Molecular mechanics

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Molecular mechanics (MM) is a computational technique used to model the behavior of molecules. It is based on classical mechanics and uses mathematical equations to describe the potential energy of a system of atoms. This method is widely used in computational chemistry, biochemistry, and materials science to predict the structure, energy, and properties of molecules.

Principles

Molecular mechanics relies on the concept of a force field, which is a set of equations and parameters that describe the potential energy of a system. The potential energy is typically divided into several components, including:

• Bond stretching: The energy associated with the stretching or compressing of bonds between atoms.
• Angle bending: The energy associated with the bending of angles between three bonded atoms.
• Torsional interactions: The energy associated with the rotation around bonds.
• Non-bonded interactions: The energy associated with interactions between atoms that are not directly bonded, including van der Waals forces and electrostatic interactions.

Force Fields

Several force fields have been developed for use in molecular mechanics, each with its own set of parameters and equations. Some of the most commonly used force fields include:

• AMBER
• CHARMM
• GROMOS
• OPLS

Each force field is parameterized to reproduce experimental data and quantum mechanical calculations for a specific set of molecules.

Applications

Molecular mechanics is used in a variety of applications, including:

• Protein folding: Predicting the three-dimensional structure of proteins from their amino acid sequences.
• Drug design: Identifying potential drug candidates by modeling the interactions between small molecules and biological targets.
• Materials science: Studying the properties of materials at the atomic level.

Advantages and Limitations

Molecular mechanics has several advantages, including its ability to handle large systems and its relatively low computational cost compared to quantum mechanics. However, it also has limitations, such as its reliance on empirical parameters and its inability to accurately model systems with significant electronic changes, such as chemical reactions.

See Also

• Molecular dynamics
• Quantum mechanics
• Computational chemistry
• Force field (chemistry)
• Protein structure prediction

Related Pages

• Computational chemistry
• Biochemistry
• Materials science
• Protein folding
• Drug design