Modeling Concepts - Prelab Exercises
Exercise 1: How many internal degrees of freedom are there in n-butane? How many of these are bond lengths, angles and dihedral angles?
Exercise 2: Look at the dipeptide, Anserine. How many rotatable bonds are there? Amide bonds are usually cis or trans (2 conformational states), but sp3-sp3 bonds are usually like butane and have 3 conformational states. Based on that, how many conformational isomers does anserine have overall?
Exercise 3: Sketch a PES for an Sn2 reaction (perhaps Br- + CH3Cl). What are the major geometry variables that change throughout this reaction? You can google "sn2 reaction diagram" for some examples to check your own result.
Exercise 4: How many bonds are there in Arginine? How many of those are unique bond types?
Exercise 5: Why use quantum mechanics rather than molecular mechanics?
Exercise 6: What happens if you need 347 steps for a minimization to reach a slope of zero, but you only allow it 100 steps? What happens if you need 347 steps for a minimization to reach a slope of zero, but you give it 5000?
Exercise 7: In an earlier exercise you sketched an Sn2 reaction profile. If you were to try to generate this profile using a coordinate scan, what variable(s) would you scan?
Exercise 8: How do you know if a Monte Carlo conformational search has actually found the global minimum energy structure?
You can go back to the main prelab page or the MGCF main page.