From owner-chemistry@ccl.net Thu Feb 21 09:54:01 2013 From: "Victor Rosas Garcia rosas.victor-#-gmail.com" To: CCL Subject: CCL: Applications for a Computational Chemistry Appliance Message-Id: <-48280-130221095012-21679-LEO38jZ5uv6jHEHDal/DCw#server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=f46d0447f094bc4eaa04d63d3020 Date: Thu, 21 Feb 2013 08:50:05 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor!^!gmail.com] --f46d0447f094bc4eaa04d63d3020 Content-Type: text/plain; charset=ISO-8859-1 I thought such a thing already existed, from Parallel Quantum Solutions http://pqs-chem.com/ Victor 2013/2/20 Devang Sachdev dsachdev^_^nvidia.com > > Sent to CCL by: "Devang Sachdev" [dsachdev::nvidia.com] > Hi > > Today computational chemists have to work with off-the-shelf server nodes > or workstations and > customizing them with applications that are needed for their research. > What if there was an appliance > that came with preconfigured hardware (processors, memory, networking, > storage, etc), OS, > management tools and commonly used computational chemistry applications. > > So the question is whether this would be useful to the computational > chemists and what kind of > applications would you like to see on such an appliance? > > You can reply privately to me if you like. > > Thanks > Devang Sachdev > NVIDIA> > > --f46d0447f094bc4eaa04d63d3020 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I thought such a thing already existed, from Parallel Quantum Solutions
=
http://pqs-chem.com/

Victor=

2013/2/20 Devang Sachdev dsachdev^_^nvidia.com <owner-chemistry(_)ccl.net>

Sent to CCL by: "Devang =A0Sachdev" [dsachdev::
nvidia.com]
Hi

Today computational chemists have to work with off-the-shelf server nodes o= r workstations and
customizing them with applications that are needed for their research. What= if there was an appliance
that came with preconfigured hardware (processors, memory, networking, stor= age, etc), OS,
management tools and commonly used computational chemistry applications.
So the question is whether this would be useful to the computational chemis= ts and what kind of
applications would you like to see on such an appliance?

You can reply privately to me if you like.

Thanks
Devang Sachdev
NVIDIA



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--f46d0447f094bc4eaa04d63d3020-- From owner-chemistry@ccl.net Thu Feb 21 10:29:00 2013 From: "Serge Lavoie sergethevoice%x%gmail.com" To: CCL Subject: CCL: ECD spectre with gaussian Message-Id: <-48281-130221084819-19072-U+L6roEC82/sKdPLiVVS/Q_._server.ccl.net> X-Original-From: "Serge Lavoie" Date: Thu, 21 Feb 2013 08:48:18 -0500 Sent to CCL by: "Serge Lavoie" [sergethevoice%x%gmail.com] Hi, I'm doctorate student at Universite of Quebec at Chicoutimi (UQAC). We need to calculate the ECD spectra of some natural products. After geometry optimisation of conformers generated with spartan (at b3lyp/6-31(d,d) level) and frequency calculation to check for absence of imaginary frequency and corrected free energy (as for boltzmann averaging), we calculate the electronic excitation with this route: # td=(singlets,nstates=60) b3lyp/6-311g(2d,2p) scrf=(iefpcm,solvent=methanol) Unfortunatly, the comparison with the experimental data is not good below 250 nm. Do you think that it's related with the fact that we only calculate for the singlet transition. Should we remove this keyword? Thank you for your help From owner-chemistry@ccl.net Thu Feb 21 11:03:00 2013 From: "Patrick Pang skpang\a/ctimail.com" To: CCL Subject: CCL: transition state in bond dissociation Message-Id: <-48282-130221103540-17653-3NFRUlseiyP5otACz449wQ+*+server.ccl.net> X-Original-From: "Patrick Pang" Date: Thu, 21 Feb 2013 10:35:39 -0500 Sent to CCL by: "Patrick Pang" [skpang*ctimail.com] Dear all, I calculate the bond dissociation of some molecules. I found that no transition state is observed in potential energy surface scan when it started from the ground state. However, when it started from the 1st excited state, a transition state appears. Why? Regards, Patrick From owner-chemistry@ccl.net Thu Feb 21 11:38:00 2013 From: "Abrash, Sam sabrash(0)richmond.edu" To: CCL Subject: CCL: Negative activation energy/non Arrhenius Message-Id: <-48283-130221105530-663-rgdtRW78hppdn7FkVAd1QQ ~ server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 21 Feb 2013 15:55:23 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash/./richmond.edu] Hi Benoit, Amy is correct if you determined the negative activation energy by theoretical means. If, on the other hand, it is an experimental result, what it means is that you have an activation barrier either of zero or sufficiently close to zero that the temperature dependence of the kinetic pre-exponential factor, A, dominates over that of the activation energy. The temperature dependence of the preexpontial factor will look like a negative activation energy. Best regards, Sam Abrash Samuel A. Abrash Department of Chemistry Coordinator, Environmental Studies Progrram University of Richmond Richmond, VA 23173 Phone (Gottwald): 804-289-8248 Phone (International Center): 804-484-1473 Fax: 804-287-1897 E-mail: sabrash a richmond.edu Web-page: http://www.richmond.edu/~sabrash "That's one of the tragedies of this life, that the men who are most in need of a beating are always enormous." Rudy Valee, as J. D. Hackensacker, III, in the Preston Sturges Film "The Palm Beach Story" -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu a ccl.net [mailto:owner-chemistry+sabrash==richmond.edu a ccl.net] On Behalf Of Amy Austin amy_jean_austin*yahoo.com Sent: Tuesday, February 19, 2013 8:54 PM To: Abrash, Sam Subject: CCL: Negative activation energy/non Arrhenius Hello Benoit, It sounds like you have missed at least one low energy intermediate along the path. You could tie everything together with some IRC's after you've identified the relevant transition states. Best,  Amy ________________________________ From: Benoit Benoit bonoit_10**yahoo.fr To: "Austin, Amy J " Sent: Tuesday, February 19, 2013 8:35 AM Subject: CCL: Negative activation energy/non Arrhenius Sent to CCL by: "Benoit  Benoit" [bonoit_10_+_yahoo.fr] Dear CCLers, I'd like to enquire about negative activation energies that some reactions can have, what's the meaning of such negative value? Does is mean that the reaction is barrierless? Any help is appreciated Best regards Benoitthe strange characters on the top line to the (_) sign. You can also      E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net or use                 --752418115-821153590-1361325269=1634 Content-Type: text/html; charset=o-8859-1 Content-Transfer-Encoding: quoted-printable
Hello Benoit,

