Energetics of Protonation

The tendency of a (basic) molecule B to accept a proton is quantitatively described by its proton affinity PA (Chap. 2.11). For such a protonation we have [3] 

In case of an intended protonation under the conditions of Cl one has to compare the PAs of the neutral analyte M with that of the complementary base B of the proton-donating reactant ion [BH] (Brpnsted acid). Protonation will occur as long as the process is exothermic, i.e., if PA(b) PA(m). The heat of reaction has basically to be distributed among the degrees of freedom of the [Mh-H] analyte ion. [12,21] This means in turn, that the minimum internal energy of the [Mh-H] ions is determined by  

Some additional thermal energy will also be contained in the [M-i-H] ions. Having PA data at hand (Table 2.6) one can easily judge whether a reagent ion will be able to protonate the analyte of interest and how much energy will be put into the [M-i-H] ion. 

Example The CHs reactant ion will protonate C2H6 because Eq. 7.13 gives APA = PA(ch4)-PA(C2H6) = 552 - 601 =-49 kJ mol . The product, protonated ethane, C2H7, immediately stabilizes by H2 loss to yield C2Hs. [17,18] In case of tetrahydrofurane, protonation is more exothermic APA = PA(ch4 -PA(C4H80) = 552-831 = -279 kJ moF.  

Due to the above energetic considerations, impurities of the reagent gas having a higher PA than the neutral reagent gas are protonated by the reactant ion. [3] Residual water is a frequent source of contamination. Higher concentrations of water in the reagent gas may even alter its properties completely, i.e., HsO becomes the predominant species in a CH4/H2O mixture under Cl conditions (Fig. 7.4). [22] 

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The enthalpy changes associated with proton transfer in the various 4, -substituted benzophenone contact radical ion pairs as a function of solvent have been estimated by employing a variety of thermochemical data [20]. The effect of substituents upon the stability of the radical IP were derived from the study of Arnold and co-workers [55] of the reduction potentials for a variety of 4,4 -substituted benzophenones. The effect of substituents upon the stability of the ketyl radical were estimated from the kinetic data obtained by Creary for the thermal rearrangement of 2-aryl-3,3-dimethylmethylenecyclopropanes, where the mechanism for the isomerization assumes a biradical intermediate [56]. The solvent dependence for the energetics of proton transfer were based upon the studies of Gould et al. [38]. The details of the analysis can be found in the original literature [20] and only the results are herein given in Table 2.2. 

Because of the complexity of hydrated PEMs, a full atomistic modeling of proton transport is impractical. The generic problem is a disparity of time and space scales. While elementary molecular dynamics events occur on a femtosecond time scale, the time interval between consecutive transfer events is usually 3 orders of magnitude greater. The smallest pore may be a few tenth of nanometer while the largest may be a few tens of nanometers. The molecular dynamics events that protons transfer between the water filled pores may have a timescale of 100-1000 ns. This combination of time and spatial scales are far out of the domain for AIMD but in the domain of MD and KMC as shown in Fig. 2. Because of this difficulty, in the models the complexity of the systems is restricted. In fact in many models the dynamics of excess protons in liquid water is considered as an approximation for proton conduction in a hydrated Nation membrane. The conformations and energetics of proton dissociation in acid/water clusters were also evaluated as approximations for those in a Nation membrane.16,19 20 22 24 25... 

P.J. Bruna et al., Beryllium-beryllium bonding. 1. Energetics of protonation and hydrogenation of beryllium dimer and its ions. J. Phys. Chem. 96, 6269-6278 (1992)... 

Figure 11. Calculated energetics of proton transfer between the catalytic cysteine and the dianionic phosphate group of the substrate in LMPTP and PTPIB.

T. Komatsuzaki and I. Ohmine, Energetics of proton transfer in liquid water. I. Ab initio study for origin of many-body interactions and potential energy surfaces, Chem. Phys., 180 (1994) 239-269. 

Figure ]4r Calculated free energy profiles for the reference reaction, 21 0 OH l HjO+ (open triangles) in water and for the proton transfer step in human carbonic anhydrase 1 (open squares). The calculated energetics of proton transfer from a zinc-bound water molecule in aqueous solution is also shown for comparison (Aqvist...

JS Klassen, P Kerbarle. Collison-induced dissociation threshold energetics of protonated glycine, glycinamide, and some related small peptides and peptide amino amides. J Am Chem Soc 119 6552—6563, 1997. 

CI) species from strong acids produced by EI of a suitable bath gas (H2, CH4...) due to a lower internal energy of the ions controlled by the energetics of proton-transfer reaction... 

Double proton exchange within a molecule was demonstrated by Destro [91]. He was able to characterize by X-ray diffraction measurements at temperatures ranging from 20 to 293 K the energetics of proton transfer betwen the two tautomeric forms of citrinine 20. 

The energetics of proton transfer along the water chains can be evaluated using methods that combine QM for a system, MM (or MD) for the protein (including internal water), and continuum electrostatics for external solvent and the membrane. (The latter can treated via generalized solvent boundary potential (GSBP) [139]). The methods of such calculations are currently well developed [32,140, 141-151], and have been reviewed recently [152], At the time of this writing, such... 

In a second study, DFT calculations on cuboidal MIr3S4 type clusters were performed by Tanaka et al, varying the heterometal centers (M=V, Cr, Mn, Fe, Co, Ni, Cu, Mo, Ru, W). This study was conducted in order to determine which of these clusters could potentially be employed for the conversion of N2 to ammonia. As a result of these calculations, the clusters with M=Ru, Mo and W were identified to activate N2, whereas no activation was found with the other metals. In order to obtain further insight into the reactivities of these clusters, calculations on the energetics of proton transfer from an external acid (lutidinium) to the coordinated N2 molecule were performed. These treatments indicated that protonation of the RU-N2 complex is associated with a high-energy barrier, in agreement with the experimental result that for this cluster no protonation of N2 could be achieved. Protonation of the Mo- and W-N2 complexes, in contrast, was predicted to be facile. 

Ab initio study of energetics of protonation and hydrogen bonding of pyridine N-oxide and its derivatives ... 

Similarly, Angell and coworkers [43] reported that the studied acid-base pairs with the high ionicity are those with a proton transfer gap of about 0.7 eV, corresponding to Ap a values of ca. 12. The very high Ap/sTa values required to achieve complete proton transfer in protic ionic liquids should be compared with those in aqueous solutions, as discussed above. It seems that the nonaqueous solvation environment of ionic liquids has a very strong effect on the energetics of proton transfer. 

Z. Latajka and S. Scheiner, Energetics of proton transfer between carbon atoms. (H3CH-CH3)-, Int. J. Quantum Chem., 29 (1986) 285. 

S. Scheiner, P. Redfem and M.M. Szczesniak, Effects of external ions on the energetics of proton transfers across hydrogen bonds, J. Phys. Chem., 89 (1985) 262. 

A general level of agreement has been established between experimental results and theoretical calculations of the energetics of proton transfer in the gas phase. The results indeed appear encouraging for the use of theory to obtain needed molecular structures of organic cations and anions. 

The relative contribution of each pathway to the final proton transfer rate depends not only on the geometry of the groups involved, but on the energetics of protonation at... 

S. Scheiner, Theoretical calculation of energetics of proton translocation through membranes. Methods Enzymol. 127 456 (1986). 

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