Water Promoting Electron Hole Transport between Tyrosine and Cysteine in Proteins via a Special Mechanism: Double Proton Coupled Electron Transfer

Enhancing the microbial advanced oxidation of P-nitrophenol in sediment through accelerating extracellular respiration with electrical stimulation

Microbial advanced oxidation, a fundamental process for pollutant degradation in nature, is limited in efficiency by the weak respiration of indigenous microorganisms. In this study, an electric field was employed to enhance microbial respiration and facilitate the microbial advanced oxidation of p-nitrophenol (PNP) in simulated wetlands with alternation of anaerobic and aerobic conditions. With intermittent air aeration, an electric field of 0.8 V promoted extracellular electron transfer to increase Fe2+ generation through dissimilatory iron reduction and the production of hydroxyl radicals (•OH) through Fenton-like reactions. As a result, the PNP removal rate of the electrically-stimulated group was higher than that of the control (72.15 % vs 46.88 %). Multiple lines of evidence demonstrated that the electrically-induced polarization of respiratory enzymes expedited proton-coupled electron transfer within the respiratory chain to accelerate microbial advanced oxidation of PNP. The polarization of respiratory enzymes with the electric field hastened proton outflow to increase cell membrane potential for adenosine triphosphate (ATP) generation, which enhanced intracellular electron transportation to benefit reactive oxygen species generation. This study provided a new method to enhance microelectrochemical remediation of the contaminant in wetlands via the combination of intermittent air aeration.

High-Power-Density and Excellent-Flexibility Thermoelectric Generator Based on All-SWCNTs/PVP Composites

Flexible polymer/single-wall carbon nanotube (SWCNT) composites are a vital component for wearable/portable electronics, but the development of their n-type counterpart is laggard. Furthermore, little attention is paid to the interaction between SWCNT and polymers, especially the unconjugated polymers, as well as the conversion mechanism of conduction characteristics. Here, the n-type flexible SWCNTs/Polyvinyl Pyrrolidone (PVP) films are successfully fabricated, where the oxygen atoms in PVP interacted with SWCNT via hydrogen bonds, which can lower the energy barrier of electron tunneling, providing the pathway for the electron transfer. Furthermore, with the increasing synthesis temperature, the hydrogen bonds strengthened and the thermal activation energy further improved, both of which enhanced the electron-donating ability of PVP, resulting in a high-power-factor value of 260 µW m-1 K-2. Based on the optimized SWCNTs/PVP films, a thermoelectric module is assembled, which achieved a power density of 400 µW cm-2 at a temperature difference of 56 K, coupled with excellent flexibility, showing a less than 1% variation of resistance after 5000 bending cycles. It shows the highest output-performance and the best flexibility among the reported SWCNT-based thermoelectric modules. This work provides significant insights into the interaction mechanism and performance optimization of hybrid thermoelectric composites, based on SWCNTs/unconjugated polymers.

The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions

Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.

Improving microbial production of value-added products through the intervention of magnetic fields

The magnetic field application is emerging as an auxiliary physical strategy to facilitate rapid biomass accumulation and intracellular production of compounds. However, the underlying mechanisms and principles governing the application of magnetic fields for microbial growth and biotransformation are not yet fully understood. Therefore, a better understanding of interdisciplinary technologies integration, expanded magnetic field application, and scaled-up industrial implementation is crucial. In this review, the magnetic field characteristics, magnetic field-assisted fermentation devices, and the working mechanism of magnetic field have been reviewed comprehensively from both physical and microbiological perspectives. The review suggests that magnetic fields affect the biochemical processes in microorganisms by mediating nutrient transport across membranes, electron transfer during photosynthesis and respiration, enzyme activity and gene expression. Moreover, the recent advances in magnetic field application for microbial fermentation and conversion in biochemical, food and agricultural fields have been summarized.

Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen Bond

Multiple proton transfer (PT) controllable by external stimuli plays a crucial role in fundamental chemistry, biological activity, and material science. However, in crystalline systems, controlling multiple PT, which results in a distinct protonation state, remains challenging. In this study, we developed a novel tridentate ligand and iron(II) complex with a short hydrogen bond (HB) that exhibits a PT-coupled spin transition (PCST). Single-crystal X-ray and neutron diffraction measurements revealed that the positions of the two protons in the complex can be controlled by temperature and photoirradiation based on the thermal- and photoinduced PCST. The obtained results suggest that designing molecules that form short HBs is a promising approach for developing multiple PT systems in crystals.

