha of 180.7 pc. Note that $R$ does not
correspond to a physical radius in the disk, but rather is the radius of a
circle with the same area as the derived emitting area. As such, it $R$ can be
considered a lower limit on the physical radius of the emission, though one
that is not motivated by any physical model. The resulting model spectra are
convolved to the resolution of the corresponding MRS band, using the average
values reported by Jones et al. (2023) for each band, then resampled to the
same wavelength grid as the observations using the SpectRes package (Carnall,
2017).

For a given sub-band, the spectral lines are fit for one molecule at a time,
following the method of Grant et al. (2023). The goodness of fit for a given
model is determined by comparing to the observations at each wavelength using
a $\chi^{2}$ routine. The $\chi^{2}$ fitting is restricted to regions where
emission from the given molecule is expected and there is no expected strong
emission from other species based on initial slab models using typical
emitting temperatures for each species. Additionally, pixels where the
continuum-subtracted flux is less than -5 mJy are excluded. This excludes both
potential absorption features and single pixels with anomalously low values.

After a best-fit model for a given molecule has been identified, this model is
subtracted from the spectrum before fitting the next species. Molecules are
fit in the following order: H2O, OH, CO, CO2, HCN, C2H2. After obtaining an
initial fit for all species, we rerun the fit for H2O with the best-fit models
from all other species subtracted in order to account for any small
contributions from other species overlapping with the water emission. This
second round of fitting results in only small variations, within the reported
uncertainty, compared to the first round, demonstrating that the emission from
other species has only a minor impact on our fitting routine, at least for
species with strong lines. For weaker lines, it is possible that this method
leads to an underestimation of the line flux. Molecular fits are only run when
the molecule is expected to emit within the sub-band. The continuum subtracted
spectra and best-fit models for the fitted regions are shown in Figures 3 & 4
and the $\chi^{2}$ maps for the model grid are shown in Figures 8-10.

Figure 3:  Top: Continuum subtracted observations (black) and cumulative model
adding the contributions from each molecule (yellow) from 4.9 to 7.6
$\mathrm{\mu}$m. Grey dots denote wavelengths used for continuum subtraction.
Black horizontal lines indicate the line-free region used to calculate the rms
noise. Other horizontal lines indicate the wavelength range considered when
fitting each molecule. Bottom: Individual LTE slab models for each molecule.

Figure 4: Top: Continuum subtracted observations (black) and cumulative model
adding the contributions from each molecule (yellow) from 13.5 to 20.7
$\mathrm{\mu}$m. Grey dots denote wavelengths used for continuum subtraction.
Black horizontal lines indicate the line-free region used to calculate the rms
noise. Other horizontal lines indicate the wavelength range considered when
fitting each molecule. Bottom: Individual LTE slab models for each molecule.

##  3 Results

The overall MIRI-MRS spectrum of SY Cha is characterized by a strong 10
$\mathrm{\mu}$m amorphous silicate feature in emission as well as evidence of
forsterite. Following the method of van Boekel et al. (2005) we measure the
ratio of the flux at 11.3 and 9.8 $\mathrm{\mu}$m, which is correlated with
the strength of the silicate feature. We find a low 11.3/9.8 $\mathrm{\mu}$m
ratio of $\sim 0.7$. This is indicative of the presence of warm silicate
grains which have not undergone a large amount of processing. This emission
originates in the inner disk and demonstrates the presence of a dusty disk at
small radii.

###  3.1 Atomic Hydrogen Emission

Atomic hydrogen emission at mid-IR wavelengths arises primarily from the hot
disk atmosphere, though jets and outflows can also contribute. We detect four
hydrogen recombination lines shortward of 10 $\mathrm{\mu}$m, with the
strongest being the HI (6-5) line at $\sim$7.5 $\mathrm{\mu}$m. We do not
detect the HI (7-6) line, which is often used as an accretion tracer, (e.g.,
Rigliaco et al., 2015; Beuther et al., 2023), though it may be masked by the
presence of multiple strong H2O lines in the vicinity.

