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Cover page of J. Comput. Chem. (Nov. 2015)

Cover page of J. Comput. Chem. (Nov. 2015) featuring the article by Sakalli and Knapp


  • Bruun, S., Stoeppler, D., Keidel, A., Kuhlmann, U., Luck, M., Diehl, A., Geiger, M.-A., Woodmansee, D., Trauner, D., Hegemann, P., et al. (2015). Light–Dark Adaptation of Channelrhodopsin Involves Photoconversion between the all-trans and 13-cis Retinal Isomers. Biochemistry 54, 5389-5400.

  • Galstyan, G., and Knapp, E.-W. (2015). Computing pKA values of hexa-aqua transition metal complexes. J Comput Chem 36, 69-78.

  • Guerra, F., Adam, S., and Bondar, A.-N. (2015). Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. J Mol Graph 58, 30-39.

  • Guerra, F., and Bondar, A.-N. (2015). Dynamics of the Plasma Membrane Proton Pump. J Membr Biol 248, 443-453.

  • Ibrahim, M., Chatterjee, R., Hellmich, J., Tran, R., Bommer, M., Yachandra, V.K., Yano, J., Kern, J., and Zouni, A. (2015). Improvements in serial femtosecond crystallography of photosystem II by optimizing crystal uniformity using microseeding procedures. Struct Dyn 2, 041705.

  • Kielb, P., Sezer, M., Katz, S., Lopez, F., Schulz, C., Gorton, L., Ludwig, R., Wollenberger, U., Zebger, I., and Weidinger, I.M. (2015). Spectroscopic Observation of Calcium-Induced Reorientation of Cellobiose Dehydrogenase Immobilized on Electrodes and its Effect on Electrocatalytic Activity. ChemPhysChem 16, 1960-1968.

  • Kim, W.K., and Netz, R.R. (2015). Barrier-induced dielectric counterion relaxation at super-low frequencies in salt-free polyelectrolyte solutions. Eur Phys J E 38, 120.

  • Kim, W.K., and Netz, R.R. (2015). The mean shape of transition and first-passage paths. J Chem Phys 143, 224108.

  • Klauss, A., Haumann, M., and Dau, H. (2015). Seven Steps of Alternating Electron and Proton Transfer in Photosystem II Water Oxidation Traced by Time-Resolved Photothermal Beam Deflection at Improved Sensitivity. J Phys Chem B 119, 2677-2689.

  • Kuhne, J., Eisenhauer, K., Ritter, E., Hegemann, P., Gerwert, K., and Bartl, F. (2015). Early Formation of the Ion-Conducting Pore in Channelrhodopsin-2. Angew Chem Int Ed 54, 4953-4957.

  • Lorch, S., Capponi, S., Pieront, F., and Bondar, A.N. (2015). Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II. J Phys Chem B 119, 12172-12181.

  • Lórenz-Fonfría, V.A., Bamann, C., Resler, T., Schlesinger, R., Bamberg, E., and Heberle, J. (2015). Temporal evolution of helix hydration in a light-gated ion channel correlates with ion conductance. Proc Natl Acad Sci USA 112, E5796-E5804.

  • Lórenz-Fonfría, V.A., Schultz, B.-J., Resler, T., Schlesinger, R., Bamann, C., Bamberg, E., and Heberle, J. (2015). Pre-Gating Conformational Changes in the ChETA Variant of Channelrhodopsin-2 Monitored by Nanosecond IR Spectroscopy. J Am Chem Soc 137, 1850-1861.

  • Luck, M., Bruun, S., Keidel, A., Hegemann, P., and Hildebrandt, P. (2015). Photochemical chromophore isomerization in histidine kinase rhodopsin HKR1. FEBS Lett 589, 1067-1071.

  • Ly, H.K., Wrzolek, P., Heidary, N., Gotz, R., Horch, M., Kozuch, J., Schwalbe, M., and Weidinger, I.M. (2015). 2nd coordination sphere controlled electron transfer of iron hangman complexes on electrodes probed by surface enhanced vibrational spectroscopy. Chem Sci 6, 6999-7007.

  • Mattioli, G., Zaharieva, I., Dau, H., and Guidoni, L. (2015). Atomistic Texture of Amorphous Manganese Oxides for Electrochemical Water Splitting Revealed by Ab Initio Calculations Combined with X-ray Spectroscopy. J Am Chem Soc 137, 10254-10267.

  • Meyer, T., and Knapp, E.W. (2015). pK(a) Values in Proteins Determined by Electrostatics Applied to Molecular Dynamics Trajectories. J Chem Theory Comput 11, 2827-2840.

  • Mueh, F., DiFiore, D., and Zouni, A. (2015). The influence of poly(ethylene glycol) on the micelle formation of alkyl maltosides used in membrane protein crystallization. Phys Chem Chem Phys 17, 11678-11691.

  • Pyta, K., Przybylski, P., and Bartl, F. (2015). Regioselective Long-Range Proton Transfer in New Rifamycin Antibiotics: A Process in which Crown Ethers Act as Stronger Br circle divide nsted Bases than Amines. ChemPhysChem 16, 938-942.

  • Resler, T., Schultz, B.-J., Lorenz-Fonfria, V.A., Schlesinger, R., and Heberle, J. (2015). Kinetic and Vibrational Isotope Effects of Proton Transfer Reactions in Channelrhodopsin-2. Biophys J 109, 287-297.

