From owner-chemistry@ccl.net Fri Feb 10 04:25:00 2006 From: "Toomas Tamm tt-ccl.*_*.kky.ttu.ee" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30838-060210041914-5635-CAK1rNZtKnzdLXYfJj0oRQ*_*server.ccl.net> X-Original-From: Toomas Tamm Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 10 Feb 2006 11:18:57 +0200 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl*_*kky.ttu.ee] Our experience with aqueous cations shows that a significant portion (up to and, in some cases, more than one elecron) of the charge is transfered from the ion to the surrounding water molecules. The ions themselves had +2 or +3 formal charges, which in some cases were reduced to +1 and below (Mulliken) in the larger water clusters. The charge resides even not on the ligating water molecules, but a significant portion of it is spread over the outer solvation shell in two-shell model clusters. For some numbers, see Uudsemaa and Tamm, Chemical Physics Letters, 342, 667-672 (2001). Many more numbers are available from us directly, if you ask. The same may happen to anions, although we have no practical experience with anions or ion pairs in water clusters. On Thu, Feb 09, 2006 at 10:07:44AM -0500, nokophala+*+aim.com wrote: > just to add again on thuis issue: Some (most?) anions have positive > homo energies. I suppose this means they do not really exist in > isolation. I wonder what the correct way of calculating the energis > in solution for such species would be. I was thinking of I want to > calculate the energy of an anionic species, A-(aq), then I can > consider the cycle: AH = A-(aq) +H+(aq). Both AH (which is neutral) > and H+ obviously hav epositive homos and so can be considered > stable, so E(AH-H+(aq)) can be considered the true energy of A- in > solution, and it may/may not differ from a direct calculation of a > hypothetical A- in solution. But then, the energy of A- can easily > depend on the nature of the counterion. Is that not a true picture > of reality, i.e. energy of an anion in solution should depend on the > nature of the surounding cation (even if it is not strongly bound)? > I hope the argument that species with positive HOMOs (think HF > energies to avoid the issue of meaning of DFT orbitals) do not exist > is true irrespective of the belief about whether orbitals are > reality or not (i do not want to re-start that debate). > > Noko > -- Toomas Tamm e-mail: tt-ccl(!)kky.ttu.ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Fri Feb 10 09:30:00 2006 From: "Georgios Dimitrakakis giwrgis#%#chemistry.uoc.gr" To: CCL Subject: CCL: ONIOM input using GaussView for Gaussian03 Message-Id: <-30839-060210060909-1147-6IznH7MFvO1Rye9whShevw*_*server.ccl.net> X-Original-From: "Georgios Dimitrakakis" Sent to CCL by: "Georgios Dimitrakakis" [giwrgis|*|chemistry.uoc.gr] Hello to all the members of this list. I am having a problem that has to do with an ONIOM implementation via GaussView. The problem is that I implemented ONIOM through GaussView with two different ways and the results were not the same. I wanted to optimize a structure using DFT->6-311++G** for the High Level and UFF for the Low Level. GaussView has its own way to introduce UFF by selecting Mechanics -> UFF. I did that (the one calculation) and I noticed that the Z-Mat had a strange structure. You can see a part here : C-C_R 0 0.000000 0.000000 0.000000 H C-C_R 0 0.000000 0.000000 1.457200 H C-C_R 0 1.378600 0.000000 1.790600 H ........................................................ .............................(etc)...................... So I tried this calculation and I tried another one by putting Custom->UFF. In this second calculation the input line was the same as previously but instead this time the Z-Mat was looking like this part: C 0 0.000000 0.000000 0.000000 H C 0 0.000000 0.000000 1.457200 H C 0 1.378600 0.000000 1.790600 H ........................................................ .........................(etc).......................... The two calculations came out with different results (for the Energy) both at the ONIOM and at the High Level. The difference was for the ONIOM on the second decimal digit while for the High on the third. Could anyone tell me why is there such a difference in the results?? And another question that may sound silly. Which of the above ways is the correct?? I mean that if I was going to implement ONIOM by hand without the use of GaussView I was never going to create I Z-Mat like the first one. Any ideas? Best regards, Georgios Dimitrakakis giwrgis(at)chemistry.uoc.gr From owner-chemistry@ccl.net Fri Feb 10 10:05:00 2006 From: "Daniel Tunega Daniel.Tunega|-|univie.ac.at" To: CCL Subject: CCL: CALL for papers - EJSS Message-Id: <-30840-060210051928-23436-Resn48DJ0cTAGIuSoT3MXg a server.ccl.net> X-Original-From: Daniel Tunega Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 10 Feb 2006 10:42:51 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Tunega [Daniel.Tunega]^[univie.ac.at] CALL FOR PAPERS European Journal of Soil Science prepares a special thematic issue on "Molecular Modeling in Soil Science" Everybody is invited to submit a contribution related to this topic. The deadline for submitting manuscripts is March 15th 2006. Further details can be found at http://blackwellpublishing.com/ejs ************************************* Daniel Tunega Institute for Theoretical Chemistry University of Vienna Waehringerstrasse 17 A-1090 Vienna, Austria Phone: +43-1-4277-52749 Fax : +43-1-4277-9527 Email: Daniel.Tunega]*[univie.ac.at ************************************* From owner-chemistry@ccl.net Fri Feb 10 10:40:01 2006 From: "nokophala-.-aim.com" To: CCL Subject: CCL: Aquous electrochemistry - Brief Message-Id: <-30841-060210090127-18136-kg9m3NOCg3GVyFgnNKeTdw%server.ccl.net> X-Original-From: nokophala_._aim.com Content-Type: multipart/alternative; boundary="--------MailBlocks_8C7FC6199A988CF_44C_591C_FWM-M08.sysops.aol.com" Date: Fri, 10 Feb 2006 09:01:18 -0500 MIME-Version: 1.0 Sent to CCL by: nokophala[a]aim.com ----------MailBlocks_8C7FC6199A988CF_44C_591C_FWM-M08.sysops.aol.com Content-Type: text/plain; charset="us-ascii" Summary (thanks to everyone, I have made significant progress in my work since the first post): Original question: ">Is anyone aware of successes in reproducing some of the > tabulated redox potentials of electrochemical reactions that > ar elisted i standard electrochemical tables, especiall those > involving single ions? e.g. Cu > --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the > selection of appropriate solvation models. I doubt if > continuum models would require inclusion of at least the > first shell of water molecules, as these are strongly bound. > As a starting point I am trying to reproduce the experimental > value of the 'reference' reaction 2H+ +2e = H2. Even this > appears tricky." Condensed summary: There is a significant quantity of literature on modelling redox reactions involving LARGE molecules, and the redox potentials can be reproduced to within a few mV. Seems like error increases slightly as molecules get smaller. Also, one must question the experimental data sometimes. Inclusion of the first solvation shell is reported to be important for some cases. In my calcs with H+, I found it necessary to include two water molecules to get the correct H+ reduction potential. With regard to the nature of charged species in solution, there is very significant charge delocalisation, such that the solute charge is smaller in solution. This can help stabilise electronically unstable anions. ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ----------MailBlocks_8C7FC6199A988CF_44C_591C_FWM-M08.sysops.aol.com Content-Type: text/html; charset="us-ascii"
 Summary (thanks to everyone, I have made significant progress in my work since the first post):
 