It sounds like you have missed at least one low energy intermediate along the path. You could tie everything together with some IRC's after you've identified the relevant transition states.

Best, 

Amy



From: Benoit Benoit bonoit_10**yahoo.fr <owner-chemistry(_)ccl.net>
To: "Austin, Amy J " <amy_jean_austin(_)yahoo.com>
Sent: Tuesday, February 19, 2013 8:35 AM
Subject: CCL: Negative activation energy/non Arrhenius


Sent to CCL by: "Benoit  Benoit" [bonoit_10_+_yahoo.fr]
Dear CCLers,

I'd like to enquire about negative activation energies that some reactions can have, what's the meaning of such negative value?
Does is mean that the reaction is barrierless?

Any help is appreciated

Best regards

Benoit


the strange characters on the top line to the (_) sign. You can also
E-mail to subscribers: CHEMISTRY(_)ccl.net or use:
     

E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     
     




From owner-chemistry@ccl.net Thu Feb 21 12:57:00 2013 From: "James Eilers jeilers[A]siue.edu" To: CCL Subject: CCL: Negative activation energy/non Arrhenius Message-Id: <-48284-130221125119-25409-pCLu+6gKjFDIg5igb/zJAQ _ server.ccl.net> X-Original-From: James Eilers Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Thu, 21 Feb 2013 11:50:58 -0600 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: James Eilers [jeilers%%siue.edu] One should work with the modified Arrhenius expresion A sqrt(T) exp(- Ea/RT) before getting all that excited or perplexed by negative experimental activation energies. On Feb 21, 2013, at 9:55 AM, Abrash, Sam sabrash(0)richmond.edu wrote: > > Sent to CCL by: "Abrash, Sam" [sabrash/./richmond.edu] > Hi Benoit, > > Amy is correct if you determined the negative activation energy by > theoretical means. If, on the other hand, it is an experimental > result, what it means is that you have an activation barrier either > of zero or sufficiently close to zero that the temperature > dependence of the kinetic pre-exponential factor, A, dominates over > that of the activation energy. The temperature dependence of the > preexpontial factor will look like a negative activation energy. > > Best regards, > Sam Abrash > > Samuel A. Abrash > Department of Chemistry > Coordinator, Environmental Studies Progrram > University of Richmond > Richmond, VA 23173 > Phone (Gottwald): 804-289-8248 > Phone (International Center): 804-484-1473 > Fax: 804-287-1897 > E-mail: sabrash~!~richmond.edu > Web-page: http://www.richmond.edu/~sabrash > "That's one of the tragedies of this life, that the men who are most > in need of a beating are always enormous." Rudy Valee, as J. D. > Hackensacker, III, in the Preston Sturges Film "The Palm Beach Story" > > -----Original Message----- >> From: owner-chemistry+sabrash==richmond.edu~!~ccl.net [mailto:owner-chemistry+sabrash==richmond.edu >> ~!~ccl.net] On Behalf Of Amy Austin amy_jean_austin*yahoo.com > Sent: Tuesday, February 19, 2013 8:54 PM > To: Abrash, Sam > Subject: CCL: Negative activation energy/non Arrhenius > > Hello Benoit, > > It sounds like you have missed at least one low energy intermediate > along the path. You could tie everything together with some IRC's > after you've identified the relevant transition states. > > Best, > > Amy > > > > > ________________________________ > From: Benoit Benoit bonoit_10**yahoo.fr > To: "Austin, Amy J " > Sent: Tuesday, February 19, 2013 8:35 AM > Subject: CCL: Negative activation energy/non Arrhenius > > > Sent to CCL by: "Benoit Benoit" [bonoit_10_+_yahoo.fr] > Dear CCLers, > > I'd like to enquire about negative activation energies that some > reactions can have, what's the meaning of such negative value? > Does is mean that the reaction is barrierless? > > Any help is appreciated > > Best regards > > Benoitthe strange characters on the top line to the (_) sign. You > can also > > > > E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net or use > > > --752418115-821153590-1361325269=1634 > Content-Type: text/html; charset=o-8859-1 > Content-Transfer-Encoding: quoted-printable > >
Hello > Benoit,

It sounds like you have missed at least one low > energy intermediate along the path. You could tie everything > together with some IRC's after you've identified the relevant > transition states.

