Electrostatic effects of substrate charge on base-catalyzed proton exchange in purines. Implications for the involvement of zwitterions

1980 ◽  
Vol 58 (1) ◽  
pp. 86-91 ◽  
Author(s):  
Spencer E. Taylor
Keyword(s):  
Aqueous Solution ◽  
Transition State ◽  
Exchange Reaction ◽  
Rate Constants ◽  
Electrostatic Interactions ◽  
Equilibrium Constants ◽  
Proton Exchange ◽  
Net Charge ◽  
Hydroxide Ion ◽  
Rate Behaviour

Rates of detritiation from the C-8 position of various ionized purine molecules have been shown to reflect electrostatic interactions occurring within the transition state of the exchange reaction. The purines are capable of existing as protonated, anionic, neutral, and zwitterionic species in aqueous solution, each of which have been shown previously to undergo specific hydroxide ion-catalyzed detritiation. The effects of substrate charge are quantified as the protonactivatingfactor, aniondeactivatingfactor, and zwitterionactivatingfactor. Localized charge and not net charge is shown to govern the reactivities of the various species, especially the zwitterions.Estimation of rate constants for the zwitterionic species (hitherto only postulated to account for the observed rate behaviour) has enabled the calculation of the corresponding zwitterionic equilibrium constants (Kzw). Kzw values calculated in this manner agree with those estimated from suitable literature pKa data.

Kinetics and mechanism of gold(III) incorporation into tetrakis(1-methylpyridium-4-yl)porphyrin in aqueous solution

2004 ◽  
Vol 08 (11) ◽  
pp. 1269-1275 ◽  
Author(s):  
Ahsan Habib ◽  
Masaaki Tabata ◽  
Ying Guang Wu
Keyword(s):  
Aqueous Solution ◽  
Rate Constants ◽  
Kinetic Data ◽  
Ph Dependence ◽  
Equilibrium Constants ◽  
Hydroxyl Group ◽  
Net Charge ◽  
First Order ◽  
Kinetics Of ◽  
Hydrolysis Of

The kinetics of the reaction of the tetrakis(1-methylpyridium-4-yl)porphyrin tetracation, [ H 2( TMPyP )]4+, with gold(III) ions were studied along with equilibria of gold(III) species in aqueous medium at 25°C, I = 0.10 M ( NaNO 3). The equilibrium constants for the formation of [ AuCl 4-n( OH ) n ]- ( n = 0,…,4), defined as β n = [ AuCl 4- n ( OH ) n ]- [ Cl -] n / [ AuCl 4-][ OH -] n were found to be that log β1 = 7.94 ± 0.03, log β2 = 15.14 ± 0.03, log β3 = 21.30 ± 0.05 and log β4 = 26.88 ± 0.05. The overall reaction was first order with respect to each of the total [ Au (III)] and [ H 2 TMPyP 4+]. On the basis of pH dependence on rate constants and the hydrolysis of gold(III), the rate expression can be written as d [ Au ( TMPyP )5+]/ dt = ( k 1[ AuCl 4-] + k2[ AuCl 3( OH )-] + k3[ AuCl 2( OH )2-] + k4[ AuCl ( OH )3-])[ H 2 TMPyP 4+], where k1, k2, k3 and k4 were found to be (2.16 ± 0.31) × 10-1, (6.56 ± 0.19) × 10-1, (1.07 ± 0.24) × 10-1, and (0.29 ± 0.21) × 10-1 M -1. s -1, respectively. The kinetic data revealed that the trichloromonohydroxogold(III) species, [ AuCl 3( OH )]-, is the most reactive. The higher reactivity of [ AuCl 3( OH )]- is explained by hydrogen bonding formation between the hydroxyl group of [ AuCl 3( OH )]- and the pyrrole hydrogen atom of [ H 2( TMPyP )]4+. Furthermore, applying the Fuoss equation to the observed rate constants at different ionic strengths, the apparent net charge of [ H 2( TMPyP )]4+ was calculated to be +3.5.

Thermochromism of Metal Exchange Reaction between Zinc(II) and Mercury(II) Porphyrins

1995 ◽  
Vol 50 (4) ◽  
pp. 545-550 ◽  
Author(s):  
Masaaki Tabata ◽  
Masahiro Ide ◽  
Kentaro Kaneko
Keyword(s):  
Aqueous Solution ◽  
Exchange Reaction ◽  
Thermodynamic Parameters ◽  
Distribution Curve ◽  
Equilibrium Constants ◽  
Metal Exchange ◽  
Free Base ◽  
Temperature Range ◽  
Base Form ◽  
Metal Exchange Reaction

Thermochromism was observed for an aqueous solution containing zinc(II) and mercury( II) cations and N-p-nitrobenzyl-5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin anion (NO2Bz(Htpps)4-) in the temperature range 10 to 70 °C. The equilibrium constants and the thermodynamic parameters of Zn(NO2Bztpps)3- and Hg(NO2Bztpps)3- have been determined spectrophotometrically to elucidate the thermochromism at 10, 15, 20, 25 and 30 °C in 0.1 mol dm-3 NaNO3. The protonation and metalation constants of NO2Bz(Htpps)4- are defined as K2 = [H2P][H+]-1[HP]-1, K3 = [H3P][H+]-1[H2P]-1 and KMP = [M P][H+][M2+]-1[HP]-1, where HP and MP denote the free base form of the prophyrin and the metalloporphyrins of zinc(II) and mercury(II), respectively. Charges of the prophyrin and metalloporphyrins are omitted for simplicity. The following values were found: logK2 = 7.75 ±0.02 (25 °C), ΔH°/kJmol-1 = -21.2±0.5 and ΔS°/Jmol-1K-1 = 77±1, logK3 = 2.55±0.02 (25 °C), ΔH°/kJmol-1 = -25±0.8 and ΔS°/Jmol-1K-1 = -35±3 and log KZnP = 0.63±0.03 (25 °C), ΔH°/kJmol-1 = 31.0±0.8 and ΔS°/Jmol-1K-1 = 116±3, logKHgP = 6.22±0.03 (25 °C), ΔH°/kJmol-1 = 4.5±0.7 and ΔS°/Jmol-1K-1 = 134±2. The distribution curve calculated from the thermodynamic parameters sufficiently agrees with the observed metal exchange reaction between the metalloporphyrins.

Aminolysis of naphthyl acetates catalyzed by cyclodextrins

1999 ◽  
Vol 77 (5-6) ◽  
pp. 950-959 ◽  
Author(s):  
Oswald S Tee ◽  
Michael J Boyd
Keyword(s):  
Aqueous Solution ◽  
Transition State ◽  
Rate Constants ◽  
Nucleophilic Attack ◽  
Reactivity Ratios ◽  
Aryl Group ◽  
First Order ◽  
Free Amine ◽  
Transition State Stabilization ◽  
Pseudo First Order

The effects of cyclodextrins (CDs) on the rate of nucleophilic attack on 1- and 2-naphthyl acetates (1-NA and 2-NA) in aqueous solution have been investigated. Analysis of the variation of the pseudo-first-order rate constants with [nucleophile] and [CD] affords rate constants for reaction of the nucleophiles with free ester (kN) and with ester bound to the CD (kcN). The reaction of 1-NA and 2-NA with the trifluoroethoxide anion is slowed down by β-CD as the ratios kcN/kN are 0.11 and 0.30, respectively. For reaction with the anion of 2-mercaptoethanol in the presence of α-CD, β-CD, "hydroxypropyl-β-CD" (hp-β-CD) and γ-CD, the reactivity ratios kcN/kN vary between 0.04 and 2.4, ranging from strong retardation to modest catalysis; the retardations arise with β-CD and hp-β-CD, which bind the esters strongly. By contrast, the attack of primary alkylamines is generally accelerated, and in many cases substantially so. For the aminolysis of 1-NA in the presence of β-CD, values of kcN/kN range from 7 to 460, assuming that free amine reacts with CD-bound ester. Alternatively, if the CD-catalyzed reaction involves free ester reacting with CD-bound amine, with rate constant kNc, the ratios kNc/kN vary from 43 to 140. Either way, there is appreciable catalysis of the aminolysis of 1-NA by β-CD. For the aminolysis of 2-NA, the effects are less dramatic: the ratios kcN/kN range from 0.19 to 17, and values of kNc/kN vary from 17 to 110. The reaction of 1-NA with n-hexylamine is also catalyzed by γ-CD. The variations of kinetic parameters with alkylamine chain length suggest that the CD-catalyzed aminolysis basically takes place by the attack of CD-bound amine on the free ester. However, there must be some stabilizing interactions between the aryl group of the ester and the CD during the reaction, since the transition state stabilization is different for 1-NA and 2-NA, as well for other esters.Key words: aminolysis, catalysis, cyclodextrin, ester cleavage, kinetics.

