Dear Cina;

Thank you so much for your prompt reply. My case study is the= dehydrogenation reaction of an amide (RCONH2 >>> RCONH + H) over = a catalysis surface. The calculated activation energy is very low (less tha= n 2 kcal/mol). however, both activation energy and activation enthalpy are = negative. The method of calculation is M062X/6-31G*.

------------------------------------------------------------= ------------------------------------------------------------------ &nb= sp;

`The man who makes no mistakes does not usually make anythin= g.'

&nb= sp; = Edward John Ph= elps (1822-1900)

--------------------------------------------------= ---------------------------------------------------------------------------= -
Mehdi D. Esrafili, Ph.D.

Assistant Professor of Physical Chem= istry
Current address: Department of Chemistry,

Faculty of Basic Sciences,University of

Maragheh, Iran. <= /div>

E-mail 1: m_esrafil= i ~~ yahoo.com
E-mail 2: = esrafili ~~ maragheh.ac.ir

-------------------------------------------------------= -----------------------------------------------------------------------

<= div style=3D"display: block;" class=3D"yahoo_quoted">

On Friday, January 30, 201= 5 5:33 AM, Cina Foroutan-Nejad canyslopus#%#yahoo.co.uk <owner-chemistry= ~~ ccl.net> wrote:

<= span>Dear Mehdi,

A common reason for negative acti= vation energy is that a reaction that you think is single-step, indeed is m= ulti-step. A good example of such reactions is SN2 reaction in gas phase wh= ere first a non-covalently bonded complex forms between nucleophile and rea= ctant then Nu and RX react and form another complex and then this complex m= ay dissociate. Comparing the energy of reactants/TS in some SN2 reactions i= n gas phase may suggest that there is a negative energy barrier for reactio= n. If I can correctly remember I saw this example in Reaction and Mechanism= in Organic Chemistry by Lowry and Richardson. If you explain more about ye= ar reaction, I may help more.

All the best,

Cina

-------------= ---------------------------------------------------------------------------= -------

Cina Foroutan-Nejad, PhD,

= CEITEC, Central European Institute of Technology,

M= asaryk University, Brno,

Czech Republic

https://muni.= academia.edu/CinaForoutanNejad

On Friday, 30 Janua= ry 2015, 12:40, Mehdi Esrafili m_esrafili]=3D[yahoo.com <owner-chemistry= |-|ccl.net> wrote:

Dear all;

<= div id=3D"yiv7904227697yui_3_16_0_1_1422613084688_3511" dir=3D"ltr">I want to know what is t= he meaning of negative activation free energy =CE=94G# for a reaction step?=

With best regards

Mehdi

-------------------------------------------------------------= ----------------------------------------------------------------- &nbs= p;

`The man who makes no mistakes does= not usually make anything.'

&nb= sp; = &nb= sp; Edward John Phelps (1822-1900)

----------------------------------------= ---------------------------------------------------------------------------= -----------
Mehdi D. Esrafili, Ph.D.

Assistant Professor of Physical Chemistry
Current address: Department of C= hemistry,

Faculty of Basic Sciences,U= niversity of

Maragheh, Iran.

E-mail 1: m_es= rafili(~)yahoo.com
E-mail 2: esrafili(~)maragheh.ac.ir

-------------------------------------------------------------= -----------------------------------------------------------------

