Generation of nitrogen functionalities on activated carbons by amidation reactions and Hofmann rearrangement: Chemical and electrochemical characterization

Nitrogen functionalization of a highly microporous activated carbon (BET surface area higher than 3000 m2/g) has been achieved using the following sequence of treatments: (i) chemical oxidation using concentrated nitric acid, (ii) amidation by acyl chloride substitution with NH4NO3 and (iii) amination by Hoffman rearrangement. This reaction pathway yielded amide and amine functional groups, and a total nitrogen content higher than 3 at.%. It is achieved producing only a small decrease (20%) of the starting microporosity, being most of it related to the initial wet oxidation of the activated carbon. Remarkably, nitrogen aromatic rings were also formed as a consequence of secondary cyclation reactions. The controlled step-by-step modification of the surface chemistry allowed to assess the influence of individual nitrogen surface groups in the electrochemical performance in 1 M H2SO4 of the carbon materials. The largest gravimetric capacitance was registered for the pristine activated carbon due to its largest apparent surface area. The nitrogen-containing activated carbons showed the highest surface capacitances. Interestingly, the amidated activated carbon showed the superior capacitance retention due to the presence of functional groups (such as lactams, imides and pyrroles) that enhance electrical conductivity through their electron-donating properties, showing a capacitance of 83 F/g at 50 A/g.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

Transition-state-theory calculations for reactions of O(3P) with halogenated olefins

The potential energy surfaces for the reactions of atomic oxygen in its ground electronic state, O(P-3), with the olefins: CF2=CCl2 and CF2=CF - CF3, have been characterized using ab initio molecular orbital calculations. Geometry optimization and vibrational frequency calculations were performed for reactants, transition states and products at the MP2 and QCISD levels of theory using the 6-31G(d) basis set. This database was then used to calculate the rate constants by means of Transition-State-Theory. To obtain a better reference and to test the reliability of the activation barriers we have also carried out computations using the CCSD(T)(fc)/6-311Gdagger, MP4(SDQ)(fc)/CBSB4 and MP2(fc)/CBSB3 single point energy calculations at both of the above levels of theory, as well as with the composite CBS-RAD procedure ( P. M. Mayer, C. J. Parkinson, D. M. Smith and L. Radom, J. Chem. Phys., 1998, 108, 604) and a modi. cation of this approach, called: CBS-RAD( MP2, MP2). It was found that the kinetic parameters obtained in this work particularly with the CBS-RAD ( MP2, MP2) procedure are in reasonable agreement with the experimental values. For both reactions it is found that the channels leading to the olefin double-bond addition predominates with respect to any other reaction pathway. However, on account of the different substituents in the alkenes we have located, at all levels of theory, two transition states for each reaction. Moreover, we have found that, for the reactions studied, a correlation exists between the activation energies and the electronic structure of the transition states which can explain the influence of the substituent effect on the reactivity of the halo-olefins.

Thermal decomposition behavior of 1,2-bis-(2,4,6-tribromophenoxy)ethane

The thermal decomposition behavior of 1,2-bis-(2,4,6-tribromophenoxy)ethane (BTBPE) widely used as flame retardant plastics additive was studied by HRTG and differential scanning calorimetries. It was pyrolysed in inert atmosphere at 240 and 340 °C in isothermal conditions, the decomposition products were collected and investigated by means of IR and GC-MS, most of them are identified. It was found that BTBPE mostly evaporates at 240 °C. The decomposition products at 340°C depend on rate of their removal from the hot reaction zone. Main primary decomposition products found in case of rapid removal are tribromophenol and vinyl tribromophenyl ether. Whereas, prolonged contact with heating zone also produces hydrogen bromide, ethylene bromide, polybrominated vinyl phenyl ethers and diphenyl ethers, and dibenzodioxins. The nature of the identified compounds are in accordance with a molecular and radical pyrolysis reaction pathway. © 2002 Elsevier Science B.V. All rights reserved.

