From owner-chemistry@ccl.net Fri Jan 26 03:44:01 2007 From: "Patrick Pang skpang#%#ctimail.com" To: CCL Subject: CCL: Windows-based software for the analysis of the DNA structure Message-Id: <-33443-070126034228-15686-hSeqCdGRdtsQeb5E4Ov3nw|*|server.ccl.net> X-Original-From: "Patrick Pang" Date: Fri, 26 Jan 2007 03:42:24 -0500 Sent to CCL by: "Patrick Pang" [skpang::ctimail.com] Dear all, Would you suggest software for the analysis of the DNA structure (e.g. major groove, minor groove, bent angle (like cisplatin binding to DNA), twist angle ...) under Windows? Regards, Patrcik My e-mail address is: skpang]_[ctimail.com From owner-chemistry@ccl.net Fri Jan 26 07:52:00 2007 From: "Jim Harrison jim456harrison*_*yahoo.com" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33444-070126014918-31149-oZxhrTzQV+8BE9HOYcjBnw .. server.ccl.net> X-Original-From: Jim Harrison Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1657244345-1169789971=:98131" Date: Thu, 25 Jan 2007 21:39:31 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jim Harrison [jim456harrison..yahoo.com] --0-1657244345-1169789971=:98131 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all I have a problem concerning optimization of molecules of more than 2 atoms. I am using Gaussian 03 to optimize and perform a frequency calculation of molecules such as for example NaCN. NaCN is a T shape molecule and has a non-linear geometry. If I input a linear initial geometry and perform an optimization, will the molecule (which is actually non-linear) converge to a non-linear geometry I have perform an optimization of linear NaCN and the stationary point was found.The optimized geometry remains linear. But when I perform optimization of non-linear NaCN with initial angle 120, the required geometry (T shaped) was obtained. My question is that must one have a knowledge of the geometry of a molecule under study in its ground state to perform optimization. If so what is the purpose of optimizing. Can an initial linear structure input converged to an optimized structure which is actually non-linear Can Gaussian 03 predict the structure of a molecule for which the geometry is unknown. If so how? I know that Gaussian 03 required an approximate initial geometry. Is there a way > from theory to determine whether the molecule in question is linear, bent or even a T shape. For example OCS molecule is linear. If one is going to calculate the adiabatic electron affinity, one has to optimise the anion OCS- which I did with a linear geometry just like with OCS. The optimize anion OCS- remains linear. But I have found from many publications that anion OCS- is actually a bent shape molecules.Again I perform an optimization of OCS- but this time with a bent shape, angle 120. This optimized geometry with angle 136.7 coincide with the publications. The angle has change significantly from angle 120 to 136.7. Why the initial linear geometry of anion OCS- did not converge to the optimised geometry with angle 136.7 note that the electron affinity computed with linear anion OCS- and the bent shaped anion OCS- are totally different. The one which coincide with the experimental value is the bent shaped as required. I perform a frequency calculation with the optimized geometry of the linear anion OCS- and obtain negative frequency (saddle point which specifies a transition state). Does a negative frequency mean the optimized geometry has not actually been optimized. Does in general a negative frequency is an indication that the initial geometry input is not correct and hence must alter the initial geometry just like I did with the bent shape. Thanking you all Best regards Jim --------------------------------- Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and get things done faster. --0-1657244345-1169789971=:98131 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all

    I have a problem concerning optimization of molecules of more than 2 atoms.
I am using Gaussian 03 to optimize and perform a frequency calculation of molecules such as for example NaCN. NaCN is a T shape molecule and has a non-linear geometry.

 If I input a linear initial geometry and perform an optimization, will the molecule (which is actually non-linear) converge to a non-linear geometry

I have perform an optimization of linear NaCN and the stationary point was found.The optimized geometry remains linear. But when I perform optimization of
non-linear NaCN with initial angle 120, the required geometry (T shaped) was obtained.

My question is that must one have a knowledge of the geometry of a molecule under study in its ground state to perform optimization. If so what is the purpose of optimizing. Can an initial linear structure input converged to an optimized structure which is actually non-linear
Can Gaussian 03 predict the structure of a molecule for which  the geometry is unknown. If so how?

I know that Gaussian 03 required an approximate initial geometry. Is there a way
from theory to determine whether the molecule in question is linear, bent or  even a T shape.

For example OCS molecule is linear. If one is going to calculate the adiabatic electron affinity, one has to optimise the anion OCS- which I did with a linear
geometry just like with OCS. The optimize anion OCS- remains linear. But I have found from many publications that anion OCS- is actually  a bent shape molecules.Again I perform an optimization of OCS- but this time with a bent shape, angle 120. This optimized geometry with angle 136.7 coincide with the publications. The angle has change  significantly from angle 120 to 136.7.

Why the initial linear geometry of anion OCS- did not converge to the optimised geometry with angle 136.7

note that the electron affinity computed with linear anion OCS- and the bent shaped anion OCS- are totally different. The one which coincide with the experimental value is the bent shaped as required.

I perform a frequency calculation with the optimized geometry of the linear anion
OCS-  and obtain negative frequency (saddle point which specifies a transition state). Does a  negative frequency mean the optimized geometry has not actually
been optimized. Does in general a negative frequency is an indication that the initial geometry input is not correct and hence must alter the initial geometry just like I did with the bent shape.

