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21 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS2011

Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

Molecular dynamics simulations were carried out in order to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistant with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive.The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be non-conducting. The conductance of the hexamer was estimated to be 115+/-34 pS and 74+/-20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K(+) and Cl(-) with their first solvation shells intact. The free energy barrier encountered by K(+) is only 2.2 kcal/mol whereas Cl(-) encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics. keywords: ion channels, peptaibols, channel conductance, molecular dynamics

Wilson, Michael A.↗
NASA NTRS2001

The Transition from Hydrogen Bonding to Ionization in (HCI)n(NH3)n and (HCI)n(H2O)n Clusters: Consequences for Anharmonic Vibrational Spectroscopy

Anharmonic vibrational frequencies and intensities are calculated for 1:1 and 2:2 (HCl)(sub n)(NH3)(sub n) and (HCl)(sub n)(H2O)(sub n) complexes, employing the correlation-corrected vibrational self-consistent field method with ab initio potential surfaces at the MP2/TZP computational level. In this method, the anharmonic coupling between all vibrational modes is included, which is found to be important for the systems studied. For the 4:4 (HCl)(sub n)(H2O)(sub n) complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Just as the (HCl)(sub n)(NH3)(sub n) structure switches from hydrogen-bonded to ionic for n=2, the (HCl)(sub n)(H2O)(sub n) switches to ionic structure for n=4. For (HCl)2(H2O)2, the lowest energy structure corresponds to the hydrogen-bonded form. However, configurations of the ionic form are separated from this minimum by a barrier of less than an O-H stretching quantum. This suggests the possibility of experiments on ionization dynamics using infrared excitation of the hydrogen-bonded form. The strong cooperative effects on the hydrogen bonding, and concomitant transition to ionic bonding, makes an accurate estimate of the large anharmonicity crucial for understanding the infrared spectra of these systems. The anharmonicity is typically of the order of several hundred wave numbers for the proton stretching motions involved in hydrogen or ionic bonding, and can also be quite large for the intramolecular modes. In addition, the large cooperative effects in the 2:2 and higher order (HCl(sub n)(H2O)(sub n) complexes may have interesting implications for solvation of hydrogen halides at ice surfaces.

Chaban, Galina M.↗
NASA NTRS2016

Computational and Experimental Study of Li-doped Ionic Liquids at Electrified Interfaces

We evaluate the influence of Li-salt doping on the dynamics, capacitance, and structure of three ionic liquid electrolytes, [pyr14][TFSI], [pyr13][FSI], and [EMIM][BF4], using molecular dynamics and polarizable force fields. In this respect, our focus is on the properties of the electric double layer (EDL) formed by the electrolytes at the electrode surface as a function of surface potential (Psi). The rates of EDL formation are found to be on the order of hundreds of picoseconds and only slightly influenced by the addition of Li-salt. The EDLs of three electrolytes are shown to have different energy storage capacities, which we relate to the EDL formation free energy. The differential capacitance obtained from our computations exhibits asymmetry about the potential of zero charge and is consistent with the camel-like profiles noted from mean field theories and experiments on metallic electrodes. The introduction of Li-salt reduces the noted asymmetry in the differential capacitance profile. Complementary experimental capacitance measurements have been made on our three electrolytes in their neat forms and with Li-salt. The measurements, performed on glassy carbon electrodes, produce U-like profiles, and Li-salt doping is shown to strongly affect capacitance at high magnitudes of Psi. Differences in the theoretical and experimental shapes and magnitudes of capacitance are rationalized in terms of the electrode surface and pseudocapacitive effects. In both neat and Li-doped liquids, the details of the computational capacitance profile are well described by Psi-induced changes in the density and molecular orientation of ions in the molecular layer closest to the electrode. Our results suggest that the addition of Li+ induces disorder in the EDL, which originates from the strong binding of anions to Li+. An in-depth analysis of the distribution of Li+ in the EDL reveals that it does not readily enter the molecular layer at the electrode surface, preferring instead to be localized farther away from the surface in the second molecular layer. This behavior is validated through an analysis of the free energy of Li+ solvation as a function of distance from the electrode. Free energy wells are found to coincide with localized concentrations of Li+, the depths of which increase with Psi and suggest a source of impedance for Li+ to reach the electrode.

Haskins, Justin B.↗