From owner-chemistry@ccl.net Tue Mar 6 03:38:01 2012 From: "Ermias Legg ermiaslegg]~[gmail.com" To: CCL Subject: CCL:G: solvent calculation Message-Id: <-46428-120306033725-31277-4BaDC5Gyy0gR9arVs68FyA^^^server.ccl.net> X-Original-From: "Ermias Legg" Date: Tue, 6 Mar 2012 03:37:24 -0500 Sent to CCL by: "Ermias Legg" [ermiaslegg{:}gmail.com] Dear all If I am to study the thermodynamics of certain organic solvent using DFT in condensed phase, is it appropriate to optimize the structures in gas phase and then use implicit solvent calculations or can I simply optimize the structures in implicit solvent calculations (e.g. using PCM). The package I intend to use is Gaussian 09. I would be very glad if anyone could point me to relevant literatures I thank you for your Help. From owner-chemistry@ccl.net Tue Mar 6 05:48:01 2012 From: "Reza Shojaei shojaei81*_*gmail.com" To: CCL Subject: CCL:G: single point calculations and g09/l508.exe and g09/l502.exe errors Message-Id: <-46429-120306054353-18406-/Qz+Uktv3h07QkbiwYlZ3g ~~ server.ccl.net> X-Original-From: "Reza Shojaei" Date: Tue, 6 Mar 2012 05:43:52 -0500 Sent to CCL by: "Reza Shojaei" [shojaei81%gmail.com] Hi Heribert, Thank you very much for your constructive suggestions. I just used scf=noincfock and it converged. Regards, Reza > "hreis[a]eie.gr hreis[a]eie.gr" wrote: > > Sent to CCL by: "hreis^-^eie.gr" [hreis^-^eie.gr] > Hi Reza, > > You could try the standard scf (no qc) with > > integral=ultrafine scf=noincfock > > and leave out 6D 10F. Sometimes nosymm also helps. > > Heribert > > > Original Message: > ----------------- > > From: Reza Shojaei shojaei81#gmail.com owner-chemistry,ccl.net > Date: Sun, 26 Feb 2012 13:52:31 -0500 > To: hreis,eie.gr > Subject: CCL:G: single point calculations and g09/l508.exe and g09/l502.exe > errors > > > > Sent to CCL by: " Reza Shojaei" [shojaei81,+,gmail.com] > Thanks for suggestions, but none of them are working. > does anyone have new Idea? > > > > "eurisco1::pochta.ru" wrote: > > > > Sent to CCL by: [eurisco1(_)pochta.ru] > > Dear Reza Shojaei, > > > > > > I guess that keywords SCF(XQC,vshift=150,maxcycle=512) will be helpful. > > > > Sincerely, > > Ol Ga > > > > > > > > ----- ----- > > > From: Reza Shojaei shojaei81[-]gmail.com > > Sent: Friday, February 24, 2012 11:15 AM > > To: Ga, Ol > > Subject: CCL:G: single point calculations and g09/l508.exe and > g09/l502.exe > > errors > > > > > > Sent to CCL by: "Reza Shojaei" [shojaei81],[gmail.com] > > Yes, there is more explanations on the errors. > > > > for g09/l502 I got this message: > > > > Convergence failure -- run terminated. > > Error termination via Lnk1e in .../g09/l502.exe > > > > and for g09/l508.exe the message was: > > > > Search did not lower the energy significantly. > > No lower point found -- try reversing direction. > > Search did not lower the energy significantly. > > No lower point found -- switch to scaled steepest descent. > > Search did not lower the energy significantly. > > Scaled steepest descent with Shift=0.000 failed. > > Search did not lower the energy significantly. > > Scaled steepest descent with Shift=0.025 failed. > > Search did not lower the energy significantly. > > Scaled steepest descent with Shift=0.050 failed. > > Search did not lower the energy significantly. > > Scaled steepest descent with Shift=0.075 failed. > > Search did not lower the energy significantly. > > No lower point found -- switch to steepest descent. > > Search did not lower the energy significantly. > > Search did not lower the energy significantly. > > Search did not lower the energy significantly. > > No lower point found -- run aborted. > > Error