The role of molecular shape similarity in specific molecular recognition

Vital significance of addition of “shape similarity” between solutes to shape complementarity for more precise molecular recognition in aqueous binary solvents

“…If the shape similarity effect is responsible for the specific recognition described above, a pair of groups with similar shape would be expected to be brought close together. Indeed, this is true for the NMe 2 group in 17 and the Me 2 CH group (R 6 ) in 18 , as demonstrated by X‐ray analysis (Figure 5) of the crystalline 1:1 complex (R 5 = Ph[CH 2 ] 2 and R 6 = Me 2 CH[CH 2 ] 2 ) 36…”

“…This section is most deeply concerned with the title. The following results36 first led us to notice extreme importance of shape similarity in molecular recognition. With the oxidation of system 1a and 2a in aqueous acetonitrile (MeCN) [ mole fraction of water ( x w ) = 0.42] at 35.0 °C, the r of 1.2 for Z = CHMe 2 has proved to be the same as that for Z = NO 2 (1.2).…”

“…The crystalline 1:1 complexes each had very characteristic color, changing from pale yellow to pale brown, dark brown, orange, reddish brown, purple, dark purple, and so on 36. It is also remarkable that, among the nine possible combinations where R 5 is a cyclohexylalkyl group (C 6 H 11 [CH 2 ] 0–2 ) and R 6 is a phenylalkyl group (Ph[CH 2 ] 0–2 ), only two afforded the crystalline 1:1 complexes, each having two spatially similar groups of the same number of carbon atoms: the pairs C 6 H 11 —Ph and C 6 H 11 [CH 2 ] 2 —Ph[CH 2 ] 2 36. If the shape similarity effect is responsible for the specific recognition described above, a pair of groups with similar shape would be expected to be brought close together.…”

Evaluation of enthalpies of cyclic alkene-benzene and ether-benzene interactions based on MO calculations

“…18 As a result, it has been clarified that three-dimensional shape similarity between interacting groups in reacting molecules is responsible for more specific and precise molecular recognition than would otherwise be achieved. 19 These findings led us to investigate weak interactions between interacting groups. Using GLPC, it has been demonstrated that (i) enthalpies of weak interactions of a phenyl group (DDH t ) with substituted benzenes, 20 alkanes, 21 alkenes, 22 ethers 22 and carbonyl compounds 20 range from À2.7 to 0.1 kcal mol À1 (1 cal = 4.184 J) and (ii) the weak interactions of a phenyl group become more attractive with a cyclic group that is similar in threedimensional shape to a phenyl group; 20 DDH t is the enthalpy of the weak interaction of a PhX molecule with the phenyl group in the stationary liquid (practically a PhH molecule) relative to the enthalpy of that of an noctane molecule with the phenyl group.…”

Structure of the 1:1 complex of 1-(p-dimethylaminophenyl)-3-(phenylacetyl)urea and 1-isobutyl-3-(p-nitrobenzoyl)urea, C17H19N3O2.C12H15N3O4

“…In order to elucidate the mechanism of the selectivity in oxidation of a pair of thiols, HSCH 2-(CONH)2C6H4N(CH3) 2 and HSCH2CH2(NHCO)2-R (R = alkyl), we have determined the crystal structures of the former compound (Uchida, Ohashi, Sasada, Kaneko & Endo, 1983) and its model compound C6HsCHE(CONH)EC6H4N(CH3) 2 (Ohashi, Uchida, Sasada, Kinoshita & Endo, 1984). Further studies on the complex formation were carried out using several pairs of acylurea derivatives, R I--(CONH)EC6H4N-(CH3) 2 and RE-(NHCO)EC6H4NO 2, where R 1 and R E are non-polar groups (Endo, Miyazawa, Endo, Uchida, Ohashi & Sasada, 1982;Endo, Miyazawa, Endo, Kato, Uchida, Ohashi '& Sasada, 1983). The p-nitrophenyl group was used since it has similar shape but opposite electronic character to the pdimethylaminophenyl group and the selectivity for C6H4NO 2 in the oxidation is approximately the same as that for C6H4N(CH3) 2.…”