First-principles investigation of isomerization by proton transfer in beta-fumaric acid crystal.

Crystal structure of fumaric acid was investigated by Car-Parrinello molecular dynamics and Path Integral molecular dynamics. We propose a mechanism of isomerization by proton transfer in the solid state. It is shown that the three conformers of fumaric acid observed in cryogenic Ar matrix are also present in the solid. Standard ab initio Car-Parrinello dynamics of the studied solid at 100 K indicates that barrier height for proton transfer is too high to enable thermal jump over the barrier. Path Integral method in this particular case significantly changes proton behavior in the hydrogen bridge, and the proton tunneling process is observed. Vibrational spectra of investigated system HOOC-CH=CH-COOH and its deuterated analog DOOC-CH=CH-COOD were calculated and compared with experimental data.

Vibrational dynamics of the hydrogen bonded complexes (CH2)2O-HF and -DF investigated by combined jet- and cell-Fourier transform infrared spectroscopy.

Fourier transform infrared spectra of the Vs stretching bands of HF and DF bonded to (CH2)2O have been recorded at 0.5 cm(-1) resolution in a cooled cell and in a supersonic expansion seeded with argon. The analysis of the congested spectra of this type of medium strength hydrogen bonded complexes exploits a combination of controlled temperature effects in the ranges 25-80 K and 200-300 K and a band contour simulation program accounting for homogeneous and inhomogeneous contributions. Significant anharmonic couplings between the donor stretch mode and three of the low frequency intermolecular modes are found to be responsible for the characteristic hot band patterns in the Vs fundamental region of cell spectra. A global analysis of sum and difference combination bands involving Vs provides reliable values of intermolecular frequencies, anharmonic coupling constants and a good estimate of the dissociation energy of the complex which compares favorably with ab initio results. The effective linewidth provides a lower bound for the predissociation lifetime of 1.5 ps for HF and 7 ps for DF containing complexes, respectively. The correlation between effective linewidths and vibrational densities of states for (CH2)2O-HF and -DF underlines the important role of intramolecular vibrational redistribution in the vibrational dynamics of these complexes while the lifetime decrease for HF (or DF) bonded to oxygenated cyclic ethers with respect to sulfured homologues might be explained by the change in the arrangement of the acid relative to the plane of the acceptor subunit.

Vibrational dynamics of medium strength hydrogen bonds: Fourier transform infrared spectra and band contour analysis of the DF stretching region of (CH2)2S-DF.

Fourier transform infrared spectra of the nu(s) band of the (CH2)(2)S-DF complex have been recorded at 0.1-0.5 cm(-1) resolution in a cooled cell and in a supersonic jet expansion seeded with argon. A sufficient density of (CH(2))(2)S-DF heterodimers is produced by a double injection nozzle device, which limits the possibility of reaction between thiirane and DF before the expansion. The observation of partially resolved PQR branch structures at cell temperatures as high as 252 K indicates relatively small effective line widths, which allow a detailed analysis of the underlying vibrational couplings and of the structural properties of the complex. The analysis of cell and free jet spectra in the temperature range 50-250 K is performed with a software package for the simulation and fitting of multiple hot band progressions in asymmetric rotors. The analysis reveals that the three low frequency hydrogen-bond modes are strongly coupled to the DF stretch with anharmonic coupling constants, which indicates a strengthening of the hydrogen bond upon vibrational excitation of DF. Rovibrational parameters and a reliable upper bound for the homogeneous line width have been extracted.

Solvent effect on hydrogen bonded ammonia-hydrogen halide complexes: continuum medium versus cluster models

The influence of water and dinitrogen environment on the structures of hydrogen bonded XH-NH3 (X = F, Cl, and Br) complexes has been investigated using the self-consistent isodensity polarizable continuum solvent model (SCI-PCM) with two values of dielectric constants, 1.5 and 78.0, respectively. The geometrical parameters, along with the interaction energies as well as harmonic frequencies were calculated at the B3M-LYP/6-311 + + G(d,p) level of theory. The results from dielectric continuum model were compared with those obtained by traditional supermolecule approach. In order to model the proton transfer in XH-NH3 systems by supermolecular approach, one should add from two to four explicit water or dinitrogen molecules to the calculations. The dielectric continuum model provides similar effect using less effort. As our results shown, the SCI-PCM model, where a solvent is treated as a continuum medium, reproduces quite accurately the molecular properties of investigated medium strong hydrogen bonded systems both with dinitrogen and water environment. In order to represent solvent effects on hydrogen-bonded complexes with less acidic HX subunit it is necessary to take explicit solvent molecules into account.

Direction of protein biosynthesis as a reflection of the prebiotic environment

Systematical analyses of the folding pathways of simple polypeptides show that for systems containing L-stereoisomers their natural tendency to be right-handed abakes when the polypeptide terminal are naturally charged. This disadvantageous effect is minimized by an introduction of charged amino acid residues into the polypeptide chain at the beginning of its synthesis. Since in the rebiotic environment negatively charged amino acids were more prominent than positively charged ones, we conclude that the fixed direction of protein biosynthesis might be a result of "a broken symmetry" of amino acid charges.Copyright 1997 Academic Press Limited Copyright 1997 Academic Press Limited