###  3.2 Molecular Emission

Figures 3 & 4 show the continuum subtracted spectra as well as the best-fit
slab models. The best-fit model parameters are given in Table 3. After
continuum subtraction, the MIRI-MRS spectrum of SY Cha is dominated by ro-
vibrational and pure rotational H2O vapor emission, which is seen in all sub-
bands (Figures 3 & 4). As with observations of other disks observed with MIRI-
MRS, e.g., Kóspál et al. (2023); Banzatti et al. (2023a); Gasman et al.
(2023), the lines at longer wavelengths preferentially trace cooler gas (Table
3). In addition to H2O, we detect CO, C2H2, HCN, CO2, and OH. The best-fit
column densities for H2O are high compared to most other disks observed with
MIRI, where typical column densities are of order $10^{18}$ cm-2, while the
column densities for the carbon bearing species are on the low end (Grant et
al., 2023; Tabone et al., 2023; Perotti et al., 2023; Banzatti et al., 2023a;
Gasman et al., 2023). Our slab model fits do not provide tight constraints on
the temperature of the emitting gas. This is likely due to the limits of
fitting multiple transitions with a single slab model. As demonstrated by
Banzatti et al. (2023b) and Banzatti et al. (2023a), H2O lines close together
in frequency space can originate from physically distinct locations, with
distinct densities and temperatures. In the future more sophisticated
modeling, e.g., using nested slab models or full radiative transfer of a model
disks, will be needed to provide tighter constraints.

As previously mentioned, CO ro-vibrational emission at 4.7 $\mathrm{\mu}$m was
not detected in ground-based observations of SY Cha (Brown et al., 2013).
However, ro-vibrational CO emission is clearly seen in our MIRI-MRS Band 1
data, which begin at 4.9 $\mathrm{\mu}$m. Given the presence of extended
emission seen in H2, it is possible that the lower J CO lines are obscured by
an absorbing disk wind between the disk and the viewer. Previous high-spectral
resolution ground-based studies have shown that lower J CO lines are more
likely to be seen in absorption than higher J lines, particularly for disks
such as SY Cha’s with inclinations greater than 40∘ (Banzatti et al., 2022).
This is interpreted as due to a disk wind component. Alternatively the 4.7
$\mathrm{\mu}$m emission could be hidden by telluric features in the ground-
based observations, as suggested by Brown et al. (2013). Our best-fit slab
model for CO gives an excitation temperature of 1570 K and an equivalent
emission radius (emitting area) of 0.13 au (0.053 au2). This is consistent
with the temperatures and emitting area derived from LTE slab model fits to
Keck-NIRSPEC data for full T Tauri disks by Salyk et al. (2011a). However,
they found transition disks tended to be best fit by a lower temperature model
and smaller emitting area. That the CO emission in SY Cha is consistent with
emission from full protoplanetary disks suggests that the inner disk in SY Cha
remains gas-rich.

13CO2 is not detected. Based on the best-fit temperature and column density
for CO2, the 13CO2 feature at 15.42 $\mathrm{\mu}$m is expected to be
extremely weak, peaking at less than 1 mJy. This feature also overlaps with a
bright H2O line, preventing constraints on the 13CO2/CO2 ratio.

Most mid-IR disk spectra show either strong H2O emission, with H2O emission
stronger than emission from other molecular species, or hydrocarbon emission
(Pascucci et al., 2013; Banzatti et al., 2020; Grant et al., 2023; Tabone et
al., 2023; Banzatti et al., 2023a; Gasman et al., 2023). The SY Cha spectrum
contains both strong H2O lines as well as, potentially, a weak C2H2 line.
Figure 5 shows the best-fit C2H2 slab model as well as the residual observed
spectrum after subtracting the best-fit H2O, OH, CO2 and HCN models. Emission
from C2H2 explains residual emission that is not well fit by the fundamental
bending mode of HCN. This potential C2H2 emission feature at 13.69
$\mathrm{\mu}$m peaks $5\sigma$ above the rms noise of 0.6 mJy. However, this
is of the same order as the residuals in other regions of the spectrum where
we do not expect molecular emission. The column density and temperature of
C2H2 are also not well constrained by the slab model fits (Figure 10). We
therefore classify the C2H2 detection as tentative. Previously reported values
for C2H2 in SY Cha could have been contaminated by emission from other species
due to the lower spectral resolution of _Spitzer_ (Salyk et al., 2011b;
Banzatti et al., 2020). Alternatively, the C2H2 column density in the inner
disk has changed in the twelve years between observations.

