From owner-chemistry@ccl.net Thu Jan 26 05:58:01 2006 From: "Roger Kevin Robinson r.robinson ~ imperial.ac.uk" To: CCL Subject: CCL:G: g3 theory Message-Id: <-30634-060126055643-10023-7OBU1sVfYvSK9+c66sCEpQ,server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 Jan 2006 10:56:42 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson*imperial.ac.uk] Hi, Im trying to calculate some thermodynamic propties using G3 theory. I thought i'd start by trying to replicate the values already creating for methane First i wanted to calculate the enthalpy of formation at 298k, to do this i think i need to calculate the atomization energy. So i did calculation for C, H and CH4 at G3B3 energy. I then took the G3 energy listed at the end of the .log file and did the following (EC+4*EH)-ECH4-EZPECH4 Atomization Energy ZPE C -37.77874 0.00000 H -0.49967 0.00000 Kcal/mol KJ/mol CH4 -40.45540 0.04341 0.63457 398.19808 1666.06091 Experim EV 17.02100 392.52128 1642.27119 (i am using this conversion factors Hartree Joule 2625.5 Hartree Cal 627.50950 ) creating a atomization energy of 1666KJ/mol when the experimental is 1642KJ/mol i know that G1 can do better than this never mind G3B3. I also tried the same thing with the G3(0 K)= G3 Enthalpy G3 Free Energy and G3B3 energy readings in the output and none of them produced 1642KJ/mol. Next i looked in Exploring chemistry with electronic structure methods 2ed. they have a worked expample of calculating the atomization energy of PH2 using B3LYP/6-31G(d) as so Atomization Energy ZPE P -341.25930 0.00000 H -0.50027 0.00000 Kcal/mol KJ/mol PH2 -342.50942 0.01322 0.23636 148.31815 620.56318 Experim EV 144.70000 605.42 Not the most accurate answer so i then ran my G3B3 calculations Atomization Energy ZPE P -341.05939 0.00000 H -0.49967 0.00000 Kcal/mol KJ/mol PH2 -342.34826 0.01293 0.27660 173.57038 726.21855 Experim EV 144.70000 605.42 Producing a considerably worse result. Anyone know where im going wrong. This is an example of my input for CH4 %chk=/home2/rkr79/gaussian/g3.B3LYP.Methane/step1.chk %mem=6MW %nproc=1 # G3B3 geom=connectivity Title Card Required 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 3 A2 2 D1 H 1 B4 4 A3 2 D2 B1 1.08942541 B2 1.08942541 B3 1.08942541 B4 1.08942541 A1 109.47122063 A2 109.47122063 A3 109.47122063 D1 -120.00000000 D2 -120.00000000 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5 and this is an example of my output for CH4 .... Diagonal vibrational polarizability: 0.0000000 0.0000000 0.0000000 Temperature= 298.150000 Pressure= 1.000000 E(ZPE)= 0.043414 E(Thermal)= 0.046286 E(QCISD(T))= -40.356011 E(Empiric)= -0.027040 DE(Plus)= -0.001744 DE(2DF)= -0.056279 E(Delta-G3)= -0.060613 E(G3-Empiric)= -0.027040 G3(0 K)= -40.458273 G3 Energy= -40.455401 G3 Enthalpy= -40.454457 G3 Free Energy= -40.475598 1\1\GINC-C28\Mixed\G3B3\G3B3\C1H4\RKR79\20-Jan-2006\0\\# G3B3 GEOM=CON NECTIVITY\\Title Card Required\\0,1\C,0,0.,0.,0.\H,0,0.,0.,1.093381706 7\H,0,1.030850159,0.,-0.3644605689\H,0,-0.5154250795,-0.8927424252,-0. 3644605689\H,0,-0.5154250795,0.8927424252,-0.3644605689\\Version=AM64L -G03RevC.02\State=1-A1\MP2/6-31G(d)=-40.3325233\QCISD(T)/6-31G(d)=-40. 3560114\MP4/6-31G(d)=-40.3548385\MP2/6-31+G(d)=-40.3340665\MP4/6-31+G( d)=-40.3565823\MP2/6-31G(2df,p)=-40.3848479\MP4/6-31G(2df,p)=-40.41111 77\MP2/GTLarge=-40.4470038\G3B3=-40.4582732\FreqCoord=0.,0.,0.,0.,0.,2 .0661919855,1.9480244856,0.,-0.6887306618,-0.9740122428,-1.6870386917, -0.6887306618,-0.9740122428,1.6870386917,-0.6887306618\PG=TD [O(C1),4C .... I have to say im not finding the G3 papers particulary easy to work though as a guide for how to use the theory. For instance they didnt mention u could just type in the G3 or G3B3 keyword and i found this is Exploring chemistry with electronic structure methods 2ed. Are there any more books like this which would have worked examples i could learn from ? Any help appreciated Roger From owner-chemistry@ccl.net Thu Jan 26 10:23:00 2006 From: "Shobe, David dshobe ~~ sud-chemieinc.com" To: CCL Subject: CCL:G: g3 theory Message-Id: <-30635-060126102024-30688-xjN4COUaplyhGUqxP0lriw[*]server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 26 Jan 2006 16:17:47 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe(!)sud-chemieinc.com] Roger, It's difficult to tell what you did exactly because Outlook's text wrapping messed up your formatting. One thing, however: the G3 enthalpy as reported by Gaussian already includes the ZPE energy. There is no need to make a second ZPE correction, and doing so will lead to an error, so perhaps that is the source of your trouble. Incidentally, when the paper introducing G3 was written, the only way to calculate a G3 enthalpy was to to add and subtract all the energies yourself (perhaps with the help of a spreadsheet). The G3 command in Gaussian was added later. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry(-)ccl.net [mailto:owner-chemistry(-)ccl.net] Sent: Thursday, January 26, 2006 6:07 AM To: Shobe, David Subject: CCL:G: g3 theory Sent to CCL by: Roger Kevin Robinson [r.robinson*imperial.ac.uk] Hi, Im trying to calculate some thermodynamic propties using G3 theory. I thought i'd start by trying to replicate the values already creating for methane First i wanted to calculate the enthalpy of formation at 298k, to do this i think i need to calculate the atomization energy. So i did calculation for C, H and CH4 at G3B3 energy. I then took the G3 energy listed at the end of the .log file and did the following (EC+4*EH)-ECH4-EZPECH4 Atomization Energy ZPE C -37.77874 0.00000 H -0.49967 0.00000 Kcal/mol KJ/mol CH4 -40.45540 0.04341 0.63457 398.19808 1666.06091 Experim EV 17.02100 392.52128 1642.27119 (i am using this conversion factors Hartree Joule 2625.5 Hartree Cal 627.50950 ) creating a atomization energy of 1666KJ/mol when the experimental is 1642KJ/mol i know that G1 can do better than this never mind G3B3. I also tried the same thing with the G3(0 K)= G3 Enthalpy G3 Free Energy and G3B3 energy readings in the output and none of them produced 1642KJ/mol. Next i looked in Exploring chemistry with electronic structure methods 2ed. they have a worked expample of calculating the atomization energy of PH2 using B3LYP/6-31G(d) as so Atomization Energy ZPE P -341.25930 0.00000 H -0.50027 0.00000 Kcal/mol KJ/mol PH2 -342.50942 0.01322 0.23636 148.31815 620.56318 Experim EV 144.70000 605.42 Not the most accurate answer so i then ran my G3B3 calculations Atomization Energy ZPE P -341.05939 0.00000 H -0.49967 0.00000 Kcal/mol KJ/mol PH2 -342.34826 0.01293 0.27660 173.57038 726.21855 Experim EV 144.70000 605.42 Producing a considerably worse result. Anyone know where im going wrong. This is an example of my input for CH4 %chk=/home2/rkr79/gaussian/g3.B3LYP.Methane/step1.chk %mem=6MW %nproc=1 # G3B3 geom=connectivity Title Card Required 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 3 A2 2 D1 H 1 B4 4 A3 2 D2 B1 1.08942541 B2 1.08942541 B3 1.08942541 B4 1.08942541 A1 109.47122063 A2 109.47122063 A3 109.47122063 D1 -120.00000000 D2 -120.00000000 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5 and this is an example of my output for CH4 ... Diagonal vibrational polarizability: 0.0000000 0.0000000 0.0000000 Temperature= 298.150000 Pressure= 1.000000 E(ZPE)= 0.043414 E(Thermal)= 0.046286 E(QCISD(T))= -40.356011 E(Empiric)= -0.027040 DE(Plus)= -0.001744 DE(2DF)= -0.056279 E(Delta-G3)= -0.060613 E(G3-Empiric)= -0.027040 G3(0 K)= -40.458273 G3 Energy= -40.455401 G3 Enthalpy= -40.454457 G3 Free Energy= -40.475598 1\1\GINC-C28\Mixed\G3B3\G3B3\C1H4\RKR79\20-Jan-2006\0\\# G3B3 GEOM=CON NECTIVITY\\Title Card Required\\0,1\C,0,0.,0.,0.\H,0,0.,0.,1.093381706 7\H,0,1.030850159,0.,-0.3644605689\H,0,-0.5154250795,-0.8927424252,-0. 3644605689\H,0,-0.5154250795,0.8927424252,-0.3644605689\\Version=AM64L -G03RevC.02\State=1-A1\MP2/6-31G(d)=-40.3325233\QCISD(T)/6-31G(d)=-40. 3560114\MP4/6-31G(d)=-40.3548385\MP2/6-31+G(d)=-40.3340665\MP4/6-31+G( d)=-40.3565823\MP2/6-31G(2df,p)=-40.3848479\MP4/6-31G(2df,p)=-40.41111 77\MP2/GTLarge=-40.4470038\G3B3=-40.4582732\FreqCoord=0.,0.,0.,0.,0.,2 .0661919855,1.9480244856,0.,-0.6887306618,-0.9740122428,-1.6870386917, -0.6887306618,-0.9740122428,1.6870386917,-0.6887306618\PG=TD [O(C1),4C ... I have to say im not finding the G3 papers particulary easy to work though as a guide for how to use the theory. For instance they didnt mention u could just type in the G3 or G3B3 keyword and i found this is Exploring chemistry with electronic structure methods 2ed. Are there any more books like this which would have worked examples i could learn from ? Any help appreciated Rogerhttp://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 Thu Jan 26 10:58:01 2006 From: "Richard Wood rwoodphd[-]yahoo.com" To: CCL Subject: CCL: CFF91 reference Message-Id: <-30636-060126104656-19353-ZizFqZ3Ok+6bTy2GfJrhzQ%x%server.ccl.net> X-Original-From: Richard Wood Content-Type: multipart/alternative; boundary="0-1423814143-1138286813=:72066" Date: Thu, 26 Jan 2006 06:46:53 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Richard Wood [rwoodphd#yahoo.com] --0-1423814143-1138286813=:72066 Content-Type: text/plain; charset=us-ascii Hi all, Does anyone know of a reference for the force field CFF91? I need it for a document that I am writing and I can't find one anywhere. Thanks in advance, Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd=yahoo.com --0-1423814143-1138286813=:72066 Content-Type: text/html; charset=us-ascii
Hi all,

