UV-driven chemistry as a signpost of late-stage planet
formation

Jenny K. Calahan, Edwin A. Bergin, Arthur D. Bosman, Evan A. Rich, Sean M. Andrews, Jennifer B. Bergner, L. Ilsedore Cleeves, Viviana V. Guzmán, Jane Huang, John D. Ilee, et al.

► To cite this version:

Jenny K. Calahan, Edwin A. Bergin, Arthur D. Bosman, Evan A. Rich, Sean M. Andrews, et al. UV-driven chemistry as a signpost of late-stage planet formation. Nature Astronomy, 2023, 7, pp.49-56. 10.1038/s41550-022-01831-8. insu-04473235

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# UV-driven chemistry as a signpost of late-stage planet formation

Received: 19 July 2022

Accepted: 14 October 2022

Published online: 8 December 2022

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Jenny K. Calahan Ⓔ<fnref n="1" />, Edwin A. Bergin Ⓔ<fnref n="1" />, Arthur D. Bosman<fnref n="1" />, Evan A. Rich<fnref n="1" />, Sean M. Andrews², Jennifer B. Bergner Ⓔ³, L. Ilsedere Cleeves⁴, Viviana V. Guzmán⁵,⁶, Jane Huang<fnref n="1" />, John D. Ilee Ⓔ⁷, Charles J. Law², Romane Le Gal⁸,⁹,¹⁰, Karin I. Öberg Ⓔ², Richard Teague¹¹, Catherine Walsh Ⓔ⁷, David J. Wilner Ⓔ² & Ke Zhang¹²

The chemical reservoir within protoplanetary disks has a direct impact on planetary compositions and the potential for life. A long-lived carbon- and nitrogen-rich chemistry at cold temperatures (≤ 50 K) is observed within cold and evolved planet-forming disks. This is evidenced by bright emission from small organic radicals in 1–10 Myr aged systems that would otherwise have frozen out onto grains within 1 Myr. We explain how the chemistry of a planet-forming disk evolves from a cosmic-ray/X-ray-dominated regime to an ultraviolet-dominated chemical equilibrium. This, in turn, will bring about a temporal transition in the chemical reservoir from which planets will accrete. This photochemical dominated gas phase chemistry develops as dust evolves via growth, settling and drift, and the small grain population is depleted from the disk atmosphere. A higher gas-to-dust mass ratio allows for deeper penetration of ultraviolet photons is coupled with a carbon-rich gas (C/O > 1) to form carbon-bearing radicals and ions. This further results in gas phase formation of organic molecules, which then would be accreted by any actively forming planets present in the evolved disk.

Protoplanetary disks are the natal environments for planets. Disks have three main components: a pebble-rich dusty midplane (dust grain radius > -1 mm), a gaseous atmosphere extending well above<fnref n="1" /> and radially beyond (by a factor of ~2; ref. ²) the pebble-rich midplane and a small dust population (radius < 10 µm) that is coupled to the gas. Each component of the protoplanetary disk has an impact on shaping the chemistry of actively forming planets. The solid cores of giant planets must form over a short timescale (~1 Myr) for the eventual planet to obtain its full mass over the course of a typical lifetime of gas in a disk (~10 Myr; ref. ³) and to explain the widely observed gap and ring

structures that are thought to be indicative of planet formation⁴. The compositions of pebbles and their icy mantles directly influence the final composition of a solid planetary core⁵,⁶. After a core becomes sufficiently massive, planets start to accrete material from the gaseous reservoir surrounding the pebble-rich midplane of a protoplanetary disk to form their atmospheres⁷. It remains difficult to directly probe the gas within the planet-forming midplane owing to the high dust densities leading to elevated dust optical depths that mask line emission, as well as cold temperatures that lead to the freezing out of common gas tracers such as CO onto dust grains. However, constraining the chemical

<footnote n="1">¹University of Michigan, Ann Arbor, MI, USA. ²Center for Astrophysics | Harvard & Smithsonian, Cambridge, MA, USA. ³University of Chicago Department of the Geophysical Sciences, Chicago, IL, USA. ⁴Department of Astronomy, University of Virginia, Charlottesville, VA, USA. ⁵Instituto de Astrofísica, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile. ⁶Núcleo Milenio de Formación Planetaria (NPF), Santiago, Chile. ⁷School of Physics & Astronomy, University of Leeds, Leeds, UK. ⁸IRAP, Université de Toulouse, CNRS, CNES, Toulouse, France. ⁹IPAG, Université Grenoble Alpes, CNRS, IPAG, Grenoble, France. ¹⁰IRAM, Saint-Martin d'Hères, France. ¹¹Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. ¹²Department of Astronomy, University of Wisconsin-Madison, Madison, WI, USA. ☎e-mail: jcalahan@umich.edu</footnote>
environment of the planet-forming midplane is essential to connect sub-millimetre observations probing the warm intermediate regions above the disk midplane to the composition of actively forming planets.

