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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

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molecular modeling

Molecular Modeling

Part I.

A Brief Introduction to

Molecular Mechanics

molecular modeling 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
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
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
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 energy6
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
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 - …]

(cubic terms give better fit

in region near minimum; inclusion

of a fourth power term eliminates the maximum in the cubic fcn.)

bond angle bending energy
Bond Angle Bending Energy

Ebend = kb/2 (q - q0)2

graph: sp3 C-C-C

(Likewise, cubic and higher

terms are added for better fit

with experimental observations)

torsional energy
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.

gauche

Eclipsed

eclipsed

Anti

torsional energy10
Torsional Energy

Etorsion = 0.5 V1 (1 + cos f) + 0.5 V2 (1 + cos 2f) +

0.5 V3 (1 + cos 3f)

van der waals energy
van der Waals Energy

EvdW = A/r12 - B/r6

Lennard-Jones or

6-12 potential

combination of a repulsive

term [A] and an attractive term [B]

van der waals energy14
van der Waals Energy...

EvdW = A (B/r ) - C/r6

Buckingham potential

(essentially repulsion only, especially at short distances)

hydrogen bonding energy
Hydrogen Bonding Energy

EH-Bond = A/r12 - B/r10

(Lennard-Jones type,

with a 10, 12 potential)

electrostatic energy
Electrostatic Energy

E electrostatic = q1q2 / cer

(attractive or repulsive, depending on relative signs of charge; value depends inversely on permitivity of free space, or the dielectric constant of the hypothetical medium)

dipole dipole energy
Dipole-Dipole Energy

Calculated as the three dimensional vector sum of the bond dipole moments, also considering the permitivity (related to dielectric constant)of the medium (typical default value is 1.5)

(this is too complicated to demonstrate!!!)

use of cut offs
Use of Cut-offs
  • Van der Waals forces, hydrogen bonding, electrostatic forces, and dipole-dipole forces have dramatic distance dependencies; beyond a certain distance, the force is negligible, yet it still “costs” the computer to calculate it.
  • To economize, “cut-offs” are often employed for these forces, typically somewhere between 10 and 15Å.
properties calculated
Properties Calculated
  • Optimized geometry (minimum energy conformation)
  • Equilibrium bond lengths, bond angles, and dihedral (torsional) angles
  • Dipole moment (vector sum of bond dipoles)
  • Enthalpy of Formation (in some programs).
enthalpy of formation
Enthalpy of Formation
  • Equal to “steric energy” plus sum of group enthalpy values (CH2, CH3, C=O, etc.), with a few correction terms
  • Not calculated by all molecular mechanics programs (e.g., HyperChem and Titan)
  • Calculated values are generally quite close to experimental values for common classes of organic compounds.
bond lengths
Bond Lengths

Sybyl MM+ MM3Expt

CH3CH3

C-C 1.554 1.532 1.531 1.526

C-H 1.095 1.115 1.113 1.109

CH3COCH3

C-C 1.518 1.517 1.516 1.522

C-H 1.107 1.114 1.111 1.110

C=O 1.223 1.210 1.211 1.222

bond angles
Bond Angles

Sybyl MM+ MM3

CH3CH3

H-C-C 109.5 111.0 111.4

H-C-H 109.4 107.9 107.5

CH3COCH3

C-C-C 116.9 116.6 116.1

H-C-H 109.1 108.3 107.9

C-C-O 121.5 121.7 122.0

common force fields
Common Force Fields
  • MM2 / MM3 (Allinger) best; general purpose
  • MMX (Gilbert) added TS’s, other elements; good
  • MM+ (Ostlund) in HyperChem; general; good
  • OPLS (Jorgenson) proteins and nucleic acids
  • AMBER (Kollman) proteins and nucleic acids +
  • BIO+ (Karplus) CHARMm; nucleic acids
  • MacroModel (Still) biopolymers, general; good
  • MMFF (Merck Pharm.) general; newer; good
  • Sybyl in Alchemy2000, general (poor).
molecular modeling programs
Molecular Modeling Programs
  • HyperChem (MM+, OPLS, AMBER, BIO+)
  • Spartan(MM3, MMFF, Sybyl; on SGI or via x-windows from pc)
  • Titan (like Spartan,but faster; MMFF)
  • Alchemy2000 (Sybyl)
  • Gaussian 03 (on our SGIs linux cluster and on unix computers at NCSU and ECU; no graphical interface; not for molecular mechanics; MO calculations only)
steps in performing molecular mechanics calculations
Steps in Performing Molecular Mechanics Calculations
  • Construct graphical representation of molecule to be modeled (“front end”)
  • Select forcefield method and termination condition (gradient, # cycles, or time)
  • Perform geometry optimization
  • Examine output geometry... is it reasonable?
  • Search for global minimum.
energy minimization
Energy Minimization
  • Local minimum vs global minimum
  • Many local minima; only ONE global minimum
  • Methods: Newton-Raphson (block diagonal), steepest descent, conjugate gradient, others.

local minima

global minimum

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