termination via Lnk1e in ...../g09/l508.exe > > > > Reza > > > > > "Dr. Vitaly V. Chaban vvchaban**gmail.com" wrote: > > > > > > Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban]^[gmail.com] > > > I suppose there should be more specific descriprion of your problem(s) > > > than just "g09/l508.exe and g09/l502.exe". > > > > > > -- > > > Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. > > > Univ. Rochester, Rochester, New York 14627-0216 > > > THE UNITED STATES OF AMERICA > > > > > > > > > > > > > > > On Thu, Feb 23, 2012 at 4:20 PM, Reza Shojaei shojaei81.:.gmail.com > > > wrote: > > > > > > > > Sent to CCL by: " Reza Shojaei" [shojaei81*gmail.com] > > > > Dear all, > > > > > > > > I do single point calculations on Biphenyl by Gaussian 09 using HPC > but > > > > I > > > > have encountered with serious problems and all my attempts failed and > I > > > > get > > > > g09/l508.exe and g09/l502.exe error messages. I have tried different > > > > keywords like scf=tight, scf(maxcycle=300), L508, scf=fermi, scf=xqc > and > > > > scf=qc, but none of them succeed. does someone have any Idea to > overcome > > > > this > > > > problem. your suggestions are highly appreciated.the input file is : > > > > > > > > %nproc=8 > > > > %mem=8gb > > > > # b3lyp/aug-cc-pvdz 6d 10f POP=FULL GFINPUT scf=qc > > > > > > > > Biphenyl twisted b3lyp mometum distribution > > > > > > > > 0 1 > > > > C 0.000000 0.000000 0.723101 > > > > C 0.000000 0.000000 -0.723101 > > > > C -0.158093 1.217136 1.466542 > > > > C -0.158093 -1.217136 -1.466542 > > > > C 0.158093 -1.217136 1.466542 > > > > C 0.158093 1.217136 -1.466542 > > > > C -0.166057 1.211550 2.847549 > > > > C 0.166057 -1.211550 2.847549 > > > > C -0.166057 -1.211550 -2.847549 > > > > C 0.166057 1.211550 -2.847549 > > > > C 0.000000 0.000000 3.549464 > > > > C 0.000000 0.000000 -3.549464 > > > > H -0.309412 2.160499 0.944666 > > > > H 0.309412 -2.160499 0.944666 > > > > H -0.309412 -2.160499 -0.944666 > > > > H 0.309412 2.160499 -0.944666 > > > > H -0.304449 2.143962 3.396690 > > > > H -0.304449 -2.143962 -3.396690 > > > > H 0.304449 2.143962 -3.396690 > > > > H 0.304449 -2.143962 3.396690 > > > > H 0.000000 0.000000 4.641585 > > > > H 0.000000 0.000000 -4.641585 > > > > > > > > > > > > Rezahttp://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://w > ww. > ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------------- > myhosting.com - Premium Microsoft Windows and Linux web and application > hosting - http://link.myhosting.com/myhosting > > From owner-chemistry@ccl.net Tue Mar 6 06:23:00 2012 From: "Wojciech Kolodziejczyk dziecial|-|icnanotox.org" To: CCL Subject: CCL:G: solvent calculation Message-Id: <-46430-120306060241-518-vgUmwcAApIXqHnRg+sWexA,server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-2 Date: Tue, 6 Mar 2012 12:02:30 +0100 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial##icnanotox.org] Hi, In my solvent calculations I am using that approach Warshel, A. No Title. Computer Modeling of Chemical Reactions in Enzymes and Solutions 1991. Florián, J.; Warshel, A. Phosphate ester hydrolysis in aqueous solution: Associative versus dissociative mechanisms. Journal of Physical Chemistry B 1998, 102, 719-734. Florián, J.; ©trajbl, M.; Warshel, A. Conformational flexibility of phosphate, phosphonate, and phosphorothioate methyl esters in aqueous solution. Journal of the American Chemical Society 1998, 120, 7959-7966. Davidson, N. No Title. Statistical Mechanics 1962. How? You can find it in my paper --> Probing the role of P{double bond, long}O stretching mode enhancement in nerve-agent sensors: Simulation of the adsorption of