From owner-chemistry@ccl.net Mon Sep 16 07:38:00 2013 From: "sania ali saniachemist[#]gmail.com" To: CCL Subject: CCL: New version of CCCBDB Message-Id: <-49173-130916011629-25924-h997le7PrzxFXxi1FTkQcg:_:server.ccl.net> X-Original-From: sania ali Content-Type: multipart/alternative; boundary=047d7b5d57100d670004e6794e21 Date: Mon, 16 Sep 2013 10:16:21 +0500 MIME-Version: 1.0 Sent to CCL by: sania ali [saniachemist]=[gmail.com] --047d7b5d57100d670004e6794e21 Content-Type: text/plain; charset=ISO-8859-1 I am sania,and interested in computational chemistery,i think cccbdb is very well and so many new students can get more knowledge from here thnks On Fri, Sep 13, 2013 at 1:39 AM, Johnson III, Russell D. Dr. russell.johnson],[nist.gov wrote: > The Computational Chemistry Comparison and Benchmark Database (CCCBDB) > has released version 16 at cccbdb.nist.gov. The CCCBDB is a collection of > experimental and computed (by quantum methods) ideal-gas thermochemistry > for 1500 small molecules and atoms. The properties include enthalpy of > formation, vibrational frequencies, geometries, rotational constants and > dipole moments. Please send questions or comments to cccbdb]^[nist.gov.*** > * > --047d7b5d57100d670004e6794e21 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I am sania,and interested in computational chemistery,i th= ink cccbdb is very well and so many new students can get more knowledge fro= m here thnks


On Fri, Sep 13, 2013 at 1:39 AM, Johnson III, Russell D. Dr. russell.johnso= n],[nist.gov <owner-chemistry[A]ccl.n= et> wrote:

The Computational Chemistry Comparison and Benchmark= Database (CCCBDB) has released version 16 at cccbdb.nist.gov. The CCCBDB is a collection of = experimental and computed (by quantum methods) =A0ideal-gas thermochemistry= for 1500 small molecules and atoms. The properties include enthalpy of formation, vibrational frequ= encies, geometries, rotational constants and dipole moments. Please send qu= estions or comments to cccbdb]^[nist.gov.