Best,  >

Amy


style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> >

size="1"> From: > Benoit Benoit bonoit_10**yahoo.fr <owner- > chemistry(_)ccl.net>
To: span> "Austin, Amy J " <amy_jean_austin(_)yahoo.com>
> Sent: Tuesday, > February 19, 2013 8:35 AM
style="font-weight: bold;">Subject: CCL: Negative > activation energy/non Arrhenius

>
Sent to CCL by: "Benoit  Benoit" [bonoit_10_ > +_yahoo.fr]
Dear CCLers,

I'd like to enquire about > negative activation energies that some reactions can have, what's > the meaning of such negative value?
Does is mean that the > reaction is barrierless?

Any help is appreciated

Best > regards

Benoit


the strange characters on > the top line to the (_) sign. You can also
E-mail to > subscribers: CHEMISTRY(_)ccl.net or use:
     

E- > mail to administrators: href="mailto:CHEMISTRY-REQUEST(_)ccl.net">CHEMISTRY- > REQUEST(_)ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message a>
    >  
    >  




> > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > James E. Eilers Professor Chemistry Department Southern Illinois University Edwardsville (618)650-3559 From owner-chemistry@ccl.net Thu Feb 21 15:07:00 2013 From: "Olasunkanmi Lukman Olawale walecomuk~~yahoo.co.uk" To: CCL Subject: CCL: Transition State Search and Activation Parameters Message-Id: <-48285-130221141953-12465-ARmof1Uer7tYW3WEbq6v/g-*-server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="1670751155-295810895-1361473985=:2866" Date: Thu, 21 Feb 2013 19:13:05 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk[*]yahoo.co.uk] --1670751155-295810895-1361473985=:2866 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,=0ACan anyone pls refer me to a material that is well-explanatory = on how to use MOPAC 2009/2012 to search for Transition State and determine = Activation Parameters. I have read a number of articles in which MOPAC was = used to study some chemical reactions in this regard, I have even read MOPA= C manuals several times, but I still do not understand how to apply MOPAC f= or the same purpose. Kindly help. Thanks.=0A=0A=A0=0AOlasunkanmi Lukman Ola= wale=0A________________________________=0ACurrent Address:=0ADepartment of = Chemistry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.=0ANigeria.= =0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A__________________________= ______ --1670751155-295810895-1361473985=:2866 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,<= /span>
Can anyone pls refer me to a material that is well-e= xplanatory on how to use MOPAC 2009/2012 to search for Transition State and= determine Activation Parameters. I have read a number of articles in which= MOPAC was used to study some chemical reactions in this regard, I have eve= n read MOPAC manuals several times, but I still do not understand how to ap= ply MOPAC for the same purpose. Kindly help. Thanks.
 = ;
Olasu= nkanmi Lukman Olawale

Current Address:
Department of Chemistry,Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.
+2
--1670751155-295810895-1361473985=:2866-- From owner-chemistry@ccl.net Thu Feb 21 17:05:00 2013 From: "Dr. Lars Goerigk lars.goerigk/./chem.usyd.edu.au" To: CCL Subject: CCL:G: ECD spectre with gaussian Message-Id: <-48286-130221164830-14810-MgYm9BVfelGV4bJrYj6S0g_+_server.ccl.net> X-Original-From: "Dr. Lars Goerigk" Content-Type: multipart/alternative; boundary="------------090307090401050904090709" Date: Fri, 22 Feb 2013 08:48:20 +1100 MIME-Version: 1.0 Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk**chem.usyd.edu.au] This is a multi-part message in MIME format. --------------090307090401050904090709 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Serge, before one considers if you can actually calculate these higher excitations with your choice of method, I would make sure that your energy-ordering of the conformers is right. So let me please elaborate on that. B3LYP with a small double-zeta basis is not good enough for accurate conformational energies, even though it is a widely-used approach for that! Particularly for theoretical ECD it is crucial to get this step right, because wrong relative energies lead to a wrong Boltzmann average, which then gives a completely wrong spectrum. You mention that you treat natural products, which means that you have to consider London-dispersion effects in your system. If you do not want to run the geometry optimisations again, I suggest to run single-point calculations on your geometries with a bigger basis set (a big triple-zeta set should be sufficient) and dispersion corrected DFT. The best conformational energies can be obtained with a double-hybrid functional and DFT-D3. Do not try to use MP2 instead! This was discussed in: PCCP 2011, 13 6670, DOI: 10.1039/c0cp02984j We showed the effect of wrong conformational energies on ECD spectra in a tutorial which is part of a book chapter: http://onlinelibrary.wiley.com/doi/10.1002/9781118120187.ch22/summary If you can not access it, I recommend that you have a look at the literature, e.g. at the works by Stefan Grimme or other big people in the area of theoretical UV/Vis and ECD. Between, the book itself is worth reading. Only if you have considered this, I would start thinking about how to actually calculate the spectra. Also here, better methods than B3LYP are available. In that book-chapter and also in peer-reviewed articles it was shown that double-hybrid functionals generate accurate ECD spectra (with very high excitations being the exception). However, if you have only Gaussian09 please DO NOT try to attempt this! It is not implemented although G09 before Rev C01 did some sort of calculation when you requested TD-B2PLYP. ORCA would be a free alternative for you. Cheers, Lars PS.: Why non-dispersion-corrected B3LYP with a small basis set should not be used was demonstrated very recently: JOC 2012, 77, 10824 ,DOI: 10.1021/jo302156p You also have an intramolecular bassis-set-superpostion error, which is not always cancelled out by the missing London-dispersion. That intramolecular BSSE can affect the conformational energy profile of a system has been known for some time in the literature, see e.g. work by T. van Mourik. -- Dr. Lars Goerigk School of Chemistry (Building F11) The University of Sydney, NSW 2006 Australia Profile: http://www.researchgate.net/profile/Lars_Goerigk List of publications: www.researcherid.com/rid/D-3717-2009 --------------090307090401050904090709 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Serge,

