[en] The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (1) retinal twisting; (2) hydrogen-bonding distances in the active site; and (3) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base

[en] The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (1) retinal twisting; (2) hydrogen-bonding distances in the active site; and (3) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base

[en] The present status of development of the density-functional-based tight-binding (DFTB) method is reviewed. As a two-centre approach to density-functional theory (DFT), it combines computational efficiency with reliability and transferability. Utilizing a minimal-basis representation of Kohn-Sham eigenstates and a superposition of optimized neutral-atom potentials and related charge densities for constructing the effective many-atom potential, all integrals are calculated within DFT. Self-consistency is included at the level of Mulliken charges rather than by self-consistently iterating electronic spin densities and effective potentials. Excited-state properties are accessible within the linear response approach to time-dependent (TD) DFT. The coupling of electronic and ionic degrees of freedom further allows us to follow the non-adiabatic structure evolution via coupled electron-ion molecular dynamics in energetic particle collisions and in the presence of ultrashort intense laser pulses. We either briefly outline or give references describing examples of applications to ground-state and excited-state properties. Addressing the scaling problems in size and time generally and for biomolecular systems in particular, we describe the implementation of the parallel 'divide-and-conquer' order-N method with DFTB and the coupling of the DFTB approach as a quantum method with molecular mechanics force fields. (author)

[en] This paper is devoted to a specific difficulty related to the electronic nonadiabatic coupling terms (NACT), namely, how to determine correctly their signs. It is well known that correct NACTs, including their signs, are crucial for any numerical treatment of the nuclear Schroedinger equation [see, i.e., A. Kuppermaan and R. Abrol, Adv. Chem. Phys. 124, 283 (2003)]. In most cases the derivation of the correct sign of the nonadiabatic coupling matrix (NACM) is done employing various continuity procedures. However, there are cases where these procedures do not suffice and for these cases we suggest to apply an additional procedure based on a mathematical lemma which asserts that the exponentiated line integral which yields the D matrix is invariant with respect to the initial point of the integration [M. Baer, J. Phys. Chem. A 104, 3181 (2000)]. In the numerical study we apply this lemma to determine the signs of the 3x3 NACM elements for the three excited states of the {H₂,O} system (some of these NACTs are presented here for the first time). It turns out that the ab initio treatment yields results from which one can form eight different 3x3 NACMs. However the application of this lemma (which does not require any significant additional numerical effort) reduces this number to two. The final selection is done by an enhanced numerical study which requires more accurate calculations