Probing the environment of cu(b) in heme-copper oxidases

Time-resolved step-scan FTIR (TRS2-FTIR) and density functional theory have been applied to probe the structural dynamics of CuB in heme-copper oxidases at room temperature. The TRS2-FTIR data of cbb3 from Pseudomonas stutzeri indicate a small variation in the frequency of the transient CO bound to CuB in the pH/pD 7-9 range. This observation in conjunction with density functional theory calculations, in which significant frequency shifts of the nu(CO) are observed upon deprotonation and/or detachment of the CuB ligands, demonstrates that the properties of the CuB ligands including the cross-linked tyrosine, in contrast to previous reports, remain unchanged in the pH 7-9 range. We attribute the small variations in the nu(CO) of CuB to protein conformational changes in the vicinity of CuB. Consequently, the split of the heme Fe-CO vibrations (alpha-, beta-, and gamma-forms) is not due to changes in the ligation and/or protonation states of the CuB ligands or to the presence of one or more ionizable groups, as previously suggested, but the result of global protein conformational changes in the vicinity of CuB which, in turn, affect the position of CuB with respect to the heme Fe.     

On the Melvin–Morton–Rozansky conjecture

We prove a conjecture stated by Melvin and Morton (and elucidated further by Rozansky) saying that the Alexander–Conway polynomial of a knot can be read from some of the coefficients of the Jones polynomials of cables of that knot (i.e., coefficients of the “colored” Jones polynomial). We first reduce the problem to the level of weight systems using a general principle, which may be of some independent interest, and which sometimes allows to deduce equality of Vassiliev invariants from the equality of their weight systems. We then prove the conjecture combinatorially on the level of weight systems. Finally, we prove a generalization of the Melvin–Morton–Rozansky (MMR) conjecture to knot invariants coming from arbitrary semi-simple Lie algebras. As side benefits we discuss a relation between the Conway polynomial and immanants and a curious formula for the weight system of the colored Jones polynomial. Oblatum 28-VII-1994 & 5-XI-1995 & 22-XI-1995     

Non-linear dynamics of the photodissociation of nitrous oxide: equilibrium points, periodic orbits, and transition states

The diffuse vibrational bands, observed in the ultraviolet photodissociation spectrum of nitrous oxide by exciting the molecule in the first (1)A' state, have recently been attributed to resonances localized mainly in the NN stretch and bend degrees of freedom. To further investigate the origin of this localization, fundamental families of periodic orbits emanating from several stationary points of the (1)A' potential energy surface and bifurcations of them are computed. We demonstrate that center-saddle bifurcations of periodic orbits are the main mechanism for creating stable regions in phase space that can support the partial trapping of the wave packet, and thus they explain the observed spectra. A non-linear mechanical methodology, which involves the calculation of equilibria, periodic orbits, and transition states in normal form coordinates, is applied for an in detail exploration of phase space. The fingerprints of the phase space structures in the quantum world are identified by solving the time dependent Schro?dinger equation and calculating autocorrelation functions. This demonstrates that different reaction channels could be controlled if exact knowledge of the phase space structure is available to guide the initial excitation of the molecule.     

Enhancing the stiffness of electrospun nanofiber scaffolds with a controlled surface coating and mineralization

A new method was developed to coat hydroxyapatite (HAp) onto electrospun poly(lactic-co-glycolic acid) (PLGA) nanofibers for tendon-to-bone insertion site repair applications. Prior to mineralization, chitosan and heparin were covalently immobilized onto the surface of the fibers to accelerate the nucleation of bone-like HAp crystals. Uniform coatings of HAp were obtained by immersing the nanofiber scaffolds into a modified, 10-fold-concentrated simulated body fluid (m10SBF) for different periods of time. The new method resulted in thicker and denser coatings of mineral on the fibers compared to those produced by previously reported methods. Scanning electron microscopy measurements confirmed the formation of nanoscale HAp particles on the fibers. A mechanical property assessment demonstrated a higher stiffness with respect to previous coating methods. A combination of the nanoscale fibrous structure and bonelike mineral coating could mimic the structure, composition, and function of mineralized tissues.     

Competing (1)πσ* mediated dynamics in mequinol: O-H versus O-CH(3) photodissociation pathways

