Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Intermolecular Enantioselective Amination Reactions Mediated by Visible Light and a Chiral Iron Porphyrin Complex

In the presence of 1 mol % of a chiral iron porphyrin catalyst, various 3-arylmethyl-substituted 2-quinolones and 2-pyridones underwent an enantioselective amination reaction (20 examples; 93-99 % ee). The substrates were used as the limiting reagents, and fluorinated aryl azides (1.5 equivalents) served as nitrene precursors. The reaction is triggered by visible light which allows a facile dediazotation at ambient temperature. The selectivity of the reaction is governed by a two-point hydrogen bond interaction between the ligand of the iron catalyst and the substrate. Hydrogen bonding directs the amination to a specific hydrogen atom within the substrate that is displaced by the nitrogen substituent either in a concerted fashion or by a rebound mechanism.

Quantifying near-symmetric molecular distortion using symmetry-coordinate structural decomposition

We imagine molecules to be perfect, but rigidified units can be designed to bend from their ideal shape, discarding their symmetric elements as they progress through vibrations and larger, more permanent distortions. The shape of molecules is either simulated or measured by crystallography and strongly affects chemical properties but, beyond an image or tabulation of atom-to-atom distances, little is often discussed of the accessed conformation. We have simplified the process of shape quantification across multiple molecular types with a new web-accessible program - SCSD - through which a molecular subunit possessing near-symmetry can be dissected into symmetry coordinates with ease. This parameterization allows a common set of numbers for comparing and understanding molecular shape, and is a simple method for database analysis; this program is available at https://www.kingsbury.id.au/scsd.

Porphyrin Atropisomerism as a Molecular Engineering Tool in Medicinal Chemistry, Molecular Recognition, Supramolecular Assembly, and Catalysis

Porphyrin atropisomerism, which arises from restricted σ-bond rotation between the macrocycle and a sufficiently bulky substituent, was identified in 1969 by Gottwald and Ullman in 5,10,15,20-tetrakis(o-hydroxyphenyl)porphyrins. Henceforth, an entirely new field has emerged utilizing this transformative tool. This review strives to explain the consequences of atropisomerism in porphyrins, the methods which have been developed for their separation and analysis and present the diverse array of applications. Porphyrins alone possess intriguing properties and a structure which can be easily decorated and molded for a specific function. Therefore, atropisomerism serves as a transformative tool, making it possible to obtain even a specific molecular shape. Atropisomerism has been thoroughly exploited in catalysis and molecular recognition yet presents both challenges and opportunities in medicinal chemistry.

Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design

Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.

Molecular Symmetry and Art: Visualizing the Near-Symmetry of Molecules in Piet Mondrian's De Stijl

Symmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties. We, as chemists, are comfortable with pictorial representations of structure, in which some nuance is lost-investigating molecular shape numerically by looking at how closely it fits a reference, such as a plane, or a set of vectors or coordinates, is informative, though far from engaging. Often relationships between chemical structure and derived values are obscured. Taking our inspiration from Piet Mondrian's Compositions, we have depicted the symmetry information encoded within 3D data as blocks of color, to show clearly how chemical arguments and resultant molecular distortion may contribute to symmetry. Great art gives us a new perspective on the world; as a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, understanding how their shape and properties are intertwined.

Porphyrin-based covalent organic frameworks from design, synthesis to biological applications

Covalent organic frameworks (COFs) constitute a class of highly functional porous materials composed of lightweight elements interconnected by covalent bonds, characterized by structural order, high crystallinity, and large specific surface area. The integration of naturally occurring porphyrin molecules, renowned for their inherent rigidity and conjugate planarity, as building blocks in COFs has garnered significant attention. This strategic incorporation addresses the limitations associated with free-standing porphyrins, resulting in the creation of well-organized porous crystal structures with molecular-level directional arrangements. The unique optical, electrical, and biochemical properties inherent to porphyrin molecules endow these COFs with diversified applications, particularly in the realm of biology. This review comprehensively explores the synthesis and modulation strategies employed in the development of porphyrin-based COFs and delves into their multifaceted applications in biological contexts. A chronological depiction of the evolution from design to application is presented, accompanied by an analysis of the existing challenges. Furthermore, this review offers directional guidance for the structural design of porphyrin-based COFs and underscores their promising prospects in the field of biology.

Spin-Flip via Subtle Electronic Perturbation in Axially Ligated Diiron(III) Porphyrin Dimer

