From owner-chemistry@ccl.net Sat Mar 14 03:21:01 2009 From: "David A. Mannock dmannock!^!ualberta.ca" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38848-090314000013-21504-BK/6d/vZG75mo0xZbh5P/g[A]server.ccl.net> X-Original-From: "David A. Mannock" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Fri, 13 Mar 2009 22:00:00 -0600 Mime-Version: 1.0 Sent to CCL by: "David A. Mannock" [dmannock]-[ualberta.ca] Jimmy, It is inevitably the case that both experimental and computer scientists get it wrong as much as they get it right. In a perfect world, we would have to do only one experiment and one calculation per system. Having just read a lot of the 1930 sterol crystallography papers (Bernal et al 1940, PTRSL), I was surprised that they got so much correct, but in my own field, there is a heck of of a lot of rubbish which you have to sift through to get to the correct answer. This is true in computer chemistry as well as in lipid biophysics. One gentleman at the Royal Free Hospital, who I knew as a grad student in London, used to bully his people and rush them into publication. As a pioneer, he did a lot of incredible things, but few of his students and postdocs stayed in science and ultimately my colleague and myself had to repeat a lot of his work to sort out the problems. It just goes to prove that sometimes wanting to be famous can be counterproductive! Hence the saying, "Rubbish in! Rubbish out!" Don't believe the numbers in every table in every reference book that you have on your book shelf. Some of that info may be a typo, or 50 years out of date! If you find a number that is wrong, look for similar measurements on the same compound on the Web of Science in addition to doing the computer calculation. Dave At 06:51 PM 13/03/2009, you wrote: >Sent to CCL by: "James J. P. Stewart" [MrMOPAC]-[att.net] > >David Mannock said, "Sometimes computational chemists forget that it >is frequently possible to perform experiments on the systems on >which they work and so generate real numbers." While true in most >cases, the converse is also true sometimes. To illustrate: The NIST >WebBook represents one of the finest collections of thermochemical >data extant. During the development of PM6, a few instances were >found in the WebBook where reference heats of formation were simply >not credible, and using semiempirical methods I generated what I >considered to be more accurate values. On being informed of this, >NIST updated the WebBook to add or replace the experimental values >with the theoretically predicted values. For a list of these >species, see: >http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mask=1 > >The point is that although experimentalists generate real numbers, >on rare occasions the numbers in compendia such as the WebBook might >be of questionable accuracy. This may be due to any one of several >reasons, for example the experimental work might involve >questionable steps, the arithmetic involved in converting from >experimental measurement to heat of formation might be faulty, the >formula used might be incorrect, there might be typographic errors >in the journal article, or the printed heat of formation might be in >error by a sign. Examples of all of these errors were found on >reviewing the original literature written by >experimentalists. Simple computational chemistry calculations, >requiring only a few seconds each, revealed the potential >errors. That the reported data were inaccurate was confirmed by >examining the original articles and identifying the error. > >As a semiempiricalist, I am acutely aware of the great debt we owe >to the experimental community for generating reference data, but to >suggest that collections of experimental data should be regarded as >infallibly accurate and that computational results should be >regarded cum granus salis is simple unwarrented. > >Jimmy > > > ( !^! !^! ) > .-----------------oOOo----(_)----oOOo--------------------------------------. > | James J. P. Stewart | | > | Stewart Computational Chemistry | E-mail: MrMOPAC*OpenMOPAC.net | > | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | > | Colorado Springs CO 80921-2512 | http://openmopac.net/ | > | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| > | .ooo0 | Phone: USA +(719) 488-9416 | > | ( ) Oooo.| | > .