Original question:
 ">Is anyone aware of successes in reproducing some of the
> tabulated redox potentials of electrochemical reactions that
> ar elisted i standard electrochemical tables, especiall those
> involving single ions? e.g. Cu
> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the
> selection of appropriate solvation models. I doubt if
> continuum models would require inclusion of at least the
> first shell of water molecules, as these are strongly bound.
> As a starting point I am trying to reproduce the experimental
> value of the 'reference' reaction 2H+ +2e = H2. Even this
> appears tricky."
 
 
Condensed summary:
 
There is a significant quantity of literature on modelling redox reactions involving LARGE molecules, and the redox potentials can be reproduced to within a few mV. Seems like error increases slightly as molecules get smaller. Also, one must question the experimental data sometimes. Inclusion of the first solvation shell is reported to be important for some cases. In my calcs with H+, I found it necessary  to include two water molecules to get the correct H+ reduction potential. With regard to the nature of charged species in solution, there is very significant charge delocalisation, such that the solute charge is smaller in solution. This can help stabilise electronically unstable anions.
 
 
 
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----------MailBlocks_8C7FC6199A988CF_44C_591C_FWM-M08.sysops.aol.com-- From owner-chemistry@ccl.net Fri Feb 10 11:15:01 2006 From: "nokophala%%aim.com" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30842-060210084334-16783-dRlXl89DXBtL303uPW76oA=-=server.ccl.net> X-Original-From: nokophala|*|aim.com Content-Type: multipart/alternative; boundary="--------MailBlocks_8C7FC5F107F4FC7_44C_57B0_FWM-M08.sysops.aol.com" Date: Fri, 10 Feb 2006 08:43:09 -0500 MIME-Version: 1.0 Sent to CCL by: nokophala\a/aim.com ----------MailBlocks_8C7FC5F107F4FC7_44C_57B0_FWM-M08.sysops.aol.com Content-Type: text/plain; charset="us-ascii" Thanks. It seems reasonable to expect that the same happens with ions. I have just seen HOMO energies of some ions turn from positive to negative in the presence of a solvent. For these I probably cannot talk of solvation energy, since they are electronically unstable in the gas phase. -----Original Message----- > From: Toomas Tamm tt-ccl.|a|.kky.ttu.ee To: Phala, Noko Sent: Fri, 10 Feb 2006 04:57:03 -0500 Subject: CCL: Aquous electrochemistry Sent to CCL by: Toomas Tamm [tt-ccl*_*kky.ttu.ee] Our experience with aqueous cations shows that a significant portion (up to and, in some cases, more than one elecron) of the charge is transfered from the ion to the surrounding water molecules. The ions themselves had +2 or +3 formal charges, which in some cases were reduced to +1 and below (Mulliken) in the larger water clusters. The charge resides even not on the ligating water molecules, but a significant portion of it is spread over the outer solvation shell in two-shell model clusters. For some numbers, see Uudsemaa and Tamm, Chemical Physics Letters, 342, 667-672 (2001). Many more numbers are available from us directly, if you ask. The same may happen to anions, although we have no practical experience with anions or ion pairs in water clusters. On Thu, Feb 09, 2006 at 10:07:44AM -0500, nokophala+*+aim.com wrote: > just to add again on thuis issue: Some (most?) anions have positive > homo energies. I suppose this means they do not really exist in > isolation. I wonder what the correct way of calculating the energis > in solution for such species would be. I was thinking of I want to > calculate the energy of an anionic species, A-(aq), then I can > consider the cycle: AH = A-(aq) +H+(aq). Both AH (which is neutral) > and H+ obviously hav epositive homos and so can be considered > stable, so E(AH-H+(aq)) can be considered the true energy of A- in > solution, and it may/may not differ from a direct calculation of a > hypothetical A- in solution. But then, the energy of A- can easily > depend on the nature of the counterion. Is that not a true picture > of reality, i.e. energy of an anion in solution should depend on the > nature of the surounding cation (even if it is not strongly bound)? > I hope the argument that species with positive HOMOs (think HF > energies to avoid the issue of meaning of DFT orbitals) do not exist > is true irrespective of the belief about whether orbitals are > reality or not (i do not want to re-start that debate). > > Noko > -- Toomas Tamm e-mail: tt-ccl_+_kky.ttu.ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ----------MailBlocks_8C7FC5F107F4FC7_44C_57B0_FWM-M08.sysops.aol.com Content-Type: text/html; charset="us-ascii"
 Thanks. It seems reasonable to expect that the same happens with ions. I have just seen HOMO energies of some ions turn from positive to negative in the presence of a solvent. For these I probably cannot talk of solvation energy, since they are electronically unstable in the gas phase.
 
 
 
-----Original Message-----
From: Toomas Tamm tt-ccl.|a|.kky.ttu.ee <owner-chemistry|a|ccl.net>
To: Phala, Noko <nokophala|a|aim.com>
Sent: Fri, 10 Feb 2006 04:57:03 -0500
Subject: CCL: Aquous electrochemistry

Sent to CCL by: Toomas Tamm [tt-ccl*_*kky.ttu.ee]
Our experience with aqueous cations shows that a significant portion
(up to and, in some cases, more than one elecron) of the charge is
transfered from the ion to the surrounding water molecules. The ions
themselves had +2 or +3 formal charges, which in some cases were
reduced to +1 and below (Mulliken) in the larger water clusters.

