No description available.

We have modelled structures and dynamics of hydrogen bond networks that form from imidazoles tethered to oligomeric aliphatic backbones in crystalline and glassy phases. We have studied the behavior of oligomers containing 5 or 10 imidazole groups. These systems have been simulated over the range 100-900 K with constantpressure molecular dynamics using the AMBER 94 force field, which was found to show good agreement with ab initio calculations on hydrogen bond strengths and imidazole rotational barriers. Hypothetical crystalline solids formed from packed 5-mers and 10-mers melt above 600 K, then form glassy solids upon cooling. Viewing hydrogen bond networks as clusters, we gathered statistics on cluster sizes and percolating pathways as a function of temperature, for comparison with the same quantities extracted from neat imidazole liquid. We have found that, at a given temperature, the glass composed of imidazole 5-mers shows the same hydrogen bond mean cluster size as that from the 10-mer glass, and that this size is consistently larger than that in liquid imidazole. Hydrogen bond clusters were found to percolate across the simulation cell for all glassy and crystalline solids, but not for any imidazole liquid. The apparent activation energy associated with hydrogen bond lifetimes in these glasses (9.3 kJ/mol) is close to that for the liquid (8.7 kJ/mol), but is substantially less than that in the crystalline solid (13.3 kJ/mol). These results indicate that glassy oligomeric solids show a promising mixture of extended hydrogen bond clusters and liquid-like dynamics. This study prompted a continued look at smaller oligomers (monomers, dimers, trimers, and pentamers). Using many of the above statistics we found that decreased chain length decreased the tendency to form global hydrogen bonding networks (percolation pathways). We also developed an reorientational correlation for the imidazole ring which allowed us to extract a timescale for reorientation. Smaller chains produce faster reorientation timescales and thus there is a trade off between faster reorientation dynamics and long global hydrogen bonding networks. Moreover we showed that homogeneity of chain length has no effect on hydrogen bonding statistics. Initial development on a multi-state empirical valence bond model has been to study proton transfer in liquid imidazole. We have shown that GAFF produces very large proton transfer barriers created by a highly repulsive N· · ·H VDW interaction at the transition point. In order to produce an acceptable fit to the potential energy surface while still producing stable dynamics this interaction must be turned off. This is in contrary to what is reported in the literature [14]. Using our model we have produced simulations with acceptable drift in the total energy (3.2 kcal/mol per ns) and negligible drift in the temperature (.12 K/ns).

No description available.

No description available.

<p dir="ltr">While electrospray ionization facilitates the mass determination of smaller analytes, ESI of macromolecular native protein complexes is complicated by narrow charge state distributions and overlapping charge states, hindering mass analysis. This problem is further exacerbated with heterogeneous protein mixtures that yield ions of similar <i>m/z</i> values. Charge-reduction of a selected precursor population via ion/ion reaction provides further <i>m/z</i> separation and utilizes an extended mass range, allowing for mass determination. All experiments were performed on a TripleTOF 5600 quadrupole TOF mass spectrometer (SCIEX), modified for ion/ion reactions. Alternatively pulsed nano-electrospray ionization allowed for sequential injection of reagent and analyte ions. Selected cations were reacted with different anions, and charge-reduced product ions were mass analyzed on a TOF with modifications and tuning for an extended <i>m/z</i> range of 200,000+. Charge reduction via proton transfer reaction (PTR) involves a perfluorinated anion reacting with a multiply charged cation and results in the loss of one proton removal at a time. Through multiple iterations of PTR, the overlapping charge states of protein ions (from an unstained protein standard mixture consisting of 12 recombinant proteins of masses10kDa-200kDa) within the <i>m/z</i> 6500-8500 and <i>m/z</i> 4000-5000 ranges, generated under native conditions by ESI, transforms to a product spectrum with single-digit charge states, thereby deconvoluting the precursor “blob”.</p>

