Electrostatic docking of a supramolecular host-guest assembly to cytochrome c probed by bidirectional photoinduced electron transfer

How neocarcerand Octacid4 self-assembles with guests into irreversible noncovalent complexes and what accelerates the assembly

Cram's supramolecular capsule Octacid4 can irreversibly and noncovalently self-assemble with small-molecule guests at room temperature, but how they self-assemble and what accelerates their assembly remain poorly understood. This article reports 81 distinct Octacid4•guest self-assembly pathways captured in unrestricted, unbiased molecular dynamics simulations. These pathways reveal that the self-assembly was initiated by the guest interaction with the cavity portal exterior of Octacid4 to increase the portal collisions that led to the portal expansion for guest ingress, and completed by the portal contraction caused by the guest docking inside the cavity to impede guest egress. The pathways also reveal that the self-assembly was accelerated by engaging populated host and guest conformations for the exterior interaction to increase the portal collision frequency. These revelations may help explain why the presence of an exterior binding site at the rim of the enzyme active site is a fundamental feature of fast enzymes such as acetylcholinesterase and why small molecules adopt local minimum conformations when binding to proteins. Further, these revelations suggest that irreversible noncovalent complexes with fast assembly rates could be developed-by engaging populated host and guest conformations for the exterior interactions-for materials technology, data storage and processing, molecular sensing and tagging, and drug therapy.

Photoinduced Electron Transfer in Encapsulated Heterocycles by Cavitands

Host-guest complexation of small heterocyclic (guest) and macrocyclic cavitands (hosts) organic molecules is still to date a very popular, inexpensive approach that bypasses the burdens of conventional covalent synthesis. Understanding the selection criteria of these chemicals is crucial to the design and potential applications of their supramolecular assemblies. This review surveys examples within the last 15 years (2005-2020) of supramolecular complexes in which the interacting photoinduced electron transfer (PET)-based chromophore and quencher fragments are commonly used in the market with reported CAS numbers. It appears from this survey that the supramolecular effects can be directed to specifically disrupt PET when the nonemissive macrocycles separately encapsulate the fluorescent acceptor or donor molecules, among other specific factors, such as when inducing conformational changes or pK_a shift of the donor. On the contrary, synergetic encapsulation of both donor and acceptor molecules, formation of ternary self-assembly at the rim or encapsulation of one component while grafting the other onto the macrocycle, among other specific factors such as the modulation of the excited-state structure of donor, will lead to the enhancement of PET process. In the event the donor or acceptor molecules have multitopic structures, the PET process can repeatedly be switched on and off. It is generally concluded that understanding the criteria for the combination of these available products for the purpose of manipulating their PET efficiency should pave the way for the facile alternative generation of new noncovalently bonded host-guest supramolecular assemblies with a more specific design tailored for more advanced, diverse and economic applications such as chemical sensing, molecular gates, drug delivery and biolabeling.

How the water-soluble hemicarcerand incarcerates guests at room temperature decoded with modular simulations

Molecular dynamics simulations of hemicarcerands and related variants allow the study of constrictive binding and offer insight into the rules of molecular complexation, but are limited because three-dimensional models of hemicarcerands are tedious to build and their atomic charges are complicated to derive. There have been no molecular dynamics simulations of the reported water-soluble hemicarcerand (Octacid4) that explain how Octacid4 encapsulates guests at 298 K and keeps them encapsulated at 298 K in NMR experiments. Herein we report a modular approach to hemicarcerand simulations that simplifies the model building and charge derivation in a manner reminiscent of the approach to protein simulations with truncated amino acids as building blocks. We also report that in aqueous molecular dynamics simulations at 298 K apo Octacid4 adopts two clusters of conformations one of which has an equatorial portal open but the guest-bound Octacid4 adopts one cluster of conformations with all portals closed. These results explain how Octacid4 incarcerates guests at room temperature and suggest that the guest-induced host conformational change that impedes decomplexation is a previously unrecognized conformational characteristic that promotes strong molecular complexation.

