phenylalanine
Enable an AI agent to identify phenylalanine, assess its form and measured condition, and select handling or use actions supported by evidence for the specific material and context.
Research draft, second pass
A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.
Researched by: Codex + Grok
Purpose and description
Enable an AI agent to identify phenylalanine, assess its form and measured condition, and select handling or use actions supported by evidence for the specific material and context.
Phenylalanine is the aromatic α-amino acid 2-amino-3-phenylpropanoic acid; animals use almost exclusively the L (2S) enantiomer as a proteinogenic essential amino acid (codons UUU and UUC) and as the substrate of phenylalanine hydroxylase in tyrosine biosynthesis.
It can be Verify phenylalanine identity and resolve or explicitly preserve uncertainty about its stereochemistry.; Select a measurement approach that distinguishes free, hydrolysis-released and total reported phenylalanine.; Calculate a transfer or dilution using verified content, chemical form and reporting basis.; Assess dissolution and sampling suitability under recorded solvent, pH and temperature conditions.; Accept, hold or reject a material for a specified use against a cited specification.; Route biological or dietary interpretations to the appropriate specimen, food or clinical model with the phenylalanine evidence attached..
Distinguishing features
Require evidence for the 2-amino-3-phenylpropanoic acid connectivity; the formula C9H11NO2 alone cannot establish identity. Reference identity: [PubChem L-phenylalanine](https://pubchem.ncbi.nlm.nih.gov/compound/phenylalanine).
Check aromatic substitution: phenylalanine has an unsubstituted phenyl side chain, whereas tyrosine has an additional ring hydroxyl group.
Require stereochemistry-sensitive evidence to distinguish L from D or a mixture; formula and an achiral identity assay cannot resolve this distinction. Reference counterpart: [PubChem D-phenylalanine](https://pubchem.ncbi.nlm.nih.gov/compound/D-Phenylalanine).
Check the alpha-amino group and carbon skeleton to distinguish phenylalanine from phenylpyruvate and phenethylamine.
Establish whether the reported material is free phenylalanine, a peptide-bound residue or phenylalanine released during hydrolysis before treating measurements as equivalent.
Scope
+ Phenylalanine identity and discrimination from related aromatic compounds.
+ L, D, mixed and unspecified stereochemical composition within the registered entry.
+ Free phenylalanine, ionic forms and the distinction between free analyte and covalently bound residue.
+ Phenylalanine amount, concentration, chemical purity and enantiomeric composition with measurement evidence.
+ Material condition, preparation compatibility and constraints on an intended use.
- Whole proteins, peptide sequences and their folding or function.
- Complete food, supplement and pharmaceutical formulations.
- Patient diagnosis, treatment targets and dietary prescriptions.
- Phenylalanine hydroxylase, genes and complete metabolic pathways.
- Independent identities and properties of tyrosine, phenylpyruvate and chemically modified phenylalanine derivatives.
Characteristics
- Molecular identity evidence
- confirmed phenylalanine connectivity | tentative identification | unresolved Prevents a name, formula or nonspecific analytical signal from being accepted as sufficient identification.
- Stereochemical composition
- L and D mole fractions or enantiomeric excess with the major enantiomer named; unknown permitted Distinguishes materials that may share chemical identity tests but differ in suitability for a stereospecific use.
- Chemical and association form
- free amino acid | specified ionic or salt form | peptide-bound residue | modified derivative relation | unresolved Determines what the identity claim and reported amount refer to without merging derivatives into phenylalanine.
- Containing material
- linked neat-material lot, solution, food, formulation or biological specimen Locates the occurrence and makes matrix-dependent interpretation possible.
- Phenylalanine amount or concentration
- mol, mg, mmol/L, µmol/L or mg/g; specify free versus total and wet versus dry basis where relevant Supports preparation and comparison without confusing incompatible reporting bases.