Exploring Proton-Coupled Electron Transfer at Multiple Scales

The coupling of electron and proton transfer is critical for chemical and biological processes spanning a wide range of length and time scales and often occurring in complex environments. Thus, diverse modeling strategies, including analytical theories, quantum chemistry, molecular dynamics, and kinetic modeling, are essential for a comprehensive understanding of such proton-coupled electron transfer reactions. Each of these computational methods provides one piece of the puzzle, and all these pieces must be viewed together to produce the full picture.

Mechanism of Radical Initiation and Transfer in Class Id Ribonucleotide Reductase Based on Density Functional Theory

Class Id ribonucleotide reductase (RNR) is a newly discovered enzyme, which employs the dimanganese cofactor in the superoxidized state (Mn^III/Mn^IV) as the radical initiator. The dimanganese cofactor of class Id RNR in the reduced state (inactive) is clearly based on the crystal structure of the Fj-β subunit. However, the state of the dimanganese cofactor of class Id RNR in the oxidized state (active) is not known. The X-band EPR spectra have shown that the activated Fj-β subunit exists in two distinct complexes, 1 and 2. In this work, quantum mechanical/molecular mechanical calculations were carried out to study class Id RNR. First, we have determined that complex 2 contains a Mn^III-(μ-oxo)₂-Mn^IV cluster, and complex 1 contains a Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV cluster. Then, based on the determined dimanganese cofactors, the mechanism of radical initiation and transfer in class Id RNR is revealed. The Mn^III-(μ-oxo)₂-Mn^IV cluster in complex 2 has not enough reduction potential to initiate radical transfer directly. Instead, it needs to be monoprotonated into Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV (complex 1) before the radical transfer. The protonation state of μ-oxo can be regulated by changing the protein microenvironment, which is induced by the protein aggregation and separation of β subunits with α subunits. The radical transfer between the cluster of Mn^III-(μ-hydroxo/μ-oxo)-Mn^IV and Trp30 in the radical-transfer chain of the Fj-β subunit (Mn^III/Mn^IV ↔ His100 ↔ Asp194 ↔ Trp30 ↔ Arg99) is a water-mediated tri-proton-coupled electron transfer, which transfers proton from the ε-amino group of Lys71 to the carboxyl group of Glu97 via the water molecule Wat551 and the bridging μ-hydroxo ligand through a three-step reaction. This newly discovered proton-coupled electron-transfer mechanism in class Id RNR is different from those reported in the known Ia-Ic RNRs. The ε-amino group of Lys71, which serves as a proton donor, plays an important role in the radical transfer.

Applying Dynamic Magnetic Field To Promote Anaerobic Digestion via Enhancing the Electron Transfer of a Microbial Respiration Chain

Electrochemical methods have been reported to strengthen anaerobic digestion, but the continuous electrical power supply and the complicated electrode installed inside the digester have restricted it from practical use. In this study, a dynamic magnetic field (DMF) was placed outside a digester to induce an electromotive force to electrically promote anaerobic digestion. With the applied DMF, an electromotive force of 0.14 mV was generated in the anaerobic sludge, and a 65.02% methane increment was obtained from the anaerobic digestion of waste-activated sludge. Experiments on each stage of anaerobic digestion showed that acidification and methanogenesis that involve electron transfer of respiration chains were promoted with the DMF, while solubilization and hydrolysis less related to respiration chains were not enhanced. Further analysis indicated that the induced electromotive force polarized the protein-like substances in the sludge to increase the conductivity and capacitance of the sludge. Electrotrophic methanogens (Methanothrix) and exoelectrogens (Exiguobacterium) were enriched with DMF. The kinetic isotope effect test confirmed that electron transfer was accelerated with DMF. Consistently, the concentration ratio of co-enzymes (NADH/NAD⁺ and F₄₂₀H₂/F₄₂₀₎ that reflects the electron exchange with respiration chains significantly increased. Applying the DMF seemed a more accessible strategy to electrically strengthen anaerobic digestion.