Spin state switching in the metal center is a crucial phenomenon in many enzymatic reactions in biology. The spin state alteration, a critical step in cytochrome P450 catalysis, is driven most likely through a weak perturbation upon substrate binding in the enzyme, which is still not well clarified. In the current work, the spin state transition of iron(III) from high to intermediate via an admixed state is observed upon a subtle electronic perturbation to the sulphonate moieties coordinated axially to a diiron(III)porphyrin dimer. While electron-donating substituents stabilize the high-spin state of iron(III), strongly electron-withdrawing groups stabilize an intermediate-spin state, whereas the moderate electron-withdrawing nature of axial ligands resulted in an admixed state. Confirmation of the molecular structures and their spin states have been made utilizing single-crystal X-ray structure analysis, Mössbauer, magnetic, EPR, and 1H NMR spectroscopic investigations. The position of the signals of the porphyrin macrocycle in the paramagnetic 1H NMR is found to be very characteristic of the spin state of the iron center in solution. The Curie plot for the pure high-spin complexes shows the signals' temperature dependency in line with the Curie law. Conversely, the pure intermediate-spin state of iron exhibits an anti-Curie temperature dependence, whereas the admixed-spin state of iron displays significant curvature of the lines in the Curie plot. An extensive DFT analysis displays a linear dependence between the energy difference between dx 2 - y 2 ${{_{x{^{2}}- y{^{2}}}}}$ and dz 2 ${{_{z{^{2}}}}}$ orbital versus Fe-Npor distance for the complexes reported here. Furthermore, a strong linear correlation between the Fe-O distance and the spin density over the oxygen atom, as well as the Fe-Npor distance for the complexes, has been observed. Thus, a slight electronic perturbation at the axial ligand of the diheme resulted in a large change in the electronic structures with a spin-flip. This is at par with the metalloenzymes, which employ minute perturbations around the periphery of the active sites, leading to spin state transitions.

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restraints for nonprotein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in chlorophyll proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C2 symmetry of photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and cryogenic electron microscopy PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to a 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restraints play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested from cyanobacteria to algae. These results highlight both the opportunities and limitations inherent in structure-based analyses of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

Reversible disassembly-reassembly of C-phycocyanin in pressurization-depressurization cycles of high hydrostatic pressure

Hydrostatic pressure can reversibly modulate protein-protein and protein-chromophore interactions of C-phycocyanin (C-PC) from Spirulina platensis. Small-angle X-ray scattering combined with UV-Vis spectrophotometry and protein modeling was used to explore the color and structural changes of C-PC under high pressure conditions at different pH levels. It was revealed that pressures up to 350 MPa were enough to fully disassemble C-PC from trimers to monomers at pH 7.0, or from monomers to detached subunits at pH 9.0. These disassemblies were accompanied by protein unfolding that caused these high-pressure induced structures to be more extended. These changes were reversible following depressurization. The trimer-to-monomer transition proceeded through a collection of previously unrecognized, L-shaped intermediates resembling C-PC dimers. Additionally, pressurized C-PC showed decayed Q-band absorption and fortified Soret-band absorption. This was evidence that the folded tetrapyrroles, which had folded at ambient pressure, formed semicyclic unfolded conformations at a high pressure. Upon depressurization, the peak intensity and shift all recovered stepwise, showing pressure can precisely manipulate C-PC's structure as well as its color. Overall, a protein-chromophore regulatory theory of C-PC was unveiled. The pressure-tunability could be harnessed to modify and stabilize C-PC's structure and photochemical properties for designing new delivery and optical materials.

Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species

Understanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III-coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin-dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x-ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.

Diversifying the functions of heme proteins with non-porphyrin cofactors

Heme proteins perform diverse biochemical functions using a single iron porphyrin cofactor. This versatility makes them attractive platforms for the development of new functional proteins. While directed evolution and metal substitution have expanded the properties, reactivity, and applications of heme proteins, the incorporation of porphyrin analogs remains an underexplored approach. This review discusses the replacement of heme with non-porphyrin cofactors, such as porphycene, corrole, tetradehydrocorrin, phthalocyanine, and salophen, and the attendant properties of these conjugates. While structurally similar, each ligand exhibits distinct optical and redox properties, as well as unique chemical reactivity. These hybrids serve as model systems to elucidate the effects of the protein environment on the electronic structure, redox potentials, optical properties, or other features of the porphyrin analog. Protein encapsulation can confer distinct chemical reactivity or selectivity of artificial metalloenzymes that cannot be achieved with the small molecule catalyst alone. Additionally, these conjugates can interfere with heme acquisition and uptake in pathogenic bacteria, providing an inroad to innovative antibiotic strategies. Together, these examples illustrate the diverse functionality that can be achieved by cofactor substitution. The further expansion of this approach will access unexplored chemical space, enabling the development of superior catalysts and the creation of heme proteins with emergent properties.

Diheme cytochromes: Effect of mixed-axial ligation on the electronic structure and electrochemical properties with cobalt porphyrin dimer

A series of six-coordinate diCo(III) porphyrin dimers, as synthetic analogues of diheme cytochromes, have been reported here having bis(imidazole), bis(pyridine) and mixed thiophenolate-pyridine/imidazole axial ligands. In the X-ray structures of bis(imidazole) and bis(pyridine) complexes, the axial ligands are in perpendicular orientation while they are parallelly oriented in their monomeric analog. The porphyrin rings are also highly ruffle-distorted in dimer but planar in monomer which reflect the effect of intramolecular interaction between two Co(porphyrin) units in dimers. In the X-ray structure of diCo(III) thiophenolate-pyridine mixed-ligated complex, the axial Co-S and Co-N(py) distances are 2.256(1) and 2.063(2) Å, respectively. The Co-N(py) distance of 2.063(2) Å is much longer than the distances of 1.961(3) and 1.972(3) Å observed in bis(pyridine) complex and the Co-S distance is larger than Co-N(py) in the mixed ligated complex which results in a displacement of Co by 0.15 Å towards the pyridine ligand from the mean porphyrin plane. Indeed, this is the first X-ray structure of a metalloporphyrin with mixed thiophenolate-pyridine axial ligands. The effect of mixed-axial ligation is demonstrated by a blue-shift of the Soret band in the UV-visible spectroscopy and also a positive shift of the Co(III)/Co(II) redox couple as compared to their bis(pyridine) analogue. The redox potentials are shifted to a large negative value just upon replacing the metal from iron to cobalt. The present investigation emphasizes the role of axial ligation, metal ions, and also the effect of heme-heme interaction in controlling the spectral and electrochemical properties.