before one considers if you can actually calculate these higher excitations with your choice of method, I would make sure that your energy-ordering of the conformers is right. So let me please elaborate on that.

B3LYP with a small double-zeta basis is not good enough for accurate conformational energies, even though it is a widely-used approach for that! Particularly for theoretical ECD it is crucial to get this step right, because  wrong relative energies lead to a wrong Boltzmann average, which then gives a completely wrong spectrum.
You mention that you treat natural products, which means that you have to consider London-dispersion effects in your system. If you do not want to run the geometry optimisations again, I suggest to run single-point calculations on your geometries with a bigger basis set (a big triple-zeta set should be sufficient) and dispersion corrected DFT. The best conformational energies  can be obtained with a double-hybrid functional and DFT-D3. Do not try to use MP2 instead! This was discussed in:

PCCP 2011, 13  6670, DOI: 10.1039/c0cp02984j  

We showed the effect of wrong conformational energies on ECD spectra in a tutorial which is part of a book chapter:

http://onlinelibrary.wiley.com/doi/10.1002/9781118120187.ch22/summary

If you can not access it, I recommend that you have a look at the literature, e.g. at the works by Stefan Grimme or other big people in the area of theoretical UV/Vis and ECD. Between, the book itself is worth reading.

Only if you have considered this, I would start thinking about how to actually calculate the spectra. Also here, better methods than B3LYP are available. In that book-chapter and also in peer-reviewed articles it was shown that double-hybrid functionals generate accurate ECD spectra (with very high excitations being the exception). However, if you have only Gaussian09 please DO NOT try to attempt this! It is not implemented although G09 before Rev C01 did some sort of calculation when you requested TD-B2PLYP. ORCA would be a free alternative for you.

Cheers,
Lars

PS.: Why non-dispersion-corrected B3LYP with a small basis set should not be used was demonstrated very recently:

JOC 2012, 77, 10824 ,DOI: 10.1021/jo302156p

You also have an intramolecular bassis-set-superpostion error, which is not always cancelled out by the missing London-dispersion. That intramolecular BSSE can affect the conformational energy profile of a system has been known for some time in the literature, see e.g. work by T. van Mourik.

