Showing papers by "Wiktor Zierkiewicz published in 2010"

Theoretical investigation of the conformation, acidity, basicity and hydrogen bonding ability of halogenated ethers.

Abstract: MP2/6-311++G(d,p) calculations have been carried out to investigate the conformation, protonation and the hydrogen bonding interactions with water of several halogenated ethers (CH3OCH2Cl, CH2ClOCH2Cl, CH3OCHCl2, CHFClOCHF2). The optimized geometries, ν(CH) harmonic vibrational frequencies and the SAPT decomposition of the interaction energies are studied. The interaction with one water molecule gives several stable structures characterized by OwHw⋯O and CH⋯Ow hydrogen bonds or by O⋯Cl halogen bonding. The MP2/CBS calculated binding energies of different complexes between the halogenated ethers and water vary between 1.7 and 7.7 kcal mol−1. The energies of these structures are discussed as a function of the proton affinity of the ethers and the deprotonation enthalpy of the CH bonds. The contraction of the CH bonds and blue shifts of the corresponding stretching vibrations in the O-protonated ethers and their O⋯HwOw complexes are compared. A natural bond orbital analysis has revealed that substitution of the H atoms by one or several halogen atoms has a great influence on the hyperconjugative effects from the two non-equivalent O lone pairs to relevant antibonding orbitals, and the subsequent geometry of the hydrogen bonded complexes.

Adenine ribbon stabilized by Watson-Crick and Hoogsteen hydrogen bonds: WFT and DFT study.

Abstract: The self-organized adenine ribbon is studied theoretically. The experimental evidence for the formation of such a ribbon has been found in the crystal structure of the supramolecular system [Dobrzynska and Jerzykiewicz, J. Am. Chem. Soc., 2004, 126, 11118], and the striking structural feature is the fact that both the Watson–Crick and Hoogsteen faces of adenine are involved in the hydrogen bonding within the ribbon. The structure and physical properties of the monomer and five clusters of adenine (Ade)n (where n = 2, 3, 4, 5, 6) with AA22 configuration have been studied by means of the B3LYP, RI-TPSS, RI-TPSS-D (augmented with the dispersion term) and RI-MP2 methods using the 6-311+G(d,p), cc-pVTZ and TZVP basis sets. It is shown that among the investigated adenine clusters only the dimer has the planar structure. The evaluation of the three-body contribution to the total binding energy of adenine trimer has been performed at different levels of theory. All the methods consistently indicate that this term is positive and small (less than 0.5 kcal mol−1) which corresponds to a weak anti-cooperative effect, in adenine trimer. The differences between the total electronic energies obtained at the RI-TPSS/TZVP-D and RI-TPSS/TZVP levels of theory have shown that the London dispersion forces stabilize the adenine cluster containing 12 or more molecules by about −8 kcal mol−1 per molecule. The results from the DFT symmetry adapted perturbation theory analysis have revealed that the contribution of dispersion to the binding energy of the adenine ribbon is about 25%.