Graphic Characterization and Taxonomy of Organic Reactions Shimaku Fujita Research Laboratories, Ashigara, Fuji Photo Film, Co., Ltd., Mlnaml-Ashigara, Kanagawa, Japan 250-01 Systematic characterization of organic reactions is a problem that has often troubled teachers and students of organic chemistry. There emerged various methods intended to solve the problem. The IUPAC nomenclature for straightforward transformations (1,2) provided a general system of verbal representation in place of various and sometimes inconsistent descriptive terms employed? Hendrickson's system (3)adopted four types of substitutions (H, R, II,and Z)on carbon reaction centers, characterized an organic reaction in the form of such a combination as HZ, RZ, or ZZ, and also proposed a character triangle and a character tetrahedron for correlation between carbon atoms of various oxidation states. Other methods were proposed mainly for the purpose of computer manipulation of organic reactions (4-7). We have critically reviewed the previous methods (8,s). Although all of the methods have their own merits in describing the respective objects they aim at, a novel system integrating them is desired in order to comprehend the total features of organic reactions (9). Especially for the educational purpose, the desired system should be compatible with the conventional system of chemical notation. We have already presented the concept of imaginary transition structures (ITS) as one of the integrated systems for re~resentineoreanic reactions (10-26). The ~ r e s e n DaDer t deks with &e &bstructures (subgraphs) of 1kS8 th; provide an effective a ~ v r o a c hto the characterization of oreanic reactions. The Convenllonal Way for Charactarlzatlon of Organic Reactions Let us work out several examples of bromination reactions (eqs 1 4 ) . How do we recognize these reactions as brominations? We start by comparing the left-hand and the righthand sides of eq 1.We then find the reaction centers whose bonds are formed or broken. Because oreanic chemistw oavs specialattention to carbon atoms, we recognize that a - C - ~ r bond formation and a C-H bond cleavaee occur at the same carbon atom. Equations 2 4 contain thesame mode of structural chanaes, as recoenized hv the same Drocesses. And finally, we perceive these reactions as belong;ng to the same cateeow and refer to these as brominations (ICPAC: bromodeh;drigenation). Although we may unconsciously take these processes of recognition as the result of our academic training, the recognition is complicated even in these simple cases and is frequently difficult for a student beginning to learn organic chemistry as wellas for an inorganic computer.
CH3(CH2)3CH2COOH +
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Journal of Chemical Education
COOH I -+ CH3(CHZ)3CH Br HBr
13)
jCN
Equations 5-9 are reaction diagrams of constructions (C-
C bond formations), a cleavage, an elimination, and an addition, respectively. The examination of how one characterizes these reactions would be a good exercise for students as well as for expert organic chemists.
lrnaglnary Transltlon Structure: A New Way When we carefully reexamine the above processes of recognition, we become aware that the recognition necessitates the strict correspondence between the atoms of the both sides. In other words, it implies the superposition of the one side onto the other of each diagram. Figure 1depicts the superposition corresponding to eq 1. The figure, at the same time, explicates the construction of
'
(2)
Or2
The iUPAC rule distinguishesthe naming of transformations from that Of reactions and from the designation of reaction mechanisms. See ref 1.
from the ITS. These operations reveal that the ITS (1) holds the whole information represented by eq 1. There emerge 15 combinations of par-, out-, andlor inbonds in ITS'S (Table 2). We call each of the combinations an imaginary bond (or an ITS bond). The imaginary bond is denoted by a pair of integers (a b) that is referred to as a comolex bond number. The inteeer a is the multiolicitv of the starting stage, and b is the digerence between the product and the startine ~ t a e eThe . ~ conceot of imaeinarv bonds is an extension of-usuz bonds (sin&, double, and triple bonds) appearing in an organic structure. ~~
~
Three-Nodal Substructure ot an ITS ( 13, 14)
Figure 1. Conobuction of an imaginary transition structure.
Table 1. Three Typa 01 Bonds In an lmaglnary TranaHlon Structure
mior monochromatic representation representation -
-
name pr-bond
&finitlona a bond appearing
both in the starting
-
-
ih-bond
-
x
wt-bond
(green)
Ired)
and product stages a bond appearing only in the produn stage a bond appearing only in the m l n g staoe
Comparison between ITS's 1-4 shows the presence of a common substructure (H++C+Br). This can be extracted by collecting one carbon reaction center and two adjacent noncarbon reaction centers. We call this type of substructures (or subgraphs) three-nodal substructures (or subgraphs), which is abbreviated to 3NS's. This can be coded as H(1-l)C(O+l)Br bv usine comolex bond numbers. ObviOU&~ the , ~ N Scorr&pon& to "bromination", because the PS and PP ooerations reeenerates the equation, H-C + Br I ~ of thein- and out-bonds, (PS) H C-BI ( P P ) ~ terms the substructure (H++C+Br) exactly represents "bromodehydrogenation" or .'bromo-dehydro-substitution" denominated by the IUPAC nomenclature. It should be noted that the complex processes of the conventional perception are replaced by the extraction of the substructure, once we formuiate the concept of ITS'S for representing organic reactions. In order to classify organic reactions, we introduce a hierarchy of 3NS's, as exemplified by Figure 3. If we consider hyperhydrogen (HH) as a superior concept of h y d ~ o g e n , ~ , ~ the substructure derived, HH++C+Br, corresponds to the
-
+
an imaginary transition structure (ITS). The resulting ITS (1) is then regarded as a structural formula that contains three kinds of bonds: par-, out-, and in-bonds (Table 1). The other reactions (eqs 2-9) are similarly represented by the ITS's (2-9).
Figure 2 illustrates projections to the starting stage (PS) and to the product stage (PP) that regenerate the original reaction diagram (eq 1) from the ITS (1).The P S operation that is the deletion of all in-honds from an ITS affords the corresponding starting stage. The product stage is regenerated hy the PPoperation that is thedeletionof all out-hunds
By using complex bond numbers (CBN's), an ITS is stored in the
form of a connection table of the ITS tor its eauivalent). The PS operation is accomplished by replacing CBN (ab) with a. The PP operation is the replacement of (am with a bin a computer. See ref
e+
starting stage
product s t a g e
Figure 2. ProJectionsto the starting stage and to the product stage
Table 2. lmaglnary Bonds and Complex Bond Numbers + - (I-1)
( I .O)
10 .!I
10
The term "hyperhydrogen" indicates such an electroposltlve atom as a hydrogen and an alkali metal. Another 3NS (KKC+Hal) of subfamily level that represents "halo-dehydro-substitution" can be derived. Volume 67 Number 4 April 1990
29 1
term "bromination" in the literal sense, because i t has no definition of the released atom. If the terminal bromine of rhe 3NS is considered to be a halogen (Hal) in a more abstract sense. we obtain HHcC+Hal for the t e r n "halogenation". A more generic descriptor, HH+tC+Z, can be obtained, if a halogen atom is classified into a Z atom (an electronegative atom). Because the displacement of H H by Z means an "oxidative" transformation, the substructure (HH+C+Z) corresponds to an "oxidative substitution". For further discussions, the classification levels of biology (phylum, class, division, section, order, family, genus, and species) are applied to designate the reaction hiearchies, as shown inFigure
(order) HHICeZ
-
(oxidative
substn.)
-
3.
Another t .v.~ of e 3NS (O++C+Br) appears in the ITS (2). .. This generates the cor;esponding substructures of "pper levels. i.e.. HetcC+Hal (family)and Z
