Combinatorial chemistry – solid phase and solution phase synthesis MCQs With Answer

Combinatorial chemistry is a powerful approach in modern drug discovery that enables rapid generation of diverse compound libraries using both solid phase synthesis and solution phase synthesis. For B. Pharm students, mastering concepts such as resin selection, linkers, split-and-mix strategies, encoding, purification, and high-throughput screening is essential for medicinal chemistry and formulation research. Solid-phase methods (e.g., SPPS) simplify purification, while solution-phase and parallel synthesis offer scalability and detailed reaction control. Understanding analytical checks (HPLC, MS) and library design principles deepens practical skills for lead identification. This set of focused, keyword-rich MCQs will reinforce theory and application. Now let’s test your knowledge with 30 MCQs on this topic.

Q1. What is the main purpose of combinatorial chemistry in drug discovery?

• To synthesize single large molecules with complex chirality
• To rapidly generate large libraries of diverse compounds
• To replace clinical trials with in vitro assays
• To only perform natural product isolation

Correct Answer: To rapidly generate large libraries of diverse compounds

Q2. Which feature best describes solid-phase synthesis?

• Reactants remain in homogeneous solution for easy monitoring
• Compounds are synthesized while covalently attached to an insoluble support
• It requires no protecting groups
• It is only used for small-scale natural product synthesis

Correct Answer: Compounds are synthesized while covalently attached to an insoluble support

Q3. What is a key advantage of solution-phase synthesis over solid-phase synthesis?

• Eliminates need for purification entirely
• Allows better reaction monitoring and scale-up feasibility
• Always gives higher yields on beads
• Prevents side reactions without protecting groups

Correct Answer: Allows better reaction monitoring and scale-up feasibility

Q4. What does the split-and-mix (split-and-pool) strategy achieve?

• Sequentially increases purity of a single compound
• Creates very large combinatorial libraries by iterative splitting and pooling of resin batches
• Encodes each bead with an electronic tag
• Eliminates need for coupling reagents

Correct Answer: Creates very large combinatorial libraries by iterative splitting and pooling of resin batches

Q5. Which method is commonly used to identify the structure of a compound on an individual bead?

• Direct NMR analysis of intact beads without cleavage
• Chemical or DNA-based encoding tags attached during synthesis
• Visual color change on the bead surface
• Measuring resin swelling only

Correct Answer: Chemical or DNA-based encoding tags attached during synthesis

Q6. Which resin type is most commonly used in solid-phase organic synthesis?

• Polystyrene cross-linked with divinylbenzene (DVB)
• Cellulose paper without crosslinking
• Silica gel with no functional groups
• Unmodified polyethylene tubing

Correct Answer: Polystyrene cross-linked with divinylbenzene (DVB)

Q7. Wang resin is characterized by which property?

• Base-labile linker cleavable with piperidine
• Acid-labile linker cleavable with trifluoroacetic acid (TFA)
• Photocleavable linker only
• Cleavable only under hydrogenolysis

Correct Answer: Acid-labile linker cleavable with trifluoroacetic acid (TFA)

Q8. What is the primary outcome when using Rink amide resin for peptide synthesis?

• Production of peptides with a free carboxylate C-terminus
• Cleavage under basic conditions only
• Formation of C-terminal amide peptides after acidic cleavage
• Inability to incorporate non-standard amino acids

Correct Answer: Formation of C-terminal amide peptides after acidic cleavage

Q9. What does resin “loading” refer to in solid-phase synthesis?

• The mechanical weight of beads per vial
• The moles of reactive functional groups per gram of resin (mmol/g)
• The volume of solvent the resin can absorb
• The percentage of crosslinker in the polymer

Correct Answer: The moles of reactive functional groups per gram of resin (mmol/g)

Q10. Which solvents are commonly used to swell polystyrene-based resins and promote reactions?

• Water and methanol
• Dichloromethane (DCM) and N,N-dimethylformamide (DMF)
• Hexane and pentane only
• Glycerol and ethylene glycol

Correct Answer: Dichloromethane (DCM) and N,N-dimethylformamide (DMF)

Q11. Which reagent is typically used for Fmoc deprotection in solid-phase peptide synthesis?

• Trifluoroacetic acid (TFA)
• Piperidine in DMF
• Hydrazine hydrate
• Sodium borohydride

Correct Answer: Piperidine in DMF

Q12. Which reagent is commonly used for Boc group deprotection?

• Triethylamine
• Trifluoroacetic acid (TFA)
• Pyridine
• Sodium hydroxide

Correct Answer: Trifluoroacetic acid (TFA)

Q13. Which coupling reagent is frequently employed for amide bond formation in both solid and solution phase?

• HATU
• Sodium chloride
• Acetic acid
• Hydrochloric acid

Correct Answer: HATU

Q14. If a split-and-mix synthesis uses 3 building blocks in step one and 4 in step two, how many unique compounds are generated (assuming complete combinatorial pairing)?