--
Dr. Lars Goerigk
School of Chemistry (Building F11)
The University of Sydney, NSW 2006
Australia
Profile: http://www.researchgate.net/profile/Lars_Goerigk
List of publications: www.researcherid.com/rid/D-3717-2009
--------------090307090401050904090709-- From owner-chemistry@ccl.net Thu Feb 21 18:15:00 2013 From: "Amy Austin amy_jean_austin-*-yahoo.com" To: CCL Subject: CCL: Negative activation energy/non Arrhenius Message-Id: <-48287-130221174028-29273-w+dTjz201F7JN2S6XgtaRw^-^server.ccl.net> X-Original-From: Amy Austin Content-Type: multipart/alternative; boundary="-790415396-1344751577-1361486421=:89304" Date: Thu, 21 Feb 2013 14:40:21 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Amy Austin [amy_jean_austin|,|yahoo.com] ---790415396-1344751577-1361486421=:89304 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Benoit,=0A=0AIf this is a computational study of the PES, there is anoth= er possibility for a negative barrier height. DFT's underestimate barrier h= eights. The hybrid functionals are better for this purpose, but B3LYP has i= ssues due to the training set. If you need a DFT for the computational expe= nse, the MPWB1K might help. =0A=0ABest,=0A=0AAmy=0A=0A=0A=0A=0A____________= ____________________=0A From: James Eilers jeilers[A]siue.edu =0ATo: "Austin, Amy J " =0A= Sent: Thursday, February 21, 2013 12:50 PM=0ASubject: CCL: Negative activat= ion energy/non Arrhenius=0A =0A=0ASent to CCL by: James Eilers [jeilers%%si= ue.edu]=0AOne should work with the modified Arrhenius expresion=A0 A sqrt(T= ) exp(-Ea/RT) before getting all that excited or perplexed by negative expe= rimental activation energies.=0A=0AOn Feb 21, 2013, at 9:55 AM, Abrash, Sam= sabrash(0)richmond.edu wrote:=0A=0A> =0A> Sent to CCL by: "Abrash, Sam" [s= abrash/./richmond.edu]=0A> Hi Benoit,=0A> =0A> Amy is correct if you determ= ined the negative activation energy by theoretical means.=A0 If, on the oth= er hand, it is an experimental result, what it means is that you have an ac= tivation barrier either of zero or sufficiently close to zero that the temp= erature dependence of the kinetic pre-exponential factor, A, dominates over= that of the activation energy.=A0 The temperature dependence of the preexp= ontial factor will look like a negative activation energy.=0A> =0A> Best re= gards,=0A> Sam Abrash=0A> =0A> Samuel A. Abrash=0A> Department of Chemistry= =0A> Coordinator, Environmental Studies Progrram=0A> University of Richmond= =0A> Richmond, VA 23173=0A> Phone (Gottwald):=A0 804-289-8248=0A> Phone (In= ternational Center): 804-484-1473=0A> Fax:=A0 804-287-1897=0A> E-mail:=A0 s= abrash~!~richmond.edu=0A> Web-page:=A0 http://www.richmond.edu/~sabrash=0A>= "That's one of the tragedies of this life, that the men who are most in ne= ed of a beating are always enormous." Rudy Valee, as J. D. Hackensacker, II= I, in the Preston Sturges Film "The Palm Beach Story"=0A> =0A> -----Origina= l Message-----=0A>> From: owner-chemistry+sabrash=3D=3Drichmond.edu~!~ccl.n= et [mailto:owner-chemistry+sabrash=3D=3Drichmond.edu~!~ccl.net] On Behalf O= f Amy Austin amy_jean_austin*yahoo.com=0A> Sent: Tuesday, February 19, 2013= 8:54 PM=0A> To: Abrash, Sam=0A> Subject: CCL: Negative activation energy/n= on Arrhenius=0A> =0A> Hello Benoit,=0A> =0A> It sounds like you have missed= at least one low energy intermediate along the path. You could tie everyth= ing together with some IRC's after you've identified the relevant transitio= n states.=0A> =0A> Best,=0A> =0A> Amy=0A> =0A> =0A> =0A> =0A> _____________= ___________________=0A> From: Benoit Benoit bonoit_10**yahoo.fr =0A> To: "Austin, Amy J " =0A>= Sent: Tuesday, February 19, 2013 8:35 AM=0A> Subject: CCL: Negative activa= tion energy/non Arrhenius=0A> =0A> =0A> Sent to CCL by: "Benoit=A0 Benoit" = [bonoit_10_+_yahoo.fr]=0A> Dear CCLers,=0A> =0A> I'd like to enquire about = negative activation energies that some reactions can have, what's the meani= ng of such negative value?=0A> Does is mean that the reaction is barrierles= s?=0A> =0A> Any help is appreciated=0A> =0A> Best regards=0A> =0A> Benoitth= e strange characters on the top line to the (_) sign. You can also=0A> =0A>= =0A> =0A>=A0 =A0 =A0 E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net= or use=0A> =0A> =0A> --752418115-821153590-1361325269=3D1634=0A> Content-T= ype: text/html; charset=3Do-8859-1=0A> Content-Transfer-Encoding: quoted-pr= intable=0A> =0A>
Hello Benoit,
It sounds like you have missed at least one low energy intermediate a= long the path. You could tie everything together with some IRC's after you'= ve identified the relevant transition states.

Best, 

Am= y


=A0

=A0 From: Benoit Benoit bonoit_10**yahoo.fr = <owner-chemistry(_)ccl.net>
To: "Austin, Amy J " <amy_jean_austin(_)yahoo.com>
<= b>Sent: Tuesday, February 19,= 2013 8:35 AM
style=3D"font-weight: bold;">Subject:= CCL: Negative activation energy/non Arrhenius

= =0A>
Sent to CCL by: "Benoit  Benoit" [bonoit_10_+_yahoo.fr]
De= ar CCLers,

I'd like to enquire about negative activation energies th= at some reactions can have, what's the meaning of such negative value?
D= oes is mean that the reaction is barrierless?

