From owner-chemistry@ccl.net Thu Jun 19 04:49:01 2014 From: "Muhammed Buyuktemiz mbtemiz3,,gmail.com" To: CCL Subject: CCL: Error in GAMESS MCQDPT Calculation Message-Id: <-50229-140619044754-12272-JjU6Jq1y6KP6D0u2BCVKlg/./server.ccl.net> X-Original-From: "Muhammed Buyuktemiz" Date: Thu, 19 Jun 2014 04:47:53 -0400 Sent to CCL by: "Muhammed Buyuktemiz" [mbtemiz3_._gmail.com] Hi CCLers I am trying to do MCQDPT calculations on top of CASSCF wfs. along a reaction coordinate, RC. Most of my runs are ending as they should be, without producing any errors. However some of the points on the RC, I get the error copied at the end of this message. What I initially thought was increasing the nstate variable in the MCQDPT block of my input. Going from 20 to 60 did not help. I am also not sure if this would mess something up with the mp2 results, because you have to increase mxbase variable with nstate too and there is nothing related to mxbase on the gamess manual . So my question is (obviously :)), what should I do when I get this error? Thank you. ------------ SOLVING FOR CAS-CI STATE FUNCTIONS. ########################## ### CAS-CI RESULTS ### ########################## *** ERROR STOP IN SUB.MQCACI *** NSTOP =100 NOWBAS = 41 ENERGY( 1) = -1731.9902749044 ENERGY( 2) = -1731.9343716341 ENERGY( 3) = -1731.9106356350 ENERGY( 4) = -1731.8603939282 ENERGY( 5) = -1731.8511232291 ENERGY( 6) = -1731.8457785674 ENERGY( 7) = -1731.7976350720 ENERGY( 8) = -1731.7652175465 ENERGY( 9) = -1731.7647695057 ENERGY( 10) = -1731.7568379467 ENERGY( 11) = -1731.7452138176 ENERGY( 12) = -1731.7407885814 ENERGY( 13) = -1731.7377709180 ENERGY( 14) = -1731.7341629282 ENERGY( 15) = -1731.7266956105 ENERGY( 16) = -1731.7229472113 ENERGY( 17) = -1731.7206673934 ENERGY( 18) = -1731.6996804154 ENERGY( 19) = -1731.6860912874 ENERGY( 20) = -1731.6840981351 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Tue Jun 17 22:58:01 2014 54052120 WORDS OF DYNAMIC MEMORY USED mb. From owner-chemistry@ccl.net Thu Jun 19 07:57:00 2014 From: "chengchangli chengcl018- -126.com" To: CCL Subject: CCL: Fisrt-order perturbed molecular orbital in magnetic field Message-Id: <-50230-140619011621-13142-hfL8UCFGZFgUqMphes/hXA#,#server.ccl.net> X-Original-From: chengchangli Content-Type: multipart/alternative; boundary="----=_Part_135505_1844336347.1403154923620" Date: Thu, 19 Jun 2014 13:15:23 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: chengchangli [chengcl018]^[126.com] ------=_Part_135505_1844336347.1403154923620 Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: base64 RGVhciBhbGwKCgpXaGVuIGNhbGN1bGF0aW5nIG9yYml0YWwgY29udHJpYnV0aW9ucyB0byB0aGUg bWFnbmV0aWNhbGx5IGluZHVjZWQgcmluZyBjdXJyZW50LCBJIGRvbid0IGtub3cgd2h5IHRoZSBm aXJzdC1vcmRlciBjaGFuZ2UgdG8gYW4gb2NjdXBpZWQgb3JiaXRhbCBpcyBzdW1tYXRpb24gb3Zl ciBhbGwgdmlydHVhbCBvcmJpdGFscywgcmF0aGVyIHRoYW4gc3VtbWF0aW9uIG92ZXIgYWxsIG9y Yml0YWxzLiAoc2VlIFN0ZWluZXIgYW5kIEZvd2xlciwgUENDUCAyMDA0LCA2LCAyNjEtMjcyKQpJ ZiBJIHdhbnQgdG8gY2FsY3VsYXRlIHRoZSBmaXJzdC1vcmRlciBjaGFnbmUgdG8gYSB2aXJ0dWFs IG9yYml0YWwsIHNob3VsZCB0aGUgc3VtbWF0aW9uIHJ1biBvdmVyIGFsbCBvY2N1cGllZCBvcmJp dGFscz8gCgoKVGhhbmtzIGluIGFkdmFuY2UKQmVzdCB3aXNoZXMKCgpDaGFuZ2xpIENoZW5nClRz aW5naHVhIFVuaXZlcnNpdHkKQmVpamluZywgQ2hpbmEKCg== ------=_Part_135505_1844336347.1403154923620 Content-Type: text/html; charset=GBK Content-Transfer-Encoding: base64 PGRpdiBzdHlsZT0ibGluZS1oZWlnaHQ6MS43O2NvbG9yOiMwMDAwMDA7Zm9udC1zaXplOjE0cHg7 