The charge resides even not on the ligating water molecules, but a
significant portion of it is spread over the outer solvation shell in
two-shell model clusters. For some numbers, see Uudsemaa and Tamm,
Chemical Physics Letters, 342, 667-672 (2001). Many more numbers are
available from us directly, if you ask.

The same may happen to anions, although we have no practical
experience with anions or ion pairs in water clusters.


On Thu, Feb 09, 2006 at 10:07:44AM -0500, nokophala+*+aim.com wrote:

> just to add again on thuis issue: Some (most?) anions have positive
> homo energies. I suppose this means they do not really exist in
> isolation. I wonder what the correct way of calculating the energis
> in solution for such species would be. I was thinking of I want to
> calculate the energy of an anionic species, A-(aq), then I can
> consider the cycle: AH = A-(aq) +H+(aq). Both AH (which is neutral)
> and H+ obviously hav epositive homos and so can be considered
> stable, so E(AH-H+(aq)) can be considered the true energy of A- in
> solution, and it may/may not differ from a direct calculation of a
> hypothetical A- in solution. But then, the energy of A- can easily
> depend on the nature of the counterion. Is that not a true picture
> of reality, i.e. energy of an anion in solution should depend on the
> nature of the surounding cation (even if it is not strongly bound)?


> I hope the argument that species with positive HOMOs (think HF
> energies to avoid the issue of meaning of DFT orbitals) do not exist
> is true irrespective of the belief about whether orbitals are
> reality or not (i do not want to re-start that debate).

>  
> Noko
>  
-- 
Toomas Tamm                                 e-mail: tt-ccl_+_kky.ttu.ee
Chair of Inorganic Chemistry                voice:  INT+372-620-2810
Tallinn University of Technology            fax:    INT+372-620-2828
Ehitajate tee 5, EE-19086 Tallinn, Estonia  http://www.kk.ttu.ee/toomas/CHEMISTRY|a|ccl.net or use:
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----------MailBlocks_8C7FC5F107F4FC7_44C_57B0_FWM-M08.sysops.aol.com-- From owner-chemistry@ccl.net Fri Feb 10 11:49:01 2006 From: "Deng, Jun jdeng]=[ppg.com" To: CCL Subject: CCL: Question on TDDFT calculation from G98 Message-Id: <-30843-060210095331-6662-1lXP93zWATjWcqWbiIZ5WA+*+server.ccl.net> X-Original-From: "Deng, Jun" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 10 Feb 2006 09:53:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Deng, Jun" [jdeng-*-ppg.com] Dear College: I am puzzled by the coefficient generated from TDDFT calculation. Here are two examples (both of them are triplet excitation of the closed shell system) Output from the First example: ....... Excited State 1: Triplet-?Sym 2.3594 eV 525.49 nm f=0.0000 49 -> 62 0.17572 50 -> 58 0.13132 52 -> 57 0.21082 52 -> 58 -0.24690 53 -> 57 0.60669 54 -> 57 0.18554 56 -> 57 0.39833 56 -> 58 0.12071 ........ Output from the second example: ..... Excited State 1: Triplet-?Sym 2.8110 eV 441.06 nm f=0.0000 150 ->162 -0.11979 151 ->163 0.11359 152 ->162 0.11210 153 ->163 -0.10921 154 ->155 0.59243 154 ->161 -0.20965 ........ If we calculate the sum of the square of the coefficient, the first one gives 0.73 and second one gives 0.45. Generally, I though this number should be less than 0.5 because the excitation for the closed shell only calculates alpha spin and only absolute coefficient larger than 0.1 is listed. How do I explain the result from the first example then?? Thanks for your help!! Jun Deng PPG From owner-chemistry@ccl.net Fri Feb 10 12:24:00 2006 From: "omar Deeb deeb2000il[#]yahoo.com" To: CCL Subject: CCL: carcinogenic database Message-Id: <-30844-060210103654-3515-uQQQypgINDId3jiHpJLVUw*server.ccl.net> X-Original-From: omar Deeb Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-532936024-1139585807=:68641" Date: Fri, 10 Feb 2006 07:36:47 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: omar Deeb [deeb2000il---yahoo.com] --0-532936024-1139585807=:68641 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear ccl, I am looking for the experimental carcinogenic database of a group of compounds, the TD50. Can you please refer me to to the different sites that I can get these values. I visit CPDB site in which it has 1485 compounds but i did not found what I am looking for. Best wishes Dr. Omar Deeb Assistant Professor , PhD Theoretical/computational chemist Chemistry and chemical technology department Faculty of science and technology Alquds University Abu-deis, Jerusalem e-mail : deeb2000il|,|yahoo.com --------------------------------- Yahoo! Mail Use Photomail to share photos without annoying attachments. --0-532936024-1139585807=:68641 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear ccl,
I am looking for the experimental carcinogenic database of a group of compounds, the TD50.
Can you please refer me to to the different sites that I can get these values.
I visit CPDB site in which it has 1485 compounds but i did not found what I am looking for.
Best wishes
 