Synthesis and Self-Assembly of β-Octa[(4-Diethoxyphosphoryl)phenyl]porphyrins

The β-substituted porphyrinoids commonly used to form functional assembled systems in nature yet are still scarcely used in material chemistry probably due to the laborious synthesis of these compounds. In this work, β-octa[(4-diethoxyphosphoryl)phenyl]porphyrin (2HOPPP) and its metal (Zn(II), Cd(II), Cu(II), and Ni(II)) complexes were prepared in good yields. These highly soluble chromophores were characterized in solution using spectroscopic (NMR, UV-vis, fluorescence), electrochemical, and spectroelectrochemical methods. Attachment of the electron-deficient residue (ArP(O)(OEt)₂) to the porphyrin macrocycle leads to easier reductions and harder oxidations of the macrocycle for all complexes studied as compared to corresponding meso-tetra[4-(diethoxyphosphoryl)phenyl]porphyrin derivatives reported previously. We demonstrated that the strong electron-deficient character of the MOPPP porphyrins results principally from the increase in the number of electron-withdrawing groups at the periphery of the tetrapyrrolic macrocycle. Electron-deficient porphyrins are highly required in supramolecular and material chemistry in part due to their ability to form supramolecular assemblies via the coordination of axial ligands to the central metal atom. According to single-crystal X-ray data, ZnOPPP forms in the crystalline phase dimers in which each of the two tetrapyrrolic macrocycles is connected through an unusual combination of hydrogen bonding of two phosphoryl groups and the water molecules axially coordinated to the zinc atom of the partner molecule. The involvement of water molecules in porphyrin binding allows for an increase of distance between two porphyrin mean N₄ planes, up to 4.478 Å. The offset of phosphoryl groups attached to the macrocycle through a 1,4-phenylene spacer withdraws the whole porphyrin macrocycle of one molecule from spatial overlap with the macrocycle of a partner molecule and increases the Zn-Zn distance up to 10.372 Å. This still unknown type of porphyrin dimers allows one to get deeper insights into the organization of naturally occurring tetrapyrrolic macrocycles. ZnOPPP also forms a labile dimeric complex in 5.3 × 10^-7-5.8 × 10^-5 M chloroform solutions. In contrast, other complexes prepared in this work exist as monomeric species under these experimental conditions. The self-association constant of ZnOPPP has been determined by electronic absorption spectroscopy.

Control of spin coupling through a redox-active bridge in a dinickel(II) porphyrin dimer: step-wise oxidations enable isolations of a chlorin-porphyrin heterodimer and a dication diradical with a singlet ground state

A dinickel(II)porphyrin dimer has been used here in which the redox-active pyrrole-moiety, similar to the tryptophan residue in diheme enzymes such as MauG and bCcP, has been placed between two Ni(II)porphyrin centers connected via a flexible, but unconjugated methylene bridge. This arrangement provides a large physical separation between the two metal centers and thus displays almost no communication between them through the bridge. Upon treatment with DDQ as an oxidant, the dinickel(II) porphyrin dimer slowly gets converted into an indolizinium-fused chlorin-porphyrin heterodimer. However, oxidations of the dinickel(II) porphyrin dimer up to two oxidizing equivalents using oxidants such as AgSbF₆ and FeCl₃ resulted in the formation of a dication diradical complex. Interestingly, in order to stabilize such a highly oxidized dication diradical, two non-conjugated methylene spacers undergo facile 2e^-/-2H⁺ oxidation to make the bridge fully π-conjugated for promoting through-bond communication. Through the oxidized and conjugated bridge, two porphyrin π-cation radicals display considerable communications leading to an efficient intramolecular spin coupling to form a singlet state. Interestingly, the redox-active nature of the bridge controls the electronic communication just by simple oxidation or reduction, and thereby, acts as a molecular switch for efficient magnetic relay.

Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation

Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV-vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies.

Nonplanar porphyrins: synthesis, properties, and unique functionalities

Porphyrins are variously substituted tetrapyrrolic macrocycles, with wide-ranging biological and chemical applications derived from metal chelation in the core and the 18π aromatic surface. Under suitable conditions, the porphyrin framework can deform significantly from regular planar shape, owing to steric overload on the porphyrin periphery or steric repulsion in the core, among other structure modulation strategies. Adopting this nonplanar porphyrin architecture allows guest molecules to interact directly with an exposed core, with guest-responsive and photoactive electronic states of the porphyrin allowing energy, information, atom and electron transfer within and between these species. This functionality can be incorporated and tuned by decoration of functional groups and electronic modifications, with individual deformation profiles adapted to specific key sensing and catalysis applications. Nonplanar porphyrins are assisting breakthroughs in molecular recognition, organo- and photoredox catalysis; simultaneously bio-inspired and distinctly synthetic, these molecules offer a new dimension in shape-responsive host-guest chemistry. In this review, we have summarized the synthetic methods and design aspects of nonplanar porphyrin formation, key properties, structure and functionality of the nonplanar aromatic framework, and the scope and utility of this emerging class towards outstanding scientific, industrial and environmental issues.

