From owner-chemistry@ccl.net Mon Jun 19 05:34:01 2006
From: "Marcin Krol mykrol[]cyf-kr.edu.pl" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: How to calculate Pka value of a compound
Message-Id: <-31952-060618173752-20279-Z14ZLPry3+EE7fzEMGp6rw]_[server.ccl.net>
X-Original-From: Marcin Krol <mykrol _ cyf-kr.edu.pl>
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Date: Sun, 18 Jun 2006 22:18:11 +0200 (METDST)
MIME-Version: 1.0
Sent to CCL by: Marcin Krol [mykrol- -cyf-kr.edu.pl]
In principle you need to calculate free energy change upon proton
dissociation. This implies calculating free energy of an acid and its
conjugated base - you need to perform calculations for two different
molecules.
For the general protocol of calculating pka read eg.
Liptak, M. D.; Gross, K. C.; Seybold, P. G.; Feldgus, S.; Shields, G. C.
Journal of the American Chemical Society 2002, 124, 6421.
Liptak, M. D.; Shields, G. C. Journal of the American Chemical Society
2001, 123, 7314.
Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. Journal of Physical Chemistry
A 2006, 110, 2493.
Gao, D.; Svoronos, P.; Wong, P. K.; Maddalena, D.; Hwang, J.; Walker, H.
Journal of Physical Chemistry A 2005, 109, 10776.
Good luck
marcin
> Sent to CCL by: "Chin Hung Lai" [chinhunglai]![ntu.edu.tw]
> Dears all:
> If I have done frequency analysis and single-point solvation energy
> calculations by Gaussian 03, how can I use these results to calculate
> the pKa value of one compound?
> Sincerely yours
> Chin-Hung Lai 2006,6,18>
>
>
From owner-chemistry@ccl.net Mon Jun 19 09:19:01 2006
From: "Srikanth Kambalapalli kambalapalli],[gmail.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL:G: Periodic Boundary Conditions calculations in G03
Message-Id: <-31953-060619030447-13439-C0JnKgGHTI+DTGhsEN8G+g/./server.ccl.net>
X-Original-From: "Srikanth Kambalapalli" <kambalapalli[]gmail.com>
Date: Mon, 19 Jun 2006 03:04:43 -0400
Sent to CCL by: "Srikanth Kambalapalli" [kambalapalli~!~gmail.com]
Dear CCLers,
I am trying Periodic boundary conditions on polyaniline using the PBC keyword in Gaussian 03. I am interested in visualising the highest occupied crystal orbital (HOCO) and lowest unoccupied crystal orbital (LUCO) for polyaniline in GaussView. The HOCO and LUCO for polyaniline are not located at K=0. Using pop=full in Gaussian 03 gives orbital coefficients for gamma point only. Does anybody have any idea how to calculate the orbitals at a different K-point from the Gaussian 03 output.
Thank You
Srikanth Kambalapalli
From owner-chemistry@ccl.net Mon Jun 19 10:00:02 2006
From: "Orlin Blajiev blajiev _ vub.ac.be" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL:G: DipoleDeriv
Message-Id: <-31954-060619040537-19030-JtA0oc4p6NXAzzogeimbEw~!~server.ccl.net>
X-Original-From: Orlin Blajiev <blajiev{}vub.ac.be>
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Date: Mon, 19 Jun 2006 09:14:02 +0200
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Sent to CCL by: Orlin Blajiev [blajiev[a]vub.ac.be]
Hi,
I will appreciate very much if somebody lets me know what are the units
of the following output fragment from Gaussian
\DipoleDeriv=-0.9812321,0.,0.,0.,-1.7018432,-0.2426153,
Are they directions, cosinuses?
