- Computational and experimental analyses converge to reveal a coherent yet malleable aptamer structure that controls chemical reactivity
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As short nucleic acids, aptamers in solution are believed to be structurally flexible. Consistent with this view, most aptamers examined for this property have been shown to bind their target molecules by mechanisms that can be described as "induced fit".
- Tianjiao, Wang,Hoy, Julie A.,Lamm, Monica H.,Nilsen-Hamilton, Marit
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- Kinetics of malachite green fading in water-ethanol-1-propanol ternary mixtures
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The rate constant of malachite green (MG+) alkaline fading was measured in water-ethanol-1-propanol ternary mixtures. This reaction was studied under pseudo-first-order conditions at 283-303 K. It was observed that the reaction rate constant increases in the presence of different weight percentages of ethanol and 1-propanol. The fundamental rate constants of MG+ fading in these solutions were obtained by SESMORTAC model. In each series of experiments, concentration of one alcohol was kept constant and the concentration of the second one was changed. It was observed that at constant concentration of one alcohol and variable concentrations of the second one, with increase in temperature, k1 values increase and this indicates that presence of ethanol (or 1-propanol) increases dissolution of 1-propanol (or ethanol) in the activated complex formed in these solutions. Also, in each zone, fundamental rate constants of reaction at each certain temperature change as k2 * k1 * k-1.
- Samiey, Babak,Zafari, Mahshid
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- Kinetic exploration supplemented by spectroscopic and molecular docking analysis in search of the optimal conditions for effective degradation of malachite green
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The degradation of malachite green (MG) by an alkaline hydrolytic process has been explored spectrophotometrically. The kinetics of the reaction have been meticulously studied under the influence of cationic alkyltrimethylammonium bromide (DTAB, TTAB and CTAB) surfactants, α-, β- and γ-cyclodextrins (CDs) and surfactant-β-CD mixed systems applying pseudo-first order conditions at 298 K. The surfactants and cyclodextrins individually catalyze the hydrolytic rate, whereas surfactant-β-CD mixed systems exhibit both an inhibiting and catalytic influence depending on the surfactant concentrations. The kinetic results have been explained precisely based on the pseudo-phase ion exchange (PIE) model of micelles and CD-catalyzed model of CD systems. The surfactants exhibit micellar surface catalysis, while CDs accelerate the rate by forming MG-CD inclusion complexes, thereby facilitating nucleophilic attack of its ionized secondary hydroxyl group on the carbocation center of MG. The encapsulation of MG within the supramolecular host cavity of the CDs has been investigated diligently using a steady-state absorption spectroscopic technique. The result shows 1:1 host-guest complexation with different relative orientations of the guest (MG) inside the hosts. Studies employing density functional theory (DFT) as well as molecular docking analysis provide valuable insight on the insertion mechanism. The results reveal that quantitative analysis can be utilized to predict the optimum conditions for the fastest degradation of MG in ambient environments.
- Dasmandal, Somnath,Mandal, Harasit Kumar,Rudra, Suparna,Kundu, Arjama,Majumdar, Tapas,Mahapatra, Ambikesh
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- Kinetics of malachite green fading in alcohol-water binary mixtures
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The rate constant of alkaline fading of malachite green (MG+) was studied in alcohol-water binary mixtures. This reaction was studied under pseudo-first-order conditions at 283-303 K. It was observed that the reaction rate constants were increased in the presence of different weight percentages of methanol, ethanol, 1-propanol, 2-propanol, ethylene glycol, 1,2-propanediol, and glycerol (up to 19.3%). In aqueous glycerol solutions higher than 19.3%, the rate constant of reaction slightly decreases, which is due to high viscosity values of solvent mixtures. The fundamental rate constants of MG+ fading in these solutions were obtained by using the SESMORTAC model. Owing to the charged character of activated complex, with an increase in the weight percentage of the used cosolvents or temperature, κ2 values change according to the trend of hydroxide ion nucleophilic parameter values. Also, using MG+ solvatochromism, a simple test, called MAGUS, is introduced for measuring the glycerol concentration in its aqueous solutions.