Zm9udC1mYW1pbHk6QXJpYWwiPjxkaXY+RGVhciBhbGw8L2Rpdj48ZGl2Pjxicj48L2Rpdj48ZGl2 PldoZW4gY2FsY3VsYXRpbmcgb3JiaXRhbCBjb250cmlidXRpb25zIHRvIHRoZSBtYWduZXRpY2Fs bHkgaW5kdWNlZCByaW5nIGN1cnJlbnQsIEkgZG9uJ3Qga25vdyB3aHkgdGhlIGZpcnN0LW9yZGVy IGNoYW5nZSB0byBhbiBvY2N1cGllZCBvcmJpdGFsIGlzIHN1bW1hdGlvbiBvdmVyIGFsbCB2aXJ0 dWFsIG9yYml0YWxzLCByYXRoZXIgdGhhbiBzdW1tYXRpb24gb3ZlciBhbGwgb3JiaXRhbHMuIChz ZWUgU3RlaW5lciBhbmQgRm93bGVyLCBQQ0NQIDIwMDQsIDYsIDI2MS0yNzIpPC9kaXY+PGRpdj5J ZiBJIHdhbnQgdG8gY2FsY3VsYXRlIHRoZSBmaXJzdC1vcmRlciBjaGFnbmUgdG8gYSB2aXJ0dWFs Jm5ic3A7PHNwYW4gc3R5bGU9ImZvbnQtc2l6ZTogMTRweDsgbGluZS1oZWlnaHQ6IDEuNzsiPm9y Yml0YWwsIHNob3VsZCB0aGUgc3VtbWF0aW9uIHJ1biBvdmVyIGFsbCBvY2N1cGllZCBvcmJpdGFs cz8mbmJzcDs8L3NwYW4+PC9kaXY+PGRpdj48c3BhbiBzdHlsZT0iZm9udC1zaXplOiAxNHB4OyBs aW5lLWhlaWdodDogMS43OyI+PGJyPjwvc3Bhbj48L2Rpdj48ZGl2PjxzcGFuIHN0eWxlPSJmb250 LXNpemU6IDE0cHg7IGxpbmUtaGVpZ2h0OiAxLjc7Ij5UaGFua3MgaW4gYWR2YW5jZTwvc3Bhbj48 L2Rpdj48ZGl2PjxzcGFuIHN0eWxlPSJmb250LXNpemU6IDE0cHg7IGxpbmUtaGVpZ2h0OiAxLjc7 Ij5CZXN0IHdpc2hlczwvc3Bhbj48L2Rpdj48ZGl2PjxzcGFuIHN0eWxlPSJmb250LXNpemU6IDE0 cHg7IGxpbmUtaGVpZ2h0OiAxLjc7Ij48YnI+PC9zcGFuPjwvZGl2PjxkaXY+PHNwYW4gc3R5bGU9 ImZvbnQtc2l6ZTogMTRweDsgbGluZS1oZWlnaHQ6IDEuNzsiPkNoYW5nbGkgQ2hlbmc8L3NwYW4+ PC9kaXY+PGRpdj48c3BhbiBzdHlsZT0iZm9udC1zaXplOiAxNHB4OyBsaW5lLWhlaWdodDogMS43 OyI+VHNpbmdodWEgVW5pdmVyc2l0eTwvc3Bhbj48L2Rpdj48ZGl2PjxzcGFuIHN0eWxlPSJmb250 LXNpemU6IDE0cHg7IGxpbmUtaGVpZ2h0OiAxLjc7Ij5CZWlqaW5nLCBDaGluYTwvc3Bhbj48L2Rp dj48ZGl2PjxzcGFuIHN0eWxlPSJmb250LXNpemU6IDE0cHg7IGxpbmUtaGVpZ2h0OiAxLjc7Ij48 YnI+PC9zcGFuPjwvZGl2PjwvZGl2Pjxicj48YnI+PHNwYW4gdGl0bGU9Im5ldGVhc2Vmb290ZXIi PjxzcGFuIGlkPSJuZXRlYXNlX21haWxfZm9vdGVyIj48L3NwYW4+PC9zcGFuPg== ------=_Part_135505_1844336347.1403154923620-- From owner-chemistry@ccl.net Thu Jun 19 08:54:01 2014 From: "liton liton.icsp-*-gmail.com" To: CCL Subject: CCL: Question regarding exothermic reactions Message-Id: <-50231-140619073348-30400-TKJJIFISb9WCHI4sikbp0Q^^^server.ccl.net> X-Original-From: liton Content-Type: multipart/alternative; boundary=089e0122f628af8c9904fc2ebf89 Date: Thu, 19 Jun 2014 17:03:41 +0530 MIME-Version: 1.0 Sent to CCL by: liton [liton.icsp|-|gmail.com] --089e0122f628af8c9904fc2ebf89 Content-Type: text/plain; charset=ISO-8859-1 Hi, I like to discuss few questions regarding exothermic reactions.. (1) Does exothermic reactions contain any activation barrier? (2) Does all the exothermic reactions are barrier less? (3) What rate formula should we used for computing the rate of an exothermic reaction? (4) What is the best and easiest way to compute the reaction rate of an exothermic reaction? I am waiting for helpful answers from all. Best Wishes, Liton ========================================== *Liton Majumdar* Department of Astrochemistry/Astrobiology, *Indian Centre for Space Physics*, 43-Chalantika, Garia Station Road, Kolkata-700084, West Bengal, India. Email - liton]^[csp.res.in, liton.icsp]^[gmail.com Phone:+91-(0)33-2436-6003 Ext.- 22, Fax:+91-(0)33-2462-2153 Ext.-28 Mob:+91-(0)8017853048 ========================================== --089e0122f628af8c9904fc2ebf89 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
=A0= =A0=A0 I like to discuss few questions regarding exothermic reactions..
=
(1) Does exothermic reactions contain any activation barrier?
=
(2) Does all the exothermic reactions are barrier less?
=A0
(3)= What rate formula should we used for computing the rate of an exothermic r= eaction?