Figure 5: Residual observed emission after subtracting the continuum, H2O, OH,
CO2, and HCN best-fit models (black). The best-fit model for C2H2 is
overplotted in magenta. Grey shading indicated the $1\sigma$ rms noise level
calculated for the continuum subtracted spectrum for 14.74-14.755
$\mathrm{\mu}$m. The emission attributed to C2H2 is of the same order as
nearby residual emission. Table 3: Best-fit model parameters per spectral
channel. The quoted uncertainties are the confidence intervals per fit
parameter, given based on the $\chi^{2}$ maps and are included only for maps
with a closed $1\sigma$ contour (see Figures 8-10).

For N the confidence intervals are given in log-space.  Molecule $N$ $T$ $R$
[cm-2] [K] [au] 4.9-5.7 $\mathrm{\mu}$m $\sigma_{5.44-5.452}=0.59$ mJy H2O
2.0${}\times 10^{19}$ 1020 0.026 CO 3.0${}\times 10^{16}$ 1570 0.13 5.7-6.6
$\mathrm{\mu}$m $\sigma_{5.998-6.004}=0.22$ mJy H2O 1.2${}\times
10^{20}$${}_{-0.7}^{+6.4}$ 1080${}_{-650}^{+580}$ 0.022${}_{-0.014}^{+0.42}$
6.6-7.6 $\mathrm{\mu}$m $\sigma_{6.89-6.90}=0.40$ mJy H2O 2.0${}\times
10^{19}$${}_{-1.0}^{+4.7}$ 970${}_{-660}^{+850}$ 0.029${}_{-0.019}^{+0.51}$
13.5-15.5 $\mathrm{\mu}$m $\sigma_{14.74-14.755}=0.62$ mJy H2O 8.4${}\times
10^{18}$${}_{-0.8}^{+1.0}$ 660${}_{-120}^{+130}$ 0.17${}_{-0.08}^{+0.35}$ OH
3.3${}\times 10^{18}$ 1750b 0.038 CO2 4.9${}\times 10^{17}$ 210 0.27 HCN
2.7${}\times 10^{13}$${}_{-0.5}^{+4.4}$ 720${}_{-190}^{+265}$
6.9${}_{-6.88}^{+3.07}$ C2H${}_{2}^{a}$ 2.3${}\times 10^{17}$ 100 2.7
15.5-17.5 $\mathrm{\mu}$m $\sigma_{16.06-16.1}=0.97$ mJy H2O 7.0${}\times
10^{18}$${}_{-0.7}^{+0.6}$ 510${}_{-65}^{+60}$ 0.24${}_{-0.08}^{+0.19}$ OH
1.2${}\times 10^{18}$ 810b 0.15 17.9-20.7 $\mathrm{\mu}$m
$\sigma_{19.1-19.153}=0.33$ mJy H2O 3.1${}\times 10^{21}$ 360 0.27 OH
1.1${}\times 10^{17}$ 3500b 0.060

Note. — aTentative detection

b Temperatures for OH reflect collisional or chemical pumping, not a physical
gas temperature

