labmate-mcp 7.0.0__py3-none-any.whl

labmate_mcp/writing.py

@@ -0,0 +1,1488 @@
+"""
+labmate-mcp writing & publication support module.
+
+Tools for the final phase of the research workflow:
+  - Citation formatting via Crossref content negotiation
+  - Experimental section templates for common reaction types
+  - Journal submission formatting guides
+  - Supporting Information (SI) checklists
+  - Standard chemistry abbreviations & symbols
+  - Thesis writing section guides
+  - Molecular formula formatting (LaTeX, HTML, Unicode)
+  - IUPAC nomenclature lookup (PubChem)
+
+No API keys required for most functions. Crossref and PubChem calls are free.
+"""
+
+from __future__ import annotations
+
+import logging
+import re
+from typing import Any
+
+import httpx
+
+logger = logging.getLogger(__name__)
+
+
+# =============================================================================
+# Citation formatting via Crossref content negotiation
+# =============================================================================
+
+# CSL style → Crossref content-negotiation style parameter
+CSL_STYLES: dict[str, str] = {
+    "acs":          "american-chemical-society",
+    "acs-nano":     "acs-nano",
+    "jacs":         "american-chemical-society",
+    "apa":          "apa",
+    "apa7":         "apa-7th-edition",
+    "rsc":          "royal-society-of-chemistry",
+    "nature":       "nature",
+    "science":      "science",
+    "angew":        "angewandte-chemie",
+    "angewandte":   "angewandte-chemie",
+    "ieee":         "ieee",
+    "vancouver":    "vancouver",
+    "chicago":      "chicago-author-date",
+    "harvard":      "harvard-cite-them-right",
+    "cell":         "cell",
+    "pnas":         "proceedings-of-the-national-academy-of-sciences",
+    "elsevier":     "elsevier-harvard",
+    "springer":     "springer-basic-author-date",
+    "wiley":        "american-chemical-society",
+    "mla":          "modern-language-association",
+}
+
+
+async def format_citation(
+    doi: str,
+    style: str = "acs",
+    locale: str = "en-US",
+) -> dict:
+    """
+    Format a DOI as a citation in the requested style using Crossref content negotiation.
+
+    Args:
+        doi: DOI string (with or without https://doi.org/ prefix)
+        style: Citation style (acs, apa, rsc, nature, angew, ieee, vancouver, etc.)
+        locale: Locale for formatting (default: en-US)
+
+    Returns:
+        dict with 'citation', 'style', 'doi' keys.
+    """
+    doi = doi.strip()
+    if doi.startswith("http"):
+        doi = doi.split("doi.org/")[-1]
+
+    csl_style = CSL_STYLES.get(style.lower(), style.lower())
+
+    url = f"https://api.crossref.org/works/{doi}/transform"
+    headers = {
+        "Accept": f"text/x-bibliography; style={csl_style}; locale={locale}",
+        "User-Agent": "labmate-mcp/7.0.0 (mailto:labmate@scholarly.dev)",
+    }
+
+    try:
+        async with httpx.AsyncClient(timeout=15, follow_redirects=True) as client:
+            resp = await client.get(url, headers=headers)
+            if resp.status_code == 200:
+                citation = resp.text.strip()
+                return {
+                    "doi": doi,
+                    "style": style,
+                    "csl_style": csl_style,
+                    "citation": citation,
+                }
+            elif resp.status_code == 404:
+                return {"error": f"DOI not found: {doi}"}
+            else:
+                return {"error": f"Crossref returned {resp.status_code}", "doi": doi}
+    except Exception as e:
+        return {"error": f"Network error: {e}", "doi": doi}
+
+
+async def build_bibliography(
+    dois: list[str],
+    style: str = "acs",
+    numbered: bool = True,
+    locale: str = "en-US",
+) -> dict:
+    """
+    Build a formatted bibliography from a list of DOIs.
+
+    Returns dict with 'bibliography' (formatted string) and 'entries' (individual citations).
+    """
+    entries = []
+    errors = []
+
+    for i, doi in enumerate(dois[:100]):  # cap at 100
+        result = await format_citation(doi, style=style, locale=locale)
+        if "error" in result:
+            errors.append({"doi": doi, "error": result["error"]})
+        else:
+            entries.append({
+                "index": i + 1,
+                "doi": doi,
+                "citation": result["citation"],
+            })
+
+    # Build formatted bibliography
+    lines = []
+    for entry in entries:
+        if numbered:
+            lines.append(f"({entry['index']}) {entry['citation']}")
+        else:
+            lines.append(entry["citation"])
+
+    return {
+        "style": style,
+        "num_entries": len(entries),
+        "num_errors": len(errors),
+        "bibliography": "\n\n".join(lines),
+        "entries": entries,
+        "errors": errors if errors else None,
+    }
+
+
+# =============================================================================
+# IUPAC name ↔ SMILES via PubChem PUG-REST
+# =============================================================================
+
+PUBCHEM_REST = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
+
+
+async def iupac_from_smiles(smiles: str) -> dict:
+    """Look up IUPAC name from a SMILES string via PubChem."""
+    url = f"{PUBCHEM_REST}/compound/smiles/property/IUPACName,MolecularFormula,MolecularWeight,IsomericSMILES/JSON"
+    params = {"smiles": smiles}
+    try:
+        async with httpx.AsyncClient(timeout=15) as client:
+            resp = await client.get(url, params=params)
+            if resp.status_code == 200:
+                data = resp.json()
+                props = data.get("PropertyTable", {}).get("Properties", [{}])[0]
+                return {
+                    "input_smiles": smiles,
+                    "iupac_name": props.get("IUPACName"),
+                    "formula": props.get("MolecularFormula"),
+                    "molecular_weight": props.get("MolecularWeight"),
+                    "canonical_smiles": props.get("IsomericSMILES"),
+                }
+            else:
+                return {"error": f"PubChem returned {resp.status_code}. Compound may not be in database.", "smiles": smiles}
+    except Exception as e:
+        return {"error": str(e), "smiles": smiles}
+
+
+async def smiles_from_name(name: str) -> dict:
+    """Look up SMILES and properties from a chemical name via PubChem."""
+    import urllib.parse
+    encoded = urllib.parse.quote(name, safe="")
+    url = f"{PUBCHEM_REST}/compound/name/{encoded}/property/IsomericSMILES,CanonicalSMILES,IUPACName,MolecularFormula,MolecularWeight,InChI,InChIKey/JSON"
+    try:
+        async with httpx.AsyncClient(timeout=15) as client:
+            resp = await client.get(url)
+            if resp.status_code == 200:
+                data = resp.json()
+                props = data.get("PropertyTable", {}).get("Properties", [{}])[0]
+                return {
+                    "input_name": name,
+                    "isomeric_smiles": props.get("IsomericSMILES"),
+                    "canonical_smiles": props.get("CanonicalSMILES"),
+                    "iupac_name": props.get("IUPACName"),
+                    "formula": props.get("MolecularFormula"),
+                    "molecular_weight": props.get("MolecularWeight"),
+                    "inchi": props.get("InChI"),
+                    "inchi_key": props.get("InChIKey"),
+                }
+            elif resp.status_code == 404:
+                return {"error": f"Compound not found: '{name}'"}
+            else:
+                return {"error": f"PubChem returned {resp.status_code}", "name": name}
+    except Exception as e:
+        return {"error": str(e), "name": name}
+
+
+# =============================================================================
+# Molecular formula formatting
+# =============================================================================
+
+
+def format_molecular_formula(
+    formula: str,
+    output_format: str = "unicode",
+) -> dict:
+    """
+    Format a molecular formula with proper subscripts.
+
+    Args:
+        formula: e.g., "C9H8O4", "Ca(OH)2", "Fe2O3"
+        output_format: "unicode", "latex", "html", or "plain"
+
+    Returns dict with formatted string.
+    """
+    f = formula.strip()
+
+    if output_format == "latex":
+        # C9H8O4 → C$_{9}$H$_{8}$O$_{4}$
+        out = re.sub(r"(\d+)", r"$_{\1}$", f)
+        # Also handle in \ce{} notation
+        ce = re.sub(r"(\d+)", r"_{\1}", f)
+        return {"formula": f, "latex_inline": out, "latex_ce": f"\\ce{{{ce}}}", "format": "latex"}
+
+    elif output_format == "html":
+        out = re.sub(r"(\d+)", r"<sub>\1</sub>", f)
+        return {"formula": f, "html": out, "format": "html"}
+
+    elif output_format == "unicode":
+        subscript_map = str.maketrans("0123456789", "₀₁₂₃₄₅₆₇₈₉")
+        out = ""
+        for ch in f:
+            if ch.isdigit():
+                out += ch.translate(subscript_map)
+            else:
+                out += ch
+        return {"formula": f, "unicode": out, "format": "unicode"}
+
+    else:  # plain
+        return {"formula": f, "plain": f, "format": "plain"}
+
+
+# =============================================================================
+# Experimental section templates
+# =============================================================================
+
+EXPERIMENTAL_TEMPLATES: dict[str, dict] = {}
+
+
+def _et(name, *, aliases=None, category="", template="", notes="", safety=""):
+    key = name.lower()
+    EXPERIMENTAL_TEMPLATES[key] = {
+        "name": name,
+        "aliases": aliases or [],
+        "category": category,
+        "template": template,
+        "notes": notes,
+        "safety": safety,
+    }
+    for a in (aliases or []):
+        EXPERIMENTAL_TEMPLATES[a.lower()] = EXPERIMENTAL_TEMPLATES[key]
+
+
+# --- Cross-Coupling Reactions ---
+
+_et("Suzuki Coupling",
+    aliases=["suzuki-miyaura", "suzuki"],
+    category="Cross-Coupling",
+    template="""**{product_name}**
+
+A flame-dried round-bottom flask equipped with a magnetic stir bar was charged with {aryl_halide} ({aryl_halide_mass} mg, {aryl_halide_mmol} mmol, {aryl_halide_equiv} equiv), {boronic_acid} ({boronic_acid_mass} mg, {boronic_acid_mmol} mmol, {boronic_acid_equiv} equiv), Pd(PPh₃)₄ ({cat_mass} mg, {cat_mmol} mmol, {cat_mol_percent} mol%), and {base} ({base_mass} mg, {base_mmol} mmol, {base_equiv} equiv). The flask was evacuated and backfilled with N₂ (3×). {solvent} ({solvent_volume} mL) was added, and the reaction mixture was stirred at {temperature} °C for {time} h. The reaction was monitored by TLC ({tlc_system}). Upon completion, the mixture was cooled to room temperature, diluted with EtOAc ({workup_volume} mL), and washed with H₂O ({workup_volume} mL) and brine ({workup_volume} mL). The organic layer was dried over Na₂SO₄, filtered, and concentrated under reduced pressure. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound as a {product_appearance} ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.