Any help is appreciate= d

Best regards

Benoit


the strange charac= ters on the top line to the (_) sign. You can also
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=A0 =0A> =0A> =0A> =0A> -=3D This is automatically added to ea= ch message by the mailing script =3D-=0A> To recover the email address of t= he author of the message, please change> Conferences: http://server.ccl.net= /chemistry/announcements/conferences/>=0A> =0A=0AJames E. Eilers=0AProfesso= r=0AChemistry Department=0ASouthern Illinois University Edwardsville=0A(618= )650-3559=0A=0A=0A=0A-=3D This is automatically added to each message by th= e mailing script =3D-=0ATo recover the email address of the author of the m= essage, please change=0Athe strange characters on the top line to the :_: sig= n. You can also=0A=0A= =0A=0A=A0 =A0 http://www.cc= l.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY= -REQUEST:_:ccl.net or use=0A=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage=0A=0ASubscribe/Unsubscribe:=A0 =A0 http://www.ccl.net/chemistry/sub_= unsub.shtml=0A=0A=0A= =0AJob: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry= /announcements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemis= try/searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 err= or, check:=0A=A0 =A0=0A=0ARTFI: http://www.= ccl.net/chemistry/aboutccl/instructions/ ---790415396-1344751577-1361486421=:89304 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Benoit,

If this is a c= omputational study of the PES, there is another possibility for a negative = barrier height. DFT's underestimate barrier heights. The hybrid functionals= are better for this purpose, but B3LYP has issues due to the training set.= If you need a DFT for the computational expense, the MPWB1K might help.
Best,

Amy



= From: James Eilers jeiler= s[A]siue.edu <owner-chemistry:_:ccl.net>
To: "Austin, Amy J " <amy_jean_austin:_:yah= oo.com>
Sent: Thursday, Febr= uary 21, 2013 12:50 PM
Subject: CCL: Negative activation energy/non Arrhenius
=

Sent to CCL by: James Eilers [jeilers%%siue.edu]
One should work= with the modified Arrhenius expresion  A sqrt(T) exp(-Ea/RT) before g= etting all that excited or perplexed by negative experimental activation en= ergies.

On Feb 21, 2013, at 9:55 AM, Abrash, Sam sabrash(0)richmond.= edu wrote:

>
> Sent to CCL by: "Abrash, Sam" [sabrash/./ri= chmond.edu]
> Hi Benoit,
>
> Amy is correct if you deter= mined the negative activation energy by theoretical means.  If, on the= other hand, it is an experimental result, what it means is that you have a= n activation barrier either of zero or sufficiently close to zero that the = temperature dependence of the kinetic pre-exponential factor, A, dominates over that of the activation energy.  The temperature depend= ence of the preexpontial factor will look like a negative activation energy= .
>
> Best regards,
> Sam Abrash
>
> Samuel= A. Abrash
> Department of Chemistry
> Coordinator, Environment= al Studies Progrram
> University of Richmond
> Richmond, VA 231= 73
> Phone (Gottwald):  804-289-8248
> Phone (Internationa= l Center): 804-484-1473
> Fax:  804-287-1897
> E-mail:&nbs= p; sabrash~!~richmond.edu
> Web-page:  http://www.richmond.edu/~sabrash<= br>> "That's one of the tragedies of this life, that the men who are mos= t in need of a beating are always enormous." Rudy Valee, as J. D. Hackensac= ker, III, in the Preston Sturges Film "The Palm Beach Story"
>
&g= t; -----Original Message-----
>> From: owner-chemistry+sabrash=3D=3Drichmond.edu~!~ccl.net [mailto:owner-chemistr= y+sabrash=3D=3Drichmond.edu~!~ccl.net] On Behalf Of Amy Austin amy_jean_aus= tin*yahoo.com
> Sent: Tuesday, February 19, 2013 8:54 PM
