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CMDL Properties ​

Text Properties ​

BigSMILES ​

  • Description: Line notation for polymers.
  • Example:
cmdl
polymer PEO-PPO {
    big_smiles: "{[][<]OCC[>][<]}{[>][<]OC(C)C[>][]}";
}

Date ​

  • Description: Describes date of occurance of sample or experiment
  • Example:

Note: Currently only supports mm/dd/yy date format.

Description ​

  • Description: Additional description text for a component or other element.
  • Example:
cmdl
component Monomer_Syringe {
    description: "NormJect 25 ml syringe"
}

Inchi Key ​

  • Description: InChi key for a small-molecule chemical
  • Example:
cmdl
chemical TEA {
    inchi_key: "ZMANZCXQSJIPKH-UHFFFAOYSA-N";
}

NMR Nuclei ​

  • Description: Nucleus for a NMR spectra (e.g. 1H, 13C, 19F).
  • Example:
cmdl
sample Test_Sample_A {
    nmr Test_NMR {
        nmr_nucleas: "1H";
    };
}

Limiting ​

  • Description: Boolean value indicting that the chemical or polymer is a limiting reagent.
  • Example:
cmdl
reaction Example_RXN {
    @Reagent1 {
        mass: 100 mg;
        roles: [ "reagent" ];
        limiting: true;
    };
}

Reaction Roles ​

  • Description: Role of a particular chemical or polymer within a chemical reaction.
  • Example:
cmdl
reaction Example_RXN {
    @Reagent1 {
        mass: 100 mg;
        roles: [ "reagent" ];
        limiting: true;
    };
}

Reactor ​

  • Description: References which reactor is used for a particular flow reaction.
  • Example:
cmdl
flow_reaction Example_RXN {
    reactor: @Example_Reactor;
}

Record Id ​

  • Description: Experimental id assigned by a database system, such as the MongoDB ObjectId.
  • Example:
cmdl
metadata {
    record_id: "620f207950c16f9dax5z3485";
}

SMILES ​

  • Description: SMILES line notation for small-molecules
  • Example:
cmdl
chemical THF {
    smiles: "C1CCOC1";
}

Tags ​

  • Description: Tags for an experiment or other record. Used in the metadata group.
  • Example:
cmdl
metadata {
    tags: [ "polymerization", "ring-opening_polymerization" ];
}

Target ​

  • Description: Node to which the current node is connected to within a reactor graph.
  • Example:

Note: The example is only a fragment of a full reactor_graph definition. See the continuous flow tutorial for a full example.

cmdl
reactor_graph Test_Reactor {
    component Monomer_Syringe {
        target: @Monomer_Pump
    };

    component Monomer_Pump {
        target: @Reactor_T_Mixer;
    }
}

Structure ​

  • Description: Reference property which assigns a reactor graph/composite tree representation to a polymer reference.
  • Example:
cmdl
polymer mPEG-OH {
   structure: @PEG_BASE;
   mn_avg: 5000 g/mol;

   @PEG_BASE.PEG_Block.p_PEO {
      degree_poly: 112.8
   };
}

Physical Properties ​

Collection Time ​

  • Description: Time after start of the continous flow run at which the sample was collected.
  • Units:
  • Example: in progress

Conversion ​

  • Description: Percent conversion of a given chemical species in a reaction.
  • Units:
    • Percent (%)
  • Example:
cmdl
char_data Test-I-123B-nmr {
   time_point: 10 s;
   sample_id: "Test-I-123B";
   technique: "nmr";

   @lLactide {
      conversion: 99%;
   };

   @mPEG-PLLA.PLLA_Block.lLac {
      degree_poly: 80;
   };
}

Degree of Polymerization ​

  • Description: Degree of polymerization of a polymeric material or component of a polymeric material.
  • Units: None
  • Example:
cmdl
char_data Test-I-123B-nmr {
   time_point: 10 s;
   sample_id: "Test-I-123B";
   technique: "nmr";

   @lLactide {
      conversion: 99%;
   };

