From owner-chemistry@ccl.net Fri May 4 04:44:01 2012 From: "VITORGE Pierre 094605 Pierre.VITORGE,,cea.fr" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46848-120504044148-11251-SYDJ03d/5BHVm8EDcoDvKA-x-server.ccl.net> X-Original-From: VITORGE Pierre 094605 Content-Language: fr-FR Content-Type: multipart/alternative; boundary="_000_F2DC62A7B720FA44B0662C84DC3E8EA715FAEDEXDAG0A1intraceaf_" Date: Fri, 4 May 2012 08:41:37 +0000 MIME-Version: 1.0 Sent to CCL by: VITORGE Pierre 094605 [Pierre.VITORGE=-=cea.fr] --_000_F2DC62A7B720FA44B0662C84DC3E8EA715FAEDEXDAG0A1intraceaf_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I imagine your complexation reaction is typically M + L -> ML where L is the polypyridine ligand, and M the transition metal ion. A usual interpretation is 1/K =3D [L]_1/2, the L concentration at the point of half reaction (similarly to pKa =3D pH_= 1/2): it depends on the unit used for [L] (activity, concentration, fugacit= y, partial pressure). If this unit is not realistic (typically partial pressure in atm for a reac= tion that is only observed in aqueous solution) you might find very big or = very small numbers. Did you first check this unit problem? -- Pierre Vitorge Directeur de recherche CEA Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LA= MBE, UMR 8587, CEA, Univ Evry, CNRS, Bd. Francois Mitterrand, Bat. Maupertuis, S 02 F-91025 Evry, France tel.01.69.47.01.40 (+33.1.69.47.01.40) http://www.lambe.univ-evry.fr/pvitorge http://www.vitorge.name Saclay : Laboratoire de Radiolyse et de la Matiere Organique, LRMO (this is the new = name of the lab.) CEA, DEN, DPC, SECR, Bat.391 Pe.121 F-91191 Gif-sur-Yvette, France. tel.01.69.08.32.65 (+33.1.69.08.32.65) De : owner-chemistry+pierre.vitorge=3D=3Dcea.fr#ccl.net [mailto:owner-chemi= stry+pierre.vitorge=3D=3Dcea.fr#ccl.net] De la part de Olasunkanmi Lukman O= lawale walecomuk^_^yahoo.co.uk Envoy=E9 : jeudi 3 mai 2012 20:42 =C0 : VITORGE Pierre 094605 Objet : CCL: Large value of equilibrium constants Dear Colleagues, I carried out some theoretical calculations on complexation of some transit= ion metal ions with a polypyridine ligand and I predicted the equilibrium c= onstants for the assumed reversible reactions. I got values of K as high as= 1 x 10^400 and in fact, an infinite value in one case.What do you think ab= out these large values? I interpretated them to mean that the reactions are= essentially irreversible. Thank you all. Olasunkanmi Lukman Olawale ________________________________ Current Address: Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Osun State. Nigeria. +234-0-80-52401564 Or +234-0-80-67161091 ________________________________ --_000_F2DC62A7B720FA44B0662C84DC3E8EA715FAEDEXDAG0A1intraceaf_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I imagine your complexation reac= tion is typically

M + L -> ML

where L is the polypyridine ligand, and M the transition metal ion.

A usual interpretation is

1/K =3D [L]_1/2,

the L concentration at the point= of half reaction (similarly to pKa =3D pH_1/2): it depends on the unit use= d for [L] (activity, concentration, fugacity, partial pressure).=

If this unit is not realistic (t= ypically partial pressure in atm for a reaction that is only observed in aq= ueous solution) you might find very big or very small numbers.

Did you first check this unit pr= oblem?

--
Pierre Vitorge
Directeur de recherche CEA

Laboratoire Analyse et Model= isation pour la Biologie et l Environnement, LAMBE,
UMR 8587, CEA, Univ Evry, CNRS,
Bd. Francois Mitterrand, Bat. Maupertuis, S 02
F-91025 Evry, France
tel.01.69.47.01.40 (+33.1.69.47.01.40)
http://www.lambe.univ-evry.fr/pvitorge
http://www.vitorge= .name

Saclay :
Laboratoire de Radiolyse et de la Matiere Organique, LRMO (this is the new name of the lab.)