Best regards,
Orlin
--
Orlin Blajiev
Department of Metallurgy, Electrochemistry and Materials Science
Faculty of Applied Science
Vrije Universiteit Brussel
Pleinlaan 2, B-1050 Brussels
Belgium
http://www.vub.ac.be/META/
tel.: 32-(0)2-6293538
fax : 32-(0)2-6293200
From owner-chemistry@ccl.net Mon Jun 19 11:14:00 2006
From: "Shobe, David dshobe-,-sud-chemieinc.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL:G: DipoleDeriv
Message-Id: <-31955-060619110936-3018-dSTmc4k7q7/tZkHuJp78Ew===server.ccl.net>
X-Original-From: "Shobe, David" <dshobe ~ sud-chemieinc.com>
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Date: Mon, 19 Jun 2006 17:08:10 +0200
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Sent to CCL by: "Shobe, David" [dshobe ~~ sud-chemieinc.com]
Orlin,
The dipole derivative should be a matrix with nine elements. If the dipole vector is (a,b,c) and the nuclear displacement vector (for a particular atom) is (x,y,z), then the dipole derivative is the matrix:
[ da/dx da/dy da/dz ]
[ db/dx db/dy db/dz ]
[ dc/dx dc/dy dc/dz ]
Note: The d's are *partial* derivatives. (I can't use the proper character.)
--David Shobe, Ph.D., M.L.S.
S�d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724
Don't bother flaming me: I'm behind a firewall.
-----Original Message-----
> From: owner-chemistry*_*ccl.net [mailto:owner-chemistry*_*ccl.net]
Sent: Monday, June 19, 2006 10:06 AM
To: Shobe, David
Subject: CCL:G: DipoleDeriv
Sent to CCL by: Orlin Blajiev [blajiev[a]vub.ac.be]
Hi,
I will appreciate very much if somebody lets me know what are the units of the following output fragment from Gaussian
\DipoleDeriv=-0.9812321,0.,0.,0.,-1.7018432,-0.2426153,
Are they directions, cosinuses?
Best regards,
Orlin
--
Orlin Blajiev
Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium
http://www.vub.ac.be/META/
tel.: 32-(0)2-6293538
fax : 32-(0)2-6293200http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message.
Thank you.
From owner-chemistry@ccl.net Mon Jun 19 14:47:01 2006
From: "Niels Hansen n.hansen],[tuhh.de" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Antiferromagnetic coupling
Message-Id: <-31956-060619120331-32536-tO4X5QYWnBxguJXfX4hl+g(_)server.ccl.net>
X-Original-From: Niels Hansen <n.hansen*o*tuhh.de>
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Date: Mon, 19 Jun 2006 17:22:13 +0200
MIME-Version: 1.0
Sent to CCL by: Niels Hansen [n.hansen..tuhh.de]
Hello,
recently I performed DFT/B3LYP calculations for the N2O decomposition on
an oxygen bridged binuclear iron complex in ZSM-5 having the structure
Z[FeOFe] where Z represents a small cluster consisting of two 5T rings
carved out from the zeolite lattice. Calculations on different spin
potential energy surfaces revealed that the strucuture with multiplicity
of Ms = 9 has the lowest energy.
Now, I would like to estimate how the consideration of antiferromagnetic
coupling would affect my relative energies in the catalytic cycle. I
think, first I have to estimate the coupling constant J from
performing a broken symmetry calculation with my system. Does anyone
has experience in setting up such a calculation with TURBOMOLE?
However, if I have succeeded in obtaining the coupling constant, how can
I use it to estimate how it changes the relative energies of my
catalytic cycle?
Any comments would be appreciated.
Many thanks,
Niels Hansen
From owner-chemistry@ccl.net Mon Jun 19 16:07:01 2006
From: "Nuno A. G. Bandeira nuno.bandeira\a/ist.utl.pt" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: Periodic Boundary Conditions calculations in G03
Message-Id: <-31957-060619104853-811-8BGWz6bLCrYazSdRpU+21A|*|server.ccl.net>
X-Original-From: "Nuno A. G. Bandeira" <nuno.bandeira**ist.utl.pt>
Content-Transfer-Encoding: 7bit
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Date: Mon, 19 Jun 2006 15:11:45 +0100
MIME-Version: 1.0
Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira**ist.utl.pt]
Srikanth Kambalapalli kambalapalli],[gmail.com wrote:
> Sent to CCL by: "Srikanth Kambalapalli" [kambalapalli~!~gmail.com]
> Dear CCLers,
>
> I am trying Periodic boundary conditions on polyaniline using the PBC keyword in Gaussian 03. I am interested in visualising the highest occupied crystal orbital (HOCO) and lowest unoccupied crystal orbital (LUCO) for polyaniline in GaussView. The HOCO and LUCO for polyaniline are not located at K=0. Using pop=full in Gaussian 03 gives orbital coefficients for gamma point only. Does anybody have any idea how to calculate the orbitals at a different K-point from the Gaussian 03 output.
