From owner-chemistry@ccl.net Fri Jun 22 02:19:01 2007 From: "Kaci Tizi_Ouzou kaci.tiziouzou:-:gmail.com" To: CCL Subject: CCL: Alchemy (Bagus, McLean and Liu) Message-Id: <-34539-070622021713-26190-Wa+6Kq9LwqWk+KxUFa8bJg-x-server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_158365_12446162.1182492993504" Date: Fri, 22 Jun 2007 00:16:33 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou+*+gmail.com] ------=_Part_158365_12446162.1182492993504 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Folks, Does anybody know where can I get the code for Alchemy (which was written back in the 1971) by Bagus, McLean, Liu and Yoshimie. Thanks all, Kass ------=_Part_158365_12446162.1182492993504 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Folks,
 
Does anybody know where can I get the code for Alchemy (which was written back in the 1971) by
Bagus, McLean, Liu and Yoshimie.
 
Thanks all,
 
 
Kass
------=_Part_158365_12446162.1182492993504-- From owner-chemistry@ccl.net Fri Jun 22 07:10:01 2007 From: "Gahungu Godefroid ggahungu],[yahoo.fr" To: CCL Subject: CCL: ELF Plot Message-Id: <-34540-070622070624-27644-TAKQx5GY6Ky8UGkokACC/A]=[server.ccl.net> X-Original-From: "Gahungu Godefroid" Date: Fri, 22 Jun 2007 07:06:21 -0400 Sent to CCL by: "Gahungu Godefroid" [ggahungu,yahoo.fr] Hello, I am looking for a program which can be used to plot the electron localization function of a molecule. Since I am working with a Windows PC, the program which can help me more should be a Windows based one! If you know such a program, please, I am waiting for your message! Thanks, ahead for your help. Best regards, Godefroid GAHUNGU E-mail: gahungu()nenu.edu.cn Norstheast Normal University Laboratory of Theoretical Chemistry Renmin Street,5268 Changchun, 130024 PR China From owner-chemistry@ccl.net Fri Jun 22 08:20:00 2007 From: "Lukasz Cwiklik lukasz.cwiklik^uochb.cas.cz" To: CCL Subject: CCL: Alchemy (Bagus, McLean and Liu) Message-Id: <-34541-070622074339-16033-Jz8tNgdJdn/jEYXBKSzjhQ++server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Jun 2007 11:59:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [lukasz.cwiklik]^[uochb.cas.cz] On 6/22/07, Kaci Tizi_Ouzou kaci.tiziouzou:-:gmail.com wrote: > Hi Folks, > > Does anybody know where can I get the code for Alchemy (which was written > back in the 1971) by > Bagus, McLean, Liu and Yoshimie. At http://www.netsci.org/Resources/Software/Modeling/QM/ contact information for Alchemy-II code are given: *** ALCHEMY-II is a set of IBM-based programs for direct CI and MCSCF on small and medium sized molecules. One-particle density matrices, one-electron properties, natural orbitals, transition density matrices. Contact: Michael Dupuis IBM Corporation Scientific and Engineering and Computations Department Department 48B Kingston, NY 12401 USA Phone: 914-385-4965 *** Best regards, Lukasz Cwiklik -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Fri Jun 22 11:32:00 2007 From: "David A. Case case*o*scripps.edu" To: CCL Subject: CCL:G: magentic susceptibility from gaussian program Message-Id: <-34542-070622112631-17091-hSeqCdGRdtsQeb5E4Ov3nw a server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 22 Jun 2007 08:26:14 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case^-^scripps.edu] On Wed, Jun 20, 2007, Mahalakshmi. S. mlakshmis/agmail.com wrote: > > In the output of g03 program for calculating the magnetic susceptibility, > its given as cgs-ppm. Magnetic anisotropy is obtained by subtracting > magnetic susceptibility_parallel and magnetic susceptibility_perpendicular. > How do you convert the magnetic anisotropy from cgs-ppm to m3/molecule ? I > would like to thank in advance the members who respond to this message. There is a table of conversion factors on p. 171 of this article: %A D. Sitkoff %A D.A. Case %T Theories of chemical shift anisotropies in proteins and nucleic acids %J Prog. NMR Spectr. %V 32 %P 165-190 %D 1998 Note that cgs-ppm is a Gaussian system, and m3/molecule is