3.1: Potential Energy Surface and Bonding Interactions In this chapter, we return to the idea of a potential energy surface and consider models for a covalent bond. The potential energy changes as a function of the relative distance between bonded atoms. As atoms come together to form molecules, the potential energy will have a minimum at the equilibrium bond distance. For diatomic molecules, the potential energy surface is one-dimensional and depends only on the distance between the two atoms in the diatomic molecule. For polyatomic molecules with 3.2: Intermolecular Forces We now discuss interactions between atoms that are not directly bonded together, called non-bonding interactions. These give rise to two common types of intermolecular interactions: electrostatic interactions between charged molecules, and van der Waals (dispersion) interactions. The Coulomb interaction between charges plays an important role in the assembly of biological structures. 3.3: Newtonian Mechanics The text discusses the application of Newton's laws of motion to atomic nuclei and larger molecules, focusing on the interaction of particles and harmonic motion. Newton's second law is formulated for forces between particles and a harmonic oscillator system, like a mass and spring. Concepts of potential energy, restoring forces, and phase space in relation to differential equations are introduced. 3.4: Molecular Dynamics Simulations 3.5: Analysis of Molecular Dynamics Trajectories 3.6: Advanced topics in Molecular Dynamics