Theoretical Insights into the Mechanism of Wavelength Regulation in Blue-Absorbing Proteorhodopsin.

Proteorhodopsin (PR) is a light-driven proton pump that is most notable for ushering in the discovery of an ever-increasing number of microbial retinal proteins that are at the forefront of fields such as optogenetics. Two variants, blue (BPR) and green (GPR) proteorhodopsin, have evolved to harvest light at different depths of the ocean. The color-tuning mechanism in PR is controlled by a single residue at position 105: in BPR it is a glutamine, whereas in GPR it is a leucine. Although the majority of studies on the spectral tuning mechanism in PR have focused on GPR, detailed understanding of the electronic environment responsible for spectral tuning in BPR is lacking. In this work, several BPR models were investigated using quantum mechanics/molecular mechanics (QM/MM) calculations to obtain fundamental insights into the color tuning mechanism of BPR. We find that the molecular mechanism of spectral tuning in BPR depends on two geometric parameters, the bond length alternation and the torsion angle deviation of the all-trans-retinyl chromophore. Both parameters are influenced by the strength of the hydrogen-bonded networks in the chromophore-binding pocket, which shows how BPR is different from other microbial rhodopsins.

Application of semiempirical electronic structure theory to compute the force generated by a single surface-mounted switchable rotaxane.

Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391-5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100-200 pN range, consistent with published experimental estimates. Graphical Abstract A single surface-mounted switchable rotaxane.

Theoretical Evidence for Multiple Charge Transfer Pathways in Bacteriorhodopsin.

The development of molecular-scale junctions utilizing biomolecules is a challenging field that requires intimate knowledge of the relationship between molecular structure and conductance characteristics. One of the key parameters to understanding conductance efficiency is the charge mobility, which strongly influences the response time of electronic devices. The charge mobility of bacteriorhodopsin (bR), a membrane protein that has been studied experimentally in detail, was theoretically investigated using extended Marcus-Hush theory. Charge mobilities of 1.3 × 10(-2) and 9.7 × 10(-4) cm(2)/(V s) for hole and electron transfer, respectively, were determined. The computed electron mobility is comparable to experimentally measured values (9 × 10(-4) cm(2)/(V s)). Interestingly, the pathways for hole and electron hopping were very distinct from each other, utilizing different transmembrane helices to traverse the protein. In particular, only the electron transfer pathway involved the retinal chromophore, indicating that the efficiency of charge transfer is directly affected by the tertiary arrangement of proteins. Our results provide a template for obtaining the molecular and electronic-level details that can reveal fundamental insights into experimental studies on protein electron transport and inform efficient design of biomolecular-based junctions on the nanoscale.

Water Splitting Processes on Mn4O4 and CaMn3O4 Model Cubane Systems.

Catalytic conversion of solar energy into chemical energy has been frequently investigated to develop clean energy sources in the last few decades. Metal oxide complexes show high potential for the catalytic conversion process, but the biochemical process in green plants has better efficiency than artificial photocatalysts consisting of metal oxides. In this work, the water splitting process is theoretically investigated using two synthetic model complexes whose structures are similar to the manganese-based oxygen evolving complex in photosystem II. Model A consists of four Mn atoms, and model B consists of three Mn atoms and a Ca atom in the core. Model A shows a better ability for water splitting than model B when comparing the highest reaction energy. The highest reaction energies are 2.56 and 2.99 eV for models A and B, respectively. In model B, the first oxidation in the water splitting process is exothermic, which is different from model A. In both models, the molecular oxygen generation step is endothermic by about 1.0-2.5 eV.

Theoretical investigation of water oxidation processes on small Mn(x)Ti(2-x)O4 (x = 0-2) complexes.