The molecules CH₃CN and HC₃N are two of many complex organic molecules (loosely defined as molecules with at least six atoms, including multiple carbon atoms) that could act as basic precursors to prebiotic molecules⁸⁻¹⁰. CH₃CN and HC₃N have been observed and spatially resolved towards the protoplanetary disks around six young stars: GM Aur, AS 209, HD 163296, MWC 480, LkCa 15 and V4046 Sgr¹¹⁻¹⁴. CH₃CN has also been spatially resolved towards the TW Hya disk¹⁵, and a small (≈ 4 source) survey has detected unresolved CH₃CN or HC₃N emission from other young stellar objects¹⁶. These molecules exhibit bright emission signifying high gas phase abundances and column densities (N<sub>total</sub> = 10¹²–10¹³ cm⁻² (refs. ¹¹,¹²)). CH₃CN is an excellent probe of gas temperature due to multiple transitions tracing a range of energy states (lower energy state (E<sub>L</sub>) ≈ 5 K, the span of lower energy states across transitions (ΔE<sub>L</sub>) = -100 K) that can be observed simultaneously. Each *J* transition (where *J* is the rotational quantum number) has a series of *K*-ladder transitions (where *K* is the quantum number of angular momentum along the molecular axis) that are only sensitive to collisions, and thus the ratio between *K* transitions depends only on the gas density and temperature. The *K* transitions span a large range of temperatures and are sufficiently close in frequency to observe in one spectral setting with the Atacama Large Millimeter/submillimeter Array (ALMA). Analyses of rotational diagrams¹⁷ made from CH₃CN observations demonstrate an origin in gas with a temperature between 25 and 50 K (ref. ¹²), well below the expected desorption temperature (100–124 K (ref. ¹⁸)). Thus, the brightly observed flux from this species and similar nitriles and organics such as HC₃N and CH₂CN (ref. ¹⁹) present a chemical conundrum as they should not be present in the gaseous state; rather, they should be frozen out on cold grain surfaces. Where CH₃CN and other carbon-rich molecules reside and how they are replenished in the gas phase has a substantial impact on our understanding of prebiotic enrichment into gaseous planet atmospheres. The traditional solution to this apparent discrepancy has been to turn to grain-surface chemistry. Simple carbon- and nitrogen-bearing molecules can undergo hydrogenation or other reactions to form complex organics on the surface of a grain that then non-thermally desorb intact from the grain. This solution has been used to explain the organic inventories locked onto pebbles and icy grains²⁰,²¹. This dust chemistry path requires both an intact photodesorption rate of CH₃CN from the grains of 10⁻³ mols per photon¹⁵,²² and a reactive desorption efficiency²³ of 1%. Laboratory experiments find an intact photodesorption efficiency of CH₃CN to be orders of magnitude less efficient (10⁻⁵ mols per photon²⁴) and reactive desorption has not been well studied in laboratory experiments for these species. We posit here that there is a simpler alternative based solely on disk evolution processes that have been previously theorized and observed, which link the disk gas chemistry to planet formation. This involves two ingredients: (1) an elevated C/O ratio in the gas and (2) greater penetration of ultraviolet (UV) photons owing to a reduction in the total surface area of the small grain population due to pebble formation. These combine to power a state of photochemical equilibrium.

There has been mounting evidence for an elevated C/O gas phase
ratio at large radial distances in evolved and cool gas-rich protoplan-
etary disks. Brighter than expected emission from small hydrocarbons
such as C<sub>2</sub>H (refs. ²⁵,²⁶) and complex organics such as c-C<sub>3</sub>H<sub>2</sub>(ref. ²⁷) in
disks and HC<sub>3</sub>N and CH<sub>3</sub>CN in photon-dominated regions²⁸ have inde-
pendently suggested a C/O ratio well above the solar abundance ratio
(C/O ≈ 0.55)²⁹. As a radical, C<sub>2</sub>H has a short lifetime (<1,000 years), but it
is found to be abundant in the gas. Bosman et al.²⁶ find that the only way
to reproduce the high column densities observed was to increase the
C/O ratio throughout the full disk to between 1 and 2. They found that it
was also necessary for C<sub>2</sub>H to exist in high density gas while remaining
above the disk midplane (height/radius ≈ 0.1–0.2) where UV photons

dominate the high-energy photon budget. Together, this produces a long-lived carbon-rich gas phase cycle in photochemical equilibrium²⁶. One critical factor is that C₂H is predicted and is observed to exist above the disk midplane³⁰. In contrast, CH₃CN has been observed to emit closer to the midplane¹². Extending the carbon-rich chemical environment that is used to explain C₂H observations to the midplane could allow for gas phase formation of complex molecules in the planet-forming zone. Elevated C/O ratios would be necessary to supply the materials to create hydrocarbons and nitriles. However, this alone would not alleviate the issue of CH₃CN and HC₃N existing in the gas at temperatures at which they should be frozen out and locked onto grains.

