From owner-chemistry@ccl.net Mon Oct 3 01:09:00 2005 From: "Perry E. Metzger perry_+_piermont.com" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ - Wrap up Message-Id: <-29465-051002234200-11546-VB1IWMwKp9CaTN+XfQazMg[*]server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Sun, 02 Oct 2005 23:41:52 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry[]piermont.com] "Konrad Hinsen" writes: >> Some friends of mine are now giant fans of Haskell. Haskell is a >> strongly typed functional language in the ML family (i.e. it does type > > .. Haskell, which I think has most of the strong points of Lisp, > plus some of its own. The big one it lacks is the fact that code is not in the form of a first class data structure of the language. Lisp macros are essentially impossible in any other language (though there have been heroic attempts) and they are the most interesting part of the language, and often the least talked about. BTW, it is fairly easy to produce a lazy extension to lisp (and indeed I've seen it done), but it is always difficult to get the implementation efficient. (As you later note, even dedicated Haskell compilers are often a bit taxed in this regard.) > I have some doubts though that the current compilers generate good > enough code for numerical applications. I'd also be surprised if > computational scientists adopted the functional approach any time > soon - it's too far from what they are used to. The irony being, of course, that functional programming is almost more suited to numerical simulation work than to most normal tasks. One is, after all, frequently posing questions that are nearly in the form of a function application, and functional languages are better suited (at least in theory) to the optimization strategies one needs here. A numerical simulation doesn't have to worry too much about using Monads and other hacks to get around a lack of state -- fundamentally, the problems are entirely stateless (though of course they're rarely implemented that way, and one does need to be able to checkpoint...) Unfortunately, though, as you note, this is not a culture, at the moment, would be widely open to the functional style -- as you hint, it is beyond alien here. >> Lastly, may I make a pitch for meta-programming? I know one researcher > > Good point. For many specialized optimizations, this is a good solution. > >> Writing programs that build programs is something I don't see done a >> lot in the CChem world even though it is frequently the case that > > True. Perhaps the most used package that uses this technique is > FFTW, which mostly consists of C code generated by an ML code > generator. Speaking of ML and Haskell, I think that it is excellent practice for the mind to try working in at least one of the languages with a Hindley-Milner type system, such as ML, Haskell, Caml, etc. -- as with Lisp, it has a profound impact on the way you think about programming. Perry From owner-chemistry@ccl.net Mon Oct 3 01:44:00 2005 From: "Dr Seth Olsen s.olsen1~~uq.edu.au" To: CCL Subject: CCL: Protein dielectric for Poisson-Boltzman calcs Message-Id: <-29466-051003005922-3074-RyAHqBdSsQDdm2UzDYx5ew],[server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 03 Oct 2005 14:59:14 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1[a]uq.edu.au] Hi CCLers, What is the current state of thought in the community regarding the best internal dielectric to use in Poisson-Boltzman calculations of pKas of titratable residues in proteins? I am constructing a model of a protein to use for later calculations. I am attempting to assign the protonation state of titratable sites in the protein using continuum Poisson-Boltzman calculations (Amber/RESP charges and Bondi radii). It seems that the state of a residue very near the region of interest (chromophore) depends upon the internal dielectric chosen in the pH region I have chosen (neutral pH). The residue is a GLU which resides in near contact with the chromophore (which has a net negative charge). The predicted pKa of the GLU is >37, 18, 8 and 3 with internal dielectics of 1,2,3 and 4 respectively. I have been using the H++ online server with external dielectric of 80 and screening parameter 0.15 (defaults). Obviously, I must make a choice, but I'd like to know that I'm making an informed one. Does anyone have any advice that might be useful? Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1(!)uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From owner-chemistry@ccl.net Mon Oct 3 03:11:00 2005 From: "John Hearns john.hearns-x-streamline-computing.com" To: CCL Subject: CCL: W:hardware for computational chemistry calculations Message-Id: <-29467-051003030130-11628-uafE97op/TVUn4U1s3BiuA|server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 03 Oct 2005 08:01:16 +0100 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns{=}streamline-computing.com] On Sun, 2005-10-02 at 10:49 -0700, Bill Ross ross[*]cgl.ucsf.edu wrote: > Power requirements and consequent air conditioning needs might > tip the equation back toward the 4100 for higher-horsepower > systems. > You make a good point. I will counter that by saying that some big centres have huge computer rooms dating from the mainframe age - they can deal with high volumes of air conditioning, but are less able to cope with spot loads. Floor loading is also a factor in very large systems. As usual, the best solution depends on your application and the constraints of your particulat location. From owner-chemistry@ccl.net Mon Oct 3 05:01:00 2005 From: "Per-Ola Norrby pon::kemi.dtu.dk" To: CCL Subject: CCL: W:LACVP Message-Id: <-29468-051003045337-9456-2RDTRT2msSiDENvGEGjzDA*_*server.ccl.net> X-Original-From: Per-Ola Norrby Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Mon, 3 Oct 2005 09:57:33 +0200 Mime-Version: 1.0 Sent to CCL by: Per-Ola Norrby [pon{:}kemi.dtu.dk] >Does anyone know where we can find the LACVP basis set? We're >interested in modeling Platinum based drug compounds. It comes with the Jaguar program, it's just the old Hay-Wadt ECP+basis. In Gaussian, you get the same basis set by specifying a GEN basis with LANL2DZ on Pt, 6-31G* on everything else, AND also read in the LANL2DZ pseudo-potentials using PSEUDO=READ. In Gaussian, you also have the option of adding some f-type polarization fro Pt without loosing too much performance, and also to split the basis a bit. Cheers, Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon^kemi.dtu.dk tel +45-45252123, fax +45-45933968 From owner-chemistry@ccl.net Mon Oct 3 06:03:00 2005 From: "Adrian Stevens astevens-#-biofocus.com" To: CCL Subject: CCL: W:Calculate electron populations of Pi systems Message-Id: <-29469-051003060128-5867-08zHajW8EAWB20JC7S1kBg _ server.ccl.net> X-Original-From: "Adrian Stevens" Sent to CCL by: "Adrian Stevens" [astevens(_)biofocus.com] Hi, I'm interested in looking at the changes in electron populations of a variety of aromatic ring systems. Although it's possible to obtain either the Mulliken or Lowdin values per atom, and thus get an estimate of the 'total ring population', I'm specifically interested in the changes in the P-orbital Pi electron populations. Is it possible to split out the populations per orbital type, so that they can be summed per atom? I'm using the PC GAMESS version of the GAMESS package and must profess to not being an expert user in QM packages, so apologies if this is an obvious question. Many thanks in advance, Adrian. From owner-chemistry@ccl.net Mon Oct 3 07:59:00 2005 From: "Drew McCormack da.mccormack*few.vu.nl" To: CCL Subject: CCL: W:CCL: Cleaning up dusty deck fortran and converting to C/C++ - Wrap up Message-Id: <-29470-051003075812-6437-gOj10RHV9tZ2TWi9MXu0wA%a%server.ccl.net> X-Original-From: Drew McCormack Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 3 Oct 2005 13:57:04 +0200 Mime-Version: 1.0 (Apple Message framework v734) Sent to CCL by: Drew McCormack [da.mccormack_-_few.vu.nl] >> are hard to ignore. I guess the reason, in the first place, that >> I jumped >> in on this thread was that it was stated that one cannot do more >> sophisticated >> algorithms and data structures in fortran, and I think this is a >> prejudice that >> should not be extended past fortran 77 to fortran 90 and its >> successors. A >> > > At least not 100%. Fortran 90 has much better data structures, but > for someone with an OO > background it is still not good enough. Which is particularly > regrettable considering that when the > standard was fixed, the utility of OO concepts was already well > established. I think it is worth noting that the most recent Fortran standard, Fortran 2003, does include OO. Of course, it will be several years before these features are well supported by compilers. > > > Language developers have largely turned away from scientific > applications, but there are still a few > projects around. Sisal was considered dead but there is a faint > resurrection attempt: > > http://sisal.sourceforge.net/ > http://www2.cmp.uea.ac.uk/~jrwg/Sisal/ > > A more recent project is Titanium, a parallel