Deoxycalyciphylline B , CAS No.619326-74-8

CAS: 619326-74-8 Cat. No.: D946571 PubChem CID: 5243215

Storage

Room temperature

Specifications

Condizioni di conservazione di stoccaggio

Room temperature

Nomi e identificatori

• Sorrisi canonici: CC1CN2C3C(CCC4C3=CCC4)C5(C6(C2C1CC6)CCC(=O)O5)C
• IUPAC Name: 6,18-dimethyl-5-oxa-16-azahexacyclo[14.5.1.01,6.07,15.010,14.019,22]docos-13-en-4-one
• InChIKey: NGQSEZXJVMCXSC-UHFFFAOYSA-N
• INCHI: 1S/C22H31NO2/c1-13-12-23-19-16-5-3-4-14(16)6-7-17(19)21(2)22(11-9-18(24)25-21)10-8-15(13)20(22)23/h5,13-15,17,19-20H,3-4,6-12H2,1-2H3
• Isomeri SMILES: CC1CN2C3C(CCC4C3=CCC4)C5(C6(C2C1CC6)CCC(=O)O5)C
• PubChem CID: 5243215
• Termini MeSH: deoxycalyciphylline B

Proprietà chimiche e fisiche

• Peso molecolare: 341.500 g/mol
• XLogP3: 3.500
• Hydrogen Bond Donor Count: 0
• Hydrogen Bond Acceptor Count: 3
• Rotatable Bond Count: 0
• Exact Mass: 341.235 Da
• Monoisotopic Mass: 341.235 Da
• Topological Polar Surface Area: 29.500 Ų
• Heavy Atom Count: 25
• Formal Charge: 0
• Complexity: 671.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 8
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 1

Application Protocols

• Item-specific tested applications: Not specified for this item; refer to CoA/Spec Sheet.

• General laboratory protocols (non-spec) for small-molecule natural products:

  • Stock preparation: Weigh accurately (analytical balance). Dissolve to 10 mM in anhydrous DMSO or MeOH. Vortex and, if needed, sonicate briefly. Store aliquots to minimize freeze–thaw.
  • HPLC/LC–MS method development: Start with C18, 0.1% FA in water and ACN, 5–95% gradient over 15 min, 0.3–1.0 mL/min. Detect at 210–230 nm and by ESI+ MS. Adjust gradient and modifiers to control retention/peak shape of basic analytes.
  • NMR acquisition: Prepare 5–15 mg/mL in CDCl3 or CD3OD. Acquire 1D/2D suite (1H, 13C, DEPT, HSQC, HMBC, COSY, NOESY/ROESY). Reference residual solvent peaks.
  • Crystallization (optional): If solid and purity permits, attempt slow evaporation from CHCl3/MeOH or EtOAc/hexanes. For salts, ether diffusion into MeOH/TFA salts can yield crystals suitable for X-ray.

• Documentation: Record lot number, preparation date, solvent, and concentration on all aliquots for traceability.

Biological Roles

• General background (literature, not item-specific):

  • Deoxycalyciphylline B is a plant-derived alkaloid of the Daphniphyllum family. Alkaloids in this family are secondary metabolites thought to contribute to plant defense and ecological interactions.
  • Structurally rigid, polycyclic alkaloids are often studied for their interactions with biological macromolecules in the context of chemical biology, target identification, and SAR exploration, but specific molecular targets for Deoxycalyciphylline B have not been specified here.
  • The presence of a basic nitrogen can influence cellular uptake and subcellular distribution (ion trapping), and salt forms can affect apparent solubility and assay performance.

• Research use only

  • This product is supplied strictly for research use. No claims are made regarding therapeutic efficacy, diagnosis, or clinical utility.

• Practical guidance for biologists/chemists:

  • Prepare DMSO stocks (e.g., 10 mM) and dilute into assay buffers to ≤1% DMSO final to limit solvent effects.
  • Evaluate adsorption losses on plastics for hydrophobic natural products; use low-bind tubes or add small amounts of carrier protein/detergent where appropriate.
  • Confirm stability in assay media (pH 7–8) and under light exposure; include time-zero and matrix-control samples for accurate interpretation.

Buffer Applications

• Not typically applicable

  • Deoxycalyciphylline B is a neutral organic small molecule (alkaloid) and is not used as a buffering agent. It does not define a useful conjugate acid/base pair within the physiological buffering range for routine buffer preparation.

• Practical note (for assays only):

  • When preparing assay buffers that will contain this compound, ensure adequate cosolvent (e.g., ≤1% DMSO or small amounts of methanol/ethanol) or use a soluble salt form (e.g., HCl, TFA) to avoid precipitation. Optimize pH to maintain the desired protonation state of the amine if target engagement is pH-dependent.

