Riet Ramaekers

Neutral and zwitterionic glycine.H2O complexes: A theoretical and matrix-isolation Fourier transform infrared study

The H-bond interaction between glycine and H2O has been studied by a combined theoretical (DFT(B3LYP)/6-31++G(**)) and experimental (matrix-isolation FT-IR) methodology. The 1:1 and 1:2 complexes of the most stable conformation (I) of glycine appear to be neutral complexes which have been vibrationally characterized in detail. The higher stoichiometry complexes (glycine).(H2O)n with n larger than 3 are demonstrated to be zwitterionic H-bonded complexes. A set of characteristic IR absorption bands for this zwitterionic structure has been observed in low-temperature Ar matrices. This would be the first experimental IR evidence for proton transfer occurring between the NH2 and COOH groups of amino acids by a H-bonded water molecular channel in isolated conditions.

On the contribution of intramolecular H-bonding entropy to the conformational stability of alanine conformations.

The experimental and theoretical rotamerization constants for the rotameric equilibrium between the two most stable conformations of the alpha-amino acid alanine are compared. The experimental technique of matrix-isolation Fourier transform infrared spectroscopy in combination with the density functional theory (DFT) (B3LYP) and the 6-31++G** basis set is used for this study. A large disagreement between the experimental and theoretical value of the equilibrium constant is found. A relatively strong intramolecular H-bond in conformation II is at the origin of this discrepancy. From the difference between the experimental and theoretical rotamerization constant, a DeltaS degrees value of -6.6 J K(-1) mol(-1) is found for the intramolecular H-bond formation.

DFT theoretical, X-ray diffraction and IR matrix-isolated studies on 4-chloro-2′-hydroxy-4′-ethoxyazobenzene

Abstract Results of X-ray diffraction, IR spectra of the solute either in an Ar matrix or in benzene and carbon tetrachloride solutions as well as DFT theoretical studies are used to discuss the structure and dynamics of 4-chloro-2′-hydroxy-4′-ethoxyazobenzene with particular attention to the OH⋯N intramolecular hydrogen bonding. The packing in the crystalline lattice suggests preferences for the formation of sandwich type dimers in stacks with OH⋯N bridges in two opposite directions. The analysis of the IR spectra supported by DFT calculations was particularly devoted to the manifestations of hydrogen bonding in the ν(OH) and γ(OH) vibrations. It is demonstrated that there is a substantial contribution of the γ(OH) overtone to the intense complex absorption in the spectral region around 1600 cm −1 . The mechanical and electrical anharmonicities of the OH group are discussed based on the H/D frequency and intensity isotope effects. The extremely small intensity of the ν(OH) band (41 km mol −1 ) is also particular in the present case.

The influence of the peptide bond on the conformation of amino acids: a theoretical and FT-IR matrix-isolation study of N-acetylproline.

A combined experimental matrix-isolation FT-IR and theoretical study has been performed to investigate the conformational behavior of N-acetylproline. The conformational landscape of N-acetylproline was explored using successively higher computational methods, i.e. HF, DFT(B3LYP) and finally MP2. The exploration resulted in 10 conformations with a relative energy difference smaller than 22 kJ.mol(-1) at the HF/3-21G level of theory. These conformations led to six different conformations after DFT(B3LYP) optimizations. Further optimization at the MP2/6-31++G** level of theory resulted in the same six conformations, all of them with an energy difference smaller than 11.5kJ.mol(-1). One conformation with an intramolecular H-bond was found which was energetically the most favorable conformation. The vibrational and thermodynamical features were calculated using the DFT and MP2 methodologies. In the experimental matrix-isolation FT-IR spectrum, the most stable conformation was dominant and at least two non-H-bonded conformations could be identified. An experimental rotamerization constant between the H-bonded and the other non-H-bonded conformations was estimated and appeared to agree reasonably well with the theoretical MP2 predictions. Some new spectral features of N-acetylproline compared to proline were discovered which might be used to discriminate between the acetylated and non-acetylated form.

Correlations between experimental and DFT(B3LYP)/6-31++G∗∗ H-bonding parameters for closed X⋯HO⋯HN (X = N, O or S) H-bonded complexes

Abstract Correlations between experimental and DFT(B3LYP)/6-31++G ∗∗ calculated parameters for a series of closed H-bonded complexes of type X⋯HO⋯HN between a water molecule and a purine or pyrimidine base are investigated. Regular relationships are observed between: (1) the calculated H-bond distance and the H-bond angle; (2) the frequency shift, −Δ ν OH b (experimental and theoretical) and the X⋯H distance/the elongation of the OH bond; (3) the experimental relative frequency shift, Δ ν (NH⋯)/ ν ° (NH) and the calculated interaction energy; and (4) the experimental and the calculated frequency shift, −Δ ν OH b . All the X⋯HO⋯HO complexes used in this work correlate similarly in all relationships, although the nature of the different H-bond-acceptor groups, i.e. X=N, O or S, is clearly expressed in some of the correlations.