-----------------------\ (----( )---------------------------------------. > \_) ) / > (_/ From owner-chemistry@ccl.net Sat Mar 14 12:26:02 2009 From: "Anatoli Korkin a_korkin%%yahoo.com" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38849-090314110104-26984-r0BS1TowSSMtKhSvt0EEhA#%#server.ccl.net> X-Original-From: Anatoli Korkin Content-Type: text/plain; charset=us-ascii Date: Sat, 14 Mar 2009 07:00:49 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [a_korkin : yahoo.com] Interesting discussion! I believe it is worth mentioning that with growing number of on-line publications and self-publications, some people, particularly the students, may have problems in identifying the right numbers and sources they can trust. Meanwhile, nowadays prior going to the library, most people first check with Mr. Google and then with more specific sources. Some people don't go in the libraries any more and even if they do most of the time they spend at the library computer anyway. "Internet research" and evaluation of the sources is becoming almost a profession on its own, sort of "internet scientist". I created a new web page - forums - at my informal educational web site, ASDN (nanotechnology for blonds, if you wish) and will appreciate references to the useful internet sources in the listed categories: http://asdn.net/asdn/links/nanoforums.shtml Best regards, Anatoli Korkin korkin<>nanoandgiga.com --- On Fri, 3/13/09, David A. Mannock dmannock!^!ualberta.ca wrote: > From: David A. Mannock dmannock!^!ualberta.ca > Subject: CCL: Computational Chemistry - Arm chair Scientists !!! > To: "Korkin, Anatoli " > Date: Friday, March 13, 2009, 9:00 PM > Sent to CCL by: "David A. Mannock" > [dmannock]-[ualberta.ca] > Jimmy, It is inevitably the case that both experimental and > computer scientists get it wrong as much as they get it > right. In a perfect world, we would have to do only one > experiment and one calculation per system. Having just read > a lot of the 1930 sterol crystallography papers (Bernal et > al 1940, PTRSL), I was surprised that they got so much > correct, but in my own field, there is a heck of of a lot of > rubbish which you have to sift through to get to the correct > answer. This is true in computer chemistry as well as in > lipid biophysics. One gentleman at the Royal Free Hospital, > who I knew as a grad student in London, used to bully his > people and rush them into publication. As a pioneer, he did > a lot of incredible things, but few of his students and > postdocs stayed in science and ultimately my colleague and > myself had to repeat a lot of his work to sort out the > problems. It just goes to prove that sometimes wanting to be > famous can be counterproductive! Hence the saying, > "Rubbish in! Rubbish out!" Don't believe the > numbers in every table in every reference book that you have > on your book shelf. Some of that info may be a typo, or 50 > years out of date! If you find a number that is wrong, look > for similar measurements on the same compound on the Web of > Science in addition to doing the computer calculation. Dave > > At 06:51 PM 13/03/2009, you wrote: > > > Sent to CCL by: "James J. P. Stewart" > [MrMOPAC]-[att.net] > > > > David Mannock said, "Sometimes computational > chemists forget that it is frequently possible to perform > experiments on the systems on which they work and so > generate real numbers." While true in most cases, the > converse is also true sometimes. To illustrate: The NIST > WebBook represents one of the finest collections of > thermochemical data extant. During the development of PM6, > a few instances were found in the WebBook where reference > heats of formation were simply not credible, and using > semiempirical methods I generated what I considered to be > more accurate values. On being informed of this, NIST > updated the WebBook to add or replace the experimental > values with the theoretically predicted values. For a list > of these species, see: > http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mask=1 > > > > The point is that although experimentalists generate > real numbers, on rare occasions the numbers in compendia > such as the WebBook might be of questionable accuracy. This > may be due to any one of several reasons, for example the > experimental work might involve questionable steps, the > arithmetic involved in converting from experimental > measurement to heat of formation might be faulty, the > formula used might be incorrect, there might be typographic > errors in the journal article, or the printed heat of > formation might be in error by a sign. Examples of all of > these errors were found on reviewing the original literature > written by experimentalists. Simple computational chemistry > calculations, requiring only a few seconds each, revealed > the potential errors. That the reported data were > inaccurate was confirmed by examining the original articles > and identifying the error. > > > > As a semiempiricalist, I am acutely aware of the great > debt we owe to the experimental community for generating > reference data, but to suggest that collections of > experimental data should be regarded as infallibly accurate > and that computational results should be regarded cum granus > salis is simple unwarrented. > > > > Jimmy > > > > > > ( !^! !^! ) > > > .