From owner-chemistry@ccl.net Tue Apr 16 00:25:00 2013 From: "Oscar U Ojeda molecular.oscar ~ gmail.com" To: CCL Subject: CCL: MCD TDDFT software recommendation Message-Id: <-48557-130415235359-27229-p8T8UUgnivA9g3SUQ2rfsQ.@.server.ccl.net> X-Original-From: "Oscar U Ojeda" Date: Mon, 15 Apr 2013 23:53:58 -0400 Sent to CCL by: "Oscar U Ojeda" [molecular.oscar()gmail.com] Hi Folks, I would like to gather your recommendations regarding a TDDFT software package that can predict MCD for organic and transition metal compounds. Your feedback is highly appreciated. Oscar Ojeda Research Associate Arizona State University From owner-chemistry@ccl.net Tue Apr 16 07:25:00 2013 From: "Dave Winkler dave.winkler..csiro.au" To: CCL Subject: CCL: AIMECS 13 international medicinal chemistry congress in Taipei, October 15-18 2013 Message-Id: <-48558-130416013144-26391-JS9b6Y1Q5T3Q76NulgrzjQ+*+server.ccl.net> X-Original-From: Dave Winkler Content-Type: multipart/alternative; boundary="Apple-Mail=_A6E52764-1749-4D65-9035-82A3713F1477" Date: Tue, 16 Apr 2013 15:31:29 +1000 Mime-Version: 1.0 (Apple Message framework v1283) Sent to CCL by: Dave Winkler [dave.winkler . csiro.au] --Apple-Mail=_A6E52764-1749-4D65-9035-82A3713F1477 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii This is an excellent international conference in Taipei, organised by = the Asian Federation for Medicinal Chemistry, sponsored by the European = Federation for Medicinal Chemistry, ACS Medicinal Chemistry and IUPAC. See http://www.aimecs13.tw or = http://www.aimecs13.tw/files/AIMECS13%20First%20Circular.pdf for = circular Cheers Dave Prof. Dave Winkler Team Leader Materials Science & Engineering Bayview Ave, Clayton 3169 Bag 10 Clayton South MDC 3169 Phone: +61 3 9545 2477 --Apple-Mail=_A6E52764-1749-4D65-9035-82A3713F1477 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii This = is an excellent international conference in Taipei, organised by the = Asian Federation for Medicinal Chemistry, sponsored by the European = Federation for Medicinal Chemistry, ACS Medicinal Chemistry and = IUPAC.

See http://www.aimecs13.tw or http= ://www.aimecs13.tw/files/AIMECS13%20First%20Circular.pdf for = circular

Cheers
Dave
Prof. Dave Winkler
Team = Leader
Materials Science & Engineering
Bayview Ave, Clayton = 3169
Bag 10 Clayton South MDC 3169
Phone: +61 3 9545 = 2477



