tag:blogger.com,1999:blog-6701417360427959244.post4293742634216200813..comments2024-03-27T07:18:00.323+01:00Comments on Molecular Modeling Basics: Finding a transition state: an Sn2 reactionJan Jensenhttp://www.blogger.com/profile/08595894308946022740noreply@blogger.comBlogger35125tag:blogger.com,1999:blog-6701417360427959244.post-55408289635017578932019-04-12T04:24:18.083+02:002019-04-12T04:24:18.083+02:00Hello sir, I am trying to calculate TS energy of O...Hello sir, I am trying to calculate TS energy of OH- + CH3Cl using your method. First I have not been able to get a negative frequency after several trials. Second, I don't know how you got the data about $HESS that you copied into your ts.inp file below the $DATA. Thanks in anticipationAnonymoushttps://www.blogger.com/profile/09698737997575237892noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-51438803977656985972012-06-06T16:53:27.372+02:002012-06-06T16:53:27.372+02:00I have PC GAMESS version 7.0 (14 August 2006).I have PC GAMESS version 7.0 (14 August 2006).Moshe Snoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-83615913285103869672012-06-06T11:27:44.857+02:002012-06-06T11:27:44.857+02:00OK, thanks for the follow up. Just curious, what ...OK, thanks for the follow up. Just curious, what version do you use. I use a fairly ancient version 12 JAN 2009 (R3) on my laptop.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-18559920007872236122012-06-06T00:11:10.918+02:002012-06-06T00:11:10.918+02:00In orer to solve the error: UNABLE TO PROJECT DLC,...In orer to solve the error: UNABLE TO PROJECT DLC, I added IFDMOD=2 to the $zmat group. IFDMOD selects a method to freeze internals in DLC. <br /><br />I also had to add AUTOFV=.f. into the $zmat group in order to allow GAMESS to read the fvalue input of 2.0. AUTOFV=.t. is the default and it tells GAMESS to generate an fvalue array automatically, thus ignoring values inputted by the user. <br /><br />I have an outdated version of GAMESS. In the newer versions of GAMESS, IFDMOD is put in by default. I'm not certain, but I think that AUTO=.f. is also added a default in the newer versions.Moshe Snoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-62870837618912156452012-05-25T07:48:42.430+02:002012-05-25T07:48:42.430+02:00That's strange. It works fine for me, i.e. I ...That's strange. It works fine for me, i.e. I copied the text from your comment, made an input file and ran it. <br /><br />I suggest posting your question to the <a href="https://groups.google.com/forum/?fromgroups#!forum/gamess" rel="nofollow"> Google GAMESS group</a> with lots of detail including version, hardware, and quotes from the output.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-23798706771910251162012-05-23T21:26:55.613+02:002012-05-23T21:26:55.613+02:00In regards to the previous post, the input code th...In regards to the previous post, the input code that I typed into GAMESS did have a space before each $. The spaces did not appear when I copied the input into the blog post.Moshe Shttps://www.blogger.com/profile/07122373307163056626noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-23300581052812068102012-05-23T21:23:24.108+02:002012-05-23T21:23:24.108+02:00Hi,
I'm trying to copy the input that you wro...Hi,<br /><br />I'm trying to copy the input that you wrote in GAMESS for optimizing the geometry for the reaction: <br /> F- + CH3Cl -> Cl- + CH3F<br />The following error message always <br />results in the output: "ERROR: UNABLE TO PROJECT DLC".<br /><br /><br />Below is the input code that I've been using. What is the reason why I recieved the error message?<br /><br /> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE <br /> ICHARG=-1 MULT=1 COORD=ZMTMPC $END<br /> $statpt opttol=0.0005 nstep=50 hssend=.t. $end<br /> $force nvib=2 $end<br /> $contrl nzvar=1 $end<br /> $zmat dlc=.t. auto=.t. nonvdw(1)=1,6 1,2 $end<br /> $zmat ifzmat(1)=1,1,6 fvalue(1)=2.0 $end<br /> $BASIS GBASIS=PM3 $END<br /> $DATA<br />CH3FCl(-1)<br />C1 1<br />C 0.0000000 0 0.0000000 0 0.0000000 0 0 0 0<br />Cl 1.7600005 1 0.0000000 0 0.0000000 0 1 0 0<br />H 1.0900004 1 109.47118 1 0.0000000 0 1 2 0<br />H 1.0899995 1 109.47124 1 -119.99998 1 1 2 3<br />H 1.0899995 1 109.47124 1 119.99998 1 1 2 3<br />F 2.0000001 1 171.80211 1 0.0000000 1 1 2 3<br /> $ENDMoshe Shttps://www.blogger.com/profile/07122373307163056626noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-54326014900584561442012-02-17T18:25:09.454+01:002012-02-17T18:25:09.454+01:00Thanks for these instructions. I used them to mod...Thanks for these instructions. I used them to model a simple Sn2 reaction for an o chem class that I teach. I ran into some problems trying to model the reactants, and wanted to share the solution so that if someone else runs into the same problem, they know what to do.