EPR, ENDOR, and HYSCORE Study of the Structure and the Stability of Vanadyl−Porphyrin Complexes Encapsulated in Silica: Potential Paramagnetic Biomarkers for the Origin of Life

Improving the molecular spin qubit performance in zirconium MOF composites by mechanochemical dilution and fullerene encapsulation

Enlarging the quantum coherence times and gaining control over quantum effects in real systems are fundamental for developing quantum technologies. Molecular electron spin qubits are particularly promising candidates for realizing quantum information processing due to their modularity and tunability. Still, there is a constant search for tools to increase their quantum coherence times. Here we present how the mechanochemical introduction of active spin qubits in the form of 10% diluted copper(ii)-porphyrins in the diamagnetic PCN-223 and MOF-525 zirconium-MOF polymorph pair can be achieved. Furthermore, the encapsulation of fullerene during the MOF synthesis directs the process exclusively toward the rare PCN-223 framework with a controllable amount of fullerene in the framework channels. In addition to the templating role, the incorporation of fullerene increases the electron spin-lattice and phase-memory relaxation times, T1 and Tm. Besides decreasing the amount of nuclear spin-bearing solvent guests in the non-activated qubit frameworks, the observed improved relaxation times can be rationalized by modulating the phonon density of states upon fullerene encapsulation.

Methods for analyzing the coordination and aggregation of metal-amyloid-β

The misfolding and aggregation of amyloid-β (Aβ) peptides are histopathological features found in the brains of Alzheimer's disease (AD). To discover effective therapeutics for AD, numerous efforts have been made to control the aggregation of Aβ species and their interactions with other pathological factors, including metal ions. Metal ions, such as Cu(II) and Zn(II), can bind to Aβ peptides forming metal-bound Aβ (metal-Aβ) complexes and, subsequently, alter their aggregation pathways. In particular, redox-active metal ions bound to Aβ species can produce reactive oxygen species leading to oxidative stress. In this review, we briefly illustrate some experimental approaches for characterizing the coordination and aggregation properties of metal-Aβ complexes.

Magnetic expression in kerogen reveals impact on fluid transport

How can the transport of fluids in a confined and complex mixed organic/inorganic matrix be far below the expected value from a topological aspect? A good example of this situation is oil shales. Oil and gas shales are source rocks in which organic matter has matured to form hydrocarbons. They exhibit a dual porous network formed by the intertwining of mineral and organic pores that leads to very low permeability. Still, the exact origin of this extremely low permeability remains somehow unclear. The present communication addresses this important question and provides novel insights on the mechanisms that strongly hinder fluid diffusion in such materials. By combining nuclear and electronic magnetic resonance techniques with SEM imaging, we show evidence that magnetic interaction occurs in kerogen. This results from a magnetic coupling between vanadyl present in porphyrins and the organic matrix. We demonstrate that such coupling retards fluid diffusion and is reversible. This key dynamical feature explains the extremely low mobility of oil in shale rocks. This phenomenon may be a more general feature occurring in several systems where fluids are confined in a complex hierarchical matrix that embeds both organic and inorganic radicals resulting from the aging process.

Insight into the structure of black coatings of ancient Egyptian mummies by advanced electron magnetic resonance of vanadyl complexes

Ancient Egyptian mummies from the Late Period to the Greco-Roman Period were covered by a black coating consisting of complex and heterogeneous mixtures of conifer resins, wax, fat and oil with variable amounts of bitumen. Natural bitumen always contains traces of vanadyl porphyrin complexes that we used here as internal probes to explore the nanoscale environment of V4 + ions in these black coatings by electron nuclear double resonance (ENDOR) and hyperfine sub-level correlation spectroscopy (HYSCORE). Four types of vanadyl porphyrin complexes were identified from the analysis of 14 N hyperfine interactions. Three types (referred to as VO-P1, VO-P2 and VO-P3) are present in natural bitumen from the Dead Sea, among which VO-P1 and VO-P2 are also present in black coatings of mummies. The absence of VO-P3 in mummies, which is replaced by another complex, VO-P4, may be due to its transformation during preparation of the black matter for embalming. Analysis of 1 H hyperfine interaction shows that bitumen and other natural substances are intimately mixed in these black coatings, with aggregate sizes of bitumen increasing with the bitumen content but not exceeding a few nanometres.

Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution

INTRODUCTION

While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past.

AREAS COVERED

Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations.

EXPERT OPINION

Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.

Ferromagnetic Coupling in Oxidovanadium(IV)-Porphyrin Radical Dimers

Three different oxidovanadium(IV) porphyrin dimers with anti, cis, and trans arrangements of the two rings have been synthesized by changing the bridge between the porphyrin macrocycles. This provides a unique opportunity to investigate the role of the bridge and spatial arrangement between the two V^IVO centers for their electronic communication and magnetic coupling. They were characterized by the combined application of XRD analysis, UV-vis and electron paramagnetic resonance (EPR) spectroscopy, cyclic voltammetry, magnetic susceptibility, and DFT calculations. One- and two-electron oxidations produce mono- and dication diradical species, respectively, which display an unusual ferromagnetic interaction between the unpaired spins of vanadium(IV) and porphyrin π-cation radical, in contrast to other metalloporphyrin dimers. The oxidized species show a dissimilar behavior between cis and trans isomers. The ferromagnetic coupling occurs between the porphyrin π-cation radical and the unpaired electron of the V^IVO ion on the d_xy orbital, orthogonal to the porphyrin-based molecular orbitals a_1u and a_2u.

Molecular Dynamics and Proton Hyperpolarization via Synthetic and Crude Oil Porphyrin Complexes in Solid and Solution States

The use of vanadyl porphyrins either in synthetic compounds or naturally occurring in asphaltenes is investigated as a source of proton hyperpolarization via dynamic nuclear polarization (DNP) in nuclear magnetic resonance (NMR) experiments. The features of dynamics and location of the vanadyl VO²⁺ complex in aggregates within the oil asphaltene molecules are studied by means of DNP, electron paramagnetic resonance (EPR), and NMR field cycling relaxometry. Both the solid effect and Overhauser DNP were observed for the asphaltene solution in benzene, as well as in the solution and solid states for synthetic compounds. By comparison with a solution of synthetic vanadyl porphyrins, it is shown that vanadyl porphyrins in asphaltene aggregates are localized outside of the interface of the asphaltene aggregates and more exposed to the maltene molecules than "free" carbon-centered radicals associated with the core of asphaltene molecules. The perceptible contribution of scalar interaction is observed in solutions for both synthetic and asphaltene vanadyl porphyrins.

Nondestructive Analysis of Mummification Balms in Ancient Egypt Based on EPR of Vanadyl and Organic Radical Markers of Bitumen

The black matter employed in the funeral context by ancient Egyptians is a complex mixture of plant-based compounds with variable amounts of bitumen. Asphaltene, the most resistant component of bitumen, contains vanadyl porphyrins and carbonaceous radicals, which can be used as paramagnetic probes to investigate embalming materials without sample preparation. Electron paramagnetic resonance (EPR) at the X-band, combining in-phase and out-of-phase detection schemes, provides new information in a nondestructive way about the presence, the origin, and the evolution of bitumen in these complex materials. It is found that the relative EPR intensity of radicals and vanadyl porphyrins is sensitive to the origin of the bitumen. The presence of nonporphyrinic vanadyl complexes in historical samples is likely due to the complexation of VO²⁺ ions by carboxylic functions at the interface between bitumen and other biological components of the embalming matter. The absence of such oxygenated vanadyl complex in natural bitumen and in one case of historical human mummy acquired by a museum in the 19th century reveals a possible, nondocumented, ancient restoration of this mummy by pure bitumen. The linear correlation between in-phase and out-of-phase EPR intensities of radicals and vanadyl porphyrins in balms and in natural bitumen reveals a nanostructuration of radicals and vanadyl porphyrin complexes, which was not affected by the preparation of the balm. This points to the remarkable chemical stability of paramagnetic probes in historical bitumen in ancient Egypt.