+{mp_or_rotation}""",
+    notes="Replace placeholders with actual values. For Pd(dppf)Cl₂ catalyst, use degassed dioxane/H₂O (4:1).",
+    safety="Pd catalysts: avoid inhalation. Boronic acids: irritants. Use fume hood.")
+
+_et("Sonogashira Coupling",
+    aliases=["sonogashira"],
+    category="Cross-Coupling",
+    template="""**{product_name}**
+
+A Schlenk flask was charged with {aryl_halide} ({aryl_halide_mass} mg, {aryl_halide_mmol} mmol, {aryl_halide_equiv} equiv), PdCl₂(PPh₃)₂ ({pd_mass} mg, {pd_mmol} mmol, {pd_mol_percent} mol%), and CuI ({cui_mass} mg, {cui_mmol} mmol, {cui_mol_percent} mol%). The flask was evacuated and backfilled with N₂ (3×). Degassed {solvent} ({solvent_volume} mL) and {amine_base} ({amine_volume} mL) were added via syringe. {alkyne} ({alkyne_mass} mg, {alkyne_mmol} mmol, {alkyne_equiv} equiv) was then added dropwise. The mixture was stirred at {temperature} °C for {time} h. The reaction was filtered through Celite, washed with EtOAc, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Use degassed solvents. CuI amount typically 5-10 mol%. Et₃N or iPr₂NH as base.",
+    safety="CuI: toxic. Pd compounds: avoid inhalation.")
+
+_et("Buchwald-Hartwig Amination",
+    aliases=["buchwald-hartwig", "c-n coupling"],
+    category="Cross-Coupling",
+    template="""**{product_name}**
+
+An oven-dried Schlenk tube was charged with Pd₂(dba)₃ ({pd_mass} mg, {pd_mmol} mmol, {pd_mol_percent} mol%), {ligand} ({lig_mass} mg, {lig_mmol} mmol, {lig_equiv} equiv), and {base} ({base_mass} mg, {base_mmol} mmol, {base_equiv} equiv). The tube was evacuated and backfilled with N₂ (3×). {aryl_halide} ({aryl_halide_mass} mg, {aryl_halide_mmol} mmol, {aryl_halide_equiv} equiv), {amine} ({amine_mass} mg, {amine_mmol} mmol, {amine_equiv} equiv), and {solvent} ({solvent_volume} mL) were added. The reaction was heated to {temperature} °C and stirred for {time} h. After cooling, the mixture was diluted with EtOAc, filtered through Celite, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Common ligands: BINAP, XPhos, SPhos, RuPhos, DavePhos, BrettPhos. Base: NaOtBu or Cs₂CO₃.",
+    safety="Pd catalysts: avoid inhalation. Strong bases: moisture-sensitive. Use glovebox or Schlenk line.")
+
+# --- Reductions ---
+
+_et("Sodium Borohydride Reduction",
+    aliases=["nabh4 reduction", "nabh4", "borohydride reduction"],
+    category="Reduction",
+    template="""**{product_name}**
+
+To a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol, {substrate_equiv} equiv) in {solvent} ({solvent_volume} mL) at {temperature} °C was added NaBH₄ ({nabh4_mass} mg, {nabh4_mmol} mmol, {nabh4_equiv} equiv) portionwise over {addition_time} min. The reaction was stirred at {temperature} °C for {time} h. The reaction was quenched by careful addition of saturated NH₄Cl solution ({quench_volume} mL) at 0 °C and extracted with {extraction_solvent} (3 × {extraction_volume} mL). The combined organic layers were washed with brine, dried over Na₂SO₄, filtered, and concentrated under reduced pressure. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound as a {product_appearance} ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Quench carefully — H₂ evolution. For ketone selectivity over ester, use MeOH at −78 °C. CeCl₃ for Luche conditions.",
+    safety="NaBH₄: flammable solid, water-reactive. Quench generates H₂ — open vessel, no sparks.")
+
+_et("LiAlH4 Reduction",
+    aliases=["lah reduction", "lialh4", "lithium aluminium hydride reduction"],
+    category="Reduction",
+    template="""**{product_name}**
+
+To a suspension of LiAlH₄ ({lah_mass} mg, {lah_mmol} mmol, {lah_equiv} equiv) in dry {solvent} ({solvent_volume} mL) at 0 °C under N₂ was added a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol, {substrate_equiv} equiv) in dry {solvent} ({substrate_solvent_volume} mL) dropwise via addition funnel over {addition_time} min. The reaction was allowed to warm to {temperature} °C and stirred for {time} h. The reaction was cooled to 0 °C and carefully quenched by sequential addition of H₂O ({fieser_water} mL), 15% NaOH ({fieser_naoh} mL), and H₂O ({fieser_water2} mL) [Fieser workup]. The resulting white precipitate was filtered through Celite and washed with {solvent}. The filtrate was dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Fieser workup: for each gram of LiAlH₄, add x mL H₂O, x mL 15% NaOH, 3x mL H₂O. Alternative: Rochelle's salt (Na/K tartrate) workup.",
+    safety="LiAlH₄: pyrophoric, water-reactive. Anhydrous conditions mandatory. Quench under N₂ at 0 °C. Fire extinguisher on hand.")
+
+_et("Catalytic Hydrogenation",
+    aliases=["hydrogenation", "pd/c hydrogenation", "h2 reduction"],
+    category="Reduction",
+    template="""**{product_name}**
+
+A round-bottom flask was charged with {substrate} ({substrate_mass} mg, {substrate_mmol} mmol), Pd/C (10 wt%, {cat_mass} mg, {cat_loading} mol% Pd), and {solvent} ({solvent_volume} mL). The flask was evacuated and backfilled with H₂ (balloon, 3×). The reaction was stirred at room temperature under H₂ atmosphere (1 atm, balloon) for {time} h. The reaction was filtered through a pad of Celite, washed with {solvent} ({wash_volume} mL), and concentrated under reduced pressure to afford the title compound as a {product_appearance} ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Pd/C: 10% w/w typical, can use 5-20%. Solvents: MeOH, EtOAc, EtOH. For debenzylation, use same conditions. Pd(OH)₂/C (Pearlman's catalyst) for stubborn substrates.",
+    safety="Pd/C: pyrophoric when dry. Always add solvent first. Never expose dry Pd/C to H₂. Filter away from open flames.")
+
+# --- Oxidations ---
+
+_et("Dess-Martin Oxidation",
+    aliases=["dmp oxidation", "dess-martin"],
+    category="Oxidation",
+    template="""**{product_name}**
+
+To a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol, 1.0 equiv) in CH₂Cl₂ ({solvent_volume} mL) at room temperature was added Dess-Martin periodinane ({dmp_mass} mg, {dmp_mmol} mmol, {dmp_equiv} equiv). The reaction was stirred at room temperature for {time} h, then quenched by addition of a 1:1 mixture of saturated NaHCO₃ and saturated Na₂S₂O₃ ({quench_volume} mL). The layers were separated, and the aqueous layer was extracted with CH₂Cl₂ (3 × {extraction_volume} mL). The combined organic layers were washed with brine, dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="1.1-1.5 equiv DMP. Na₂S₂O₃ reduces excess periodinane and iodinane byproducts. No over-oxidation to carboxylic acid.",
+    safety="DMP: oxidizer, shock-sensitive when dry. Store cold. Waste: treat with Na₂S₂O₃ before disposal.")
+
+_et("Swern Oxidation",
+    aliases=["swern"],
+    category="Oxidation",
+    template="""**{product_name}**
+
+To a solution of oxalyl chloride ({oxchloride_volume} μL, {oxchloride_mmol} mmol, {oxchloride_equiv} equiv) in CH₂Cl₂ ({solvent_volume} mL) at −78 °C was added DMSO ({dmso_volume} μL, {dmso_mmol} mmol, {dmso_equiv} equiv) dropwise. The mixture was stirred for 15 min, then a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol, 1.0 equiv) in CH₂Cl₂ ({substrate_solvent_volume} mL) was added dropwise. The reaction was stirred at −78 °C for {time} min, then Et₃N ({et3n_volume} mL, {et3n_mmol} mmol, {et3n_equiv} equiv) was added. The reaction was allowed to warm to room temperature over 1 h, then diluted with CH₂Cl₂ ({dilute_volume} mL) and washed with H₂O, 1 M HCl, saturated NaHCO₃, and brine. The organic layer was dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Order of addition critical: (COCl)₂ first, then DMSO, then substrate, then Et₃N. Keep at −78 °C until Et₃N added.",
+    safety="Oxalyl chloride: highly toxic, corrosive, lachrymator. DMSO/oxalyl chloride: exothermic at >−60 °C. Use dry ice/acetone bath. Fume hood mandatory.")
