14039-15-7Relevant academic research and scientific papers
The 4,4′-dimethoxytrityl carbenium ion by ionization of 4,4′-dimethoxytrityl alcohol in acetonitrile - Aqueous perchloric and nitric acids containing electrolytes: Kinetics, equilibria, and ion-pair formation
Crugeiras, Juan,Maskill, Howard
, p. 530 - 536 (1999)
We have studied the equilibration shown in eq. [3] of 4,4′-dimethoxytrityl alcohol in aqueous perchloric and nitric acids containing low proportions of acetonitrile using stopped-flow kinetics techniques. The rate constants for the overall progress to equilibrium, kobs, have been resolved into forward and reverse components using the equilibrium UV absorbance and a value for the molar absorptivity of the 4,4′-dimethoxytrityl carbenium ion determined in concentrated aqueous perchloric acid. The forward reaction (rate constant kf) is first order in both the alcohol and the acid concentrations; the reverse reaction (rate constant Kr) is pseudo first order with respect to the carbocation. At constant hydronium ion concentration, the forward rate constant increases linearly with the concentration of electrolyte, whereas the reverse rate constant decreases. These effects depend upon the nature of the anion, but not the cation, and are not ionic strength effects. At constant anion concentrations, kf in both acids, and kr in perchloric acid, are independent of hydronium ion concentration; however, kr decreases with increasing hydronium ion concentration at constant nitrate concentration. At nonconstant ionic strength, changes in kr and Kr observed in increasing concentrations of perchloric acid are attributable wholly to changes in perchlorate concentration. A mechanism is proposed which involves pre-equilibrium protonation of the alcohol, heterolysis of the protonated alcohol to give a 4,4′-dimethoxytrityl carbenium ion - water ion-molecule pair, then conversion of this into a dissociated carbenium ion in equilibrium with ion pairs. To account for the strong effects of perchlorate and nitrate upon the forward rate constants, it is proposed that these anions provide additional reaction channels from the ion-molecule pair. However, we find no evidence of acid catalysis in the reaction of the ion-molecule pair (in contrast to our finding for the reaction of the corresponding ion-molecule pair formed from dimethoxytritylamine in acidic media). Some of the elementary rate and equilibrium constants of the proposed mechanism have been evaluated.
The kinetics and mechanism of the acid-catalysed detritylation of nucleotides in non-aqueous solution
Russell, Mark A.,Laws, Andrew P.,Atherton, John H.,Page, Michael I.
, p. 52 - 57 (2009)
The kinetics and mechanism of the deprotection (detritylation) of 5′-O-(4,4′-dimethoxytrityl)-2′-deoxythymidine nucleoside catalysed by dichloroacetic acid to give a 4,4′-dimethoxytrityl carbocation have been studied in toluene, dichloromethane and acetonitrile. There is little or no effect of solvent polarity on the equilibrium and rate constants. Entropies of activation are highly negative ～-105 J K -1 mol-1 and similarly show little variation with solvent. Addition of small amounts of water to the reaction medium reduces the detritylation rate, presumably through its effect on the solution acidity. All observations are compatible with detritylation occurring through a concerted general acid-catalysed mechanism rather than a stepwise A1 process.
Molar Absorptivity and pKR+ of the 4,4'-Dimethoxytrityl Carbenium Ion in Methanolic Water, and its Equilibrium with Chloride Ion
Lee, Won Heui,Maskill, H.
, p. 1463 - 1466 (1994)
The 4,4'-dimethoxytrityl carbenium ion has been generated in 80:20 (v/v) water-methanol containing perchloric acid in a rapid reaction from 4,4'-dimethoxytrityl alcohol and in a slower reaction from 4,4'-dimethoxytritylamine.The pK (-0.95; K=8.98) and molar absorptivity (ε=297 000) of the cation have been measured directly under equilibrium conditions in this highly aqueous medium at ionic strength = 1.0 mol dm-3 by a convenient spectrophotometric method at 25 deg C.In addition, the pK has been measured at other temperatures, which allows the determination of the standard enthalpy (ΔH = -11.4 kJ mol-1) and entropy (ΔS = -20 J K-1 mol-1) of the reaction of the cation with the solvent, and at other ionic strengths.The equilibrium constant for the formation of 4,4'-dimethoxytrityl chloride from the cation and chloride has also been measured in the same medium (KRCl = 8.20 at 25.0 deg C, ionic strength = 1.0 mol dm-3) by generating the cation from the alcohol and perchloric acid in the presence of 0.10 mol dm-3 sodium chloride.