A non-thermal desorption mechanism is needed to increase the number of molecules that are being desorbed from the grains, either intact or as fragments of larger molecules. If the disk atmosphere is small-dust rich, with a gas-to-dust ratio close to the typical interstellar medium (ISM) mass ratio (gas-to-dust = 100) then UV radiation cannot penetrate deep into the disk. In this case, only high-energy radiation (X-rays and cosmic rays) can penetrate the dust and gas and drive the chemistry within and near the midplane. Small dust grains are the main opacity source for UV photons, which are readily produced by the young and active star. As the protoplanetary disk evolves, small dust grains agglomerate and eventually settle downwards and drift inwards radially as they grow in size⁴,³¹, decreasing the total surface area of the small grain population. As the main opacity source begins to deplete, UV photons can penetrate deeper into the disk. Here complete desorption of CH₃CN or HC₃N is inhibited because of the dense and cold environment²⁸. This mechanism would have an effect on all molecules residing on grains, and a brief discussion regarding this can be found in the Supplementary Discussion, in the section ‘Implications on other molecules’.

The combined effect of a high C/O ratio and excess UV flux allows complex molecules to exist within the gas phase at cold, midplane temperatures. Thus, bright hydrocarbon and nitrile (that is C₂H, CH₃CN) emission from the cold midplane acts as a signpost for an evolved dust population, coincident with an advanced stage of planet formation including the accumulation of gas-giant atmospheres. The chemical scenario we put forward, comparing early and late-stage disk environments is shown in Fig. 1. The disks observed in the Molecules with ALMA at Planet-forming Scales (MAPS) large programme³² provide plausible support for this theory. The youngest disks in the MAPS sample reside around IM Lup and AS 209, which are on the order of 1–2 Myr old³². Towards the youngest source, IM Lup, there is no detection of CH₃CN nor HC₃N. AS 209 has detections of CH₃CN and HC₃N, which suggest both molecules emit from height/radius (z/r) > 0.1. The disk systems surrounding stars > 6 Myr old have CH₃CN detected at z/r < 0.1 as determined by the modelled thermal structure and detected rotational temperature from the *K*-ladder transitions. This complex organic-rich midplane will influence the atmospheres of planetary companions. It is worth noting that the oldest disk systems in the MAPS program exist around Herbig stars whereas the youngest systems are T Tauri stars. The UV-bright spectrum innate to Herbig stars may additionally influence the push of complex molecules towards the planet-forming midplane. Currently, the MAPS sample contains the bulk of the resolved CH₃CN and HC₃N data towards protoplanetary disks. To explore the effect of the stellar spectrum on CH₃CN and HC₃N emission, more disks with a wide range of stellar host masses would need to be observed.

To test the validity of this proposed end-stage chemistry, we first explored single point models representative of the disk midplane with corresponding cold temperatures and high gas densities (approximately 35 K, 5 × 10¹¹ mol cm⁻³). We varied the gas-to-dust mass ratio and initial carbon abundance among other physical and chemical variables including the nitrogen abundance, dust extinction and ionization rate (Table 1). We found that the gas phase CH₃CN abundance was the most sensitive to the gas-to-dust ratio and initial gas phase carbon abundance. We then produced a thermochemical model representing the disk around the Herbig Ae star HD 163296 (Table 1). This disk
<figure><img src="image_3.png" /><figcaption>**Fig. 1 |** A schematic highlighting the physical evolution of a disk and how that physical environment can affect the chemistry. At the top, we show a disk with a large amount of small dust that acts to block UV photons. As the</figcaption></figure>

small dust settles, UV photons make their way deeper into the disk, allowing for photodesorption of complex species off grains. Now, there is a cycle of carbon chemistry that can be observed in the gas phase.

<table><caption>**Table 1 |** Modelling parameters for TW Hya and HD 163296</caption><thead><tr><th rowspan="2">Parameters</th><th colspan="3">TW Hya</th><th colspan="3">HD 163296</th></tr><tr><th>Gas</th><th>Small dust</th><th>Large dust</th><th>Gas</th><th>Small dust</th><th>Large dust<sup>a</sup></th></tr></thead><tbody><tr><td>Mass (M<sub>c</sub>)</td><td>0.025</td><td>1.0×10<sup>-4</sup></td><td>4.0×10<sup>-4</sup></td><td>0.14</td><td>2.6×10<sup>-5</sup></td><td>0.024</td></tr><tr><td>ψ</td><td>1.1</td><td>1.2</td><td>1.2</td><td>1.08</td><td>1.08</td><td>1.08</td></tr><tr><td>γ</td><td>0.75</td><td>0.75</td><td>1.0</td><td>0.8</td><td>0.8</td><td>0.1</td></tr><tr><td>h<sub>c</sub> (au)</td><td>42</td><td>42</td><td>8.4</td><td>8.44</td><td>8.44</td><td>NA</td></tr><tr><td>r<sub>e</sub> (au)</td><td>400</td><td>400</td><td>400</td><td>165</td><td>165</td><td>NA</td></tr><tr><td>r<sub>in</sub> (au)</td><td>0.1</td><td>0.5</td><td>1</td><td>0.45</td><td>0.45</td><td>0.45</td></tr><tr><td>r<sub>out</sub> (au)</td><td>200</td><td>200</td><td>200</td><td>600</td><td>600</td><td>240</td></tr></tbody></table>

