MCSCF and DFT calculations of EPR parameters of sulfur centered radicals

Effect of Pyrrolidinedithiocarbamate Ligand on the Luminescence Properties of Heteroligand Samarium and Europium Complexes: Experimental and Theoretical Study

The photophysical properties of two isostructural heteroligand lanthanide complexes of general formula Ln(pdtc)3(phen) (pdtc = pyrrolidinedithiocarbamate anion, phen = 1,10-phenanthroline), Ln = Sm3+ (1), Eu3+ (2)) were studied in solid state and dichloromethane (DCM) solution. The two lanthanide complexes were investigated by experimental techniques for structural (single-crystal X-ray diffraction analysis of 1, powder XRD, TG-DTA) and spectroscopic [electron paramagnetic resonance (EPR), infrared (IR), ultraviolet-visible (UV-vis), photoluminescence (PL)] characterization. DFT/TDDFT/ωB97xD and multireference SA-CASSCF/NEVPT2 calculations with perturbative spin-orbit coupling corrections were applied to construct the Jablonski energy diagrams and to discuss the excited state energy transfer mechanism with competing excited state processes and possible sensitized mechanism of metal-centered emission. The first excited state (S1) involved in the excited state energy transfer L(antenna)-to-Ln was predicted to have interligand (pdtc-to-phen) charge transfer character in contrast to the previously predicted ligand-to-metal charge transfer character. The theoretical consideration showed similar relaxation paths and luminescence quenching channels and appropriate Donor*(phen)-Acceptor*(Ln3+) energy gap for 1 and 2. The experimental measurements in the solid state, however, showed efficient luminescence and good ability to convert UV to visible light only for the Sm(pdtc)3(phen) complex. The minor emission of 2 was explained by partial reduction of Eu3+, confirmed by EPR and calculated electron density distribution data.

Formation of free radicals in human hair under strain: Combined electron paramagnetic resonance (EPR) - Strain technique

In this work, the formation of free radicals in human hair and the evolution of the radical concentration under strain, using a combined electron paramagnetic resonance (EPR) - strain technique, has been investigated. The radicals formed in the hair as a result of homolytic bond cleavage in cystine residues of polypeptide chains were identified. Stability of the radicals formed in dry hair and in the presence of water were studied. The spin-strain curves for the grey human hair in dry state and in water are presented and compared with conventional hair stress vs. strain curves. The evolution of sulfur radical species has been found to only occur at strains of above ca. 25%, corresponding with the Post-Yield region of the stress vs. strain behaviour for hair; this indicates that the matrix of the hair in this region behaves like a highly crosslinked gel and helps to explain the reversibility in hair mechanical behaviour below the Post-Yield region.

Evidence for a Long-Lived, Cu-Coupled and Oxygen-Inert Disulfide Radical Anion in the Assembly of Metallothionein-3 Cu(I)4-Thiolate Cluster

The human copper-binding protein metallothionein-3 (MT-3) can reduce Cu(II) to Cu(I) and form a polynuclear Cu(I)4-Cys5-6 cluster concomitant with intramolecular disulfide bonds formation, but the cluster is unusually inert toward O2 and redox-cycling. We utilized a combined array of rapid-mixing spectroscopic techniques to identify and characterize the transient radical intermediates formed in the reaction between Zn7MT-3 and Cu(II) to form Cu(I)4Zn(II)4MT-3. Stopped-flow electronic absorption spectroscopy reveals the rapid formation of transient species with absorption centered at 430-450 nm and consistent with the generation of disulfide radical anions (DRAs) upon reduction of Cu(II) by MT-3 cysteine thiolates. These DRAs are oxygen-stable and unusually long-lived, with lifetimes in the seconds regime. Subsequent DRAs reduction by Cu(II) leads to the formation of a redox-inert Cu(I)4-Cys5 cluster with short Cu-Cu distances (<2.8 Å), as revealed by low-temperature (77 K) luminescence spectroscopy. Rapid freeze-quench Raman and electron paramagnetic resonance (EPR) spectroscopy characterization of the intermediates confirmed the DRA nature of the sulfur-centered radicals and their subsequent oxidation to disulfide bonds upon Cu(II) reduction, generating the final Cu(I)4-thiolate cluster. EPR simulation analysis of the radical g- and A-values indicate that the DRAs are directly coupled to Cu(I), potentially explaining the observed DRA stability in the presence of O2. We thus provide evidence that the MT-3 Cu(I)4-Cys5 cluster assembly process involves the controlled formation of novel long-lived, copper-coupled, and oxygen-stable disulfide radical anion transient intermediates.

