From owner-chemistry@ccl.net Thu Mar 29 07:59:01 2012 From: "Zoubeyr Boudene zoubeyr.boudene#%#ifpen.fr" To: CCL Subject: CCL:G: IRC calculations on Gaussian Message-Id: <-46590-120329044053-16242-Pz8wOHYgfJQn7t7vbQMueA(_)server.ccl.net> X-Original-From: "Zoubeyr Boudene" Date: Thu, 29 Mar 2012 04:40:50 -0400 Sent to CCL by: "Zoubeyr Boudene" [zoubeyr.boudene{:}ifpen.fr] Hello, I'm a Phd-student at the French Institute of Petroleum (IFPEN). Im carrying on calculations on Iron complexes reactivity. Ive already obtain a transition state and Im trying to perform an IRC calculation using Gaussian9. The input heading is as follows: %chk=checkpoint.chk %Mem=20GB %NProcShared=16 #P IRC(rcfc,forward,maxpoints=10) scf=(maxcycle=6000,Conver=6) uM06/gen pseudo=read Nosymm geom=Check guess=Read The job is supposed to read atoms coordinates and frequencies from the file checkpoint.chk (containing the TS properties) and generate 10 geometrical steps. The problem is that the calculation ends after the very first step and I obtain the following message at the output file: ------------------------------------------------------------------- Cartesian Forces: Max 0.000431700 RMS 0.000069619 Leave Link 716 at Thu Mar 29 05:53:07 2012, MaxMem= 2684354560 cpu: 0.9 (Enter /soft/irsrvsoft1/expl/Gaussian_09_PGI80Lib105/g09/l9999.exe) This type of calculation cannot be archived. THOSE WHO ARE UNABLE TO LEARN FROM PAST MEETINGS ARE CONDEMNED TO REPEAT THEM. Job cpu time: 10 days 14 hours 38 minutes 3.8 seconds. File lengths (MBytes): RWF= 993 Int= 0 D2E= 0 Chk= 82 Scr= 1 Normal termination of Gaussian 09 at Thu Mar 29 05:53:07 2012. I would like to know the origin of the problem and how to fix it. Sincerely yours, Zoubeyr Boudene IFPEN, Rueil-Malmaison France From owner-chemistry@ccl.net Thu Mar 29 11:28:00 2012 From: "Jaccob Madhavan chemjaccob(~)yahoo.co.in" To: CCL Subject: CCL: calcualtion of kinetic isotopic effect values Message-Id: <-46591-120329112655-15220-ee9Z4tw7a2KL1DO1P/sxVQ++server.ccl.net> X-Original-From: "Jaccob Madhavan" Date: Thu, 29 Mar 2012 11:26:51 -0400 Sent to CCL by: "Jaccob Madhavan" [chemjaccob _ yahoo.co.in] Dear Friends, Greetings! For the calculation of kinetic isotopic effect(KIE) values, optimization with deutrium is needed or only frequency calcualtion is enough. Any help in this regard will be highily appreciated. with best regards Jaccob From owner-chemistry@ccl.net Thu Mar 29 12:31:01 2012 From: "Joe Corkery jcorkery(~)eyesopen.com" To: CCL Subject: CCL: Congratulations to the winners of the OpenEye Outstanding Junior Faculty Award Message-Id: <-46592-120329120751-22605-m8lXXb/GjNTeJzAkirBL3w_-_server.ccl.net> X-Original-From: Joe Corkery Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_CB9A010A16B58jcorkeryeyesopencom_" Date: Thu, 29 Mar 2012 09:07:38 -0700 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery[-]eyesopen.com] --_000_CB9A010A16B58jcorkeryeyesopencom_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable OpenEye Scientific Software congratulates the winners of the OpenEye Outsta= nding Junior Faculty Award at the Spring 2012 ACS National Meeting in San D= iego. Dr. Anthony Nicholls, President and CEO of OpenEye, was on hand to present = each recipient with their award certificate and $1,000 cash prize during th= e COMP division poster session on March 27, 2012. The Outstanding Junior Faculty are: * Prof. Patrick Charbonneau, Duke University Monte Carlo Algorithms for Studying Microphase and Cluster-Crystal Formers * Prof. Lasse Jensen, Penn State University Understanding and Controlling Molecule-plasmon Interactions * Prof. Li Xiaosong, University of Washington Energy-specific Linear Response TDHF/TDDFT Method for Calculating High-ener= gy Excited States * Prof. Joseph E. Subotnik, University of Pennsylvania Surface Hopping Predicts The Incorrect Scaling for Marcus=92s Electron Tran= sfer Rate: Why Decoherence Saves the Day About the OpenEye Outstanding Junior Faculty Award The OpenEye Outstanding Junior Faculty Award is designed to recognize the w= ork of and assist rising new faculty members in gaining visibility within t= he COMP community. The Award is granted semi-annually at the ACS National M= eetings. The application deadline for the Fall 2012 Philadelphia meeting is= Tuesday, April 3rd. For application and eligibility details, please visit:= http://web2011.acscomp.org/awards/the-comp-acs-outstanding-junior-faculty-= award. About OpenEye Scientific Software OpenEye Scientific Software Inc. is a privately held company headquartered = in Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg,= France and Tokyo, Japan. It was founded in 1997 to develop large-scale mol= ecular modeling applications and toolkits. Primarily aimed towards drug dis= covery and design, areas of application include: * chemical informatics * structure generation * shape comparison * docking * fragment replacement * electrostatics * crystallography * visualization The software is designed for scientific rigor, as well as speed, scalabilit= y and platform independence. OpenEye makes most of its technology available= as toolkits - programming libraries suitable for custom development. OpenE= ye software typically is distributable across multiple processors, supports= 64-bit processing, and runs on Linux, Windows and Mac OS X. For further in= formation on the company and its products, see www.eyesopen.com For additional information Joseph Corkery, M.D. Vice President, Business Development +1-505-473-7385 x76 jcorkery:eyesopen.com --_000_CB9A010A16B58jcorkeryeyesopencom_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
OpenEye Sc= ientific Software congratulates the winners of the OpenEye Outs= tanding Junior Faculty Award at the Spring 2012 ACS National Meeting in San= Diego.