Does anyone know of a reference for the force field CFF91?  I need it for a document that I am writing and I can't find one anywhere.

Thanks in advance,
Richard


 
Richard L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030
rwoodphd=yahoo.com

--0-1423814143-1138286813=:72066-- From owner-chemistry@ccl.net Thu Jan 26 11:33:00 2006 From: "Mills, Nancy S. nmills ~ trinity.edu" To: CCL Subject: CCL: calculating area of a ring Message-Id: <-30637-060126111054-28573-POAPULWf6pdTT7PgYw0xuw|-|server.ccl.net> X-Original-From: "Mills, Nancy S." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 26 Jan 2006 09:23:43 -0600 MIME-Version: 1.0 Sent to CCL by: "Mills, Nancy S." [nmills_._trinity.edu] Is there a program that uses cartesian coordinates (effectively x,y coordinates) to calculate the area of a flat ring? I am interested in rings that are not necessarily perfect polygons. Thanks. Nancy Nancy S. Mills, Ph. D. Phone, (210) 999-7317 Professor Fax, (210) 999-7569 Department of Chemistry nmills(a)trinity.edu Trinity University One Trinity Place San Antonio, TX 78212-7200 From owner-chemistry@ccl.net Thu Jan 26 12:38:00 2006 From: "David F. Green dfgreen.{=}.ams.sunysb.edu" To: CCL Subject: CCL: calculating area of a ring Message-Id: <-30638-060126123528-7714-EbehKq4ZMINKcP/qQbFjeA{=}server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 Jan 2006 12:35:09 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen _ ams.sunysb.edu] I'm not aware of any such program, but it should be trivial to write one. Just place a point anywhere inside the ring, and sum up the area of the triangles formed by connecting each edge to the central point. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Mills, Nancy S. nmills ~ trinity.edu wrote: > Sent to CCL by: "Mills, Nancy S." [nmills_._trinity.edu] > Is there a program that uses cartesian coordinates (effectively x,y coordinates) to calculate the area of a flat ring? I am interested in rings that are not necessarily perfect polygons. > > Thanks. > > Nancy > > Nancy S. Mills, Ph. D. Phone, (210) 999-7317 > Professor Fax, (210) 999-7569 > Department of Chemistry nmills]=[trinity.edu > Trinity University > One Trinity Place > San Antonio, TX 78212-7200> > > From owner-chemistry@ccl.net Thu Jan 26 13:12:00 2006 From: "Luis Simn luissimonrubio _ hotmail.com" To: CCL Subject: CCL:G: PCM and thermochemistry in Gaussian Message-Id: <-30639-060126113650-11710-gDlegs7WHYIiIpFQHKfOag|server.ccl.net> X-Original-From: "Luis Simn" Sent to CCL by: "Luis Simn" [luissimonrubio-,-hotmail.com] Dear all: I have been performing few calculations on G03W using PCM solvation model. I have also calculated the frequencies. One surprissing result is that after adding the "thermal correction to Gibbs Free Energy" to the "total free energy in solution" (bellow I include an exammple) I sometimes obtain a different result than the "Sum of electronic and thermal Free Energies" (which, unless I am completelly wrong, should be the addition of previous terms). The same is observed for zero point corrected energies. In the example bellow (dimethylamine), the difference is arround 0.4 kcal/mol, although in most of the cases I obtain no difference at all. I have full optimized structures, and none of the hessian eigenvalues are negative. Which of the two different figures is more reliable? What is the reason for this difference? Thanks: Luis Variational PCM results ======================= (a.u.) = -135.173988 (a.u.) = -135.175037 Total free energy in solution: with all non electrostatic terms (a.u.) = -135.175691 (...) Zero-point correction= 0.092555 (Hartree/Particle) Thermal correction to Energy= 0.096932 Thermal correction to Enthalpy= 0.097876 Thermal correction to Gibbs Free Energy= 0.067118 Sum of electronic and zero-point Energies= -135.082482 Sum of electronic and thermal Energies= -135.078105 Sum of electronic and thermal Enthalpies= -135.077161 Sum of electronic and thermal Free Energies= -135.107919 From owner-chemistry@ccl.net Thu Jan 26 13:47:00 2006 From: "help,gaussian.com" To: CCL Subject: CCL:G: UV calculations with Gaussian Message-Id: <-30640-060126122629-2419-4bm8XK9cdcXkUxY/HZw0zw.:.server.ccl.net> X-Original-From: help---gaussian.com Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 26 Jan 2006 11:35:52 -0500 Mime-Version: 1.0 Sent to CCL by: help~!~gaussian.com Dr. Papadopoulos, This message does not really suggest any problem and my crystal ball is a bit foggy today. Can you send one of these input file and the last 50 lines or so of the output? Also include details on your site so I can check which version of G03 you are using. On Wed, Jan 25, 2006 at 09:47:04AM -0500, Anastasios Papadopoulos anastp,,chem.auth.gr wrote: > Sent to CCL by: Anastasios Papadopoulos [anastp,+,chem.auth.gr] > Dear CCL users, > > I am running UV calculations of Ag,Cu clusters in Gaussian 03,using > BP86/lanl2dz method. All calculations abnormally end during link l914 without > any error message. > Could anybody inform me about the causes of this problem? > > Yours, > Tasos G. Papadopoulos> -- Douglas J. Fox Technical Support Gaussian, Inc. help,+,gaussian.com From owner-chemistry@ccl.net Thu Jan 26 14:22:00 2006 From: "Bruno Catalanotti brucatal*o*unina.it" To: CCL Subject: CCL: CFF91 reference Message-Id: <-30641-060126115735-19995-Z+UhPaN1b9okh7SHQ6pPQA/a\server.ccl.net> X-Original-From: Bruno Catalanotti Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 26 Jan 2006 18:00:19 +0100 MIME-Version: 1.0 Sent to CCL by: Bruno Catalanotti [brucatal##unina.it] Maple, JR et al. (1994) JComput. Chem., 15,162-185 Hwang M. (1994) JACS 116,2515-2525 Richard Wood rwoodphd[-]yahoo.com wrote: >Sent to CCL by: Richard Wood [rwoodphd#yahoo.com] >--0-1423814143-1138286813=:72066 >Content-Type: text/plain; charset=us-ascii > >Hi all, > > Does anyone know of a reference for the force field CFF91? I need it for a document that I am writing and I can't find one anywhere. > > Thanks in advance, > Richard > > > >Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd a yahoo.com > > >--0-1423814143-1138286813=:72066 >Content-Type: text/html; charset=us-ascii > >
Hi all,
>
>Does anyone know of a reference for the force field CFF91?  I need >it for a document that I am writing and I can't find one anywhere.
>
>Thanks in advance,
>Richard
>
>
 
