Organic Compounds Database

The abbreviation QSAR stands for quantitative structure-activity relationships. QSPR means quantitative structure-property relationships. As the properties of an organic compound usually cannot be predicted directly from its molecular structure, an indirect approach Is used to overcome this problem. In the first step numerical descriptors encoding information about the molecular structure are calculated for a set of compounds. Secondly, statistical methods and artificial neural network models are used to predict the property or activity of interest, based on these descriptors or a suitable subset. A typical QSAR/QSPR study comprises the following steps structure entry or start from an existing structure database), descriptor calculation, descriptor selection, model building, model validation. 

OtherD t b ses. Available from different vendors (Table 8). For example, the researcher can obtain physical properties by usiag the Merck Index Online or the Dictionary of Organic Compounds available by Chapman and Hall Chemical Database. In DIALOG, numeric databases are collected under the name of CHEMPROP. 

Chapman and Hall Chemical Database Chapman and Hall, Ltd. Dialog Dictiona of Organic Compounds (5th ed.), Dictiona of Organometallic Compounds, Carbohydrates, Mmino Mcids, Peptides, Dictionay of Antibiotics and Eelated Compounds, and Dictionay of Organophosphorus Compounds... 

Bcl-2 is one of the many factors that control apoptosis, and overexpression of Bcl-2 has been observed in many different cancers. A homology model of Bcl-2 was derived from the NMR 3D structure of the Bcl-XL complex with a Bak BH3 peptide. This model served to search the NCI 3D database of 206,876 organic compounds for potential Bcl-2 inhibitors, which bind to the Bak BH3 binding site of Bcl-2. Full conformational flexibility of the ligands was taken into account in the program DOCK. Thirty-five potential inhibitors were tested, and seven of them had IC50 values from 1.6 to W.OpM. One of... 

A variety of commercial kits and automated systems are available to test the abilities of bacteria to assimilate, ferment, decarboxylate, or cleave selected organic compounds.46 Their reliability for species identification is usually greater with cultures from clinical samples, where a limited number of bacteria are commonly encountered, and less with environmental soil and water samples, where a great many uncommon or previously unidentified species not in the database are likely to be present.29,45 Additional tests beyond those found in the commercial kits may be necessary for example, the hydrolysis of various nitriles and amides is useful for identifying Rhodococcus spp.47 Some commercial kits for clinical use feature antimicrobial susceptibility testing.21... 

Moreover, this model counts with a substance database for both organic and inorganic substances as well as default values when a parameter is unknown. In addition, the model can conduct calculations for different substances at the same time. However, the model is more developed for the organic compounds than for the inorganic ones. 

First of all it is helpful to check the presence of similar spectra in the available spectral databases. Ideally the task may be completely resolved at this stage. The library search may help to refer the sample to a certain class of organic compounds, to get some clues on the presence of heteroatoms and functional groups. 

We have attempted to collect in appendix B a list of the most used thermochemical databases. Each one has been built with a particular class of substances and a specific set of properties in mind. We can find compilations of thermochemical values for gas-phase ions, for condensed and gas-phase pure organic compounds, for organometallic molecules, for gas-phase organic free radicals, for inorganic substances, and so on. Most are available in printed form, some are distributed in a software package, and a few can be used online, through the World Wide Web. 

The choice of a given database as source of auxiliary values may not be straightforward, even for a thermochemist. Consistency is a very important criterion, but factors such as the publication year, the assignment of an uncertainty to each value, and even the scientific reputation of the authors or the origin of the database matter. For instance, it would not be sensible to use the old NBS Circular 500 [22] when the NBS Tables of Chemical Thermodynamic Properties [17], published in 1982, is available. If we need a value for the standard enthalpy of formation of an organic compound, such as ethanol, we will probably prefer Pedley s Thermodynamic Data and Structures of Organic Compounds [15], published in 1994, which reports the error bars. Finally, if we are looking for the standard enthalpy of formation of any particular substance, we should first check whether it is included in CODATA Key Values for Thermodynamics [16] or in the very recent Active Thermochemical Tables [23,24],... 

In summary, we selected one database (Pedley s) to quote the standard enthalpies of formation of the pure organic compounds and another database (NBS) to derive the solution enthalpies. Although these databases are not mutually consistent, that did not affect our final result because the experimental enthalpies of solution were calculated with NBS data only. The exercise illustrates the sort of caution one should keep in mind whenever two or more nonconsistent databases are used. 

The most reliable values of Laidler terms that can applied to a wide variety of compounds are those recommended by Cox and Pilcher [89]. They were derived from a consistent database that includes experimentally determined standard enthalpies of formation for hundreds of organic compounds. This lengthy but simple exercise involves the choice of a set of bond enthalpy terms that affords the best agreement between experimental and calculated standard enthalpies of... 

Entropy and Heat Capacity of Organic Compounds Compiled by Glushko Thermocenter, Moscow. In NIST Chemistry WebBook NIST Standard Reference Database Number 69 P. J. Linstrom, W. G. Mallard, Eds. National Institute of Standards and Technology Gaithersburg, June 2005 (webbook.nist.gov). 

This database supersedes those in Cox and Pilcher [54], Pedley 77 [45], and Pedley 86 [38]. An empirical scheme, developed by the author, to estimate enthalpies of formation of organic compounds in gas and condensed phases, is also described. 

This useful and simple-to-use software package relies on Benson s group additivity scheme [47] to estimate thermochemical data for organic compounds in the gas phase. It also contains values from several NIST databases, including NIST Positive Ion Energetics [32] and JANAF Tables [22]. The first version of... 

E. S. Domalsky, E. D. Hearing, V J. Hearing Jr.. NIST Estimation of the Chemical Thermodynamic Properties for Organic Compounds at 298.15 K. NIST Standard Reference Database 18 National Institute of Standards and Technology Gaithersburg, 1994. 

This has been, for many years, the main source of standard enthalpies of formation of neutral organic compounds. It is a classic work on thermochemistry and has set a standard for thermochemical databases. Superseded by Pedley s 1994 compilation [26]. 

Shah JJ, Heyerdahl EK. 1988. National ambient volatile organic compounds (VOCs) database update. US Environmental Protection Agency. Research Triangle Park, NC US Environmental Protection Agency, Atmospheric Sciences Research Laboratory. EPA 600/S3-88-010, 1-11. 

EPA. 1988b. U.S. Environmental Protection Agency National ambient volatile organic compounds (VOCS) Database update. EPA/600/3-88/010. 

Gherini, S.A., Sutmners, K.V., Munson, R.K., and Mills, W.B. Chemical Data for Predicting the Fate of Organic Compounds in Water, Volume 2 Database (Lafayette, CA Tetra Tech, 1988), 433 p. 

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