C5R CORP.

Synthesize and detect an amide

Physical end-to-end experiments
Task space

Confirm product formation by LCMS when synthesizing N-benzyl-4-methylbenzamide from p-toluic acid and benzylamine.

Synthesizing and verifying a target molecule is a core task in medicinal chemistry. Here, agents make N-benzyl-4-methylbenzamide from p-toluic acid and benzylamine through a single amide-forming reaction. They select reagents, design and execute a protocol, quench the reaction, and characterize the product by LC-MS.

The task tests the full workflow: adapting to available equipment and reagents, preparing samples, developing an analytical method, and interpreting the resulting chromatograms and spectra.

Scoring

Pass all five required conditions: adequately quench the LC–MS sample and the reserved aliquot, detect the product by LC–MS, correctly interpret the LC–MS result, and retain product in the reserved aliquot.

RESULTS

Synthesize N-benzyl-4-methylbenzamide from p-toluic acid and benzylamine, then verify the product by LC–MS.
ModelPass@1Cost ($)Model/API inference cost only, averaged per task attempt. Lab and labor costs are not reported. Repeats are averaged using the same task and family weights as scores.
Claude Fable 5.1xhigh100.0%$44.35
GPT–6 Astraxhigh50.0%$75.39
Claude Opus 5xhigh50.0%$63.52
GPT–5.6 Solxhigh0.0%$25.13
Gemini 3.8 Flashhigh0.0%$5.79
Grok 4.6xhigh0.0%$22.33
0%50%100%

Whiskers show ±1 standard error from repeats.

Run progress

Elapsed time from task receipt. Milestones use published annotations or the first matching recorded Facility action. A red × marks when a run stopped, at its last reached milestone.

Task receivedProtocol execution startedPowder and liquid transferredLC–MS acquiredEnd of recorded run01h2h3h4.6hElapsed time / hoursGPT–5.6 Sol · Task received: 0m; 1/1 attemptsGPT–5.6 Sol · Protocol execution started: 41m; 1/1 attemptsGPT–5.6 Sol · Powder and liquid transferred: 50m; 1/1 attemptsGPT–5.6 Sol · LC–MS acquired: 2h 16m; 1/1 attemptsGPT–5.6 Sol · End of recorded run: 2h 21m; 1/1 attempts20.0 %Claude Opus 5 · Task received: 0m; 1/1 attemptsClaude Opus 5 · Protocol execution started: 56m; 1/1 attemptsClaude Opus 5 · Powder and liquid transferred: 1h 16m; 1/1 attemptsClaude Opus 5 · LC–MS acquired: 2h 36m; 1/1 attemptsClaude Opus 5 · End of recorded run: 4h 35m; 1/1 attempts100.0 %Gemini 3.8 Flash · Task received: 0m; 1/1 attemptsGemini 3.8 Flash · Protocol execution started: 41m; 1/1 attemptsGemini 3.8 Flash · Powder and liquid transferred: 46m; 1/1 attemptsGemini 3.8 Flash · LC–MS acquired: 1h 26m; 1/1 attemptsGemini 3.8 Flash · End of recorded run: 1h 28m; 1/1 attempts0.0 %Claude Fable 5.1 · Task received: 0m; 1/1 attemptsClaude Fable 5.1 · Protocol execution started: 38m; 1/1 attemptsClaude Fable 5.1 · Powder and liquid transferred: 1h 22m; 1/1 attemptsClaude Fable 5.1 · LC–MS acquired: 3h 23m; 1/1 attemptsClaude Fable 5.1 · End of recorded run: 3h 49m; 1/1 attempts100.0 %

Model trajectories

One example per model.

Run grading

Fail
MeasurementRecorded resultOutcome
Score60.0 %× Fail

Pass condition: Pass all five required conditions: adequately quench the LC–MS sample and the reserved aliquot, detect the product by LC–MS, correctly interpret the LC–MS result, and retain product in the reserved aliquot.

