Nonbonded interaction energy

In LN, the bonded interactions are treated by the approximate linearization, and the local nonbonded interactions, as well as the nonlocal interactions, are treated by constant extrapolation over longer intervals Atm and At, respectively). We define the integers fci,fc2 > 1 by their relation to the different timesteps as Atm — At and At = 2 Atm- This extrapolation as used in LN contrasts the modern impulse MTS methods which only add the contribution of the slow forces at the time of their evaluation. The impulse treatment makes the methods symplectic, but limits the outermost timestep due to resonance (see figures comparing LN to impulse-MTS behavior as the outer timestep is increased in [88]). In fact, the early versions of MTS methods for MD relied on extrapolation and were abandoned because of a notable energy drift. This drift is avoided by the phenomenological, stochastic terms in LN. 

United atom force fields (see United versus All Atom Force Fields on page 28) are sometimes used for biomolecules to decrease the number of nonbonded interactions and the computation time. Another reason for using a simplified potential is to reduce the dimensionality of the potential energy surface. This, in turn, allows for more samples of the surface. 

The hardness parameters for MM+ are the dissociation energies of the nonbonded interactions of two identical atoms divided by 1.125, 8=Dq/1.125. The values of Dq used are ... 

This value is in excellent agreement with the calculated free energy value by the consideration of various nonbonded interactions in the epimers (69 and 70) [(2 X 1,3-diaxial Me—H interaction) — (1 x 1,3-diaxial Me—H interaction + 1 X l,2- < Me—H interaction) = (0.9 x 2) — (0.9 + 0.6) = 0.3 kcal/mole]. Hydrolysis of the enamine with dilute acetic acid gave a 3 2 mixture of cis and trans isomers of the ketone, thus confirming the assignments made to the enamine components. 

Try to explain the conformational preference in terms of steric repulsion. Which ring atom(s) in the higher-energy conformer approach the CH3 group most closely (Make sure that you find all significant nonbonded interactions.) Which of these interactions are absent in the lower-energy conformer Can interactions that appear in both conformers account for the conformational preference ... 

Identify the preferred conformer for each. Are the energy differences in line with your expectations, or are there significant deviations If the latter, what additional nonbonded interactions can explain these deviations Which factor plays the larger role in determining conformational preferences, the additional interactions or CHs-ring interactions ... 

Compare energies for equatorial and axial chair conformers for methylcyclohexane, R = Me, and tert-butylcyclohexane, R = CMe3. Which is more stable in each molecule Use equation (1) to calculate the ratio of major to minor conformers for each system at 298 K. Which molecule shows a larger preference Why (Hint Compare nonbonded interactions and/or geometrical distortions in the higher-energy conformers that are absent in the lower-energy conformers.)... 

Examine space-filling models for the two conformers and identify any likely unfavorable nonbonded interactions. Based on steric effects, which conformer would you anticipate would be the more stable Compare energies of anti-1,2-ethanediol and gauche-1,2-ethanediol to see if you are correct. Is this the same ordering of conformer energies as seen for n-butane (see Chapter 5, Problem 3)7... 

Energies in kcal/mol, distances in A, angles in radians, and charges in atomic charge units. / b describes the nonbonded interactions between the solute atoms, while t/ b is used for the ... 

See also Energy minimization methods computer program for, 130-132 Nonbonded interactions, 56,61 Normal modes analysis, 117-119 computer program for, 132-134... 

---