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Chemical Reactivity Modeling and Visualization: Insights into Kinetics & Thermodynamics

Explore electron density surfaces, frontier molecular orbitals, and reactivity susceptibility in chemical reactions. Learn about reactivity visualization and control mechanisms. Discover insights into catalysis, polyester weatherability, and urethane polymerization.

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Chemical Reactivity Modeling and Visualization: Insights into Kinetics & Thermodynamics

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  1. Modeling Chemical Reactivity • Visualization of chemical reactivity • Kinetic & thermodynamics * David Gallagher Mount St. Helens, WA, USA, May 18, 1980

  2. • - • Partial charges HOMO + Largest negative charge on para & ortho positions Largest HOMO density on para & ortho positions Highest frontier density on para & ortho positions Fukui’s Frontier Density* HOMO on electron iso-density surface Electrophilic susceptibility** Visualization of Reactivity Susceptibility to electrophilic attack? (phenol) * K. Fukui et al, J. Chem. Phys.,11. 1433-1442 (1953) ** Also, nucleophilic, radical, electrostatic potential, superdelocalizability, etc.

  3. Susceptibility to Attack Electrophilic (occupied obitals) Nucleophilic (unoccupied orbitals) Radical (all valence orbitals) *Fukui’s frontier density on electron isodensity surface

  4. Polyester Weatherability* • New methyl propane diol based Polyester introduced • Competitor claims “Norrish type II” degradation mechanisms mean rapid degradation of diols with beta hydrogens under UV radiation, unlike competitor’s neopentyl based polyester H neopentyl diol methyl propane diol

  5. CAChe & Tests Disprove Claims* • Experimental accelerated test results inconsistent with “Norrish” • “Radical susceptibilty” surfaces similar for both polyesters H neopentyl polyester methyl propane polyester * Published in Journal of Coatings Technology Vol. 67, No. 847, August ‘95 by Carl J. Sullivan & Charles F. Cooper, ARCO Chemical Company

  6. Why does iron tricarbonyl apparently catalyse this reaction? Fe(CO)3 Disrotatory ? Insights into Catalysis X Conrotatory sterically hindered tricyclo-octadiene bicyclo-octatriene A. R. Pinhas, B. K. Carpenter, J.C.S. Chem. Comm., 1980, 15.

  7. Iron carbonyl changes symmetry of frontier orbital (HOMO) Disrotatory Sterically allowed Fe Frontier MO Control of Stereochemistry • Thermal reaction: most reactive electrons in HOMO Conrotatory Sterically hindered CAChe MOPAC AM1-d

  8. Improve Yield, Minimize Byproducts • Thermodynamic control? Isomers have same Hf, - No! • Kinetic control? syn-product T-state is lower energy, - Yes! • Why is syn lower? Visualize energy terms of T-state* methylnitrone 83% syn ? + 17% anti monofluoroallene *Purvis III, G. D., J. Computer Aided Molecular Design, 5 (1991) 55-80

  9. Sterics of the Transition-state • Sterics, Frontier orbitals & Electrostatics all influence transition state • Sterics slightly favor anti-product: but inconsistent with experiment (17%) steric hindrance? methylnitrone MFA syn-addition (83%) anti-addition (17%)

  10. Orbitals of the Transition-state • Closest energy frontier orbitals are nitrone HOMO & MFA LUMO • Frontier orbital overlap suggest both transition states equally allowed + + nitrone HOMO + + + + MFA LUMO + + anti-addition (17%) syn-addition (83%)

  11. Electrostatic Control of Yield • Anti-addition shows +/+ repulsion, syn seems energetically favored • Product ratios are consistent with electrostatic control (strongest long-range) • Thus, changing solvent (dielectric) or substituents could control product yield +/+ red: +ve nitrone blue: -ve MFA syn-addition (83%) anti-addition (17%) Electrostatic isopotential surfaces: proton repelled by 20 kcals on red surface.