(4)=A0 What is the best and easiest way to compute th= e reaction rate of an exothermic reaction?

I am waiting for helpful answers from all.

Best Wis= hes,
=A0=A0=A0 Liton
=A0

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D
*Liton Majumdar*
Department of Astrochemistry/Astrobiology,
*Indian Centre for Space Phys= ics*,
43-Chalantika, Garia Station Road,
Kolkata-700084, West Bengal,= India.
Email - liton]^[csp.res.in= , liton.icsp]^[gmail.com
Phone:+91-(0)33-2436-6003 Ext.- 22,
Fax:+91-(0)33-2462-2153 Ext.-28
= Mob:+91-(0)8017853048
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D

--089e0122f628af8c9904fc2ebf89-- From owner-chemistry@ccl.net Thu Jun 19 11:34:00 2014 From: "Radoslaw Kaminski rkaminski.rk,+,gmail.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50232-140619113318-13147-FiUFH4iflH8VO2rKgSH4Lg.:.server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Thu, 19 Jun 2014 11:33:17 -0400 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] Dear All, A trivial question. I have a XYZ file with a molecule in some coordinate system. I would like to have a Z axis be in a certain direction along A...B atoms. Is there any program that can easily change my coordinate system by choosing some 3 atoms? I can of course do all transformations by hand (for example in Excel) but its tedious. I know that ADF is capable of transforming the coordinates to some specified coordination system (Prof. Baerends' CCL post > from several years ago), but is there any other program that can just make such transformations quickly? Thanks in advance, Radek From owner-chemistry@ccl.net Thu Jun 19 12:11:01 2014 From: "Robert Molt r.molt.chemical.physics|-|gmail.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50233-140619120953-29697-LsIH1fyhEAZQHOwO/iPUmg_-_server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Jun 2014 12:09:45 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics]|[gmail.com] I personally found it worthwhile to write a script to use rotation matrices to transform coordinates as one pleases. This is one of those things that crops up now and again that it's worth it to have for your own. Just look up the rotation matrices from Goldstein's classical mechanics or the like. Dr. Robert Molt Jr., Ph.D. r.molt.chemical.physics=gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 On 6/19/14 11:33 AM, Radoslaw Kaminski rkaminski.rk,+,gmail.com wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post >> from several years ago), but is there any other program that can just make such > transformations quickly? > > Thanks in advance, > > Radek> > From owner-chemistry@ccl.net Thu Jun 19 12:45:00 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor[-]fluor.quimica.uniovi.es" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50234-140619123246-14321-aUHecUVBCKmAcWPfI1SXkg^-^server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Thu, 19 Jun 2014 18:25:34 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]|[fluor.quimica.uniovi.es] On Thu, Jun 19, 2014 at 11:33:17AM -0400, Radoslaw Kaminski rkaminski.rk,+,gmail.com wrote: > > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post > > from several years ago), but is there any other program that can just make such > transformations quickly? > Radek, It's not so trivial. May I suggest S.K. Kearsley, "On the orthogonal transformation used for structural % comparisons", Acta Cryst. A 45 (1989) 208--210. It's not difficult to do the transformation using matlab or gnu-octave and write an script using your favorite language. Best regards, Dr. Víctor Luaña -- \|/a "After years of trying to solve a problem XXXXX exclaimed: |^.^| what an idiot I am ... the solution is trivial!' +---!OO--\_/--OO!------------------------------+----------------------- ! Dr.Víctor Luaña ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor|-|fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Thu Jun 19 13:21:00 2014 From: "Michel Petitjean petitjean.chiral]~[gmail.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50235-140619123719-18076-1kRxxUwPnFP7nSj2R5qDJA__server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=UTF-8 Date: Thu, 19 Jun 2014 18:37:12 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral ~ gmail.com] Dear Radek, You would like to have the new Z axis along vector AB. Compute the angle t=(Z->AB) Compute the vector product V=Z*AB. Once you have the axis V and the angle t, use the Rodrigues' rotation formula to rotate any vector you like in your data. Of course that is not automatic, you need to write some lines of code, but it should work. Best regards, Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral%x%gmail.com (preferred), michel.petitjean%x%univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2014-06-19 17:33 GMT+02:00 Radoslaw Kaminski rkaminski.rk,+,gmail.com : > > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post >> from several years ago), but is there any other program that can just make such > transformations quickly? > > Thanks in advance, > > Radek From owner-chemistry@ccl.net Thu Jun 19 13:55:00 2014 From: "berger%x%chem.helsinki.fi" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50236-140619124735-5400-GKHktYWhdU2/66/WTL6srg- -server.ccl.net> X-Original-From: berger|a|chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 19 Jun 2014 19:47:19 +0300 MIME-Version: 1.0 Sent to CCL by: berger##chem.helsinki.fi Dear Radek, a "simple" GUI solution with molden: open the xyz with molden. goto edit zmatrix, and there to reorder zmatrix. click first on atom A then on atom B and then on all others in some order. save the zmatrix when finished. close molden. open molden with the zmatrix and then save the file as xyz. here you might have to permute the x and z column still. best regards Raphael > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along > A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of > transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL > post >> from several years ago), but is there any other program that can just >> make such > transformations quickly? > > Thanks in advance, > > Radek> > > From owner-chemistry@ccl.net Thu Jun 19 14:31:00 2014 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor+*+fluor.quimica.uniovi.es" To: CCL Subject: CCL: Question regarding exothermic reactions Message-Id: <-50237-140619094830-4239-MRROhva5d7CEKizadbssPw{=}server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Thu, 19 Jun 2014 15:41:15 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor a fluor.quimica.uniovi.es] On Thu, Jun 19, 2014 at 05:03:41PM +0530, liton liton.icsp-*-gmail.com wrote: > Hi, > I like to discuss few questions regarding exothermic reactions.. I don't recognize this questions from a well versed professional of CCL. maybe you should start describing who you are and what is the purpose of the questions. > > (1) Does exothermic reactions contain any activation barrier? They use to have. ¿Why not? If it were is no activation barrier the original system would reacct espontaneously. > (2) Does all the exothermic reactions are barrier less? There are cases of barrier less reactions. Let me stop here and recommend you any good book in chemical kinetics. There are many, but I like very much the next, Introduction to the Physics of the Earth's Interior, 2nd Edition Jean-Paul Poirier (March 2000, Cambridge UP) Manufactured on demand: supplied direct from the printer isbn: 9780521663922 Remember that STP conditions are not the only ones and G(p,T) is the thermodynammic potential to examine. Regards, Dr. Víctor Luaña -- \|/a "After years of trying to solve a problem XXXXX exclaimed: |^.^| what an idiot I am ... the solution is trivial!' +---!OO--\_/--OO!------------------------------+----------------------- ! Dr.Víctor Luaña ! ! Departamento de Química Física y Analítica ! ! Universidad de Oviedo, 33006-Oviedo, Spain ! ! e-mail: victor|*|fluor.quimica.uniovi.es ! ! phone: +34-985-103491 fax: +34-985-103125 ! +----------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Thu Jun 19 15:06:00 2014 From: "Robert Molt Jr r.molt.chemical.physics**gmail.com" To: CCL Subject: CCL: Question regarding exothermic reactions Message-Id: <-50238-140619102201-16332-/UGctulQn66/ppCb8S6C+Q=-=server.ccl.net> X-Original-From: Robert Molt Jr Content-Type: multipart/alternative; boundary="------------080607050303010702040709" Date: Thu, 19 Jun 2014 10:21:53 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt Jr [r.molt.chemical.physics,+,gmail.com] This is a multi-part message in MIME format. --------------080607050303010702040709 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Questions 1.) and 2.) Sometimes exothermic reactions have barriers. Depends on the sign of the thermodynamic functions and what variables you are holding constant. Question 3:) See Eyring equation of transition state theory Question 4:) This question is impossible to answer. You need to specify a system and a needed accuracy of your result. On 06/19/2014 07:33 AM, liton liton.icsp-*-gmail.com wrote: > Hi, > I like to discuss few questions regarding exothermic reactions.. > > (1) Does exothermic reactions contain any activation barrier? > > (2) Does all the exothermic reactions are barrier less? > > (3) What rate formula should we used for computing the rate of an > exothermic reaction? > > (4) What is the best and easiest way to compute the reaction rate of > an exothermic reaction? > > I am waiting for helpful answers from all. > > Best Wishes, > Liton > > > ========================================== > *Liton Majumdar* > Department of Astrochemistry/Astrobiology, > *Indian Centre for Space Physics*, > 43-Chalantika, Garia Station Road, > Kolkata-700084, West Bengal, India. > Email - liton[*]csp.res.in , > liton.icsp[*]gmail.com > Phone:+91-(0)33-2436-6003 Ext.- 22, > Fax:+91-(0)33-2462-2153 Ext.-28 > Mob:+91-(0)8017853048 > ========================================== > --------------080607050303010702040709 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Questions 1.) and 2.)

