Phase 1Synthesis and reaction
01Incoming identification and quality check of raw materials and reagents (incoming testing, raw material identification)
Starting-material purity determines the quality of the whole synthesis, and impurities from the first step are carried through to later steps.
- Standard method
- Identification by FT-IR (infrared spectroscopy) + purity confirmation by HPLC
- Reagents and materials
- HPLC mobile phase solvents, API reference standards and impurity standards (CRS)
Why it is the standard. ICH Q7 (GMP for APIs) requires identification testing of starting materials and reagents. IR gives rapid identification from the functional-group fingerprint and is a standard identification method in the pharmacopoeias (USP/JP/EP). Purity is complemented by HPLC.
Check also. FT-IR (infrared spectroscopy) can rapidly identify 'what compound it is' from the fingerprint of its functional groups, but it cannot distinguish enantiomers, crystal polymorphs or trace structural analogues. The purity and stereochemistry of the starting material are covered by tests based on other principles, such as HPLC and chiral analysis.
About this step and the alternatives
Think of it as inspecting the ingredients in cooking. Before charging to the reactor, this step checks at the door that the raw material or reagent is really the target compound and that its purity is within specification.
The procedure is simple. Infrared spectroscopy (FT-IR) identifies the molecular skeleton like a fingerprint, and high-performance liquid chromatography (HPLC) measures purity. Together, the two pin down both identity and quality.
The outcome of a synthesis is determined by the purity of the starting materials. If poor-quality material gets in at the first step, impurities are carried through to the later steps. The key is therefore to stop quality problems at the entrance.
Synthesis is determined by the purity of the starting materials. If poor-quality material enters the first step, impurities are carried through to the later steps. So before charging to the reaction, confirm 'is this really the target compound?' and 'is the purity within specification?'
Alternatives in practice
- Rapid identification by near-infrared/Raman spectroscopy · Bruker MPA II (NIR)/Thermo Scientific TruScan RM (handheld Raman, raw material identification through the container) — Effective for nondestructive identification through the container at receipt. Discriminating variants requires building a library first.
- Gas chromatography (volatile raw materials and solvents) · Agilent 8890 GC (FID)/Shimadzu Nexis GC-2030 — For confirming the purity/impurities of volatile liquid raw materials and solvents.
- Confirmation of physical constants such as melting point and optical rotation · Mettler Toledo MP90 melting point apparatus/Anton Paar MCP 5100 polarimeter — A simple supporting identification. Low molecular specificity, so unsuitable as a primary method.
02Reaction progress monitoring and endpoint determination (in-process control) (in-process control/reaction monitoring)
Misjudging the stop point leaves unreacted starting material or increases by-products. Endpoint determination governs yield.
- Standard method
- Monitoring of conversion and impurity profile by HPLC (sampled in-process analysis)
- Reagents and materials
- HPLC mobile phase solvents, API reference standards and impurity standards (CRS)
Why it is the standard. ICH Q7 requires in-process control (IPC). HPLC is the industry standard for confirming reaction completion and can quantitatively track residual starting material, intermediates and impurities at the same time (consistent with practical descriptions such as Pharmaguideline).
With Racemic synthesis + optical resolution (diastereomeric salt crystallization)
- Intermediate isolation doubles as optical resolution
- Method: Add the resolving agent to the racemic intermediate to form diastereomeric salts, then crystallize the target salt preferentially, or by fractional recrystallization (repeated as needed), based on the solubility difference to enrich it optically. Racemization and recycling of the opposite enantiomer in the mother liquor are considered
- Reagents: Resolving agent (tartaric acid derivatives, mandelic acid, CSA, etc.) + recrystallization solvent system
- Check also: The theoretical yield is at most 50% per stage. Preferential crystallization is possible only for conglomerates, and most cases are salt-formation-type resolutions
About this step and the alternatives
A mid-process check to judge when to 'stop' the reaction. Like tasting a simmering dish, you check partway how far the running reaction has progressed.
The method is to draw a small amount of liquid from the reaction vessel and follow the conversion and the appearance of impurities by high-performance liquid chromatography (HPLC). This is called in-process control.
Misjudging the stop point is costly. Too early and unreacted starting material remains; too late and over-reaction increases by-products. Determine the optimal endpoint before moving on to the next operation.
If you do not check how far the reaction has progressed along the way, you will misjudge when to stop. Stop too early and unreacted starting material remains; too late and over-reaction increases by-products. Track the conversion in real time or by sampling, and move on at the optimal endpoint.
Alternatives in practice
- In situ ATR-FTIR (real-time reaction tracking) · Mettler Toledo ReactIR 702L (DiComp/SiComp probes) — Monitors reaction start and endpoint in real time without sampling. Better suited to understanding behavior than to quantitation.
- TLC (simple reaction tracking) · Merck TLC silica gel 60 F254 plates + UV cabinet (CAMAG UV Cabinet 4) — Quick at the bench. Low quantitation, so it complements the primary method.
- In-line/benchtop NMR, NIR · Bruker Fourier 80 (benchtop NMR)/Bruker Matrix-F (process NIR) — Depends on the solvent and reaction system, but allows nondestructive continuous monitoring.