CEA, DEN, DPC, SECR, Bat.391 Pe= .121
F-91191 Gif-sur-Yvette, France.
tel.01.69.08.32.65 (+33.1.69.08.32.65)

De : owne= r-chemistry+pierre.vitorge=3D=3Dcea.fr#ccl.net [mailto:owner-chemistry&= #43;pierre.vitorge=3D=3Dcea.fr#ccl.net] De la part de Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk
Envoy=E9 : jeudi 3 mai 2012 20:42
=C0 : VITORGE Pierre 094605
Objet : CCL: Large value of equilibrium constants

Dear Colleagues,

I carried out some theoretical calculations on complexation of some tran= sition metal ions with a polypyridine ligand and I predicted the equilibriu= m constants for the assumed reversible reactions. I got values of K as high as 1 x 10^400 and in fact, an infinit= e value in one case.What do you think about these large values? I interpret= ated them to mean that the reactions are essentially irreversible.

Thank you all.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.

+234-0-80-52401564 = Or +234-0-80-67161091=

--_000_F2DC62A7B720FA44B0662C84DC3E8EA715FAEDEXDAG0A1intraceaf_-- From owner-chemistry@ccl.net Fri May 4 08:09:00 2012 From: "Gkourmpis, Thomas Thomas.Gkourmpis###borealisgroup.com" To: CCL Subject: CCL: Tinker Force Field Explorer - installation Message-Id: <-46849-120504014008-16364-smfFR2MD+h40mgsnT3n8PA(0)server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 4 May 2012 07:39:46 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis:borealisgroup.com] Hi John If I remember correctly the FFE has been removed in order to sort out some bugs and functionality issues before being re-released (no idea when this will happen). I might be wrong though so if anyone knows anything more on the subject please do correct me. Thomas Thomas Gkourmpis Researcher Borealis AB | SE-444 86 Stenungsund | Sweden Tel. +46 303 205 576 | Mobile +46 766 378 106 | Fax +46 303 866 49 www.borealisgroup.com | 556078-6633 | Swedish Companies Registration Office ___________________________________ Borealis - Shaping the Future with Plastics -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com\a/ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com\a/ccl.net] On Behalf Of John Keller jwkeller~~alaska.edu Sent: Thursday, May 03, 2012 9:05 PM To: Gkourmpis, Thomas Subject: CCL: Tinker Force Field Explorer - installation Sent to CCL by: "John Keller" [jwkeller__alaska.edu] Where are the installation files for the Tinker Force Field Explorer (FFE) program? I cannot see them on the Tinker website.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Fri May 4 09:07:00 2012 From: "DJUKIC Jean-Pierre djukic^unistra.fr" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46850-120504090505-1137-lyLVK3CYjpJgBU3G27hiQw+*+server.ccl.net> X-Original-From: DJUKIC Jean-Pierre Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 May 2012 15:04:47 +0200 MIME-Version: 1.0 Sent to CCL by: DJUKIC Jean-Pierre [djukic]=[unistra.fr] It is a principle in physics and maths that a logarithm (of whatever form, neperian or decimal or other) can only be calculated for a dimension-less number. Therefore ln(K) makes sense only if K is dimension-less, and in principle it is, because activities are dimension-less too. Signed: a concerned chemist. Le 04/05/2012 10:41, VITORGE Pierre 094605 Pierre.VITORGE,,cea.fr a �crit : > I imagine your complexation reaction is typically > > M + L -> ML > > where L is the polypyridine ligand, and M the transition metal ion. > > A usual interpretation is > > 1/K = [L]_1/2, > > the L concentration at the point of half reaction (similarly to pKa = > pH_1/2): it depends on the unit used for [L] (activity, concentration, > fugacity, partial pressure). > > If this unit is not realistic (typically partial pressure in atm for a > reaction that is only observed in aqueous solution) you might find very > big or very small numbers. > > Did you first check this unit problem? > > > -- > Pierre Vitorge > Directeur de recherche CEA > > Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, > LAMBE, > UMR 8587, CEA, Univ Evry, CNRS, > Bd. Francois Mitterrand, Bat. Maupertuis, S 02 > F-91025 Evry, France > tel.01.69.47.01.40 (+33.1.69.47.01.40) > http://www.lambe.univ-evry.fr/pvitorge > http://www.vitorge.name > > Saclay : > Laboratoire de Radiolyse et de la Matiere Organique, LRMO *(this is the > new name of the lab.)* > > CEA, DEN, DPC, SECR, Bat.391 Pe.121 > F-91191 Gif-sur-Yvette, France. > tel.01.69.08.32.65 (+33.1.69.08.32.65) > > *De :*owner-chemistry+pierre.vitorge==cea.fr:-:ccl.net > [mailto:owner-chemistry+pierre.vitorge==cea.fr:-:ccl.net] *De la part > de* Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk > *Envoy� :* jeudi 3 mai 2012 20:42 > *� :* VITORGE Pierre 094605 > *Objet :* CCL: Large value of equilibrium constants > > Dear Colleagues, > > I carried out some theoretical calculations on complexation of some > transition metal ions with a polypyridine ligand and I predicted the > equilibrium constants for the assumed reversible reactions. I got values > of K as high as 1 x 10^400 and in fact, an infinite value in one > case.What do you think about these large values? I interpretated them to > mean that the reactions are essentially irreversible. > > Thank you all. > > *Olasunkanmi Lukman Olawale* > > ------------------------------------------------------------------------ > > *Current Address:* > *Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria.* > > *+*2*34-0-80-52401564 Or +234-0-80-67161091* > > ------------------------------------------------------------------------ -- From owner-chemistry@ccl.net Fri May 4 10:36:00 2012 From: "Alain Borel alain.borel^epfl.ch" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46851-120504103336-29587-cQh0tjDwxnUX350HDx7A/w*server.ccl.net> X-Original-From: Alain Borel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 04 May 2012 16:33:26 +0200 MIME-Version: 1.0 Sent to CCL by: Alain Borel [alain.borel=-=epfl.ch] On 04.05.12 10:41, VITORGE Pierre 094605 Pierre.VITORGE,,cea.fr wrote: > I imagine your complexation reaction is typically > M + L -> ML > where L is the polypyridine ligand, and M the transition metal ion. If this is exactly the system the OP was calculating, it is probably not too surprising that the binding constant was every high: a transition metal ion alone in vacuum will gladly bind to anything electronegative it can find on its path. A more realistic model would be: M(H2O)n + L -> ML(H2O)m + (n-m)H2O Best regards, Alain Borel EPFL Biblioth�que Rolex Learning Center Station 20 CH-1015 LAUSANNE (SUISSE) T�l�phone: +41 (0)21 693.98.01 T�l�fax: +41 (0)21 693.51.00 From owner-chemistry@ccl.net Fri May 4 12:30:00 2012 From: "Olasunkanmi Lukman Olawale walecomuk.:.yahoo.co.uk" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46852-120504122414-3966-i9RZM/+66KUIOqYenAwodQ_._server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="-1142916560-971991493-1336148645=:80733" Date: Fri, 4 May 2012 17:24:05 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk[-]yahoo.co.uk] ---1142916560-971991493-1336148645=:80733 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Cina & Andrew: Thank you for your response. Here is the brief description o= f what I actually did. M+=A0=A0 +=A0=A0=A0=A0 L=A0=A0=A0=A0 =3D=A0=A0=A0=A0= ML+=0ADelta G(rxn) =3D Delta H(rxn) - TxDelta S(rxn).=0AI used PM6 Hamilto= nian in semiempirical quantum chemical calculation software (MOPAC). I got = Delta H(rxn) from the Delta H(formation) of the species; and Delta S(rxn) f= rom the difference in absolute entropies of the species. I calculated K (eq= uilibrium constant) from Delta G(rxn).=0AValues of K as high as 1 x 10^400 = and infinity were obtained.=0AWhat do you suggest?=0AThank you.=0A=0A=A0=0A= Olasunkanmi Lukman Olawale=0A________________________________=0ACurrent Add= ress:=0ADepartment of Chemistry,=0AObafemi Awolowo University,=0AIle-Ife, O= sun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A_____= ___________________________=0A =0A=0A=0A________________________________=0A= From: cina foroutan canyslopus()yahoo.co.uk =0ATo= : "Olasunkanmi, Olawale Lukman " =0ASent: T= hursday, 3 May 2012, 13:48=0ASubject: CCL: Large value of equilibrium const= ants=0A =0A=0ADear Olasunkanmi,=0A=0AWould you please mention at which theo= retical level you performed the computations. Is it an ab initio or DFT or = it is of semi-empirical/molecular mechanic level? This might be a systemati= c error due to the computational level. Would you please also mention the a= mount of the binding energies between the metal and ligands. If the binding= energy is very large, you must improve your computational level.=0ASee thi= s reference as an example of wrong computational level selection: Sensors, = 2007, 7, 3119.=0A=0AGood Luck!=0ACina=0A***********************************= *************************************************************=0A=0ACina For= outan-Nejad, Ph.D.=0ASchool of Chemistry, College of Science=0AUniversity o= f Tehran, Tehran, Iran=0Ahttp://independent.academia.edu/CinaForoutanNejad= =0A=0A=0A=0A________________________________=0A From: Olasunkanmi Lukman Ol= awale walecomuk^_^yahoo.co.uk =0ATo: "Foroutan-N= ejad, Cina " =0ASent: Thursday, 3 May 2012, 22:4= 2=0ASubject: CCL: Large value of equilibrium constants=0A =0A=0ADear Collea= gues,=0AI carried out some theoretical calculations on complexation of some= transition metal ions with a polypyridine ligand and I predicted the equil= ibrium constants for the assumed reversible reactions. I got values of K as= high as 1 x 10^400 and in fact, an infinite value in one case.What do you = think about these large values? I interpretated them to mean that the react= ions are essentially irreversible.=0AThank you all.=0A=0A=A0=0AOlasunkanmi = Lukman Olawale=0A________________________________=0ACurrent Address:=0ADepa= rtment of Chemistry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.= =0ANigeria.=0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A_______________= _________________ ---1142916560-971991493-1336148645=:80733 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Cina &= Andrew: Thank you for your response. Here is the brief description of what= I actually did. M+ + L &nbs= p; =3D ML+