##  4 Discussion

The strong H2O flux relative to carbon bearing species suggests the inner disk
of SY Cha is H2O rich, with a sub-solar carbon to oxygen ratio ($C/O<0.5$).
The H2O column density from our slab models ranges from 7${}\times 10^{18}$ to
3.1${}\times 10^{21}$ cm-2 for the different wavelength ranges fitted. This is
sufficient for H2O to be self-shielded from dissociating UV emission (Bethell
& Bergin, 2009). It is possible that the high H2O column also shields other
species from UV photons (e.g., Bosman et al., 2022), resulting in emission
from both H2O and carbon bearing species. The best fit temperatures for H2O
emission in our models also vary from several hundred Kelvin to over a
thousand Kelvin, with the best fit temperature generally decreasing with
increasing wavelength. This can be explained by the H2O transitions at shorter
wavelengths having preferentially higher excitation temperatures (Banzatti et
al., 2023b), and has been observed in several other protoplanetary disks
(Gasman et al., 2023; Banzatti et al., 2023a). The emission at different
excitation temperatures likely also probes different radial regions in the
disk: a much smaller area of the disk is able to reach temperatures warmer
than 1000 K compared to a few hundred Kelvin. Thus, the best-fit emitting area
decreases as the best fit temperature increases.

Prompt emission from OH is the result of H2O photodissociation by UV photons
forming OH in a rotationaly excited state (Harich et al., 2000; van Harrevelt
& van Hemert, 2000). In this circumstance, OH emission should be seen
throughout the wavelength range covered by MIRI-MRS, with OH lines shortward
of 10 $\mathrm{\mu}$m brighter than those at longer wavelengths (Tabone et
al., 2021). We do not detect OH emission at wavelengths shorter than 13
$\mathrm{\mu}$m, nor do the detected OH quadruplets display the asymmetry
expected from prompt emission. While weak OH emission at short wavelengths
could be hidden in the forest of water lines, the lack of asymmetry in the
observed quadruplets leads us to conclude that the observed OH emission is not
primarily the result of UV dissociation of H2O. Instead, OH is likely excited
via collisions or chemical pumping. Similar results were found for the disk
around Sz 98 by Gasman et al. (2023).

The large cavity observed in the millimeter continuum has not resulted in a
H2O poor inner disk. This is not surprising given that the spatially resolved
millimeter 12CO emission observed with ALMA does not show an inner cavity,
suggesting that there are not large gaps in the radial gas distribution. SY
Cha’s infrared spectral index, as well as the presence of silicate emission,
is also indicative of disk material at small radii (e.g., Banzatti et al.,
2020).

Most mechanisms proposed to form substructures such as dust rings in
protoplanetary disks do so by creating a pressure trap (Bae et al., 2023).
Pressure traps are able to stop the inward drift of large, millimeter sized,
dust particles, which can lead to gaps seen in millimeter continuum emission.
Pressure traps do not inhibit the movement of gas or the small, micron-sized,
particles which are more coupled to the gas. Gas and small grains can instead
be cleared by photo-evaporation or interaction with a perturber, such as a
planet or an infall stream (Lin & Papaloizou, 1979; Lubow et al., 1994;
Suriano et al., 2019; Kuznetsova et al., 2022). Based on the high column
density of molecules in the inner disk, particularly H2O as well as the high
infrared spectral index and resolved CO emission, we conclude that the
mechanism which created the millimeter dust ring at 100 au has not prevented
the inward motion of gas and sub-micron dust in SY Cha. If the millimeter
cavity in SY Cha has been created by a planet, such a planet would need to be
massive enough to create a pressure trap but below the mass needed to clear a
gap in the gas (Kley & Nelson, 2012; Zhu et al., 2012).

