From owner-chemistry@ccl.net Tue Jun 20 04:11:01 2006 From: "Orlin Blajiev blajiev=-=vub.ac.be" To: CCL Subject: CCL:G: DipoleDeriv Message-Id: <-31961-060620033601-2692-soeyZvYaGV439UAMqSy5PQ##server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 20 Jun 2006 08:40:35 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev##vub.ac.be] David, Thank you very much for the answer. I am really sorry, but the problem is still unclear to me because of the following. I counted the numbers between the \DipoleDeriv and Polarizability keywords and it is 3N , but 9N (N is the number of atoms). Maybe another way to clarify the question is what Gaussview is plotting as a Transitional Moment for each vibrational frequency. What I, in fact need, is how transitional dipole moment is oriented towards the molecular frame I will appreciate some advice. Orlin Shobe, David dshobe-,-sud-chemieinc.com wrote: > 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. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > > 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 > -- 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 Tue Jun 20 08:39:00 2006 From: "Marcel Swart marcel.swart[A]icrea.es" To: CCL Subject: CCL: Antiferromagnetic coupling Message-Id: <-31962-060620064933-10858-gu7g1hgt+uOKLCJ49kwThg-$-server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-1-683545481 Date: Tue, 20 Jun 2006 09:43:57 +0200 Mime-Version: 1.0 (Apple Message framework v750) Sent to CCL by: Marcel Swart [marcel.swart_+_icrea.es] --Apple-Mail-1-683545481 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Look at papers by Noodleman and co-workers (for example J.Phys.Chem.A =20= 1998, 102, 6311-6324), that explain how to obtain pure spin state energies from broken-=20 spinstate energies, and also how to obtain the J coupling constant. Note also that B3LYP overstabilizes high spin states. [see for instance J.Inor.Bioch. 2006, 100, 786-800] On Jun 19, 2006, at 9:30 PM, Niels Hansen n.hansen],[tuhh.de wrote: > Sent to CCL by: Niels Hansen [n.hansen..tuhh.de] > Hello, > > recently I performed DFT/B3LYP calculations for the N2O =20 > decomposition on > an oxygen bridged binuclear iron complex in ZSM-5 having the =20 > 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 =20 > multiplicity > of Ms =3D 9 has the lowest energy. > Now, I would like to estimate how the consideration of =20 > 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, =20 > 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 =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) T +34-972-418359 F +34-972-418356 E marcel.swart|a|icrea.es W http://www.icrea.es/pag.asp?id=3DMarcel.Swart W http://iqc.udg.es/~marcel =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-1-683545481 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252 Look at papers by Noodleman and = co-workers (for example J.Phys.Chem.A 1998, 102, 6311-6324),
that = explain how to obtain pure spin state energies from broken-spinstate = energies,
and also how to obtain the J coupling = constant.

Note = also that B3LYP overstabilizes high spin states.
[see for = instance J.Inor.Bioch. 2006, 100, 786-800]

On = Jun 19, 2006, at 9:30 PM, Niels Hansen n.hansen],[tuhh.de = wrote:

Sent to CCL by: Niels Hansen = [n.hansen..tuhh.de]
Hello,

recently = I performed DFT/B3LYP calculations for the N2O decomposition on=A0
an = oxygen bridged binuclear=A0 = iron complex in ZSM-5 having the structure=A0
Z[FeOFe] = where Z represents a small cluster consisting of two 5T rings=A0
carved = out from the zeolite lattice. Calculations on different spin=A0
=A0
of Ms =3D 9 has the lowest energy.
Now, I would like to estimate how the consideration = of antiferromagnetic=A0
coupling = would affect my relative energies in the catalytic cycle. I=A0
think, = first I have to estimate the coupling constant J=A0 from =A0
=A0 anyone =A0
has = experience in setting up such a calculation with TURBOMOLE?
However, if I have succeeded in obtaining the = coupling constant, how can=A0
I use it = to estimate how it changes the relative energies of my=A0
Any comments would be = appreciated.