Delta G(rxn= ) =3D Delta H(rxn) - TxDelta S(rxn).

I used PM6 Hami= ltonian in semiempirical quantum chemical calculation software (MOPAC). I g= ot Delta H(rxn) from the Delta H(formation) of the species; and Delta S(rxn= ) from the difference in absolute entropies of the species. I calculated K = (equilibrium constant) from Delta G(rxn).

Values of = K as high as 1 x 10^400 and infinity were obtained.

= What do you suggest?

Thank you.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemis= try,
Obafemi Awolowo Universit= y,
Ile-Ife, Osun State.=
Nigeria.

<= span style=3D"color: rgb(0, 0, 191); font-weight: bold;">+234-0-80-52401564 Or +234-0-80-67161091

From: cina foroutan canyslopus()yahoo.co.uk <owner-chemist= ry#ccl.net>
To: "Ol= asunkanmi, Olawale Lukman " <walecomuk#yahoo.co.uk>
<= span style=3D"font-weight: bold;">Sent: Thursday, 3 May 2012, 13= :48
Subject: CCL: Larg= e value of equilibrium constants

Dear Olasunkanmi,

Wo= uld you please mention at which theoretical level you performed the computations. Is it a= n ab initio or DFT or it is of semi-empirical/molecular mechanic level? Thi= s might be a systematic error due to the computational level. Would you ple= ase also mention the amount of the binding energies between the metal and l= igands. If the binding energy is very large, you must improve your computat= ional level.

See this reference as an example of wro= ng computational level selection: Sensors, 2007, 7, 3119.

=

Good Luck!

Cina

******************************************************= ******************************************

Cina= =0A Foroutan-Nejad, Ph.D.

School of Chemistry, Colle= ge of Science

University of Tehran, Tehran, Iran

http://independent.academia.edu/CinaForoutanNejad

From: Olasunkanmi Lukman Olawale walecomuk^_^yah= oo.co.uk <owner-chemistry]^[ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus]^[yahoo.co.= uk>
Sent: Thursday= , 3 May 2012, 22:42
Subject: CCL: Large value of equilibrium constants

Dear Colleagues,

I carr= ied out some theoretical calculations on complexation of some transition me= tal ions with a polypyridine ligand and I predicted the equilibrium constan= ts for the assumed reversible reactions. I got values of K as high as 1 x 1= 0^400 and in fact, an infinite value in one case.What do you think about th= ese large values? I interpretated them to mean that the reactions are essen= tially irreversible.