###  4.1 Comparison to PDS 70

The MIRI-MRS spectra of another transition disk, PDS 70, was recently studied
by Perotti et al. (2023). The SY Cha and PDS 70 disks are superficially
similar in the millimeter continuum, with a small inner disk, a wide ($>$40
au) dust cavity, an outer ring of millimeter grains, at roughly 70 au and 45
au respectively, and moderate inclinations of $51.1\mbox{${}^{\circ}$}$ and
$51.7\mbox{${}^{\circ}$}$ (Benisty et al., 2021; Orihara et al., 2023). Both
disks have been observed with ALMA at $\sim 20$ milli-arcsecond resolution,
though the rms noise in the PDS 70 observations is significantly lower. The
inner disk of PDS 70 is marginally resolved by ALMA, extending out to 18 au,
while the inner disk in SY Cha is unresolved but constrained to be smaller
than 3.5 au. As previously mentioned, PDS 70 is one of the only transition
disks known to host young massive planets within its dust cavity. However, the
MIRI-MRS spectra of these two systems are vastly different, with the SY Cha
continuum a factor of 3-6 stronger and much stronger molecular and atomic
emission when PDS 70 is scaled to the distance of SY Cha (Figure 6). The shape
of the continuum is also different. The slope of the continuum at short
wavelengths is extremely steep in PDS 70 when compared to most T Tauri disks.
The crystalline forsterite feature at 11 $\mathrm{\mu}$m, indicative of a past
heating event, is more pronounced in PDS 70, while the slope of the continuum
beyond 15 $\mathrm{\mu}$m is steeper for SY Cha.

Figure 6: Comparison between the _JWST_ -MIRI MRS spectrum of SY Cha (black)
and PDS 70 scaled to the distance of SY Cha (grey). SY Cha exhibits stronger
flux in both the line and continuum emission.

The best-fit slab models for H2O from 6.7-7.3 $\mathrm{\mu}$m give similar
temperatures and emitting areas for both sources, roughly 600 K and 0.04 au.
However, the column density for SY Cha is several orders of magnitude greater,
at 5.2${}\times 10^{21}$ cm-2 compared to 1.4${}\times 10^{18}$ cm-2 in PDS
70. Emission lines from other atomic and molecular species are likewise much
stronger for SY Cha.

There are several potential explanations for the different chemical
composition in the inner disks of these two systems. With a bolometric
luminosity of 0.35 L⊙, PDS 70 is less luminous than SY Cha (Pecaut & Mamajek,
2016). Thus, the incident ionizing flux from the central star, a driver of
disk evolution, is different. The inner disk in SY Cha could be less evolved,
with less gas depletion, than the PDS 70 disk. Although the ages of these
systems are highly uncertain, the best estimates suggest SY Cha is roughly 2
Myr younger than PDS 70 (Müller et al., 2018; Galli et al., 2021).

Alternatively, it is possible that the dust cavity in SY Cha was not carved by
massive planets, instead being formed by other methods (e.g., Flock et al.,
2015) or smaller planets, which are less efficient at preventing the inward
motion of gas and small dust grains. In the case of planets, the strength of
the pressure trap increases with increasing planet mass, as well as depending
on the disk temperature and viscosity (e.g., Fung et al., 2014; Kanagawa et
al., 2015; Asensio-Torres et al., 2021). There is no published data on SY Cha
from optical/near-IR surveys searching for planets in transition disks.
Likewise, the published observations of SY Cha with ALMA are not sensitive
enough to detect emission from protoplanets of similar brightness to the ones
detected in PDS 70. The 12CO gas observed by ALMA does not display a central
cavity, while the less abundant $\mathrm{{}^{13}CO}$ and C18O isotopologues
exhibit a ring-like morphology. In PDS 70 all molecular species, apart from
the optically thick 12CO, observed with ALMA appear depleted inside of
$0\farcs{2}$ and modeling of the disk finds a gas surface density minimum at
20 au (Keppler et al., 2019; Facchini et al., 2021; Portilla-Revelo et al.,
2023). The cavity in PDS 70 is clearly far more depleted than that in SY Cha.
This is likely the cause of the different chemical compositions in the inner
disk.

If the cavity in SY Cha is carved by less massive planets this would point to
the composition of the inner disk being strongly linked to the mass of, not
just the presence of, planets at larger radii. Confirmation of this idea will
require additional _JWST_ observations of transition disks to constrain the
inner disk composition as well as deep searches for sub-stellar companions.
Overall, the molecular column densities in the inner disk of SY Cha are more
similar to those derived for the full protoplanetary disk of Sz 98 despite its
different millimeter dust morphology (Gasman et al., 2023). The Sz 98 disk is
a full protoplanetary disks with several narrow gaps observed in the sub-
millimeter continuum. Its dust disk extends to $R=278$ au, compared to $\sim
140$ au for the SY Cha disk (Tazzari et al., 2017; Orihara et al., 2023).