Many thanks,
Niels = Hansen

=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96<= /DIV>
dr. Marcel Swart

ICREA researcher=A0at
Institut de Qu=EDmica = Computacional
Universitat de Girona

Campus Montilivi
17071 Girona
Catalunya = (Spain)

T=A0=A0+34-972-418359
E=A0=A0marcel.swart|a|icrea.es
W=A0=A0http://iqc.udg.es/~marcel
=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96<= /DIV>


=

= --Apple-Mail-1-683545481-- From owner-chemistry@ccl.net Tue Jun 20 10:05:00 2006 From: "Jens Spanget-Larsen spanget * ruc.dk" To: CCL Subject: CCL:G: DipoleDeriv Message-Id: <-31963-060620081853-17466-H6VlZCK0i7MOy1t2vGiyug-#-server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 20 Jun 2006 13:20:27 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget]=[ruc.dk] Orlin Blajiev wrote: .... What I, in fact need, is how transitional dipole moment is oriented towards the molecular frame. Dear Orlin, include iop(7/33=1) with the freq job, for example: #t B3LYP/DGDZVP freq iop(7/33=1) This will produce a lot of output, part of which will look like this: Dipole derivatives wrt mode 1: 5.01266D-01 -1.87527D-02 -4.66685D-09 Vibrational polarizability contributions from mode 1 0.3823903 0.0005352 0.0000000 Vibrational hyperpolarizability contributions from mode 1 0.0000000 0.0000000 0.0000000 Dipole derivatives wrt mode 2: -3.51910D-08 1.43984D-08 -5.64392D-01 Vibrational polarizability contributions from mode 2 0.0000000 0.0000000 0.1731243 .......etc. The information you need to determine the orientation of the transition moments for the computed normal vibrational modes is contained in the entries "Dipole derivatives wrt mode 1:" and so forth. The following three numbers on the line give you the derivatives of the molecular dipole moment with respect to the x, y, and z components of the normal coordinate in question. These three numbers correspond to the x, y, and z components of the transition moment vector. The components are given in the same coordinate system as the nuclear coordinates in the gaussian "Standard Orientation". OK? Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget|,|ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ From owner-chemistry@ccl.net Tue Jun 20 11:26:01 2006 From: "JunJun Liu ljjlp03*|*gmail.com" To: CCL Subject: CCL:G: G03: Operation on file out of range Message-Id: <-31964-060620112037-9520-jsMWQUARX4KjRfKWsLgCNQ++server.ccl.net> X-Original-From: "JunJun Liu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Tue, 20 Jun 2006 11:10:03 -0300 MIME-Version: 1.0 Sent to CCL by: "JunJun Liu" [ljjlp03||gmail.com] Hi All, Maybe I didn't describe my problem clear. Actually, I've problem in restarting an aborted ONIOM calculation. The abortion of that ONIOM may be caused by an I/O problem, but I don't care about this. I'm interested in how to restart this calculation, because I got an "operation on file out of range" error message when applying opt=restart. Thanks! On Mon, 19 Jun 2006 19:09:18 -0300, JunJun Liu ljjlp03|-|gmail.com wrote: > 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 Tue Jun 20 12:00:03 2006 From: "Shobe, David dshobe.:.sud-chemieinc.com" To: CCL Subject: CCL:G: DipoleDeriv Message-Id: <-31965-060620111005-8806-LGhwaRQqKfwA6MVOuz86TA!^!server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 20 Jun 2006 17:09:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe++sud-chemieinc.com] OK here's a physics question for the list. Is there a reason that the off-diagonal elements of this matrix should be zero? In other words, can the motion of a nucleus perpendicular to the dipole affect the dipole? --David Shobe, Ph.D., M.L.S. Süd-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: Tuesday, June 20, 2006 4:13 AM To: Shobe, David Subject: CCL:G: DipoleDeriv Sent to CCL by: Orlin Blajiev [blajiev##vub.ac.be] David, Thank you very much for the answer. I am really sorry, but the problem is still unclear to me because of the following. I counted the numbers between the \DipoleDeriv and Polarizability keywords and it is 3N , but 9N (N is the number of atoms). Maybe another way to clarify the question is what Gaussview is plotting as a Transitional Moment for each vibrational frequency. What I, in fact need, is how transitional dipole moment is oriented towards the molecular frame I will appreciate some