crownether-Host-guest-C-docked.ppt
Chiral Recognition by NMR Spectroscopy- A Theoretical approach.
Illustrating modeling strategies with organic molecules
with overtones for Modeling of Bio-molecules
An Abstract
This material may be availed as Internet Resource:
Display the web subdirectory: http://www.ugc-inno-nehu.com/CRNMR/
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S.Aravamudhan
7/6/2012 11:50:10 AM
Aravamudhan: Chiral Recognition by NMR
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While trying to find out the host-guest interactions the thrust has also been to make use of (1) an
as much versatile software for the theoretical calculations (2) and a software which is also easily
accessible for beginners that would enable them to learn the features of a software for theoretical
(Quantum mechanics/ Molecular mechanics) Calculations. Such a report of the facts of
investigation would put the beginners on the path for learning about the compromises required in
a (macro-)molecular modeling. Typically the trade off between molecular sizes and available
computer memory, together with the necessity to minimize the computational time (which could
be a matter of computational costs).
The computational chemistry package used for the current work is the online remote
computational facility located at http://www.webmo.net . The strong point first of all is the
simplicity of access and the student-proof way the web administration manages the Working
Demo of this computational chemistry website. The second, but no less important is the fact that
this working demo has one of the most advanced features for choosing the computational
methods by providing several software engines with each one of them capable of being
configured for several properties of molecules to be calculated. Computation, and the way the
entire Job parameter can be archived in the resident disc for uploading into the Demo for
subsequent calculations at any later time, and the way the results and job parameters can be
exported to process and review in off-line mode are not features to which beginners can have
access as readily as it is in this working Demo. There is no way as per the current version of the
Demo to increase the computational time available per job to more than one minute. This
provides an experience in choosing model systems for addressing specific theoretical queries even
in the small molecule regime.
18 July 2012
Aravamudhan Chiral discrimination NMR
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hyperlink
All G.O. are MM Calculations
18Crown6etherFlig1-S-F at6 zaxis
18Crown6ether18Crown6etherFlig1-S-F at6 zaxis-UFF-GO
Flig2-R-Fat6zaxis
hyperlink
View in
Str. Editor
View in
Str. Editor
hyperlink
18Crown6etherFlig1-S-N at6 zaxis
18Crown6ether18Crown6ether-Flig1-SFlig2-R-Nat6zaxis
Nat6zaxis-UFF-GO
hyperlink
View in
Str. Editor
View in
Str. Editor
18 July 2012
Aravamudhan Chiral discrimination NMR
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All G.O. are MM Calculations
hyperlink
18Crown6etherFlig2-R-Fat6zaxis
18Crown6etherFlig2-R-Fat6zaxis-UFF-GO
hyperlink
View in
Str. Editor
hyperlink
View in
Str. Editor
18Crown6etherFlig2-R-Nat6zaxis
18Crown6etherFlig2-R-Nat6zaxis-UFF-GO
hyperlink
View in
Str. Editor
View in
Str. Editor
18 July 2012
Aravamudhan Chiral discrimination NMR
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The typical constraint of a time limit of 1 min . per job rendered the G.O. by QM ab initio
methods as most inconvenient to opt .
However the corresponding geometry ( obtained by the G.O. using any other time saving
means) of these molecules could be conveniently put through the one-minute jobs for
NMR chemical shift calculations at the “WEBMO”. All the NMR spectra of the different
isomers (of the Cs -several lines in spectrum - and of the D3d – towlines spectrum ) of the
18Crown6Ether were obtained by ab initio SCF/STO 3G choice with G.I.A .O. for the
chemical shift calculation.
When it becomes the host (18Crown6ether) –guest (ligand) the NMR calculations
exceeded the time limit and hence no calculated spectrum could result for comparison
with unbound Host spectrum and the free ligand spectrum (even for the simplest chiral
molecule one could envisage as derivative of a methane structure) . Thus even before
knowing the actualities of binding criteria which enable the Chiral Discrimination, it
became necessary to resort to a modeling strategy, essentially to decrease the size of the
molecule and thus in detail know about the theoretical explanations for the possible
discrimination. With this situation at the outset, a search for a model.
Two major criteria emerges from the Calculations of the docking type and the
corresponding NMR spectra: 1) as much a simple NMR pattern for assigning the protons
to track the distinct changes due to chirality of guest. 2) Much of the complexing is
determined by the interaction with the oxygen centers of the host and hence the
importance of Crown Ether.
18 July 2012
Aravamudhan Chiral discrimination NMR
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