  • Richter, C., Schneider, C., Quick, M.T., Volz, P., Mahrwald, R., Hughes, J., Dick, B., Alexiev, U., and Ernsting, N.P. (2015). Dual-fluorescence pH probe for bio-labelling. Phys Chem Chem Phys 17, 30590-30597.

  • Richter, F., Scheib, U.S., Mehlhorn, J., Schubert, R., Wietek, J., Gernetzki, O., Hegemann, P., Mathes, T., and Moeglich, A. (2015). Upgrading a microplate reader for photobiology and all-optical experiments. Photochem Photobiol Sci 14, 270-279.

  • Rinne, K.F., Schulz, J.C.F., and Netz, R.R. (2015). Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water. J Chem Phys 142, 215104.

  • Rost, B.R., Schneider, F., Grauel, M.K., Wozny, C., G Bentz, C., Blessing, A., Rosenmund, T., Jentsch, T.J., Schmitz, D., Hegemann, P., et al. (2015). Optogenetic acidification of synaptic vesicles and lysosomes. Nat Neurosci 18, 1845-1852.

  • Sakalli, I., and Knapp, E.-W. (2015). pKA in proteins solving the Poisson–Boltzmann equation with finite elements. J Comput Chem 36, 2147-2157.

  • Scheib, U., Stehfest, K., Gee, C.E., Korschen, H.G., Fudim, R., Oertner, T.G., and Hegemann, P. (2015). The rhodopsin-guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling. Sci Signal 8, rs8.

  • Schneider, F., Grimm, C., and Hegemann, P. (2015). Biophysics of Channelrhodopsin. Annu Rev Biophys 44, 167-186.

  • Schwierz, N., Horinek, D., and Netz, R.R. (2015). Specific Ion Binding to Carboxylic Surface Groups and the pH Dependence of the Hofmeister Series. Langmuir 31, 215-225.

  • Sezer, M., Kielb, P., Kuhlmann, U., Mohrmann, H., Schulz, C., Heinrich, D., Schlesinger, R., Heberle, J., and Weidinger, I.M. (2015). Surface Enhanced Resonance Raman Spectroscopy Reveals Potential Induced Redox and Conformational Changes of Cytochrome c Oxidase on Electrodes. J Phys Chem B 119, 9586-9591.

  • Skandary, S., Hussels, M., Konrad, A., Renger, T., Muh, F., Bommer, M., Zouni, A., Meixner, A.J., and Brecht, M. (2015). Variation of Exciton-Vibrational Coupling in Photosystem II Core Complexes from Thermosynechococcus elongatus As Revealed by Single-Molecule Spectroscopy. J Phys Chem B 119, 4203-4210.

  • Song, C., Velazquez Escobar, F., Xu, X.-L., Narikawa, R., Ikeuchi, M., Siebert, F., Gärtner, W., Matysik, J., and Hildebrandt, P. (2015). A Red/Green Cyanobacteriochrome Sustains Its Color Despite a Change in the Bilin Chromophore’s Protonation State. Biochemistry 54, 5839-5848.

  • Stensitzki, T., Muders, V., Schlesinger, R., Heberle, J., and Heyne, K. (2015). The primary photoreaction of channelrhodopsin-1: Wavelength dependent photoreactions induced by ground-state heterogeneity. Front Mol Biosci 2, 41.

  • Velazquez Escobar, F., Piwowarski, P., Salewski, J., Michael, N., Fernandez Lopez, M., Rupp, A., Muhammad Qureshi, B., Scheerer, P., Bartl, F., Frankenberg-Dinkel, N., et al. (2015). A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes. Nat Chem 7, 423-430. [Link to news section.]

  • Velazquez Escobar, F., von Stetten, D., Günther-Lütkens, M., Keidel, A., Michael, N., Lamparter, T., Essen, L.-O., Hughes, J., Gärtner, W., Yang, Y., et al. (2015). Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes. Front Mol Biosci 2, 37.

  • Vogt, A., Guo, Y., Tsunoda, S.P., Kateriya, S., Elstner, M., and Hegemann, P. (2015). Conversion of a light-driven proton pump into a light-gated ion channel. Sci Rep 5, 16450.

  • Volz, P., Boreham, A., Wolf, A., Kim, T.-Y., Balke, J., Frombach, J., Hadam, S., Afraz, Z., Rancan, F., Blume-Peytavi, U., et al. (2015). Application of Single Molecule Fluorescence Microscopy to Characterize the Penetration of a Large Amphiphilic Molecule in the Stratum Corneum of Human Skin. Int J Mol Sci 16, 6960-6977.

  • Weidinger, I.M. (2015). Analysis of structure–function relationships in cytochrome c oxidase and its biomimetic analogs via resonance Raman and surface enhanced resonance Raman spectroscopies. Biochim Biophys Acta 1847, 119-125.

  • Wietek, J., Beltramo, R., Scanziani, M., Hegemann, P., Oertner, T.G., and Simon Wiegert, J. (2015). An improved chloride-conducting channelrhodopsin for light-induced inhibition of neuronal activity in vivo. Sci Rep 5, 14807.

  • Zhang, C., Chen, C., Dong, H., Shen, J.-R., Dau, H., and Zhao, J. (2015). A synthetic Mn4Ca-cluster mimicking the oxygen-evolving center of photosynthesis. Science 348, 690-693.