+
+# --- Amide Coupling ---
+
+_et("Amide Coupling",
+    aliases=["peptide coupling", "hatu coupling", "edc coupling", "amidation"],
+    category="Amide Bond Formation",
+    template="""**{product_name}**
+
+To a solution of {acid} ({acid_mass} mg, {acid_mmol} mmol, {acid_equiv} equiv) in {solvent} ({solvent_volume} mL) at {temperature} °C was added {coupling_reagent} ({coupling_mass} mg, {coupling_mmol} mmol, {coupling_equiv} equiv) and {base} ({base_volume} μL, {base_mmol} mmol, {base_equiv} equiv). The mixture was stirred for {preactivation_time} min, then {amine} ({amine_mass} mg, {amine_mmol} mmol, {amine_equiv} equiv) was added. The reaction was stirred at room temperature for {time} h. The reaction was diluted with EtOAc ({dilute_volume} mL) and washed sequentially with 1 M HCl, saturated NaHCO₃, and brine. The organic layer was dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Coupling reagents: HATU > HBTU > TBTU > EDC·HCl/HOBt. Bases: DIPEA (iPr₂NEt), NMM, Et₃N. Solvents: DMF, CH₂Cl₂, or DMF/CH₂Cl₂ mixtures. Pre-activation with coupling reagent + base for 5-15 min improves yields.",
+    safety="HATU/HBTU: skin sensitizers, irritants. DMF: reproductive toxicant — avoid skin contact.")
+
+# --- SPPS ---
+
+_et("Solid-Phase Peptide Synthesis",
+    aliases=["spps", "fmoc spps", "peptide synthesis"],
+    category="Peptide Chemistry",
+    template="""**Solid-Phase Peptide Synthesis of {peptide_name}**
+
+Peptide synthesis was performed manually on a {resin_type} resin (loading: {resin_loading} mmol/g, {resin_mass} mg, {scale} mmol scale) using standard Fmoc/tBu chemistry.
+
+*Fmoc Deprotection*: The resin was treated with 20% piperidine in DMF (2 × {deprot_volume} mL, 5 + 15 min) and washed with DMF (5 × {wash_volume} mL).
+
+*Amino Acid Coupling*: Fmoc-{aa_name}-OH ({aa_equiv} equiv), {coupling_reagent} ({coupling_equiv} equiv), and {base} ({base_equiv} equiv) were dissolved in DMF ({coupling_volume} mL) and added to the resin. The mixture was agitated for {coupling_time} min at room temperature. Coupling completion was monitored by the Kaiser (ninhydrin) test. If positive, the coupling was repeated.
+
+*Wash Cycles*: Between each step: DMF (5×), CH₂Cl₂ (3×), DMF (3×).
+
+*Cleavage*: The peptide was cleaved from the resin using TFA/{scavenger_cocktail} ({cleavage_ratio}, {cleavage_volume} mL) for {cleavage_time} h at room temperature. The resin was filtered off, and the filtrate was concentrated under N₂ flow. The crude peptide was precipitated with cold diethyl ether ({ether_volume} mL), centrifuged (4000 rpm, 5 min), and the pellet was washed with cold ether (2×). The crude peptide was dissolved in {dissolve_solvent} and lyophilized to afford a {product_appearance} ({crude_mass} mg).
+
+*Purification*: The crude peptide was purified by preparative RP-HPLC (Column: {hplc_column}; gradient: {hplc_gradient}; flow rate: {hplc_flow} mL/min; detection: λ = 220/280 nm). Pure fractions were pooled and lyophilized to afford the title peptide as a {pure_appearance} ({pure_mass} mg, {yield_percent}% overall).
+
+Analytical HPLC: tR = {hplc_rt} min (purity: {hplc_purity}%, {hplc_conditions}).
+MALDI-TOF MS: m/z calcd for {ms_formula} [M+H]⁺ {ms_calcd}, found {ms_found}.
+{additional_characterization}""",
+    notes="Scavenger cocktails: TFA/TIS/H₂O (95:2.5:2.5) standard. For Cys-containing: TFA/TIS/H₂O/EDT (94:1:2.5:2.5). For Met/Trp-containing: add EDT or DODT. Kaiser test: ninhydrin/pyridine/KCN; blue = free amine (incomplete coupling), yellow = complete.",
+    safety="TFA: highly corrosive, strong acid. Piperidine: highly toxic, flammable. EDT: foul-smelling thiol. Use fume hood for all operations.")
+
+# --- Click Chemistry ---
+
+_et("CuAAC Click Reaction",
+    aliases=["click chemistry", "copper click", "cuaac", "azide-alkyne cycloaddition"],
+    category="Cycloaddition",
+    template="""**{product_name}**
+
+To a solution of {azide} ({azide_mass} mg, {azide_mmol} mmol, {azide_equiv} equiv) and {alkyne} ({alkyne_mass} mg, {alkyne_mmol} mmol, {alkyne_equiv} equiv) in {solvent} ({solvent_volume} mL) was added CuSO₄·5H₂O ({cuso4_mass} mg, {cuso4_mmol} mmol, {cu_mol_percent} mol%) and sodium ascorbate ({asc_mass} mg, {asc_mmol} mmol, {asc_equiv} equiv). The mixture was stirred at room temperature for {time} h. The reaction was diluted with EtOAc ({dilute_volume} mL), washed with saturated NH₄Cl ({wash_volume} mL), H₂O, and brine. The organic layer was dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the 1,4-disubstituted 1,2,3-triazole product ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="CuSO₄/sodium ascorbate (in situ Cu(I)). Typically 5-10 mol% Cu. Solvents: t-BuOH/H₂O (1:1), DMF/H₂O, DMSO. TBTA ligand accelerates. Exclusively 1,4-regioisomer.",
+    safety="Organic azides: potentially explosive — never isolate low-MW azides. CuSO₄: irritant. Ascorbate: safe.")
+
+# --- Protection/Deprotection ---
+
+_et("Boc Deprotection",
+    aliases=["boc removal", "tfa deprotection", "boc cleavage"],
+    category="Protection/Deprotection",
+    template="""**{product_name}**
+
+To a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol) in CH₂Cl₂ ({solvent_volume} mL) at 0 °C was added TFA ({tfa_volume} mL, {tfa_equiv} equiv). The reaction was stirred at room temperature for {time} h. The reaction was concentrated under reduced pressure. The residue was azeotroped with toluene (3×) to remove residual TFA, affording the TFA salt of the title compound as a {product_appearance} ({product_mass} mg, {yield_percent}%).
+
+{characterization}""",
+    notes="Typical: 25-50% TFA in CH₂Cl₂ (v/v). For acid-sensitive substrates: 4 M HCl in dioxane or TMSOTf/2,6-lutidine. Free-base by dissolving in CH₂Cl₂ and washing with saturated NaHCO₃.",
+    safety="TFA: highly corrosive. Use fume hood. Neutralize waste with NaHCO₃ before disposal.")
+
+_et("TBS Protection",
+    aliases=["tbs silylation", "tbdms protection", "silyl protection"],
+    category="Protection/Deprotection",
+    template="""**{product_name}**
+
+To a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol, 1.0 equiv) and imidazole ({imid_mass} mg, {imid_mmol} mmol, {imid_equiv} equiv) in {solvent} ({solvent_volume} mL) at {temperature} °C was added TBSCl ({tbs_mass} mg, {tbs_mmol} mmol, {tbs_equiv} equiv). The reaction was stirred at room temperature for {time} h. The reaction was quenched with H₂O ({quench_volume} mL) and extracted with {extraction_solvent} (3 × {extraction_volume} mL). The combined organic layers were washed with brine, dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="TBSCl/imidazole in DMF for 1° alcohols. For 2°: TBSOTf/2,6-lutidine in CH₂Cl₂ at −78°C to 0°C. DMAP catalytic amount can accelerate.",
+    safety="TBSCl: corrosive. Imidazole: irritant.")
+
+_et("TBAF Desilylation",
+    aliases=["tbaf deprotection", "tbs removal", "silyl removal"],
+    category="Protection/Deprotection",
+    template="""**{product_name}**
+
+To a solution of {substrate} ({substrate_mass} mg, {substrate_mmol} mmol, 1.0 equiv) in THF ({solvent_volume} mL) at {temperature} °C was added TBAF (1.0 M in THF, {tbaf_volume} mL, {tbaf_mmol} mmol, {tbaf_equiv} equiv). The reaction was stirred at room temperature for {time} h, then quenched with saturated NH₄Cl ({quench_volume} mL). The mixture was extracted with EtOAc (3 × {extraction_volume} mL), washed with brine, dried over Na₂SO₄, filtered, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="1.0-2.0 equiv TBAF. Add AcOH to buffer if substrate is base-sensitive. Alternative: HF·pyridine (Olah's reagent) for hindered silyl ethers.",
+    safety="TBAF: corrosive, hygroscopic. HF·pyridine: extremely dangerous — HF burns are life-threatening.")
+
+# --- Recrystallization & Purification ---
+
+_et("Recrystallization",
+    aliases=["recrystallization", "crystallization"],
+    category="Purification",
+    template="""**Recrystallization of {compound_name}**
+
+Crude {compound_name} ({crude_mass} mg) was dissolved in minimum hot {solvent} (~{dissolve_temp} °C, {solvent_volume} mL). The solution was allowed to cool slowly to room temperature, then placed at {cool_temp} °C for {cool_time} h. The resulting crystals were collected by vacuum filtration, washed with cold {wash_solvent} ({wash_volume} mL), and dried under vacuum to afford pure {compound_name} as {crystal_appearance} ({product_mass} mg, {recovery_percent}% recovery).
+
+mp: {melting_point} °C.
+{additional_characterization}""",
+    notes="Solvent pairs: EtOAc/hexanes, CH₂Cl₂/hexanes, MeOH/H₂O, acetone/hexanes, EtOH/H₂O. Seed crystals improve nucleation. Slow cooling = larger, purer crystals.",
+    safety="Use appropriate solvent safety precautions. Hot solvent: burn risk.")
+
+# --- General Procedures ---
+
+_et("Wittig Reaction",
+    aliases=["wittig olefination", "wittig"],
+    category="C-C Bond Formation",
+    template="""**{product_name}**
+
+To a suspension of {phosphonium_salt} ({salt_mass} mg, {salt_mmol} mmol, {salt_equiv} equiv) in THF ({solvent_volume} mL) at {base_temp} °C was added {base} ({base_volume} mL/mg, {base_mmol} mmol, {base_equiv} equiv) dropwise. The resulting orange/red ylide solution was stirred for {ylide_time} min. A solution of {aldehyde} ({aldehyde_mass} mg, {aldehyde_mmol} mmol, 1.0 equiv) in THF ({aldehyde_solvent_volume} mL) was added dropwise at {addition_temp} °C. The reaction was stirred at {reaction_temp} °C for {time} h. The reaction was quenched with saturated NH₄Cl, extracted with EtOAc (3×), washed with brine, dried over Na₂SO₄, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%, E:Z = {ez_ratio}).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Non-stabilized ylides: preferentially Z-alkene. Stabilized ylides: preferentially E-alkene. Bases: n-BuLi, NaHMDS, KHMDS. For E-selective olefination, use HWE (Horner-Wadsworth-Emmons) instead.",
+    safety="n-BuLi: pyrophoric. Use syringe techniques under inert atmosphere.")