advice. Orlin Shobe, David dshobe-,-sud-chemieinc.com wrote: > 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. > Süd-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > > > > 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 > -- 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 Tue Jun 20 12:35:00 2006 From: "Fiona Case fhcase/a\hotmail.com" To: CCL Subject: CCL: Prediction of physical properties vapor pressures and viscosities Message-Id: <-31966-060619161922-31548-G2a39anfKjDUeqjnOtizCQ#server.ccl.net> X-Original-From: "Fiona Case" Content-Type: text/plain; format=flowed Date: Mon, 19 Jun 2006 15:32:04 -0400 Mime-Version: 1.0 Sent to CCL by: "Fiona Case" [fhcase%%hotmail.com] Do you use theory/modeling/simulation to predict physical properties such as vapor pressures and viscosities? Two challenges have been set as part of the third Industrial Fluid Property Simulation Challenge (IFPSC) contest. Any theory/modeling/simulation method can be used (within the rules and limitations set out at the IFPSC contest website). This is a blind test. The new experimental data that will be used to judge the entries will not be revealed until the contest closes. Entries should be submitted by September 30th 2006. All participants are invited to present their result at a special session during the AIChE annual meeting, November 12-17, when the champions of the 3rd IFPSC will be announced, and prizes will be awarded. Authors of papers that are acceptable to our judging panel of world renowned modeling and property prediction experts will also be invited to contribute to a special edition of Fluid Phase Equilibria. We invite you to participate in this exciting event. 1: A test of the ability of property prediction methods to extrapolate from one state point to another (state conditions transferability). For a binary mixture of ethanol and 1,1,1,2,3,3,3-heptafluoropropane compute the bubble point (or total vapor pressure) at constant temperature T = 343.13 K (69.98 °C) for seven different mole fractions. Bubble point pressures for mixtures at 283.17 K (10.02 °C) are provided. 2: A test of the ability of theory/modeling/simulation methods to predict properties for a range of related materials, using the same input parameters. For the following molecules: (i) 1,4-butanediol (ii) 1,3-butanediol (iii) 1,2-butanediol (iv) 2-methyl-1,3-propanediol (v) 1,2,4-butanetriol Compute the low-strain rate limit (Newtonian) viscosity at (a) T = 373K, P=0.1Mpa, (b) T = 373K, P=250MPa Full details are available at http://fluidproperties.org/ The IFPSC is an industry-led initiative aimed at promoting and encouraging the development of techniques for the prediction of industrially relevant fluid properties. The activities of the group are supported by the Computational Molecular Science and Engineering Forum (CoMSEF) of the American Institute of Chemical Engineers (AIChE), the Computational Chemistry (COMP) and Physical Chemistry (PHYS) divisions of the American Chemical Society (ACS), The Dow Chemical Company, BP Amoco, NIST, Case Scientific, ExxonMobil, Mitsubishi Chemical, 3M Company, and DuPont. From owner-chemistry@ccl.net Tue Jun 20 13:55:00 2006 From: "vechism]^[netscape.net" To: CCL Subject: CCL:G: How can I calculate pKa value of a cpmpound Message-Id: <-31967-060620101107-25459-h7v+U/Z01R6x9TQ7FULQkQ~!~server.ccl.net> X-Original-From: vechism::netscape.net Content-Type: multipart/alternative; boundary="--------MailBlocks_8C8628578871838_1CF4_42EB_mblkn-m07.sysops.aol.com" Date: Tue, 20 Jun 2006 09:35:03 -0400 MIME-Version: 1.0 Sent to CCL by: vechism]=[netscape.net ----------MailBlocks_8C8628578871838_1CF4_42EB_mblkn-m07.sysops.aol.com Content-Type: text/plain; charset="us-ascii" Chin-Hung, I found the following reference useful as a starting point: M. D Liptak et al., J. Am. Chem. Soc, 124, 6421-6427 (2002) useful. Sergio. -----Original Message----- > From: chinhunglai::ntu.edu.tw To: Vechi,Sergio Modesto Sent: Sat, 17 Jun 2006 22:47:06 -0400 Subject: CCL:G: How can I calculate pKa value of a cpmpound Sent to CCL by: 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 2006,6,17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt----------MailBlocks_8C8628578871838_1CF4_42EB_mblkn-m07.sysops.aol.com Content-Type: text/html; charset="us-ascii"
Chin-Hung,
 