• 7
• 12
• 1
• 24

Correct Answer: 12

Q15. What is positional scanning deconvolution used for in mixture-based libraries?

• To purify individual compounds without analysis
• To identify active substituents by testing systematic positional mixtures
• To increase resin swelling
• To encode beads chemically

Correct Answer: To identify active substituents by testing systematic positional mixtures

Q16. What is a major advantage of mixture-based combinatorial libraries in screening?

• They eliminate the need for secondary assays completely
• They reduce the number of initial biological assays by testing pools of compounds
• They always ensure single-compound activity signals
• They bypass the need for any analytical characterization

Correct Answer: They reduce the number of initial biological assays by testing pools of compounds

Q17. Which statement best defines parallel synthesis?

• All compounds are synthesized on a single resin bead
• Each compound is synthesized in a separate reaction vessel under controlled conditions
• Compounds are generated randomly without design
• Only identical compounds are synthesized repeatedly

Correct Answer: Each compound is synthesized in a separate reaction vessel under controlled conditions

Q18. Which analytical technique is most useful for confirming mass of a compound cleaved from solid support?

• Ultraviolet-visible spectrophotometry (UV-Vis) only
• Mass spectrometry (MS)
• Polarimetry
• Density measurement

Correct Answer: Mass spectrometry (MS)

Q19. What is the ultimate goal of applying combinatorial chemistry in pharmaceutical research?

• To slow down the lead discovery process
• To accelerate lead identification and optimization
• To eliminate target validation studies
• To produce only one optimized drug candidate without testing

Correct Answer: To accelerate lead identification and optimization

Q20. What does diversity-oriented synthesis (DOS) emphasize when generating libraries?

• Maximizing structural and stereochemical diversity of scaffolds
• Producing only linear peptides
• Using only a single building block repeatedly
• Avoiding any scaffold variation

Correct Answer: Maximizing structural and stereochemical diversity of scaffolds

Q21. What is a common limitation of split-and-mix solid-phase libraries?

• They always produce pure compounds without work-up
• Difficulty in identifying the structure on an individual bead without encoding or cleavage
• They are impossible to screen biologically
• They only allow one-step reactions

Correct Answer: Difficulty in identifying the structure on an individual bead without encoding or cleavage

Q22. Which cleavage condition is typically used to release molecules from an acid-labile linker on resin?

• Strong base such as NaOH
• Acidic cleavage using trifluoroacetic acid (TFA)
• High-temperature pyrolysis
• Light without special linkers

Correct Answer: Acidic cleavage using trifluoroacetic acid (TFA)

Q23. Why must linkers be chosen carefully in solid-phase synthesis?

• They determine color of the final product only
• They must be stable to reaction conditions yet cleavable under controlled conditions
• Linkers are irrelevant to purification strategy
• They automatically encode compound identity

Correct Answer: They must be stable to reaction conditions yet cleavable under controlled conditions

Q24. What is an advantage of on-bead (on-resin) screening?

• It always gives quantitative potency values directly
• It can identify binders without initial cleavage of compounds
• On-bead screening removes the need for secondary validation
• It eliminates false positives completely

Correct Answer: It can identify binders without initial cleavage of compounds

Q25. Solution-phase parallel synthesis is particularly advantageous for which reason?

• It prevents any need for work-up or purification
• It facilitates scale-up and detailed reaction monitoring for each compound
• It requires no reagents
• It only works for peptide chemistry

Correct Answer: It facilitates scale-up and detailed reaction monitoring for each compound

Q26. Automated peptide synthesizers commonly use which protection strategy for solid-phase peptide synthesis?

• Boc strategy with repetitive hydrogenolysis
• Fmoc/tBu strategy with Fmoc removal by piperidine
• Unprotected amino acid coupling only
• Protease-catalyzed chain elongation

Correct Answer: Fmoc/tBu strategy with Fmoc removal by piperidine

Q27. What is a scaffold-based library?

• A library where each compound shares a common core scaffold and varies at defined positions
• A random collection of unrelated natural products
• A single compound tested at multiple concentrations
• A library made only from peptides

Correct Answer: A library where each compound shares a common core scaffold and varies at defined positions

Q28. Which parameter is important when assessing the diversity of a combinatorial library?

• Chemical space coverage and diversity of molecular properties
• Only the physical color of beads
• Number of vials used irrespective of compound structures
• The supplier of the resin

Correct Answer: Chemical space coverage and diversity of molecular properties

Q29. Which analytical method is routinely used to analyze crude mixtures from solution-phase combinatorial reactions?

• High-performance liquid chromatography (HPLC)
• Paper chromatography only
• Refractive index without separation
• Simple titration

Correct Answer: High-performance liquid chromatography (HPLC)

Q30. In ideal split-and-pool bead-based synthesis, what is the intended number of unique compounds per bead?

• Zero compounds per bead
• Approximately one unique compound per bead
• Hundreds of different compounds per bead
• Identical mixtures on every bead

Correct Answer: Approximately one unique compound per bead

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