One-color resonance two-photo ionization (R2PI) spectra of mixed clusters of styrene molecule (S) with polar molecules [water (W), methanol (M), ethanol (E), and trifuoroethanol (T)] were measured through the S1←S0 transition of the styrene molecule. The spectra reveal a rapid increase in complexity with the number of polar molecules in the cluster, associated with van der Waal modes and isomeric forms. The spectral shifts of the cluster origins from the S1-S0 transition of the bare styrene molecule reflect the nature of the intermolecular interactions within the binary clusters. The obtained R2PI spectra xv were compared with the spectra of the analogous benzene containing clusters. The styrene-water and the styrene-methanol complexes exhibited very different spectral shifts and structures as compared to the benzene-water and benzene-methanol complexes, respectively. The favorable interactions of polar molecules with the olefin group of styrene may explain the strong inhibition effects of exerted by small concentrations of water and alcohols on the cationic polymerization of styrene. Size-specified intracluster proton transfer reactions were observed for mixed clusters of styrene dimer with water, methanol and ethanol molecules. It was proposed that the polar molecules tend to aggregate around the olefin center, which promotes the transfer of the charge from the propagating chain to the hydrogen-bonded polar molecules subcluster. The minimum number of polar molecules required for a proton transfer to take place exothermically depends on the proton affinity of the polar molecules subcluster. The estimated upper limit value for the proton affinity of styrene dimer radical was evaluated based on the energetic of the proton transfer reaction to be ≤ 220.4 kcal/mol. No intracluster reaction was observed for styrene-trifluoroethanol (STn) system. In order to provide a comparison between the styrene and benzene systems, the benzene-ethanol (BEn) and benzene-trifluoroethanol (BTn) clusters were studied by using the R2PI technique via the 6¹0 transition of the benzene molecule. Both dissociative electron transfer and dissociative proton transfer reactions were observed within the BEn clusters, where n = 2 and 3, respectively. Proton transfer reactions were observed following dissociative electron transfer reactions within the (BTn) clusters, where n = 4, to generate the protonated clusters (H+Tn).

As antocianinas compreendem o maior conjunto de pigmentos solúveis em água do reino vegetal. A absorção da luz por estes compostos, responsáveis pelas cores vermelha, azul e roxa da maioria das frutas e flores, é produto de combinações de vários fatores, como o número de substituintes, a presença ou não de outras moléculas capazes de estabilizar a cor (“co-pigmentos"), o pH local do meio e a natureza do microambiente em que a antocianina se encontra. A reatividade química e fotoquímica das antocianinas já é relativamente complexa em solução aquosa na ausência de micelas, onde cada um dos processos químicos e fotoquímicos ocorre numa faixa de tempo distinta. Uma forma de se diminuir o número de espécies em solução é o emprego de antocianinas sintéticas com estruturas simplificadas, conhecidas como sais de flavílio, cuja variação no número, posição e tipo químico de substituinte permite um certo controle sobre as frações molares das espécies. Neste estudo procurou-se compreender os processos que regem o equilíbrio ácido-base e a hidratação do cátion flavílio em ambiente micelar. Estes dois processos exercem um papel central na estabilização da cor em antocianinas. Foram utilizados três sais de flavílio: o 4-carboxi-7-hidroxi-4\'-metoxiflavílio (CHMF), o 2-fenilbenzopirílio e o 4\'-metoxiflavílio. Os dois grupos ionizáveis do CHMF possuem pKas distintos (pKa1 = 0,73; pKa2 = 4,84), cujas dinâmicas de protonação/desprotonação são influenciadas pelas micelas de SDS de modos diferentes. O cátion é estabilizado preferencialmente pelas micelas aniônicas em relação ao zwitterion (pKa1SDS = 2,77), que por sua vez é mais favorecido que a base quinonoidal (pKa2SDS = 5,64). A estabilização do cátion está relacionada com as fortes interações eletrostáticas entre a espécie e a micela carregada negativamente. A base quinonoidal, que no caso específico do CHMF tem carga negativa, é desfavorecida em relação ao zwitterion. Adicionalmente, em SDS praticamente não se observa hidrólise da espécie zwitteriônica. Com relação ao 2-fenilbenzopirílio (pKw = 3,01) e o 4\'-metoxiflavílio (pKw = 4,47), a primeira observação feita é que a inclusão do grupo metoxi na posição C4\' estabiliza o cátion flavílio, diminuindo a extensão da hidrólise por meio de transferência de carga para o anel central. O efeito de estabilização do cátion pelo ambiente micelar, verificado pelo aumento do pKw, é mais pronunciado no 2-fenilbenzopirílio (pKwSDS = 4,73) do que no 4\'-metoxiflavílio (pKwSDS = 5,05). Os processos cinéticos mostram que a reação de hidratação (kw) do flavílio sem substituintes diminui 65 vezes em SDS, enquanto que a reação no sentido inverso se mantém dentro da mesma ordem de magnitude. Já no caso do 4\'-metoxiflavílio, foi verificado que ambas as constantes de velocidade aumentam, mas a constante de desidratação do hemicetal (k-w), que depende da concentração de prótons, é a mais afetada, aumentando cerca de 15 vezes. Este fato é um indicativo de que o pH na interface micelar é o fator de estabilização do cátion do 4\'-metoxiflavílio. Adicionalmente foram feitos cálculos computacionais de transições eletrônicas, pKa e potenciais de redução em nível ab initio para um conjunto cátions flavílios e respectivas bases quinonoidais. Os valores de pKa calculados apresentaram um desvio médio de +/- 0,5 unidade de pKa. / Anthocyanins comprise the major water-soluble pigment group in the Plant Kingdom. Light absorption by these compounds is responsible for the diverse colors in many flowers and fruits and can be modulated by phenomena such as self-association of flavylium cations or anhydrobases, copigmentation with other polyphenols and flavonoids, complexation with metal ions, incorporation of anthocyanins into microaggregates like micelles and the pH of the medium. The chemical and photochemical reactivity of anthocyanins is quite complex in aqueous solution and each process occurs in a different time range. The use of structurally simplified synthetic flavylium salts permits a certain control over the mole fractions of the various species in solution. In this study we used the synthetic flavylium ions 4-carboxy-7-hydroxy-4\'-methoxyflavylium (CHMF), 2-phenylbenzopyrylium and 4´-methoxyflavylium to investigate the main processes that influence the acid-base equilibrium and hydration of the flavylium cation in micellar environments. Such reactions play a central role in color stabilization of anthocyanins. CHMF has two ionizable groups with distinct pKas (pKa1 = 0,73; pKa2 = 4,84), and the protonation/deprotonation dynamics of these groups are affected differently by SDS micelles. The results show that SDS micelles stabilize the cationic form rather than the zwitterion (pKa1SDS = 2,77), which is favored relative to the quinonoidal base (pKa2SDS = 5,64). The preferential stabilization of the cation is related to electrostatic interactions of this form with the anionic micelle. The quinonoidal base, which in the specific case of CHMF is an anion, is disfavored relative to the zwitterion. In addition, the hydrolysis of the zwitterionic form is substantially reduced in micellar SDS solutions. The comparison of 2-phenylbenzopyrylium (pKw = 3,01) and 4´-methoxyflavylium (pKw = 4,47) shows that the methoxy group at the C4´ position stabilizes the cationic form, reducing the hydration by charge transfer to the central ring. The stabilization of the cationic form by the micellar environment, which is reflected in the increase of the pKw, is more pronounced for the 2-phenylbenzopyrylium cation (pKwSDS = 4,73) than for 4´-methoxyflavylium (pKwSDS = 5,05). Kinetic studies of the 2-phenylbenzopyrylium ion in SDS indicate a 65-fold reduction in the hydration rate constant (kw), while the inverse reaction has the same magnitude as in water. In the case of the 4´-methoxyflavylium ion, both rate constants associated with the equilibrium between the flavylium cation and hemicetal increased. However, the [H+]-dependent rate constant for dehydration of the hemicetal is affected to a greater extent, increasing about 15 fold, indicating stabilization of the 4\'-methoxyflavylium cation by the micellar interface. Finally, computational calculations were performed at the ab initio level for several flavylium cations and anhydrobases to estimate the electronic transitions, pKa and reduction potentials. The quality of the calculated pKa results were compared with experimental data and the mean absolute deviation is +/- 0.5 pKa unit.