<= /html> ------=_Part_2808821_1540953144.1422631204896-- From owner-chemistry@ccl.net Fri Jan 30 11:22:01 2015 From: "Mahmoud A. A. Ibrahim m.ibrahim-$-compchem.net" To: CCL Subject: CCL:G: Hardware Specs: Connectivity vs Performance Message-Id: <-50977-150130112011-9334-1b0gFmq+9LKAduNV6os+8g-*-server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Date: Fri, 30 Jan 2015 11:20:09 -0500 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim,,compchem.net] Dear All We are going to install a switching system for our new CompChem Cluster. The Cluster is around 12 servers; each one with two 2.2GHz octa-core process and four 32G RAM, plus a storage system. The point is that what level of connectivity should be used to connect the servers and to read/write from the servers and the storage system? Because of the fact that the budget dedicated for the switch system is very limited, we decided to purchase 1G ethernet switch, and each server will be connected to the switch via 4 cables (teaming up to give a total performance of 4G). We are afraid this low level of connectivity (4G) will reduce the performance of the servers. Anyone there would like to place a comment based on his experience. By the way, we are using quantum and molecular mechanics packages such as Gaussian and AMBER. Thanks in advance Sincerely; M. Ibrahim From owner-chemistry@ccl.net Fri Jan 30 16:11:00 2015 From: "Yingbin Ge yingbin.ge#gmail.com" To: CCL Subject: CCL: =?UTF-8?Q?Re=3A_CCL=3A_Negative_activation_free_energy_=CE=94G=23?= Message-Id: <-50978-150130144655-11286-W/XDt2QhANvMs54im7plXw]*[server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=001a11c00372a2e9b7050de3dd4d Date: Fri, 30 Jan 2015 11:46:50 -0800 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge(-)gmail.com] --001a11c00372a2e9b7050de3dd4d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Mehdi, There are 3 common reasons for a negative Gibbs energy of activation: 1) There's an intermediate between the reactant(s) and the product(s). This intermediate has lower Gibbs energy than the reactant(s) and is mistaken to be the transition state. 2) The reaction is energetically downhill and thus does not have a well-defined transition state. A simple example is CH3 + CH3 -> C2H6. It is possible to calculate the partition functions of H3C---CH3 with a stretched C-C bond and still construct a "Gibbs energy surface" for the reaction path to find the so called generalized transition state (GTS). Prof. Donald G Trular's published many papers on generalized transition state theory. (These types of reactions have no potential energy barriers and thus are often collision controlled or diffusion controlled.) 3) The transition state structures you get, from calculations using most quantum chemistry software, are the structures with the highest electronic energy along the reaction path; it may not be the structure with the highest Gibbs energy. A negative Gibbs energy of activation can also be due to 4) inaccurate computational method being used, 5) inaccurate modeling (e.g., not including the surface effect properly for a surface reaction). There can be many other reasons for a negative Gibbs energy of activation. But I am guessing, very boldly, it might be due to reason 2), 3), or 5) for your case (RCONH + H -> RCONH2 on a surface). Sincerely, Yingbin Yingbin Ge, Associate Professor Science Building 207A Department of Chemistry Central Washington University 400 E University Way On Fri, Jan 30, 2015 at 2:20 AM, Mehdi Esrafili m_esrafili]=3D[yahoo.com < owner-chemistry*ccl.net> wrote: > Dear all; > I want to know what is the meaning of negative activation free energy =CE= =94G# > for a reaction step? > With best regards > Mehdi > > > > -------------------------------------------------------------------------= ----------------------------------------------------- > `The man who makes no mistakes does not usually make anything.' > Edward John Phelps (1822-1900) > -------------------------------------------------------------------------= ----------------------------------------------------- > > Mehdi D. Esrafili, Ph.D. > Assistant Professor of Physical Chemistry > *Current address*: Department of Chemistry, > Faculty of Basic Sciences,University of > Maragheh, Iran. > E-mail 1: m_esrafili(~)yahoo.com > E-mail 2: esrafili(~)maragheh.ac.ir > > -------------------------------------------------------------------------= ----------------------------------------------------- > --001a11c00372a2e9b7050de3dd4d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Mehdi,

There are 3 common= reasons for a negative Gibbs energy of activation:

1) There&= #39;s an intermediate between the reactant(s) and the product(s). This inte= rmediate has lower Gibbs energy than the reactant(s) and is mistaken to be = the transition state.

