From owner-chemistry@ccl.net Sat Aug 23 10:26:01 2014 From: "Alan Shusterman alan:-:reed.edu" To: CCL Subject: CCL: Frequencies of Optimized Minima Message-Id: <-50427-140822211616-13787-XQgbHFkI4CAcusvWbDmiOg=-=server.ccl.net> X-Original-From: Alan Shusterman Content-Type: multipart/alternative; boundary=001a11c2a3ec60ed49050141b28a Date: Fri, 22 Aug 2014 18:16:00 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan-$-reed.edu] --001a11c2a3ec60ed49050141b28a Content-Type: text/plain; charset=UTF-8 The s-cis conformation of 1,3-butadiene is a transition state between two nonplanar ("skew") conformations. This may be the case for your enones. Alan On Fri, Aug 22, 2014 at 2:56 PM, Matthew Chen mchen148..aol.com < owner-chemistry%%ccl.net> wrote: > > Sent to CCL by: "Matthew Chen" [mchen148!=!aol.com] > Dear Colleagues, > > I am attempting to perform an optimization on the structures of various > enones. The s-trans conformations converged to a minimum without problems; > however, the s-cis conformations frequently demonstrate an imaginary > frequency. I manually checked the geometry of one of the simpler enones and > it looks exactly like the minimum should, so I don't know why this is > happening. > > What factors govern whether a functional will or will not provide > imaginary frequencies for minima? What may be done to stop it from doing so? > > Sincerely, > Matthew Chen> > > -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23 --001a11c2a3ec60ed49050141b28a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
The s-cis conformation of 1,3-butadiene is a transiti= on state between two nonplanar ("skew") conformations. This may b= e the case for your enones.
Alan


On Fri, Aug 22, 2014 at 2:56 PM, Matthew= Chen mchen148..aol.com &l= t;owner-chemis= try%%ccl.net> wrote:

Sent to CCL by: "Matthew=C2=A0 Chen" [mchen148!=3D!aol.com]
Dear Colleagues,

I am attempting to perform an optimization on the structures of various eno= nes. The s-trans conformations converged to a minimum without problems; how= ever, the s-cis conformations frequently demonstrate an imaginary frequency= . I manually checked the geometry of one of the simpler enones and it looks= exactly like the minimum should, so I don't know why this is happening= .

What factors govern whether a functional will or will not provide imaginary= frequencies for minima? What may be done to stop it from doing so?

