The calculation of hydrogen positions is a common preprocessing step when working with crystal structures of protein-ligand complexes. An explicit description of hydrogen atoms is generally needed in order to analyze the binding mode of particular ligands or to calculate the associated binding energies. Due to the large number of degrees of freedom resulting from different chemical moieties and the high degree of mutual dependence this problem is anything but trivial. In addition to an efficient algorithm to take care of the complexity resulting from complicated hydrogen bonding networks, a robust chemical model is needed to describe effects such as tautomerism and ionization consistently. We present a novel method for the placement of hydrogen coordinates in protein-ligand complexes which takes tautomers and protonation states of both protein and ligand into account. Our method generates the most probable hydrogen positions on the basis of an optimal hydrogen bonding network using an empirical scoring function. The high quality of our results could be verified by comparison to the manually adjusted Astex diverse set and a remarkably low rate of undesirable hydrogen contacts compared to other tools.

Lateral diffusion of three different dye molecules (terrylene and two perylene diimides) in 4 to 225 nm thin films of 8CB liquid crystals in the smectic-A phase has been investigated on a single molecule level. The influence of film thickness on tracer diffusion can be qualitatively modeled by a hydrodynamic approach. Molecular tracking experiments as well as fluorescence correlation (FCS) studies reveal the presence of diffusion dynamics which span a range of at least more than one order of magnitude in time, which is much larger than the reported anisotropic self-diffusion observed for 8CB bulk samples. We tentatively assign the heterogeneity to the formation of diffusion limiting domains on a micrometer scale within the 8CB films or at the interfaces.

The electronic response of doped manganites at the transition from the paramagnetic insulating to the ferromagnetic metallic state in La 1−x Ca x MnO 3 for x = 0.3 and 0.2 was investigated by dc conductivity, ellipsometry, and vacuum ultraviolet reflectance for energies between 0 and 22 eV. A stabilized Kramers-Kronig transformation yields the optical conductivity and reveals changes in the optical spectral weight up to 22 eV at the metal-to-insulator transition. In the observed energy range, the spectral weight is conserved within 0.3%. The redistribution of spectral weight in this surprisingly broad energy range has important ramifications for the effective low-energy physics. We discuss the importance of the charge-transfer, Coulomb on-site, Jahn-Teller, and long-range Coulomb screening effects to the electronic structure. Among strongly correlated materials, the manganites exhibit a wealth of novel properties. For example, some hexagonal insulating materials exhibit multiferroic behavior and the cubic doped manganites show charge ordering and the colossal magnetoresistance ͑CMR͒ effect.1,2 It is clear that the two key ingredients responsible for these diverse phenomena are, first, the high geometrical and spin frustration and, second, the large number of competing interactions, the most important of which are the electron-electron and electron-phonon interactions. 1,[3][4][5][6][7][8][9] There is a deep disagreement as to which of these interactions is the primary driving force behind either the insulating phase of the manganites or the metal-to-insulator transition in the doped manganites. Models describing these phenomena involve double exchange, Jahn-Teller ͑JT͒, superexchange, and Coulomb on-site ͑Hubbard U͒ interactions that yield effective low-energy Hamiltonians, which predict different types of quasiparticle excitations, such as spin excitations, lattice polarons, spin polarons, or orbitons. 3,4,[6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] However, the effective Hamiltonians used to describe the manganites typically ignore the oxygen p bands and consider only an effective manganese d band. It is also generally assumed that the high-energy degrees of freedom can be neglected by a "down folding" of the large number of bands into a single effective band. This implies that there is no redistribution of electronic states between low-energy and high-energy degrees of freedom. On the other hand, if one considers the importance of local interactions and hybridization in correlated materials, one would expect quite pronounced effects at higher energies that are connected to charge-transfer or Mott-Hubbard physics. 15,[22][23][24] Thus, the important test for the effective low-energy picture is to study whether one finds strong exchanges of spectral weight between low and high energies.Therefore, it is crucial to test the complex nature of the band structure explicitly. The most direct experiment is to measure the dielectric response of a material as a function of temperature and doping. Unfort...

Orbital ordering leads to an unconventional excitation spectrum that we investigate by resonance Raman scattering using incident photon energies between 1.7 and 5.0 eV. We use spectral ellipsometry to determine the corresponding dielectric function. Our results show resonant behavior of the phonon Raman cross section when the laser frequency is close to the orbiton-excitation energy of 2 eV in LaMnO3. We show an excellent agreement between theoretical calculations based on the Franck-Condon mechanism activating multiphonon Raman scattering in first order of the electron-phonon coupling and the experimental data of phonons with different symmetries.