It is also possible that the strong molecular emission lines in SY Cha are
indicative of some level of dust grain growth in the inner disk. As dust
grains grow, the dust opacity is reduced, exposing a larger gas column and
resulting in stronger molecular line emission without a large change in the
SED at infrared wavelengths (Antonellini et al., 2023). In this case the
unresolved inner disk emission seen with ALMA should be from dust emission,
rather than free-free emission or an ionized wind. Additional observations at
longer wavelengths would help clarify the origin of the sub-millimeter
emission. It should be noted that the _JWST_ data presented in the current
work demonstrates the presence of small dust grains in the inner disk but does
not rule out the presence of larger grains.

###  4.2 Temporal Variability

As discussed in Section 2.2, there is substantial variability observed in the
continuum flux between the _JWST_ observations and the three _Spitzer_ epochs.
To determine whether the molecular line flux is likewise variable we degrade
the MIRI-MRS spectrum to the resolution of the _Spitzer_ high resolution
observations from 2004 and 2008. Continuum subtraction is then carried out as
described in Section 2, with the same points used for all epochs. We then
integrate over the same wavelength range to get the total line flux. The
wavelength ranges used for C2H2, HCN, and CO2 are the same as those used by
Banzatti et al. (2020) while the wavelength range for H2O is taken from Najita
et al. (2013). The results are given in Table 4.

Figure 7: Continuum subtracted spectra from _Spitzer_ high resolution and MIRI
MRS observations, with the MIRI spectra degraded to the same resolution as
_Spitzer_ before continuum subtraction. Epochs are offset by 0.02 Jy for
readability. The grey shaded regions indicate the wavelength range used when
integrating line fluxes. The line flux shows noticeable variation between
epochs, though the changes are within the flux calibration uncertainty.

The total line flux appears to vary not just between the _JWST_ and _Spitzer_
observations, but also between the two _Spitzer_ epochs. This apparent change
in brightness is of the same order as that reported by Banzatti et al. (2012)
for EX Lupi for similar wavelength ranges. EX Lupi is the prototype of the
highly variable T Tauri sources know as EXors and the changes were seen when
comparing observations during quiescent and outbursting epochs. However, the
luminosity of the line emission in SY Cha is weaker than that in EX Lupi.

To determine if the variability seen in the molecular line emission for SY Cha
is significant, we calculate the uncertainty in the flux ratio between two
epochs, where the uncertainty for a single observation is the calculated rms
noise added in quadrature to the spectro-photometric accuracy of the
instrument. Given the spectro-photometric accuracy of both _Spitzer_ -IRS and
_JWST_ -MIRI, the variability in line flux in SY Cha is not statistically
significant. The potential variability in line emission seen in SY Cha, which
has not undergone any known recent outbursts, suggests that the physical
conditions in the inner regions of even quiescent protoplanetary disks could
change on observable timescales. Careful study of line emission in a single
source at high signal-to-noise over multiple epochs is needed to confirm this
idea.

Table 4: Comparison of Integrated Line Flux in _Spitzer_ and _JWST_ Observations. Error is the rms noise error. Molecule | Wavelength |  _Spitzer_ 2004 | Err |  _Spitzer_ 2008 | Err |  _JWST_ 2022 | Err
---|---|---|---|---|---|---|---
|  $\mathrm{\mu}$m | ($10^{-14}$ erg s-1 cm${-2}$) | ($10^{-14}$ erg s-1 cm${-2}$) | ($10^{-14}$ erg s-1 cm${-2}$)
C2H2 | 13.648-13.729 | $0.28$ | $0.18$ | $0.66$ | $0.25$ | $0.22$ | $0.14$
HCN | 13.914-14.055 | $0.29$ | $0.34$ | $1.12$ | $0.47$ | $0.96$ | $0.27$
CO2 | 14.93-15.04 | $0.51$ | $0.21$ | $0.51$ | $0.29$ | $0.28$ | $0.17$
H2O | 17.077-17.1555 | $0.45$ | $0.15$ | $0.18$ | $0.25$ | $0.156$ | $0.094$
H2O | 17.183-17.261 | $0.32$ | $0.11$ | $0.22$ | $0.19$ | $0.258$ | $0.073$
H2O | 17.2998-17.4200 | $0.59$ | $0.23$ | $0.37$ | $0.38$ | $0.13$ | $0.15$

