A QM/MM study of the nature of the entatic state in plastocyanin

Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study

Molecular mechanics rely on existing experimental and theoretical inputs to confidently calculate the trajectories of molecular systems. These calculations, however, are often hindered by missing force field parameters. A notable subject of this problem is metal centers of proteins. This study parameterized, through an adaptive force matching (AFM) workflow, the copper cofactor of plastocyanin in its two oxidation states. New 12-6 Lennard-Jones (LJ) parameters and atomic partial charges were generated to complete the non-bonded description of the copper site. Our models show uniform distorted tetrahedral structures for reduced plastocyanin, Cu(I), and oxidized plastocyanin, Cu(II). These structures align with the QM/MM MD results and existing crystallography studies. TD-DFT calculations, meanwhile, showed that conformations with elongated axial Cu-SMet and shortened equatorial Cu-SCys bonds retain the experimental UV-Vis profile of blue copper (BC) proteins, thus signifying the importance of Cu-S interactions on BC proteins' unique spectroscopic properties.

Tailored Charge Transfer Kinetics in Precursors for Organic Radical Batteries: A Joint Synthetic-Theoretical Approach

The development of sustainable energy storage devices is crucial for the transformation of our energy management. In this scope, organic batteries attracted considerable attention. To overcome the shortcomings of typically applied materials from the classes of redox-active conjugated polymers (i. e., unstable cell voltages) and soft matter-embedded stable organic radicals (i. e., low conductivity), a novel design concept was introduced, integrating such stable radicals within a conductive polymer backbone. In the present theory-driven design approach, redox-active (2,2,6,6-tetramethylpiperidin-1-yl)oxyls (TEMPOs) were incorporated in thiophene-based polymer model systems, while structure-property relationships governing the thermodynamic properties as well as the charge transfer kinetics underlying the charging and discharging processes were investigated in a systematical approach. Thereby, the impact of the substitution pattern, the length as well as the nature of the chemical linker, and the ratio of TEMPO and thiophene units was studied using state-of-the-art quantum chemical and quantum dynamical simulations for a set of six molecular model systems. Finally, two promising candidates were synthesized and electrochemically characterized, paving the way to applications in the frame of novel organic radical batteries.

Symmetry Breaking in Solution-Phase [Cu(tsc)2(H2O)2]2+: Emergent Asymmetry in Cu-S Distances and in Covalence

The structure of aqueous Cu(II)-bis-thiosemicarbazide, [Cu(tsc)₂]²⁺, is reported following EXAFS and MXAN analyses of the copper K-edge X-ray absorption (XAS) spectrum. The rising K-edge feature at 8987.1 eV is higher energy than those of crystalline models, implying unique electronic and structural solution states. EXAFS analysis (k = 2-13 Å^-1; 2 × Cu-N = 2.02 ± 0.01 Å; 2 × Cu-S = 2.27 ± 0.01 Å; Cu-O_ax = 2.41 ± 0.04 Å) could not resolve 5- versus 6-coordinate models. However, MXAN fits converged to an asymmetric broken symmetry 6-coordinate model with cis-disposed TSC ligands (Cu-O_ax = 2.07 and 2.54 Å; Cu-N = 1.94 Å, 1.98 Å; Cu-S = 2.20 Å, 2.41 Å). Transition dipole integral evaluation of the sulfur K-edge XAS 1s → 3p valence transition feature at 2470.7 eV yielded a Cu-S covalence of 0.66 e^-, indicating Cu^1.34+. The high Cu-S covalence and short Cu-S bond in aqueous [Cu(tsc)₂(H₂O)₂]²⁺ again contradict the need for a protein rack to explain the unique structure of the blue copper active site. MXAN models of dissolved Cu(II) complex ions have invariably featured broken centrosymmetry. The potential energy ground state for dissolved Cu(II) evidently includes the extended solvation field, providing a target for improved physical theory. A revised solvation model for aqueous Cu(II), |[Cu(H₂O)₅]·14H₂O|²⁺, is presented.

Electrostatic regulation of blue copper sites

In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to the and vectors in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu–S_Met bond distance, Cu(ii)–S_Cys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(ii/i) reduction potential and the relative absorption intensities at 450 nm and 600 nm.

Intramolecular electric fields in blue copper proteins are oriented in a fixed way to modulate properties of their copper sites: they control the first-shell copper interactions to influence geometric, spectroscopic, and redox behavior.

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

CuA-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential

Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.

Hypothesis: entaticversusecstatic states in metalloproteins

Biological metal sites are optimized for function by conformational properties of the protein macroligand.

Theoretical Investigation of the Electron-Transfer Dynamics and Photodegradation Pathways in a Hydrogen-Evolving Ruthenium-Palladium Photocatalyst

Time-dependent density functional theory calculations combined with the Marcus theory of electron transfer (ET) were applied on the molecular photocatalyst [(tbbpy)₂ Ru(tpphz)PdCl₂ ]²⁺ in order to elucidate the light-induced relaxation pathways populated upon excitation in the longer wavelength range of its absorption spectrum. The computational results show that after the initial excitation, metal (Ru) to ligand (tpphz) charge transfer (MLCT) triplet states are energetically accessible, but that an ET toward the catalytic center (PdCl₂ ) from these states is a slow process, with estimated time constants above 1 ns. Instead, the calculations predict that low-lying Pd-centered states are efficiently populated-associated to an energy transfer toward the catalytic center. Thus, it is postulated that these states lead to the dissociation of a Cl^- and are consequently responsible for the experimentally observed degradation of the catalytic center. Following dissociation, it is shown that the ET rates from the MLCT states to the charge separated states are significantly increased (i.e. 10⁴ -10⁶ times larger). This demonstrates that alteration of the catalytic center generates efficient charge separation.

Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory

Blue copper proteins, such as azurin, show dramatic changes in Cu²⁺/Cu⁺ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high‐level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long‐range electrostatic changes and hence can be modeled accurately with continuum electrostatics.

A QM/MM study of the nature of the entatic state in plastocyanin

Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory‐based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.