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## Molecular Visualization and Simulation with HyperChem

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**Molecular Visualizationand Simulation with HyperChem**Thomas K. Green Department of Chemistry University of Alaska Fairbanks**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**“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**Features of Molecular Modeling**• Structure • Stability • Reactivity • Properties**Structural Models**• 2-D Drawing Ethanol • 3-D Models of HyperChem Sticks Tubes Ball and Stick Space-Filling CH3CH2OH**Computational Methods**• Molecular Mechanics • Semi-Empirical • abinitio**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.**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.**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**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.**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**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**S-Cis**S-Trans**Space-Filling Model of S-Cis Conformation**Steric Repulsion of Hydrogen Atoms**Stability of Benzyl Carbocation**900 Planar Hf 222 kcal/mol Perpendicular Hf 253 kcal/mol**Resonance Stabilizationof Benzyl Carbocation**More Stable Less Stable**Molecular Orbitals of Planar Benzyl Carbocation**• Molecular Orbital is where the electrons are located • Lowest Unoccupied Molecular Orbital represents distribution of positive charge.**Spin Density of Allyl Radical**Unpaired electron**Electrostatic Potentialof Ammonia**• Electrostatic potential reveals site of protonation in acid-base reaction. :NH3 + H+ NH4+