From owner-chemistry %-% at %-% ccl.net Mon May  9 11:02:00 2016
From: "Debopreeti Mukherjee debopreeti91 ~ gmail.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: TD-DFT calculations performed for simulation of peptide CD spectrum
Message-Id: <-52186-160509103656-1664-ZJRwhxFR3RiONkS4qUwa5w%server.ccl.net>
X-Original-From: "Debopreeti  Mukherjee" <debopreeti91++gmail.com>
Date: Mon, 9 May 2016 10:36:55 -0400


Sent to CCL by: "Debopreeti  Mukherjee" [debopreeti91(-)gmail.com]
Hello,

I am trying to simulate the CD spectrum of a peptide using TD-DFT. In my 
peptide, I expect to see an excitonic coupling band arising as a result of 
interactions between two aromatic amino acids (seen from experiment). In 
order to calculate the rotational strength of this band, I need to 
construct a Hamiltonian based on dipole-dipole interactions between the 
aromatic amino acid residues, diagonalize it and then use the eigen vector 
components. I would also need the transition dipole moment values 
corresponding to each aromatic chromophore.

I ran a TD-DFT calculation (no solvent model, counterpoise for two aromatic 
fragments; according to the paper - 
http://onlinelibrary.wiley.com/doi/10.1002/chir.20792/full) and then tried 
to use Matlab to construct the matrices. However, I am confused regarding 
the rotational strength units and the values also seem way off.

If anyone has done these kind of calculations before, can you please help 
me? 
Thank you so much.

Regards,
Debopreeti Mukherjee
Email id: debopreeti91#,#gmail.com