= --Apple-Mail=_A6E52764-1749-4D65-9035-82A3713F1477-- From owner-chemistry@ccl.net Tue Apr 16 08:00:00 2013 From: "Ruud Kenneth kenneth.ruud^^^uit.no" To: CCL Subject: CCL: MCD TDDFT software recommendation Message-Id: <-48559-130416043243-11039-0Oua38rbQh4imOlDcufFfA!A!server.ccl.net> X-Original-From: Ruud Kenneth Content-ID: Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 16 Apr 2013 08:32:34 +0000 MIME-Version: 1.0 Sent to CCL by: Ruud Kenneth [kenneth.ruud#uit.no] Dear Oscar, Dalton (www.daltonprogram.org) can do this, but note that the program is restricted to closed-shell molecules. With some shameless self-promotion, you can check out "The ab initio calculation of magnetic circular dichroism.": T.Kjærgaard, S.Coriani and K.Ruud. WIREs Comput.Mol.Sci. 2, 443 (2012). Best regards, Kenneth Kenneth Ruud Director, CTCC President, Norwegian Chemical Society Telephone: +47 77623101 http://www.ctcc.no/people/senior-scientists/ruud/index.html On Apr 16, 2013, at 5:53 AM, Oscar U Ojeda molecular.oscar ~ gmail.com wrote: > > Sent to CCL by: "Oscar U Ojeda" [molecular.oscar()gmail.com] > Hi Folks, > I would like to gather your recommendations regarding a TDDFT software package that can predict MCD for organic and transition metal compounds. > Your feedback is highly appreciated. > Oscar Ojeda > Research Associate > Arizona State University> > From owner-chemistry@ccl.net Tue Apr 16 08:34:00 2013 From: "Zakieh Yousefi zakiehyousefi##yahoo.com" To: CCL Subject: CCL: Negative Frequencies in Tetrammer constructed by copper complex Message-Id: <-48560-130416074610-14937-fbiJ8S24KCoLl+21ZxNysg_-_server.ccl.net> X-Original-From: Zakieh Yousefi Content-Type: multipart/alternative; boundary="1862148595-1383920138-1366112761=:34973" Date: Tue, 16 Apr 2013 12:46:01 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Zakieh Yousefi [zakiehyousefi#,#yahoo.com] --1862148595-1383920138-1366112761=:34973 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Yes, I did optimization of the structure at B3lyp with 6-31g(d,p) and ECP f= or Cu atom and computed freq with them.=0A=0A=0A=0A________________________= ________=0A From: Andrew Yeung andrew.yeung*chem.tamu.edu =0ATo: "Yousefi, Zakieh " =0ASent= : Monday, 15 April 2013, 13:11:37=0ASubject: CCL: Negative Frequencies in T= etrammer constructed by copper complex=0A =0A=0A=0ADid you optimize the str= ucture at the given theory/basis set to begin with?=0A=0AAndrew Yeung=0ADon= ald J. Darensbourg Research Group=0ADepartment of Chemistry, Texas A&M Univ= ersity=0A3255 TAMU=0ACollege Station, TX 77843-3255 Tel: 979 845 4837=0AFax= : 979 845 0158=0AOn 2013-04-15 1:34 PM, Victor Rosas Garcia rosas.victor(!)= gmail.com wrote:=0A=0Awhat basis set did you use? If you are using ECPs (I'= m guessing due to the presence of Cu) I am not surprised you got many imagi= nary frequencies.=A0 Same thing has happened to me in the past when using E= CPs (although not specifically with Cu).=0A>=0A>=0A>=0A>=0A>2013/4/14 zboro= wsk[#]chemia.uj.edu.pl =0A>=0A>=0A>>Sent to CCL = by: zborowsk]^[chemia.uj.edu.pl=0A>>=0A>>=0A>>>=0A>>> Sent to CCL by: "Zaki= eh =A0Yousefi" [zakiehyousefi/./yahoo.com]=0A>>>=0A>>> Dear Sir/Madam=0A>>>= =0A>>> Several month ago, I had a problem with computation=0A = of frequencies of=0A>>> H-bonded tetramer constructed by Cu complex. I got= =0A such an error:=0A>>>=0A>>> =A0dumping /fiocom/, unit =3D 3= NFiles =3D =A0 =A0 1 SizExt =3D =A0=0A =A0524288 WInBlk =3D= =0A>>> =A0 512=0A>>> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0defal =3D T Lst= Wrd =3D =A0 =A0 =A0 67072=0A FType=3D2 FMxFil=3D10000=0A>>>=0A= >>> =A0Number =A0 =A0 =A0 =A0 =A0 0=0A>>> =A0Base =A0 =A0 =A0 =A0 20480=0A>= >> =A0End =A0 =A0 =A0 =A0 =A067072=0A>>> =A0End1 =A0 =A0 =A0 =A0 67072=0A>>= > =A0Wr Pntr =A0 =A0 =A020480=0A>>> =A0Rd Pntr =A0 =A0 =A020480=0A>>> =A0Le= ngth =A0 =A0 =A0 46592=0A>>> =A0Error termination in NtrErr:=0A>>> =A0NtrEr= r called from FIOCnC.=0A>>>=0A>>> After Consultation with CCl subscriber, I= ran the=0A program with linux,=0A>>> Now, I have 67 negative = frequencies,=0A>>=0A>>=0AWow, a New World Record, I think=0A>>=0A>>Sorry, b= ut i norder to help =A0you one must see your result, I=0A mean o= ne must=0A>>see the structure you calculated.=0A>>=0A>>=0A>>> Of =A0course = the compound has been=0A>>> optimized and then Stable=3Drepopt has been don= e for=0A it.=0A>>>=0A>>> %chk=3D3Cu-pydc2.chk=0A>>> =A0%mem=3D= 3000MB=0A>>> =A0%nprocshared=3D4=0A>>> =A0Will use up to =A0 =A04 processor= s via shared memory.=0A>>>=0A =A0-----------------------------= -----------------------------------------=0A>>> =A0#p freq=3Dnoraman b3lyp = chkbas geom=3Dallcheck=0A scf=3D(direct,maxcycle=3D400,ti=0A>>= > =A0ght)=0A>>> =A0.=0A>>> =A0.=0A>>> =A0.=0A>>> =A0.=0A>>> =A0.=0A>>> =A0S= toichiometry =A0 =A0C44H32Cu4N16O16(5)=0A>>> =A0Framework group =A0CI[X(C44= H32Cu4N16O16)]=0A>>> =A0Deg. of freedom =A0 165=0A>>> =A0Full point group = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 CI =A0 =A0 =A0NOp =A0 2=0A>>> =A0Largest Ab= elian subgroup =A0 =A0 =A0 =A0 CI =A0 =A0 =A0NOp =A0 2=0A>>> =A0Largest con= cise Abelian subgroup CI =A0 =A0 =A0NOp =A0 2=0A>>> =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0Standard orientation:>=0A>>>=0A>>>=0A>>=0A>>=0A= >>=0A--=0A>>=0A>>https://www.youtube.com/watch?v=3DtKmW1cLzo8Q=0A>>=0A>>=0A= >>Krzysztof K. Zborowski=0A>>Faculty of Chemistry=0A>>Jagiellonian Universi= ty=0A>>3 Ingardena Street=0A>>30-060 Krakow=0A>>Poland=0A>>phone: +48(12)63= 2-4888 ext. 2064 or 2067=0A>>fax: =A0+48(12)634-05-15=0A>>email: zborowsk:c= hemia.uj.edu.pl=0A>>gg 3817259=0A>>skype kzys70=0A>>www.chemia.uj.edu.pl/~z= borowsk=0A>>=0A>>=0A>>=0A>>=0A>>=0A>>E-mail to subscribers: CHEMISTRY:_:ccl= .net or use:=0A>>=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e=0A>>=0A>>E-mail to administrators: CHEMISTRY-REQUEST:_:ccl.net or use=0A>= >=A0 =A0 =A0=0A>>=0A>>Subsc= ribe/Unsubscribe:=0A>>=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sh= tml=0A>>=0A=0A>>=0A= >>Job: http://www.ccl.net/jobs=0A>>Conferences: http://server.ccl.net/chemi= stry/announcements/conferences/=0A>>=0A>>Search Messages: http://www.ccl.ne= t/chemistry/searchccl/index.shtml=0A>>=0A>>=A0 =A0 =A0 http://www.ccl.net/s= pammers.txt=0A>>=0A>>RTFI: http://www.ccl.net/chemistry/aboutccl/instructio= ns/=0A>>=0A>>=0A>>=0A>>=0A>>=0A> --1862148595-1383920138-1366112761=:34973 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Yes, I did optimization of the structure at B3lyp with 6-31g(d,p) and ECP= for Cu atom and computed freq with them.