diisopropylfluorophosphate on the model MgO and CaO surfaces Chemical Physics Letters Volume 450, Issue 1-3, 14 December 2007, Pages 138-143 Best regards W. 2012/3/6 Ermias Legg ermiaslegg]~[gmail.com : > > Sent to CCL by: "Ermias  Legg" [ermiaslegg{:}gmail.com] > Dear all > If I am to study the thermodynamics of certain organic solvent using DFT in > condensed phase, is it appropriate to optimize the structures in gas phase and > then use implicit solvent calculations or can I simply optimize the structures > in implicit solvent calculations (e.g. using PCM). The package I intend to use > is Gaussian 09. I would be very glad if anyone could point me to relevant > literatures > I thank you for your Help.>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Tue Mar 6 11:45:00 2012 From: "John McKelvey jmmckel^gmail.com" To: CCL Subject: CCL:G: solvent calculation Message-Id: <-46431-120306114150-4171-9aI+TdHefOa3avoPRmHMNQ]-[server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=e89a8ff2447f8f8ff204ba95b78a Date: Tue, 6 Mar 2012 11:41:39 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel..gmail.com] --e89a8ff2447f8f8ff204ba95b78a Content-Type: text/plain; charset=ISO-8859-2 Content-Transfer-Encoding: quoted-printable If I understand the question being asked concerning how to apply solvation I believe there are several previous CCL posts on this which could provide opinions on both sides of the issue, including solvation or applying at the end of gas phase calculations.. John 2012/3/6 Wojciech Kolodziejczyk dziecial|-|icnanotox.org < owner-chemistry]![ccl.net> > > Sent to CCL by: Wojciech Kolodziejczyk [dziecial##icnanotox.org] > Hi, In my solvent calculations I am using that approach > > > > Warshel, A. No Title. Computer Modeling of Chemical Reactions in > Enzymes and Solutions 1991. > > Flori=E1n, J.; Warshel, A. Phosphate ester hydrolysis in aqueous > solution: Associative versus dissociative mechanisms. Journal of > Physical Chemistry B 1998, 102, 719-734. > > Flori=E1n, J.; =A9trajbl, M.; Warshel, A. Conformational flexibility of > phosphate, phosphonate, and phosphorothioate methyl esters in aqueous > solution. Journal of the American Chemical Society 1998, 120, > 7959-7966. > > Davidson, N. No Title. Statistical Mechanics 1962. > > > > How? You can find it in my paper --> > > Probing the role of P{double bond, long}O stretching mode enhancement > in nerve-agent sensors: Simulation of the adsorption of > diisopropylfluorophosphate on the model MgO and CaO surfaces > Chemical Physics Letters > Volume 450, Issue 1-3, 14 December 2007, Pages 138-143 > > > Best regards > W. > > > 2012/3/6 Ermias Legg ermiaslegg]~[gmail.com : > > > > Sent to CCL by: "Ermias Legg" [ermiaslegg{:}gmail.com] > > Dear all > > If I am to study the thermodynamics of certain organic solvent using DF= T > in > > condensed phase, is it appropriate to optimize the structures in gas > phase and > > then use implicit solvent calculations or can I simply optimize the > structures > > in implicit solvent calculations (e.g. using PCM). The package I intend > to use > > is Gaussian 09. I would be very glad if anyone could point me to releva= nt > > literatures > > I thank you for your Help.> > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel]![gmail.com --e89a8ff2447f8f8ff204ba95b78a Content-Type: text/html; charset=ISO-8859-2 Content-Transfer-Encoding: quoted-printable If I understand the question being asked concerning how to apply solvation = I believe there are several previous CCL posts on this which could provide = opinions on both sides of the issue, including solvation or applying at the= end of gas phase calculations..

