Matches function fragment

The largest difference between force fields is probably how they handle electrostatics. Each force field uses its own definition of what functions and data should be used. The well-known MM2 force field describes all electrostatic interactions by bond dipoles (4), but most other force fields utilize atomic point charges. The charges may in turn be obtained from fragment matching (34), from bond-type-dependent charge flux (35), or from more complex schemes that can also respond to the environment (36). 

This is the fragment key for phenol. The key function can be used to compute and store values of the fragment key in tables of molecular structures. It can also be used to compute values of fragment keys for substructures to be used as a prescreen during a full substructure search using the matches function. 

The following function is analogous to the fragment key function above. It uses a relational table to define fragments, a function to match SMILES and SMARTS (in this case count matches), and an aggregate SQL function to tally the results over all matched fragments. 

This function returns a length 166 fragment key. The input text string ( 1 in the function body) is a SMILES, as expected by the matches function. The table of fragments is based on the MACCS 166 public keys1 and is shown in Table A.5.3 of this Appendix. 

This function computes the polar surface area of an input SMILES structure. It uses the table for tpsa fragment SMARTS and fragment partial polar surface areas shown in Table A.3. It relies on the count matches function described in Chapter 7. 

Consider now the behaviour of the HF wave function 0 (eq. (4.18)) as the distance between the two nuclei is increased toward infinity. Since the HF wave function is an equal mixture of ionic and covalent terms, the dissociation limit is 50% H+H " and 50% H H. In the gas phase all bonds dissociate homolytically, and the ionic contribution should be 0%. The HF dissociation energy is therefore much too high. This is a general problem of RHF type wave functions, the constraint of doubly occupied MOs is inconsistent with breaking bonds to produce radicals. In order for an RHF wave function to dissociate correctly, an even-electron molecule must break into two even-electron fragments, each being in the lowest electronic state. Furthermore, the orbital symmetries must match. There are only a few covalently bonded systems which obey these requirements (the simplest example is HHe+). The wrong dissociation limit for RHF wave functions has several consequences. 

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