Typing rules, atom

Atom types represen t the chemical environment of an atom. The atom types associated with a given force field could be hard-wired to have specific vahiesand meaning. llyperChem also allows flexible definitions of the atom types and the associated chemical en vironmen Is. Th e ch em ical en viron men t of an atom (a set of rules for defining a type) and the default rules are in a standard ASCII text file, chem.nil. included with llyperChem. You can modify this file and compile it m a binary form that llyperChem... 

To redefine an atom type associated with a force field, adpist the rules in th e ch cm, ru 1 file to represent the new ehernical environment for a particular type and then compile the new types. It is always desirable to save the origin a I eh cm. nil un dcr an oth cr n am c prior to modifying chem.rul. Having modified chem. nil, you can... 

The force fields in HyperChem that use the above 6-12 potential allow six ways of specifying the constants Ay and B.. three by single atom type and three by pairs of atom types. Single atom type means that there are constants for individual atom types, i, that are combined by a combining rule that results in a parameters for a specific pair, ij, of atom types. Pairs of atom types means that parameter files contain explicit parameters for a pair of atom types... 

The form that single atom type constants take is selected by setting the Registry/chem.ini parameter set entry 6-12AtomVDWFormat to one of RStarEpsilon, SigmaEpsilon or SlaterKirkwood. This specifies the combination rules that are used for the file pointed to by the 6-12AtomVDW entry in the Registry or the chem.ini file for the same parameter set. 

The OPLS atom types are a superset of the AMBER united atom types and the bonding parameters are just those of AMBER, supplemented where needed by the OPLS developers. The bond stretch, angle bending, dihedral angle and improper dihedral angle terms are identical to those of AMBER. Unlike AMBER, different combination rules are used for the van der Waals parameters, no hydrogen bonding term is used and no lone pairs are used. 

Newer, published CHARMM parameter sets override some of the combination rule generated parameters for some atom type pairs. These parameters are found in the file pointed to by the 6-12PairVDW entry for the parameter set, usually called npr.txt(dbf). The values of Ay and By for these are computed using equations (22) and (23) on page 178 by setting the 6-12PairVDWFormat entry to RStarEpsilon. 

Atom-based methods [40, 57-68] cut molecules down to single atoms and commonly do not apply correction rules. According to Eq. (9) they work by summing the products of the contribution of an atom type i times the frequency of its presence in a query molecule ... 

Our current ionization and tautomer model encodes biased and balanced equilibria with 108 and 35 rules respectively. Extensive use is made of atom typing to specify chemistry in as generic a manner as possible, which reduces the number of rules required, for example, a number of heteroaromatic nitrogen types, including selected 2-aminopyridines and imidazoles, are aggregated into a definition of bases with pK ... 

Such a process is structurally very unlikely. It would be expected to have a very small A factor as well as a fairly high activation energy. If we rule this type of process out then we are forced to assume that the CH2 attacks the H atom initially in very much the same way that it might for a metathetical process. If we follow this process through, then we see that if the H-atom abstraction is successful, we have still a transition state in which two radicals, the newly formed methyl and the residual alkyl, arc in very close proximity, being essentially H-bonded. However, we have already noted as an empirical fact that the cross sections for alkyl radical recombinations are extremely high. We should thus like to propose that the H-bonded radical pair simply rotates into the favorable position for C-C bond formation before separation can take place. The pathway for the insertion reaction would then take the form ... 

The last term in the formula (1-196) describes electrostatic and Van der Waals interactions between atoms. In the Amber force field the Van der Waals interactions are approximated by the Lennard-Jones potential with appropriate Atj and force field parameters parametrized for monoatomic systems, i.e. i = j. Mixing rules are applied to obtain parameters for pairs of different atom types. Cornell et al.300 determined the parameters of various Lenard-Jones potentials by extensive Monte Carlo simulations for a number of simple liquids containing all necessary atom types in order to reproduce densities and enthalpies of vaporization of these liquids. Finally, the energy of electrostatic interactions between non-bonded atoms is calculated using a simple classical Coulomb potential with the partial atomic charges qt and q, obtained, e.g. by fitting them to reproduce the electrostatic potential around the molecule. 

Muegge I, Martin YC (1999) Atomtypes assigned by SMARTS rules. Problems with insufficient data in PDB for some atom types, J Med Chem, 42 791-804... 

In the case of normal rare earth intermetallic compounds, it is quite plausible to assume that the rare earth has well-defined 4fn configuration with an oxidation state of +3. Thus the behaviour of the rare earth ion in a metallic system is similar to insulators. The 4/ electrons are strongly correlated in atomic type configurations characterized by total angular momentum quantum levels, J in accordance with Hund s rules. 

---