Thanking you all

 Best regards

Jim


Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and get things done faster. --0-1657244345-1169789971=:98131-- From owner-chemistry@ccl.net Fri Jan 26 09:08:00 2007 From: "Jens Spanget-Larsen spanget-*-ruc.dk" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33445-070126082414-19451-3KfiUAmzQ75pnmbDi0qadg**server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 26 Jan 2007 14:24:01 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget * ruc.dk] Dear Jim, when you input a geometry that displays symmetry, e.g., a linear molecule, the forces on the nuclei reflects that symmetry. Hence, the optimization algorithm will produce zero force gradients in directions that violate this symmetry, and the molecule will stay within the initial symmetry during the optimization procedure. This is perfectly normal! The optimized geometry obtained in this way will not necessarily be an equilibrium structure corresponding to a minimum. A frequency calculation may turn out to obtain one or more negative force constants (imaginary wavenumbers), indicating that the structure corresponds to a saddle point. In order to find the true minimum, you must repeat the calculation with no symmetry restriction. Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*_*ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Jim Harrison jim456harrison*_*yahoo.com wrote: > Dear all > > I have a problem concerning optimization of molecules of more than 2 > atoms. I am using Gaussian 03 to optimize and perform a frequency > calculation of molecules such as for example NaCN. NaCN is a T shape > molecule and has a non-linear geometry. > > If I input a linear initial geometry and perform an optimization, > will the molecule (which is actually non-linear) converge to a > non-linear geometry > > I have perform an optimization of linear NaCN and the stationary > point was found.The optimized geometry remains linear. But when I > perform optimization of non-linear NaCN with initial angle 120, the > required geometry (T shaped) was obtained. > > My question is that must one have a knowledge of the geometry of a > molecule under study in its ground state to perform optimization. If > so what is the purpose of optimizing. Can an initial linear structure > input converged to an optimized structure which is actually > non-linear Can Gaussian 03 predict the structure of a molecule for > which the geometry is unknown. If so how? > > I know that Gaussian 03 required an approximate initial geometry. Is > there a way > >> from theory to determine whether the molecule in question is >> linear, bent or even a T shape. > > > For example OCS molecule is linear. If one is going to calculate the > adiabatic electron affinity, one has to optimise the anion OCS- which > I did with a linear geometry just like with OCS. The optimize anion > OCS- remains linear. But I have found from many publications that > anion OCS- is actually a bent shape molecules.Again I perform an > optimization of OCS- but this time with a bent shape, angle 120. This > optimized geometry with angle 136.7 coincide with the publications. > The angle has change significantly from angle 120 to 136.7. > > Why the initial linear geometry of anion OCS- did not converge to the > optimised geometry with angle 136.7 > > note that the electron affinity computed with linear anion OCS- and > the bent shaped anion OCS- are totally different. The one which > coincide with the experimental value is the bent shaped as required. > > I perform a frequency calculation with the optimized geometry of the > linear anion OCS- and obtain negative frequency (saddle point which > specifies a transition state). Does a negative frequency mean the > optimized geometry has not actually been optimized. Does in general a > negative frequency is an indication that the initial geometry input > is not correct and hence must alter the initial geometry just like I > did with the bent shape. > > Thanking you all > > Best regards > > Jim > > > > > --------------------------------- Check out the all-new Yahoo! Mail > beta - Fire up a more powerful email and get things done faster. From owner-chemistry@ccl.net Fri Jan 26 10:56:01 2007 From: "Phil Hultin hultin(~)cc.umanitoba.ca" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33446-070126104511-28852-2Eoq11JL2Tz8fvtKMoZ9kg,server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 26 Jan 2007 09:06:35 -0600 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin_+_cc.umanitoba.ca] Jens is also pointing out something important - he is quite correct that Gaussian will maintain the initial symmetry during a minimization unless told otherwise. Add that to my comments on the nature of minimization and you should begin to have a clearer picture of how this all works. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin _ cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net] Sent: January 26, 2007 7:24 AM To: Hultin, Philip G. Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Sent to CCL by: Jens Spanget-Larsen [spanget * ruc.dk] Dear Jim, when you input a geometry that displays symmetry, e.g., a linear molecule, the forces on the nuclei reflects that symmetry. Hence, the optimization algorithm will produce zero force gradients in directions that violate this symmetry, and the molecule will stay within the initial symmetry during the optimization procedure. This is perfectly normal! The optimized geometry obtained in this way will not necessarily be an equilibrium structure corresponding to a minimum. A frequency calculation may turn out to obtain one or more negative force constants (imaginary wavenumbers), indicating that the structure corresponds to a saddle point. In order to find the true minimum, you must repeat the calculation with no symmetry restriction. Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*o*ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Jim Harrison jim456harrison*_*yahoo.com wrote: > Dear all > > I have a problem concerning optimization of molecules of more than 2 > atoms. I am using Gaussian 03 to optimize and perform a frequency > calculation of molecules such as for example NaCN. NaCN is a T shape > molecule and has a non-linear geometry. > > If I input a linear initial geometry and perform an optimization, > will the molecule (which is actually non-linear) converge to a > non-linear geometry > > I have perform an optimization of linear NaCN and the stationary > point was found.The optimized geometry remains linear. But when I > perform optimization of non-linear NaCN with initial angle 120, the > required geometry (T shaped) was obtained. > > My question is that must one have a knowledge of the geometry of a > molecule under study in its ground state to perform optimization. If > so what is the purpose of optimizing. Can an initial linear structure > input converged to an optimized structure which is actually > non-linear Can Gaussian 03 predict the structure of a molecule for > which the geometry is unknown. If so how? > > I know that Gaussian 03 required an approximate initial geometry. Is > there a way > >> from theory to determine whether the molecule in question is >> linear, bent or even a T shape. > > > For example OCS molecule is linear. If one is going to calculate the > adiabatic electron affinity, one has to optimise the anion OCS- which > I did with a linear geometry just like with OCS. The optimize anion > OCS- remains linear. But I have found from many publications that > anion OCS- is actually a bent shape molecules.Again I perform an > optimization of OCS- but this time with a bent shape, angle 120. This > optimized geometry with angle 136.7 coincide with the publications. > The angle has change significantly from angle 120 to 136.7. > > Why the initial linear geometry of anion OCS- did not converge to the > optimised geometry with angle 136.7 > > note that the electron affinity computed with linear anion OCS- and > the bent shaped anion OCS- are totally different. The one which > coincide with the experimental value is the bent shaped as required. > > I perform a frequency calculation with the optimized geometry of the > linear anion OCS- and obtain negative frequency (saddle point which > specifies a transition state). Does a negative frequency mean the > optimized geometry has not actually been optimized. Does in general a > negative frequency is an indication that the initial geometry input > is not correct and hence must alter the initial geometry just like I > did with the bent shape. > > Thanking you all > > Best regards > > Jim > > > > > --------------------------------- Check out the all-new Yahoo! Mail > beta - Fire up a more powerful email and get things done faster.http://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 Fri Jan 26 11:30:00 2007 From: "Sergio Emanuel Galembeck segalemb{}usp.br" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33447-070126092203-6041-T88YDG0aWyj0wHPFAtgYig/a\server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 26 Jan 2007 11:21:36 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb ~ usp.br] Dear Jim, The problem with OCS-, is that Gaussian, and some other programs, mantain the initial symmetry, in this case Dinfh. The imaginary (negative) frequency indicates that you are in a transition state. In order to obtain the minima, you need to decrease the bond angle to reduce the symmetry to Cs. Hope this help you, Sergio Citando "Jim Harrison jim456harrison*_*yahoo.com" : > Dear all > > I have a problem concerning optimization of molecules of more than 2 > atoms. > I am using Gaussian 03 to optimize and perform a frequency calculation of > molecules such as for example NaCN. NaCN is a T shape molecule and has a > non-linear geometry. > > If I input a linear initial geometry and perform an optimization, will the > molecule (which is actually non-linear) converge to a non-linear geometry > > I have perform an optimization of linear NaCN and the stationary point was > found.The optimized geometry remains linear. But when I perform optimization > of > non-linear NaCN with initial angle 120, the required geometry (T shaped) was > obtained. > > My question is that must one have a knowledge of the geometry of a molecule > under study in its ground state to perform optimization. If so what is the > purpose of optimizing. Can an initial linear structure input converged to an > optimized structure which is actually non-linear > Can Gaussian 03 predict the structure of a molecule for which the geometry > is unknown. If so how? > > I know that Gaussian 03 required an approximate initial geometry. Is there a > way > > from theory to determine whether the molecule in question is linear, bent > or even a T shape. > > For example OCS molecule is linear. If one is going to calculate the > adiabatic electron affinity, one has to optimise the anion OCS- which I did > with a linear > geometry just like with OCS. The optimize anion OCS- remains linear. But I > have found from many publications that anion OCS- is actually a bent shape > molecules.Again I perform an optimization of OCS- but this time with a bent > shape, angle 120. This optimized geometry with angle 136.7 coincide with the > publications. The angle has change significantly from angle 120 to 136.7. > > Why the initial linear geometry of anion OCS- did not converge to the > optimised geometry with angle 136.7 > > note that the electron affinity computed with linear anion OCS- and the bent > shaped anion OCS- are totally different. The one which coincide with the > experimental value is the bent shaped as required. > > I perform a frequency calculation with the optimized geometry of the linear > anion > OCS- and obtain negative frequency (saddle point which specifies a > transition state). Does a negative frequency mean the optimized geometry has > not actually > been optimized. Does in general a negative frequency is an indication that > the initial geometry input is not correct and hence must alter the initial > geometry just like I did with the bent shape. > > Thanking you all > > Best regards > > Jim > > > > > --------------------------------- > Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and > get things done faster. From owner-chemistry@ccl.net Fri Jan 26 12:05:00 2007 From: "Xunlei Ding dingxunlei-$-gmail.com" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33448-070126112340-9964-bC0iaebMnKWNHgRZX4OMxw]=[server.ccl.net> X-Original-From: Xunlei Ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 26 Jan 2007 16:36:13 +0100 MIME-Version: 1.0 Sent to CCL by: Xunlei Ding [dingxunlei!A!gmail.com] Dear Jim, Two reasons: 1. Symmetry restrict: Linear one has higher symmetry than non-linear one, and the symmetry will be kept in the optimization. So you can try to set the angle as 179.0, to see whether it can get a non-linear result. 2. Local minimal: Ordinary optimazation is to find local minimum in the energy surface, not the global minimun. So if linear geometry is a local minimal, even you start with a angle of 179.0, you will still get linear result. The first reason may lead to negative frequency and the second one will not. Yours sincerely, Ding Jim Harrison jim456harrison*_*yahoo.com wrote: > Dear all > > I have a problem concerning optimization of molecules of more than > 2 atoms. > I am using Gaussian 03 to optimize and perform a frequency calculation > of molecules such as for example NaCN. NaCN is a T shape molecule and > has a non-linear geometry. > > If I input a linear initial geometry and perform an optimization, > will the molecule (which is actually non-linear) converge to a > non-linear geometry > > I have perform an optimization of linear NaCN and the stationary point > was found.The optimized geometry remains linear. But when I perform > optimization of > non-linear NaCN with initial angle 120, the required geometry (T > shaped) was obtained. > > My question is that must one have a knowledge of the geometry of a > molecule under study in its ground state to perform optimization. If > so what is the purpose of optimizing. Can an initial linear structure > input converged to an optimized structure which is actually non-linear > Can Gaussian 03 predict the structure of a molecule for which the > geometry is unknown. If so how? > > I know that Gaussian 03 required an approximate initial geometry. Is > there a way > from theory to determine whether the molecule in question is linear, > bent or even a T shape. > > For example OCS molecule is linear. If one is going to calculate the > adiabatic electron affinity, one has to optimise the anion OCS- which > I did with a linear > geometry just like with OCS. The optimize anion OCS- remains linear. > But I have found from many publications that anion OCS- is actually a > bent shape molecules.Again I perform an optimization of OCS- but this > time with a bent shape, angle 120. This optimized geometry with angle > 136.7 coincide with the publications. The angle has change > significantly from angle 120 to 136.7. > > Why the initial linear geometry of anion OCS- did not converge to the > optimised geometry with angle 136.7 > > note that the electron affinity computed with linear anion OCS- and > the bent shaped anion OCS- are totally different. The one which > coincide with the experimental value is the bent shaped as required. > > I perform a frequency calculation with the optimized geometry of the > linear anion > OCS- and obtain negative frequency (saddle point which specifies a > transition state). Does a negative frequency mean the optimized > geometry has not actually > been optimized. Does in general a negative frequency is an indication > that the initial geometry input is not correct and hence must alter > the initial geometry just like I did with the bent shape. > > Thanking you all > > Best regards > > Jim > > > ------------------------------------------------------------------------ > Check out the all-new Yahoo! Mail beta > > - Fire up a more powerful email and get things done faster. From owner-chemistry@ccl.net Fri Jan 26 12:40:01 2007 From: "David Sherrill sherrill---gatech.edu" To: CCL Subject: CCL: Georgia Tech Summer Theory Program 2007 Message-Id: <-33449-070125184125-13204-KHIFoPfBwp2c13Y7XL4TnA:server.ccl.net> X-Original-From: David Sherrill Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 25 Jan 2007 18:11:24 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: David Sherrill [sherrill-$-gatech.edu] Georgia Tech will host its annual Summer Theory Program as part of its NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 21 to July 27 and is open to students who will be in their junior or senior years during the 2006-2007 academic year. Theory students will work with Professors David Sherrill, Rigoberto Hernandez, or Jean-Luc Bredas in the areas of electronic structure theory, nonequilibrium dynamics, or the electronic properties of organic materials. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $4000, a travel allowance, and housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html The deadline for applications is February 15, 2007. -- C. David Sherrill, Ph.D. Associate Professor School of Chemistry & Biochemistry and College of Computing Georgia Institute of Technology www.chemistry.gatech.edu/faculty/sherrill/ sherrill+/-gatech.edu, tel: 404-894-4037, fax: 404-894-7452 From owner-chemistry@ccl.net Fri Jan 26 13:15:00 2007 From: "Gabriele Cruciani meeting2007**moldiscovery.com" To: CCL Subject: CCL: 2nd Molecular Discovery Users` Meeting: first announcement Message-Id: <-33450-070126110638-1920-SlvpKfEwnKb78QfOjvV/1Q%a%server.ccl.net> X-Original-From: "Gabriele Cruciani" Date: Fri, 26 Jan 2007 11:06:35 -0500 Sent to CCL by: "Gabriele Cruciani" [meeting2007 . moldiscovery.com] The 2nd Molecular Discovery Users Meeting on Novel Computational Methods for Cheminformatics, Rational Drug Design, ADME and DMPK Prediction. 27th - 31st May, 2007 We are pleased to announce the second MD Users Meeting which will be held in Perugia, Italy, from the 27th to 31st of May, 2007. The main focus of the Meeting will be on the practical use of the MD Programmes in real research applications, and participants will be able to work with the latest release of each Programme. They will also have a unique opportunity to evaluate and try some of the novel software projects which are currently being developed by the scientists at Molecular Discovery. Preliminary agenda for the meeting: DAY 0 (Sunday 27th May): Arrival and welcome party in the evening. DAY 1 (Monday 28th May): Predicting the site of metabolism for xenobiotics. MetaSite DAY 2 (Thusday 29th May): What's new in in silico ADME-methods. VolSurf+ DAY 3 (Wednesday 30th May): In silico pKa prediction. MoKa DAY 4 (Thursday 31st May): Scaffold hopping from proteins. SHOP Recommendation: The number of rooms for attendees is limited, so a registration should be made as soon as possible. Venue: The meeting will be held in Relais Borgo Brufa, a wonderful resort centre overlooking luxuriant valleys cloaked in olive groves and vineyards. A green oasis of silence for nature lovers, made even more irresistible by a unique range of services and technology, located in the hills surrounding Perugia. Snapshots of the locations are reported in the web page: http://www.borgobrufa.it For any question please feel free to contact Prof. G.Cruciani gabri[A]chemiome.chm.unipg.it or meeting2007[A]moldiscovery.com From owner-chemistry@ccl.net Fri Jan 26 13:50:01 2007 From: "Joe Kwiatkowski joseph-john.kwiatkowski .. imperial.ac.uk" To: CCL Subject: CCL:G: Zindo parameters Message-Id: <-33451-070126115132-29852-UP1pVvE8MvjmwdYTJ91/VQ**server.ccl.net> X-Original-From: Joe Kwiatkowski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 26 Jan 2007 16:49:00 +0000 MIME-Version: 1.0 Sent to CCL by: Joe Kwiatkowski [joseph-john.kwiatkowski**imperial.ac.uk] Dear All. I am attempting to input Zindo1 parameters into Gaussian using IOP(3/41=100). My question is what should I be entering? For each atom the manual asks for: 1) Scale 2) HDiag(1,2,3) 3) Beta(1,2,3) I am taking these to mean: 1) Slater exponent (same for s, p and d) 2) Ionisation energy of s, p and d orbitals 3) Bond parameter for resonance integral of s, p, d However, the calculation doesn't work. Help! Am I entering the correct information? Many thanks, Joe Kwiatkowski Imperial College London From owner-chemistry@ccl.net Fri Jan 26 14:25:01 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas+*+chem.elte.hu" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33452-070126123957-29689-nIjecOVyu92Qw9gYdighwg=server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 26 Jan 2007 18:38:25 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas]![chem.elte.hu] Hi Jim (and Jens), Jens was right, when the initial structure of the molecule has any sort of symmetry (includes linearity and planarity) there is no force which violates this symmetry (assuming that there are no external charges, field, etc.). Releasing the symmetry restrictions may only help if due to numerical error force components violate the symmetry and the optimization can move away from the critical point. In general, the final structure should be analyzed using a frequency (second derivative, force constant) calculation. If no imaginary frequency (negative eigenvalue of the force constant matrix) found than the optimized geometry is a true local minimum. Otherwise, the structure should be moved out from the stationary point and re-optimized. This can be done manually in GaussView or automatically via doing some steps of molecular dynamics (BOMD or ADMP) and then re-optimize. An IRC calculation may also help. Best wishes, Ödön On Thu, 2007-01-25 at 21:39 -0800, Jim Harrison jim456harrison*_*yahoo.com wrote: > Dear all > > I have a problem concerning optimization of molecules of more than > 2 atoms. > I am using Gaussian 03 to optimize and perform a frequency calculation > of molecules such as for example NaCN. NaCN is a T shape molecule and > has a non-linear geometry. > > If I input a linear initial geometry and perform an optimization, > will the molecule (which is actually non-linear) converge to a > non-linear geometry > > I have perform an optimization of linear NaCN and the stationary point > was found.The optimized geometry remains linear. But when I perform > optimization of > non-linear NaCN with initial angle 120, the required geometry (T > shaped) was obtained. > > My question is that must one have a knowledge of the geometry of a > molecule under study in its ground state to perform optimization. If > so what is the purpose of optimizing. Can an initial linear structure > input converged to an optimized structure which is actually non-linear > Can Gaussian 03 predict the structure of a molecule for which the > geometry is unknown. If so how? > > I know that Gaussian 03 required an approximate initial geometry. Is > there a way > from theory to determine whether the molecule in question is linear, > bent or even a T shape. > > For example OCS molecule is linear. If one is going to calculate the > adiabatic electron affinity, one has to optimise the anion OCS- which > I did with a linear > geometry just like with OCS. The optimize anion OCS- remains linear. > But I have found from many publications that anion OCS- is actually a > bent shape molecules.Again I perform an optimization of OCS- but this > time with a bent shape, angle 120. This optimized geometry with angle > 136.7 coincide with the publications. The angle has change > significantly from angle 120 to 136.7. > > Why the initial linear geometry of anion OCS- did not converge to the > optimised geometry with angle 136.7 > > note that the electron affinity computed with linear anion OCS- and > the bent shaped anion OCS- are totally different. The one which > coincide with the experimental value is the bent shaped as required. > > I perform a frequency calculation with the optimized geometry of the > linear anion > OCS- and obtain negative frequency (saddle point which specifies a > transition state). Does a negative frequency mean the optimized > geometry has not actually > been optimized. Does in general a negative frequency is an indication > that the initial geometry input is not correct and hence must alter > the initial geometry just like I did with the bent shape. > > Thanking you all > > Best regards > > Jim > > > > > > ______________________________________________________________________ > > Check out the all-new Yahoo! Mail beta - Fire up a more powerful email > and get things done faster. -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Fri Jan 26 15:00:00 2007 From: "Pablo Vitoria pablo.vitoria|ehu.es" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33453-070126124107-31105-XF4pxY5lL6qDWJ/X00zYDw##server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Type: multipart/alternative; boundary="----=_NextPart_000_014E_01C74171.02626060" Date: Fri, 26 Jan 2007 17:40:03 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria" [pablo.vitoria|ehu.es] This is a multi-part message in MIME format. ------=_NextPart_000_014E_01C74171.02626060 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Jim, The behaviour of your calculations is normal, at least in Gaussian. G03, by default, does not change the symmetry point group of the input = molecular coordinates. When you start a calculation with a perfectly = linear NaCN (or OCS-) molecule, whose point group is Cinfv, the = optimization will never reach the bent geometry, of lower Cs symmetry. = In order to optimize a bent (or T shape) geometry you should start from = a bent molecule. Any of these optimizations (linear or bent) will finish = in a stationary point in the PES (potential energy surface), which could = be a local minimum or a saddle point, depending on number of negative = frequencies in the frequency calculation: none means local minimum in = the PEs, one means transition state (first order saddle point), and more = a higher order saddle point. If you want to know if your molecule is linear or bent (which includes T = shape), you don't really need any knowledge of the experimental = geometry, at least with these small, triatomic systems. You can optimize = both a linear and a bent (it does not matter the input angle, it will = eventually reach the experimental) molecule, and then run a frequency = calculation in both. The might be both local minimums, and the = experimental geometry (at least in the gas phase) should correspond to = the one whose energy is lower, which is the global minimum in the PES. = Or one of them may be a transition state and the other one a local = minimum. For more complicated systems, the calculation is (much) faster if you = start from a high symmetry geometry, and check the frequencies. If there = are any negative ones, decrease the symmetry (as indicated by the normal = mode corresponding to the negative frequency) and optimize again. =20 In the case of OCS-, the negative frequency for the linear molecule = indicates that the geometry has been optimized to the nearest stationary = point of linear symmetry, which happens to be a transition state. In = fact, the Gaussian output indicates that the negative frequency = corresponds to a movement of the atoms away from linearity. On the other = hand, the bent OCS- optimizes to a local minimum, with an angle of about = 136=BA and no negative frequencies.=20 The linear OCS could have been another local minimum, but much higher in = energy than the bent one. I hope this helps you a little bit Best regards Pablo ----- Original Message -----=20 From: Jim Harrison jim456harrison*_*yahoo.com=20 To: Vitoria, Pablo =20 Sent: Friday, January 26, 2007 6:39 AM Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - = negative frequency Dear all I have a problem concerning optimization of molecules of more than = 2 atoms. I am using Gaussian 03 to optimize and perform a frequency calculation = of molecules such as for example NaCN. NaCN is a T shape molecule and = has a non-linear geometry. If I input a linear initial geometry and perform an optimization, = will the molecule (which is actually non-linear) converge to a = non-linear geometry I have perform an optimization of linear NaCN and the stationary point = was found.The optimized geometry remains linear. But when I perform = optimization of=20 non-linear NaCN with initial angle 120, the required geometry (T = shaped) was obtained.=20 My question is that must one have a knowledge of the geometry of a = molecule under study in its ground state to perform optimization. If so = what is the purpose of optimizing. Can an initial linear structure input = converged to an optimized structure which is actually non-linear Can Gaussian 03 predict the structure of a molecule for which the = geometry is unknown. If so how? I know that Gaussian 03 required an approximate initial geometry. Is = there a way from theory to determine whether the molecule in question is linear, = bent or even a T shape. For example OCS molecule is linear. If one is going to calculate the = adiabatic electron affinity, one has to optimise the anion OCS- which I = did with a linear=20 geometry just like with OCS. The optimize anion OCS- remains linear. = But I have found from many publications that anion OCS- is actually a = bent shape molecules.Again I perform an optimization of OCS- but this = time with a bent shape, angle 120. This optimized geometry with angle = 136.7 coincide with the publications. The angle has change = significantly from angle 120 to 136.7.=20 Why the initial linear geometry of anion OCS- did not converge to the = optimised geometry with angle 136.7 note that the electron affinity computed with linear anion OCS- and = the bent shaped anion OCS- are totally different. The one which coincide = with the experimental value is the bent shaped as required. I perform a frequency calculation with the optimized geometry of the = linear anion=20 OCS- and obtain negative frequency (saddle point which specifies a = transition state). Does a negative frequency mean the optimized = geometry has not actually=20 been optimized. Does in general a negative frequency is an indication = that the initial geometry input is not correct and hence must alter the = initial geometry just like I did with the bent shape. Thanking you all Best regards Jim -------------------------------------------------------------------------= ----- Check out the all-new Yahoo! Mail beta - Fire up a more powerful email = and get things done faster. ------=_NextPart_000_014E_01C74171.02626060 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Jim,
 