Dr. Anthony Nicholls, President and CEO of OpenEye, w= as on hand to present each recipient with their award certificate and $1,00= 0 cash prize during the COMP division poster session on March 27, 2012.

=

The= Outstanding Junior Faculty are:

  • Pro= f. Patrick Charbonneau, Duke University
    Monte Carlo Algorithms for St= udying Microphase and Cluster-Crystal Formers

  • Prof. Lasse J= ensen, Penn State University
    Understanding and Controlling Molecule-p= lasmon Interactions

  • Prof. Li Xiaosong, University of Washin= gton
    Energy-specific Linear Response TDHF/TDDFT Method for Calculatin= g High-energy Excited States

  • Prof. Joseph E. Subotnik, Univ= ersity of Pennsylvania
    Surface Hopping Predicts The Incorrect Scaling= for Marcus=92s Electron Transfer Rate: Why Decoherence Saves the Day

About the OpenEye Outstanding Junior Faculty Award

Th= e OpenEye Outstanding Junior Faculty Award is designed to recognize the wor= k of and assist rising new faculty members in gaining visibility within the= COMP community. The Award is granted semi-annually at the ACS National Mee= tings. The application deadline for the Fall 2012 Philadelphia meeting is T= uesday, April 3rd. For application and eligibility details, please visit:&n= bsp;http://web2011.acscomp.org/awards/the-comp-acs-outstanding-juni= or-faculty-award.

About OpenEye Scientific Software

Op= enEye Scientific Software Inc. is a privately held company headquartered in= Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg, F= rance and Tokyo, Japan. It was founded in 1997 to develop large-scale molec= ular modeling applications and toolkits. Primarily aimed towards drug disco= very and design, areas of application include:

The software is designed = for scientific rigor, as well as speed, scalability and platform independen= ce. OpenEye makes most of its technology available as toolkits - programmin= g libraries suitable for custom development. OpenEye software typically is = distributable across multiple processors, supports 64-bit processing, and r= uns on Linux, Windows and Mac OS X. For further information on the company = and its products, see www.eyesopen.com

For additional information

Joseph Corker= y, M.D.
Vice President, Business Development
+1-505-473-7385 x76<= br>jcorkery:eyesopen.com


--_000_CB9A010A16B58jcorkeryeyesopencom_-- From owner-chemistry@ccl.net Thu Mar 29 13:05:00 2012 From: "=?iso-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jordi.villafreixa/./gmail.com" To: CCL Subject: CCL: calcualtion of kinetic isotopic effect values Message-Id: <-46593-120329125917-27432-em5pTxP4vAx7vF19ejgd+A---server.ccl.net> X-Original-From: =?iso-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Type: multipart/alternative; boundary=Apple-Mail-2-398341299 Date: Thu, 29 Mar 2012 18:59:03 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: =?iso-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jordi.villafreixa=-=gmail.com] --Apple-Mail-2-398341299 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 just calculation on H, as the PES is identical. So, frequency calculation is enough On Mar 29, 2012, at 5:26 PM, Jaccob Madhavan chemjaccob(~)yahoo.co.in = wrote: >=20 > Sent to CCL by: "Jaccob Madhavan" [chemjaccob _ yahoo.co.in] > Dear Friends, >=20 > Greetings! For the calculation of kinetic isotopic effect(KIE) values, = optimization with deutrium is needed or only frequency calcualtion is = enough. Any help in this regard will be highily appreciated. >=20 > with best regards > Jaccob >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --=20 Jordi Vill=E0 i Freixa Computational Biochemistry and Biophysics lab GRIB/IMIM/UPF - PRBB C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: jordi.villa[A]upf.edu=20 web: http://cbbl.imim.es http://www.ascidea.com Twitter: [A]JVillaFreixa [A]aScidea Linkedin: http://es.linkedin.com/in/jordivf --Apple-Mail-2-398341299 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 just = calculation on H, as the PES is identical.
So, frequency calculation = is enough