Richard L. Wood, Ph. D. >
>Computational Chemist >
>Cockeysville, MD 21030 >
>rwoodphd a yahoo.com

>--0-1423814143-1138286813=:72066--> > > > > > -- Il messaggio e' stato analizzato alla ricerca di virus o contenuti pericolosi da MailScanner, ed e' risultato non infetto. From owner-chemistry@ccl.net Thu Jan 26 18:15:00 2006 From: "Mills, Nancy S. nmills:-:trinity.edu" To: CCL Subject: CCL: calculating area of a ring Message-Id: <-30642-060126135159-16669-sWg8F8a/77EqIElgG4L4Xw_+_server.ccl.net> X-Original-From: "Mills, Nancy S." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 26 Jan 2006 12:51:48 -0600 MIME-Version: 1.0 Sent to CCL by: "Mills, Nancy S." [nmills]|[trinity.edu] I had thought of that approach but wondered if someone had already done the program. Thanks. Nancy Nancy S. Mills, Ph. D. Phone, (210) 999-7317 Professor Fax, (210) 999-7569 Department of Chemistry nmills%x%trinity.edu Trinity University One Trinity Place San Antonio, TX 78212-7200 -----Original Message----- > From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net] Sent: Thursday, January 26, 2006 12:05 PM To: Mills, Nancy S. Subject: CCL: calculating area of a ring Sent to CCL by: "David F. Green" [dfgreen _ ams.sunysb.edu] I'm not aware of any such program, but it should be trivial to write one. Just place a point anywhere inside the ring, and sum up the area of the triangles formed by connecting each edge to the central point. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Mills, Nancy S. nmills ~ trinity.edu wrote: > Sent to CCL by: "Mills, Nancy S." [nmills_._trinity.edu] > Is there a program that uses cartesian coordinates (effectively x,y coordinates) to calculate the area of a flat ring? I am interested in rings that are not necessarily perfect polygons. > > Thanks. > > Nancy > > Nancy S. Mills, Ph. D. Phone, (210) 999-7317 > Professor Fax, (210) 999-7569 > Department of Chemistry nmills]=[trinity.edu > Trinity University > One Trinity Place > San Antonio, TX 78212-7200http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jan 26 18:50:00 2006 From: "Young Leh youngleh-#-gmail.com" To: CCL Subject: CCL:G: composite energy method with transition metal Message-Id: <-30643-060126134107-11501-/COChbspKCb8gIdBYLCb2Q .. server.ccl.net> X-Original-From: "Young Leh" Sent to CCL by: "Young Leh" [youngleh]_[gmail.com] Dear Ccler, I have been collecting information on the application of composite energy methods to transition metals for a long time. All the popular composite energy methods, Gaussian-n, Complete Basis Set, and multi-coefficent, are only calibarited with first, second, and third row elements excluding transition metals. Is there any composite energy method that can be applied to transition metal at all? Or if I am going to use those methods to transition metals, how wrong could I be? thank you all for the reponse and any suggestion is greatly appreciated. Sincerely, Young Leh From owner-chemistry@ccl.net Thu Jan 26 19:25:01 2006 From: "Christopher Cramer cramer]~[chem.umn.edu" To: CCL Subject: CCL:G: PCM and thermochemistry in Gaussian Message-Id: <-30644-060126145350-20130-iBf92X4AFubLX7Dx+3n0BQ(!)server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-5--1063249026 Date: Thu, 26 Jan 2006 13:53:44 -0600 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Christopher Cramer [cramer!^!chem.umn.edu] --Apple-Mail-5--1063249026 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Looks like a small bug. The thermal "correction" (not really a correction, but a "contribution", I would say) to go from U to G is being added to without including the non- electrostatic terms. No doubt the variable name in the frequency section is set to something like EELEC but the output in the SCRF section reports EELEC+ENONELEC... Chris Cramer On Jan 26, 2006, at 12:44 PM, Luis Simn luissimonrubio _ hotmail.com wrote: > Sent to CCL by: "Luis Simn" [luissimonrubio-,-hotmail.com] > Dear all: > > I have been performing few calculations on G03W using PCM solvation > model. I have also calculated the frequencies. One surprissing > result is that after adding the "thermal correction to Gibbs Free > Energy" to the "total free energy in solution" (bellow I include an > exammple) I sometimes obtain a different result than the "Sum of > electronic and thermal Free Energies" (which, unless I am > completelly wrong, should be the addition of previous terms). The > same is observed for zero point corrected energies. In the example > bellow (dimethylamine), the difference is arround 0.4 kcal/mol, > although in most of the cases I obtain no difference at all. > > I have full optimized structures, and none of the hessian > eigenvalues are negative. Which of the two different figures is > more reliable? What is the reason for this difference? > > Thanks: Luis > > Variational PCM results > ======================= > (a.u.) = -135.173988 > (a.u.) = -135.175037 > Total free energy in solution: > with all non electrostatic terms (a.u.) = -135.175691 > (...) > > Zero-point correction= 0.092555 (Hartree/ > Particle) > Thermal correction to Energy= 0.096932 > Thermal correction to Enthalpy= 0.097876 > Thermal correction to Gibbs Free Energy= 0.067118 > Sum of electronic and zero-point Energies= -135.082482 > Sum of electronic and thermal Energies= -135.078105 > Sum of electronic and thermal Enthalpies= -135.077161 > Sum of electronic and thermal Free Energies= -135.107919 > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer*pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-5--1063249026 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Looks like a small bug. The = thermal "correction" (not really a correction, but a "contribution", I = would say) to go from U to G is being added = to=A0<psi(f)|H+V(f)/2|psi(f)> without including the = non-electrostatic terms. No doubt the variable name in the frequency = section is set to something like EELEC but the output in the SCRF = section reports EELEC+ENONELEC...

