From owner-chemistry@ccl.net Mon Dec 3 02:03:00 2007 From: "Soren Eustis soreneustis\a/gmail.com" To: CCL Subject: CCL:G: Band gap Message-Id: <-35750-071202235129-27368-j6Ghnm4KP+NZ8m3CGAMazg!^!server.ccl.net> X-Original-From: "Soren Eustis" Content-Type: multipart/alternative; boundary="----=_Part_6033_9973848.1196654035194" Date: Sun, 2 Dec 2007 22:53:55 -0500 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soreneustis=-=gmail.com] ------=_Part_6033_9973848.1196654035194 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Naser, These are in a.u. or Hartrees. This corresponds to a gap of 1.09 eV, which seems reasonable. Soren Eustis On Dec 2, 2007 8:36 PM, Naser Eltaher Eltayeb nasertaha90-$-yahoo.co.uk < owner-chemistry[a]ccl.net> wrote: > > Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 ~ yahoo.co.uk] > Dear All > > 1-Could any one give me details about How can I calculate the band gap > (HOMO-LUMO) energy,using Gaussian 03. > > 2- I am tring to calculate the band gap by generating the molecular > orbital after optimization, then I looked to energy of HOMO and LUMO , I > found the energy of HOMO= -0.261 and the energy of LUMO = -0.221. First > what the unit of energy of HOMO and LUMO in Gasssian 03, secondly is the > band gap 0.04 acceptable?> > > ------=_Part_6033_9973848.1196654035194 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Naser,

   These are in a.u. or Hartrees.  This corresponds to a gap of 1.09 eV, which seems reasonable. 

Soren Eustis

On Dec 2, 2007 8:36 PM, Naser Eltaher Eltayeb nasertaha90-$- yahoo.co.uk <owner-chemistry[a]ccl.net> wrote:

Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 ~ yahoo.co.uk]
Dear All

1-Could any one give me details about How can I calculate the band gap (HOMO-LUMO) energy,using Gaussian 03.

2- I am tring to calculate the band gap by generating the molecular orbital after optimization, then I looked to energy of HOMO and LUMO , I found the energy of HOMO= -0.261 and the energy of LUMO = -0.221. First what the unit of energy of HOMO and LUMO in Gasssian 03, secondly is the band gap 0.04 acceptable?



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------=_Part_6033_9973848.1196654035194-- From owner-chemistry@ccl.net Mon Dec 3 11:50:01 2007 From: "irfan ahmad irfaahmad*gmail.com" To: CCL Subject: CCL:G: Band gap Message-Id: <-35751-071203090021-1138-H1vothDqOzZrBNL3Ismp1A]~[server.ccl.net> X-Original-From: "irfan ahmad" Content-Type: multipart/alternative; boundary="----=_Part_8103_19916394.1196686477346" Date: Mon, 3 Dec 2007 20:54:37 +0800 MIME-Version: 1.0 Sent to CCL by: "irfan ahmad" [irfaahmad##gmail.com] ------=_Part_8103_19916394.1196686477346 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline yes it is 0.04, unit are hatrees. if u multiply with 27.2116 it will be 1.088 eV On 12/3/07, Naser Eltaher Eltayeb nasertaha90-$-yahoo.co.uk < owner-chemistry,+,ccl.net> wrote: > > > Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 ~ yahoo.co.uk] > Dear All > > 1-Could any one give me details about How can I calculate the band gap > (HOMO-LUMO) energy,using Gaussian 03. > > 2- I am tring to calculate the band gap by generating the molecular > orbital after optimization, then I looked to energy of HOMO and LUMO , I > found the energy of HOMO= -0.261 and the energy of LUMO = -0.221. First > what the unit of energy of HOMO and LUMO in Gasssian 03, secondly is the > band gap 0.04 acceptable?> > > ------=_Part_8103_19916394.1196686477346 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline yes it is 0.04, unit are hatrees. if u multiply with 27.2116 it will be 1.088 eV

On 12/3/07, Naser Eltaher Eltayeb nasertaha90-$-yahoo.co.uk <owner-chemistry,+,ccl.net > wrote:

Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 ~ yahoo.co.uk ]
Dear All

1-Could any one give me details about How can I calculate the band gap (HOMO-LUMO) energy,using Gaussian 03.