The nature of the transition state in diarylmethyl cation – nucleophile combination reactions as probed by secondary α-deuterium isotope effects

2001 ◽  
Vol 79 (12) ◽  
pp. 1887-1897
Author(s):  
Thuy Van Pham ◽  
Robert A McClelland
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Rate Constant ◽  
Rate Constants ◽  
Flash Photolysis ◽  
Isotope Effects ◽  
Equilibrium Constants ◽  
Bond Formation ◽  
Kinetic Isotope ◽  
Rate Limiting

Transition-state structures for the carbocation–nucleophile combination reactions of (4-substituted-4'- methoxydiphenyl)methyl cations with water, chloride, and bromide ions in acetonitrile–water mixtures have been investigated by measuring the secondary α-deuterium kinetic and equilibrium isotope effects. Rate constants in the combination direction were measured with laser flash photolysis. Equilibrium constants were measured for the water reaction by a comparison method in moderately concentrated sulfuric acid solutions, for the bromide reaction via the observation of reversible combination, and for the chloride reaction from the ratio of the combination rate constant and the rate constant for the ionization of the diarylmethyl chloride product. The fraction of bond making in the transition state has been calculated as the ratio log (kinetic isotope effect):log (equilibrium isotope effect). For the water reaction, there is 50–65% bond making in the transition state; this is also true for cations that are many orders of magnitude less reactive. The same conclusions, 50–65% bond formation in the transition state independent of reactivity, have previously been made in correlations of log kw vs. log KR. Thus, two quite different measures of transition structure provide the same result. The kH:kD values for the halide combinations in 100% acetonitrile are within experimental error of unity. This is consistent with suggestions that these reactions are occurring with diffusional encounter as the rate-limiting step. Addition of water has a dramatic retarding effect on the halide reactions, with rate constants decreasing steadily with increased water content. Small inverse kinetic isotope effects are observed (in 20% acetonitrile:80% water) indicating that carbon—halogen bond formation is rate-limiting. Comparison of the kinetic and equilibrium isotope effects shows ~25 and ~40% bond formation in the transition states for the reactions with bromide and chloride, respectively.Key words: carbocation, isotope effect, transition state, halide.

scholarly journals Mechanism of Allosteric Modulation of Rod Cyclic Nucleotide–gated Channels

1999 ◽  
Vol 113 (5) ◽  
pp. 601-620 ◽  
Author(s):  
Elizabeth R. Sunderman ◽  
William N. Zagotta
Keyword(s):  
Transition State ◽  
Rate Constant ◽  
Rate Constants ◽  
Cyclic Nucleotide ◽  
Equilibrium Constants ◽  
Rod Photoreceptor ◽  
Open Probability ◽  
Allosteric Transition ◽  
Cng Channel ◽  
Single Channel Currents

