From owner-chemistry@ccl.net Tue Jan 29 06:48:01 2008 From: "Ramachandrann chelat rcchelat-$-rediffmail.com" To: CCL Subject: CCL: Full-CI calculations Message-Id: <-36139-080129064359-9953-eTV4VU/pEWHPZfJVxI97+A-,-server.ccl.net> X-Original-From: "Ramachandrann chelat" Date: Tue, 29 Jan 2008 06:43:56 -0500 Sent to CCL by: "Ramachandrann chelat" [rcchelat*rediffmail.com] CCL'rs , I did one molpro calculation for a triatomic linear system containing 3 electron HeH2+ linear. Earlier the energy for this system was reported to be MRCI CASSCF HF-SCF -3.51818587 -3.48901389 -3.47036561 using th input ***,HeH2plus Memory,100,M geometry={H; H1,H,r1; He,H,r2,H1,a1} r1=2.075338 r2=1.931059 a1= 180.0 basis=v5Z {HF occ,2,0,0,0 wf,charge=1,symmetry=1,spin=1 } casscf mrci I tried to redo the problem using Full-CI calculations I tried it in 3 different ways as I have not done any full CI calculations before... when I tried with the keyword fci alone without specifying anything else it terminated with the error saying that orbital record not found. Then I specified the wavefunction details as above, still the same error. Then I did the fci followed taking previous hf wavefunction and also another calculation in which fci taking casscf wavefunction as follows, ***,HeH2+intermediate-example-FCI memory,50,m geometry={H; H1,H,r1; He,H,r2,H1,a1} r1=2.075338 r2=1.931059 a1= 180.0 basis,H=v5z !define basis hf {fci occ,2,0,0,0 wf,charge=1,symmetry=1,spin=1 } and ***,HeH2+intermediate-example-FCI memory,50,m geometry={H; H1,H,r1; He,H,r2,H1,a1} r1=2.075338 r2=1.931059 a1= 180.0 basis,H=v5z {casscf occ,2,0,0,0 wf,charge=1,symmetry=1,spin=1 } {fci } both gives the same energy as -3.50605528 Hartrees As you see this energy is very much different from the values they reported through MRCI calculations.... I was expecting a lower energy through full CI calculations. Is something wrong....?? Can anyone advice me with some details? Thanks in advance Ramachandran From owner-chemistry@ccl.net Tue Jan 29 09:04:00 2008 From: "Ross Walker ross:-:rosswalker.co.uk" To: CCL Subject: CCL: Computational Spectroscopy Message-Id: <-36140-080128203653-30934-w7cKBpxAa3daA/RbQ5k0ow|*|server.ccl.net> X-Original-From: "Ross Walker" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0060_01C861CB.F20E2DD0" Date: Mon, 28 Jan 2008 16:36:32 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross*|*rosswalker.co.uk] This is a multi-part message in MIME format. ------=_NextPart_000_0060_01C861CB.F20E2DD0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi Sina, You could try the method discussed in the following papers to explicitly calculate the emission spectrum (including widths and stokes shift): Mercer, I.P., Gould, I.R., Klug, D.A., "A quantum mechanical/molecular mechanical approach to relaxation dynamics: Calculation of the optical properties of solvated bacteriochlorophyll-a" JOURNAL OF PHYSICAL CHEMISTRY B 103 (36): 7720-7727 SEP 9 1999 Walker RC, de Souza MM, Mercer IP, et al. Large and fast relaxations inside a protein: Calculation and measurement of reorganization energies in alcohol dehydrogenase JOURNAL OF PHYSICAL CHEMISTRY B 106 (44): 11658-11665 NOV 7 2002 All the best Ross /\ \/ |\oss Walker | Assistant Research Professor | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross.|*|.rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. _____ > From: owner-chemistry.|*|.ccl.net [mailto:owner-chemistry.|*|.ccl.net] Sent: Monday, January 28, 2008 13:58 To: Walker, Ross Subject: CCL: Computational Spectroscopy I just wanted to bring up my question once more to see if anybody has an answer On Jan 23, 2008 11:49 AM, Sina T reli sinatureli[#]gmail.com wrote: Sent to CCL by: "Sina T reli" [sinatureli ~ gmail.com] Hello, I have some questions regarding computational spectroscopy. My aim is to find the spectral orbital overlap between some molecules (namely chlorophylls). I use arguslab to produce the transition wavelengths and use a homogenous linewidth of 2nm to produce graphs of absorption with width. However I need a method for determining also their emission spectra and for that since they are quite immobile in their enviroment a mirror image about the 0->0 transition is suggested in some literatures and books. My question is is there a way in which I can find where in the graph is this 0->0 transition is supposed to be. I know it is near the end but since I am going to calculate spectral overlap of molecules, I need a more precise way of finding it.. Or is there any tool that will produce the emission spectra of molecules? Second question comes to users of arguslab. When a spectral analysis is done on the molecule at any given transition dipole electric length and state dipole length. Are these measured in debye or do they just give the directions of the dipoles. If I am looking for the magnitute of transition dipole moment of any given transition, is the length of this transition dipole electric length that will give me the value? Thanks in advance for your answers. 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------=_NextPart_000_0060_01C861CB.F20E2DD0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Sina,
 
