How closely related are the effective and the real temperature

The determination of proton affinity (PA) of 2Ј-deoxyadenosine (dA) is used as a case study for the evaluation of possible drawbacks in the determination of the PA of the nucleic acid molecules by the kinetic method. The observed ⌬PA among the different values obtain for dA by applying this procedure in its different extensions was 0.64 Kcal/mol, which is within the uncertainties of any theoretical or experimental approach. It was demonstrated that nucleosides can be generally used as reference compounds to measure the PA of an unknown nucleoside. The evaluation of ⌬⌬S value for two competing reaction channels taken by proton-bound heterodimers formed by two nucleosides provides clear information on the reference base which has to be discarded from the set of reference compounds used for the estimation of an unknown PA. The PA of dA obtained with the most elaborated kinetic method (237.00 Ϯ 0.07 kcal/mol) is consistent with the value of 237.0 kcal/mol obtained by a simple treatment of the relative intensities of the product ions generated by two couples of the proton bound dimers formed by the nucleoside and two reference amines. The kinetic method can be, therefore, confidently used to assess the proton affinity of the multifunctional molecules such as nucleosides and nucleobases. (J Am Soc Mass Spectrom 2004, 15, 1080 -1086

Section: Resultsmentioning

confidence: 99%

A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules

Donna

Napoli

Sindona

et al. 2004

“…It is well established that the effective temperature depends on the amplitude degree of excitation, the time-scale window of the dissociation processes, and a number of other parameters [43,44]. The measurements of proline basicity, performed by our group [47], underline the advantage of the combination of experimental results obtained with an ion trap and triple quadrupole instruments.…”

Section: Methodsmentioning

confidence: 96%

“…This approach is based on the eq 2 with GA T eff app ͑A 0 , A i ͒ ϭ ⌬H°a cid ͑A 0 ͒ Ϫ T eff ⌬⌬S°a cid ͑A 0 , A i ͒ (T eff : effective temperature in K [42][43][44]; R: Boltzmann constant ϳ 8.31 J mol Ϫ1 K Ϫ1 , and GA T eff app : apparent gas-phase acidity in kJ mol Ϫ1 [45]. In this regard, it should be noted that the A i references require similar chemical and physicochemical properties with each other and a ⌬H°a cid (A i ) ϳ [⌬H°a cid (A 0 ) Ϯ 10] kJ mol Ϫ1 [44].…”

Section: Methodsmentioning

confidence: 99%

“…The slope and the x-intercept of this curve are Ϫ1/RT eff and GA T eff app , respectively. In the case of the extended method, this experiment is performed under variable CID conditions allowing to change the effective temperature (fictitious value, which describes the behavior of ions dissociating in the time window of analyzer with non-thermal internal energy distribution) [42][43][44]. Finally, the relation of GA T eff app versus T eff yields a linear dependence that allows an estimation of ⌬H°a cid (A 0 ) and Ϫ⌬⌬S°(A 0 , A i ) corresponding to the y-intercept and the slope, respectively.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Stereochemical effects during [M-H]⁻ dissociations of epimeric 11-OH-17β-estradiols and distant electronic effects of substituents at C₍₁₁₎ position on gas phase acidity