2- I am tring to calculate the band gap by generating the molecular orbital after optimization, then I looked to energy of HOMO and LUMO , I found the energy of HOMO= - 0.261 and the energy of LUMO = -0.221. First what the unit of energy of HOMO and LUMO in Gasssian 03, secondly is the band gap 0.04 acceptable?



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------=_Part_8103_19916394.1196686477346-- From owner-chemistry@ccl.net Mon Dec 3 12:25:00 2007 From: "may abdelghani may01dz#%#yahoo.fr" To: CCL Subject: CCL: structural isomerism and fluxional isomerism Message-Id: <-35752-071203043832-10921-8pF/qKXZfvpkajLefYGJIg:+:server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1560657719-1196671410=:3861" Date: Mon, 3 Dec 2007 09:43:30 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz+/-yahoo.fr] --0-1560657719-1196671410=:3861 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit dear CCLers, First, what is the different between the structural isomerism and fluxional isomerism? How we can distinct between them? How we can expect, or study theoretically, the fluxional behaviour of some molecules (from the shape of the orbital and its interaction with each other, for exemple)? thanks --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-1560657719-1196671410=:3861 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit dear CCLers,

First, what is the different between the structural isomerism and fluxional isomerism?
How we can distinct between them?
 How we can expect, or study theoretically, the fluxional behaviour of some molecules (from the shape of the orbital and its interaction with each other, for exemple)?

