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tokens: We thank an anonymous referee for useful comments that helped to improve the paper. We are grateful to Ted Bergin for the use of his non-equilibrium code. We benefited from many discussions with him and his (former) graduate student Ilse Cleeves on astrochemical codes and analysis. Additionally, we thank Til Birnstiel, Roy van Boekel, Cornelis Dullemond, Thomas Henning, Hubert Klahr, Oliver Gressel and Dmitry Semenov for interesting discussions and feedback on this work. The work made use of the Shared Hierarchical Academic Research Computing Network (SHARCNET: www.sharcnet.ca ) and Compute/Calcul Canada. AJC acknowledges funding from the National Sciences and engineering Research Council (NSERC) through the Alexander Graham Bell CGS/PGS Doctoral Scholarship. REP is supported by an NSERC Discovery Grant. MA acknowledges funding by an Ontario Graduate Scholarship (OGS) and NSERC CGS-M scholarship. REP also thanks the MPIA and the Institut fur Theoretische Astrophysik (ITA) in the Zentrum fur Astronomie Heidelberg for support during his sabbatical leave (2015/16) during the final stages of this project. AJC also thanks MPIA and the Institut fur Theoretische Astrophysik (ITA) in the Zentrum fur Astronomie Heidelberg for their hospitality during his 1 month stay in 2016.