Scaling Up Electronic Spin Qubits into a Three-Dimensional Metal-Organic Framework

Practical implementation of highly coherent molecular spin qubits for challenging technological applications, such as quantum information processing or quantum sensing, requires precise organization of electronic qubit molecular components into extended frameworks. Realization of spatial control over qubit-qubit distances can be achieved by coordination chemistry approaches through an appropriate choice of the molecular building blocks. However, translating single qubit molecular building units into extended arrays does not guarantee a priori retention of long quantum coherence and spin-lattice relaxation times due to the introduced modifications over qubit-qubit reciprocal distances and molecular crystal lattice phonon structure. In this work, we report the preparation of a three-dimensional (3D) metal-organic framework (MOF) based on vanadyl qubits, [VO(TCPP-Zn₂-bpy)] (TCPP = tetracarboxylphenylporphyrinate; bpy = 4,4'-bipyridyl) (1), and the investigation of how such structural modifications influence qubits' performances. This has been done through a multitechnique approach where the structure and properties of a representative molecular building block of formula [VO(TPP)] (TPP = tetraphenylporphyrinate) (2) have been compared with those of the 3D MOF 1. Pulsed electron paramagnetic resonance measurements on magnetically diluted samples in titanyl isostructural analogues revealed that coherence times are retained almost unchanged for 1 with respect to 2 up to room temperature, while the temperature dependence of the spin-lattice relaxation time revealed insights into the role of low-energy vibrations, detected through terahertz spectroscopy, on the spin dynamics.

Interaction of antidiabetic vanadium compounds with hemoglobin and red blood cells and their distribution between plasma and erythrocytes

The interaction of V(IV)O(2+) ion with hemoglobin (Hb) was studied with the combined application of spectroscopic (EPR), spectrophotometric (UV-vis), and computational (DFT methods) techniques. Binding of Hb to V(IV)O(2+) in vitro was proved, and three unspecific sites (named α, β, and γ) were characterized, with the probable coordination of His-N, Asp-O(-), and Glu-O(-) donors. The value of log β for (VO)Hb is 10.4, significantly lower than for human serum apo-transferrin (hTf). In the systems with V(IV)O potential antidiabetic compounds, mixed species cis-VOL2(Hb) (L = maltolate (ma), 1,2-dimethyl-3-hydroxy-4(1H)-pyridinonate (dhp)) are observed with equatorial binding of an accessible His residue, whereas no ternary complexes are observed with acetylacetonate (acac). The experiments of uptake of [VO(ma)2], [VO(dhp)2], and [VO(acac)2] by red blood cells indicate that the neutral compounds penetrate the erythrocyte membrane through passive diffusion, and percent amounts higher than 50% are found in the intracellular medium. The biotransformation of [VO(ma)2], [VO(dhp)2], and [VO(acac)2] inside the red blood cells was proved. [VO(dhp)2] transforms quantitatively in cis-VO(dhp)2(Hb), [VO(ma)2] in cis-VO(ma)2(Hb), and cis-VO(ma)2(Cys-S(-)), with the equatorial coordination of a thiolate-S(-) of GSH or of a membrane protein, and [VO(acac)2] in the binary species (VO)xHb and two V(IV)O complexes with formulation VO(L(1),L(2)) and VO(L(3),L(4)), where L(1), L(2), L(3), and L(4) are red blood cell bioligands. The results indicate that, in the studies on the transport of a potential pharmacologically active V species, the interaction with red blood cells and Hb cannot be neglected, that a distribution between the erythrocytes and plasma is achieved, and that these processes can significantly influence the effectiveness of a V drug.