Marcus Relationship Maintained During Ultrafast Electron Transfer Across a Supramolecular Capsular Wall

Photoinduced electron transfer across an organic capsular wall between excited donors and ground-state acceptors is established to occur with rate constants varying in the range 0.32-4.0 × 10¹¹ s^-1 in aqueous buffer solution. The donor is encapsulated within an anionic supramolecular capsular host, and the cationic acceptor remains closer to the donor separated by the organic frame through Coulombic attraction. Such an arrangement results in electron transfer proceeding without diffusion. Free energy of the reaction (ΔG°) and the rate of electron transfer show Marcus relation with inversion. From the plot, λ and V_el were estimated to be 1.918 and 0.0058 eV, respectively. Given that the donor remains within the nonpolar solvent-free confined space, and there is not much change in the environment around the acceptor, the observed λ is believed to be because of "internal" reorganization rather than "solvent" reorganization. A similarity exists between the capsular assembly investigated here and glass and crystals at low temperature where the medium is rigid. The estimated electronic coupling (V_el) implies the existence of interaction between the donor and the acceptor through the capsular wall. Existence of such an interaction is also suggested by ¹H NMR spectra. Results of this study suggest that molecules present within a confined space could be activated from outside. This provides an opportunity to probe the reactivity and dynamics of radical ions within an organic capsule.

Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction

The iron storage protein bacterioferritin (Bfr) binds up to 12 hemes b at specific sites in its protein shell. The heme b can be substituted with the photosensitizer Zn(II)-protoporphyrin IX (ZnPP), and photosensitized reductive iron release from the ferric oxyhydroxide {[FeO(OH)]n} core inside the ZnPP-Bfr protein shell was demonstrated [Cioloboc, D., et al. (2018) Biomacromolecules 19, 178-187]. This report describes the X-ray crystal structure of ZnPP-Bfr and the effects of loaded iron on the photophysical properties of the ZnPP. The crystal structure of ZnPP-Bfr shows a unique six-coordinate zinc in the ZnPP with two axial methionine sulfur ligands. Steady state and transient ultraviolet-visible absorption and luminescence spectroscopies show that irradiation with light overlapping the Soret absorption causes oxidation of ZnPP to the cation radical ZnPP•+ only when the ZnPP-Bfr is loaded with [FeO(OH)]n. Femtosecond transient absorption spectroscopy shows that this photooxidation occurs from the singlet excited state (1ZnPP*) on the picosecond time scale and is consistent with two oxidizing populations of Fe3+, which do not appear to involve the ferroxidase center iron. We propose that [FeO(OH)]n clusters at or near the inner surface of the protein shell are responsible for ZnPP photooxidation. Hopping of the photoinjected electrons through the [FeO(OH)]n would effectively cause migration of Fe2+ through the inner cavity to pores where it exits the protein. Reductive iron mobilization is presumed to be a physiological function of Bfrs. The phototriggered Fe3+ reduction could be used to identify the sites of iron mobilization within the Bfr protein shell.

Structural, Photophysical, and Photochemical Characterization of Zinc Protoporphyrin IX in a Dimeric Variant of an Iron Storage Protein: Insights into the Mechanism of Photosensitized H2 Generation

Some of us have previously reported the preparation of a dimeric form of the iron storage protein, bacterioferritin (Bfr), in which the native heme b is substituted with the photosensitizer, Zn(II)-protoporphyrin IX (ZnPP-Bfr dimer). We further showed that the ZnPP-Bfr dimer can serve as a photosensitizer for platinum-catalyzed H₂ generation in aqueous solution without the usually added electron relay between photosensitizer and platinum ( Clark , E. R. , Inorg. Chem. 2017 , 56 , 4584 - 4593 ). We proposed reductive or oxidative quenching pathways involving the ZnPP anion radical (ZnPP^•-) or the ZnPP cation radical, (ZnPP^•+), respectively. The present report describes structural, photophysical, and photochemical properties of the ZnPP in the ZnPP-Bfr dimer. X-ray absorption spectroscopic studies at 10 K showed a mixture of five- and six-coordinated Zn centers with axial coordination by one long Zn-SγMet distance of ∼2.8 Å and ∼40% having an additional shorter Zn-S distance of ∼2.4 Å, in addition to the expected 4 nitrogen atom coordination from the porphyrin. The ZnPP in ZnPP-Bfr dimer was prone to photosensitized oxidation to ZnPP^•+. The ZnPP^•+ was rapidly reduced by ascorbic acid, which we previously determined was essential for photosensitized H₂ production in this system. These results are consistent with an oxidative quenching pathway involving electron transfer from ³ZnPP* to platinum, which may be assisted by a flexible ZnPP axial coordination sphere. However, the low quantum yield for H₂ production (∼1%) in this system could make reductive quenching difficult to detect, and can, therefore, not be completely ruled out. The ZnPP-Bfr dimer provides a simple but versatile framework for mechanistic assessment and optimization of porphyrin-photosensitized H₂ generation without an electron relay between porphyrin and the platinum catalyst.

