Transcript 0_specific - ugc-inno

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. Geometrical Variations
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 wateramino acid interaction within the coordinate sphere of
the amino acid, and find how the bilk water medium could
further facilitate.
details
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.
This is what is the most popularly known conditions
in Biological media.
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?
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.
If M.E.P. is of relevance
would it be better to
have H+ and OH in
Preliminary assessment
with dipole moments and
energies of system.
Additive and Non additive
energy contributions to
clusters
(Glycine:1W) is slightly
more stable than the
system of infinitely
separated molecules
the medium?
Dipole
Moments
MEP_1
MEP_2
An Example of
arranging water
molecules
MEP
Possible space for intramolecular
proton transfer
Arrangement 1
Consider two
water molecules
placed near
glycine molecule
Know the difference
between the two
arrrangements
Arrangement 2
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
Thismediate
part is ain the
more
specific
proton
transfer
water-amino
acid
from ammonium
interaction
to carboxylate of
glycine
Water molecules orient conveniently
for the proton to reach for the oxygen
of water
How?
At iterative
step 15
STO3G basis
gave error
-
OH
Basis set changed
to B3-21G
Changes of O-H
16 also
is H+
15 is a
Output
Step 33
-
ion orientation
indicates a specific
interaction with
COOH functional of
amino acid
-
OH
H+
Output
Step 50
Output
Step 65
G.O. indicates
the Zwitterion
stabilization
Edited
output
Proton transfer from
carboxylic acid group
to alpha Amino group
Larger
size