[QE-users] Lodwin Charges - analysis concern

Paolo Costa paolo.costa85 at gmail.com
Mon Mar 4 21:33:35 CET 2019


Thanks Giuseppe. I confused myself by focusing on the filling of vacant p
orbital of boron by the lone pair of nitrogen.
However, as you said, nitrogen is more electronegative than boron.


Il giorno lun 4 mar 2019 alle ore 15:11 Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> ha scritto:

>
> Well, according to the Pauling electronegativity table, boron is the
> “most positive” element in your molecule. I’m not surprised by the
> fact that it loses charge and nitrogen acquires it.
> HTH
> Giuseppe
>
>
> Paolo Costa <paolo.costa85 at gmail.com> ha scritto:
>
> > Dear Giuseppe,
> >
> > thanks for your reply!  I still do not understand the partial charge on
> > Boron and Nitrogen.
> > On BODIPY molecule the boron is tetracoordinated, thus it should have a
> > negative charge, while the nitrogens positive charge. However, now the
> > charges on B and N are the opposite.
> > Do you know why?
> >
> > Thanks again.
> >
> > Paolo
> >
> > Il giorno lun 4 mar 2019 alle ore 11:53 Giuseppe Mattioli <
> > giuseppe.mattioli at ism.cnr.it> ha scritto:
> >
> >>
> >> Dear Paolo
> >> It is just the opposite!
> >> F has 7 electrons, thus it gains ~0.34 electrons in your molecule (a
> >> partial -0.34 charge), at least by using the Lowdin partitioning. H
> >> has 1 electron and it loses ~0.24 electrons (a partial +0.24 charge).
> >> HTH
> >> Giuseppe
> >>
> >> Paolo Costa <paolo.costa85 at gmail.com> ha scritto:
> >>
> >> > Dear QE users,
> >> >
> >> > I calculated the Lodwin analysis of a BODIPY  molecule. If I
> understood
> >> > correctly, to obtain the partial charges, I have to subtract the total
> >> > charge with the anticipated number of electrons.
> >> > However, by doing so, I noticed that fluorines own positive partial
> >> charge
> >> > and hydrogen negative partial charge. I guess it should be opposite.
> >> > Am I doing something wrong?
> >> > Here the total charge, partial charge and below the coordinates of the
> >> > structure.
> >> > Thanks.
> >> >
> >> > Paolo
> >> >
> >> > Element Total Charge (from Lodwin Analysis) Partial Charge
> >> > B 2.375 -0.625
> >> > N 5.1304 0.1304
> >> > C 3.8606 -0.1394
> >> > C 3.9568 -0.0432
> >> > C 3.8606 -0.1394
> >> > N 5.13 0.13
> >> > C 3.9493 -0.0507
> >> > C 4.1393 0.1393
> >> > C 4.1395 0.1395
> >> > C 4.1326 0.1326
> >> > H 0.7777 -0.2223
> >> > C 4.1326 0.1326
> >> > H 0.7778 -0.2222
> >> > C 4.1317 0.1317
> >> > H 0.7699 -0.2301
> >> > H 0.7699 -0.2301
> >> > H 0.7702 -0.2298
> >> > C 4.1696 0.1696
> >> > C 3.893 -0.107
> >> > C 4.1698 0.1698
> >> > C 3.893 -0.107
> >> > F 7.3363 0.3363
> >> > F 7.3371 0.3371
> >> > C 4.1772 0.1772
> >> > C 4.1773 0.1773
> >> > H 0.7659 -0.2341
> >> > H 0.7542 -0.2458
> >> > H 0.7659 -0.2341
> >> > H 0.7541 -0.2459
> >> > Br 6.8341 -0.1659
> >> > Br 6.8342 -0.1658
> >> > Coordinates Structure
> >> > ATOMIC_POSITIONS (angstrom)
> >> > B       17.439513804  25.625322834  20.973045091
> >> > N       16.882879284  26.046299295  19.588650891
> >> > C       17.611417570  26.577761866  18.547638252
> >> > C       18.981473543  26.847480834  18.679994501
> >> > C       19.627787526  26.552801209  19.889428726
> >> > N       18.946313574  25.987021043  20.943865411
> >> > C       19.725048002  27.421306063  17.572506985
> >> > C       20.966884035  26.898825182  17.199885814
> >> > C       19.215753256  28.507049461  16.854272118
> >> > C       21.672475010  27.442583578  16.143363528
> >> > H       21.355632883  26.025431956  17.736034285
> >> > C       19.928670364  29.053299943  15.803815775
> >> > H       18.258129871  28.943219988  17.161656267
> >> > C       21.158317994  28.523222279  15.442553524
> >> > H       22.636034674  27.008532757  15.854570202
> >> > H       19.522552264  29.915432507  15.263514196
> >> > H       21.720598110  28.955759334  14.608217851
> >> > C       16.755699795  26.709363581  17.431198041
> >> > C       15.626387791  25.867384471  19.148113264
> >> > C       20.961586499  26.780304609  20.296707620
> >> > C       19.816776014  25.851045266  21.957660446
> >> > F       16.805285541  26.335760829  21.963860569
> >> > F       17.299909483  24.267118687  21.135505695
> >> > C       15.503982739  26.269192895  17.814655089
> >> > C       21.080018363  26.329060350  21.596854814
> >> > H       21.734290190  27.249658971  19.687403597
> >> > H       21.957537020  26.337873981  22.242787824
> >> > H       17.056054376  27.071432630  16.447685129
> >> > H       14.590507636  26.219539022  17.222738922
> >> > Br      19.337204180  25.130245441  23.585145081
> >> > Br      14.294364702  25.162791887  20.209885331
> >> > --
> >> > Paolo Costa, Ph.D.
> >> > Postdoctoral Researcher
> >> > Department of Chemistry and Biomolecular Sciences
> >> > University of Ottawa
> >> > 10 Marie Curie, Ottawa, ON K1N 6N5, Canada
> >> > Room number: DRO 326 (D'Iorio Hall)
> >>
> >>
> >>
> >> GIUSEPPE MATTIOLI
> >> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >> Via Salaria Km 29,300 - C.P. 10
> >> I-00015 - Monterotondo Scalo (RM)
> >> Mob (*preferred*) +39 373 7305625
> >> Tel + 39 06 90672342 - Fax +39 06 90672316
> >> E-mail: <giuseppe.mattioli at ism.cnr.it>
> >>
> >> _______________________________________________
> >> users mailing list
> >> users at lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
> >>
> >
> >
> > --
> > Paolo Costa, Ph.D.
> > Postdoctoral Researcher
> > Department of Chemistry and Biomolecular Sciences
> > University of Ottawa
> > 10 Marie Curie, Ottawa, ON K1N 6N5, Canada
> > Room number: DRO 326 (D'Iorio Hall)
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
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