Final values of the TW Hya and HD 163296 models that reproduce CO, HD, CH₃CN, HCN and HCN observations when available. *r*<sub>in</sub> and *r*<sub>out</sub> are the radial inner and outer limits of the disk, respectively, beyond which there is assumed to be no gas nor dust. <sup>a</sup>The surface density of the large dust distribution in HD 163296 is empirically set by continuum observations, and thus it is not smooth and it is not dictated by the parametric equations. NA, not applicable.

is old (approximately 7.6 Myr)³³ and is nearby at 101 pc (ref. ³⁴) and has observed jets and winds³⁵,³⁶. The HD 163296 disk has been widely observed in multiple gas and dust tracers with high spatial resolution (-10 au) with clear gap and ring structures typically assumed to be associated with active planet formation³²,³⁷. There is bright CH₃CN emission coming from ~35 K gas as well as bright emission from HC₃N and HCN¹²,³⁸. Our modelling efforts follow that of Zhang et al.³⁹, and Calahan et al.⁴⁰, who set up a thermochemical model of the HD 163296 disk by reproducing the millimetre dust-continuum observations, the spectral-energy distribution (SED), the full line intensity and morphology of six CO isotopologue transitions, and the vertical distribution of the optically thick lines. The model of HD 163296 started with a gas-to-small dust ratio of the disk equal to 500 (ref. ³⁹), which was needed to reproduce the disk's SED.

## Results

To produce this end-stage chemical environment, we deplete the small dust mass by a factor of 10 throughout the disk of HD 163296 making the new gas-to-dust mass ratio above the pebble disk midplane equal

to 5,000. We then enhanced the initial gas phase carbon abundance in the system in the form of C, CH₄ or C₂H, increasing the overall gas phase carbon-to-oxygen ratio in both disks to above unity. There are two possible sources for excess carbon in protoplanetary disks, either through the destruction of refractory carbon grains⁴¹ or CO depletion through mechanisms such as reactions with ionized molecules and atoms such as He⁺ or H⁺ (ref. ⁴²) and a series of chemical and freeze-out processes. We note that while signatures of CO depletion are found in the HD 163296 disk³⁹,⁴⁰, CO destruction probably only occurs in environments with a high cosmic-ray flux (2 × 10⁻¹⁷ s⁻¹)⁴². Additionally, CO destruction would supply equal amounts of carbon and oxygen, while we seek to enhance carbon over oxygen. Our thermochemical model is run for a full mega-year (Myr), after which the chemistry reaches an equilibrium. Notable chemical feedback due to dust evolution is predicted to occur over scales of ~1 Myr (refs. ⁴³,⁴⁴), and thus we use ~1 Myr as an approximate length of time for the chemical environment to transition from 'early-stage' to 'late-stage' dust evolution and subsequently exist in a state of photochemical equilibrium. Gas phase chemical reactions and rates were taken from the chemical network derived in Bosman et al.⁴⁵, which in turn relies on the UMIST Database for Astrochemistry Rate12 version⁴⁶ (see Methods section for more details). We found that, regardless of the carrier of carbon, using a C/O = 1-2 and a factor of 10 depletion of small dust roughly reproduces line ratios and fluxes of the radial intensity profiles of CH₃CN, HC₃N and HCN (Fig. 2). In this proposed scenario, ~96% of the total mass of CH₃CN continues to reside frozen out onto grains, but the increase in UV flux allows for sufficient CH₃CN to exist and be formed in the gas to reproduce the observed radial intensity profiles and column densities. Figure 3 shows the two-dimensional number densities of CH₃CN and HC₃N. The inner ~20 au exhibited brighter or more centrally peaked emission than was seen in observations if the C/O ratio = 2 throughout the full disk. To counteract this, we set the C/O ratio to the ISM ratio (0.47), inside of (~20 au) where Zhang et al.³⁹ found an ISM ratio of CO/H₂ (Supplementary Fig. 2). The inner disk emission remains slightly brighter than that observed in HCN and CH₃CN (Fig. 2) with this alteration. This could be accounted for via a depletion in the nitrogen abundance within the N₂ ice line, a strong buildup of pebbles around the water ice line (~5 au), a lower HCN desorption energy or a combination of these effects. Additionally, the observations may also be affected by processes such as beam smearing and a
<figure><img src="image_4.png" /><figcaption>**Fig. 2 | Radial intensity profiles of the observed complex organic molecules and HCN towards the disk around HD 163296.** The molecules shown are CH₃CN, HCN and HC₃N (left to right with two transitions of CH₃CN shown in the first two panels). Solid thick lines in the background correspond to the observations derived from Ilee et al.¹² and Guzmán et al.⁷⁹ (utilizing the results of Law et al.⁵³),</figcaption></figure>