The behaviour of your calculations is = normal, at=20 least in Gaussian.
G03, by default, does not change the = symmetry point=20 group of the input molecular coordinates. When you start a calculation = with a=20 perfectly linear NaCN (or OCS-) molecule, whose point group is Cinfv, = the=20 optimization will never reach the bent geometry, of lower Cs symmetry. = In order=20 to optimize a bent (or T shape) geometry you should start from a bent=20 molecule. Any of these optimizations (linear or bent) will finish = in a=20 stationary point in the PES (potential energy surface), which could be a = local=20 minimum or a saddle point, depending on number of negative frequencies = in the=20 frequency calculation: none means local minimum in the PEs, one means = transition=20 state (first order saddle point), and more a higher order saddle=20 point.
 
If you want to know if your molecule is = linear or=20 bent (which includes T shape), you don't really need any knowledge of = the=20 experimental geometry, at least with these small, triatomic systems. You = can=20 optimize both a linear and a bent (it does not  matter the input = angle, it=20 will eventually reach the experimental) molecule, and then run a = frequency=20 calculation in both. The might be both local minimums, and the = experimental=20 geometry (at least in the gas phase) should correspond to the one whose = energy=20 is lower, which is the global minimum in the PES. Or one of them may be = a=20 transition state and the other one a local minimum.
For more complicated systems, the = calculation is=20 (much) faster if you start from a high symmetry geometry, and check the=20 frequencies. If there are any negative ones, decrease the symmetry = (as=20 indicated by the normal mode corresponding to the negative frequency) = and=20 optimize again.
 
In the case of OCS-, the negative = frequency for the=20 linear molecule indicates that the geometry has been optimized to the = nearest=20 stationary point of linear symmetry, which happens to be a transition = state. In=20 fact, the Gaussian output indicates that the negative frequency = corresponds to a=20 movement of the atoms away from linearity. On the other hand, the bent = OCS-=20 optimizes to a local minimum, with an angle of about 136=BA and no = negative=20 frequencies.
The linear OCS could have been another = local=20 minimum, but much higher in energy than the bent one.
 
I hope this helps you a little = bit
Best regards
 
Pablo
----- Original Message -----
From:=20 Jim=20 Harrison jim456harrison*_*yahoo.com
Sent: Friday, January 26, 2007 = 6:39=20 AM
Subject: CCL:G: Gaussian 03 -=20 optimization (linear, non linear) - negative frequency

Dear all

    I have a problem = concerning=20 optimization of molecules of more than 2 atoms.
I am using Gaussian = 03 to=20 optimize and perform a frequency calculation of molecules such as for = example=20 NaCN. NaCN is a T shape molecule and has a non-linear=20 geometry.

 If I input a linear initial geometry and = perform an=20 optimization, will the molecule (which is actually non-linear) = converge to a=20 non-linear geometry

I have perform an optimization of linear = NaCN and=20 the stationary point was found.The optimized geometry remains linear. = But when=20 I perform optimization of
non-linear NaCN with initial angle 120, = the=20 required geometry (T shaped) was obtained.

My question is that = must=20 one have a knowledge of the geometry of a molecule under study in its = ground=20 state to perform optimization. If so what is the purpose of = optimizing. Can an=20 initial linear structure input converged to an optimized structure = which is=20 actually non-linear
Can Gaussian 03 predict the structure of a = molecule for=20 which  the geometry is unknown. If so how?

I know that = Gaussian 03=20 required an approximate initial geometry. Is there a way
from = theory to=20 determine whether the molecule in question is linear, bent or  = even a T=20 shape.

For example OCS molecule is linear. If one is going to = calculate=20 the adiabatic electron affinity, one has to optimise the anion OCS- = which I=20 did with a linear
geometry just like with OCS. The optimize anion = OCS-=20 remains linear. But I have found from many publications that anion = OCS- is=20 actually  a bent shape molecules.Again I perform an optimization = of OCS-=20 but this time with a bent shape, angle 120. This optimized geometry = with angle=20 136.7 coincide with the publications. The angle has change  = significantly=20 from angle 120 to 136.7.