+
+_et("Grignard Reaction",
+    aliases=["grignard addition", "grignard"],
+    category="C-C Bond Formation",
+    template="""**{product_name}**
+
+Mg turnings ({mg_mass} mg, {mg_mmol} mmol, {mg_equiv} equiv) were flame-dried under vacuum in a round-bottom flask. Dry THF ({thf_volume} mL) and a crystal of I₂ were added. {halide} ({halide_volume} μL, {halide_mmol} mmol, {halide_equiv} equiv) in THF ({halide_thf_volume} mL) was added dropwise at a rate to maintain gentle reflux. After addition, the mixture was refluxed for {grignard_time} h to ensure complete consumption of Mg. The Grignard reagent was cooled to {addition_temp} °C, and a solution of {electrophile} ({electrophile_mass} mg, {electrophile_mmol} mmol, 1.0 equiv) in THF ({electrophile_thf_volume} mL) was added dropwise. The reaction was stirred at {reaction_temp} °C for {time} h, then quenched with saturated NH₄Cl at 0 °C. The mixture was extracted with EtOAc (3×), washed with brine, dried over Na₂SO₄, and concentrated. Purification by column chromatography (SiO₂, {column_eluent}) afforded the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Anhydrous conditions essential. Activation: I₂, 1,2-dibromoethane, or DIBAL-H. Solvents: THF or Et₂O. Titrate Grignard with menthol/1,10-phenanthroline before use.",
+    safety="Grignard formation is exothermic — control addition rate. Mg turnings: flammable. Anhydrous ether/THF: fire hazard.")
+
+_et("Mitsunobu Reaction",
+    aliases=["mitsunobu"],
+    category="Substitution",
+    template="""**{product_name}**
+
+To a solution of {alcohol} ({alcohol_mass} mg, {alcohol_mmol} mmol, 1.0 equiv), {nucleophile} ({nuc_mass} mg, {nuc_mmol} mmol, {nuc_equiv} equiv), and PPh₃ ({pph3_mass} mg, {pph3_mmol} mmol, {pph3_equiv} equiv) in THF ({solvent_volume} mL) at 0 °C was added DIAD ({diad_volume} μL, {diad_mmol} mmol, {diad_equiv} equiv) dropwise. The reaction was allowed to warm to room temperature and stirred for {time} h. The reaction was concentrated and purified directly by column chromatography (SiO₂, {column_eluent}) to afford the title compound ({product_mass} mg, {yield_percent}%).
+
+¹H NMR ({nmr_freq} MHz, {nmr_solvent}): δ {nmr_data_1h}
+¹³C NMR ({nmr_freq_13c} MHz, {nmr_solvent}): δ {nmr_data_13c}
+HRMS ({ms_method}): m/z calcd for {ms_formula} [M+{ms_ion}]⁺ {ms_calcd}, found {ms_found}.""",
+    notes="Nucleophile pKₐ < 11 required. DIAD or DEAD as azodicarboxylate. Inversion of configuration at stereocenter. TPPO byproduct can be problematic — use polymer-bound PPh₃ or Fluorous-PPh₃ for easier removal.",
+    safety="DIAD/DEAD: toxic, eye/skin irritant. PPh₃: sensitizer.")
+
+
+def lookup_experimental_template(query: str) -> dict | list[dict] | None:
+    """
+    Look up an experimental section template by reaction name.
+
+    Returns template dict or list of partial matches.
+    """
+    q = query.strip().lower()
+    if q in EXPERIMENTAL_TEMPLATES:
+        return EXPERIMENTAL_TEMPLATES[q]
+
+    # Fuzzy search
+    matches = []
+    for key, tmpl in EXPERIMENTAL_TEMPLATES.items():
+        if q in key or q in tmpl.get("category", "").lower():
+            if tmpl not in matches:
+                matches.append(tmpl)
+    return matches if matches else None
+
+
+# =============================================================================
+# Journal formatting guides
+# =============================================================================
+
+JOURNAL_GUIDES: dict[str, dict] = {}
+
+
+def _jg(name, *, aliases=None, publisher="", issn="", citation_style="",
+        word_limit="", abstract_limit="", figure_limit="",
+        reference_format="", si_allowed=True, graphical_abstract="",
+        submission_url="", open_access="", apc="", scope="",
+        file_formats="", special_notes=""):
+    key = name.lower()
+    JOURNAL_GUIDES[key] = {
+        "name": name,
+        "aliases": aliases or [],
+        "publisher": publisher,
+        "issn": issn,
+        "citation_style": citation_style,
+        "word_limit": word_limit,
+        "abstract_limit": abstract_limit,
+        "figure_limit": figure_limit,
+        "reference_format": reference_format,
+        "si_allowed": si_allowed,
+        "graphical_abstract": graphical_abstract,
+        "submission_url": submission_url,
+        "open_access": open_access,
+        "apc": apc,
+        "scope": scope,
+        "file_formats": file_formats,
+        "special_notes": special_notes,
+    }
+    for a in (aliases or []):
+        JOURNAL_GUIDES[a.lower()] = JOURNAL_GUIDES[key]
+
+
+_jg("Journal of the American Chemical Society",
+    aliases=["jacs", "j. am. chem. soc."],
+    publisher="ACS", issn="0002-7863",
+    citation_style="ACS (superscript numbered)",
+    word_limit="Articles: no strict limit (typically 8000-12000 words). Communications: 4 journal pages (~3500 words + figures).",
+    abstract_limit="200 words max",
+    figure_limit="No strict limit for articles. Communications: typically 3-4 figures.",
+    reference_format="ACS style: superscript numbers, numbered in order of appearance. Format: Author(s). Title. J. Abbrev. Year, Vol, Pages. DOI.",
+    graphical_abstract="Required. 3.25 × 1.75 inches, max 600 dpi.",
+    submission_url="https://pubs.acs.org/journal/jacsat",
+    open_access="Hybrid. ACS AuthorChoice (CC-BY or CC-BY-NC-ND).",
+    apc="~$5000 (ACS AuthorChoice)",
+    scope="All areas of chemistry — emphasis on significance and broad interest.",
+    file_formats="Manuscript: Word or LaTeX. Figures: TIFF, EPS, PDF (300+ dpi). SI: single PDF.",
+    special_notes="TOC graphic required. ORCID mandatory for corresponding author. Data availability statement required.")
+
+_jg("Angewandte Chemie International Edition",
+    aliases=["angew", "angew. chem. int. ed.", "angewandte"],
+    publisher="Wiley-VCH", issn="1433-7851",
+    citation_style="Angew style: superscript numbered, numbered in order of citation.",
+    word_limit="Communications: 4 pages (~2500 words + refs). Reviews: by invitation.",
+    abstract_limit="200 words max",
+    figure_limit="Communications: 3-5 figures/schemes/tables combined.",
+    reference_format="Angew format: [N] a) Author, Journal Year, Vol, Pages; b) ... Multiple sub-references with a), b), c).",
+    graphical_abstract="Table of Contents graphic required. Max 5 × 5 cm.",
+    submission_url="https://onlinelibrary.wiley.com/journal/15213773",
+    open_access="Hybrid. OnlineOpen (CC-BY, CC-BY-NC).",
+    apc="~€4500",
+    scope="All areas — must be of very high importance and broad interest.",
+    file_formats="Word preferred. Figures: TIFF, EPS (300+ dpi).",
+    special_notes="Very selective (~15% acceptance). Highlight (5 keywords) and catch-phrase for TOC required.")
+
+_jg("Nature Chemistry",
+    aliases=["nat. chem.", "nature chem"],
+    publisher="Nature Publishing Group / Springer Nature", issn="1755-4330",
+    citation_style="Nature style: superscript numbered, numbered in order of citation.",
+    word_limit="Articles: ~3000 words (main text, excluding methods, refs, figure legends). Letters: ~1500 words.",
+    abstract_limit="150 words max (no references in abstract)",
+    figure_limit="Articles: up to 6 display items (figures/tables). Letters: up to 4.",
+    reference_format="Nature style: Author(s). Title. Journal Abbrev. Vol, Pages (Year). Max 30 refs for Letters, 50 for Articles.",
+    graphical_abstract="Not required (Nature uses own design for TOC).",
+    submission_url="https://www.nature.com/nchem/",
+    open_access="Hybrid. Gold OA available.",
+    apc="~€9500 (Gold OA)",
+    scope="All areas of chemistry — emphasis on novelty and broad significance.",
+    file_formats="Word or LaTeX. Figures: separate files, 300+ dpi.",
+    special_notes="Extremely selective. Methods section separate from main text. Extended Data figures allowed (8 max). Cover letter essential.")
+
+_jg("Chemical Science",
+    aliases=["chem. sci.", "chem sci"],
+    publisher="Royal Society of Chemistry (RSC)", issn="2041-6520",
+    citation_style="RSC style: superscript numbered.",
+    word_limit="Edge articles: ~5 journal pages. Full articles: ~8 journal pages.",
+    abstract_limit="200 words max",
+    figure_limit="Reasonable (typically 4-8 figures).",
+    reference_format="RSC format: N. Author, J. Abbrev., Year, Vol, Pages. ESI references numbered separately.",
+    graphical_abstract="Table of Contents entry: max 8 × 4 cm.",
+    submission_url="https://www.rsc.org/journals-books-databases/about-journals/chemical-science/",
+    open_access="Full Gold OA (CC-BY). No APC — funded by RSC.",
+    apc="Free (no APC)",
+    scope="Chemistry of exceptional significance. All areas.",
+    file_formats="Word or LaTeX. Figures: TIFF, EPS.",
+    special_notes="Flagship RSC journal. Free open access (unique!). ESI (Electronic Supplementary Information) strongly encouraged.")