03Isolation and purity confirmation of intermediates (key intermediates and registered starting materials) — in multistep synthesis, the intermediate is isolated after each reaction by crystallization, filtration, etc., and brought into conformance with the IPC specification before moving to the next step (intermediate isolation and IPC)
In multistep synthesis, each intermediate is isolated and brought into specification so that impurities are not carried forward
- Standard method
- Isolation of intermediates by crystallization and filtration, with in-process control (purity, content and impurity confirmation by HPLC/GC)
- Reagents and materials
- Bulk organic solvents, API reference standards and impurity standards (CRS)
Why it is the standard. Intermediate isolation is a step that standardly must be passed in multistep API synthesis and is the most important control point for cutting off impurity carry-over.
Check also. Which intermediate is designated as the registered starting material (RSM) in the filing is a matter to be agreed with the regulatory authority; all steps and impurities from that point on become subject to control. Where the line is drawn determines the later filing burden, so it is not decided by internal judgment alone.
About this step and the alternatives
A checkpoint: each time a reaction in a multistep synthesis finishes, the key intermediate or registered starting material (RSM/KSM) is taken out of the liquid, its purity is confirmed, and only then is it passed on.
It is isolated as a solid by crystallization and filtration, dried, and then judged for purity, content and impurities against the specification. If it does not pass, it does not go on to the next reaction.
Why check at every stage? Because the more impurities are removed at the intermediate stage, the more stable the quality of the final API. What is built up along the way determines the final quality.
In the standard multistep synthesis of a small-molecule API, it is usual to isolate and dry the key intermediates and registered starting materials (RSM/KSM) after the reaction ends, and to judge purity and impurity profile against the specification before moving to the next reaction. Removing impurities at the intermediate stage directly affects the quality of the final API.
Alternatives in practice
- Telescoping (carrying the intermediate into the next reaction without isolation) · Mettler Toledo OptiMax 1001 (with ReactIR for in-line concentration monitoring) — Shortens the process and improves yield. The risk is that the quality of each intermediate cannot be controlled directly.
- Intermediate purification by column chromatography · Biotage Selekt (Sfär Silica cartridges)/Teledyne ISCO CombiFlash NextGen — Effective for hard-to-separate intermediates. At large scale, cost and solvent load are high.
Phase 2Workup and crystallization
04Primary purification of the crude product by extraction, phase separation and washing (extraction, phase separation, water washing)
Primary purification that removes salts, catalyst and water-soluble impurities coarsely by phase separation, reducing the load on the later crystallization.
- Standard method
- Liquid-liquid extraction, phase separation and washing (water wash, acid/base wash)
- Reagents and materials
- Bulk organic solvents
Why it is the standard. Standard workup for chemically synthesized APIs. Phase separation removes water-soluble impurities and inorganic salts efficiently, and in ICH Q11 process design it is also positioned as a basic primary purification operation.
About this step and the alternatives
The liquid after the reaction is a 'hodgepodge' in which salts, catalyst, unreacted material and solvent are mixed in with the target compound. This is the primary purification that first washes out the bulk of them.
The liquid is washed after being separated into a layer compatible with water (aqueous layer) and a layer compatible with oil (organic layer). Water-soluble impurities and inorganic salts are moved to the aqueous side and discarded, and the target stays in the organic layer.
The more is removed coarsely here, the cleaner the later crystallization proceeds. It is, so to speak, the prep work that makes the finishing crystallization easier.
In addition to the target compound, the reaction liquid contains salts, catalyst, unreacted material and solvent. Separating it into aqueous and organic layers and washing first removes water-soluble impurities and inorganic salts to a large extent. The more is removed coarsely here, the easier the later crystallization becomes.
Alternatives in practice
- Activated carbon treatment + filtration (decolorization and removal of trace impurities) · Cabot NORIT powdered activated carbon + Pall SUPRApak depth filter/Sartorius Sartoclear depth filter — Effective for pigments and polar impurities. Watch for API loss and the handling of carbon.
- Quench + filtration (removal of solid by-products) · Agitated Nutsche Filter (Rosenmund RVNF/De Dietrich Guedu) — A simple way to remove salts and inorganic solids.
- Continuous countercurrent extraction (continuous liquid-liquid extraction) · Sulzer centrifugal extractor/Koch-Glitsch countercurrent extraction column — Suited to large-volume, continuous production. Capital investment and emulsion management are the challenges.
05Decolorization (activated carbon treatment) and clarifying (polish) filtration — activated carbon is added to the crude product solution and stirred to adsorb and remove colored impurities, trace metals and fine particles, and the carbon and foreign matter are removed by clarifying filtration before the solution goes to crystallization (decolorization and clarifying filtration/carbon treatment)
To remove colored impurities, trace metals and foreign matter by activated carbon and clarifying filtration before crystallization and obtain high-purity crystals
- Standard method
- Activated carbon treatment
- Reagents and materials
- Activated carbon decolorizing adsorbents, Filter aids and flocculants
Why it is the standard. Activated carbon decolorization + clarifying filtration before crystallization is a step that standardly must be passed in small-molecule API purification.
Check also. Activated carbon adsorbs colored substances and trace metals well, but it can also adsorb the API itself and lower the yield. The amount of carbon and the contact time are set by balancing decolorizing effect against recovery, and attention is also paid to adsorption properties that vary from lot to lot.