Sometimes exothermic reactions have barriers.  Depends on the sign of the thermodynamic functions and what variables you are holding constant.

Question 3:)

See Eyring equation of transition state theory

Question 4:)

This question is impossible to answer.  You need to specify a system and a needed accuracy of your result.

On 06/19/2014 07:33 AM, liton liton.icsp-*-gmail.com wrote:
Hi,
    I like to discuss few questions regarding exothermic reactions..

(1) Does exothermic reactions contain any activation barrier?

(2) Does all the exothermic reactions are barrier less?
 
(3) What rate formula should we used for computing the rate of an exothermic reaction?

(4)  What is the best and easiest way to compute the reaction rate of an exothermic reaction?

I am waiting for helpful answers from all.

Best Wishes,
    Liton
 

==========================================
*Liton Majumdar*
Department of Astrochemistry/Astrobiology,
*Indian Centre for Space Physics*,
43-Chalantika, Garia Station Road,
Kolkata-700084, West Bengal, India.
Email - liton[*]csp.res.in, liton.icsp[*]gmail.com
Phone:+91-(0)33-2436-6003 Ext.- 22,
Fax:+91-(0)33-2462-2153 Ext.-28
Mob:+91-(0)8017853048
==========================================


--------------080607050303010702040709-- From owner-chemistry@ccl.net Thu Jun 19 15:41:00 2014 From: "Jean-Pierre DJUKIC djukic]*[unistra.fr" To: CCL Subject: CCL: Question regarding exothermic reactions Message-Id: <-50239-140619111901-32010-TOHoiYrCKZlisJ8lkTVOSQ]=[server.ccl.net> X-Original-From: Jean-Pierre DJUKIC Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 19 Jun 2014 17:19:00 +0200 MIME-Version: 1.0 Sent to CCL by: Jean-Pierre DJUKIC [djukic ~ unistra.fr] Le 19/06/2014 13:33, liton liton.icsp-*-gmail.com a écrit : > Hi, > I like to discuss few questions regarding exothermic reactions.. > > (1) Does exothermic reactions contain any activation barrier? > yes, most of them do. > (2) Does all the exothermic reactions are barrier less? > no exothermicity is related to the enthalpy variation of a reaction, iot its "heat release"; it is a thermo**chemical** consideration...it does not tell anything special about the kinetics of the reaction, which depend much on the activation barrier(s) of its elementary steps. A + B -> A-B , heat release out of the chemical system = exothermicity = thermochemistry, says nothing about the kinetics. A + B -> [A,B] -> [A...B]# -> A-B each step has its "thermochemistry", some is exo some endothermic, what will determine the rate is the highest endo**ergonic** step going to a transition state, since the latter is necessary for the transformation to occur (bond cleavage and formation) and the reaction profile to make sense in most cases... If you consider the second law of thermodynamics, what becomes important is whether the Gibbs free enthalpy variation is negative or not for an overall reaction like A + B -> A-B, that is whether the transformation is spontaneous or not under given conditions of temperature and pressure. This again doesn't tell more about the feasability of the reaction from a kinetic point of view because this info is hidden within the reaction profile and the transition states. At least it tells you whether the reaction is favored thermodynamically or not. For example: catalysis promotes reactions that MUST be thermodynamically favored (DG<0), but which in the absence of catalyst won't move a finger because the activation barriers are too prohibitive. > (3) What rate formula should we used for computing the rate of an > exothermic reaction? > see 4 > (4) What is the best and easiest way to compute the reaction rate of an > exothermic reaction? > Gibbs "free" enthalpy variation from a reactant complex to a related transition state (TS) is related to the rate constant of the elementary step implying conversion of the reactant complex into some product associated with the TS. This is what you can read in textbooks. As you want to establish a reaction profile, it is essential to track down all the reasonable transitions states and from these determine what could be the rate-limiting step of the overall process to get a rough idea of how your computed rate constant k fits the experimental value. There are excellent textbooks on the topic. > I am waiting for helpful answers from all. > Hope it helps clarifying a bit... > Best Wishes, > Liton > > > ========================================== > *Liton Majumdar* > Department of Astrochemistry/Astrobiology, > *Indian Centre for Space Physics*, > 43-Chalantika, Garia Station Road, > Kolkata-700084, West Bengal, India. > Email - liton[*]csp.res.in , > liton.icsp[*]gmail.com > Phone:+91-(0)33-2436-6003 Ext.- 22, > Fax:+91-(0)33-2462-2153 Ext.-28 > Mob:+91-(0)8017853048 > ========================================== > -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr Jean-Pierre DJUKIC (Äukić)(DR CNRS) Laboratoire de Chimie et Systémique OrganoMétalliques (LCSOM) http://lcsom.u-strasbg.fr Adresse postale: LCSOM, Institut de Chimie de Strasbourg UMR 7177 CNRS / Université de Strasbourg 4, rue Blaise Pascal 67000 Strasbourg Cedex. me joindre: Institut Le bel, aile nord, 9ème étage, pièce 942b, tel: +33 (0)368851523 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ a.k.a. F4HCV http://qrz.com/db/F4HCV ================================================================== Attention le présent document est un courrier. Il n'est diffusable qu'avec l'accord explicite de son expéditeur. Le contenu de ce courriel et ses eventuelles pièces jointes sont confidentiels. Ils s'adressent exclusivement à la personne destinataire. Si cet envoi ne vous est pas destiné, ou si vous l'avez reçu par erreur, et afin de ne pas violer le secret des correspondances, vous ne devez pas le transmettre à d'autres personnes ni le reproduire. Merci de le renvoyer à l'émetteur et de le détruire. Attention : L'Organisme de l'émetteur du message ne pourra être tenu responsable de l'altération du présent courriel. Il appartient au destinataire de vérifier que les messages et pièces jointes reçus ne contiennent pas de virus. Les opinions contenues dans ce courriel et ses éventuelles pièces jointes sont celles de l'émetteur. Elles ne reflètent pas la position de l'Organisme sauf s'il en est disposé autrement dans le présent courriel. From owner-chemistry@ccl.net Thu Jun 19 16:15:00 2014 From: "Adam Tenderholt atenderholt,,gmail.com" To: CCL Subject: CCL:G: Coordinate system rotation Message-Id: <-50240-140619125334-11270-fXiAtCTXmcEsuf3eAk9hyw ~~ server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=089e0111d160460e0204fc3337a3 Date: Thu, 19 Jun 2014 09:53:07 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt[-]gmail.com] --089e0111d160460e0204fc3337a3 Content-Type: text/plain; charset=UTF-8 Hi Radek, I think QMForge (http://qmforge.sourceforge.net/) probably can do what you need. It lets you select (using a GUI) one atom to center the molecule, two atoms to rotate that bond (or vector) to an axis, and three atoms to rotate into a plane. You can download an older version ( https://sourceforge.net/projects/qmforge/files/qmforge/) for free. I just tested v2.1 on Mac, and it opens an XYZ file. Note that v2.3.2 does not read XYZ files directly, but you can access the same functionality if you open a logfile from a supported QM program (e.g. Gaussian, ORCA, GAMESS, ADF, etc.). Please let me know (via direct email) if you have any problems. Adam On Thu, Jun 19, 2014 at 8:33 AM, Radoslaw Kaminski rkaminski.rk,+,gmail.com wrote: > > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of > transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL > post > > from several years ago), but is there any other program that can just > make such > transformations quickly? > > Thanks in advance, > > Radek> > > --089e0111d160460e0204fc3337a3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Radek,