+
+_jg("Organic Letters",
+    aliases=["org. lett.", "orglett"],
+    publisher="ACS", issn="1523-7060",
+    citation_style="ACS style: superscript numbered.",
+    word_limit="Communications only: max 4 printed pages (~2500 words).",
+    abstract_limit="150 words max",
+    figure_limit="Typically 2-4 schemes + 1-2 figures/tables.",
+    reference_format="ACS style: superscript numbers.",
+    graphical_abstract="TOC graphic required.",
+    submission_url="https://pubs.acs.org/journal/orlef7",
+    open_access="Hybrid (ACS AuthorChoice).",
+    apc="~$5000",
+    scope="Organic and bioorganic chemistry — synthesis, mechanisms, theory, new reagents.",
+    file_formats="Word or LaTeX. SI: single PDF.",
+    special_notes="Short communications only. Highly competitive. Experimental + full characterization in SI.")
+
+_jg("The Journal of Organic Chemistry",
+    aliases=["joc", "j. org. chem."],
+    publisher="ACS", issn="0022-3263",
+    citation_style="ACS style: superscript numbered.",
+    word_limit="Full articles: no strict limit (typically 6000-12000). Notes: 4 pages.",
+    abstract_limit="200 words max",
+    figure_limit="Reasonable for full articles.",
+    reference_format="ACS style: superscript numbers.",
+    graphical_abstract="TOC graphic required.",
+    submission_url="https://pubs.acs.org/journal/joceah",
+    open_access="Hybrid.",
+    apc="~$5000",
+    scope="Organic chemistry: synthesis, mechanisms, theory, natural products, methodology.",
+    file_formats="Word or LaTeX.",
+    special_notes="Full experimental details in main manuscript (not SI). Complete NMR data for all new compounds.")
+
+_jg("ACS Catalysis",
+    aliases=["acs catal.", "acs catalysis"],
+    publisher="ACS", issn="2155-5435",
+    citation_style="ACS style.",
+    word_limit="Letters: 3000 words. Articles: no strict limit.",
+    abstract_limit="200 words",
+    figure_limit="Reasonable.",
+    reference_format="ACS style.",
+    graphical_abstract="TOC graphic required.",
+    submission_url="https://pubs.acs.org/journal/accacs",
+    open_access="Hybrid.",
+    apc="~$5000",
+    scope="Heterogeneous, homogeneous, bio-, and electro-catalysis. Mechanisms and applications.",
+    file_formats="Word or LaTeX.",
+    special_notes="Scope includes computational catalysis. Turnover numbers/frequencies expected.")
+
+_jg("Journal of Medicinal Chemistry",
+    aliases=["jmc", "j. med. chem."],
+    publisher="ACS", issn="0022-2623",
+    citation_style="ACS style.",
+    word_limit="Articles: 7500-10000 words. Letters: 3000 words. Perspectives: 10000 words.",
+    abstract_limit="250 words",
+    figure_limit="Reasonable.",
+    reference_format="ACS style.",
+    graphical_abstract="TOC graphic required.",
+    submission_url="https://pubs.acs.org/journal/jmcmar",
+    open_access="Hybrid.",
+    apc="~$5000",
+    scope="Drug design, SAR, ADME, computational med chem, chemical biology.",
+    file_formats="Word or LaTeX.",
+    special_notes="Requires biological data + SAR analysis. SMILES strings for all compounds. Molecular formula strings for HRMS.")
+
+_jg("Chemical Communications",
+    aliases=["chemcomm", "chem. commun.", "chem commun"],
+    publisher="RSC", issn="1359-7345",
+    citation_style="RSC style.",
+    word_limit="Communications: 3500 words max (including refs and captions).",
+    abstract_limit="No formal abstract — use first paragraph as summary.",
+    figure_limit="4 figures/tables max.",
+    reference_format="RSC format.",
+    graphical_abstract="TOC entry + graphical abstract preferred.",
+    submission_url="https://www.rsc.org/journals-books-databases/about-journals/chemcomm/",
+    open_access="Hybrid. Gold OA available.",
+    apc="~£2000",
+    scope="All areas of chemistry. Short, urgent communications.",
+    file_formats="Word. Figures: TIFF.",
+    special_notes="Very short format. All experimental details must go in ESI. Rapid publication.")
+
+_jg("Dalton Transactions",
+    aliases=["dalton", "dalton trans."],
+    publisher="RSC", issn="1477-9226",
+    citation_style="RSC style.",
+    word_limit="Communications: 4 pages. Full papers: no strict limit.",
+    abstract_limit="200 words",
+    figure_limit="Reasonable.",
+    reference_format="RSC format.",
+    graphical_abstract="TOC graphic.",
+    submission_url="https://www.rsc.org/journals-books-databases/about-journals/dalton-transactions/",
+    open_access="Hybrid.",
+    apc="~£2000",
+    scope="Inorganic, organometallic, bioinorganic chemistry. Catalysis, materials.",
+    file_formats="Word.",
+    special_notes="CIF files required for crystal structures. CCDC deposition mandatory.")
+
+_jg("Chemistry - A European Journal",
+    aliases=["chem. eur. j.", "cej", "chem eur j"],
+    publisher="Wiley-VCH", issn="0947-6539",
+    citation_style="Wiley (numbered).",
+    word_limit="Communications: 2500 words. Full papers: no strict limit.",
+    abstract_limit="200 words",
+    figure_limit="Reasonable.",
+    reference_format="Wiley format: numbered.",
+    graphical_abstract="Required.",
+    submission_url="https://chemistry-europe.onlinelibrary.wiley.com/journal/15213765",
+    open_access="Hybrid.",
+    apc="~€3500",
+    scope="All areas of chemistry.",
+    file_formats="Word.",
+    special_notes="Part of Chemistry Europe family of journals.")
+
+_jg("ACS Nano",
+    aliases=["acs nano"],
+    publisher="ACS", issn="1936-0851",
+    citation_style="ACS style.",
+    word_limit="Articles: no strict limit. Letters: ~3000 words.",
+    abstract_limit="250 words",
+    figure_limit="Reasonable.",
+    reference_format="ACS style.",
+    graphical_abstract="TOC graphic required.",
+    submission_url="https://pubs.acs.org/journal/ancac3",
+    open_access="Hybrid.",
+    apc="~$5000",
+    scope="Nanoscience and nanotechnology — synthesis, assembly, properties, applications.",
+    file_formats="Word or LaTeX.",
+    special_notes="Strong emphasis on characterization (TEM, AFM, DLS, etc.).")
+
+
+def lookup_journal_guide(query: str) -> dict | list[dict] | None:
+    """Look up journal formatting guide by name or alias."""
+    q = query.strip().lower()
+    if q in JOURNAL_GUIDES:
+        return JOURNAL_GUIDES[q]
+
+    matches = []
+    for key, guide in JOURNAL_GUIDES.items():
+        if q in key or q in guide.get("publisher", "").lower() or q in guide.get("scope", "").lower():
+            if guide not in matches:
+                matches.append(guide)
+    return matches if matches else None
+
+
+# =============================================================================
+# Supporting Information (SI) checklist
+# =============================================================================
+
+SI_REQUIREMENTS: dict[str, dict] = {
+    "1h_nmr": {
+        "name": "¹H NMR Spectrum",
+        "required_info": "Frequency (MHz), solvent, chemical shifts (δ in ppm), multiplicity (s, d, t, q, m, dd, dt, etc.), coupling constants (J in Hz), number of protons, assignment.",
+        "format": "δ X.XX (mult, J = X.X Hz, NH, assignment)",
+        "example": "δ 7.42 (dd, J = 8.2, 1.5 Hz, 2H, ArH), 3.85 (s, 3H, OCH₃)",
+        "common_mistakes": "Missing coupling constants. Wrong multiplicity for overlapping signals. Using 'br s' without explanation. Missing residual solvent peak assignment.",
+        "spectrum_required": True,
+        "checklist": [
+            "All peaks assigned",
+            "Coupling constants for non-singlets",
+            "Correct integration ratios",
+            "Residual solvent peak identified",
+            "Spectrum clean (no impurities >5%)",
+            "Baseline flat",
+        ],
+    },
+    "13c_nmr": {
+        "name": "¹³C NMR Spectrum",
+        "required_info": "Frequency (MHz), solvent, chemical shifts (δ in ppm). DEPT or HSQC data for multiplicity assignment recommended.",
+        "format": "δ X.X (Cₓ assignment, optional)",
+        "example": "δ 170.2 (C=O), 138.5 (C-Ar), 128.3 (CH-Ar), 55.2 (OCH₃)",
+        "common_mistakes": "Missing peaks (check molecule has correct number of unique carbons). Quaternary carbons sometimes weak/missing.",
+        "spectrum_required": True,
+        "checklist": [
+            "Number of peaks matches expected unique carbons",
+            "All peaks listed in text",
+            "Solvent peaks identified (CDCl₃: 77.16; DMSO-d₆: 39.52)",
+            "Spectrum shows adequate S/N for all peaks",
+        ],
+    },
+    "19f_nmr": {
+        "name": "¹⁹F NMR Spectrum",
+        "required_info": "Frequency (MHz), solvent, chemical shifts (δ in ppm referenced to CFCl₃ or internal standard), multiplicity, coupling constants.",
+        "format": "δ -X.X (mult, J = X.X Hz)",
+        "example": "δ −62.3 (s, 3F, CF₃), −110.5 (dd, J = 10.2, 8.5 Hz, 1F, ArF)",
+        "spectrum_required": True,
+        "checklist": ["Reference standard stated", "All F-containing groups assigned"],
+    },
+    "31p_nmr": {
+        "name": "³¹P NMR Spectrum",
+        "required_info": "Frequency (MHz), solvent, chemical shifts (δ referenced to H₃PO₄ = 0 ppm), multiplicity.",
+        "format": "δ X.X (mult)",
+        "example": "δ 26.5 (s)",
+        "spectrum_required": True,
+        "checklist": ["Reference standard stated", "Decoupled and/or coupled spectra"],
+    },
+    "2d_nmr": {
+        "name": "2D NMR (COSY, HSQC, HMBC, NOESY)",
+        "required_info": "Type of 2D experiment, frequency, solvent. Cross-peaks should be annotated.",
+        "format": "HSQC, HMBC, or NOESY cross-peaks listed or annotated on spectrum.",
+        "spectrum_required": True,
+        "checklist": [
+            "2D spectra included for structure elucidation of novel complex structures",
+            "Key cross-peaks labeled",
+            "Axis labels (¹H and ¹³C/¹H chemical shift axes)",
+        ],
+    },
+    "ir": {
+        "name": "Infrared Spectroscopy",
+        "required_info": "Method (KBr pellet, ATR, film), key absorptions in cm⁻¹ with assignment.",
+        "format": "IR (ATR): ν̃ = XXXX, XXXX, XXXX cm⁻¹",
+        "example": "IR (ATR): ν̃ = 3350 (br, O-H), 1720 (s, C=O), 1600, 1510 (Ar C=C) cm⁻¹",
+        "spectrum_required": True,
+        "checklist": ["Key functional group absorptions listed", "Method stated"],
+    },
+    "hrms": {
+        "name": "High-Resolution Mass Spectrometry",
+        "required_info": "Ionization method (ESI, EI, APCI, MALDI), ion type ([M+H]⁺, [M+Na]⁺, [M-H]⁻), calculated mass, found mass, molecular formula.",
+        "format": "HRMS (method): m/z calcd for C₁₂H₁₅NO₃ [M+ion]⁺ XXX.XXXX, found XXX.XXXX.",
+        "example": "HRMS (ESI): m/z calcd for C₁₂H₁₆NO₃ [M+H]⁺ 222.1125, found 222.1128.",
+        "common_mistakes": "Wrong molecular formula (forgetting to add H for [M+H]⁺). Mass accuracy >5 ppm. Wrong isotope pattern.",
+        "spectrum_required": True,
+        "checklist": [
+            "Correct molecular formula including ion",
+            "Mass accuracy within 5 ppm",
+            "Ionization method stated",
+            "Spectrum shows isotope pattern consistent with formula",
+        ],
+    },
+    "melting_point": {
+        "name": "Melting Point",
+        "required_info": "Range (onset-endset), method (capillary, DSC), corrected/uncorrected.",
+        "format": "mp X-Y °C (uncorrected)",
+        "example": "mp 152-154 °C (uncorrected)",
+        "spectrum_required": False,
+        "checklist": ["Range not too broad (<3 °C for pure compounds)", "Method stated"],
+    },
+    "optical_rotation": {
+        "name": "Optical Rotation",
+        "required_info": "Specific rotation [α], wavelength (D-line, 589 nm), temperature, concentration (g/100 mL), solvent.",
+        "format": "[α]²⁵_D = +/-X.X (c = Y.Y, solvent)",
+        "example": "[α]²⁵_D = −45.2 (c = 1.0, CHCl₃)",
+        "spectrum_required": False,
+        "checklist": ["Temperature stated", "Concentration and solvent stated", "Sign and magnitude reported"],
+    },
+    "hplc": {
+        "name": "HPLC Chromatogram",
+        "required_info": "Column type and dimensions, mobile phase (gradient or isocratic), flow rate, detection wavelength, retention time, purity.",
+        "format": "HPLC: tR = X.X min (purity: XX.X%, Column, gradient, λ = XXX nm)",
+        "example": "HPLC: tR = 12.3 min (purity: 99.2%, Phenomenex Luna C18 250×4.6 mm, H₂O/MeCN 0.1% TFA, 10-90% over 30 min, 1.0 mL/min, λ = 254 nm)",
+        "spectrum_required": True,
+        "checklist": [
+            "Full method reported (column, eluent, gradient, flow, detector)",
+            "Purity stated (≥95% for biological testing)",
+            "Retention time stated",
+            "Chromatogram included in SI",
+        ],
+    },
+    "chiral_hplc": {
+        "name": "Chiral HPLC",
+        "required_info": "Chiral column, eluent, flow rate, detection, retention times for both enantiomers, ee%.",
+        "format": "Chiral HPLC: tR(major) = X.X min, tR(minor) = X.X min, ee = XX% (column, eluent, flow)",
+        "spectrum_required": True,
+        "checklist": [
+            "Both enantiomers resolved (even if minor not detected)",
+            "Racemic reference shown",
+            "ee% calculated correctly",
+        ],
+    },
+    "xray": {
+        "name": "X-ray Crystallography",
+        "required_info": "Crystal data, data collection parameters, structure solution/refinement details, R-factors, CCDC number.",
+        "format": "CIF file deposited with CCDC (deposition number XXXXXXX).",
+        "spectrum_required": False,
+        "checklist": [
+            "CIF file deposited with CCDC",
+            "CCDC deposition number stated in manuscript",
+            "ORTEP or ellipsoid plot included",
+            "Crystal data table (a, b, c, α, β, γ, space group, Z, R₁, wR₂)",
+            "CheckCIF alerts addressed",
+            "Hydrogen atoms located or placed in calculated positions",
+        ],
+    },
+    "elemental_analysis": {
+        "name": "Elemental Analysis (CHN)",
+        "required_info": "Calculated and found percentages for C, H, N (and other elements). Must agree within 0.4%.",
+        "format": "Anal. Calcd for C₁₂H₁₅NO₃: C, 65.14; H, 6.83; N, 6.33. Found: C, 65.02; H, 6.79; N, 6.28.",
+        "spectrum_required": False,
+        "checklist": [
+            "Calcd and found within 0.4% for each element",
+            "Molecular formula includes any solvate/salt",
+        ],
+    },
+    "uv_vis": {
+        "name": "UV-Vis Spectroscopy",
+        "required_info": "Solvent, wavelength of maxima (λmax in nm), extinction coefficients (ε in M⁻¹cm⁻¹ or L mol⁻¹ cm⁻¹).",
+        "format": "UV-Vis (solvent): λmax (ε) = XXX nm (XXXX)",
+        "example": "UV-Vis (MeCN): λmax (ε) = 345 nm (12,500 M⁻¹cm⁻¹), 420 nm (8,200)",
+        "spectrum_required": True,
+        "checklist": ["Solvent stated", "ε values calculated from Beer-Lambert", "Concentration stated"],
+    },
+    "fluorescence": {
+        "name": "Fluorescence Spectroscopy",
+        "required_info": "Excitation wavelength, emission wavelength, quantum yield (Φ), solvent, concentration.",
+        "format": "Fluorescence (solvent): λex = XXX nm, λem = XXX nm, Φ = X.XX",
+        "spectrum_required": True,
+        "checklist": ["Reference standard for Φ stated", "Excitation and emission wavelengths"],
+    },
+    "tga": {
+        "name": "Thermogravimetric Analysis (TGA)",
+        "required_info": "Heating rate, atmosphere (N₂ or air), temperature range, mass loss events.",
+        "spectrum_required": True,
+        "checklist": ["Heating rate stated", "Atmosphere stated", "Onset temperatures identified"],
+    },
+    "dsc": {
+        "name": "Differential Scanning Calorimetry (DSC)",
+        "required_info": "Heating/cooling rate, temperature range, Tg, Tm, Tc values.",
+        "spectrum_required": True,
+        "checklist": ["Heating/cooling rates stated", "Cycle number stated (1st, 2nd heating)"],
+    },
+    "gc_ms": {
+        "name": "GC-MS",
+        "required_info": "Column, temperature program, carrier gas, injection mode, MS ionization.",
+        "format": "GC-MS: tR = X.X min, m/z (% relative intensity) = XXX [M]⁺ (XX), XXX (100).",
+        "spectrum_required": True,
+        "checklist": ["Method details stated", "Major fragments assigned", "M⁺ peak identified"],
+    },
+}
+
+
+def get_si_checklist(
+    content_types: list[str] | None = None,
+    compound_type: str = "small molecule",
+) -> dict:
+    """
+    Generate a Supporting Information checklist.
+
+    Args:
+        content_types: List of analytical methods (e.g., ['1h_nmr', '13c_nmr', 'hrms', 'hplc']).
+                       If None, returns the standard minimum for the compound type.
+        compound_type: 'small molecule', 'peptide', 'polymer', 'material', 'natural product'
+
+    Returns dict with checklist items and formatting guidance.
