From owner-chemistry@ccl.net Fri Oct 21 02:02:00 2016 From: "Jeya Vimalan jeyavimalan2k++gmail.com" To: CCL Subject: CCL: Formation Energy - Summary Message-Id: <-52456-161021015044-13457-hEhcF13bsahu0VJSU5xhSw/a\server.ccl.net> X-Original-From: Jeya Vimalan Content-Type: multipart/alternative; boundary=001a114491ece75bd7053f599e69 Date: Fri, 21 Oct 2016 11:20:33 +0530 MIME-Version: 1.0 Sent to CCL by: Jeya Vimalan [jeyavimalan2k%%gmail.com] --001a114491ece75bd7053f599e69 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear All, Thanks for your response. I am summarizing the replies. vimal Question : =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dear All, I have three composition. A1-B3-C4 A2-B4-C5 A4-B3-C7 I would like to understand which structures are stable and hence decided to calculate formation (or Cohesive) energy. Lets take the first two cases and calculate Formation energy by the below formulae. Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 -(Energy of 1*A + Energy of 3*B + Energy of 4*C). Formation Energy of 1 (E2) =3D Total energy of A2-B4-C5 -(Energy of 2*A + Energy of 4*B + Energy of 5*C). Does the direct comparison (E1, E2) makes sense? Can i conclude if E1>E2, then composition 1 is more stable. I feel, i am missing something. Your help would be appreciable. Best regards, Vimal =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =3D=3D=3D Dear Vimal, I would say that your approach is valid, under the condition that the A, B, and C and sensible moieties. It reminds a bit of atomization energies. However, I would say that if E1 > E2 (e.g. +2 vs. -10) that 2 is more stable, not 1. Marce Prof Dr Marcel Swart, FRSC ICREA Research Professor at Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi (IQCC) Univ. Girona (Spain) COST Action CM1305 (ECOSTBio) chair Girona Seminar 2016 organizer IQCC director Young Academy of Europe (Board) member Web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =3D=3D=3D=3Dl Dear Vimal: Unfortunately, the concept of stability is not that straightforward. Thermodynamics does not provide the final answer. The stability of a molecule not only depends on its formation energy, but it depends also on the relative energies of its neighboring local minima on its potential energy surface and the energy barrier between the minimum and its immediate neighboring minima (kinetic stability). To begin, I would rather check the depth of minimum energy well by looking at frequencies. In the next step ab initio/MC/DFT- MD simulations can provide more insight toward the kinetic stability. Then of course we can define stability with respect to a particular reaction. Is your molecule stable when it is in the presence of air/water/light/etc. You must be more precise about stability. I hope my general answer can help you to solve your problem. Good luck, Cina -------------------------------------------------------------- Cina Foroutan-Nejad, PhD CEITEC-Central European Institute of Technology Kamenice 5/A4, Masaryk University, Brno, Czech Republic https://muni.academia.edu/CinaForoutanNejad =3D=3D=3D=3D Hi Vimal: I am not exactly certain what you want to do but if you want to estimate is composition A1-B3-C4 is more stable than A2-B4-C5, you should calculate the energy of this "reaction" ... A1-B3-C4 + A + B + C --> A2-B4-C5 Now you have a mass balanced equation. Assuming the energies of these components are negative, then if E(Right Hand Side) - E(Left Hand Side) is negative the LHS is more stable. This means A2-B4-C5 as a compound is more stable than A1-B3-C4 and an extra A, B, and C. Regards, Joe Golab jtgolab59(~)gmail.com =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dear Jeya, how are you? The comparison kind of makes sense, but to get the correct energies it is not enough to calculate the single points without the thermodynamic corrections (and using the correct stoichiometry in your equations). Please, if you can, take a look at this link[1] (it is in Portuguese, but maybe Google Translator can deal with this issue for you). All the best [1] - http://ab.cheminformatics.xyz/dft/uma-busca-pela-entalpia-de-formacao= / henriquecsj(~)gmail.com =3D=3D=3D Thanks and best regards, vimal --001a114491ece75bd7053f599e69 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear All,

Thanks for your response.
I am summarizing the replies.
vimal

Question :


=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dear = All,

I have three composition.

