134. If the energy of a protein structure is calculated using molecular mechanics forcefield, which of the following
energy components CANNOT have a negative value?
1. Bond energy
2. Dihedral energy
3. van der Waals energy
4. Electrostatic energy

Question

If the energy of a protein structure is calculated using molecular mechanics forcefield, which of the following energy components CANNOT have a negative value?

1. Bond energy

2. Dihedral energy

3. van der Waals energy

4. Electrostatic energy

Detailed Explanation

Molecular mechanics is a computational method used to predict the energy of a molecule based on its structure. The forcefield used in molecular mechanics consists of various energy components that describe the interactions between atoms in a molecule. These energy components are calculated using specific mathematical functions, and each contributes to the overall energy of the system.

Here are the main components:

1. Bond Energy:

   • Bond energy refers to the energy associated with the formation and stretching of chemical bonds between atoms in a molecule.

   • It is typically positive for bond stretching, as energy is required to stretch or compress bonds, but bond energy is inherently non-negative because it represents the strength of the bond.

2. Dihedral Energy:

   • Dihedral energy arises from the torsional strain of rotating around a bond, influencing the conformation of a molecule.

   • This energy can be negative when the conformation of the molecule leads to a more stable arrangement (favorable torsion angles) or positive when the conformation is less stable (unfavorable torsion angles).

3. van der Waals Energy:

   • Van der Waals interactions are the attractive forces between atoms or molecules that are close together but not chemically bonded.

   • Van der Waals energy is typically negative when atoms are at an optimal distance and attract each other, leading to a more stable arrangement. However, if the atoms are too close (overlapping electron clouds), the energy becomes positive, indicating repulsion.

4. Electrostatic Energy:

   • Electrostatic energy arises from interactions between charged particles (e.g., ions or dipoles).

   • Electrostatic interactions can be both negative (attractive interactions between oppositely charged ions) and positive (repulsive interactions between similarly charged ions).

   • However, in molecular mechanics, electrostatic energy is typically negative when charges are favorably interacting (opposite charges attracting each other).

✅ Correct Answer: 1. Bond Energy

• Bond energy cannot be negative because bond stretching or compression requires energy input, and thus it is always positive in nature. The bond is a stable, but positive energy contribution in molecular mechanics forcefields.

Conclusion

In molecular mechanics forcefields, the bond energy is the only energy component that cannot have a negative value. This is because bond stretching always requires energy input, while other energy components like dihedral, van der Waals, and electrostatic interactions can have both positive and negative values depending on the molecular conformation and interactions between atoms.