Login / Signup

RMG Database for Chemical Property Prediction.

Matthew S JohnsonXiaorui DongAlon Grinberg DanaYunsie ChungDavid FarinaRyan J GillisMengjie LiuNathan W YeeKatrin BlondalEmily J MazeauColin A GrambowA Mark PayneKevin A SpiekermannHao-Wei PangC Franklin GoldsmithRichard H WestWilliam H Green
Published in: Journal of chemical information and modeling (2022)
The Reaction Mechanism Generator (RMG) database for chemical property prediction is presented. The RMG database consists of curated datasets and estimators for accurately predicting the parameters necessary for constructing a wide variety of chemical kinetic mechanisms. These datasets and estimators are mostly published and enable prediction of thermodynamics, kinetics, solvation effects, and transport properties. For thermochemistry prediction, the RMG database contains 45 libraries of thermochemical parameters with a combination of 4564 entries and a group additivity scheme with 9 types of corrections including radical, polycyclic, and surface absorption corrections with 1580 total curated groups and parameters for a graph convolutional neural network trained using transfer learning from a set of >130 000 DFT calculations to 10 000 high-quality values. Correction schemes for solvent-solute effects, important for thermochemistry in the liquid phase, are available. They include tabulated values for 195 pure solvents and 152 common solutes and a group additivity scheme for predicting the properties of arbitrary solutes. For kinetics estimation, the database contains 92 libraries of kinetic parameters containing a combined 21 000 reactions and contains rate rule schemes for 87 reaction classes trained on 8655 curated training reactions. Additional libraries and estimators are available for transport properties. All of this information is easily accessible through the graphical user interface at https://rmg.mit.edu. Bulk or on-the-fly use can be facilitated by interfacing directly with the RMG Python package which can be installed from Anaconda. The RMG database provides kineticists with easy access to estimates of the many parameters they need to model and analyze kinetic systems. This helps to speed up and facilitate kinetic analysis by enabling easy hypothesis testing on pathways, by providing parameters for model construction, and by providing checks on kinetic parameters from other sources.
Keyphrases
  • convolutional neural network
  • adverse drug
  • molecular dynamics simulations
  • emergency department
  • randomized controlled trial
  • healthcare
  • rna seq
  • systematic review
  • resistance training
  • machine learning