   @mPEG-PLLA.PLLA_Block.lLac {
      degree_poly: 80;
   };
}

Density ​

  • Description: Density of a chemical compound. Required for chemical references whose physical state is a liquid and where volumetric quantity is used in a reaction or solution.
  • Units:
    • g/ml
  • Example:
cmdl
chemical THF {
    molecular_weight: 72.1 g/mol;
    density: 0.88 g/ml;
    smiles: "C1CCOC1";
}

Dispersity ​

  • Description: Molecular weight dispersity of a polymeric material.
  • Units: None
  • Example:
cmdl
char_data Test-I-123A-gpc {
   time_point: 5 s;
   sample_id: "Test-I-123A";
   technique: "gpc";

   @mPEG-PLLA {
      dispersity: 1.45;
      mn_avg: 14000 g/mol;
   };
}

Flow Rate ​

  • Description: Rate of flow for a given input for a flow reaction.
  • Units:
    • ml/min
  • Example:
cmdl
flow_reaction FlowTest {
    reactor: @ReactorTest;
    temperature: 22 degC;

    @Monomer_Solution {
      flow_rate: 10 ml/min;
    };

    @Catalyst_Solution {
      flow_rate: 10 ml/min;
    };

    @Quench_Solution {
      flow_rate: 10 ml/min;
    };
}

Glass Transition Temperature ​

  • Description: Glass transition temperature of a polymeric material.
  • Units:
    • degC
    • degK
  • Example:

HC50 ​

  • Description: HC50 value of a chemical compound or material.
  • Units:
    • mg/l
    • µg/ml
  • Example: in progress

Hydrodynamic Diameter ​

  • Description: Hydrodynamic diameter (Dh) of a material.
  • Units:
    • nm
  • Example: in progress

Hydrodynamic Diameter Dispersity ​

  • Description: Dispersity of the hydrodynamic diameter of a material.
  • Units: None
  • Example: in progress

Lambda Max Absorbtion ​

  • Description: Absorbtion maximum of a compound or material.
  • Units:
    • nm
  • Example: in progress

Lamda Max Emission ​

  • Description: Emission maximum of a compound or material.
  • Units:
  • Example:

Length ​

  • Description: Length of a reactor component or other element.
  • Units:
  • Example:
cmdl
reactor QuenchReactor {
    component Quench_Mixer {
        description: "PEEK T-Mixer (0.1 cm ID) ";
        inner_diameter: 0.1 cm;
        target: @Quench_Reactor;
    };
    component Quench_Reactor {
        description: "PFA Reactor Tubing (2 cm, 0.1 cm ID)";
        inner_diameter: 0.1 cm;
        length: 2 cm;
        volume: 0.0157 ml;
        target: @Collection;
    };
}

Loading Capacity ​

  • Description: Loading capacity of a micelle or other superamolecular complex for a small-molecule cargo
  • Units:
    • wt %;
  • Example: in progress

Molecular Weight ​

  • Description: Molecular weight of a chemical compound
  • Units:
    • g/mol
  • Example:
cmdl
chemical THF {
    molecular_weight: 72.1 g/mol;
    density: 0.88 g/ml;
    smiles: "C1CCOC1";
}

Outer Diameter ​

  • Description: Outer diameter of a piece of tubing.
  • Units:
    • mm
  • Example: in progress

Inner Diameter ​

  • Description: Inner diameter of a piece of tubing
  • Units:
    • mm
  • Example:
cmdl
reactor QuenchReactor {
    component Quench_Mixer {
        description: "PEEK T-Mixer (0.1 cm ID) ";
        inner_diameter: 0.1 cm;
        target: @Quench_Reactor;
    };
}

Mn ​

  • Description: Number average molecular weight.
  • Units:
    • g/mol
    • Da
    • kDa
  • Example:
cmdl
char_data Test-I-123A-gpc {
   time_point: 5 s;
   sample_id: "Test-I-123A";
   technique: "gpc";