I think QMForge (http://qmforge.sourceforge.net/) probab= ly can do what you need. It lets you select (using a GUI) one atom to cente= r the molecule, two atoms to rotate that bond (or vector) to an axis, and t= hree atoms to rotate into a plane.=C2=A0

You can download an older version (https://sourceforge.net/pro= jects/qmforge/files/qmforge/) for free. I just tested v2.1 on Mac, and = it opens an XYZ file. Note that v2.3.2 does not read XYZ files directly, bu= t you can access the same functionality if you open a logfile from a suppor= ted QM program (e.g. Gaussian, ORCA, GAMESS, ADF, etc.).

Please let me know (via direct email) if you have any p= roblems.

Adam



On Thu, Jun 19, 2014 at= 8:33 AM, Radoslaw Kaminski rkaminski.rk,+,gma= il.com <owner-chemistry{:}ccl.net> wrote:

Sent to CCL by: "Radoslaw =C2=A0Kaminski" [rkaminski.rk]=3D[gmail.com]
Dear All,

A trivial question. I have a XYZ file with a molecule in some coordinate system. I would like to have a Z axis be in a certain direction along A...B=
atoms. Is there any program that can easily change my coordinate system by<= br> choosing some 3 atoms? I can of course do all transformations by hand (for<= br> example in Excel) but its tedious. I know that ADF is capable of transformi= ng
the coordinates to some specified coordination system (Prof. Baerends' = CCL post
> from several years ago), but is there any other program that can just = make such
transformations quickly?

Thanks in advance,

Radek



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--089e0111d160460e0204fc3337a3-- From owner-chemistry@ccl.net Thu Jun 19 16:50:01 2014 From: "Mezei, Mihaly mihaly.mezei=mssm.edu" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50241-140619130612-22188-bC93tMjzFu/L3kiT0DKIDg^_^server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 19 Jun 2014 17:06:02 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei(a)mssm.edu] Greetings, one of the options of my program Simulaid (http://inka.mssm.edu/~mezei/simulaid) is to rotate a molecule so a bond (actually, a pair of atoms) is along the X axis and select the a third atom that has to be in the X-Y plane. Regards, Mihaly Mezei Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://www.mssm.edu/departments-and-institutes/structural-and-chemical-biology From owner-chemistry@ccl.net Thu Jun 19 17:25:00 2014 From: "Elaine Meng meng[a]cgl.ucsf.edu" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50242-140619125912-16348-29PLc8rc3jD9fb8OduO8HA]-[server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 19 Jun 2014 12:59:10 -0400 Sent to CCL by: "Elaine Meng" [meng{=}cgl.ucsf.edu] Hi Radek, With Chimera you could align 2 atoms front->back and then save a PDB file with the transformed coordinates. Not sure if that is exactly what you needed, or whether it is quick enough, but you could automate looping through multiple files with a little bit of Python. (1) open XYZ file (e.g. menu FileOpen, choose file.xyz, or command "open file.xyz") http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html That will automatically assign unique atom names by element and order in file, for example the first C will be C1, the first N will be N1. (2) use "align" command to put atoms A,B in center of view along the line of sight (laboratory Z axis) with A in front and B in back (e.g.: align **c1**o1) http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html (3) save PDB with transformed coordinates (e.g. menu FileSave PDB, un-check "use untransformed coordinates" or command something like "write #0 file.pdb") http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html (4) close structure (e.g. command "close #0" or "close all") if multiple structures to process, loop back to step 1. See here for writing looping scripts for Chimera: http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 From owner-chemistry@ccl.net Thu Jun 19 18:00:00 2014 From: "Olasunkanmi Lukman Olawale walecomuk]-[yahoo.co.uk" To: CCL Subject: CCL: Symmetry vs Non-symmetry impostition Message-Id: <-50243-140619124705-4786-W2OYbZhCPGGDsppjaLWivg|*|server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="862858767-2105263782-1403196417=:76916" Date: Thu, 19 Jun 2014 17:46:57 +0100 MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk:+:yahoo.co.uk] --862858767-2105263782-1403196417=:76916 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CClers,=0A=0AI have carried out geometry optimizations and frequency c= alculations on some set of heteroaromatic molecules using DFT/B3LYP/6-311G*= * level of theory in G09W. The calculations were done first without symmetr= y constraint and later with symmetry constraint using a specific symmetry p= oint group, which I expect the molecules to adopt. In each case I have got = different energy values (not unexpected) but the results with symmetry impo= sition returned some imaginary frequencies which left me with the conclusio= n that the molecules are not in the ground state upon imposition =A0of such= symmetry. The energy values from symmetry imposed calculations are slightl= y higher than those without symmetry constraint.=0AMy questions are:=0A- is= it not possible to get the ground state configurations of these molecules = at the particular symmetry point group I imposed on them?=0A- can I conclud= e that the geometry with a less order symmetry point group is more stable t= han the more symmetric one (somewhat against the rule of stability!)?=0A=0A= Your contributions will be appreciated.=0AThank you.=0A=0A=A0=0ALukman Olaw= ale Olasunkanmi=0A=0ACurrent Address:=0ADepartment of Chemistry,=0AFaculty = of Agriculture, Science and Technology,=0ANorth West University (Mafikeng C= ampus),=0ASouth Africa.=0ACell: +27710156252 OR +27747614116=0A=0APermanent= Address:=0ADepartment of Chemistry,=0AObafemi Awolowo University,=0AIle-If= e,=0ANigeria.=0ACell: +234 805 240 1564=0A --862858767-2105263782-1403196417=:76916 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CClers,

