From owner-chemistry@ccl.net Tue Feb 10 07:52:01 2015 From: "Igors Mihailovs igors.mihailovs0**gmail.com" To: CCL Subject: CCL:G: Gaussian ListWindow Message-Id: <-51019-150210075022-10571-9lH8Vxz7UkPdIV5BTNGMvg(~)server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=047d7b34362a06d4fb050ebb541b Date: Tue, 10 Feb 2015 14:49:54 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0- -gmail.com] --047d7b34362a06d4fb050ebb541b Content-Type: text/plain; charset=UTF-8 Dear Mr. Nieman, I agree, usage of Frozen Core options are REALLY poorly documented in G09 manual, first of all because it is not stressed that these are OPTIONS and not KEYWORDS. I myself spent a lot of time struggling to understand that... If I do remember correctly, You should write #P B3LYP(ListWindow=(2 4))/6-311g* SP pop=reg gfinput gfprint iop(6/7=3) SCF=direct I hope this helps, Igors Mihailovs Institute of Solid State Physics University of Latvia 2015-02-06 21:19 GMT+02:00 Reed Nieman reed.nieman*o*ttu.edu < owner-chemistry : ccl.net>: > > Sent to CCL by: "Reed Nieman" [reed.nieman,+,ttu.edu] > I am having trouble implementing the keyword ListWindow in g09. I am > looking to freeze several non-sequential orbitals in a fairly large system > and from the documentation at the bottom of this page: > http://www.gaussian.com/g_tech/g_ur/k_fc.htm , it looked like it would be > exactly what I needed. However, the wording as to how one should use this > feature is rather vague and anytime I try to run a test calculation on > water freezing orbitals 2 and 4, the output file says that ListWindow is an > invalid keyword. The line I use in the input file looks like this (on a > single line): > > #P B3LYP/6-311g* SP pop=reg gfinput gfprint iop(6/7=3) SCF=direct > ListWindow=(2 4) > > I would greatly appreciate any help or guidance with this issue. > > Best, > Reed Nieman > reed.nieman~~ttu.edu> > > --047d7b34362a06d4fb050ebb541b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Mr. Nieman,

I agree, usage of Frozen Core options are= REALLY poorly documented in G09 manual, first of all because it is not str= essed that these are OPTIONS and not KEYWORDS. I myself spent a lot of time= struggling to understand that...
If I do remember correctly, You should w= rite
#P B3LYP(ListWindow=3D(2 4))/6-311g* SP pop=3Dreg gfin= put gfprint iop(6/7=3D3) SCF=3Ddirect

I hope this helps,
Igors Mihailovs
<= div>
Institute of Solid= State Physics
University of Latvia

<= /div>

2015-02-06 21:19 GMT+02:00 Reed Nieman reed.= nieman*o*ttu.edu <owner-chemistry : ccl= .net>:

Sent to CCL by: "Reed=C2=A0 Nieman" [reed.nieman,+,ttu.edu]
I am having trouble implementing the keyword ListWindow in g09. I am lookin= g to freeze several non-sequential orbitals in a fairly large system and fr= om the documentation at the bottom of this page: http://www.gaussian.com/g_= tech/g_ur/k_fc.htm , it looked like it would be exactly what I needed. = However, the wording as to how one should use this feature is rather vague = and anytime I try to run a test calculation on water freezing orbitals 2 an= d 4, the output file says that ListWindow is an invalid keyword. The line I= use in the input file looks like this (on a single line):

#P B3LYP/6-311g* SP pop=3Dreg gfinput gfprint iop(6/7=3D3) SCF=3Ddirect Lis= tWindow=3D(2 4)

I would greatly appreciate any help or guidance with this issue.

