The study of the role of Hydronium ion in Proton transfer essentially provides an evidence that the bulk water presence is a viable medium for proton transfer to occur.

At least what happens in isolated amino acid molecule Geometry Optimization starting with Zwitterion form can happen unhindered even in presence of water even if water does not seem to be significantly faciliting what happens without its presence.

At this juncture the question of greater concern seems to be to find ways for proton transfer from the carboxylic acid function (of the nonionic amino acid) to the alpha amino group in the molecule.

This requires much closely the possible specific water-amino acid interaction within the coordinate sphere of the amino acid, and find how the bilk water medium could further facilitate.

Geometrical Variations

The main inference by the results considered till now is that the ZWITTERION form of the amino acid exhibits the proton releasing tendency of the ammonium group at provocation of the presence of an Oxygen containing system in the neighborhood and that in the absence of any other molecule, the carboxylate ion of the isolated amino acid receives the proton readily.

Is it possible to investigate the role of water mediation to such an extent that, the zwitterion form becomes more stable in such a surrounding as compared to the nonionic form?

This is what is the most popularly known conditions in Biological media.

details

The methods of Molecular Electrostatic Potential in the Computational Chemistry tries to derive the benefit of Chemist’s intuition imagining as if a proton can be placed around the molecule, and try to find out its energy values due to the electrostatic interaction with the molecular charges. Essentially molecular environment favoring certain dispositions which eventually makes possible certain reactivities for the given structure.

In a similar way by examining the dipole moment of the molecule and placing a water molecule in the neighbor hood is it possible to find a favorable number of water molecules in the coordination sphere and the relative disposition of these molecules to influence the proton transfers to take place in such a way that proton prefers to get lodged at the ammonium ion region rather than the carboxylate ion region of the amino acid?

In the following slide such a environmental information is attempted at with two water molecules in the neighborhood.

Preliminary assessment with dipole moments and energies of system.

(Glycine:1W) is slightly more stable than the system of infinitely separated molecules

An Example of arranging water molecules

If M.E.P. is of relevance would it be better to

have H+ and OH- in the medium?

Additive and Non additive energy contributions to clusters

MEP_1

MEP_2

Dipole Moments

+

- MEP

Arrangement 1

Arrangement 2

Possible space for intramolecular proton transfer

Causes a crowding to sterically hinder ammonium proton from getting directed towards oxygen of carboxylate

Warer molecules have to get rearranged near to the carboxylate

Water molecules orient conveniently for the proton to reach for the oxygen of water

Water molecules mediate in the proton transfer from ammonium to carboxylate of glycine

This part is a more specific water-amino acid interaction

Know the difference between the two arrrangements

Consider two water molecules placed near glycine molecule

How?

15 is a H+

16 also

is H+

OH-

OH-

At iterative step 15 STO3G basis gave error

Basis set changed to B3-21G

Output Step 33

Output Step 50

Output Step 65 Edited

outputProton transfer from carboxylic acid group to alpha Amino group

G.O. indicates the Zwitterion stabilization

Changes of

ion orientation indicates a specific interaction with COOH functional of amino acid

O-H -

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