> To: = Abrash, Sam
> Subject: CCL: Negative activation energy/non Arrhenius<= br>>
> Hello Benoit,
>
> It sounds like you have mis= sed at least one low energy intermediate along the path. You could tie ever= ything together with some IRC's after you've identified the relevant transi= tion states.
>
> Best,
>
> Amy
>
> <= br>>
>
> ________________________________
> From: Be= noit Benoit bonoit_10**yahoo.fr <owner-chemistry(_)ccl.net>
> T= o: "Austin, Amy J " <amy_jean_austin(_)yahoo.com>
> Sent: Tuesd= ay, February 19, 2013 8:35 AM
> Subject: CCL: Negative activation ene= rgy/non Arrhenius
>
>
> Sent to CCL by: "Benoit  Benoit" [bonoit_10_+_yahoo.fr]
> Dear CCLers,
>
> I'd l= ike to enquire about negative activation energies that some reactions can h= ave, what's the meaning of such negative value?
> Does is mean that t= he reaction is barrierless?
>
> Any help is appreciated
>= ;
> Best regards
>
> Benoitthe strange characters on th= e top line to the (_) sign. You can also
>
>
>
>=       E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net = or use
>
>
> --752418115-821153590-1361325269=3D1634> Content-Type: text/html; charset=3Do-8859-1
> Content-Transfer-= Encoding: quoted-printable
>
> <html><body><div= style=3D"color:#000; background-color:#fff; font-family:arial, helvetica, = sans-serif;font-size:12pt">Hello Benoit,<br><br>It sounds li= ke you have missed at least one low energy intermediate along the path. You could tie everything together with some IRC's after you've identified = the relevant transition states.<br><br>Best,&nbsp; <br&g= t;<br>Amy<br><div><span><br></span><= /div><div><br></div>  <div style=3D"font-famil= y: arial, helvetica, sans-serif; font-size: 12pt;"> <div style=3D"fon= t-family: times new roman, new york, times, serif; font-size: 12pt;"> &l= t;div dir=3D"ltr"> <font face=3D"Arial" size=3D"2"> <hr size=3D= "1">  <b><span style=3D"font-weight:bold;">From:</sp= an></b> Benoit Benoit bonoit_10**yahoo.fr &lt;owner-chemistry(= _)ccl.net&gt;<br> <b><span style=3D"font-weight: bold;"&= gt;To:</span></b> "Austin, Amy J " &lt;amy_jean_austin(_)ya= hoo.com&gt; <br> <b><span style=3D"font-weight: bold;"&g= t;Sent:</span></b> Tuesday, February 19, 2013 8:35 AM<br> <b><span
> style=3D"font-weight: bold;">Subject:</spa= n></b> CCL: Negative activation energy/non Arrhenius<br> <= ;/font> </div> <br>
> <br>Sent to CCL by: "Benoi= t&nbsp; Benoit" [bonoit_10_+_yahoo.fr]<br>Dear CCLers,<br>&= lt;br>I'd like to enquire about negative activation energies that some r= eactions can have, what's the meaning of such negative value?<br>Does= is mean that the reaction is barrierless?<br><br>Any help is a= ppreciated<br><br>Best regards<br><br>Benoit<br&= gt;<br><br><br<br<br>the strange characters on the = top line to the (_) sign. You can also<br<br><br>E-mail to s= ubscribers: <a ymailto=3D"mailto:CHEMISTRY(_)ccl.net" href=3D"mailto:CHE= MISTRY(_)ccl.net">CHEMISTRY(_)ccl.net</a> or use:<br>&nb= sp; &nbsp; &nbsp;<br><br>E-mail to administrators: <a ymailto=3D"mailto:CHEMISTRY-REQUEST(_)ccl.net"
> href=3D"mailt= o:CHEMISTRY-REQUEST(_)ccl.net">CHEMISTRY-REQUEST(_)ccl.net</a> or = use<br>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.c= cl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank">http://www= .ccl.net/cgi-bin/ccl/send_ccl_message</a><br><br<br&g= t;&nbsp; &nbsp; &nbsp;<br><br<br><br<br<= ;br><br<br><br<br>&nbsp; &nbsp; &nbsp;<= br><br<br><br><br><br><br> </div>= </div>  </div></body></html>
>
>=
>
> -=3D This is automatically added to each message by the = mailing script =3D-
> To recover the email address of the author of t= he message, please change> Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/>
>