"The need for an efficient, non-polluting power source for vehicles in urban environments has resulted in increased attention to the option of fuel cell powered vehicles of high efficiency and low emissions. Of various fuel cell systems considered, the proton exchange membrane (PEM) fuel cell technology seems to be the most suitable one for the terrestrial transportation applications. This is thanks to its low temperature of operation (hence, fast cold start), and a combination of high power density and high energy conversion efficiency. Besides automobile and stationary applications (distributed power for homes, office buildings, and as back-up for critical applications such as hospitals and credit card centers), future consumer electronics also demands compact long-lasting sources of power, and fuel cell is a promising candidate in these applications. The goal of a cost effective and high performance fuel cell has resulted in very active multidisciplinary research. Although significant progress has been made on PEM fuel cells over the last twenty years, further progress in fuel cell research is still needed before the commercially viable fuel cell utilization in transportation, potable and stationary applications. A chief goal among others is the design of PEM fuel cells that can operate with impure hydrogen containing traces of CO, which has been the objective of this research. Standard Pt and PtRu anode catalyst has been studied systematically under practical fuel cell conditions, in an attempt to understand the mechanism and kinetics of H2/CO electrooxidation on these noble metal catalysts. In the study of Pt as anode catalyst, it was found that the fuel cell performance was strongly affected by the anode flow rate and cathode oxygen pressure. A CO electrooxidation kinetic model was developed taking into account the CO inventory in the anode, which can successfully simulate the experimental results. It was found that there is finite CO electrooxidation even on Pt anode with H2/CO as anode feed. Thus, anode overpotential and outlet CO concentration is a function of anode inlet flow rate at a constant current density. The on-line monitoring of CO concentration in PEM fuel cell anode exit has proved that the ~{!0~}ligand mechanism~{!1~} and ~{!0~}bifunctional mechanism~{!1~} coexist as the CO tolerance mechanisms for PtRu anode catalyst. For PtRu anode catalyst, sustained potential oscillations were observed when the fuel cell was operated at constant current density with H2/CO as anode feed. Temperature was found to be the key bifurcation parameter besides current density and the anode flow rate for the onset of potential oscillations. The anode kinetic model was extended further to unsteady state which can reasonably reproduce and adequately explain the oscillatory phenomenon. The potential oscillations are due to the coupling of anode electrooxidation of H2 and CO on PtRu alloy surface, on which OHad can be formed more facile, preferably on top of Ru atoms at lower overpotentials. One parameter bifurcation and local linear stability analysis have shown that the bifurcation experienced during the variation of fuel cell temperature is a Hopf bifurcation, which leads to stable potential oscillations when the fuel cell is set at constant current density. It was further found that a PEM fuel cell operated in an autonomous oscillatory state produces higher time-averaged cell voltage and power density as compared to the stable steady-state operation, which may be useful for developing an operational strategy for improved management of power output in PEM fuel cells with the presence of CO in anode feed. Finally, an Electrochemical Preferential Oxidation (ECPrOx) process is proposed to replace the conventional PrOx for cleaning CO from reformate gas, which can selectively oxidized CO electrochemically while generating supplemental electrical power without wasting hydrogen."

