Stochastic unraveling of Redfield master equations and its application to electron transfer problems

A method for stochastic unraveling of general time-local quantum master equations (QMEs) is proposed. The present kind of jump algorithm allows a numerically efficient treatment of QMEs which are not in Lindblad form, i.e. are not positive semidefinite by definition. The unraveling can be achieved by allowing for trajectories with negative weights. Such a property is necessary, e.g. to unravel the Redfield QME and to treat various related problems with high numerical efficiency. The method is successfully tested on the damped harmonic oscillator and on electron transfer models including one and two reaction coordinates. The obtained results are compared to those from a direct propagation of the reduced density matrix (RDM) as well as from the standard quantum jump method. Comparison of the numerical efficiency is performed considering both the population dynamics and the RDM in the Wigner phase space representation.Comment: accepted in J. Chem. Phys.; 26 pages, 6 figures; the order of authors' names on the title page correcte

A density matrix approach to photoinduced electron injection

Electron injection from an adsorbed molecule to the substrate (heterogeneous electron transfer) is studied. One reaction coordinate is used to model this process. The surface phonons and/or the electron-hole pairs together with the internal degrees of freedom of the adsorbed molecule as well as possibly a liquid surrounding the molecule provide a dissipative environment, which may lead to dephasing, relaxation, and sometimes excitation of the relevant system. In the process studied the adsorbed molecule is excited by a light pulse. This is followed by an electron transfer from the excited donor state to the quasi-continuum of the substrate. It is assumed that the substrate is a semiconductor. The effects of dissipation on electron injection are investigated

Exciton scattering in light-harvesting systems of purple bacteria

Using the reduced density matrix formalism the exciton scattering in light-harvesting systems of purple bacteria is calculated. The static disorder (fluctuations of the site energies) as well as the dynamic disorder (dissipation) is taken into account in this work. Circular aggregates with 18 pigments are studied to model the B850 ring of bacteriochlorophylls with LH2 complexes. It can be shown that the influence of dissipation may not be neglected in the simulation of the time-dependent anisotropy of fluorescence. Also an elliptical deformation of the ring could be essential

Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump

Background Efflux pumps of the Resistance-Nodulation-cell Division superfamily confer multi-drug resistance to Gram-negative bacteria. The most-studied polyspecific transporter belonging to this class is the inner-membrane trimeric antiporter AcrB of Escherichia coli. In previous studies, a functional rotation mechanism was proposed for its functioning, according to which the three monomers undergo concerted conformational changes facilitating the extrusion of substrates. However, the molecular determinants and the energetics of this mechanism still remain unknown, so its feasibility must be proven mechanistically. Methods A computational protocol able to mimic the functional rotation mechanism in AcrB was developed. By using multi-bias molecular dynamics simulations we characterized the translocation of the substrate doxorubicin driven by conformational changes of the protein. In addition, we estimated for the first time the free energy profile associated to this process. Results We provided a molecular view of the process in agreement with experimental data. Moreover, we showed that the conformational changes occurring in AcrB enable the formation of a layer of structured waters on the internal surface of the transport channel. This water layer, in turn, allows for a fairly constant hydration of the substrate, facilitating its diffusion over a smooth free energy profile. Conclusions Our findings reveal a new molecular mechanism of polyspecific transport whereby water contributes by screening potentially strong substrate-protein interactions. General significance We provided a mechanistic understanding of a fundamental process related to multi-drug transport. Our results can help rationalizing the behavior of other polyspecific transporters and designing compounds avoiding extrusion or inhibitors of efflux pumps

The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics

The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity

Influence of Static and Dynamic Disorder on the Anisotropy of Emission in the Ring Antenna Subunits of Purple Bacteria Photosynthetic Systems

Using the reduced density matrix formalism the time dependence of the exciton scattering in light-harvesting ring systems of purple bacteria is calculated. In contrast to the work of Kumble and Hochstrasser (J. Chem. Phys. 109 (1998) 855) static disorder (fluctuations of the site energies) as well as dynamic disorder (dissipation) is taken into account. For the description of dissipation we use Redfield theory in exciton eigenstates without secular approximation. This is shown to be equivalent to the Markovian limit of Capek's theory in local states. Circular aggregates with 18 pigments are studied to model the B850 ring of bacteriochlorophyls within LH2 complexes. It can be demonstrated that the dissipation is important for the time-dependent anisotropy of the fluorescence. Smaller values of static disorder are sufficient to produce the same decay rates in the anisotropy in comparison with the results by Kumble and Hochstrasser

Correction: Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

Correction for ‘Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes’ by Beatrix M. Bold et al., Phys. Chem. Chem. Phys., 2020, 22, 10500–10518, https://doi.org/10.1039/C9CP05753F. The authors have recognised two errors in the data for the published version of this article. The first one concerns the reported QM/MM calculations on the Fenna–Matthews–Olson (FMO) complex, and the second error affects all Coulomb couplings presented. In brief, the most important changes are: (i) the ZINDO site energies for the individual pigments are closer to each other and the ZINDO site energy fluctuations are smaller; (ii) the couplings are smaller and now in better agreement with reference data; and (iii) as a consequence, the exciton splitting is decreased. These errors do not change the conclusions of the study but only lead to small corrections of the reported results, as detailed below

Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree–Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna–Matthews–Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future

Structural basis for chitin acquisition by marine <i>Vibrio </i>species

Chitin degrading bacteria are important for marine ecosystems. Here the authors structurally and functionally characterize the Vibrio harveyi outer membrane diffusion channel chitoporin and give mechanistic insights into chito-oligosaccharide uptake