Ultrafast Vibrational Cooling Inside of a Molecular Container

Vibrational cooling of azulene encapsulated in a hemicarcerand molecular container was studied by pump-probe spectroscopy. Within 1.5 ps of excitation of azulene to the S₁ state, rapid internal conversion through a conical intersection leads to the formation of a vibrationally hot (∼1080 K) ground state, the subsequent cooling of which can be monitored by tracking the evolution of the red-shifted hot band at the edge of the ground-state absorption. It was found that the cooling of the hot S₀ state of azulene in the host-guest complex (hemicarceplex) is 2-4 times faster than that in common organic solvents. Such large acceleration points to a high density of matching vibrational modes and efficient mechanical coupling between the guest and the host. The experimental observations were fully corroborated by the results of molecular dynamics simulations.

Choosing sides: unusual ultrafast charge transfer pathways in an asymmetric electron-accepting cyclophane that binds an electron donor

Photo-driven electron transfer is faster from an electron donor guest to the harder to reduce acceptor in an asymmetric cyclophane host.

Constructing functional molecular systems for solar energy conversion and quantum information science requires a fundamental understanding of electron transfer in donor–bridge–acceptor (D–B–A) systems as well as competitive reaction pathways in acceptor–donor–acceptor (A–D–A) and acceptor–donor–acceptor′ (A–D–A′) systems. Herein we present a supramolecular complex comprising a tetracationic cyclophane having both phenyl-extended viologen (ExV²⁺) and dipyridylthiazolothiazole (TTz²⁺) electron acceptors doubly-linked by means of two p-xylylene linkers (TTzExVBox⁴⁺), which readily incorporates a perylene (Per) guest in its cavity (Per ⊂ TTzExVBox⁴⁺) to establish an A–D–A′ system, in which the ExV²⁺ and TTz²⁺ units serve as competing electron acceptors with different reduction potentials. Photoexcitation of the Per guest yields both TTz⁺˙–Per⁺˙–ExV²⁺ and TTz²⁺–Per⁺˙–ExV⁺˙ in <1 ps, while back electron transfer in TTz²⁺–Per⁺˙–ExV⁺˙ proceeds via the unusual sequence TTz²⁺–Per⁺˙–ExV⁺˙ → TTz⁺˙–Per⁺˙–ExV²⁺ → TTz²⁺–Per–ExV²⁺. In addition, selective chemical reduction of TTz²⁺ gives Per ⊂ TTzExVBox³⁺˙, turning the complex into a D–B–A system in which photoexcitation of TTz⁺˙ results in the reaction sequence ²*TTz⁺˙–Per–ExV²⁺ → TTz²⁺–Per–ExV⁺˙ → TTz⁺˙–Per–ExV²⁺. Both reactions TTz²⁺–Per⁺˙–ExV⁺˙ → TTz⁺˙–Per⁺˙–ExV²⁺ and TTz²⁺–Per–ExV⁺˙ → TTz⁺˙–Per–ExV²⁺ occur with a (16 ± 1 ps)^–1 rate constant irrespective of whether the bridge molecule is Per⁺˙ or Per. These results are explained using the superexchange mechanism in which the ionic states of the perylene guest serve as virtual states in each case and demonstrate a novel supramolecular platform for studying the effects of bridge energetics within D–B–A systems.

Bidirectional Electron-Transfer in Polypeptides with Various Secondary Structures

The protein-mediated bidirectional electron transfer (ET) is the foundation of protein molecular wire, and plays an important role in the rapid detection of oxo-guanine-adenine DNA mismatches by MutY glycosylase. However, the influences of structural transitions on bidirectional ET are still not clear. In this work, the modified through-bond coupling (MTBC) model was further refined to correlate the structural transition and ET rate more quantitatively. With this model, various polyglycine structures (3₁₀-helix, α-helix, β-sheets, linear, polyproline helical I and II) were studied to explore the influences of structural transitions on bidirectional ET. It was found that the HOMO-LUMO gaps (ΔE) in CN (from the carboxyl to amino terminus) direction are much lower than that in opposite direction, except for polypro I. However, with the equal tunneling energy, the differences between bidirectional ET rates are slight for all structures. In structural transitions, we found that the ET rates are not only affected by the Ramachandran angles, but also correlated to the alignment of C = O vectors, the alignment of peptide planes and the rearrangement of other structure factors. The detailed information can be used to rationalize the inhomogeneous ET across different protein structures and design more efficient protein molecular wires.