Best,
Reed Nieman
reed.nieman~~ttu.edu



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--047d7b34362a06d4fb050ebb541b-- From owner-chemistry@ccl.net Tue Feb 10 09:26:01 2015 From: "Igors Mihailovs igors.mihailovs0(-)gmail.com" To: CCL Subject: CCL: Homo-lumo gap significance Message-Id: <-51020-150210053805-18170-jvngxKRWrFRD6QntGnU5VA{:}server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary=047d7b3a8298f69599050eb97ae8 Date: Tue, 10 Feb 2015 12:37:38 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igors.mihailovs0..gmail.com] --047d7b3a8298f69599050eb97ae8 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear all, I agree, of course, that eigenvalues are not at all that best values to be used for gap calculations from the formal (and, frequently, also from the practical point of view), but, nevertheless, they DO provide SOME approximation. Eigenvalues, naturally, look like 'approximation for everything', as we are talking both about MO-to-MO transitions when considering UV-Vis spectra and about electron removal from some orbital / electron addition to some orbital, talking about ionization or electron capture. Of course, in reality one and the same quantity cannot describe both. However, it is well known that, for example, Koopmans' theorem often provides quite good results (okay, it's due to error compensation). Eigenvalue differences are also the first approximation in TD methods. I want also to emphasize that the person asking was dealing with HOMO-LUMO gap in a TRANSITION STATE. From more physical point of view, Mr. van Sittert should compute ionization potential of electron donor in his reaction and electron affinity of the acceptor, according to =CE=94 (or =CE= =94SCF) methodology (energy difference). However, I do not know if this would be easy task to perform in transition state, correctly including the polarization of other molecules in the reaction center. Eigenvalues, on the contrary, are ready available from every optimization run; that's why I did not comment anything in my first answer. We are now, actually, concerned with something similar, currently reconciling ourselves with Mulliken charges of surrounding molecules for the polarization field (but we are not dealing with the transition state). Is it correct enough to consider reactants as separate electronic systems in the transition state at all? With best wishes, Igors Mihailovs Institute of Solid State Physics University of Latvia 2015-02-09 23:58 GMT+02:00 Tymofii Nikolaienko tim_mail[A]ukr.net < owner-chemistry(_)ccl.net>: > Can I try to exaggerate this discussion a bit? > > It is well known that a concept of 'orbital' has historically originated > from Hartree-Fock approximation, and that in fact molecular orbital > is no more than a mathematical tool for building an approximate > wavefunction. > Some authors have advocated the viewpoint that in reality orbitals simply > do not exist! For example: > * Mart=C3=ADn Labarca, Olimpia Lombardi "Why orbitals do not exist?" > [Foundations of Chemistry, 2010, Volume 12, Issue 2, pp 149-157, DOI > 10.1007/s10698-010-9086-5 ] > * J. F. Ogilvie, "The nature of the chemical bond=E2=80=941990: There are= no such > things as orbitals!" [J. Chem. Educ., 1990, 67 (4), p 280, DOI: > 10.1021/ed067p280 ] > > With that in mind, *do HOMO and LUMO have any importance,* - except for > adding another 'beautiful picture' to some paper with HOMO and/or LUMO > isosurfaces and withOUT any discussion of what *consequences* does their > shapes imply , - for understanding physical properties and chemical > reactivity ? > > Similar doubts about an importance apply to the *HOMO-LUMO gap*, but here > I'd like to recall that, ofr example, replacing ONE (filled) orbital (HOM= O) > in > a Slatter determinant with ONE unfilled orbital (e.g., LUMO) does NOT > produce even approximate wavefunction of an excited state, since the > crudest approximation to that wavefunction comes with CIS method, where a > linear combination of (many!) singly substituted determinants is used > in order to get (a not so good) wavefunction of an excited state. So, > there seems to be no *physical *ground for associating the HOMO-LUMO gap > with > characteristic wavelengths in a UV-Vis-like spectra. > > So, *why to care about HOMO / LUMO* unless we are not dealing with solids > ?... > > Best regards, > Tymofii, > a physicist ;) > > > > > > > > 09.02.2015 20:49, Tom Albright talbright1234=3D-=3Dgmail.com wrote: > > The units are in Hartrees. HOWEVER, to categorically say that the > HOMO-LUMO gap is a measure of thermodynamic or kinetic stability is not > true. Let me take a simple example: cyclobutadiene (in its ground state) = is > very reactive and one can rightfully say that it is a consequence of a > small HOMO-LUMO gap. On the other hand tetrakis(t-butyl)cyclobutadiene ca= n > be isolated, crystallized and stored indefinitely at room temperature and > its HOMO-LUMO gap is similar to that in the parent molecule. You have thr= ee > different transition states - should be done is to carefully compare the > bonding in each. See, for example, Albright, Burdett and Whangbo, "Orbita= l > Interactions in Chemistry, 2nd edition, J. Wiley 2013). > On Feb 9, 2015, at 11:50 AM, Igors Mihailovs igors.mihailovs0{}gmail.com > wrote: > > Dear Mr. van Sittert, > > Which units are Your eigenvalues/gap values in? Possibly hartrees? You > could possibly convert these gap values to joules and compare with k_B*T, > as suggests, for instance, plain Arrhenius formula... > With best wishes, > Igors Mihailovs > Institute of Solid State Physics > University of Latvia > > > 2015-02-09 14:16 GMT+02:00 Cornie Van Sittert Cornie.VanSittert^nwu.ac.za > : > >> Good afternoon, >> >> I was wondering if anybody could help me. I would like to ask you about >> the HOMO-LUMO energy gap. >> >> I have three transition states to compare, TS1, TS2 and TS3. The >> HOMO-LUMO was calculated for each on the whole system, so I have my HOMO= on >> my Nu- and my LUMO on my electrophile. For the HOMO-LUMO energy gap, I >> subtracted the LUMO energy from the HOMO energy and got the absolute val= ue >> (column 2). Column 3 is the HOMO-LUMO energy gap within the transition >> state structure. >> >> In the table below I compare the HOMO-LUMO energy gaps, and it seems tha= t >> at the transition state (TS, column 3), the N9 has the biggest energy ga= p, >> followed by N3, and then N7. I read that all transition states reach the >> most stable form, which is the TS with the largest HOMO-LUMO energy gap. >> This follows the trend in the lab where we made the N9>N3>>N7. The >> HOMO-LUMO energy gap of transition state minus the HOMO-LUMO energy gap = of >> reactants (column 4) shows the N9> will follow the one with the smallest gap, and this agrees with my >> experimental work. >> From what I read in literature, the HOMO-LUMO energy gap for the >> transition state should be as big as possible so that the total HOMO-LUM= O >> energy gap is small: (column 4) >> E(total) gap =3D E(reactants) gap - E(transition state) gap >> >> >> pathway >> >> HOMO-LUMO gapR >> >> HOMO-LUMO gapTS >> >> HOMO-LUMO gap(TS-R) >> >> N3 >> >> 0.15009 >> >> 0.12572 >> >> 0.02439 >> >> N7 >> >> 0.14983 >> >> 0.12340 >> >> 0.02643 >> >> N9 >> >> 0.14973 >> >> 0.12767 >> >> 0.02206 >> >> >> >> The question that no one seems to answer is if these values (shown above= ) >> are significantly different from each other. >> >> Is the difference on the 3rd decimal place in the eigenvalues for the TS >> significant? or would all the reactions occur? When can the difference = be >> taken as significant? >> >> Kind regards, >> Cornie van Sittert >> >> >> >> >> Vrywaringsklousule / Disclaimer: *http://www.nwu.ac.za/it/gov-man/discla= imer.html >> * >> > > > With Best Regards > Tom Albright > > > > --047d7b3a8298f69599050eb97ae8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear all,

