Molecular mechanics
From Free net encyclopedia
The term molecular mechanics refers to the use of Newtonian mechanics to model molecular systems. Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics simulations, Monte Carlo simulations and ligand docking simulations. Molecular mechanics is used to study small chemical systems with a few atoms, or large biological systems or material assemblies with many thousands to millions of atoms. These sytems can be investigation either in vacuum or in presence of solvent such as water. The simulations in vacuum are referred to as gas-phase simulations while the presence of solvent molecules are referred to as explicit solvent simulations. In another type of simulations, the effect of solvent is estimated by use of empirical mathematical expression, known as implicit solvation simulations.
Molecular mechanics methods are based on the following principles:
- Nuclei and electrons are considered as a single atom-like particle
- Atom-like particles are spherical (radii is obtained from measurements or theoritical considerations) and is assigned a net charge (obtained from theoretical considerations),
- Interactions are based on springs (representing bonds) and classical potentials,
- Interactions must be preassigned to specific sets of atoms,
- Interactions determine the spatial distribution of atom-like particles and their energies.
<math>\ E = E_{bonds} + E_{angle} + E_{dihedral} + E_{non-bonded} </math>
<math>\ E_{non-bonded} = E_{electrostatic} + E_{van der Waals} </math>
This function, referred to as potential function, computes the molecular potential energy as a sum of energy terms that describe the deviation of bond lengths, bond angles and torsion angles away from equilibrium values, plus terms for non-bonded pairs of atoms describing Van der Waals and electrostatic interactions. The set of parameters consisting of equilibrium bond lengths, bond angles, partial charge values, force constants and Van der Waals parameters are collectively known as force field. Different implementations of molecular mechanics use slightly different mathematical expressions, and therefore, different constants for potential function. The common force-fields in use today, have been developed by using high level quantum calculations and fitting to experimental data. The technique, known as energy minimization, is used to minimize the potential function. Lower energy states are more stable and are commonly investigated due to their role in chemical and biological processes. A molecular dynamics simulation, on the other hand, computes the behavior of system as a function of time. It involves solving Newton's equation of motion, F = ma. Integration of Newton's laws of motion, using different integration algorithms, leads to atomic trajectories in space and time. The force on atoms are defined as the negative gradient of the potential energy function. The energy minimization technique is useful for obtaining a static picture for comparison between states or similar systems, while molecular dynamics provides information about the dynamic processes with the inclusion of temperature effects.
Software Packages
Limited list; many more are available
External links
- VigyaanCD: A free software workbench that includes molecular mechanics.
References
- U. Burkert and N.L. Allinger, Molecular Mechanics, 1982, ISBN 0841208859
- O. Becker, A.D. MacKerell, Jr., B. Roux and M. Watanabe, Editors, Computational Biochemistry and Biophysics, Marcel Dekker Inc., New York, 2001, ISBN 082470455X
- MacKerell, A.D., Jr., Empirical Force Fields for Biological Macromolecules: Overview and Issues, Journal of Computational Chemistry, 25: 1584-1604, 2004fr:Mécanique moléculaire