The solid electrolyte interface ͑SEI͒ formation on composite graphite and highly oriented pyrolytic graphite in a vinylene carbonate ͑VC͒-containing electrolyte was analyzed using evolved gas analysis, Fourier transform infrared analysis, twodimensional nuclear magnetic resonance, X-ray photoelectron spectroscopy, time of flight-secondary-ion mass spectrometry, and scanning electron microscopy. We found that the SEI layers derived from VC-containing electrolytes consist of polymer species such as poly ͑vinylene carbonate͒ ͑poly͑VC͒͒, an oligomer of VC, a ring-opening polymer of VC, and polyacetylene. Moreover, lithium vinylene dicarbonate, (CHOCO 2 Li) 2 , lithium divinylene dicarbonate, (CHvCHOCO 2 Li) 2 , lithium divinylene dialkoxide, (CHvCHOLi) 2 , and lithium carboxylate, RCOOLi, were formed on graphite as VC reduction products. The presence of VC in the ethylene carbonate ͑EC͒-based electrolyte caused a decrease in the reductive gases of the EC dimethyl carbonate solvent such as C 2 H 4 , CH 4 , and CO. The VC-derived SEI layer was formed at a potential more positive than 1.0 V vs. Li/Li ϩ . Effective SEI formation by reduction of VC progresses before that of EC. The thermal decomposition temperature of the SEI layer derived from VC shifted to a higher temperature compared to that derived from the VC-free electrolytes. We concluded that the thermal stability of the VC-derived SEI layer has a close relation to high-temperature storage characteristics at elevated temperatures.

We develop a hybrid quantum mechanical/molecular mechanical-configuration interaction (QM/MM-CI) method for calculating the absorption maxima of photoreceptor proteins such as bacteriorhodopsin. A unique point of our method, discriminating it from usual QM/MM methods, is that the ground-state electronic structure of the whole protein is first evaluated by a linear scaling-molecular orbital calculation. The resultant electronic distribution is utilized to construct a modified Fock matrix for subsequent CI calculation. In the excitation energy calculation, only the chromophore located at the photoactive center of a protein is treated quantum mechanically and the surrounding environment is approximated by classical electrostatics. Another feature of the method is that the classical region is instantaneously polarized in response to the excitation of the chromophore. This corresponds to the incorporation of electronic polarization effects of the protein part. To allow the polarization of amino acid residues, each bond of them is approximated by a cylindrical dielectric with a given polarizability. The polarization in the classical part is determined self-consistently. Here, the above method is applied to the wild type of bacteriorhodopsin (bR568) and its mutants. It is revealed that their absorption maxima are not reproduced without taking into account the effect of electronic polarization of the protein part. In particular, the polarization of Trp86, Trp182, and Tyr185 plays a predominant role in causing a bathochromic shift in the absorption band of bR568.

We apply a SCRF-PCM-CI calculation to elucidate the mechanism of spectral tuning in photoactive yellow protein (PYP). It is shown that the calculation well reproduces solvatochromic shifts observed for some model compounds of the PYP chromophore. By regression analysis, we obtain an empirical equation to predict solvatochromic shifts of these compounds for a given set of dielectric constant and refractive index. Next, using a classical electrostatic theory and the crystal structure of PYP, the value of refractive index is calculated for the chromophore-binding pocket. The value of the dielectric constant is estimated from the fact that the binding pocket is highly hydrophobic. On the basis of these results we predict the absorption maximum of PYP. In addition, the spectral tuning mechanism in PYP is divided into three factors, that is, counterion effect, hydrogen-bonding effect, medium effect of the protein matrix, and each contribution is quantitatively evaluated. It is shown that the electronic polarization effects of the protein matrix plays a nonnegligible role in tuning the absorption maximum of PYP as similar to the case of bacteriorhodopsin.

In this study, integrated (MOZYME + DFT) method (Ohno et al. Chem. Phys. Lett. 2001, 341, 387.) is applied to elucidate how the pK a 's of retinal Schiff base (RSB) and Asp85 in bacteriorhodopisn (bR) are controlled by the surrounding protein matrix, especially a hydrogen bonding network involving RSB. The whole protein is divided into two layers. Layer 1 contains only the hydrogen bonding network and is treated at the DFT level of theory. The rest of the protein is calculated using a linear-scaling molecular orbital method called MOZYME that can explicitly take into account the protein three-dimensional structure. Here we focus our attention on the pK a changes of RSB and Asp85 on going from the ground state to the M intermediate, because they are key factors of the proton translocation mechanism in bR. The three-dimensional structures of both states are taken from corresponding X-ray data. The calculation successfully reproduces the experimental fact that RSB and Asp85 form the zwitterions in the ground state. On the other hand, the fact that these residues are in the neutral form in the M intermediate is reproduced only when the side chain of Thr89 takes a special orientation capable of forming hydrogen bond(s) with Asp85. It is shown that such hydrogen bond formation and the disappearance of water 402 are the major factors stabilizing the neutral state of the (RSB + Asp85) system in the M intermediate. Finally, we discuss a role of Thr89 in the proton translocation process.

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