You could try the method discussed in the = following=20 papers to explicitly calculate the emission spectrum (including widths = and=20 stokes shift):
 
Mercer, I.P., Gould, I.R., Klug, D.A., "A = quantum=20 mechanical/molecular mechanical approach to relaxation dynamics: = Calculation of=20 the optical properties of solvated bacteriochlorophyll-a"
JOURNAL OF = PHYSICAL=20 CHEMISTRY B 103 (36): 7720-7727 SEP 9 1999
 
Walker=20 RC, de Souza MM, Mercer IP, et al.
Large and fast relaxations inside = a=20 protein: Calculation and measurement of reorganization energies in = alcohol=20 dehydrogenase
JOURNAL OF PHYSICAL CHEMISTRY B 106 (44): 11658-11665 = NOV 7=20 2002
All=20 the best
Ross

/\
\/
|\oss Walker

| Assistant Research = Professor=20 |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | = EMail:-=20 ross.|*|.rosswalker.co.uk |
| http://www.rosswalker.co.uk | = PGP Key=20 available on request |

Note: Electronic Mail is not secure, has = no=20 guarantee of delivery, may not be read every day, and should not be used = for=20 urgent or sensitive issues.

 

From: owner-chemistry.|*|.ccl.net=20 [mailto:owner-chemistry.|*|.ccl.net]
Sent: Monday, January 28, = 2008=20 13:58
To: Walker, Ross
Subject: CCL:=20 Computational Spectroscopy

I just wanted to bring up my question once more to see if = anybody=20 has an answer

On Jan 23, 2008 11:49 AM, Sina T reli=20 sinatureli[#]gmail.com <owner-chemistry]|[ccl.net&g= t;=20 wrote:

Sent=20 to CCL by: "Sina  T  reli" [sinatureli ~ gmail.com]
Hello,

I have=20 some questions regarding computational spectroscopy. My aim is to = find the=20 spectral orbital overlap between some molecules (namely = chlorophylls). I use=20 arguslab to produce the transition wavelengths and use a homogenous=20 linewidth of 2nm to produce graphs of absorption with width. However = I need=20 a method for determining also their emission spectra and for that = since they=20 are quite immobile in their enviroment a mirror image about the = 0->0=20 transition is suggested in some literatures and books. My question = is is=20 there a way in which I can find where in the graph is this 0->0=20 transition is supposed to be. I know it is near the end but since I = am going=20 to calculate spectral overlap of molecules, I need a more precise = way of=20 finding it.. Or is there any tool that will produce the emission = spectra of=20 molecules?

Second question comes to users of arguslab. When a = spectral analysis is done on the molecule at any given transition = dipole=20 electric length and state dipole length. Are these measured in debye = or do=20 they just give the directions of the dipoles. If I am looking for = the=20 magnitute of transition dipole moment of any given transition, is = the length=20 of this transition dipole electric length that will give me the=20 value?

Thanks in advance for your=20 answers.



E-mail to subscribers: CHEMISTRY]|[ccl.net or = use:
 =20    http://www.ccl.net/cgi-bin/ccl/send_ccl_message
E-mail=20 to administrators: CHEMISTRY-REQUEST]|[ccl.net or=20 use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
Subscribe/Unsubscribe:
 =20    http://www.ccl.net/chemistry/sub_unsub.shtml

B= efore=20 posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences= /

Search=20 Messages: http://www.ccl.net/htdig  (login: ccl, = Password:=20 search)
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


