Proton-Deficient Hydrogen Bonds

Due to proton deficiency, crystal structures of amino acids display a much higher proportion of three-center hydrogen bonds. Their geometries, given in Th-bles 8.6 and 8.7, are based on neutron diffraction data, of which a relatively large number is available for this class of biological molecules. 

The three-center bonds represent — 70% of the total number of hydrogen bonds in the crystal structures surveyed (Thble 2.3). This is a significantly higher proportion than in the other biological molecules, and was attributed to proton deficiency, which occurs because the amino acids form zwitterionic crystal structures where the predominant hydrogen bonding is between the -NH3 and the... 

Proteins contain, on average, more acceptor than donor sites [596]. Similar proton deficiency in the amino acid zwitterion crystal structures results in the formation of three-center hydrogen bonds rather than in unsatisfied acceptor sites [74] (Part I A, Chap. 2.6). There is less flexibility in the orientation of hydrogen-bond donor and acceptor groups in proteins which would lead to a relatively larger number of unsatisfied acceptor sites. Some of the more unsymmetrical three-center bonds which might have been missed in the survey [596] because of the 3.5 A X - A cut-off limit will also contribute to reduce the number of unsatisfied acceptors in side-chains. 

The [TcO]3+ core is sufficiently electron deficient to deprotonate secondary aliphatic amines, and in 36 and analogs neutrality is achieved by loss of both amine protons and one oxime proton, with the remaining oxime proton being intramolecularly hydrogen bonded. Features of the structures are Tc=0 bond distances in the range 1.670(4)-1.682(5) A and the displacement of Tc above the N4 plane, which for 36 is 0.678(1) A. Also, for 36 the distance between Tc and the deprotonated N (imino) atoms of 1.913 A (av.) is considerably shorter than the Tc-N(oxime) distance of 2.090 A (av.) (453). The y(TcO) IR absorption in the rather... 

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