I agree, of course, that eigen= values are not at all that best values to be used for gap calculations from= the formal (and, frequently, also from the practical point of view), but, = nevertheless, they DO provide SOME approximation. Eigenvalues, naturally, l= ook like 'approximation for everything', as we are talking both abo= ut MO-to-MO transitions when considering UV-Vis spectra and about electron = removal from some orbital / electron addition to some orbital, talking abou= t ionization or electron capture. Of course, in reality one and the same qu= antity cannot describe both. However, it is well known that, for example, K= oopmans' theorem often provides quite good results (okay, it's due = to error compensation). Eigenvalue differences are also the first approxima= tion in TD methods.
I want also to emphasize that the person asking was = dealing with HOMO-LUMO gap in a TRANSITION STATE. From more physical point = of view, Mr. van Sittert should compute ionization potential of electron do= nor in his reaction and electron affinity of the acceptor, according to =CE= =94 (or =CE=94SCF) methodology (energy difference). However, I do not know = if this would be easy task to perform in transition state, correctly includ= ing the polarization of other molecules in the reaction center. Eigenvalues= , on the contrary, are ready available from every optimization run; that= 9;s why I did not comment anything in my first answer.

We are now, a= ctually, concerned with something similar, currently reconciling ourselves = with Mulliken charges of surrounding molecules for the polarization field (= but we are not dealing with the transition state). Is it correct enough to = consider reactants as separate electronic systems in the transition state a= t all?

With best wishes,
Igors Mihailovs<= br>
Institute of Solid State Physics
University of = Latvia


2015-02-09 23:58 GMT+02:00 Tymofii Nikolaien= ko tim_mail[A]ukr.net <= owner-chemistr= y(_)ccl.net>:
=20 =20 =20
Can I try to exaggerate this discussion a bit?