 
I found the following reference useful as a starting point:
 
M. D Liptak et al., J. Am. Chem. Soc, 124, 6421-6427 (2002) useful.
 
 
Sergio.
 
 
-----Original Message-----
From: chinhunglai::ntu.edu.tw <owner-chemistry^_^ccl.net>
To: Vechi,Sergio Modesto <vechism^_^netscape.net>
Sent: Sat, 17 Jun 2006 22:47:06 -0400
Subject: CCL:G: How can I calculate pKa value of a cpmpound

Sent to CCL by: 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  2006,6,17E-mail to subscribers: CHEMISTRY^_^ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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----------MailBlocks_8C8628578871838_1CF4_42EB_mblkn-m07.sysops.aol.com-- From owner-chemistry@ccl.net Tue Jun 20 17:27:00 2006 From: "Steve Williams willsd_+_appstate.edu" To: CCL Subject: CCL:G: computation of franck condon factors for O2 cation Message-Id: <-31968-060620172326-29461-fpUGS4QmSpjaCMEn/KzFbQ^server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Tue, 20 Jun 2006 16:40:36 -0400 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd,,appstate.edu] I am looking at a problem that seemed simple but looks more complicated. I'd like to compute Franck Condon factors for the lowest 5 or so vibrational states of the quartet pi excited state of O2+ going to the lowest 10 or so vibrational states of the doublet pi ground state (of O2+). I have what I think will be a useful method (Thanks to Russell Johnson for his fgh1d code) for computing vibrational wavefunctions and energies from a discrete set representation of the PES for a given state. My problem is computing the PES... I know that I can get excellent minima (experiment is 1.1164 A and computation gives 1.11637 A) and pretty good frequencies for both states using ccsd(t) with the aug-cc-pvtz basis set. I have done some PES scans (for the ground state only so far) with ACESII, QCHEM 3, and G03, and all show problems. At very short bond lengths (say 0.8 A) down to the minimum the energy drops smoothly then rises in a way that looks quite like a Morse function, but at longer distances bad things happen. The ccsd(t) reaches a maximum at about 1.9 A, falls smoothly to about 2.2 A, then drops very rapidly. In ACESII the cc equations will not converge at bond lengths greater than 2.263 A. In QCHEM 3 the MP2/aug-cc-pvqz PES is similar: a maximum at about 1.5 A; by 1.9 A the energy is well below the "minimum". I think what I am seeing is interaction between the doublet pi ground state surface and the quartet pi excited state (or maybe some other excited state). Fig 2 in J. Phys. Chem. Ref. Data, Vol 1, No2, 1972 implies a crossing of these surfaces near 2 A. Does anyone have suggestions of better ways to generate the potential energy surfaces I need for these states? I suspect that something like EOM-CCSD may be better, but I am unsure how to use such methods. I have access to Gaussian, ACESII and QCHEM 3 (at least for a while on the latter two). Thanks, Steve Williams From owner-chemistry@ccl.net Tue Jun 20 18:41:01 2006 From: "Serguei Patchkovskii ps.:.ned.sims.nrc.ca" To: CCL Subject: CCL:G: computation of franck condon factors for O2 cation Message-Id: <-31969-060620183807-23009-8ioe+jfcGJnTQQtXcplU3w%x%server.ccl.net> X-Original-From: Serguei Patchkovskii Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 20 Jun 2006 18:38:05 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Serguei Patchkovskii [ps===ned.sims.nrc.ca] On Tue, 20 Jun 2006, Steve Williams willsd_+_appstate.edu wrote: > Sent to CCL by: Steve Williams [willsd,,appstate.edu] > I am looking at a problem that seemed simple but looks more > complicated. I'd like to compute Franck Condon factors