High yield detritylation of surface-attached nucleosides with photoacid generated in an overlying solid film: Roles of translational diffusion and scavenging
Garland, Peter B.,Serafinowski, Pawel J.
body text, p. 451 - 459 (2009/07/18)
Conventional solid-phase oligonucleotide synthesis overcomes the reversibility of acid-dependent detritylation by washing away the released dimethoxytrityl cations (DMT+) with acid. This option is unavailable if the acid is photogenerated in an overlying solid film, as in the photolithographic fabrication of oligonucleotide arrays on planar surfaces. To overcome the resulting reversibility problem we developed methods of achieving ≥98% detritylation of glass-attached 5′-O-DMT-thymidine, a model for 5′-O-DMT-protected oligonucleotides, by the photogeneration of trichloroacetic acid in a solid film. Enhanced intrafilm diffusion, insufficient to degrade the photolithographic resolution but enabling DMT+ to move from its plane of release into the overlying photoacid-generating film, increased detritylation from ≤30% to ≥98%. Inclusion of an intrafilm carbocation scavenger such as a triarylsilane hydride converted the detritylation into a time-dependent irreversible process proceeding to ≥99% detritylation within 60 s following brief photoacid generation. Light sensitivity is high, exceeding direct photodeprotection methods by 15-100 fold. The Royal Society of Chemistry 2009.
Fluorous affinity purification of oligonucleotides
Pearson, William H.,Berry, David A.,Stoy, Patrick,Jung, Kee-Yong,Sercel, Anthony D.
, p. 7114 - 7122 (2007/10/03)
Nucleoside phosphoramidites bearing a fluorous dimethoxytrityl (FDMT) group were used to synthesize fluorous-tagged oligonucleotides, which were subjected to solid-phase extraction using a pH-stable fluorinated adsorbent. On-column detritylation afforded
Kinetics and thermodynamics of ionization of 4,4′-dimethoxytrityl alcohol in acetonitrile-aqueous acids: Determination of enthalpies and entropies of activation and of reaction
Crugeiras, Juan,Maskill, Howard
, p. 441 - 445 (2007/10/03)
We have studied the equilibration shown in eqn. (2) of 4,4′-dimethoxytrityl alcohol in aqueous perchloric, nitric, and hydrochloric acids containing 20% acetonitrile at different temperatures using stopped-flow kinetics techniques. The observed overall pseudo first-order rate constant for equilibration, Kobs, decreases with increasing electrolyte concentrations at constant hydronium ion concentration; kobs, has been resolved into forward and reverse components using the equilibrium UV absorbance and the temperature-independent molar absorptivity of the 4,4′-dimethoxytrityl carbenium ion. The forward reaction (rate constant kf) is first order in both the alcohol and the acid; the reverse reaction (rate constant kf) is pseudo first order with respect to the carbocation. At constant hydronium ion concentration, the forward rate constant increases with the concentration of electrolyte whereas the reverse rate constant decreases. Quantitative effects for perchlorate, nitrate, and chloride are different. Results are accommodated by a mechanism which involves pre-equilibrium protonation of the alcohol, heterolysis of the protonated alcohol to give a 4,4′-dimethoxytrityl carbenium ion-water ion-molecule pair, then conversion of this into the dissociated carbenium ion in equilibrium with ion pairs. There are additional parallel reaction channels from the protonated alcohol and electrolyte anions. Some of the elementary rate constants have been evaluated, and enthalpies and entropies of activation have been determined. Correspondingly, some equilibrium constants of the proposed mechanism have been evaluated, and associated enthalpies and entropies of reaction have been determined.