while dashed lines correspond to modelled radial profiles. Our final model includes an increase in C/O ratio beyond 20 au and a depletion of small dust and represents 1 Myr of chemistry. This model can simultaneously fit the flux, line ratios and general morphology of the observed radial profiles of these complex organic molecules.

<figure><img src="image_5.png" /><figcaption>**Fig. 3 | The radial and vertical number density distributions of CH₃CN and HC₃N.** The density distributions were determined by our final HD 163296 model with an increase in C/O ratio beyond 20 au and a depletion of small dust. This distribution produced the radial profiles shown in Fig. 2. A $z/r < 0.1$ is a good</figcaption></figure>

approximation for the midplane of the disk, and both CH₃CN and HC₃N emit partially from the midplane. A comparison can be made with Supplementary Fig. 6, which lacks the inclusion of small dust depletion.

higher dust opacity than modelled. A comparison model without a depletion in small dust mass is shown in Supplementary Fig. 5.

## Discussion

HC₃N and CH₃CN are built up in the gas from simple carbon and nitrogen-based volatiles (see Methods section 'Chemical reactions' for details). A reservoir of these more simple molecules is maintained in the gas phase because of photodesorption from dust grain surfaces by an enhanced UV field. The main destruction products from CH₃CN and HC₃N are simple volatiles that can cycle back to create larger nitrile molecules including their original parent molecule. Although there are enough complex organic molecules in the gas phase to observe bright emission, the majority of the CH₃CN, HC₃N and HCN near the midplane still remain frozen out onto grains. The carbon-rich gas reservoir and UV-dominated disk together allow for a cycle of carbon chemistry to remain active in the gas phase. This implies that actively accreting gas giants will build their atmosphere out of this complex nitrile-enhanced material. Gas-giant planets with atmospheres containing a chemical make-up with a C/O ratio > 1 can be explained by the natural evolution of dust and the observed high C/O ratios within protoplanetary disks. This environment could be extended to the inner disk in some cases, as studies such as Najita et al.⁴⁷ and Anderson et al.⁴⁸ posit a higher than solar C/O ratio within the inner disk to account for Spitzer observations of HCN and C₂H₂ around T Tauri stars.

The implications of this end-stage chemistry are far-reaching. Primarily, we put forward a chemically and physically coupled picture

of planet formation and its direct impact on the chemistry of forming planet atmospheres. Within the early stages of planet formation, pebble growth and accretion into solid planet cores has begun, and chemistry onto these cores are influenced primarily by the chemical make-up of large pebbles and their icy mantles. The chemistry active in the midplane during this stage of formation is dominated by X-rays and cosmic rays⁴⁹. After timescales of order 1 Myr, at the end-stage of pebble formation, small grains have grown and settled towards the midplane, allowing for UV photons to penetrate deeper in the disk than previously assumed. This excess UV flux in concert with an above solar C/O ratio produces a carbon-rich gas phase cycle of production and destruction in the gas surrounding actively forming planets. Bright emission from CH₃CN, HC₃N and other carbon-rich molecules emitting at cold temperatures are a signpost of this evolved chemical environment. These forming gas giants may accrete this surrounding gas and its chemical signature into their atmosphere, and may be responsible for high C/O measurements that have been observed in exo-planetary atmospheres as compared to their host star⁵⁰. In addition, the deeper penetration of UV photons pushes the CO and H₂ self-shielding layers deeper into the disk. Consequently, there are more ions such as C⁺ and H⁺ throughout the disk than would have been present with a regular (ISM) level of small dust surface area. As the ion-fraction increases so does the area of the disk that is subject to magneto-rotational instability (MRI). In our final model, the UV field increases by a factor of 3–5 in the atmosphere and between 1 and 2 near the midplane, and 13 times more gas mass is MRI active, most notably the gas midplane within 10 au and
<figure><img src="image_6.png" /><figcaption>**Fig. 4 | A comparison of the MRI active region within a non-elevated UV environment and an elevated UV environment.** The two left-most plots show regions within the HD 163296 disk that are MRI activated in an environment where small dust is depleted by a factor of 10 in total mass (gas/dust = 5,000, middle plot) and where small dust is not depleted (gas/dust = 500, left plot). The colour corresponds to the gas density in mol cm⁻³, highlighting the substantial</figcaption></figure>