Why the initial linear geometry of = anion OCS-=20 did not converge to the optimised geometry with angle = 136.7

note that=20 the electron affinity computed with linear anion OCS- and the bent = shaped=20 anion OCS- are totally different. The one which coincide with the = experimental=20 value is the bent shaped as required.

I perform a frequency = calculation=20 with the optimized geometry of the linear anion
OCS-  and = obtain=20 negative frequency (saddle point which specifies a transition state). = Does=20 a  negative frequency mean the optimized geometry has not = actually=20
been optimized. Does in general a negative frequency is an = indication that=20 the initial geometry input is not correct and hence must alter the = initial=20 geometry just like I did with the bent shape.

Thanking you=20 all

 Best regards

Jim


Check out the=20 all-new Yahoo! Mail beta - Fire up a more powerful email and get = things=20 done faster. ------=_NextPart_000_014E_01C74171.02626060-- From owner-chemistry@ccl.net Fri Jan 26 15:35:00 2007 From: "Pablo Vitoria pablo.vitoria!^!ehu.es" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33454-070126124202-32444-DhvkCYMZPYuc+pChcLNVDw(_)server.ccl.net> X-Original-From: "Pablo Vitoria" Content-Type: multipart/alternative; boundary="----=_NextPart_000_01CC_01C74179.A00467C0" Date: Fri, 26 Jan 2007 18:41:43 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Vitoria" [pablo.vitoria|*|ehu.es] This is a multi-part message in MIME format. ------=_NextPart_000_01CC_01C74179.A00467C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Jim, The behaviour of your calculations is normal, at least in Gaussian. G03, by default, does not change the symmetry point group of the input = molecular coordinates. When you start a calculation with a perfectly = linear NaCN (or OCS-) molecule, whose point group is Cinfv, the = optimization will never reach the bent geometry, of lower Cs symmetry. = In order to optimize a bent (or T shape) geometry you should start from = a bent molecule. Any of these optimizations (linear or bent) will finish = in a stationary point in the PES (potential energy surface), which could = be a local minimum or a saddle point, depending on number of negative = frequencies in the frequency calculation: none means local minimum in = the PEs, one means transition state (first order saddle point), and more = a higher order saddle point. If you want to know if your molecule is linear or bent (which includes T = shape), you don't really need any knowledge of the experimental = geometry, at least with these small, triatomic systems. You can optimize = both a linear and a bent (it does not matter the input angle, it will = eventually reach the experimental) molecule, and then run a frequency = calculation in both. The might be both local minimums, and the = experimental geometry (at least in the gas phase) should correspond to = the one whose energy is lower, which is the global minimum in the PES. = Or one of them may be a transition state and the other one a local = minimum. For more complicated systems, the calculation is (much) faster if you = start from a high symmetry geometry, and check the frequencies. If there = are any negative ones, decrease the symmetry (as indicated by the normal = mode corresponding to the negative frequency) and optimize again. In the case of OCS-, the negative frequency for the linear molecule = indicates that the geometry has been optimized to the nearest stationary = point of linear symmetry, which happens to be a transition state. In = fact, the Gaussian output indicates that the negative frequency = corresponds to a movement of the atoms away from linearity. On the other = hand, the bent OCS- optimizes to a local minimum, with an angle of about = 136=BA and no negative frequencies.=20 The linear OCS could have been another local minimum, but much higher in = energy than the bent one. I hope this helps you a little bit Best regards Pablo ----- Original Message -----=20 From: Jim Harrison jim456harrison*_*yahoo.com=20 To: Vitoria, Pablo =20 Sent: Friday, January 26, 2007 6:39 AM Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - = negative frequency Dear all I have a problem concerning optimization of molecules of more than = 2 atoms. I am using Gaussian 03 to optimize and perform a frequency calculation = of molecules such as for example NaCN. NaCN is a T shape molecule and = has a non-linear geometry. If I input a linear initial geometry and perform an optimization, = will the molecule (which is actually non-linear) converge to a = non-linear geometry I have perform an optimization of linear NaCN and the stationary point = was found.The optimized geometry remains linear. But when I perform = optimization of=20 non-linear NaCN with initial angle 120, the required geometry (T = shaped) was obtained.=20 My question is that must one have a knowledge of the geometry of a = molecule under study in its ground state to perform optimization. If so = what is the purpose of optimizing. Can an initial linear structure input = converged to an optimized structure which is actually non-linear Can Gaussian 03 predict the structure of a molecule for which the = geometry is unknown. If so how? I know that Gaussian 03 required an approximate initial geometry. Is = there a way from theory to determine whether the molecule in question is linear, = bent or even a T shape. For example OCS molecule is linear. If one is going to calculate the = adiabatic electron affinity, one has to optimise the anion OCS- which I = did with a linear=20 geometry just like with OCS. The optimize anion OCS- remains linear. = But I have found from many publications that anion OCS- is actually a = bent shape molecules.Again I perform an optimization of OCS- but this = time with a bent shape, angle 120. This optimized geometry with angle = 136.7 coincide with the publications. The angle has change = significantly from angle 120 to 136.7.=20 Why the initial linear geometry of anion OCS- did not converge to the = optimised geometry with angle 136.7 note that the electron affinity computed with linear anion OCS- and = the bent shaped anion OCS- are totally different. The one which coincide = with the experimental value is the bent shaped as required. I perform a frequency calculation with the optimized geometry of the = linear anion=20 OCS- and obtain negative frequency (saddle point which specifies a = transition state). Does a negative frequency mean the optimized = geometry has not actually=20 been optimized. Does in general a negative frequency is an indication = that the initial geometry input is not correct and hence must alter the = initial geometry just like I did with the bent shape. Thanking you all Best regards Jim -------------------------------------------------------------------------= ----- Check out the all-new Yahoo! Mail beta - Fire up a more powerful email = and get things done faster. ------=_NextPart_000_01CC_01C74179.A00467C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Jim,
 
The behaviour of your calculations is = normal, at=20 least in Gaussian.
G03, by default, does not change the = symmetry point=20 group of the input molecular coordinates. When you start a calculation = with a=20 perfectly linear NaCN (or OCS-) molecule, whose point group is Cinfv, = the=20 optimization will never reach the bent geometry, of lower Cs symmetry. = In order=20 to optimize a bent (or T shape) geometry you should start from a bent=20 molecule. Any of these optimizations (linear or bent) will finish = in a=20 stationary point in the PES (potential energy surface), which could be a = local=20 minimum or a saddle point, depending on number of negative frequencies = in the=20 frequency calculation: none means local minimum in the PEs, one means = transition=20 state (first order saddle point), and more a higher order saddle=20 point.
 
If you want to know if your molecule is = linear or=20 bent (which includes T shape), you don't really need any knowledge of = the=20 experimental geometry, at least with these small, triatomic systems. You = can=20 optimize both a linear and a bent (it does not  matter the input = angle, it=20 will eventually reach the experimental) molecule, and then run a = frequency=20 calculation in both. The might be both local minimums, and the = experimental=20 geometry (at least in the gas phase) should correspond to the one whose = energy=20 is lower, which is the global minimum in the PES. Or one of them may be = a=20 transition state and the other one a local minimum.
For more complicated systems, the = calculation is=20 (much) faster if you start from a high symmetry geometry, and check the=20 frequencies. If there are any negative ones, decrease the symmetry = (as=20 indicated by the normal mode corresponding to the negative frequency) = and=20 optimize again.
 
In the case of OCS-, the negative = frequency for the=20 linear molecule indicates that the geometry has been optimized to the = nearest=20 stationary point of linear symmetry, which happens to be a transition = state. In=20 fact, the Gaussian output indicates that the negative frequency = corresponds to a=20 movement of the atoms away from linearity. On the other hand, the bent = OCS-=20 optimizes to a local minimum, with an angle of about 136=BA and no = negative=20 frequencies.
The linear OCS could have been another = local=20 minimum, but much higher in energy than the bent one.
 
I hope this helps you a little = bit
Best regards
 
Pablo
----- Original Message -----
From:=20 Jim=20 Harrison jim456harrison*_*yahoo.com
Sent: Friday, January 26, 2007 = 6:39=20 AM
Subject: CCL:G: Gaussian 03 -=20 optimization (linear, non linear) - negative frequency

Dear all

    I have a problem = concerning=20 optimization of molecules of more than 2 atoms.
I am using Gaussian = 03 to=20 optimize and perform a frequency calculation of molecules such as for = example=20 NaCN. NaCN is a T shape molecule and has a non-linear=20 geometry.

