Literature and Databases

When we need the properties of a chemical compound, such as the boiling point of benzene, the fastest and least expensive method is a forward search from the structure to the properties by consulting a database. The sources of such experimental information are first published in primary research journals, and then pass through professional editors and panels to make their way to secondary textbooks and handbooks. 

These are the traditional passive databases of books, handbooks, reference books, journals, and catalogs. They have passed the inspection of editors of committees, and are generally reliable and accurate. 

A general reference often consulted today for the physical and chemical properties of common chemicals is Lange s Handbook of Chemistry (Dean 1999), which lists many chemical compounds and their most important properties. It is organized into separate chapters of Physical constants of organic molecules with 4300 compounds and Physical constants of inorganic molecules, and lists each compound alphabetically by name. Some of these properties are very sensitive to temperature, but less sensitive to pressure, and they are listed as tables, or more compactly as equations of the form /(T) for example, liquid heats of evaporation, heat capacities of multi-atom gases, vapor pressures over liquids, liquid and solid solubilities in liquids, and liquid viscosities. Some of these properties are sensitive both to temperature and pressure. 

Other important handbooks include Chemical Properties Handbook (Yaws 1999) and the CRC Handbook of Chemistry and Physics (Weast and Tide 1989) Tables of Physical and Chemical Constants (Kaye and Laby 1986) is a more compact handbook of physical and chemical data. One should be on guard that sometimes, when experimental results are not available, the editors may list estimated values in a handbook, which are of less certain accuracy. A printed handbook normally has only limited reverse search capability, of going from a set of properties to the structures that have these properties. 

Specialized properties that are not covered in these standard databases can be found in specialized books. The properties of food can be found in Physical Properties of Foods (Peleg and Bagley 1983). The properties of many petroleum products can be found in Petroleum Products Handbook (Guthrie 1960). The Merck Index (1996) lists chemicals, drugs, and biologicals. 

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Typical examples of such accidents with consequences on people and property are quoted in Sections 16.2.1 through 16.2.3 and may be found in detail in relevant literature and databases [12,15,16]. 

To use approximate ad hoc functions, such as power-law or lin-log kinetics, makes it difficult to incorporate available biochemical information. For example, in a worst case scenario, all kinetic constants have to be estimated de novo and cannot be obtained from or compared to existing literature and databases on reaction kinetics. 

Certain short DNA sequences with lengths of 3-12 nucleotides can be defined as more or less stable sequence motifs. Many DNA motifs play a known functional role, e.g., promoter-binding sites for various transcription factors. The functions of other DNA motifs might be yet unknown. The variety of motif seqnences can be found in the scientific literature and databases or can be determined empirically (Table I). 

There are many reviews on constitutes a mouse model for human diseases (5-7), as well as models for specific diseases (8-22). It is beyond the scope of this chapter to discuss the pros and cons of each of these potential models, especially since a recent scan of the public literature and databases revealed over 1200 genetically engineered and spontaneous mouse mutations that have skin diseases that potentially serve as models for specific human diseases. Information on these are and where to find them is discussed below. Further, this chapter will not describe the usefulness of the mouse to study wound healing, and the reader is referred to other reviews on such (23, 24). 

The Canadian Environmental Protection Act, 1999 (CEPA 1999) requires the Ministers of the Environment and Health to categorize the substances on the Canadian Domestic Substances List (DSL). The DSL contains 23 000 substances that are subject to categorization (i.e., prioritization). Generally the data selection process involves a search of the scientific literature and databases for quality experimental data for persistence, bioaccumulation potential and inherent toxicity to humans and nonhuman species. If acceptable data are not found, QSARs or other models are used to estimate the persistence, bioaccumulation, and aquatic toxicity of substances based on structure and physical - chemical properties. 

Once the structure of the PBPK model is formulated, the next step is specifying the model parameters. These can be classified into a chemical-independent set of parameters (such as physiological characteristics, tissue volumes, and blood flow rates) and a chemical-specific set (such as blood/tissue partition coefficients, and metabolic biotransformation parameters). Values for the chemical-independent parameters are usually obtained from the scientific literature and databases of physiological parameters. Specification of chemical-specific parameter values is generally more challenging. Values for one or more chemical-specific parameters may also be available in the literature and databases of biochemical and metabolic data. Values for parameters that are not expected to have substantial interspecies differences (e.g., tissue/blood partition coefficients) can be imputed based on parameter values in animals. Parameter values can also be estimated by conducting in vitro experiments with human tissue. Partitioning of a chemical between tissues can be obtained by vial equilibration or equilibrium dialysis studies, and metabolic parameters can be estimated from in vitro metabolic systems such as microsomal and isolated hepatocyte syterns. Parameters not available from the aforementioned sources can be estimated directly from in vivo data, as discussed in Section 43.4.5. 

Unfortunately, even in this case we are facing several difficulties. First, different reactions included into a complex kinetic scheme cannot be preliminarily studied to the same extent using independent methods. So, if for some reactions numerous data are available in corresponding literature and databases, in other cases not a single reliable value could be found. This means that in the framework of one kinetic model we have to use parameters obtained using very different experimental methods (direct and indirect) and also by more or less well-grounded evaluations. 

Nowadays, most stmctural results are published in non-crystallographic journals as part and in support of chemical studies. Regrettably, referees frequently receive insufficient information to judge the adequacy of the analysis—in particular when very limited crystallographic details are given, often stuffed in a footnote or a CSD reference number. Some journals seem not even to include a trained crystallographer as one of the referees because this holds-up rapid publication of important chemistry. Unfortunately also those only marginally checked structures subsequently go into the literature and databases as a refereed publication. 

Then it was possible to collect reaction rates in form of simple functions of a single parameters with Arrhenius formulas, which are quite common in literature and databases of chemical kinetics and reaction rates. The use of electron temperature as a parameter does not prevent the capability to make comparison with other existing models, since it could be related, in a one to one correspondence, with experimental informations on the streamer electric field. Indeed electron temperature is trivially connected with the mean electron energy, which is determined by the local electric field in the Boltzmann equation (Raizer, 1991). This is sufficient to make straightforward a direct comparison between this simulation and other existing ones or experimental data. In the following we considered as reference an electron temperature value of 4 eV (Kulikovsky, 1998). 

Literature—and Database Search. Ifthe same or a similar substance has already been immobilized on any support material, it may be successfully used for experiments. 

This page is in Portuguese, as is the vast majority of the literature and databases and general information however, a translator may allow recovering the information. 

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