From owner-chemistry@ccl.net Sun Feb 18 09:52:00 2007 From: "Abraham George abraham.mankavil=-=gmail.com" To: CCL Subject: CCL: Gamess Message-Id: <-33636-070218092842-23365-9P5A8PsTgh2xd7Zn/liw3Q-#-server.ccl.net> X-Original-From: "Abraham George" Date: Sun, 18 Feb 2007 09:28:39 -0500 Sent to CCL by: "Abraham George" [abraham.mankavil_-_gmail.com] Sir, How can we do the geometry optimisation of a coordination compound with a 3-d transition metal at the centre? I know how to optimise and calculate the vibrational frequencies for simple organic compounds using GAMESS. But the procedure fails for metal complexes. Expecting help, Dr.Abraham George, Kerala, India. abraham.mankavil-.-gmail.com From owner-chemistry@ccl.net Sun Feb 18 13:28:00 2007 From: "Gopakumar gopakumar|,|chem.kuleuven.be" To: CCL Subject: CCL: Gamess Message-Id: <-33637-070218121908-31223-G5+60m8nkCGU4+XslxiZag[a]server.ccl.net> X-Original-From: Gopakumar Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 18 Feb 2007 17:23:33 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Gopakumar [gopakumar#chem.kuleuven.be] probably you can join here and ask the gamess users.. https://lists.ciw.edu/mailman/listinfo/gamess This is the discussion forum for gamess users. btw what is the error message? On Sun, 18 Feb 2007, Abraham George abraham.mankavil=-=gmail.com wrote: > > Sent to CCL by: "Abraham George" [abraham.mankavil_-_gmail.com] > Sir, > How can we do the geometry optimisation of a coordination > compound with a 3-d transition metal at the centre? I know how to > optimise and calculate the vibrational frequencies for simple organic > compounds using GAMESS. But the procedure fails for metal complexes. > Expecting help, Dr.Abraham George, Kerala, India. > abraham.mankavil!A!gmail.com> > > > -- __________________________________________________________ G. Gopakumar, Division of Quantum Chemistry and Physical Chemistry, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Leuven), Belgium. e-mail: gopakumar/a\chem.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Sun Feb 18 15:48:00 2007 From: "Gustavo Mercier gamercier^yahoo.com" To: CCL Subject: CCL: Gamess Message-Id: <-33638-070218135505-20674-w0OTmlK8tzb5w6a91DEmag%a%server.ccl.net> X-Original-From: Gustavo Mercier Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1448442676-1171821293=:69577" Date: Sun, 18 Feb 2007 09:54:53 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Gustavo Mercier [gamercier||yahoo.com] --0-1448442676-1171821293=:69577 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit HI! The procedure in principle is no different. However, coordination complexes have their own set of "issues", and the most common simple level of theory for organic compounds, say HF with 6-31g**, is grossly inadequate for most coordination compounds. In general, DFT methods are preferred for coordination compounds. The choice of functional is another issue and depends on what you want to do. B3LYP is still reasonable for geometry optimization, although this may be inadequate for spectroscopy. Make sure that you have the right charge and spin multiplicity. You are likely to need a spin unrestricted