Flash-Photolysis Generation and Reactivities of Triarylmethyl and Diarylmethyl Cations in Aqueous Solutions
McClelland, Robert A.,Kanagasabapathy, V. M.,Banait, Narinder S.,Steenken, Steen
, p. 3966 - 3972 (2007/10/02)
A series of 18 triarylmethyl cations and 10 diarylmethyl cations have been generated by nanosecond laser flash photolysis of cyanide, 4-cyanophenyl ether, and acetate precursors in acetonitrile/water (AN/W) solutions and first-order rate constants for their reaction with the solvent (ks) have been directly measured following the decay in their optical density.In the standard solvent employed, 1:2 AN/W, the triarylmethyl cations which were studied had ks values at 20 deg C ranging from 1E1 s-1 (for the 4,4',4''-(MeO)3-substituted ion) to 9*1E6 s-1 (4,4'-(CF3)2), while diarylmethyl cations had ks values ranging from 1E5 s-1 (4,4'-(MeO)2) to 3*1E7 s-1 (4,4'-Me2).The parent diphenylmethyl cation and its derivative with one 4-methyl substituent were too short-lived (s of varying the amounts of acetonitrile were investigated for several cations.As water is added to 100percent acetonitrile, ks increases significantly, but at around 15percent by volume water, there is a leveling and from that point to 100percent water, ks is almost unchanged, decreasing by about 20percent.A plot of log ks versus ?+ constructed for the triarylmethyl cations shows significant deviations from linearity for the points for the ? donors, in the direction which indicates that ?+ is underestimating the stabilizing effect of these substituents for a fully formed cation.A plot versus ?C+, a parameter obtained from the analysis of NMR spectra of solutions of carbocations, is reasonably linear.A two-parameter correlation indicates that polar andresonance interactions of substituents do not proceed in parallel along the reaction coordinate, the addition of water to cation resulting at the transition state in the loss of 73percent of the equilibrium resonance effect but only a 33percent loss of the polar effect.A rate-equilibrium plot (log ks versus pKR) was constructed which covers 23 pKR units.A single line of slope 0.64 can be drawn to include the entire set of data for both triarylmethyl and diarylmethyl cations.From a small extrapolation the ks value for the tert-butyl cation in water is obtained as 1E10.5 s-1.
Bio-organic Applications of Mass Spectrometry. Part 6. Selective Deprotection of Nucleotides by Fast Atom Bombardment Mass Spectrometry
Liguori, Angelo,Sindona, Giovanni,Uccella, Nicola
, p. 1661 - 1666 (2007/10/02)
The fully protected nucleoside S-methyl O-2,4-dichlorophenyl phosphorothioates (2) and (3) undergo selective removal of the protecting groups when exposed, in liquid matrices, to 9.5 KeV Xe bombardment.Dimethoxytrityl and 9-phenylxanthen-9-yl cations are formed when the reactivity of the protonated species is examined, while solvolytic removal of the 2,4-dichlorophenyl protecting group afforded the nucleosides phosphodiester anions (6) and (8) as a result of matrix-substrate interaction in the energized condensed phase.The same substrates are competitively demethylated at the sulphur atom when thioglycerol is present in the solvation sphere of the reactants.Anions (6) and (8), desorbed into the gas phase by fast atom bombardment of their triethylammonium salts, displayed the same metastable ion kinetic energy spectra as those produced from nucleotides (2) and (3) by applying the same methodology.
A CHEMICAL 5'-PHOSPHORYLATION OF OLIGODEOXYRIBONUCLEOTIDES THAT CAN BE MONITORED BY TRITYL CATION RELEASE
Horn, Thomas,Urdea, Mickey S.
, p. 4705 - 4708 (2007/10/02)
A new phosphoramidite-derived reagent, (2-cyanoethoxy)-2-(2'-O-4,4'-dimethoxytrityloxyethylsulfonyl)ethoxy-N,N-diisopropylaminophosphine, for the 5'-phosphorylation of oligodeoxyribonucleotides has been developed.Phosphorylation efficiency can be determined by the release of 4,4'-dimethoxytrityl cation in acid.