It is well known that a concept of 'orbital' has historically originated from Hartree-Fock approximation, and that in fact molecular orbital
is no more than a mathematical tool for building an approximate wavefunction.
Some authors have advocated the viewpoint that in reality orbitals simply do not exist! For example:
* Mart=C3=ADn Labarca, Olimpia Lombardi "Why orbitals do not exist= ?" [Foundations of Chemistry, 2010, Volume 12, Issue 2, pp 149-157,=C2=A0 DOI 10.1007/s10698-010-9086-5 ]
* J. F. Ogilvie, "The nature of the chemical bond=E2=80=941990: Th= ere are no such things as orbitals!" [J. Chem. Educ., 1990, 67 (4), p 280, DO= I: 10.1021/ed067p280 ]

With that in mind, do HOMO and LUMO have any importance, - except for adding another 'beautiful picture' to some paper wit= h HOMO and/or LUMO
isosurfaces and withOUT any discussion of what consequences does their shapes imply , -=C2=A0 for understanding physical properties and chemical reactivity ?

Similar doubts about an importance apply to the HOMO-LUMO gap, but here I'd like to recall that, ofr example, replacing ONE (filled) orbital (HOMO) in
a Slatter determinant with ONE unfilled orbital (e.g., LUMO) does NOT produce even approximate wavefunction of an excited state, since the
crudest approximation to that wavefunction comes with CIS method, where a linear combination of (many!) singly substituted determinants is used
in order to get (a not so good) wavefunction of an excited state. So, there seems to be no physical ground for associating the HOMO-LUMO gap with
characteristic wavelengths in a UV-Vis-like spectra.

So, why to care about HOMO / LUMO unless we are not dealing with solids ?...

Best regards,
Tymofii,
a physicist ;)







09.02.2015 20:49, Tom Albright talbright1234=3D-=3Dgmail.com wrote:
The units are in Hartrees. HOWEVER, to catego= rically say that the HOMO-LUMO gap is a measure of thermodynamic or kinetic stability is not true. Let me take a simple example: cyclobutadiene (in its ground state) is very reactive and one can rightfully say that it is a consequence of a small HOMO-LUMO gap. On the other hand tetrakis(t-butyl)cyclobutadiene can be isolated, crystallized and stored indefinitely at room temperature and its HOMO-LUMO gap is similar to that in the parent molecule. You have three different transition states - should be done is to carefully compare the bonding in each. See, for example, Albright, Burdett and Whangbo, "Orbital Interactions in Chemistry, 2nd edition, J. Wiley 2013).
On Feb 9, 2015, at 11:50 AM, Igors Mihailovs igors.mihailovs0{}= gmail.com wrote:

Dear Mr. van Sittert,

Which units are Your eigenvalues/gap values in? Possibly hartrees? You could possibly convert these gap values to joules and compare with k_B*T, as suggests, for instance, plain Arrhenius formula...
With best wishes,
Igors Mihailovs
Institute of Solid State Physics
University of Latvia


2015-02-09 14:16 GMT+02:00 Cornie Van Sittert Cornie.VanSittert^nwu.ac.za <owner-chemistry]*[ccl.net>= ;:
Good afternoon,
=C2=A0
I was wondering if anybody could help me.=C2=A0 I would like to ask you about the HOMO-LUMO energy gap.
=C2=A0
I have three transition states to compare, TS1, TS2 and TS3. The HOMO-LUMO was calculated for each on the whole system, so I have my HOMO on my Nu- and my LUMO on my electrophile. For the HOMO-LUMO energy gap,=C2=A0I subtracted the LUMO energy from th= e HOMO energy and got the absolute value (column 2).=C2=A0 Column 3=C2=A0is the HOMO-LUMO energy gap w= ithin the transition state structure.
=C2=A0
In the table below=C2=A0I compare the HOMO-LUMO energy gaps, and it seems that at the transition state (TS, column 3), the N9 has the biggest energy gap, followed by N3, and then N7. I read that all transition states reach the most stable form, which is the TS with the largest HOMO-LUMO energy gap. This follows the trend in the lab where we made the N9>N3>>N7. The HOMO-LUMO energy gap of transition state minus the HOMO-LUMO energy gap of reactants (column 4) shows the N9<N3<N7 trend. Articles say that reactions will follow the one with the smallest gap, and this agrees with=C2=A0my experimental work.<= br>
From what=C2=A0I read in literature, the HOMO-LUMO energy gap for the transition state should be as big as possible so that the total=C2=A0HOMO-LUMO ener= gy gap is small: (column 4)
E(total) gap =3D E(reactants) gap - E(transition state) gap
=C2=A0

pa= thway

HO= MO-LUMO gapR

HO= MO-LUMO gapTS

HO= MO-LUMO gap(TS-R)