I have carried out geometry optimizations and freque= ncy calculations on some set of heteroaromatic molecules using DFT/B3LYP/6-= 311G** level of theory in G09W. The calculations were done first without sy= mmetry constraint and later with symmetry constraint using a specific symme= try point group, which I expect the molecules to adopt. In each case I have got different energy values (not unexpected) but the results with sym= metry imposition returned some imaginary frequencies which left me with the= conclusion that the molecules are not in the ground state upon imposition =  of such symmetry. The energy values from symmetry imposed calculation= s are slightly higher than those without symmetry constraint.
<= div style=3D"color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNe= ue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; backgr= ound-color: transparent; font-style: normal;">My questions are:
- is it not pos= sible to get the ground state configurations of these molecules at the part= icular symmetry point group I imposed on them?
- can I conclude that the = geometry with a less order symmetry point group is more stable than the mor= e symmetric one (somewhat against the rule of stability!)?

Your contributions will be appreciated.
Than= k you.

 
Lukman Olawale Olasunkanmi

Current Address:
Department of Chemistry,
Faculty of Agriculture, Science and Technology,
North = West University (Mafikeng Campus),
South Africa.
<= /span>Cell: +27710156252 OR +27747614116

<= /span>Permanent Address:
Dep= artment of Chemistry,
Obafemi Awolowo University,
Ile-Ife,
Nigeria.
Cell: +234 805 240 1564
--862858767-2105263782-1403196417=:76916-- From owner-chemistry@ccl.net Thu Jun 19 18:35:00 2014 From: "Brad Rose brose^^live.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50244-140619133059-12818-+4ZjaptIjBvKQ6Z7i0CcvQ#server.ccl.net> X-Original-From: Brad Rose Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Thu, 19 Jun 2014 10:31:36 -0700 MIME-Version: 1.0 Sent to CCL by: Brad Rose [brose(0)live.com] It might be worth checking out Chemcraft. It has some coordinate transformation options. Regards, Brad Rose On 6/19/2014 8:33 AM, Radoslaw Kaminski rkaminski.rk,+,gmail.com wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A...B > atoms. Is there any program that can easily change my coordinate system by > choosing some 3 atoms? I can of course do all transformations by hand (for > example in Excel) but its tedious. I know that ADF is capable of transforming > the coordinates to some specified coordination system (Prof. Baerends' CCL post >> from several years ago), but is there any other program that can just make such > transformations quickly? > > Thanks in advance, > > Radek> > From owner-chemistry@ccl.net Thu Jun 19 19:11:00 2014 From: "Hao-Bo Guo guohaobo a gmail.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50245-140619143138-14779-DUxjutQWQLGgcy5ZkTtgow*_*server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=089e0149cd42f7629f04fc349549 Date: Thu, 19 Jun 2014 14:31:31 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo]|[gmail.com] --089e0149cd42f7629f04fc349549 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable apparently you can do it using vmd. a simple tcl script will work. On Thu, Jun 19, 2014 at 12:25 PM, V=C3=ADctor Lua=C3=B1a Cabal victor[-] fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor]|= [ > fluor.quimica.uniovi.es] > On Thu, Jun 19, 2014 at 11:33:17AM -0400, Radoslaw Kaminski rkaminski.rk,= +, > gmail.com wrote: > > > > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=3D[gmail.com] > > A trivial question. I have a XYZ file with a molecule in some coordinat= e > > system. I would like to have a Z axis be in a certain direction along > A...B > > atoms. Is there any program that can easily change my coordinate system > by > > choosing some 3 atoms? I can of course do all transformations by hand > (for > > example in Excel) but its tedious. I know that ADF is capable of > transforming > > the coordinates to some specified coordination system (Prof. Baerends' > CCL post > > > from several years ago), but is there any other program that can just > make such > > transformations quickly? > > > Radek, > > It's not so trivial. May I suggest > > S.K. Kearsley, "On the orthogonal transformation used for structural > % comparisons", Acta Cryst. A 45 (1989) 208--210. > > It's not difficult to do the transformation using matlab or gnu-octave > and write an script using your favorite language. > > Best regards, > Dr. V=C3=ADctor Lua=C3=B1a > > -- > \|/a "After years of trying to solve a problem XXXXX exclaimed= : > |^.^| what an idiot I am ... the solution is trivial!' > +---!OO--\_/--OO!------------------------------+----------------------- > ! Dr.V=C3=ADctor Lua=C3=B1a ! > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor---fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --089e0149cd42f7629f04fc349549 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
apparently you can do it using vmd. a simple tcl script wi= ll work.


On Thu, Jun 19, 2014 at 12:25 PM, V=C3=ADctor Lua=C3=B1a Cabal victor[= -]fluor.quimica.uniovi.es <owner-chemistry_+_ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor]|[<= a href=3D"http://fluor.quimica.uniovi.es" target=3D"_blank">fluor.quimica.u= niovi.es]
On Thu, Jun 19, 2014 at 11:33:17AM -0400, Radoslaw Kaminski rkaminski.rk,+,= gmail.com wrote:
>
> Sent to CCL by: "Radoslaw =C2=A0Kaminski" [rkaminski.rk]=3D[= gmail.com]
> A trivial question. I have a XYZ file with a molecule in some coordina= te
> system. I would like to have a Z axis be in a certain direction along = A...B
> atoms. Is there any program that can easily change my coordinate syste= m by
> choosing some 3 atoms? I can of course do all transformations by hand = (for
> example in Excel) but its tedious. I know that ADF is capable of trans= forming
> the coordinates to some specified coordination system (Prof. Baerends&= #39; CCL post
> > from several years ago), but is there any other program that can = just make such
> transformations quickly?
>
Radek,

It's not so trivial. May I suggest

S.K. Kearsley, "On the orthogonal transformation used for structural % comparisons", Acta Cryst. A 45 (1989) 208--210.