Nuclear magnetic biosignatures in the carbonaceous matter of ancient cherts: comparison with carbonaceous meteorites

The search for organic biosignatures is motivated by the hope of understanding the conditions of emergence of life on Earth and the perspective of finding traces of extinct life in martian sediments. Paramagnetic radicals, which exist naturally in amorphous carbonaceous matter fossilized in Precambrian cherts, were used as local structural probes and studied by electron paramagnetic resonance (EPR) spectroscopy. The nuclear magnetic resonance transitions of elements inside and around these radicals were detected by monitoring the nuclear modulations of electron spin echo in pulsed EPR. We found that the carbonaceous matter of fossilized microorganisms with age up to 3.5 billion years gives specific nuclear magnetic signatures of hydrogen (¹H), carbon (¹³C), and phosphorus (³¹P) nuclei. We observed that these potential biosignatures of extinct life are found neither in the carbonaceous matter of carbonaceous meteorites (4.56 billion years), the most ancient objects of the Solar System, nor in any carbonaceous matter resulting from carbonization of organic and bioorganic precursors. These results indicate that these nuclear signatures are sensitive to thermal episodes and can be used for Archean cherts with metamorphism not higher than the greenschist facies.

Electron paramagnetic resonance study of a photosynthetic microbial mat and comparison with Archean cherts

Organic radicals in artificially carbonized biomass dominated by oxygenic and non-oxygenic photosynthetic bacteria, Microcoleus chthonoplastes-like and Chloroflexus-like bacteria respectively, were studied by Electron Paramagnetic Resonance (EPR) spectroscopy. The two bacteria species were sampled in mats from a hypersaline lake. They underwent accelerated ageing by cumulative thermal treatments to induce progressive carbonization of the biological material, mimicking the natural maturation of carbonaceous material of Archean age. For thermal treatments at temperatures higher than 620 °C, a drastic increase in the EPR linewidth is observed in the carbonaceous matter from oxygenic photosynthetic bacteria and not anoxygenic photosynthetic bacteria. This selective EPR linewidth broadening reflects the presence of a catalytic element inducing formation of radical aggregates, without affecting the molecular structure or the microstructure of the organic matter, as shown by Raman spectroscopy and Transmission Electron Microscopy. For comparison, we carried out an EPR study of organic radicals in silicified carbonaceous rocks (cherts) from various localities, of different ages (0.42 to 3.5 Gyr) and having undergone various degrees of metamorphism, i.e. various degrees of natural carbonization. EPR linewidth dispersion for the most primitive samples was quite significant, pointing to a selective dipolar broadening similar to that observed for carbonized bacteria. This surprising result merits further evaluation in the light of its potential use as a marker of past bacterial metabolisms, in particular oxygenic photosynthesis, in Archean cherts.

A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation

The standard molecular clock describes a constant rate of molecular evolution and provides a powerful framework for evolutionary timescales. Here, we describe the existence and implications of a molecular clock of folds, a universal recurrence in the discovery of new structures in the world of proteins. Using a phylogenomic structural census in hundreds of proteomes, we build phylogenies and time lines of domains at fold and fold superfamily levels of structural complexity. These time lines correlate approximately linearly with geological timescales and were here used to date two crucial events in life history, planet oxygenation and organism diversification. We first dissected the structures and functions of enzymes in simulated metabolic networks. The placement of anaerobic and aerobic enzymes in the time line revealed that aerobic metabolism emerged about 2.9 billion years (giga-annum; Ga) ago and expanded during a period of about 400 My, reaching what is known as the Great Oxidation Event. During this period, enzymes recruited old and new folds for oxygen-mediated enzymatic activities. Remarkably, the first fold lost by a superkingdom disappeared in Archaea 2.6 Ga ago, within the span of oxygen rise, suggesting that oxygen also triggered diversification of life. The implications of a molecular clock of folds are many and important for the neutral theory of molecular evolution and for understanding the growth and diversity of the protein world. The clock also extends the standard concept that was specific to molecules and their timescales and turns it into a universal timescale-generating tool.