<p>Cytochrome <i>cd</i>₁ nitrite reductase is a bifunctional enzyme, which catalyses the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of oxygen to water. The latter is a cytochrome oxidase reaction. Both reactions occur on the <i>d</i>₁ haem iron of the enzyme.</p><p>Time resolved crystallographic studies presented here show that the mechanisms of nitrite and oxygen reduction share common elements. This is of interest from an evolutionary point of view since aerobic respiratory enzymes are thought to have evolved from denitrifying enzymes. Despite of similarities, the results also imply different requirements for the timing of electron transfer to the active site in these reactions.</p><p>Quantum chemical calculations suggest that nitric oxide, the product of nitrite reduction, is not spontaneously released from the haem iron while this is not the case with water. Reduction of the haem while nitric oxide is still bound to it would result in a tight dead-end complex. A mechanism must therefore exist for the selective control of electron transfer during the reaction.</p><p>Structural studies with a product analogue (carbon monoxide) combined with flash photolysis of the complex in solution revealed an unexpected proton uptake by the active site as the neutral CO molecule left the enzyme. This led to the suggestion that the increased positive potential of the active site triggers preferential electron transfer when the active site is empty.</p><p>Crystallisation and structure determination of the reduced enzyme revealed extremely large domain rearrangements. These results offer insights into the role of tethered electron shuttle proteins in complex redox systems, and suggests a mechanism for conformational gating in catalysis.</p>

Cytochrome cd1 nitrite reductase is a bifunctional enzyme, which catalyses the one-electron reduction of nitrite to nitric oxide, and the four-electron reduction of oxygen to water. The latter is a cytochrome oxidase reaction. Both reactions occur on the d1 haem iron of the enzyme. Time resolved crystallographic studies presented here show that the mechanisms of nitrite and oxygen reduction share common elements. This is of interest from an evolutionary point of view since aerobic respiratory enzymes are thought to have evolved from denitrifying enzymes. Despite of similarities, the results also imply different requirements for the timing of electron transfer to the active site in these reactions. Quantum chemical calculations suggest that nitric oxide, the product of nitrite reduction, is not spontaneously released from the haem iron while this is not the case with water. Reduction of the haem while nitric oxide is still bound to it would result in a tight dead-end complex. A mechanism must therefore exist for the selective control of electron transfer during the reaction. Structural studies with a product analogue (carbon monoxide) combined with flash photolysis of the complex in solution revealed an unexpected proton uptake by the active site as the neutral CO molecule left the enzyme. This led to the suggestion that the increased positive potential of the active site triggers preferential electron transfer when the active site is empty. Crystallisation and structure determination of the reduced enzyme revealed extremely large domain rearrangements. These results offer insights into the role of tethered electron shuttle proteins in complex redox systems, and suggests a mechanism for conformational gating in catalysis.