- Chemical purity
- mass fraction or assay-specific percentage with method and water correction stated Separates actual phenylalanine content from chromatographic area percentage and enantiomeric purity.
- Physical presentation
- solid | dissolved | partly dissolved | suspension; solid form if established Determines whether sampling and transfer can deliver a representative amount.
- Solution conditions
- pH, temperature in °C, and linked solvent composition Provides conditions needed to interpret dissolution, ionic state and preparation compatibility.
- Condition assessment
- within cited specification | outside cited specification | untested | evidence expired Makes usability an evidence-based assessment rather than an inference from appearance.
- Intended-use qualification
- linked use, applicable specification, supporting evidence and unresolved restrictions Prevents a research reagent or analytical measurement from being treated as authorization for consumption or clinical action.
Where this came from
wikidata · CC0 1.0
Also registered as vr.tr.phenylalanine
Drafted structure
Bundle to layer to finding to question, as the second pass will find it: 6 bundles · 11 layers · 18 findings · 31 questions.
Molecular and stereochemical identity Establish what is being identified as phenylalanine and how precisely its stereochemistry is known.
A generic phenylalanine name does not resolve connectivity evidence, L versus D composition or confusion with related aromatic compounds.
Connectivity and neighbours
Test the molecular identity against plausible alternatives.
Phenylalanine connectivity
Record evidence for the amino-acid backbone and benzyl side chain, including the alternatives the evidence excludes.
- What evidence establishes phenylalanine connectivity rather than only a matching formula or nominal mass? definition
- Does the identification distinguish tyrosine, phenylpyruvate and other plausible components of this sample? boundary
Enantiomer resolution
Separate stereochemical claims from evidence that establishes only chemical identity.
L and D composition
Represent L, D and mixed composition without defaulting an unspecified registry name to L-phenylalanine.
- Is the material claimed to be L, D, racemic, another measured mixture or stereochemically unspecified? definition
- Which stereochemistry-sensitive method establishes the composition, and with what detection limit for the minor enantiomer? measurement
Chemical form and occurrence Identify the form in which phenylalanine occurs and the material containing it.
Free amino acid, salt-associated material and peptide-bound phenylalanine cannot be substituted indiscriminately in identification or amount calculations.
Free, ionic and bound forms
State whether phenylalanine is a free molecular constituent or represented through a chemical relationship.
Form and identity boundary
Record ionic or salt form and distinguish peptide residues and modified derivatives from free phenylalanine.
- Is the occurrence free phenylalanine, a specified salt or ionic form, or a residue covalently incorporated in another molecule? definition
- Does a protecting group or other covalent modification require linking to a separate compound identity? boundary
Matrix and release history
Connect the occurrence to its source material and any process that released phenylalanine.
Occurrence origin
Preserve the distinction between phenylalanine originally present as free analyte and phenylalanine obtained through sample processing.
- Which lot, formulation, food or biological specimen contains this occurrence? provenance
- Was phenylalanine measured directly or after extraction, digestion or hydrolysis, and which procedure was used? provenance
Quantification and analytical confidence Make phenylalanine quantities interpretable and assess whether analytical evidence supports a decision.
Free versus total content, matrix effects and stereochemical selectivity can produce materially different answers under the same analyte name.
Measurand and reporting basis
Define precisely what a phenylalanine value counts.
Interpretable phenylalanine quantity
Attach chemical form, free or total basis, units and uncertainty to every quantity used for comparison or preparation.
- Does the value represent free phenylalanine, hydrolysis-released content or an operationally defined total? definition
- What are the value, units, uncertainty and mass or volume basis, including any water or salt correction? measurement
Selectivity and reference evidence
Assess whether the assay measures the intended phenylalanine population reliably.
Assay fitness
Record calibration, matrix validation and unresolved interference separately from the reported numerical result.