Sincerely,
Matthew Chen



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--
Alan S= husterman
Chemistry Department
Reed College
3203 SE Woodstock Blvd=
Portland, OR 97202-8199
503-517-7699
http://blogs.reed.edu/alan/
"Nature doesn't make long speeches." Lao Tzu 23
--001a11c2a3ec60ed49050141b28a-- From owner-chemistry@ccl.net Sat Aug 23 14:06:00 2014 From: "Jing Kong jingkong[-]gmail.com" To: CCL Subject: CCL: Symposium on Accurate Theories for Small and Large Systems Message-Id: <-50428-140823133133-5078-5evXSggXnibZB+3WyvNp+Q||server.ccl.net> X-Original-From: "Jing Kong" Date: Sat, 23 Aug 2014 13:31:32 -0400 Sent to CCL by: "Jing Kong" [jingkong()gmail.com] Dear All, You are cordially invited to a symposium titled Accurate Theories for Small and Large Systems at SERMACS (southeast regional meeting of American chemical society) 2014. The meeting will be held in Nashville from Oct 16 to 19 and the symposium will be on Saturday, Oct. 18. Computational chemistry has seen ever increasing applications in molecular and materials sciences. Still, it faces a number of challenges. How to treat strong correlation is one of them. Another challenge is to model systems of many thousands of atoms accurately, with electronic effects treated concurrently with dynamics. This symposium aims to bring together leading scientists in the Southeast Region and around the world to address these challenges. It will also provide students in the region an exposure to the latest developments in computational methodology. The following is an incomplete list of potential speakers. Please note that you have until Friday, Aug. 29 to submit an abstract for the conference http://www.sermacs2014.org/. Let me know if you have to be late in submitting the abstract. The registration deadline is later (Sept 25). Attached is the advertisement of SERMACS 2014 on C&EN. Confirmed speakers: Axel Becke (Dalhousie University, Canada, keynote speaker) Matt Challacombe (Las Alamos National Lab) Dan Cheney (Bristol Meyers Squibb) Daniel Crawford (Virginia Tech) Tom Darden (Openeye) Hao Hu (Univ. Hong Kong) Gary Kedziora (Dynamics Research Corp.) Ruth Pachter (Air Force Research Lab) David Sherrill (Georgia Tech) Weitao Yang (Duke University) Sincerely, Jing Kong, Ph.D., Associate Prof., Chemistry/Computational Science, MTSU http://www.mtsu.edu/chemistry/faculty/jkong.php From owner-chemistry@ccl.net Sat Aug 23 20:40:01 2014 From: "Billy McCann thebillywayne . gmail.com" To: CCL Subject: CCL: Frequencies of Optimized Minima Message-Id: <-50429-140823202526-22805-UGHowgqKglTiwrZ6nR4SDg ~~ server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=90e6ba614f0c0ae8b30501551b50 Date: Sat, 23 Aug 2014 20:25:05 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne:gmail.com] --90e6ba614f0c0ae8b30501551b50 Content-Type: text/plain; charset=UTF-8 Matthew, The strategy that I would adopt would be 1) begin the geometry optimization of the s-cis conformer such that the cis dihedral isn't 0. I would place it at 30 degrees. As Alan stated, the 0 degree dihedral is a TS. The "skew" conformation is a balance between conjugative stabilization and steric repulsion. The conjugative stabilization for simple enones is somewhat small. The steric repulsion between the two hydrogens of the archetypal buta-1,3-diene is enough to force a slight break in the conjugation. I recommend "Modern Physical Organic Chemistry" by Anslyn and Dougherty to sharpen your chemical intuition (though maybe if it needs sharpening, it isn't intuitive?). 2) tighten the geometry and scf convergence criteria. If using DFT, use an ultrafine grid. Should you do this, and you are planning to compare energies between the conformers, you'll need to use the same convergence criteria and grid. 3) if I were still having problems, I would consider recalculating the force constants every few trial geometries. If affordable, calculate the force constants for every trial geometry. The activation barrier for passing through the 0 degree s-cis conformation is very small for unsubstitued enones. I expect that calculating the force constants will help the optimization travel away from the saddle point, down the potential energy surface, toward the local minimum. If I google "s-cis enone skew transition state", I find plentiful resources regarding this particular phenomenon. As with most molecular geometry problems, the explanation is "sterics and electronics." Anslyn's book will help you to rationalize which one is the dominant factor. Also, you'll see plenty of examples of electronic effects (typically explained through fragment or natural orbitals) or "stereoelectronics." Hope that helps, BW --90e6ba614f0c0ae8b30501551b50 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Matthew,

The strategy that I would adopt would be

1)=C2=A0 begin the geometry opt= imization of the s-cis conformer such that the cis dihedral isn't 0.=C2= =A0 I would place it at 30 degrees.=C2=A0 As Alan stated,
the = 0 degree dihedral is a TS.=C2=A0 The "skew" conformation is a bal= ance between conjugative stabilization and steric repulsion.=C2=A0 The conj= ugative stabilization for simple enones is somewhat small.=C2=A0=C2=A0 The = steric repulsion between the two hydrogens=C2=A0 of the archetypal buta-1,3= -diene is enough to force a slight break in the conjugation.=C2=A0 I recomm= end "Modern Physical Organic Chemistry" by Anslyn and Dougherty t= o sharpen your chemical intuition (though maybe if it needs sharpening, it = isn't intuitive?).

=
2)= =C2=A0 tighten the geometry and scf convergence criteria.=C2=A0 If using DF= T, use an ultrafine grid.=C2=A0 Should you do this, and you are planning to= compare energies between the conformers, you'll need to use the same c= onvergence criteria and grid.=C2=A0

= 3) if I were still having problems, I would consider recalculating the forc= e constants every few trial geometries.=C2=A0 If affordable, calculate the = force constants for every trial geometry.=C2=A0

= The activation barrier for passing through the 0 degree s-cis conformation = is very small for unsubstitued enones.=C2=A0 I expect that calculating the = force constants will help the optimization travel away from the saddle poin= t, down the potential energy surface, toward the local minimum.=C2=A0


If I google "s-cis enone skew transition state", I find plent= iful resources regarding this particular phenomenon.=C2=A0 As with most mol= ecular geometry problems, the explanation is "sterics and electronics.= "=C2=A0 Anslyn's book will help you to rationalize which one is th= e dominant factor.=C2=A0 Also, you'll see plenty of examples of electro= nic effects (typically explained through fragment or natural orbitals) or &= quot;stereoelectronics."


Hope that helps,

BW
--90e6ba614f0c0ae8b30501551b50--