From owner-chemistry@ccl.net Sun Aug 23 01:41:01 2009 From: "Gerald Knizia knizia~~theochem.uni-stuttgart.de" To: CCL Subject: CCL: Atomic Oxygen 3P starting to make sense Message-Id: <-40055-090823013838-13497-2hOr27a7oHdOIwV9IU7jjQ a server.ccl.net> X-Original-From: Gerald Knizia Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 23 Aug 2009 07:38:18 +0200 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia^-^theochem.uni-stuttgart.de] Gerald Knizia wrote: > > What I am still confused is what is the correct value here. Oxygen atom > > is non-spherical, so I fail to see how enforcing spherical symmetry is > > justified. What would a correct symmetry group be here? > > The /geometry/ of the O atom is spherically symmetric. Consequently, the > Hamilton operator H of the system is supposed to commute with every > symmetry element of the point group. As commuting operators can be > diagonalized together, in principle each hypothetical exact wave function > can be chosen in such a way that it is at the same time an eigenvector to > both H and every element of a minimal generator set of the symmetry > group[1]. > > This symmetry-operator-eigenvector property means that applying any > symmetry operator to the wave function should reproduce the original wave > function, except for an (irrelevant) phase factor. Thus, an exact wave > function of the O atom /should/ be spherically symmetric. I'd like to expand my prior statement: - For atomic oxygen, the ground state is three times degenerate. There are three different, equivalent, exact, orthogonal, FCI wave functions |Psi_i> (i=x,y,z) -- one for each of the p_x/y/z orbitals being doubly occupied and the rest singly occupied. Each of these three functions is not spherically symmetric. - Any linear combination of the three |Psi_i> is also an eigenvector of the Hamiltonian, for the same ground state energy. In particular, sqrt(1/3)(|Psi_x> + |Psi_y> + |Psi_z>) is. This is a pure state, not an ensemble average. - Unlike its also-exact component FCI wave functions, this averaged wave function /is/ spherically symmetric. So a spherically symmetric exact wave function /can/ indeed be chosen -- but it doesn't have to be. The non-spherical polarized ones, which are more compatible with chemical intuition, are just as valid. In total I'd conclude that concentrating on just one of the equivalent states (i.e., doing a non-spherical calculation) is fine theoretically. -- Gerald Knizia From owner-chemistry@ccl.net Sun Aug 23 06:00:00 2009 From: "VITORGE Pierre 094605 Pierre.VITORGE ~~ cea.fr" To: CCL Subject: CCL:G: =?iso-8859-1?Q?RE=A0=3A_G=3A_TS_energy_slightly_lower_than_minimum_energy?= Message-Id: <-40056-090822030209-6695-GHa3AL4khZxupve5hNN5Dw[a]server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CA22EA.AD941E3F" Date: Sat, 22 Aug 2009 07:37:46 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE|a|cea.fr] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA22EA.AD941E3F Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Is a 3 kcal/mol "barrier" enough to interpret your result as a TS?=20 Your "TS" probably is one of the states that is effectively observed = through thermal agitation. In that case static approaches migh not be = much accurate, especially the thermal corrections (harmonic = approximation). =20 Pierre Vitorge ________________________________ De: owner-chemistry+pierre.vitorge=3D=3Dcea.fr**ccl.net de la part de = Johannes Johansson johjo76%gmail.com Date: ven. 8/21/2009 20:24 =C0: VITORGE Pierre 094605 Objet : CCL:G: TS energy slightly lower than minimum energy Dear Andreas, =20 this is quite common for very low barriers like the one you show here = (which is less than 3 kcal/mol). Regarding the way we search for TS, = i.e. at the electronic energy "level" and the approximations involved in = the ideal gas statistical mechanics used to obtain "corrections" for the = thermodynamic potentials (by for example Gaussian) this is not strange = at all, actually it is quite common in the literature when the barrier = is low. (Also, you can see in your values that it is in the entropy term = that the picture changes and that part is known to be the least = accurately described by the ideal gas stat mech used.) For your case this probably means nothing and the quality of your = prediction based on the calculated "barrier" is most likely as good as = for any other barrier you calculated the same way, i.e. with an = uncertainty of 3-5 kcal/mol for a TM containing system. Also, the same thing could happen when you calculate dielectric effects = for a low barrier TS located in gas phase. If you are interested in this issues you can read Donald Truhlars papers = on "Generalized TST", for example =20 J. Chem. Phys. 119, 5828 (2003). Best regards/Johannes, RWTH ;-) 2009/8/21 Andreas Uhe andiuhe]|[gmx.de = Sent to CCL by: "Andreas Uhe" [andiuhe..gmx.de ] Dear CCLers, =09 I hope you can help me explain the following result: Using Gaussian03 I calculated a transition state and the respective = energetic minima connected by the transition state (I checked with an = IRC calculation). As one expects the electronic energy of the TS is = higher than the electronic energy of the minimum. The problem is that = this is reversed for the Gibbs free energy obtained by frequency = calculations: =09 E Ezpe H G transition state -1624,071411 -1623,310413 -1623,269941 = -1623,378578 following minimum -1624,075219 -1623,311174 -1623,270443 = -1623,378231 =09 =09 Is there a chemical or physical explanation for this? Or is it an = artefact of the calculations? How can I interpret this result? =09 Thanks for your help! Andi =09 =09 =09 -=3D This is automatically added to each message by the mailing script = =3D- =09 =09 =09 E-mail to subscribers: CHEMISTRY],[ccl.net or use:=09 E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use=09http://www.ccl.net/chemistry/sub_unsub.shtml =09= =20 =09=09=09 =09=09=09 =09 =09 --=20 Adam Johannes Johansson Ph.D., M.Sc. Institut f=FCr Organische Chemie RWTH Aachen University Landoltweg 1 52056 Aachen Germany Cell phone:0708178487 E-mail:johjo76],[gmail.com =20 Research web page:www.physto.se/~johjo ------_=_NextPart_001_01CA22EA.AD941E3F-- From owner-chemistry@ccl.net Sun Aug 23 09:03:01 2009 From: "James Stewart MrMOPAC{}OpenMOPAC.net" To: CCL Subject: CCL: Atomic Oxygen 3P starting to make sense Message-Id: <-40057-090823090110-8298-SPus8hWK/kqeYFDR1IAFuw() server.ccl.net> X-Original-From: "James Stewart" Date: Sun, 23 Aug 2009 09:01:06 -0400 Sent to CCL by: "James Stewart" [MrMOPAC__OpenMOPAC.net] At 11:38 PM 8/22/2009, you wrote: Sent to CCL by: Gerald Knizia [knizia^-^theochem.uni-stuttgart.de] Gerald Knizia wrote: > > This symmetry-operator-eigenvector property means that applying any > symmetry operator to the wave function should reproduce the original wave > function, except for an (irrelevant) phase factor. Thus, an exact wave > function of the O atom /should/ be spherically symmetric. - I'd like to expand my prior statement: - - For atomic oxygen, the ground state is three times degenerate. There are - three different, equivalent, exact, orthogonal, FCI wave functions |Psi_i> - (i=x,y,z) -- one for each of the p_x/y/z orbitals being doubly occupied and - the rest singly occupied. Each of these three functions is not spherically - symmetric. - - Any linear combination of the three |Psi_i> is also an eigenvector of the - Hamiltonian, for the same ground state energy. In particular, sqrt(1/3)(|Psi_x> + |Psi_y> + |Psi_z>) - is. This is a pure state, not an ensemble average. - - Unlike its also-exact component FCI wave functions, this averaged wave - function /is/ spherically symmetric. So a spherically symmetric exact wave - function /can/ indeed be chosen -- but it doesn't have to be. The - non-spherical polarized ones, which are more compatible with chemical - intuition, are just as valid. - In total I'd conclude that concentrating on just one of the equivalent - states (i.e., doing a non-spherical calculation) is fine theoretically. The state sqrt(1/3)(|Psi_x> + |Psi_y> + |Psi_z>) has equal contributions from each of the p-orbitals. To that degree it has spherical symmetry. But the off-diagonal terms give it exactly the same asymmetry that a pure p-orbital would have. That is, any linear combination of p-orbitals is also a p-orbital. So I disagree with the statements that "Unlike its also-exact component FCI wave functions, this averaged wave function /is/ spherically symmetric. So a spherically symmetric exact wave function /can/ indeed be chosen -- but it doesn't have to be." It is not merely difficult to get a single state that has spherical symmetry for oxygen - it is impossible. Only by adding the contributions from the three degenerate states can spherical symmetry be achieved. However, I agree that by solving for one of the three degenerate components, all physical properties relating to the completely spherical oxygen can be determined. That is, I do agree with "In total I'd conclude that concentrating on just one of the equivalent states (i.e., doing a non-spherical calculation) is fine theoretically." Quite often we hear of "non-spherical atoms." This is a misnomer. Atoms have spherical symmetry, just sometimes the math is done wrong and the resulting solutions for the wavefunction are non-spherical. The fact that they are non-spherical does not alter the fact that both the exact (using degenerate states)and time-average solutions predict exact spherical symmetry in every case. Jimmy Stewart ( ** ** ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: MrMOPAC**OpenMOPAC.