With Racemic synthesis + optical resolution (diastereomeric salt crystallization)
- Ordinary crystallization → fractional crystallization of diastereomeric salts
- Method: In addition to controlled crystallization of the polymorph and solid form, fractional recrystallization is performed using the solubility difference of the diastereomeric salts. After resolution, the salt is decomposed with acid/base to regenerate the free-form enantiomer, and the final crystallization of the API is then performed
- Reagents: Chiral resolving agent salt; acid/base for salt decomposition (HCl, NaOH/NaHCO3, etc.)
- Check also: The endpoint of fractional recrystallization is determined by chiral purity (optical rotation/chiral HPLC), and residual resolving agent and the opposite diastereomer are controlled as impurities
About this step and the alternatives
A 'polishing' step done just before crystallization. Activated carbon is added to the crude product solution and stirred, so that colored substances, residual metals and trace impurities are soaked up onto the carbon surface.
After adsorption, clarifying (polish) filtration filters off carbon grains and insoluble foreign matter. This gives a clear, clean solution, ready for crystallization.
Activated carbon treatment before crystallization is the norm in API purification. If color and trace impurities are removed first, the target crystal form can be precipitated cleanly in the crystallization that follows.
In API purification, it is standard to treat with activated carbon immediately before crystallization to adsorb and remove colored substances, residual metals and trace impurities. The clarifying (polish) filtration that follows removes carbon particles and insoluble foreign matter, and the target crystal form is precipitated from a clean solution.
Alternatives in practice
- Removal of residual catalyst (Pd, etc.) with metal scavenger resins · Johnson Matthey QuadraPure TU/Smopex fibers, SiliCycle SiliaMetS Thiol/Thiourea — Selective removal of residual Pd/metals. Decolorization is limited, so choose between it and carbon treatment as appropriate.
- In-line passage through cartridge-type activated carbon · 3M Zeta Plus activated carbon cartridges (CUNO)/Pall Seitz AKS carbon modules — Decolorization in a closed system, avoiding the addition of powdered carbon. Capacity is smaller than with depth-type carbon.
06Purification by crystallization and building the target solid form (polymorph, salt form) (crystallization and polymorph control)
The most important step, handling purification and solid form determination at once; polymorph and salt determine solubility, stability and manufacturability.
- Standard method
- Controlled crystallization (cooling/antisolvent/reactive crystallization) + seeding and PAT monitoring
- Reagents and materials
- Bulk organic solvents
Why it is the standard. ICH Q6A requires control of polymorphs and solid forms. Supersaturation control by seeding and PAT (FBRM/ATR-FTIR) is the standard approach for obtaining the target polymorph, particle size and purity reproducibly (consistent with the practice of Crystal Pharmatech and others).
Check also. Crystallization is the most important step, handling purification and solid form determination at once, but there is no guarantee that the targeted crystal polymorph or salt form will reproduce on scale-up. Behavior changes with stirring, cooling rate and seed crystals, and an undesired polymorph can occasionally appear suddenly, so PAT (process analytical technology) monitoring and polymorph control are carried out in parallel.
About this step and the alternatives
The peak of the synthesis, handling purification and solid-form building at the same time. The solution is cooled or an antisolvent is added so that only the target precipitates as crystals.
With conditions set properly, impurities stay in the mother liquor (the remaining liquid) and only the target comes out as crystals. Seed crystals are added, and precipitation is controlled while being monitored by process analytical technology (PAT).
In addition, which crystal polymorph or salt form is produced is also decided here. It is the most important stage, which also determines the solid form and thereby affects ease of dissolution, stability and ease of manufacture.
Crystallization is the most important step, handling purification and solid form determination at the same time. With conditions set properly, impurities stay in the mother liquor and only the target comes out as crystals. Moreover, which crystal polymorph or salt is produced determines solubility, stability and ease of manufacture.
Alternatives in practice
- Simple cooling recrystallization · Mettler Toledo EasyMax 102 (programmed cooling) — Simple, but control of polymorph and particle size is limited.
- Salt and cocrystal screening · Technobis Crystal16/Crystalline (multi-reactor crystallization screener) — Comprehensive exploration of solubility and polymorphs. Small scale.
- Continuous crystallization (MSMPR/continuous flow) · Alconbury Weston/Cambridge Reactor Design continuous crystallizers, monitored with Mettler Toledo PAT — Uniform particle size and higher productivity. Startup and control are complex.
07Removal of solvent from wet crystals by filtration and drying (filtration and drying/filter dryer, ANFD)
Meet residual solvent and moisture specifications and avoid polymorph transition and decomposition by carefully setting the drying temperature and time.
- Standard method
- Vacuum filtration/centrifugal filtration + vacuum drying (conical/tray)
- Reagents and materials
- Bulk organic solvents
Why it is the standard. ANFD (agitated Nutsche filter dryer) performs filtration, washing and drying in a single vessel and, being closed, limits cross-contamination and exposure; it is the standard equipment for chemically synthesized APIs. Meeting the ICH Q3C residual solvent limits is built up in the drying step.
Check also. Drying is not mere solvent removal; heating and desolvation can also transition the crystal polymorph or break down hydrates. If temperature and time are pushed too hard, the targeted solid form is lost, so the polymorph is checked after drying in another step, such as XRPD (powder X-ray diffraction).
