Effect of Anchoring Dynamics on Proton-Coupled Electron Transfer in the Ru(bda) Coordination Oligomer on a Graphitic Surface.

The oligomeric ruthenium-based water oxidation catalyst, Ru(bda), is known to be experimentally anchored on graphitic surfaces through CH-π stacking interactions between the auxiliary bda ([2,2'-bipyridine]-6,6'-dicarboxylate) ligand bonded to ruthenium and the hexagonal rings of the surface. This anchoring provides control over their molecular coverage and enables efficient catalysis of water oxidation to dioxygen. The oligomeric nature of the molecule offers multiple anchoring sites at the surface, greatly enhancing the overall stability of the hybrid catalyst-graphitic surface anode through dynamic bonding. However, the impact of this dynamic anchoring on the overall catalytic mechanism is still a topic of debate. In this study, a crucial proton-coupled electron transfer event in the catalytic cycle is investigated using DFT-based molecular dynamics simulations plus metadynamics. The CH-π stacking anchoring plays a critical role not only in stabilizing this hybrid system but also in facilitating the proton-coupled electron transfer event with possible vibronic couplings between the anchoring bonds motion and charge fluctuations at the catalyst - graphitic surface interface. Furthermore, this computational investigation displays the presence of a quartet spin state intermediate that can lead to the experimentally observed and thermodynamically more stable doublet spin state.

Observation of Dark States in Two-Dimensional Electronic Spectra of Chlorosomes.

Observations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are necessary for providing novel insights into the nature and function of dark states, especially since these are not directly accessible in spectroscopy experiments. Here, we will focus on signatures of dark-type states in chlorosomes, a light-harvesting complex from green sulfur bacteria well-known for uniting a broad absorption band with very efficient energy transfer. In agreement with experiments, our simulations of two-dimensional electronic spectra capture the ultrafast exciton transfer occurring in 100s of femtoseconds within a single chlorosome cylinder. The sub-100 fs process corresponds to relaxation within the single-excitation manifold in a single chlorosome tube, where all initially created populations in the bright exciton states are quickly transferred to dark-type exciton states. Structural inhomogeneities on the local scale cause a redistribution of the oscillator strength, leading to the emergence of these dark-type exciton states, which dominate ultrafast energy transfer. The presence of the dark-type exciton states suppresses energy loss from an isolated chlorosome via fluorescence quenching, as observed experimentally. Our results further question whether relaxation to dark-exciton states is a leading process or merely competes with transfer to the baseplate within the photosynthetic apparatus of green sulfur bacteria.

An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum.

Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ.

Covalent Benzenesulfonic Functionalization of a Graphene Nanopore for Enhanced and Selective Proton Transport.

A fundamental understanding of proton transport through graphene nanopores, defects, and vacancies is essential for advancing two-dimensional proton exchange membranes (PEMs). This study employs ReaxFF molecular dynamics, metadynamics, and density functional theory to investigate the enhanced proton transport through a graphene nanopore. Covalently functionalizing the nanopore with a benzenesulfonic group yields consistent improvements in proton permeability, with a lower activation barrier (≈0.15 eV) and increased proton selectivity over sodium cations. The benzenesulfonic functionality acts as a dynamic proton shuttle, establishing a favorable hydrogen-bonding network and an efficient proton transport channel. The model reveals an optimal balance between proton permeability and selectivity, which is essential for effective proton exchange membranes. Notably, the benzenesulfonic-functionalized graphene nanopore system achieves a theoretically estimated proton diffusion coefficient comparable to or higher than the current state-of-the-art PEM, Nafion. Ergo, the benzenesulfonic functionalization of graphene nanopores, firmly holds promise for future graphene-based membrane development in energy conversion devices.

MetalDock: An Open Access Docking Tool for Easy and Reproducible Docking of Metal Complexes.

