AMBER Archive (2009)

Subject: Re: [AMBER] Re: COOH troubling

From: Dean Cuebas (deancuebas_at_missouristate.edu)
Date: Sat Dec 12 2009 - 10:47:42 CST

Dear Jiomm,

I just wanted to clarify that the three ring structure is completely
aromatic only when the phenolic proton is removed... for the protonated
phenol structure (-1 or 0 charge) only the phenolic ring is aromatic, just
as Junmei demonstrated for you. After reading the article you provided in a
bit more detail, I realize that only the neutral compound would be soluble
in CH2Cl2. Junmei's got the correct answers for your situation.
(Being a biochemist, I always work in physiologic solutions... :-)

Good luck with your work!

Dean

Dr. Dean Cuebas, Associate Professor of Chemistry
deancuebas_at_missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

> From: Junmei Wang <junmwang_at_gmail.com>
> Reply-To: AMBER Mailing List <amber_at_ambermd.org>
> Date: Thu, 10 Dec 2009 15:45:43 -0600
> To: AMBER Mailing List <amber_at_ambermd.org>
> Subject: Re: [AMBER] Re: COOH troubling
>
> Hi,
> I have carefully examined your molecule. The structure should be correct
> (forming C=O, neutral). I am not sure how you did QM calculations and how
> you set the radii for Iodine. I calculated HF/CEP-121G (the radii for I was
> set to 1.98) optimization for your ligand molecule and derived the resp
> charges. I can see the difference between yours and mine is enormous. Please
> see the attached prepi file.
>
> After that, I tried to repeat your MD results. Using your charges, the 1-4
> interaction became unrealistic negative and led the program to crash for
> both minimization and MD. However, with my RESP charges based on HF/CEP-121G
> (I think HF/CEP-31G, which mimics the HF/6-31G* better, should be used), the
> minimization and MD were run smoothly. Please see the attached sander
> outputs.
>
> According to my experience, gaff can handle most organic molecules well and
> I have successfully run MD simulations for at least 500 organic molecules,
> all in TIP3P water or the other organic solvents. The trouble molecules I
> met are those containing high positive or negative charges (>1.5 and < -1.5)
> or those are gases at the simulation contidions. For most trouble molecules,
> I still can make MD running by modifing MD inputs and minimizing the unideal
> strctures.
>
> Good luck
>
> Junmei
>
>
>
> On Thu, Dec 10, 2009 at 5:03 AM, Jio M <jiomm_at_yahoo.com> wrote:
>
>> Dear Dr. Dean and J. Wang;
>>
>>
>>
>>> Either get rid of the double bond and add a negative charge to make a
>>
>> phenolate ion, or make a C-O-H by adding a hydrogen to the oxygen to make a
>>
>> phenolic group, like you have on the opposite side of your anthracene ring
>>
>> system.
>>
>>
>>
>> I am sending link which shows my structure.
>>
>> http://www.wag.caltech.edu/publications/sup/pdf/370.pdf
>>
>> But I have used RESP charges. There some other charge method is used. I
>> think it is C double bond O.
>>
>>
>>
>> thanks and regards;
>>
>> JIomm
>>
>>
>>
>>
>>
>>
>>
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