The cyclic nucleotide–gated (CNG) channel of retinal rod photoreceptor cells is an allosteric protein whose activation is coupled to a conformational change in the ligand-binding site. The bovine rod CNG channel can be activated by a number of different agonists, including cGMP, cIMP, and cAMP. These agonists span three orders of magnitude in their equilibrium constants for the allosteric transition. We recorded single-channel currents at saturating cyclic nucleotide concentrations from the bovine rod CNG channel expressed in Xenopus oocytes as homomultimers of α subunits. The median open probability was 0.93 for cGMP, 0.47 for cIMP, and 0.01 for cAMP. The channels opened to a single conductance level of 26–30 pS at +80 mV. Using signal processing methods based on hidden Markov models, we determined that two closed and one open states are required to explain the gating at saturating ligand concentrations. We determined the maximum likelihood rate constants for two gating schemes containing two closed (denoted C) and one open (denoted O) states. For the C ↔ C ↔ O scheme, all rate constants were dependent on cyclic nucleotide. For the C ↔ O ↔ C scheme, the rate constants for only one of the transitions were cyclic nucleotide dependent. The opening rate constant was fastest for cGMP, intermediate for cIMP, and slowest for cAMP, while the closing rate constant was fastest for cAMP, intermediate for cIMP, and slowest for cGMP. We propose that interactions between the purine ring of the cyclic nucleotide and the binding domain are partially formed at the time of the transition state for the allosteric transition and serve to reduce the transition state energy and stabilize the activated conformation of the channel. When 1 μM Ni2+ was applied in addition to cyclic nucleotide, the open time increased markedly, and the closed time decreased slightly. The interactions between H420 and Ni2+ occur primarily after the transition state for the allosteric transition.

Hydrogen exchange studies. XIV. Kinetics and mechanism of base-catalyzed hydrogen exchange in 1,3-dinitrobenzene in aqueous dimethylformamide and relationship with σ-complex formation

1981 ◽  
Vol 59 (22) ◽  
pp. 3177-3187 ◽  
Author(s):  
Erwin Buncel ◽  
Allen W. Zabel
Keyword(s):  
Complex Formation ◽  
Rate Constants ◽  
Hydrogen Exchange ◽  
Equilibrium Constants ◽  
Medium Composition ◽  
Proton Exchange ◽  
Ion Concentrations ◽  
First Order ◽  
Order Rate ◽  
Insight Into

Kinetic data have been evaluated for hydrogen exchange in 1,3-dinitrobenzene (DNB), occurring at the 2-position, in dimethylformamide (DMF) – D2O mixtures containing deuteroxide ion. The pseudo first order rate constants for exchange, kobs, show inverse dependence on the initial DNB concentration, which can be quantitatively related to the extent of σ-complex formation in these systems. The profile for kobs as function of medium composition exhibits a maximum at ca. 70 mol% DMF, and εapp for σ-complex formation reaches a plateau at about the same medium composition. The equilibrium constants for σ-complex formation, Ke, are used to calculate the free, or uncomplexed, deuteroxide ion concentrations, which then allow one to calculate k2, the second order rate constants for exchange. The k2 values show a uniformly increasing tendency with increased DMF content. Correlations with medium basicity are examined, and the nature of the log k2 and log Ke vs. H− plots afford insight into the origin of the medium dependence of proton exchange. The results of the present study are consistent with the σ-complex being an unreactive form of the substrate towards exchange, which occurs via uncomplexed DNB present in small concentration. The study also rules out the possibility that the colored species present in these systems is the carbanion formed on deprotonation of DNB.

Rate and equilibrium constants for formation and hydrolysis of 9-formylfluorene oxime: diffusion-controlled trapping of a protonated aldehyde by hydroxylamine

2000 ◽  
Vol 78 (12) ◽  
pp. 1594-1612 ◽  
Author(s):  
RA More O'Ferrall ◽  
D M O'Brien ◽  
D G Murphy
Keyword(s):  
Aqueous Solution ◽  
Acetic Acid ◽  
Reaction Pathway ◽  
Equilibrium Constants ◽  
Diffusion Control ◽  
General Measure ◽  
Hydroxide Ion ◽  
Diffusion Controlled ◽  
Enol Tautomer ◽  
Hydrolysis Of