Despite the proven potential of metal complexes as therapeutics, the lack of computational tools available for the high-throughput screening of their interactions with proteins is a limiting factor toward clinical developments. To address this challenge, we introduce MetalDock, an easy-to-use, open access docking software for docking metal complexes to proteins. Our tool integrates the AutoDock docking engine with three well-known quantum software packages to automate the docking of metal-organic complexes to proteins. We used a Monte Carlo sampling scheme to obtain the missing Lennard-Jones parameters for 12 metal atom types and demonstrated that these parameters generalize exceptionally well. Our results show that the poses obtained by MetalDock are highly accurate, as they predict the binding geometries experimentally determined by crystal structures with high spatial reproducibility. Three different case studies are presented that demonstrate the versatility of MetalDock for the docking of diverse metal-organic compounds to different biomacromolecules, including nucleic acids.

Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates.

Chlorosomes from green bacteria perform the most efficient light capture and energy transfer, as observed among natural light-harvesting antennae. Hence, their unique functional properties inspire developments in artificial light-harvesting and molecular optoelectronics. We examine two distinct organizations of the molecular building blocks as proposed in the literature, demonstrating how these organizations alter light capture and energy transfer, which can serve as a mechanism that the bacteria utilize to adapt to changes in light conditions. Spectral simulations of polarization-resolved two-dimensional electronic spectra unravel how changes in the helicity of chlorosomal aggregates alter energy transfer. We show that ultrafast anisotropy decay presents a spectral signature that reveals contrasting energy pathways in different chlorosomes.

Elucidation of the Electrocatalytic Nitrite Reduction Mechanism by Bio-Inspired Copper Complexes.

Mononuclear copper complexes relevant to the active site of copper nitrite reductases (CuNiRs) are known to be catalytically active for the reduction of nitrite. Yet, their catalytic mechanism has thus far not been resolved. Here, we provide a complete description of the electrocatalytic nitrite reduction mechanism of a bio-inspired CuNiR catalyst Cu(tmpa) (tmpa = tris(2-pyridylmethyl)amine) in aqueous solution. Through a combination of electrochemical studies, reaction kinetics, and density functional theory (DFT) computations, we show that the protonation steps take place in a stepwise manner and are decoupled from electron transfer. The rate-determining step is a general acid-catalyzed protonation of a copper-ligated nitrous acid (HNO2) species. In view of the growing urge to convert nitrogen-containing compounds, this work provides principal reaction parameters for efficient electrochemical nitrite reduction. This contributes to the investigation and development of nitrite reduction catalysts, which is crucial to restore the biogeochemical nitrogen cycle.

Photon Energy-Dependent Ultrafast Exciton Transfer in Chlorosomes of Chlorobium tepidum and the Role of Supramolecular Dynamics.

The antenna complex of green sulfur bacteria, the chlorosome, is one of the most efficient supramolecular systems for efficient long-range exciton transfer in nature. Femtosecond transient absorption experiments provide new insight into how vibrationally induced quantum overlap between exciton states supports highly efficient long-range exciton transfer in the chlorosome of Chlorobium tepidum. Our work shows that excitation energy is delocalized over the chlorosome in <1 ps at room temperature. The following exciton transfer to the baseplate occurs in ∼3 to 5 ps, in line with earlier work also performed at room temperature, but significantly faster than at the cryogenic temperatures used in previous studies. This difference can be attributed to the increased vibrational motion at room temperature. We observe a so far unknown impact of the excitation photon energy on the efficiency of this process. This dependency can be assigned to distinct optical domains due to structural disorder, combined with an exciton trapping channel competing with exciton transfer toward the baseplate. An oscillatory transient signal damped in <1 ps has the highest intensity in the case of the most efficient exciton transfer to the baseplate. These results agree well with an earlier computational finding of exciton transfer driven by low-frequency rotational motion of molecules in the chlorosome. Such an exciton transfer process belongs to the quantum coherent regime, for which the Förster theory for intermolecular exciton transfer does not apply. Our work hence strongly indicates that structural flexibility is important for efficient long-range exciton transfer in chlorosomes.

Ligand Rigidity Steers the Selectivity and Efficiency of the Photosubstitution Reaction of Strained Ruthenium Polypyridyl Complexes.