=
From: Andr= ew Yeung andrew.yeung*chem.tamu.edu <owner-chemistry**ccl.net>
= To: "Yousefi, Zakieh = " <zakiehyousefi**yahoo.com>
Subject: CCL: Negative Frequencies in Tetramme= r constructed by copper complex

=0A =0A=0A =0A =0A
=0A
Did you optimize the structure at the=0A gi= ven theory/basis set to begin with?
=0A 
Andrew Yeung=0ADonald J. Darensbourg Research Group=0ADepart=
ment of Chemistry, Texas A&M University=0A3255 TAMU=0ACollege Station, =
TX 77843-3255=0A=0ATel: 979 845 4837=0AFax: 979 845 0158
=0A On 2= 013-04-15 1:34 PM, Victor Rosas Garcia=0A rosas.victor(!)gmail.com wro= te:
=0A
=0A
=0A
what basis set did you use? If you are using ECPs=0A (I'm guessi= ng due to the presence of Cu) I am not surprised you=0A got many ima= ginary frequencies.  Same thing has happened to me=0A in the pa= st when using ECPs (although not specifically with Cu).
=0A
= =0A

=0A
=0A =
2013/4/14 zborowsk[#]chemia.uj.edu= .pl=0A <owner-chemistry:_:ccl.net>
=0A <= blockquote class=3D"yiv1508143288gmail_quote" style=3D"margin:0 0 0 .8ex;bo= rder-left:1px #ccc solid;padding-left:1ex;">
=0A Sent to CCL = by: zborowsk]^[chemia.uj.edu.pl
=0A