an SI (rationalized MKS) unit. So there is a factor of 4*pi involved (related to the definition of susceptibility, which differs in the two unit systems): it's not just changing cm to m, and mol to molecule! ...good luck...dave case From owner-chemistry@ccl.net Fri Jun 22 12:07:01 2007 From: "Christian Herhaus christian.herhaus]*[merck.de" To: CCL Subject: CCL: Using GIS technology to represent molecule dependencies? Message-Id: <-34543-070622102345-8277-nDdxlT4yoLO+/uSz8p7RKg-#-server.ccl.net> X-Original-From: "Christian Herhaus" Date: Fri, 22 Jun 2007 10:23:42 -0400 Sent to CCL by: "Christian Herhaus" [christian.herhaus|,|merck.de] Dear all, inspired by the work of the Novartis/MPI team around Stefan Wetzel and Ansgar Schuffenhauer I am already looking for a while for appropriate tools to interactively display representations of dependencies between different molecules comparable to the scaffold trees described by these two colleagues (JCIM 2007 47(1),47-58). As real-life dependencies are in most cases more complicated than trees it should ideally also be able to cope with network-like graphs. But graphs add complexity in an extent which makes it difficult to meaningfully display dependancies spanning more than 2-3 levels of hierarchy. I tried a combination of Cytoscope and yEd and was successful in generating graphs containing bitmap structure images, but the complexity of the generated illustrations was only difficultly to interprete. Recently I thought if hierarchical dependancy information could also be displayed in a way well-known from modern Geographical Information System (GIS) like Google Earth or NASAs WorldWind which basically have to cope with similar problems. The huge complexity of full geographical information is revealed on demand by zooming through different hierarchical levels like continents, countries, cities and buildings. Comparably, a "molecular landscape" could also be seen as organized e.g in clusters, Murcko-fragment series, single molecules etc.. I can imagine that a representation in a GIS-like interactive way which allows a user to zoom in on only the area of interest, without getting lost in complexity on the one hand but without losing the dependancy information on the other hand, could be highly attractive. Therefore I would like to ask if anybody had already gathered experience in this field. Particularly WorldWind could be interesting in this respect as it is open source, contains a C/VB/JScript/.NET plugin interface and is available in a Java version since May. Thanks in advance, and kind regards, Christian From owner-chemistry@ccl.net Fri Jun 22 12:42:01 2007 From: "Shrinwantu Pal paul=jncasr.ac.in" To: CCL Subject: CCL:G: excited state dipole moment Message-Id: <-34544-070622021558-26093-i7MolOr78a2JneqASf5FOQ]_[server.ccl.net> X-Original-From: "Shrinwantu Pal" Date: Fri, 22 Jun 2007 02:15:53 -0400 Sent to CCL by: "Shrinwantu Pal" [paul|,|jncasr.ac.in] dear colleagues, i happen not to figure out how to compute excited state dipole moment in adf or gaussian.. any help will be thankfully acknowledged.. reagards, shrinwantu pal TSU JNCASR India From owner-chemistry@ccl.net Fri Jun 22 13:17:01 2007 From: "Krishna Chaitanya S skchetu*_*gmail.com" To: CCL Subject: CCL: using CHELPG-SVD Message-Id: <-34545-070622083026-5389-PeIwST49s53Wz3jkzj0sRg|-|server.ccl.net> X-Original-From: "Krishna Chaitanya S" Date: Fri, 22 Jun 2007 08:30:22 -0400 Sent to CCL by: "Krishna Chaitanya S" [skchetu^gmail.com] Hi all, I would like to use CHELPG with SVD(singular value decomposition) for fitting atomic partial charges to a protein. The potential around the protein is calculated using Poisson-Boltzamann equation and I would like to fit charges(to protein atoms) using this potential. I am using CHARMM and wanted to know if there is any option in CHARMM to do the same. If not, could someone tell me how to do it. Waiting for positive response. Regards Krishna From owner-chemistry@ccl.net Fri Jun 22 13:52:01 2007 From: "Reinaldo Pis Diez reinaldo.pisdiez(~)gmail.com" To: CCL Subject: CCL: ELF Plot Message-Id: <-34546-070622103244-9627-oVS5ofrK3YuyycctTn+j7A|server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Jun 2007 10:38:02 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez.:.gmail.com] Dear Godefroid, You can use gOpenMol to plot ELF functions. The same procedure to plot MEPs must be used. Let me know if you don´t know how to do this, I could send you a short how-to I wrote. Regards, Reinaldo Gahungu Godefroid ggahungu],[yahoo.fr escribió: > Sent to CCL by: "Gahungu Godefroid" [ggahungu,yahoo.fr] > Hello, > > > > I am looking for a program which can be used to plot the electron localization function of a molecule. Since I am working with a Windows PC, the program which can help me more should be a Windows based one! > If you know such a program, please, I am waiting for your message! > > Thanks, ahead for your help. > > Best regards, > Godefroid GAHUNGU > > E-mail: gahungu^_^nenu.edu.cn > Norstheast Normal University > Laboratory of Theoretical Chemistry > Renmin Street,5268 > Changchun, 130024 PR China> > > > From owner-chemistry@ccl.net Fri Jun 22 15:32:00 2007 From: "Reynier Suardiaz reynier.suardiaz*_*uam.es" To: CCL Subject: CCL: s character of a C-C bond? Message-Id: <-34547-070622151231-2425-ocJHkatGDOQhb0/7z2zEGA]_[server.ccl.net> X-Original-From: "Reynier Suardiaz" Date: Fri, 22 Jun 2007 15:12:26 -0400 Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz a uam.es] Dear CCL Is there any attempt to assign s or p hybridization to a bond instead of an atom? Is it correct at all? I would like to relate the s character of both C of a C-C bond with a physical property. I know about attempts to relate one bond nmr coupling constants with the multiplication of the %s of both atoms. Is it possible to relate it with an "s character" of the bond? Best reynier From owner-chemistry@ccl.net Fri Jun 22 16:34:00 2007 From: "Shobe, David David.Shobe[]sud-chemie.com" To: CCL Subject: CCL: s character of a C-C bond? Message-Id: <-34548-070622163104-1737-i9OKTMeMop7+Q38KC5/xaA:+:server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Jun 2007 22:30:16 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe*sud-chemie.com] You could do a Natural Population analysis of the bond to find out which natural orbitals contribute to the bond. The %s character of the bond between C1 and C2 would be the % contribution by the s orbital of C1 + the % contribution by the s orbital of C2. Whether this turns out to be a useful quantity, or just some useless statistic like the number of H's in Shakespeare's Macbeth, remains to be seen... Regards, --David Shobe -----Original Message----- > From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net] Sent: Friday, June 22, 2007 3:12 PM To: Shobe, David Subject: CCL: s character of a C-C bond? Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz a uam.es] Dear CCL Is there any attempt to assign s or p hybridization to a bond instead of an atom? Is it correct at all? I would like to relate the s character of both C of a C-C bond with a physical property. I know about attempts to relate one bond nmr coupling constants with the multiplication of the %s of both atoms. Is it possible to relate it with an "s character" of the bond? Best reynierhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Jun 22 17:15:00 2007 From: "Shobe, David David.Shobe,,sud-chemie.com" To: CCL Subject: CCL: s character of a C-C bond? Message-Id: <-34549-070622171128-24789-SP8qyzEMwm+dd7GXss6qyw::server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Jun 2007 23:10:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe|-|sud-chemie.com] To be pedantic, the hybridization belongs to an atom, but the %s character describes what an atom contributes to a bond or lone pair. Any carbon in a normal valence environment has 1.0 s and 3.0 p but these are allocated to the various sigma bonds, pi bonds, and to the lone pair or the SOMO in the case