Analysis of degradation mechanism of disperse orange 25 in supercritical water oxidation using molecular dynamic simulations based on the reactive force field

4-[N-(2-cyanoethyl)-N-ethylamino]-4′-nitroazo-benzene (disperse orange 25, DO25) is one of the main components in dyeing wastewater. In this work, supercritical water oxidation (SCWO) process of DO25 has been investigated using the molecular dynamic simulations based on the reactive force field (ReaxFF). For the SCWO system, the effects of temperature, the molecular ratio of DO25, O₂ and H₂O as well as the reaction time have been analyzed. The simulated results showed that the aromatic rings in DO25 could be attacked by hydroxyl radical, oxygen molecule, and hydroxyl radical together with oxygen molecule, respectively, which caused the aromatic ring-opening reaction to happen mainly through three different pathways. The hydroxyl radicals were mainly from water clusters and H₂O₂ (which was produced from oxygen molecules reacting with water clusters). However, for the SCW system as comparison, the aromatic rings in DO25 could be attacked by hydroxyl radical only, and the OH radicals just come from water clusters. During the DO25 SCWO degradation process, we also found that N elements in one DO25 molecule were difficult to be converted into environmentally friendly N₂ molecules because of steric hindrance, but increasing the number of DO25 molecules could improve the possibility for the connection of N elements, thus promoting N element converting into N₂. Extending reaction time could also improve N elements in DO25 to transform into N₂ rather than carbonitride.

Open image in new window

Graphical Abstract The processes of making DO25 wastewater by SCWO into clean water

     

Imidazole Ring Opening of 7-Methylguanosine at Physiological pH

Abstract

It is shown by carbon-13 NMR that the only product of the imidazole ring-opening of 7-methyl-guanosine at physiological pH is 2-amino-6-hydroxy-5-N-methylformamido-4-(N-β-ribofurano-sylamino)pyrimidine and that, contrary to previous results, the hydrolysis of the glycosylic bond at pH=7.2 is a much slower process than the ring opening. The ring opened formamidopyrimidine derivative is a very mobile molecule existing under different conformations depending on the solvent, and in water it is capable of giving different kinds of aggregates. Possible biochemical implications of these results are discussed.     

The reaction of nitro-blue tetrazolium with d,l-L-tetrahydrofolate: The effect of pH,oxygen, formaldehyde and palladium(II)

d,l-L-Tetrahydrofolate (d,l-L-FH₄) transfers two electrons to nitro-blue tetrazolium (NBT) in oxygen-free buffers to form the highly coloured nitro-blue formazan and oxidized folate. Both the rate and extent of this reaction are affected by the pH, the nature of the buffer and the oxygen concentration. Inhibition of both the rate and extent of this reaction in air-saturated solutions by superoxide dismutase (SOD) indicates that the superoxide anion is an intermediate in the reaction so that formazan can be produced by both superoxide independent and superoxide dependent routes in air-saturated solutions.In oxygen-free solutions several lines of evidence can be interpreted to mean that the reduced pteridine ring of tetrahydrofolate is the electron donor in the reaction with NBT. Ionization of the amide hydrogen of the pteridine ring and subsequent increase in electron density of that ring might explain the large increases observed in the rate and extent of the reaction of tetrahydrofolate with NBT as the pH increases. Formaldehyde reacts non-enzymatically with tetrahydrofolate to form a methylene bridge between nitrogens 5 and 10 of methylenetetrahydrofolate. This molecule is much less reactive with nitro-blue tetrazolium than tetrahydrofolate. Complexes formed between tetrahydrofolate and palladium(II) ions are also less reactive with NBT than the tetrahydrofolate alone. This result provides added evidence that palladium(II) ions interact with tetrahydrofolate at the nitrogen 5, nitrogen 10 site of the molecule.     

Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits

Extradiol dioxygenases facilitate microbial aerobic degradation of catechol and its derivatives by activating molecular dioxygen and incorporating both oxygen atoms into their substrates. Experimental and theoretical studies have focused on the mechanism of the reaction at the active site. However, whether the catalytic rate is limited by O₂ access to the active site has not yet been explored. Here, we choose a recently solved X-ray structure of homoprotocatechuate 2,3-dioxygenase as a typical example to determine potential pathways for O₂ migration from the solvent into the enzyme center. On the basis of the trajectories of two 10-ns molecular dynamics simulations, implicit ligand sampling was used to calculate the 3D free energy map for O₂ inside the protein. The energetically optimal routes for O₂ diffusion were identified for each subunit of the homotetrameric protein structure. The O₂ tunnels formed because of thermal fluctuations were also characterized by connecting elongated cavities inside the protein. By superimposing the favorable O₂ tunnels on to the free energy map, both energetically and geometrically preferred O₂ pathways were determined, as also were the amino acids that may be critical for O₂ passage along these paths. Our results demonstrate that identical subunits possess quite distinct O₂ tunnels. The order of O₂ affinity of these tunnels is generally consistent with the order of the catalytic rate of each subunit. As a consequence, the probability of finding the reaction product is highest in the subunit containing the highest O₂ affinity pathway.     

