From owner-chemistry@ccl.net Mon Aug 3 00:15:01 2009 From: "kevin hauser 84hauser||gmail.com" To: CCL Subject: CCL: difference between CI single and double excitations Message-Id: <-39906-090802161936-20405-HRt02wi6rU1oYmJTjOJirw=server.ccl.net> X-Original-From: kevin hauser <84hauser%x%gmail.com> Content-Type: multipart/alternative; boundary=000e0cd14aea32a3f004702e5ec5 Date: Sun, 2 Aug 2009 13:19:18 -0700 MIME-Version: 1.0 Sent to CCL by: kevin hauser [84hauser~!~gmail.com] --000e0cd14aea32a3f004702e5ec5 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, Aditya, I believe your questions on restricted/unrestriced CI is concerning the reference HF calculation. Restricted HF references have equal spatial wavefunctions (matrix elements) for alpha and beta spin. For most systems (which have even number of electrons) whose equilibrium structure is desired, as opposed to studying dissociation PES's, RHF is preferred because it's easier computationally. Now if you're trying to find a dissociation curve for a system, you must use Unrestricted reference HF, or else your dissociation curve may not predict the proper structure...In the next few weeks, the art of quantum chemistry will become clearer to you. See Szabo and Ostlund's "Modern Quantum Chemistry" text and Stanton and Bartlett's "Post-Hartree Fock Methods: A Tutorial" for more rigorous and useful commentaries... Good luck, kevin On Sat, Aug 1, 2009 at 2:09 AM, aditya khandavelli svk003:-:latech.edu < owner-chemistry*|*ccl.net> wrote: > Dr. Close & Dr. Sukumar, > My special thanks to you for responding. I actually performed ground state > optimization on a system using a DFT technique. After that i want to > optimize the excited states of that system, for that i wanted to use CI > method. I was confused with the CIS and CID methods and which one to use and > which one is more accurate. And one more question i would like to ask you is > about the restricted CI and unrestricted CI, the difference between the two. > Kindly help me in this regard. I thank you one again for your help > > Regards, > Aditya Khandavelli. > > > -- HK --------------------------------------- Quantum Theory Project New Physics Building 2224 The University of Florida Gainesville, Florida 32611 ------------------------------------------- 84hauser*|*gmail.com 561-635-1848 8962 SE North Passage Way, Tequesta, FL 33469 Kevin Eduard Hauser --000e0cd14aea32a3f004702e5ec5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Aditya,


I believe your questions on r= estricted/unrestriced CI is concerning the reference HF calculation. Restri= cted HF references have equal spatial wavefunctions (matrix elements) for a= lpha and beta spin. For most systems (which have even number of electrons) = whose equilibrium structure is desired, as opposed to studying dissociation= PES's, RHF is preferred because it's easier computationally. Now i= f you're trying to find a dissociation curve for a system, you must use= Unrestricted reference HF, or else your dissociation curve may not predict= the proper structure...In the next few weeks, the art of quantum chemistry= will become clearer to you.

See Szabo and Ostlund's "Modern Quantum Chemis= try" text and Stanton and Bartlett's "Post-Hartree Fock Metho= ds: A Tutorial" for more rigorous and useful commentaries...


Good luck,
kevin

On Sat, Aug 1, 2009 at 2:09 AM, aditya khandavelli svk= 003:-:latech.edu <owner-chemistry*|*ccl.net> wrote:
Dr. Close & Dr. Sukumar,

=
My special thanks to you for responding. I actually performed ground s= tate optimization on a system using a DFT technique. After that =A0i want t= o optimize the excited states of that system, for that i wanted to use CI m= ethod. I was confused with the CIS and CID methods and which one to use and= which one is more accurate. And one more question i would like to ask you = is about the restricted CI and unrestricted CI, the difference between the = two. Kindly help me in this regard. I thank you one again for your help

Regards,
Aditya Khandavelli.