About this step and the alternatives
The crystals produced by crystallization are still in a 'wet' state, containing mother liquor and solvent. They are separated from the liquid and the remaining solvent is driven off to finish a dry API.
After the liquid is removed by vacuum filtration or centrifugal filtration, vacuum drying removes moisture and solvent to within specification. Temperature and time are carefully set in a conical dryer or by tray drying.
Judgment is key here. Inadequate drying puts residual solvent out of specification, and overdoing it can cause the crystal polymorph to transition or decompose.
Crystals obtained by crystallization contain mother liquor and solvent. Filtration removes the liquid, and drying drives off the remaining solvent. Inadequate drying leaves residual solvent and moisture out of specification, and excessive drying can cause polymorph transition or decomposition, so temperature and time are carefully set.
Alternatives in practice
- Fluid bed drying · GEA/Glatt fluid bed dryers (GPCG series) — Fast and uniform drying. Watch for fine-powder scattering and static charge.
- Freeze drying (heat-sensitive/amorphous APIs) · SP VirTis/Millrock freeze dryers (GMP-compliant) — Effective for heat-labile products. High cost and long time.
- Rotary vacuum drying (double cone) · GEA/Italvacuum double-cone vacuum dryers — Gentle mixing-drying. More product-discharge steps than with ANFD.
Phase 4Quality attributes and analytics
10Confirmation of chemical structure (identification test) (structure confirmation/NMR, MS)
Retention time cannot guarantee structure, so spectroscopy and mass spectrometry finally prove that it is the target molecule.
- Standard method
- Structure confirmation by NMR (1H/13C, plus 19F/31P as needed) + mass spectrometry
- Reagents and materials
- HPLC mobile phase solvents
Why it is the standard. NMR is the reference method for primary structure analysis, able to establish structure at the atomic level. MS confirms the molecular weight and provides identification on a different principle. The two are routinely used together for structure confirmation of a new API (ICH Q6A identification test).
About this step and the alternatives
An identification test that finally proves 'whether what was made is really the target molecule.' Chromatographic retention time alone cannot guarantee structure.
Nuclear magnetic resonance (NMR) reads the skeleton and the arrangement of functional groups, and mass spectrometry corroborates the molecular weight. Layering several spectroscopic methods makes the structure certain.
A step that is the linchpin of consistent 'identity confirmation' from the starting materials to the final API. If this wavers, the foundation for discussing purity collapses.
Finally proves that 'what was made is really the target molecule.' HPLC retention time alone cannot guarantee structure, so the skeleton, functional groups and molecular weight are corroborated by several spectroscopic methods. It is the linchpin of identification from the starting materials through to the final API.
Alternatives in practice
- FT-IR (functional group identification, comparison with reference standard) · Thermo Scientific Nicolet iS20/Bruker ALPHA II — Effective for confirming functional groups and comparing against a reference. Cannot determine the full structure.
- UV-Vis spectroscopy · Agilent Cary 60/Thermo Evolution UV-Vis — A supplementary check for chromophores.
- Elemental analysis (CHN) · Elementar vario MICRO cube/Thermo Flash 2000 CHNS — Supports confirmation of the empirical formula. Cannot determine the structure itself.
11Assay (content) and quantitation of organic impurities and related substances (assay and related substances/HPLC quantitation)
Quantify the content responsible for efficacy and the related substances from synthesis and degradation to secure the core of quality.
- Standard method
- Quantitation by reverse-phase HPLC/UHPLC (UV detection, stability-indicating method)
- Reagents and materials
- HPLC mobile phase solvents, API reference standards and impurity standards (CRS)
Why it is the standard. The industry standard based on ICH Q3A (impurities in drug substances), Q6A and Q2 (analytical method validation). HPLC/UHPLC-UV can quantify content and related substances at the same time, and stability-indicating capability is assured by validation (many method development examples such as PMC11371568).
Check also. UV detection in reverse-phase HPLC works well for impurities with a chromophore, but it misses impurities that barely absorb UV, as well as inorganic salts and counterions. When the mass balance does not close, complement it with other detection principles such as CAD/ELSD (evaporative light scattering) or mass spectrometry.
About this step and the alternatives
The main event of quality testing, measuring the core of API purity. It looks at the 'content (assay)' responsible for efficacy and the related substances that get mixed in, together.
Content is quantified by reverse-phase HPLC/UHPLC, and related substances from synthesis and degradation are separated and tracked one by one. This reveals which impurities are present and how much.
Stability studies also follow how degradation products increase, so a 'stability-indicating method' that can properly separate degradation products is indispensable. The story of purity is told here.
How pure the API is, and which impurities are present and how much, is the core of quality. The content responsible for efficacy is measured, and related substances derived from synthesis and degradation are followed one by one. Stability studies also look at how degradation products increase, so a method that can separate the degradation products is essential.
Alternatives in practice
- LC-MS/MS (assignment and quantitation of trace impurities) · Sciex Triple Quad 7500/Waters Xevo TQ-XS — Effective for impurities with weak UV absorption and for structural assignment.
- Ion chromatography · Thermo Scientific Dionex Integrion/Metrohm 940 Professional IC — For quantifying counterions and inorganic ions.