Modified Cellulose Proton-Exchange Membranes for Direct Methanol Fuel Cells

A direct methanol fuel cell (DMFC) is an excellent energy device in which direct conversion of methanol to energy occurs, resulting in a high energy conversion rate. For DMFCs, fluoropolymer copolymers are considered excellent proton-exchange membranes (PEMs). However, the high cost and high methanol permeability of commercial membranes are major obstacles to overcome in achieving higher performance in DMFCs. Novel developments have focused on various reliable materials to decrease costs and enhance DMFC performance. From this perspective, cellulose-based materials have been effectively considered as polymers and additives with multiple concepts to develop PEMs for DMFCs. In this review, we have extensively discussed the advances and utilization of cost-effective cellulose materials (microcrystalline cellulose, nanocrystalline cellulose, cellulose whiskers, cellulose nanofibers, and cellulose acetate) as PEMs for DMFCs. By adding cellulose or cellulose derivatives alone or into the PEM matrix, the performance of DMFCs is attained progressively. To understand the impact of different structures and compositions of cellulose-containing PEMs, they have been classified as functionalized cellulose, grafted cellulose, acid-doped cellulose, cellulose blended with different polymers, and composites with inorganic additives.

Intermittent voltage induced sludge polarization to enhance anaerobic digestion

Intermittent voltage supply has been reported to improve the performance of electro-assisted anaerobic digestion but has not been well understood. In this study, an intermittent voltage of 0.6 V (1 day on-1 day off) was applied in an electro-assisted anaerobic digester to explore its effects. Compared to those without the voltage, the methane yield increased nearly by 20.0%, and organic decomposition increased by 9.5% with the intermittent voltage, which was similar to those with the continuous voltage. The amide groups of the sludge protein after the electro-treatment were polarized to enhance electron transfer and electron storage of protein-like substances of the sludge. Although the voltage was supplied intermittently, the increased conductivity and capacitance of the sludge and EPS could effectively transport electrons between exoelectrogens and electrotrophs (such as Firmicutes and Methanothrix) to promote the anaerobic digestion. This study explained the essence of electrochemical enhancement of anaerobic digestion from the perspective of molecular structure, that is, the polarization of functional groups by voltage could improve the sludge electro-activity to maintain effective interspecies electron transfer in the periodic voltage supply.

Chalcogen Atoms as Electron Donors in Proton-Coupled Electron Transfer Reactions

Proton-coupled electron transfer (PCET) reactions are crucial for the optimal functioning of a broad scope of chemical and biological processes. In this report, we present an unprecedented type of concerted PCET (cPCET), in which a chalcogen atom acts as the electron donor. The nature of this mechanism is key for understanding the reactivity of different radical-trapping antioxidants having heavy chalcogens (S, Se, or Te) in their structures. Moreover, this chalcogen-assisted cPCET is likely to be occurring in multiple systems of biological interest.

Kinetic model for reversible radical transfer in ribonucleotide reductase

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.

19F Electron-Nuclear Double Resonance Reveals Interaction between Redox-Active Tyrosines across the α/β Interface of E. coli Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to deoxyribonucleotides, thereby playing a key role in DNA replication and repair. Escherichia coli class Ia RNR is an α₂β₂ enzyme complex that uses a reversible multistep radical transfer (RT) over 32 Å across its two subunits, α and β, to initiate, using its metallo-cofactor in β₂, nucleotide reduction in α₂. Each step is proposed to involve a distinct proton-coupled electron-transfer (PCET) process. An unresolved step is the RT involving Y₃₅₆(β) and Y₇₃₁(α) across the α/β interface. Using 2,3,5-F₃Y₁₂₂-β₂ with 3,5-F₂Y₇₃₁-α₂, GDP (substrate) and TTP (allosteric effector), a Y₃₅₆^• intermediate was trapped and its identity was verified by 263 GHz electron paramagnetic resonance (EPR) and 34 GHz pulse electron–electron double resonance spectroscopies. 94 GHz ¹⁹F electron-nuclear double resonance spectroscopy allowed measuring the interspin distances between Y₃₅₆^• and the ¹⁹F nuclei of 3,5-F₂Y₇₃₁ in this RNR mutant. Similar experiments with the double mutant E₅₂Q/F₃Y₁₂₂-β₂ were carried out for comparison to the recently published cryo-EM structure of a holo RNR complex. For both mutant combinations, the distance measurements reveal two conformations of 3,5-F₂Y₇₃₁. Remarkably, one conformation is consistent with 3,5-F₂Y₇₃₁ within the H-bond distance to Y₃₅₆^•, whereas the second one is consistent with the conformation observed in the cryo-EM structure. The observations unexpectedly suggest the possibility of a colinear PCET, in which electron and proton are transferred from the same donor to the same acceptor between Y₃₅₆ and Y₇₃₁. The results highlight the important role of state-of-the-art EPR spectroscopy to decipher this mechanism.