- Samiey, Babak,Toosi, Ali Raoof
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- Study of malachite green fading in water-ethanol-ethylene glycol ternary mixtures
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The rate constant of malachite green (MG+) alkaline fading was measured in water-ethanol-ethylene glycol ternary mixtures. This reaction was studied under pseudo-first-order conditions at 283-303 K. In each series of experiments, the concentration of ethanol was kept constant and the concentration of ethylene glycol was changed. It was shown that due to hydrogen bonding and hydrophobic interaction between MG+ and alcohol molecules the observed reaction rate constant, kobs, increased in the water-ethanol-ethylene glycol ternary mixtures. The fundamental rate constants of MG+ fading in these solutions (k1, k- 1 and k2) were obtained by the SESMORTAC model. Analysis of k1 and k2 values in solutions containing constant ethanol concentrations show that in low concentrations of ethylene glycol, hydrogen bonding formed between ethanol and ethylene glycol molecules and in high concentrations of ethylene glycol, ethanol as a solvent for ethylene glycol affected the reaction rate.
- Samiey, Babak,Ahmadi, Somayeh
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- Kinetic investigations on alkaline fading of malachite green in the presence of micelles and reverse micelles
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The kinetics of alkaline hydrolysis of malachite green (MG+) have been studied spectrophotometrically in the presence of cetyltrimethylammonium bromide (CTAB) under pseudo-first-order condition at buffered of pH 11 and 298 K. The rate increases slightly up to the critical micelle concentration of CTAB then increases rapidly for surface catalysis of the micelles. The reaction has also been studied in the water pools of the CTAB/1-butanol/heptane/water reverse micelles and found 4-8 times faster over its rate in aqueous phase but the rate decreases exponentially with its water pool (w) size. The CTAB micellar medium has been characterized using steady state emission spectroscopy and tensiometry at the reaction condition for better explanation of the experimental findings. The thermodynamic activation parameters for the hydrolysis reaction have also been determined for comparison of the kinetic behavior in different environments.
- Dasmandal, Somnath,Mandal, Harasit Kumar,Kundu, Arjama,Mahapatra, Ambikesh
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- Synthesis method of malachite green salt
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The invention relates to a synthesis method of malachite green salt. The method completely abandons traditional synthesis methods in the prior art, and tries to adopt a brand new synthesis route. A Grignard reagent is prepared, and a nucleophilic addition is carried out to synthesize leucomalachite green, and it is accidentally found that the method has the advantages of very few byproducts, and very high yield of the product; the malachite green salt prepared from the synthesized leucomalachite contains few impurities, and can be used as a high-quality candidate for a malachite green standardsubstance; and compared with the traditional synthesis methods, the method of the invention has the advantages of mild reaction conditions, and simplicity in operation.
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Paragraph 0045-0048; 0056-0063
(2019/12/25)
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- Kinetics of fading of some triphenylmethane dyes: Effects of electric charge, substituent, and aqueous binary mixtures of dimethyl sulfoxide and 2-propanol
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The rate constants of alkaline fading of a number of triphenylmethane (TPM) dyes including methyl green (ME2+), brilliant green (BG +), fuchsin acid (FA2-), and bromophenol blue (BPB 2-) were obtained in aqueous binary mixtures of 2-propanol (protic solvent) and dimethyl sulfoxide (DMSO) (aprotic solvent) at different temperatures. It was observed that the reaction rate constants of BG+ and ME2+ increased and those of FA2- and BPB2- decreased with an increase in weight percentages of aqueous 2-propanol and DMSO binary mixtures. 2-Propanol and DMSO interact with the used TPM molecules through hydrogen bonding and ion-dipole interaction, respectively, in addition to their hydrophobic interaction with TPM dyes. The fundamental rate constants of a fading reaction in these solutions were obtained by the SESMORTAC model. Also, the effect of electric charge and substituent groups of a number of TPM dyes on their alkaline fading rate was studied.
