Center reaction

BittI R, van der Est A, Kamlowski A, Lubitz W and Stehlik D 1994 Time-resolved EPR of the radical pair bacterial reaction centers. Observation of transient nutations, quantum beats and... 

Prisner T F, van der Est A, BittI R, Lubitz W, Stehlik D and Mdbius K 1995 Time-resolved W-band (95 GHz) EPR spectroscopy of Zn-substituted reaction centers of Rhodobacter sphaeroides R-26 Chem. Phys. 194 361-70... 

Vos M H, Jones M R, Hunter C N, Breton J and Martin J-L 1994 Coherent nuclear dynamics at room temperature in bacterial reaction centers Proc. Natl Acad. Sci. USA 91 12 701-5... 

Vos M H, Jones M R, Breton J, Lambry J-C and Martin J-L 1996 Vibrational dephasing of long- and short-lived primary donor states in mutant reaction centers ot Rhodobacter sphaeroides Biochemistry 35 2687-92... 

Stanley R J and Boxer S G 1995 Oscillations in the spontaneous fluorescence from photosynthetic reaction centers J. Phys. Chem. 99 859-63... 

Walker G C, Maiti S, Cowen B R, Moser C C, Dutton P L and Hochstrasser R M 1994 Time resolution of electronic transitions of photosynthetic reaction centers in the infrared J. Phys. Chem. 

Haran G, Wynne K, Moser 0 0, Dutton P L and Hochstrasser R M 1996 Level mixing and energy redistribution in bacterial photosynthetic reaction centers J. Rhys. Chem. 100 5562-9... 

Kirmaier C and Holten D 1988 Subpicosecond spectroscopy of charge separation in Rhodobacter capsulatus reaction centers Isr. J. Chem. 28 79-85... 

Breton J, Martin J-L, Fleming G R and Lambry J-C 1988 Low-temperature femtosecond spectroscopy of the initial step of electron transfer in reaction centers from photosynthetic purple bacteria Biochemistry 27 8276... 

Holzapfel W, Finkele U, Kaiser W, Oesterhelt D, Scheer H, Stilz H U and Zinth W 1989 Observation of a bacteriochlorophyll anion radical during the primary charge separation in a reaction center Chem. Rhys. Lett. 160 1-7... 

Stanley R J, King B and Boxer S G 1996 Excited state energy transfer pathways in photosynthetic reaction centers. 1. Structural symmetry effected. Phys. Chem. 100 12 052-9... 

Deisenhofer J, Epp O, Miki K, Huber R and Michei H 1984 X-ray structure anaiysis of a membrane-protein compiex eiectron density map at 3 A resoiution and a modei of the chromophores of the photosynthetic reaction center from Rhode pseudomonas viridis J. Mol. Biol. 180 385-98... 

To appreciate the reaction center and its importance in reaction searching... 

Unfortunately, in most cases not all the available information on a reaction is given in the reaction equation in a publication, and even less so in reaction databases. To obtain a fuller picture of the reaction that was performed, the text describing the experimental procedure in the publication or a lab journal) would have to be consulted. Reaction products that are considered as trivial, such as water, alcohol, ammonia, nitrogen, etc., are generally not included in the reaction equation or mentioned in the text describing the experimental work. This poses serious problems for the automatic identification of the reaction center. It is highly desirable to have the full stoichiometry of a reaction specified in the equation. 

Consideration of the reaction center or reaction site is of central importance in reaction searching. It does not suffice to specify the functional groups in the starting materials and in the products of a reaction when one is interested in a certain transformation. On top of that, one also has to specify that these functional groups shotfid participate directly in the reaction - that they should be part of the reaction center. 

The reaction center has either to be spedfied when inputting a reaction into a database, or it has to be determined automatically. Specification on input is time-consuming but it can benefit from the insight of the human expert, particularly so if the reaction input is done by the primary investigator as is the case in an electronic notebook. Automatic determination of reaction centers is difficult, particularly so when incomplete readion equations are given where the stoichiometry of a reaction is not balanced see Section 3.1). One approach is to try first to complete the stoichiometry of a reaction equation by filling in the missing molecules such as water, N2, etc. and then to start with reaction center determination. A few systems for automatic reaction center specification are available. However, little has been published on this matter and therefore it is not discussed in any detail here. 

From among the many reaction classification schemes, only a few are mentioned here. The first model concentrates initially on the atoms of the reaction center and the next approach looks first at the bonds involved in the reaction center. These are followed by systems that have actually been implemented, and whose performance is demonstrated. 

On this basis Hendrickson classified organic reactions. A distinction is made between refiinctionalization reactions and skeletal alteration reactions. Refiinctiona-lizations in almost all cases have no more than four carbon atoms in the reaction center. Construction or fragmentation reactions have no more than three carbon atoms in each joining or cleaving part of the molecule. Thus, these parts are treated... 

Reactions should be represented by the shifting of bonds and electrons in the reaction center. 

Gelemter and Rose [25] used machine learning techniques Chapter IX, Section 1.1 of the Handbook) to analyze the reaction center. Based on the functionalities attached to the reaction center, the method of conceptual clustering derived the features a reaction needed to possess for it to be assigned to a certain reaction type. A drawback of this approach was that it only used topological features, the functional groups at the reaction center, and its immediate environment, and did not consider the physicochemical effects which are so important for determining a reaction mechanism and thus a reaction type. 

We will show here the classification procedure with a specific dataset [28]. A reaction center, the addition of a C-H bond to a C=C double bond, was chosen that comprised a variety of different reaction types such as Michael additions, Friedel-Crafts alkylation of aromatic compounds by alkenes, or photochemical reactions. We wanted to see whether these different reaction types can be discerned by this... 

The next question is how to represent the reacting bonds of the reaction center. We wanted to develop a method for reaction classification that can be used for knowledge extraction from reaction databases for the prediction of the products of a reaction. Thus, we could only use physicochemical values of the reactants, because these should tell us what products we obtain. 

Figure 3-19. Reaction center of the dataset of 120 reactions (reacting bonds are indicated by broken lines), and some reaction instances of this dataset.

Table 3-4. Seven physiocheinical property data used to characterize each reaction center.

Figure 3-22 shows a nucleophilic aliphatic substitution with cyanide ion as a nucleophile, i his reaction is assumed to proceed according to the S f2 mechanism with an inversion in the stereochemistry at the carbon atom of the reaction center. We have to assign a stereochemical mechanistic factor to this reaction, and, clearly, it is desirable to assign a mechanistic factor of (-i-1) to a reaction with retention of configuration and (-1) to a reaction with inversion of configuration. Thus, we want to calculate the parity of the product, of 3 reaction from the parity of the... 

It is essential to indicate also the reaction center and the bonds broken and made In a reaction - In essence, to specify how electrons are shifted during a reaction. In this sense, the representation of chemical reactions should consider some essential features of a reaction mechanism. 

Further insight into the driving forces of chemical reactions can be gained by considering major physicochemical effects at the reaction center. 

Specification of the reaction center is important for many queries to reaction databases. 

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

This reaction data set of 626 reactions was used as a training data set to produce a knowledge base. Before this data set is used as input to a neural Kohonen network, each reaction must be coded in the form of a vector characterizing the reaction event. Six physicochemical effects were calculated for each of five bonds at the reaction center of the starting materials by the PETRA (see Section 7.1.4) program system. As shown in Figure 10,3-3 with an example, the physicochemical effects of the two regioisomeric products arc different. 

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