--047d7b5d57100d670004e6794e21-- From owner-chemistry@ccl.net Mon Sep 16 08:13:00 2013 From: "salma bibi shah salmachemist88 : gmail.com" To: CCL Subject: CCL: HOMO-LUMO of a charged molecule Message-Id: <-49174-130916014059-26938-x+qlvR4iHXLAHxW+hDs8HA!=!server.ccl.net> X-Original-From: "salma bibi shah" Date: Mon, 16 Sep 2013 01:40:57 -0400 Sent to CCL by: "salma bibi shah" [salmachemist88^gmail.com] Hi dears. I am a new student of computational chemistry.I experience a lot of problems due to lake of supervision.now a days i am working with small molecules for practice purpose.At the present i got the problem in determining HOMO-LUMO of excited molecules.When i performed open shell calculations with charge one i got alpha and beta both types of orbitals.Which orbital will be the HOMO and which one the LUMO. It will be either that of alpha or beta orbitals? Best regards From owner-chemistry@ccl.net Mon Sep 16 09:31:00 2013 From: "chandra shekar s chandrashekar . iisertvm.ac.in" To: CCL Subject: CCL: relation between basis functions, processors and cpu Message-Id: <-49175-130916092649-29618-JOAsb+USbxQmmUG90R3M/A*|*server.ccl.net> X-Original-From: "chandra shekar s" Date: Mon, 16 Sep 2013 09:26:47 -0400 Sent to CCL by: "chandra shekar s" [chandrashekar|,|iisertvm.ac.in] Hi, what is the relationship between the the number of basis functions, processors and the memory. i just want to know how to calculate the CPU time for a given number of atoms (geometry optimization), processors and the memory in guassian 09 using DFT. From owner-chemistry@ccl.net Mon Sep 16 10:06:00 2013 From: "Herbert Fruchtl herbert.fruchtl%st-andrews.ac.uk" To: CCL Subject: CCL: HOMO-LUMO of a charged molecule Message-Id: <-49176-130916094816-7510-WH5Ot1LEgx23bcA5RJ0LNw*|*server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 Sep 2013 14:47:47 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl-x-st-andrews.ac.uk] Dear Salma, You are mixing a few concepts, or at least using the expressions interchangeably. The ones you need to understand are: Charged molecule This only means that the number of electrons is not balancing the nuclear charge. In itself, has no influence on how you calculate the excitation gap. Open-shell molecule You have at least one singly occupied orbital. If you do an unrestricted calculation, you get orbital energies for alpha and beta electrons. If you are looking for optical excitation energies, the gap you are looking for is the one > from the highest occupied orbital to the lowest unoccupied of the same spin (but see below). If there is a lower empty orbital of opposite spin, you won't get there with a single-photon excitation (it's spin-forbidden), but there may be other mechanisms to allow it. Excited state An electron is sitting in an orbital of higher energy than the LUMO. Keep in mind that Koopman's Theorem, which tells you that the excitation energy is roughly the difference between HOMO and LUMO, is a) not exact, because there is orbital relaxation after excitation, and b) even more inexact if you rely on HF or DFT orbitals, because these theories give rather inaccurate energies for virtual orbitals. Hope this helps, Herbert On 16/09/13 06:40, salma bibi shah salmachemist88 : gmail.com wrote: > > Sent to CCL by: "salma bibi shah" [salmachemist88^gmail.com] > Hi dears. > I am a new student of computational chemistry.I experience a lot of problems due to lake of supervision.now a days i am working with small molecules for practice purpose.At the present i got the problem in determining HOMO-LUMO of excited molecules.When i performed open shell calculations with charge one i got alpha and beta both types of orbitals.Which orbital will be the HOMO and which one the LUMO. It will be either that of alpha or beta orbitals? > Best regards> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Mon Sep 16 11:18:01 2013 From: "Krisztian Niesz kniesz#chemaxon.com" To: CCL Subject: CCL: free software for metabolites prediction Message-Id: <-49177-130916095339-9577-CM+jN/Zc8FaWSvYSsaUUrg*o*server.ccl.net> X-Original-From: Krisztian Niesz Content-Type: multipart/mixed; boundary="------------050409060201050605090002" Date: Mon, 16 Sep 2013 15:53:21 +0200 MIME-Version: 1.0 Sent to CCL by: Krisztian Niesz [kniesz+/-chemaxon.com] This is a multi-part message in MIME format. --------------050409060201050605090002 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Andrew, ChemAxon might have a solution for you. Metabolizer is a metabolic pathway prediction tool that allows users to identify major metabolites of substrates in phase-1 human bio-transformation reactions. Please check out this website for further information. http://www.chemaxon.com/products/metabolizer/ Best regards, - Appsci team P.S. Comments are appreciated (as always) On 9/9/2013 8:08 AM, Andrew Voronkov drugdesign[A]yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign##yandex.ru] > Dear CCL users, are you aware of some free software programs (analogs to MetaCore, MetaSite and MetaDrug for example), which can estimate metabolic transformations and metabolism products for the small molecules? > > Best regards, > Andrew> > > --------------050409060201050605090002 Content-Type: text/x-vcard; charset=utf-8; name="kniesz.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="kniesz.vcf" begin:vcard fn:Krisztian Niesz n:Niesz;Krisztian org:ChemAxon Ltd. adr:;;Zahony ut 7.;Budapest;;1031;Hungary email;internet:kniesz!A!chemaxon.com title:Application Scientist tel;cell:+36.70.343.4041 url:www.chemaxon.com version:2.1 end:vcard --------------050409060201050605090002--