Non-bonding interaction

According to Bartell (1961a), the relative motion of the interacting non-bonded atoms is described by means of a harmonic oscillator when the two atoms are bonded to the same atom, and by means of two superimposed harmonic oscillators when the atoms are linked to each other via more than one intervening atom. It is the second case which is of interest in connection with the biphenyl inversion transition state. The non-bonded interaction will of course introduce anharmonicity, but since a first-order perturbation calculation of the energy only implies an... 

Steric interaction Non-bonded or van der Waals interaction has been demonstrated to be no different from, albeit weaker than, both covalent and ionic interactions. It has in fact been demonstrated [88] that all pairwise interactions in a molecule are correctly simulated by the point-charge model of section 5.3. 

TransannUlar interaction Literally cross-ring interactions. Non-bonded interaction between ligands attached to nonadjacent atoms in a ring, for example in a cyclohexane boat or in medium-sized rings. 

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

In addition, the non-bonded forces can be divided into several regions according to pair distances. The near region is normally more important than the distant region because the non-bonded forces decay with distance. Since most of the CPU time in a MD simulation is spent in the calculation of these non-bonded interactions, the separation in pair distance results in valuable speedups. Using a 3-fold distance split, the non-bonded forces are separated in 3 regions near, medium, and fax distance zones. Thus, the Liouville operator can be express as a sum of five terms... 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

In the next step, the suggested models are translated into 3D space by subsequently combining the templates. Again, each model is assessed and ranked according to various structural criteria, such as the geometric fit of the 3D templates and non-bonding interactions (steric clashes). If none of the solu-... 

Figure 2-99. Elimination of non-bonded interactions (close contacts).

Figure 7-8. Bonded (upper row) and non-bonded (lower row) contributions to a typioal molecular mechanics force field potential energy function. The latter two types of Interactions can also occur within the same molecule.

The PEF is a sum of many individual contributions, Tt can be divided into bonded (bonds, angles, and torsions) and non-bonded (electrostatic and van der Waals) contributions V, responsible for intramolecular and, in tlic case of more than one molecule, also intermoleculai interactions. Figure 7-8 shows schematically these types of interactions between atoms, which arc included in almost all force field implementations. 

Vn is often called the barrier of rotation. This is intuitive but misleading, because the exact energetic barrier of a particular rotation is the sum of all V components and other non-bonding interactions with the atoms under consideration. The multiplicity n gives the number of minima of the function during a 360° rotation of the dihedral angle o). The phase y defines the exact position of the minima. 

It is noteworthy that it is not obligatory to use a torsional potential within a PEF. Depending on the parameterization, it is also possible to represent the torsional barrier by non-bonding interactions between the atoms separated by three bonds. In fact, torsional potentials and non-bonding 1,4-interactions are in a close relationship. This is one reason why force fields like AMBER downscale the 1,4-non-bonded Coulomb and van der Waals interactions. 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

The raie gas atoms reveal through their deviation from ideal gas behavior that electrostatics alone cannot account for all non-bonded interactions, because all multipole moments are zero. Therefore, no dipole-dipole or dipole-induced dipole interactions are possible. Van der Waals first described the forces that give rise to such deviations from the expected behavior. This type of interaction between two atoms can be formulated by a Lennaid-Jones [12-6] function Eq. (27)). 

A second idea to save computational time addresses the fact that hydrogen atoms, when involved in a chemical bond, show the fastest motions in a molecule. If they have to be reproduced by the simulation, the necessary integration time step At has to be at least 1 fs or even less. This is a problem especially for calculations including explicit solvent molecules, because in the case of water they do not only increase the number of non-bonded interactions, they also increase the number of fast-moving hydrogen atoms. This particular situation is taken into account... 

Figure 7-14. All-atom and united-atom representation of the amino acid isoleucine. In this example, 13 atoms, which are able to form explicit non-bonding interactions, are reduced to only four pseudo-atoms,...

Ways to circumvent the above-mentioned problems have been to simply increase the cutoff distance to larger values, to use more than one cutoff value with different update frequencies, or to define more sophisticated cutoff schemes. In the last case, a truncation of the non-bonded interactions was replaced by shifting the interaction energies to zero or by additionally applying a switched sigmoidal func-... 

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