N3=

0.= 15009

0.= 12572

0.= 02439

N7=

0.= 14983

0.= 12340

0.= 02643

N9=

0.= 14973

0.= 12767

0.= 02206
=C2=A0
=C2=A0
The question that no one=C2=A0seems to answer is i= f these values (shown above) are significantly different from each other.
=C2=A0
Is the difference on the 3rd decimal place in the eigenvalues for the TS significant? or would all the reactions occur?=C2=A0 When can the differenc= e be taken as significant?
=C2=A0
Kind regards,
Cornie van Sittert
=C2=A0
=C2=A0
=C2=A0

Vrywaringsklousule / Disclaimer: http://www.nwu.ac.za/it/gov-man/disclaimer.html



With Best Regards
Tom Albright




--047d7b3a8298f69599050eb97ae8-- From owner-chemistry@ccl.net Tue Feb 10 13:04:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor[a]fluor.quimica.uniovi.es" To: CCL Subject: CCL: Homo-lumo gap significance Message-Id: <-51021-150210120931-12425-rjXIhwMh7sQJt4wesqmS9g*server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 10 Feb 2015 18:04:45 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor_+_fluor.quimica.uniovi.es] On Tue, Feb 10, 2015 at 12:37:38PM +0200, Igors Mihailovs igors.mihailovs0(-)gmail.com wrote: > We are now, actually, concerned with something similar, currently > reconciling ourselves with Mulliken charges of surrounding molecules for > the polarization field (but we are not dealing with the transition state). > Is it correct enough to consider reactants as separate electronic systems > in the transition state at all? > > With best wishes, > Igors Mihailovs > Institute of Solid State Physics > University of Latvia Igors, Maybe you find interesting this article: http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.102.226401 It's not mine ... Regards, Dr. Víctor Luaña -- . . "La suma de la mediocridad y de la creatividad es / `' \ constante: a más de la una menos de la otra" /(o)(o)\ (Jorge Wasenberg, 2015) /`. \/ .'\ "mediocrity+creativity=constant" / '`'` \ (First Principle of thermodynamics,Universal version) | \'`'`/ | "Lo mediocre es peor que lo bueno, pero también es peor | |'`'`| | que lo malo, porque la mediocridad no es un grado, es una \/`'`'`'\/ actitud" ===(((==)))==================================+========================= ! Dr.Víctor Luaña ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor . fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Tue Feb 10 18:00:00 2015 From: "Gennady L Gutsev gennady.gutsev[]famu.edu" To: CCL Subject: CCL:G: Fermi coupling constants for singlet AF states Message-Id: <-51022-150210175827-7394-yiqhJmvx8LTZodidpisMeg]|[server.ccl.net> X-Original-From: "Gennady L Gutsev" Date: Tue, 10 Feb 2015 17:58:26 -0500 Sent to CCL by: "Gennady L Gutsev" [gennady.gutsev%%famu.edu] Good afternoon, we got a problem with interpreting the results of calculations of Fermi contact coupling constants for antiferromagnetic singlet states. Generally, a singlet cannot be seen in ESR experiments because the hyperfine coupling SAI should be zero if S = 0. However, if we perform BPW91/6-311+G* computations on MnAl dimer for 2S+1 = 5, 3 and 1 states then we get: 2S+1 = 5 Mulliken atomic spin densities: 1 Mn 4.652563 2 Al -0.652563 Isotropic Fermi Contact Couplings Atom a.u. MegaHertz Gauss 10(-4) cm-1 1 Mn(55) 1.01027 279.17681 99.61722 93.12336 2 Al(27) 0.08368 24.38532 8.70129 8.13407 2S+1 = 3 Mulliken atomic spin densities: 1 Mn 3.409175 2 Al -1.409175 Isotropic Fermi Contact Couplings Atom a.u. MegaHertz Gauss 10(-4) cm-1 1 Mn(55) -1.86537 -1030.94712 -367.86756 -343.88694 2 Al(27) -0.53709 -313.02370 -111.69464 -104.41347 2S+1 = 1 Mulliken atomic spin densities: 1 Mn 0.100879 2 Al -0.100879 Isotropic Fermi Contact Couplings Atom a.u. MegaHertz Gauss 10(-4) cm-1 1 Mn(55) 0.75916 419.56836 149.71242 139.95294 2 Al(27) 0.03470 20.22439 7.21657 6.74613 That is, the singlet state has non-zero Fermi coupling constants (because there are excess spin sensities on atoms). But this singlet is considered to be not seen in ESR experiments. On another hand, the Mn Fermi coupling constant is zero in the singlet state of MnO4-, which is right, and there is no excess spin density on the Mn site. Now, the question is what Gaussian09 actually computes for AF singlet state? and how it can be related to ESR experiments? Thank you very much, Gennady Gutsev