Green Alternatives

• Context: While the compound itself is fixed, greener choices relate to solvent selection, purification, and waste minimization when handling Deoxycalyciphylline B.

• Greener solvent substitutions (general guidance):

  • Replace CHCl3/DCM with 2-MeTHF, CPME, EtOAc, or alcohols where solubility allows.
  • Use EtOH/MeOH–water mixes for LC when compatible, instead of ACN-intensive methods.
  • For amine-containing analytes, buffered aqueous-organic systems (MeOH/H2O with 0.1% FA) often match performance while reducing halogenated waste.

• Small comparison (general):

  • DCM/CHCl3: excellent solvency; high EHS impact; easy evaporation.
  • EtOAc/2-MeTHF: good solvency for nonpolar to mid-polar; lower toxicity; slightly higher bp may lengthen evaporation times.
  • EtOH/MeOH: renewable sourcing possible; good for salts; protic nature can alter selectivity.

• Process considerations:

  • Favor reverse-phase purification to reduce chlorinated solvent use.
  • Concentrate fractions using energy-efficient rotovaps; pool only pure fractions to minimize rework.
  • Use mini-columns or preparative SFC (with CO2 + alcohol modifier) where available to cut solvent consumption.

• Note: Validate analyte stability in alternative media; tertiary amines can show different retention/ionization behavior across greener systems.

Pharmaceutical Uses

• Not specified for this item; refer to CoA/Spec Sheet.

• General context (non-clinical, research/manufacturing):

  • Natural product alkaloids such as Deoxycalyciphylline B may be used as analytical reference standards in quality control labs, in metabolite identification workflows, or as tool compounds in preclinical discovery studies.
  • No compendial (USP/EP/JP) monograph is indicated for this item. It is not supplied as an excipient. Any use in drug product manufacturing would require independent qualification and regulatory assessment by the user.

• Formulation considerations for research use:

  • Prepare concentrated stocks in DMSO or ethanol; for aqueous systems, consider converting to a defined salt to enhance solubility and handling consistency.
  • Light and oxidation control may be important for long-term solution stability; verify by stability-indicating HPLC.

Physical Properties

• Item-specific from Product Data

  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Storage conditions: Room temperature (per Product Data)

• Not specified for this item; refer to CoA/Spec Sheet (do not treat the following literature guidance as specifications):

  • Melting point (typical for polycyclic alkaloids): often solid at ambient conditions with mp in the 100–250 °C range (literature-general for the class; exact value for Deoxycalyciphylline B should be confirmed from primary sources).
  • Solubility (general guidance): sparingly soluble in water; soluble in organic media such as chloroform, dichloromethane, methanol, ethanol, acetonitrile, and DMSO (literature-general for lipophilic tertiary-amine natural products). Salt formation (e.g., HCl, TFA salts) increases water/methanol solubility.
  • pKa: tertiary amine pKa typically in the ~7.5–10.5 range for Daphniphyllum-type alkaloids; the exact basicity depends on substitution and ring constraints (literature-general).
  • LogP: expected to be high (lipophilic) due to polycyclic hydrocarbon content; exact value not verified (literature-general).
  • UV-vis: many alkaloids show modest UV absorbance in the 200–230 nm range; specific λmax/ε for this compound not verified (literature-general).

• Practical notes (general):

  • Prepare analytical stocks at 1–10 mg/mL in DMSO, MeOH, or CHCl3 for NMR/LC–MS. Sonication or gentle warming (≤40 °C) can aid dissolution. Filter (0.2 µm PTFE) before chromatographic use.

Quality and Grades

• Item-specific from Product Data

  • Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.

• Interpreting grade (general guidance):

  • When available, “research-grade” or “analytical standard” designations indicate suitability for discovery chemistry, method development, or reference use. Purity for natural products is commonly determined by HPLC/UPLC area %, NMR purity, and LC–MS profile.
  • For structural, SAR, or bioassay work, review: purity (area %), residual solvent profile, counterion content if supplied as a salt, and water content (Karl Fischer). If chiral, check enantiomeric/diastereomeric ratios.

• Stabilizers/additives:

  • No stabilizers are specified for this item. If present in a given lot, they will be disclosed on the CoA/SDS. Absence of additives is typical for small-molecule natural products, but verify if salt forms (e.g., HCl) are used to enhance solubility or stability.

• Recommendations:

  • Request recent CoA before critical work. For quantitative applications (qNMR, calibration curves), consider in-house verification of purity and assignment by 1H/13C NMR and LC–MS.

