From owner-chemistry@ccl.net Tue Sep 25 05:07:01 2012 From: "Nguyen Minh Ly nguyenminhly2209*|*yahoo.com" To: CCL Subject: CCL:G: SN1 reaction Message-Id: <-47657-120925050542-28343-MQwEw5E67ds5F8ifYeK1aA|server.ccl.net> X-Original-From: "Nguyen Minh Ly" Date: Tue, 25 Sep 2012 05:05:39 -0400 Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209,yahoo.com] I have a problem to discuss. I survey the SN1 reaction of tert-butyl chloride and OH- by: 1 / Optimization of structures with Gaussian 2 / Optimize to find the transition state in the first stage of the SN1 reaction (using QST2 keyword) As we all know, this reaction depends on the concentration of OH-. If concentration of OH- is low (dilute solution), the reaction will occur SN1. If concentration of OH- is high (special solution), the reaction will occur E1. But in GaussView, when I optimized to find the transition state in the first stage of the SN1 reaction, I can only draw a molecule C4H9Cl and a OH- in Reactants window, a molecule C4H9OH and a Cl- in products window. This means that the rate of C4H9Cl and OH- concentration in the solution was 1:1 (corresponding to the high concentration of OH-). So E1 reaction will occur! But I want to find the transition state in the first stage of the SN1 reaction. How can do this ? Please help me Thank you From owner-chemistry@ccl.net Tue Sep 25 05:41:00 2012 From: "Kunal Roy kroy++pharma.jdvu.ac.in" To: CCL Subject: CCL: The rm2 calculator: An open access web service for judging quality o Message-Id: <-47658-120925052729-4946-wGpVCS5b21y4WZaV+Y96QA]_[server.ccl.net> X-Original-From: "Kunal Roy" Date: Tue, 25 Sep 2012 05:27:28 -0400 Sent to CCL by: "Kunal Roy" [kroy.:.pharma.jdvu.ac.in] An open access web service rm2 calculator (http://203.200.173.43:8080/rmsquare) for judging quality of QSAR predictions has been developed by the Drug Theoretics and Cheminformatics Laboratory ( https://sites.google.com/site/kunalroyindia/ ) , Department of Pharmaceutical Technology, Jadavpur University in association with APT Software Avenues Pvt. Ltd., Kolkata ( http://aptsoftware.com/ ). The details about the rm2 metrics developed by this laboratory can be checked at https://sites.google.com/site/rm2forqsarvalidation/ . Kunal Roy, Ph.D. Associate Professor, Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Email : kroy=pharma.jdvu.ac.in , kunalroy_in=yahoo.com URL : http://sites.google.com/site/kunalroyindia/ From owner-chemistry@ccl.net Tue Sep 25 06:16:00 2012 From: "Rzepa, Henry S h.rzepa*imperial.ac.uk" To: CCL Subject: CCL:G: SN1 reaction Message-Id: <-47659-120925060834-9004-Tky9fw16z4WX+fs740W+yQ .. server.ccl.net> X-Original-From: "Rzepa, Henry S" Content-ID: Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 25 Sep 2012 10:08:08 +0000 MIME-Version: 1.0 Sent to CCL by: "Rzepa, Henry S" [h.rzepa_._imperial.ac.uk] On 25 Sep 2012, at 10:05, Nguyen Minh Ly nguyenminhly2209*|*yahoo.com wrote: > > Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209,yahoo.com] > I have a problem to discuss. I survey the SN1 reaction of tert-butyl chloride > and OH- by: > 1 / Optimization of structures with Gaussian > 2 / Optimize to find the transition state in the first stage of the SN1 > reaction (using QST2 keyword) > > As we all know, this reaction depends on the concentration of OH-. If > concentration of OH- is low (dilute solution), the reaction will occur SN1. If > concentration of OH- is high (special solution), the reaction will occur E1. > > But in GaussView, when I optimized to find the transition state in the first > stage of the SN1 reaction, I can only draw a molecule C4H9Cl and a OH- in > Reactants window, a molecule C4H9OH and a Cl- in products window. This means > that the rate of C4H9Cl and OH- concentration in the solution was 1:1 > (corresponding to the high concentration of OH-). So E1 reaction will occur! > > But I want to find the transition state in the first stage of the SN1 reaction. > How can do this ? An intrinsic reaction coordinate for the SN1 reaction of t-butyl chloride in water is shown at http://www.ch.imperial.ac.uk/rzepa/blog/?p=5228 Normally, Sn1 reactions require solvation, both explicit and continuum, to characterise. From owner-chemistry@ccl.net Tue Sep 25 07:15:00 2012 From: "Bruce Palfey brupalf() umich.edu" To: CCL Subject: CCL:G: SN1 reaction Message-Id: <-47660-120925071406-28403-kkED8Vpic2zePE35rY/hUw^_^server.ccl.net> X-Original-From: Bruce Palfey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Sep 2012 07:13:50 -0400 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Bruce Palfey [brupalf]|[umich.edu] Physically speaking, wouldn't the placement of the two reactants in the small volume of the simulation be equivalent to high concentrations? I would think that excluding OH- would simulate dilute solution and allow the intermediate to form. ciao, Bruce On Sep 25, 2012, at 5:05 AM, Nguyen Minh Ly nguyenminhly2209*|*yahoo.com wrote: > > Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209,yahoo.com] > I have a problem to discuss. I survey the SN1 reaction of tert-butyl chloride > and OH- by: > 1 / Optimization of structures with Gaussian > 2 / Optimize to find the transition state in the first stage of the SN1 > reaction (using QST2 keyword) > > As we all know, this reaction depends on the concentration of OH-. If > concentration of OH- is low (dilute solution), the reaction will occur SN1. If > concentration of OH- is high (special solution), the reaction will occur E1. > > But in GaussView, when I optimized to find the transition state in the first > stage of the SN1 reaction, I can only draw a molecule C4H9Cl and a OH- in > Reactants window, a molecule C4H9OH and a Cl- in products window. This means > that the rate of C4H9Cl and OH- concentration in the solution was 1:1 > (corresponding to the high concentration of OH-). So E1 reaction will occur! > > But I want to find the transition state in the first stage of the SN1 reaction. > How can do this ? > > Please help me > Thank you> > > > From owner-chemistry@ccl.net Tue Sep 25 10:01:01 2012 From: "Mauro Barbosa de Amorim maurobdeamorim-#-gmail.com" To: CCL Subject: CCL:G: SN1 reaction Message-Id: <-47661-120925092827-9447-eVSsykVV6fwoYB7zBlM3Ug[a]server.ccl.net> X-Original-From: Mauro Barbosa de Amorim Content-Type: multipart/alternative; boundary=f46d04083a8bce10ff04ca86ad3f Date: Tue, 25 Sep 2012 10:28:17 -0300 MIME-Version: 1.0 Sent to CCL by: Mauro Barbosa de Amorim [maurobdeamorim|gmail.com] --f46d04083a8bce10ff04ca86ad3f Content-Type: text/plain; charset=ISO-8859-1 Dear Nguyen, Unimolecular reactions, implicit in terms E1 and SN1, pass through unimolecular transitions states, involving just the substrate molecule, t-butyl chloride. So, we cannot simulate their transition states using both the nucleophile or base (OH-) and the substrate (t-BuCl). The first step of these reactions would be the Cl-C(CH3)3 bond breaking, followed, as a second step, by the attack of OH- as a base on one of the H atoms (in E1 reaction) or as a nucleophile on the cationic carbon (SN1). Otherwise, you may want to study the bimolecular processes (E2 and SN2), which occur in just one step. In this case, you should direct the attack of the anioic species (OH-) to the central carbon (SN2) or to one os the methyl hydrogens (E2) (that are statistically more prone to attack: 9 to 1, justifying the E2 preference in high OH- conentrations). You should also consider that OH- is more basic than nucleophilic, favoring E2 reactions. My best regards from a sunny Rio. Mauro 2012/9/25 Nguyen Minh Ly nguyenminhly2209*|*yahoo.com < owner-chemistry[]ccl.net> > > Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209,yahoo.com] > I have a problem to discuss. I survey the SN1 reaction of tert-butyl > chloride > and OH- by: > 1 / Optimization of structures with Gaussian > 2 / Optimize to find the transition state in the first stage of the SN1 > reaction (using QST2 keyword) > > As we all know, this reaction depends on the concentration of OH-. If > concentration of OH- is low (dilute solution), the reaction will occur > SN1. If > concentration of OH- is high (special solution), the reaction will occur > E1. > > But in GaussView, when I optimized to find the transition state in the > first > stage of the SN1 reaction, I can only draw a molecule C4H9Cl and a OH- in > Reactants window, a molecule C4H9OH and a Cl- in products window. This > means > that the rate of C4H9Cl and OH- concentration in the solution was 1:1 > (corresponding to the high concentration of OH-). So E1 reaction will > occur! > > But I want to find the transition state in the first stage of the SN1 > reaction. > How can do this ? > > Please help me > Thank you> > > --f46d04083a8bce10ff04ca86ad3f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Nguyen,