of carbanions and radicals. For example in ethylene, each C atom has: 0.33 s and 0.67 p in each C-H bond (33% s and 67% p), 0.34 s and 1.66 p in the C=C bond (17% s and 67% p), which includes 0.34 s and 0.66 p for the C-C sigma bond (34% s and 66% p) and 0.00 s and 1.00 p for the C-C pi bond (0% s and 100% p) In methane, each C atom has 25% s and 75% p in each C-H bond. So you can see that the %s character, as normally employed by organic chemists, already is associated with the bond as well as with the atom. --David Shobe -----Original Message----- > From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net] Sent: Friday, June 22, 2007 3:12 PM To: Shobe, David Subject: CCL: s character of a C-C bond? Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz a uam.es] Dear CCL Is there any attempt to assign s or p hybridization to a bond instead of an atom? Is it correct at all? I would like to relate the s character of both C of a C-C bond with a physical property. I know about attempts to relate one bond nmr coupling constants with the multiplication of the %s of both atoms. Is it possible to relate it with an "s character" of the bond? Best reynierhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri Jun 22 17:49:00 2007 From: "Mustafa Hussein mustafa.hussein86|yahoo.com" To: CCL Subject: CCL: Density Matrix Methods Message-Id: <-34550-070622133927-15101-nqmQoTyoRs2cpFWeBFFaHw]=[server.ccl.net> X-Original-From: "Mustafa Hussein" Date: Fri, 22 Jun 2007 13:39:24 -0400 Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86 ~~ yahoo.com] Hi all, Is there a difference between: Reduced Density Matrix Theory (RDMT) Density Matrix Variational Theory (DMVT) Density Matrix Functional Theory (DMFT) I know about the variational Reduced Density Matrix Theory, is it different from the DMVT?? Any help is appreciated Thanks From owner-chemistry@ccl.net Fri Jun 22 18:40:00 2007 From: "Soren Eustis soren*_*jhu.edu" To: CCL Subject: CCL: Vertical Detachment Energy Calculation and ZPE Message-Id: <-34551-070622183739-22524-qeYIX9VRTuRenK4mELML8g^-^server.ccl.net> X-Original-From: "Soren Eustis" Date: Fri, 22 Jun 2007 18:37:36 -0400 Sent to CCL by: "Soren Eustis" [soren/a\jhu.edu] I have a question regarding the calculation of vertical detachment energy calculations (i.e. the difference between the anion and the neutral at the anion geometry). For an electron affinity calculation the two zero-point energies must be included for the calculation to make sense realistically. These generally cancel out (or make minor adjustments to the EA. However, for VDE calculations it seems standard not to use the zero-point energy of the anion (rather, the bottom of the potential well is used). For the neutral, it is clear that no ZPE correction is needed since the neutral is not close to equilibrium geometry and thus the energy will be well above the zero-point energy. However, for the anion this is not a satisfactory claim. Clearly, the anion is at an energy corresponding to the zero-point energy (assuming 0 K). If you perform a zero-point corrected calculation for the VDE of a molecule with many modes (E(neutral at anion geometry)-(E(anion)+ZPE(anion)), the result is often far too small to correspond with reality due to the large number of modes present. So, two problems/questions: 1) non-zero-point corrected VDE values seem to correspond well with experiment. How is this true if 2) the calculation clearly relies on a false assumption about the energy of the anion? Thanks in advance for all replies. From owner-chemistry@ccl.net Fri Jun 22 19:32:00 2007 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL: s character of a C-C bond? Message-Id: <-34552-070622172525-2540-3XweqWmwTNJJOR08UQeRyw::server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Jun 2007 21:46:55 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]|[ist.utl.pt] Reynier Suardiaz reynier.suardiaz*_*uam.es wrote: > Sent to CCL by: "Reynier Suardiaz" [reynier.suardiaz a uam.es] > Dear CCL > Is there any attempt to assign s or p hybridization to a bond instead of an atom? Is it correct at all? > I would like to relate the s character of both C of a C-C bond with a physical property. I know about attempts to relate one bond nmr coupling constants with the multiplication of the %s of both atoms. Is it possible to relate it with an "s character" of the bond? Yes. You can use the NBO formalism or localise the molecular orbitals and look at their final composition. Regards, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student .. IST,Lisbon -- From owner-chemistry@ccl.net Fri Jun 22 21:33:01 2007 From: "Jeff Hammond jeff.science[]gmail.com" To: CCL Subject: CCL: Density Matrix Methods Message-Id: <-34553-070622212824-26294-FdeTEabSUI0c6gme4nr9KQ#%#server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 22 Jun 2007 21:28:12 -0400 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science{}gmail.com] Mustafa, Variational reduced-density-matrix (RDM) theory and density matrix variational theory are the same thing. The former is the name used by Mazziotti and coworkers for work beginning with these two papers: D. A. Mazziotti and R. M. Erdahl, Phys. Rev. A 63, 042113 (2001). "Uncertainty relations and reduced density matrices: Mapping many-body quantum mechanics onto four particles" D. A. Mazziotti, Phys. Rev. A 65, 062511 (2002). "Variational minimization of atomic and molecular ground-state energies via the two-particle reduced density matrix" while latter is the name used by Nakatsuji and coworkers beginning with these papers: M. Nakata, H. Nakatsuji, M. Ehara, M. Fukuda, K. Nakata and K. Fujisawa, J. Chem. Phys. 114, 8282 (2001). "Variational calculations of fermion second-order reduced density matrices by semidefinite programming algorithm" M. Nakata, M. Ehara, and H. Nakatsuji, J. Chem. Phys. 116, 5432 (2002). "Density matrix variational theory: Application to the potential energy surfaces and strongly correlated systems" The original work in the field is probably C. Garrod, M. V. Mihailovic and M. Rosina, J. Math. Phys. 16, 868 (1975). "The variational approach to the two–body density matrix" Although just my opinion, the naming convention of Mazziotti is more consistent with the original work and is more precise than the naming of Nakatsuji and coworkers. Density matrix variational theory is general enough to describe other methods, such as the density matrix renormalization group (DMRG), while the association of variational and reduced-density-matrix has only ever been used in the context of approximate solution of the N-representability problem and 2-RDM methods. On the subject of nomenclature in variational RDM theory, the naming of N-representability conditions is also different between groups. Nakatsuji and coworkers, as well as others, have used PQG to denote constraints on the three variants of the 2-RDM (see the papers for details), while Mazziotti and coworkers use DQG and 2-positivity (2POS) for this set of conditions. The latter convention became necessary when higher positivity conditions were developed by Mazziotti and Erdahl (see above). Density matrix functional theory (DMFT) is an extension of DFT which uses the off-diagonal elements of the 1-particle reduced-density-matrix (1-RDM) to incorporate exact-exchange. This is not my area of expertise so perhaps an expert can add something useful. Jeff PS All of Mazziotti's papers can be found here: mazziotti.uchicago.edu (click on publications), while Nakatsuji's papers are here: http://quanta.synchem.kyoto-u.ac.jp/publist_public.htm. Mustafa Hussein mustafa.hussein86|yahoo.com wrote: > Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86 ~~ yahoo.com] > Hi all, > Is there a difference between: > Reduced Density Matrix Theory (RDMT) > Density Matrix Variational Theory (DMVT) > Density Matrix Functional Theory (DMFT) > > I know about the variational Reduced Density Matrix Theory, is it different from the DMVT?? > > Any help is appreciated > > Thanks