Supramolecular Photochemistry in Solution and on Surfaces: Encapsulation and Dynamics of Guest Molecules and Communication between Encapsulated and Free Molecules

Supramolecular assemblies that help to preorganize reactant molecules have played an important role in the development of concepts related to the control of excited-state processes. This has led to a persistent search for newer supramolecular systems (hosts), and this review briefly presents our work with octa acid (OA) to a host to control excited-state processes of organic molecules. Octa acid, a water-soluble host, forms 1:1, 2:1, and 2:2 (host-guest) complexes with various organic molecules. A majority of the guest molecules are enclosed within a capsule made up of two molecules of OA whereas OA by itself remains as a monomer or aggregates. Luminescence and (1)H NMR spectroscopy help to characterize the structure and dynamics of these host-guest complexes. The guest molecule as well as the host-guest complex as a whole undergoes various types of motion, suggesting that the guests possess freedom inside the confined space of the octa acid capsule. In addition, the confined guests are not isolated but are able to communicate (energy, electron, and spin) with molecules present closer to the capsule. The host-guest complexes are stable even on solid surfaces such as silica, clay, α-Zr phosphate, TiO2, and gold nanoparticles. This opens up new opportunities to explore the interaction between confined guests and active surfaces of TiO2 and gold nanoparticles. In addition, this allows the possibility of performing energy and electron transfer between organic molecules that do not adsorb on inert surfaces of silica, clay, or α-Zr phosphate. The results summarized here, in addition to providing a fundamental understanding of the behavior of molecules in a confined space provided by the host OA, are likely to have a long-range effect on the capture and release of solar energy.

Bidirectional Photoinduced Electron Transfer in Ruthenium(II)-Tris-bipyridyl-Modified PpcA, a Multi-heme c-Type Cytochrome from Geobacter sulfurreducens

PpcA, a tri-heme cytochrome c7 from Geobacter sulfurreducens, was investigated as a model for photosensitizer-initiated electron transfer within a multi-heme "molecular wire" protein architecture. Escherichia coli expression of PpcA was found to be tolerant of cysteine site-directed mutagenesis, demonstrated by the successful expression of natively folded proteins bearing cysteine mutations at a series of sites selected to vary characteristically with respect to the three -CXXCH- heme binding domains. The introduced cysteines readily reacted with Ru(II)-(2,2'-bpy)2(4-bromomethyl-4'-methyl-2,2'-bipyridine) to form covalently linked constructs that support both photo-oxidative and photo-reductive quenching of the photosensitizer excited state, depending upon the initial heme redox state. Excited-state electron-transfer times were found to vary from 6 × 10(-12) to 4 × 10(-8) s, correlated with the distance and pathways for electron transfer. The fastest rate is more than 10(3)-fold faster than previously reported for photosensitizer-redox protein constructs using amino acid residue linking. Clear evidence for inter-heme electron transfer within the multi-heme protein is not detected within the lifetimes of the charge-separated states. These results demonstrate an opportunity to develop multi-heme c-cytochromes for investigation of electron transfer in protein "molecular wires" and to serve as frameworks for metalloprotein designs that support multiple-electron-transfer redox chemistry.

Symmetrized photoinitiated electron flow within the [myoglobin:cytochrome b₅] complex on singlet and triplet time scales: energetics vs dynamics

We report here that photoinitiated electron flow involving a metal-substituted (M = Mg, Zn) myoglobin (Mb) and its physiological partner protein, cytochrome b5 (cyt b5) can be "symmetrized": the [Mb:cyt b5] complex stabilized by three D/E → K mutations on Mb (D44K/D60K/E85K, denoted MMb) exhibits both oxidative and reductive ET quenching of both the singlet and triplet photoexcited MMb states, the direction of flow being determined by the oxidation state of the cyt b5 partner. The first-excited singlet state of MMb ((1)MMb) undergoes ns-time scale reductive ET quenching by Fe(2+)cyt b5 as well as ns-time scale oxidative ET quenching by Fe(3+)cyt b5, both processes involving an ensemble of structures that do not interconvert on this time scale. Despite a large disparity in driving force favoring photooxidation of (1)MMb relative to photoreduction (δ(-ΔG(0)) ≈ 0.4 eV, M = Mg; ≈ 0.2 eV, M = Zn), for each M the average rate constants for the two reactions are the same within error, (1)k(f) > 10(8) s(-1). This surprising observation is explained by considering the driving-force dependence of the Franck-Condon factor in the Marcus equation. The triplet state of the myoglobin ((3)MMb) created by intersystem crossing from (1)MMb likewise undergoes reductive ET quenching by Fe(2+)cyt b5 as well as oxidative ET quenching by Fe(3+)cyt b5. As with singlet ET, the rate constants for oxidative ET quenching and reductive ET quenching on the triplet time scale are the same within error, (3)k(f) ≈ 10(5) s(-1), but here the equivalence is attributable to gating by intracomplex conversion among a conformational ensemble.