- Samiey,Dalvand
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- Stabilities of trityl-protected substrates: The wide mechanistic spectrum of trityl ester hydrolyses
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Ionization rates of para-substituted triphenylmethyl (trityl) acetates, benzoates, and para-nitrobenzoates have been determined in aqueous acetonitrile and aqueous acetone at 25 °C. Conventional and stoppedflow techniques have been used to evaluate rate constants ranging from 1.38 × 10-5 to 2.15 × 102S-1 by conductimetry and photospectrometry methods. The varying stabilities of the differently substituted tritylium ions account for a gradual change of reaction mechanism. Poorly stabilized carbocations are generated slowly by the ionization of their covalent precursors and trapped fast by water. Better stabilized carbocations are generated more rapidly and accumulate, so that ionization and trapping by water can be observed as separate steps in a single experiment. Finally, highly stabilized tritylium ions do not react with water, and only the rates of their formation could be measured. The ionization rate constants correlate linearly with Winstein's ionizing powers Y; the low slopes (0.17 + parameters is excellent for symmetrically substituted tritylium derivatives, deviations for unsymmetrically substituted systems are observed. The failing rate-equilibrium relationship between the rates of ionizations (log kion) and the stabilities of the carbocations in aqueous solution (pKR+) may be explained by the late " development of resonance between a p-amino group and the carbocationic center of the tritylium ion during the ionization process.
- Horn, Markus,Mayr, Herbert
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supporting information; experimental part
p. 7469 - 7477
(2010/09/11)
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- The optical properties of triphenylmethane dye molecules and chromogens
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Industrial dye monomers, including malachite green, crystal violet, brilliant green, and methyl violet, were isolated by extraction with the use of heptane. UV light absorption bands characteristic of pure molecules were determined. The molecules of the dyes studied, which were ion pairs (formed by dye cations and oxalate or chlorine anions), did not absorb light in the visible range; that is, they were not chromogens. The conclusion was drawn that chromogen particles responsible for chromaticity were supramolecular dimers of nonchromogenic triphenylmethane series molecules. This conclusion was substantiated by trends in spectral transformations with the participation of immonium hydroxides obtained from dyes and side products of the synthesis of industrial dyes with quinoid molecular structures.
- Mikheev,Guseva,Ershov
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body text
p. 1580 - 1588
(2009/02/04)
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- Influence of colloid suspensions of humic acids upon the alkaline fading of carbocations
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The influence of humic substances (HSs) upon the alkaline hydrolysis of crystal violet (CV) and malachite green (MG) has been studied. Important inhibition of hydrolysis reaction has been reported. This inhibition has been explained in terms of association of reactants to the humic substances. Kinetic results have been modelized using the micellar pseudophase model. Copyright
- Arias-Estevez,Astray,Cid,Fernandez-Gandara,Garcia-Rio,Mejuto
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experimental part
p. 555 - 560
(2009/04/04)
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- Synthesis and characterization of N-demethylated metabolites of malachite green and leucomalachite green
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Malachite green (MG), a triphenylmethane dye used to treat fungal and protozoan infections in fish, undergoes sequential oxidation to produce various N-demethylated derivatives (monodes-, dides(sym)-, dides(unsym)-, trides-, and tetrades-) both before and after reduction to leucomalachite green (LMG). The close structure resemblance of the metabolites with aromatic amine carcinogens implicates a potential genotoxicity from exposure to MG. The availability of the synthetic standards is important for metabolic and DNA adduct studies of MG. This paper describes a simple and versatile method for the synthesis of MG, LMG, and their N-demethylated metabolites. The synthesis involves a coupling of 4-(dimethylamino)-benzophenone or 4-nitrobenzophenone with the aryllithium reagents derived from appropriately substituted 4-bromoaniline derivatives, followed by treatment with HCl in methanol. The resulting cationic MG and their leuco analogues showed systematic UV/vis spectral and tandem mass fragmentation patterns consistent with sequential N-demethylation. The extensive 1H and 13C spectral assignments of the metabolites were aided by the availability of 13C7-labeled MG and LMG. The results indicate the existence of a resonance structure with the cationic charge located in the central methane carbon (C7). The synthetic procedure is general in scope so that it can be extended to the preparation of N-demethylated metabolites of other structurally related N-methylated triphenylmethane dyes.