<br /><br />When the two reactants were close together (<6Å or so), I could do minimization and energy computations with DFT just fine. But when the reactants were farther apart, turning DFT on made GAMESS abort because it could not get the SCF to converge. I eventually figured out that the problem was my DFT method. I was using B3LYP, which isn't designed for long-range correlations, like the separation between two reactants before their orbitals start to interact. Changing the DFT method to BLYP and turning on the long-range correlation correction in GAMESS by adding <b>$DFT LC=.t.</b> to the input file fixed the problem. Now the SCF converges just fine.Sorenhttps://www.blogger.com/profile/09127721889533199793noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-58023110068758896692012-01-23T12:35:49.405+01:002012-01-23T12:35:49.405+01:00The discussion with Paolo lead to this post.The discussion with Paolo lead to <a href="http://molecularmodelingbasics.blogspot.com/2012/01/negative-activations-energies-in.html" rel="nofollow">this post</a>.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-12212329635692327442012-01-15T12:43:25.755+01:002012-01-15T12:43:25.755+01:00:):)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-43592938504078082832012-01-15T10:59:37.251+01:002012-01-15T10:59:37.251+01:00Now, I understand. You have
R1 + R2 -> R1/R2 ...Now, I understand. You have<br /><br />R1 + R2 -> R1/R2 -> TS -> P<br /><br />and E(R1)+E(R2) > E(TS)<br /><br />This can happen and there is nothing (necessarily) wrong with your calculations. <br /><br />If you are trying to model a reaction in solution, then your activation energy is<br /><br />Ea = E(TS)-E(R1/R2)<br /><br />This is because the energy liberated by binding is lost to the environment before it can be used to react.<br /><br />If you are trying to model a reaction in the gas phase, then you would say that this is a barrier-less reaction and the reaction rate is proportional to the collision frequency. This is because the energy cannot escape the complex, and can be used to overcome the barrier. However, this will be pressure dependent (higher pressure, worse assumption).<br /><br />PS. I am really happy to hear you found the blog useful. Thanks for telling me.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-61002069899287688832012-01-14T20:13:17.869+01:002012-01-14T20:13:17.869+01:00:)
My way to build the PES:
Reactants---->TS-...:)<br /><br />My way to build the PES:<br /><br />Reactants---->TS---->Product<br /><br />Reactants = react1 + react2<br /><br /><br />In your way to build IRC we use only the TS geometry so the reactants are considered interacting. In my way no. Is the simple sum of the energies.<br /><br />However thanks a lot Prof.<br /><br /><br />P.S<br />After reading your post one year ago I learned to use GAMESS, I graduated myself with a magnificent Mass spectrometry thesis with some computational features (all learned by you!!!!!!)<br /><br />Now I got a Research bourse in computational chemistry!!!<br /><br />So thanks a lot!!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-41673860615325263802012-01-14T20:09:58.928+01:002012-01-14T20:09:58.928+01:00Sorry, I don't understandSorry, I don't understandJan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-17404836091230697282012-01-14T19:33:13.641+01:002012-01-14T19:33:13.641+01:00To construct the Potential Energy Surface I use to...To construct the Potential Energy Surface I use to optimize the reactants singly, the TS, and the product. After that I plot the three steps: in this way I get a negative activation energy and the reaction seems to be barrierless.<br /><br />My idea is that in this case the sum of the optimized reactants,each one considered at infinity distance from the other one, is higher in energy respect to the TS.<br /><br />I hope you understand now.....thanks for your help, really!!<br /><br />PaoloAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-82109800953353108742012-01-14T16:33:54.710+01:002012-01-14T16:33:54.710+01:00If thats the IRC why do you say "plotting the...If thats the IRC why do you say "plotting the Potential Energy Surface the calculated TS gives to me a negative activation energy"?Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-36625398362290434152012-01-14T16:06:08.335+01:002012-01-14T16:06:08.335+01:00I follow exactly the procedure that has been expl...I follow exactly the procedure that has been explained in your post concerning the Intrinsic Reaction Coordinate.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-81201077843765366742012-01-14T15:56:27.358+01:002012-01-14T15:56:27.358+01:00I dont understand 4. Can you explain exactly how y...I dont understand 4. Can you explain exactly how you obtained this plot?Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-37142148678328294492012-01-14T13:15:11.934+01:002012-01-14T13:15:11.934+01:00Sure:
1. the value of the imaginary frequency is ...Sure:<br /><br />1. the value of the imaginary frequency is 225.3 cm^-1<br /><br />2.yes<br /><br />3. around 5 kcal/mol lower than reactant<br /><br />4. yes<br /> The pattern show a not barrierless reaction<br /> link:http: //db.tt/dOfu7iAz<br /><br />How I can explain this?<br /><br />PaoloAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-37952593576742000392012-01-14T11:43:46.956+01:002012-01-14T11:43:46.956+01:00If you found a proper TS, then its energy has to b...If you found a proper TS, then its energy has to be higher than the reactant and product it connects (this does not account for single point energies).<br /><br />But without knowing more it's hard to tell what's wrong:<br /><br />1. What's the value of the imaginary frequency?<br /><br />2. Do you use NVIB=2 in the Hessian calculation?<br /><br />3. What's the value of the (negative) activation energy at the PM3 level? <br /><br />4. Are you sure you found the lowest energy conformation of your reactant.<br /><br />5. Have you computed <a href="http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html" rel="nofollow">an IRC</a>?Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-51024283609337592452012-01-13T20:49:36.450+01:002012-01-13T20:49:36.450+01:00Hi Jan,
I have a question for you that makes me ma...Hi Jan,<br />I have a question for you that makes me mad: I computed a transition state of a complex system; I got the imaginary frequency and the vectors seem concord to the mechanism. Now, plotting the Potential Energy Surface the calculated TS gives to me a negative activation energy. So the reaction seems to be barrierless. Is it possible? I know that usually increasing the temperature in real systems we can have a barrierless reaction but in a simulation seems strange. I used a PM3 method and I think that this probably is the reason. Performing the single point energy with a B3LYP/6311-G-(2d,p) the energy gap decrease but the TS energy remains 9 kcal lower than the reactants.<br /><br />Help me please and thanks for your time <br /><br />PaoloAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-36906319208278902082010-11-20T15:47:03.418+01:002010-11-20T15:47:03.418+01:00I have made a post on computing an IRC, which shou...I have made a <a href="http://molecularmodelingbasics.blogspot.com/2009/10/get-reaction-intrinsic-reaction.html" rel="nofollow">post on computing an IRC</a>, which should hopefully help.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-6984822277235887872010-11-20T15:15:52.357+01:002010-11-20T15:15:52.357+01:00By the way, here's the reaction that I will do...By the way, here's the reaction that I will do. Thanks!<br /><br />[IMG]http://i51.tinypic.com/2e2gx3q.jpg[/IMG]<br /><br />RalphUnknownhttps://www.blogger.com/profile/08125205617838593710noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-80803781681651760382010-11-20T15:11:55.265+01:002010-11-20T15:11:55.265+01:00Hi, I've been following your blog. I would lik...Hi, I've been following your blog. I would like to learn about Molecular Modeling for my thesis. So I was assigned to make an IRC calculation on the reaction of Carnosine with 4-hydroxynonenal. Can help me out? What do I do first? Thanks in advance.<br /><br />RalphUnknownhttps://www.blogger.com/profile/08125205617838593710noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-80632759074807779462010-10-20T09:12:37.883+02:002010-10-20T09:12:37.883+02:00First check if this structure has an imaginary fre...First check if this structure has an imaginary frequency with a mode that looks like what you want.<br /><br />If it does, use it for a runtyp=sadpoint run.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-63056820619944281112010-10-19T16:50:51.259+02:002010-10-19T16:50:51.259+02:00I have add all the rings freezing the the TS regio...I have add all the rings freezing the the TS region, but now in which way I have to use the new structure? I have to optimize the geometry or find another transition state?<br /><br />PaoloAnonymousnoreply@blogger.com