Dr. Omar Deeb
Assistant Professor , PhD
Theoretical/computational chemist
Chemistry and chemical technology department
Faculty of science and technology
Alquds University
Abu-deis, Jerusalem
e-mail : deeb2000il|,|yahoo.com

Yahoo! Mail
Use Photomail to share photos without annoying attachments. --0-532936024-1139585807=:68641-- From owner-chemistry@ccl.net Fri Feb 10 12:59:03 2006 From: "omar Deeb deeb2000il+/-yahoo.com" To: CCL Subject: CCL: satbility of a salt Message-Id: <-30845-060210105253-14253-2KJSg84hV53WOP19UJg3cw---server.ccl.net> X-Original-From: omar Deeb Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1104942139-1139586768=:6425" Date: Fri, 10 Feb 2006 07:52:48 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: omar Deeb [deeb2000il|a|yahoo.com] --0-1104942139-1139586768=:6425 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCl, I would like to ask about a way or method to calculate theoretically the stability of a salt as well as the solubility of it.. Any suggestions. Best wishes Omar Dr. Omar Deeb Assistant Professor , PhD Theoretical/computational chemist Chemistry and chemical technology department Faculty of science and technology Alquds University Abu-deis, Jerusalem e-mail : deeb2000il{}yahoo.com --------------------------------- Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail. --0-1104942139-1139586768=:6425 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
      Dear CCl,
  I would like to ask about a way or method to calculate theoretically
the stability of a salt as well as the solubility of it..
  Any suggestions.
  Best wishes
  Omar


Dr. Omar Deeb
Assistant Professor , PhD
Theoretical/computational chemist
Chemistry and chemical technology department
Faculty of science and technology
Alquds University
Abu-deis, Jerusalem
e-mail : deeb2000il{}yahoo.com