=0A >
=0A > Sent to CCL by: "= Zakieh  Yousefi" [zakiehyousefi/./yahoo.com]
=0A >
=0A= > Dear Sir/Madam
=0A >
=0A = > Several month ago, I had a problem with computation=0A = of frequencies of
=0A > H-bonded tetramer constructed = by Cu complex. I got=0A such an error:
=0A >= ;
=0A >  dumping /fiocom/, unit =3D 3 NFiles =3D &n= bsp;   1 SizExt =3D  =0A  524288 WInBlk =3D
= =0A >   512
=0A >     &nb= sp;              defal =3D T LstWrd =3D =       67072=0A FType=3D2 FMxFil=3D10000
=0A = >
=0A >  Number      = ;     0
=0A >  Base       =   20480
=0A >  End        =  67072
=0A >  End1        = ; 67072
=0A >  Wr Pntr      20480=0A >  Rd Pntr      20480
=0A = >  Length       46592
=0A &g= t;  Error termination in NtrErr:
=0A >  NtrErr= called from FIOCnC.
=0A >
=0A > Afte= r Consultation with CCl subscriber, I ran the=0A program with = linux,
=0A > Now, I have 67 negative frequencies,
=0A=
=0A
=0A Wow, a New World Reco= rd, I think
=0A
=0A Sorry, but i norder to hel= p  you one must see your result, I=0A mean one must
=0A = see the structure you calculated.
=0A

=0A > Of  course the compound= has been
=0A > optimized and then Stable=3Drepopt has b= een done for=0A it.
=0A >
=0A = > %chk=3D3Cu-pydc2.chk
=0A >  %mem=3D3000MB=0A >  %nprocshared=3D4
=0A > &nb= sp;Will use up to    4 processors via shared memory.
=0A = >=0A  ----------------------------------------= ------------------------------
=0A >  #p freq=3Dnor= aman b3lyp chkbas geom=3Dallcheck=0A scf=3D(direct,maxcycle=3D= 400,ti
=0A >  ght)
=0A >  .=
=0A >  .
=0A >  .
=0A = >  .
=0A >  .
=0A = >  Stoichiometry    C44H32Cu4N16O16(5)
=0A = >  Framework group  CI[X(C44H32Cu4N16O16)]
=0A = >  Deg. of freedom   165
=0A >  = Full point group                 CI=      NOp   2
=0A >  Largest Ab= elian subgroup         CI      NOp  = ; 2
=0A >  Largest concise Abelian subgroup CI &nbs= p;    NOp   2
=0A >       =                    Standa= rd orientation:>
=0A >
=0A >
= =0A
=0A
=0A
=0A = --
=0A
=0A https://www.yo= utube.com/watch?v=3DtKmW1cLzo8Q
=0A
=0A =0A Krzysztof K. Zborowski
=0A Faculty of Chemis= try
=0A Jagiellonian University
=0A 3 Ingardena= Street
=0A 30-060 Krakow
=0A Poland
=0A = phone: +48(12)632-4888 ext. 2064 or 2067
=0A fax: &nb= sp;+48(12)634-05-15
=0A email: zborowsk:chemia.uj.edu.pl
= =0A gg 3817259
=0A skype kzys70
=0A = www.chemia.uj.edu.pl/~zborowsk
=0A
=0A
=0A
=0A
=0A
= =0A E-mail to subscribers: CHEMISTRY:_:ccl.net=0A or use:
=0A =       http://www.ccl.net/cgi-bin= /ccl/send_ccl_message
=0A
=0A = E-mail to administrators: CHEMISTRY-REQUEST:_:ccl.net=0A or use
=0A =       http://www.ccl.net/cg= i-bin/ccl/send_ccl_message
=0A
=0A = Subscribe/Unsubscribe:
=0A       http://www.ccl.net/chemistry/sub_unsub.shtml
=0A =
=0A Before posting, check wait time at: <= a rel=3D"nofollow" target=3D"_blank" href=3D"http://www.ccl.net/">http://ww= w.ccl.net
=0A
=0A Job: http://www= .ccl.net/jobs
=0A Conferences: http://server.ccl.net/chemistry/announcements/conferences/=0A
=0A Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
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=0A=0A