Ratiometric Oxygen Sensing with H-NOX Protein Conjugates

Ratiometric sensors are self-referencing constructs that are functional in cells and tissues, and the read-out is independent of sensor concentration. One strategy for ratiometric sensing is to utilize two-color emission, where one component possesses analyte-dependent emission and the other is independent of analyte concentration, serving as an internal standard. In this way, the intensity ratio of the two components is a quantitative measure of the analyte. In this study, protein-based ratiometric oxygen sensors are prepared using the heme nitric oxide/oxygen-binding protein (H-NOX) from the thermophilic bacterium Caldanaerobacter subterraneus. The native heme cofactor is replaced with a Pd(II) or Pt(II) porphyrin as the oxygen-responsive phosphor. Mutagenesis is performed to incorporate a cysteine residue on the protein surface for thiol/maleimide coupling of the oxygen-insensitive dye, which serves as a Förster resonance energy transfer (FRET) donor for the porphyrin. While both Pd(II)- and Pt(II)-based sensors are responsive over biologically relevant ranges, the Pd sensor exhibits greater sensitivity at lower oxygen concentrations. Together, these sensors represent a new class of protein-based ratiometric oxygen sensors, and the modular platform allows the oxygen sensitivity to be tailored for a specific application. This proof-of-principle study has identified the key considerations and optimal methodologies to develop and subsequently refine protein-based ratiometric oxygen sensors.

Highly Oxidized Cobalt Porphyrin Dimer: Control of Spin Coupling via a Bridge

A cobalt porphyrin dimer is constructed in which two Co(II)porphyrins are connected covalently through a redox-active diethylpyrrole moiety via a flexible but "nonconjugated" methylene bridge. Upon oxidation with even a mild oxidant such as iodine, each cobalt(II) center and porphyrin ring undergo 1e^- oxidation, leading to the formation of a 4e^--oxidized cobalt(III)porphyrin dication diradical complex. Other oxidants such as Cl₂ and Br₂ also produce similar results. To stabilize such highly oxidized dication diradicals, the "nonconjugated" methylene spacer undergoes a facile and spontaneous oxidation to form a methine group with a drastic structural change, thereby making the bridge fully π-conjugated and enabling through-bond communication. This results in a strong spin coupling between two π-cation radicals which stabilizes the singlet state. The experimental observations are also strongly supported by extensive density functional theory calculations. The present study highlights the crucial role played by the nature of the bridge in the long-range electronic communication.

Metal Complexes of Singly, Doubly and Triply Linked Porphyrins and Corroles: An Insight into the Physicochemical Properties

Metal complexes of multi‐porphyrins and multi‐corroles are unique systems that display a host of extremely interesting properties. Availability of free meso and β positions allow formation of different types of directly linked bis‐porphyrins giving rise to intriguing optical and electronic properties. While the fields of metalloporphyrin and corroles monomer have seen exponential growth in the last decades, the chemistry of metal complexes of bis‐porphyrins and bis‐corroles remain rather underexplored. Therefore, the impact of covalent linkages on the optical, electronic, (spectro)electrochemical, magnetic and electrocatalytic activities of metal complexes of bis‐porphyrins and ‐corroles has been summarized in this review article. This article shows that despite the (still) somewhat difficult synthetic access to these molecules, their extremely exciting properties do make a strong case for pursuing research on these classes of compounds.

Detection of Hypertension-Induced Changes in Erythrocytes by SERS Nanosensors

Surface-enhanced Raman spectroscopy (SERS) is a promising tool that can be used in the detection of molecular changes triggered by disease development. Cardiovascular diseases (CVDs) are caused by multiple pathologies originating at the cellular level. The identification of these deteriorations can provide a better understanding of CVD mechanisms, and the monitoring of the identified molecular changes can be employed in the development of novel biosensor tools for early diagnostics. We applied plasmonic SERS nanosensors to assess changes in the properties of erythrocytes under normotensive and hypertensive conditions in the animal model. We found that spontaneous hypertension in rats leads (i) to a decrease in the erythrocyte plasma membrane fluidity and (ii) to a decrease in the mobility of the heme of the membrane-bound hemoglobin. We identified SERS parameters that can be used to detect pathological changes in the plasma membrane and submembrane region of erythrocytes.

Corrole–protein interactions in H-NOX and HasA

Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.