language based on Java: > > http://titanium.cs.berkeley.edu/ Sun is also working on a scientific language, called Fortress. Let's hope it becomes the Java of scientific programming languages, at least in terms of adoption: http://it.slashdot.org/article.pl?sid=05/04/30/1749205&from=rss Drew From owner-chemistry@ccl.net Mon Oct 3 08:53:00 2005 From: "G. Vergoten Gerard.Vergoten^_^univ-lille1.fr" To: CCL Subject: CCL: In gaussian, how to output second derivative (Hessian) matrix in cartesian coordinate? Message-Id: <-29471-051003034957-32395-N35B8OrhimRn0HSdvZG5fw_+_server.ccl.net> X-Original-From: "G. Vergoten" Content-Type: multipart/mixed; boundary="=====================_1606890==_" Date: Mon, 03 Oct 2005 09:25:32 +0200 Mime-Version: 1.0 Sent to CCL by: "G. Vergoten" [Gerard.Vergoten_+_univ-lille1.fr] --=====================_1606890==_ Content-Type: multipart/alternative; boundary="=====================_1606900==.ALT" --=====================_1606900==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Use the checkpoint file!You have first to transform the .chk file into a formatted file using the formchk command: formchk *.chk *.fchk where * is the name of your file Then, within Gaussian, there is a script called "demofc" that you can use to output the hessian in cartesian coordinates. Just create a small input file like the attached demofc.inp and execute: demofc hessian.out & I hope this help, let me know. Gerard At 08:27 PM 9/30/2005, you wrote: >Dear CLLers, > >I want to output second derivative matrix(hessian matrix) of energy in >cartesian coordinate in gaussian03, how to do it? >I found at the end of freq job, g03 will output one matrix, but in interan >coordinate. But now I want that in a different coordinate. >Thank you for any suggestion in advance! > > >Yahoo! for Good >Click here to donate to the >Hurricane Katrina relief effort. --=====================_1606900==.ALT Content-Type: text/html; charset="us-ascii" Hi
Use the checkpoint file!You have first to transform the .chk file into a formatted file using the formchk command:
formchk *.chk *.fchk where * is the name of your file
Then, within Gaussian, there is a script called "demofc" that you can use to output the hessian in cartesian coordinates. Just create a small input file like the attached demofc.inp and execute:
demofc <demofc.inp >hessian.out &

I hope this help, let me know.
Gerard



At 08:27 PM 9/30/2005, you wrote:
Dear CLLers,
 
I want to output second derivative matrix(hessian matrix) of energy in cartesian coordinate in gaussian03, how to do it?
I found at the end of freq job, g03 will output one matrix, but in interan coordinate. But now I want that in a different coordinate.
Thank you for any suggestion in advance!


Yahoo! for Good
Click here to donate to the Hurricane Katrina relief effort.
--=====================_1606900==.ALT-- --=====================_1606890==_ Content-Type: text/plain; charset="us-ascii" Content-Disposition: attachment; filename="demofc.inp" *.fchk Cartesian Force Constants quit --=====================_1606890==_-- From owner-chemistry@ccl.net Mon Oct 3 09:28:00 2005 From: "Achim Lienke achim.lienke+/-unilever.com" To: CCL Subject: CCL: W:Unsubscribe Message-Id: <-29472-051003033702-31557-6wLar54wKAFuGwz0cmMrTQ]|[server.ccl.net> X-Original-From: "Achim Lienke" Sent to CCL by: "Achim Lienke" [achim.lienke:+:unilever.com] Hallo, could you please Unsubscribe me. Kind regards Achim Lienke From owner-chemistry@ccl.net Mon Oct 3 10:03:00 2005 From: "Sulev Sild sul(-)chem.ut.ee" To: CCL Subject: CCL: W:CCL: Cleaning up dusty deck fortran and converting to C/C++ - Wrap up Message-Id: <-29473-051003034623-32050-U8S5dE6NcecHXrJ3Sk0TsA^-^server.ccl.net> X-Original-From: Sulev Sild Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 3 Oct 2005 09:46:18 +0300 Mime-Version: 1.0 Sent to CCL by: Sulev Sild [sul\a/chem.ut.ee] Hello, On Oct 02, Konrad Hinsen khinsen|-|cea.fr wrote: > > Language developers have largely turned away from scientific applications, but there are still a few > projects around. Sisal was considered dead but there is a faint resurrection attempt: > It seems to me that scientific community is not completely negleted by language developers. Take a look at the following article by Guy Steele: http://research.sun.com/minds/2005-0302/ This article is about a new language developed at Sun, called Fortress. Here is a nice quote from the article: Fortress focuses on the needs of programmers who work in mathematical disciplines and disciplines such as physics and chemistry that rely extensively on mathematics. While there is no actual implementation available for download, as far as I know, the specification can be found at: http://research.sun.com/projects/plrg/fortress0707.pdf. Looks very promising... If done right, it may have enough potential to become the second generation fortran for another 50 years :) Best wishes, Sulev From owner-chemistry@ccl.net Mon Oct 3 10:38:01 2005 From: "SANDEEP KUMAR skumar23~!