------=_NextPart_000_0060_01C861CB.F20E2DD0-- From owner-chemistry@ccl.net Tue Jan 29 09:38:01 2008 From: "Didier MATHIEU didier.mathieu:_:cea.fr" To: CCL Subject: CCL: estimating ability of molecules to diffuse through pores Message-Id: <-36141-080129090123-18279-WA20riSxXTvA9mMA+VdWsw%%server.ccl.net> X-Original-From: "Didier MATHIEU" Date: Tue, 29 Jan 2008 09:01:19 -0500 Sent to CCL by: "Didier MATHIEU" [didier.mathieu(!)cea.fr] Hi, some colleagues ask me to compute the 'size' of some molecules. In fact, they would like to know whether these compounds are small enough to diffuse into a nanoporous material. This seems to be a common problem, but I cannot find out whether there are well-established definition of 'size' in this context, or alternative criteria (preferably purely geometric or topological, because I lack a reliable potential) to assess the ability of small molecules to diffuse pores ? Thanks. Didier From owner-chemistry@ccl.net Tue Jan 29 10:14:00 2008 From: "Pieter Stouten Pieter.Stouten]-[glpg.com" To: CCL Subject: CCL: CRT monitors for hardware stereo Message-Id: <-36142-080129075243-18599-D4wf5evuzSHrKN9jYUzeHQ-,-server.ccl.net> X-Original-From: "Pieter Stouten" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 29 Jan 2008 13:55:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com] I am looking for monitors for use with hardware stereo. I used to use the Samsung SyncMaster 1100DF and I was very happy with it. A colleague recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to have been discontinued. To have an adequate refresh rate and no ghost images, the rule of thumb was that only a CRT monitor would do. Is that still the case? If you have good hardware stereo experiences with a specific monitor (CRT or otherwise), could you please let me know? And what stereo-emitter and stereo-glasses work well for you? Any opinions, hints or pointers are much appreciated. And yes, in case you were wondering, we do have job openings: http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml Thanks, Pieter Pieter Stouten Group Leader Computational Chemistry Galapagos NV, Mechelen, Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. From owner-chemistry@ccl.net Tue Jan 29 10:49:00 2008 From: "Bob Snyder noordwijkerhout a comcast.net" To: CCL Subject: CCL: Call for Papers: 8th International Conference on Chemical Structures Message-Id: <-36143-080129092329-27373-xWYC+K4Jj3yW7JW3WRfmHQ-*-server.ccl.net> X-Original-From: "Bob Snyder" Date: Tue, 29 Jan 2008 09:23:25 -0500 Sent to CCL by: "Bob Snyder" [noordwijkerhout[A]comcast.net] This is the third "Call for Papers" for the 8th International Conference on Chemical Structures (ICCS). Please note that abstracts can now be submitted at the conference web site at http://www.int-conf-chem-structures.org/. The deadline for the submission of abstracts is 15 February 2008. The conference is now open for attendee registration at the same address. The deadline to take advantage of the early registration discount is 25 March 2008. We hope to see you in Noordwijkerhout. Bob Snyder, ICCS Program Chair Markus Wagener, ICCS Vice Chair ------------------------------------------------------------------ C A L L F O R P A P E R S 8th International Conference on Chemical Structures NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 1 - 5 June 2008 Visit the conference website at www.int-conf-chem-structures.org for more information. Joint Organizers: o Division of Chemical Information of the American Chemical Society (CINF) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the Society of German Chemists (GDCh) o Royal Netherlands Chemical Society (KNCV) o Chemical Information Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) The 8th International Conference on Chemical Structures is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > molecular similarity and diversity > library analysis and profiling > chemical information visualization > representation and searching of conformationally flexible compounds o Structure-Activity and Structure-Property Prediction > data fusion, consensus modeling and multi-property optimization > prediction of ADME/Tox properties > industrialized and large-scale QSAR/QSPR model building o Structure-Based Drug Design and Virtual Screening > protein flexibility in docking > improved chemical models and scoring functions > integration of virtual and high-throughput screening o Analysis of Large Data Sets > data mining of HTS data > analysis of large chemistry spaces > machine learning o Informatics for Bridging Between Chemistry and Biology > integrative discovery informatics > virtual pharmacology > target family based approaches to drug discovery o Virtual Chemistry > structure- and ligand-based de-novo design > synthesis planning and design > mining electronic lab journals > reaction networks, reaction databases and reaction retrieval We encourage the submission of papers on both applications and case studies as well as on method development and algorithmic work. The final program will be a balance of these two aspects. Posters can be submitted for any of the above and related areas, but we also welcome contributions in any aspect of the computer handling of chemical structure information, such as: o representation and manipulation of organic and inorganic compounds, biomacromolecules and polymers o new algorithms for searching and managing chemical structures and reactions o 3D databases and pharmacophore modeling o (automatic) structure elucidation o combinatorial chemistry, diversity analysis o web technology and its effect on chemical information o electronic publishing o searching/dealing with patent spaces o MM or QM/MM simulations o practical free energy calculations o material sciences The conference will feature a new product review session for commercial presentations. Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 15 February 2008. We hope to see you in Noordwijkerhout. Bob Snyder, ICCS Program Chair Markus Wagener, ICCS Vice Chair From owner-chemistry@ccl.net Tue Jan 29 11:24:00 2008 From: "Nagesh Babu Idupulapati nbi002{=}LaTech.edu" To: CCL Subject: CCL:G: energy barriers Message-Id: <-36144-080129014431-31685-l7JbWj9EZhG5U+EyJp+mmw**server.ccl.net> X-Original-From: Nagesh Babu Idupulapati Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 28 Jan 2008 23:57:54 -0600 MIME-Version: 1.0 Sent to CCL by: Nagesh Babu Idupulapati [nbi002*_*LaTech.edu] Dear CCL members I am performing Transition state calculations on a particular enzyme oxidation mechanism by obtaining reactant, intermediates and product using gaussian calculations. Iam getting energy barriers between 20-30 kcal/mol between different intermediates and transition states involved in the mechanism. Actually, there is no experimental evidence for me to compare these barriers for that particular enzyme. can anybody please let me know, whether there are any "general kinetic requirements for an enzymatic catalytic process i.e. the energy barriers calculated shouldn't exceed a particular value"?? I really need to justify my results, if they are ok I would really appreciate anybody's help. Regards Nagesh ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Tue Jan 29 12:00:01 2008 From: "Joe Corkery jcorkery[A]eyesopen.com" To: CCL Subject: CCL: CRT monitors for hardware stereo Message-Id: <-36145-080129111528-15376-oPIPDmYBVGf6mFCj1pObMg . server.ccl.net> X-Original-From: Joe Corkery Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 Jan 2008 11:15:07 -0500 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery%x%eyesopen.com] Hi Peter, I've been very happy with my iiyama Vision Master Pro 514 CRT for stereo visualization. It was rather hard to obtain in the US and one of the two that we ordered was broken on arrival. We've been unable to get a replacement for the broken one. If you can get more than one, I would recommend it because these monitors are becoming increasingly scarce. That being said, I do recall seeing a number of European / UK online vendors carrying it. You should also check out ebay as occasionally a number of stereo-capable CRTs will appear there when a failing company is liquidating its assets. With regards to stereo-emitter and glasses. I've been using the same pair of StereoGraphics CrystalEyes for a long time and they have worked well for me on multiple different machines and operating systems. Good luck, Joe Joseph Corkery, M.D. Principal Developer OpenEye Scientific Software, Inc. 222 Third Street, Suite 3120 Cambridge, MA 02142 Pieter Stouten Pieter.Stouten]-[glpg.com wrote: > Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com] > I am looking for monitors for use with hardware stereo. I used to use > the Samsung SyncMaster 1100DF and I was very happy with it. A colleague > recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to > have been discontinued. > > To have an adequate refresh rate and no ghost images, the rule of thumb > was that only a CRT monitor would do. Is that still the case? > > If you have good hardware stereo experiences with a specific monitor > (CRT or otherwise), could you please let me know? And what > stereo-emitter and stereo-glasses work well for you? Any opinions, hints > or pointers are much appreciated. > > And yes, in case you were wondering, we do have job openings: > > http://www.glpg.com/careers/openings.htm > http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml > > Thanks, > > Pieter > > Pieter Stouten > Group Leader Computational Chemistry > Galapagos NV, Mechelen, Belgium > > -- > This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently. > > Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. > > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Tue Jan 29 12:33:01 2008 From: "Michel Petitjean michel.petitjean[*]cea.fr" To: CCL Subject: CCL: estimating ability of molecules to diffuse through pores Message-Id: <-36146-080129104537-22713-PQpIwvNQopYT19nGeOWqnQ%a%server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 29 Jan 2008 16:40:26 +0100 Mime-Version: 1.0 Sent to CCL by: Michel Petitjean [michel.petitjean(0)cea.fr] Hi Mathieu, There are several possible answers to that: Largest size, smallest size, minimal enclosing sphere, minimal polyhedral hull, and so on. The RADI2 freeware computes several geometric parameters: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean:-:itodys.jussieu.fr, michel.petitjean:-:cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. ................................................................ Sent to CCL by: "Didier MATHIEU" [didier.mathieu(!)cea.fr] Hi, some colleagues ask me to compute the 'size' of some molecules. In fact, they would like to know whether these compounds are small enough to diffuse into a nanoporous material. This seems to be a common problem, but I cannot find out whether there are well-established definition of 'size' in this context, or alternative criteria (preferably purely geometric or topological, because I lack a reliable potential) to assess the ability of small molecules to diffuse pores ? Thanks. Didier From owner-chemistry@ccl.net Tue Jan 29 13:09:00 2008 From: "Warren DeLano warren~!~delsci.com" To: CCL Subject: CCL: CRT monitors for hardware stereo Message-Id: <-36147-080129123613-15496-zP4Of7hiYRzip7Yg9i7+iw^^server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 29 Jan 2008 09:34:55 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren[-]delsci.com] It's a bit out of date, but the following page may help in finding a nice "pre-owned" cathode ray tube display for doing stereo. http://pymol.sf.net/stereo3d.html -----Original Message----- > From: owner-chemistry(_)ccl.net [mailto:owner-chemistry(_)ccl.net]=20 Sent: Tuesday, January 29, 2008 8:12 AM To: Warren DeLano Subject: CCL: CRT monitors for hardware stereo Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com] I am looking for monitors for use with hardware stereo. I used to use the Samsung SyncMaster 1100DF and I was very happy with it. A colleague recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to have been discontinued. To have an adequate refresh rate and no ghost images, the rule of thumb was that only a CRT monitor would do. Is that still the case? If you have good hardware stereo experiences with a specific monitor (CRT or otherwise), could you please let me know? And what stereo-emitter and stereo-glasses work well for you? Any opinions, hints or pointers are much appreciated. And yes, in case you were wondering, we do have job openings: http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml Thanks, Pieter Pieter Stouten Group Leader Computational Chemistry Galapagos NV, Mechelen, Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently.=20 Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jan 29 13:46:00 2008 From: "Abdeladim Guermoune lguermoune]![hotmail.com" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36148-080129132020-19336-kUVK9JsSt7gUrbvj1Qs8pg*server.ccl.net> X-Original-From: "Abdeladim Guermoune" Date: Tue, 29 Jan 2008 13:20:16 -0500 Sent to CCL by: "Abdeladim Guermoune" [lguermoune-$-hotmail.com] Dear members, Thanks for your answers, Moreover, I need more clarification about some suggestions. So first, the Gaussian job is just to get the wfn file which will be treated with aim2000 program or other. But the following error: THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! In the running job, abort the formation of wfn file. How to force Gaussian job to done wfn file in this situation? Secondly, using only electronic density that means the instruction keywords will be as below: #p B3P86 6-311++G(3df,2p) density=current scf=(tight,save) output=wfn scfcyc=250 guess=huckel if so, what about the keyword: aim=???? (May be aim=cp?); If not, how? Finally, an interesting remark raised by Henry Rzepa, when one of the elements has a pseudopotential? Some critical points and ring points are missing. Whats the useful to do in this case? Best regards, -----------------------------------> GUERMOUNE Abdeladim. University Cadi Ayyad> Morocco. From owner-chemistry@ccl.net Tue Jan 29 15:07:00 2008 From: "Sergio Emanuel Galembeck segalemb/a\usp.br" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36149-080129140420-18344-RhV1HDCWQaLw7vKHD6EGkw-#-server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Tue, 29 Jan 2008 16:04:03 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb]_[usp.br] Hello, I recomend AIMAll. It is very fast, easy to use and have several options for the integration of atomic basins. For more information visit http://aim.tkgristmill.com/ Best regards, Sergio Galembeck Citando "zborowsk+/-chemia.uj.edu.pl" : > > Sent to CCL by: zborowsk-x-chemia.uj.edu.pl > Hi > Try AIMPAC, its free and good > (there are also Morphy and AIM2000 but they are not free) > I have not tried to perform the AIM analysis in Gaussian so far because > all my "AIM teachers" always said that at this point Gaussian is useless. > > regards > > Kzys > >> >> Sent to CCL by: "abdeladim guermoune" [lguermoune,hotmail.com] >> Dear members, >> I try to run a calculation in G03 with aim instructions >> To find a critical points for geometries including >> Iron and bridged hydrogen between borons atoms (tree centers two >> electrons) >> But I get de following message in the end of the output file: >> >> THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! >> Error termination via Lnk1e in /users/g03/l609.exe at Sun Jan 27 23:33:3= 6 >> 2008. >> >> >> I used as keywords in the input file: >> >> #p B3P86 6-311++G(3df,2p) aim=3Dall density=3Dcurrent scf=3D(tight,save) >> output=3Dwfn scfcyc=3D250 guess=3Dhuckel >> >> Can any one have suggestions to result this problem? >> (sorry for my English, its the third foreigner language for me) >> Yours, >> >> ----------------------------------- >> GUERMOUNE Abdeladim. >> University Cadi Ayyad >> Morocco.> >> >> > > > -- > Krzysztof Zborowski > Faculty of Chemistry > Jagiellonian University > 3 Ingardena Street > 30-060 Krakow > Poland > phone: +48(12)632-4888 ext. 2064 or 2067 > fax: +48(12)634-05-15 > email: zborowsk*|*chemia.uj.edu.pl > ICQ 158385743 > gg 3817259 > skype kzys70 > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Tue Jan 29 15:49:00 2008 From: "Eduard Matito ematito|-|gmail.com" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36150-080129154440-8745-gDBwKSJ/+K4BQaT3ehQnYg!^!server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 29 Jan 2008 20:42:15 +0100 MIME-Version: 1.0 Sent to CCL by: Eduard Matito [ematito||gmail.com] Well, the point is you should not use "aim" keyword in the gaussian job, then such message should not appear. Gaussian will punch the wfn file as long as put "out=wfn" on your input. Using exactly what you suggest mail should do the work. > #p B3P86 6-311++G(3df,2p) density=current scf=(tight,save) output=wfn scfcyc=250 guess=huckel > When pseudopotentials are used, I would simply remove the spurious CP around the nucleus, and place an attractor at the nucleus position. Then check for safety that Poincaré-Hopf condition is fulfilled. It's a lousy solution, but there is not much more you can do... Eduard -- Eduard Matito Postdoctoral Researcher Lundbeck Foundation, Center for Theoretical Chemistry University of Aarhus, Aarhus (Denmark) http://lctc.dcmedia.dk/index.php?id=77 From owner-chemistry@ccl.net Tue Jan 29 18:41:01 2008 From: "Kalju Kahn kalju:_:chem.ucsb.edu" To: CCL Subject: CCL: CRT monitors for hardware stereo Message-Id: <-36151-080129183220-28540-o2me5X82r6JwgOxWqD42tA^server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 29 Jan 2008 15:32:04 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju||chem.ucsb.edu] Hi Peter, I use ViewSonic G225fB as a monitor and NuVision 60GX for glasses. The G225FB is discontinued but it looks like PenguinExpress has one refurbished model on sale right now. The NuVision glasses work well and are cheaper than CrystalEyes but the latter felt more comfortable on my big nose. Cheers, Kalju > > Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com] > I am looking for monitors for use with hardware stereo. I used to use > the Samsung SyncMaster 1100DF and I was very happy with it. A colleague > recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to > have been discontinued. > > To have an adequate refresh rate and no ghost images, the rule of thumb > was that only a CRT monitor would do. Is that still the case? > > If you have good hardware stereo experiences with a specific monitor > (CRT or otherwise), could you please let me know? And what > stereo-emitter and stereo-glasses work well for you? Any opinions, hints > or pointers are much appreciated. > > And yes, in case you were wondering, we do have job openings: > > http://www.glpg.com/careers/openings.htm > http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml > > Thanks, > > Pieter > > Pieter Stouten > Group Leader Computational Chemistry > Galapagos NV, Mechelen, Belgium > > -- > This e-mail and its attachment(s) (if any) may contain confidential and/or > proprietary information and is intended for its addressee(s) only. Any > unauthorized use of the information contained herein (including, but not > limited to, alteration, reproduction, communication, distribution or any > other form of dissemination) is strictly prohibited. If you are not the > intended addressee, please notify the orginator promptly and delete this > e-mail and its attachment(s) (if any) subsequently. > > Galapagos nor any of its affiliates shall be liable for direct, special, > indirect or consequential damages arising from alteration of the contents > of this message (by a third party) or as a result of a virus being passed > on.