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 < [email protected]> 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 <[email protected]> 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 < > > [email protected]> 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 <[email protected]> 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: <[email protected]> > >> > >> _______________________________________________ > >> users mailing list > >> [email protected] > >> 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: <[email protected]> > > _______________________________________________ > users mailing list > [email protected] > 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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