   @mPEG-PLLA {
      dispersity: 1.45;
      mn_avg: 14000 g/mol;
   };
}

Mw ​

  • Description: Weighte average molecular weight.
  • Units:
    • g/mol
    • Da
    • kDa
  • Example:
cmdl
char_data Test-I-123A-gpc {
   time_point: 5 s;
   sample_id: "Test-I-123A";
   technique: "gpc";

   @mPEG-PLLA {
      dispersity: 1.45;
      mn_avg: 14000 g/mol;
      mw_avg: 16080 g/mol;
   };
}

Mass ​

  • Description: Mass of a chemical compound.
  • Units:
  • Example:
cmdl
reaction BatchRxn {
   temperature: 22 degC;
   reaction_time: 10 s;

   @kOtBu {
      mass: 5 mg;
      roles: [ "catalyst", "reagent" ];
   };
}

Melting Temperature ​

  • Description: Melting temperature of a chemical compound.
  • Units:
    • degc
    • degK
  • Example: in progress

Minimum Inhibitory Concentration ​

  • Description: Minimum inhibitory concentration of a chemical compound or material.
  • Units:
    • mg/l
    • µg/ml
  • Example: in progress

Moles ​

  • Description: Moles of a chemical compound.
  • Units:
  • Example:
cmdl
reaction BatchRxn {
   temperature: 22 degC;
   reaction_time: 10 s;

   @kOtBu {
      moles: 0.3 mmol;
      roles: [ "catalyst", "reagent" ];
   };
}

Onset Temperature ​

  • Description: Onset temperature for degredation of a material.
  • Units:
  • Example: in progress

Pressure ​

  • Description: Pressure of a chemical compound.
  • Units:
  • Example: in progress

Pressure Rate ​

  • Description: Rate of pressure change in a process.
  • Units:
  • Example: in progress

Reaction Time ​

  • Description: Total time of a chemical reaction.
  • Units:
  • Example:

Run Time ​

  • Description:
  • Units:
  • Example:
cmdl
reaction BatchRxn {
   temperature: 22 degC;
   reaction_time: 10 s;

   @kOtBu {
      moles: 0.3 mmol;
      roles: [ "catalyst", "reagent" ];
   };
}

Sublimation Temperature ​

  • Description: Temperature of sublimation of a substance.
  • Units:
  • Example: in progress

Time Point ​

  • Description: Time point, during the reaction time, for a sample being analyzed.
  • Units:
  • Example:
cmdl
char_data Test-I-123A-gpc {
   time_point: 5 s;
   sample_id: "Test-I-123A";
   technique: "gpc";

   @mPEG-PLLA {
      dispersity: 1.45;
      mn_avg: 14000 g/mol;
      mw_avg: 16080 g/mol;
   };
}

Treatment Concentration ​

  • Description: Concentration at which a chemical compound or material is administered.
  • Units:
  • Example: in progress

Temperature ​

  • Description: Temperature of a substance or process.
  • Units:
  • Example:
cmdl
reaction BatchRxn {
   temperature: 22 degC;
   reaction_time: 10 s;

   @kOtBu {
      moles: 0.3 mmol;
      roles: [ "catalyst", "reagent" ];
   };
}

Wavelength ​

  • Description: Wavelength of a light-driven process
  • Units:
  • Example: in progress

Wavenumber ​

  • Description: Wavenumber of a stretching frequency
  • Units:
  • Example: in progress

Volume ​

  • Description: Volume of a chemical or reactor
  • Units:
  • Example:
cmdl
reaction BatchRxn {
   temperature: 22 degC;
   reaction_time: 10 s;

   @THF {
      volume: 0.3 ml;
      roles: [ "solvent" ];
   };
}

Yield ​

  • Description: Yield of a chemical or material as determined by a given characterization technique.
  • Units:
  • Example:
cmdl
char_data Test-I-123B-nmr {
   time_point: 10 s;
   sample_id: "Test-I-123B";
   technique: "nmr";

   @lLactide {
      conversion: 99%;
   };

   @mPEG-PLLA {
      yield: 80%;
   }
}

Zeta Potential ​

  • Description: Zeta potential of a material.
  • Units:
  • Example: in progress