Ketones in hydrothermal petroleums and sediments from Guaymas Basin

The polar compound (NSO) fractions of seabed petroleums and sediment extracts from the Guaymas Basin hydrothermal system have been analyzed by gas chromatography and gas chromatography-mass spectrometry. The oils were collected from the interiors and exteriors of high temperature hydrothermal vents and represent hydrothermal pyrolysates that have migrated to the seafloor by hydrothermal fluid circulation. The downcore samples are representative of both thermally unaltered and thermally altered sediments. The survey has revealed the presence of oxygenated compounds correlated with samples exhibiting a high degree of thermal maturity. Several homologous series of related ketone isomers are enriched in the interiors of the hydrothermal vent samples or in hydrothermally-altered sequences of the downcore sediments (DSDP Holes 477 and 481A). The n-alkanones range in carbon number from C11 to C33 with a Cmax from 14 to 23, distributions that are similar to those of the n-alkanes. The alkan-2-ones are usually in highest concentrations, with lower amounts of 3-, 4-, 5-, 6-, 7- (and higher) alkanones, and they exhibit no carbon number preference (there is an odd carbon number preference of alkanones observed for downcore samples). The alkanones are enriched in the interiors of the hydrothermal vent spires or in downcore hydrothermally-altered sediments, indicating an origin at depth or in the hydrothermal fluids and not from an external biogenic deposition. Minor amounts of C13 and C18 isoprenoid ketones are also present. Simulation of the natural hydrothermal alternation process by laboratory hydrous pyrolysis techniques provided information regarding the mode of alkanone formation. Hydrous pyrolysis of n-C32H66 at 350°C for 72 h with water only or water with inorganic additives has been studied using a stainless steel reaction vessel. In each experiment oxygenated hydrocarbons, including alkanones, were formed from the n-alkane. The product distributions indicate a reaction pathway consisting of n-alkanes and a-olefins as primary cracking products with internal olefins and alkanones as secondary reaction products. Hydrous pyrolyses of Messel shale spiked with molecular probes have been performed under similar time and temperature constraints to produce alkanone distributions like those found in the hydrothermal vent petroleums.

Thermal degradation studies on Edible Oil during Deep Fat Frying Process

Deep fat frying process is one of the widely followed cooking practices throughout the world. Cooking oils serve as a medium for frying food for transferring heat and makes fried food tasty and palatable. Frying process is a most complex process involving numerous physicochemical changes which are complicated to understand. Frying leads to thermal degradation of oil through thermo-oxidation, hydrolysis, and polymerization. Hydrolysis results in formation of free fatty acids whereas oxidation process produces hydroperoxides and small molecular carbonyl compounds. This whole process leads to the formation of polar compounds and degradation of antioxidants that further degrades frying oil. Eventually, through mass transfer process these degradation products accumulate into fried food and reduce the nutritional quality of both oil and food. Thus, the frying process is of research interest calls for detailed systematic study which is chosen for the present study. The primary objective of this study is to understand the mechanism of degradation and characterization ofdegraded products which helps in arriving at the limits for frying oil utilization in terms of number of frying cycles. The mechanistic studies and the knowledge on the degraded products help to understand the way to retard the deterioration of oil for stability and enhancement of frying cycles. The study also explores the formation of the predominant polar compounds and their structural elucidation through mass spectrometry. Oxidation of oil is another important factor that ignites the degradation phenomena. One of the best ways to increase thermal stability of any oil is addition of potent antioxidants. But, most of the natural and synthetic antioxidants are unstable and ineffective at frying temperatures. Therefore, it is necessary to screen alternative antioxidants for their activity in the refined oils which are devoid of any added antioxidants. In this context, this study discussed the efficacy of several natural and synthetic antioxidants to retard the formation of polar compounds and thermooxidation during prolonged frying conditions. Similarly, the advantage of blending of two different oils to improve the thermal stability was explored. The present study brings out the total picture on the type of degradation products formed during frying and the ways of retarding the determination to improve upon the stability of the oil and enhancement of frying cycles.