increase in mass that is MRI active. The right-most plot shows a comparison of the UV field strength through a 'regular' disk and a dust depleted disk. The UV field increases upwards of a factor of 3–5 in the atmosphere of the disk and 1–2 below a $z/r = 0.2$. This has notable effects on the chemistry of the midplane. $G_0$ is a UV flux unit that is normalized to the typical ISM value. $G_0 = 1 = F_{UV} = 1.6 \times 10^{-3}$ ergs s⁻¹ cm⁻².

then at a $z/r = 0.1–0.2$ within 30 au (Fig. 4). This could be a source of accretion⁵¹ for older disks. Our proposed UV-dominated carbon-rich gas phase chemistry is a major shift in our understanding of the astro-chemistry of planet formation. This transition will have a strong effect on the composition of actively forming planets, disk MRI-activity and subsequent disk accretion.

## Methods

### Observations

For a thorough description of the observations and the techniques used to obtain the CLEAN-ed images and radial profiles of CH₃CN, HCN and HC₃N towards HD 163296 see Czekala et al.⁵², Law et al.⁵³ and Öberg et al.³². A description of the observations of CH₃CN towards TW Hya can be found in Loomis et al.¹⁵. A brief summary of these observations are as follows.

**HD 163296.** The data for HD 163296 is from the MAPS large programme (Project ID 2018.1.01055.L)³². The image cubes were produced using the tclean task in the Common Astronomy Software Applications (CASA) package, v.6.1.0 (ref.⁵⁴). Keplerian masks based on the disk geometric parameters were used in the CLEANing process and the final images were then corrected for the Jorsater and van Moorsel effect⁵⁵ to ensure that the image residuals are in units consistent with that of the CLEAN model. For all lines, we used the beam-circularized and UV-tapered images, which had synthesized beam sizes of 0.3". All radial intensity profiles were generated by deprojecting and azimuthally averaging zeroth moment maps using the GoFish python package.

**TW Hya.** CH₃CN was observed towards TW Hya as a part of ALMA project 2016.1.01046.S. Each emission line was individually imaged using CLEAN and the synthesized beam for each transition were matched using small UV tapers to 1.05" × 0.83". A Keplerian mask was used to extract the flux for each transition. See Loomis et al.¹⁵ for more details.

### Modelling

Simple single point models of the disk environment were utilized to quickly and efficiently understand the chemical impacts of different physical and initial chemical conditions. Our chemical network is derived from Bosman et al.⁴⁵, which in turn is derived from the UMIST 'RATE12' network⁴⁶, and for this study we disregarded most grain-surface chemical reactions to isolate gas phase formation of CH₃CN. After our results from the modelling suggested a higher gas/dust ratio and carbon content, we turned to more comprehensive thermochemical codes that model the thermal physics and chemical evolution throughout the whole disk. The code RAC2D (ref.⁵⁶) was used to create models of the disks around TW Hya and HD 163296. The 2D

temperature, density and molecular abundance results were used to simulate observations of each disk with a ray-tracing code: RADMC-3D (ref.⁵⁷). A brief description of the physical code of RAC2D is given below; a detailed description of the code can be found in Calahan et al.⁵⁸.

RAC2D takes into account a gas and dust structure and stellar radiation field and computes the gas and dust temperature and chemical structure over time. Our model consists of three mass components: gas, small dust and large dust grains. The spatial extent of each component is given by a global surface density distribution⁵⁹, which is widely used in protoplanetary disk modelling and corresponds to the self-similar solution of a viscously evolved disk:

$$ \Sigma(r) = \Sigma_c \left(\frac{r}{r_c}\right)^{-\gamma} \exp \left[ - \left(\frac{r}{r_c}\right)^{2-\gamma} \right], \quad (1) $$

$r_c$ is the characteristic radius at which the surface density is $\Sigma_c/e$ where $\Sigma_c$ is the characteristic surface density, and $\gamma$ is the power-law index that describes the radial behaviour of the surface density.

A two-dimensional density profile for the gas and dust populations can be derived from the surface density profile and a scale height:

$$ \rho(r, z) = \frac{\Sigma(r)}{\sqrt{2\pi h(r)}} \exp \left[ -\frac{1}{2} \left( \frac{z}{h(r)} \right)^2 \right], \quad (2) $$

$$ h = h_c \left( \frac{r}{r_c} \right)^{\psi}, \quad (3) $$

where $h_c$ is the scale height at the characteristic radius and $\psi$ is a power index that characterizes the flaring of the disk structure. The modeling parameters used for TW Hya and HD 163296 are shown in Table 1.