Crystal Structure of 04-Methyl Uridine: Stacking Induced Changes in the Geometry of the Pyrimidine Ring and Its Mutagenic Role

Abstract

The geometric properties of the pyrimidine ring of O⁴-methyl uridine more closely resemble those of cytidine than diketo uridine. Differences between the independent molecules of O⁴-methyl uridine are observed in the C(7)-O(4)-C(4)-C(5)-C(6) bond orders and the planarity of the pyrimidine rings. These differences are attributed to the monopole-induced dipole interactions between the ribose ring oxygen atom and a neighboring base of molecule A. A survey of the literature reveals that similar stacking-induced effects occur in other structures, involving both pyrimidine and purines. Finally, two base pairing schemes between O⁴-methyl uridine and guanosine, in which two hydrogen bonds can form, have been presented. Of these two the mispair with Watson-Crick geometry is favored.     

Thermal stability of water polyhedra with square faces

The remarkable properties of pristine B₃O₃ nanosheet as a nanocarrier for adsorption and desorption of TEPA anticancer drug for designing potential drug delivery platform were investigated using periodic DFT calculations. We studied the adsorption energy of all stable complexes formed between the drug molecule and B₃O₃ in gas and aqueous phases along with electronic structure analysis of complexes. Different adsorption configurations were studied for drug/B₃O₃ complexes, including the interaction of the C atom of the triangular ring, O atom in the TEPA drug with the B atom in B₃O₃, and indirect drug interaction the middle of the R1 ring cavity of the B₃O₃ nanosheet. The take-up of TEPA prompts a substantial change of 68.13% in the band gap (E_g) of the B₃O₃ nanosheet in the most stable complex. The present study results affirmed the application of B₃O₃ nanosheet as a potential vehicle for TEPA drugs in the treatment of cancerous tissues.

     

Theoretical study on the initial reaction mechanisms of <Emphasis Type="Italic">ansa</Emphasis>-metallocene zirconium precursor on hydroxylated Si(1 0 0) surface

The initial reaction mechanisms for depositing ZrO₂ thin films using ansa-metallocene zirconium (Cp₂CMe₂)ZrMe₂ precursor were studied by density functional theory (DFT) calculations. The (Cp₂CMe₂)ZrMe₂ precursor could be absorbed on the hydroxylated Si(1 0 0) surface via physisorption. Possible reaction pathways of (Cp₂CMe₂)ZrMe₂ were proposed. For each reaction, the activation energies and reaction energies were compared, and stationary points along the reaction pathways were shown. In addition, the influence of dispersion effects on the reactions was evaluated by non-local dispersion corrected DFT calculations.     

Ring-Opening of 3-β-D-Ribofuranosyl-3,7,8,9-Tetrahydropyrimido [1,2-i]Purin-8-ol and Preparation of 2-Thio- and 2-aza-Adenosine Derivatives

The adduct 3-β-D-ribofuranosyl-3,7,8,9-tetrahydropyrimido[1,2-i]purin-8-ol (2), obtained from adenosine and epichlorohydrin, underwent ring fission at basic conditions. The initial ring-opening took place at C2 of the pyrimidine unit resulting in 2-(5-amino-1-β-D-ribofuranosyl-imidazol-4-yl)-1,4,5,6-tetrahydropyrimidin-5-ol (3). Also the tetrahydropyrimidine ring of 3 could be opened resulting in 5-amino-1-(β-D-ribofuranosyl)-imidazole-4-(N-3-amino-2-hydroxyl-propyl)-carboxamide (4). In hot acid conditions, 2 was both deglycosylated and ring-opened yielding 2-(5-amino-imidazol-4-yl)-1,4,5,6-tetrahydropyrimidin-5-ol (7) as the final product. When reacting 3 with CS₂ or HNO₂ ring-closure took place and 3-β-D-ribofuranosyl-3,4,7,8,9-pentahydropyrimido[1,2-i]purin-8-ol-5-thione (5), and 3-β-D-ribofuranosyl-imidazo[4,5-e]-3,7,8,9-tetrahydropyrimido[1,2-c][1,2,3]triazine-8-ol (6), respectively, were obtained. Also, the pyrimidine ring of the epichlorohydrin adduct with adenine, 10-imino-5,6-dihydro-4H,10H-pyrimido[1,2,3-cd]purin-5-ol (10), underwent ring fission and the product was identified as 3-hydroxy-1,2,3,4-tetrahydroimidazo[1,5-a]pyrimidine-8-carboximidamide (11).     