- CAD/ELSD detection · Thermo Scientific Vanquish Charged Aerosol Detector (CAD)/Agilent 1290 Infinity II ELSD — General-purpose quantitation of compounds without UV absorption.
12Ultra-trace control of mutagenic impurities and nitrosamines (ultra-trace nitrosamine analysis)
Reliably control impurities that are carcinogenic even in trace amounts at ppb levels, orders of magnitude lower than ordinary tests.
- Standard method
- Ultra-trace quantitation by LC-MS/MS (or GC-MS/MS)
- Reagents and materials
- HPLC mobile phase solvents, API reference standards and impurity standards (CRS)
Why it is the standard. Control based on ICH M7 (mutagenic impurities). Nitrosamines and genotoxic impurities require ppb-level control, and LC-MS/MS is the standard for its high selectivity and sensitivity (consistent with the methods of LCGC/Shimadzu/PMC12655250). HS-GC-MS/ECD is also used for volatile alkyl halides.
Check also. For mutagenic impurities and nitrosamines, the practice is first to assess from the synthetic route and reagents whether they could form, as a structural alert, and then to measure at the ppb level only the compounds that are needed. Since the 2018 sartan drug product problem, regulation (ICH M7, etc.) and the control targets continue to be updated, so operate in line with the latest notifications.
About this step and the alternatives
A special control step that watches for impurities that are carcinogenic even in trace amounts at concentrations orders of magnitude lower. It deals with a range that ordinary purity testing cannot reach.
Alkylating agents and nitrosamines are the leading examples. They are quantified at the parts-per-billion (ppb) level using methods with extremely low detection limits, such as LC-MS/MS.
Since nitrosamine contamination was discovered in the 2018 sartan drug product (antihypertensive) problem, regulation has tightened all at once. It is a test at the front line of safety.
Impurities that carry a carcinogenic risk even at very low levels need to be controlled at ppb levels, orders of magnitude lower than in ordinary purity testing. Alkylating agents and nitrosamines are representative, and regulation has tightened since the 2018 sartan drug product problem. They are reliably controlled with methods that have extremely low detection limits.
Alternatives in practice
- HS-GC-MS (volatile nitrosamines) · Agilent 8890 GC/7000E MS+7697A headspace — Effective for volatile low-molecular-weight nitrosamines.
- GC-ECD (volatile alkyl halides, etc.) · Agilent 8890 GC+ECD detector — High-sensitivity detection of halogenated compounds. Limited versatility.
- HRMS screening/process purge assessment · Thermo Orbitrap Exploris/Waters Xevo G3 QTof (HRMS) — Supports the search for unknown nitroso compounds and measured purge factors.
13Quantitation of residual organic solvents (residual solvents/headspace GC)
Quantify residual solvents, whose limits differ with toxicity, as a final check of drying adequacy and safety.
- Standard method
- Quantitation of residual solvents by headspace GC-FID (HS-GC)
- Equipment
- Residual solvent GC headspace
- Reagents and materials
- Bulk organic solvents, API reference standards and impurity standards (CRS)
Why it is the standard. Standard method based on ICH Q3C (residual solvents) and USP<467>. HS-GC-FID separates volatile solvents from a nonvolatile matrix and quantifies them with high sensitivity, and is the method specified in the pharmacopoeias (consistent with methods such as PMC12614197).
With Racemic synthesis + optical resolution (diastereomeric salt crystallization)
- Precious metal catalyst residues drop out of the control scope
- Equipment: ICP-MS (microwave acid digestion pretreatment)
- Reagents: Because the resolution route does not use asymmetric metal catalysts (Rh/Ru, etc.), monitoring of precious metal residues of the ICH Q3D classes such as Ru/Rh is normally unnecessary. Instead, the focus shifts to elements that can be introduced in the salt formation and decomposition steps (such as Na) and to those derived from the equipment used
- Check also: In contrast, on the asymmetric synthesis side, Ru/Rh/Pd residues derived from catalysts such as BINAP-Ru/Rh are the main targets of ICP-MS monitoring
About this step and the alternatives
A safety test that confirms no trace of the solvents used in synthesis and crystallization remains in the API. It also serves as a final check that drying was sufficient.
Quantified by headspace gas chromatography (HS-GC), which warms the sample and captures the vaporized solvent. It efficiently picks up readily volatile solvents.
Toxicity differs by solvent type, so stricter limits are set for the more toxic ones. Pass/fail is judged by comparing the residual amount with the limit.
Solvents used in synthesis and crystallization remain in the API in trace amounts. Toxicity differs by type, so the more toxic the solvent, the stricter the limit set. It also serves as a final check that drying was sufficient, making it a test directly tied to safety.
Alternatives in practice
- HS-GC-MS (when identification is needed) · Agilent 8890 GC/5977B MSD+7697A headspace — Effective for identifying peaks of unknown solvents. Quantitative reproducibility is somewhat inferior to FID.
- Direct injection GC · Agilent 8890 GC-FID (direct liquid injection) — For high-boiling, hard-to-volatilize solvents. Watch for matrix contamination.
- Karl Fischer (water measured separately) · Metrohm 851 Titrando/Mettler Toledo C20S — Residual water cannot be measured by GC, so a separate method is needed.
14Quantitation of elemental impurities and metal catalyst residues (elemental impurities/ICP-MS)
Control metal catalyst residues, toxic even in trace amounts, within permitted limits and make a final check that removal was sufficient.
