The Scope of this Book

This book is conceived as a textbook for application in teaching and self-learning of chemoinfoimatics. We aim to present a comprehensive overview of the field of che-moinformatics for students, teachers, and scientists from other areas of chemistry, from biology, informatics, and medicine. Those interested in a more in-depth presentation and analysis of the topics in this Textbook are referred to an accompanying set of four volumes. 

Handbook of Chemoirfonnatics - From Data to Knowledge where many of the issues are presented in greater detail by leading experts in the various fields. 

Clearly, some of the subjects touched upon deserve entire books of their own. This is particularly true for the methods discussed in Chapters 7 and 9. 

References cited in the corresponding chapters of this book direct the interested reader to these books that provide much more detail in greater depth than is possible here. We can present only the major foundations, methods, and uses of these subjects as we have deemed necessary. 

Some aspects, such as the computer representation and manipulation of proteins and nucleic acids, could not be covered. Even the modeling of the interactions of small molecules with proteins, as dealt with in docking software or software for de novo design could not be included in the Textbook, although chapters in the Handbook do treat these subjects. 

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Dislocation theory as a portion of the subject of solid-state physics is somewhat beyond the scope of this book, but it is desirable to examine the subject briefly in terms of its implications in surface chemistry. Perhaps the most elementary type of defect is that of an extra or interstitial atom—Frenkel defect [110]—or a missing atom or vacancy—Schottky defect [111]. Such point defects play an important role in the treatment of diffusion and electrical conductivities in solids and the solubility of a salt in the host lattice of another or different valence type [112]. Point defects have a thermodynamic basis for their existence in terms of the energy and entropy of their formation, the situation is similar to the formation of isolated holes and erratic atoms on a surface. Dislocations, on the other hand, may be viewed as an organized concentration of point defects they are lattice defects and play an important role in the mechanism of the plastic deformation of solids. Lattice defects or dislocations are not thermodynamic in the sense of the point defects their formation is intimately connected with the mechanism of nucleation and crystal growth (see Section IX-4), and they constitute an important source of surface imperfection. 

An excellent treatment of molecular quantum mechanics, on a level comparable to that of Szabo and Ostiund. The scope of this book is quite different, however, as it focuses mainly on the basic principles of quantum mechanics and the theoretical treatment of spectroscopy. 

The detailed theory of bonding in transition metal complexes is beyond the scope of this book, but further references will be made to the effects of the energy splitting in the d orbitals in Chapter 13. 

The hydrides of beryllium and magnesium are both largely covalent, magnesium hydride having a rutile (p. 36) structure, while beryllium hydride forms an electron-deficient chain structure. The bonding in these metal hydrides is not simple and requires an explanation which goes beyond the scope of this book. 

Carbon forms a number of oxides in addition to carbon monoxide and dioxide but they are beyond the scope of this book. 

This is not to say that we deem these topics not to be important. On the contrary, we think that those interested in chemoinformatics should strive to obtain a basic knowledge of these subjects. We even think that all professionals in natural sciences and engineering should in future obtain a minimum of training in these fields during their studies. However, presentation here of those aspects of informatics would go beyond the scope of this book. 

If you wish to modify SHMO or mn it on a machine that is different from the machine that it was compiled on, you may have to recompile. Compiling EORTRAN programs is outside the scope of this book but is described in detail in... 

The prime importance of these biological applications, far beyond the scope of this book, has in recent years focused interest on biological applications of thiazoles instead of on typical chemical research (at least for those described in Chapter 3). In the tables of products, thiazoles that are of biological interest are indicated... 

Note that the environments that produce SCC are not necessarily corrosive to the metals in the unstressed state. Other factors that may also influence susceptibility to SCC are listed here discussion of these items is, however, beyond the scope of this book. 

Nearly every manufacturing, shipping, and installation process is a potential source of a defect. Manufacturers, in recognition of this, mount major efforts to minimize or eliminate defects. Although an exhaustive list of defects is beyond the scope of this book, some common ones will be discussed. 

The full technical details of these processes are beyond the scope of this book (see Further reading for further enlightenment), but it is worth having a slightly closer look at them to get a feel for the engineering context in which each is used. 

Molecular modelling calculations using values of smaller than 3 Angstrom units for these proton-proton distances can be performed to obtain an optimized picture of the molecule. But this exceeds the scope of this book. 

The solutions to a problem of this magnitude can be found in references [3, 7] and others. Figures 9-16 and 9-17 are torsional mode shape diagrams of some typical systems. While the rigorous solution to the multimass damped system is not within the scope of this book, several interesting points should be made. 

The technical requirements for such applications are highly specific, and the technology is also highly specialised and beyond the scope of this book. 

