Molecular Visualization and Simulation with HyperChem

1. Molecular Visualizationand Simulation with HyperChem Thomas K. Green Department of Chemistry University of Alaska Fairbanks

2. Is the Time Right? “Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry. It would occasion a rapid and widespread degeneration of that science” A. Compte 1798-1857

3. “The more progress physical sciences make the more they tend to enter the domain of mathematics, which is a kind of centre to which they all converge. We may judge the degree of perfection to which a science has arrived by the facility with which it may be submitted to calculation.” Adolphe Quetelet 1796-1874

4. Features of Molecular Modeling • Structure • Stability • Reactivity • Properties

5. Structural Models • 2-D Drawing Ethanol • 3-D Models of HyperChem Sticks Tubes Ball and Stick Space-Filling CH3CH2OH

6. Periodic Table

7. Ethanol HOCH2CH3

8. Tubes

9. Ball and Stick

10. Space-filling

11. Nucleic Acids

12. DNA

15. Amino Acids

16. Protein

21. Computational Methods • Molecular Mechanics • Semi-Empirical • abinitio

22. Molecular Mechanics • Describes the energy of molecule in terms of distortions of bond distances and angles away from idealized values, with contributions from nonbonded interactions. • Provides equilibrium geometry very quickly. • Does not provide reliable relative energies of isomers or of reaction energies.

23. Semi-Empirical Method • Based on more sophisticated quantum mechanical methods but with time-saving approximations , including incorporation of experimentally-derived parameters. • Provides good account of equilibrium structures but less satisfactory for reaction thermochemistry than ab initio method. • AM1 method is most popular present-generation method.

24. ab initio Methods • Quantum Mechanical methods successful in providing equilibrium and transition state geometries • Relative computation times are much longer than semi-empirical methods and therefore more costly. • 3-21G and 6-31G* are most popular. H E

25. Stability and Geometry Optimization • Geometry optimization alters molecular geometry to lower the energy of the system to yield a more stable conformation. • Derivative of the energy with respect to all coordinates, called the gradient, is near zero. • Several different minima are possible.

26. Energy Minima

27. Saddle Point

29. Conformational Analysis of Cyclohexane Chair Global Minimum Twist Boat Local Minimum 1.33 kcal/mol 7.22 kcal/mol Boat Saddle point 8.31 kcal/mol

30. Bond Rotation of Butadiene S-Trans S-Cis S-Trans 1800 0.0 kcal/mol 1500 900 1.62 kcal/mol 5.35 kcal/mol 600 300 S-Cis 00 3.40 kcal/mol 2.80 kcal/mol 3.46 kcal/mol

31. S-Cis S-Trans

32. Space-Filling Model of S-Cis Conformation Steric Repulsion of Hydrogen Atoms

33. Stability of Benzyl Carbocation 900 Planar Hf 222 kcal/mol Perpendicular Hf 253 kcal/mol

34. Resonance Stabilizationof Benzyl Carbocation More Stable Less Stable

35. Molecular Orbitals of Planar Benzyl Carbocation • Molecular Orbital is where the electrons are located • Lowest Unoccupied Molecular Orbital represents distribution of positive charge.

37. Perpendicular Benzyl Carbocation

38. Spin Density of Allyl Radical Unpaired electron

39. Electrostatic Potentialof Ammonia • Electrostatic potential reveals site of protonation in acid-base reaction. :NH3 + H+ NH4+

40. Infrared Spectrum of Ethanol

41. The O-H Stretch