1 / 27

A pplications of ETS-NOCV method in description of various t ypes of chemical bonds

A pplications of ETS-NOCV method in description of various t ypes of chemical bonds. Mariusz P. Mitoraj. Jagiellonian University Cracow, Poland Department of Theoretical Chemistry. ADF webinar, Kraków-rest-of-the-world, 28th Feb., 2014.

yaron
Download Presentation

A pplications of ETS-NOCV method in description of various t ypes of chemical bonds

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Applications of ETS-NOCVmethodin description of various types of chemicalbonds MariuszP. Mitoraj Jagiellonian University Cracow, Poland Department of Theoretical Chemistry ADF webinar, Kraków-rest-of-the-world, 28th Feb., 2014

  2. Examples of theoretical quantities for visualization of chemical bond ADF webinar, Kraków-restoftheworld, 28th Feb., 2014

  3. Formation of chemical bond in H2 –  based picture 1. Start from promolecular state (atom/fragments) H H H2 H=1s2 H=1s2 H H Deformation density (Differential density) (1) qualitative data by inspection of the sign of : negative (outflow), positive (inflow) of density due to bond formation ADF webinar, Kraków-restoftheworld, 28th Feb., 2014

  4. NOCV’s ( ) diagonalize the deformation density matrix: where P=P-P0 , density matrix of the combined molecule, P0- density matrix of the considered molecular fragments. NOCV’s also decompose the deformation density : useful qualitative data by inspection of the sign of : negative (outflow), positive (inflow) of density NOCV’s are in pairs: Radoń, M. Theor Chem Account 2008, 120,337. The Natural Orbitals for Chemical Valence (NOCV) Mitoraj, M.; Michalak, A. Organometallics 2007, 26(26); 6576., Michalak, A.; Mitoraj, M.; Ziegler, T. J. Phys. Chem. A. 2008, 112 (9), 1933, Mitoraj, M.; Michalak, A. J. Mol. Model., 2008, 14, 681, Mitoraj, M.; Zhu, H.; Michalak, A.; Ziegler, T. 2008, International Journal of Quantum Chemistry, DOI: 10.1002/qua.21910., Mitoraj, M.; Michalak, A. J. Mol. Model.2008, 14, 681.

  5. donation back donation back donation The contours of the deformation density () and the contributions from the pairs of complementary orbitals for the heme/CO system q = 0.74 q = 1.04

  6. -De=Etotal= Edist + Eelstat + EPauli + Eorb ETS: NOCV: ETS-NOCV: Energetic estimation of k A combination of ETS and NOCV - (ETS-NOCV) electronic factor Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler „A combined charge and energy decom- Position scheme for bond analysis” J. Chem. Theory Comput., 2009, 5 (4), pp 962–975.

  7. (CO)5Cr=CH2 donation :CN- > PH3>NH3>C2H4 >CS>CO > N2>NO+ :NO+>CS>CO > N2>C2H4>PH3>CN-> NH3 for Ni(NH3)3 X complexes: back donation Donor/acceptor properties of ligands Dativebonds – systems with symmetry Mitoraj Mariusz, Michalak A (2007) „ Donor-Acceptor Properties of Ligands from the Natural Orbitals for Chemical Valence” Organometallics, 26, 6576-6580

  8. Dative Bond NH3BH3 - Calculations • Defineclosedshellfragments, NH3 and BH3 • Run SP calculations to get the fragment MO’s • Run SP ETS-NOCV calculations for wholemolecule in the basis • of previouslycalculated fragment MO’s

  9. Dative Bond NH3BH3 - Calculations M.Mitoraj J. Phys. Chem. A, 2011, 115 (51), pp 14708–14716

  10. Crystal of AmmoniaBorane, NH3BH3 M.Mitoraj J. Phys. Chem. A, 2011, 115 (51), pp 14708–14716

  11. Adenine-Thymine Inter-Molecular-Hydrogen Bonds Eorb=-22.0 Os*(H-N) Ns*(H-N) O-H Rafał Kurczab, Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler J. Phys. Chem. A,2010, 114, 8581. H-N covalency!

  12. Hydrogen Bond A-TCalculations • Defineclosedshellfragments, Adenine and Thymine • Run SP calculations to get the fragment MO’s • Run SP ETS-NOCV calculations for wholemolecule in the basis • of previouslycalculated fragment MO’s ADF webinar, Kraków-restoftheworld, 28th Feb., 2014

  13. H3CCCCH3 GeH2=GeH2 CH2=CH2 CH3-CH3 Covalent bonds

  14. 1[-65.5 kcal/mol] [-84.3 kcal/mol] 2[-65.5 kcal/mol] [-1.3 kcal/mol] Quadruple bond; Re2Cl82-

  15. Typical-Multiple bonds-TM Cr2, formally sixtuple bond, bCr2-Nal = 6.01 Etotal=-31.3kcal/mol Eorb=-242.7 Esteric=211.4 Eorb=-242.7 kcal/mol J. Chem. Theory Comput., 2009, 5 (4), pp 962–975.

