Covalent force field

While nonbonded atom pairs will typically not come within 1A of each other, it is possible for covalently bound pairs, either directly bounds, as in 1-2 pairs, or at the vertices of an angle, as in 1-3 pairs. Accordingly it may be considered desirable to omit the 1-2 and 1-3 dipole-dipole interactions as is commonly performed on additive force fields for the Coulombic and van der Waals terms. However, it has been shown that inclusion of the 1-2 and 1-3 dipole-dipole interactions is required to achieve anistropic molecular polarizabilites when using isotropic atomic polariz-abilites [50], For example, in a Drude model of benzene in which isotropic polarization was included on the carbons only inclusion of the 1-2 and 1-3 dipole-dipole interactions along with the appropriate damping of those interactions allowed for reproduction of the anisotropic molecular polarizability of the molecule [64], Thus, it may be considered desirable to include these short range interactions in a polarizable force field. 

The basic idea of the QM/MM methods [32, 33] is to partition the system into an inner quantum zone, in which the interesting chemistry happens, and an outer classical force field region. While this division is physically sensible, it can be quite tricky to handle the boundary between the two domains. If there is no covalent bond linking the QM and MM regions, the partitioning is simpler. If the boundary cuts through chemical bonds, however, the partitioning is more difficult. Several approaches have... 

Molecular mechanics force fields rest on four fundamental principles. The first principle is derived from the Bom-Oppenheimer approximation. Electrons have much lower mass than nuclei and move at much greater velocity. The velocity is sufficiently different that the nuclei can be considered stationary on a relative scale. In effect, the electronic and nuclear motions are uncoupled, and they can be treated separately. Unlike quantum mechanics, which is involved in determining the probability of electron distribution, molecular mechanics focuses instead on the location of the nuclei. Based on both theory and experiment, a set of equations are used to account for the electronic-nuclear attraction, nuclear-nuclear repulsion, and covalent bonding. Electrons are not directly taken into account, but they are considered indirectly or implicitly through the use of potential energy equations. This approach creates a mathematical model of molecular structures which is intuitively clear and readily available for fast computations. The set of equations and constants is defined as the force... 

Carosati, E., Sciabola, S. and Cruciani, G. (2004) Hydrogen bonding interactions of covalently bonded fluorine atoms from crystallographic data to a new angular function in the GRID force field. Journal of Medicinal Chemistry, 47, 5114-5125. 

Figure 3. Structural representation of the computational models A-F. Models B, D, and E are combined QM/MM models where the regions enclosed in the dotted polygons represent the QM region. The regions outside the polygons are treated by a molecular mechanics force field. For the electronic structure calculation of the QM region, the covalent bonds that traverse the QM/MM boundary (the dotted polygon), have been capped with hydrogen atoms. In model A the atoms labelled 1 through 4 are the atoms that have been fixed in the calculations of models A through E.

Debeau and Poulet 2S1> reported an interesting study of 31 crystalline hexa-chloro MC16 and hexabromo MBr6 metallates and the force constants are calculated with a modified Urey-Bradley force field the relation between the metal-X stretching frequency and the MX covalency is discussed. 

A very promising recent approach to modeling angular geometries, the VAL-BOND model[30], is based on Pauling s 1931 paper1311 that established the fundamental principles of directed covalent bonds formed by hybridization. The VALBOND force field, which uses conventional terms for bond stretching, torsions, improper tor-... 

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