~jhem.jhu.edu" To: CCL Subject: CCL: Protein dielectric for Poisson-Boltzman calcs Message-Id: <-29474-051003085725-3727-bSQL9LKEmzgAz3lzw43fig ~ server.ccl.net> X-Original-From: SANDEEP KUMAR Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 03 Oct 2005 08:57:17 -0400 MIME-Version: 1.0 Sent to CCL by: SANDEEP KUMAR [skumar23##jhem.jhu.edu] Dear Seth: I usually use an internal dielectric of 20 for proteins, because it appears more reasonable, especially in the binding site region where you could have a number of charged residues. Of''course I cross validate the results with dielectric of 4 as well. Generally, if the trends in the two calculations match, the results would be reliable. Sincerely, Sandeep ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan ~~ jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/ ----- Original Message ----- > From: "Dr Seth Olsen s.olsen1~~uq.edu.au" Date: Monday, October 3, 2005 0:59 am Subject: CCL: Protein dielectric for Poisson-Boltzman calcs > > Sent to CCL by: Dr Seth Olsen [s.olsen1[a]uq.edu.au] > > Hi CCLers, > > What is the current state of thought in the community regarding the > bestinternal dielectric to use in Poisson-Boltzman calculations of > pKas of > titratable residues in proteins? > > I am constructing a model of a protein to use for later > calculations. I > am attempting to assign the protonation state of titratable sites > in the > protein using continuum Poisson-Boltzman calculations (Amber/RESP > charges and Bondi radii). It seems that the state of a residue very > near the region of interest (chromophore) depends upon the internal > dielectric chosen in the pH region I have chosen (neutral pH). The > residue is a GLU which resides in near contact with the chromophore > (which has a net negative charge). The predicted pKa of the GLU is > >37,18, 8 and 3 with internal dielectics of 1,2,3 and 4 > respectively. I > have been using the H++ online server with external dielectric of > 80 and > screening parameter 0.15 (defaults). > > Obviously, I must make a choice, but I'd like to know that I'm > making an > informed one. Does anyone have any advice that might be useful? > > Cheers, > > Seth > > > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group > Centre for Computational Molecular Science > Chemistry Building, > The University of Queensland > Qld 4072, Brisbane, Australia > > tel (617) 33653732 > fax (617) 33654623 > email: s.olsen1!=!uq.edu.au > Web: www.ccms.uq.edu.au > > ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ~~ sign. You can > also> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Mon Oct 3 11:13:01 2005 From: "Noel O Boyle noel.oboyle2|*|mail.dcu.ie" To: CCL Subject: CCL: What keeps a molecule adsorbed? Message-Id: <-29475-051003102119-19347-7/wWlOOY1Wx0xMPIKqzDGw++server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 03 Oct 2005 15:20:42 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [noel.oboyle2++mail.dcu.ie] Dear all, I have been trying to explain the results of a DFT study (using G03) where a molecule adsorbs onto a gold cluster through its nitrogen atom. I created an isosurface of the change in the electron density associated with the adsorption (by calculating the electron densities of the molecule and the gold cluster separately at the geometry of the adsorbed system). This shows that electron density *decreases* in the area between the adsorbate and the surface. This is the opposite of what I expected. A paper by Bilic, Reimers, Hush and Hafner (JCP, 2002, 116, 8981) shows the same effect for ammonia on an infinite surface of gold(111). It shows the same result, and says that this is evidence that covalent bonding effects are not so important (they also have other evidence). It seems that I do not understand bonding very well - what keeps the molecule stuck to the surface, if it isn't a shared electron or two? Regards, Noel -- Dr. Noel M. O'Boyle, Group of Dr. John Mitchell (http://www-mitchell.ch.cam.ac.uk), Unilever Centre for Molecular Science Informatics, Dept. of Chemistry, University of Cambridge, U.K. From