Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

The Steady March toward Biomimetic Nanoelectronics

Steady progress is being made in unveiling nature's long-range charge transport mechanisms in redox proteins and in the development of versatile self-assembling scaffolds and de novo proteins by design-two separate fields that soon may intersect to yield the first artificial bioelectronic wires. Here, we summarize compelling developments in these areas that put a spotlight on the prospect of their convergence, featuring, in particular, work by Dai et al. in this issue of ACS Nano that illustrates success in intentional design with nuanced control, binding multiple c-type hemes into a specific ordered array bearing the essential hallmarks of heme chains in bacterial multiheme cytochromes.

How the Donor/Acceptor Spin States Affect the Electronic Couplings in Molecular Charge-Transfer Processes?

The electronic coupling matrix element H_AB is an essential ingredient of most electron-transfer theories. H_AB depends on the overlap between donor and acceptor wave functions and is affected by the involved states’ spin. We classify the spin-state effects into three categories: orbital occupation, spin-dependent electron density, and density delocalization. The orbital occupancy reflects the diverse chemical nature and reactivity of the spin states of interest. The effect of spin-dependent density is related to a more compact electron density cloud at lower spin states due to decreased exchange interactions between electrons. Density delocalization is strongly connected with the covalency concept that increases the spatial extent of the diabatic state’s electron density in specific directions. We illustrate these effects with high-level ab initio calculations on model direct donor–acceptor systems relevant to metal oxide materials and biological electron transfer. Obtained results can be used to benchmark existing methods for H_AB calculations in complicated cases such as spin-crossover materials or antiferromagnetically coupled systems.

Whole-cell circular dichroism difference spectroscopy reveals an in vivo-specific deca-heme conformation in bacterial surface cytochromes

Our novel analytical framework to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell revealed that the heme alignment in reduced MtrC is distinct from that in purified system.

We established whole-cell circular dichroism difference spectroscopy to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell. Our data showed that the heme alignment of reduced MtrC in whole cell is distinct from that in purified one, suggesting the in vivo specific electron transport kinetics.

Diabatic States at Construction (DAC) through Generalized Singular Value Decomposition

A procedure, called generalized diabatic-at-construction (GDAC), is presented to transform adiabatic potential energy surfaces into a diabatic representation by generalized singular value decomposition. First, we use a set of localized, valence bond-like configuration state functions, called DAC, as the basis states. Then, the adiabatic ground and relevant excited states are determined using multistate density functional theory (MSDFT). GDAC differs in the opposite direction from traditional approaches based on adiabatic-to-diabatic transformation with certain property restraints. The method is illustrated with applications to a model first-order bond dissociation reaction of CH₃OCH₂Cl polarized by a solvent molecule, the ground- and first-excited-state potential energy surfaces near the minimum conical intersection for the ammonia dimer photodissociation, and the multiple avoided curve crossings in the dissociation of lithium hydride. The GDAC diabatization method may be useful for defining charge-localized states in studies of electron transfer and proton-coupled electron transfer reactions in proteins.

Corresponding Orbitals Derived from Periodic Bloch States for Electron Transfer Calculations of Transition Metal Oxides

An approach for modeling electron transfer in solids and at surfaces of iron-(oxyhydr)oxides and other redox active solids has been developed for electronic structure methods (i.e., plane-wave density functional theory) capable of performing calculations with periodic cells and large system sizes efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, V _AB, and the electron transfer transmission factor, κ_el. This method is an extension of the valence bond theory electron transfer method for molecules and clusters implemented by Dupuis and others and used extensively by Rosso and co-workers in which scaled corresponding orbitals derived from the Bloch states are used to calculate the off-diagonal matrix elements H _AB and S _AB. A key development of the present work is the formulation of algorithms to improve the accuracy of the integration of the exact exchange integral in periodic boundary conditions. This method is demonstrated on model systems for electron small polaron transfer in iron-(oxyhydr)oxides, including bare Fe²⁺-Fe³⁺ ions, and in [Fe³⁺(OH₂)₂ (OH^-)₂)] _nⁿ⁺ chains representing the common edge-sharing Fe octahedral motif in these materials.

