A Chemical Bond From the Natural Orbitals for Chemical Valence (NOCV) Perspective. Mariusz P. Mitoraj

Transcription

1 Bonding Analysis Workshop 2015, 05, 18-22, Marburg A hemical Bond From the Natural Orbitals for hemical Valence (NOV) Perspective Mariusz P. Mitoraj Jagiellonian University racow, Poland Department of Theoretical hemistry

2 Experimental visualization chemical bond? Bonding Analysis Workshop 2015, 05, 18-22, Marburg Atomic Force Microscopy Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy J. Zhang et al., Science, 2013, 342,

3 Experimental seeing the chemical reaction at quantum level? Bonding Analysis Workshop 2015, 05, 18-22, Marburg

4 Examples of theoretical quantities for visualization of chemical bond

5 Quantum Theory of Atoms in Molecules (QTAIM) by Richard Bader *start- electron (charge) density from wavefunction (ψ) (N electrons, with positions x 1, x 2,.x N ): dihydrogen charge density is delocalized over the whole molecule, how then extract any information about bonding between selected atoms - or -? ethane

6 Quantum Theory of Atoms in Molecules (QTAIM) by Richard Bader *construct the essian matrix (second derivatives of density) and perform diagonalization to obtain various critical points.

7 Quantum Theory of Atoms in Molecules (QTAIM) by Richard Bader, ethane( 2 6 ),water( 2 O), sodium chloride (Nal), benzene( 6 6 ) examples a.u a.u. Lap BP =-0.31a.u. (covalent bond) 0.32a.u. O l 0.03a.u. Lap BP =+0.16a.u. Ionic bond) Na a.u. Ring-ritical-Point RP (3,+1) π-electrons Two eigenvalues positive (in plane axes) and one negative (perpendicular)

8 Examples of theoretical quantities for visualization of chemical bond Bonding Analysis Workshop 2015, 05, 18-22, Marburg

9 Bonding Analysis Workshop 2015, 05, 18-22, Marburg Formation of chemical bond in 2 ρ based picture 1. Start from promolecular state (atom/fragments) ρ 2 ρ =1s 2 ρ =1s 2 ρ = ρ 2 2ρ Deformation density (Differential density) (1) qualitative data by inspection of the sign of ρ: negative (outflow), positive (inflow) of density due to bond formation

10 Bonding Analysis Workshop 2015, 05, 18-22, Marburg Experimental visualization of chemical bond vs calculated ρ Tetramer of 8-hydroxyquinoline connected via hydrogen bonds ρ Red-outflow Blue-inflow N O O O O Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy J. Zhang et al., Science, 2013, 342, N N ρ=ρ molecule - ρ 1 - ρ 2 -ρ 3 -ρ 4

11 Bonding Analysis Workshop 2015, 05, 18-22, Marburg Formation of chemical bond in hem-o; ρ based picture In the A/B resolution (fragment / ligand) : ρ = ρ AB ( r) ρ ( r) ρ ( r) A B

12 Formation of chemical bond in hem-o; ρ based picture difficult to extract σ- or π-contributions of Fe- bond

13 NOV s ( The Natural Orbitals for hemical Valence (NOV) ψ i = i NOV s also decompose the deformation density ρ: ρ(r) ij * λ = ) diagonalize the deformation density matrix: i P i = v i i ; i =1, M where P=P-P 0, density matrix of the combined molecule, P 0 - density matrix of the considered molecular fragments. NOV s are in pairs: ρ(r) = M / 2 M k= 1 v 2 k ψk (r) v k [ ψ 2 2 k (r) +ψ k (r)] = ρ k (r) k=1 M / 2 k=1 Radoń, M. Theor hem Account 2008, 120,337. useful qualitative data by inspection of the sign of ρ: negative (outflow), positive (inflow) of density Mitoraj, M.; Michalak, A. Organometallics 2007, 26(26); 6576., Michalak, A.; Mitoraj, M.; Ziegler, T. J. Phys. hem. A. 2008, 112 (9), 1933, Mitoraj, M.; Michalak, A. J. Mol. Model., 2008, 14, 681, Mitoraj, M.; Zhu,.; Michalak, A.; Ziegler, T. 2008, International Journal of Quantum hemistry, DOI: /qua , Mitoraj, M.; Michalak, A. J. Mol. Model. 2008, 14, 681.

14 The contours of the deformation density ( ρ) and the contributions from the pairs of complementary orbitals for the heme/o system n ρ( r) = ν ϕ i= 1 i 2 i ( r) donation back donation back donation

15 A combination of ETS/EDA and NOV - (ETS-NOV) -D e = E total = E dist + E elstat + E Pauli + E orb ETS/EDA: NOV: orb = E P orb ETS-NOV: λ N / 2 k= 1 μ orb λμ F TS λμ 2 2 k (r) + ψk(r)] = N / 2 ρ (r) = v [ ψ ρ k k= 1 k (r) electronic factor E orb = Tr( P orb F TS ) = Tr ( + P orb + F TS ) = N / 2 k= 1 v k [ F TS k, k + F TS k, k ] = N / 2 k= 1 E orb k M / 2 TS TS Eorb = vk[ F k + F k ] = E k= 1 M / 2 k k orb Energetic estimation of ρ k Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler A combined charge and energy decom- Position scheme for bond analysis J. hem. Theory omput., 2009, 5 (4), pp

