Determining the key vibrations for spin relaxation in ruffled Cu(ii) porphyrins via resonance Raman spectroscopy† † Electronic supplementary information (ESI) available. CCDC 2303071. For ESI and crystallographic data in CIF or other electronic format see DOI: https://doi.org/10.1039/d3sc05774g
Ontology highlight
ABSTRACT:
SUBMITTER: Kazmierczak N
PROVIDER: S-EPMC10866354 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:To design molecular spin qubits with enhanced quantum coherence, a control of the coupling between the local vibrations and the spin states is crucial, which could be realized in principle by engineering molecular structures via coordination chemistry. To this end, understanding the underlying structural factors that govern the spin relaxation is a central topic. Here, we report the investigation of the spin dynamics in a series of chemically designed europium(II)-based endohedral metallofullerenes (EMFs). By introducing a unique structural difference, i. e. metal-cage binding site, while keeping other molecular parameters constant between different complexes, these manifest the key role of the three low-energy metal-displacing vibrations in mediating the spin-lattice relaxation times (T1 ). The temperature dependence of T1 can thus be normalized by the frequencies of these low energy vibrations to show an unprecedentedly universal behavior for EMFs in frozen CS2 solution. Our theoretical analysis indicates that this structural difference determines not only the vibrational rigidity but also spin-vibration coupling in these EMF-based qubit candidates.
| S-EPMC8518920 | biostudies-literature
Project description:A new method has been developed to determine α-helical and β-sheet secondary structural components of aqueous and membrane-bound proteins using pulsed electron paramagnetic resonance (EPR) spectroscopy. The three-pulse electron spin echo envelope modulation (ESEEM) technique was used to detect weakly coupled (2)H-labeled nuclei on side chains in the proximity of a strategically placed nitroxide spin-label up to 8 Å away. Changes in the ESEEM spectra for different samples correlate directly to periodic structural differences between α-helical and β-sheet motifs. These distinct trends were demonstrated with α-helical (M2δ subunit of the acetylcholine receptor) and β-sheet (ubiquitin) peptides in biologically relevant sample environments.
| S-EPMC3535504 | biostudies-literature
Project description:Excited state vibrations are crucial for determining the photophysical and photochemical properties of molecular compounds. Stimulated Raman scattering can coherently stimulate and probe molecular vibrations with optical pulses, but it is generally restricted to ground state properties. Working under resonance conditions enables cross-section enhancement and selective excitation to a targeted electronic level but is hampered by an increased signal complexity due to the presence of overlapping spectral contributions. Here, we show how detailed information about ground and excited state vibrations can be disentangled by exploiting the relative time delay between Raman and probe pulses to control the excited state population, combined with a diagrammatic formalism to dissect the pathways concurring with the signal generation. The proposed method is then exploited to elucidate the vibrational properties of the ground and excited electronic states in the paradigmatic case of cresyl violet. We anticipate that the presented approach holds the potential for selective mapping of the reaction coordinates pertaining to transient electronic stages implied in photoactive compounds.
| S-EPMC7735730 | biostudies-literature
Project description:Presented herein is a first major density functional theory (BP86/D3/STO-TZ2P) survey of the energetics of saddling versus ruffling for a wide range of dodecasubstituted metalloporphyrins with M = Ni, Cu, Zn, Pd, and Pt. For the majority of X8TPP (i.e., β-octasubstituted-meso-tetraphenylporphyrin), the calculations indicated a clear preference for the saddled conformation, consistent with a large body of experimental data. The preference for the saddled conformation relative to the ruffled conformation was found to vary from about ∼0.3-0.4 eV for Me8TPP derivatives up to 1 eV for I8TPP and (CF3)8TPP derivatives. For X = Ph, that is, dodecaphenylporphyrins, the saddled and the ruffled conformation are almost equienergetic, with even a slight preference for the ruffled conformation in some cases. This finding provides a satisfactory explanation for the X-ray crystallographic observation of both saddled and ruffled conformations for dodecaphenylporphyrin complexes as well as for spectroscopic evidence for conformational mobility of these complexes in solution. The calculations also indicate near-equienergetic saddled and ruffled conformations for meso-tetraacetylenyltetrabenzoporphyrins, again consonant with key crystallographic findings. By and large, both the energetics and nonplanar distortions of the metalloporphyrin derivatives correlated well with the Charton and Sterimol B1 steric parameters of the peripheral substituents.
| S-EPMC6644939 | biostudies-literature
Project description:Myoglobin has been demonstrated to function as a nitrite reductase to produce nitric oxide during hypoxia. One of the most intriguing aspects of the myoglobin/nitrite interactions revealed so far is the unusual O-binding mode of nitrite to the ferric heme iron, although conflicting data have been reported for the electronic structure of this complex also raising the possibility of linkage isomerism. In this work, we applied resonance Raman spectroscopy in a temperature-dependent approach to investigate the binding of nitrite to ferric myoglobin and the properties of the formed adduct from ambient to low temperatures (293 K to 153 K). At ambient temperature the high spin state of the ferric heme Fe-O-N[double bond, length as m-dash]O species is present and upon decreasing the temperature the low spin state is populated, demonstrating that a thermally-induced spin crossover phenomenon takes place analogous to what has been observed in many transition metal complexes. The observed spin crossover is fully reversible and is not due to linkage isomerism, since the O-binding mode is retained upon the spin transition. The role of the heme pocket environment in controlling the nitrite binding mode and spin transition is discussed.