Impact of UV Radiation on the Raman Signal of Cystine: Implications for the Detection of S-rich Organics on Mars

Traces of life may have been preserved in ancient martian rocks in the form of molecular fossils. Yet the surface of Mars is continuously exposed to intense UV radiation detrimental to the preservation of organics. Because the payload of the next rovers going to Mars to seek traces of life will comprise Raman spectroscopy tools, laboratory simulations that document the effect of UV radiation on the Raman signal of organics appear critically needed. The experiments conducted here evidence that UV radiation is directly responsible for the increase of disorder and for the creation of electronic defects and radicals within the molecular structure of S-rich organics such as cystine, enhancing the contribution of light diffusion processes to the Raman signal. The present results suggest that long exposure to UV radiation would ultimately be responsible for the total degradation of the Raman signal of cystine. Yet because the degradation induced by UV is not instantaneous, it should be possible to detect freshly excavated S-rich organics with the Raman instruments on board the rovers. Alternatively, given the very short lifetime of organic fluorescence (nanoseconds) compared to most mineral luminescence (micro- to milliseconds), exploiting fluorescence signals might allow the detection of S-rich organics on Mars. In any case, as illustrated here, we should not expect to detect pristine S-rich organic compounds on Mars, but rather by-products of their degradation.

A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase

The class III ribonucleotide reductases (RNRs) are glycyl radical (G•) enzymes that provide the balanced pool of deoxynucleotides required for DNA synthesis and repair in many facultative and obligate anaerobic bacteria and archaea. Unlike the class I and II RNRs, where reducing equivalents for the reaction are delivered by a redoxin (thioredoxin, glutaredoxin, or NrdH) via a pair of conserved active site cysteines, the class III RNRs examined to date use formate as the reductant. Here, we report that reaction of the Escherichia coli class III RNR with CTP (substrate) and ATP (allosteric effector) in the absence of formate leads to loss of the G• concomitant with stoichiometric formation of a new radical species and a "trapped" cytidine derivative that can break down to cytosine. Addition of formate to the new species results in recovery of 80% of the G• and reduction of the cytidine derivative, proposed to be 3'-keto-deoxycytidine, to dCTP and a small amount of cytosine. The structure of the new radical has been identified by 9.5 and 140 GHz EPR spectroscopy on isotopically labeled varieties of the protein to be a thiosulfuranyl radical [RSSR2]•, composed of a cysteine thiyl radical stabilized by an interaction with a methionine residue. The presence of a stable radical species on the reaction pathway rationalizes the previously reported [(3)H]-(k(cat)/K(M)) isotope effect of 2.3 with [(3)H]-formate, requiring formate to exchange between the active site and solution during nucleotide reduction. Analogies with the disulfide anion radical proposed to provide the reducing equivalent to the 3'-keto-deoxycytidine intermediate by the class I and II RNRs provide further evidence for the involvement of thiyl radicals in the reductive half-reaction catalyzed by all RNRs.