Reaction and Applications

• Applications (research context):

  • Reference standard and analytical spike-in for method development (LC–MS/NMR) on Daphniphyllum alkaloids.
  • Structural studies: conformational analysis, stereochemical assignment, and computational benchmarking against experimental spectra.
  • Derivatization chemistry to adjust solubility or create analytical handles (e.g., acylation of the amine to reduce basicity for improved chromatographic behavior; quaternization for permanent charge in ESI-MS).

• Natural product chemistry (general):

  • Deoxycalyciphylline B belongs to a class widely targeted in total synthesis. The compound can serve as a comparator for spectral data, impurity profiling, and as a substrate for selective functionalization studies on rigid polycyclic frameworks.

• Practical notes:

  • Handle under inert atmosphere during prolonged manipulations if oxidative sensitivity is suspected; many polycyclic alkaloids withstand air but can be sensitive to strong acids/oxidants.
  • For reaction screening, start with small-scale (0.5–5 mg) using high-concentration stocks in dry CH2Cl2, MeOH, or ACN. Monitor by LC–MS with acidic modifiers to track protonated species.

• Examples of transformations (literature-general):

  • N-oxidation (mCPBA) to amine N-oxides; reductive acylation/alkylation at nitrogen; formation of mineral-acid salts; mild hydrogenations if olefinic motifs are present. Exact functional groups for this specific molecule should be verified before attempting.

Reaction Conditions

• General derivatization conditions for tertiary-amine natural products (literature-general; not item-specific specifications):

  • Salt formation: treat with HCl(g) in ether or TFA in DCM/MeOH at 0–25 °C to give crystalline ammonium salts; isolate by concentration and trituration.
  • N-oxidation: mCPBA (1.1–1.5 equiv) in DCM at 0 °C to rt for 0.5–4 h; monitor by TLC/LC–MS. Work up with aqueous Na2CO3 to remove acid by-products.
  • Quaternization: MeI or MeOTf (1.1–3 equiv) in MeCN or acetone at 0–25 °C; reaction times 1–24 h depending on sterics. Employ inert atmosphere to limit side reactions.
  • Acylation via iminium: activate with acid anhydrides or use reductive acylation strategies (e.g., Ac2O then NaBH(OAc)3) under strictly anhydrous conditions.

• Analytical conditions (method development):

  • LC–MS: C18 column, 5–95% ACN/H2O with 0.1% formic acid over 10–20 min; ESI+ favored. Typical injection 1–10 µL of 0.1 mg/mL stock.
  • NMR: 600 MHz recommended for complex signal dispersion; acquire 1H, 13C, HSQC, HMBC, NOESY for stereochemical analysis.

• Yields and selectivity:

  • Expect moderate to high conversions for salt formation and quaternization; N-oxidations can be high-yielding but may require careful temperature control to avoid over-oxidation. Exact yields depend on the specific structural features of Deoxycalyciphylline B (not specified here).

Safety and Handling

• Item-specific from Product Data

  • GHS: Not specified for this item; refer to SDS.
  • Signal word / H-statements / Pictograms: Not specified for this item; refer to SDS.
  • Research use note: For research use only.

• General laboratory safety (non-spec; follow institutional SDS-driven policies):

  • PPE: lab coat, safety glasses, and appropriate chemical-resistant gloves (e.g., nitrile). Avoid inhalation, ingestion, and skin contact.
  • Engineering controls: handle powders/solids in a fume hood; minimize dust/aerosol generation. Use closed containers for solutions.
  • First aid (overview): rinse skin/eyes with water for ≥15 minutes upon contact; seek medical evaluation if irritation persists. If inhaled, move to fresh air. If ingested, do not induce vomiting; seek medical attention.
  • Incompatibilities: strong oxidizers and strong acids/bases may cause decomposition or rearrangement of sensitive polycyclic alkaloids. Avoid prolonged exposure to light and heat.
  • Environmental: prevent release to the environment; collect waste in halogenated or non-halogenated organic waste streams according to the solvent used.

• Special notes for alkaloids (general):

  • Many plant alkaloids are bioactive; avoid dermal exposure and accidental ingestion. Use microbalance technique to reduce exposure to particulates.
  • Always defer to the official SDS for authoritative hazard classification and emergency measures for this SKU.

Solvent Selection

• Polarity and dissolution (general for lipophilic tertiary-amine alkaloids):

  • Readily soluble: DCM, CHCl3, MeOH, EtOH, ACN, THF, DMSO.
  • Poorly soluble: water at neutral pH. Aqueous solubility can be increased by forming protonated salts (e.g., adding TFA/HCl to give a water/methanol-soluble ammonium salt).

