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Model[Molecule]

Model information for a group of atoms held together via covalent and/or ionic bonds.

Organizational Information

    Name

    Name of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: A string.

    ID

    ID of this Object.
    Format: Single
    Class: String
    Programmatic Pattern: _String
    Pattern Description: The ID of this object.

    Object

    Object of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Model[Molecule, _String]
    Pattern Description: The object reference of this object.

    Type

    Type of this Object.
    Format: Single
    Class: Expression
    Programmatic Pattern: Model[Molecule]
    Pattern Description: Model[Molecule]

    Notebook

    Notebook this object belongs to.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Pattern Description: An object of that matches ObjectP[Object[LaboratoryNotebook]].

    Synonyms

    List of possible alternative names this model goes by.
    Format: Multiple
    Class: String
    Programmatic Pattern: _String

    Authors

    The people who created this model.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[User]

    Molecule

    The chemical structure that represents this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: MoleculeP | _?StructureQ | _?StrandQ

    UNII

    Unique Ingredient Identifier of this molecule, as given by the unified identification scheme of the FDA.
    Format: Single
    Class: String
    Programmatic Pattern: _String

    InChI

    The International Chemical Identifer (InChI) that uniquely identifies this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: InChIP

    InChIKey

    The hashed version of the International Chemical Identifer (InChI) that uniquely identifies this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: InChIKeyP

    CAS

    Chemical Abstracts Service (CAS) registry number for this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: _String

    IUPAC

    International Union of Pure and Applied Chemistry (IUPAC) name for this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: _String

Inventory

    DefaultSampleModel

    Specifies the model of sample that will be used if this model is specified to be used in an experiment.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Sample]

Physical Properties

    MolecularFormula

    Chemical formula of this molecule (e.g. H2O, NH2, etc.).
    Format: Single
    Class: String
    Programmatic Pattern: _String

    DetectionLabel

    Indicates whether this molecule (e.g. Alexa Fluor 488) can be attached to another molecule and act as a tag that can indicate the presence and amount of the other molecule.
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    AffinityLabel

    Indicates whether this molecule has high binding capacity with certain material and can be attached to another molecule (e.g. His Tag).
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    DetectionLabels

    Indicates the tags (e.g. Alexa Fluor 488) that the molecule contains, which can indicate the presence and amount of the molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: ObjectP[Model[Molecule]]
    Relation: Model[Molecule]

    AffinityLabels

    Indicates the tags that the molecule contains (e.g. His Tag), which has high binding capacity with other materials.
    Format: Multiple
    Class: Link
    Programmatic Pattern: ObjectP[Model[Molecule]]
    Relation: Model[Molecule]

    Targets

    Target molecules (e.g. proteins or antibodies) to which this molecule binds selectively.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link

    State

    The physical state of a pure sample of this molecule at room temperature and pressure.
    Format: Single
    Class: Expression
    Programmatic Pattern: Solid | Liquid | Gas

    Density

    The density of a pure sample of this molecule at room temperature and pressure.
    Format: Single
    Class: Real
    Unit: 1 gram per milliliter
    Programmatic Pattern: 0 Gram Hold[GreaterP[------ Milli]] Liter

    ExtinctionCoefficients

    A measure of how strongly this molecule absorbs light at a particular wavelength.
    Format: Multiple

    [Wavelength]

      Header: Wavelength
      Class: VariableUnit

    [ExtinctionCoefficient]

      Header: ExtinctionCoefficient
      Class: VariableUnit

    Fluorescent

    Indicates if this molecule can re-emit light upon excitation.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    FluorescenceExcitation Maximums

    The wavelengths corresponding to the highest peak of each Fluorescent moiety's excitation spectrum.
    Format: Multiple
    Class: Real
    Unit: 1 nanometer
    Programmatic Pattern: GreaterP[0 Nanometer]

    FluorescenceEmissionMaximums

    For each member of FluorescenceExcitationMaximums, the corresponding highest peak of the fluorescent moiety's emission spectrum.
    Format: Multiple
    Class: Real
    Unit: 1 nanometer
    Programmatic Pattern: GreaterP[0 Nanometer]

    MolecularWeight

    The molecular weight of this molecule (the mass of one mole of the molecule).
    Format: Single
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    ExactMass

    The most abundant mass of the molecule calculated using the natural abundance of isotopes on Earth.
    Format: Single
    Class: Real
    Unit: 1 gram per mole
    Programmatic Pattern: 0 Gram Hold[GreaterP[------]] Mole

    StructureImageFile

    An image depicting the molecule's chemical structure.
    Format: Single
    Class: Link
    Programmatic Pattern: ObjectP[Object[EmeraldCloudFile]]

    StructureFile

    A file that contains the molecule's chemical structure.
    Format: Single
    Class: Link
    Programmatic Pattern: ObjectP[Object[EmeraldCloudFile]]

    MeltingPoint

    Melting temperature of a pure sample of this molecule at atmospheric pressure.
    Format: Single
    Class: Real
    Unit: 1 degree Celsius
    Programmatic Pattern: GreaterP[0 Kelvin]

    BoilingPoint

    Temperature at which a pure sample of this molecule boils under atmospheric pressure.
    Format: Single
    Class: Real
    Unit: 1 degree Celsius
    Programmatic Pattern: GreaterP[0 Kelvin]

