Thanks so much in advance DIV>

Best wishes

Hossein

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On Oct 28, = 2007, at 9:19 AM, yorth kos yortama2003^_^yahoo.ca wrote:

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Date: October 21, 2007 7:36:28 AM = MDT

Subject: = The caretesian coordintes of fullerenes
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Dear Folks

=A0 I'm interested to have a full = information regarding to the Cartesian coordinates(xyz) of different = carbon nanotubes and their derivatives.It is appreciated if anyone could = kindly give me a clear address about them .

=A0 Thanks so much in = advance
=A0 Best wishes
=A0 = Hossein

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<DIV>Dear = Folks</DIV>=A0 = <DIV> </DIV>=A0 <DIV>I'm interested to = have a full information regarding to the Cartesian coordinates(xyz) of = different carbon nanotubes and their derivatives.It is appreciated if = anyone could kindly give me a clear address about them = .</DIV>=A0 = <DIV> </DIV>=A0 <DIV>Thanks so much in = advance</DIV>=A0 = <DIV>Best wishes</DIV>=A0 = <DIV>Hossein</DIV><p> 
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= --Apple-Mail-4-553612760-- From owner-chemistry@ccl.net Mon Oct 29 11:23:00 2007 From: "David Gallagher gallagher.da:_:gmail.com" To: CCL Subject: CCL: Fluorescence spectra Message-Id: <-35517-071029112035-6198-5ntI5CsinuADGjqzj/Ti/Q^server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 29 Oct 2007 08:21:46 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da * gmail.com] Hi Naser, I am not aware of any specific programs for fluorescence prediction, but I have used the following approach with some success: Fluorescence emission usually occurs from the first excited singlet state to the ground singlet state. After excitation, as the rate constant for fluorescence is typically much slower than the rate constant for vibrational relaxation, the molecule will have time for the geometry to relax to an excited-singlet geometry before fluorescing. However, the rate of photon emission is so fast that the excited-singlet geometry does not have time to relax during the fluorescence (Frank-Condon principle applies). As the probability of emission and absorption are the same, a UV-visible absorption spectrum calculation such as ZINDO (C.I.) on the excited-singlet geometry should provide a reasonable approximation to the fluorescence emission. However, just as with UV-visible absorption spectra, ZINDO estimates only pure S0 - S1 electronic transitions without any vibrational fine structure, so vibrational fine structure is not reproduced. Also, although, trends are usually well predicted with ZINDO (providing the geometries are good), the results often benefit from experimental calibration. Regards, David Gallagher CAChe Research At 02:05 AM 10/29/2007, Naser Eltaher Eltayeb nasertaha90(0)yahoo.co.uk wrote: >Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90-x-yahoo.co.uk] >Dear All > >Is there any programme can calculate and predict the fluorescence spectra? > > >thank you > >Naser Eltaher Eltayeb From owner-chemistry@ccl.net Mon Oct 29 11:59:01 2007 From: "Steve Bowlus chezbowlus _ comcast.net" To: CCL Subject: CCL: More about STERIMOL parameters Message-Id: <-35518-071029095040-11844-bjC6uj7NpIFy8q5EzADyIw**server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 29 Oct 2007 06:31:38 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus^-^comcast.net] The supplemental documentation for STERIMOL, now available at the CCL site, includes correspondence that addresses this point. The conformation dependence of the parameters is clear. So long as the investigator strictly adopts a consistent scheme, consistent _differences_ emerge. Remember, these are QSAR descriptors: it is their variances that is modeled, not the absolute magnitudes. But take a look at the documentation ... Steve Bowlus Tamas Gunda tgunda2(_)puma.unideb.hu wrote: > > Sent to CCL by: "Tamas Gunda" [tgunda2[*]puma.unideb.hu] > The problem with the sterimol parameters is that the values are strongly > depending on the input geometry of the residue and which bond has been > used to create the residue. In case of an ethyl group there aren't too > much possibilities, but as the residues grow the number of input > variations grow accordingly. For example, in the case of propane you > can create geomertically two different propyl residues depending on > which of the CH3 hydrogens has been removed. The obtained sterimol > parameters: > > Propyl (1): > > L: 5.05 > B1 - B5: 1.55, 1.91, 1.91, 3.51, 3.51 > L/B1: 3.25 > B4/B1: 2.26 > > > or propyl(2): > > L: 4.17 > B1 - B5: 1.56, 1.92, 3.16, 4.22, 4.43 > L/B1: 2.68 > B4/B1: 2.71 > > > Dr. Tamas E. Gunda > University of Debrecen > Department of Pharmaceutical Chemistry > H-4010 Debrecen, POB 36, Hungary > tgunda2 {at} puma.unideb.hu > > > > > > > ----- Original Message ----- > >> From: "Jinsong Zhao jszhao*mail.hzau.edu.cn" > > To: "Gunda, Tamas E " > Sent: Sunday, October 28, 2007 14:34 PM > Subject: CCL: More about STERIMOL parameters > > >> >> Sent to CCL by: "Jinsong Zhao" [jszhao__mail.hzau.edu.cn] >> Dear