State of the art in nail dosimetry: free radicals identification and reaction mechanisms

Until very recently, analysis of bone biopsies by means of the method of electron paramagnetic resonance (EPR) collected after surgery or amputation has been considered as the sole reliable method for radiation dose assessment in hands and feet. EPR measurements in finger- and toenail have been considered for accident dosimetry for a long time. Human nails are very attractive biophysical materials because they are easy to collect and pertinent to whole body irradiation. Information on the existence of a radiation-induced signal in human nails has been reported almost 25 years ago. However, no practical application of EPR dosimetry on nails is known to date because, from an EPR perspective, nails represent a very complex material. In addition to the radiation-induced signal (RIS), parasitic and intense signals are induced by the mechanical stress caused when collecting nail samples (mechanically induced signals-MIS). Moreover, it has been demonstrated that the RIS stability is strongly influenced not only by temperature but also by humidity. Most studies of human nails were carried out using conventional X-band microwave band (9 GHz). Higher frequency Q-band (37 GHz) provides higher spectral resolution which allows obtaining more detailed information on the nature of different radicals in human nails. Here, we present for the first time a complete description of the different EPR signals identified in nails including parasitic, intrinsic and RIS. EPR in both X- and Q-bands was used. Four different MIS signals and five different signals specific to irradiation with ionizing radiation have been identified. The most important outcome of this work is the identification of a stable RIS component. In contrast with other identified (unstable) RIS components, this component is thermally and time stable and not affected by the physical contact of fingernails with water. A detailed description of this signal is provided here. The discovery of stable radiation-induced radical(s) associated with the RIS component mentioned opens a way for broad application of EPR dosimetry in human nails. Consequently, several recent dosimetry assessments of real accident cases have been performed based on the described measurements and analyses of this component.

Thiol redox biochemistry: insights from computer simulations

Thiol redox chemical reactions play a key role in a variety of physiological processes, mainly due to the presence of low-molecular-weight thiols and cysteine residues in proteins involved in catalysis and regulation. Specifically, the subtle sensitivity of thiol reactivity to the environment makes the use of simulation techniques extremely valuable for obtaining microscopic insights. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of selected relevant issues in thiol redox biochemistry, such as investigations on (1) the protonation state of cysteine in protein, (2) two-electron oxidation of thiols by hydroperoxides, chloramines, and hypochlorous acid, (3) mechanistic and kinetics aspects of the de novo formation of disulfide bonds and thiol-disulfide exchange, (4) formation of sulfenamides, (5) formation of nitrosothiols and transnitrosation reactions, and (6) one-electron oxidation pathways.

Investigating the intermediates in the reaction of ribonucleoside triphosphate reductase from Lactobacillus leichmannii: An application of HF EPR-RFQ technology

In this investigation high-frequency electron paramagnetic resonance spectroscopy (HFEPR) in conjunction with innovative rapid freeze-quench (RFQ) technology is employed to study the exchange-coupled thiyl radical-cob(II)alamin system in ribonucleotide reductase from a prokaryote Lactobacillus leichmannii. The size of the exchange coupling (Jex) and the values of the thiyl radical g tensor are refined, while confirming the previously determined (Gerfen et al. (1996) [20]) distance between the paramagnets. Conclusions relevant to ribonucleotide reductase catalysis and the architecture of the active site are presented. A key part of this work has been the development of a unique RFQ apparatus for the preparation of millisecond quench time RFQ samples which can be packed into small (0.5 mm ID) sample tubes used for CW and pulsed HFEPR--lack of this ability has heretofore precluded such studies. The technology is compatible with a broad range of spectroscopic techniques and can be readily adopted by other laboratories.

Spectroscopic studies on the [4Fe-4S] cluster in adenosine 5'-phosphosulfate reductase from Mycobacterium tuberculosis

Mycobacterium tuberculosis adenosine 5'-phosphosulfate reductase (MtAPR) is an iron-sulfur protein and a validated target to develop new antitubercular agents, particularly for the treatment of latent infection. The enzyme harbors a [4Fe-4S](2+) cluster that is coordinated by four cysteinyl ligands, two of which are adjacent in the amino acid sequence. The iron-sulfur cluster is essential for catalysis; however, the precise role of the [4Fe-4S] cluster in APR remains unknown. Progress in this area has been hampered by the failure to generate a paramagnetic state of the [4Fe-4S] cluster that can be studied by electron paramagnetic resonance spectroscopy. Herein, we overcome this limitation and report the EPR spectra of MtAPR in the [4Fe-4S](+) state. The EPR signal is rhombic and consists of two overlapping S = &frac12; species. Substrate binding to MtAPR led to a marked increase in the intensity and resolution of the EPR signal and to minor shifts in principle g values that were not observed among a panel of substrate analogs, including adenosine 5'-diphosphate. Using site-directed mutagenesis, in conjunction with kinetic and EPR studies, we have also identified an essential role for the active site residue Lys-144, whose side chain interacts with both the iron-sulfur cluster and the sulfate group of adenosine 5'-phosphosulfate. The implications of these findings are discussed with respect to the role of the iron-sulfur cluster in the catalytic mechanism of APR.