- Which reference material and calibration establish the result, and do they match the claimed stereochemical scope? provenance
- What recovery, interference, quantification-limit and sample-preparation evidence supports this method in this matrix? measurement
- Is the evidence sufficient for the intended comparison, or is confirmatory analysis required? action
Physical condition and preparation Assess whether the phenylalanine material can be sampled, dissolved and transferred as intended.
An identity-correct phenylalanine material may still give incorrect delivered amounts through incomplete dissolution, water content or an unsuitable preparation history.
Phase and dissolution
Relate the observed physical state to a proposed preparation.
Preparation homogeneity
Require evidence that phenylalanine is distributed as assumed before sampling or concentration calculations.
- Is phenylalanine present as a solid, fully dissolved solute or partly dissolved material under the recorded conditions? measurement
- What solvent, pH, temperature and concentration support the proposed dissolution or representative sampling step? action
Purity and condition history
Evaluate chemical content and condition using lot-specific evidence.
Material condition evidence
Keep chemical purity, enantiomeric purity, water content and condition history distinct when assessing usable phenylalanine content.
- Which measured impurities, water content and enantiomeric composition determine the usable phenylalanine content? measurement
- Which storage or preparation events fall outside the conditions supported by the lot's stability evidence? provenance
- Does the applicable specification permit use, require retesting or require the material to be held? action
Biological context and use decisions Connect phenylalanine evidence to intended uses while keeping clinical and formulation decisions with their owning models.
Chemical identity alone does not establish biological equivalence, dietary suitability or the meaning of a biological concentration.
Biological interpretation boundary
Preserve the context needed by a biological or clinical model.
Metabolic context link
Link relevant metabolic context: phenylalanine hydroxylase participates in conversion of phenylalanine to tyrosine, and deficiency can elevate phenylalanine; this relation does not establish a diagnosis from a material record. [NCBI Genes and Disease](https://www.ncbi.nlm.nih.gov/sites/books/NBK22253/).
- Which specimen, collection time and linked biological context belong to this phenylalanine measurement? provenance
- Which external clinical model owns interpretation, reference intervals and any proposed response to the result? boundary
Use-specific qualification
Judge a proposed use against its phenylalanine-specific requirements.
Permitted use evidence
Match stereochemistry, content, impurities and material grade to an explicit use rather than assuming all phenylalanine materials are interchangeable.
- Does the proposed analytical, synthetic, nutritional or formulation use require a particular enantiomer, chemical form or purity specification? action
- Which qualification evidence supports that use, and which missing evidence prevents a decision? provenance
- If consumption is proposed, which linked product or clinical model determines suitability and any phenylalanine-related restrictions? boundary
Evidence and external alignment What the world already says about this thing, gathered so the model can be checked against it.
A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.
Reported evidence
Findings from the breadth pass, kept separate from the structural claims.
Kinds and varieties
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- L-phenylalanine (proteinogenic 2S enantiomer; the nutritional and pharmaceutical substance)
- D-phenylalanine (2R enantiomer; occurs in some peptides and is sold as a distinct supplement)
- DL-phenylalanine (racemate, marketed as a dietary supplement)
- Protein-bound phenylalanyl residues in peptides and food proteins
- Free phenylalanine in plasma, tissues, and crystalline amino-acid mixes
- Isotopically labelled L-phenylalanine (¹³C, ¹⁵N, ²H) used as a metabolic tracer
- Which of these kinds and varieties hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Identifiers and schemes
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- Wikidata - Q170545 - Item commonly used for phenylalanine / L-phenylalanine as the chemical entity.
- CAS Registry Number - 63-91-2 - L-phenylalanine; D-enantiomer 673-06-3; racemate 150-30-1.
- PubChem CID - 6140 - L-phenylalanine.
- ChEBI - CHEBI:17295 - L-phenylalanine; D-enantiomer CHEBI:28044.
- IUPAC-IUB amino-acid code - Phe / F - Residue codes in sequences; free acid still named phenylalanine.