Equilibrium constants Kadd = 440 and Kox = 3.0 × 108 for formation of a carbinolamine adduct and oxime, respectively from 9-formylfluorene and hydroxylamine, and pKa = –1.62 for protonation of the oxime, have been evaluated at 25°C in aqueous solution, based on measurements in hydroxylamine buffers, acetic acid buffers, and dilute HCl. Rate constants for hydrolysis of the oxime have been measured in the acidity range pH 4–12 M HClO4. At the highest acidities, a reaction pathway via protonated carbinolamine has been identified: evidence is presented that the reverse of this reaction involves rate-determining attack of hydroxylamine upon protonated 9-formylfluorene. By assuming that the attack of hydroxylamine is diffusion-controlled, with rate constant 3 × 109 M –1 s–1, a pKa for O-protonation of the aldehyde (–4.5) is derived. Taking account of the equilibrium constant for enolization of 9-formylfluorene (KE = 16.6), a pKa for for C-protonation of the enol tautomer ((–5.7) may also be obtained. Comparison of this pKa with that of the enol of acetophenone shows that the enol of 9-formylfluorene is less basic by a factor of 1010. By combining pKas for protonation of the aldehyde and oxime with measured or estimated equilibrium constants for addition of water, hydroxide ion, and hydroxylamine to 9-formylfluorene, it is also possible to obtain values of pKR = –5.3, 4.1, and 12.25 for the protonated 9-formylfluorene, protonated oxime, and 9-formylfluorene, respectively. The usefulness of pKR in providing a general measure of equilibrium constants for electrophile-nucleophile combination reactions is discussed.Key words: oxime, formyfluorene, hydrolysis, protonation, diffusion-control.

OXIDATION OF MANGANATE BY HYPOCHLORITE

1961 ◽  
Vol 39 (1) ◽  
pp. 96-101
Author(s):  
M. W. Lister ◽  
Y. Yoshino
Keyword(s):  
Activation Energy ◽  
Potassium Permanganate ◽  
Rate Constants ◽  
Effective Activation Energy ◽  
Equilibrium Constants ◽  
Intermediate Formation ◽  
Ion Concentration ◽  
Effective Activation ◽  
Text Data ◽  
Hydroxide Ion

The oxidation of potassium manganate to potassium permanganate by potassium hypochlorite has been examined. The rate of the reaction is proportional to the square of the manganate concentration and the first power of the hypochlorite, and it is inversely proportional to the permanganate concentration and to the square of the hydroxide ion concentration. It seems probable that the reaction involves the intermediate formation of hypomanganate ions from a relatively fast disproportionation of manganate, followed by a slower oxidation by hypochlorite. The following mechanism is tentatively proposed:[Formula: see text]Data on the over-all rate and effective activation energy (19.6 kcal/g-molecule) are given; but at present it is not possible to separate all the rate constants and equilibrium constants.

On the relationship between the rate constants for racemization and isotopic exchange

1998 ◽  
Vol 76 (6) ◽  
pp. 643-648 ◽  
Author(s):  
John MW Scott ◽  
Danny Summers
Keyword(s):  
Transition State ◽  
Exchange Reaction ◽  
Rate Constants ◽  
Isotopic Exchange ◽  
Alkyl Halides ◽  
Sufficient Condition ◽  
Isotopic Exchange Kinetics ◽  
Halide Exchange ◽  
Exchange Kinetics ◽  
The Relationship

The relationship between the rate constants that describe the halide ion catalysis of the racemization (kr) of optically alkyl halides and the related isotopic halide exchange reaction (ke) is shown to be valid in two distinct cases. The first is when the racemization and exchange mechanisms follow the classical and conventional SN2 path characterized by a symmetrical trigonal (sp2) transition state. The second envisages the trigonal species characteristic of the SN2 reaction as an intermediate instead of a transition state. The latter mechanism is also shown to be characterized by the relationship kr = 2ke, and hence this diagnostic test is seen to be a necessary but not a sufficient condition for invoking the SN2 mechanism.Key words: racemization, isotopic exchange, kinetics, bimolecular substitution, inversion.

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