 If I input a linear initial geometry and = perform an=20 optimization, will the molecule (which is actually non-linear) = converge to a=20 non-linear geometry

I have perform an optimization of linear = NaCN and=20 the stationary point was found.The optimized geometry remains linear. = But when=20 I perform optimization of
non-linear NaCN with initial angle 120, = the=20 required geometry (T shaped) was obtained.

My question is that = must=20 one have a knowledge of the geometry of a molecule under study in its = ground=20 state to perform optimization. If so what is the purpose of = optimizing. Can an=20 initial linear structure input converged to an optimized structure = which is=20 actually non-linear
Can Gaussian 03 predict the structure of a = molecule for=20 which  the geometry is unknown. If so how?

I know that = Gaussian 03=20 required an approximate initial geometry. Is there a way
from = theory to=20 determine whether the molecule in question is linear, bent or  = even a T=20 shape.

For example OCS molecule is linear. If one is going to = calculate=20 the adiabatic electron affinity, one has to optimise the anion OCS- = which I=20 did with a linear
geometry just like with OCS. The optimize anion = OCS-=20 remains linear. But I have found from many publications that anion = OCS- is=20 actually  a bent shape molecules.Again I perform an optimization = of OCS-=20 but this time with a bent shape, angle 120. This optimized geometry = with angle=20 136.7 coincide with the publications. The angle has change  = significantly=20 from angle 120 to 136.7.

Why the initial linear geometry of = anion OCS-=20 did not converge to the optimised geometry with angle = 136.7

note that=20 the electron affinity computed with linear anion OCS- and the bent = shaped=20 anion OCS- are totally different. The one which coincide with the = experimental=20 value is the bent shaped as required.

I perform a frequency = calculation=20 with the optimized geometry of the linear anion
OCS-  and = obtain=20 negative frequency (saddle point which specifies a transition state). = Does=20 a  negative frequency mean the optimized geometry has not = actually=20
been optimized. Does in general a negative frequency is an = indication that=20 the initial geometry input is not correct and hence must alter the = initial=20 geometry just like I did with the bent shape.

Thanking you=20 all

 Best regards

Jim


Check out the=20 all-new Yahoo! Mail beta - Fire up a more powerful email and get = things=20 done faster. ------=_NextPart_000_01CC_01C74179.A00467C0-- From owner-chemistry@ccl.net Fri Jan 26 16:12:00 2007 From: "Kanchana Sahan Thanthiriwatte amarasara**gmail.com" To: CCL Subject: CCL: Cartesian to Spherical Harmonics inter-conversion? Message-Id: <-33455-070126133755-7346-brVKYB9LK4i9T6Vu71IvQQ!=!server.ccl.net> X-Original-From: Kanchana Sahan Thanthiriwatte Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 26 Jan 2007 11:32:50 -0600 MIME-version: 1.0 Sent to CCL by: Kanchana Sahan Thanthiriwatte [amarasara%a%gmail.com] Dear CCLers, I am dealing with higher order multipolar moments. I need to convert them from Cartesian values to Spherical Harmonics values and again from Spherical Harmonics values to Cartesian values. How do I do this inter-conversion? I went through the book "The theory of intermolecular forces" of A.J.Stone. It was very useful but it did not discuss Cartesian to Spherical Harmonics inter-conversions for higher order multipolar moments in a more general way. Appendix E has Cartesian - Spherical conversion table up to L =4, but I need inter-convert higher order multipolar moments. Can anyone tell me how to perform the Cartesian - Spherical inter-conversion? Thank you. Best regards, -Sahan- Anselm.Horn#chemie.uni-erlangen.de wrote: > Sent to CCL by: Anselm.Horn/./chemie.uni-erlangen.de > > >> I am dealing with higher order multipolar moments. I need to convert them >> >>> from Cartesian values to Spherical Harmonics values and again from >>> Spherical Harmonics values to Cartesian values. How do I do this inter-conversion? >>> > > Maybe you'll find the book "The theory of intermolecular forces" of > A.J.Stone (Clarendon Press, Oxford 1996-2002) helpful, especially Appendix > B "Spherical tensors". > > Regards, > > Anselm> > > > > From owner-chemistry@ccl.net Fri Jan 26 16:45:00 2007 From: "Phil Hultin hultin : cc.umanitoba.ca" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33456-070126150754-3308-zFSMSXi5lueLT8kpUE89Cw() server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0194_01C74153.553F6EE0" Date: Fri, 26 Jan 2007 14:07:25 -0600 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin .. cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_0194_01C74153.553F6EE0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Jim: This message was supposed to appear BEFORE my previous one but seems to have been eaten by the server. If it shows up twice on CCL, sorry about that. It is a misnomer to call this calculation an "optimization" - or at least, it is a distortion. What you are doing is finding the nearest local minimum on the potential energy surface. Whether this is the "optimal" solution - i.e. the global minimum - is another issue. You don't have to know the structure to find the structure, but if you do not have some idea then you do have to search for it. Finding the global minimum can be labour intensive, although for a system of only three atoms you can easily work through the possibilities. It sounds to me like you have already done so, in fact. Was the calculated energy of the T-shaped geometry lower than that of the linear geometry at the level of theory you used? Bear in mind, most minimization algorithms (including those used in Gaussian calculations) can ONLY go downhill in energy. Thus, if you start your calculation on the other side of an energy barrier from a given minimum, you will never converge to that minimum. You can only move down to the bottom of the energy well you are currently in. I would strongly urge you to go get either Chris Cramer's book on Computational Chemistry, or Andrew Leach's book "Molecular Modeling" (or both) and read up a bit on minimizations and searching the potential surface. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin=-=cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin _____ > From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net] Sent: January 25, 2007 11:40 PM To: Hultin, Philip G. Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Dear all I have a problem concerning optimization of molecules of more than 2 atoms. I am using Gaussian 03 to optimize and perform a frequency calculation of molecules such as for example NaCN. NaCN is a T shape molecule and has a non-linear geometry. If I input a linear initial geometry and perform an optimization, will the molecule (which is actually non-linear) converge to a non-linear geometry I have perform an optimization of linear NaCN and the stationary point was found.The optimized geometry remains linear. But when I perform optimization of non-linear NaCN with initial angle 120, the required geometry (T shaped) was obtained. My question is that must one have a knowledge of the geometry of a molecule under study in its ground state to perform optimization. If so what is the purpose of optimizing. Can an initial linear structure input converged to an optimized structure which is actually non-linear Can Gaussian 03 predict the structure of a molecule for which the geometry is unknown. If so how? I know that Gaussian 03 required an approximate initial geometry. Is there a way > from theory to determine whether the molecule in question is linear, bent or even a T shape. For example OCS molecule is linear. If one is going to calculate the adiabatic electron affinity, one has to optimise the anion OCS- which I did with a linear geometry just like with OCS. The optimize anion OCS- remains linear. But I have found from many publications that anion OCS- is actually a bent shape molecules.Again I perform an optimization of OCS- but this time with a bent shape, angle 120. This optimized geometry with angle 136.7 coincide with the publications. The angle has change significantly from angle 120 to 136.7. Why the initial linear geometry of anion OCS- did not converge to the optimised geometry with angle 136.7 note that the electron affinity computed with linear anion OCS- and the bent shaped anion OCS- are totally different. The one which coincide with the experimental value is the bent shaped as required. I perform a frequency calculation with the optimized geometry of the linear anion OCS- and obtain negative frequency (saddle point which specifies a transition state). Does a negative frequency mean the optimized geometry has not actually been optimized. Does in general a negative frequency is an indication that the initial geometry input is not correct and hence must alter the initial geometry just like I did with the bent shape. Thanking you all Best regards Jim _____ Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and get things done faster. ------=_NextPart_000_0194_01C74153.553F6EE0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Jim:

 

This message was supposed to appear = BEFORE my previous one but seems to have been eaten by the server.  If it = shows up twice on CCL, sorry about that.

 

It is a misnomer to call this = calculation an “optimization” – or at least, it is a distortion.  What you are doing is finding the nearest local minimum on the = potential energy surface.  Whether this is the “optimal” solution – i.e. the global minimum – is another = issue.

 

You don’t have to know the = structure to find the structure, but if you do not have some idea then you do have = to search for it.  Finding the global minimum can be labour intensive, although for a system of only three atoms you can easily work through = the possibilities.  It sounds to me like you have already done so, in = fact.  Was the calculated energy of the T-shaped geometry lower than that = of the linear geometry at the level of theory you = used?