On Mar 29, 2012, at 5:26 PM, Jaccob = Madhavan chemjaccob(~)yahoo.co.in wrote:


Sent to CCL by: "Jaccob  Madhavan" = [chemjaccob _ yahoo.co.in]
Dear Friends,

Greetings! For the = calculation of kinetic isotopic effect(KIE) values, optimization with = deutrium is needed or only frequency calcualtion is enough. Any help in = this regard will be highily appreciated.

with best = regards
Jaccob



-=3D This is automatically added to = each message by the mailing script =3D-
To recover the email address = of the author of the message, please change
the strange characters on = the top line to the [A] sign. You can also
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RTFI: http://www.cc= l.net/chemistry/aboutccl/instructions/


<= /div>


-- 
Jordi Vill=E0 = i Freixa
Computational Biochemistry and Biophysics lab GRIB/IMIM/UPF = - PRBB
C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
Tel: +34 93 = 316 0504 // Fax: +34 93 316 0550
e-mail: jordi.villa[A]upf.edu 
web: = http://cbbl.imim.es http://www.ascidea.com
Twitter: = [A]JVillaFreixa [A]aScidea
Linkedin: http://es.linkedin.com/in/jordi= vf

= --Apple-Mail-2-398341299-- From owner-chemistry@ccl.net Thu Mar 29 15:46:01 2012 From: "Sanjay Bharathwaj computationalchemist.:.gmail.com" To: CCL Subject: CCL: Possible questions? Message-Id: <-46594-120329123925-30842-bdq0JDAV4heSV8GMhZU1Bw- -server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=e89a8f642ec674204404bc645d73 Date: Thu, 29 Mar 2012 18:39:17 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist() gmail.com] --e89a8f642ec674204404bc645d73 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I have been invited recently to conduct a job interview based on computational chemistry for a start-up company where the role is to conduct research based on computational techniques. I have something on my mind, but i would like you all to share possible technical questions in computational chemistry, that one can use to handle PHD candidates. (apart from asking them to explain their work) Thanks in Advance Dr. Sanjay., -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --e89a8f642ec674204404bc645d73 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

I have been inv= ited recently to conduct a
job interview based on computati= onal chemistry
for a start-up company where the role is to = conduct research
based on computational techniques.

I have something on my mind, but i would like you all to
share possible=A0technical questions in computational chemistry, that= one=A0
can use to handle PHD candidates. (apart from asking them to exp= lain their work)

Thanks in Advance
Dr. Sanjay.,=A0

--
Regards,
Dr. San= jay Bharathwaj Kumar,
Dharmendra Institute of Technology,
India.
--e89a8f642ec674204404bc645d73-- From owner-chemistry@ccl.net Thu Mar 29 16:21:01 2012 From: "Sebastian Kozuch kozuchs,,yahoo.com" To: CCL Subject: CCL: calcualtion of kinetic isotopic effect values Message-Id: <-46595-120329131744-10398-v7BNGxGL3Ap5YFxaW15iGQ/a\server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="630850330-1120368410-1333041429=:4455" Date: Thu, 29 Mar 2012 10:17:09 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs(0)yahoo.com] --630850330-1120368410-1333041429=:4455 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Although the X-D and X-H bond distances are very slightly different, I don'= t know any program that can calculate that difference. The optimizations ar= e done in the Born-Oppenheimer approximation and the mass of the nuclei are= not taken into account, only their charge. As far as I know (and as far as= all QM software know) deuterium and protium have the same charge, so no re= optimization is necessary. Anyway, the error of the theoretical method is w= ay bigger than the difference in the real bond lengths.=0A=0AMaybe this is = a good opportunity to recommend an essay by Simmons and Hartwig that just a= ppeared in ACIE regarding the analysis of the KIE for inter and intramolecu= lar competition, an issue that has been overlooked an has been the root of = more than one error:=0A Angewandte Chemie International Edition 2012, 51, 3= 066=E2=80=933072.=0ABest,=0ASebastian.=0A=0A=0A=0A_________________________= _______=0A From: Jaccob Madhavan chemjaccob(~)yahoo.co.in =0ATo: "Kozuch, Sebastian " =0ASent: Th= ursday, March 29, 2012 5:26 PM=0ASubject: CCL: calcualtion of kinetic isoto= pic effect values=0A =0A=0ASent to CCL by: "Jaccob=C2=A0 Madhavan" [chemjac= cob _ yahoo.co.in]=0ADear Friends,=0A=0AGreetings! For the calculation of k= inetic isotopic effect(KIE) values, optimization with deutrium is needed or= only frequency calcualtion is enough. Any help in this regard will be high= ily appreciated.=0A=0Awith best regards=0AJaccob=0A=0A=0A=0A-=3D This is au= tomatically added to each message by the mailing script =3D-=0ATo recover t= he email address of the author of the message, please change=0Athe strange = characters on the top line to the ~ sign. You can also=0Alook up the X-Orig= inal-From: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY ~ c= cl.net or use:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_c= cl_message=0A=0A= =0A=C2=A0 =C2=A0 =C2=A0=0A= =0A=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemis= try/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://www.ccl= .net=0A=0A=0AConferences: http://server.ccl.ne= t/chemistry/announcements/conferences/=0A=0ASearch Messages: http://www.ccl= .net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CCL wit= h 5.7.1 error, check:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.tx= t=0A=0A--630850330-1120368410-1333041429=:4455 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Although the <= span>X-D and X-H bond distances are very slightly different, I= don't know any program that can calculate that difference. The optimizatio= ns are done in the Born-Oppenheimer approximation and the mass of the nucle= i are not taken into account, only their charge. As far as I know (and as f= ar as all QM software know) deuterium and protium have the same charge, so = no reoptimization is necessary. Anyway, the error of the theoretical method= is way bigger than the difference in the real bond lengths.