Role of Water in Proton-Coupled Electron Transfer between Tyrosine and Cysteine in Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides and is critical for DNA synthesis and repair in all organisms. Its mechanism requires radical transfer along a ∼32 Å pathway through a series of proton-coupled electron transfer (PCET) steps. Previous simulations suggested that a glutamate residue (E623) mediates the PCET reaction between two stacked tyrosine residues (Y730 and Y731) through a proton relay mechanism. This work focuses on the adjacent PCET reaction between Y730 and a cysteine residue (C439). Quantum mechanical/molecular mechanical free energy simulations illustrate that when Y730 and Y731 are stacked, E623 stabilizes the radical on C439 through hydrogen bonding with the Y730 hydroxyl group. When Y731 is flipped away from Y730, a water molecule stabilizes the radical on C439 through hydrogen bonding with Y730 and lowers the free energy barrier for radical transfer from Y730 to C439 through electrostatic interactions with the transferring hydrogen but does not directly accept the proton. These simulations indicate that the conformational motions and electrostatic interactions of the tyrosines, cysteine, glutamate, and water strongly impact the thermodynamics and kinetics of these two coupled PCET reactions. Such insights are important for protein engineering efforts aimed at altering radical transfer in RNR.

Mechanism of DOPA radical generation and transfer in metal-free class Ie ribonucleotide reductase based on density functional theory

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The mechanism of DOPA radical generation, transfer and regeneration is revealed.

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The superoxide O₂^•− should be protonated to HO₂^• prior to oxidizing Tyr126 to DOPA radical.

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The protonation of Asp88 is the prerequisite for the DOPA radical generation and radical transfer.

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Lys213 is a key residue for the transfer of the DOPA radical.

Quantum mechanical/molecular mechanical (QM/MM) calculations were carried out to investigate the mechanisms of the generation, transfer, and regeneration of the DOPA radical for metal-free class Ie ribonucleotide reductase. The crystal structure of MfR2 (Nature, 2018, 563, 416–420) was adopted for the calculations. The QM/MM calculations have revealed several key points that are vital for understanding the mechanisms. The superoxide O₂^•− provided by the flavoprotein NrdI cannot directly oxidize the residue Tyr126 to the DOPA radical. It should be protonated to HO₂^•. The calculation results suggest that the covalent modification of Tyr126 and the DOPA radical generation can be carried out with no involvement of metal cofactors. This addresses the concerns of the articles (Nature, 2018, 563, 416–420; PNAS, 2018, 115, 10022–10027). Another concern from the articles is that how the DOPA radical is transferred from the radical trap. The DFT calculations have demonstrated that Lys213 is a key residue for the radical transfer from the DOPA radical. The ε-amino group of Lys213 is used not only as a bridge for the electron transfer but also as a proton donor. It can provide a proton to DOPA126 via a water molecule, and thus the radical transfer from DOPA126 to Trp52 is facilitated. It has also been revealed that the protonation of Asp88 is the prerequisite for the DOPA radical generation and the radical transfer in class Ie. Once the radical is quenched, it can be regenerated via the oxidations by superoxide O₂^•− and hydroperoxyl radical HO₂^•.

Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC

The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por^•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por^•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ^• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.