--1862148595-1383920138-1366112761=:34973-- From owner-chemistry@ccl.net Tue Apr 16 09:10:00 2013 From: "Haya Kornweitz hayak[]ariel.ac.il" To: CCL Subject: CCL: transition state Message-Id: <-48561-130416085430-31072-yC5aiGwXsv5aHEvyCxykkQ,server.ccl.net> X-Original-From: "Haya Kornweitz" Date: Tue, 16 Apr 2013 08:54:28 -0400 Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il] Dear CCLers I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I have found the same transition in all the methods, but the TS is quite similar to my product, similar I mean its geometry and its energy. The TS has one negative frequency while the reactant and product don't have any negative frequency. Can someone explain these results? From owner-chemistry@ccl.net Tue Apr 16 10:47:00 2013 From: "Cina Foroutan-Nejad canyslopus/./yahoo.co.uk" To: CCL Subject: CCL: transition state Message-Id: <-48562-130416104513-21538-bxN0iylOVhLV9wH9tWVGfg * server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="1453005445-363240232-1366123505=:21240" Date: Tue, 16 Apr 2013 15:45:05 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus_-_yahoo.co.uk] --1453005445-363240232-1366123505=:21240 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Haya,=0A=0AI don't know what type of reaction you are studying but it = seems that your initial guess is already the TS! I recommend you running an= IRC calculation to find reactant and product. In addition, be careful abou= t negative frequencies... A negative frequency does not necessarily mean th= e TS of your reaction! Check if the frequency is really along your reaction= coordinate or it is a trivial negative frequency, arising from some inter-= molecular rotational barrier; something like the rotational barriers of alk= yl groups, etc.=0A=0AGood luck,=0ACina=0A++++++++++++++++++++++++++++++++++= ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=0ACina Forouta= n-Nejad, PhD=0Ahttp://muni.academia.edu/CinaForoutanNejad=A0=0A=0A=0A______= __________________________=0A From: Haya Kornweitz hayak[]ariel.ac.il =0ATo: "Foroutan-Nejad, Cina " =0ASent: Tuesday, 16 April 2013, 14:54=0ASubject: CCL: transition = state=0A =0A=0A=0ASent to CCL by: "Haya=A0 Kornweitz" [hayak[]ariel.ac.il]= =0ADear CCLers=0AI study a reaction, and I looked for a TS using QST2 QST3 = and IRC in G09. I =0Ahave found the same transition in all the methods, but= the TS is quite similar =0Ato my product, similar=A0 I mean its geometry a= nd its energy. The TS has one =0Anegative frequency while the reactant and = product don't have any negative =0Afrequency.=0ACan someone explain these r= esults?=0A=0A=0A=0A-=3D This is automatically added to each message by the = mailing script =3D-=0ATo recover the email address of the author of the mes= sage, please change=0Athe strange characters on the top line to the .. sign.= You can also=0A=0A=0A==0A=A0 =A0 =A0 http://www.c= cl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTR= Y-REQUEST..ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_= ccl_message=0A=0A=0A=A0 =A0 =A0 http://www.ccl.net/c= hemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://ww= w.ccl.net=0A=0A=0AConferences: http://server.c= cl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://ww= w.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from CC= L with 5.7.1 error, check:=0A=A0 =A0 =A0=0A= =0A--1453005445-363240232-1366123505=:21240 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Hay= a,

I d= on't know what type of reaction you are studying but it seems that your ini= tial guess is already the TS! I recommend you running an IRC calculation to= find reactant and product. In addition, be careful about negative frequenc= ies... A negative frequency does not necessarily mean the TS of your reacti= on! Check if the frequency is really along your reaction coordinate or it i= s a trivial negative frequency, arising from some inter-molecular rotational barrier; something like the rotational barriers of alkyl groups= , etc.

Good luck,
Cina
= +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++= +++++++++++++++++++++++++
Cina Foroutan-= Nejad, PhD

=
From: Haya Kornwei= tz hayak[]ariel.ac.il <owner-chemistry..ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus..yahoo.co.uk>
= Sent: Tuesday, 16 April 2013, 14:54
Subject: CCL: transition state
=


Sent to CCL by: "Haya  Kornweit= z" [hayak[]ariel.ac.il]
Dear CCLers
I study a reaction, and I looked = for a TS using QST2 QST3 and IRC in G09. I
have found the same transiti= on in all the methods, but the TS is quite similar
to my product, simil= ar  I mean its geometry and its energy. The TS has one
negative fr= equency while the reactant and product don't have any negative
frequenc= y.
Can someone explain these results?