Universal Theoretical Approach to Extract Anisotropic Spin Hamiltonians

Monometallic Ni(II) and Co(II) complexes with large magnetic anisotropy are studied using correlated wave function based ab initio calculations. Based on the effective Hamiltonian theory, we propose a scheme to extract both the parameters of the zero-field splitting (ZFS) tensor and the magnetic anisotropy axes. Contrarily to the usual theoretical procedure of extraction, the method presented here determines the sign and the magnitude of the ZFS parameters in any circumstances. While the energy levels provide enough information to extract the ZFS parameters in Ni(II) complexes, additional information contained in the wave functions must be used to extract the ZFS parameters of Co(II) complexes. The effective Hamiltonian procedure also enables us to confirm the validity of the standard model Hamiltonian to produce the magnetic anisotropy of monometallic complexes. The calculated ZFS parameters are in good agreement with high-field, high-frequency electron paramagnetic resonance spectroscopy and frequency domain magnetic resonance spectroscopy data. A methodological analysis of the results shows that the ligand-to-metal charge transfer configurations must be introduced in the reference space to obtain quantitative agreement with the experimental estimates of the ZFS parameters.

Theoretical investigation of the EPR hyperfine coupling constants in amino derivatives

The HFCCs of the radical cations of a series of amines have been determined at different levels of approximation including the CISD, QCISD, and CCSD ab initio correlated methods and density functional theory approaches employing the B3LYP, PBE0, BHandHLYP, TPSS, and BLYP exchange-correlation functionals. Although quantitative differences with respect to experimental data have been noticed, these are mostly systematic within a given class of N and H atoms. As a consequence, these different levels of theory are reliable in most cases to account for the substituent and structure effects on the HFCCs of amines. Linear regression fits have then been performed to reach quantitative agreement between the theoretical and experimental values. This has finally been substantiated by considering the EPR signal of the recently synthesized radical cations of two derivatives of [10-(4-aminophenyl)-9-anthryl]aniline as well as in confirming a recent assignment of the EPR signal of n-propylamine.

Calculation of Solvent Shifts on Electronic g-Tensors with the Conductor-Like Screening Model (COSMO) and Its Self-Consistent Generalization to Real Solvents (Direct COSMO-RS)

The conductor-like screening model (COSMO) was used to investigate the solvent influence on electronic g-values of organic radicals. The previously studied diphenyl nitric oxide and di-tert-butyl nitric oxide radicals were taken as test cases. The calculations employed spin-unrestricted density functional theory and the BP and B3LYP density functionals. The g-tensors were calculated as mixed second derivative properties with respect to the external magnetic field and the electron magnetic moment. The first-order response of the Kohn-Sham orbitals with respect to the external magnetic field was determined through the coupled-perturbed DFT approach. The spin-orbit coupling operator was treated using an accurate multicenter spin-orbit mean-field (SOMF) approach. Provided that important hydrogen bonds are explicitly modeled by a supermolecule approach and that the basis set is sufficiently saturated, the COSMO calculations lead to accurate predictions of isotropic g-shifts with deviations of not more than 100 ppm relative to experiment. Very accurate results were obtained by employing a recently developed self-consistent modification of the COSMO method to real solvents (COSMO-RS), which we briefly introduce in this paper as direct COSMO-RS (D-COSMO-RS). This model gives isotropic g-shifts of similar high accuracy for water without using the supermolecule approach. This is an important result because it solves many of the problems associated with the supermolecule approach such as local minima and the choice of a suitable model system. Thus, the self-consistent D-COSMO-RS incorporates some specific solvation effects into continuum models, in particular it appears to successfully model the effects of hydrogen bonding. Although not yet widely validated, this opens a novel approach for the calculation of properties which so far only could be calculated by the inclusion of explicit solvent molecules in continuum solvation methods.

