From owner-chemistry@ccl.net Sat Aug 4 03:06:00 2012 From: "Elham Abdolhamidi flight.66.ab],[gmail.com" To: CCL Subject: CCL:G: Gaussian Message-Id: <-47317-120804025936-28434-IUvi+NwhUtjJ9X94q3glPw**server.ccl.net> X-Original-From: "Elham Abdolhamidi" Date: Sat, 4 Aug 2012 02:59:33 -0400 Sent to CCL by: "Elham Abdolhamidi" [flight.66.ab^_^gmail.com] Dear Members; I'm working with gaussian and when I calculate the energy levels of Polypyrrole(using PBC), for 10 levels (using 5/103=10) , I find the HOMO and LUMO in k=0,0,0 :-3.529 ev and -1.954 ev respectively. But when I find the energy levels in gamma point I find -15.863 ev and -9.8 ev for HOMO and LUMO. I wanted to know why the energies in gamma point and in k=0,0,0 are not the same. Regards. From owner-chemistry@ccl.net Sat Aug 4 07:23:00 2012 From: "may abdelghani may01dz**yahoo.fr" To: CCL Subject: CCL: Re : CCL: %age composition of fragments Message-Id: <-47318-120804065522-1427-6ty23C/ez9ysQ4yY9zRPgw:-:server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="-559650306-1219447079-1344077715=:27863" Date: Sat, 4 Aug 2012 11:55:15 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz(0)yahoo.fr] ---559650306-1219447079-1344077715=:27863 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0ATry AOMix=20 http://www.sg-chem.net/aomix/ =0A=0A --- En date de=A0: Ven 3.8.12, meishway linkon meishwaylinkon*_*yahoo.com <= owner-chemistry- -ccl.net> a =E9crit=A0: De: meishway linkon meishwaylinkon*_*yahoo.com Objet: CCL: %age composition of fragments =C0: "Abdelghani, May " Date: Vendredi 3 ao=FBt 2012, 10h31 Sent to CCL by: "meishway=A0 linkon" [meishwaylinkon]|[yahoo.com] Hello ! =A0 =A0 =A0 =A0 =A0 can someone tell me how to calculate %age composition o= f donor and acceptor fragements for a donor molecules, e.g. if there is a d= onor X , it has two donor fragment=A0 a, b=A0 and one acceptor fragemen c ,= then how i will calculate that HOMO of X donor have how much contribution = > from a, b and c . -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0---559650306-1219447079-1344077715=:27863 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A<= p class=3D"MsoNormal" style=3D"text-align:left;direction:ltr;unicode-bidi:e= mbed">Try AOMix
=

http://www.sg-chem.net/aomix/

=0A=0A

--- E= n date de : Ven 3.8.12, meishway linkon meishwaylinkon*_*yahoo.com = <owner-chemistry- -ccl.net> a =E9crit :

De: meishway linkon meishwaylinkon*_*yahoo.com <owner-c= hemistry- -ccl.net>
Objet: CCL: %age composition of fragments
=C0: "= Abdelghani, May " <may01dz- -yahoo.fr>
Date: Vendredi 3 ao= =FBt 2012, 10h31


Sent to CCL by: "meish= way  linkon" [meishwaylinkon]|[yahoo.com]
Hello !
    =       can someone tell me how to calculate %age composition = of donor and acceptor fragements for a donor molecules, e.g. if there is a = donor X , it has two donor fragment  a, b  and one acceptor frage= men c , then how i will calculate that HOMO of X donor have how much contri= bution from a, b and c .



-=3D This is automatically added to each message by the mailing script =3D-
To recover the email a= ddress of the author of the message, please change
the strange character= s on the top line to the - - sign. You can also
look up the X-Original-Fro= m: line in the mail header.

E-mail to subscribers: CHEMISTR= Y- -ccl.net or use:
      http://www.ccl.net/cgi-bin= /ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net or use
      ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscr= ibe:
      http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br>
Search Messages: http://www.ccl.net/chemistry/searchccl/index.= shtml
=       http://www.ccl.net/spammers.txt