Surface Activity and Bulk Defect Chemistry of Solid Oxide Fuel Cell Cathodes

In the first half of this thesis, a new robotic instrument called a scanning impedance probe is presented that can acquire electrochemical impedance spectra in automated fashion from hundreds of thin film microelectrodes with systematically varied properties. Results from this instrument are presented for three catalyst compositions that are commonly considered for use in state-of-the-art solid oxide fuel cell cathodes. For (La_0.8Sr_0.2)_0.95Mn_O3+δ (LSM), the impedance spectra are well fit by a through-the-film reaction pathway. Transport rates are extracted, and the surface activity towards oxygen reduction is found to be correlated with the number of exposed grain boundary sites, suggesting that grain boundaries are more surface-active than grains. For La_0.5Sr_0.5Co_O3-δ (LSC), the surface activity degrades ~50x initially and then stabilizes at a comparable activity to that of previously measured Ba_0.5Sr_0.5Co_0.8Fe_0.2O3-δ films. For Sr_0.06Nb_0.06Bi_1.87O₃ (SNB), an example of a doped bismuth oxide, the activity of the metal-SNB boundary is measured.

In the second half of this thesis, SrCo_0.9Nb_0.1O_3-δ is selected as a case study of perovskites containing Sr and Co, which are the most active oxygen reduction catalysts known. Several bulk properties are measured, and synchrotron data are presented that provide strong evidence of substantial cobalt-oxygen covalency at high temperatures. This covalent bonding may be the underlying source of the high surface activity.

Reactions of tetrahalogeno-1,2-benzoquinones. Part III. Reaction of tetrachloro-1,2-benzoquinone with tetralones and naphthols: Pathway to the condensates

With a view to understanding the mechanism of the formation of 6-methoxy-2,2-(tetrachloro--phenylenedioxy)-naphthalen-1 (2H)-one (IIIa) in the reaction of 6-methoxy-1-tetralone (Ia) with tetrachloro-1,2-benzoquinone (II), the reaction of (II) with various tetralones and naphthols has been studied. Reaction with either α-tetralone or α-naphthol gives 2,2-(tetrachloro-o-phenylenedioxy)naphthalen-1 (2H)-one (IIIb), whereas reaction with either β-tetralone or β-naphthol gives a mixture of (IIIb) and ,1-(tetrachloro-o-phenylenedioxy)-naphthalen-2 (1H)-one (IX), with the former predominating. Further, reactions of (II) with 7-methoxy-3,4-dihydrophenanthren- 1 (2H)-one and m-methoxyphenol gave respectively 7-methoxy- ,2-(tetrachloro-o- phenylenedioxy)phenanthren-1 (2H)-one (VII) and 3-methoxy-6,6-(tetrachloro-o- phenylenedioxy)cyclohexa-2,4-dien-1-one (VIII). Structures of all these compounds have been proved on the basis of i.r. and n.m.r. data. The pathway to the formation of the condensates (III) is discussed.

The underlying pathway structure of biochemical reaction networks

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function.

Identification of the proton pathway in bacterial reaction centers: Replacement of Asp-M17 and Asp-L210 with Asn reduces the proton transfer rate in the presence of Cd2+

The reaction center (RC) from Rhodobacter sphaeroides converts light into chemical energy through the reduction and protonation of a bound quinone molecule QB (the secondary quinone electron acceptor). We investigated the proton transfer pathway by measuring the proton-coupled electron transfer, kAB(2) [QA⨪QB⨪ + H+ → QA(QBH)−] in native and mutant RCs in the absence and presence of Cd2+. Previous work has shown that the binding of Cd2+ decreases kAB(2) in native RCs ≈100-fold. The preceding paper shows that bound Cd2+ binds to Asp-H124, His-H126, and His-H128. This region represents the entry point for protons. In this work we investigated the proton transfer pathway connecting the entry point with QB⨪ by searching for mutations that greatly affect kAB(2) (≳10-fold) in the presence of Cd2+, where kAB(2) is limited by the proton transfer rate (kH). Upon mutation of Asp-L210 or Asp-M17 to Asn, kH decreased from ≈60 s−1 to ≈7 s−1, which shows the important role that Asp-L210 and Asp-M17 play in the proton transfer chain. By comparing the rate of proton transfer in the mutants (kH ≈ 7 s−1) with that in native RCs in the absence of Cd2+ (kH ≥ 104 s−1), we conclude that alternate proton transfer pathways, which have been postulated, are at least 103-fold less effective.