While photosubstitution reactions in metal complexes are usually thought of as dissociative processes poorly dependent on the environment, they are, in fact, very sensitive to solvent effects. Therefore, it is crucial to explicitly consider solvent molecules in theoretical models of these reactions. Here, we experimentally and computationally investigated the selectivity of the photosubstitution of diimine chelates in a series of sterically strained ruthenium(II) polypyridyl complexes in water and acetonitrile. The complexes differ essentially by the rigidity of the chelates, which strongly influenced the observed selectivity of the photosubstitution. As the ratio between the different photoproducts was also influenced by the solvent, we developed a full density functional theory modeling of the reaction mechanism that included explicit solvent molecules. Three reaction pathways leading to photodissociation were identified on the triplet hypersurface, each characterized by either one or two energy barriers. Photodissociation in water was promoted by a proton transfer in the triplet state, which was facilitated by the dissociated pyridine ring acting as a pendent base. We show that the temperature variation of the photosubstitution quantum yield is an excellent tool to compare theory with experiments. An unusual phenomenon was observed for one of the compounds in acetonitrile, for which an increase in temperature led to a surprising decrease in the photosubstitution reaction rate. We interpret this experimental observation based on complete mapping of the triplet hypersurface of this complex, revealing thermal deactivation to the singlet ground state through intersystem crossing.

Correction: Automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells.

Correction for 'Automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells' by Jelena Belic et al., Phys. Chem. Chem. Phys., 2022, 24, 197-210, https://doi.org/10.1039/D1CP04218A.

In vivo metallophilic self-assembly of a light-activated anticancer drug.

Self-assembling molecular drugs combine the easy preparation typical of small-molecule chemotherapy and the tumour-targeting properties of drug-nanoparticle conjugates. However, they require a supramolecular interaction that survives the complex environment of a living animal. Here we report that the metallophilic interaction between cyclometalated palladium complexes generates supramolecular nanostructures in living mice that have a long circulation time (over 12 h) and efficient tumour accumulation rate (up to 10.2% of the injected dose per gram) in a skin melanoma tumour model. Green light activation leads to efficient tumour destruction due to the type I photodynamic effect generated by the self-assembled palladium complexes, as demonstrated in vitro by an up to 96-fold cytotoxicity increase upon irradiation. This work demonstrates that metallophilic interactions are well suited to generating stable supramolecular nanotherapeutics in vivo with exceptional tumour-targeting properties.

Challenges in Elucidating the Free Energy Scheme of the Laccase Catalyzed Reduction of Oxygen.

Artificial redox catalysts are typically limited by unfavorable scaling relations of reaction intermediates leading to a significant overpotential in multi-electron redox reactions such as for example the oxygen reduction reaction (ORR). The multicopper oxidase laccase is able to catalyze the ORR in nature. In particular the high-potential variants show a remarkably low overpotential for the ORR and apparently do not suffer from such unfavorable scaling relations. Although laccases are intensively studied, it is presently unknown why the overpotential for ORR is so low and a clear description regarding the thermodynamics of the catalytic cycle and the underlying design principles is lacking. In order to understand the laccase catalyzed ORR from an electrochemical perspective, elucidation of the free energy scheme would be of high value. This article reviews the energetics of the proposed laccase catalyzed ORR mechanisms based on experimental and computational studies. However, there are still remaining challenges to overcome to elucidate the free energy scheme of laccase. Obtaining thermodynamic data on intermediates is hard or even impossible with analytical techniques. On the other hand, several computational studies have been performed with significantly different parameters and conditions, thus making a direct comparison difficult. For these reasons, a consensus on a clear free energy scheme is still lacking. We anticipate that ultimately conquering these challenges will result in a better understanding of laccase catalyzed ORR and will allow for the design of low overpotential redox catalysts.

Manifestation of Hydrogen Bonding and Exciton Delocalization on the Absorption and Two-Dimensional Electronic Spectra of Chlorosomes.