Thank you all.

=

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
<= span style=3D"color: rgb(0, 0, 191); font-weight: bold;">Obafemi Awolowo Un= iversity,
Ile-Ife, Osun State.=
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091

=

---1142916560-971991493-1336148645=:80733-- From owner-chemistry@ccl.net Fri May 4 13:16:00 2012 From: "DJUKIC Jean-Pierre djukic.:.unistra.fr" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46853-120504131437-23879-8sdgjAkOmJSYgSgCtUH87g_-_server.ccl.net> X-Original-From: DJUKIC Jean-Pierre Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 May 2012 19:14:02 +0200 MIME-Version: 1.0 Sent to CCL by: DJUKIC Jean-Pierre [djukic(_)unistra.fr] Dear Obafemi, I would not be surprized by a huge K if the reaction in question is quasi irreversible, i.e if it has a huge thermodynamic drive. Experimentally we do measure in host-guest interactions "apparently" irreversible processes wherein non covalent interactions are mostly involved, with Ks of 5 orders of magnitude in water. Good luck. JPD Le 04/05/2012 18:24, Olasunkanmi Lukman Olawale walecomuk.:.yahoo.co.uk a �crit : > Cina & Andrew: Thank you for your response. Here is the brief > description of what I actually did. M+ + L = ML+ > Delta G(rxn) = Delta H(rxn) - TxDelta S(rxn). > I used PM6 Hamiltonian in semiempirical quantum chemical calculation > software (MOPAC). I got Delta H(rxn) from the Delta H(formation) of the > species; and Delta S(rxn) from the difference in absolute entropies of > the species. I calculated K (equilibrium constant) from Delta G(rxn). > Values of K as high as 1 x 10^400 and infinity were obtained. > What do you suggest? > Thank you. > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > *From:* cina foroutan canyslopus()yahoo.co.uk > *To:* "Olasunkanmi, Olawale Lukman " > *Sent:* Thursday, 3 May 2012, 13:48 > *Subject:* CCL: Large value of equilibrium constants > > Dear Olasunkanmi, > > Would you please mention at which theoretical level you performed the > computations. Is it an ab initio or DFT or it is of > semi-empirical/molecular mechanic level? This might be a systematic > error due to the computational level. Would you please also mention the > amount of the binding energies between the metal and ligands. If the > binding energy is very large, you must improve your computational level. > See this reference as an example of wrong computational level selection: > Sensors, 2007, 7, 3119. > > Good Luck! > Cina > ************************************************************************************************ > Cina Foroutan-Nejad, Ph.D. > School of Chemistry, College of Science > University of Tehran, Tehran, Iran > http://independent.academia.edu/CinaForoutanNejad > > > ------------------------------------------------------------------------ > *From:* Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk > > *To:* "Foroutan-Nejad, Cina " > *Sent:* Thursday, 3 May 2012, 22:42 > *Subject:* CCL: Large value of equilibrium constants > > Dear Colleagues, > I carried out some theoretical calculations on complexation of some > transition metal ions with a polypyridine ligand and I predicted the > equilibrium constants for the assumed reversible reactions. I got values > of K as high as 1 x 10^400 and in fact, an infinite value in one > case.What do you think about these large values? I interpretated them to > mean that the reactions are essentially irreversible. > Thank you all. > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ > > > > -- From owner-chemistry@ccl.net Fri May 4 15:07:01 2012 From: "Prashant Singh Rana psrana%a%gmail.com" To: CCL Subject: CCL: Face this Molecular Modelling Challenge: Design of Novel Scaffolds for Inhibitors of Complex III Message-Id: <-46854-120504150407-10690-T74XnrkTPyYOe6E5XTmiHQ/./server.ccl.net> X-Original-From: Prashant Singh Rana Content-Type: multipart/alternative; boundary=20cf300faf2d1e49b704bf3a95ae Date: Sat, 5 May 2012 00:33:57 +0530 MIME-Version: 1.0 Sent to CCL by: Prashant Singh Rana [psrana[A]gmail.com] --20cf300faf2d1e49b704bf3a95ae Content-Type: text/plain; charset=UTF-8 Face this Molecular Modelling Challenge: Design of Novel Scaffolds for Inhibitors of Complex III https://www.innocentive.com/ar/challenge/9932885 -- Thanks & Regards Prashant Singh Rana PhD Research Scholar Department of Information & Communication Technology ABV-Indian Institute of Information Technology & Management (IIITM), Gwalior, MP, India. Contact: +91-9098236997 +91-9313889932 Email : psrana**iiitm.ac.in psrana**gmail.com "Try to Fail, BUT Don't Fail to Try" --20cf300faf2d1e49b704bf3a95ae Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Face this Molecular Modelling Challenge: Design = of Novel Scaffolds for Inhibitors of Complex III

