Proton computational approaches

A density functional theory computational approach has been used " to investigate the [1,5]-hydrogen shift in (z)-penta-l,3-diene. Ab initio calculations of the activation barriers to proton transfer in nitrogen derivatives have been computed and these values used to show that the proton transfer in pyrazole is formally a... 

In the next chapter by Ibon Alkorta and Jose Elguero, applying computational approaches presents interrelations between aromaticity and chemical and physicochemical properties of heterocycles. The following problems and properties are considered tautomerism, conformation analysis, acid-base equilibria, H-bonding and proton transfer, energetics, reactivity, IR-, NMR-, and MW-spectroscopies. At the end is a discussion of problems related to supramolecules and macrocycles. 

Computational approach. Singleton, Beak and Lee explored the pathways of decarboxylation of 1-methylorotic acid 11 via the 2-protonated zwitterion 4b and the 4-protonated zwitterion 6b using Becke3LYP calculations with a 6-31 + G basis set.46... 

This conclusion appears to agree fully with the concept of the aforementioned thermodynamically favorable four-electron mechanism of N2 reduction (Likhtenshtein and Shilov, 1970) and with the evolution of free hydrazine at the acid or base treatment of nitrogenase during turn-over (Lowe et al., 1993), (5) Histidine is the only aniino acid side chain capable of donating protons in neutral pH. The Fe atoms are not saturated. Though aforementioned theoretical calculations are based on simplified truncated models of FeMoco and use an approximate computational approach, they allow the... 

Prior to 2001, when the first serious computational approaches to the problem appeared in print, four mechanistic proposals had been offered for understanding the Hajos-Parrish-Wiechert-Eder-Sauer reaction (Scheme 6.8). Hajos and Parrish proposed the first two mechanisms Mechanisms A and B. Mechanism A is a nucleophilic substitution reaction where the terminal enol attacks the carbinolamine center, displacing proUne. The other three mechanisms start from an enamine intermediate. Mechanism B invokes an enaminium intermediate, which undergoes C-C formation with proton transfer from the aminium group. Mechanism C, proposed by Agamii to account for the nonlinear proline result, has the proton transfer assisted by the second proline molecule. Lastly, Mechanism D, proffered by Jung, proposed that the proton transfer that accompanies C-C bond formation is facilitated by the carboxylic acid group of proline. 

Calculations using conventional TST and the Bigeleisen-Wolfsberg [16] treatment for isotope effects have demonstrated that thd = 1-44 is a useful benchmark for primary hydrogen isotope effects. Using empirical harmonic force fields and various reactant-state and transition-state geometries, More O Ferrall and Kouba [30] found, for proton-transfer models, that the exponents were within 2% of the 1.44 value, and similar computational approaches gave Xhd = 1.43-1.45 (343 K)... 

Fig. 3 a Proposed mechanism of ODCase-catalyzed decarboxylation of OMP by 02 protonation. Both the protonation and decarboxylation steps would be expected to be slightly sensitive to isotopic substitution at Nl. b Model reactions used to assess the feasibility of the 02 protonation mechanism, or any mechanism with a pre-decarboxylation step that is isotopically sensitive at Nl, and the measured Nl equilibrium and kinetic isotope effects, a Data from [31]. b Data from [30]. c Model reactions for which Nl equilibrium and kinetic isotope effects were determined using computational approaches, and the computed values [32]... 

The possibility of using 2,6-disubstituted pyridines and 2,6,7-trisubstituted quinuclidines, where the substituents feature remote atoms with lone pairs to stabilize the hydrogen upon protonation, are proposed snperbases that have been explored by computational approaches. There is interest in synthesizing macrocyclic proton chelaters as catalytically active organic snperbases,and a new strnctnral motif for snperbases featuring caged secondary amines has been reported. The alkali metal hydroxides, of eqnal basicity in aqueous solution, have proton affinities in the order LiOH (1000 kJ/mol) < NaOH < KOH < CsOH (1118 kJ/mol). This order matches the increasing ionic character of the alkah metal-hydroxide bonds. 

The velocity dr/dt of the relative motion of the proton b, approaching the H-atom, can be computed in a center-of-mass coordinate system from the classical kinetic energy expression... 

As a final example, we also illustrate how a computational approach was used in a study on possible tautomerism. Molecule VI, studied in the second CCDC blind test [57] may form three different stable polymorphs, aU observed as sidfonimides. However, in one of these forms, a sUght shift in the proton positions within a dimer core of the crystal structure gives the sulfonamide tautomer. Therefore, we initiated a study to elucidate the energy difference between suffonimide and sulfonamide tautomers of VI (Fig. 7.22). 

Computational approaches that have been employed to understand the structure and transport properties of water and protons in swollen Nation membranes include ab initio (Eikerling et al., 2003 Roudgar et al., 2006, 2008 Vartak et al., 2013), classical all-atom (Cui et al., 2007 Devanathan et al., 2007a,b Goddard et al., 2006 Spohr et al., 2002 Vishnyakov and Neimark, 2000, 2001), and coarse-grained descriptions (Galperin and Khokhlov, 2006 Wescott et al., 2006) of the system. 

The computational approach also makes it possible to gain insight into the effect of solvation on the enthalpy of formation without conducting experiments. A calculation performed in the absence of solvent molecules estimates the properties of the molecule of interest in the gas phase. Computational methods are available that allow for the inclusion of several solvent molecules around a solute molecule, thereby taking into account the effect of molecular interactions with the solvent on the enthalpy of formation of the solute. Again, the numerical results are only estimates, and the primary purpose of the calculation is to predict whether interactions with the solvent increase or decrease the enthalpy of formation. As an example, consider the amino acid glycine, which can exist in a neutral (5) or zwitterionic (6) form, in which the amino group is protonated and the... 

At any rate, even within these widely employed NMR protocols, computational approaches can play an important role. In particular, the choice among alternative structural hypotheses can often be guided by the correspondence between measured and computed spectroscopic parameters. Instances where this approach has led to disprove a seemingly reliable structural assignment are not uncommon. As a matter of fact, it is reasonable to foresee that this kind of validation will become even more widespread in the near future rather than any difficulty in the actual calculation of magnetic resonance parameters, stumbling blocks along this direction may be represented by issues of flexibility, protonation microstates, and... 

This review summarises and discusses the advances of computational photochemistry in 2012 and 2013 in both methodology and applications fields. The methodological developments of models and tools used to study and simulate non-adiabatic processes are highlighted. These developments can be summarised as assessment studies, new methods to locate conical intersections, tools for representation, interpretation and visualisation, new computational approaches and studies introducing simpler models to rationalise the quantum dynamics near and in the conical intersection. The applied works on the topics of photodissociation, photostability, photoisomerisations, proton/charge transfer, chemiluminescence and bioluminescence are summarised, and some illustrative examples of studies are analysed in more detail, particularly with reference to photostability and chemi/ bioluminescence. In addition, theoretical studies analysing solvent effects are also considered. We finish this review with conclusions and an outlook on the future. 

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