> > > From owner-chemistry@ccl.net Tue Jan 29 20:13:00 2008 From: "zborowsk__chemia.uj.edu.pl" To: CCL Subject: CCL:G: problem with aim calculation. Message-Id: <-36152-080129162844-6612-z8IrXOTAUBlwVEMiamJnNQ ~~ server.ccl.net> X-Original-From: zborowsk]~[chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 29 Jan 2008 21:50:33 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk*o*chemia.uj.edu.pl in order to obtain the wave function #p B3P86 6-311++G(3df,2p) scf=tight output=wfn is enough I have had never problems with wave function printing regards Kzys > > Sent to CCL by: "Abdeladim Guermoune" [lguermoune-$-hotmail.com] > Dear members, > Thanks for your answers, > Moreover, I need more clarification about some suggestions. > So first, the Gaussian job is just to get the wfn file which will be > treated with aim2000 program or other. But the following error: THE > MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! In the running job, > abort the formation of wfn file. > How to force Gaussian job to done wfn file in this situation? > Secondly, using only electronic density that means the instruction > keywords will be as below: > #p B3P86 6-311++G(3df,2p) density=current scf=(tight,save) output=wfn > scfcyc=250 guess=huckel > if so, what about the keyword: aim=???? (May be aim=cp?); If not, how? > Finally, an interesting remark raised by Henry Rzepa, when one of the > elements has a pseudopotential? Some critical points and ring points are > missing. > Whats the useful to do in this case? > > Best regards, > > -----------------------------------> > GUERMOUNE Abdeladim. > University Cadi Ayyad> Morocco.> > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk|chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Tue Jan 29 20:47:00 2008 From: "Bruno O Villoutreix Bruno.Villoutreix- -gmail.com" To: CCL Subject: CCL: links to free computer tools in chemistry and bioinformatics Message-Id: <-36153-080129113715-1763-bnBpSQAMm6G0KeDIeSZD9Q/./server.ccl.net> X-Original-From: "Bruno O Villoutreix" Date: Tue, 29 Jan 2008 11:37:11 -0500 Sent to CCL by: "Bruno O Villoutreix" [Bruno.Villoutreix[-]gmail.com] Dear Colleagues I have been collecting a list of computer tools of possible interest during these last few years, i post them in my personal web site, at, www.vls3d.com then, enter the site and click links. Some tools are very new, some others are not...some involve links to compound collections, others to ADME filters, .... well, let me know if useful or not...some links are broken, i just leave them such that people can contact the authors directly. sincerely Bruno Villoutreix Director of Research Inserm, University of Paris 5 and 7 Paris France From owner-chemistry@ccl.net Tue Jan 29 21:22:00 2008 From: "serge.christmann-franck]*[merck.fr" To: CCL Subject: CCL: RE CCL: CRT monitors for hardware stereo Message-Id: <-36154-080129121859-1475-tf95/L6URAONwJYYxRFMTw-,-server.ccl.net> X-Original-From: serge.christmann-franck|a|merck.fr Content-Type: multipart/mixed; boundary= "==_ DisclaimeR ff7ce54e.b0ce5404 _==" Date: Tue, 29 Jan 2008 17:47:18 +0100 MIME-Version: 1.0 Sent to CCL by: serge.christmann-franck() merck.fr This is the disclaimer envelope of a multipart messsage in MIME format. --==_ DisclaimeR ff7ce54e.b0ce5404 _== Content-Type: multipart/alternative; boundary="=_alternative 005C37E5C12573DF_=" Message en plusieurs parties au format MIME --=_alternative 005C37E5C12573DF_= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1" dear Pieter i'm using a IIYAMA Vision Master Pro 514 CRT monitor with NuVison 60GX=20 glasses and that works just fine for me good luck with your 3D experiences, Cordialement / Best regards / Gr=FCsse, =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Serge CHRISTMANN-FRANCK, Ph.D. Drug Discovery Informatics, Bio- & Chemoinformatics Merck Sant=E9 Tel : 00(33)1 69 79 24 71 Fax : 00(33)1 69 79 92 55 e-Mail: serge.christmann-franck-.-merck.fr 4 avenue du Pr=E9sident Fran=E7ois Mitterrand 91380 Chilly-Mazarin, France =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Si=E8ge social : Merck Sant=E9 s.a.s. 37 rue Saint-Romain 69008 Lyon capital social : 77.797.247 euros - FR 75 572 028 033 - RCS Lyon 572 028=20 033 "Pieter Stouten Pieter.Stouten]-[glpg.com" =20 Envoy=E9 par : owner-chemistry-.-ccl.net 29/01/2008 13:55 Veuillez r=E9pondre =E0 "CCL Subscribers" A "Christmann-franck, Serge " cc Objet CCL: CRT monitors for hardware stereo=20 Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com] I am looking for monitors for use with hardware stereo. I used to use the Samsung SyncMaster 1100DF and I was very happy with it. A colleague recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to have been discontinued. To have an adequate refresh rate and no ghost images, the rule of thumb was that only a CRT monitor would do. Is that still the case? If you have good hardware stereo experiences with a specific monitor (CRT or otherwise), could you please let me know? And what stereo-emitter and stereo-glasses work well for you? Any opinions, hints or pointers are much appreciated. And yes, in case you were wondering, we do have job openings: http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml Thanks, Pieter Pieter Stouten Group Leader Computational Chemistry Galapagos NV, Mechelen, Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or = proprietary information and is intended for its addressee(s) only. Any=20 unauthorized use of the information contained herein (including, but not=20 limited to, alteration, reproduction, communication, distribution or any=20 other form of dissemination) is strictly prohibited. If you are not the=20 intended addressee, please notify the orginator promptly and delete this=20 e-mail and its attachment(s) (if any) subsequently.=20 Galapagos nor any of its affiliates shall be liable for direct, special,=20 indirect or consequential damages arising from alteration of the contents=20 of this message (by a third party) or as a result of a virus being passed=20 on. -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 005C37E5C12573DF_= Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="ISO-8859-1"
dear Pieter