While detailed discussion of the merits of PEN fibres is largely outside the scope of this book mention may be made of the success in preliminary trials of (yacht) sailcloths made from PEN fibre. PEN fibres have a modulus roughly 2.5 X that of PET, exhibit excellent flex life and also show very good UV resistance. It is understood that the one yacht fitted with PEN sailcloth in the 1996 Olympics won the gold medal in its event. 

The bulk of bituminous materials are used for road making and building applications which are outside the scope of this book. Only a very small percentage is used in moulding compositions and few data have been made publicly available concerning the properties of these compositions. 

In 1994 the Oak Ridge National Laboratory hosted an American Carbon Society Workshop entitled Carbon Materials for Advanced Technologies . The inspiration for this book came from that workshop. By late 1995 a suitable group of contributors had been identified such that the scope of this book would be sufficiently broad to make a useful contribution to the literature. 

A number of alternative methods for manufacturing the desired products are available however, it is beyond the scope of this book to discuss these processes and products. 

Some six hundred structures of naturally occurring carbogenic molecules appe on the pages which follow, together with the name of each compound and references to the original literature of successful chemical synthesis. Thus, Part Three of this book is effectively a key to the literature of chemical synthesis as applied to the complex molecules of nature. The survey does not include oligomeric or polymeric structures, such as peptides, proteins, carbohydrates and polynucleotides, which fall outside the scope of this book because they can be assembled by repetitive procedures. 

More rigorous techniques for optimizing outlet composition are described by ]-Halwagi and Manousiouthakis (1990b), Garrison cral, (1995), and Gupta and Manousiouthakis (1995) and is beyond the scope of this book. 

Manufacturing efficiency embodies a wide variety of topics far beyond the scope of this book. However, a materials utilization factor will be defined and characterized for composite materials and metals as a... 

The design of heaters and waste heat recovery units is beyond the scope of this book. Sizing and design are best left to manufacturers. However, the concepts discussed in this chapter and in Chapter 2 can be used to verify the manufacturer s proposals. 

The Ryan-Holmes distillation process uses cryogenic distillation to remove acid gases from a gas stream. This process is applied to remove COi for LPG separation or where it is desired to produce COt at high pressure for reservoir injection. This complicated process is beyond the scope of this book. 

The following descriptions are meant to briefly describe the various generic valve types. Within each type there are numerous different design details that separate one valve manufacturer s valves from the ne of these speciuc models have good points and bad points all can h correctly and incorrectly. It is beyond the scope of this book to c each valve manufacturer s design. However, the various valve sal will be more than pleased to contrast the benefits of their valve s ft with that of the competition. The reader is cautioned that hight valves do not necessarily mean better valves, and that expensive can result in a significant waste of money when a less expensive but adequate valve will perform satisfactorily. 

There are many configurations of plugs and seats ( trim ) that create different control responses. The design specification of control valves is beyond the scope of this book. 

A rigorous treatment of dispersion in soils is beyond the scope of this book. However, some qualitative discussion is warranted because of the potential and existing problems already described. Two ntain problems arise bceause dispersion in soil (or land) is anisotropic (i.e., it varies with direction) and the penneability is not only a variable but also att unknown. 

Although an in-depth treatment is outside the scope of this book, it may be instructive to point out some of the features and problems in a relativistic quantum description of atoms and molecules. 

Since working with the full four-component wave function is so demanding, different approximate methods have been developed where the small component of the wave function is eliminated to a certain order in 1/c or approximated (like the Foldy-Wouthuyserd or Douglas-Kroll transformations thereby reducing the four-component wave function to only two components. A description of such methods is outside the scope of this book. 

A detailed description of methods for studying dynamic (i.e. time-dependent) phenomena and condensed phases is outside the scope of this book. The common feature for all these methods, however, is the need for an energy surface upon which the dynamics can take place. The generation of such a surface normally relies at least partly on results from calculations of the types discussed in Chapters 2-6, and it may therefore be of interest to briefly discuss the fundamentals. 

Given the diversity of different SCRF models, and the fact that solvation energies in water may range from a few kcal/mol for say ethane to perhaps 100 kcal/mol for an ion, it is difficult to evaluate just how accurately continuum methods may in principle be able to represent solvation. It seems clear, however, that molecular shaped cavities must be employed, the electiostatic polarization needs a description either in terms of atomic charges or quite high-order multipoles, and cavity and dispersion terms must be included. Properly parameterized, such models appear to be able to give absolute values with an accuracy of a few kcal/mol." Molecular properties are in many cases also sensitive to the environment, but a detailed discussion of this is outside the scope of this book. ... 

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