In this problem you will use molecular mechanics software of your instructors choice to

Chapter 19, Problem 19.22

(choose chapter or problem)

In this problem you will use molecular mechanics software of your instructors choice to gain some appreciation for the complexity of the calculations that lead to plots such as those in Fig. 19.29. Our model for the protein is the dipeptide (15) in which the terminal methyl groups replace the rest of the polypeptide chain. (a) Draw three initial conformers of the dipeptide with R = H: one with = +75, = 65, a second with = = +180, and a third with = +65, = +35. Use a molecular mechanics routine to optimize the geometry of each conformer and measure the total potential energy and the final and angles in each case. (Although any force field will work satisfactorily, the AMBER force field is strongly recommended, as it is optimized for calculations on biopolymers.) Did all of the initial conformers converge to the same final conformation? If not, what do these final conformers represent? Rationalize any observed differences in total potential energy of the final conformers. (b) Use the approach in part (a) to investigate the case R = CH3, with the same three initial conformers as starting points for the calculations. Rationalize any similarities and differences between the final conformers of the dipeptides with R = H and R = CH3.