--
HK
-----------------= ----------------------
Quantum Theory Project
New Physics Building 22= 24
The University of Florida
Gainesville, Florida 32611
----------= ---------------------------------
84hauser*|*gmail.com
561-635-184= 8
8962 SE North Passage Way,
Tequesta, FL 33469

Kevin Eduard H= auser
--000e0cd14aea32a3f004702e5ec5-- From owner-chemistry@ccl.net Mon Aug 3 07:31:01 2009 From: "Geoffrey Hutchison geoffh..pitt.edu" To: CCL Subject: CCL: reorganization energy Message-Id: <-39907-090803000337-11394-glZJ62Hh8//WH8b8VA0vCg[*]server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sun, 2 Aug 2009 23:30:50 -0400 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Geoffrey Hutchison [geoffh||pitt.edu] > I want to calculate the total reorganization energy of a molecule > (from the family of organic field effect transistors). The total > reorganization energy can be divided into two terms (1) internal > reorganization energy (2) external reorganization energy. Well, you mention that you're looking at OFET molecules, so it gets slightly complicated to define the external reorganization energy. Are you looking at the reorganization energy for a solid-state charge transfer -- if so, there's no solvent. > my 2nd question is that if i calculate reorganization energy in > solvent, can i say it is solvent reorganization energy From the way you wrote that, you would be calculating the reorganization energy of the molecule using a solvation model. The solvent reorganization energy is created by the change in the geometry of the solvent (or other environment). Certainly if you're considering charge transfer in solution, the internal reorganization energy will be calculated more accurately in a solvent model. If you want to calculate the real external reorganization in a lattice, you have to consider how the lattice would change upon charge transfer (polarization, polaron deformation, etc.) Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 From owner-chemistry@ccl.net Mon Aug 3 11:11:01 2009 From: "sadaf iqbal sadaf_chem26,yahoo.com" To: CCL Subject: CCL: subsite specificity Message-Id: <-39908-090803072048-19079-35fPAQyuEpBo8i2akzbSsg||server.ccl.net> X-Original-From: "sadaf iqbal" Date: Mon, 3 Aug 2009 07:20:45 -0400 Sent to CCL by: "sadaf iqbal" [sadaf_chem26+*+yahoo.com] Hello all, I have modeled a 3D structure of a protein by homology modeling using MOE. Now i want to analyze the difference in both (target and template) proteins in terms of their active site volumes and electrostatic maps. In this way i would be able to analyze the subsite specificity of the modeled protein just by computational means. Anybody can help me in this regard that how this task will be done on chimera, vmd, or any other visualizing or docking software. Or is there any alternative way? Thanks in advance. Sadaf Iqbal Junior Research fellow ICCBS From owner-chemistry@ccl.net Mon Aug 3 11:46:01 2009 From: "sadaf iqbal sadaf_iqbal * iccs.edu" To: CCL Subject: CCL: subsite specificity Message-Id: <-39909-090803072308-19290-v6xXTkHzr5CdUy2eDZ1Kiw:+:server.ccl.net> X-Original-From: "sadaf iqbal" Date: Mon, 3 Aug 2009 07:23:02 -0400 Sent to CCL by: "sadaf iqbal" [sadaf_iqbal ~~ iccs.edu] Hello all, I have modeled a 3D structure of a protein by homology modeling using MOE. Now i want to analyze the difference in both (target and template) proteins in terms of their active site volumes and electrostatic maps. In this way i would be able to analyze the subsite specificity of the modeled protein just by computational means. Anybody can help me in this regard that how this task will be done on chimera, vmd, or any other visualizing or docking software. Or is there any alternative way? Thanks in advance. Sadaf Iqbal Junior Research fellow ICCBS From owner-chemistry@ccl.net Mon Aug 3 12:23:00 2009 From: "Sadaf Iqbal sadaf_chem26_._yahoo.com" To: CCL Subject: CCL: subsite analysis Message-Id: <-39910-090803025946-16443-fpUGS4QmSpjaCMEn/KzFbQ]=[server.ccl.net> X-Original-From: "Sadaf Iqbal" Date: Mon, 3 Aug 2009 02:59:43 -0400 Sent to CCL by: "Sadaf Iqbal" [sadaf_chem26===yahoo.com] Hello all, I have modeled a 3D structure of a protein by homology modeling using MOE. Now i want to analyze the difference in both (target and template) proteins in terms of their active site volumes and electrostatic maps. In this way i would be able to analyze the subsite specificity of the modeled protein just by computational means. Anybody can help me in this regard that how this task will be done on chimera, vmd, or any other visualizing or docking software. Or is there any alternative way? Thanks in advance. Sadaf Junior Research Fellow ICCBS From owner-chemistry@ccl.net Mon Aug 3 12:56:00 2009 From: "Elaine Meng meng^cgl.ucsf.edu" To: CCL Subject: CCL: subsite specificity Message-Id: <-39911-090803122825-32372-uj/8LOjrRkRRvkHZCbog7A**server.ccl.net> X-Original-From: "Elaine Meng" Date: Mon, 3 Aug 2009 12:28:21 -0400 Sent to CCL by: "Elaine Meng" [meng(-)cgl.ucsf.edu] Hello Sadaf, If you don't mind uploading your coordinates to a web server, I have a couple of suggestions. Both servers provide some visualization but also allow you to download or have mailed to you the full results, which can be viewed in Chimera. (1) for electrostatic comparisons, "webPIPSA: web server for Protein Interaction Property Similarity Analysis" http://pipsa.eml.org/pipsa/ focused on performing calculations on multiple proteins and comparing them (won't let you proceed until you specify at least two), choice of using UHBD or APBS for electrostatic potential calculations. input: upload PDB files or specify PDB IDs, email address for getting results output: dendrogram and heat map comparing the results for the multiple proteins, optional download of zip file with intermediate results (includes map files and corresponding PDBs). In Chimera, should probably only view these maps along with the corresponding PDBs since the structures may have been transformed (rotated and translated). Chimera reads both UHBD and APBS electrostatic potential maps: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html (2) for site volume comparisons, the CASTp server http://sts-fw.bioengr.uic.edu/castp/calculation.php If you have results e-mailed to you, Chimera has a convenient interface for looking through the list of pockets