Examples and Exercises
Malate Dehydrogenase: PDB code 1EMD, rendered in VMD
Citric acid and NAD in VDW.
Nicotine: modeled in HyperChem
Acetylcholine: modeled in HyperChem
Nicotine binds in the same site as acetylcholine
View in Webviewer : Examine the overlay of the two by using selections (double right click)
Acetylcholinesterase: Rendered in VMD with RESTYPE and Cartoon rendering
View in HyperChem Webviewer
“Peptide” bond rotation
trans N-methylacetamide AM1 semiempirical quantum chemical calculation in Hyperchem
Heat of formation: -46.9 kcal/mole
cis N-methylacetamide AM1 semiempirical quantum chemical calculation in Hyperchem
Heat of formation: -47.2 kcal/mole ® D = 0.3 kcal/mole
90 ° structure (transition state) –32.4 kcal/mole ® barrier = -14.5 kcal/mole
Visual Pigments
11-cis retinal: HyperChem
Examine electronic spectrum in WebViewer
trans-retinal: Hyperchem
Examine electronic spectrum in WebViewer
Tautomerism of 7-Aminopyrazolo pyrimidine
N7H: Heat of Formation 89.5 kcal/mole
N8H: Heat of Formation 95.6 kcal/mole
Stable Conformers of Alanine Dipeptide
Lowest energy confirmation using AMBER in Hyperchem
View in Webviewer
Conformational Search: Hyperchem with Excel macro phipsi.xlm
Created
by Jonathan M. Smith
Department of Chemistry
Copyright 2001