valuesets 0.3.1__py3-none-any.whl

valuesets/schema/chemistry/reactions.yaml

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+name: reactions
+title: Chemical Reactions Value Sets
+description: 'Value sets for chemical reactions, reaction types, mechanisms, and kinetics.
+
+  '
+id: https://w3id.org/valuesets/chemistry/reactions
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  RXNO: http://purl.obolibrary.org/obo/RXNO_
+  MOP: http://purl.obolibrary.org/obo/MOP_
+  REX: http://purl.obolibrary.org/obo/REX_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  GO: http://purl.obolibrary.org/obo/GO_
+  EC: https://enzyme.expasy.org/EC/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  reaction_type:
+    description: Types of chemical reactions
+    range: ReactionTypeEnum
+  reaction_mechanism:
+    description: Reaction mechanism types
+    range: ReactionMechanismEnum
+  catalyst_type:
+    description: Types of catalysts
+    range: CatalystTypeEnum
+  reaction_condition:
+    description: Reaction conditions
+    range: ReactionConditionEnum
+  reaction_rate_order:
+    description: Reaction rate orders
+    range: ReactionRateOrderEnum
+  enzyme_class:
+    description: EC enzyme classification
+    range: EnzymeClassEnum
+  solvent_class:
+    description: Classes of solvents
+    range: SolventClassEnum
+  thermodynamic_parameter:
+    description: Thermodynamic parameters
+    range: ThermodynamicParameterEnum
+enums:
+  ReactionTypeEnum:
+    description: Types of chemical reactions
+    permissible_values:
+      SYNTHESIS:
+        description: Combination reaction (A + B → AB)
+        annotations:
+          aliases: combination, addition
+          pattern: A + B → AB
+      DECOMPOSITION:
+        description: Breakdown reaction (AB → A + B)
+        annotations:
+          aliases: analysis
+          pattern: AB → A + B
+      SINGLE_DISPLACEMENT:
+        description: Single replacement reaction (A + BC → AC + B)
+        annotations:
+          aliases: single replacement
+          pattern: A + BC → AC + B
+      DOUBLE_DISPLACEMENT:
+        description: Double replacement reaction (AB + CD → AD + CB)
+        annotations:
+          aliases: double replacement, metathesis
+          pattern: AB + CD → AD + CB
+      COMBUSTION:
+        description: Reaction with oxygen producing heat and light
+        annotations:
+          reactant: oxygen
+          products: usually CO2 and H2O
+      SUBSTITUTION:
+        title: substitution reaction
+        description: Replacement of one group by another
+        meaning: MOP:0000790
+        annotations:
+          subtypes: SN1, SN2, SNAr
+      ELIMINATION:
+        title: elimination reaction
+        description: Removal of atoms/groups forming double bond
+        meaning: MOP:0000656
+        annotations:
+          subtypes: E1, E2, E1cB
+      ADDITION:
+        title: addition reaction
+        description: Addition to multiple bond
+        meaning: MOP:0000642
+        annotations:
+          subtypes: electrophilic, nucleophilic, radical
+      REARRANGEMENT:
+        description: Reorganization of molecular structure
+        annotations:
+          examples: Claisen, Cope, Wagner-Meerwein
+      OXIDATION:
+        description: Loss of electrons or increase in oxidation state
+        annotations:
+          electron_change: loss
+      REDUCTION:
+        description: Gain of electrons or decrease in oxidation state
+        annotations:
+          electron_change: gain
+      DIELS_ALDER:
+        title: Diels-Alder reaction
+        description: '[4+2] cycloaddition reaction'
+        meaning: RXNO:0000006
+        annotations:
+          type: pericyclic
+          components: diene + dienophile
+      FRIEDEL_CRAFTS:
+        title: Friedel-Crafts reaction
+        description: Electrophilic aromatic substitution
+        meaning: RXNO:0000369
+        annotations:
+          subtypes: alkylation, acylation
+      GRIGNARD:
+        title: Grignard reaction
+        description: Organometallic addition reaction
+        meaning: RXNO:0000014
+        annotations:
+          reagent: RMgX
+      WITTIG:
+        title: Wittig reaction
+        description: Alkene formation from phosphonium ylide
+        meaning: RXNO:0000015
+        annotations:
+          product: alkene
+      ALDOL:
+        title: aldol condensation
+        description: Condensation forming β-hydroxy carbonyl
+        meaning: RXNO:0000017
+        annotations:
+          mechanism: enolate addition
+      MICHAEL_ADDITION:
+        title: Michael addition
+        description: 1,4-addition to α,β-unsaturated carbonyl
+        meaning: RXNO:0000009
+        annotations:
+          type: conjugate addition
+  ReactionMechanismEnum:
+    description: Reaction mechanism types
+    permissible_values:
+      SN1:
+        description: Unimolecular nucleophilic substitution
+        annotations:
+          rate_determining: carbocation formation
+          stereochemistry: racemization
+      SN2:
+        description: Bimolecular nucleophilic substitution
+        annotations:
+          rate_determining: concerted
+          stereochemistry: inversion
+      E1:
+        description: Unimolecular elimination
+        annotations:
+          intermediate: carbocation
+      E2:
+        description: Bimolecular elimination
+        annotations:
+          requirement: antiperiplanar
+      E1CB:
+        description: Elimination via conjugate base
+        annotations:
+          intermediate: carbanion
+      RADICAL:
+        description: Free radical mechanism
+        annotations:
+          initiation: homolytic cleavage
+      PERICYCLIC:
+        description: Concerted cyclic electron reorganization
+        annotations:
+          examples: Diels-Alder, Cope
+      ELECTROPHILIC_AROMATIC:
+        description: Electrophilic aromatic substitution
+        annotations:
+          intermediate: arenium ion
+      NUCLEOPHILIC_AROMATIC:
+        description: Nucleophilic aromatic substitution
+        annotations:
+          requirement: electron-withdrawing groups
+      ADDITION_ELIMINATION:
+        description: Addition followed by elimination
+        annotations:
+          intermediate: tetrahedral
+  CatalystTypeEnum:
+    description: Types of catalysts
+    permissible_values:
+      HOMOGENEOUS:
+        description: Catalyst in same phase as reactants
+        annotations:
+          phase: same as reactants
+          examples: acid, base, metal complexes
+      HETEROGENEOUS:
+        description: Catalyst in different phase from reactants
+        annotations:
+          phase: different from reactants
+          examples: Pt/Pd on carbon, zeolites
+      ENZYME:
+        title: cofactor
+        description: Biological catalyst
+        meaning: CHEBI:23357
+        annotations:
+          type: protein
+          specificity: high
+      ORGANOCATALYST:
+        description: Small organic molecule catalyst
+        annotations:
+          metal_free: 'true'
+          examples: proline, thiourea
+      PHOTOCATALYST:
+        description: Light-activated catalyst
+        annotations:
+          activation: light
+          examples: TiO2, Ru complexes
+      PHASE_TRANSFER:
+        description: Catalyst facilitating reaction between phases
+        annotations:
+          function: transfers reactant between phases
+      ACID:
+        description: Acid catalyst
+        annotations:
+          mechanism: proton donation
+      BASE:
+        description: Base catalyst
+        annotations:
+          mechanism: proton abstraction
+      METAL:
+        description: Metal catalyst
+        annotations:
+          examples: Pd, Pt, Ni, Ru
+      BIFUNCTIONAL:
+        description: Catalyst with two active sites
+        annotations:
+          sites: multiple
+  ReactionConditionEnum:
+    description: Reaction conditions
+    permissible_values:
+      ROOM_TEMPERATURE:
+        description: Standard room temperature (20-25°C)
+        annotations:
+          temperature: 20-25°C
+      REFLUX:
+        description: Boiling with condensation return
+        annotations:
+          temperature: solvent boiling point
+      CRYOGENIC:
+        description: Very low temperature conditions
+        annotations:
+          temperature: <-150°C
+          examples: liquid N2, liquid He
+      HIGH_PRESSURE:
+        description: Elevated pressure conditions
+        annotations:
+          pressure: '>10 atm'
+      VACUUM:
+        description: Reduced pressure conditions
+        annotations:
+          pressure: <1 atm
+      INERT_ATMOSPHERE:
+        description: Non-reactive gas atmosphere
+        annotations:
+          gases: N2, Ar
+      MICROWAVE:
+        description: Microwave heating
+        annotations:
+          heating: microwave irradiation
+      ULTRASOUND:
+        description: Ultrasonic conditions
+        annotations:
+          activation: ultrasound
+      PHOTOCHEMICAL:
+        description: Light-induced conditions
+        annotations:
+          activation: UV or visible light
+      ELECTROCHEMICAL:
+        description: Electrically driven conditions
+        annotations:
+          activation: electric current
+      FLOW:
+        description: Continuous flow conditions
+        annotations:
+          type: continuous process
+      BATCH:
+        description: Batch reaction conditions
+        annotations:
+          type: batch process
+  ReactionRateOrderEnum:
+    description: Reaction rate orders
+    permissible_values:
+      ZERO_ORDER:
+        description: Rate independent of concentration
+        annotations:
+          rate_law: rate = k
+          integrated: '[A] = [A]₀ - kt'
+      FIRST_ORDER:
+        description: Rate proportional to concentration
+        annotations:
+          rate_law: rate = k[A]
+          integrated: ln[A] = ln[A]₀ - kt
+      SECOND_ORDER:
+        description: Rate proportional to concentration squared
+        annotations:
+          rate_law: rate = k[A]²
+          integrated: 1/[A] = 1/[A]₀ + kt
+      PSEUDO_FIRST_ORDER:
+        description: Apparent first order (excess reagent)
+        annotations:
+          condition: one reagent in large excess
+      FRACTIONAL_ORDER:
+        description: Non-integer order
+        annotations:
+          indicates: complex mechanism
+      MIXED_ORDER:
+        description: Different orders for different reactants
+        annotations:
+          example: rate = k[A][B]²
+  EnzymeClassEnum:
+    description: EC enzyme classification
+    permissible_values:
+      OXIDOREDUCTASE:
+        title: Oxidoreductases
+        description: Catalyzes oxidation-reduction reactions
+        meaning: EC:1
+        annotations:
+          EC_class: '1'
+          examples: dehydrogenases, oxidases
+      TRANSFERASE:
+        title: Transferases
+        description: Catalyzes group transfer reactions
+        meaning: EC:2
+        annotations:
+          EC_class: '2'
+          examples: kinases, transaminases
+      HYDROLASE:
+        title: Hydrolases
+        description: Catalyzes hydrolysis reactions
+        meaning: EC:3
+        annotations:
+          EC_class: '3'
+          examples: proteases, lipases
+      LYASE:
+        title: Lyases
+        description: Catalyzes non-hydrolytic additions/removals
+        meaning: EC:4
+        annotations:
+          EC_class: '4'
+          examples: decarboxylases, aldolases
+      ISOMERASE:
+        title: Isomerases
+        description: Catalyzes isomerization reactions
+        meaning: EC:5
+        annotations:
+          EC_class: '5'
+          examples: racemases, epimerases
+      LIGASE:
+        title: Ligases
+        description: Catalyzes formation of bonds with ATP
+        meaning: EC:6
+        annotations:
+          EC_class: '6'
+          examples: synthetases, carboxylases
+      TRANSLOCASE:
+        title: Translocases
+        description: Catalyzes movement across membranes
+        meaning: EC:7
+        annotations:
+          EC_class: '7'
+          examples: ATPases, ion pumps
+  SolventClassEnum:
+    description: Classes of solvents
+    permissible_values:
+      PROTIC:
+        description: Solvents with acidic hydrogen
+        annotations:
+          H_bonding: donor
+          examples: water, alcohols, acids
+      APROTIC_POLAR:
+        description: Polar solvents without acidic H
+        annotations:
+          H_bonding: acceptor only
+          examples: DMSO, DMF, acetone
+      APROTIC_NONPOLAR:
+        description: Nonpolar solvents
+        annotations:
+          H_bonding: none
+          examples: hexane, benzene, CCl4
+      IONIC_LIQUID:
+        description: Room temperature ionic liquids
+        annotations:
+          state: liquid salt
+          examples: imidazolium salts
+      SUPERCRITICAL:
+        description: Supercritical fluids
+        annotations:
+          state: supercritical
+          examples: scCO2, scH2O
+      AQUEOUS:
+        description: Water-based solvents
+        annotations:
+          base: water
+      ORGANIC:
+        description: Organic solvents
+        annotations:
+          base: organic compounds
+      GREEN:
+        description: Environmentally friendly solvents
+        annotations:
+          property: low environmental impact
+          examples: water, ethanol, scCO2
+  ThermodynamicParameterEnum:
+    description: Thermodynamic parameters
+    permissible_values:
+      ENTHALPY:
+        description: Heat content (ΔH)
+        annotations:
+          symbol: ΔH
+          units: kJ/mol
+      ENTROPY:
+        description: Disorder (ΔS)
+        annotations:
+          symbol: ΔS
+          units: J/mol·K
+      GIBBS_ENERGY:
+        description: Free energy (ΔG)
+        annotations:
+          symbol: ΔG
+          units: kJ/mol
+      ACTIVATION_ENERGY:
+        description: Energy barrier (Ea)
+        annotations:
+          symbol: Ea
+          units: kJ/mol
+      HEAT_CAPACITY:
+        description: Heat capacity (Cp)
+        annotations:
+          symbol: Cp
+          units: J/mol·K
+      INTERNAL_ENERGY:
+        description: Internal energy (ΔU)
+        annotations:
+          symbol: ΔU
+          units: kJ/mol