CMDL Groups

WARNING

CMDL is undergoing significant revisions to improve conciseness and ease of use. This page will be undergoing updates as the type of CMDL groups is revised.

• Chemical
• Complex
• Component
• Container
• Flow Reaction
• Polymer
• Polymer Graph
• Reaction
• Reactor
• Reactor Graph
• Solution

Chemical

---

• Description: Describes a small-molecule chemical reference for use in an experiment.

• Member Of: None

• Reference Group Properties: None

• Properties:

  • Molecular Weight
  • Density
  • State
  • SMILES
  • InChi
  • InChi Key

• Example:

  chemical lLactide {
      molecular_weight: 144.12 g/mol;
      state: "solid";
      smiles: "C[C@H]1C(=O)O[C@H](C(=O)O1)C";
  }

Complex

---

• Description: Describes a reference of a macromolecular complex for use in experiments and assays. May consist of both polymeric and small-molecule components.
• Member Of: None
• Reference Group Properties:
  • Ratio
• Properties:
  • Critical Micelle Concentration
  • Hydrodynamic Radius
  • Hydrodynamic Radius Dispersity
  • Loading Capacity
• Example:

Component

---

• Description: Describes a physical component in a continuous flow reactor.

• Member Of:

  • Reactor Graph
  • Reactor

• Reference Group Properties: None

• Properties:

  • Length
  • Volume
  • Inner Diameter
  • Outer Diameter

• Example:

  Note: The following illustrate valid arrangements of the component group. For more detailed description of a reactor_graph setup see the flow reaction tutorial.

  reactor_graph FlowReactorA {
      reactor PolymerizationReactor {
          component Mixer {
              description: "PEEK T-Mixer (0.05 cm ID)";
              inner_diameter: 0.05 cm;
          };
  
          component Reactor_Tubing {
              description: "PFA Reactor Tubing (14 cm, 0.05 cm ID)";
              inner_diameter: 0.05 cm;
              length: 14 cm;
              volume: 0.02749 ml;
          };
      };
  }

  reactor_graph FlowReactorA {
      component Monomer_Syringe {
        description: "NormJect Syringe (10 mL)";
  	    volume: 10 ml;
  	    target: @Monomer_Pump;
    };
  }

Container

---

• Description: Describes a container group in a polymer_graph representation. Contains references to edges, nodes, and other container groups for describing the polymer structure

• Member Of:

  • Polymer Graph
  • Container

• Reference Group Properties: None

• Properties:

  • Nodes
  • Connections

• Example:

  polymer_graph mPEG_Graph {
      nodes: [ @eg_MeO ];
      <@eg_MeO.R => @PEG_Block.p_PEO.R>;
  
      container PEG_Block {
          nodes: [ @p_PEO ]
          <@p_PEO.Q => @p_PEO.R>;
      };
  }

Flow Reaction

---

• Description:
• Member Of:
• Properties:
• Example:

Polymer

---

• Description: Defines a polymer reference for use within an experiment record.

• Member Of: None

• Reference Group Properties: None

• Properties:

  • M_n
  • M_w
  • Dispersity
  • State
  • Tree
  • BigSMILES

• Example:

    polymer mPEG-OH {
        tree: @PEG_BASE;
        mn_avg: 5000 g/mol;
  
        @PEG_BASE.PEG_Block.p_PEO {
            degree_poly: 112.8
        };
    }

Polymer Graph

---

• Description: Defines a graph representation for a polymeric material.

• Member Of: None

• Reference Group Properties: None

• Properties:

  • Nodes
  • Connections

• Example:

  polymer_graph PEG_PLLA_Base {
      nodes: [ @eg_MeO ];
      <@eg_MeO.R => @PEG_Block.p_PEO.R>;
  
      container PEG_Block {
          nodes: [ @p_PEO ];
          <@p_PEO.Q => @p_PEO.R>;
      };
  
      container PLLA_Block {
          nodes: [ @p_Llac ];
          <@p_Llac.Q => @p_Llac.R>;
      };
  }

Reaction

---

• Description: Defines a batch reaction for an experimental record.

• Member Of: None

• Reference Group Properties:

  • Mass
  • Volume
  • Moles
  • Pressure
  • Roles

• Properties:

  • Temperature
  • Volume
  • Reaction Time

• Example:

  reaction BatchRxn {
      temperature: 22 degC;
      reaction_time: 10 s;
  
      @mPEG-OH {
          mass: 5 mg;
          roles: [ "initiator" ];
          limiting: true;
      };
  
      @kOtBu {
          mass: 5 mg;
          roles: [ "catalyst", "reagent" ];
      };
  
      @lLactide {
          mass: 1440 mg;
          roles: [ "monomer" ];
      };
  
      @THF {
          volume: 2 ml;
          roles: [ "solvent" ];
      };
  
      @mPEG-PLLA {
          roles: [ "product" ];
      };
  }

Reactor

---

• Description: Defines a container for component elements that belong to a single reactor element within a reactor graph. Treated as a single volume for computing residence times and stoichiometry.

• Member Of:

  • Reactor Graph

• Reference Group Properties: None

• Properties: None

• Example:

  Note: The following example would be nested inside a reactor graph

  reactor PolymerizationReactor {
      component Mixer {
          description: "PEEK T-Mixer (0.05 cm ID)";
          inner_diameter: 0.05 cm;
      };
  
      component Reactor_Tubing {
          description: "PFA Reactor Tubing (14 cm, 0.05 cm ID)";
          inner_diameter: 0.05 cm;
          length: 14 cm;
          volume: 0.02749 ml;
      };
  };

Reactor Graph

---

• Description: Defines a reactor graph representation that can be used within a flow reaction group.

• Member Of: None

• Reference Group Properties: None

• Properties: None

• Example:

  reactor_graph FlowReactorA {
      reactor PolymerizationReactor {
          component Mixer {
              description: "PEEK T-Mixer (0.05 cm ID)";
              inner_diameter: 0.05 cm;
          };
  
          component Reactor_Tubing {
              description: "PFA Reactor Tubing (14 cm, 0.05 cm ID)";
              inner_diameter: 0.05 cm;
              length: 14 cm;
              volume: 0.02749 ml;
          };
      };
  }

Solution

---

• Description: Describes a stock solution of reagents for use in a flow reaction.

• Member Of: None

• Reference Group Properties:

  • Mass
  • Volume
  • Moles
  • Pressure
  • Roles

• Properties: None

• Example:

    solution Catalyst_Solution {
        @KOMe {
            mass: 144 mg;
            roles: [ "catalyst" ];
        };
  
        @UreaCatalyst {
            mass: 500 mg;
            roles: [ "catalyst" ];
        };
  
        @THF {
            volume: 8 ml;
            roles: [ "solvent" ];
        };
    }