Van der Waals attractive and repulsive

FIG. 15-3. Diagram illustrating van der Waals attraction and repulsion in relation to electron distribution of inonatomic moletules ol argon. 

The fourth summation corresponds to an energy function for all atoms j not directly bonded to atom /, and represented by a van der Waals attractive and repulsive energy term. This term is essential for nucleic acid model building in order to maintain a reasonable base stacking such that the stacked base planes are approximately parallel and separated by about 3.4 A. In addition to this, the fourth summation is used to constrain certain specified pairs of atoms at hydrogen bond distances. Thus, we initially specified in the refinement the base-paired secondary structure as well as the tertiary structure hydrogen bonds which could be seen in the MIR and partial group structure Fourier maps. 

The crystal binding, or cohesive energy, of single component molecular materials is often referred to as the lattice energy and can be calculated by summing all the interactions between a central molecule and aU the surrounding molecules in the crystal lattice (Docherty and Meenan 1999). Each atom-atom interaction pair consists of a van der Waals attractive and repulsive... 

The internal energies of each of the sixteen possible Ci conformations of the aldopentopyranoses (i.e. the ol- and j8-anomers of both the d- and L-forms) have been derived from Monte-Carlo calculations that take into account contributions made by van der Waals attractive and repulsive forces, polar interactions, and... 

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