Identification of the proton pathway in bacterial reaction centers: Inhibition of proton transfer by binding of Zn2+ or Cd2+

The reaction center (RC) from Rhodobacter sphaeroides converts light into chemical energy through the light induced two-electron, two-proton reduction of a bound quinone molecule QB (the secondary quinone acceptor). A unique pathway for proton transfer to the QB site had so far not been determined. To study the molecular basis for proton transfer, we investigated the effects of exogenous metal ion binding on the kinetics of the proton-assisted electron transfer kAB(2) (QA−•QB−• + H+ → QA(QBH)−, where QA is the primary quinone acceptor). Zn2+ and Cd2+ bound stoichiometrically to the RC (KD ≤ 0.5 μM) and reduced the observed value of kAB(2) 10-fold and 20-fold (pH 8.0), respectively. The bound metal changed the mechanism of the kAB(2) reaction. In native RCs, kAB(2) was previously shown to be rate-limited by electron transfer based on the dependence of kAB(2) on the driving force for electron transfer. Upon addition of Zn2+ or Cd2+, kAB(2) became approximately independent of the electron driving force, implying that the rate of proton transfer was reduced (≥ 102-fold) and has become the rate-limiting step. The lack of an effect of the metal binding on the charge recombination reaction D+•QAQB−• → DQAQB suggests that the binding site is located far (>10 Å) from QB. This hypothesis is confirmed by preliminary x-ray structure analysis. The large change in the rate of proton transfer caused by the stoichiometric binding of the metal ion shows that there is one dominant site of proton entry into the RC from which proton transfer to QB−• occurs.

Identification of the proton pathway in bacterial reaction centers: Both protons associated with reduction of QB to QBH2 share a common entry point

The reaction center from Rhodobacter sphaeroides uses light energy for the reduction and protonation of a quinone molecule, QB. This process involves the transfer of two protons from the aqueous solution to the protein-bound QB molecule. The second proton, H+(2), is supplied to QB by Glu-L212, an internal residue protonated in response to formation of QA− and QB−. In this work, the pathway for H+(2) to Glu-L212 was studied by measuring the effects of divalent metal ion binding on the protonation of Glu-L212, which was assayed by two types of processes. One was proton uptake from solution after the one-electron reduction of QA (DQA→D+QA−) and QB (DQB→D+QB−), studied by using pH-sensitive dyes. The other was the electron transfer kAB(1) (QA−QB→QAQB−). At pH 8.5, binding of Zn2+, Cd2+, or Ni2+ reduced the rates of proton uptake upon QA− and QB− formation as well as kAB(1) by ≈an order of magnitude, resulting in similar final values, indicating that there is a common rate-limiting step. Because D+QA− is formed 105-fold faster than the induced proton uptake, the observed rate decrease must be caused by an inhibition of the proton transfer. The Glu-L212→Gln mutant reaction centers displayed greatly reduced amplitudes of proton uptake and exhibited no changes in rates of proton uptake or electron transfer upon Zn2+ binding. Therefore, metal binding specifically decreased the rate of proton transfer to Glu-L212, because the observed rates were decreased only when proton uptake by Glu-L212 was required. The entry point for the second proton H+(2) was thus identified to be the same as for the first proton H+(1), close to the metal binding region Asp-H124, His-H126, and His-H128.

