From owner-chemistry@ccl.net Sun Sep 10 13:05:00 2006 From: "Guosheng Wu wu_guosheng2002---yahoo.com" To: CCL Subject: CCL: sp2 or sp3 for the single-bonded ester oxygen atom Message-Id: <-32510-060910112706-25926-IsH6p8pmmCic0hgdCNXfpw()server.ccl.net> X-Original-From: Guosheng Wu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 10 Sep 2006 07:26:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Guosheng Wu [wu_guosheng2002!^!yahoo.com] Dear Kalju, Thanks a lot for your nice and informatic response. It is obvious that you think sp3 hybridization is more appropriate to describe that oxygen atom in ester. However, I have different understandings over some of your reasons. For CH3C(=O)OCH3, I name the carbonyl O as O1, and the other O(also in the topic) as O2. > One justification behind ester oxygen being sp3 is in bond lengths and > angles in esters. The C(sp2)-O bond in esters is about 1.33-1.34 Ang. > This is closer to the C-O(sp3) bond in alcohols and ethers > (1.41-1.42) than to the C=O(sp2) bond in carbonyl compounds > (1.20-1.21). It is not "fair" arrive the conclusion based on comparing the bond lengths of those two O atoms (the C=O and the C-O-C in ester), since O1 is double-bonded to a carbon, but O2 is single-bonded to atoms. Similar argument applies for the comparison for pyridine N and amide N, since both N atoms are sp2, but quite different situations. > Also, the QM potential-based partial charge on this > oxygen is more similar to alcohols than to carbonyls. You are right, but still it can not justify the hybridization. I think O2 in ester is much less polar than the alcohol O, certainly not comparable. Also, point charge model might be one of the most misleading component in molecular modelling, no matter how it is calculated. So I think polarized charge models could make lots of improvements for modelling, although it takes much time for its development and in applications. >Liquid simulations with the OPLS-AA force field suggest that Lennard-Jones > parameters of ether oxygen should be similar to ether and not to > carbonyl oxygen. However, many force fields reconize the uniqueness > of this oxygen by using a special atom type for the ether and > carboxylic acid oxygens. Typing O2 as sp2 or O3 does not necessary mean that one has to use all of the parameters of carbonyl O or ether O. The L-J parameter does not have much to do with sp2 or sp3, which is more about electrostatic interaction. Also, the simulations are dependent on many factors, so the conclusion from OPLS-AA has its limitations. (I feel the last "ether" in your email above is a typo for "ester") Certainly the O2 is very unique, quite different from carbonyl or ether O, so it's appropriate to name it specially, but it seems not clean what kinds of its physical properties are captured in the force fields. > It in not necessarily true that the coplanar structure of esters > arises only from p-pi conjugation. The repulsion of negative charges > on the carbonyl oxygen and the two tetrahedrally-arranged electron > pairs on sp3 oxygen would also predict planar structures, with > Z-conformer (in which both e-pairs point away from the C=O oxygen) > much more favorable than the E conformation (e-pairs surrounding C=O > oxygen). This is somewhat similar to glyoxal (HOC-CHO), which is > planar with a *long* C-C bond. Also note that the classical Lewis > resonance structure would make the ester oxygen positively charged, > something that would not fit well with the electronegative nature of > the oxygen. I agree with you that steric effect and lone-pair interactions have a role in the structure of ester. (Lewis structure has lots limitations, so I do not even mention it.) > The ester (sp3) oxygen is known to be weak H-bond acceptor so your > finding of limited number of structures is OK. I wonder if anybody > has done a gas phase QM study to see the difference between > tetrahedrally positioned H-bond acceptor and coplanar one? > > P.S. Some details about ester force fields are hidden in our own > "Parameterization of OPLS-AA force field for the conformational > analysis of macrocyclic polyketides", in J. Comp. Chem. 23, 977 (2002) In order to get deep understanding of the electronic structure of ester, I think one has to use very high level of QM theories and do very careful analysis. Something like NBO(natural bond orbital) analysis might be helpful and more relevant, which was reminded by one of the responses I got from this list. However I am limited to the resources, so I posted it out and hope someone would be interested in it. Certainly it could be a good porject for the students if anyone is teaching QM or Comp. Chem. Nevertheless, I think it would be more reasonable to assign sp2 hybridization for O2. Electronically, O in ester is much like NH in amide, which is popular in protein structures. I can not believe anyone would say that the N atom in amide is sp3. Other p-pi conjugation examples can be found in PhOH(Ph=benzene), PhOCH3, furan, pyridine, pyrrole, etc. The common feature for all of them is that O or N atom is connected to a pi system, either C=O or benzene, or whatever, so that one of the lone-pairs is more like pi electrons, becoming less polar, and not good for being a H-bond acceptor. One special case is substituted anilines that are often away from coplanar structures because the steric effect of the substituted groups, while aniline itself is complete flat. Thanks, Guosheng > > ------------------- > > Sent to CCL by: Guosheng Wu [wu_guosheng2002]^[yahoo.com] > > Hi there, > > > > For the first O atom in ester like CH3OC(=O)CH3, what kind of hybrid > state we should assign? > > > > Certainly it's within the context of molecular mechanics, although I > tried a little QM study with > > electrostatic potential and electron density calculation, and did > not get a clue. (Any QM expert > > can help me on it ?) > > > > I looked up the literature or the web(google), but all I