owner-chemistry@ccl.net Mon Oct 3 11:58:00 2005 From: "S.I.Gorelsky gorelsky(0)stanford.edu" To: CCL Subject: CCL: W:Calculate electron populations of Pi systems Message-Id: <-29476-051003115604-18434-pWuOQY6hNzcEJYDSBVGa7g]-[server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 3 Oct 2005 08:55:57 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky[a]stanford.edu] Hello, you can do per-orbital Mulliken and Lowdin populations as well as per-used-defined-fragment (groups of atoms and/or orbitals) using the AOMix-L program. For more details, please check: www.sg-chem.net Best regards, S. Gorelsky On Mon, 3 Oct 2005, Adrian Stevens astevens-#-biofocus.com wrote: > > Sent to CCL by: "Adrian Stevens" [astevens(_)biofocus.com] > Hi, > > I'm interested in looking at the changes in electron populations of a variety of aromatic ring systems. Although it's possible to obtain either the Mulliken or Lowdin values per atom, and thus get an estimate of the 'total ring population', I'm specifically interested in the changes in the P-orbital Pi electron populations. Is it possible to split out the populations per orbital type, so that they can be summed per atom? I'm using the PC GAMESS version of the GAMESS package and must profess to not being an expert user in QM packages, so apologies if this is an obvious question. > > Many thanks in advance, > > Adrian.> > > ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From owner-chemistry@ccl.net Mon Oct 3 12:32:00 2005 From: "George Fitzgerald gxf%accelrys.com" To: CCL Subject: CCL: W:Iodo NMR chemical shifts Message-Id: <-29477-051003110233-8322-gVcmctjJCAqJ8yt20fhfmA%server.ccl.net> X-Original-From: George Fitzgerald Content-Type: multipart/alternative; boundary="=_alternative 004E97EA8825708F_=" Date: Mon, 3 Oct 2005 07:18:29 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [gxf===accelrys.com] This is a multipart message in MIME format. --=_alternative 004E97EA8825708F_= Content-Type: text/plain; charset="US-ASCII" The CASTEP DFT program has NMR capability that has been used for heavy elements. This can be applied to both molecular and solid state systems. I don't know that they have examples of Iodine in particular, but there are examples of other heavy elements like Ag. ____________________________________________ George Fitzgerald, Ph.D. gxf[#]accelrys.com Accelrys, Inc. Tel: +1 858 799 5360 10188 Telesis Court Fax: +1 858 799 5100 Suite 100 Mobile: +1 858 692 8722 San Diego, CA 92121 "CCL" Sent by: owner-chemistry[#]ccl.net 09/28/2005 10:11 PM Please respond to "CCL Subscribers" To "Fitzgerald, George " cc Subject CCL: W:Iodo NMR chemical shifts Sent to CCL by: "Gisele deFreitas Gauze" [giselegauze()yahoo.com.br] --Replace strange characters with the "at" sign to recover email address--. I am calculating chemical shifts to alfa iodine ketones, with Gaussian (3-21G and lanl2dz) and the results are very poor. Anyone knows about specific iodine basis set to perform these calculation. Thanks for while Gisele de Freitas Gauze giselegauze[#]yahoo.com.br Maring-Paran-Brasillookup the X-Original-From: line in the mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_messageJob advertising: http://www.ccl.net/jobs-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/CoEFM2KEWkMeWfjiws0!1Ognos4+MFXc+Wv0Ykg2WOYO3yUbjL0CgxUoYdy9HTLk!KiCdhBGxr7HojgCrpEpwKArRB9NLGXgIJpYAxAJnDWCsZS6dxrNw0PfyR0fpbLypOdjT5a+poXav30C8wWPITLOExhCtbxI2+qtRS6L4Hn23FI4yDkyWNBT6RuF2ID5ecYBmP1vWbuoV2JwgT4t762gE20VSCsy --=_alternative 004E97EA8825708F_= Content-Type: text/html; charset="US-ASCII"
The CASTEP DFT program has NMR capability that has been used for heavy elements. This can be applied to both molecular and solid state systems. I don't know that they have examples of Iodine in particular, but there are examples of other heavy elements like Ag.

____________________________________________
George Fitzgerald, Ph.D.       gxf[#]accelrys.com
Accelrys, Inc.                             Tel:  +1 858 799 5360
10188 Telesis Court                 Fax: +1 858 799 5100
Suite 100                                     Mobile: +1 858 692 8722
San Diego, CA 92121


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CCL: W:Iodo NMR chemical shifts






Sent to CCL by: "Gisele deFreitas Gauze" [giselegauze()yahoo.com.br]

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I am calculating chemical shifts to alfa iodine ketones, with Gaussian (3-21G and lanl2dz) and the results are very poor. Anyone knows about specific iodine basis set to perform these calculation.