Bourgoin-Voillard

Zins

Fournier

et al. 2009

The affinity of estradiol derivatives for the estrogen receptor (ER) depends strongly on nature and stereochemistry of substituents in C (11) position of the 17␤-estradiol (I). In this work, the stereochemistry effects of the 11␣-OH-17␤-estradiol (III ␣ ) and 11␤-OH-17␤-estradiol (III ␤ ) were investigated using CID experiments and gas-phase acidity (⌬H°a cid ) determination. The CID experiments showed that the steroids decompose via different pathways involving competitive dissociations with rate constants depending upon the ␣/␤ C (11) stereochemistry. It was shown that the fragmentations of both deprotonated [III ␣ -H] Ϫ and [III ␤ -H] Ϫ epimers were initiated by the deprotonation of the most acidic site, i.e. the phenolic hydroxyl at C (3) . This view was confirmed by H/D exchange and double resonance experiments. Furthermore, the ⌬H°a cid of both epimers (III ␣ and III ␤ ), 17␤-estradiol (I), and 17-desoxyestradiol (II) was determined using the extended Cooks' kinetic method. The resulting values allowed us to classify steroids as a function of their gas-phase acidity as follows:Interestingly, the ␣/␤ C (11) stereochemistry appeared to influence strongly the gas-phase acidity. This phenomenon could be explained through stereospecific proton interaction with -orbital cloud of A ring, which was confirmed by theoretical calculation. . The E 2 /ER␣ complex is stabilized by hydrogen contacts occurring between, on the one hand, the hydroxyl group of phenolic A ring (E 2 ) and Glu-353 as well as Arg-394 of the hormone binding pocket (HBP), and on the other hand, between the 17␤-hydroxyl of D-ring and His-524 (Scheme 1a) [5][6][7]. Moreover, position around the functionalized site at the C (11) position (C ring) seems to contribute to the anchorage of the hormone within this pocket of the receptor [7][8][9][10][11][12][13], suggesting that steric effects at this position are important for binding affinity. Accordingly, we may consider that the proton donor character efficiency could be reinforced through electrostatic effects mediated by the nature and the stereochemistry of substituent in position 11 [14].Mass spectrometry is widely used to characterize diastereoisomeric compound through stereochemical effects [15,16]. Many reviews have described stereochemistry differentiation of the hydroxyl group in gas phase on rigid rings [17][18][19][20][21][22]. The stereochemical effects could provide evidence that the chemical pathways for ion-molecule reaction as well as the dissociation mechanisms promoted by negative charge from stereoisomeric ion species prepared in chemical ionization and electrospray [23]. For instance, the differentiation of alkoxides of trans and cis-cyclohexanediols has been widely described in negative chemical ionization [24 -26]. This technique turned out to be also appropriate to distinguish more complex polycyclic molecules, such as mono-or polyhydroxyl norborneols, saccharides, and steroids [27][28][29][30]. The origin of stereochemical effects in these systems has been described in terms of...

“…The effective temperature is an empirical parameter that depends on several experimental variables and properties of the proton-bound dimers [15][16][17][18][19][20]. The term ⌬(⌬S) is the difference of the activation entropies between the two competing dissociation channels, ⌬S (with k) -⌬S (with k i ).…”

Section: Methodsmentioning

confidence: 99%

Determination of the gas-phase acidities of cysteine-polyalanine peptides using the extended kinetic method

Tan

Ren

2007

We determined the gas-phase acidities of two cysteine-polyalanine peptides, HSCA 3 and HSCA 4 , using a triple-quadrupole mass spectrometer through application of the extended kinetic method with full entropy analysis. Five halogenated carboxylic acids were used as the reference acids. The negatively charged proton-bound dimers of the deprotonated peptides with the conjugate bases of the reference acids were generated by electrospray ionization. Collision-induced dissociation (CID) experiments were carried out at three collision energies. The enthalpies of deprotonation (⌬ acid H) of the peptides were derived according to the linear relationship between the logarithms of the CID product ion branching ratios and the differences of the gas-phase acidities. The values were determined to be ⌬ acid H(HSCA 3 ) ϭ 317.3 Ϯ 2.4 kcal/mol and ⌬ acid H (HSCA 4 ) ϭ 316.2 Ϯ 3.9 kcal/mol. Large entropy effects (⌬(⌬S) ϭ 13-16 cal/mol K) were observed for these systems. Combining the enthalpies of deprotonation with the entropy term yielded the apparent gas-phase acidities (⌬ acid G app ) of 322.1 Ϯ 2.4 kcal/mol (HSCA 3 ) and 320.1 Ϯ 3.9 kcal/mol (HSCA 4 ), in agreement with the results obtained from the CID-bracketing experiments. Compared with that in the isolated cysteine residue, the thiol group in HSCA 3,4 has a stronger gas-phase acidity by about 20 kcal/mol. This increased acidity is likely due to the stabilization of the negatively charged thiolate group through internal solvation. (J Am Soc Mass Spectrom 2007, 18, 188 -194)