Brings words and photos together (easily) with
PhotoMail - it's free and works with Yahoo! Mail. --0-1104942139-1139586768=:6425-- From owner-chemistry@ccl.net Fri Feb 10 13:34:01 2006 From: "Anselm HC Horn anselm.horn]*[chemie.uni-erlangen.de" To: CCL Subject: CCL: Visualization of quadrupole moments Message-Id: <-30846-060210105144-12608-EOmCd4/Go49WtPKkjDkfvQ=server.ccl.net> X-Original-From: "Anselm HC Horn" Sent to CCL by: "Anselm HC Horn" [anselm.horn_._chemie.uni-erlangen.de] Dear all, I wonder whether there is a way to easily visualize arbitrary quadrupole moments. For dipoles (x,y,z component) a simple arrow (vector) is sufficient, as used in many visualization programs. However, quadrupole moments consist of a traceless symmetrical 3x3 matrix, so there are six different values (Qxx, Qyy, Qzz, Qxy, Qxz, Qyz). In textbooks quadrupole moments of planar molecules are often represented by a set of four charges around a center. So, a possible solution could be to extend this set of charges; but this results in a cloud of charges (the size of which could be represented by different sphere radii), that seems unsuited for visualization. Any hints and ideas are welcome! Best regards, Anselm Horn Computer Chemie Centrum Friedrich-Alexander-Universiaet Erlangen-Nuernberg From owner-chemistry@ccl.net Fri Feb 10 14:09:01 2006 From: "T. Daniel Crawford crawdad[a]exchange.vt.edu" To: CCL Subject: CCL:G: Question on TDDFT calculation from G98 Message-Id: <-30847-060210124150-24534-kt2YMBDyE0MtFOL8fZ67Ng=-=server.ccl.net> X-Original-From: "T. Daniel Crawford" Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Fri, 10 Feb 2006 12:41:42 -0500 Mime-version: 1.0 Sent to CCL by: "T. Daniel Crawford" [crawdad{:}exchange.vt.edu] The normalization is probably over spatial orbitals rather than spin orbitals, and so the sum of the squares of the coefficients should give 1.0 rather than 0.5. In addition, it is likely that G03 is printing only the largest contributions, so you don't get a complete excitation vector with which to compute the norm. Also, given that you have numerous "large" coefficients, it would not be surprising to find that there are many non-negligible contributions from coefficients not printed here. -Daniel On 2/10/06 12:24 PM, "Deng, Jun jdeng]=[ppg.com" wrote: > Sent to CCL by: "Deng, Jun" [jdeng-*-ppg.com] > Dear College: > > I am puzzled by the coefficient generated from TDDFT calculation. Here are > two examples (both of them are triplet excitation of the closed shell system) > > Output from the First example: > ...... > Excited State 1: Triplet-?Sym 2.3594 eV 525.49 nm f=0.0000 > 49 -> 62 0.17572 > 50 -> 58 0.13132 > 52 -> 57 0.21082 > 52 -> 58 -0.24690 > 53 -> 57 0.60669 > 54 -> 57 0.18554 > 56 -> 57 0.39833 > 56 -> 58 0.12071 > ....... > > Output from the second example: > .... > Excited State 1: Triplet-?Sym 2.8110 eV 441.06 nm f=0.0000 > 150 ->162 -0.11979 > 151 ->163 0.11359 > 152 ->162 0.11210 > 153 ->163 -0.10921 > 154 ->155 0.59243 > 154 ->161 -0.20965 > ....... > > If we calculate the sum of the square of the coefficient, the first one gives > 0.73 and second one gives 0.45. Generally, I though this number should be > less than 0.5 because the excitation for the closed shell only calculates > alpha spin and only absolute coefficient larger than 0.1 is listed. How do I > explain the result from the first example then?? > > Thanks for your help!! > > Jun Deng > PPG> > > -- T. Daniel Crawford Department of Chemistry crawdad ~ vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From owner-chemistry@ccl.net Fri Feb 10 14:44:01 2006 From: "Maryline Bourotte maryline.bourotte|,|univ-orleans.fr" To: CCL Subject: CCL: use of Corina with FlexX Message-Id: <-30848-060210115548-19330-qShz1YcrWhzYeMTdX9eKRQ**server.ccl.net> X-Original-From: "Maryline Bourotte" Sent to CCL by: "Maryline Bourotte" [maryline.bourotte{=}univ-orleans.fr] Hello, The FlexX program can use CORINA for the generation of low-energy conformations of ring systems. How does it work? I hadn't find a solution to exploit this functionnality of CORINA. What is the procedure to insert CORINA in the FlexX program? Please help!!! Thanks to all Best regards, Maryline Bourotte maryline.bourotte.:.univ-orleans.fr From owner-chemistry@ccl.net Fri Feb 10 15:19:00 2006 From: "Chunyi Sung juneyi1^yahoo.com.tw" To: CCL Subject: CCL:G: Basis set for Barium in Gaussian Message-Id: <-30849-060210132010-20348-V/kjT8pyaXrhbNuXy66UEQ##server.ccl.net> X-Original-From: "Chunyi Sung" Sent to CCL by: "Chunyi Sung" [juneyi1/./yahoo.com.tw] Hi, I'm doing some calculations that involves barium, oxygen, and aluminum atoms. I used to use LANL2DZ for all atoms the above system, but I wonder if there will be a better best basis set for barium than LANL2DZ. I've seen people calculating barium dihalides using CRENBL or WB MEFIT