For both the TW Hya and HD 163296 models, each dust population follows an Mathis, Rumpl and Nordsieck grain distribution $n(a) \propto a^{-3.5}$ (ref.⁶⁰), where a indicates the size of the grain. The small dust grains have radii between $5 \times 10^{-3}$ and $1 \mu$m, and the large grains have radii between $5 \times 10^{-3}$ and $10^3 \mu$m. The large dust population is settled in the midplane with a smaller vertical extent and radial extent (gas extends - 5 and 2.5 times above and beyond, respectively). This settled large grain population is the result of dust evolution, namely growth in concert with vertical settling to the midplane and radial drift. For the HD 163296 model, the large grain population has a unique, non-smooth, surface density profile that reproduces the millimetre continuum observations of the HD 163296 disk³⁹,⁶¹. Opacity values for the dust are calculated based on Birnstiel et al.⁶². Large dust grains consist of water ice⁶³, silicates⁶⁴, troilites and refractory organics⁶⁵.
<table><caption>**Table 2 | Dust surface reactions**</caption><thead><tr><td>Reaction</td><td>Reference</td></tr></thead><tbody><tr><td>gH + gH → gH<sub>2</sub></td><td>Hasegawa et al.<sup>72</sup></td></tr><tr><td>gH + gOH → gH<sub>2</sub>O</td><td>Ioppolo et al.<sup>75</sup></td></tr><tr><td>gH + gH<sub>2</sub>O<sub>2</sub> → gH<sub>2</sub>O + gOH</td><td>Ioppolo et al.<sup>74</sup></td></tr><tr><td>gH + gCH<sub>3</sub>OH → gH<sub>2</sub> + gCH<sub>2</sub>OH</td><td>Extrapolated from Fuchs et al.<sup>76</sup></td></tr><tr><td>gH + gCH<sub>2</sub>OH → gCH<sub>3</sub>OH</td><td>Extrapolated from Fuchs et al.<sup>76</sup></td></tr><tr><td>gH<sub>2</sub> + gOH → gH<sub>2</sub>O + gH</td><td>Oba et al.<sup>77</sup></td></tr><tr><td>gOH + gCO → gCO<sub>2</sub> + gH<sup>a</sup></td><td>Ruffle and Herbst<sup>78</sup></td></tr><tr><td>gO + gCO → gCO<sub>2</sub><sup>a</sup></td><td>Goumans and Brown<sup>73</sup></td></tr><tr><td>gO + gHCO → gCO<sub>2</sub> + gH</td><td>Goumans and Brown<sup>73</sup></td></tr><tr><td>gH + gNH<sub>2</sub> → gNH<sub>3</sub></td><td>Allen and Robinson<sup>71</sup></td></tr></tbody></table>

The complete list of dust surface reactions accounted for in this study. <sup>a</sup>This reaction has additional special treatment for three-body reactions.

Small dust grains consist of 50% silicates and 50% refractory organics. Further discussion on the modelling efforts for TW Hya can be found in Calahan et al.<sup>58</sup> and for HD 163296 in Calahan et al.<sup>40</sup>.

The thermochemical model resulted in two-dimensional distributions of the gas and dust temperature, density and molecular abundances. These were used as inputs for the ray-tracing code RADMC-3D<sup>37</sup>. The molecular properties of CH<sub>3</sub>CN, HC<sub>3</sub>N and HCN were taken from the Leiden Atomic and Molecular Database<sup>66</sup>, with some molecular parameters updated according to data from the Cologne Database for Molecular Spectroscopy<sup>67,68</sup>. The result from RADMC-3D was a three-dimensional image cube of the molecular emission across velocity space. We utilized GoFish<sup>69</sup> to compress these three-dimensional images into zeroth moment maps and radial profiles, which were then directly compared to the azimuthally averaged observations.

## Chemical reactions

The chemical reaction network utilized in this work comes from Bosman et al.<sup>45</sup>, which in turn relies on the Rate12 version of the UMIST Database for Astrochemistry<sup>46</sup>, a network that is widely used across astrochemical modelling efforts. In our network there are 6,302 gas phase reactions and we have limited the grain-surface reactions to 12. We kept grain-surface reactions that involved the formation of H<sub>2</sub>, CH<sub>2</sub>OH, CH<sub>3</sub>OH, CO<sub>2</sub>, H<sub>2</sub>O and NH<sub>3</sub> because each of these species is well studied in the laboratory and comes with strong evidence for active two-body chemistry on dust grains<sup>70–77</sup> (Table 2). Both thermal adsorption and desorption are taken into account for every molecule in the network. Our network contains molecules with at most 11 carbon atoms and at most 12 total atoms. We run our thermochemical model for 1 Myr as the CH<sub>3</sub>CN and HC<sub>3</sub>N chemistry reaches an equilibrium after this time period (Supplementary Fig. 3). In our evolved disk model, the main formation pathway for CH<sub>3</sub>CN once the chemistry has reached equilibrium is as follows:

$$CH_3^+ + HCN \rightarrow CH_3CNH^+ + e^- \rightarrow CH_3CN + H$$

This reaction in the gas phase is the primary formation pathway for CH<sub>3</sub>CN, and thus there is a strong reliance on HCN existing in the gas phase even at cold temperatures below its measured sublimation temperature (-85–103 K (ref. 78)) and an ionization source (UV photons) to produce CH<sub>3</sub>^+.