Prediction of electrocatalytic activity of some nitrogen-doped polyaromatic hydrocarbons by molecular modelling

Density function theory calculations of minimum energy structure of an oxygen molecule and oxygen atom bonded to the two dimensional molecules, C₂₃NH₁₂, coronene and C₂₁NH₁₄, pentacene doped with nitrogen, indicate the structures are at a minimum on the potential energy surface having no imaginary frequencies. Calculation of the bond dissociation energy (BDE) to remove an oxygen atom from nitrogen-doped pentacene to which is bonded O₂, (C₂₁NH₁₄O₂) shows it is less than that to dissociate O₂. However, this is not the case for nitrogen-doped coronene. This suggests that nitrogen-doped pentacene could be an effective catalyst for the oxygen reduction reaction in fuel cells assuming it is O₂ dissociation. It is also shown that O₂H can bond to nitrogen-doped coronene and pentacene and that the BDE to remove OH is less than that to remove OH from O₂H indicating that N-doped coronene and pentacene could also catalyse this reaction. The calculated adsorption energy for O₂ and O₂H on these molecules is negative indicating they can bond to N-doped coronene and pentacene.     

Synthesis of Novel Polycyclic Nucleoside Analogs

Abstract

We have synthesized polycyclic nucleoside derivatives by a novel, one pot procedure by reacting 4-0-TPS-pyrimidine nucleosides with aromatic diamines. The reaction is limited in scope but provides easy access to certain previously unknown heterocyclic ring systems.₂ 4-0-Triisopro- pylphenylsulfonyl-pyrimidine nucleosides were reacted with aromatic diamines leading to fused, polycyclic ring systems: o-phenylenediamine yielded the pyrimido[1,6-a]benzimidazole, 2.3- diaminonaphthalene gave the naphth[2′,3′:4,5]imidam [1.2-flpyrimidine and 1.8-diaminonaph- thalene led to the pyrimido[l,6-a]perimidine ring system. The reaction is unique because two connected nucleophilic centers react with the pyrimidine nucleoside to form an extended ring system. However, reactions of pyrimidine nucleosides with electrophiles are well known. E.g., reaction of cytidine and adenosine with bromoacetaldehyde yields ethenocytidine and ethenoadenosine) and on reaction of cytidine with 1′-methylthiaminium salts dipyrimido[1,6-a:4′,5′-d]pyrimidine derivatives are obtained.₄ Other polycyclic bases have been made from cytidine and adenosine by photochemical reactions₅.     

1,2,4-triazolo[4,3-a]pyrimidines: a new kind of ligands. Structure of the silver(I) dimer with the 7-oxo derivative

This paper describes the silver dinuclear complex [Ag₂L₂(NO₃)₂] · 2H₂O, where L represents the bridging ligand 7,8-dihydro-7-oxo-1,2,4-triazolo[4,3-a]pyrimidine, this being the first example of a coordination compound of a 1,2,4-triazolo[4,3-a]pyrimidine derivative. As a difference with the most studied 1,2,4-triazolo[1,5-a]pyrimidine derivatives, the coordination takes place through the contiguous nitrogen atoms of the triazole ring, closing a six member Ag₂N₄ core with a higher intermetallic distance, 3.4791(3) Å. Linear coordination of silver is not possible in this geometry, so flat trigonal coordination involving also the nitrate counteranion is found instead.     

Reductive elimination pathway for homocysteine to methionine conversion in cobalamin-dependent methionine synthase

Density functional theory has been applied to investigate the methyl transfer from methylcobalamin (MeCbl) cofactor to homocysteine (Hcy) as catalyzed by methionine synthase (MetH). Specifically, the S_N2 and the reductive elimination pathways have been probed as the possible mechanistic pathways for the methyl transfer reaction. The calculations indicate that the activation barrier for the reductive elimination reaction (24.4 kcal mol⁻¹) is almost four times higher than that for the S_N2 reaction (7.3 kcal mol⁻¹). This high energy demand of the reductive elimination pathway is rooted in the structural distortion of the corrin ring that is induced en route to the formation of the triangular transition state. Furthermore, the reductive elimination reaction demands the syn accommodation of the methyl group and the substrate over the upper face of the corrin ring, which also accounts for the high energy demand of the reaction. Consequently, the reductive elimination pathway for MetH-catalyzed methyl transfer from MeCbl to Hcy cannot be considered as one of the possible mechanistic routes.     

