Announcements:• Final Projects – 1stitem due next Monday•we will have class this Friday 4:15-5:30 in 5 LSB• we’ll start discussing electronic structure next class• I’ll be sending an e-mail about teams Today:• a few comments on Exam I• comments on Assignment 5• Assignment 5.5 problems #1 & 3 (+)64657276788082848595Exam I Scores:talk to me today or Wed. if you have questions about the gradingexcellentgoodreasonabledisappointing• according to the syllabus, Exam I constitutes 12.5% of your course grade • a low score is far from fatal but still cause for concern average = 783 energies: force field energy, steric energy, and strain energyQuestion #4:I graded this problem but then gave everyone full credit, because there was some confusion (on all of our parts) on the definitions of strain energy Jensen (p. 29): “The force field energy, EFFis often called the steric energy as in some sense it is the excess energy relative to a hypothetical molecule with non-interacting fragments.”In the text Molecular Mechanics Across Chemistry, Rappe & Casewit use the terms steric, strain, and force-field energy synonymouslyCramer (p.40): “a ‘strain-free’ molecule is one in which every coordinate adopts its equilibrium value”... “so neglecting non-bonded terms for the moment, we see that the raw force-field energy can be called the ‘strain energy’, since it represents the positive deviation from a hypothetical strain-free system.”=?Leach (p. 226): equates force-field energy to steric energy. He then defines strain as follows: “To determined the strain energy it is usual to define some ‘strainless’ reference point. The references points can be chosen in many ways and so many different definitions of strain energy have been proposed in the literature. For example, Allinger and coworkers defined the reference point using a set of ‘strainless’ compounds such as the all-trans conformations of the straight-chain alkanes from methane to hexane. From this set of compounds it was possible to derive a set of strainless energy parameters for constituent parts of molecules. The inherent strain energy of a hydrocarbon is then obtained by subtracting the reference ‘strainless’energy from the actual steric energy calculated using the force field.”Jensen, p. 45Question #5:NCHCOHROHHNCHCOHROHHR=CH3φψExample: Simple Water Models for Liquid Simulations from: Jorgensen et al., J. Chem. Phys. 79, 926 (1983).Table 4.3 & Figs. from Leech2.27 2.18 2.352.17μ/ D(σ/A, ε/kB/K)(3.17, 78) (3.17, 78) (2.96, 157) (3.15, 78)(3.15, 77) (3.10, 38)μgas= 1.85 Dμliq~ 2.6 DJensen, p. 47Assignment #5EnergyOptimization Step0 20406080100Energy E-Emin / kcal mol-102004006008001000EnergyOptimization Step0 20406080100Energy E-Emin / kcal mol-110-310-210-1100101102103S.D.CG(PR)BD NRCG(FR)R2R3R4R5R1θ1θ2R2R3R4R5R1θ1θ2Molecule
View Full Document
Unlocking...