https://www= .innocentive.com/ar/challenge/9932885

--

Thanks & Regards

Prashant Singh Rana
PhD Res= earch Scholar
Department of Information & Communication TechnologyABV-Indian Institute of Information Technology & Management (IIITM), = Gwalior, MP, India.

Contact:=C2=A0 +91-9098236997
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0=C2=A0 +91-9313889932
Email=C2=A0=C2=A0 :=C2=A0=C2=A0 psrana**iiitm.ac.in
= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 psrana**gmail.com

"Try to Fail, BUT Don't Fail to Try"
--20cf300faf2d1e49b704bf3a95ae-- From owner-chemistry@ccl.net Fri May 4 16:20:00 2012 From: "VITORGE Pierre 094605 Pierre.VITORGE[#]cea.fr" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46855-120504161745-2381-/AnAKzdO8VHpqf0Ptd8jIw__server.ccl.net> X-Original-From: VITORGE Pierre 094605 Content-Language: fr-FR Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 4 May 2012 20:17:33 +0000 MIME-Version: 1.0 Sent to CCL by: VITORGE Pierre 094605 [Pierre.VITORGE+*+cea.fr] Yes, ln(K) is dimension-less. Namely K has the meaning of the activity at the point of half reaction, this is consistent because activity is dimension-less, now the activity scale is defined from the value of typically the partial pressure in the reference state, typically 1 atm. (neglecting non ideality) [L], the activity of L is linked to P_L, the partial pressure of L as [L] = P_L / Po where Po is the pressure of the reference state, for this reason, by definition Po = 1 and it is often omitted in formula, as typically the well known pKa = pH_1/2 -- Pierre Vitorge -----Message d'origine----- De�: owner-chemistry+pierre.vitorge==cea.fr^-^ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr^-^ccl.net] De la part de DJUKIC Jean-Pierre djukic^unistra.fr Envoy�: vendredi 4 mai 2012 15:05 ��: VITORGE Pierre 094605 Objet�: CCL: Large value of equilibrium constants Sent to CCL by: DJUKIC Jean-Pierre [djukic]=[unistra.fr] It is a principle in physics and maths that a logarithm (of whatever form, neperian or decimal or other) can only be calculated for a dimension-less number. Therefore ln(K) makes sense only if K is dimension-less, and in principle it is, because activities are dimension-less too. Signed: a concerned chemist. Le 04/05/2012 10:41, VITORGE Pierre 094605 Pierre.VITORGE,,cea.fr a �crit : > I imagine your complexation reaction is typically > > M + L -> ML > > where L is the polypyridine ligand, and M the transition metal ion. > > A usual interpretation is > > 1/K = [L]_1/2, > > the L concentration at the point of half reaction (similarly to pKa = > pH_1/2): it depends on the unit used for [L] (activity, concentration, > fugacity, partial pressure). > > If this unit is not realistic (typically partial pressure in atm for a > reaction that is only observed in aqueous solution) you might find very > big or very small numbers. > > Did you first check this unit problem? > > > -- > Pierre Vitorge > Directeur de recherche CEA > > Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, > LAMBE, > UMR 8587, CEA, Univ Evry, CNRS, > Bd. Francois Mitterrand, Bat. Maupertuis, S 02 > F-91025 Evry, France > tel.01.69.47.01.40 (+33.1.69.47.01.40) > http://www.lambe.univ-evry.fr/pvitorge > http://www.vitorge.name > > Saclay : > Laboratoire de Radiolyse et de la Matiere Organique, LRMO *(this is the > new name of the lab.)* > > CEA, DEN, DPC, SECR, Bat.391 Pe.121 > F-91191 Gif-sur-Yvette, France. > tel.01.69.08.32.65 (+33.1.69.08.32.65) > > *De :*owner-chemistry+pierre.vitorge==cea.fr:-:ccl.net > [mailto:owner-chemistry+pierre.vitorge==cea.fr:-:ccl.net] *De la part > de* Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk > *Envoy� :* jeudi 3 mai 2012 20:42 > *� :* VITORGE Pierre 094605 > *Objet :* CCL: Large value of equilibrium constants > > Dear Colleagues, > > I carried out some theoretical calculations on complexation of some > transition metal ions with a polypyridine ligand and I predicted the > equilibrium constants for the assumed reversible reactions. I got values > of K as high as 1 x 10^400 and in fact, an infinite value in one > case.What do you think about these large values? I interpretated them to > mean that the reactions are essentially irreversible. > > Thank you all. > > *Olasunkanmi Lukman Olawale* > > ------------------------------------------------------------------------ > > *Current Address:* > *Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria.* > > *+*2*34-0-80-52401564 Or +234-0-80-67161091* > > ------------------------------------------------------------------------ --http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri May 4 16:54:00 2012 From: "William Fernandes will.black.soad_+_gmail.com" To: CCL Subject: CCL: TDDFT UVVIS Message-Id: <-46856-120504111447-7275-6rjfma+RD+CcVDiUFt00Vg-,-server.ccl.net> X-Original-From: "William Fernandes" Date: Fri, 4 May 2012 11:14:46 -0400 Sent to CCL by: "William Fernandes" [will.black.soad]|[gmail.com] Hi mrs, How can I att the electronic transitions of the UV-VIS spectrum bands calculated with TDDFT in G09? Thanks From owner-chemistry@ccl.net Fri May 4 17:29:00 2012 From: "Andrew Yeung andrew.yeung[]chem.tamu.edu" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46857-120504131952-30953-/XpCIFhiSbd64I78zd8lHw++server.ccl.net> X-Original-From: Andrew Yeung Content-Type: multipart/alternative; boundary="------------080908020407050607070905" Date: Fri, 04 May 2012 12:19:30 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung:+:chem.tamu.edu] This is a multi-part message in MIME format. --------------080908020407050607070905 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Yes, I don't think that approach works too well. I've tried this approach with a simple organic A <=> B interconversion at a relatively high level but got unrealistic results. The problem is, the derived value for K is very sensitive to small changes in Delta G. Play around with the numbers in Excel or some other spreadsheet program, and you can see what I mean. I think it's easier to compare the enthalpy in this series and discuss which ones bind more strongly (more exothermic complexation). One of our colleagues here mentioned that it is more realistic to consider the reaction M(H2O)6(n+) + L --> ML(n+) + 6 H2O or similar; I agree with that. Maybe you can also model the thermodynamics of the reaction M(L1) + L2 --> M(L2) + L1 I think the entropy term might be less poorly estimated that way. Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-05-04 11:24 AM, Olasunkanmi Lukman Olawale walecomuk.:.yahoo.co.uk wrote: > Cina & Andrew: Thank you for your response. Here is the brief > description of what I actually did. M+ + L = ML+ > Delta G(rxn) = Delta H(rxn) - TxDelta S(rxn). > I used PM6 Hamiltonian in semiempirical quantum chemical calculation > software (MOPAC). I got Delta H(rxn) from the Delta H(formation) of > the species; and Delta S(rxn) from the difference in absolute > entropies of the species. I calculated K (equilibrium constant) from > Delta G(rxn). > Values of K as high as 1 x 10^400 and infinity were obtained. > What do you suggest? > Thank you. > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > *From:* cina foroutan canyslopus()yahoo.co.uk > *To:* "Olasunkanmi, Olawale Lukman " > *Sent:* Thursday, 3 May 2012, 13:48 > *Subject:* CCL: Large value of equilibrium constants > > Dear Olasunkanmi, > > Would you please mention at which theoretical level you performed the > computations. Is it an ab initio or DFT or it is of > semi-empirical/molecular mechanic level? This might be a systematic > error due to the computational level. Would you please also mention > the amount of the binding energies between the metal and ligands. If > the binding energy is very large, you must improve your computational > level. > See this reference as an example of wrong computational level > selection: Sensors, 2007, 7, 3119. > > Good Luck! > Cina > ************************************************************************************************ > Cina Foroutan-Nejad, Ph.D. > School of Chemistry, College of Science > University of Tehran, Tehran, Iran > http://independent.academia.edu/CinaForoutanNejad > > > ------------------------------------------------------------------------ > *From:* Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk > > *To:* "Foroutan-Nejad, Cina " > *Sent:* Thursday, 3 May 2012, 22:42 > *Subject:* CCL: Large value of equilibrium constants > > Dear Colleagues, > I carried out some theoretical calculations on complexation of some > transition metal ions with a polypyridine ligand and I predicted the > equilibrium constants for the assumed reversible reactions. I got > values of K as high as 1 x 10^400 and in fact, an infinite value in > one case.What do you think about these large values? I interpretated > them to mean that the reactions are essentially irreversible. > Thank you all. > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ > > > > --------------080908020407050607070905 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Yes, I don't think that approach works too well. I've tried this approach with a simple organic A <=> B interconversion at a relatively high level but got unrealistic results.