- InChIKey - COLNVLDHVKWLRT-QMMMGPOBSA-N - Standard InChIKey of L-phenylalanine.
- EC inventory (EINECS) - 200-568-1 - L-phenylalanine as a listed substance.
- KEGG COMPOUND - C00079 - L-phenylalanine in metabolic maps (e.g. phenylalanine, tyrosine and tryptophan biosynthesis).
- HMDB - HMDB0000159 - Human metabolome entry for L-phenylalanine.
- Which of these identifiers and schemes hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Standards and regulation
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983): amino-acid names and Phe/F symbolism.
- European Pharmacopoeia monograph 'Phenylalanine' (EDQM): identity, purity and assay of the pharmaceutical substance.
- United States Pharmacopeia-National Formulary, Phenylalanine (USP): pharmaceutical quality standard.
- U.S. FDA, 21 CFR 172.804 (aspartame): mandatory statement 'PHENYLKETONURICS: CONTAINS PHENYLALANINE'.
- Regulation (EU) No 1169/2011 (European Parliament and Council): foods with aspartame or aspartame-acesulfame salt must state that they contain a source of phenylalanine.
- WHO/FAO/UNU, Protein and Amino Acid Requirements in Human Nutrition, TRS 935 (2007): reference aromatic-amino-acid requirement.
- National newborn-screening programmes (state/national public-health authorities): blood-spot phenylalanine as the PKU case-finding analyte.
- Which of these standards and regulation hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Real-world use
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- Residue in essentially all dietary proteins; intake tracks ordinary protein consumption.
- The amino acid that must be restricted, and then titrated, in phenylketonuria medical foods and low-protein diets.
- Component of crystalline L-amino-acid solutions for parenteral nutrition.
- Industrial starting material, with L-aspartic acid, for aspartame (methyl L-α-aspartyl-L-phenylalaninate).
- Protected building block in peptide manufacture (typically Fmoc-L-Phe-OH).
- Over-the-counter L- or DL-phenylalanine capsules sold as supplements.
- Stable-isotope tracer of whole-body protein metabolism (e.g. L-[1-¹³C]phenylalanine infusion or breath tests).
- Which of these real-world use hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Typical measurements
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- molar mass (C9H11NO2) - 165.19 (exact molecular mass of the free acid) - g·mol⁻¹
- adult fasting plasma L-phenylalanine - about 35-85 - µmol·L⁻¹
- PKU treatment target (European guidelines, through childhood) - 120-360 - µmol·L⁻¹
- adult aromatic-amino-acid requirement (Phe + Tyr), WHO/FAO/UNU 2007 - 25 - mg·kg⁻¹·day⁻¹
- aqueous solubility of L-phenylalanine near 25 °C - about 27 - g·L⁻¹
- acid-base constants (α-COOH / α-NH3+) - about 2.2 / 9.2 - pKa
- Which of these typical measurements hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Failure modes and hazards
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- Phenylalanine hydroxylase deficiency (phenylketonuria): hyperphenylalaninemia with impaired neurotransmitter synthesis and irreversible developmental injury if untreated in infancy.
- Maternal PKU: teratogenic effect of high maternal blood phenylalanine.
- Tetrahydrobiopterin-recycling defects that raise phenylalanine and can be missed if only dietary PKU is assumed.
- Over-restriction of dietary phenylalanine: protein-energy failure, growth faltering, and tyrosine deficiency.
- Undeclared or unrecognised aspartame exposing people with PKU to a phenylalanine load.
- Racemisation or Strecker degradation in harsh food processing, which removes nutritionally available L-phenylalanine.
- Which of these failure modes and hazards hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Regional variation
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- Clinic units: Europe reports blood phenylalanine in µmol·L⁻¹; some North American records still use mg·dL⁻¹ (1 mg·dL⁻¹ ≈ 60 µmol·L⁻¹).