John=A0

2012/3/6 Wojciech Kolodziejc= zyk dziecial|-|icnanotox.org <owner-chemistry]![ccl= .net>

Sent to CCL by: Wojciech Kolodziejczyk [dziecial##icnanotox.org]
Hi, In my solvent calculations I am using that approach



Warshel, A. No Title. Computer Modeling of Chemical Reactions in
Enzymes and Solutions 1991.

Flori=E1n, J.; Warshel, A. Phosphate ester hydrolysis in aqueous
solution: Associative versus dissociative mechanisms. Journal of
Physical Chemistry B 1998, 102, 719-734.

Flori=E1n, J.; =A9trajbl, M.; Warshel, A. Conformational flexibility of
phosphate, phosphonate, and phosphorothioate methyl esters in aqueous
solution. Journal of the American Chemical Society 1998, 120,
7959-7966.

Davidson, N. No Title. Statistical Mechanics 1962.



How? You can find it in my paper -->

Probing the role of P{double bond, long}O stretching mode enhancement
in nerve-agent sensors: Simulation of the adsorption of
diisopropylfluorophosphate on the model MgO and CaO surfaces
Chemical Physics Letters
Volume 450, Issue 1-3, 14 December 2007, Pages 138-143


Best regards
W.


2012/3/6 Ermias Legg ermiaslegg]~[gmail.com <owner-chemistry=3Dccl.net>:
>
> Sent to CCL by: "Ermias =A0Legg" [ermiaslegg{:}gmail.com]
> Dear all
> If I am to study the thermodynamics of certain organic solvent using D= FT in
> condensed phase, is it appropriate to optimize the structures in gas p= hase and
> then use implicit solvent calculations or can I simply optimize the st= ructures
> in implicit solvent calculations (e.g. using PCM). The package I inten= d to use
> is Gaussian 09. I would be very glad if anyone could point me to relev= ant
> literatures
> I thank you for your Help.> =A0 =A0 =A0http://www.ccl.net/= cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-b= in/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub= _unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt>
>



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY]![ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST]![ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
John McKelv= ey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel]![gmail.com
--e89a8ff2447f8f8ff204ba95b78a-- From owner-chemistry@ccl.net Tue Mar 6 14:16:00 2012 From: "Jan H Jensen jhjensen]![chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: recent important articles Message-Id: <-46432-120306135209-5229-2X83GAVIEedvRl+Xn+blrQ^server.ccl.net> X-Original-From: "Jan H Jensen" Date: Tue, 6 Mar 2012 13:52:08 -0500 Sent to CCL by: "Jan H Jensen" [jhjensen _ chem.ku.dk] The first (February) issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2012_02_01_archive.html CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. Table of content for the February issue featuring contributions from CCH editors Jan Jensen and Steven Bachrach: Total Synthesis of Oxidized Welwitindolinones and (-)-N-Methylwelwitindolinone C Isonitrile Roaming-mediated isomerization in the photodissociation of nitrobenzene Assessment of Popular DFT and Semiempirical Molecular Orbital Techniques for Calculating Relative Transition State Energies and Kinetic Product Distributions in Enantioselective Organocatalytic Reactions Regiochemical Substituent Switching of Spin States in Aryl(trifluoromethyl)carbenes NMR Structure Determination for Larger Proteins Using Backbone-Only Data Interested in more? There are already several contributions to the March issue and there are many ways to subscribe to updates. http://www.compchemhighlights.org/p/get-cch-updates.html