Proton-transfer dynamics in the (HCO3-)2 dimer of KHCO3 from Car-Parrinello and path-integrals molecular dynamics calculations.
ABSTRACT The proton motion in the (HCO(3)(-))(2) dimer of KHCO(3) at 298 K has been studied with Car-Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298 K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1 fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20 fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations.
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ABSTRACT: Protonated methane, CH5+, continues to elude definitive structural assignment, as large-amplitude vibrations and hydrogen scrambling challenge both theory and experiment. Here, the infrared spectrum of bare CH5+ is presented, as detected by reaction with carbon dioxide gas after resonant excitation by the free electron laser at the FELIX facility in the Netherlands. Comparison of the experimental spectrum at approximately 110 kelvin to finite-temperature infrared spectra, calculated by ab initio molecular dynamics, supports fluxionality of bare CH5+ under experimental conditions and provides a dynamical mechanism for exchange of hydrogens between CH3 tripod positions and the three-center bonded H2 moiety, which eventually leads to full hydrogen scrambling. The possibility of artificially freezing out scrambling and internal rotation in the simulations allowed assignment of the infrared spectrum despite this pronounced fluxionality.Science 09/2005; 309(5738):1219-22. · 31.20 Impact Factor
- Acta Crystallographica 01/1952; 5(2):292-292.
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ABSTRACT: Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.Proceedings of the National Academy of Sciences 05/2007; 104(17):6980-5. · 9.74 Impact Factor