An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings

Long-range hole transfer of proteins plays an important role in many biological processes of living organisms. Therefore, it is highly useful to examine the possible hole stepping stones, which can facilitate hole transfer in proteins. However, the structures of stepping stones are diverse because of the complexity of the protein structures. In the present work, we proposed a series of special stepping stones, which are instantaneously formed by three and four packing aromatic side chains of amino acids to capture a hole, corresponding to three-π five-electron (π:π∴π↔π∴π:π) and four-π seven-electron (π:π∴π:π↔π:π:π∴π) resonance bindings with appropriate binding energies. The aromatic amino acids include histidine (His), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp). The formations of these special stepping stones can effectively reduce the local ionization potential of the high π-stacking region to efficiently capture the migration hole. The quick formations and separations of them promote the efficient hole transfer in proteins. More interestingly, we revealed that a hole cannot delocalize over infinite aromatic rings along the high π-π packing structure at the same time and the micro-surroundings of proteins can modulate the formations of π:π∴π↔π∴π:π and π:π∴π:π↔π:π:π∴π bindings. These results may contribute a new avenue to better understand the potential hole transfer pathway in proteins.

Remote Water-Mediated Proton Transfer Triggers Inter-Cu Electron Transfer: Nitrite Reduction Activation in Copper-Containing Nitrite Reductase

The copper-containing nitrite reductase (CuNiR) catalyzes the biological conversion of nitrite to nitric oxide; key long-range electron/proton transfers are involved in the catalysis. However, the details of the electron-/proton-transfer mechanism are still unknown. In particular, the driving force of the electron transfer from the type-1 copper (T1Cu) site to the type-2 copper (T2Cu) site is ambiguous. Here, we explored the two possible proton-transfer channels, the high-pH proton channel and the primary proton channel, by using two-layered ONIOM calculations. Our calculation results reveal that the driving force for electron transfer from T1Cu to T2Cu comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the T2Cu site. These findings explain the detailed proton-/electron-transfer mechanisms of copper-containing nitrite reductase and could extend our understanding of the diverse proton-coupled electron-transfer mechanisms in complicated proteins.

Quantitative analysis of the coupling between proton and electron transport in peptide/manganese oxide hybrid films

A novel platform is proposed to quantify the coupling phenomenon between electrons and protons in tyrosine-rich peptide/manganese oxide hybrid films at room temperature.

Fouling-resistant biofilter of an anaerobic electrochemical membrane reactor

Membrane fouling is a considerable challenge for the stable operation of anaerobic membrane-based bioreactors. Membrane used as a cathode is a common measure to retard fouling growth in anaerobic electrochemical membrane bioreactors (AnEMBR), which; however, cannot avoid the fouling growth. Here we report a strategy using the membrane as an anode to resist membrane fouling in an AnEMBR. Although aggravating in the initial stage, the fouling on the anode membrane is gradually alleviated by the anode oxidation with enriching exoelectrogens to finally achieve a dynamic equilibrium between fouling growth and decomposition to maintain the operation stable. A mesh-like biofilter layer composed of cells with less extracellular polymeric substance (EPS) is formed on the membrane surface to lower the trans-membrane pressure and promote the interception of the anode membrane. The membrane has high electron storage and transfer capacities to accelerate the oxidation of the intercepted fouling materials, especially, the redundant EPSs of the biofilter layer.

Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.

Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer

We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.

The Role of Water Distribution Controlled by Transmembrane Potentials in the Cytochrome c-Cardiolipin Interaction: Revealing from Surface-Enhanced Infrared Absorption Spectroscopy

The interaction of cytochrome c (cyt c) with cardiolipin (CL) plays a crucial role in apoptotic functions, however, the changes of the transmembrane potential in governing the protein behavior at the membrane-water interface have not been studied due to the difficulties in simultaneously monitoring the interaction and regulating the electric field. Herein, surface-enhanced infrared absorption (SEIRA) spectroelectrochemistry is employed to study the mechanism of how the transmembrane potentials control the interaction of cyt c with CL membranes by regulating the electrode potentials of an Au film. When the transmembrane potential decreases, the water content at the interface of the membranes can be increased to slow down protein adsorption through decreasing the hydrogen-bond and hydrophobic interactions, but regulates the redox behavior of CL-bound cyt c through a possible water-facilitated proton-coupled electron transfer process. Our results suggest that the potential drop-induced restructure of the CL conformation and the hydration state could modify the structure and function of CL-bound cyt c on the lipid membrane.

A controllable mechanistic transition of charge transfer in helical peptides: from hopping to superexchange

A controllable mechanistic transition of charge transfer in helical peptides is demonstrated as a direct result of side-bridge gating.

Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities

Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups.

Ferryl protonation in oxoiron(IV) porphyrins and its role in oxygen transfer

Ferryl porphyrins, P-Fe(IV)═O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe(IV)TMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe(IV)TDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P-Fe(IV)═O ⇆ P(+)-Fe(III)(OH2)2. Reversible pKa values in the range of 4-6.3 have been measured for this process by pH-jump, UV-vis spectroscopy. Ferryl protonation has important ramifications for C-H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O-H and substrate C-H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO-H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe(IV)TMPS(+) and oxoFe(IV)TDClPS(+) species to be ∼92-94 kcal/mol. Similar values were calculated from the two-proton P(+)-Fe(III)(OH2)2 pKa(obs) and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C-H bond scission.

Hydrogen bond network between amino acid radical intermediates on the proton-coupled electron transfer pathway of E. coli α2 ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all organisms. In all Class Ia RNRs, initiation of nucleotide diphosphate (NDP) reduction requires a reversible oxidation over 35 Å by a tyrosyl radical (Y122•, Escherichia coli) in subunit β of a cysteine (C439) in the active site of subunit α. This radical transfer (RT) occurs by a specific pathway involving redox active tyrosines (Y122 ⇆ Y356 in β to Y731 ⇆ Y730 ⇆ C439 in α); each oxidation necessitates loss of a proton coupled to loss of an electron (PCET). To study these steps, 3-aminotyrosine was site-specifically incorporated in place of Y356-β, Y731- and Y730-α, and each protein was incubated with the appropriate second subunit β(α), CDP and effector ATP to trap an amino tyrosyl radical (NH2Y•) in the active α2β2 complex. High-frequency (263 GHz) pulse electron paramagnetic resonance (EPR) of the NH2Y•s reported the gx values with unprecedented resolution and revealed strong electrostatic effects caused by the protein environment. (2)H electron-nuclear double resonance (ENDOR) spectroscopy accompanied by quantum chemical calculations provided spectroscopic evidence for hydrogen bond interactions at the radical sites, i.e., two exchangeable H bonds to NH2Y730•, one to NH2Y731• and none to NH2Y356•. Similar experiments with double mutants α-NH2Y730/C439A and α-NH2Y731/Y730F allowed assignment of the H bonding partner(s) to a pathway residue(s) providing direct evidence for colinear PCET within α. The implications of these observations for the PCET process within α and at the interface are discussed.

Gas-phase tyrosine-to-cysteine radical migration in model systems

Radical migration, both intramolecular and intermolecular, from the tyrosine phenoxyl radical Tyr(O(∙)) to the cysteine radical Cys(S(∙)) in model peptide systems was observed in the gas phase. Ion-molecule reactions (IMRs) between the radical cation of homotyrosine and propyl thiol resulted in a fast hydrogen atom transfer. In addition, radical cations of the peptide LysTyrCys were formed via two different methods, affording regiospecific production of Tyr(O(∙)) or Cys(S(∙)) radicals. Collision-induced dissociation of these isomeric species displayed evidence of radical migration from the oxygen to sulfur, but not for the reverse process. This was supported by theoretical calculations, which showed the Cys(S(∙)) radical slightly lower in energy than the Tyr(O(∙)) isomer. IMRs of the LysTyrCys radical cation with allyl iodide further confirmed these findings. A mechanism for radical migration involving a proton shuttle by the C-terminal carboxylic group is proposed.

Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations

QM cluster and QM/MM protein models have been employed to understand aspects of the reaction mechanism of plant allene oxide synthase (pAOS). In this study we have investigated two reaction mechanisms for pAOS. The standard pAOS mechanism was contrasted with an alternative involving an additional active site molecule which has been shown to facilitate proton coupled electron transfer (PCET) in related systems. Firstly, we found that the results from QM/MM protein model are comparable with those from the QM cluster model, presumably due to the large active site used. Furthermore, the results from the QM cluster model show that the Fe(III) and Fe(IV) pathways for the standard mechanism have similar energetic and structural properties, indicating that the reaction mechanism may well proceed via both pathways. However, while the PCET process is facilitated by an additional active site bound water in other related families, in pAOS it is not, suggesting this type of process is not general to all closely related family members.