Binding Pockets and Pathways for Dioxygen through the KijD3 N‐Oxygenase in Complex with Flavin Mononucleotide Cofactor and a 3‐Aminoglucose Substrate: Predictions from Molecular Dynamics Simulations

In this work, two protein systems, Kij3D? FMN? AKM? O₂ and Kij3D? FMN? O₂, made of KijD3 N‐oxygenase, flavin mononucleotide (FMN) cofactor, dTDP‐3‐amino‐2,3,6‐trideoxy‐4‐keto‐3‐methyl‐D ‐glucose (AKM) substrate, and dioxygen (O₂), have been assembled by adding a molecule of O₂, and removing (or not) AKM, to crystal data for the Kij3D? FMN? AKM complex. Egress of AKM and O₂ from these systems was then investigated by applying a tiny external random force, in turn, to their center of mass in the course of molecular dynamics in explicit H₂O. It turned out that the wide AKM channel, even when emptied, does not constitute the main route for O₂ egress. Other routes appear to be also viable, while various binding pockets (BPs) outside the active center are prone to trap O₂. By reversing the reasoning, these can also be considered as routes for uptake of O₂ by the protein, before or after AKM uptake, while BPs may serve as reservoirs of O₂. This shows that the small molecule O₂ is capable of permeating the protein by exploiting all nearby interstices that are created on thermal fluctuations of the protein, rather than having necessarily to look for farther, permanent channels.     

On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. II. Proton shifts in the ribose ring of purine nucleosides as a function of the torsion angle about the glycosyl bond

The variations of the ring current, the local diamagnetic susceptibility anisotropy and the polarization contributions to the chemical shift of the non exchangeable protons of the ribose ring of purine nucleosides are computed as a function of the torsion angle about the glycosyl bond, χ_CN. The results show that the ring current effect is relatively more important in the purines than in the pyrimidines. In addition, N₃ of purines has a local magnetic anisotropy effect similar to the one of the carbonyl group C₂O₂ of pyrimidine nucleosides. The experimental differences between the chemical shift of the ribose protons of purine nucleosides and of 8 substituted derivatives are discussed in relation to the theoretical variations.     

5-Halogenopyrimidines

Microbial enzymatic hydroxylation of 4-hydroxy-5-halogeno-pyrimidines was shown to take place at the C₂ of the pyrimidine ring, giving rise to corresponding 5-halogeno-uracils. The analogous 2-hydroxy-5-fluoropyridine was never hydroxylated by microorganisms at the C₄ to give rise to 5-fluorouracil. An inhibitory effect was found only with 4-hydroxy-5-fluoropyrimidine (the starting substance) and its transformation metabolite (5-fluorouracil). In this case the metabolite formed possessed a greater inhibitory effect than did the original pyrimidine derivative.     

Singlet oxygen‐triggered chloroplast‐to‐nucleus retrograde signalling pathways: An emerging perspective

Singlet oxygen (¹O₂) is a prime cause of photo‐damage of the photosynthetic apparatus. The chlorophyll molecules in the photosystem II reaction center and in the light‐harvesting antenna complex are major sources of ¹O₂ generation. It has been thought that the generation of ¹O₂ mainly takes place in the appressed regions of the thylakoid membranes, namely, the grana core, where most of the active photosystem II complexes are localized. Apart from being a toxic molecule, new evidence suggests that ¹O₂ significantly contributes to chloroplast‐to‐nucleus retrograde signalling that primes acclimation and cell death responses. Interestingly, recent studies reveal that chloroplasts operate two distinct ¹O₂‐triggered retrograde signalling pathways in which β‐carotene and a nuclear‐encoded chloroplast protein EXECUTER1 play essential roles as signalling mediators. The coexistence of these mediators raises several questions: their crosstalk, source(s) of ¹O₂, downstream signalling components, and the perception and reaction mechanism of these mediators towards ¹O₂. In this review, we mainly discuss the molecular genetic basis of the mode of action of these two putative ¹O₂ sensors and their corresponding retrograde signalling pathways. In addition, we also propose the possible existence of an alternative source of ¹O₂, which is spatially and functionally separated from the grana core.     