Chris = Cramer

On Jan 26, 2006, at 12:44 PM, Luis Simn = luissimonrubio _ hotmail.com wrote:

Sent to CCL by: "Luis=A0 Simn" = [luissimonrubio-,-hotmail.com]
Dear = all:

I have been performing few calculations on G03W = using PCM solvation model. I have also calculated the frequencies. One = surprissing result is that after adding the "thermal correction to Gibbs = Free Energy" to the "total free energy in solution" (bellow I include an = exammple) I sometimes obtain a different result than the "Sum of = electronic and thermal Free Energies" (which, unless I am completelly = wrong, should be the addition of previous terms). The same is observed = for zero point corrected energies. In the example bellow = (dimethylamine), the difference is arround 0.4 kcal/mol, although in = most of the cases I obtain no difference at all.

I have = full optimized structures, and none of the hessian eigenvalues are = negative. Which of the two different figures is more reliable? What is = the reason for this difference?

Thanks: Luis=A0

Variational = PCM results
=A0=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=A0<psi(f)| =A0 H=A0 =A0 |psi(f)> =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = (a.u.) =3D=A0 =A0 = -135.173988
=A0<psi(f)|H+V(f)/2|psi(f)> = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 (a.u.) =3D=A0 =A0 = -135.175037
=A0Total free energy in = solution:
=A0 with all non electrostatic = terms=A0 =A0 =A0 =A0 =A0 =A0 = (a.u.) =3D=A0 =A0 = -135.175691
(...)

=A0Zero-point correction=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 0.092555 (Hartree/Particle)
=A0Therma= l correction to Energy=3D=A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.096932
=A0Therma= l correction to Enthalpy=3D=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.097876
=A0Thermal correction to Gibbs = Free Energy=3D =A0 =A0 =A0 =A0 = 0.067118
=A0Sum of electronic and = zero-point Energies=3D =A0 =A0 =A0 = =A0 =A0 -135.082482
=A0Sum of electronic and thermal = Energies=3D=A0 =A0 =A0 =A0 =A0 =A0 = =A0 -135.078105
=A0Sum of electronic and thermal = Enthalpies=3D=A0 =A0 =A0 =A0 =A0 =A0= -135.077161
=A0Sum of electronic and thermal = Free Energies=3D =A0 =A0 =A0 =A0 = -135.107919


-=3D = This is automatically added to each message by the mailing script = =3D-
To recover the email address of = the author of the message, please change
the = strange characters on the top line to the * sign. You can also
look up the X-Original-From: line in the mail = header.

