Introduction to Molecular Modeling

Introduction to Molecular Modeling - Introduction to...

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Introduction to Molecular Modeling
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Natalie Chartrand Lab Section 3 October 3, 2007 Acyclic Aliphatic Hydrocarbons Aliphatic compounds:   Molecules having hydrocarbon chains that usually contain portions of carbon atoms  with four  single  bonds 1 . Methane Bond length:  1.09  Ǻ Bond angle: 109.5˚ Dichloromethane E= -671.9023 C-Cl bond length: 1.74    Ǻ C-H bond length: 1.11  Ǻ Cl-C-Cl bond angle: 112.998˚ Cl-C-H bond angle: 107.941˚ H-C-H bond angle 112.144˚ Ethane-Staggered C-C-H bond angle: 110.723˚ H-C-H bond angle: 108.191˚ Distance between H atoms: cis:  2.51791  Ǻ trans:  3.1009  Ǻ Ethane-Eclipsed E= -670.6617 C-C-H bond angle: 110.043˚ H-C-H bond angle: 107.855˚ Note: Ethane, in its staggered conformation, is more stable mainly because the hydrogen atoms are slightly  farther apart. Propane C 1 -C 2  hydrogen atoms eclipsed:   E= -952.5695 C 1 -C 2  and C 2 -C 3  hydrogen atoms eclipsed:  E= -950.9236
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Staggered (all hydrogen atoms):  E= -953.8936 Note:  According to the calculated energy values for the molecules, propane, in which all of the hydrogen  atoms are staggered, is the most stable conformer for this substance.  Again, this is due to the fact that the  hydrogen atoms are slightly farther apart when staggered than they are when eclipsed. Butane Anti:    E= -1235.3671 Distance from C 1 -C 4 :  3.83718  Ǻ Anticlinal Eclipsed:  E= -1234.3617 Distance from C 1 -C 4 : 3.59408  Ǻ Gauche: E= -1235.0991 Distance from C 1 -C 4 :  3.07541  Ǻ Syn-periplanar: E= -1232.6130 Distance from C 1 -C 4 : 2.79952  Ǻ Note: Based on their energies, the conformers of butane, from most stable to least, are Anti, Gauche,  Anticlinal eclipsed, and Syn-periplanar.
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Chart 1 Relative Energies of Butane Conformations - 12 3 6 .0 - 12 3 5.5 - 12 3 5.0 - 12 3 4 .5 - 12 3 4 .0 - 12 3 3 .5 - 12 3 3 .0 - 12 3 2 .5 - 12 3 2 .0 0 60 120 180 Angle Between Methane Groups of Adjacent Carbon Atoms Relative Energy Cyclic Aliphatic Hydrocarbons Alicyclic:  (aliphatic cyclic) A term indicating that a molecule has one or more rings but lacks the  conjugated   bonds that characterize an aromatic compound. π 1 Cyclopropane E= - 807.6188 C-C-C bond angles: 60˚ Distance H-H: cis:  2.57442  Ǻ trans:  3.15728  Ǻ
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