The problem is, the derived value for K is very sensitive to small changes in Delta G. Play around with the numbers in Excel or some other spreadsheet program, and you can see what I mean.

I think it's easier to compare the enthalpy in this series and discuss which ones bind more strongly (more exothermic complexation). One of our colleagues here mentioned that it is more realistic to consider the reaction M(H2O)6(n+) + L --> ML(n+) + 6 H2O or similar; I agree with that.

Maybe you can also model the thermodynamics of the reaction

M(L1) + L2 --> M(L2) + L1

I think the entropy term might be less poorly estimated that way.

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837

On 2012-05-04 11:24 AM, Olasunkanmi Lukman Olawale walecomuk.:.yahoo.co.uk wrote:

Cina & Andrew: Thank you for your response. Here is the brief description of what I actually did. M+ + L = ML+

Delta G(rxn) = Delta H(rxn) - TxDelta S(rxn).

I used PM6 Hamiltonian in semiempirical quantum chemical calculation software (MOPAC). I got Delta H(rxn) from the Delta H(formation) of the species; and Delta S(rxn) from the difference in absolute entropies of the species. I calculated K (equilibrium constant) from Delta G(rxn).

Values of K as high as 1 x 10^400 and infinity were obtained.

What do you suggest?

Thank you.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091

From: cina foroutan canyslopus()yahoo.co.uk <owner-chemistry%x%ccl.net>
To: "Olasunkanmi, Olawale Lukman " <walecomuk%x%yahoo.co.uk>
Sent: Thursday, 3 May 2012, 13:48
Subject: CCL: Large value of equilibrium constants

Dear Olasunkanmi,

Would you please mention at which theoretical level you performed the computations. Is it an ab initio or DFT or it is of semi-empirical/molecular mechanic level? This might be a systematic error due to the computational level. Would you please also mention the amount of the binding energies between the metal and ligands. If the binding energy is very large, you must improve your computational level.

See this reference as an example of wrong computational level selection: Sensors, 2007, 7, 3119.

Good Luck!

Cina

************************************************************************************************

Cina Foroutan-Nejad, Ph.D.

School of Chemistry, College of Science

University of Tehran, Tehran, Iran

http://independent.academia.edu/CinaForoutanNejad

From: Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk <owner-chemistry]^[ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus]^[yahoo.co.uk>
Sent: Thursday, 3 May 2012, 22:42
Subject: CCL: Large value of equilibrium constants

Dear Colleagues,

I carried out some theoretical calculations on complexation of some transition metal ions with a polypyridine ligand and I predicted the equilibrium constants for the assumed reversible reactions. I got values of K as high as 1 x 10^400 and in fact, an infinite value in one case.What do you think about these large values? I interpretated them to mean that the reactions are essentially irreversible.

Thank you all.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091

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