##  5 Conclusions

We report the first results from _JWST_ -MIRI MRS observations of the SY Cha
protoplanetary disk, observed as part of the MINDS GTO program. We detect
emission from HI, [NeII], H2, H2O, OH, CO, CO2, and HCN as well as a marginal
detection of C2H2. The line fluxes for all species are relatively high
compared to the other T Tauri disks observed thus far with MIRI-MRS, with the
emission from H2O particularly strong (Grant et al., 2023; Perotti et al.,
2023; Banzatti et al., 2023a; Gasman et al., 2023). Based on these results we
conclude that the high molecular column densities in the inner disk are likely
due to the inward drift of gas and small grains while large grains are caught
by a weak pressure trap. The superior spectral resolution of MIRI-MRS allows
us to isolate the mid-infrared OH lines in the source for the first time.
Based on the lack of OH emission observed shortward of 13 $\mathrm{\mu}$m and
the lack of asymmetry in the observed quadruplets, we conclude the OH excited
then H2O is dissociated by UV photons. We also find that SY Cha is highly
variable in the mid-IR continuum. This is consistent with previous studies of
protoplanetary disks, particularly those with large millimeter dust cavities.
We further find hints of molecular line variability. Higher signal-to-noise
observations will be needed to confirm this.

Determining how common gas-rich inner disks co-existing with large millimeter
cavities are will require a large _JWST_ survey of protoplanetary disks with a
range of dust morphologies. Further, multiple epochs of high spectral
resolution observations with MIRI-MRS will be required to determine if
variability of both line and continuum flux is common, while modeling will be
needed to determine if this is due to changes in chemical abundance,
temperature, or disk morphology.

##  6 Acknowledgments

This work is based on observations made with the NASA/ESA/CSA James Webb Space
Telescope. The data were obtained from the Mikulski Archive for Space
Telescopes at the Space Telescope Science Institute, which is operated by the
Association of Universities for Research in Astronomy, Inc., under NASA
contract NAS 5-03127 for JWST. These observations are associated with program
1282. The following National and International Funding Agencies funded and
supported the MIRI development: NASA; ESA; Belgian Science Policy Office
(BELSPO); Centre Nationale d’Etudes Spatiales (CNES); Danish National Space
Centre; Deutsches Zentrum fur Luft und Raumfahrt (DLR); Enterprise Ireland;
Ministerio De Economía y Competividad; Netherlands Research School for
Astronomy (NOVA); Netherlands Organisation for Scientific Research (NWO);
Science and Technology Facilities Council; Swiss Space Office; Swedish
National Space Agency; and UK Space Agency.

The data presented in this article were obtained from the Mikulski Archive for
Space Telescopes (MAST) at the Space Telescope Science Institute. The specific
observations analyzed can be accessed via https://doi.org/10.17909/8ref-ye65
(catalog DOI).