Gaussian supplies the values of HOCO and LUCO, by default, where they
have the smallest numerical difference so it's not necessarily given at
the gamma point. You have to take a look at the band structure output to
see how the bands look like and then think about what you want.
At the moment you can't visualize orbitals at different k points (this
is a problem I presented to their development team a while back) but I
think you can see the coefficients if you request #p and pop=full along
with iop(5/33=3) (beware! massive amounts of output)
You must use IOp(5/103=N) to request that the energies of the N highest
occupieds and N lowest virtuals at each k-point be printed. If N<=5
these are on one line per k-point, if N>5 then the occupied and virtual
energies are printed on separate lines.
Regards,
--
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student ^ IST,Lisbon
--
From owner-chemistry@ccl.net Mon Jun 19 16:41:01 2006
From: "Marcelo Zaldini zaldini[a]ufpe.br" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: CUBE file with MEP in NWCHEM ?
Message-Id: <-31958-060619161037-22117-b4cDBNUe1xUPFQ/ZVeKORw]=[server.ccl.net>
X-Original-From: "Marcelo Zaldini" <zaldini*_*ufpe.br>
Content-Type: multipart/alternative;
boundary="----=_NextPart_000_004E_01C693BA.E3A2DF60"
Date: Mon, 19 Jun 2006 16:10:31 -0300
MIME-Version: 1.0
Sent to CCL by: "Marcelo Zaldini" [zaldini[a]ufpe.br]
This is a multi-part message in MIME format.
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Dear CCLers,
I would like to know if it is possible to generate a CUBE file with =
electrostatic potential in NWCHEM, using the function DPLOT =
(http://www.emsl.pnl.gov/docs/nwchem/doc/user/node28.html) ?
Does anyone have experience with that ?
Best Regards,
Marcelo Z.H.
UFPE
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charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2900.2912" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear CCLers,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I would like to know if it is possible =
to generate=20
a CUBE file with electrostatic potential in NWCHEM, using the function =
DPLOT (<A=20
href=3D"http://www.emsl.pnl.gov/docs/nwchem/doc/user/node28.html">http://=
www.emsl.pnl.gov/docs/nwchem/doc/user/node28.html</A>)=20
?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Does anyone have experience with that=20
?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Best Regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Marcelo Z.H.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>UFPE</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV></BODY></HTML>
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From owner-chemistry@ccl.net Mon Jun 19 17:58:00 2006
From: "JunJun Liu ljjlp03|-|gmail.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL:G: G03: Operation on file out of range
Message-Id: <-31959-060619171931-29831-O7XG1NDYSKCLmqnD4fNlVQ/a\server.ccl.net>
X-Original-From: "JunJun Liu" <ljjlp03+*+gmail.com>
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Date: Mon, 19 Jun 2006 16:02:52 -0300
MIME-Version: 1.0
Sent to CCL by: "JunJun Liu" [ljjlp03^-^gmail.com]
Hi All,
I'm doing a ONIOM calculation with addredundant keyword for PES(potential
energy surface) scan. It stoped at step 14, point 9. Then I restarted the
calculation with opt=restart. The restarted calculation looks good because
it started at step 15, point 9, and the QM part and MM parts seem to be
already finished. But it still gave out a strange error message "Operation
on file out of range". I tried many times but got the same error message.
Could anybody who knows the problem please diagnoses it and gives me some
suggestions? Thanks a lot! In the following there's some more detailed
information about my input, outputs and Gaussian version.
===== Output for the first run of PES scan ===============================
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Internal Forces: Max 0.010302263 RMS 0.000625233
Search for a local minimum.
Step number 14 out of a maximum of 388 on scan point 9 out of 11
..............................
..... information omitted ....
..............................
8258 1 -0.000011802 -0.000107472 -0.000111981
8259 1 -0.000010240 -0.000075319 -0.000157084
-------------------------------------------------------------------
Cartesian Forces: Max 0.010279078 RMS 0.000093894
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Internal Forces: Max 0.010145186 RMS 0.000589130
Erroneous write. write -1 instead of 80000.
fd = 5
Erroneous write. write -1 instead of 80000.
fd = 5
writwa
writwa: Unknown error
Segmentation fault
==============================================================================
===== Restart Keywords that I used for the second run ====
%chk=int3-PES-6-31gs.chk
%nproc=8
# opt=restart oniom(hf/6-31g*:amber)
==========================================================
===== Output for the restarted(second) PES scan ====
..............................