-----------------oOOo----(_)----oOOo--------------------------------------. > > | James J. P. Stewart | > | > > | Stewart Computational Chemistry | E-mail: > MrMOPAC*OpenMOPAC.net | > > | 15210 Paddington Circle | 39/03/15 N, > 104/49/29 W | > > | Colorado Springs CO 80921-2512 | > http://openmopac.net/ | > > | USA | SKYPE: > Jimmy.Stewart2 GMT 1500 - 0200| > > | .ooo0 | Phone: USA > +(719) 488-9416 | > > | ( ) Oooo.| > | > > .-----------------------\ (----( > )---------------------------------------. > > \_) ) / > > (_/ > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the (~) sign. You > can alsoConferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml From owner-chemistry@ccl.net Sat Mar 14 16:40:00 2009 From: "m sabir shabbir3790###hotmail.com" To: CCL Subject: CCL: stability of two different systems Message-Id: <-38850-090314163743-29334-nXy6X3jRg2bddQy3KUQZQw%a%server.ccl.net> X-Original-From: "m sabir" Date: Sat, 14 Mar 2009 16:37:39 -0400 Sent to CCL by: "m sabir" [shabbir3790,+,hotmail.com] Hello dear ccl users, I have theoretically designed an alkali metal complex with cluster and now, wondering about its stability. I have calculated its vertical ionization potential that is about 6.53ev which is 4eV less that its cluster used in its complex formation. Although HOMO-LUMO gap has also decreased after the formation of alkali metal-cluster complex. Now my question are; 1- Is there any limit of ionization potential value above which we can say that the compounds with this or higher value will be stable? 2- Any other parameter besides above that can compare the stability of two different systems i.e. cluster and alkali-cluster complex? I have dire need of comments about this problem. Thanks for kind cosidrations! shabbir]|[nenu.edu.cn From owner-chemistry@ccl.net Sat Mar 14 17:24:01 2009 From: "Anindita De de.anindita]![gmail.com" To: CCL Subject: CCL:G: NBO problem Message-Id: <-38851-090314143328-13494-G3/oCO6gvKBz9uz1yNCquQ|a|server.ccl.net> X-Original-From: "Anindita De" Date: Sat, 14 Mar 2009 14:33:23 -0400 Sent to CCL by: "Anindita De" [de.anindita(_)gmail.com] Hi, While doing a NBO calculation of a Copper complex with Gaussian 03 programme I am always getting a error like this Sorting of NBOs: 282 224 213 230 220 259 265 248 273 258 Sorting of NBOs: 279 228 229 236 244 234 274 219 227 246 Sorting of NBOs: 270 211 210 215 216 202 218 206 226 285 Sorting of NBOs: 288 207 198 242 256 209 278 199 266 284 Sorting of NBOs: 287 243 254 260 264 241 271 238 240 214 Sorting of NBOs: 204 289 205 197 201 196 267 235 249 233 NBStor is confused about NOcc. Error termination via Lnk1e in C:\G03W\l607.exe at Sat Mar 07 15:46:25 2009. Job cpu time: 0 days 2 hours 26 minutes 38.0 seconds. File lengths (MBytes): RWF= 91 Int= 0 D2E= 0 Chk= 3 Scr= 1 I am using pop=(nbo, savenbo) keyword. Can anybody please tell me what is the problem? regards, Anindita From owner-chemistry@ccl.net Sat Mar 14 17:58:00 2009 From: "Kaliappan Muthukumar muthukumar2k3,+,gmail.com" To: CCL Subject: CCL: Turbomole 5.8: Generating localized orbitals Message-Id: <-38852-090314055326-28446-OH3oD4NwFSmlcnXP0Y2nxQ(-)server.ccl.net> X-Original-From: Kaliappan Muthukumar Content-Type: multipart/alternative; boundary=001636c5b47e4025d0046510c051 Date: Sat, 14 Mar 2009 09:22:06 +0000 MIME-Version: 1.0 Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3() gmail.com] --001636c5b47e4025d0046510c051 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Thomas, Use the ridft -proper or dscf -proper with the pointval option (mentioning the no of orbitals that you find in eiger) in a single processor. You will end up with the .plt files and .xyz which are the input files. Then follow the last section of the following tutorial. http://www.cosmologic.de/data/Tutorial_6-0.pdf Best regards, Muthu On Fri, Mar 13, 2009 at 3:07 PM, Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner,tugraz.at wrote: > > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner.. > tugraz.at] > Hello! > I am trying to generate localized orbitals for plotting in gOpenMol with > Turbomole 5.8. However, the documentation is rather unclear on how to > prepare the input file, whether to use the (unsupported) moloch program > or the dscf program, how to choose the orbitals to be plotted etc. > > Could anyone give me a sample input file (or rather the keywords needed) > to perform the localization of mos? > > Thank you, > > Thomas> > > -- ---------------------------------------------------------- With My Best Wishes, Kaliappan Muthukumar, ------------------------------------------------------------ --001636c5b47e4025d0046510c051 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Thomas,
=A0
Use the ridft -proper or dscf -proper with the pointval option (mentio= ning the no of orbitals that you find in eiger) in a single processor.
=A0
You will end up with the .plt files and .xyz which are the input files= .
=A0
Then follow the last section of the following tutorial.
=A0
Best regards,
Muthu