Reaction of magnesium dibromide etherate with 2,3-anhydroaldopyranosides

The reaction of some 2,3-anhydroaldo-hexo- and -pento-pyranoside derivatives with MgBr₂-etherate was found to afford bromodeoxy products in high yield. In the absence of any free hydroxyl group in the molecule, rigid bicyclic, and flexible monocyclic, 2,3-anhydro-α-d-aldopyranoside derivatives, mainly yielded 3-bromo-3-deoxy products through an unusual, diequatorial opening of the oxirane ring. In contrast, similar 2,3-anhydro derivatives having a free hydroxyl group in the molecule underwent the usual, diaxial opening of the oxirane ring, affording the 2-bromo-2-deoxy product. However, methyl 2,3-anhydro-4-O-methyl-β-d-ribopyranoside, despite the absence of a free hydroxyl group, underwent trans-diaxial opening of the oxirane ring.     

Hemin-mediated para-hydroxylation of aniline: A potential model for oxygen activation and insertion reactions of mixed function oxidases

The activation of molecular oxygen by alkaline hemin (ferriprotoporphyrin IX) has been studied. In the presence of reductant nicotineamide adenine dinucleotide (NADH) or nicotineamide adenine dinucleotide phosphate (NADPH) and organic substrate, aniline, hemin activates oxygen to the hydroperoxide anion (HO₂^?) and subsequently mediates insertion of active oxygen into the benzene ring of the substrate to form p-aminophenol, with a high degree of regiospecificity. Oxygen activation does not occur in the absence of aniline. Stoichiometry of the reaction indicates that two electrons are required per molecule of oxygen activated or atom of oxygen inserted into the substrate aromatic ring system. Direct measurements of H₂O₂ and of the pK_a for maximum rate of p-aminophenol formation (11.7 ± 0.1) indicate participation of the hydroperoxide anion as the active oxygen species in the rate-determining step of the insertion reaction. Powerful scavengers of the hydroxyl radical (OH′) have little effect on the formation of H₂O₂ or p-aminophenol by the system. Superoxide dismutase (10^?7 mol dm^?3) inhibited both p-aminophenol and H₂O₂ formation, when added to the system immediately prior to initiation of the reaction. Studies involving N-phenylhydroxylamine indicate that aromatic ring hydroxylation is occurring directly and not by rearrangement of an N-hydroxylated intermediate. Implications of hemin-mediated hydroxylation reactions for those of enzymatic mixed function oxidase activity are discussed.     

Inactivation of Hydrogenase in Cell-free Extracts and Whole Cells of Chlamydomonas reinhardi by Oxygen

O₂ irreversibly inactivates hydrogenase from Chlamydomonas reinhardi. The mechanism for the inactivation involves the reaction of one molecule of hydrogenase with one molecule of O₂ (or two oxygen atoms) in the transition complex of the rate-limiting step. The second order rate constant for this reaction is 190 atmospheres⁻¹ minute⁻¹ (1.4 × 10⁵ molar⁻¹ minute⁻¹). At levels above 0.01 atmosphere O₂, the increased numbers of O₂ molecules may compete for the site of inactivation hindering the proper orientation for inactivation of any one O₂ molecule and resulting in lowered rates of inactivation.     

Mechanism of the gas phase reactions of the C5H5Ni and C5H5Co ions with substituted pyridines. A combined experimental and theoretical study

Different products have been observed in the reactions of C₅H₅Co⁺ and C₅H₅Ni⁺ ions with halogen-substituted pyridines (XPy) that have been studied by ion trap mass spectrometry (ITMS) techniques. In particular, an addition product C₅H₅M(XPy)⁺ and a product ion C₅H₄M(Py)⁺ corresponding to a loss of a HX molecule (X = F, Cl, Br) have been detected. The relative yield of these products is determined by the nature of the metal and by the nature and position of the halogen on the pyridine ring. A computational study at the DFT level on model-systems formed by 2-fluoro and 2-bromopyridine reacting either with the C₅H₅Ni⁺ or the C₅H₅Co⁺ ion has been carried out. This study shows the existence of a general mechanistic pattern. The rate-determining step of this mechanism is the migration of the halogen from the pyridine ring to the metal. A final hydrogen abstraction step carried out by the halogen leads to the expulsion of a HX molecule. The existence of avoided crossings between surfaces of different multiplicities (ground and first excited state) allows the system to follow lower energy reaction pathways. The barrier determined for the reactions involving 2-bromopyridine is significantly lower than that found for 2-fluoropyridine. This is mainly due to the poor migrating/leaving character and low polarizability of fluorine compared to that of bromine.