Subject: questions

From: Vlad Cojocaru <[email-masked]>
Date: Thu, 30 May 2002 16:06:25 +0200

I am trying to calculate the electron density and electrostatic 
potential for some pteridine analogues. I have several questions about that.
I am using as model the desciption of this type of calculation for 
azulene and nafthalene described on www.gaussian.com. I also must say 
that I am a beginner with Gaussian.
1. If I am using RBecke3LYP method for calculating the density and ep is 
it necessary that the optimization run prior to these calculations is 
done using the same method or can I simply use a structure that was 
optimized using HF.
2. By your experience which DFMethod gives the best results for the 
electron density and ep?
3. I found this explaination on the site ("The theoretical model used in 
this study was the RBecke3LYP method with a 6-31G(D) basis set. The 
optimized geometry was determined by minimizing the energy with respect 
to the nuclear coordinates. This was followed by a calculation of the 
frequencies of vibration to verify that the structure was a minimum and 
to compute the thermal energy at 300 Kelvin"). Can somebody explain how 
can one verify from the freq. of vibration if the structure was a minimum?
4. Did somebody ever calculated these properties for 2-amino purine in 
order to compare them to that of Adenine. If yes could you please supply 
me a reference so that I can look up.

Thanks in advance for any kind of suggestions,
vlad

-- 
Vlad Cojocaru 
Max Planck Institut for Biophysical Chemistry 
Deparment: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1389 
e-mail: [email-masked]

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From: "Alimet S. Ozen" <[email-masked]>
Date: Thu, 30 May 2002 23:18:35 +0300 (EET DST)

I might have an answer for that question:
On Thu, 30 May 2002, Vlad Cojocaru wrote:
> can one verify from the freq. of vibration if the structure was a minimum> 
> 
I couldn't find the explanation you mentioned but as far as I know,
a stationary point(a local or a global minumum or a transition state) on a
potential energy surface is where the net force is zero, meaning the first
derivative of energy wrt nuclear coordinates (or the gradient) is zero.In
addition to that, at minimum, the second derivative of energy must be
greater than 0 or in other words all the eigenvalues of the hessian matrix
must be positive.(If one eigenvalue is negative then this is a transition state)
Second derivatives of energy are related to the harmonic force constants
that are further related to the vibrational frequencies.So, if you have
all-positive frequencies than this verifies that the structure is a
minimum..but cannot tell if it is a global or a local one..
If you have one negative or 'imaginary' frequency than this is a
transition state..maximum in one dimension but minimum in all the
others..
you can refer Alan Hinchliffe's book 'modelling molecular structures'
(or Frank Jensen's 'introduction to computational chemistry') for
a better discussion..
Best regards
Alimet

"Real value: is not the one whose presence fills an empty space
but the one whose absence creats one" Ozdemir Asaf
 [email-masked]
 [email-masked]
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