The ionic products from bredigite bioceramics induced cementogenic differentiation of periodontal ligament cells via activation of the Wnt/β-catenin signalling pathway

Periodontitis results from the destructive inflammatory reaction of the host elicited by a bacterial biofilm adhering to the tooth surface and if left untreated, may lead to the loss of the teeth and the surrounding tissues, including the alveolar bone. Cementum is a specialized calcified tissue covering the tooth root and an essential part of the periodontium which enables the attachment of the periodontal ligament to the root and the surrounding alveolar bone. Periodontal ligament cells (PDLCs) represent a promising cell source for periodontal tissue engineering. Since cementogenesis is the critical event for the regeneration of periodontal tissues, this study examined whether inorganic stimuli derived from bioactive bredigite (Ca7MgSi4O16) bioceramics could stimulate the proliferation and cementogenic differentiation of PDLCs, and further investigated the involvement of the Wnt/β-catenin signalling pathway during this process via analysing gene/protein expression of PDLCs which interacted with bredigite extracts. Our results showed that the ionic products from bredigite powder extracts led to significantly enhanced proliferation and cementogenic differentiation, including mineralization–nodule formation, ALP activity and a series of bone/cementum-related gene/protein expression (ALP, OPN, OCN, BSP, CAP and CEMP1) of PDLCs in a concentration dependent manner. Furthermore, the addition of cardamonin, a Wnt/β-catenin signalling inhibitor, reduced the pro-cementogenesis effect of the bredigite extracts, indicating the involvement of the Wnt/β-catenin signalling pathway in the cementogenesis of PDLCs induced by bredigite extracts. The present study suggests that an entirely inorganic stimulus with a specific composition of bredigite bioceramics possesses the capacity to trigger the activation of the Wnt/β-catenin signalling pathway, leading to stimulated differentiation of PDLCs toward a cementogenic lineage. The results indicate the therapeutic potential of bredigite ceramics in periodontal tissue engineering application.

Osteogenic differentiation of bone marrow MSCs by β-tricalcium phosphate stimulating macrophages via BMP2 signalling pathway

Immune reactions play important roles in determining the in vivo fate of bone substitute materials, either in new bone formation or inflammatory fibrous tissue encapsulation. The paradigm for the development of bone substitute materials has been shifted from inert to immunomodulatory materials, emphasizing the importance of immune cells in the material evaluation. Macrophages, the major effector cells in the immune reaction to implants, are indispensable for osteogenesis and their heterogeneity and plasticity render macrophages a primer target for immune system modulation. However, there are very few reports about the effects of macrophages on biomaterial-regulated osteogenesis. In this study, we used b-tricalcium phosphate (b-TCP) as a model biomaterial to investigate the role of macrophages on the material stimulated osteogenesis. The macrophage phenotype switched to M2 extreme in response to b-TCP extracts, which was related to the activation of calcium-sensing receptor (CaSR) pathway. Bone morphogenetic protein 2 (BMP2) was also significantly upregulated by the b-TCP stimulation, indicating that macrophage may participate in the b-TCP stimulated osteogenesis. Interestingly, when macrophageconditioned b-TCP extracts were applied to bone marrow mesenchymal stem cells (BMSCs), the osteogenic differentiation of BMSCs was significantly enhanced, indicating the important role of macrophages in biomaterial-induced osteogenesis. These findings provided valuable insights into the mechanism of material-stimulated osteogenesis, and a strategy to optimize the evaluation system for the in vitro osteogenesis capacity of bone substitute materials.

RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway

RNA interference (RNAi) is widely used to silence genes in plants and animals. It operates through the degradation of target mRNA by endonuclease complexes guided by approximately 21 nucleotide (nt) short interfering RNAs (siRNAs). A similar process regulates the expression of some developmental genes through approximately 21 nt microRNAs. Plants have four types of Dicer-like (DCL) enzyme, each producing small RNAs with different functions. Here, we show that DCL2, DCL3 and DCL4 in Arabidopsis process both replicating viral RNAs and RNAi-inducing hairpin RNAs (hpRNAs) into 22-, 24- and 21 nt siRNAs, respectively, and that loss of both DCL2 and DCL4 activities is required to negate RNAi and to release the plant's repression of viral replication. We also show that hpRNAs, similar to viral infection, can engender long-distance silencing signals and that hpRNA-induced silencing is suppressed by the expression of a virus-derived suppressor protein. These findings indicate that hpRNA-mediated RNAi in plants operates through the viral defence pathway.