Deactivation of excited electronic states through coupling to dissociative (1)πσ* states in heteroaromatic systems has received considerable attention in recent years, particularly as a mechanism that contributes to the ultraviolet (UV) photostability of numerous aromatic biomolecules and their chromophores. Recent studies have expanded upon this work to look at more complex species, which involves understanding competing dynamics on two different (1)πσ* potential energy surfaces (PESs) localized on different heteroatom hydride coordinates (O-H and N-H bonds) within the same molecule. In a similar spirit, the work presented here utilizes ultrafast time-resolved velocity map ion imaging to study competing dissociation pathways along (1)πσ* PESs in mequinol (p-methoxyphenol), localized at O-H and O-CH(3) bonds yielding H atoms or CH(3) radicals, respectively, over an excitation wavelength range of 298-238 nm and at 200 nm. H atom elimination is found to be operative via either tunneling under a conical intersection (CI) (298 ≥ λ ≥ 280 nm) or ultrafast internal conversion through appropriate CIs (λ ≤ 245 nm), both of which provide mechanisms for coupling onto the dissociative state associated with the O-H bond. In the intermediate wavelength range of 280 ≥ λ ≥ 245 nm, mediated H atom elimination is not observed. In contrast, we find that state driven CH(3) radical elimination is only observed in the excitation range 264 ≥ λ ≥ 238 nm. Interpretation of these experimental results is guided by: (i) high level complete active space with second order perturbation theory (CASPT2) calculations, which provide 1-D potential energy cuts of the ground and low lying singlet excited electronic states along the O-H and O-CH(3) bond coordinates; and (ii) calculated excitation energies using CASPT2 and the equation-of-motion coupled cluster with singles and doubles excitations (EOM-CCSD) formalism. From these comprehensive studies, we find that the dynamics along the O-H coordinate generally mimic H atom elimination previously observed in phenol, whereas O-CH(3) bond fission in mequinol appears to present notably different behavior to the CH(3) elimination dynamics previously observed in anisole (methoxybenzene).     

Understanding solvent effects in the selective conversion of fructose to 5-hydroxymethyl-furfural: a molecular dynamics investigation

Selective conversion of fructose to 5-hydroxymethyl-furfural (HMF) involves the participation of high-boiling solvents like dimethyl sulfoxide (DMSO). In order to replace DMSO with low-boiling solvents, it is imperative that we understand the effect of DMSO solvation in protecting (i) HMF from rehydration and humins formation reactions and (ii) fructose from side reactions, other than its dehydration to HMF. In the present work, molecular dynamics simulations of HMF and fructose in water and in water-DMSO mixtures are carried out using the OPLS-AA force field. Radial pair distribution functions, coordination numbers and the hydrogen-bond network between the HMF/fructose molecule and the solvent molecules are analysed. The local 3-dimensional picture of the arrangement of solvent molecules around the solute, which cannot be accessed from pair distribution functions, is also computed. We show preferential coordination of DMSO around HMF and explain how this could provide a shielding effect to the HMF molecule, thus protecting it from further rehydration to levulinic acid and formic acid and from humins formation. In the case of fructose, the presence of DMSO also reduces the number of water molecules in the immediate vicinity of fructose. Though fewer water molecules coordinate around fructose, they are bound strongly to it. Analysis of the local 3-dimensional arrangement of DMSO molecules suggests that it protects the fructose molecule from side reactions that would lead to condensation or reversion products. However, the presence of DMSO molecules does not hamper the water molecules coming into contact with the oxygen atom of the hydroxyl groups of fructose, which is required for a proton transfer from water to fructose, to initiate the dehydration reaction to HMF.     

3D microoptical elements formed in a photostructurable germanium silicate by direct laser writing

We present our investigations into the fabrication of three-dimensional microoptical elements by the direct femtosecond laser writing of a germanium–silicon photosensitive hybrid material. Germanium glass composites are very interesting for optical applications as they are photosensitive, and maintain high optical transparency in the visible and near-infrared bands of the spectrum. Here, we have used a germanium containing hybrid material to make nanophotonic structures and microoptical elements such as photonic crystal templates, prisms and spatial polarization plates, both on flat surfaces and fiber tips. Our results show that this germanium silicate composite is an excellent material for microoptics fabrication.     

Photosensitive, all-glass AgPO3/silicaphotonic bandgap fiber

Photonic bandgap (PBG) guidance is observed in a solid core photonic crystal fiber (PCF) consisting of silver metaphosphate (AgPO(3)) glass embedded into a silica cladding, realized by vacuum-assisted infiltration of the molten glass into the hollow channels of a commercial silica PCF. Morphologic analysis of the cladding microstructure by optical and scanning electron microscopy reveals the formation of highly homogeneous glass strands along the PCF length. The characteristic transmission spectrum of the fiber shows PBG guidance in the range between 350 and 1650 nm. The exposure of the cladding glass matrix, using 355 nm, 150 ps laser irradiation, allows photo-induced enhancement of the transmission-to-stop-band extinction ratio by ～60 dB/cm and bandwidth tuning. Numerical calculations of the transmission pattern of the fabricated AgPO(3)/silica bandgap fiber are in good agreement with experiments.     

Bragg grating recording in low-defect optical fibers using ultraviolet femtosecond radiation and a double-phase mask interferometer

The fabrication of Bragg reflectors in fluorine depressed cladding silicate glass and SMF-28 fibers by employing a double-phase mask interferometer and 248 nm, 500 fs laser radiation is demonstrated here. The maximum refractive index changes obtained were of the order of 6 x 10(-4) for pulse intensities of 220 GW/cm(2) and accumulated energy densities of 3.5 kJ/cm(2). The Bragg gratings fabricated in the F-doped fiber endured temperatures greater than 700 degrees C, while those inscribed in the standard telecom fiber demarcated at 900 degrees C. The experimental results presented depict that the combination of the two phase mask interferometer and the 248 nm photon at sub-TW/cm(2) intensities constitute an efficient route in the fabrication of Bragg gratings in low-defect silicate glass optical fibers.