Multimerization of solution-state proteins by tetrakis(4-sulfonatophenyl)porphyrin

Surface binding and interactions of anionic porphyins bound to cationic proteins have been studied for nearly three decades and are relevant as models for protein surface molecular recognition and photoinitiated electron transfer. However, interpretation of data in nearly all reports explicitly or implicitly assumed interaction of porphyrin with monodisperse proteins in solutions. In this report, using small-angle X-ray scattering with solution phase samples, we demonstrate that horse heart cytochrome (cyt) c, triheme cytochrome c7 PpcA from Geobacter sulfurreducens, and hen egg lysozyme multimerize in the presence of zinc tetrakis(4-sulfonatophenyl)porphyrin (ZnTPPS). Multimerization of cyt c showed a pH dependence with a stronger apparent binding affinity under alkaline conditions and was weakened in the presence of a high salt concentration. Ferric-cyt c formed complexes larger than those formed by ferro-cyt c. Free base TPPS and FeTPPS facilitated formation of complexes larger than those of ZnTPPS. No increase in protein aggregation state for cationic proteins was observed in the presence of cationic porphyrins. All-atom molecular dynamics simulations of cyt c and PpcA with free base TPPS corroborated X-ray scattering results and revealed a mechanism by which the tetrasubstituted charged porphyrins serve as bridging ligands nucleating multimerization of the complementarily charged protein. The final aggregation products suggest that multimerization involves a combination of electrostatic and hydrophobic interactions. The results demonstrate an overlooked complexity in the design of multifunctional ligands for protein surface recognition.

Zinc-substituted cytochrome P450cam: characterization of protein conformers F420 and F450 by photoinduced electron transfer

Metal substitution of heme proteins is widely applied in the study of biologically relevant electron transfer (ET) reactions. It has been shown that many modified proteins remain in their native conformation and can provide useful insights into the molecular mechanism of electron transfer between the native protein and its substrates. We investigated ET reactions between zinc-substituted cytochrome P450(cam) and small organic compounds such as quinones and ferrocene, which are capable of accessing the protein's hydrophobic channel and binding close to the active site, like its native substrate, camphor. Following the substitution method developed by Gunsalus and co-workers [Wagner, G. C., et al. (1981) J. Biol. Chem. 256, 6262-6265], we have identified two dominant forms of the zinc-substituted protein, F450 and F420, that exhibit different photophysical and photochemical properties. The ET behavior of F420 suggests that hydrophobic redox-active ligands are able to penetrate the hydrophobic channel and place themselves in the direct vicinity of the Zn-porphyrin. In contrast, the slower ET quenching rates observed in the case of F450 indicate that the association is weak and occurs outside of the protein channel. Therefore, we conclude that F420 corresponds to the open structure of the native cytochrome P450(cam) while F450 has a closed or partially closed channel that is characteristic of the camphor-containing cytochrome P450(cam). The existence of two distinct conformers of Zn-bound P450(cam) is consistent with the findings of Goodin and co-workers [Lee, Y.-T., et al. (2010) Biochemistry 49, 3412-3419] and has significant consequences for future electron transfer studies on this popular metalloenzyme.

Multicomponent assembly of cavitand-based polyacylhydrazone nanocapsules

The thermodynamically controlled syntheses of different di-, tetra-, and hexacavitand polyacylhydrazone nanocapsules are reported. [2+4]-, [4+8]-, and [6+12]-nanocapsules assemble upon reacting a tetraformyl cavitand with two equivalents of isophthalic dihydrazide, or terephthalic dihydrazide in the presence of trifluoroacetic acid, whereby the building blocks are linked together through 8, 16, or 24 newly formed acylhydrazone bonds. Futhermore, the reaction of the tetraformylcavitands with different trigonal planar trihydrazides, simultaneously leads to the formation of [2+4]- and [6+8]-nanocapsules in varying ratios that depend on the cavitand to trihydrazide ratio and the nature of the cavitand and trihydrazide building blocks. The product ratios are rationalized with the different conformational strain of the acylhydrazone linkages in these nanocapsules. Diffusion NMR experiments with the hexacavitand polyacylhydrazone nanocapsules yield solvodynamic radii that range from 1.6 to 2.5 nm, consistent with estimates from force field calculations, and support, that these capsules have solvent filled, spherical interiors, the sizes of which approaches those of smaller proteins.