for the lowest 5 > or so vibrational states of the quartet pi excited state of O2+ going to > the lowest 10 or so vibrational states of the doublet pi ground state > (of O2+). I have what I think will be a useful method (Thanks to > Russell Johnson for his fgh1d code) for computing vibrational > wavefunctions and energies from a discrete set representation of the PES > for a given state. Why not simply use the experimental RKKR energy surfaces for both states? These are likely to be (much) more accurate than anything you could compute with reasonable amount of work. "Constants of Diatomic Molecules" by Huber and Herzberg give the relevant references for both states you are interested in. The references are also available online at: http://webbook.nist.gov/cgi/cbook.cgi?ID=C12185078&Units=SI&Mask=1000 If you -really- want to calculate the curves yourself, standard single- reference coupled cluster methods are probably not the best choice, particularly away from the equilibrium geometry. Completely renormalized coupled-cluster methods, such as CR-CCSD(T) may give better results (see Piecuch, Kowalski, Pimienta, and McGuire, Int. Rev. Phys. Chem. 21 527-655 (2002)). An implementation of CR-CC methods is available in GAMESS-US. However, if you are really serious about getting the right answers for the right reasons at large internuclear distances, you should be using a multi-reference method. My personal favorite would be multi-reference quasi-degenerate perturbation theory (MR-QDPT2, also available in GAMESS-US). You should be able to get essentially identical results with CASPT2 (available in Gaussian) or one of the flavours of multi-reference CI. Serguei From owner-chemistry@ccl.net Tue Jun 20 21:54:00 2006 From: "Yi wen Dong yyyy2469\a/163.com" To: CCL Subject: CCL:G: How to calculate excited states of Cu(II) complexes by G98? Message-Id: <-31970-060620202504-23858-NXACPGNVAmxstGhXBYAG3w_+_server.ccl.net> X-Original-From: "Yi wen Dong" Date: Tue, 20 Jun 2006 20:25:03 -0400 Sent to CCL by: "Yi wen Dong" [yyyy2469[-]163.com] Would anybody likes to tell me how to calculate the excited states of Cu(II) complexes? The Cu(II) complexes have a Cu-d9 configuretion, so the multiplicities for these complexes are 2, not 1 and 3. The CIS, TDDFT and Zindo levels of G98 have no option, Doublet, therefore it is concluded that the excited states for these complexes would be impossible for calculation by G98. Is it Ok? If not, how to calculate them? I will be very appreciated if you can send me a calculating example input file for such complexes or give some comments or suggestion. Dr. Yi-wen Dong yyyy2469 : 163.com From owner-chemistry@ccl.net Tue Jun 20 23:29:00 2006 From: "Patrick Pang skpang(0)ctimail.com" To: CCL Subject: CCL: implication of HOMO and LUMO location in SN2 reaction Message-Id: <-31971-060620232511-3377-jsMWQUARX4KjRfKWsLgCNQ%%server.ccl.net> X-Original-From: "Patrick Pang" Date: Tue, 20 Jun 2006 23:25:09 -0400 Sent to CCL by: "Patrick Pang" [skpang*o*ctimail.com] Dear all, For SN2 reaction involving square planar complexes(e.g.: PtX2L2), the metal centre (Pt) must contribute to LUMO of PtX2L2 compounds for accepting the electons from attacking/incoming ligands. The leaving ligands (L) of PtX2L2 may contribute to HOMO in order that the leaving ligands (L) with the highest MO energy can depart easy when compared with other coordinated ligands (X). Is it Right? Please comment! In SN2 reactions, is it necessary for the metal centre (Pt) to largely contribute to HOMO? Are there any books or papers explaining the role of HOMO and LUMO in SN2 reactions? Regards, Patrick Pang My e-mail address is "skpang:-:ctimail.com".