thanks

Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-1560657719-1196671410=:3861-- From owner-chemistry@ccl.net Mon Dec 3 13:00:01 2007 From: "Mark Mackey mark#,#cresset-bmd.com" To: CCL Subject: CCL: FieldTemplater - find bioactive conformations from ligand data alone Message-Id: <-35753-071203115627-19024-1GVZF2h8ZYMk/aluPRPKRQ%%server.ccl.net> X-Original-From: "Mark Mackey" Date: Mon, 3 Dec 2007 11:56:23 -0500 Sent to CCL by: "Mark Mackey" [mark],[cresset-bmd.com] Cresset BioMolecular Discovery Ltd announces the release of FieldTemplater (GUI version) version 2 for Windows or Linux workstations. This is an upgrade of our Linux command line FieldTemplater program to give the benefits of a user-friendly front-end and simple operation on a local PC. FieldTemplater is a unique application that generates bioactive conformation hypotheses ('field templates') from ligand data alone. The models it produces go far beyond traditional three- or four-point pharmacophores: FieldTemplater can suggest not only what the bioactive conformation of each active is, but also the relative alignment of the molecules in the binding site. All that is required is the 2D structure of three active molecules: no protein data is required. It is thus ideal for generating bioactive conformation models for GPCRs and ion channel ligands. FieldTemplater is based on the assumption that each protein active site requires a complementary electrostatic and steric field pattern in its ligands. Thus ligands that bind at the same site should display a common field pattern in their bioactive conformations. FieldTemplater uses Cressets field similarity technology to find those conformations of each ligand that can display a common field pattern and presents these as hypotheses for the bioactive conformation. You can use FieldTemplater to generate a bioactive conformation model and then use Cressets FieldAlign program to overlay multiple other molecules (from 2D) onto the template. This allows rapid exploration of SAR in terms of molecular fields, as well as suggesting targets for synthesis. Together, FieldTemplater and FieldAlign provide a valuable lead optimisation tool for modelers and chemists to explore new chemotypes and substitution patterns and compare these to their bioactive conformation model. In this way, field SAR can be explored and refined in a qualitative way. The FieldTemplater front-end is based on our popular FieldAlign GUI program and therefore extends the range of our hit-to-lead and lead optimisation software that can be used by both molecular modellers and medicinal chemists. Download a free 30 day fully-functional evaluation of FieldAlign and FieldTemplater from our website: http://www.cresset-bmd.com/fieldalign.shtml http://www.cresset-bmd.com/fieldtemplater.shtml -- Dr Mark Mackey Director, Development Cresset Biomolecular Discovery Ltd From owner-chemistry@ccl.net Mon Dec 3 13:35:00 2007 From: "errol lewars elewars||trentu.ca" To: CCL Subject: CCL:G: basis set erroneous concept Message-Id: <-35754-071203103811-10101-uvQzj3GqZ5FEXaaNlnanjA(_)server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Dec 2007 10:38:14 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars[a]trentu.ca] 2007 Dec 3 Hello, re "question is: 6-31G basis set for C_sp3 is similar to 6-31G basis set for C_sp2 ." Basis sets are sets of mathematical functions whose purpose is to approximate, via molecular orbitals and a (or more than one) Slater determinant, the molecular wavefunction. The standard procedure is to put basis functions on atoms, so in an oversimplified way they are akin to conventional atomic orbitals. What you do with basis functions other than approximating a molecular wavefunction is optional. Hybridization, for example, is only a kind of mathematical trick, a convenient way of viewing the electron distribution around an atom. E. Lewars === John McKelvey jmmckel _ gmail.com wrote: > This is a very good question!! > > The short answer is that the iterative SCF process, whether > Hartree-Fock or DFT, allows the distribution of electrons to be > optimal for any local chemical environment. This process has optimal > chance of representing the "true chemical picture" the larger the > number of mathematical electronic distribution functions, here basis > orbitals. Hence, a simple Slater orbital, or its popular Gaussian > approximation STO-nG, is at the most restrictive end of the spectrum, > while something like 6-311++G** is in the direction of the much more > flexible set of distribution functions, but not necessarily _the_ most > flexible, but may be close enough for practical application. Now > something like 6-31G is in between, among many other possibilities. > Which of the intermediate set of functions one chooses is controlled > by how well it allows the most suitable results for a given application. > > There are many papers by the Pople group published during the > development of various basis sets, just to mention one of many places > to read about this. > > Hope this helps! > > Cheers, > > John McKelvey > > On Dec 1, 2007 6:35 AM, mohamed aish mhmdaish!^!yahoo.com > > wrote: > > Hi All; > I am a new in computational chemistry field. Now, I am reading > about the basis sets. There are something confused me and would be > appreciative if anyone helps me to correct my erroneous concepts. > Suppose that we have a compound containing carbons with sp^2 and > sp^3 hybridization, for example CH_3 CH=CH_2 , and the basis set > is 6-31G. Now my question is: 6-31G basis set for C_sp3 is similar > to 6-31G basis set for C_sp2 . Is this right??!! Please correct my > concept. > > Thanks a Lot > > > ------------------------------------------------------------------------ > Be a better sports nut! Let your teams follow you with Yahoo > Mobile. Try it now. > > > From owner-chemistry@ccl.net Mon Dec 3 14:10:00 2007 From: "Roman D. Gorbunov rgorbuno*aecom.yu.edu" To: CCL Subject: CCL:G: Gaussian problem: What is PrismC? Message-Id: <-35755-071203125141-22560-sGUO2sZgdih+gQ+9RbyHhg]-[server.ccl.net> X-Original-From: "Roman D. Gorbunov" Date: Mon, 3 Dec 2007 12:51:38 -0500 Sent to CCL by: "Roman D. Gorbunov" [rgorbuno++aecom.yu.edu] Dear CCL Subscribers, I run a set of similar Gaussian jobs (geometry optimization + normal mode frequencies calculations for system consisting of 61 atoms). All this calculations have been finished with the "Normal Termination". However, I am not able to get "Normal Termination" if I slightly change the system. I just remove some atoms and add new ones (so that the totals size of the system increases to 64 atoms). In the "problematic" case I have no error message. Gaussian just stops. In the and of the output file I find the following: Number of processors reduced from 4 to 1 for far-field. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. Number of processors reduced from 4 to 1 for far-field. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. Number of processors reduced from 4 to 1 for far-field. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. PrismC: NFx= 2048 NFxT= 4 NFxU= 4. It is repeating many times and the Gaussian stops with the following message: 3 vectors were produced by pass224. Number of processors reduced from 4 to 1 for far-field. PrismC: NFx= 2048 NFxT= 4 NFxU= 3. PrismC: NFx= 2048 NFxT= 4 NFxU= 3. PrismC: NFx= 2048 NFxT= 4 NFxU= 3. PrismC: NFx= 2048 NFxT= 4 NFxU= 3. 3 vectors were produced by pass225. Number of processors reduced from 4 to 1 for far-field. Does any body know what Gaussian try to do here and why it cannot finish that? Thank you in advance, Roman