+    """
+    # Standard minimums by compound type
+    standard_minimums = {
+        "small molecule": ["1h_nmr", "13c_nmr", "hrms", "melting_point"],
+        "peptide": ["hplc", "hrms", "1h_nmr"],
+        "polymer": ["1h_nmr", "13c_nmr", "tga", "dsc"],
+        "material": ["1h_nmr", "tga", "dsc", "uv_vis"],
+        "natural product": ["1h_nmr", "13c_nmr", "2d_nmr", "hrms", "optical_rotation", "ir"],
+    }
+
+    if content_types is None:
+        content_types = standard_minimums.get(compound_type.lower(), standard_minimums["small molecule"])
+
+    items = []
+    for ct in content_types:
+        ct_lower = ct.lower().replace(" ", "_").replace("-", "_")
+        if ct_lower in SI_REQUIREMENTS:
+            items.append(SI_REQUIREMENTS[ct_lower])
+        else:
+            # Fuzzy match
+            for key, val in SI_REQUIREMENTS.items():
+                if ct_lower in key or ct_lower in val["name"].lower():
+                    items.append(val)
+                    break
+
+    return {
+        "compound_type": compound_type,
+        "requested_content": content_types,
+        "num_items": len(items),
+        "checklist": items,
+        "general_tips": [
+            "Number compounds sequentially (1, 2a, 2b, 3, ...)",
+            "Include General Information section (reagent sources, instrument models)",
+            "Provide spectra as images (not raw data) unless journal requests FIDs",
+            "Label all spectra with compound number and solvent",
+            "Include a table of contents for the SI document",
+            "Purity: ≥95% for compounds submitted for biological testing",
+        ],
+    }
+
+
+# =============================================================================
+# Standard chemistry abbreviations
+# =============================================================================
+
+ABBREVIATIONS: dict[str, dict[str, str]] = {
+    "solvents": {
+        "ACN": "acetonitrile (MeCN)",
+        "DCE": "1,2-dichloroethane",
+        "DCM": "dichloromethane (CH₂Cl₂)",
+        "DMA": "N,N-dimethylacetamide",
+        "DME": "1,2-dimethoxyethane",
+        "DMF": "N,N-dimethylformamide",
+        "DMSO": "dimethyl sulfoxide",
+        "EtOAc": "ethyl acetate",
+        "EtOH": "ethanol",
+        "Et₂O": "diethyl ether",
+        "Hex": "hexane(s)",
+        "MeCN": "acetonitrile",
+        "MeOH": "methanol",
+        "NMP": "N-methyl-2-pyrrolidone",
+        "PE": "petroleum ether",
+        "iPrOH": "2-propanol (isopropanol)",
+        "THF": "tetrahydrofuran",
+        "TFE": "2,2,2-trifluoroethanol",
+        "tol": "toluene",
+    },
+    "reagents": {
+        "AIBN": "azobisisobutyronitrile",
+        "BHT": "butylated hydroxytoluene",
+        "Boc": "tert-butyloxycarbonyl",
+        "Boc₂O": "di-tert-butyl dicarbonate",
+        "BPO": "benzoyl peroxide",
+        "Cbz": "benzyloxycarbonyl",
+        "CSA": "camphorsulfonic acid",
+        "DABCO": "1,4-diazabicyclo[2.2.2]octane",
+        "DBU": "1,8-diazabicyclo[5.4.0]undec-7-ene",
+        "DCC": "N,N′-dicyclohexylcarbodiimide",
+        "DDQ": "2,3-dichloro-5,6-dicyano-1,4-benzoquinone",
+        "DEAD": "diethyl azodicarboxylate",
+        "DIAD": "diisopropyl azodicarboxylate",
+        "DIBAL-H": "diisobutylaluminium hydride",
+        "DIPEA": "N,N-diisopropylethylamine (Hünig's base)",
+        "DMAP": "4-(dimethylamino)pyridine",
+        "DMP": "Dess-Martin periodinane",
+        "EDC": "1-ethyl-3-(3-dimethylaminopropyl)carbodiimide",
+        "Fmoc": "9-fluorenylmethyloxycarbonyl",
+        "HATU": "hexafluorophosphate azabenzotriazole tetramethyl uronium",
+        "HBTU": "hexafluorophosphate benzotriazole tetramethyl uronium",
+        "HOBt": "1-hydroxybenzotriazole",
+        "IBX": "2-iodoxybenzoic acid",
+        "LAH": "lithium aluminium hydride (LiAlH₄)",
+        "LDA": "lithium diisopropylamide",
+        "LiHMDS": "lithium bis(trimethylsilyl)amide",
+        "mCPBA": "meta-chloroperoxybenzoic acid",
+        "MOM": "methoxymethyl",
+        "Ms": "methanesulfonyl (mesyl)",
+        "NaHMDS": "sodium bis(trimethylsilyl)amide",
+        "NBS": "N-bromosuccinimide",
+        "NCS": "N-chlorosuccinimide",
+        "NMO": "N-methylmorpholine N-oxide",
+        "NOBIN": "2-amino-2′-hydroxy-1,1′-binaphthyl",
+        "PDC": "pyridinium dichromate",
+        "PCC": "pyridinium chlorochromate",
+        "PMB": "para-methoxybenzyl",
+        "PTSA": "para-toluenesulfonic acid",
+        "SEM": "2-(trimethylsilyl)ethoxymethyl",
+        "TBAF": "tetrabutylammonium fluoride",
+        "TBAI": "tetrabutylammonium iodide",
+        "TBDMS": "tert-butyldimethylsilyl (= TBS)",
+        "TBS": "tert-butyldimethylsilyl",
+        "TBDPS": "tert-butyldiphenylsilyl",
+        "TCA": "trichloroacetic acid",
+        "TEMPO": "(2,2,6,6-tetramethylpiperidin-1-yl)oxyl",
+        "TES": "triethylsilyl",
+        "Tf": "trifluoromethanesulfonyl (triflyl)",
+        "TFA": "trifluoroacetic acid",
+        "TfOH": "triflic acid",
+        "TIPS": "triisopropylsilyl",
+        "TMS": "trimethylsilyl",
+        "Ts": "para-toluenesulfonyl (tosyl)",
+        "Xantphos": "4,5-bis(diphenylphosphino)-9,9-dimethylxanthene",
+    },
+    "catalysts_ligands": {
+        "BINAP": "2,2′-bis(diphenylphosphino)-1,1′-binaphthyl",
+        "BrettPhos": "2-(dicyclohexylphosphino)-3,6-dimethoxy-2′,4′,6′-triisopropyl-1,1′-biphenyl",
+        "cod": "1,5-cyclooctadiene",
+        "Cy": "cyclohexyl",
+        "dba": "dibenzylideneacetone",
+        "DavePhos": "2-dicyclohexylphosphino-2′-(N,N-dimethylamino)biphenyl",
+        "dppf": "1,1′-bis(diphenylphosphino)ferrocene",
+        "dppe": "1,2-bis(diphenylphosphino)ethane",
+        "dppp": "1,3-bis(diphenylphosphino)propane",
+        "JohnPhos": "2-(di-tert-butylphosphino)biphenyl",
+        "P(o-tol)₃": "tri(ortho-tolyl)phosphine",
+        "PCy₃": "tricyclohexylphosphine",
+        "Pd/C": "palladium on carbon",
+        "Pd₂(dba)₃": "tris(dibenzylideneacetone)dipalladium(0)",
+        "Pd(OAc)₂": "palladium(II) acetate",
+        "Pd(PPh₃)₄": "tetrakis(triphenylphosphine)palladium(0)",
+        "PPh₃": "triphenylphosphine",
+        "RuPhos": "2-dicyclohexylphosphino-2′,6′-diisopropoxybiphenyl",
+        "SPhos": "2-dicyclohexylphosphino-2′,6′-dimethoxybiphenyl",
+        "XPhos": "2-dicyclohexylphosphino-2′,4′,6′-triisopropylbiphenyl",
+        "IPr": "1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (NHC ligand)",
+    },
+    "spectroscopy": {
+        "ATR": "attenuated total reflectance",
+        "COSY": "correlated spectroscopy",
+        "DEPT": "distortionless enhancement by polarization transfer",
+        "DQF-COSY": "double quantum filtered COSY",
+        "EI": "electron ionization",
+        "ESI": "electrospray ionization",
+        "FAB": "fast atom bombardment",
+        "FID": "free induction decay",
+        "HMBC": "heteronuclear multiple bond correlation",
+        "HSQC": "heteronuclear single quantum coherence",
+        "HRMS": "high-resolution mass spectrometry",
+        "LRMS": "low-resolution mass spectrometry",
+        "MALDI": "matrix-assisted laser desorption/ionization",
+        "MS": "mass spectrometry",
+        "NMR": "nuclear magnetic resonance",
+        "NOESY": "nuclear Overhauser effect spectroscopy",
+        "ROESY": "rotating frame Overhauser effect spectroscopy",
+        "TOCSY": "total correlation spectroscopy",
+        "TOF": "time-of-flight",
+        "UV-Vis": "ultraviolet-visible spectroscopy",
+    },
+    "analytical": {
+        "CD": "circular dichroism",
+        "CE": "capillary electrophoresis",
+        "DLS": "dynamic light scattering",
+        "DSC": "differential scanning calorimetry",
+        "FPLC": "fast protein liquid chromatography",
+        "GC": "gas chromatography",
+        "GPC": "gel permeation chromatography",
+        "HPLC": "high-performance liquid chromatography",
+        "ICP-MS": "inductively coupled plasma mass spectrometry",
+        "ITC": "isothermal titration calorimetry",
+        "LC-MS": "liquid chromatography-mass spectrometry",
+        "MPLC": "medium-pressure liquid chromatography",
+        "ORD": "optical rotatory dispersion",
+        "PAGE": "polyacrylamide gel electrophoresis",
+        "RP-HPLC": "reversed-phase HPLC",
+        "SEC": "size exclusion chromatography",
+        "SEM": "scanning electron microscopy",
+        "SFC": "supercritical fluid chromatography",
+        "SPR": "surface plasmon resonance",
+        "TEM": "transmission electron microscopy",
+        "TGA": "thermogravimetric analysis",
+        "TLC": "thin-layer chromatography",
+        "UPLC": "ultra-performance liquid chromatography",
+        "XPS": "X-ray photoelectron spectroscopy",
+        "XRD": "X-ray diffraction",
+    },
+    "general": {
+        "aq": "aqueous",
+        "br": "broad (NMR)",
+        "cat.": "catalytic",
+        "conc.": "concentrated",
+        "d": "doublet (NMR)",
+        "dd": "doublet of doublets (NMR)",
+        "dt": "doublet of triplets (NMR)",
+        "ee": "enantiomeric excess",
+        "er": "enantiomeric ratio",
+        "dr": "diastereomeric ratio",
+        "equiv": "equivalent(s)",
+        "m": "multiplet (NMR)",
+        "M": "molar (mol/L)",
+        "mp": "melting point",
+        "MW": "molecular weight",
+        "ppm": "parts per million",
+        "q": "quartet (NMR)",
+        "quant.": "quantitative",
+        "Rf": "retention factor (TLC)",
+        "RT": "room temperature",
+        "s": "singlet (NMR)",
+        "sat.": "saturated",
+        "t": "triplet (NMR)",
+        "tR": "retention time",
+        "v/v": "volume per volume",
+        "w/w": "weight per weight",
+    },
+    "biochemistry": {
+        "ATP": "adenosine triphosphate",
+        "BSA": "bovine serum albumin",
+        "cDNA": "complementary DNA",
+        "DMEM": "Dulbecco's modified Eagle medium",
+        "DNA": "deoxyribonucleic acid",
+        "DTT": "dithiothreitol",
+        "EDTA": "ethylenediaminetetraacetic acid",
+        "ELISA": "enzyme-linked immunosorbent assay",
+        "FBS": "fetal bovine serum",
+        "FRET": "Förster resonance energy transfer",
+        "GSH": "glutathione (reduced)",
+        "GSSG": "glutathione (oxidized)",
+        "IC₅₀": "half-maximal inhibitory concentration",
+        "Kd": "dissociation constant",
+        "Ki": "inhibition constant",
+        "Km": "Michaelis constant",
+        "mRNA": "messenger RNA",
+        "NAD⁺/NADH": "nicotinamide adenine dinucleotide (oxidized/reduced)",
+        "PBS": "phosphate-buffered saline",
+        "PCR": "polymerase chain reaction",
+        "PDB": "Protein Data Bank",
+        "PI": "propidium iodide",
+        "RNA": "ribonucleic acid",
+        "SAR": "structure-activity relationship",
+        "SDS": "sodium dodecyl sulfate",
+        "siRNA": "small interfering RNA",
+        "TRIS": "tris(hydroxymethyl)aminomethane",
+        "WT": "wild-type",
+    },
+}
+
+
+def get_abbreviations(category: str = "all") -> dict:
+    """
+    Get standard chemistry abbreviations.