- Standard method
- Elemental quantitation by ICP-MS (microwave acid digestion pretreatment)
- Equipment
- ICP-MS and ICP-OES
- Reagents and materials
- API reference standards and impurity standards (CRS)
Why it is the standard. Standard method based on ICH Q3D (elemental impurities) and USP<232>/<233>. ICP-MS quantifies many elements simultaneously from ppb to ppt and covers catalyst residues (Pd/Pt/Ni, etc.) and environment-derived metals (As/Cd/Hg/Pb) (consistent with the methods of PMC9433241/PMC10987250).
Check also. ICP-MS measures the total amount of an element but does not distinguish the chemical form (valence, species) that determines toxicity. Permitted amounts are set by ICH Q3D risk assessment for each route of administration, and the measurement is used only as a final check that catalyst residue removal was sufficient.
With Racemic synthesis + optical resolution (diastereomeric salt crystallization)
- Chiral HPLC is promoted to the rate-determining IPC
- Method: Chiral HPLC (enantiomer separation and ee quantitation with a chiral stationary phase, CSP). On the resolution route, it is used as a rate-determining process control item for building up ee (endpoint determination of fractional recrystallization, in-process checks after each crystallization)
- Equipment: Chiral HPLC (polysaccharide CSP: amylose/cellulose derivative columns, etc.)
- Check also: On the asymmetric synthesis side, ee is set by the catalyst, and chiral HPLC is mainly a confirmatory test at release. On the resolution side, it becomes a key analysis that governs the process
About this step and the alternatives
A step that measures the 'leftovers' of metal catalysts used in synthesis. If palladium, nickel and the like remain in the API even in trace amounts, toxicity becomes a concern.
After pretreatment in which the sample is dissolved in acid, elements are quantified by inductively coupled plasma mass spectrometry (ICP-MS). Even trace metals are picked up accurately.
Permitted amounts are set for each route of administration. The elements specified by regulation are reliably measured, providing final support that catalyst removal was sufficient.
If metal catalysts used in synthesis, such as palladium and nickel, remain in the API even in trace amounts, toxicity becomes a concern. Permitted amounts are set for each route of administration, so the elements specified by regulation are reliably measured. It is also the final check that catalyst removal was sufficient.
Alternatives in practice
- ICP-OES (for high-concentration elements) · Agilent 5800/5900 ICP-OES/Thermo iCAP PRO — Simple and robust for high-concentration elements. Trace-level (ppb) sensitivity is inferior to ICP-MS.
- AAS (atomic absorption) · Agilent 240/280 AA/PerkinElmer PinAAcle 900 — For single-element targets. Simultaneous multi-element measurement is not possible.
- Colorimetric methods/simple kits (limit tests) · Merck heavy metal limit test kits/Agilent Cary 60 UV-Vis — Simple judgment in the manner of a limit test. Low quantitative accuracy and selectivity.
15Confirmation of chiral purity and enantiomeric excess (ee) (chiral purity/chiral HPLC)
An unwanted enantiomer changes efficacy and safety, so it is separated and quantified to assure the success of asymmetric synthesis.
- Standard method
- Enantiomer separation and quantitation by chiral HPLC (chiral stationary phase, CSP)
- Reagents and materials
- HPLC mobile phase solvents, Payload linker system suitability standards
Why it is the standard. Chiral HPLC (polysaccharide CSP) is the most established technique for enantiomer separation and corresponds to the chiral API specification (enantiomeric purity) of ICH Q6A. The Daicel CHIRALPAK series is used as the industry standard.
About this step and the alternatives
A test to confirm that the molecule that is the mirror image (enantiomer), with left and right reversed as if reflected in a mirror, has not been mixed in on the unwanted side. It is essential for optically active APIs.
Enantiomers, related like left and right hands, can differ in efficacy and safety. The two are separated by HPLC with a chiral stationary phase and quantified as an impurity.
Did asymmetric synthesis or chiral resolution work as intended? A stereochemical quality check that assures the result in the form of enantiomeric excess (ee).
In an optically active API, if the enantiomer (a molecule related like left and right hands) is mixed in, efficacy and safety change. The unwanted enantiomer is separated and quantified as one impurity. This test assures that asymmetric synthesis or chiral resolution worked as intended.
Alternatives in practice
- Chiral SFC (supercritical fluid chromatography) · Waters ACQUITY UPC2/Agilent 1260 Infinity II SFC+Daicel CHIRALPAK columns — Fast and low in solvent, and also advantageous for preparative work. Requires equipment investment.
- Optical rotation measurement · Anton Paar MCP 5100/JASCO P-2000 polarimeters — Simple, but unsuited to high-precision quantitation of enantiomeric excess.
- Chiral GC · Agilent 8890 GC + cyclodextrin-based chiral column (Agilent CP-Chirasil-Dex CB) — Effective for volatile chiral compounds. Limited range of application.
16Confirmation of crystal polymorph and crystallinity (crystal polymorph/powder X-ray diffraction, XRPD)
Polymorph differences change solubility, stability and absorption, so consistent manufacture of the target polymorph is confirmed lot by lot.