  16. EthaneBuilt from twomethylradicals 1. Define CH3 regions (uneven number of electrons); 2. Run SP RESTRICTED ! Calculations for CH3 fragments to get the fragment MO’s; (1/2 + 1/2 electrons for SOMO of CH3) 3. Use fragoccupations keyword in order to keep the right occupations for each CH3 fragoccupations f1 A 5 // 4 subend f2 A 4 // 5 subend End 4. Run SP ETS-NOCV calculations for whole molecule in the basis of previously calculated fragment MO’s -alpha-and beta-NOCV’s

  17. Typical-Multiplebonds-TM Cr2, sextuple bond, bCr2-Nal = 6.01 Etotal=-31.3kcal/mol Eorb=-242.7 Esteric=211.4 Eorb=-242.7 kcal/mol J. Chem. Theory Comput., 2009, 5 (4), pp 962–975.

  18. Cr2Built from two Cr+Cr 1. Define Cr regions (unevennumber of electrons); 2. Run SP RESTRICTED ! Calculations for Cr fragments usingOCCUPATIONkeyword (A 18 1 1 1 1 1 1); Should be like Cr but itisCr 6* (1/2 + 1/2) so we must: 3. Usefragoccupationskeyword in order to keep the rightoccupations for each Cr. fragoccupations Region_1 A 15//9 subend Region_2 A 9//15 subend End 4. Run SP ETS-NOCV calculations for wholemolecule in the basis of previouslycalculated fragment MO’s Cr Cr

  19. Better Fragment MO’s from unrestriced run: advanced ’manual’ usage ADF uses in principle only ‚rectricted’ fragments, however, one might cheat him 1. Run open shell calculations for a given fragment; 2. Save tape21  ascii (dmpkf) copy the final MO’s (from the section Eig-CoreSFO_A, MO’s expressed in SFO); 3. Run fragment calculations by setting SCF=0 wrong MO’s save tape21asciifind Eig-CoreSFO_A section, then: 4. Take MO’s and occupations, energies, from step 2 and paste them to Tape21 from step 3…..it gives you right fragment MO’s Transform asciibinary(udmpkf); 5. Rerun final ETSNOCV calculations (do not recalculate the fragments!)

  20. Ni-diimine cationic Brookhart model catalyst Agostic intramolecular RH---Metal interaction Cb-H polarization Ca-Cb Ni-Ca Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler „On the Nature of the Agostic Bond between Metal Centers and -Hydrogen Atoms in Alkyl Complexes. An Analysis Based on the Extended Transition State Method and the Natural Orbitals for Chemical Valence Scheme (ETS-NOCV)” Organometallics, 2009, 28 (13), pp 3727

  21. Halogen Bonding CF3I---NH3 from ETS-NOCV perspective Charge outflow, increase positive charge ETSNOCV(red-outflow,blue-inflow) -8.3 kcal/mol N-I covalency Ns*(C-F) charge accumulation, increase s-character (pointed out by prof. Grabowski) Grabowski S. Chem. Rev., 2011, 111 (4), pp 2597–2625

  22. Halogen Bonding CF3I---NH3 from ETS-NOCV perspective Domination of the electrostatic factor is due to the presense of σ-hole on iodine atom: I F F F (Politzer P, Lane P, Concha MC, Ma Y, Murray J (2007) JMolModel, 13, 305, „An Overview of Halogen Bonding”

  23. Halogen Bonding CF3I---NH3 from ETS-NOCV perspective Prof. Politzer, „Program & Book of Abstracts”, MIB 2011, „….The weakness of this interpretation (electrostatic) is that it is simple and straightforward, and therefore is viewed by some with suspicion. s(C-F) bond s-hole I F F Electrostatic potential picture F Charge Anisotropy ETS-NOCV picture

  24. Can ETS-NOCV discriminate between halogen and hydrogen bonding within the same molecule? Anion receptor based on urea, which involve hydrogen and halogen Bonding at the same time|: Chudzinski, et all, JACS, 2011, 133, 10559

  25. Can ETS-NOCV discriminate between halogen and hydrogen bonding within the same molecule? -22.3 kcal/mol -6.3 kcal/mol Yes: ETS-NOCV can separate halogen and hydrogen connections

  26. Cl- / rest • Defineclosedshellfragments, Cl minus + rest of the complex • Run SP calculations to get the fragment MO’s • Run SP ETS-NOCV calculations for wholemolecule in the basis • of previouslycalculated fragment MO’s ADF webinar, Kraków-restoftheworld, 28th Feb., 2014

  27. Thank You very much for Your Attention! ADF webinar, Kraków-restoftheworld, 28th Feb., 2014

More Related