Unimolecular reactions, implicit in terms E= 1 and SN1, pass through unimolecular transitions states, involving just the= substrate molecule, t-butyl chloride. So, we cannot simulate their transit= ion states using both the nucleophile or base (OH-) and the substrate (t-Bu= Cl). The first step of these reactions would be the Cl-C(CH3)3 bond breakin= g, followed, as a second step, by the attack of OH- as a base on one of the= H atoms (in E1 reaction) or as a nucleophile on the cationic carbon (SN1).= Otherwise, you may want to study the bimolecular processes (E2 and SN2), w= hich occur in just one step. In this case, you should direct the attack of = the anioic species (OH-) to the central carbon (SN2) or to one os the methy= l hydrogens (E2) (that are statistically more prone to attack: 9 to 1, just= ifying the E2 preference in high OH- conentrations). You should also consid= er that OH- is more basic than nucleophilic, favoring E2 reactions.

My best regards from a sunny Rio.

<= div>Mauro

2012/9/25 Nguyen Minh Ly nguyen= minhly2209*|*yahoo.com &= lt;owner-chemi= stry[]ccl.net>

Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209,yahoo.com]
I have a problem to discuss. I survey the SN1 reaction of tert-butyl chlori= de
and OH- by:
1 / Optimization of structures with Gaussian
2 / Optimize to find the transition state in the first stage of the SN1
reaction (using QST2 keyword)

As we all know, this reaction depends on the concentration of OH-. If
concentration of OH- is low (dilute solution), the reaction will occur SN1.= If
concentration of OH- is high (special solution), the reaction will occur E1= .

But in GaussView, when I optimized to find the transition state in the firs= t
stage of the SN1 reaction, I can only draw a molecule C4H9Cl and a OH- in Reactants window, a molecule C4H9OH and a Cl- in products window. This mean= s
that the rate of C4H9Cl and OH- concentration in the solution was 1:1
(corresponding to the high concentration of OH-). So E1 reaction will occur= !

But I want to find the transition state in the first stage of the SN1 react= ion.
How can do this ?

Please help me
Thank you



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--f46d04083a8bce10ff04ca86ad3f-- From owner-chemistry@ccl.net Tue Sep 25 16:39:01 2012 From: "Marc marc-andre.belanger a umontreal.ca" To: CCL Subject: CCL: Reference Request: Nomenclature of peri-condensed benzenoids Message-Id: <-47662-120925163144-19795-8C0g+ljStKNIOw0DC7utbA%a%server.ccl.net> X-Original-From: Marc Content-Type: multipart/alternative; boundary=Apple-Mail-1-930708214 Date: Tue, 25 Sep 2012 16:31:35 -0400 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Marc [marc-andre.belanger|umontreal.ca] --Apple-Mail-1-930708214 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Hi, Balaban and Harary have described a nomenclature for cata-condensed = benzenoids centered around their concept of a molecule's characteristic = graph. Their nomenclature is described in these publications: http://dx.doi.org/10.1016/S0040-4020(01)82523-0 http://dx.doi.org/10.1016/S0040-4020(01)82827-1 Does anybody know if a follow up was made on the nomenclature of = peri-condensed benzenoids? I cannot find papers about it. Thank you, Marc-Andr=E9 B=E9langer Universit=E9 de Montr=E9al= --Apple-Mail-1-930708214 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 http://dx.doi.org= /10.1016/S0040-4020(01)82523-0

Does anybody = know if a follow up was made on the nomenclature of = peri-condensed benzenoids? I cannot find papers about = it.

Thank = you,

Marc-Andr=E9 B=E9langer
Universit=E9= de Montr=E9al
= --Apple-Mail-1-930708214-- From owner-chemistry@ccl.net Tue Sep 25 19:39:00 2012 From: "Nguyen Minh Ly nguyenminhly2209:-:yahoo.com" To: CCL Subject: CCL:G: SN1 reaction Message-Id: <-47663-120925193802-26832-rqcJMfMwtDZzFoprJLxzbg+*+server.ccl.net> X-Original-From: "Nguyen Minh Ly" Date: Tue, 25 Sep 2012 19:38:01 -0400 Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209 . yahoo.com] Dear sir, I survey for various types of reactions: 1/1 C4H9Cl molecule (tert-butyl chloride) are surrounded by many OH-(I do like this: http://www.ch.imperial.ac.uk/rzepa/blog/?p=5228 ) 2 / I'm just drawing a molecule C4H9Cl in reactants window (GaussView), a carbocation C4H9 + and a Cl- in products window (I want to find the transition state in the first stage of the SN1 reaction) In the first case, I can not be performed due to insufficient hardware conditions. In the second case, I optimized by use QST2 keyword (Gaussian) to find the transition state in the first phase of the SN1 reaction. Although there is only one C4H9Cl molecule in reactants window (there is no OH-) but I still can not find the transition state (Link die in a state that C4H9Cl almost split off HCl molecule) Command as follows: # opt=qst2 b3lyp/6-31g(d) scrf=(solvent=water) nosymm geom=connectivity scf=tight How can I survey the SN1 reaction? Please help me ! Thank you