all, >> >> Recently, I read the paper about STERIMOL parameters in drug design*. >> And fortunately, I get the STERIMOL program written by W. >> Hoogenstraaten, and ported to PC by Stephen B. Bowlus. >> >> I have read the rules of molecule notation carefully, which is kindly >> provided by Stephen B. Bowlus. However, I also can not get the same >> results published by A. Verloop et al. for substituent CH2CH3, though >> I think the input card HC(H,H)C(H,H,H)* is correct. Therefore, I think >> there must be something wrong in my input file, otherwise, the results >> published may be wrong. >> >> So I hop to get help from you, if you would like to give me one or >> more examples on how to prepare the input file for STERIMOL program, >> or help me to contact the author of the paper published in 1976 (I can >> not find their recent address). >> >> *Verloop, A., Hoogenstraaten, W. and Tipker, J. Development and >> applications of new steric substituent parameters in drug design. In: >> Ariens, E. J. (Editor) Drug design. 1976, Vol. 7. 165-207. New York: >> Academic Press. >> >> Thank you very much for your attention on this topic, and look forward >> to your reply. >> >> Best regards, >> >> Jinsong >> >> -- >> Dr. Jinsong Zhao >> College of Resources and Environment >> Huazhong Agricultural University >> No.1 Shizishan Road, Wuhan 430070 >> P.R. China >> E-mail: jszhao .. mail.hzau.edu.cnhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > From owner-chemistry@ccl.net Mon Oct 29 12:34:01 2007 From: "Karol Langner karol.langner]_[kn.pl" To: CCL Subject: CCL: error in CCSD calculation in g03 Message-Id: <-35519-071029115509-32356-so8TpQrysyKA77EkGtNVMA-.-server.ccl.net> X-Original-From: Karol Langner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 29 Oct 2007 17:43:41 -0400 MIME-Version: 1.0 Sent to CCL by: Karol Langner [karol.langner[*]kn.pl] On Monday 29 October 2007 05:26, Pablo Echenique echenique.p(~)gmail.com wrote: > Now, if I try to perform a single point energy calculation at > CCSD/aug-cc-pVTZ with the following header: > > %mem=1500MB > # CCSD/aug-cc-pVTZ 5D 7F SCF=Tight TrackIO GFInput > MaxDisk=32GB > > on formamide (HCONH2), I get the following error: > > Estimate disk for full transformation 1395760528 words. > Semi-Direct transformation. > ModeAB= 2 MOrb= 204 LenV= 195422800 > LASXX= 201330812 LTotXX= 293577723 LenRXX= 604717200 > LTotAB= 19144000 MaxLAS= 604717200 LenRXY= 19144000 > NonZer= 616154970 LenScr= 927215616 LnRSAI= 0 > LnScr1= 0 LExtra= 4174627 Total= 1555251443 > MaxDsk= 4294967296 SrtSym= F ITran= 5 > JobTyp=0 Pass 1: I= 1 to 204. > Erroneous read. Read 0 instead of 6258688. > fd = 4 > g_read Your rwf file is probably larger than MaxDisk. If you have more disk space, raise the value. -- written by Karol Langner Mon Oct 29 17:41:51 EDT 2007 From owner-chemistry@ccl.net Mon Oct 29 13:40:01 2007 From: "Reinaldo Pis Diez reinaldo.pisdiez() gmail.com" To: CCL Subject: CCL:G: UV-Vis spectra Message-Id: <-35520-071028210522-15522-0dm2CA95KKNCZ9XrXWvlkA__server.ccl.net> X-Original-From: "Reinaldo Pis Diez" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 28 Oct 2007 21:02:02 -0300 MIME-Version: 1.0 Sent to CCL by: "Reinaldo Pis Diez" [reinaldo.pisdiez!^!gmail.com] Dear Jerome, Did you make a conformational search before calculating uvvis spectra? It's quite possible that you weren't dealing with lowest-energy conformers but with some lower-energy ones, instead. On the other hand, I'm not sure if you can expect quantitative results in such cases. You are having a qualitative red shift after all! Best wishes, Reinaldo 2007/10/28, Jerome Kieffer jerome.Kieffer]*[terre-adelie.org : > Dear CCLers, > > I have a question regarding the simulation of electronic transitions : > I calculated the UV-Vis spectra of two molecules using TD-DFT with a > B3LYP/6-31G(d,p) + PCM > > The results are very good for one of the two moleules and very bad > for the other. > The two molecules are based on a 1-10-phenanthroline substituted in > position 3 & 8 by two bithienyls. The spectrum of this molecule is very > well reproduced. If I add 2 methyls in position 2 & 9 of the > phenanthroline this induces a twist and breaks a bit the conjugaison. > For this second molecule, the experimental spectrum shows a red shift > of 70nm but only 20nm according to the calculation. > > Do you have an idea of the reason of this differance ? is it linked with > the geo-optimisation (should I increase the basis set size ?) or with > TDDFT ? > > Another question : is it possible to calculate fluorescence spectra > using Gaussian or another QM software ? > > Thank you for your help, best regards. > > -- > J=E9r=F4me KIEFFER : http://www.terre-adelie.org > > From owner-chemistry@ccl.net Mon Oct 29 15:08:01 2007 From: "errol lewars elewars#,#trentu.ca" To: CCL Subject: CCL:G: global optimisation Message-Id: <-35521-071029134156-30798-0+AbhS9wttQ/mlzuVX9k4Q**server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 29 Oct 2007 12:43:12 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars%x%trentu.ca] 2007 Oct 29 If you're interested in locating the global minimum corrsponding to a particular