Steric Repulsion Induced Conformational Switch in Supramolecular Structures

Inspired by the rigidified architecture of ‘picket‐fence’ systems, we propose a strategy utilizing strain to impose intramolecular tension in already peripherally overcrowded structures leading to selective atropisomeric conversion. Employing this approach, tuneable shape‐persistent porphyrin conformations were acquired exhibiting distinctive supramolecular nanostructures based on the orientation of the peripheral groups. The intrinsic assemblies driven by non‐covalent bonding interactions form supramolecular polymers while encapsulating small molecules in parallel channels or solvent‐accessible voids. The developed molecular strain engineering methodologies combined with synthetic approaches have allowed the introduction of the pivalate units creating a highly strained molecular skeleton. Changes in the absorption spectrum indicated the presence of severe steric repulsions between the peripheral groups which were confirmed by single crystal X‐ray analysis. To release the steric strain introduced by the peripheral units, thermal equilibration strategies were used to selectively convert the most abundant atropisomer to the desirable minor one.

meso-Tetra-(4-pyridyl)porphyrin/palladium(II) complexes as anticancer agents

This study reports the synthesis, structural characterization and cytotoxic activity of four new palladium/pyridylporphyrin complexes, with the general formula {TPyP[PdCl(P-P)]₄}(PF₆)₄, where P-P is 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)butane (dppb) or 1,1'-bis(diphenylphosphino)ferrocene (dppf). The complexes were characterized by elemental analysis, and by FT-IR, UV/Vis, ¹H and ³¹P{¹H} NMR (1D/2D) spectroscopy. The slow evaporation of a methanolic solution of {TPyP[PdCl(dppb)]₄}(PF₆)₄ (in an excess of NaBF₄ salt) resulted in single crystals suitable for X ray diffraction, allowing the determination of the tridimensional structure of this complex, which crystallized in the P2₁/a space group. The cytotoxicity of the complexes against MDA-MB-231 (breast cancer cells) and MCF-10A (non-tumor breast cancer cells), was determined by the colorimetric MTT method, which revealed that all four complexes show selective indexes close to 1.2, lower than that of cisplatin for the same cells (12.12). The interaction of the complexes with CT-DNA was evaluated by UV-visible and viscosity measurements and it was determined that the complexes interact moderately with CT-DNA, probably by H-bonding/π-π stacking and electrostatic interactions.

Chirogenesis in Zinc Porphyrins: Theoretical Evaluation of Electronic Transitions, Controlling Structural Factors and Axial Ligation

In the present work, sixteen different zinc porphyrins (possessing different meso substituents) with and without a chiral guest were modelled using DFT and TD-DFT approaches in order to understand the influence of various controlling factors on electronic circular dichroism (ECD) spectra. Two major aspects are influenced by these factors: excitation energy of the electronic transitions and their intensity. In the case of excitation energy, the influence increases in the following order: orientation of the peripheral substituents Collapse

Key Words

• circular dichroism
• density functional calculations
• porphyrins
• supramolecular chemistry
• transition metals

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MESH Headings Collapse

Grants

• PUTJD749 Estonian Research Council
• PRG399 Estonian Research Council
• 828779 European Union's H2020-FETOPEN
• Estonian Research Council

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Affiliation(s)

Irina Osadchuk Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance
Riina Aav Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
Victor Borovkov Department of Chemistry and BiotechnologySchool of ScienceTallinn University of Technology AddressAkadeemia tee 1512618TallinnEstonia
Eric Clot ICGMUniv MontpellierCNRS, ENSCMMontpellierFrance

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PorphyStruct: A Digital Tool for the Quantitative Assignment of Non-Planar Distortion Modes in Four-Membered Porphyrinoids

PorphyStruct, a new digital tool for the analysis of non‐planar distortion modes of different porphyrinoids, and its application to corrole structures is reported. The program makes use of the normal‐coordinate structure decomposition technique (NSD) and employs sets of normal modes equivalent to those established for porphyrins in order to describe the out‐of‐plane dislocation pattern of perimeter atoms from corroles, norcorroles, porphycenes and other porphyrinoids quantitatively and in analogy to the established terminology. A comparative study of 17 porphyrin structures shows very similar results to the original NSD analysis and no systematic error. Application to corroles is successful and reveals the necessity to implement an extended basis of normal modes for a large share of experimental structures. The results frequently show the concomitant occurence of several modes but remain interpretable. For group XI metal corroles the phenomenon of supersaddling was unravelled, allowing for more in‐depths discussions of structure‐function correlations.

Conformational Control of Chemical Reactivity for Surface-Confined Ru-Porphyrins

We assess the crucial role of tetrapyrrole flexibility in the CO ligation to distinct Ru-porphyrins supported on an atomistically well-defined Ag(111) substrate. Our systematic real-space visualisation and manipulation experiments with scanning tunnelling microscopy directly probe the ligation, while bond-resolving atomic force microscopy and X-ray standing-wave measurements characterise the geometry, X-ray and ultraviolet photoelectron spectroscopy the electronic structure, and temperature-programmed desorption the binding strength. Density-functional-theory calculations provide additional insight into the functional interface. We unambiguously demonstrate that the substituents regulate the interfacial conformational adaptability, either promoting or obstructing the uptake of axial CO adducts.