from this server, as described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html Or instead of using PIPSA, you could run electrostatics calculations on your own with DelPhi, GRASP, APBS, or UHBD and just look at the surfaces colored by ESP map values side by side. Yet another option is the quick "Coulombic Surface Coloring" tool in recent versions (daily builds) or Chimera: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Mon Aug 3 16:35:00 2009 From: "Manish Sud msud-,-san.rr.com" To: CCL Subject: CCL: Somewhat chemistry related question Message-Id: <-39912-090803163249-15383-/COChbspKCb8gIdBYLCb2Q(a)server.ccl.net> X-Original-From: "Manish Sud" Date: Mon, 3 Aug 2009 16:32:45 -0400 Sent to CCL by: "Manish Sud" [msud- -san.rr.com] It's definitely not a computational chemistry question, but I thought some of the chemists out there who read CCL might know the names and structures of the key molecules responsible for the lemony smell and the yellow color of the solution extracted from the zest of ripe lemons using alcohol. Limonene, a colorless liquid, appears to be one of the molecule involved the smell and the color probably comes from the molecules in the Cartenoids family. I'm interested in finding out which Cartenoids are responsible for the color, and what other molecules might be involved in the smell and the color? Those of you who might be wondering: Why am I interested in this information? Well, it's a long story and the answer would not qualify as a posting on CCL. Please send me a direct email and I would be glad to share it with you. Thanks, Manish Sud msud ~~ san.rr.com From owner-chemistry@ccl.net Mon Aug 3 17:13:00 2009 From: "Nilesh Tawari tawari.nilesh*_*gmail.com" To: CCL Subject: CCL: Query regarding iron complex optimization using MOPAC Message-Id: <-39913-090803134549-26840-cy9PbAnPL6H0G4Vcf8VcmA ~ server.ccl.net> X-Original-From: "Nilesh Tawari" Date: Mon, 3 Aug 2009 13:45:45 -0400 Sent to CCL by: "Nilesh Tawari" [tawari.nilesh[*]gmail.com] Hello everyone, I want to optimize an iron (Fe+++) hexacoordinated complex with my molecule using MOPAC using PM3 can you please suggest the essential keywords and the precautions to be taken in this calculations and get some properties like energy and heat of formation. As i am beginner for MOPAC any help would be of great importance to me. If possible please suggest any tutorial for the same. Thanks in advance -nilesh From owner-chemistry@ccl.net Mon Aug 3 17:48:01 2009 From: "Wayne Steinmetz WES04747 : pomona.edu" To: CCL Subject: CCL: Somewhat chemistry related question Message-Id: <-39914-090803173745-20835-2AEzyXEopGJV+9qSif+eTA|a|server.ccl.net> X-Original-From: Wayne Steinmetz Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 3 Aug 2009 14:37:30 -0700 MIME-Version: 1.0 Sent to CCL by: Wayne Steinmetz [WES04747(~)pomona.edu] You will find a full discussion of your questions in H.-D Belitz & W. Grosc= h, Food Chemistry, Springer-Verlag. This monograph is a classic. I once h= ad the data as I developed an undergraduate experiment dealing the analysis= of the composition of odors from food stuffs. I have retired. After seve= ral moves, I have lost the information. Wayne E. Steinmetz Professor Emeritus of Chemistry USFS Volunteer Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz-*-pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- > From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu-*-ccl.net [mailto:= owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu-*-ccl.net] On Behalf Of = Manish Sud msud-,-san.rr.com Sent: Monday, August 03, 2009 1:33 PM To: Wayne Steinmetz Subject: CCL: Somewhat chemistry related question Sent to CCL by: "Manish Sud" [msud- -san.rr.com] It's definitely not a computational chemistry question, but I thought some = of the chemists out there who read CCL might know the names and structures = of the key molecules responsible for the lemony smell and the yellow color = of the solution extracted from the zest of ripe lemons using alcohol. Limonene, a colorless liquid, appears to be one of the molecule involved th= e smell and the color probably comes from the molecules in the Cartenids fa= mily. I'm interested in finding out which Cartenoids are responsible for th= e color, and what other molecules might be involved in the smell and the co= lor? Those of you who might be wondering: Why am I interested in this informatio= n? Well, it's a long story and the answer would not qualify as a posting on= CCL. Please send me a direct email and I would be glad to share it with yo= u. Thanks, Manish Sud msud(a)san.rr.com -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D From owner-chemistry@ccl.net Mon Aug 3 20:28:02 2009 From: "David Gallagher gallagher.da-*-gmail.com" To: CCL Subject: CCL: Query regarding iron complex optimization using MOPAC Message-Id: <-39915-090803202539-18152-/Uwc7qogDMMO1pFcXLoQEw{=}server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary=0003255765f642ebec047045d9e1 Date: Mon, 3 Aug 2009 17:20:06 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da(-)gmail.com] --0003255765f642ebec047045d9e1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Nilesh, Unless you have a good reason to stick with PM3, I would recommend MOPAC2009 with PM6, as it has higher accuracy for geometries and heats of formation. MOPAC2009 is free for academics. The 'UHF' keyword generally gives the most reliable results for transition metal complexes. You can find links for the MOPAC manual and download (free for academics) at: http://cacheresearch.com/mopac.html#mopac-support Good luck, David Gallagher CACheResearch.com On Mon, Aug 3, 2009 at 10:45 AM, Nilesh Tawari tawari.nilesh*_*gmail.com < owner-chemistry|ccl.net> wrote: > > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh[*]gmail.com] > Hello everyone, > I want to optimize an iron (Fe+++) hexacoordinated complex with my molecule > using MOPAC using PM3 can you please suggest the essential keywords and the > precautions to be taken in this calculations and get some properties like > energy and heat of formation. As i am beginner for MOPAC any help would be > of great importance to me. If possible please suggest any tutorial for the > same. > Thanks in advance > -nilesh> > > --0003255765f642ebec047045d9e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Nilesh,