• Practical choices by application:

  • NMR: CDCl3 or CD3OD are typical; DMSO-d6 if required for sparingly soluble samples. Add a drop of TFA-d if line-broadening from basicity occurs.
  • LC–MS: ACN/H2O with 0.1% formic acid supports protonation and robust [M+H]+ signals; isocratic vs gradient chosen by retention.
  • Purification: normal-phase silica with CH2Cl2/MeOH or hexanes/EtOAc/MeOH mixtures; basic modifiers (0.1–1% Et3N) can suppress tailing of amines. Reverse-phase C18 with MeOH/H2O or ACN/H2O plus 0.1% TFA/FA is effective for polar salt forms.

• Comparison (general):

  • CHCl3/DCM: excellent dissolution, easy rotary evaporation; less green.
  • MeOH/EtOH: protic, good for salts and UV detection, greener than chlorinated.
  • DMSO: highest solvating power; residues can be persistent.

• Tip: Pre-test solubility at 1 mg/mL in several solvents; choose the minimal-toxicity solvent compatible with downstream analytics.

Storage and Reconstitution

• Item-specific from Product Data

  • Storage conditions: Room temperature.
  • Shipped in: Not specified for this item; refer to CoA/Spec Sheet.

• General storage guidance (non-spec):

  • Keep tightly closed in an inert, light-protective container. Store in a dry place with desiccant to limit moisture uptake. Avoid prolonged exposure to light and heat.
  • For long-term archiving, many users store natural products at 2–8 °C or -20 °C in the dark; equilibrate to room temperature before opening to prevent condensation.

• Reconstitution (solution preparation):

  • Prepare concentrated stocks in dry DMSO, MeOH, or CHCl3 at 1–10 mg/mL. Filter (0.2 µm PTFE) if particles persist. For aqueous work, form an acid salt in situ (e.g., add a small amount of TFA or HCl) to improve solubility.
  • Aliquot solutions into amber vials to minimize freeze–thaw and photodegradation.

• Stability checks:

  • Verify concentration and integrity periodically by HPLC/LC–MS and 1H NMR, especially after extended storage or if solutions show discoloration or precipitation.

• Note: For definitive stability and handling instructions for this SKU/lot, consult the CoA and SDS.

Structure and Identity

• Item-specific from Product Data

  • SKU: D946571
  • Product name: Deoxycalyciphylline B
  • CAS: 619326-74-8
  • CID: 5243215 (PubChem)
  • InChIKey: 238065 (as provided; note: not the standard 27-character format)
  • SMILES: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.

• Literature/structural context (non-spec):

  • Deoxycalyciphylline B is a member of the Daphniphyllum alkaloids, a family of complex, polycyclic plant secondary metabolites.
  • Typical features of this scaffold class include: a multi-fused carbocyclic “cage-like” framework, one incorporated nitrogen (often as a tertiary amine), multiple bridgeheads, and numerous stereogenic centers.
  • 2D structural description (generic to the calyciphylline-type alkaloids): a compact polycyclic backbone with fused five-, six-, and/or seven-membered rings, a bridge across the polycycle creating a caged topology, and a basic nitrogen embedded within the framework; oxygenation level varies among congeners, with “deoxy” analogs having fewer oxygenated functionalities.

• Notes

  • If exact constitutional/absolute configuration details are required for this lot, please consult the CoA/SDS or request the structure file from technical support. All structural assertions above are literature-general to the class and not item-specific.

Synthetic Utility

• Functional group logic (general for Daphniphyllum-type alkaloids):

  • Tertiary amine: accessible to salt formation, quaternization (e.g., MeI/MeOTf), acylation after prior activation (e.g., via iminium formation), and N-oxidation (mCPBA) leading to downstream rearrangements (Polonovski-type chemistry).
  • Polycyclic hydrocarbon framework: opportunities for selective C–H functionalization, hydrogenation of olefinic sites (if present), and oxidative unveiling of hidden functionality under carefully tuned conditions.

• Uses in synthesis research:

  • Benchmarking spectral data and absolute configuration in total synthesis campaigns of calyciphylline-type targets.
  • Scaffold diversification: late-stage functionalization to generate analog libraries for SAR, leveraging innate reactivity and conformational bias of the cage structure.
  • Analytical derivatization to improve chromatographic behavior (e.g., carbamate formation, dansylation for fluorescence).

• Practical considerations:

  • The rigid framework can confer high chemoselectivity but also steric hindrance; reagents and catalysts that operate under mild conditions (photoredox, electrochemical, or Rh/Pd C–H activation with directing groups) may be advantageous.
  • Verify exact functional groups for Deoxycalyciphylline B from primary characterization before attempting specific named transformations; natural product congeners differ subtly in oxidation state and substitution.

Target Specificity

• Not applicable to this product type.
  • Deoxycalyciphylline B is a small-molecule natural product, not an antibody or biologic. No antigen/epitope/isotype information applies.
  • If biological target engagement is being investigated, this must be determined empirically by the user; no target specificity is provided in the Product Data.