Maybe this is a good opportunity to re= commend an essay by Simmons and Hartwig that just appeared in ACIE regardin= g the analysis of the KIE for inter and intramolecular competition, an issu= e that has been overlooked an has been the root of more than one error:
Angewandte Chemie International Edition<= /i> 2012, 51, 3066=E2=80=933072.
=0A
=0A =0A
Best,
Sebastian.

From: Jaccob Madhavan chemjaccob(~)yahoo.co.in <own= er-chemistry ~ ccl.net>
To: "Kozuch, Sebastian " <kozuchs ~ yahoo.com>
Sent: Thursday, March 29, 2012 5:2= 6 PM
Subject: CCL: cal= cualtion of kinetic isotopic effect values

=0A
Se= nt to CCL by: "Jaccob  Madhavan" [chemjaccob _ yahoo.co.in]
Dear Fr= iends,

Greetings! For the calculation of kinetic isotopic effect(KIE= ) values, optimization with deutrium is needed or only frequency calcualtio= n is enough. Any help in this regard will be highily appreciated.

wi= th best regards
Jaccob



-=3D This is automatically added t= o each message by the mailing script =3D-
To recover the email address o= f the author of the message, please change
the strange characters on the= top line to the ~ sign. You can also
look up the X-Original-From: line = in the mail header.

E-mail to subscribers: CHEMISTRY ~ ccl.net or u= se:
     =

E-mail to administrators: CHEMISTRY-REQUEST ~ ccl.net or= use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_mes= sage
      http://www.= ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at= : http://www.ccl.net
Conferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/

Search Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your ma= il bounces from CCL with 5.7.1 error, check:
      http:/= /www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutcc= l/instructions/




--630850330-1120368410-1333041429=:4455-- From owner-chemistry@ccl.net Thu Mar 29 22:01:00 2012 From: "Yesu Feng immanuelsvera,gmail.com" To: CCL Subject: CCL: about spinspin and mixed for pseudo potential in NMR calculation Message-Id: <-46596-120329220012-15460-uFr9CYZH50mgZFKcIqgvlg-#-server.ccl.net> X-Original-From: "Yesu Feng" Date: Thu, 29 Mar 2012 22:00:09 -0400 Sent to CCL by: "Yesu Feng" [immanuelsvera[]gmail.com] Dear all, I am using nmr=(giao,spinspin,mixed) b3lyp/genecp scf=tight integral= (grid=ultrafine) to perform a mixed two step calculation of j couplings. The system has a Pt atom, for which I use pseudo potential, so the input goes like: #p nmr=(giao,spinspin,mixed) b3lyp/genecp scf=tight integral=(grid=ultrafine) ....... 0 1 molecule structure -C -H -O -N 6-311+G(d,p) **** -Pt lanl2dz **** -Pt F 1 1.00 0.9930000000D+00 0.1000000000D+01 **** -Pt lanl2dz and the output error is Pseudo-potential data read from chk file. Unrecognized value of NGIC in SetDat. Error termination via Lnk1e in /home/dbchem/mapete/chem/g09-A.02-ifort- static/g09/l301.exe at Wed Mar 28 23:04:04 2012. it seems the second step goes wrong when trying to read pseudo potential from the chk file. Has anyone encountered the similar problem? thank you very much! Immanuel