It's not difficult to do the transformation using matlab or gnu-octave<= br> and write an script using your favorite language.

Best regards,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Dr. V=C3=ADctor Lua=C3=B1a<= br>
--
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0\|/a =C2=A0 "After years of trying t= o solve a problem XXXXX exclaimed:
=C2=A0 =C2=A0 =C2=A0 =C2=A0 |^.^| =C2=A0 =C2=A0 what an idiot I am ... the = solution is trivial!'
+---!OO--\_/--OO!------------------------------+-----------------------
! =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Dr.V=C3=ADctor Lua=C3=B1a =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 !
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica =C2=A0 !
! Universidad de Oviedo, 33006-Oviedo, Spain =C2=A0 !
! e-mail: =C2=A0 victor---fluor.quimica.uniovi.es =C2=A0 =C2=A0 !
! phone: +34-985-10= 3491 =C2=A0fax: +34-985-103125 =C2=A0 !
+----------------------------------------------+
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/ =C2=A0(being reworked)



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--089e0149cd42f7629f04fc349549-- From owner-chemistry@ccl.net Thu Jun 19 19:45:00 2014 From: "Nicolas Cheron nicolas.cheron.boulot|*|gmail.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50246-140619143457-18764-sXWv6zCFLUbBRLDabqUdVw%x%server.ccl.net> X-Original-From: Nicolas Cheron Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 19 Jun 2014 14:34:08 -0400 MIME-Version: 1.0 Sent to CCL by: Nicolas Cheron [nicolas.cheron.boulot|gmail.com] Hello, Let's say you want to align the vector U(uX,uY,uZ) with the vector V(vX,vY,vZ), both being normalized. We call Alpha the angle between the two vectors. I assume that the xyz coordinates are stored in an array of doubles (oldMolecule[size][3]); the new ones will be stored in newMolecule[size][3]. In C++, you can use something like the following: // You must define uX, uY, uZ, vX, vY, vZ before, using the coordinates of your atoms. // We define W=UxV/||UxV||. double wX = (uY*vZ - uZ*vY)/sqrt(pow(uY*vZ - uZ*vY,2) + pow(uZ*vX - uX*vZ,2) + pow(uX*vY - uY*vX,2)); double wY = (uZ*vX - uX*vZ)/sqrt(pow(uY*vZ - uZ*vY,2) + pow(uZ*vX - uX*vZ,2) + pow(uX*vY - uY*vX,2)); double wZ = (uX*vY - uY*vX)/sqrt(pow(uY*vZ - uZ*vY,2) + pow(uZ*vX - uX*vZ,2) + pow(uX*vY - uY*vX,2)); // We know U.V = U*V*cos(alpha) and sin(alpha) = det(W, U, V) double cosAlpha = uX*vX + uY*vY + uZ*vZ; double sinAlpha = (wX*uY*vZ + uX*vY*wZ + vX*wY*uZ) - (vX*uY*wZ + wX*vY*uZ + uX*wY*vZ); // Let's write the rotation matrix around the vector W (http://en.wikipedia.org/wiki/Rotation_matrix#Rotation_matrix_from_axis_and_angle). double rotationMatrix[3][3]; rotationMatrix[0][0] = cosAlpha + pow(wX,2)*(1-cosAlpha); rotationMatrix[0][1] = wX*wY*(1-cosAlpha) + wZ*sinAlpha; rotationMatrix[0][2] = wX*wZ*(1-cosAlpha) - wY*sinAlpha; // rotationMatrix has the following form: rotationMatrix[1][0] = wX*wY*(1-cosAlpha) - wZ*sinAlpha; // [0][0] [1][0] [2][0] rotationMatrix[1][1] = cosAlpha + pow(wY,2)*(1-cosAlpha); // [0][1] [1][1] [2][1] rotationMatrix[1][2] = wY*wZ*(1-cosAlpha) + wX*sinAlpha; // [0][2] [1][2] [2][2] rotationMatrix[2][0] = wX*wZ*(1-cosAlpha) + wY*sinAlpha; rotationMatrix[2][1] = wY*wZ*(1-cosAlpha) - wX*sinAlpha; rotationMatrix[2][2] = cosAlpha + pow(wZ,2)*(1-cosAlpha); // Then you can do the alignement. double newMolecule[size][3]; for (unsigned int j=0; j: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]|[fluor.quimica.uniovi.es] > On Thu, Jun 19, 2014 at 11:33:17AM -0400, Radoslaw Kaminski rkaminski.rk,+,gmail.com wrote: >> >> Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=[gmail.com] >> A trivial question. I have a XYZ file with a molecule in some coordinate >> system. I would like to have a Z axis be in a certain direction along A...B >> atoms. Is there any program that can easily change my coordinate system by >> choosing some 3 atoms? I can of course do all transformations by hand (for >> example in Excel) but its tedious. I know that ADF is capable of transforming >> the coordinates to some specified coordination system (Prof. Baerends' CCL post >> > from several years ago), but is there any other program that can just make such >> transformations quickly? >> > Radek, > > It's not so trivial. May I suggest > > S.K. Kearsley, "On the orthogonal transformation used for structural > % comparisons", Acta Cryst. A 45 (1989) 208--210. > > It's not difficult to do the transformation using matlab or gnu-octave > and write an script using your favorite language. > > Best regards, > Dr. Víctor Luaña > > -- > \|/a "After years of trying to solve a problem XXXXX exclaimed: > |^.^| what an idiot I am ... the solution is trivial!' > +---!OO--\_/--OO!------------------------------+----------------------- > ! Dr.Víctor Luaña ! > ! Departamento de Química Física y Analítica ! > ! Universidad de Oviedo, 33006-Oviedo, Spain ! > ! e-mail: victor---fluor.quimica.uniovi.es ! > ! phone: +34-985-103491 fax: +34-985-103125 ! > +----------------------------------------------+ > GroupPage : http://azufre.quimica.uniovi.es/ (being reworked)> > From owner-chemistry@ccl.net Thu Jun 19 20:20:00 2014 From: "uekstrom|a|gmail.com uekstrom|a|gmail.com" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50247-140619120449-27128-/XpCIFhiSbd64I78zd8lHw/./server.ccl.net> X-Original-From: "uekstrom-x-gmail.com" Content-Type: multipart/alternative; boundary=047d7bf10a1cfb26bf04fc3288f6 Date: Thu, 19 Jun 2014 18:04:43 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom-$-gmail.com" [uekstrom-$-gmail.com] --047d7bf10a1cfb26bf04fc3288f6 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Radek, I made a command line program many years ago to do this (and other things). It still compiles, and you can get it from https://www.dropbox.com/s/croyi7dg6gzvtlp/mol_tool.tgz There is not much help, but the syntax is Usage: moltool -r MOLECULE RX RY RZ [ANGLE] Where the RX,RY,RZ is the axis. I hope this can be helpful. Regards, Ulf Ekstr=C3=B6m 2014-06-19 17:33 GMT+02:00 Radoslaw Kaminski rkaminski.rk,+,gmail.com < owner-chemistry()ccl.net>: > > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk]=3D[gmail.com] > Dear All, > > A trivial question. I have a XYZ file with a molecule in some coordinate > system. I would like to have a Z axis be in a certain direction along A..= .B > atoms. Is there any program that can easily change my coordinate system b= y > choosing some 3 atoms? I can of course do all transformations by hand (fo= r > example in Excel) but its tedious. I know that ADF is capable of > transforming > the coordinates to some specified coordination system (Prof. Baerends' CC= L > post > > from several years ago), but is there any other program that can just > make such > transformations quickly? > > Thanks in advance, > > Radek > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --047d7bf10a1cfb26bf04fc3288f6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Radek,=C2=A0
I made a command line program many y= ears ago to do this (and other things). It still compiles, and you can get = it from=C2=A0https://www.dropbox.com/s/croyi7dg6gzvtlp/mol_tool.tgz=C2=A0
There is not much help, but the syntax is