-=3D This is automa= tically added to each message by the mailing script =3D-
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the strange ch= aracters on the top line to the .. sign. You can also
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=
--1453005445-363240232-1366123505=:21240-- From owner-chemistry@ccl.net Tue Apr 16 11:22:00 2013 From: "Brad Rose brose---live.com" To: CCL Subject: CCL: transition state Message-Id: <-48563-130416103842-12663-TA/flhChCzMQ2xt7FjGEXA * server.ccl.net> X-Original-From: "Brad Rose" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 16 Apr 2013 07:38:43 -0700 MIME-Version: 1.0 Sent to CCL by: "Brad Rose" [brose]-[live.com] If your intuition is questioning the TS one way to check the energetics is to do an IRC calculation from the TS going to back to the reactant and one > from the TS going to the product. If you have a reasonable amount of steps you can plot of step # vs energy, and if it is a TS it should be the highest energy along the paths. Brad Rose -----Original Message----- > From: Haya Kornweitz hayak[]ariel.ac.il Sent: Tuesday, April 16, 2013 5:54 AM To: Rose, Bradley Subject: CCL: transition state Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il] Dear CCLers I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I have found the same transition in all the methods, but the TS is quite similar to my product, similar I mean its geometry and its energy. The TS has one negative frequency while the reactant and product don't have any negative frequency. Can someone explain these results?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Apr 16 11:56:00 2013 From: "Alessandro Contini alessandro.contini()unimi.it" To: CCL Subject: CCL: transition state Message-Id: <-48564-130416110031-12494-eKs0HrPPeKh2L1eJ1ZBKBA]*[server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7bit Content-type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 16 Apr 2013 17:00:19 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini,+,unimi.it] Hi, did you try to visualize the vibration associated to the single imaginary frequency you obtained? Does it correspond to the expected transition (i.e. stretching of forming/breaking bonds)? You can visualize frequencies with gaussview or with other open source codes (molekel, molden, webmo...). Sometimes, when starting from a geometry that is to close to the expected product, the TS search algorithm fails and push the geometry toward the product and the single imaginary frequency correspond to some conformational change (i.e. the rotation of an alkyl group). Best regards Alessandro Il 16/04/2013 14:54, Haya Kornweitz hayak[]ariel.ac.il ha scritto: > Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il] > Dear CCLers > I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I > have found the same transition in all the methods, but the TS is quite similar > to my product, similar I mean its geometry and its energy. The TS has one > negative frequency while the reactant and product don't have any negative > frequency. > Can someone explain these results?> > > -- Alessandro Contini, PhD Dipartimento di Scienze Farmaceutiche Sezione di Chimica Generale e Organica "A. Marchesini" Via Venezian, 21 20133 Milano tel. +390250314480 e-mail alessandro.contini**unimi.it skype alessandrocontini From owner-chemistry@ccl.net Tue Apr 16 12:31:00 2013 From: "jp.djukic jp.djukic-x-orange.fr" To: CCL Subject: CCL: transition state Message-Id: <-48565-130416115840-29766-Qi/15h0q537V5ifM5IZkKA[#]server.ccl.net> X-Original-From: "jp.djukic" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Apr 2013 17:58:32 +0200 MIME-Version: 1.0 Sent to CCL by: "jp.djukic" [jp.djukic+/-orange.fr] One way to locate a decent TS candidate for further accurate TS search is to use the linear transit procedure (LT procedure; can be run with ADF) assuming that you already have a good idea of how your system evolves in terms of elementary reactions and bonds being broken or made in the key reactions, etc...LT is a good alternative to serendipity in most cases. Le 16/04/2013 16:45, Cina Foroutan-Nejad canyslopus/./yahoo.co.uk a écrit : > Dear Haya, > > I don't know what type of reaction you are studying but it seems that your initial guess is already the TS! I recommend you running an IRC calculation to find reactant and product. In addition, be careful about negative frequencies... A negative frequency does not necessarily mean the TS of your reaction! Check if the frequency is really along your reaction coordinate or it is a trivial negative frequency, arising from some inter-molecular rotational barrier; something like the rotational barriers of alkyl groups, etc. > > Good luck, > Cina > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Cina Foroutan-Nejad, PhD > http://muni.academia.edu/CinaForoutanNejad > > > ________________________________ > From: Haya Kornweitz hayak[]ariel.ac.il > To: "Foroutan-Nejad, Cina " > Sent: Tuesday, 16 April 2013, 14:54 > Subject: CCL: transition state > > > > Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il] > Dear CCLers > I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I > have found the same transition in all the methods, but the TS is quite similar > to my product, similar I mean its geometry and its energy. The TS has one > negative frequency while the reactant and product don't have any negative > frequency. > Can someone explain these results?> the strange characters on the top line to the !=! sign. You can also > > > ==0A> > E-mail to administrators: CHEMISTRY-REQUEST!=!ccl.net or use> > > --1453005445-363240232-1366123505=:21240 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: quoted-printable > >
Dear Haya,

I don't know what type of reaction you are studying but it seems that your initial guess is already the TS! I recommend you running an IRC calculation to find reactant and product. In addition, be careful about negative frequencies... A negative frequency does not necessarily mean the TS of your reaction! Check if the frequency is really along your reaction coordinate or it is a trivial negative frequency, arising from some inter-molecular > rotational barrier; something like the rotational barriers of alkyl groups, etc.