  12. Sterics • space-filling • VdW (electron isodensity) • MM conformation search • Electrostatics(AM1) • partial charges (menu) • electrostatics on surface • electrostatic isopotential • Frontier orbitals • HOMO, LUMO, etc. • susceptibility*, (substrate only) • superdelocalizability*, (both reactants) Visualization of Reactivity • * K. Fukui et al, J. Chem. Phys., 11, 1433-1442 (1953)

  13. 2. Kinetics (activation energy) Etransition-state - Ereactants T-state Et Activation energy Ea = Et – Er k = A*exp(-Ea/R*T) Energy of reaction = Ep – Er Thermodynamics & Kinetics • 1. Thermodynamics (heat of reaction) Eproducts – Ereactants Reactant Er Product Ep Heats of Formation are calculated by MOPAC PM3 http://www.shodor.org/UNChem/advanced/kin/arrhenius.html

  14. 2) Ortho: 171 Kcals 1) Para: 167 Kcals 3) Meta: 183 Kcals Substitution Position by Kinetics Transition states for electrophilic attack by Br+ on phenol Br Br Br Lowest energy* transition state = fastest reaction = main product

  15. Model transition states, then calculate catalyst & solvent effects RCatalystSolventActivation E methyl 43.7 kcal phenyl 41.3 kcal methyl N(CH3)3 32.0 kcal phenyl N(CH3)3 26.9 kcal phenyl N(CH3)3 CH3OH 16.7 kcal Urethane Polymerization Reaction • Lower temperature would reduce costs and thermal decomposition • To save time & money, CAChe used to explore reaction conditions R Catalyst Project successful, saving many months & cost of chemicals for pilot scale R-N=C=O + CH3OH = RNHCOOCH3 *Malwitz, N., Reaction Kinetic Modeling from PM3 Transition State Calculations, J. Phys. Chem., Vol 99, No. 15, 1995 p. 5291

  16. Literature states lone-pair of trimethylamine ‘attacks’ + of carbonyl ‘C’ Unexpected Insights • Modeling does NOT support this (lone pair of catalyst attaches to proton) • New insight reveals alternative (or true?) mechanism R Catalyst *Malwitz, N., Reaction Kinetic Modeling from PM3 Transition State Calculations, J. Phys. Chem., Vol 99, No. 15, 1995 p. 5291

  17. Polyurethane: “Summary” • “... capable of offering insight useful toward • minimizing unwanted side reactions • optimizing yields • suggesting reaction conditions • and determining polymer composition...” *Malwitz, N., Reaction Kinetic Modeling from PM3 Transition State Calculations, J. Phys. Chem., Vol 99, No. 15, 1995 p. 5291

  18. Exothermic Endothermic low temp high temp CPD Dimerization & Temperature * * * * G = H - T S

  19. MOPAC & DFT Accuracy Hf RMS errors (kcal.mol-1) compared to experiment *Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, James J. P. Stewart, J Mol Model (2004) 10:6-12

  20. 1. Sketch a ‘guess’ 2. Modify similar TS 3. Map reaction 4. Search for saddle Strategies for locating T-States

  21. Map the Reaction Diels Alder MOPAC PM3 Optimized Grid Screen capture with “SNAP32”, AVI movie made with “GIF Movie Gear”

  22. 2. Copy & name it “Product” 3. Edit to “Product” structure 4. Copy “Reactant”, name “T-state” 5. Experiment: Search for Saddle T-state Product Search for Saddle (keto-enol) 1. Sketch “Reactant” with atom #s Reactant

  23. 1. Refine 2. Verify (IR spectrum) Verifying the T-State

  24. 2. Do atom-distances seem reasonable? “Adjust | Define geometry label” 3. Do calculated bond-orders seem reasonable? “View | Pt. Chg. & Calc. Bond Order” 1. Single negative vibration? “Verify T-state” Verify Transition State

  25. Intermediates? ? ? Intrinsic Reaction Coordinate (IRC)

  26. Reaction Path (IRC) Water-catalyzed keto-enol tautomerization, reaction path Intrinsic Reaction Coordinate (IRC)

  27. Solvents & Radicals

  28. 1. Create an approximate T-state 2. Refine (consider solvents & radicals) 3. Verify (neg. vibration, bonds) 4. Check reaction path for intermediates Summary for locating T-States

  29. Safe Laboratory Practice “The purpose of computing is insight, not numbers” Amdahl “Calibrate before use!” (experiment or ab initio) Old Chemists never die… they simply fail to react

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