E-mail to subscribers: CHEMISTRY*ccl.net or = use:

E-mail to administrators: CHEMISTRY-REQUEST*ccl.net = or use

Subscribe/Unsubscribe:=A0

Before posting, check wait time = at: http://www.ccl.net

http:/= /server.ccl.net/chemistry/announcements/conferences/

Search = Messages: http://www.ccl.net/htdig=A0 (login: ccl, Password: = search)

If your mail bounces from CCL with 5.7.1 error, = check:






--


Christopher J. Cramer

University of Minnesota

Department of Chemistry

207 Pleasant St. = SE

Minneapolis, MN 55455-0431

--------------------------

=

Phone:=A0 (612) 624-0859 || FAX:=A0 (612) 626-2006

Mobile: (952) = 297-2575

cramer*pollux.chem.umn.edu<= /FONT>

http://pollux.chem.umn.edu/~cr= amer

(website = includes information about the textbook "Essentials

=A0 =A0 of Computational = Chemistry:=A0 Theories and = Models, 2nd Edition")


= --Apple-Mail-5--1063249026-- From owner-chemistry@ccl.net Thu Jan 26 20:00:03 2006 From: "German I. Sastre Navarro gsastre ~ itq.upv.es" To: CCL Subject: CCL: CFF91 reference Message-Id: <-30645-060126143410-6091-+GhX4eaWQ3iMthEwCRFPIQ^-^server.ccl.net> X-Original-From: "German I. Sastre Navarro" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 26 Jan 2006 19:05:44 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "German I. Sastre Navarro" [gsastre|*|itq.upv.es] Hi Richard, CFF91 references: U. Dinur and A. T. Hagler, "New Approaches to Empirical Force fields" in Reviews of Computational Chemistry Chapter 4, 1991. J. R. Maple, U. Dinur, and A. T. Hagler, Proc. Natl. Acad. Sci. USA 1988, 85, 5350-5354. Regards German > Sent to CCL by: Richard Wood [rwoodphd#yahoo.com] > --0-1423814143-1138286813=:72066 > Content-Type: text/plain; charset=us-ascii > > Hi all, > > Does anyone know of a reference for the force field CFF91? I need it for a document that I am writing and I can't find one anywhere. > > Thanks in advance, > Richard > > > > Richard L. Wood, Ph. D. > Computational Chemist > Cockeysville, MD 21030 > rwoodphd a yahoo.com > > > --0-1423814143-1138286813=:72066 > Content-Type: text/html; charset=us-ascii > >
Hi all,
>
> Does anyone know of a reference for the force field CFF91?  I need > it for a document that I am writing and I can't find one anywhere.
>
> Thanks in advance,
> Richard
>
>
 
Richard L. Wood, Ph. D. >
> Computational Chemist >
> Cockeysville, MD 21030 >
> rwoodphd a yahoo.com