Good luck,
Cina
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cina Foroutan-Nejad, PhD

From: Haya Kornweitz hayak[]ariel.ac.il <owner-chemistry!=!ccl.net>
To: "Foroutan-Nejad, Cina " > <canyslopus!=!yahoo.co.uk>
Sent: Tuesday, 16 April 2013, 14:54
Subject: CCL: transition state


Sent to CCL by: "Haya  Kornweitz" [hayak[]ariel.ac.il]
Dear CCLers
I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I
have found the same transition in all the methods, but the TS is quite similar
to my product, similar  I mean its geometry and its energy. The TS has one
negative frequency while the reactant and product don't have any negative
frequency.
Can someone explain these results?


the strange characters on the top line to the !=! sign. You can also
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From owner-chemistry@ccl.net Tue Apr 16 13:07:00 2013 From: "David Gallagher gallagher.da.(!).gmail.com" To: CCL Subject: CCL: transition state Message-Id: <-48566-130416125921-18259-Q2Hvg6vQ/DFCf0HZFAN3nQ(!)server.ccl.net> X-Original-From: David Gallagher Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Apr 2013 09:51:47 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da__gmail.com] Hi Haya, A "transition state" that is remarkably close in energy and geometry to either the reactant or product, could well be a conformational transition state of the reactant or product, such as the rotation of a terminal group. If you cannot confidently judge this by viewing the 3D models, then running IRC calculations backwards and forwards should lead to the reactants and products respectively. If it doesn't go to both, then it probably isn't the transition state you are looking for (though it could still be one step of a multi-step reaction). There are some general guidelines for finding transition states about halfway down this page: http://www.cacheresearch.com/presentations.html If you were to provide the coordinates for your structures, some kind CCLer may be predisposed to take a closer look for you (a picture is worth a thousand words). David Gallagher On 4/16/2013 5:54 AM, Haya Kornweitz hayak[]ariel.ac.il wrote: > Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il] > Dear CCLers > I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I > have found the same transition in all the methods, but the TS is quite similar > to my product, similar I mean its geometry and its energy. The TS has one > negative frequency while the reactant and product don't have any negative > frequency. > Can someone explain these results?> > > From owner-chemistry@ccl.net Tue Apr 16 21:17:01 2013 From: "WMC Sameera chamil|a|chalmers.se" To: CCL Subject: CCL: transition state Message-Id: <-48567-130416110611-23389-ttpvJCbchIGac3BQn+J/7g*|*server.ccl.net> X-Original-From: WMC Sameera Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_5D530D598B1F7546B5B4D5539295A7A255FBE5gruntitachalmerss_" Date: Tue, 16 Apr 2013 15:06:02 +0000 MIME-Version: 1.0 Sent to CCL by: WMC Sameera [chamil]=[chalmers.se] --_000_5D530D598B1F7546B5B4D5539295A7A255FBE5gruntitachalmerss_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Haya, It is possible to observe a late transition state for a reaction, but the r= eaction barrier is usually high. So, please check the reaction barrier of t= he reaction. Suggestions: - You should check the second derivative matrix of the transition state str= ucture, where you can identify the eigenvectors required to have negative v= alues. From these, you can identify the key structural parameters (bond len= gths, angles, etc) that are connected to the negative frequency. - You should carefully look at the displacements of the atoms in your negat= ive frequency. This will give you an idea about bond forming/breaking. Also= , you can displace your TS structure towards the reactant and product. - Additionally, you should do a relaxed scan over the reaction coordinate. Hope this would help. Best regards, Sameera. =85.. Dr. W. M. C. Sameera LASSIE-ER FP7 ITN Department of Chemistry and Molecular Biology University of Gothenburg SE-412 96, Kemivagen 04 Gothenburg Sweden. On Apr 16, 2013, at 1:54 PM, Haya Kornweitz hayak[]ariel.ac.il > wrote: Sent to CCL by: "Haya Kornweitz" [hayak[]ariel.ac.il] Dear CCLers I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I have found the same transition in all the methods, but the TS is quite simi= lar to my product, similar I mean its geometry and its energy. The TS has one negative frequency while the reactant and product don't have any negative frequency. Can someone explain these results? -=3D This is automatically added to each message by the mailing script =3D-E-mail to subscribers: CHEMISTRY*ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_5D530D598B1F7546B5B4D5539295A7A255FBE5gruntitachalmerss_ Content-Type: text/html; charset="Windows-1252" Content-ID: Content-Transfer-Encoding: quoted-printable Dear Haya,

It is possible to observe a late transition state for a reaction, but = the reaction barrier is usually high. So, please check the reaction barrier= of the reaction. 