i'm using a IIYAMA Vision Master Pro 514 CRT monitor  with NuVison 60GX glasses and that works just fine for me

good luck with your 3D experiences,<= br>
Cordialement / Best regards / Gr=FCsse,
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F

Serge CHRISTMANN-FRANCK, Ph.D.
Drug Discovery Informatics, Bio- & Chemoinformatics
Merck Sant=E9
Tel : 00(33)1 69 79 24 71
Fax : 00(33)1 69 79 92 55
e-Mail: serge.christmann-franck-.-merck.fr
4 avenue du Pr=E9sident Fran=E7ois Mitterrand 91380 Chilly-Mazarin, France<= br> =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
Si=E8ge social : Merck Sant=E9 s.a.s. 37 rue Saint-Romain 69008 Lyon
capital social : 77.797.247 euros - FR 75 572 028 033 - RCS Lyon 572 028 033


"Pieter Stouten = Pieter.Stouten]-[glpg.com" <owner-chemistry-.-ccl.net>
Envoy=E9 par : owner-chemistry-.-ccl.n= et

29/01/2008 13:55
Veuillez r=E9pondre = =E0
"CCL Subscribers" <chemistry-.-ccl.net>
A
"Christmann-franck, Serge -id#5= 5p-" <serge.christmann-franck-.-merck.fr>
cc
Objet
CCL: CRT monitors for hardware stereo






Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com]
I am looking for monitors for use with hardware stereo. I used to use
the Samsung SyncMaster 1100DF and I was very happy with it. A colleague
recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to
have been discontinued.

To have an adequate refresh rate and no ghost images, the rule of thumb
was that only a CRT monitor would do. Is that still the case?

If you have good hardware stereo experiences with a specific monitor
(CRT or otherwise), could you please let me know? And what
stereo-emitter and stereo-glasses work well for you? Any opinions, hints
or pointers are much appreciated.

And yes, in case you were wondering, we do have job openings:

http://www.glpg.com/careers/openings.htm
http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml

Thanks,

Pieter

Pieter Stouten
Group Leader Computational Chemistry
Galapagos NV, Mechelen, Belgium

--
This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently.

Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
     http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
     http://www.ccl.net/chemistry/sub=5Funsub.shtml