    VaporPressure

    Vapor pressure of a pure sample of this molecule at room temperature.
    Format: Single
    Class: Real
    Unit: 1 kilopascal
    Programmatic Pattern: GreaterEqualP[0 Kilo Pascal]

    Viscosity

    The viscosity of a pure sample of this molecule at room temperature.
    Format: Single
    Class: Real
    Unit: 1 second pascal
    Programmatic Pattern: GreaterEqualP[0 Pascal Second]

    pKa

    The logarithmic acid dissociation constants of a pure sample of this molecule at room temperature.
    Format: Multiple
    Class: Real
    Programmatic Pattern: NumericP

    NMRSolventPeak

    The known chemical shift for a given nucleus for this molecule.
    Format: Multiple

    [Nucleus]

      Header: Nucleus
      Class: String

    [ChemicalShift]

      Header: ChemicalShift
      Class: Real
      Unit: 1 part per million

    Chiral

    Indicates if this molecule is a enantiomer, that cannot be superposed on its mirror image by any combination of rotations and translations.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Racemic

    Indicates if this molecule represents equal amounts of left- and right-handed enantiomers of a chiral molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    EnantiomerForms

    If this molecule is racemic (Racemic -> True), indicates models for its left- and right-handed enantiomers.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Molecule]

    RacemicForm

    If this molecule is one of the enantiomers (Chiral -> True), indicates the model for its racemic form.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Molecule]

    EnantiomerPair

    If this molecule is one of the enantiomers (Chiral -> True), indicates the model for its non-superimposable mirror imaged molecule (stereoisomer).
    Format: Single
    Class: Link
    Programmatic Pattern: _Link
    Relation: Model[Molecule]

    pH

    The logarithmic concentration of hydrogen ions of a pure sample of this molecule at room temperature and pressure.
    Format: Single
    Class: Real
    Programmatic Pattern: RangeP[0, 14]

Health & Safety

    Radioactive

    Indicates if this molecule emits substantial ionizing radiation.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Ventilated

    Indicates if a pure sample of this molecule must be handled in a ventilated enclosures.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Flammable

    Indicates if a pure sample of this molecule is easily set aflame at room temperature and pressure.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Acid

    Indicates if pure samples of this molecule are strong acids (pH <= 2).
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Base

    Indicates if pure samples of this molecule are strong acids (pH >= 12).
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Pyrophoric

    Indicates if pure samples of this molecule can ignite spontaneously upon exposure to air.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    WaterReactive

    Indicates if pure samples of this molecule react spontaneously upon exposure to water.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Fuming

    Indicates if pure samples of this molecule emit fumes spontaneously when exposed to air.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    HazardousBan

    Indicates this molecule is currently banned from usage in the ECL because the facility isn't yet equiped to handle it.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    ExpirationHazard

    Indicates if pure samples of this molecule become hazardous once they are expired and must be automatically disposed of when they pass their expiration date.
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    ParticularlyHazardous Substance

    Indicates if special precautions should be taken in handling this molecule, as indicated by the MSDS classification.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    DrainDisposal

    Indicates if this molecule may be safely disposed down a standard drain.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    Pungent

    Indicates if pure samples of this molecule have a strong odor.
    Format: Single
    Class: Boolean
    Programmatic Pattern: BooleanP

    MSDSRequired

    Indicates if an MSDS is required for this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    MSDSFile

    The PDF of the MSDS (Materials Saftey Data Sheet) of this molecule.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link

    NFPA

    The National Fire Protection Association (NFPA) 704 hazard diamond classification for this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: NFPAP

    DOTHazardClass

    The Department of Transportation hazard classification for this molecule.
    Format: Single
    Class: String
    Programmatic Pattern: DOTHazardClassP

    BiosafetyLevel

    The Biosafety classification for this molecule.
    Format: Single
    Class: Expression
    Programmatic Pattern: BiosafetyLevelP

Storage Information

    LightSensitive

    Indicates if this molecule reacts or degrades in the presence of light.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

Compatibility

    IncompatibleMaterials

    A list of materials that would be damaged if wetted by this molecule.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: MaterialP | None

    LiquidHandlerIncompatible

    Indicates if pure samples of this molecule cannot be reliably aspirated or dispensed on an automated liquid handling robot.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    PipettingMethod

    The pipetting parameters used to manipulate pure samples of this model.
    Format: Single
    Class: Link
    Programmatic Pattern: _Link

    UltrasonicIncompatible

    Indicates if pure samples of this molecule cannot be performed via the ultrasonic distance method due to vapors interfering with the reading.
    Format: Single
    Class: Expression
    Programmatic Pattern: BooleanP

    FluorescenceLabelingTarget

    The types of molecules that cause fluorescence enhancement upon binding to this fluorophore.
    Format: Multiple
    Class: Expression
    Programmatic Pattern: FluorescenceLabelingTargetTypeP

Experimental Results

    ReferenceNMR

    Data that exemplify the expected NMR spectrum for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

    ReferenceMassSpectra

    Data that exemplify the expected mass spectrometry spectrum for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

    ReferenceChromatographs

    Data that exemplify expected analytical HPLC traces for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

    ReferenceTLC

    Data that exemplify expected thin layer chromatography results for this molecule.
    Format: Multiple
    Class: Link
    Programmatic Pattern: _Link
    Relation: Object[Data]

Analysis & Reports

Last modified on Mon 26 Sep 2022 15:43:55