density. Check for spin contamination -- in DFT this is usually a small component. As for basis set, it is best to use effective core potentials, ECP's. Gamess has several. With ECP's you don't waste extra functions in trying to represent the core of your transition metal. Just remember that you computation will miss the core electrons, and you may need to keep track of that in the "bean counting". Finally, try to use delocalized coordinates because this makes the optimization of geometries more efficient. Gamess will generate these automatically, and it certainly is an improvement if you have any king of ring system. As an illustration, I include part of an input file. (The format is a bit screwed up due to copying and pasting, but you should get the idea.) ! Single Point with default; DFT-B3LYP/UHF/SBKJC,6-31G*//mine,hs optimization ! $CONTRL ICHARG=1 MPLEVL=0 EXETYP=RUN MOLPLT=.T. SCFTYP=UHF MAXIT=40 RUNTYP=OPTIMIZE NZVAR=105 MULT=5 UNITS=ANGS INTTYP=HONDO QMTTOL=3.0E-06 ITOL=20 ICUT=10 COORD=UNIQUE ECP=READ $END $ZMAT DLC=.T. AUTO=.T. $END $SCF CONV=1.0E-06 FDIFF=.F. DIIS=.T. SHIFT=.F. $END $DFT DFTTYP=B3LYP METHOD=GRID NRAD=96 NTHE=36 NPHI=72 NRAD0=48 NTHE0=12 NPHI0=24 ! NRAD0=96 NTHE0=36 NPHI0=72 SWITCH=1.0E-4 $END $SYSTEM TIMLIM=50000 MWORDS=16 MEMDDI=0 $END $STATPT NSTEP=200 OPTTOL=1.0E-06 $END ! $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=0 ! DIFFSP=.F. $END $GUESS GUESS=MOREAD NORB=418 $END ! ESP/CONNOLLY CHARGES !$ELPOT IEPOT=1 WHERE=PDC OUTPUT=PUNCH $END !$PDC PTSEL=CONNOLLY CONSTR=NONE $END $ECP MN-ECP SBKJC N-ECP NONE N-ECP NONE N-ECP NONE N-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE C-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE H-ECP NONE $END $DATA Mn(III)Porphyrin DFT-B3LYP/UHF/SBKJC,6-31g*//(geo mine) 1,5 opt run Dnh 4 Mn 25.0 0.000 0.000 0.000 SBKJC N1 7.0 1.991 0.000 0.000 N31 6 D 1 1 0.800000000 1.00000000 C1A 6.0 2.776 1.098 0.000 N31 6 D 1 1 0.800000000 1.00000000 C2B 6.0 4.154 0.681 0.000 N31 6 D 1 1 0.800000000 1.00000000 C20M 6.0 2.466 2.466 0.000 N31 6 D 1 1 0.800000000 1.00000000 H2B 1.0 5.021 1.325 0.000 N31 6 H20M 1.0 3.230 3.230 0.000 N31 6 $END --- OPEN SHELL ORBITALS --- GENERATED AT Sun Nov 14 21:05:40 2004 Mn(III)Porphyrin UHF/SBKJC,6-31g*//(geo mine) 1,5 E(UHF)= -1084.7652048146, E(NUC)= 2226.0210041029, 18 ITERS $VEC .... these are cut-off Hope this helps! Gustavo Mercier, jr "Abraham George abraham.mankavil=-=gmail.com" wrote: Sent to CCL by: "Abraham George" [abraham.mankavil_-_gmail.com] Sir, How can we do the geometry optimisation of a coordination compound with a 3-d transition metal at the centre? I know how to optimise and calculate the vibrational frequencies for simple organic compounds using GAMESS. But the procedure fails for metal complexes. Expecting help, Dr.Abraham George, Kerala, India. abraham.mankavil!A!gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Gustavo A. Mercier, Jr. MD,PhD Boston Medical Center Radiology - Nuclear Medicine gamercier!=!yahoo.com (preferred e-mail address) Gustavo.Mercier!=!bmc.org gumercie!=!bu.edu cell: 469-396-6750 --0-1448442676-1171821293=:69577 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
HI!
 