 

Bear in mind, most minimization = algorithms (including those used in Gaussian calculations) can ONLY go downhill in = energy.  Thus, if you start your calculation on the other side of an energy barrier from a given minimum, you will never converge to that minimum.  You can only move down to the bottom of the energy well you are = currently in.

 

I would strongly urge you to go get = either Chris Cramer’s book on Computational Chemistry, or Andrew = Leach’s book “Molecular Modeling” (or both) and read up a bit on minimizations and searching the potential = surface.

 

Dr. Philip G. = Hultin

Professor of = Chemistry,

University of = Manitoba

Winnipeg, MB

R3T = 2N2

hultin=-=cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

From: owner-chemistry=-=ccl.net [mailto:owner-chemistry=-=ccl.net]
Sent: January 25, 2007 = 11:40 PM
To: Hultin, Philip G. =
Subject: CCL:G: Gaussian = 03 - optimization (linear, non linear) - negative = frequency

 

Dear all

    I have a problem concerning optimization of molecules = of more than 2 atoms.
I am using Gaussian 03 to optimize and perform a frequency calculation = of molecules such as for example NaCN. NaCN is a T shape molecule and has a non-linear geometry.

 If I input a linear initial geometry and perform an optimization, = will the molecule (which is actually non-linear) converge to a non-linear = geometry

I have perform an optimization of linear NaCN and the stationary point = was found.The optimized geometry remains linear. But when I perform = optimization of
non-linear NaCN with initial angle 120, the required geometry (T shaped) = was obtained.

My question is that must one have a knowledge of the geometry of a = molecule under study in its ground state to perform optimization. If so what is = the purpose of optimizing. Can an initial linear structure input converged = to an optimized structure which is actually non-linear
Can Gaussian 03 predict the structure of a molecule for which  the geometry is unknown. If so how?

I know that Gaussian 03 required an approximate initial geometry. Is = there a way
> from theory to determine whether the molecule in question is linear, = bent or  even a T shape.

For example OCS molecule is linear. If one is going to calculate the = adiabatic electron affinity, one has to optimise the anion OCS- which I did with a = linear
geometry just like with OCS. The optimize anion OCS- remains linear. But = I have found from many publications that anion OCS- is actually  a bent = shape molecules.Again I perform an optimization of OCS- but this time with a = bent shape, angle 120. This optimized geometry with angle 136.7 coincide with = the publications. The angle has change  significantly from angle 120 to = 136.7.

Why the initial linear geometry of anion OCS- did not converge to the = optimised geometry with angle 136.7

note that the electron affinity computed with linear anion OCS- and the = bent shaped anion OCS- are totally different. The one which coincide with the experimental value is the bent shaped as required.

I perform a frequency calculation with the optimized geometry of the = linear anion
OCS-  and obtain negative frequency (saddle point which specifies a transition state). Does a  negative frequency mean the optimized = geometry has not actually
been optimized. Does in general a negative frequency is an indication = that the initial geometry input is not correct and hence must alter the initial = geometry just like I did with the bent shape.

Thanking you all

 Best regards

Jim

 

Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and get = things done faster.

------=_NextPart_000_0194_01C74153.553F6EE0-- From owner-chemistry@ccl.net Fri Jan 26 17:24:01 2007 From: "Shobe, David David.Shobe^sud-chemie.com" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33457-070126152420-14517-cg0oOfyBIXnAFaMkwAzoQA^_^server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C74187.E8D0BDCA" Date: Fri, 26 Jan 2007 21:23:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe:sud-chemie.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C74187.E8D0BDCA Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Jim, =20 You've received several answers by now. The practical consequences of the = theory you have learned are as follows: =20 1. You *do* have to guess whether the molecule / ion is linear or bent.=20 =20 2. However, if the molecule is bent, you don't have to know the angle. =20 3. If you guess the molecule is linear and it's actually bent, you will get= those imaginary (negative) frequencies. If you animate the frequencies i= n a program such as Gaussview, you will see the molecule "trying" to bend.= =20 =20 (It's *always* a good idea to calculate frequencies and check that there ar= e no negative/imaginary frequencies!) =20 4. If you guess the molecule is bent and it's actually linear, Gaussian wil= l optimize the angle to ~179.9 degrees, and then will (usually) crash with = an error message. =20 Regards, --David Shobe S=FCd-Chemie, Inc. =20 Attention to detial is essentail. ________________________________ > From: owner-chemistry() ccl.net [mailto:owner-chemistry() ccl.net]=20 Sent: Friday, January 26, 2007 12:40 AM To: Shobe, David Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative = frequency Dear all I have a problem concerning optimization of molecules of more than 2 at= oms. I am using Gaussian 03 to optimize and perform a frequency calculation of m= olecules such as for example NaCN. NaCN is a T shape molecule and has a non= -linear geometry. If I input a linear initial geometry and perform an optimization, will the= molecule (which is actually non-linear) converge to a non-linear geometry I have perform an optimization of linear NaCN and the stationary point was = found.The optimized geometry remains linear. But when I perform optimizatio= n of=20 non-linear NaCN with initial angle 120, the required geometry (T shaped) wa= s obtained.=20 My question is that must one have a knowledge of the geometry of a molecule= under study in its ground state to perform optimization. If so what is the= purpose of optimizing. Can an initial linear structure input converged to = an optimized structure which is actually non-linear Can Gaussian 03 predict the structure of a molecule for which the geometry= is unknown. If so how? I know that Gaussian 03 required an approximate initial geometry. Is there = a way > from theory to determine whether the molecule in question is linear, bent o= r even a T shape. For example OCS molecule is linear. If one is going to calculate the adiaba= tic electron affinity, one has to optimise the anion OCS- which I did with = a linear=20 geometry just like with OCS. The optimize anion OCS- remains linear. But I = have found from many publications that anion OCS- is actually a bent shape= molecules.Again I perform an optimization of OCS- but this time with a ben= t shape, angle 120. This optimized geometry with angle 136.7 coincide with = the publications. The angle has change significantly from angle 120 to 136= .7.=20 Why the initial linear geometry of anion OCS- did not converge to the optim= ised geometry with angle 136.7 note that the electron affinity computed with linear anion OCS- and the ben= t shaped anion OCS- are totally different. The one which coincide with the = experimental value is the bent shaped as required. I perform a frequency calculation with the optimized geometry of the linear= anion=20 OCS- and obtain negative frequency (saddle point which specifies a transit= ion state). Does a negative frequency mean the optimized geometry has not = actually=20 been optimized. Does in general a negative frequency is an indication that = the initial geometry input is not correct and hence must alter the initial = geometry just like I did with the bent shape. Thanking you all Best regards Jim ________________________________ Check out the all-new Yahoo! Mail beta - Fire up a more powerful e= mail and get things done faster.=20 This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, 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 an= d delete this message.=20 Thank you. ------_=_NextPart_001_01C74187.E8D0BDCA Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Jim,
 
You've received several answers by now.  The = practical=20 consequences of the theory you have learned are as=20 follows:
 
1. You *do* have to guess whether the molecule / i= on is=20 linear or bent. 
 
2. However, if the molecule is bent, you don't hav= e to know=20 the angle.
 
= 3. If you guess the molecule is l= inear and=20 it's actually bent, you will get those imaginary  (negative) frequencies.  = If you=20 animate the frequencies in a program such as Gaussview, you will see the=20 molecule "trying" to bend. 
 
(It's *always* = a good=20 idea to calculate frequencies and check that there are no=20 negative/imaginary frequencies!)
 
= 4. If you guess the molecule is b= ent and=20 it's actually linear, Gaussian will optimize the angle to ~179.9 degrees, a= nd=20 then will (usually) crash with an error=20 message.
 
Regards,
--David Shobe
  S=FCd-Chemie, Inc.
 
Attention to detial is=20 essentail.

From: owner-chemistry() ccl.net=20 [mailto:owner-chemistry() ccl.net]
Sent: Friday, January 26, 2007 = 12:40=20 AM
To: Shobe, David
Subject: CCL:G: Gaussian 03 -=20 optimization (linear, non linear) - negative frequency

Dear all

    I have a problem concerning= =20 optimization of molecules of more than 2 atoms.
I am using Gaussian 03 t= o=20 optimize and perform a frequency calculation of molecules such as for examp= le=20 NaCN. NaCN is a T shape molecule and has a non-linear geometry.

&nbs= p;If=20 I input a linear initial geometry and perform an optimization, will the mol= ecule=20 (which is actually non-linear) converge to a non-linear geometry

I h= ave=20 perform an optimization of linear NaCN and the stationary point was found.T= he=20 optimized geometry remains linear. But when I perform optimization of=20
non-linear NaCN with initial angle 120, the required geometry (T shaped= ) was=20 obtained.