- Cho, Bongsup P.,Yang, Tianle,Blankenship, Lonnie R.,Moody, Joanna D.,Churchwell, Mona,Beland, Frederick A.,Culp, Sandra J.
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p. 285 - 294
(2007/10/03)
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- A study on equilibrium and kinetics of carbocation-to-carbinol conversion for di- and tri- arylmethane dye cations in aqueous solutions: Relative stabilities of dye carbocations and mechanism of dye carbinol formation
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Arylmethane dye cations form a structurally interesting set of stable carbocations. A detailed study on rate-equilibria of carbinol formation from two diarylmethane and nine triarylmethane dye carbocations in aqueous solutions has been carried out using spectrophotometric measurements. The conclusions reached are : (i) The stability order found (auramine O>crystal violet = methyl violet > victoria blue R > victoria pure blue BO = ethyl violet > pararosaniline > brilliant green > malachite green > carbocation form of Michler's hydrol > methyl green), seems to be determined by an interplay of dye carbocation / carbinol conformation and stereoelectronic effects of substituents; and (ii) carbinol formation is general base catalysed and occurs by the rate determining attack of a H2O molecule on the dye carbocation centre via two kinetic pathways one mediated by another H2O molecule and the other by a OH ion.
- Sen Gupta,Mishra,Radha Rani
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p. 703 - 708
(2007/10/03)
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- Equilibrium and Kinetic Studies on the Formation of Triphenylmethanols from Triphenylmethane Dyes
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For five kinds of triphenylmethane dyes, the rate constants of hydration and dehydration reactions, and equilibrium constants in an aqueous solution were measured by a stopped-flow method.An increase in the number of dialkylamino groups caused a decrease in the rates and the equilibrium constants of the hydration, and the more the electron-donating effect of the dialkylamino groups, the slower the hydration rate became.The more protonated quinonoids were easily converted to the corresponding alcohols.On the basis of the equilibrium constants, Malachite Green was ascertained to be the best reagent of the five dyes for ion association with heteropolyacids in an aqueous medium.
- Hagiwara, Takuyuki,Motomizu, Shoji
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p. 390 - 397
(2007/10/02)
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- Carbenium ion-carbinol equilibration for basic triarylmethane dyes: Relative reactivities of dyes in aq. solutions
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Equilibria and kinetics of carbenium ion-to-carbinol base reactions for a set of selected basic triarylmethane dyes in aq. buffer solutions of low ionic strength have been measured spectrophotometrically.Relative reactivities of the dyes towards nucleophilic attack by hydroxide ion, on the basis of both equilibrium constant and forward rate constant of the reaction, have been found to follow the same order: malachite green (MG)> brillant green (BG)>> Victoria pure blue BO(VB)> methyl violet (MV) = crystal violet (CV)> ethyl vioet (EV).A fairly good correlation between elec trophilicities of the dyes and ?R+ parameters of their 4-alkylamino substituents has been obtained
- Gupta, Susanta K. Sen,Arvind, Udai
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p. 998 - 1000
(2007/10/02)
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- Reactions of Carbocations with a Functionalized Hydrophobic Ammonium Ion
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At high pH (2-hydroxyethyl)tri-n-octylammonium bromide and mesylate 2 react readily with Malachite Green or Crystal Violet to give the corresponding ethers.Reaction is promoted by association of the carbocations with clusters of 2 and involves the nucleophilic zwitterion of 2.Reactions are considerably faster than those with OH- or the cholinate zwitterion, but second-order rate constants in the clusters are lower than in micelles of (2-hydroxyethyl)dimethylhexadecylammonium bromide (1) by a factor of ca. 4.
