Simulating the interaction between amino acids and DNA: a combined matrix-isolation FT-IR and theoretical study of the 1-methyluracil·glycine H-bond complexes using a dual sublimation furnace

J Phys Chem B. 2012 Oct 4;116(39):11890-8. doi: 10.1021/jp307388e. Epub 2012 Sep 24.

Abstract

The H-bond complex formation between 1-methyluracil and glycine has been investigated by theoretical calculations and the most stable complex configurations have been identified by FT-IR spectroscopy in Ar matrices. The importance of this H-bonding system is huge since all DNA biological functions are dependent on the interactions with proteins. The theoretical optimizations have revealed six different closed H-bond complexes between 1-methyluracil and glycine. The obtained energies have demonstrated that the uracil C(4)═O site is a better H-acceptor site than the C(2)═O site. The stabilization energy of the most stable complex is -47.83 (MP2) or -54.14 kJ·mol(-1) (DFT). The DFT(B3LYP)/6-31G optimized geometries have been evaluated, and the obtained energies appeared to be in agreement with the results of the computational more expensive DFT(B3LYP)6-31++G** approach. In order to identify the 1:1 complexes in an argon matrix, a new dual miniature furnace has been developed which allows to sublimate both complex partners at their optimal temperature. The presence of three different glycine·1-methyluracil complexes has been demonstrated by analysis of the H-bond shifted modes. The H-bond parameters have been evaluated and previously obtained correlations for different H-bond complexes have been confirmed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Glycine / chemistry*
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Conformation
  • Phase Transition*
  • Quantum Theory
  • Spectroscopy, Fourier Transform Infrared*
  • Uracil / analogs & derivatives*
  • Uracil / chemistry

Substances

  • Uracil
  • 1-methyluracil
  • DNA
  • Glycine