Interactions between partial charges

The Coulomb interaction between charges is our starting point for the discussion of the assembly of biological structures. 

Atoms in molecules in general have partied cheffges. Table 11.2 gives the partial charges typically found on the atoms in peptides. If these charges were separated by a vacuum, they would attract or repel each other in accordance with Coulomb s law Fundamentals F.3), and we would write 

The energy of interaction between a partial charge of—0.36 (that is, Qi=—0.36e) on the N atom of a peptide link and the partial charge of-1-0.45 (Q2=-l-0.45e) on the carbonyl C atom at a distance of 3.0 nm on the assumption that the medium between them is a vacuum is 

24 The Coulomb potential energy of two charges Qi and Q2 and its dependence on their separation. The two curves correspond to different relative permittivities e, =1 for a vacuum, 3 for a fluid). 

This energy (after multiplication by Avogadros constant) corresponds to -7.5 kj mol . However, if the medium has a typical relative permittivity of 3.5, then the interaction energy is reduced to -2.1 kJ moh. For bulk water as the medium, with the HjO molecules able to rotate in response to a field, the energy of interaction would be reduced by a factor of 78, to only-0.96 kJ mob.  

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We consider a generic donor-acceptor complex solute at infinite dilution in a polyatomic solvent. Both the solute and solvent molecules are represented by rigid and non-polarizable ISM models. In the ISM models the potential energy of interaction between two molecules is a sum of pairwise-additive site-site terms, including Coulombic interactions between partial charges located at the molecular sites. Throughout the paper the subscript A refers to interaction sites of the solute, while the subscript aj refers to interaction site j of solvent molecule a. 

Here cr is the collision diameter and e is the depth of the potential well at the minimum of zz(r). For molecules we often use combinations of atomic pair potentials, adding several body potentials that describe bending or torsion when needed. For dipolar fluids we have to add dipole-dipole interactions (or, in a more sophisticated description. Coulomb interactions between partial charges on the atoms) and for ionic solutions also Coulomb interactions between the ionic charges. 

The most dominant interaction is the electrostatic interaction between partial charges of neighboring atoms. 

Nonbonded interactions are typically modeled as electrostatic interactions between partial charges on the atoms, London dispersion forces due to correlated fluctuations of the electronic clouds of the atoms, and exclusion forces at short distances. They depend on the distance between the atoms / y = r, — tj, and are represented as a sum of Coulomb and Lennard-Jones potentials. 

Interaction between partial charges. If the partial charges Q, and Qj on the atoms i and j are known, a Coulombic contribution of the form given in eqn 11.13 can be included, using the partial charges quoted in Table 11.2. 

The interaction between partial charges does away with the need to take dipole-dipole interactions into account, for they are taken care of by dealing with each partial charge explicitly. 

Hydrogen bonding. In some models of structure, the interaction between partial charges is judged to take into account the effect of hydrogen bonding. 

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