Density Functional Physicality in Electronic Coupling Estimation: Benchmarks and Error Analysis

Electronic coupling estimates from constrained density functional theory configuration interaction (CDFT-CI) depend critically on choice of density functional. In this Letter, the orbital multielectron self-interaction error (OMSIE), vertical electron affinity (VEA), and vertical ionization potential (VIP) are shown to be the key indicators inherited from the density functional that determine the accuracy of electronic coupling estimates. An error metric η is derived to connect the three properties, based on the linear proportionality between electronic coupling and overlap integral, and the hypothesis that the slope of this line is a function of VEA/VIP, η = (1/N_testset)Σ_i^testset|-VE^Ref × OMSIE + ΔVE - ΔVE × OMSIE|_i. Based on η, BH&HLYP and LRC-ωPBEh are suggested as the best functionals for electron and hole transfer, respectively. Error metric η is therefore a useful predictor of errors in CDFT-CI electronic coupling, showing that the physical correctness of the density functional has a direct effect on the accuracy of the electronic coupling.

Elaborately Tuning Intramolecular Electron Transfer Through Varying Oligoacene Linkers in the Bis(diarylamino) Systems

The research efforts on oligoacene systems are still relatively limited mainly due to the synthetic challenge and the extreme instability of longer acenes. Herein, these two issues have been overcome through elaborative modification and the stable pentacene species has been successfully synthesized. Additionally, a series of bis(diarylamino) compounds linked by variable-length oligoacene bridges ranging from one to five fused rings (benzene (1a), naphthalene (1b), anthracene (1c), tetracene (1d) and pentacene (1e)) have been prepared to probe the effect of the extent of π-conjugation on the electron transfer properties. Compound 1c exhibits a high planarity between the anthracyl bridge and the two nitrogen cores and the molecular packing shows a two-dimensional herringbone characteristic. Combined studies based on electrochemistry and spectroelectrochemistry demonstrate that (i) the electronic coupling across the oligoacene linkers between two diarylamine termini exponentially decrease with a moderate attenuation constant (β) of 0.14 Å⁻¹ in these length-modulated systems and (ii) the associated radical cations [1a]⁺–[1e]⁺ are classified as the class II Robin–Day mixed-valence systems. Furthermore, density functional theory (DFT) calculations have been conducted to gain insight into the nature of electron transfer processes in these oligoacene systems.

Multistate Density Functional Theory for Effective Diabatic Electronic Coupling

Multistate density functional theory (MSDFT) is presented to estimate the effective transfer integral associated with electron and hole transfer reactions. In this approach, the charge-localized diabatic states are defined by block localization of Kohn-Sham orbitals, which constrain the electron density for each diabatic state in orbital space. This differs from the procedure used in constrained density functional theory that partitions the density within specific spatial regions. For a series of model systems, the computed transfer integrals are consistent with experimental data and show the expected exponential attenuation with the donor-acceptor separation. The present method can be used to model charge transfer reactions including processes involving coupled electron and proton transfer.

Intramolecular electron transfer in the dihaem cytochrome c peroxidase of Pseudomonas aeruginosa

Mutant forms of the enzyme cytochrome c peroxidase from Pseudomonas aeruginosa, in which the peroxidatic haem ligand (H71) and putative haem-bridging amino acid (W94) have been mutated, were produced in an E. coli expression system as a means of investigating possible mechanisms of intramolecular electron transfer within the enzyme. EPR spectroscopy indicated the presence of a high-spin, presumably five-coordinate, peroxidatic haem site in the H71G and H71G/W94A mutants, whilst the W94A mutant apparently retained the normal six-coordinate haem structures. In turnover experiments, these mutants show 55, 4, and <1% activity, respectively, as compared to the wild-type enzyme. The W94A mutant shows essentially no activity in turnover experiments. Circular dichroism spectroscopy indicates no measurable difference in the secondary structure of the H71G mutant from that of the native enzyme, whilst some small differences are observed for the double mutant. Treatment of the oxidised mutant proteins with hydrogen peroxide, in the absence of preactivation or exogenous reductants, yields products that suggest the formation of a tryptophan radical species in the case of the H71 mutant and the production of a porphyrin radical in the case of the double mutant. These results are discussed in terms of the intramolecular electron transfer in this enzyme.

Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations. II

A new database (HAB7-) of electronic coupling matrix elements (Hab) for electron transfer in seven medium-sized negatively charged π-conjugated organic dimers is introduced. Reference data are obtained with spin-component scaled approximate coupled cluster method (SCS-CC2) and large basis sets. Assessed DFT-based approaches include constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), self-consistent charge density functional tight-binding (FODFTB) and the recently described analytic overlap method (AOM). This complements the previously reported HAB11 database where only cationic dimers were considered. The CDFT method in combination with a functional based on PBE and including 50% of exact exchange (HFX) was found to provide best estimates, with a mean relative unsigned error (MRUE) of 8.2%. CDFT couplings systematically increase with decreasing fraction of HFX as a consequence of increasing delocalisation of the SOMO orbital. The FODFT method is found to be very robust underestimating electronic couplings by 28%. The FODFTB and AOM methods, although orders of magnitude more efficient in terms of computational effort than the DFT approaches, perform well with reasonably small errors of 54% and 29%, respectively, translating in errors in the non-adiabatic electron transfer rate of a factor of 2.4 and 1.7, respectively. We discuss carefully various sources of errors and the scope and limitations of all assessed methods taking into account the results obtained for both HAB7- and HAB11 databases.

Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.

Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H(ab) values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

Possible dynamically gated conductance along heme wires in bacterial multiheme cytochromes

The staggered cross decaheme configuration of electron transfer cofactors in the outer-membrane cytochrome MtrF serves as a prototype for conformationally gated multiheme electron transport. Derived from the bacterium Shewanella oneidensis, the staggered cross configuration reveals intersecting c-type octaheme and tetraheme "wires" containing thermodynamic "hills" and "valleys" (Proc. Natl. Acad. Sci. U. S. A. 2014, 11, 611-616), suggesting that the protein structure may include a dynamical mechanism for conductance and pathway switching depending on enzymatic functional need. Here, we applied classical molecular and statistical mechanics calculations of large-amplitude protein dynamics in MtrF, to address its potential to modulate pathway conductance, including assessment of the effect of the total charge state. Explicit solvent molecular dynamics simulations of fully oxidized and fully reduced MtrF showed that the slowest mode of collective decaheme motion is 90% similar between the oxidized and reduced states and consists primarily of interheme separation with minor rotational contributions. The frequency of this motion is 1.7 × 10(7) s(-1), both for fully oxidized and fully reduced MtrF, slower than the downhill electron transfer rates between stacked heme pairs at the octaheme termini and faster than the electron transfer rates between parallel hemes in the tetraheme chain. This implies that MtrF uses slow conformational fluctuations to modulate electron flow along the octaheme pathway, apparently for the purpose of increasing the residence time of electrons on lowest potential hemes 4 and 9. This apparent gating mechanism should increase the success rate of electron transfer from MtrF to low potential environmental acceptors via these two solvent-exposed hemes.

Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c

Cytochrome (cyt) c is an important electron transfer protein. The ruffling deformation of its heme cofactor has been suggested to relate to its electron transfer rate. However, there is no direct experimental evidence demonstrating this correlation. In this work, we studied Pseudomonas aeruginosa cytochrome c551 and its F7A mutant. These two proteins, although similar in their X-ray crystal structure, display a significant difference in their heme out-of-plane deformations, mainly along the ruffling coordinate. Resonance Raman and vibrational coherence measurements also indicate significant differences in ruffling-sensitive modes, particularly the low-frequency γa mode found between ∼50-60 cm(-1). This supports previous assignments of γa as having a large ruffling content. Measurement of the photoreduction kinetics finds an order of magnitude decrease of the photoreduction cross-section in the F7A mutant, which has nearly twice the ruffling deformation as the WT. Additional measurements on cytochrome c demonstrate that heme ruffling is correlated exponentially with the electron transfer rates and suggest that ruffling could play an important role in redox control. A major relaxation of heme ruffling in cytochrome c, upon binding to the mitochondrial membrane, is discussed in this context.

Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials

The naturally widespread process of electron transfer from metal reducing bacteria to extracellular solid metal oxides entails unique biomolecular machinery optimized for long-range electron transport. To perform this function efficiently, microorganisms have adapted multiheme c-type cytochromes to arrange heme cofactors into wires that cooperatively span the cellular envelope, transmitting electrons along distances greater than 100 Å. Implications and opportunities for bionanotechnological device design are self-evident. However, at the molecular level, how these proteins shuttle electrons along their heme wires, navigating intraprotein intersections and interprotein interfaces efficiently, remains a mystery thus far inaccessible to experiment. To shed light on this critical topic, we carried out extensive quantum mechanics/molecular mechanics simulations to calculate stepwise heme-to-heme electron transfer rates in the recently crystallized outer membrane deca-heme cytochrome MtrF. By solving a master equation for electron hopping, we estimate an intrinsic, maximum possible electron flux through solvated MtrF of 10(4)-10(5) s(-1), consistent with recently measured rates for the related multiheme protein complex MtrCAB. Intriguingly, our calculations show that the rapid electron transport through MtrF is the result of a clear correlation between heme redox potential and the strength of electronic coupling along the wire: thermodynamically uphill steps occur only between electronically well-connected stacked heme pairs. This observation suggests that the protein evolved to harbor low-potential hemes without slowing down electron flow. These findings are particularly profound in light of the apparently well-conserved staggered cross-heme wire structural motif in functionally related outer membrane proteins.

Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex

Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged propionates of the two hemes.

Revisiting electronic couplings and incoherent hopping models for electron transport in crystalline C60 at ambient temperatures

We assess the validity of incoherent hopping models that have previously been used to describe electron transport in crystalline C(60) at room temperature. To this end we present new density functional theory based calculations of the electron transfer parameter defining these models. Specifically, we report electronic coupling matrix elements for several ten thousand configurations that are thermally accessible to the C(60) molecules through rotational diffusion around their lattice sites. We find that the root-mean-square fluctuations of the electronic coupling matrix element (11 meV) are almost as large as the average value (14 meV) and that the distribution is well approximated by a Gaussian. Importantly, due to the small reorganisation energy of the C(60) dimer (≈0.1 eV), the ET is almost activationless for the majority of configurations. Yet, for a small but significant fraction of orientations the coupling is so strong compared to reorganisation energy that no charge-localised state exists, a situation that is aggravated if zero-point motion of the nuclei is taken into account. The present calculations indicate that standard hopping models do not provide a sound description of electron transport in C(60), which might be the case for many other organics as well, and that approaches are needed that solve the electron dynamics directly.

The 'porin-cytochrome' model for microbe-to-mineral electron transfer

Many species of bacteria can couple anaerobic growth to the respiratory reduction of insoluble minerals containing Fe(III) or Mn(III/IV). It has been suggested that in Shewanella species electrons cross the outer membrane to extracellular substrates via 'porin-cytochrome' electron transport modules. The molecular structure of an outer-membrane extracellular-facing deca-haem terminus for such a module has recently been resolved. It is debated how, once outside the cells, electrons are transferred from outer-membrane cytochromes to insoluble electron sinks. This may occur directly or by assemblies of cytochromes, perhaps functioning as 'nanowires', or via electron shuttles. Here we review recent work in this field and explore whether it allows for unification of the electron transport mechanisms supporting extracellular mineral respiration in Shewanella that may extend into other genera of Gram-negative bacteria.

Kinetics of the terminal electron transfer step in cytochrome c oxidase

Cytochrome c oxidase (cco) catalyzes the oxygen reduction reaction in most aerobically respiring organisms. Decades of research have uncovered many aspects relating to structure and function of this enzyme. However, the origin of the unusually fast terminal electron transfer step from heme a to heme a(3) in cco has been the subject of intense discussions over recent years. Yet, no satisfactory consensus has been achieved. Carrying out large-scale molecular dynamics simulation of the protein embedded in a solvated membrane, we obtain a reorganization free energy λ = 0.57 eV. Evaluation of the quantized single-mode rate equation using the experimental rate and the computed reorganization free energy gives a value of 1.5 meV for the average electronic coupling (H(ab)) between heme a and heme a(3). Thus, according to our calculations, the nanosecond electron transfer (ET) is due to a small but significant activation barrier (ΔG(‡) = 0.12 eV) in combination with effective electronic coupling between the two cofactors. The activation free energy is caused predominantly by collective reorganization of protein residues. We show that our results are consistent with the weak temperature dependence observed in experiment if one allows for very minor variations in the donor-acceptor distance as the temperature changes.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q(-)) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, (<|H(ab)|(2)>)(1/2)=6.7 mH, is significantly higher than the value obtained for the minimum energy structure, |H(ab)|=3.8 mH. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q(-) in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Molecular details of multielectron transfer: the case of multiheme cytochromes from metal respiring organisms

Shewanella are facultative anaerobic bacteria of remarkable respiratory versatility that includes the dissimilatory reduction of metal ores. They contain a large number of multiheme c-type cytochromes that play a significant role in various anaerobic respiratory processes. Of all the cytochromes found in Shewanella, only the two most abundant periplasmic cytochromes, the small tetraheme cytochrome (STC) and flavocytochrome c(3) (Fcc(3)) have been structurally characterized. For these two proteins the molecular bases for their redox properties were determined using spectroscopic methods based on paramagnetic NMR, that allow the contribution of specific hemes to be discriminated. In this perspective these results are reviewed in the context of the continuing effort to understand the molecular mechanisms of electron transfer in the respiratory chains of these organisms.