$$N + CH_2CCH \rightarrow HC_3N + H_2$$

$$CN + C_2H_2 \rightarrow HC_3N + H$$

$$H + C_3N^- \rightarrow HC_3N + e^-$$

The formation of HC<sub>3</sub>N strongly relies on the existence of carbon-rich molecules including radicals (CN) and ions (C<sub>3</sub>N<sup>-</sup>).

## Data availability

The data that support the findings of this study can be obtained as part of the MAPS programme and are publicly available via alma-maps. info. This paper makes use of the following ALMA data: ADS/JAO. ALMA#2018.1.01055.L. and 2016.1.01046.S. Data regarding TW Hya can be obtained via data-rich figures in the online version of ref. 58. ALMA is a partnership of European Southern Observatory (ESO) (representing its member states), NSF (USA) and National Institutes of Natural Sciences (Japan), together with National Research Council (Canada), Ministry of Science and Technology and Academia Sinica Institute of Astronomy and Astrophysics (Taiwan), and Korea Astronomy and Space Science Institute (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, Associated Universities Inc/National Radio Astronomy Observatory and National Astronomical Observatory of Japan. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.

## Code availability

This study relied on the following publicly available coding packages: rac2d https://github.com/fjdu/rac-2d, RADMC-3D https://www.itau.uni-heidelberg.de/-dullemond/software/radmc-3d/ and GoFish https://github.com/richteague/gofish. TORUS is a private code developed by T. Harries and collaborators.

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## Acknowledgements

J.K.C. acknowledges support from the National Science Foundation Graduate Research Fellowship under grant no. DGE 1256260 and the National Aeronautics and Space Administration FINESST grant, under grant no. 80NSSC19K1534. E.A.B. acknowledges support from National Science Foundation (NSF) AAG grant no. 1907653. A.D.B. acknowledges support from NSF AAG grant no. 1907653. E.A.R. acknowledges support from NSF AST grant no. 1830728. J.B.B. acknowledges support from NASA through the NASA Hubble Fellowship grant no. HST-HF2-51429.001-A, awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. Support for J.H. was provided by NASA through the NASA Hubble Fellowship grant no. HST-HF2-51460.001-A awarded

by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract no. NAS5-26555. This work was supported by a grant from the Simons Foundation 686302 and by an award from the Simons Foundation 321183FY19 (to K.I.Ö.). This material is based upon work supported by the National Science Foundation under grant no. AST-1907832. J.D.I. acknowledges support from an STFC Ernest Rutherford Fellowship (no. ST/W004119/1) and a University Academic Fellowship from the University of Leeds. C.W. acknowledges financial support from the University of Leeds, the Science and Technology Facilities Council and UK Research and Innovation (grant nos. ST/T000287/1 and MR/ T040726/1). V.V.G. gratefully acknowledges support from FONDECYT Regular 1221352, ANID BASAL projects nos. ACE210002 and FB210003, and ANID - Millennium Science Initiative Program - NCN19_171. We thank T. Harries for help with and providing access to the TORUS modelling program.

## Author contributions

J.K.C. is the lead author, produced thermochemical models and led the group effort to put forward this new chemical theory. E.A.B. contributed to the text, provided advisement throughout the modelling process, contributed heavily to the scientific theory, and is a principle investigator of the large observing programme these models and theory rely on. A.D.B contributed to the text, provided advisement throughout the modelling process, and contributed heavily to the scientific theory and the SED modelling. E.A.R. contributed to the text and provided and contributed to the SED modelling. K.I.Ö. and V.V.G. contributed to the text and discussion on the scientific theory, and are principle investigators of the large observing programme these models and theory rely on. C.W. contributed to the text and discussion on the scientific theory, compiled the gas-grain chemical network and is a PI of the large observing programme these models and theory rely on. S.M.A., J.B.B., L.I.C., J.H., J.D.I., C.J.L, R.LG., R.T., D.J.W. and K.Z. contributed significantly to discussion of the theory and writing and editing of the text.

## Competing interests

The authors declare no competing interests

## Additional information

**Supplementary information** The online version contains supplementary material available at https://doi.org/10.1038/s41550-022-01831-8.

**Correspondence and requests for materials** should be addressed to Jenny K. Calahan.

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