Zinc- and Cadmium meso-Aryl-Isoporphyrins: Non-Aromatic NIR Dyes with Distinct Conformational Features

A series of pyrrolyl and dipyrrinyl isoporphyrins carrying different phenyl and thienyl groups is reported. The compounds are obtained by a one-pot approach in the presence of a template reagent. Thienyl derivatives gave better yields, and were the only subclass to form with steric hindrance. The structural analyses carried out on compounds 1 and 14 revealed distinct conformational differences which are likely to result from an intramolecular NH… Cl hydrogen bridge of the pyrrolyl subclass. In addition, this hydrogen bridge strongly favors one of the two possible atropisomers. Hindered rotation of the meso-aryl groups is observed only in the cases of methylbenzothienyl derivatives 10 and 15 and leads to the observation of several diastereomers. NIR absorptions up to 923 nm are found throughout. Electrochemical investigations into the 1e- and 2e- reduced species unravel axial ligand exchange dynamics for the zinc isoporphyrin radical, and the probable formation of a zinc phlorinate.

2D Porphyrinic Metal-Organic Frameworks Featuring Rod-Shaped Secondary Building Units

Metal-organic frameworks (MOFs) encompass a rapidly expanding class of materials with diverse potential applications including gas storage, molecular separation, sensing and catalysis. So-called 'rod MOFs', which comprise infinitely extended 1D secondary building units (SBUs), represent an underexplored subclass of MOF. Further, porphyrins are considered privileged ligands for MOF synthesis due to their tunable redox and photophysical properties. In this study, the CuII complex of 5,15-bis(4-carboxyphenyl)-10,20-diphenylporphyrin (H2L-CuII, where H2 refers to the ligand's carboxyl H atoms) is used to prepare two new 2D porphyrinic rod MOFs PROD-1 and PROD-2. Single-crystal X-ray analysis reveals that these frameworks feature 1D MnII- or CoII-based rod-like SBUs that are coordinated by labile solvent molecules and photoactive porphyrin moieties. Both materials were characterised using infrared (IR) spectroscopy, powder X-ray diffraction (PXRD) spectroscopy and thermogravimetric analysis (TGA). The structural attributes of PROD-1 and PROD-2 render them promising materials for future photocatalytic investigations.

Structural effects of meso-halogenation on porphyrins

The use of halogens in the crystal engineering of supramolecular porphyrin assemblies has been a topic of strong interest over the past decades. With this in mind we have characterized a series of direct meso-halogenated porphyrins using single crystal X-ray crystallography. This is accompanied by a detailed conformational analysis of all deposited meso-halogenated porphyrins in the CSD. In this study we have used the Hirshfeld fingerprint plots together with normal-coordinate structural decomposition and determined crystal structures to elucidate the conformation, present intermolecular interactions, and compare respective contacts within the crystalline architectures. Additionally, we have used density functional theory calculations to determine the structure of several halogenated porphyrins. This contrasts conformational analysis with existing X-ray structures and gives a method to characterize samples that are difficult to crystallize. By using the methods outlined above we were able to deduce the impact a meso halogen has on a porphyrin, for example, meso-halogenation is dependent on the type of alternate substituents present when forming supramolecular assemblies. Furthermore, we have designed a method to predict the conformation of halogenated porphyrins, without need of crystallization, using DFT calculations with a high degree of accuracy.

A Dynamic Substrate is Required for MhuD-Catalyzed Degradation of Heme to Mycobilin

The noncanonical heme oxygenase MhuD from Mycobacterium tuberculosis binds a heme substrate that adopts a dynamic equilibrium between planar and out-of-plane ruffled conformations. MhuD degrades this substrate to an unusual mycobilin product via successive monooxygenation and dioxygenation reactions. This article establishes a causal relationship between heme substrate dynamics and MhuD-catalyzed heme degradation, resulting in a refined enzymatic mechanism. UV/vis absorption (Abs) and electrospray ionization mass spectrometry (ESI-MS) data demonstrated that a second-sphere substitution favoring the population of the ruffled heme conformation changed the rate-limiting step of the reaction, resulting in a measurable buildup of the monooxygenated meso-hydroxyheme intermediate. In addition, UV/vis Abs and ESI-MS data for a second-sphere variant that favored the planar substrate conformation showed that this change altered the enzymatic mechanism resulting in an α-biliverdin product. Single-turnover kinetic analyses for three MhuD variants revealed that the rate of heme monooxygenation depends upon the population of the ruffled substrate conformation. These kinetic analyses also revealed that the rate of meso-hydroxyheme dioxygenation by MhuD depends upon the population of the planar substrate conformation. Thus, the ruffled heme conformation supports rapid heme monooxygenation by MhuD, but further oxygenation to the mycobilin product is inhibited. In contrast, the planar substrate conformation exhibits altered heme monooxygenation regiospecificity followed by rapid oxygenation of meso-hydroxyheme. Altogether, these data yielded a refined enzymatic mechanism for MhuD where access to both substrate conformations is needed for rapid incorporation of three oxygen atoms into heme yielding mycobilin.