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | http://openmopac.net/ | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| | .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo.| | .-----------------------\ (----( )---------------------------------------. \_) ) / (_/ From owner-chemistry@ccl.net Sun Aug 23 14:33:01 2009 From: "Madi Narayanan madi7sk,+,gmail.com" To: CCL Subject: CCL:G: A question about ONIOM calculation in G03 Message-Id: <-40058-090823143212-24899-R+wSrfjB6RvfzNcMj8HGEA%x%server.ccl.net> X-Original-From: "Madi Narayanan" Date: Sun, 23 Aug 2009 14:32:09 -0400 Sent to CCL by: "Madi Narayanan" [madi7sk..gmail.com] Hi All, I am trying to run a ONIOM job using G03 as a test. This is a two layered oniom calculation. The model system being a organic molecule and it was optimized at HF/3-21G. It is surrounded my 5 water molecules, treated at AM1. I am interested in the dipole moment of the organic molecule after it is solvated by these waters. When I go through the output using chemcraft, the minimum energy conformation occurs at step 26. At this step, I see the following output Dipole moment= -0.384745 -0.953906 0.845786 Cartesian Forces: Max 0.070185324 RMS 0.022519929 SvSCFP is copying densities from files 528 and 530 to 603. ONIOM: saving gridpoint 1 ONIOM: restoring gridpoint 3 ONIOM: calculating energy. ONIOM: gridpoint 1 method: low system: model energy: 0.193909638221 ONIOM: gridpoint 2 method: high system: model energy: -500.715675862807 ONIOM: gridpoint 3 method: low system: real energy: -0.320806003300 ONIOM: extrapolated energy = -501.230391504329 ONIOM: calculating first derivatives. ONIOM: calculating electric field derivatives. ONIOM: Dipole =-1.30382196D-01-7.75259554D-02 6.33586444D-02 ONIOM: Dipole moment (Debye): X= -0.3314 Y= -0.1971 Z= 0.1610 Tot= 0.4178 I was wondering if I am correct in looking at the dipole moment at this step?? If I am correct, then how would I figure out the dipole moment of my molecule? Also I would greatly appreciate it if someone could explain to me what ONIOM dipole below is referring to. I do not understand the format of the statement below. ONIOM: Dipole =-1.30382196D-01-7.75259554D-02 6.33586444D-02 Thank you very much for your time. Madi From owner-chemistry@ccl.net Sun Aug 23 17:28:01 2009 From: "Barbault Florent florent.barbault|*|univ-paris-diderot.fr" To: CCL Subject: CCL: protein-ligand binding simulation times with molecular dynamics Message-Id: <-40059-090823122445-25657-0tFPSyCEWmCOfjLiq9O69g_._server.ccl.net> X-Original-From: "Barbault Florent" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Sun, 23 Aug 2009 17:31:01 +0200 MIME-Version: 1.0 Sent to CCL by: "Barbault Florent" [florent.barbault[#]univ-paris-diderot.fr] Hello, Definition of the time required for a MD trajectory is always problematic. In my opinion, the best way to do is to plot the RMSD=f(time) graphs for whole complex, ligand alone, ligand and binding pocket. On the two last plots you must reach a plateau. For the first plot you could still see some fluctuations which can belongs to some peptide loops. From my knowledge, estimation of a free-energy of binding with MMPBSA for an organic compound in interaction with a protein could be done between 1 to 10ns, generally 5 ns is enough. I Hope this will help you. Regards, Florent Barbault On Sat, 22 Aug 2009 09:11:44 +0400 "Andrew Voronkov drugdesign[-]yandex.ru" wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign[*]yandex.ru] > Dear CCl users, > How much time it will take to assess organic compound's binding with >Mw=300-400 to the protein's potential binding site with molecular >dynamics? Is 1-5 nanoseconds enough? > The goal is to assess the stability of protein-ligand complex and >then to evaluate its stability by MM-PBSA for selection from ligands >databases? > > Best regards, > Andrew > > > > -= This is automatically added to each message by the mailing script >=- > To recover the email address of the author of the message, please >change> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/> > ------------------------------------------------- Dr Florent Barbault Maitre de conferences / Assistant professor NEW ADDRESS !!! Universite Paris Diderot Laboratoire ITODYS 15 rue Jean de Baïf, bâtiment Lavoisier 75013 Paris FRANCE http://www.itodys.univ-paris7.fr/ tel : (33) 01-57-27-88-50 e-mail : florent.barbault-$-univ-paris-diderot.fr -------------------------------------------------