=A0
On Fri, Mar 13, 2009 at 3:07 PM, Dipl.-Ing. Thom= as Mitterfellner thomas.mitterfellner,tugraz.a= t <owne= r-chemistry^^^ccl.net> wrote:

Sent to CCL by: "Dipl.-= Ing. Thomas Mitterfellner" [thomas.mitterfellner..tugraz.at]
Hello!
I am trying to generate localized orbitals for plotting in gOpenM= ol with
Turbomole 5.8. However, the documentation is rather unclear on h= ow to
prepare the input file, whether to use the (unsupported) moloch pr= ogram
or the dscf program, how to choose the orbitals to be plotted etc.

C= ould anyone give me a sample input file (or rather the keywords needed)
= to perform the localization of mos?

Thank you,

Thomas



-=3D This is automatically added to each message by the mailing= script =3D-
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--
--------------= --------------------------------------------
With My Best Wishes,
Kaliappan Muthukumar,
-------------------------= -----------------------------------
--001636c5b47e4025d0046510c051-- From owner-chemistry@ccl.net Sat Mar 14 23:51:01 2009 From: "Arthur computationalboy[*]gmail.com" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38853-090314234818-22332-2HvhIEUMNt6hhT6fjhJV6w-*-server.ccl.net> X-Original-From: Arthur Content-Type: multipart/alternative; boundary=000e0cd2426241e83204652033b3 Date: Sun, 15 Mar 2009 11:48:00 +0800 MIME-Version: 1.0 Sent to CCL by: Arthur [computationalboy%a%gmail.com] --000e0cd2426241e83204652033b3 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, Anandarup, the Tripos Benchware 3D Explorer can reach your requirement. It is commercially available, though you can request a free evaluation copy for one month. http://www.tripos.com/index.php?family=modules,SimplePage,lab_informatics Regards! Arthur On Thu, Mar 5, 2009 at 7:54 AM, Anandarup Goswami ananda1911[A]gmail.com < owner-chemistry---ccl.net> wrote: > Hi all, > I am using powewrpoint in my mac to make presentation. I have to put some > calculated structures in my slides. I have been using chemcraft and > gaussview to make the picture. But it would have been much better if I could > allow some of my structures to rotate freely (like a movie file) during my > presentation. I am relatively new to this field and have no experience in > this kind of 3D effect particularly in mac. Any help regarding this would be > highly appreciated. > Thanks, > Anandarup Goswami > -- Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China Tel : +86 24 23986419 Fax: +86 24 23995043 E-Mail: wjmed(at)126.com ; computationalboy(at)gmail.com --000e0cd2426241e83204652033b3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi, Anandarup, the Tripos Benchware 3D Explorer can reach your require= ment.
It is commercially available, though you can request a free evaluation= copy for one month.
Regards!
Arthur

On Thu, Mar 5, 2009 at 7:54 AM, Anandarup Goswam= i ananda1911[A]gmail.com <owner-chemistry---ccl.net= > wrote:
Hi all,
I am using powewrpoin= t in my mac to make presentation. I have to put some calculated structures = in my slides. I have been using chemcraft and gaussview to make the picture= . But it would have been much better if I could allow some of my structures= to rotate freely (like a movie file) during my presentation. I am relative= ly new to this field and have no experience in this kind of 3D effect parti= cularly in mac. Any help regarding this would be highly appreciated.
Thanks,
Anandarup Goswami



--
Arthur J. Wang
Shenyang Pharmace= utical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenya= ng,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail: =A0wjmed(at)126.com ;
=A0 =A0 =A0computationalboy(at)gmail.com
--000e0cd2426241e83204652033b3--