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Substituent Effects on Hydrogen Bonding in Watson–Crick Base Pairs. A Theoretical Study

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Abstract

We have theoretically analyzed Watson–Crick AT and GC base pairs in which purine C8 and/or pyrimidine C6 positions carry a substituent X = H, F, Cl or Br, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P. The purpose is to study the effects on structure and hydrogen bond strength if X = H is substituted by a halogen atom. Furthermore, we wish to explore the relative importance of electrostatic attraction versus orbital interaction in the above multiply hydrogen-bonded systems, using a quantitative bond energy decomposition scheme. We find that replacing X = H by a halogen atom has relatively small yet characteristic effects on hydrogen bond lengths, strengths and bonding mechanism. In general, it reduces the hydrogen-bond-accepting- and increases the hydrogen-bond-donating capabilities of a DNA base. The orbital interaction component in these hydrogen bonds is found for all substituents (X = H, F, Cl, and Br) to contribute about 41% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining 59% of the attraction.

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  1. Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands

    Célia Fonseca Guerra, Tushar van der Wijst & F. Matthias Bickelhaupt

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  1. Célia Fonseca Guerra
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  2. Tushar van der Wijst
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  3. F. Matthias Bickelhaupt
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Correspondence to F. Matthias Bickelhaupt.

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Guerra, C.F., van der Wijst, T. & Bickelhaupt, F.M. Substituent Effects on Hydrogen Bonding in Watson–Crick Base Pairs. A Theoretical Study. Struct Chem 16, 211–221 (2005). https://doi.org/10.1007/s11224-005-4453-x

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