The procedure in principle is no different. However, coordination complexes have their own set of "issues", and the most
common simple level of theory for organic compounds, say HF with 6-31g**, is grossly inadequate for most coordination compounds.
 
In general, DFT methods are preferred for coordination compounds. The choice of functional is another issue and depends on what you want to do. B3LYP is still reasonable for geometry optimization, although this may be inadequate for spectroscopy. Make sure that you have the right charge and spin multiplicity. You are likely to need a spin unrestricted density. Check for spin contamination -- in DFT this is usually a small component. As for basis set, it is best to use effective core potentials, ECP's. Gamess has several. With ECP's you don't waste extra functions in trying to represent the core of your transition metal. Just remember that you computation will miss the core electrons, and you may need to keep track of that in the "bean counting".
 
Finally, try to use delocalized coordinates because this makes the optimization of geometries more efficient. Gamess will generate these automatically, and it certainly is an improvement if you have any king of ring system.
 
As an illustration, I include part of an input file. (The format is a bit screwed up due to copying and pasting, but you
should get the idea.)
 
! Single Point with default; DFT-B3LYP/UHF/SBKJC,6-31G*//mine,hs optimization
!
$CONTRL ICHARG=1 MPLEVL=0 EXETYP=RUN MOLPLT=.T.
SCFTYP=UHF MAXIT=40 RUNTYP=OPTIMIZE NZVAR=105
MULT=5 UNITS=ANGS INTTYP=HONDO
QMTTOL=3.0E-06 ITOL=20 ICUT=10
COORD=UNIQUE ECP=READ $END
$ZMAT DLC=.T. AUTO=.T. $END
$SCF CONV=1.0E-06 FDIFF=.F. DIIS=.T.
SHIFT=.F. $END
$DFT DFTTYP=B3LYP METHOD=GRID
NRAD=96 NTHE=36 NPHI=72
NRAD0=48 NTHE0=12 NPHI0=24
! NRAD0=96 NTHE0=36 NPHI0=72
SWITCH=1.0E-4 $END
$SYSTEM TIMLIM=50000 MWORDS=16 MEMDDI=0 $END
$STATPT NSTEP=200 OPTTOL=1.0E-06 $END
! $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=0
! DIFFSP=.F. $END
$GUESS GUESS=MOREAD NORB=418 $END
! ESP/CONNOLLY CHARGES
!$ELPOT IEPOT=1 WHERE=PDC OUTPUT=PUNCH $END
!$PDC PTSEL=CONNOLLY CONSTR=NONE $END
$ECP
MN-ECP SBKJC
N-ECP NONE
N-ECP NONE
N-ECP NONE
N-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
C-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
H-ECP NONE
$END
$DATA
Mn(III)Porphyrin DFT-B3LYP/UHF/SBKJC,6-31g*//(geo mine) 1,5 opt run
Dnh 4
Mn 25.0 0.000 0.000 0.000
SBKJC
N1 7.0 1.991 0.000 0.000
N31 6
D 1
1 0.800000000 1.00000000
C1A 6.0 2.776 1.098 0.000
N31 6
D 1
1 0.800000000 1.00000000
C2B 6.0 4.154 0.681 0.000
N31 6
D 1
1 0.800000000 1.00000000
C20M 6.0 2.466 2.466 0.000
N31 6
D 1
1 0.800000000 1.00000000
H2B 1.0 5.021 1.325 0.000
N31 6
H20M 1.0 3.230 3.230 0.000
N31 6
$END
--- OPEN SHELL ORBITALS --- GENERATED AT Sun Nov 14 21:05:40 2004
Mn(III)Porphyrin UHF/SBKJC,6-31g*//(geo mine) 1,5
E(UHF)= -1084.7652048146, E(NUC)= 2226.0210041029, 18 ITERS
$VEC
.... these are cut-off
 
Hope this helps!
 
Gustavo Mercier, jr

"Abraham George abraham.mankavil=-=gmail.com" <owner-chemistry!=!ccl.net> wrote:

Sent to CCL by: "Abraham George" [abraham.mankavil_-_gmail.com]
Sir,
How can we do the geometry optimisation of a coordination compound with a 3-d transition metal at the centre? I know how to optimise and calculate the vibrational frequencies for simple organic compounds using GAMESS. But the procedure fails for metal complexes.
Expecting help,
Dr.Abraham George, Kerala, India.
abraham.mankavil!A!gmail.com


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt






--
Gustavo A. Mercier, Jr. MD,PhD
Boston Medical Center
Radiology - Nuclear Medicine
gamercier!=!yahoo.com (preferred e-mail address)
cell: 469-396-6750
--0-1448442676-1171821293=:69577--