Thanks for while

Gisele de Freitas Gauze
giselegauze[#]yahoo.com.br
Maring-Paran-Brasil


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--=_alternative 004E97EA8825708F_=-- From owner-chemistry@ccl.net Mon Oct 3 14:17:00 2005 From: "Mariusz Sterzel msterzel(a)buffalo.edu" To: CCL Subject: CCL: What keeps a molecule adsorbed? Message-Id: <-29478-051003141526-25902-oFUubBI8b8HYIDholY4Ciw#server.ccl.net> X-Original-From: Mariusz Sterzel Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 3 Oct 2005 13:15:18 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Mariusz Sterzel [msterzel^_^buffalo.edu] Dear Noel, Following Ruedenberg, the simple answer is electrons kinetic energy. For more details look at K. Ruedenberg, Reviews of Modern Physics, 34(2):326-376, (1962) and M.S. Gordon, J.H.Jensen, Theoretical Chemistry Accounts, 103:248-251, (2000) Mariusz -- Mariusz Sterzel Email: msterzel/^at^\buffalo.edu On Mon, 3 Oct 2005, Noel O Boyle noel.oboyle2|*|mail.dcu.ie wrote: > > Sent to CCL by: "Noel O'Boyle" [noel.oboyle2++mail.dcu.ie] > Dear all, > > I have been trying to explain the results of a DFT study (using G03) > where a molecule adsorbs onto a gold cluster through its nitrogen atom. > > I created an isosurface of the change in the electron density associated > with the adsorption (by calculating the electron densities of the > molecule and the gold cluster separately at the geometry of the adsorbed > system). This shows that electron density *decreases* in the area > between the adsorbate and the surface. This is the opposite of what I > expected. > > A paper by Bilic, Reimers, Hush and Hafner (JCP, 2002, 116, 8981) shows > the same effect for ammonia on an infinite surface of gold(111). It > shows the same result, and says that this is evidence that covalent > bonding effects are not so important (they also have other evidence). > > It seems that I do not understand bonding very well - what keeps the > molecule stuck to the surface, if it isn't a shared electron or two? > > Regards, > Noel > -- > Dr. Noel M. O'Boyle, > Group of Dr. John Mitchell (http://www-mitchell.ch.cam.ac.uk), > Unilever Centre for Molecular Science Informatics, > Dept. of Chemistry, > University of Cambridge, > U.K.> > > > > From owner-chemistry@ccl.net Mon Oct 3 15:08:01 2005 From: "Ary Junior junior!A!aryjr.com" To: CCL Subject: CCL: W:Scientific Linux Message-Id: <-29479-051003150606-14153-g/hHM0zXYbU0/cDjQSbwcA(_)server.ccl.net> X-Original-From: "Ary Junior" Sent to CCL by: "Ary Junior" [junior[]aryjr.com] Hello. What about Scientific Linux? What's the advantage of use this distribution instead my Slackware? Thanks very much, Ary Junior From owner-chemistry@ccl.net Mon Oct 3 15:43:00 2005 From: "John McKelvey jmmckel#attglobal.net" To: CCL Subject: CCL: MOPAC QM/MM ...NOTHING TO DO WITH C++/F77 ...[:-) Message-Id: <-29480-051003145216-13307-/r9cjpIQUS9LJ2SyxJK2GQ[*]server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Oct 2005 13:49:44 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel**attglobal.net] All, Using MOPAC I would like to optimize excited state geometries of molecules imbeded in a solvent cage. Is there such a QM/MM code in the public domain? I would like to use my own version of MOPAC in such a program, or modify an existing one. Best regards, John McKelvey From owner-chemistry@ccl.net Mon Oct 3 17:12:00 2005 From: "John Hearns john.hearns*o*streamline-computing.com" To: CCL Subject: CCL: W:Scientific Linux Message-Id: <-29481-051003171123-6718-lMa2rxGoPKIwKIJiypRXig!^!server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 03 Oct 2005 22:11:10 +0100 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns::streamline-computing.com] On Mon, 2005-10-03 at 15:09 -0400, Ary Junior junior!A!aryjr.com wrote: > Sent to CCL by: "Ary Junior" [junior[]aryjr.com] > Hello. What about Scientific Linux? What's the advantage of use this distribution instead my Slackware? There is a little confusion about Scientific Linux. It is not a distribution which bundles lots and lots of scientific applications. However, it is intended for use by scientific/engineering sites. Scientific Linux started life at Fermilab in Illinois. At around the same time, CERN in Geneva were looking at their future roadmap. Redhat 9 was the end of the Redhat line, and Redhat Enterprise would be the long-term stable distribution. Fedora is not a good choice for a large scientific cluster - its lifetime is too short. Scientific