..... information omitted ....
..............................
Item Value Threshold Converged?
Maximum Force 0.002802 0.000450 NO
RMS Force 0.000254 0.000300 YES
Maximum Displacement 0.017675 0.001800 NO
RMS Displacement 0.003921 0.001200 NO
Maximum MM Force 0.000045 0.000045 YES
RMS MM Force 0.000001 0.000030 YES
Predicted change in Energy=-7.494930D-06
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
NRF= 0 NRA= 0 NVA=8184 HaveQM=F
Convergence limit is 0.300E-04 MaxStp= 25827 StMxLn= 1.00D-04 StpMin=
1.00D-06.
Convergence criteria 0.00004500 0.00003000 0.00018000
0.00012000
Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS
Disp. Energy Flag
1 0 0 F T 1.00D+00 0.00203949 0.00003219 0.00203949
0.00003219 -28.1357411 ---+
2 0 0 F F 8.66D-01 0.00203949 0.00003219 0.00203949
0.00003219 -28.1357597 ---+
..............................
..... information omitted ....
..............................
76 0 0 F T 1.72D+00 0.00002060 0.00000075 0.00002028
0.00000076 -28.1357893 ====
Operation on file out of range.
PROGRAM ABORTED : IEEE divide by zero
PROCEDURE TRACEBACK:
(0) 0x400000000015f1f0 FTN_GETARITRAP + 0x570
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(1) 0x400000000015ff70 U_CATCH_ARITHMETIC_TRAP + 0x3b0
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(2) 0xe000000190002660 _user_sendsig + 0x2660 [***_Kernel_Gateway_***]
(3) 0x400000000012fa71 fileio_ + 0x3091
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(4) 0x40000000002a0360 rdwclr_ + 0x50
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(5) 0x400000000029fb70 rdwrb1_ + 0x2d0
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(6) 0x400000000029e7f0 rdwrb_ + 0x6a0
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(7) 0x400000000029e0a0 updbcor_ + 0xb0
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(8) 0x400000000014d560 optmz_ + 0x3d80
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(9) 0x40000000000f0db0 ml103 + 0x1d0
[/opt/cluster/apps/g03-C.02.M1/g03/l103.exe]
(10) 0xc00000000004e070 main_opd_entry + 0x50 [/usr/lib/hpux64/dld.so]
============================================================================
========= Gaussian Version =========
******************************************
Gaussian 03: IA64H-G03RevC.02 12-Jun-2004
16-Jun-2006
******************************************
OS: HP-UX superdome
=====================================
Regards!
Liu
From owner-chemistry@ccl.net Mon Jun 19 23:27:01 2006
From: "Green Power powergreen|,|gmail.com" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: Converting between pdb file to zmatix
Message-Id: <-31960-060619125618-7694-bOks999WgniutYl2Hjk8pA],[server.ccl.net>
X-Original-From: "Green Power" <powergreen#%#gmail.com>
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Date: Mon, 19 Jun 2006 12:00:12 -0400
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Sent to CCL by: "Green Power" [powergreen++gmail.com]
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Hi,
Anybody can tell me how to transfer pbd file to zmatix using the funtion
using Guassion03. I try to do it with the function of NEWZMAT, but it always
meets errors as follows,
"Atom 36 needs variable 3= 1.1044460150 but is 1.0971932032
Input z-matrix variables are not compatible with final structure.
Conversion to new Z-matrix failed."
Thanks
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<div>Hi,</div>
<div> </div>
<div>Anybody can tell me how to transfer pbd file to zmatix using the funtion using Guassion03. I try to do it with the function of NEWZMAT, but it always meets errors as follows,</div>
<div> </div>
<div>"Atom 36 needs variable 3= 1.1044460150 but is 1.0971932032<br> Input z-matrix variables are not compatible with final structure.<br> Conversion to new Z-matrix failed."<br> </div>
<div>Thanks</div>
<div> </div>
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