James E. Eilers
Pr= ofessor
Chemistry Department
Southern Illinois University Edwardsvill= e
(618)650-3559



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---790415396-1344751577-1361486421=:89304-- From owner-chemistry@ccl.net Thu Feb 21 22:50:00 2013 From: "Stefan Grimme grimme|thch.uni-bonn.de" To: CCL Subject: CCL: ECD spectre with gaussian Message-Id: <-48288-130221162100-12874-mx7/zdeHAjw+cfpaSTCQpQ*|*server.ccl.net> X-Original-From: "Stefan Grimme" Date: Thu, 21 Feb 2013 16:20:46 -0500 Sent to CCL by: "Stefan Grimme" [grimme(_)thch.uni-bonn.de] >I'm doctorate student at Universite of Quebec at Chicoutimi (UQAC). We need >to >calculate the ECD spectra of some natural products. After geometry >optimisation >of conformers generated with spartan (at b3lyp/6-31(d,d) level) and frequency >calculation to check for absence of imaginary frequency and corrected free >energy (as for boltzmann averaging), we calculate the electronic excitation >with this route: ># td=(singlets,nstates=60) b3lyp/6-311g(2d,2p) scrf=(iefpcm,solvent=methanol) >Unfortunatly, the comparison with the experimental data is not good below 250 >nm. Do you think that it's related with the fact that we only calculate for >the >singlet transition. Should we remove this keyword? Dear Serge, for (closed-shell) molecules containing only light elements you will observe only singlet-singlet transitionsi in ECD so this can not be the problem. According to my experience there are three main sources of error in such calculations: 1. for various (understandable) reasons the TDDFT accuracy with standard functionals decreases with increasing excitation energy 2. conformational energies at your level are too inaccurate and hence the corresponding Boltzmann populations can be bad 3. you missed important conformations Analysis and assignment of ECD bands sometimes improves when in addition theoretical and experimental UV spectra are compared (because different conformers often have very similar UV but quite different ECD spectra). Cheers! Stefan Grimme ____________________________________________________________ Prof. Dr. Stefan Grimme (grimme[-]thch.uni-bonn.de) Chair of Theoretical Chemistry Mulliken Center for Theoretical Chemistry University of Bonn Beringstr. 4, D-53115 Bonn, Germany http://www.thch.uni-bonn.de/tc/ ____________________________________________________________ From owner-chemistry@ccl.net Thu Feb 21 23:25:00 2013 From: "Ambrish K Srivastava ambrishphysics++gmail.com" To: CCL Subject: CCL: Comparing Compounds Message-Id: <-48289-130221214938-4447-YYZYwnxo6fxpKDVP9okNcQ(_)server.ccl.net> X-Original-From: Ambrish K Srivastava Content-Type: multipart/alternative; boundary=14dae9cc9f96a3a45904d6473d7a Date: Fri, 22 Feb 2013 08:19:31 +0530 MIME-Version: 1.0 Sent to CCL by: Ambrish K Srivastava [ambrishphysics ~~ gmail.com] --14dae9cc9f96a3a45904d6473d7a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sanjay, HOMO-LUMO gap calculation may help if you are not aware of such procedures mentioned aboves. it may simply be calculated by choosing a fully optimized geometry (no imag. freq.). Larger the gap, better the stability. Ambrish K. Srivastava On Wed, Feb 20, 2013 at 10:19 PM, Jean-Pierre DJUKIC djukic() unistra.fr < owner-chemistry:_:ccl.net> wrote: > > Sent to CCL by: Jean-Pierre DJUKIC [djukic|unistra.fr] > > Sanjay, > > Behind the term "stability" there is a lot of underlying issues: > -kinetic stability, which implies that one knows how some species among > others in a complex mixture can convert into something else, i.e by what > mechanism, with what activation barrier, etc... > -thermodynamic stability, which implies thermodynamic reversibility > between considered species, for example in the process of their (competin= g) > formation. > and "persistence", a notion that merges kinetic and thermodynamic > stability in a very environment-dependent way: some species are persisten= t, > but not intrinsically "stable", a variation of some environmental > parameters may lead to their disappearance or to their > proliferation/accumulation. > > I would suggest you first to clear up the whole problem by having a look > at the thermodynamics of your system: are these species competing each > other, is their formation a competitive process ? > > Is the process leading to their formation reversible or not, fully , > partly ? > > What is experiment telling you ? > > Are they decomposing or evolving into each other or into something else, > are some of them not evolving spontaneously ? > > Things can get very complicated, it depends a lot on how good one is at > understanding experimentally the system in question. > > Once you have answered these questions, then you may adapt your > computational approach and chose the criteria, the observables that will > characterize the system in the best way. > > Hope this helps... > > Jean-Pierre > > > > > > Le 20/02/2013 16:38, Sanjay Bharathwaj computationalchemist_._gmail.**com= a =E9crit : > > Dear All, >> >> I have four compounds (say for example A2B, A3B, A4B2, A6B5). >> >> I would like to know, how one can explain by computational methods, >> which of these is more stable. >> (You can't compare the total energy because of different composition) >> >> Is calculating enthalpy of formation for each of these species is a good >> idea? >> If so, can any one suggest me how should obtain this value for each >> species. >> >> Any help would be more appreciable. >> >> Sanjay >> >> >> >> >> -- >> Regards, >> Dr. Sanjay Bharathwaj Kumar, >> Dharmendra Institute of Technology, >> India. >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --=20 *Ambrish K. Srivastava CSIR Junior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* --14dae9cc9f96a3a45904d6473d7a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sanjay,
=A0
HOMO-LUMO gap calculation may help if you are not aw= are of such procedures mentioned aboves. it may simply be calculated by cho= osing a fully optimized geometry (no imag. freq.). Larger the gap, better t= he stability.

Ambrish K. Srivastava



On Wed,= Feb 20, 2013 at 10:19 PM, Jean-Pierre DJUKIC djukic() unistra.fr <owner-chemistry:_:ccl.net> wro= te:

Sent to CCL by: Jean-Pierre DJUKIC [djukic|unistra.fr]

Sanjay,

Behind the term "stability" there is a lot of underlying issues:<= br> -kinetic stability, which implies that one knows how some species among oth= ers in a complex mixture can convert into something else, i.e by what mecha= nism, with what activation barrier, etc...
-thermodynamic stability, which implies thermodynamic reversibility between= considered species, for example in the process of their (competing) format= ion.
and "persistence", a notion that merges kinetic and thermodynamic= stability in a very environment-dependent way: some species are persistent= , but not intrinsically "stable", a variation of some environment= al parameters may lead to their disappearance or to their proliferation/acc= umulation.

I would suggest you first to clear up the whole problem by having a look at= the thermodynamics of your system: are these species competing each other,= is their formation a competitive process =A0?

Is the process leading to their formation reversible or not, fully , partly= ?

What is experiment telling you ?

Are they decomposing or evolving into each other or into something else, ar= e some of them not evolving spontaneously ?

Things can get very complicated, it depends a lot on how good one is at und= erstanding experimentally the system in question.

Once you have answered these questions, then =A0you may adapt your computat= ional approach and chose the criteria, the observables that will characteri= ze the system in the best way.

Hope this helps...

Jean-Pierre





Le 20/02/2013 16:38, Sanjay Bharathwaj computationalchemist_._gmail.com a =E9crit :

Dear All,

I have four compounds (say for example A2B, A3B, A4B2, A6B5).

I would like to know, how one can explain by computational methods,
which of these is more stable.
(You can't compare the total energy because of different composition)
Is calculating enthalpy of formation for each of these species is a good idea?
If so, can any one suggest me how should obtain this value for each
species.

Any help would be more appreciable.

Sanjay




--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technology,
India.



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--
Ambrish K. Srivastava
CSIR Junior Research Fel= low
Department of Physics
University of Lucknow
Lucknow, India-22= 6007
--14dae9cc9f96a3a45904d6473d7a--