can find > out for this problem is that it > > has been called sp3 at many occasions. One paper (Kresimir Molcanov > et al, Acta Crys. B, 2004, > > B60, 424) and some force fields (CVFF, AMBER,...) explicitly > call/type it as sp3. > > > > However, that conflicts my chemistry intuition, since 2 electrons of > that O should form so-called > > p-pi conjugation with C=O, so it should be in sp2 hybrid state. > That also explains the coplanar > > structure of ester or simple organic acids. > > > > Like the paper mentioned above, I did some CSD search for that O as > H-bond acceptor, there are > > only ~200 hits (dependent on parameter such as resolution, bond > length etc), so it's certainly not > > much statistically meaningful, but still what I found out is that > most of the O..H-X > > (X=O or N) H-bonds are more or less in the same plane of the ester. > So shall we call it sp2 > > oxygen in the future when we talk about molecular mechanics, and > apply this concept in any related > > study? > > > > I find this an interesting study, and hope to receive your insights, > especially those who work in > > QM areas. > > > > Thanks for your attention, > > -Guosheng > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sun Sep 10 13:50:01 2006 From: "Sherin Alfalah shireen.alfalah^yahoo.com" To: CCL Subject: CCL: Energy convergence around conical intersection Message-Id: <-32511-060910133458-660-ov8zyDGw+p7SJkV9dgawtA||server.ccl.net> X-Original-From: "Sherin Alfalah" Date: Sun, 10 Sep 2006 13:34:57 -0400 Sent to CCL by: "Sherin Alfalah" [shireen.alfalah-*-yahoo.com] Dear CCL users, We are trying to run energy calculations for some points around a conical intersection. I am facing some problems in convergence for the excited state. To reach MCSCF convergence, we try to read some molecular orbitals of other close points or to run the energy calculations for the excited state with more weight of the ground state for example "0.1 or 0.2". In the conical intersection region, reading different vectors may lead to different stationary points with different energies. I am a bit confused about the most proper way to have convergence. Shall it be the choice of method that gave the lowest energy or what? How can I know that I am not over shooting the minimum? We are using GAMESS, I am wondering if the results we have are due to chemical reasons or some artificial results of GAMESS software. I think that having more weights of the ground state, is reasonable since the points are within the conical intersection area? I am wondering about the most proper way to obtain convergence? and also if some one has any experience or know some tricks that may be useful to obtain convergence? Also, any information or discussion for this issue would be highly appreciated. Thanks in advance. ************************************** Sherin Alfalah PhD Student Theoretical Chemist Chemistry Department AlQuds University ************************************** From owner-chemistry@ccl.net Sun Sep 10 18:38:00 2006 From: "David Case case.().scripps.edu" To: CCL Subject: CCL: Announcement: version 5.1 of Nucleic Acid Builder is released Message-Id: <-32512-060910010102-5247-IjGPtZdnRh5hn9Pq31LHhA()server.ccl.net> X-Original-From: David Case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sat, 9 Sep 2006 21:56:52 -0700 Mime-Version: 1.0 Sent to CCL by: David Case [case _ scripps.edu] ANNOUNCEMENT: version 5.1 of the NAB (Nucleic Acid Builder) molecular manipulation language is now available Thomas J. Macke, W.A. Svrcek-Seiler, Russell A. Brown and David A. Case NAB was originally designed as a small modeling language with a principal focus on constructing models for non-helical nucleic acids. As the code developed, an implementation of the AMBER force field was added, which includes the AMBER implementation of the generalized Born model for solvation effects. Version 5 adds analytical second derivatives, opening the way to new types of simulations. Force-field calculations can be carried out on proteins and small molecules, as well as nucleic acids, making NAB a useful platform for a variety of modeling tasks. NAB consists of a language specification that has special support for macromolecules and their components, along with more general-purpose constructs such as strings, regular expressions and hashed arrays. There is also a support library (primarily coded in C) that implements rigid-body transformations, distance geometry, energy minimzation, molecular dynamics and normal mode analysis. Version 5 was a major update and consolidation, and version 5.1 adds support for parallel calculations using MPI on clusters; this complements the shared-memory, openMP support of earlier versions. NAB implements for the first time second derivatives of the GB solvation model. (See R.A. Brown and D.A. Case. Second derivatives in generalized Born theory. J. Comput. Chem. 27: 1662-1675, 2006). NAB is distributed as source code under the GNU General Public License (GPL). It runs on Linux, Mac OSX, Windows (under cygwin), and on most flavors of UNIX. For more information, and to download the code, please visit our web site: http://www.scripps.edu/case/nab.html We encourage NAB users to contribute to the code, or to help us integrate it into other environments. Please contact Dave Case, if you wish to help out. ....dave case From owner-chemistry@ccl.net Sun Sep 10 19:41:01 2006 From: "Wai-To Chan chan,+,curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: Energy convergence around conical intersection Message-Id: <-32513-060910193756-25161-/zIMBxLz+DhXBJXOwOyQyA_+_server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Sun, 10 Sep 2006 19:49:53 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan]^[curl.gkcl.yorku.ca] When running into convergence difficulites with CASSCf using GAMESS I would turn on the second order method as set by FULLNR=.TRUE. in $MCSCF. This method is considerably more time consuming than the default method. My experience is that what affect convergence most is the initial guess you use. For open shell systems I always stick with Pulay's procedure of using UHF-UNO. This procedure can be difficult for partial biradicals which requires you to obtain a broken spin-symmetry solution for a closed shell system. The stable=opt option in Gaussian might help if you know how to import the stable UHF solutions to GAMESS. I once considered this option but gave up later. Usually it just takes some extra effort to 'teach' GAMESS to produce the same stable UHF solution obtained from Gaussian by experimenting with various options. The extra work always pays off as GAMESS has far superior CASSCF convergence capability. I assume you are running energy calculations not geometry optimization. I believe GAMESS can only do MCSCF calculation of the energy gradient of a pure state. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<< Sent to CCL by: "Sherin Alfalah" [shireen.alfalah-*-yahoo.com] Dear CCL users, We are trying to run energy calculations for some points around a conical intersection. I am facing some problems in convergence for the excited state. To reach MCSCF convergence, we try to read some molecular orbitals of other close points or to run the energy calculations for the excited state with more weight of the ground state for example "0.1 or 0.2". In the conical intersection region, reading different vectors may lead to different stationary points with different energies. I am a bit confused about the most proper way to have convergence. Shall it be the choice of method that gave the lowest energy or what? How can I know that I am not over shooting the minimum? We are using GAMESS, I am wondering if the results we have are due to chemical reasons or some artificial results of GAMESS software. I think that having more weights of the ground state, is reasonable since the points are within the conical intersection area? I am wondering about the most proper way to obtain convergence? and also if some one has any experience or know some tricks that may be useful to obtain convergence? Also, any information or discussion for this issue would be highly appreciated. >>>>>>>>>>>>>>>>>>>>>>>.. From owner-chemistry@ccl.net Sun Sep 10 23:49:00 2006 From: "Seth Olsen s.olsen1=uq.edu.au" To: CCL Subject: CCL: Energy convergence around conical intersection Message-Id: <-32514-060910213919-26047-Mg8pfjGiQCzjNpv+Rkdt/g%%server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 11 Sep 2006 10:49:49 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1|a|uq.edu.au] Hi Sherin, Changing the weighting of the states in a state-averaged CAS calculation will give you convergence problems if the states are close together just because it doesn't take much variation in the energy of either state in order to flip the roots. I'm a bit confused as to what your objective is, though, since any weighting scheme other than 0.5/0.5 would be expected to overbias one state or the other. This would change the energy and the position of the intersection, and it's not clear to me that this would happen in a regular fashion. The question of what weighting is 'right' to describe the intersection (in the sense of getting the 'right answer for the right reason') does not seem to be very relevant because the 'right' weighting will probably vary depending on the state and the system. In this case, even if the 'right' answer is achieved, the weighting has become just a tuning parameter and its not clear that the it is 'right for the right reason'. When you vary the weighting, are you then comparing to something more trustworthy (like evenly-weighted MCQDPT or MRCI)? I've often thought that there isn't that information about state-averaging in the literature, given that it is the currently the most popular method for computational photochemical modeling. The rate of change of weighting of a state averaged CAS solution has been suggested as a diagnostic for the quality of the wavefunction (Stalring et al, Mol. Phys. v.2 pp.103-114 (2001)). In this work it is also pointed out that only for an evenly-weighted wave function is the final solution invariant to projections within the state-averaged subspace (in addition to the usual CASSCF orbital rotation invariance). This in turn has implications for the Lagrangian used to determine analytic gradients w/ respect to geometry. Good luck. :-) Cheers, Seth Sherin Alfalah shireen.alfalah^yahoo.com wrote: >Sent to CCL by: "Sherin Alfalah" [shireen.alfalah-*-yahoo.com] >Dear CCL users, >We are trying to run energy calculations for some points around a conical intersection. I am facing some problems in convergence for the excited state. To reach MCSCF convergence, we try to read some molecular orbitals of other close points or to run the energy calculations for the excited state with more weight of the ground state for example "0.1 or 0.2". In the conical intersection region, reading different vectors may lead to different stationary points with different energies. I am a bit confused about the most proper way to have convergence. Shall it be the choice of method that gave the lowest energy or what? How can I know that I am not over shooting the minimum? > >We are using GAMESS, I am wondering if the results we have are due to chemical reasons or some artificial results of GAMESS software. > >I think that having more weights of the ground state, is reasonable since the points are within the conical intersection area? > >I am wondering about the most proper way to obtain convergence? and also if some one has any experience or know some tricks that may be useful to obtain convergence? Also, any information or discussion for this issue would be highly appreciated. > >Thanks in advance. > > > > >************************************** >Sherin Alfalah >PhD Student >Theoretical Chemist >Chemistry Department >AlQuds University >**************************************> > > > >