Understanding the water oxidation process on small metal oxide complexes is fundamental for developing photocatalysts for solar fuel production. Titanium oxide and manganese oxide complexes have high potential as components of a cheap, nontoxic, and stable photocatalyst. In this theoretical work, the water oxidation process on Mn(x)Ti(2-x)O4 (x = 0-2) clusters is investigated at the BP86 level of theory using two water molecules and fully saturated systems. In the oxidation cycle using two water molecules, Mn reduces the reaction energy; however, Mn does not reduce the reaction energy on the fully saturated system. When two water molecules are used, the highest reaction energy in the water oxidation cycle is lower than 3 eV, but the highest reaction energy is higher than 3 eV on fully saturated systems except for the pure titanium oxide complex which has a highest reaction energy of 2.56 eV. Dehydrogenation processes in the water oxidation cycle require higher energy than the O-O formation or water adsorption processes. The overall dehydrogenation energy is usually smaller on complexes including at least one Mn atom and it is smallest on the Mn2O4 complex that has two water molecules. Considering the highest reaction energy in the overall water oxidation cycle, water oxidation at the manganese atom of MnTiO4 hydrated with two water molecules is the most favorable in energy.

Water adsorption and dissociation processes on small Mn-doped TiO2 complexes.

Metal oxide complexes have high catalytic potential in many fields, such as oxidation, dehydrogenation, dehydration, reductive coupling, etc. The adsorption of molecules is a fundamental process in catalytic reactions on the metal oxide complex. In this study, water adsorption and dissociation processes on small Mn-doped TiO2 complexes are investigated at the density functional theory (DFT) level of theory. Water adsorption at terminal Mn atoms is typically found to have an energy around -0.7 eV, which is smaller than the -1.2 eV observed at terminal Ti atoms. Dissociation energies at Mn atoms are determined to be about -0.6 eV, which are also smaller than the approximately -1.2 eV dissociation energies at Ti atoms. Molecular adsorption without dissociation is favorable in energy after water adsorbs at each metal atom. Mn doping reduces the reaction energy; the reaction energy of the doped system is not similar to that of the pure manganese oxide complex.

Prediction of Charge Mobility in Amorphous Organic Materials through the Application of Hopping Theory.

The application of hopping theory to predict charge (hole) mobility in amorphous organic molecular materials is studied in detail. Application is made to amorphous cells of N,N'-diphenyl-N,N'-bis-(3-methylphenylene)-1,1'-diphenyl-4,4'-diamine (TPD), 1,1-bis-(4,4'-diethylaminophenyl)-4,4-diphenyl-1,3,butadinene (DEPB), N4,N4'-di(biphenyl-3-yl)-N4,N4'-diphenylbiphenyl-4,4'-diamine (mBPD), N1,N4-di(naphthalen-1-yl)-N1,N4-diphenylbenzene-1,4-diamine (NNP), and N,N'-bis[9,9-dimethyl-2-fluorenyl]-N,N'-diphenyl-9,9-dimethylfluorene-2,7-diamine (pFFA). Detailed analysis of the computation of each of the parameters in the equations for hopping rate is presented, including studies of their convergence with respect to various numerical approximations. Based on these convergence studies, the most robust methodology is then applied to investigate the dependence of mobility on such parameters as the monomer reorganization energy, the monomer-monomer coupling, and the material density. The results give insight into what will be required to improve the accuracy of predictions of mobility in amorphous organic materials, and what factors should be controlled to develop materials with higher (or lower) charge (hole) mobility.

The effect of trap density on the space charge formation in polymeric photorefractive composites.

The effect of trap density on the space charge formation of polymeric photorefractive (PR) composites was studied using the modified Schildkraut differential equation. The densities of electrons, holes, and traps, as well as the rates of generation, recombination, trapping, and detrapping are examined. The steady-state and temporal behaviors of photocurrent and space charge field (E(sc)) formation dependence on the trap density are also discussed. The charge transport dynamics influenced by the presence of the trap molecules controls the formation of E(sc) via charge trapping, charge detrapping, and charge recombination. Experimental studies of photocurrent and E(sc) in poly[methyl-3-(9-carbazolyl) propylsiloxane]-based polymeric PR composites were carried out to demonstrate the applicability of the model.