K.S. and T.H. acknowledge support from the European Research Council under the
Horizon 2020 Framework Program via the ERC Advanced Grant Origins 83 24 28.
G.P. gratefully acknowledges support from the Max Planck Society. D.B. and
M.M.C. have been funded by Spanish MCIN/AEI/10.13039/501100011033 grants
PID2019-107061GB-C61 and No. MDM-2017-0737. I.K., A.M.A., and E.v.D.
acknowledge support from grant TOP-1 614.001.751 from the Dutch Research
Council (NWO). I.K. and J.K. acknowledge funding from H2020-MSCA-ITN-2019,
grant no. 860470 (CHAMELEON). E.v.D. acknowledges support from the ERC grant
101019751 MOLDISK and the Danish National Research Foundation through the
Center of Excellence “InterCat” (DNRF150). A.C.G. acknowledges from PRIN-MUR
2022 20228JPA3A “The path to star and planet formation in the JWST era (PATH)”
and by INAF-GoG 2022 “NIR-dark Accretion Outbursts in Massive Young stellar
objects (NAOMY)” and Large Grant INAF 2022 “YSOs Outflows, Disks and
Accretion: towards a global framework for the evolution of planet forming
systems (YODA)”. V.C. acknowledges funding from the Belgian F.R.S.-FNRS. D.G.
thanks the Belgian Federal Science Policy Office (BELSPO) for the provision of
financial support in the framework of the PRODEX Programme of the European
Space Agency (ESA). T.P.R. acknowledges support from ERC grant 743029 EASY.
D.R.L. acknowledges support from Science Foundation Ireland (grant number
21/PATH-S/9339). M.T. acknowledges support from the ERC grant 101019751
MOLDISK.

JWST, Spitzer

##  Appendix A Continuum Subtraction

In Table 5 we list the points used to define the spline fit used to subtract
continuum.

Table 5: Points used in continuum subtraction. Covered Transitions | Value
---|---
CO, H2O | 4.926, 4.947, 4.987, 5.1, 5.168, 5.338, 5.439, 5.575, 5.702, 5.73
HI 10-6 | 5.073, 5.1, 5.168, 5.1925, 5.225
H2O | 5.728,5.893,6.0,6.084,6.164,6.18,6.192,6.21,6.429,6.463,6.607
H2O | 6.608,6.761,6.895,7.159,7.267,7.444,7.56,7.626
HI 12-7 | 6.749, 6.782, 6.7896, 6.801
HI 6-5 | 7.4, 7.4250, 7.4950, 7.528
HI 8-6, HI 11-7 | 7.425, 7.4775, 7.492, 7.528
$\mathrm{[NeII]}$ 2P1/2-2P${}_{3/2}^{a}$ | 12.77,12.802,12.860,12.88
H2O, OH, CO2 C2H2, HCN | 13.52,13.59,13.746,14.101,14.573,14.7,15.208,15.393,15.5
H2O, OH | 15.565,15.71,15.826,15.905,16.084,16.36,16.675,17.075,17.367,17.43,17.48,17.592,17.823
H2O, OH | 17.876,18.299,18.615,18.735,19.125,19.40,19.9,20.21,20.36,20.685

##  Appendix B $\chi^{2}$ maps of fits

The $\chi^{2}$ per molecule and per fitted region are presented here (Figures
8-10).

Figure 8: $\chi^{2}$ maps for the slab model fits to H2O. The color map shows
$\chi^{2}_{min}/\chi^{2}$ such that the best-fit is given a value of 1. The
red, orange, and yellow contours give the $1\sigma$, $2\sigma$, and $3\sigma$
uncertainty levels for 2 degrees of freedom. The white contours show the best-
fit emitting radius, with labels in au. Figure 9: $\chi^{2}$ maps for the slab
model fits to OH. The color map shows $\chi^{2}_{min}/\chi^{2}$ such that the
best-fit is given a value of 1. The red, orange, and yellow contours give the
$1\sigma$, $2\sigma$, and $3\sigma$ uncertainty levels for 2 degrees of
freedom. The white contours show the best-fit emitting radius, with labels in
au. The OH lines are poorly constrained by slab models. Figure 10: $\chi^{2}$
maps for the slab model fits to CO, C2H2, HCN, and CO2. The color map shows
$\chi^{2}_{min}/\chi^{2}$ such that the best-fit is given a value of 1. The
red, orange, and yellow contours give the $1\sigma$, $2\sigma$, and $3\sigma$
uncertainty levels for 2 degrees of freedom. The white contours show the best-
fit emitting radius, with labels in au.

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