> --0-1423814143-1138286813=:72066--> > > \|/ (o o) ------------------------------------------oOO-(_)-OOo------------------ German Sastre http://www.upv.es/~gsastre Instituto de Tecnologia Quimica (UPV-CSIC) e-mail: gsastre]~[itq.upv.es Universidad Politecnica de Valencia Phone: +34-96-387-7803 Av. Los Naranjos s/n, 46022 Valencia (Spain) Fax: +34-96-387-7809 ----------------------------------------------------------------------- oo0 0oo From owner-chemistry@ccl.net Thu Jan 26 20:35:04 2006 From: "Michel Petitjean ptitjean++itodys.jussieu.fr" To: CCL Subject: CCL: calculating area of a ring Message-Id: <-30646-060126165249-22159-HoDEEnBG54Dl6BhfKvDBdQ++server.ccl.net> X-Original-From: Michel Petitjean Date: Thu, 26 Jan 2006 21:54:48 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean,+,itodys.jussieu.fr] To: Subject: CCL: Re: calculating area of a ring Sent to CCL by: "Mills, Nancy S." [nmills_._trinity.edu] > Is there a program that uses cartesian coordinates (effectively x,y coordinates) to calculate the area of a flat ring? I am interested in rings that are not necessarily perfect polygons. Assuming that your are working in the plane, and that the polygon is convex, you should download from the web a planar convex hull algorithm. Once known the convex hull, calculating the area is trivial: use the the mean center of the vertices of the hull, and add the areas of the triangles. If your are working in the 3D space, download the freware RADI: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI (calculates surface and volume of the convex hull, and some shape coefficients). Michel Petitjean, Email: petitjean^^^itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean^^^ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Thu Jan 26 21:10:01 2006 From: "Matthias Rarey rarey:+:zbh.uni-hamburg.de" To: CCL Subject: CCL: calculating area of a ring Message-Id: <-30647-060126145234-19884-Vv8/lDI8lg6si7vU9T00wg,+,server.ccl.net> X-Original-From: Matthias Rarey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 26 Jan 2006 20:11:19 +0100 MIME-Version: 1.0 Sent to CCL by: Matthias Rarey [rarey]^[zbh.uni-hamburg.de] Assuming your polygon has n points (x[i],y[i]), 0 <= i < n, then the following loop should do the job: area= 0; for(i=0; i Sent to CCL by: "Mills, Nancy S." [nmills_._trinity.edu] > Is there a program that uses cartesian coordinates (effectively x,y coordinates) to calculate the area of a flat ring? I am interested in rings that are not necessarily perfect polygons. > From owner-chemistry@ccl.net Thu Jan 26 21:45:00 2006 From: "Zaki Safi zaki.safi(~)gmail.com" To: CCL Subject: CCL: Help Message-Id: <-30648-060126171354-26793-ZYTHldgG3BcBP2czlrZ18Q*o*server.ccl.net> X-Original-From: Zaki Safi Content-Type: multipart/alternative; boundary="----=_Part_37775_5131408.1138309883881" Date: Thu, 26 Jan 2006 23:11:23 +0200 MIME-Version: 1.0 Sent to CCL by: Zaki Safi [zaki.safi,+,gmail.com] ------=_Part_37775_5131408.1138309883881 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 Content-Disposition: inline SGkKRG9lcyBldmVyeSBvbmUgaGVscCBtZSBpbiB1bmRlcnN0YW5kaW5nIHRoZSBmb2xsb3dpbmcg RzAzJ3MgbWVzc2VnZQpJIGRvIGNhbGN1bGF0aW9uIGZvciBzb21lIG9yZ2FuaWMgY29tcG91bmRz IGFuZCBleGFjdGx5IGkgZG8gZnJlcXVlbmN5CmNhbGN1bGF0aW9ucy4KVGhlIGZvbGxvd2luZyB0 d28gbWVzc2VnZXMgaGF2ZSBiZWVuIHNob3duLgoxKVdhcm5pbmcgLS0gYXNzdW1wdGlvbiBvZiBj bGFzc2ljYWwgYmVoYXZpb3IgZm9yIHJvdGF0aW9uLCAgICBtYXkgY2F1c2UKc2lnbmlmaWNhbnQg ZXJyb3IKMilXYXJuaW5nIC0tIGV4cGxpY2l0IGNvbnNpZGVyYXRpb24gb2YgMTYgZGVncmVlcyBv ZiBmcmVlZG9tIGFzLCAgdmlicmF0aW9ucwptYXkgY2F1c2Ugc2lnbmlmaWNhbnQgZXJyb3IKCklu IHRoaXMgbWVhbiB0aGF0IGkgbXVzdCByZS1vcHRpbWl6ZSBteSBzdHJ1Y3R1cmUgYW5kIHJlcGVh dCB0aGUKYWxjdWxhdGlvbnMuClRoYW5rcy4KCi0tCj09PT09PT09PT09PT09PT09PT09PT09PT09 PT09PT09PT09PT09PT09PT0KRHIuIFpha2kgU2FmaQpBc3Npc3RhbnQgUHJvZi4gb2YgUXVhbnR1 bSBDaGVtaXN0cnkKQ2hlbWlzdHJ5IERlcGFydG1lbnQsIEZhY3VsdHkgb2YgU2NpZW5jZQpBbC1B emhhciBVbml2ZXJzaXR5IC0gR2F6YQpHYXphLCBQYWxlc3RpbmUK ------=_Part_37775_5131408.1138309883881 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 Content-Disposition: inline PGRpdj48YnIgY2xlYXI9ImFsbCI+SGk8L2Rpdj4KPGRpdj5Eb2VzIGV2ZXJ5IG9uZSBoZWxwIG1l IGluIHVuZGVyc3RhbmRpbmcgdGhlIGZvbGxvd2luZyBHMDMncyBtZXNzZWdlIDwvZGl2Pgo8ZGl2 PkkgZG8gY2FsY3VsYXRpb24gZm9yIHNvbWUgb3JnYW5pYyBjb21wb3VuZHMgYW5kIGV4YWN0bHkg aSBkbyBmcmVxdWVuY3kgY2FsY3VsYXRpb25zLjwvZGl2Pgo8ZGl2PlRoZSBmb2xsb3dpbmcgdHdv IG1lc3NlZ2VzIGhhdmUgYmVlbiBzaG93bi48L2Rpdj4KPGRpdj4xKTxmb250IHNpemU9IjIiPldh cm5pbmcgLS0gYXNzdW1wdGlvbiBvZiBjbGFzc2ljYWwgYmVoYXZpb3IgZm9yIHJvdGF0aW9uLCZu YnNwOyZuYnNwOyZuYnNwOyA8L2ZvbnQ+PGZvbnQgc2l6ZT0iMiI+PGZvbnQgZmFjZT0iVGltZXMg TmV3IFJvbWFuIj5tYXkgY2F1c2Ugc2lnbmlmaWNhbnQgZXJyb3I8L2ZvbnQ+PC9mb250PjwvZGl2 Pgo8ZGl2Pjxmb250IGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgc2l6ZT0iMiI+Mik8Zm9udCBzaXpl PSIyIj5XYXJuaW5nIC0tIGV4cGxpY2l0IGNvbnNpZGVyYXRpb24gb2YgMTYgZGVncmVlcyBvZiBm