| S-EPMC10025812 | biostudies-literature
Project description:Cu(II) is an essential element for life but is also associated with numerous and serious medical conditions, particularly neurodegeneration. Structural modeling of crystallization-resistant biological Cu(II) species relies on detailed spectroscopic analysis. Electron paramagnetic resonance (EPR) can, in principle, provide spin hamiltonian parameters that contain information on the geometry and ligand atom complement of Cu(II). Unfortunately, EPR spectra of Cu(II) recorded at the traditional X-band frequency are complicated by (i) strains in the region of the spectrum corresponding to the g(∥) orientation and (ii) potentially very many overlapping transitions in the g(⊥) region. The rapid progress of density functional theory computation as a means to correlate EPR and structure, and the increasing need to study Cu(II) associated with biomolecules in more biologically and biomedically relevant environments such as cells and tissue, have spurred the development of a technique for the extraction of a more complete set of spin hamiltonian parameters that is relatively straightforward and widely applicable. EPR at L-band (1-2 GHz) provides much enhanced spectral resolution and straightforward analysis via computer simulation methods. Herein, the anisotropic spin hamiltonian parameters and the nitrogen coordination numbers for two hitherto incompletely characterized Cu(II)-bound species of a prion peptide complex are determined by analysis of their L-band EPR spectra.
| S-EPMC3150385 | biostudies-literature
Project description:Resonance Raman spectroscopy (rR) is a powerful spectroscopic probe that is widely used for studying the geometric and electronic structure of metalloproteins. In this focused review, we detail how resonance Raman spectroscopy has contributed to a greater understanding of electronic structure, geometric structure, and the reaction mechanisms of pyranopterin molybdenum enzymes. The review focuses on the enzymes sulfite oxidase (SO), dimethyl sulfoxide reductase (DMSOR), xanthine oxidase (XO), and carbon monoxide dehydrogenase. Specifically, we highlight how Mo-Ooxo, Mo-Ssulfido, Mo-Sdithiolene, and dithiolene CC vibrational modes, isotope and heavy atom perturbations, resonance enhancement, and associated Raman studies of small molecule analogs have provided detailed insight into the nature of these metalloenzyme active sites.
| S-EPMC10575615 | biostudies-literature
Project description:Hemoglobins M (Hbs M) are human hemoglobin variants in which either the α or β subunit contains a ferric heme in the α2β2 tetramer. Though the ferric subunit cannot bind O2, it regulates O2 affinity of its counterpart ferrous subunit. We have investigated resonance Raman spectra of two Hbs, M Iwate (α87His → tyrosine [Tyr]) and M Boston (α58His → Tyr), having tyrosine as a heme axial ligand at proximal and distal positions, respectively, that exhibit unassigned resonance Raman bands arising from ferric (not ferrous) hemes at 899 and 876 cm-1. Our quantum chemical calculations using density functional theory on Fe-porphyrin models with p-cresol and/or 4-methylimidazole showed that the unassigned bands correspond to the breathing-like modes of Fe3+-bound Tyr and are sensitive to the Fe-O-C(Tyr) angle. Based on the frequencies of the Raman bands, the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston were predicted to be 153.5° and 129.2°, respectively. Consistent with this prediction, x-ray crystallographic analysis showed that the Fe-O-C(Tyr) angles of Hbs M Iwate and M Boston in the T quaternary structure were 153.6° and 134.6°, respectively. It also showed a similar Fe-O bond length (1.96 and 1.97 Å) and different tilting angles.
| S-EPMC9382339 | biostudies-literature
Project description:We investigated the normal mode composition and the aqueous solvation dependence of the primary amide vibrations of propanamide. Infrared, normal Raman, and UV resonance Raman (UVRR) spectroscopy were applied in conjunction with density functional theory (DFT) to assign the vibrations of crystalline propanamide. We examined the aqueous solvation dependence of the primary amide UVRR bands by measuring spectra in different acetonitrile/water mixtures. As previously observed in the UVRR spectra of N-methylacetamide, all of the resonance enhanced primary amide bands, except for the Amide I (AmI), show increased UVRR cross sections as the solvent becomes water-rich. These spectral trends are rationalized by a model wherein the hydrogen bonding and the high dielectric constant of water stabilizes the ground state dipolar (-)O-C═NH2(+) resonance structure over the neutral O═C-NH2 resonance structure. Thus, vibrations with large C-N stretching show increased UVRR cross sections because the C-N displacement between the electronic ground and excited state increases along the C-N bond. In contrast, vibrations dominated by C═O stretching, such as the AmI, show a decreased displacement between the electronic ground and excited state, which result in a decreased UVRR cross section upon aqueous solvation. The UVRR primary amide vibrations can be used as sensitive spectroscopic markers to study the local dielectric constant and hydrogen bonding environments of the primary amide side chains of glutamine (Gln) and asparagine (Asn).
| S-EPMC5065019 | biostudies-literature
Project description:Pulsed dipolar electron spin resonance spectroscopy (PDS) is a powerful tool for measuring distances in solution-state macromolecules. Paramagnetic metal ions, such as Cu2+, are used as spin probes because they can report on metalloprotein features and can be spectroscopically distinguished from traditional nitroxide (NO)-based labels. Here, we demonstrate site-specific incorporation of Cu2+ into non-metalloproteins through the use of a genetically encodable non-natural amino acid, 3-pyrazolyltyrosine (PyTyr). We first incorporate PyTyr in cyan fluorescent protein to measure Cu2+-to-NO distances and examine the effects of solvent conditions on Cu2+ binding and protein aggregation. We then apply the method to characterize the complex formed by the histidine kinase CheA and its target response regulator CheY. The X-ray structure of CheY-PyTyr confirms Cu labeling at PyTyr but also reveals a secondary Cu site. Cu2+-to-NO and Cu2+-to-Cu2+ PDS measurements of CheY-PyTyr with nitroxide-labeled CheA provide new insights into the conformational landscape of the phosphotransfer complex and have implications for kinase regulation.
| S-EPMC6215709 | biostudies-literature