Connectivity stack method

Figure 2 shows an example for the enumeration of chemical graphs by using the connectivity stack method. Nodes W, X, Y, Z in this figure have atomic valences 2, 2, 1, 1, respectively, and the priority order of these nodes is assumed to be W > X > Y = Z. Furthermore, nodes Y and Z are equivalent in this example. The connectivity stack starts by creating a bond between W and X on a connectivity matrix (ai2 = 1, i.e., bi = 1). The principles for the creation of a connectivity stack are to start to create a bond from the head of a connectivity stack, to examine the valency of each node, and not to generate separated chemical graphs (examination of connectivity). 

In the connectivity stack method, the isomorphic check (.see Isomorphism) of a substructure can be done, i.e., it is examined whether a graph obtained by permutation of equivalent nodes satisfies condition (2) for canonicalization. Here, a noncanon-ical form of the connectivity stack is discarded as a duplicate graph. 

If the generation of a connectivity stack and the permutation or substitution of equivalent nodes are carried out without effective algorithms, the number of generated stacks might be astronomical and the calculation time is very time-consuming. It is clear that the connectivity stack method also includes methods for avoiding these problems. 

Strictly, the structure generator in CHEMICS consists of two roles one is generation of any possible sets of fragments (called components in CHEMICS). and the other is generation of structures from these sets by using the connectivity stack method. In this section, the core of the generator, i.e the latter part, has been described above. 

Many systems of notation and classification have been proposed. The well-known books by R. W. G. Wyckoff, A. F. Wells, F. C. Phillips, L. Bragg, M. J. Buerger, L. V. Azakoff, D. M Adams, and W. B. Pearson (Appendix A, Further Reading) have discussed these proposals. These proposals include close packing of atoms, nets, or prism connections, stacking of coordination polyhedra and even a crystal-algebra method. Application of most of these proposals requires familiarity with the features of many structures. Only specialists can be expected to have... 

The electronic coupling of donor and acceptor sites, connected via a t-stack, can either be treated by carrying out a calculation on the complete system or by employing a divide-and-conquer (DC) strategy. With the Hartree-Fock (HF) method or a method based on density functional theory (DFT), full treatment of a d-a system is feasible for relatively small systems. Whereas such calculations can be performed for models consisting of up to about ten WCPs, they are essentially inaccessible even for dimers when one attempts to combine them with MD simulations. Semiempirical quantum chemical methods require considerably less effort than HF or DFT methods also, one can afford application to larger models. However, standard semiempirical methods, e.g., AMI or PM3, considerably underestimate the electronic couplings between r-stacked donor and acceptor sites and, therefore, a special parameterization has to be invoked (see below). 

The whole database access code is surrounded by a try-finally block. There is no catch because the exceptions are rethrown by the code. However, the finally block is necessary because the ResultSet, Statement, and Connection objects must be closed properly whether an exception is thrown, or otherwise there will be database resource leaks. The database cleanup is implemented in a Util class. The initialization of the Connection object is purposely left out from the code. It can be either from a connection pool or from a Thread Local variable that is set earlier in the method call stack. Thread Local will be discussed further in Chapter 15. 

The frameworks of zeolites can be viewed as being constructed from the stacking of simple 3-connected 2-D nets. Akporiaye and Price developed an approach to enumerate systematically the structures of zeolites based on the analysis of the frameworks in terms of component sheets.[16] This method uses simple operator sequences in describing the repeating pattern of the component sheets, which is efficient to describe known zeolite structures and enumerate theoretical structures systematically. 

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