Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage.

The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different Fe and Fe active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined.

Microscopic observation of hidden Johari-Goldstein-β process in glycerol.

The Johari-Goldstein-β (JG-β) process is widely observed in a variety of glass-forming systems and recognized as an intrinsic process in deeply supercooled and glassy states. However, in some systems, e.g.

Relationship between Viscosity and Acyl Tail Dynamics in Lipid Bilayers.

Membrane viscosity is a fundamental property that controls molecular transport and structural rearrangements in lipid membranes. Given its importance in many cell processes, various experimental and computational methods have been developed to measure the membrane viscosity, yet the estimated values depend highly on the method and vary by orders of magnitude. Here we investigate the molecular origins of membrane viscosity by measuring the nanoscale dynamics of the lipid acyl tails using x-ray and neutron spectroscopy techniques.

Direct coordination of pterin to Fe enables neurotransmitter biosynthesis in the pterin-dependent hydroxylases.

The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the Fe active site to form a highly reactive Fe = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-Fe = O intermediate and characterized its structure as a Fe-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies.

Nuclear Resonance Vibrational Spectroscopic Definition of the Facial Triad Fe═O Intermediate in Taurine Dioxygenase: Evaluation of Structural Contributions to Hydrogen Atom Abstraction.

The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin Fe═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the Fe═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the Fe═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate.

Nuclear Resonance Vibrational Spectroscopy Definition of O Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity.

The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O-4NC species and a Fe-O-4NC peroxy bridged species.

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites.

Fe-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement.

61Ni synchrotron radiation-based Mössbauer spectroscopy of nickel-based nanoparticles with hexagonal structure.

We measured the synchrotron-radiation (SR)-based Mössbauer spectra of Ni-based nanoparticles with a hexagonal structure that were synthesised by chemical reduction. To obtain Mössbauer spectra of the nanoparticles without (61)Ni enrichment, we developed a measurement system for (61)Ni SR-based Mössbauer absorption spectroscopy without X-ray windows between the (61)Ni84V16 standard energy alloy and detector. The counting rate of the (61)Ni nuclear resonant scattering in the system was enhanced by the detection of internal conversion electrons and the close proximity between the energy standard and the detector.

Slow processes in supercooled o-terphenyl: relaxation and decoupling.

We mapped the relaxation times of inter- and intramolecular correlations in o-terphenyl by a quasielastic scattering method using nuclear resonant scattering of synchrotron radiation. From the obtained map, we found that the slow β process is decoupled from the α process at 278 K, and this temperature is clearly below the previous decoupling temperature of 290 K, at which the α-relaxation dynamics changes. Then, it was also concluded that sufficient solidlike condition achieved by further cooling from 290 K is required to decouple the slow β process from the α process and, due to the difference of the length scales between the α and the slow β processes, these two averaged relaxation times <τ> are concluded not to cross as an extrapolation assumed so far.