Usage: moltool -r MOLECULE RX RY RZ [ANGLE]

= Where the RX,RY,RZ is the axis. I hope this can be helpful.

Regards,

Ulf Ekstr=C3=B6m





2014-06-19 17:33 GMT+02:00 Radoslaw Kaminski rkaminski.rk,+,gmail.com <owner-chemistry()ccl.net>= ;:

Sent to CCL by: "Radoslaw =C2=A0Kaminski" [rkaminski.rk]=3D[gmail.com]
Dear All,

A trivial question. I have a XYZ file with a molecule in some coordinate system. I would like to have a Z axis be in a certain direction along A...B=
atoms. Is there any program that can easily change my coordinate system by<= br> choosing some 3 atoms? I can of course do all transformations by hand (for<= br> example in Excel) but its tedious. I know that ADF is capable of transformi= ng
the coordinates to some specified coordination system (Prof. Baerends' = CCL post
> from several years ago), but is there any other program that can just = make such
transformations quickly?

Thanks in advance,

Radek



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--047d7bf10a1cfb26bf04fc3288f6-- From owner-chemistry@ccl.net Thu Jun 19 20:55:00 2014 From: "canyslopus-,-yahoo.co.uk canyslopus-,-yahoo.co.uk" To: CCL Subject: CCL: Coordinate system rotation Message-Id: <-50248-140619135436-13542-NHZa6DBUD/lP5juGy8wXIg(0)server.ccl.net> X-Original-From: "canyslopus/a\yahoo.co.uk" Content-Type: multipart/alternative; boundary="-1378300412-1224804684-1403200467=:76184" Date: Thu, 19 Jun 2014 18:54:27 +0100 MIME-Version: 1.0 Sent to CCL by: "canyslopus],[yahoo.co.uk" [canyslopus],[yahoo.co.uk] ---1378300412-1224804684-1403200467=:76184 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Radek,=0A=0AThe best program I know is Chemcraft. Go to www.chemcraftp= rog.com and download it. It's free for 160 days. =0A=0ACiao, =0ACina=0A----= --------------------=0ACina Foroutan-Nejad, PhD=0ANational Center for Biomo= lecular Researches,=0AMasaryk University,=A0 Brno, =0ACzech Republic=0Ahttp= s://muni.academia.edu/CinaForoutanNejad=0A=0ASent from Yahoo Mail on Androi= d=0A=0A ---1378300412-1224804684-1403200467=:76184 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Radek,

=0A

The best program I know is = Chemcraft. Go to www.chemcraftprog.com and download it. It's free for 160 d= ays.

=0A

Ciao,
=0ACina
=0A------------------------=0ACina Foroutan-Nejad, PhD
=0ANational Center for Biomolecular Resear= ches,
=0AMasaryk University, Brno,
=0ACzech Republic
=0Ahttps://= muni.academia.edu/CinaForoutanNejad

=0A

Sent from Yahoo Mail on A= ndroid

=0A
=0A =
=0A
=0A
= =0A
=0A =
=0A =0A = From:=0A = =0A Radoslaw Kaminsk= i rkaminski.rk,+,gmail.com <owner-chemistry{=}ccl.net>; =
=0A =0A = To:=0A = =0A Foroutan-Nejad, Cina &= lt;canyslopus{=}yahoo.co.uk>; =
=0A =0A = Subject:=0A =0A CCL: C= oordinate system rotation
=0A = =0A Sent:=0A =0A = Thu, Jun 19, 2014 3:33:17 PM
=0A=
=0A
=0A = =0A =0A = =0A =0A = =0A =0A =
<= BR>Sent to CCL by: "Radoslaw  Kaminski" [rkaminski.rk]=3D[gmail.com]Dear All,

A trivial question. I have a XYZ file with a molecule in= some coordinate
system. I would like to have a Z axis be in a certain = direction along A...B
atoms. Is there any program that can easily chang= e my coordinate system by
choosing some 3 atoms? I can of course do all= transformations by hand (for
example in Excel) but its tedious. I know= that ADF is capable of transforming
the coordinates to some specified = coordination system (Prof. Baerends' CCL post
> from several years a= go), but is there any other program that can just make such
transformat= ions quickly?

Thanks in advance,

Radek



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