- Bunton, Clifford A.,Dorwin, Ellen L.
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p. 4093 - 4096
(2007/10/02)
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- Base-Catalyzed Reactions of Triarylmethyl Carbocations with Water
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The general base catalyzed addition of water to a series of triarylmethyl carbocations has been studied in aqueous solution with a series of substituted quinuclidines as base catalysts.Broensted β values for general base catalysis range from 0.33 for trianisylmethyl carbocation, TAM (pKR(1+)=0.82), to 0.52 for Malachite Green, MG (pKR(1+)=6.94).There is a slight tendency for the β values to decrease with decreasing carbocation stability.The rate constants for the "water"-catalyzed reactions show a large positive deviation (800-fold in the case of Malachite Green) and the rate constants for the hydroxide ion catalyzed reactions a small negative deviation from Broensted plots based on quinuclidine catalysis.These results are consistent with a concerted mechanism for the buffer-catalyzed reactions, a stepwise mechanism that proceeds through an oxonium ion intermediate for the "water"-catalyzed reactions (this mechanism corresponds to an A-1 mechanism in the microscopic reverse direction), and either a concerted or preassociation mechanism for the hydroxide ion catalyzed reactions.The positive deviation of water and the negative deviation of the hydroxide ion from the Broensted relationship are opposite the deviations that are normally observed for these species in related reactions: compared to these related reactions, the pH range where buffer catalysis is strongest is shifted to higher pH values.These results also explain why the early attempts to find general base catalysis of the addition of water to triarylmethyl carbocations with acetate buffers proved unsuccessful.
- Gandler, Joseph R.
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p. 8218 - 8223
(2007/10/02)
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- Volume Profiles for Reactions of Malachite Green with Anionic Nucleophiles
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Volumes of activation and volumes of reaction for the reaction Malachite Green+ + Y- -> Malachite Green-Y have been measured for six different Y- in eight different solvents.The volumes of activation are negative (-4 to -20 cm3 mol-1) whereas volumes of reaction are positive (+10 to +30 cm3 mol-1) which is expected for a reaction involving charge neutralisation.In these solvents, contributions to the volumes of activation from reaction of neutral solvent are absent and the explanation of the negative values is sought in two possible models.Either, the reaction requires an initial anion separation from its counterion with which it exists as a relatively unreactive ion-pair or, the activation process requires rehybridisation and charge concentration on the Malachite Green central carbon leading to an increase in electrostriction during activation.
- Abed, Obaid Hassan,Isaacs, Neil S.
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p. 839 - 842
(2007/10/02)
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- Effect of Pressure on the Rate of Alkaline Fading of Triphenylmethane Dyes in Cationic Micelles
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The rates of alkaline fading of triphenylmethane dyes in cationic micelles have been measured at pressures up to about 2 kbar and at 25 deg C in 0.1 M Tris buffer solution.These rates follow the kinetics of the Michaelis-Menten type.The volume changes for the incorporation of dyes in the micellar phase are 14-15 cm3/mol for ethyl violet and brilliant green and 3-4 cm3/mol for crystal violet and malachite green.It was confirmed that these differences are due to the hydrophobicity of dyes.The activation volumes for the fading reaction in micellar phases are positive except in the case of the crystal violet-cetyltrimethylammonium bromide micellar system.However, the activation volumes in nonmicellar aqueous solutions are negative.The differences of the activation volumes between micellar and nonmicellar systems are discussed from the point of view of the general base catalysis, which contains both the water and hydroxide ion pathways.It was clear that micelles change the water control into hydroxide ion control.
- Taniguchi, Yoshihiro,Iguchi, Akira
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p. 6782 - 6786
(2007/10/02)
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