Rowan MCP Server

# ROWAN MCP TEST QUERIES Natural language test queries for all Rowan MCP tools. ✅: passed with expected results ⚠️: passed-ish (submitted/ran, but maybe unexpected results or needs some tweaking) ❌: failed --- # simple queries ## core calculations ### geometry optimizations - Optimize the geometry of aspirin ✅ - Run a multistage optimization on caffeine ⚠️ (Unexpected Imaginary Frequency An unexpected large imaginary frequency was encountered, meaning that the calculation is far from a critical point on the PES. It's likely this structure has not been successfully optimized! Thermochemical results will be unreliable.) - Get the best structure for benzene ✅ ### electronic props - Calculate the HOMO and LUMO of benzene ✅ - Get the electronic properties of nicotine ✅ - What are the molecular orbitals of methanol? ✅ ### conformational analysis - can you test a ❌ - stuck on "running" - Generate 5 conformers of butane ✅ - What are the different shapes ethanol can adopt? ✅ ### scans - Scan the C-C bond in ethane from 1.3 to 1.8 Angstroms ✅ ### spin states - What spin states are possible for iron(III) complex? ✅ - Calculate different spin multiplicities for NO radical ✅ - calculated doublet and quartet states (?) - Check if iron porphyrin prefers singlet or triplet state ⚠️ log files indicate that this run finished, but doesn't say "finished" on rowan UI. stopped ## cheimcal properties ### redox - What's the reduction potential of benzoquinone? ✅ (Large Oxidation Potential Predicted. The predicted oxidation potential is very large. The workflow not been thoroughly tested on values in this range—results may be less accurate!) - Can vitamin E be easily oxidized? ⚠️ log files indicate that this run finished, but doesn't say "finished" on rowan UI. stopped - Predict the redox behavior of phenol ✅ ### solubility - How soluble is aspirin in water?✅ - How soluble is caffeine in different solvents? Pick 5, and run them at 5 different temps in ascending order. ✅ ### descriptors - Generate descriptors for benzene ✅ - Get QSAR features for ethanol ✅ ### pka - What's the pKa of acetic acid? ✅ - What's the pKa of caffeine? ✅ - What are the pKa values of citric acid? ✅ ### bond dissociation energy (no access) ### hydrogen bond basicity (no access) ## reactions / dynamics ### reactivity (fukui) - Where will electrophiles attack benzene? ✅ - Find the most reactive sites in phenol ✅ ### rxn coordinate/irc ❌ - Find the transition state for hydrogen migration in formic acid, then trace the reaction path to confirm it connects HCOOH and HOCOH isomers ❌ ### molecular dynamics - Run a short MD simulation of water ✅ (use molecule='water', not 'O') - Simulate the flexibility of ethanol for 500 steps ✅ - Run molecular dynamics on butanol for 1000 steps ✅ ## drug discovery ### admet - Predict drug-likeness of aspirin (follow-up: is it orally bioavailable?) ✅ - Calculate ADMET for KarXT from Karuna Therapeutics ✅ ### docking (couldn't resolve) ❌ - Dock aspirin to COX-2 enzyme - Find binding pose of this ligand - Predict protein-drug interaction ### tautomers - What tautomers does acetylacetone have? ✅ - Find tautomers of barbituric acid ✅ - What keto-enol tautomers does phenol have? ✅ ## workflow management ### data retrieval - Get results from this calculation UUID ✅ - List 5 most recent workflows ✅ - Update name of most recent workflow to "x" ✅ ### project organization - Create a new project folder for drug discovery (and delete) ✅ - List all folders in my account ✅ - "Move KarXT-related calculations into the folder" ✅ - fix list folders ❌ ### server administration - Check server status ✅ # more comprehensive queries tbd... ### to do - reaction coordinates, irc, docking - rowan folder list - i think there's a bug - tried paramter filtering (non-None params to avoid sending empty strings) - direct API calls with rowan.Folder.list() with no params - string, None, type checks - used the example directly from Rowan's API docs (after adding redox folder), still getting 500 error - edit descriptions for one-liners to feed into the mcp tool - break up the folder and workflow mega tools