Characterization of an electron conduit between bacteria and the extracellular environment

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning beta-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment.

Quantum mechanical investigations of heme structure and vibrational spectra: effects of conformation, oxidation state, and electric field

Three conformers of a complex consisting of a Fe-porphyrin ring with axial imidazole groups FeP(Im)(2) that differed by orientation of axial imidazole groups were studied with quantum mechanical calculations in both reduced (neutral) and oxidized (cationic) states. In the reduced state, all three conformers correspond to local minima. On the other hand, in the oxidized state the conformer with the imidazole groups perpendicular to one another does not have a local minimum, which suggests that there could be changes in the structure of heme groups depending on oxidation state. The relative energy differences between conformers are small as well the differences of orbital energies. However, the populations of Fe 3d orbitals, and hence charge distributions, are predicted to change significantly between conformations. The orientation of heme groups can affect the kinetics of interheme electron transfer, so this electronic population redistribution will affect electron transfer kinetics. A comparison of calculated Raman spectra with measured surface-enhanced Raman spectra (Biju et al. Langmuir 2007, 23, 1333) shows excellent agreement for frequencies, but correlations of Raman intensities are less satisfactory. Possible explanations of the observed discrepancies could arise due to a problem in assignments of vibration bands in the experiment, a dependence of Raman spectra on heme complex on oxidation state, long-range protein structure, or membrane electric field are discussed. In particular, it was shown that the oxidation state does not dramatically alter the calculated Raman spectrum. However, the cell membrane electric field can significantly modify Raman spectra. An interpretation of the experimental oxidized cytochrome surface-enhanced Raman spectra is discussed.

Ligand preference and orientation in b- and c-type heme-binding proteins

Hemes are often incorporated into designed proteins. The importance of the heme ligand type and its orientation is still a matter of debate. Here, heme ligands and ligand orientation were investigated using a nonredundant (87 structures) and a redundant (1503 structures) set of structures to compare and contrast design features of natural b- and c-type heme-binding proteins. Histidine is the most common ligand. Marked differences in ligation motifs between b- and c-type hemes are higher occurrence of His-Met in c-type heme binding motifs (16.4% vs. 1.4%) and higher occurrence of exchangeable, small molecules in b-type heme binding motifs (67.6% vs. 9.9%). Histidine ligands that are part of the c-type CXXCH heme-binding motif show a distinct asymmetric distribution of orientation. They tend to point between either the heme propionates or between the NA and NB heme nitrogens. Molecular mechanics calculations show that this asymmetry is due to the bonded constraints of the covalent attachment between the heme and the protein. In contrast, the orientations of b-type hemes histidine ligands are found evenly distributed with no preference. Observed histidine heme ligand orientations show no dominating influence of electrostatic interactions between the heme propionates and the ligands. Furthermore, ligands in bis-His hemes are found more frequently perpendicular rather than parallel to each other. These correlations support energetic constraints on ligands that can be used in designing proteins.

Kinetics of reduction of Fe(III) complexes by outer membrane cytochromes MtrC and OmcA of Shewanella oneidensis MR-1

Because of their cell surface locations, the outer membrane c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 have been suggested to be the terminal reductases for a range of redox-reactive metals that form poorly soluble solids or that do not readily cross the outer membrane. In this work, we determined the kinetics of reduction of a series of Fe(III) complexes with citrate, nitrilotriacetic acid (NTA), and EDTA by MtrC and OmcA using a stopped-flow technique in combination with theoretical computation methods. Stopped-flow kinetic data showed that the reaction proceeded in two stages, a fast stage that was completed in less than 1 s, followed by a second, relatively slower stage. For a given complex, electron transfer by MtrC was faster than that by OmcA. For a given cytochrome, the reaction was completed in the order Fe-EDTA > Fe-NTA > Fe-citrate. The kinetic data could be modeled by two parallel second-order bimolecular redox reactions with second-order rate constants ranging from 0.872 microM(-1) s(-1) for the reaction between MtrC and the Fe-EDTA complex to 0.012 microM(-1) s(-1) for the reaction between OmcA and Fe-citrate. The biphasic reaction kinetics was attributed to redox potential differences among the heme groups or redox site heterogeneity within the cytochromes. The results of redox potential and reorganization energy calculations showed that the reaction rate was influenced mostly by the relatively large reorganization energy. The results demonstrate that ligand complexation plays an important role in microbial dissimilatory reduction and mineral transformation of iron, as well as other redox-sensitive metal species in nature.