Strategic Synthesis of 'Picket Fence' Porphyrins Based on Nonplanar Macrocycles

Traditional 'picket fence' porphyrin systems have been a topic of interest for their capacity to direct steric shielding effects selectively to one side of the macrocycle. Sterically overcrowded porphyrin systems that adopt macrocycle deformations have recently drawn attention for their applications in organocatalysis and sensing. Here we explore the combined benefits of nonplanar porphyrins and the old molecular design to bring new concepts to the playing field. The challenging ortho-positions of meso-phenyl residues in dodecasubstituted porphyrin systems led us to transition to less hindered para- and meta-sites and develop selective demethylation based on the steric interplay. Isolation of the symmetrical target compound [2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(3,5-dipivaloyloxyphenyl)porphyrin] was investigated under two synthetic pathways. The obtained insight was used to isolate unsymmetrical [2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(2-nitro-5-pivaloyloxyphenyl)porphyrin]. Upon separation of the atropisomers, a detailed single-crystal X-ray crystallographic analysis highlighted intrinsic intermolecular interactions. The nonplanarity of these systems in combination with 'picket fence' motifs provides an important feature in the design of supramolecular ensembles.

UV-trained and metal-enhanced fluorescence of biliverdin and biliverdin nanoparticles

Increasing the fluorescence quantum yield of fluorophores is of great interest for in vitro and in vivo biomedical imaging applications. At the same time, photobleaching and photodegradation resulting from continuous exposure to light are major considerations in the translation of fluorophores from research applications to industrial or healthcare applications. A number of tetrapyrrolic compounds, such as heme and its derivatives, are known to provide fluorescence contrast. In this work, we found that biliverdin (BV), a naturally-occurring tetrapyrrolic fluorophore, exhibits an increase in fluorescence quantum yield, without exhibiting photobleaching or degradation, in response to continuous ultraviolet (UV) irradiation. We attribute this increased fluorescence quantum yield to photoisomerization and conformational changes in BV in response to UV irradiation. This enhanced fluorescence can be further altered by chelating BV with metals. UV irradiation of BV led to an approximately 10-fold increase in its 365 nm fluorescence quantum yield, and the most favorable combination of UV irradiation and metal chelation led to an approximately 18.5-fold increase in its 365 nm fluorescence quantum yield. We also evaluated these stimuli-responsive behaviors in biliverdin nanoparticles (BVNPs) at the bulk-state and single-particle level. We determined that UV irradiation led to an approximately 2.4-fold increase in BVNP 365 nm quantum yield, and the combination of UV irradiation and metal chelation led to up to a 6.75-fold increase in BVNP 365 nm quantum yield. Altogether, these findings suggest that UV irradiation and metal chelation can be utilized alone or in combination to tailor the fluorescence behavior of imaging probes such as BV and BVNPs at selected wavelengths.

Spectral tuning of chlorophylls in proteins - electrostatics vs. ring deformation

In photosynthetic complexes, tuning of chlorophyll light-absorption spectra by the protein environment is crucial to their efficiency and robustness. Recombinant type II water soluble chlorophyll-binding proteins from Brassicaceae (WSCPs) are useful for studying spectral tuning mechanisms due to their symmetric homotetramer structure, and the ability to rigorously modify the chlorophyll's protein surroundings. Our previous comparison of the crystal structures of two WSCP homologues suggested that protein-induced chlorophyll ring deformation is the predominant spectral tuning mechanism. Here, we implement a more rigorous analysis based on hybrid quantum mechanics and molecular mechanics calculations to quantify the relative contributions of geometrical and electrostatic factors to the absorption spectra of WSCP-chlorophyll complexes. We show that when considering conformational dynamics, geometry distortions such as chlorophyll ring deformation accounts for about one-third of the spectral shift, whereas the direct polarization of the electron density accounts for the remaining two-thirds. From a practical perspective, protein electrostatics is easier to manipulate than chlorophyll conformations, thus, it may be more readily implemented in designing artificial protein-chlorophyll complexes.

Classic highlights in porphyrin and porphyrinoid total synthesis and biosynthesis

Porphyrins feature prominently in nature, be it as enzymatic cofactors, electron and exciton shuffles, as photoactive dyes, or as signaling substances. Their involvement in the generation, storage and use of oxygen is pivotal to life, while their photochemical properties are central to the biochemical functioning of plants. When complexed to metals, porphyrins can engage in a multitude of contemporary applications ranging from solar energy generation to serving as catalysts for important chemical reactions. They are also able to function as useful theranostic agents, and as novel materials for a wide range of applications. As such, they are widely considered to be highly valuable molecules, and it almost goes without saying that synthetic organic chemistry has dramatically underpinned all the key advances made, by providing reliable access to them. In fact, strategies for the synthesis of functionalized porphyrins have now reached a state of refinement where pretty well any desired porphyrin can successfully be synthesized with the approaches that are available, including a cornucopia of related macrocycle-modified porphyrinoids. In this review, we are going to illustrate the development of this exciting field by discussing a number of classic syntheses of porphyrins. Our coverage will encompass the natural protoporphyrins and chlorophylls, while also covering general strategies for the synthesis of unsymmetrical porphyrins and chlorins. Various industrial syntheses of porphyrins will also be discussed, as will other routes of great practical importance, and avenues to key porphyrinoids with modified macrocycles. A range of selected examples of contemporary functionalization reactions will be highlighted. The various key syntheses will be described and analyzed from a traditional mechanistic organic chemistry perspective to help student readers, and those who are new to this area. The aim will be to allow readers to mechanistically appreciate and understand how many of these fascinating ring-systems are built and further functionalized.