+
+    Args:
+        category: 'solvents', 'reagents', 'catalysts_ligands', 'spectroscopy',
+                  'analytical', 'general', 'biochemistry', or 'all'
+
+    Returns dict of abbreviation → full name mappings.
+    """
+    cat = category.strip().lower()
+    if cat == "all":
+        combined = {}
+        for cat_name, abbrevs in ABBREVIATIONS.items():
+            for k, v in abbrevs.items():
+                combined[k] = f"{v} [{cat_name}]"
+        return {
+            "category": "all",
+            "num_abbreviations": len(combined),
+            "abbreviations": combined,
+        }
+
+    # Fuzzy match
+    for key, data in ABBREVIATIONS.items():
+        if cat in key or key in cat:
+            return {
+                "category": key,
+                "num_abbreviations": len(data),
+                "abbreviations": data,
+            }
+
+    return {"error": f"Unknown category: {category}. Available: {', '.join(ABBREVIATIONS.keys())}"}
+
+
+def lookup_abbreviation(query: str) -> dict:
+    """Look up what a specific abbreviation means."""
+    q = query.strip()
+    results = {}
+    for cat, abbrevs in ABBREVIATIONS.items():
+        for abbr, full in abbrevs.items():
+            if q.lower() == abbr.lower() or q.lower() in abbr.lower():
+                results[abbr] = {"meaning": full, "category": cat}
+    if not results:
+        # Reverse search: look in full names
+        for cat, abbrevs in ABBREVIATIONS.items():
+            for abbr, full in abbrevs.items():
+                if q.lower() in full.lower():
+                    results[abbr] = {"meaning": full, "category": cat}
+
+    return {
+        "query": q,
+        "num_results": len(results),
+        "results": results,
+    }
+
+
+# =============================================================================
+# Thesis section writing guide
+# =============================================================================
+
+THESIS_GUIDES: dict[str, dict] = {
+    "abstract": {
+        "name": "Abstract",
+        "purpose": "Concise summary of the entire thesis/paper. Should stand alone.",
+        "structure": [
+            "Background / Context (1-2 sentences)",
+            "Research gap / Objective (1 sentence)",
+            "Methods / Approach (1-2 sentences)",
+            "Key results (2-3 sentences)",
+            "Significance / Conclusions (1 sentence)",
+        ],
+        "word_limit": "Thesis: 300-500 words. Papers: 150-250 words (journal-specific).",
+        "tips": [
+            "Write LAST, after all other sections",
+            "No references in the abstract",
+            "No abbreviations without definition (or avoid altogether)",
+            "Every sentence should convey essential information",
+            "Include key numerical results (yields, ee's, Ki values)",
+            "Use past tense for results, present tense for conclusions",
+        ],
+        "common_mistakes": [
+            "Too vague — no specific results",
+            "Too detailed — reads like a methods section",
+            "Including information not in the main text",
+            "Using jargon without definition",
+        ],
+    },
+    "introduction": {
+        "name": "Introduction",
+        "purpose": "Establish context, identify the gap, state your contribution.",
+        "structure": [
+            "Broad context: What is the field? Why does it matter? (1-2 paragraphs)",
+            "Literature review: What has been done? Key developments. (3-5 paragraphs)",
+            "The gap: What remains unknown or unsolved? (1 paragraph)",
+            "Your contribution: What did you do and why? (1 paragraph)",
+            "Outline: Brief overview of thesis structure (for thesis only)",
+        ],
+        "tips": [
+            "Funnel structure: broad → specific → your work",
+            "Cite primary literature, not just reviews",
+            "Be objective about others' work — acknowledge strengths and limitations",
+            "Don't bury your contribution at the very end",
+            "State your hypothesis clearly if applicable",
+            "Use present tense for established facts, past tense for specific studies",
+        ],
+        "common_mistakes": [
+            "Too broad introduction that reads like a textbook",
+            "Literature review without clear narrative thread",
+            "Gap statement is too vague ('little is known about...')",
+            "Missing connection between gap and your work",
+            "Citing too many reviews, not enough primary literature",
+        ],
+    },
+    "results_discussion": {
+        "name": "Results and Discussion",
+        "purpose": "Present findings with interpretation. Can be combined or separate sections.",
+        "structure": [
+            "Organize by logical theme, not chronological order",
+            "Each subsection: aim → approach → results → interpretation",
+            "Figures and schemes should drive the narrative",
+            "Compare with literature — agree? disagree? why?",
+            "Address unexpected results honestly",
+        ],
+        "tips": [
+            "Lead with your strongest result",
+            "Every figure/table should be referenced and discussed in text",
+            "Don't just describe data — interpret it",
+            "Use schemes for reaction development, figures for data",
+            "Discuss selectivity, scope, and limitations",
+            "Compare yields/selectivities with literature benchmarks",
+            "Use 'we observed' not 'it was observed' (active voice)",
+        ],
+        "common_mistakes": [
+            "Chronological 'lab diary' organization instead of logical narrative",
+            "Figures not discussed in text",
+            "Over-interpreting insignificant differences",
+            "Not acknowledging limitations",
+            "Repeating numbers from tables in running text",
+        ],
+    },
+    "experimental": {
+        "name": "Experimental Section",
+        "purpose": "Enable exact reproduction by a competent chemist.",
+        "structure": [
+            "General Information: instruments, reagent sources, purification of solvents",
+            "General Procedures (if applicable): used for repetitive reactions",
+            "Specific Compound Procedures: one per new compound",
+            "Each procedure: substrate, reagent amounts (mass, mmol, equiv), conditions, workup, purification, yield",
+            "Full characterization data for each new compound",
+        ],
+        "tips": [
+            "Be specific: '5 mL' not 'some', '80 °C' not 'heated'",
+            "Report actual amounts used, not theoretical",
+            "Include equiv for each reagent",
+            "State how reaction progress was monitored (TLC, LC-MS)",
+            "Report yield as mass and percentage",
+            "Use consistent formatting for all procedures",
+            "Known compounds: cite literature preparation, provide ¹H NMR to confirm identity",
+        ],
+        "common_mistakes": [
+            "Missing equivalents for reagents",
+            "Vague: 'worked up in the usual manner'",
+            "Inconsistent formatting between procedures",
+            "Missing characterization for new compounds",
+            "Not specifying which NMR solvent was used",
+            "Reporting yields > 100% without explanation",
+        ],
+    },
+    "conclusion": {
+        "name": "Conclusion",
+        "purpose": "Summarize key findings and their significance. Look forward.",
+        "structure": [
+            "Restate the problem / objective (1 sentence)",
+            "Key findings — what was accomplished (2-3 paragraphs)",
+            "Significance — why this matters (1 paragraph)",
+            "Future work — what comes next (1 paragraph)",
+        ],
+        "tips": [
+            "Don't just repeat the abstract",
+            "Be specific about what was achieved",
+            "Be honest about limitations",
+            "Future work should be realistic and specific",
+            "End on a forward-looking, positive note",
+        ],
+        "common_mistakes": [
+            "Simply repeating the abstract",
+            "Introducing new results not in the main text",
+            "Overly speculative future work",
+            "Too brief — dismissive of own work",
+        ],
+    },
+    "supporting_information": {
+        "name": "Supporting Information",
+        "purpose": "Provide complete analytical data, additional experiments, and full characterization.",
+        "structure": [
+            "Table of Contents",
+            "General Information",
+            "Synthetic Procedures (if not in main text)",
+            "Characterization Data (organized by compound number)",
+            "NMR Spectra (¹H, ¹³C, 2D if applicable)",
+            "HPLC/GC traces",
+            "HRMS data",
+            "X-ray crystallographic data (CIF reference)",
+            "Computational details (if applicable)",
+            "Additional tables and figures",
+        ],
+        "tips": [
+            "Number compounds consistently with main text",
+            "Include a table of contents for SI > 20 pages",
+            "Label every spectrum with compound number and conditions",
+            "Include full-page spectra, not cropped fragments",
+            "Arrange spectra in compound number order",
+        ],
+        "common_mistakes": [
+            "Unlabeled spectra",
+            "Missing ¹³C NMR for new compounds",
+            "HRMS without isotope pattern",
+            "NMR spectra with obvious impurities not acknowledged",
+        ],
+    },
+}
+
+
+def get_thesis_guide(section: str) -> dict | None:
+    """
+    Get writing guidance for a thesis/paper section.
+
+    Args:
+        section: 'abstract', 'introduction', 'results_discussion', 'experimental',
+                 'conclusion', 'supporting_information'
+    """
+    s = section.strip().lower().replace(" ", "_")
+    if s in THESIS_GUIDES:
+        return THESIS_GUIDES[s]
+
+    # Fuzzy match
+    for key, guide in THESIS_GUIDES.items():
+        if s in key or s in guide.get("name", "").lower():
+            return guide
+
+    return {"error": f"Unknown section: {section}. Available: {', '.join(THESIS_GUIDES.keys())}"}