Linux came about as a collaboration between Fermi and CERN. It is the equivalent of Redhat Linux - ie. it is a recompile from source, in the same way as CentOS etc. are. It has Kerberos and AFS support, as these are used at the big labs. It also has a long lifetime for each release, before they are declared end-of-life. We support Scientific Linux on customer clusters, though our default distribution is SuSE. I would say that Scientific Linux is a good choice if you are running scientific applications. Just don't expect those applications to be delivered to you as part of the distribution - the people who build this are high energy physicists. From owner-chemistry@ccl.net Mon Oct 3 21:13:00 2005 From: "Dr Seth Olsen s.olsen1[]uq.edu.au" To: CCL Subject: CCL: MOPAC QM/MM ...NOTHING TO DO WITH C++/F77 ...[:-) Message-Id: <-29482-051003210529-24836-5tHrVfTFXE04V4vaWBcYyQ . server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 04 Oct 2005 11:05:17 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1_._uq.edu.au] Hi John, If you're using Mopac 7, then I think that the MD library 'DYNAMO' has an interface. I believe also that Ghemical can run QM/MM with Mopac 7. If you're optimizing excited state geometries it may be useful to reparametrize the method against ab initio data. Some common semiempirical excited state methods (ZINDO) are parametrized against spectroscopic data - if the excited state dynamics leads out of the region where the field couples the states than the results might not be correct. I would refer you to works by Toniolo, Granucci and Martinez regarding this issue (udoubtedly this list is incomplete, but these names are at the top of my mind right now). Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1 _ uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- > From: "John McKelvey jmmckel#attglobal.net" Date: Tuesday, October 4, 2005 4:49 am Subject: CCL: MOPAC QM/MM ...NOTHING TO DO WITH C++/F77 ...[:-) > > Sent to CCL by: John McKelvey [jmmckel**attglobal.net] > All, > > Using MOPAC I would like to optimize excited state geometries of > molecules imbeded in a solvent cage. Is there such a QM/MM code > in the > public domain? I would like to use my own version of MOPAC in such > a > program, or modify an existing one. > > Best regards, > > John McKelvey > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the _ sign. You can > also> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Mon Oct 3 21:48:00 2005 From: "Joseph Han jhh3851:-:yahoo.com" To: CCL Subject: CCL: What keeps a molecule adsorbed? Message-Id: <-29483-051003175310-20447-070kFbdsCnN5V6NYnQ5SvQ%%server.ccl.net> X-Original-From: Joseph Han Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 3 Oct 2005 13:52:56 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joseph Han [jhh3851/a\yahoo.com] If the adsorption energy is small (< 5 kcal/mol), it might also be one of the following: (1) Basis set superposition error. You might need to do a counterpoise correction to address this. (2) Dipole-dipole interaction (e.g. van der Waals) where you induce a dipole in the gold cluster leading to weak electrostaic attraction. Joseph --- "Noel O Boyle noel.oboyle2|*|mail.dcu.ie" wrote: > > Sent to CCL by: "Noel O'Boyle" [noel.oboyle2++mail.dcu.ie] > Dear all, > > I have been trying to explain the results of a DFT study (using G03) > where a molecule adsorbs onto a gold cluster through its nitrogen atom. > > I created an isosurface of the change in the electron density associated > with the adsorption (by calculating the electron densities of the > molecule and the gold cluster separately at the geometry of the adsorbed > system). This shows that electron density *decreases* in the area > between the adsorbate and the surface. This is the opposite of what I > expected. > > A paper by Bilic, Reimers, Hush and Hafner (JCP, 2002, 116, 8981) shows > the same effect for ammonia on an infinite surface of gold(111). It > shows the same result, and says that this is evidence that covalent > bonding effects are not so important (they also have other evidence). > > It seems that I do not understand bonding very well - what keeps the > molecule stuck to the surface, if it isn't a shared electron or two? > > Regards, > Noel > -- > Dr. Noel M. O'Boyle, > Group of Dr. John Mitchell (http://www-mitchell.ch.cam.ac.uk), > Unilever Centre for Molecular Science Informatics, > Dept. of Chemistry, > University of Cambridge, > U.K.> > > >