- Standard method
- Polymorph identification by powder X-ray diffraction (XRPD)
- Equipment
- XRPD polymorph
- Reagents and materials
- No reagents required (Cu Kα source, λ=1.5406 Å). Zero-background sample holder (single-crystal Si) used.
Why it is the standard. XRPD is the reference method for polymorph identification, giving a fingerprint of the crystal structure. Crystals show sharp Bragg peaks and amorphous material a broad halo, and it is standard both for polymorph control under ICH Q6A and for patent protection (consistent with Malvern Panalytical's explanations).
About this step and the alternatives
Even for the same molecule, a different arrangement within the crystal (polymorph) makes it behave like a different substance. Ease of dissolution, stability and absorption change.
Powder X-ray diffraction (XRPD) reads the arrangement of the crystal like a fingerprint and confirms that the target polymorph is being made consistently.
Transition to an unwanted polymorph or to the amorphous form leads directly to problems with efficacy and stability. That is why the identity of the crystal is watched lot by lot.
Even for the same molecule, a different arrangement of the crystal (polymorph) changes solubility, stability and absorption. Whether the target polymorph is being produced consistently is confirmed like a fingerprint. Transition to an unwanted polymorph or to the amorphous form leads directly to problems with efficacy and stability, so it is checked lot by lot.
Alternatives in practice
- Solid-state NMR (ss-NMR) · Bruker AVANCE NEO 400 WB+CP-MAS probe — Strong at discriminating local structure of polymorphs and amorphous forms. Instrumentation and analysis are advanced.
- Raman/FT-IR spectroscopy · Thermo DXR3 Raman/Bruker ALPHA II FT-IR — Effective for polymorph screening and mapping. Quantitative polymorph ratios require calibration.
- Polarized light microscopy (PLM) · Olympus BX53P polarizing microscope/Leica DM2700 P — Confirmation of crystallinity and crystal habit. Supports polymorph identification.
17Confirmation of melting point, thermal behavior and water/solvation (thermal analysis and water/DSC, TGA, KF)
Grasp polymorph stability and hydration/solvation from thermal behavior, and the effect of water content on stability and content calculation.
- Standard method
- DSC+TGA (thermal analysis) + Karl Fischer titration (water)
- Equipment
- Thermal analysis (DSC, TGA), Karl Fischer titration
- Reagents and materials
- DSC/TGA: no reagents required (high-purity nitrogen purge, Al/Pt crucibles). KF: Honeywell Hydranal reagents (Composite 5/2 for volumetric, Coulomat AG for coulometric).
Why it is the standard. The standard combination: DSC evaluates melting point, transitions and polymorph conversion, and TGA evaluates solvation/hydration and thermal stability (consistent with Agno/Malvern explanations). For water, KF titration is the reference method specified by the pharmacopoeia (USP<921>).
About this step and the alternatives
A thermal analysis step that reads the 'behavior' of the API when heated. From the melting temperature, transition temperature and weight changes, it probes polymorph stability and whether the material is a hydrate or solvate.
Differential scanning calorimetry (DSC) follows the heat flow in and out, thermogravimetry (TGA) follows the loss of weight, and Karl Fischer titration measures water at the same time.
Water is controlled separately. Because it affects stability and content calculation, it is separated from thermal behavior and measured accurately.
The temperatures of melting and transitions on heating, and changes in weight, tell whether a polymorph is stable and whether it is a hydrate or solvate. Water content is also measured accurately. Water affects stability and content calculation, so it is controlled separately.
Alternatives in practice
- Dynamic vapor sorption (DVS) · Surface Measurement Systems DVS Intrinsic/TA Instruments Q5000 SA — Effective for understanding hygroscopicity and hydrate formation behavior.
- Hot-stage microscopy (thermal microscopy) · Linkam THMS600 hot stage + Olympus polarizing microscope/Mettler Toledo FP90 — Melting and transitions are confirmed visually. Quantitative heat measurement depends on DSC.
- Loss on drying (LOD) · Mettler Toledo HC103 halogen moisture analyzer/Sartorius MA37 infrared moisture analyzer — Simple measurement of volatiles. Cannot distinguish water from solvent.
18Quantitation of water (water content) — water in the API is quantified by the Karl Fischer method to confirm hydrate state, hygroscopicity and compliance with the loss-on-drying specification (water determination/Karl Fischer)
To control the API water content by specification and assure hydration state, hygroscopicity and stability
- Standard method
- Coulometric Karl Fischer method (absolute quantitation of trace water, with a heating evaporation oven as needed)
- Equipment
- Karl Fischer titration
- Reagents and materials
- Honeywell Hydranal Coulomat AG (coulometric anolyte, product number 34836), also usable in cells without a diaphragm. When used with an oven, Hydranal Coulomat AG-Oven (product number 34739).
Why it is the standard. Karl Fischer water determination is mandatory in the standard API release tests.
About this step and the alternatives
A step that measures the water contained in the API itself, as an absolute amount. The water content required in the release specification is established here.
Trace water is directly quantified by coulometric Karl Fischer titration. If needed, an oven that heats the sample to drive out the water is used with it, picking up even tightly held water.
Used to judge hydrate stoichiometry, hygroscopicity and compliance with the loss-on-drying specification. Separately from thermal analysis (DSC/TGA), it is a test that treats water as the main subject.