Unless you have a good reason to stick with P= M3, I would recommend MOPAC2009 with PM6, as it has higher accuracy for geo= metries and heats of formation. =A0MOPAC2009 is free for academics.

The 'UHF' keyword generally gives the most reliable = results for transition metal complexes.=A0

You can= find links for the MOPAC manual and download (free for academics) at:=A0

Good= luck,
David Gallagher
CACheResearch.com


On Mon, Aug 3, 2009 at 10:45 AM, Nilesh Tawa= ri tawari.nilesh*_*gmail.com <owner-chemistry|ccl.net= > wrote:

Sent to CCL by: "Nilesh =A0Tawari" [tawari.nilesh[*]gmail.com]
Hello everyone,
I want to optimize an iron (Fe+++) hexacoordinated complex with my molecule= using MOPAC using PM3 can you please suggest the essential keywords and th= e precautions to be taken in this calculations and get some properties like= energy and heat of formation. As i am beginner for MOPAC any help would be= of great importance to me. If possible please suggest any tutorial for the= same.
Thanks in advance
-nilesh



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--0003255765f642ebec047045d9e1-- From owner-chemistry@ccl.net Mon Aug 3 21:04:00 2009 From: "Roman Petrenko rpetrenko[#]gmail.com" To: CCL Subject: CCL: NMR in protein structure determination Message-Id: <-39916-090803193512-12735-TSV2hu6xlMayg7/XHIT1vQ-#-server.ccl.net> X-Original-From: "Roman Petrenko" Date: Mon, 3 Aug 2009 19:35:09 -0400 Sent to CCL by: "Roman Petrenko" [rpetrenko]~[gmail.com] Dear all, what software is usually used for comparison of expermintal NMR data with data derived from molecular dynamics trajectories? Is it possible to compute chemical shifts from trajectories? Regards, Roman Petrenko University of Cincinnati rpetrenko.x.gmail.com