Suggestions:
- You should check the second derivative matrix of the transition stat= e structure, where you can identify the eigenvectors required to have negat= ive values. From these, you can identify the key structural parameters (bon= d lengths, angles, etc) that are connected to the negative frequency.     
- You should carefully look at the displacements of the atoms in your = negative frequency. This will give you an idea about bond forming/breaking.= Also, you can displace your TS structure towards the reactant and product.=  
- Additionally, you should do a relaxed scan over the reaction coordin= ate.     

Hope this would help.

Best regards,
Sameera. 

=85..
Dr. W. M. C. Sameera
LASSIE-ER FP7 ITN
Department of Chemistry and Molecular Biology
University of Gothenburg
SE-412 96, Kemivagen 04
Gothenburg
Sweden.

On Apr 16, 2013, at 1:54 PM, Haya Kornweitz hayak[]ariel.ac.il <= owner-chemistry*ccl.net> wrote:


Sent to CCL by: "Haya  Kornweitz" [hayak[]ariel.ac.il]
Dear CCLers
I study a reaction, and I looked for a TS using QST2 QST3 and IRC in G09. I=
have found the same transition in all the methods, but the TS is quite simi= lar
to my product, similar  I mean its geometry and its energy. The TS has= one
negative frequency while the reactant and product don't have any negative <= br> frequency.
Can someone explain these results?



-=3D This is automatically added to each message by the mailing script =3D-=
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--_000_5D530D598B1F7546B5B4D5539295A7A255FBE5gruntitachalmerss_-- From owner-chemistry@ccl.net Tue Apr 16 22:24:01 2013 From: "Mohammad Rezaei rezaei.4]*[osu.edu" To: CCL Subject: CCL: Software for formal charges of ligand atoms Message-Id: <-48568-130416222128-1461-i1WUxH4DXlDCu4OZ2H+2kQ%x%server.ccl.net> X-Original-From: "Mohammad Rezaei" Date: Tue, 16 Apr 2013 22:21:27 -0400 Sent to CCL by: "Mohammad Rezaei" [rezaei.4-$-osu.edu] Dear all, I need to check a dataset of PDB files (all are protein+ligand complexes) and see the formal charges on the ligand atoms. For this purpose, I wonder which software can give me the formal charges of ligand atoms and more importantly in a way that can be automated by scripting for a large dataset. Up to now, I only have thought about LigPrep in Schroedinger Suite, by Python API scripting, but is there any easier way? [As an example, suppose that I should have the formal charges on atoms of the two ligands "MES" and "VWW" in the PDB file "10GS.pdb": http://www.pdb.org/pdb/explore/explore.do?structureId=10gs] Any suggestion is greatly appreciated, Mohammad Rezaei From owner-chemistry@ccl.net Tue Apr 16 23:53:00 2013 From: "Benjamin Stein benjamin.w.stein(~)gmail.com" To: CCL Subject: CCL: MCD TDDFT software recommendation Message-Id: <-48569-130416225116-17770-XkVvko+N4sBQ+5McTisWnA]-[server.ccl.net> X-Original-From: Benjamin Stein Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 16 Apr 2013 20:51:05 -0600 Mime-Version: 1.0 (Mac OS X Mail 6.3 \(1503\)) Sent to CCL by: Benjamin Stein [benjamin.w.stein..gmail.com] Hi Oscar, ADF (www.scm.com) can calculate MCD spectra (A, B, and C terms) with TD-DFT. In my experience it works pretty well, provided of course that the system is well treated by (TD-)DFT (no large multi-reference character, etc). For a free alternative, ORCA (cec.mpg.de/forum) can calculate MCD spectra using CASSCF or MRCI methods. While not nearly as "black box" as TD-DFT, with a little practice and thought these methods are quite useful for even large-ish systems (especially CASSCF) and potentially much more accurate than TD-DFT. Good luck! -Ben Benjamin Stein Graduate Student University of New Mexico On Apr 15, 2013, at 9:53 PM, Oscar U Ojeda molecular.oscar ~ gmail.com wrote: > > Sent to CCL by: "Oscar U Ojeda" [molecular.oscar()gmail.com] > Hi Folks, > I would like to gather your recommendations regarding a TDDFT software package that can predict MCD for organic and transition metal compounds. > Your feedback is highly appreciated. > Oscar Ojeda > Research Associate > Arizona State University> >