2) The reaction is energetically do= wnhill and thus does not have a well-defined transition state. A simple exa= mple is CH3 + CH3 -> C2H6. It is possible to calculate the partition fun= ctions of H3C---CH3 with a stretched C-C bond and still construct a "G= ibbs energy surface" for the reaction path to find the so called gener= alized transition state (GTS). Prof. Donald G Trular's published many p= apers on generalized transition state theory. (These types of reactions hav= e no potential energy barriers and thus are often collision controlled or d= iffusion controlled.)

3) The transition state structures = you get, from calculations using most quantum chemistry software, are the s= tructures with the highest electronic energy along the reaction path; it ma= y not be the structure with the highest Gibbs energy.

A negative Gibbs energy of activation can also be due to 4) inaccu= rate computational method being used, 5) inaccurate modeling (e.g., not inc= luding the surface effect properly for a surface reaction).

There can be many other reasons for a negative Gibbs energy of activatio= n. But I am guessing, very boldly, it might be due to reason 2), 3), or 5) = for your case (RCONH + H -> RCONH2 on a surface).

Sincerely,

Yingbin

Yingbin Ge, Associat= e Professor
Science Building 207A
Department of Chemistry
Centr= al Washington University
400 E University Way

On Fri, Jan 30, 2015 at 2:20 AM, = Mehdi Esrafili m_esrafili]=3D[yahoo.com <owner-chemistry*ccl.net> wrote:

Dear all;
I want to know what is the meaning of negative activation free energy = =CE=94G# for a reaction step?
With best = regards
Mehdi
=C2=A0
=C2=A0
------------------------------------------------------= ------------------------------------------------------------------------=C2= =A0=C2=A0
`The man who makes no mistakes does not usually make anyt= hing.'
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Edwar= d John Phelps (1822-1900)
-----------------------------------------= ---------------------------------------------------------------------------= ----------
Mehdi D. Esrafili, Ph.D.
Assistant Professor of Phys= ical Chemistry=C2=A0
Current address:=C2=A0Department of Chemistr= y,
Faculty of Basic Sciences,University of
Maragheh, Iran.=
E-mail 1: = m_esrafili(~)yahoo.com
E-mail 2: es= rafili(~)maragheh.ac.ir
----------------------------------------------------------------= --------------------------------------------------------------

--001a11c00372a2e9b7050de3dd4d-- From owner-chemistry@ccl.net Fri Jan 30 20:06:00 2015 From: "Jim Kress jimkress35(_)gmail.com" To: CCL Subject: CCL:G: Hardware Specs: Connectivity vs Performance Message-Id: <-50979-150130182231-4878-JSIENBhnwSwxnF88kg2VOQ*o*server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 30 Jan 2015 18:22:12 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35 . gmail.com] If you are doing Molecular Dynamics work, the latency of an Ethernet connection will kill performance. I use Infiniband and get far superior performance to a 10Gb Ethernet switch, even with an SDR IB switch and IB cards. EBay has a good selection of these items at reasonable prices. Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com-x-ccl.net [mailto:owner-chemistry+jimkress35==gmail.com-x-ccl.net] On Behalf Of Mahmoud A. A. Ibrahim m.ibrahim-$-compchem.net Sent: Friday, January 30, 2015 11:20 AM To: Kress, Jim Subject: CCL:G: Hardware Specs: Connectivity vs Performance Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim,,compchem.net] Dear All We are going to install a switching system for our new CompChem Cluster. The Cluster is around 12 servers; each one with two 2.2GHz octa-core process and four 32G RAM, plus a storage system. The point is that what level of connectivity should be used to connect the servers and to read/write from the servers and the storage system? Because of the fact that the budget dedicated for the switch system is very limited, we decided to purchase 1G ethernet switch, and each server will be connected to the switch via 4 cables (teaming up to give a total performance of 4G). We are afraid this low level of connectivity (4G) will reduce the performance of the servers. Anyone there would like to place a comment based on his experience. By the way, we are using quantum and molecular mechanics packages such as Gaussian and AMBER. Thanks in advance Sincerely; M. Ibrahimhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt