From owner-chemistry@ccl.net Sun Oct 2 10:04:01 2011 From: "Raphael Martinez raphaelmartinez1983-,-gmail.com" To: CCL Subject: CCL:G: TDDFT calculations Message-Id: <-45564-111002100326-14631-9Mn8eBeOvKthsqLZDbviHw ~~ server.ccl.net> X-Original-From: "Raphael Martinez" Date: Sun, 2 Oct 2011 10:03:24 -0400 Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983===gmail.com] Hi Everyone, First of all, thank you for any help you could give me with this question. I am trying to learn as much as I can about how to take advantage of the TDDFT calculation, mainly for exited states, using Gaussian 03. Although I am able to find good information about how to create the input file, and some general theoretical explanation of how it works, I would like to learn how to "read" the output file. What kind of information is the one that will be useful, Does anyone know a good tutorial that focus on the output file? If so, Would you please share that information with me. Thank you so much for the help. Raphael Martinez From owner-chemistry@ccl.net Sun Oct 2 11:56:01 2011 From: "=?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=?= hayak[-]ariel.ac.il" To: CCL Subject: CCL:G: catalysis on metallic nanoparticles Message-Id: <-45565-111002032828-8595-gb9EHjL0WCtMD5NZ66Sw1w(~)server.ccl.net> X-Original-From: =?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=?= Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CC80D4.DB9EE7B6" Date: Sun, 2 Oct 2011 09:27:58 +0200 MIME-Version: 1.0 Sent to CCL by: =?windows-1255?B?5+nkIPfl+PDl5en1IC0g4/gvSGF5YSBLb3Jud2VpdHogLSBEcic=?= [hayak{=}ariel.ac.il] This is a multi-part message in MIME format. ------_=_NextPart_001_01CC80D4.DB9EE7B6 Content-Type: text/plain; charset="windows-1255" Content-Transfer-Encoding: quoted-printable thank you =20 Dr. Haya Kornweitz Department of Biological Chemistry Ariel University Center In Samaria P.O.B. 3, Ariel 44837 ISRAEL Tel. +972-3-9066347 Tel.(home) +972-2-9973630 Cel. 054-5372630 FAX(home): +972-2-9709032 e-mail: hayak()ariel.ac.il =20 ________________________________ =EE=E0=FA: owner-chemistry+hayak=3D=3Dariel.ac.il()ccl.net =E1=F9=ED = CySilicoTech zeinalip . gmail.com =F0=F9=EC=E7: =E1 26/09/2011 08:03 =E0=EC: =E7=E9=E4 =F7=E5=F8=F0=E5=E5=E9=F5 - =E3=F8/Haya Kornweitz - Dr' =F0=E5=F9=E0: CCL:G: catalysis on metallic nanoparticles Hello Haya, =20 Take a look at =20 =20 Constantinos D. Zeinalipour-Yazdi and Angelos M. Efstathiou, =93The = preadsorbed water-mediated mechanism of the Water-Gas Shift reaction=94, = J. Phys. Chem. C 112, 19030-19039,2008=20 =20 where we have used DFT to find the reaction mechanism of the water-gas = shift reaction on a rhodium nanocluster. The nanocluster was = tetra-atomic, so if you don=92t have access to supercomputing time I = would not attempt to perform calculations on a larger metal cluster. If = you have any questions let me know. =20 Best regards, Constantinos. =20 Constantinos D. Zeinalipour, Ph.D. =20 C. CySilicoTech Research Limited 64 Kronou Street, Strovolos 2048 Nicosia, Cyprus. tel: +357-22-105580 fax: +357-22-331995 e-mail: zeinalip/a\insilicotech.com url: http://www.insilicotech.com =20 > from molecules to innovative materials =20 =20 =20 =20 > From: owner-chemistry+zeinalip=3D=3Ducy.ac.cy/a\ccl.net = [mailto:owner-chemistry+zeinalip=3D=3Ducy.ac.cy/a\ccl.net] On Behalf Of = Sergio Manzetti sergio.manzetti,,gmail.com Sent: 25 September 2011 23:14 To: Zeinalipour-Yazdi, Constantinos D.=20 Subject: CCL:G: catalysis on metallic nanoparticles =20 Hi Haya. You should prepare a lattice of metal ions in Gaussian, find the relaxed = state using MP-methods, then perform calculations of the reactions with = and without the lattice using Gaussian by B3LYP/HF. The results can be = quite interesting! Good luck! Best wishes Sergio On Sun, Sep 25, 2011 at 9:02 PM, Haya Kornweitz hayak|ariel.ac.il = > wrote: Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il = ] Dear CCL Subscribers Can someone recommend a program for calculating catalysis on metallic = nano-particles? The interaction with the surface should be QM. -=3D This is automatically added to each message by the mailing script = =3D-
= or use:E-mail to administrators: CHEMISTRY-REQUEST^ccl.net = or usehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20 To: CCL Subject: CCL: Question on catalytic mechanism Message-Id: <-45566-111002115716-10003-c16cNucpV4ro9HKO4ohh7A.@.server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf307810462d262e04ae52e99b Date: Sun, 2 Oct 2011 17:57:09 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti{:}gmail.com] --20cf307810462d262e04ae52e99b Content-Type: text/plain; charset=ISO-8859-1 Hi everyone, the adduct formation between epoxides and guanosine amine groups has been postulated by several sources to occur through the formation of a carbanion. However, I cannot fit in the description of the reactants how it is possible for the epoxy-carbon in a epoxy-PAH to gain a negatiive charge when the epoxy oxygen really deprotonates the amine group first. Does someone know if these sources quoting carbanions really ment carbocations? Best wishes Sergio --20cf307810462d262e04ae52e99b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi everyone,=A0 the adduct formation between= epoxides and guanosine amine groups has been postulated by several sources= to occur through the formation of a carbanion. However, I cannot fit in th= e description of the reactants how it is possible for the epoxy-carbon in a= epoxy-PAH to gain a negatiive charge when the epoxy oxygen really deproton= ates the amine group first.

Does someone know if these sources quoting carbanions really ment carbo= cations?

Best wishes

Sergio


--20cf307810462d262e04ae52e99b-- From owner-chemistry@ccl.net Sun Oct 2 13:45:00 2011 From: "Arne Dieckmann adieckma%x%googlemail.com" To: CCL Subject: CCL: Question on catalytic mechanism Message-Id: <-45567-111002130534-1597-wJwNshkEyLZO6wNfOip0ug###server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 2 Oct 2011 10:05:15 -0700 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: Arne Dieckmann [adieckma a googlemail.com] Hi Sergio, could you point us to a paper postulating these carbanions? This sounds highly unlikely to me. Also, you do not need to deprotonate an amino-group to facilitate the attack to an epoxide. Normally, the amino-group would attack and lose a proton to the alcohol oxigen afterwards. Cheers, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Arne Dieckmann Houk Research Lab University of California, Los Angeles email: adieckma-,-googlemail.com On Oct 2, 2011, at 8:57 AM, Sergio Manzetti sergio.manzetti]![gmail.com wrote: > > Hi everyone, the adduct formation between epoxides and guanosine amine groups has been postulated by several sources to occur through the formation of a carbanion. However, I cannot fit in the description of the reactants how it is possible for the epoxy-carbon in a epoxy-PAH to gain a negatiive charge when the epoxy oxygen really deprotonates the amine group first. > > Does someone know if these sources quoting carbanions really ment carbocations? > > Best wishes > > Sergio > > From owner-chemistry@ccl.net Sun Oct 2 15:46:00 2011 From: "Sergio Manzetti sergio.manzetti[a]gmail.com" To: CCL Subject: CCL: Question on catalytic mechanism Message-Id: <-45568-111002154433-5462-dNE3NGwe0JO6veqr1QVh3A!=!server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=20cf30780c32f4be3604ae5615b0 Date: Sun, 2 Oct 2011 21:44:25 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti~~gmail.com] --20cf30780c32f4be3604ae5615b0 Content-Type: text/plain; charset=ISO-8859-1 Hi Arne, I am sorry but I cannot find the reference. It must have said carbocation and I need new glasses. How would the epoxide bond be issolved, if not by the protons effect? Best wishes On Sun, Oct 2, 2011 at 7:05 PM, Arne Dieckmann adieckma%x%googlemail.com < owner-chemistry\a/ccl.net> wrote: > > Sent to CCL by: Arne Dieckmann [adieckma a googlemail.com] > Hi Sergio, > > could you point us to a paper postulating these carbanions? This sounds > highly unlikely to me. Also, you do not need to deprotonate an amino-group > to facilitate the attack to an epoxide. Normally, the amino-group would > attack and lose a proton to the alcohol oxigen afterwards. > > > Cheers, > Arne > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Dr. Arne Dieckmann > Houk Research Lab > University of California, Los Angeles > email: adieckma[A]googlemail.com > > > On Oct 2, 2011, at 8:57 AM, Sergio Manzetti sergio.manzetti]![gmail.comwrote: > > > > > Hi everyone, the adduct formation between epoxides and guanosine amine > groups has been postulated by several sources to occur through the formation > of a carbanion. However, I cannot fit in the description of the reactants > how it is possible for the epoxy-carbon in a epoxy-PAH to gain a negatiive > charge when the epoxy oxygen really deprotonates the amine group first. > > > > Does someone know if these sources quoting carbanions really ment > carbocations? > > > > Best wishes > > > > Sergio> > > --20cf30780c32f4be3604ae5615b0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Arne, I am sorry but I cannot find the reference.=A0 It must have said c= arbocation and I need new glasses.
How would the epoxide bond be issolve= d, if not by the protons effect?

Best wishes




On Sun, Oct 2, 2011 at 7:05 PM, Arne Dieckmann adieckma%x%googlemail.com <owner-chemistry\a/ccl.net> wrote:
=

Sent to CCL by: Arne Dieckmann [adieckma a googlemail.com]
Hi Sergio,

could you point us to a paper postulating these carbanions? This sounds hig= hly unlikely to me. Also, you do not need to deprotonate an amino-group to = facilitate the attack to an epoxide. Normally, the amino-group would attack= and lose a proton to the alcohol oxigen afterwards.


Cheers,
Arne

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Dr. Arne Dieckmann
Houk Research Lab
University of California, Los Angeles
email: adieckma[A]googl= email.com


On Oct 2, 2011, at 8:57 AM, Sergio Manzetti sergio.manzetti]![gmail.com wrote:

>
> Hi everyone, =A0the adduct formation between epoxides and guanosine am= ine groups has been postulated by several sources to occur through the form= ation of a carbanion. However, I cannot fit in the description of the react= ants how it is possible for the epoxy-carbon in a epoxy-PAH to gain a negat= iive charge when the epoxy oxygen really deprotonates the amine group first= .
>
> Does someone know if these sources quoting carbanions really ment carb= ocations?
>
> Best wishes
>
> Sergio
>
>



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--20cf30780c32f4be3604ae5615b0-- From owner-chemistry@ccl.net Sun Oct 2 21:26:01 2011 From: "Arne Dieckmann adieckma-$-googlemail.com" To: CCL Subject: CCL: Question on catalytic mechanism Message-Id: <-45569-111002211935-14099-Fh1CSICbuv18jae4Qr3/8A_+_server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 2 Oct 2011 18:19:26 -0700 Mime-Version: 1.0 (Apple Message framework v1244.3) Sent to CCL by: Arne Dieckmann [adieckma^googlemail.com] Hi Sergio, what would a "proton effect" be? General textbook knowledge suggests that the amino group attacks the epoxide, which might already be protonated at this stage. However, you do not need to deprotonate the amino-group to increase its nucleophilicity, its neutral form is already a good nucleophile. The amino-group is most likely deprotonated after the attack to lose the formal positive charge. Cheers, Arne On Oct 2, 2011, at 12:44 PM, Sergio Manzetti sergio.manzetti[a]gmail.com wrote: > Hi Arne, I am sorry but I cannot find the reference. It must have said carbocation and I need new glasses. > How would the epoxide bond be issolved, if not by the protons effect? > > Best wishes > > > > > On Sun, Oct 2, 2011 at 7:05 PM, Arne Dieckmann adieckma%x%googlemail.com wrote: > > Sent to CCL by: Arne Dieckmann [adieckma a googlemail.com] > Hi Sergio, > > could you point us to a paper postulating these carbanions? This sounds highly unlikely to me. Also, you do not need to deprotonate an amino-group to facilitate the attack to an epoxide. Normally, the amino-group would attack and lose a proton to the alcohol oxigen afterwards. > > > Cheers, > Arne > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Dr. Arne Dieckmann > Houk Research Lab > University of California, Los Angeles > email: adieckma[A]googlemail.com > > > On Oct 2, 2011, at 8:57 AM, Sergio Manzetti sergio.manzetti]![gmail.com wrote: > > > > > Hi everyone, the adduct formation between epoxides and guanosine amine groups has been postulated by several sources to occur through the formation of a carbanion. However, I cannot fit in the description of the reactants how it is possible for the epoxy-carbon in a epoxy-PAH to gain a negatiive charge when the epoxy oxygen really deprotonates the amine group first. > > > > Does someone know if these sources quoting carbanions really ment carbocations? > > > > Best wishes > > > > Sergio> > > > E-mail to subscribers: CHEMISTRY..ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST..ccl.net or use> > > >