Chlorosomes are supramolecular aggregates that contain thousands of bacteriochlorophyll molecules. They perform the most efficient ultrafast excitation energy transfer of all natural light-harvesting complexes. Their broad absorption band optimizes light capture. In this study, we identify the microscopic sources of the disorder causing the spectral width and reveal how it affects the excited state properties and the optical response of the system. We combine molecular dynamics, quantum chemical calculations, and response function calculations to achieve this goal. The predicted linear and two-dimensional electronic spectra are found to compare well with experimental data reproducing all key spectral features. Our analysis of the microscopic model reveals the interplay of static and dynamic disorder from the molecular perspective. We find that hydrogen bonding motifs are essential for a correct description of the spectral line shape. Furthermore, we find that exciton delocalization over tens to hundreds of molecules is consistent with the two-dimensional electronic spectra.

In Silico Optimization of Charge Separating Dyes for Solar Energy Conversion.

Dye-sensitized photoelectrochemical cells are promising devices in solar energy conversion. However, several limitations still have to be addressed, such as the major loss pathway through charge recombination at the dye-semiconductor interface. Charge separating dyes constructed as push-pull systems can increase the spatial separation of electron and hole, decreasing the recombination rate. Here, a family of dyes, consisting of polyphenylamine donors, fluorene bridges, and perylene monoimide acceptors, was investigated in silico using a combination of semi-empirical nuclear dynamics and a quantum propagation of photoexcited electron and hole. To optimize the charge separation, several molecular design strategies were investigated, including modifying the donor molecule, increasing the π-bridge length, and decoupling the molecular components through steric effects. The combination of a triphenylamine donor, using an extended 2-fluorene π-bridge, and decoupling the different components by steric hindrance from side groups resulted in a dye with significantly improved charge separation properties in comparison to the original supramolecular complex.

Freestanding non-covalent thin films of the propeller-shaped polycyclic aromatic hydrocarbon decacyclene.

Molecularly thin, nanoporous thin films are of paramount importance in material sciences. Their use in a wide range of applications requires control over their chemical functionalities, which is difficult to achieve using current production methods. Here, the small polycyclic aromatic hydrocarbon decacyclene is used to form molecular thin films, without requiring covalent crosslinking of any kind. The 2.5 nm thin films are mechanically stable, able to be free-standing over micrometer distances, held together solely by supramolecular interactions. Using a combination of computational chemistry and microscopic imaging techniques, thin films are studied on both a molecular and microscopic scale. Their mechanical strength is quantified using AFM nanoindentation, showing their capability of withstanding a point load of 26 ± 9 nN, when freely spanning over a 1 µm aperture, with a corresponding Young's modulus of 6 ± 4 GPa. Our thin films constitute free-standing, non-covalent thin films based on a small PAH.

The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes.

The most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification of chlorosomes as a unique tubular plastic crystal and we attribute the robust energy transfer in chlorosomes to this unique nature. To systematically study the role of supramolecular tube chirality by molecular simulation, a role that has remained unresolved, we share a protocol for generating realistic tubes at atomic resolution. We find that both the optical and the mechanical behavior are strongly dependent on chirality. The optical-chirality relation enables a direct interpretation of experimental spectra in terms of overall tube chirality. The mechanical response shows that the overall chirality regulates the hardness of the tube and provides a new characteristic for relating chlorosomes to distinct chirality. Our protocol also applies to other TMA systems and will inspire other systematic studies beyond lattice models.

Analytical Nonadiabatic Couplings and Gradients within the State-Averaged Orbital-Optimized Variational Quantum Eigensolver.

We introduce several technical and analytical extensions to our recent state-averaged orbital-optimized variational quantum eigensolver (SA-OO-VQE) algorithm (see Yalouz et al. Quantum Sci. Technol. 2021, 6, 024004). Motivated by the limitations of current quantum computers, the first extension consists of an efficient state-resolution procedure to find the SA-OO-VQE eigenstates, and not just the subspace spanned by them, while remaining in the equi-ensemble framework. This approach avoids expensive intermediate resolutions of the eigenstates by postponing this problem to the very end of the full algorithm. The second extension allows for the estimation of analytical gradients and nonadiabatic couplings, which are crucial in many practical situations ranging from the search of conical intersections to the simulation of quantum dynamics, in, for example, photoisomerization reactions. The accuracy of our new implementations is demonstrated on the formaldimine molecule CH2NH (a minimal Schiff base model relevant for the study of photoisomerization in larger biomolecules), for which we also perform a geometry optimization to locate a conical intersection between the ground and first-excited electronic states of the molecule.

Automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells.

Sustainable solutions for hydrogen production, such as dye-sensitized photoelectrochemical cells (DS-PEC), rely on the fundamental properties of its components whose modularity allows for their separate investigation. In this work, we design and execute a high-throughput scheme to tune the ground state oxidation potential (GSOP) of perylene-type dyes by functionalizing them with different ligands. This allows us to identify promising candidates which can then be used to improve the cell's efficiency. First, we investigate the accuracy of different theoretical approaches by benchmarking them against experimentally determined GSOPs. We test different methods to calculate the vertical oxidation potential, including GW with different levels of self-consistency, Kohn-Sham (KS) orbital energies and total energy differences. We find that there is little difference in the performance of these methods. However, we show that it is crucial to take into account solvent effects as well as the structural relaxation of the dye after oxidation. Other thermodynamic contributions are negligible. Based on this benchmark, we decide on an optimal strategy, balancing computational cost and accuracy, to screen more than 1000 dyes and identify promising candidates which could be used to construct more robust DS-PECs.

Intracellular Dynamic Assembly of Deep-Red Emitting Supramolecular Nanostructures Based on the Pt Pt Metallophilic Interaction.

Many drug delivery systems end up in the lysosome because they are built from covalent or kinetically inert supramolecular bonds. To reach other organelles, nanoparticles hence need to either be made from a kinetically labile interaction that allows re-assembly of the nanoparticles inside the cell following endocytic uptake, or, be taken up by a mechanism that short-circuits the classical endocytosis pathway. In this work, the intracellular fate of nanorods that self-assemble via the Pt…Pt interaction of cyclometalated platinum(II) compounds, is studied. These deep-red emissive nanostructures (638 nm excitation, ≈700 nm emission) are stabilized by proteins in cell medium. Once in contact with cancer cells, they cross the cell membrane via dynamin- and clathrin-dependent endocytosis. However, time-dependent confocal colocalization and cellular electron microscopy demonstrate that they directly move to mitochondria without passing by the lysosomes. Altogether, this study suggests that Pt…Pt interaction is strong enough to generate emissive, aggregated nanoparticles inside cells, but labile enough to allow these nanostructures to reach the mitochondria without being trapped in the lysosomes. These findings open new venues to the development of bioimaging nanoplatforms based on the Pt…Pt interaction.

Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: Combining GFN-xTB and density functional theory.

Photocatalytic water oxidation remains the bottleneck in many artificial photosynthesis devices. The efficiency of this challenging process is inherently linked to the thermodynamic and electronic properties of the chromophore and the water oxidation catalyst (WOC). Computational investigations can facilitate the search for favorable chromophore-catalyst combinations. However, this remains a demanding task due to the requirements on the computational method that should be able to correctly describe different spin and oxidation states of the transition metal, the influence of solvation and the different rates of the charge transfer and water oxidation processes. To determine a suitable method with favorable cost/accuracy ratios, the full catalytic cycle of a molecular ruthenium based WOC is investigated using different computational methods, including density functional theory (DFT) with different functionals (GGA, Hybrid, Double Hybrid) as well as the semi-empirical tight binding approach GFN-xTB. A workflow with low computational cost is proposed that combines GFN-xTB and DFT and provides reliable results. GFN-xTB geometries and frequencies combined with single-point DFT energies give free energy changes along the catalytic cycle that closely follow the full DFT results and show satisfactory agreement with experiment, while significantly decreasing the computational cost. This workflow allows for cost efficient determination of energetic, thermodynamic and dynamic properties of WOCs.