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


=
---559650306-1219447079-1344077715=:27863-- From owner-chemistry@ccl.net Sat Aug 4 12:27:01 2012 From: "Jan Jensen jhjensen|,|chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: July issue Message-Id: <-47319-120804061534-32146-pCLu+6gKjFDIg5igb/zJAQ a server.ccl.net> X-Original-From: "Jan Jensen" Date: Sat, 4 Aug 2012 06:15:31 -0400 Sent to CCL by: "Jan Jensen" [jhjensen|a|chem.ku.dk] The July issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2012_07_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 this issue features contributions from CCH editors Steven Bachrach, Grant Hill, and Robert Paton: Aromatic Transition States in Nonpericyclic Reactions: Anionic 5 -Endo Cyclylizations are Aborted Sigmatropic Shifts http://www.compchemhighlights.org/2012/07/aromatic-transition-states-in.html Chemical Networks (Triple Header!) http://www.compchemhighlights.org/2012/07/chemical-networks-triple-header.html A Paramagnetic Bonding Mechanism for Diatomics in Strong Magnetic Fields http://www.compchemhighlights.org/2012/07/a-paramagnetic-bonding-mechanism-for.html Dynamic Origin of the Stereoselectivity of a Nucleophilic Substitution Reaction http://www.compchemhighlights.org/2012/07/dynamic-origin-of-stereoselectivity-of.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html From owner-chemistry@ccl.net Sat Aug 4 15:37:00 2012 From: "Dillen, Jan jlmd##sun.ac.za JLMD##sun.ac.za" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47320-120804032930-5868-vw/gNbuF+bUOGeik9S1bsw*server.ccl.net> X-Original-From: "Dillen, Jan " Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Sat, 4 Aug 2012 07:29:12 +0000 MIME-Version: 1.0 Sent to CCL by: "Dillen, Jan [jlmd()sun.ac.za]" If you are seeking a transition state, then one frequency should be negative (imaginary). So your "problem" is only a problem if the lowest frequency is positive. You do not mention the software that you are using, but whatever it is there should be options to thighten the convergence criteria. I suggest to try that first. A negative barrier is mathematically impossible. So either your structure is not a transition state or it is a TS for a different reaction path. Please do an IRC to check. Jan Dillen -----Original Message----- > From: owner-chemistry+jlmd==sun.ac.za.:.ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za.:.ccl.net] On Behalf Of Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com Sent: 03 August 2012 16:06 To: Dillen, Jan Subject: CCL: Negative Barrier Height Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com] Dear All, I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism? Any suggestions is highly appreciated. Sincerely Bhupesh Kumar Mishra(Ph.D.) UGC-Dr. D. S. Kothari Post Doctoral Fellow Department of Chemical Sciences Tezpur University Tezpur- ASSAM INDIAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige lêers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail. From owner-chemistry@ccl.net Sat Aug 4 16:12:00 2012 From: "Amy J Austin amy_jean_austin*yahoo.com" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47321-120804130105-23880-EQwFv3o0Kmc6bEgkcRRNCg() server.ccl.net> X-Original-From: "Amy J Austin" Date: Sat, 4 Aug 2012 13:01:02 -0400 Sent to CCL by: "Amy J Austin" [amy_jean_austin||yahoo.com] Hello Bhupesh, It sounds like a multi-step reaction in which there is an intermediate that is lower in energy than the reactants, and that you have found the transition state for that intermediate, which is also lower in energy than reactants. Best, Amy > "Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com" wrote: > > Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com] > Dear All, > I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism? > Any suggestions is highly appreciated. > > Sincerely > Bhupesh Kumar Mishra(Ph.D.) > UGC-Dr. D. S. Kothari Post Doctoral Fellow > Department of Chemical Sciences > Tezpur University > Tezpur- ASSAM > INDIA > > From owner-chemistry@ccl.net Sat Aug 4 22:00:01 2012 From: "David Gallagher gallagher.da*gmail.com" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47322-120804170904-9881-0OBvB4FGENHgK7RcBoHSnA|*|server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="------------070609090002050705080006" Date: Sat, 04 Aug 2012 14:09:02 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da|a|gmail.com] This is a multi-part message in MIME format. --------------070609090002050705080006 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Bhupesh, As some other respondents have indicated, if there are no negative vibrations then you have found a (local) energy minimum. A true transition state is indicated by a single negative vibration. There are some suggested strategies for locating transition states posted at http://cacheresearch.com/presentations.html (about halfway down the page). Although these were written for MOPAC, the principles apply to most quantum methods. Once you have characterized the transition state, you should run an intrinsic reaction coordinate (IRC) to verify that it does go to the expected reactants and products, i.e. to make sure that it belongs to the correct reaction path. Good luck. David Gallagher CAChe Research On 8/3/2012 7:05 AM, Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com wrote: > Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com] > Dear All, > I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism? > Any suggestions is highly appreciated. > > Sincerely > Bhupesh Kumar Mishra(Ph.D.) > UGC-Dr. D. S. Kothari Post Doctoral Fellow > Department of Chemical Sciences > Tezpur University > Tezpur- ASSAM > INDIA> > > --------------070609090002050705080006 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Bhupesh,

As some other respondents have indicated, if there are no negative vibrations then you have found a (local) energy minimum.  A true transition state is indicated by a single negative vibration. 

There are some suggested strategies for locating transition states posted at http://cacheresearch.com/presentations.html (about halfway down the page).  Although these were written for MOPAC, the principles apply to most quantum methods.

Once you have characterized the transition state, you should run an intrinsic reaction coordinate (IRC) to verify that it does go to the expected reactants and products, i.e. to make sure that it belongs to the correct reaction path.

Good luck.
David Gallagher
CAChe Research
On 8/3/2012 7:05 AM, Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com wrote:
Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com]
Dear All,
I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism?
 Any suggestions is highly appreciated.

Sincerely
Bhupesh  Kumar Mishra(Ph.D.)
UGC-Dr. D. S. Kothari Post Doctoral Fellow
Department of Chemical Sciences
Tezpur University
Tezpur- ASSAM
INDIAE-mail to subscribers: CHEMISTRY]|[ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST]|[ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

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

--------------070609090002050705080006--