Water (water content) is a mandatory item in API release specifications, and trace water is quantified directly by the Karl Fischer method. Separately from the thermal behavior seen by DSC/TGA, it is used to judge hydrate stoichiometry, hygroscopicity and compliance with the loss-on-drying specification.
Alternatives in practice
- Volumetric Karl Fischer method (for items with high water content) · Metrohm 901 Titrando/Mettler Toledo V20S+Hydranal Composite 5 — Suitable for items with water of 1% or more. Higher upper limit than the coulometric method.
- Loss on drying (LOD) · Mettler Toledo HC103 halogen moisture analyzer/vacuum dryer + electronic balance — Simple, but includes volatile solvents and is not water-specific.
19Confirmation of physical properties related to formulability, such as particle size distribution and specific surface area (particle size distribution/laser diffraction)
Particle size variation affects solubility, flowability and drug product uniformity, so it is controlled as a critical quality attribute.
- Standard method
- Particle size distribution measurement by laser diffraction (Dv10/Dv50/Dv90)
- Equipment
- Laser diffraction particle size analyzer: Malvern Panalytical Mastersizer 3000 (Aero dry/Hydro wet units)/Sympatec HELOS+RODOS/Microtrac SYNC.
- Reagents and materials
- Dry: oil-free compressed air/nitrogen. Wet: dispersion medium (water or isoparaffin-based, with surfactant added, e.g., Tween 20/lecithin).
Why it is the standard. Laser diffraction is the industry standard that gives the particle size distribution as Dv10/50/90 quickly and with high reproducibility, and is widely adopted for particle size control of micronized APIs (the relevant ICH Q6A specification) (consistent with the practice of SK pharmteco/Malvern).
About this step and the alternatives
A physical property test that measures variation in particle size. Particle size affects dissolution, flowability and the uniformity of the final drug product, so it is an important quality attribute related to formulability.
The particle size distribution is measured by laser diffraction, and Dv10, Dv50 and Dv90 are read from the cumulative distribution from the small side. It confirms whether micronization gave the target distribution.
Especially for poorly soluble drugs, particle size is directly tied to variation in effect. That is why it is controlled as a critical quality attribute, down to the shape of the distribution.
Variation in particle size affects dissolution, flowability and the uniformity of the final drug product. Measure whether micronization gave the target distribution and, if needed, look at surface area as well. For poorly soluble drugs, particle size is directly tied to variation in effect, so it is controlled as a critical quality attribute.
Alternatives in practice
- BET specific surface area measurement · Micromeritics TriStar II Plus/3Flex (N2 adsorption) — An indicator of fine powder and adsorption surface area. Does not give the particle size distribution itself.
- Dynamic image analysis · Malvern Morphologi 4/Sympatec QICPIC — Particle size analysis accompanied by shape information. Watch sample amount and statistics.
- Sieving/microscopy · Retsch AS 200 sieve shaker/Olympus optical microscope + image analysis — A simple method for coarse particles. Low resolution in the fine-powder range.
20Confirmation of microbial limits and endotoxin (when needed) (microbial limits and endotoxin)
Check for microbial contamination before formulation. For raw materials of sterile drug products, pyrogens are also controlled according to the route of administration.
- Standard method
- Microbial limits test (TAMC/TYMC) + BET (LAL method) when needed
Why it is the standard. Standard based on USP<61>/<62> and <85>, and ICH Q6A. Microbial limits for oral/non-sterile APIs, and endotoxin as well for raw materials of sterile drug products. rFC is increasingly adopted as an alternative to animal-derived reagents.
Check also. Whether microbial limits or endotoxin testing is needed depends on which drug product and route of administration the API finally goes to. The level required differs greatly between oral solid dosage forms and injectables, so tests are chosen by working backward from downstream requirements rather than imposed uniformly at the API stage.
About this step and the alternatives
An API is a chemical, but this step confirms there is no microbial contamination before it goes on to formulation. The required tests are chosen according to the route of administration.
The microbial limits test measures the viable count (total aerobic microbial count, total yeast and mold count) to determine how many microbes are present. This is the basic check.
When the API becomes a raw material for a sterile drug product such as an injectable, endotoxin, a pyrogen, also becomes a concern. It is confirmed by BET (LAL method), putting a double safety net in place.
An API is a chemical, but before it goes on to formulation, it is checked for microbial contamination. Especially when it becomes a raw material for a sterile drug product such as an injectable, not only the microbial count but also pyrogens (endotoxin) are a concern. The required tests are chosen according to the route of administration of the product.
Alternatives in practice
- Recombinant factor C (rFC) method · Lonza PyroGene rFC Assay/Charles River Endosafe Trillium rCR cartridges — Independent of horseshoe crabs and sustainable. Requires validation against each pharmacopoeia and method.
- Rapid microbiological methods (RMM) · bioMérieux BacT/ALERT/Rapid Micro Biosystems Growth Direct — Speeds up results. An equivalence study is required at introduction.
- Sterility test (for sterile APIs) · Sartorius Sterisart/Merck Steritest Symbio (membrane sterility test) — For sterile APIs. Not applicable to limit testing of non-sterile products.
The reference (“gold standard”) method is the one broadly recognized in published practice and guidelines; your process, product and regulator may justify another. Makers and products are examples, not endorsements. This map is translated from the Japanese edition, where it is updated first (Japanese version).