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
     http://www.ccl.net/spammers.txt
--=_alternative 005C37E5C12573DF_=-- --==_ DisclaimeR ff7ce54e.b0ce5404 _== Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset= "iso-8859-1" This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck does not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck does not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. --==_ DisclaimeR ff7ce54e.b0ce5404 _==-- From owner-chemistry@ccl.net Tue Jan 29 21:58:00 2008 From: "L E Johnson lejohn07 ~ louisville.edu" To: CCL Subject: CCL:G: Problem with aim calculation Message-Id: <-36155-080129124055-19084-GCUcejhP4Bz0gSj/ofO6Tw|*|server.ccl.net> X-Original-From: "L E Johnson" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=US-ASCII Date: Tue, 29 Jan 2008 11:42:29 -0500 Mime-Version: 1.0 Sent to CCL by: "L E Johnson" [lejohn07-$-louisville.edu] Be careful if you are writing wave functions with Gaussian 03, version D. T= he wfn will be written using the wrong coordinates, causing strange and inc= orrect AIM calculations. Any earlier versions do not have this problem, and= I'm not sure if it's been fixed in G03 version E. For the pseudopotential problem, I've used ECP basis for a Pd atom, then ra= n the AIM analysis, and the potentials show up as (3,-3) CPs. The BCPs you = see are likely connecting the (3,-3) charge concentrations, which may not h= ave shown up in the CP search. Word of warning, when I calculated the bond = paths with those CPs, AIM2000 shut down. You can delete the BPs involving t= he potentials, but I'm not sure what the consequence of that exactly is. >>> "Rzepa, Henry h.rzepa[a]imperial.ac.uk" 01/28= /08 10:44 AM >>> Sent to CCL by: "Rzepa, Henry" [h.rzepa^imperial.ac.uk] >Sent to CCL by: "abdeladim guermoune" [lguermoune,hotmail.com] >Dear members, >I try to run a calculation in G03 with aim instructions >To find a critical points for geometries including >Iron and bridged hydrogen between borons atoms (tree centers two electrons= ) >But I get de following message in the end of the output file: > >THE MOLECULAR GRAPH IS DISCONNECTED ... ABORTING! > Error termination via Lnk1e in /users/g03/l609.exe at Sun Jan 27 23:33:36= 2008. The G03 implementation is both old and unsupported/undocumented. Old code never seems to die in Gaussian, it just fades away. Even if you get past the above message, more often than not the Poincare-Hopf condition will not be satisfied either! You are better transferring the wfn file to a program such as AIM2000 or Morphy. By the way, if anyone does plan on using output=3Dwfn, you will have to edit the resulting file if you have more than 99 atoms, since the good old Fortran output statement is I2,1X, and hence the 100th atom will catenate. If however, spaces are added to the relevant output (or the Gaussian format statement changed), all is OK. Oh, can any expert on AIM comment on the interesting "artefacts" obtained when one of the elements has a pseudopotential? Various bond critical bonds very close to the nucleus appear. Do they mean anything? --=20 Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs|mac.com (i= Chat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7= 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). -=3D This is automatically added to each message by the mailing script =3D-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 Jan 29 22:34:01 2008 From: "Eve G Zoebisch eve===ripariansoftware.com" To: CCL Subject: CCL: Molecular scale electrostatic equations Message-Id: <-36156-080129183504-28912-upGBhozGR69XWydT51LP5g~!~server.ccl.net> X-Original-From: "Eve G Zoebisch" Date: Tue, 29 Jan 2008 18:35:00 -0500 Sent to CCL by: "Eve G Zoebisch" [eve ~ ripariansoftware.com] In light of discussions, I thought the comp chem community would appreciate access to microscopic electrostatic equations. The equation used in force fields is an approximate, macroscopic equation which is reasonable for large distances. The molecular scale equation does not have a dielectric constant. Instead it uses total charge which includes induced charge as well as initial (partial) charges. At short distances from a charge electronic, polarization is only partially realized. For example, it can be shown that at vdW radius from a charged atom, the electrostatic field is the field calculated when D=1.0, as opposed to the D=2-4 generally used. (see Example 2 at the bottom of http://www.ripariansoftware.com/TechBackgrd.html ). D=1.0 is consistent with charge model development. A classic text in EE by Frederick Wooten provides a very good overview of microscopic and macroscopic equations, including the approximations made. The relevant pages of Wootens text are at http://www.ripariansoftware.com/Wooten_pg16-18,25-26.pdf To guide you through the text: Maxwells 1st equation is essentially a mathematical transformation of Coulombs Law, pg 16 has the microscopic version of Maxwells equation, pg17 has the macroscopic version, pg 25 has the approximations used for isotropic media, and pg 26 has the approximate macroscopic version of Maxwells equations. Thanks to Ture Gustafson (EE Berkeley) for recommending the Wooten text. Eve G. Zoebisch Riparian Software ripariansoftware.com From owner-chemistry@ccl.net Tue Jan 29 23:55:01 2008 From: "Darren Simpson darren.simpson%a%unisa.edu.au" To: CCL Subject: CCL:G: Gaussian test job Message-Id: <-36157-080129235209-13937-1e/eNgEBYWZUY6WgOvrDVQ#%#server.ccl.net> X-Original-From: "Darren Simpson" Date: Tue, 29 Jan 2008 23:52:05 -0500 Sent to CCL by: "Darren Simpson" [darren.simpson:unisa.edu.au] Dear CCL members, I have been looking for more details on Gaussian Test Job 330 (Part 1): IrCl6 opt with point charges, without success. Does anybody know if there are any references related to this input? Is there a Part 2? I am curious about the basis set used for Ir (below) and would like to know if there is an equivalent basis for Pt. Thanks, Darren Simpson Applied Centre for Structural and Synchrotron Studies University of South Australia Mawson Lakes SA 5095 Ph: +61-8-8302 5580 Fax: +61-8-8302 5545 E-mail: darren.simpson_-_unisa.edu.au Ir 0 S 4 1.0 90962.830 0.0162417 13710.357 0.1144733 3117.1690 0.4266289 843.75834 0.5722416 S 3 1.0 1253.6453 -.1167227 146.47251 0.6668475 66.243506 0.4040007 S 2 1.0 128.70190 0.2956966 21.869728 -1.146088 S 2 1.0 27.373123 -.3279275 4.6374705 1.1580332 S 2 1.0 6.1403068 -.2355173 0.7792355 1.0974544 S 2 1.0 0.09714598 -.5762571 0.03334092 -.4730399 P 4 1.0 4553.757 0.0223568 1074.1305 0.1553305 339.78244 0.4821554 120.55051 0.4940634 P 2 1.0 52.631119 0.4847056 21.665748 0.5725427 P 2 1.0 9.8588661 0.5355099 4.1013555 0.5208878 P 2 1.0 1.5381293 0.5349342 0.57928496 0.5339232 D 4 1.0 645.35836 0.0309533 191.21219 0.1944859 69.822136 0.5177984 26.516524 0.4457431 D 2 1.0 14.891020 0.4811845 5.0294583 0.6304681 D 3 1.0 2.4517796 0.2119183 0.84907800 0.5665945 0.27363471 0.4190297 F 3 1.0 46.890487 0.1737015 13.939088 0.5310884 4.1426684 0.5629138 P 1 1.0 0.102 1.0 P 1 1.0 0.44396 1.0 S 1 1.0 0.0434 1.0 D 1 1.0 0.27363471 1.0