Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on superoxide reductase: role of the axial thiolate in reactivity

Superoxide reductase (SOR) is a non-heme iron enzyme that reduces superoxide to peroxide at a diffusion-controlled rate. Sulfur K-edge X-ray absorption spectroscopy (XAS) is used to investigate the ground-state electronic structure of the resting high-spin and CN- bound low-spin FeIII forms of the 1Fe SOR from Pyrococcus furiosus. A computational model with constrained imidazole rings (necessary for reproducing spin states), H-bonding interaction to the thiolate (necessary for reproducing Fe-S bond covalency of the high-spin and low-spin forms), and H-bonding to the exchangeable axial ligand (necessary to reproduce the ground state of the low-spin form) was developed and then used to investigate the enzymatic reaction mechanism. Reaction of the resting ferrous site with superoxide and protonation leading to a high-spin FeIII-OOH species and its subsequent protonation resulting in H2O2 release is calculated to be the most energetically favorable reaction pathway. Our results suggest that the thiolate acts as a covalent anionic ligand. Replacing the thiolate with a neutral noncovalent ligand makes protonation very endothermic and greatly raises the reduction potential. The covalent nature of the thiolate weakens the FeIII bond to the proximal oxygen of this hydroperoxo species, which raises its pKa by an additional 5 log units relative to the pKa of a primarily anionic ligand, facilitating its protonation. A comparison with cytochrome P450 indicates that the stronger equatorial ligand field from the porphyrin results in a low-spin FeIII-OOH species that would not be capable of efficient H2O2 release due to a spin-crossing barrier associated with formation of a high-spin 5C FeIII product. Additionally, the presence of the dianionic porphyrin pi ring in cytochrome P450 allows O-O heterolysis, forming an FeIV-oxo porphyrin radical species, which is calculated to be extremely unfavorable for the non-heme SOR ligand environment. Finally, the 5C FeIII site that results from the product release at the end of the O2- reduction cycle is calculated to be capable of reacting with a second O2-, resulting in superoxide dismutase (SOD) activity. However, in contrast to FeSOD, the 5C FeIII site of SOR, which is more positively charged, is calculated to have a high affinity for binding a sixth anionic ligand, which would inhibit its SOD activity.     

Cyclization cascade of allenyl azides: a dual mechanism

A density functional theory based computational approach to describing the mechanistic course of the allene azide cycloaddition cascade sequence has been developed. The results of these calculations permit characterization of key reactive intermediates (diradicals and/or indolidenes) and explain the different behaviors observed in the experimental studies between conjugated and nonconjugated species. Furthermore, computational analysis of certain intermediates offer insight into issues of regioselectivity and stereoselectivity in cases where different reaction channels are in competition, suggesting suitable substitutions to achieve a single regioisomer in the indole synthesis via azide-allene cyclization.     

Multiscale modeling of materials based on force and charge density fidelity

The approximate representation of a quantum solid as an equivalent composite semiclassical solid is considered for insulating materials. The composite is comprised of point ions moving on a potential energy surface. In the classical bulk domain this potential energy is represented by potentials constructed to give the same structure and elastic properties as the underlying quantum solid. In a small local quantum domain the potential is determined from a detailed quantum calculation of the electronic structure. The new features of this well-studied problem are (1) a clearly stated theoretical context in which approximations leading to the model are introduced, (2) the representation of the classical domain by potentials focused on reproducing the specific quantum response being studied, (3) development of "pseudoatoms" for a realistic treatment of charge densities where bonds have been broken to define the environment of the quantum domain, and (4) inclusion of polarization effects on the quantum domain due to its distant bulk environment. This formal structure is illustrated in detail for a SiO(2) nanorod. More importantly, each component of the proposed modeling is tested quantitatively for this case, verifying its accuracy as a faithful multiscale model of the original quantum solid. To do so, the charge density of the entire nanorod is calculated quantum mechanically to provide the reference by which to judge the accuracy of the modeling. The construction of the classical potentials, the rod, the pseudoatoms, and the multipoles is discussed and tested in detail. It is then shown that the quantum rod, the rod constructed from the classical potentials, and the composite classical/quantum rod all have the same equilibrium structure and response to elastic strain. In more detail, the charge density and forces in the quantum subdomain are accurately reproduced by the proposed modeling of the environmental effects even for strains beyond the linear domain. The accuracy of the modeling is shown to apply for two quite different choices for the underlying quantum chemical method: transfer Hamiltonian and density functional methods.     

