Base pairs special stability

J. R. Quinn, S. C. Zimmerman, J. E. Del Bene, and I. Shavitt, Prebiotic Selection of the AT Base Pair A Physical Organic Approach to Understanding AT Base-Pair Stability Indicates Special Stability, in ACS Symposium Series (2009), 1025 Chemical Evolution 11), pp. 95-107. 

A Physical Organic Approach to Understanding AT Base-Pair Stability Indicates Special Stability (1, 2)... 

The AT and G-C base-pairs have been investigated experimentally and computationally to examine whether they contain any special stability relative to other base pairs. An empirically based relationship between overall complex stability (-AG°) and various possible component interactions is developed to probe the question in a large set of experimentally determined base-pairs and their analogs. Unexpected stability is observed in the A T pair, and its origin is examined computationally. The results and their possible relationship to prebiotic chemistry are described. 

To further examine the question of special stability and potentially quantify it, we took a decidedly physical organic and theoretical approach. The goal is to develop a method of empirically predicting base pair stability with the idea that a linear relationship between predicted and experimental values would allow us to identify examples that deviate from expectations. 

A quantitative analysis of relationship between the local structure and local energetics of PWCs is based on a special decomposition of stabilization energy within the framework of additive models of interaction. In this approximation, the stabilization energy of PWCs is equal to the sum of all pair interactions. We define the effective pair interaction in PWCs (effective energy of H-bond) as the following ... 

Amides are much less reactive than esters toward nucleophilic acyl substitution. They have greater resonance stabilization by the nitrogen lone pair, and they have a poorer leaving group (NH, in acid, and NH2 in base). Amides do show some special reactions the possibility of deprotonation of the nitrogen in 1° or 2C amides, reduction reactions that may form either amines or aldehydes, and a new process, the Hofmann rearrangement. 

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