- Newborn-screening cut-offs, second-tier tests, and confirmatory algorithms differ by programme.
- Access to sapropterin, pegvaliase, and glycomacropeptide low-phenylalanine foods is highly jurisdiction-dependent.
- Pharmacopoeial and food-label names: Phenylalanin (German), phénylalanine (French), alongside the English name.
- Background dietary phenylalanine load follows local staple proteins (dairy, legumes, meat, rice) more than any difference in the molecule itself.
- Which of these regional variation hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Neighbouring kinds and how to tell them apart
Reported by the breadth pass; each item needs checking against its source before it becomes normative.
- L-tyrosine - Extra 4-hydroxy group on the ring (+16 Da); separated by reversed-phase HPLC or by MS, and by the phenolic UV/colorimetric response tyrosine gives and phenylalanine does not.
- L-tryptophan - Indole side chain rather than phenyl; strong absorbance near 280 nm versus phenylalanine's weak phenyl band near 257 nm, and a 204 versus 165 Da free-acid mass.
- D-phenylalanine (when the analyte is specified as L) - Same constitution, opposite configuration; chiral HPLC, optical rotation, or an L-amino-acid-oxidase/PAH enzymatic assay.
- phenylpyruvate - 2-oxo acid, not an α-amino acid; no primary amine (ninhydrin-negative as an amino acid), detected as the hydrazone or by GC/LC-MS, and elevated in untreated PKU urine.
- L-homophenylalanine - One extra methylene in the side chain (+14 Da) and a later reversed-phase retention time.
- phenylglycine - One fewer methylene (−14 Da); the aryl group is attached directly to the α-carbon.
- aspartame - A methyl dipeptide ester (E951) that yields phenylalanine only after digestion; identified as a high-intensity sweetener, not as the free amino acid.
- Which of these neighbouring kinds and how to tell them apart hold for the sense of phenylalanine this model covers, and on what evidence? provenance
Sources
- Nomenclature and Symbolism for Amino Acids and Peptides (Recommendations 1983) - IUPAC-IUB Joint Commission on Biochemical Nomenclature, Pure and Applied Chemistry / European Journal of Biochemistry - Systematic name, three- and one-letter codes (Phe, F), and the distinction of L/D enantiomers.
- PubChem Compound Summary for CID 6140, L-Phenylalanine - National Center for Biotechnology Information, U.S. National Library of Medicine - Formula C9H11NO2, molar mass, CAS 63-91-2, InChIKey, and the identity of the L-enantiomer.
- Protein and Amino Acid Requirements in Human Nutrition - WHO Technical Report Series 935, World Health Organization / FAO / United Nations University (2007) - Adult aromatic-amino-acid (phenylalanine plus tyrosine) requirement used under measurements.
- Regulation (EU) No 1169/2011 on the provision of food information to consumers - European Parliament and Council, Official Journal of the European Union - Mandatory 'contains a source of phenylalanine' labelling for aspartame-containing foods.
- 21 CFR 172.804 Aspartame - U.S. Food and Drug Administration - U.S. phenylketonuric warning on aspartame and the regulatory link between the sweetener and phenylalanine load.
- The complete European guidelines on phenylketonuria: diagnosis and treatment - van Wegberg et al., Orphanet Journal of Rare Diseases (2017) - Clinical blood-phenylalanine target ranges and the medical hazard of untreated hyperphenylalaninemia.
What the second pass must settle
- Does the registry intend phenylalanine to encompass L, D and mixtures, or is an L-specific definition documented elsewhere?
- Does an existing Vercy world model already own this concept, requiring this registry entry to link to it?
- Which salt forms, solid forms and isotope-labelled variants should be represented within this entry rather than through neighbouring registered things?
- Which validated methods and reporting conventions should govern free, hydrolysis-released and total phenylalanine in each intended matrix?
- Which authoritative, form-specific sources establish dissolution conditions, storage limits and acceptance specifications for the intended uses?