A1-B3-C4
A2-B4= -C5
A4-B3-C7

= I would like to understand
which structures are stable a= nd hence
decided to calculate formation (or Cohesive) en= ergy.

Lets take the first two ca= ses and=C2=A0
calculate Formation energy by the below fo= rmulae.


= Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 -(Energy of 1*A + E= nergy of 3*B + Energy of 4*C).
Formation Energy of 1 (E2= ) =3D Total energy of A2-B4-C5 -(Energy of 2*A + Energy of 4*B + Energy of = 5*C).


Do= es the direct comparison (E1, E2) makes sense?
Can i con= clude if E1>E2, then composition 1 is more stable.
I feel, i am missing something.
Yo= ur help would be appreciable.

Be= st regards,
Vimal
=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D
=3D=3D=3D
Dear Vimal,

I would say that your approach is valid, u= nder the condition that the A, B, and C and
sensible moieties. It reminds a bit of atomization energies.

Howe= ver, I would say that if E1 > E2 (e.g. =C2=A0+2 =C2=A0vs. -10) that 2 is= more stable, not 1.

Marce

Prof Dr Marcel Swart, FRSC
ICREA Research Professor at
Institut de Qu=C3=ADmica Computacional= i Cat=C3=A0lisi (IQCC)
Univ. Girona (Spain)

COST Action CM1305 (= ECOSTBio) chair
Girona Seminar 2016 organizer
IQCC director
Young = Academy of Europe (Board) member

=3D=3D=3D=3Dl


Dear Vim= al:

Unfortunately, the concept of = stability is not that straightforward. Thermodynamics does not provide the = final answer. The stability of a molecule not only depends on its formation= energy, but it depends also on the relative energies of its neighboring lo= cal minima on its potential energy surface and the energy barrier between t= he minimum and its immediate neighboring minima (kinetic stability). To beg= in, I would rather check the depth of minimum energy well by looking at fre= quencies. In the next step ab initio/MC/DFT- MD simulations can provide mor= e insight toward the kinetic stability. Then of course we can define stabil= ity with respect to a particular reaction. Is your molecule stable when it = is in the presence of air/water/light/etc.
You must be more precise about stability.=C2= =A0

I hope my general answer can h= elp you to solve your problem.

Good lu= ck,
Cina

--------------------------------------------------------= ------
Cina Foro= utan-Nejad, PhD
CEITEC-Central European Institute of Technology
Kamenice 5/A4, Masaryk University, Br= no, Czech Republic

=3D=3D=3D=3D
Hi Vimal:

I am not exactly certain what you wan= t to do but if you want to estimate is composition A1-B3-C4 is more stable = than A2-B4-C5, you should calculate the energy of this "reaction"= ...

A1-B3-C4 + A + B + C --> A2-B4= -C5

Now you have a mass balanced equat= ion. Assuming the energies of these components are negative, then if E(Righ= t Hand Side) - E(Left Hand Side) is negative=C2=A0the LHS is more stable. T= his means=C2=A0A2-B4-C5 as a compound is more stable than=C2=A0A1-B3-C4 and= an extra A, B, and C.

Regards,
Joe Golab
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Dear Jeya, how a= re you?
The comparison kind of makes = sense, but to get the correct energies it is not enough to calculate the si= ngle points without the thermodynamic corrections (and using the correct st= oichiometry in your equations).
Please, if you= can, take a look at this link[1] (it is in Portuguese, but maybe Google Tr= anslator can deal with this issue for you).
All the best
<= br>
[1] -=C2=A0http:= //ab.cheminformatics.xyz/dft/uma-busca-pela-entalpia-de-formacao/=
henriquecsj(~)gmail.com
=3D=3D=3D


Thanks= and best regards,
vimal
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