A novel catechol-based universal support for oligonucleotide synthesis

A novel universal support for deoxyribo- and ribonucleic acid synthesis has been developed. The support, constructed from 1,4-dimethoxycatechol, represents an improvement over existing universal supports because of its ability to cleave and deprotect under mild conditions in standard reagents. Because no nonvolatile additives are required for cleavage and deprotection, the synthesized oligonucleotides do not require purification prior to use in biochemical assays. Using reverse phase HPLC and electrospray mass spectroscopy, it was determined that oligonucleotides synthesized on the universal support (UL1) 3'-dephosphorylate quickly (9 h in 28-30% ammonium hydroxide (NH4OH) at 55 degrees C, 2 h in 28-30% NH4OH at 80 degrees C, or <1 h in ammonium hydroxide/methylamine (1:1) (AMA) at 80 degrees C). Oligonucleotides used as primers for the polymerase chain reaction (PCR) assay were found to perform identically to control primers, demonstrating full biological compatibility. In addition, a method was developed for sintering the universal support directly into a filter plug which can be pressure fit into the synthesis column of a commercial synthesizer. The universal support plugs allow the synthesis of high-quality oligonucleotides at least 120 nucleotides in length, with purity comparable to non-universal commercial supports and approximately 50% lower reagent consumption. The universal support plugs are routinely used to synthesize deoxyribo-, ribo-, 3'-modified, 5'-modified, and thioated oligonucleotides. The flexibility of the universal support and the efficiency of 3'-dephosphorylation are expected to increase the use of universal supports in oligonucleotide synthesis.     

Phase transitions and surface morphology of surfactant-coated aerosol particles

Probe molecule spectroscopy and hygroscopic growth curves characterize the morphology of surfactant-coated aerosol particles as a function of relative humidity (RH). This study focuses on particles composed of either potassium iodide or sodium chloride and sodium dodecyl sulfate (SDS). At high RH, these mixed particles assume a reverse micelle type structure, and at low RH, they comprise a solid core of either KI or NaCl coated with SDS and water. The deliquescence relative humidity (DRH) and efflorescence relative humidity (ERH) of the inorganic fraction of the mixed particles are very similar to those of the pure salts. The surface polarity and morphology sampled by the coumarin 314 probe molecule ranges from that of a water-organic interface to that of an ionic surface and depends strongly on the RH and the amount of SDS. When the SDS coverage of the droplet just prior to efflorescence reaches approximately one monolayer, a thin soap film persists on the surface to values of RH much lower than the ERH. Both the electronic spectroscopy and photoelectric charging efficiency show a separate efflorescence for this layer at RH < 5%. The spectroscopy further reveals that there is a hysteresis associated with this low RH phase transition for both KI and NaCl cores.     

Coherently controlled ultrafast four-wave mixing spectroscopy

A novel approach to coherent nonlinear optical spectroscopy based on two-dimensional femtosecond pulse shaping is introduced. Multiple phase-stable output beams are created and overlapped at the sample in a phase-matched boxcars geometry via two-dimensional femtosecond pulse shaping. The pulse timing, shape, phase, and spectral content within all beams may be specified, yielding an unprecedented level of control over the interacting fields in nonlinear spectroscopic experiments. Heterodyne detection and phase cycling of the nonlinear signal are easily implemented due to the excellent phase stability among all output beams. This approach combines the waveform generation capabilities of magnetic resonance spectroscopy with the wavevector specification and phase matching of nonlinear optical spectroscopy, yielding the control capabilities and signal selectivity of both. Results on four prototype systems are used to illustrate some of the novel possibilities of this method.     

Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling,synthesis and biological testing

Journal of Computer-Aided Molecular Design - The problem of designing new antiviral drugs against Human Cytomegalovirus (HCMV) was addressed using the Online Chemical Modeling Environment (OCHEM)....     

Existence of minimisers for nonlinear strain-gradient elastoplasticity with finite or infinite cross-hardening

Consideration is given to the existence of minimisers for a family of variational models of finite-strain single-crystal elastoplasticity with infinite cross-hardening. The non-convex cross-hardening condition on the plastic slip necessitates the use of special analytical tools, in particular the combination of the div-curl Lemma with a slip-exclusion Lemma of Conti & Ortiz [1], if one wishes to prove existence for physically reasonable parameters. A regularised model with a cross-hardening matrix is also briefly discussed - existence of minimisers for this model also follows by a div-curl argument, at least if one goes over to the case of linearised elasticity. Moreover, in this case one can also prove that the regularised model Γ-converges to the infinite-cross-hardening model as the hardening matrix becomes unboundedly large. (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

The use of physical and virtual infrastructures for the validation of algal cryopreservation methods in international culture collections

Two cryopreservation methods, colligative cryoprotection coupled with controlled cooling and vitrification-based, encapsulation-dehydration were validated by five members of the EU research infrastructure consortium, COBRA, and two independent external validators. The test strain Chlorella vulgaris SAG 211-11b was successfully cryopreserved using two-step cooling employing passive (Mr Frosty) and Controlled Rate Freezers (CRF) attaining the desired recovery target within 15% of the median viability level (94%). Significant differences (p < 0.05) between cooling regimes were observed where Mr Frosty was more variable (Inter-Quartile Range being 21.5%, versus 13.0% for CRF samples). Viability assessment using fluorescein diacetate gave significantly (P < 0.0001) higher survival than growth in agar with median values being 96% and 89%, respectively. On employing encapsulation-dehydration, greater variability between some validators was observed, with six labs observing recovery in 100% of the beads (84-95% of cells surviving) and one lab observing survival in 80% of the treated beads. Bead disruption followed by algal growth in agar was considered the most reliable and accurate method of assessing cell survival for encapsulation-dehydration.