The Influence of Solid-State Molecular Organization on the Reaction Paths of Thiyl Radicals

Electron paramagnetic resonance (EPR) spectroscopy has been employed to investigate the effect of solid-state molecular organization on the reaction of thiyl radicals with thiols. In an irradiated C18H37SH/thiourea clathrate, the conversion of thiyl to perthiyl radicals is substantial, due to the head-to-head arrangement of the reactants within the channels and the suppression of other possible competing reactions due to hindrance by the clathrate walls. The perthiyl radical was identified using EPR analysis of its molecular dynamics within the clathrate channels. Irradiated polyethylene film containing 30% C18H37SH afforded a negligible conversion of thiyl to perthiyl radicals because of the random distribution of reactants. These results suggest that in the absence of favorable structure-control effects, the reaction between RS* and RSH is unimportant with respect to other competing reactions. Perthiyl radicals are also the major product in the vacuum solid-state radiolysis of lysozyme. A proposal of the mechanism involved in all cases is based on the equilibrium RS* + RSH <==> RSS*(H)R, followed by the irreversible conversion of the sulfuranyl radical to the perthiyl radical. As the equilibrium is strongly shifted to the left, the intermediate sulfuranyl radicals were not detected, but the lack of other competing reactions for the thiyl radicals caused the formation of perthiyl radicals to become the major path in the clathrate and in solid lysozyme radiolysis.

Electronic g-tensors of solvated molecules using the polarizable continuum model

We present the implementation of density functional response theory combined with the polarizable continuum model (PCM), enabling first principles calculations of molecular g-tensors of solvated molecules. The calculated g-tensor shifts are compared with experimental g-tensor shifts obtained from electron paramagnetic resonance spectra for a few solvated species. The results indicate qualitative agreement between the calculations and the experimental data for aprotic solvents, whereas PCM fails to reproduce the electronic g-tensor behavior for protic solvents. This failure of PCM for protic solvents can be resolved by including into the model those solvent molecules which are involved in hydrogen bonding with the solute. The results for the protic solvents show that the explicit inclusion of the solvent molecules of the first solvation sphere is not sufficient in order to reproduce the behavior of the electronic g-tensor in protic solvents, and that better agreement with experimental data can be obtained by including the long-range electrostatic effects accounted for by the PCM approach on top of the explicit hydrogen-bonded complexes.

Electronic structure of the cysteine thiyl radical: a DFT and correlated ab initio study

The electronic structure and the unusual EPR parameters of sulfur-centered alkyl thiyl radical from cysteine are investigated by density functional theory (DFT) and correlated ab initio calculations. Three geometry-optimized, staggered conformations of the radical are found that lie within 630 cm(-1) in energy. The EPR g-values are sensitive to the energy difference between the nearly-degenerate singly occupied orbital and one of the lone-pair orbitals (excitation energies of 1732, 1083, and 3429 cm(-1) from Multireference Configuration Interaction calculations for the structures corresponding to the three minima), both of which are almost pure sulfur 3p orbitals. Because of the near degeneracy, the second order correction to the g tensor, which is widely used to analyze g-values of paramagnetic systems, is insufficient to obtain accurate g-values of the cysteine thiyl radical. Instead, an expression for the g tensor must be used in which third order corrections are taken into account. The near-degeneracy can be affected to roughly equal extents by changes in the structure of the radical and by hydrogen bonds to the sulfur. The magnitude of the hyperfine coupling constants for the beta protons of the cysteine thiyl radical is found to depend on the structure of the radical. On the basis of a detailed comparison between experimental and calculated g-values and hyperfine coupling constants an attempt is made to identify the structure of thiyl radicals and the number of hydrogen bonds to the sulfur.