My question is that must one have a knowledge of the geom= etry=20 of a molecule under study in its ground state to perform optimization. If s= o=20 what is the purpose of optimizing. Can an initial linear structure input=20 converged to an optimized structure which is actually non-linear
Can Gau= ssian=20 03 predict the structure of a molecule for which  the geometry is unkn= own.=20 If so how?

I know that Gaussian 03 required an approximate initial= =20 geometry. Is there a way
from theory to determine whether the molecule i= n=20 question is linear, bent or  even a T shape.

For example OCS=20 molecule is linear. If one is going to calculate the adiabatic electron=20 affinity, one has to optimise the anion OCS- which I did with a linear=20
geometry just like with OCS. The optimize anion OCS- remains linear. Bu= t I=20 have found from many publications that anion OCS- is actually  a bent = shape=20 molecules.Again I perform an optimization of OCS- but this time with a bent= =20 shape, angle 120. This optimized geometry with angle 136.7 coincide with th= e=20 publications. The angle has change  significantly from angle 120 to 13= 6.7.=20

Why the initial linear geometry of anion OCS- did not converge to t= he=20 optimised geometry with angle 136.7

note that the electron affinity= =20 computed with linear anion OCS- and the bent shaped anion OCS- are totally= =20 different. The one which coincide with the experimental value is the bent s= haped=20 as required.

I perform a frequency calculation with the optimized=20 geometry of the linear anion
OCS-  and obtain negative frequency= =20 (saddle point which specifies a transition state). Does a  negative=20 frequency mean the optimized geometry has not actually
been optimized. = Does=20 in general a negative frequency is an indication that the initial geometry = input=20 is not correct and hence must alter the initial geometry just like I did wi= th=20 the bent shape.

Thanking you all

 Best=20 regards

Jim


Check out the=20 all-new Yahoo! Mail beta - Fire up a more powerful email and get things= done=20 faster.=20
This e-mail message may contain confidential and / or privileged informatio= n. If you are not an addressee or otherwise authorized to receive this mess= age, 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 an= d delete this message.
Thank you.
------_=_NextPart_001_01C74187.E8D0BDCA-- From owner-chemistry@ccl.net Fri Jan 26 17:55:01 2007 From: "MolSoft Training andy%x%molsoft.com" To: CCL Subject: CCL: ICM Workshop - Protein Structure and Drug Discovery - March and May 2007 Message-Id: <-33458-070126155725-4602-Phas3tJNPJ0oTVm364yr1Q-*-server.ccl.net> X-Original-From: MolSoft Training Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 26 Jan 2007 11:38:49 -0800 MIME-Version: 1.0 Sent to CCL by: MolSoft Training [andy|-|molsoft.com] Molsoft LLC (www.molsoft.com) would like to invite you to an ICM Workshop entitled “Protein Structure and Drug Discovery” to be held on March 22nd – 23rd 2007 in La Jolla, CA, USA. The course is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate in this workshop. We will also be holding an Advanced ICM Workshop on May 17th-18th 2007 for more experienced ICM users. See www.molsoft.com/training.html for more information. This workshop consists of lectures, demonstrations and “hands-on” computational experiments and will cover: - Sequence and Structure Analysis - Protein Modeling - Small Molecule Docking - Protein-Protein Docking - Mutation and Binding Site Prediction - Simulations - QSAR - ADME-TOX - Virtual Ligand Screening - Cheminformatics “The objective of this training workshop is to help computational chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools.” Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or e mail info{:}molsoft.com or call (858) 625 2000 ext.108. MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Fri Jan 26 18:34:01 2007 From: "jim harrison jim456harrison+*+yahoo.com" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33459-070126003945-26550-1dsOW4BgeyDb/slBg8DKHA^^server.ccl.net> X-Original-From: "jim harrison" Date: Fri, 26 Jan 2007 00:32:04 -0500 Sent to CCL by: "jim harrison" [jim456harrison[]yahoo.com] Dear all I have a problem concerning optimization of molecules of more than 2 atoms. I am using Gaussian 03 to optimize and perform a frequency calculation of molecules such as for example NaCN. NaCN is a T shape molecule and has a non-linear geometry. If I input a linear initial geometry and perform an optimization, will the molecule (which is actually non-linear) converge to a non-linear geometry I have perform an optimization of linear NaCN and the stationary point was found.The optimized geometry remains linear. But when I perform optimization of non-linear NaCN with initial angle 120, the required geometry (T shaped) was obtained. My question is that must one have a knowledge of the geometry of a molecule under study in its ground state to perform optimization. If so what is the purpose of optimizing. Can an initial linear structure input converged to an optimized structure which is actually non-linear Can Gaussian 03 predict the structure of a molecule for which the geometry is unknown. If so how? I know that Gaussian 03 required an approximate initial geometry. Is there a way > from theory to determine whether the molecule in question is linear, bent or even a T shape. For example OCS molecule is linear. If one is going to calculate the adiabatic electron affinity, one has to optimise the anion OCS- which I did with a linear geometry just like with OCS. The optimize anion OCS- remains linear. But I have found from many publications that anion OCS- is actually a bent shape molecules.Again I perform an optimization of OCS- but this time with a bent shape, angle 120. This optimized geometry with angle 136.7 coincide with the publications. The angle has change significantly from angle 120 to 136.7. Why the initial linear geometry of anion OCS- did not converge to the optimised geometry with angle 136.7 note that the electron affinity computed with linear anion OCS- and the bent shaped anion OCS- are totally different. The one which coincide with the experimental value is the bent shaped as required. I perform a frequency calculation with the optimized geometry of the linear anion OCS- and obtain negative frequency (saddle point which specifies a transition state). Does a negative frequency mean the optimized geometry has not actually been optimized. Does in general a negative frequency is an indication that the initial geometry input is not correct and hence must alter the initial geometry just like I did with the bent shape. Thanking you all Best regards Jim From owner-chemistry@ccl.net Fri Jan 26 19:51:00 2007 From: "zborowsk++chemia.uj.edu.pl" To: CCL Subject: CCL:G: Gaussian 03 - optimization (linear, non linear) - negative frequency Message-Id: <-33460-070126101757-26589-er1nFeQgxQ3KBxsq40Lppg*o*server.ccl.net> X-Original-From: zborowsk]-[chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Fri, 26 Jan 2007 15:42:16 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk.:.chemia.uj.edu.pl It is obvious If you run calculations on linar molecule you must obtain linear molecule There is no force that can destroy linearity in your molecule, all forces are balanced > Dear all > > I have a problem concerning optimization of molecules of more than 2 > atoms. > I am using Gaussian 03 to optimize and perform a frequency calculation of > molecules such as for example NaCN. NaCN is a T shape molecule and has a > non-linear geometry. > > If I input a linear initial geometry and perform an optimization, will > the molecule (which is actually non-linear) converge to a non-linear > geometry > > I have perform an optimization of linear NaCN and the stationary point was > found.The optimized geometry remains linear. But when I perform > optimization of > non-linear NaCN with initial angle 120, the required geometry (T shaped) > was obtained. > > My question is that must one have a knowledge of the geometry of a > molecule under study in its ground state to perform optimization. If so > what is the purpose of optimizing. Can an initial linear structure input > converged to an optimized structure which is actually non-linear > Can Gaussian 03 predict the structure of a molecule for which the > geometry is unknown. If so how? > > I know that Gaussian 03 required an approximate initial geometry. Is there > a way >> from theory to determine whether the molecule in question is linear, >> bent or even a T shape. > > For example OCS molecule is linear. If one is going to calculate the > adiabatic electron affinity, one has to optimise the anion OCS- which I > did with a linear > geometry just like with OCS. The optimize anion OCS- remains linear. But I > have found from many publications that anion OCS- is actually a bent > shape molecules.Again I perform an optimization of OCS- but this time with > a bent shape, angle 120. This optimized geometry with angle 136.7 coincide > with the publications. The angle has change significantly from angle 120 > to 136.7. > > Why the initial linear geometry of anion OCS- did not converge to the > optimised geometry with angle 136.7 > > note that the electron affinity computed with linear anion OCS- and the > bent shaped anion OCS- are totally different. The one which coincide with > the experimental value is the bent shaped as required. > > I perform a frequency calculation with the optimized geometry of the > linear anion > OCS- and obtain negative frequency (saddle point which specifies a > transition state). Does a negative frequency mean the optimized geometry > has not actually > been optimized. Does in general a negative frequency is an indication that > the initial geometry input is not correct and hence must alter the initial > geometry just like I did with the bent shape. > > Thanking you all > > Best regards > > Jim > > > > > --------------------------------- > Check out the all-new Yahoo! Mail beta - Fire up a more powerful email and > get things done faster. -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk]^[chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70