instead of LANL2DZ in Gaussian, which I don't know how to use. (J. Phys. Chem. A 2002, 106, 1060; J. Phys. Chem. A 2000, 104, 1950) It seems that they are not implemented in Gaussian. I've also been thinking about adding some d polarizations functions to some ECP. Can somebody give me some suggestions about what to use? thanks juneyi From owner-chemistry@ccl.net Fri Feb 10 18:03:01 2006 From: "Cory Pye cpye#crux.smu.ca" To: CCL Subject: CCL: ONIOM input using GaussView for Gaussian03 Message-Id: <-30850-060210171402-31498-MEAxJg+sxvq2MVgktdvekA-*-server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 10 Feb 2006 17:03:21 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye|-|crux.smu.ca] Hello, Georgious: Could it be possible that the two calculations are using different types of carbon atoms in the force field? The different labels may suggest that the Low-Level calculation is producing a different energy. Another possibility is that one is using Angstroms and the other atomic units. -Cory On Fri, 10 Feb 2006, Georgios Dimitrakakis giwrgis#%#chemistry.uoc.gr wrote: > Sent to CCL by: "Georgios Dimitrakakis" [giwrgis|*|chemistry.uoc.gr] > Hello to all the members of this list. > > I am having a problem that has to do with an ONIOM implementation via GaussView. > > The problem is that I implemented ONIOM through GaussView with two different ways and the results were not the same. > > I wanted to optimize a structure using DFT->6-311++G** for the High Level and UFF for the Low Level. > > GaussView has its own way to introduce UFF by selecting Mechanics -> UFF. I did that (the one calculation) and I noticed that the Z-Mat had a strange structure. You can see a part here : > > C-C_R 0 0.000000 0.000000 0.000000 H > C-C_R 0 0.000000 0.000000 1.457200 H > C-C_R 0 1.378600 0.000000 1.790600 H > ....................................................... > ............................(etc)...................... > > So I tried this calculation and I tried another one by putting Custom->UFF. > > In this second calculation the input line was the same as previously but instead this time the Z-Mat was looking like this part: > > C 0 0.000000 0.000000 0.000000 H > C 0 0.000000 0.000000 1.457200 H > C 0 1.378600 0.000000 1.790600 H > ....................................................... > ........................(etc).......................... > > The two calculations came out with different results (for the Energy) both at the ONIOM and at the High Level. The difference was for the ONIOM on the second decimal digit while for the High on the third. > > > Could anyone tell me why is there such a difference in the results?? > > And another question that may sound silly. Which of the above ways is the correct?? I mean that if I was going to implement ONIOM by hand without the use of GaussView I was never going to create I Z-Mat like the first one. > > Any ideas? > > > Best regards, > > Georgios Dimitrakakis > > giwrgis(at)chemistry.uoc.gr> > > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye[A]crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Fri Feb 10 20:54:00 2006 From: "Matthias Rarey rarey_._zbh.uni-hamburg.de" To: CCL Subject: CCL: use of Corina with FlexX Message-Id: <-30851-060210180504-13044-zJXZZYML/P27CJnjavTKag###server.ccl.net> X-Original-From: Matthias Rarey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 10 Feb 2006 23:23:53 +0100 MIME-Version: 1.0 Sent to CCL by: Matthias Rarey [rarey ~ zbh.uni-hamburg.de] Hi Maryline, that's easy. FlexX loads a configuration file called config.dat during start up. Open this file with an editor, then 1. Search for the variable RCGENERATOR and set this variable to RCGENERATOR /corina -d flexx -i dummies 2. Search for the variable RING_MODE and set this variable to RING_MODE 1 Corina will automatically create a set of low-energy conformations for each ring system with up to 8 atoms per elementary ring during loading a ligand molecule. The conformation set will then be considered during docking calculations without any additional change. Matthias Maryline Bourotte maryline.bourotte|,|univ-orleans.fr schrieb: > Sent to CCL by: "Maryline Bourotte" [maryline.bourotte{=}univ-orleans.fr] > Hello, > > The FlexX program can use CORINA for the generation of low-energy conformations of ring systems. How does it work? I hadn't find a solution to exploit this functionnality of CORINA. What is the procedure to insert CORINA in the FlexX program? > > Please help!!! > Thanks to all > > Best regards, > > Maryline Bourotte > maryline.bourotte=-=univ-orleans.fr> > > > > -- ------------------------------------------------------------------------------ Prof. Dr. Matthias Rarey Tel. : +49 40 42838 7350 Zentrum für Bioinformatik, Universität Hamburg Fax : +49 40 42838 4352 Bundesstraße 43, 20146 Hamburg; Germany eMail: rarey+/-zbh.uni-hamburg.de