molecular formula (e.g. the lowest-energy C4H4O structure) look at: J Wales, H A Scheraga, "Global optimization...", Science, 1999, 285 (27 August), 1368 X. Yang,..., "Global investigation of the potential energy surface...", J Phys Chem A, 2005, 109(32), 7310 H. F. Schaefer, P. v. R. Schleyer, "Mindless Chemistry", J Phys Chem A, 2006, 110(13), 4287 E. Lewars ==== Pierre Archirel pierre.archirel*o*lcp.u-psud.fr wrote: > > Sent to CCL by: Pierre Archirel [pierre.archirel^lcp.u-psud.fr] > Dear Yangsoo Kim, > I am afraid you mistake local minima and transition states: > 1- imaginary frequencies caracterise points that are not minimas, > like saddle points. > 2- all the local minimas and the global minimum as well, > do have real frequencies. > 3- if your system has several local minimas, the only way to find > the global one is to perform several optimisations with several > starting points. If your system is big, force fields can help you > in building these starting points. > This job can be tedious, but can be done with g03. > Best wishes, > P.A. > > __________________________________________________________ > > Pierre Archirel > Groupe de Chimie Th�orique > Laboratoire de Chimie Physique Tel: 01 69 15 63 86 > Bat 349 Fax: 01 69 15 61 88 > 91405 Orsay Cedex > France pierre.archirel!^!lcp.u-psud.fr > __________________________________________________________http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Oct 29 22:04:00 2007 From: "John McKelvey jmmckel::gmail.com" To: CCL Subject: CCL:G: UV-Vis spectra Message-Id: <-35522-071029200645-17333-fA+22vO2sbYOEdAewBZhOw!^!server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_1015_13540299.1193702792599" Date: Mon, 29 Oct 2007 20:06:32 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel]_[gmail.com] ------=_Part_1015_13540299.1193702792599 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hello! Could I comment on this, please? I've been working with Zerner's INDO/S [and also the program package ZINDO] for approximately forty (40 !) years, and for the last five years or so I've tried reparameterizing for the general case, i.e.across multiple structure spaces simultaneously. Even with high quality geometries, i.e.x-ray or DFT, it's (almost) impossible to get a uniform set of parameters for multiple different structure spaces!! Further, within a given structure space one might get a good linear correlation with good statistics, but the intercept will not likely be approximately zero, and th= e slope of the line will not (likely) be one!! Errors of 0.1 to 0.2 EV shoul= d not be shocking, though will likely be quite disappointing. Further, across multiple structure spaces the "best" DFT functional, the best affordable basis set, and high quality geometries are not a guarantee that in the absolute sense you'll do better than 0.1EV, and maybe 0.15 to 0.2 EV. It can be difficult enough even within a given structure space. Is it heresy to say still that understanding trends give us a significant portion of our understanding in chemistry (starting with the periodic table!!) ? Conclusion: Regardless of the method you use you have to calibrate, calibrate, calibrate... Constructive, illuminating comments are welcome!! Cheers! John McKelvey On 10/28/07, Reinaldo Pis Diez reinaldo.pisdiez() gmail.com < owner-chemistry!A!ccl.net> wrote: > > > Sent to CCL by: "Reinaldo Pis Diez" [reinaldo.pisdiez!^!gmail.com] > > Dear Jerome, > > Did you make a conformational search before calculating uvvis spectra? > It's quite possible that you weren't dealing with lowest-energy > conformers but with some lower-energy ones, instead. > On the other hand, I'm not sure if you can expect quantitative results > in such cases. You are having a qualitative red shift after all! > Best wishes, > > Reinaldo > > 2007/10/28, Jerome Kieffer jerome.Kieffer]*[terre-adelie.org > : > > Dear CCLers, > > > > I have a question regarding the simulation of electronic transitions : > > I calculated the UV-Vis spectra of two molecules using TD-DFT with a > > B3LYP/6-31G(d,p) + PCM > > > > The results are very good for one of the two moleules and very bad > > for the other. > > The two molecules are based on a 1-10-phenanthroline substituted in > > position 3 & 8 by two bithienyls. The spectrum of this molecule is very > > well reproduced. If I add 2 methyls in position 2 & 9 of the > > phenanthroline this induces a twist and breaks a bit the conjugaison. > > For this second molecule, the experimental spectrum shows a red shift > > of 70nm but only 20nm according to the calculation. > > > > Do you have an idea of the reason of this differance ? is it linked wit= h > > the geo-optimisation (should I increase the basis set size ?) or with > > TDDFT ? > > > > Another question : is it possible to calculate fluorescence spectra > > using Gaussian or another QM software ? > > > > Thank you for your help, best regards. > > > > -- > > J=E9r=F4me KIEFFER : http://www.terre-adelie.org > > > > > > > > - This is automatically added to each message by the mailing script -> > > > ------=_Part_1015_13540299.1193702792599 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hello!

