Molecular Modeling.pptVIP

Molecular Modeling Part I. A Brief Introduction to Molecular Mechanics Molecular Modeling (Mechanics) Calculation of preferred (lowest energy) molecular structure and energy based on principles of classical (Newtonian) physics “Steric energy” based on energy increments due to deviation from some “ideal” geometry Components include bond stretching, bond angle bending, torsional angle deformation, dipole-dipole interactions, van der Waals forces, H-bonding and other terms. Components of “Steric Energy” E steric = E stretch + E bend + E torsion + E vdW + E stretch-bend + E H- bonding + E electrostatic + E dipole-dipole + E other Bond Stretching Energy A Morse potential best describes energy of bond stretching ( compression), but it is too complex for efficient calculation and it requires three parameters for each bond. n(l) = De{1- exp [-a (l - l0)]}2 if: De = depth of potential energy minimum, a = w?(m/2De) where m is the reduced mass and w is related to the bond stretching frequency by w = ?(k/m) Morse potential Hooke’s Law Most bonds deviate in length very little from their equilibrium values, so simpler mathematical expressions, such as the harmonic oscillator (Hooke’s Law) have been used to model the bond stretching energy: n(l) = k/2(l - l0)2 Bond Stretching Energy Estretch = ks/2 (l - l0)2 (Hooke’s law force... harmonic oscillator) graph: C-C; C=O Higher order terms give better fit With cubic and higher terms: n(l) = k/2(l - l0)2 [1- k’(l - l0) - k’’(l - l0)2 - k’’’(l - l0)3 - …] Bond Angle Bending Energy Ebend = kb/2 (q - q0)2 graph: sp3 C-C-C Torsional Energy Related to the rotation “barrier” (which also includes some other contributions, such as van der Waals interactions). The potential energy increases periodically as eclipsing interactions occur during bond rotation. Torsional Energy Etorsion = 0.5 V1 (1 + cos f) + 0.5 V2 (1 + cos 2f) + 0.5 V3 (1