cmVlZG9tIGFzPC9mb250Pjxmb250IGZhY2U9IkNvdXJpZXIgTmV3IChBcmFiaWMpIiBzaXplPSIy Ij4sJm5ic3A7IDwvZm9udD48Zm9udCBzaXplPSIyIj48Zm9udCBmYWNlPSJUaW1lcyBOZXcgUm9t YW4iPgp2aWJyYXRpb25zIG1heSBjYXVzZSBzaWduaWZpY2FudCBlcnJvcjwvZm9udD48L2ZvbnQ+ PC9mb250PjwvZGl2Pgo8ZGl2Pjxmb250IGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgc2l6ZT0iMiI+ PC9mb250PiZuYnNwOzwvZGl2Pgo8ZGl2Pjxmb250IGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgc2l6 ZT0iMiI+SW4gdGhpcyBtZWFuIHRoYXQgaSBtdXN0IHJlLW9wdGltaXplIG15IHN0cnVjdHVyZSBh bmQgcmVwZWF0IHRoZSBhbGN1bGF0aW9ucy48L2ZvbnQ+PC9kaXY+CjxkaXY+PGZvbnQgZmFjZT0i VGltZXMgTmV3IFJvbWFuIiBzaXplPSIyIj5UaGFua3MuPC9mb250PjwvZGl2Pgo8ZGl2Pjxicj4t LSA8YnI+PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PTxicj5Eci4g WmFraSBTYWZpPGJyPkFzc2lzdGFudCBQcm9mLiBvZiBRdWFudHVtIENoZW1pc3RyeTxicj5DaGVt aXN0cnkgRGVwYXJ0bWVudCwgRmFjdWx0eSBvZiBTY2llbmNlPGJyPkFsLUF6aGFyIFVuaXZlcnNp dHkgLSBHYXphPGJyPkdhemEsIFBhbGVzdGluZSA8L2Rpdj4K ------=_Part_37775_5131408.1138309883881-- From owner-chemistry@ccl.net Thu Jan 26 22:19:01 2006 From: "David J Anick david.anick * rcn.com" To: CCL Subject: CCL: calculating area of a ring Message-Id: <-30649-060126185958-5940-9olITfLdW3zKA+Y29fZX5w**server.ccl.net> X-Original-From: "David J Anick" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 26 Jan 2006 18:59:26 -0500 MIME-Version: 1.0 Sent to CCL by: "David J Anick" [david.anick[A]rcn.com] Dear Nancy et al, Here is a very easy formula for the area of a polygon based on Green's theorem. If the coordinates of the vertices are (in order) (a1,b1), (a2,b2), (a3,b3), ... , (aN,bN), then back to (a1,b1), the formula is: Area = [(b2-b1)*(a1+a2) + (b3-b2)*(a2+a3) + ... + (b1-bN)*(aN+a1)] / 2 . I.e., for each edge of the polygon, you compute (the difference of the y-coords times the sum of the x-coords); add these up and divide by 2. It really works. Make sure you don't accidentally do (bN-b1) instead for the last step. You have to list the vertices so that they trace the polygon in a counterclockwise fashion; if clockwise you get minus the area (or just ignore orientation but be sure to take the abs value of the answer). Enjoy, David Anick PhD MD [my PhD was in math] ----- Original Message ----- > From: "Mills, Nancy S. nmills:-:trinity.edu" To: "Anick, David " Sent: Thursday, January 26, 2006 6:16 PM Subject: CCL: calculating area of a ring > Sent to CCL by: "Mills, Nancy S." [nmills]|[trinity.edu] > I had thought of that approach but wondered if someone had already done the program. > Thanks. > Nancy > > Nancy S. Mills, Ph. D. Phone, (210) 999-7317 > Professor Fax, (210) 999-7569 > Department of Chemistry nmills%trinity.edu > Trinity University > One Trinity Place > San Antonio, TX 78212-7200 > > > -----Original Message----- > > From: owner-chemistry%ccl.net [mailto:owner-chemistry%ccl.net] > Sent: Thursday, January 26, 2006 12:05 PM > To: Mills, Nancy S. > Subject: CCL: calculating area of a ring > > > Sent to CCL by: "David F. Green" [dfgreen _ ams.sunysb.edu] > I'm not aware of any such program, but it should be trivial to write > one. Just place a point anywhere inside the ring, and sum up the area > of the triangles formed by connecting each edge to the central point. > > ======================================================================== > David F. Green > Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ > Applied Mathematics and Statistics > Stony Brook University Office: +1-631-632-9344 > Math Tower, Room 1-117 Mobile: +1-617-953-3922 > Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 > ======================================================================== > > > Mills, Nancy S. nmills ~ trinity.edu wrote: > > Sent to CCL by: "Mills, Nancy S." [nmills_._trinity.edu] > > Is there a program that uses cartesian coordinates (effectively x,y coordinates) to calculate the area of a flat ring? I am interested in rings that are not necessarily perfect polygons. > > > > Thanks. > > > > Nancy > > > > Nancy S. Mills, Ph. D. Phone, (210) 999-7317 > > Professor Fax, (210) 999-7569 > > Department of Chemistry nmills]=[trinity.edu > > Trinity University > > One Trinity Place > > San Antonio, TX 78212-7200http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Thu Jan 26 22:54:02 2006 From: "Cesar Millan pachequin:-:gmail.com" To: CCL Subject: CCL: HEME group and FAD (Flavine Adenine Dinucleotide) CVFF parameters Message-Id: <-30650-060126203843-3185-CB9+/DfIXsd2Xp7TIVFGDw*o*server.ccl.net> X-Original-From: "Cesar Millan" Sent to CCL by: "Cesar Millan" [pachequin{=}gmail.com] Hi every body I'm trying to use InsightII for making some calculations using HEME group and FAD molecules but I don't have any .car files or parameters for those molecules. Does anybody have these files or any hint to construct those molecules on insightII? Thank You everybody.