Corrole-Substituted Fluorescent Heme Proteins

Although fluorescent proteins have been utilized for a variety of biological applications, they have several optical limitations, namely weak red and near-infrared emission and exceptionally broad (>200 nm) emission profiles. The photophysical properties of fluorescent proteins can be enhanced through the incorporation of novel cofactors with the desired properties into a stable protein scaffold. To this end, a fluorescent phosphorus corrole that is structurally similar to the native heme cofactor is incorporated into two exceptionally stable heme proteins: H-NOX from Caldanaerobacter subterraneus and heme acquisition system protein A (HasA) from Pseudomonas aeruginosa. These yellow-orange emitting protein conjugates are examined by steady-state and time-resolved optical spectroscopy. The HasA conjugate exhibits enhanced fluorescence, whereas emission from the H-NOX conjugate is quenched relative to the free corrole. Despite the low fluorescence quantum yields, these corrole-substituted proteins exhibit more intense fluorescence in a narrower spectral profile than traditional fluorescent proteins that emit in the same spectral window. This study demonstrates that fluorescent corrole complexes are readily incorporated into heme proteins and provides an inroad for the development of novel fluorescent proteins.

Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts

Fe-Mimochrome VI*a is a synthetic peroxidase and peroxygenase, featuring two different peptides that are covalently-linked to deuteroheme. To perform a systematic structure/function correlation, we purposely shortened the distance between the distal peptide and the heme, allowing for the separation and characterization of two regioisomers. They differ in both His axial-ligand orientation, as determined by paramagnetic NMR shifts, and activity. These findings highlight that synthetic metalloenzymes may provide an efficient tool for disentangling the role of axial ligand orientation over peroxidase activity.

Nucleophilic Aromatic Substitution (SNAr) and Related Reactions of Porphyrinoids: Mechanistic and Regiochemical Aspects

The nucleophilic substitution of aromatic moieties (SNAr) has been known for over 150 years and found wide use for the functionalization of (hetero)aromatic systems. Currently, several "types" of SNAr reactions have been established and notably the area of porphyrinoid macrocycles has seen many uses thereof. Herein, we detail the SNAr reactions of seven types of porphyrinoids with differing number and type of pyrrole units: subporphyrins, norcorroles, corroles, porphyrins, azuliporphyrins, N-confused porphyrins, and phthalocyanines. For each we analyze the substitution dependent upon: a) the type of nucleophile and b) the site of substitution (α, β, or meso). Along with this we evaluate this route as a synthetic strategy for the generation of unsymmetrical porphyrinoids. Distinct trends can be identified for each type of porphyrinoid discussed, regardless of nucleophile. The use of nucleophilic substitution on porphyrinoids is found to often be a cost-effective procedure with the ability to yield complex substituent patterns, which can be conducted in non-anhydrous solvents with easily accessible simple porphyrinoids.

Proton conductivity as a function of the metal center in porphyrinylphosphonate-based MOFs

The rational design of metal-organic frameworks (MOFs) is highly important for the development of new proton conductors. Porphyrinylphosphonate-based MOFs, providing the directed tuning of physical and chemical properties of materials through the modification of a macrocycle, are potentially high-conducting systems. In this work the synthesis and characterization of novel anionic Zn-containing MOF based on palladium(ii) meso-tetrakis(3-(phosphonatophenyl))porphyrinate, IPCE-2Pd, are reported. Moreover, the proton-conductive properties and structures of two anionic Zn-containing MOFs based on previously described nickel(ii) and novel palladium(ii) porphyrinylphosphonates, IPCE-2M (M = Ni(ii) or Pd(ii)), are compared in details. The high proton conductivity of 1.0 × 10-2 S cm-1 at 75 °C and 95% relative humidity (RH) is revealed for IPCE-2Ni, while IPCE-2Pd exhibits higher hydrolytic and thermal stability of the material (up to 420 °C) simultaneously maintaining a comparable value of conductivity (8.11 × 10-3 S cm-1 at 95 °C and 95% RH). The nature of the porphyrin metal center is responsible for the features of crystal structure of materials, obtained under identical reaction conditions. The structures of IPCE-2Pd and its dehydrated derivative IPCE-2Pd-HT are determined from the synchrotron powder diffraction data. The presence of phosphonic groups in compared materials IPCE-2M affords a high concentration of proton carriers that together with the sorption of water molecules leads to a high proton conductivity.

Synthesis of novel porphyrin derivatives and their self-assemblies to enhance photocatalytic performance

Preparation of new porphyrin derivatives and their self-assemblies to improve photocatalytic performance.

A dinuclear porphyrin-macrocycle as efficient catalyst for the hydrogen evolution reaction

We report an unprecedented dinuclear catalyst for the electrochemical hydrogen evolution reaction (HER). A macrocyclic porphyrin complex comprising two nickel centres connected via redox mediating linker molecules gives rise to efficient catalysis, significantly outperforming a mononuclear reference catalyst.