  • ×
    adequate quench
  • ✓
    correct interpretation
  • ✓
    product detected
  • ✓
    reserved aliquot product
  • ×
    reserved aliquot quench
Synthesize and detect an amideGrok 4.6 xhigh
Run gradingFail
00:0000:01

Model activity

Model transcript

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Appendix

Equipment and materials in the configured task environment.

Main equipment2 items
Opentrons

Opentrons Flex Robot

OPENTRONS:999-00191

Automated liquid handling and deck orchestration

Waters

ACQUITY UPLC H-Class with QDa and PDA

WATERS:176003208

Liquid chromatography with mass and UV detection

Supporting equipment7 items
ItemBrandSKURole
Flex 1-Channel Pipette, 5–1,000 µLOpentronsOPENTRONS:999-00187Reaction, control, and analytical-sample transfers
Flex Gripper GEN1OpentronsOPENTRONS:999-00194Plate and lid movement
Heater-Shaker Module, Flex configurationOpentronsOPENTRONS:991-00115-FL-UNActivation, reaction, and dilution mixing
Deep Well Plate Adapter for Heater-ShakerOpentronsOPENTRONS:991-00066Secures the reaction plate on the Heater-Shaker
Picus 2 Pipette, 5–120 µLSartoriusSARTORIUS:LH-747041Manual preparation of the LC–MS diluent
Picus 2 Pipette, 100–5,000 µLSartoriusSARTORIUS:LH-747101Stock and source-vial preparation
Analog Vortex Mixer, 120 VFisherbrandTHERMO-FISHER:02215414Dissolution of the p-toluic acid and HATU stocks
Consumables7 items
ItemBrandSKURole
Flex Tips, 1,000 µL, filteredOpentronsOPENTRONS:991-00106Automated liquid transfers
96-well deep-well plate, V-bottom, 2 mLNESTNEST:503501Reactions, no-HATU control, and LC–MS samples
Tough Universal LidOpentronsOPENTRONS:999-00261Covers the plate during mixing
SafetySpace filter tips, 2–120 µLSartoriusSARTORIUS:790101FManual low-volume transfers
Optifit tips, 100–5,000 µLSartoriusSARTORIUS:780304Manual stock and source-vial transfers
Clear glass vial with cap, 15 mLUlineULINE:S-25276CHATU stock and reagent source vessels
ACQUITY UPLC BEH C18 column, 2.1 × 100 mm, 1.7 µmWatersWATERS:186002352LC–MS separation
Reagents10 items
ItemBrandSKURole
p-Toluic acid, 98%ChEBI 36635 Sigma-AldrichSIGMA-ALDRICH:T36803-500GCarboxylic-acid substrate; prepared as a 650 mM stock in DMF
Butyric acid, 99%+ChEBI 30772 Thermo Fisher ScientificTHERMO-FISHER:L13189.APCarboxylic-acid substrate
HATU, 97%PubChem 6409673 Sigma-AldrichSIGMA-ALDRICH:445460Coupling reagent; prepared as a 107.333 mg/mL stock in DMF
N,N-Diisopropylethylamine, ≥99%ChEBI 193590 Sigma-AldrichSIGMA-ALDRICH:D125806Base
Benzylamine, 99%ChEBI 40538 Thermo Fisher ScientificTHERMO-FISHER:105855000Amine substrate
Cyclohexylamine, 99%ChEBI 15773 Thermo Fisher ScientificTHERMO-FISHER:111280010Amine substrate
N,N-Dimethylformamide, 99.9%ChEBI 17741 Thermo Fisher ScientificTHERMO-FISHER:447090025Stock and reaction solvent; no-HATU control
Methanol, HPLC gradeChEBI 17790 Fisher ChemicalTHERMO-FISHER:A452-4LC–MS diluent
Water, Optima LC/MS gradeChEBI 15377 Fisher ChemicalTHERMO-FISHER:W6-4LC–MS diluent
Formic acid, Optima LC/MS gradeChEBI 30751 Fisher ChemicalTHERMO-FISHER:A11750LC–MS diluent additive