Could I comment on this, please?

I've been working with Zerner's INDO/S [and also the program package ZINDO] for approximately forty (40 !) years, and for the last five years or so I've tried reparameterizing for the general case, i.e.across mult= iple structure spaces simultaneously. Even with high quality geometr= ies, i.e.x-ray or DFT, it's (almost) impossible to get a uniform set o= f parameters for multiple different structure spaces!! Further, within = a given structure space one might get a good linear correlation with good statistics, but the intercept will not likely be approximately zero, and the slope of the line will not (likely) be one!! Errors of 0.1 to 0.2 EV should not be shocking, though will likely be quite disappointing.

Further, across multiple structure spaces the "best" DFT functional, the b= est affordable basis set, and high quality geometries are not a guarantee that in the absolute sense you'll do better than 0.1EV, and maybe 0.15 to 0.2 EV. It can be difficult enough even within a given structure space.

Is it heresy to say still that understanding trends give us a significant portion of our understanding in chemistry (starting with the periodic table!!) ?

Conclusion: Regardless of the method you use you have to cali= brate, calibrate, calibrate...

Constructive, illuminating comments are welcome!!

Cheers!

John McKelvey

On 10/28/07, Reinaldo Pis Diez reinaldo= .pisdiez () gmail.com <owner-chemistry!A!ccl.net> wrote:
Sent to CCL by: "Reinaldo Pis Diez" [reinaldo.pisdiez!^!gmail= .com]

Dear Jerome,

Did you make a conformational search befor= e calculating uvvis spectra?
It's quite possible that you weren'= t dealing with lowest-energy
conformers but with some lower-energy ones, instead.
On the other ha= nd, I'm not sure if you can expect quantitative results
in such case= s. You are having a qualitative red shift after all!
Best wishes,

Reinaldo

2007/10/28, Jerome Kieffer jerome.Kieffer]*[terre-adelie.org
<owner-chemistry/./ccl.= net>:
> Dear CCLers,
>
> I have a question regarding t= he simulation of electronic transitions :
> I calculated the UV-Vis spectra of two molecules using TD-DFT with= a
> B3LYP/6-31G(d,p) + PCM
>
> The results are very good= for one of the two moleules and very bad
> for the other.
> Th= e two molecules are based on a 1-10-phenanthroline substituted in
> position 3 & 8 by two bithienyls. The spectrum of this molecul= e is very
> well reproduced. If I add 2 methyls in position 2 & 9= of the
> phenanthroline this induces a twist and breaks a bit the co= njugaison.
> For this second molecule, the experimental spectrum shows a red sh= ift
> of 70nm but only 20nm according to the calculation.
>
= > Do you have an idea of the reason of this differance ? is it linked wi= th
> the geo-optimisation (should I increase the basis set size ?) or w= ith
> TDDFT ?
>
> Another question : is it possible to ca= lculate fluorescence spectra
> using Gaussian or another QM software = ?
>
> Thank you for your help, best regards.
>
> --<= br>> J=E9r=F4me KIEFFER  : http://www.terre-adelie.org
>
>

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