16 Dative bonds systems with symmetry (O) 5 r= 2 donation back donation Donor/acceptor properties of ligands for Ni(N 3 ) 3 X complexes: σ:n - > P 3 > N 3 > 2 4 > S > O > N 2 > NO + π:no + > S > O > N 2 > 2 4 > P 3 > N - > N 3 Mitoraj Mariusz, Michalak A (2007) Donor-Acceptor Properties of Ligands from the Natural Orbitals for hemical Valence Organometallics, 26,

17 Bonding Analysis Workshop 2015, 05, 18-22, Marburg Experimental visualization of chemical bond vs calculated ρ Tetramer of 8-hydroxyquinoline connected via hydrogen bonds ρ N O O O O Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy J. Zhang et al., Science, 2013, 342, N N ρ=ρ molecule - ρ 1 - ρ 2 -ρ 3 -ρ 4

18 ETS-NOV- tetra-8-hydroxyquinoline ρ 1 ρ 2 O N O O Eorb(1)=-12.2 kcal/mol Eorb(2)=-6.3kcal/mol

19 ETS-NOV- tetra-8-hydroxyquinoline Δρ 3 Δρ 4 O O N N Eorb(3)=-2.0 kcal/mol Eorb(4)=-1.0 kcal/mol

20 Dative Bond N 3 B 3 - alculations Define closed shell fragments, N 3 and B 3 Run SP calculations to get the fragment MO s Run SP ETS-NOV calculations for whole molecule in the basis of previously calculated fragment MO s In order to perform EDA/ETS in NOV resolution one must add the keywords: ETSNOV PRINT ETSLOWDIN and NOSYM must be used

21 Dative Bond N 3 B 3 - alculations M.Mitoraj J. Phys. hem. A, 2011, 115 (51), pp

22 Inter-Molecular-ydrogen Bonds Adenine-Thymine E orb =-22.0 N σ*(-n) kcal/mol, (BP86/TZ2P) A-T E int E orb E Pauli 38.7 E prep 2.1 E elstat total - experiment 99 E total other theoretical results O σ*(-n) O- -N covalency! Rafał Kurczab, Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler J. Phys. hem. A,2010, 114, 8581.

23 Bonding Analysis Workshop 2015, 05, 18-22, Marburg ydrogen Bond A-T alculations Define closed shell fragments, Adenine and Thymine Run SP calculations to get the fragment MO s Run SP ETS-NOV calculations for whole molecule in the basis of previously calculated fragment MO s

24 ovalent bonds = 2 Ge 2 =Ge 2 3 3

25 Quadruple bond; Re 2 l 8 2- σ[-84.3 kcal/mol] π1[-65.5 kcal/mol] π2[-65.5 kcal/mol] δ[-1.3 kcal/mol]

26 Ethane Built from two methyl radicals 1. Define 3 regions (uneven number of electrons); 2. Run SP RESTRITED! alculations for 3 fragments to get the fragment MO s; (1/2α + 1/2β electrons for SOMO of 3 ) 3. Use fragoccupations keyword in order to keep the right occupations for each 3 fragoccupations f1 A 5 // 4 subend f2 A 4 // 5 subend End 4. Run SP ETS-NOV calculations for whole molecule in the basis of previously calculated fragment MO s -alpha-and beta-nov s

27 Agostic intramolecular R---Metal interaction Ni-diimine cationic Brookhart model catalyst β - polarization Ni- α α - β Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler On the Nature of the Agostic Bond between Metal enters and β-ydrogen Atoms in Alkyl omplexes. An Analysis Based on the Extended Transition State Method and the Natural Orbitals for hemical Valence Scheme (ETS-NOV) Organometallics, 2009, 28 (13), pp 3727

28 Role of Agostic Interaction in ydride Transfer Release of Ethene Molecule W

29 ETS-NOV in a description chemical reactions Diels Alder cycloaddition: ethene + 1,3-butadiene ρ 1 trajectory Mitoraj MP, Parafiniuk M, Srebro M, andzlik M, Buczek, A, Michalak A JMolModel, 2011, 17,

30 Dehydrogenation of Ammonia Borane by Ru-complex

31 Mechanism obtained from DFT/PMD calculations E ~ 13 kcal/mol AB binding concerted transfers to NMe 2 formation Organometallics, 2013, 32, R

32 Ammonia Borane binding to the Ru-catalyst AB binds to NMe of the catalyst by B- and B-π interactions

33 alogen Bonding F 3 I---N 3 from ETS-NOV perspective ETSNOV(red-outflow,blue-inflow) F N I F F harge outflow, increase positive charge N-I covalency -8.3 kcal/mol N σ*(-f) charge accumulation, increase s-character (pointed out by prof. Grabowski) Grabowski S. hem. Rev., 2011, 111 (4), pp

34 alogen Bonding F 3 I---N 3 from ETS-NOV perspective Domination of the electrostatic factor is due to the presense of σ-hole on iodine atom: F I F F (Politzer P, Lane P, oncha M, Ma Y, Murray J (2007) JMolModel, 13, 305, An Overview of alogen Bonding

35 Mitoraj M, Michalak A JMolModel, 2013, DOI /s , Dyduch K., Mitoraj M, Michalak A, JMolModel, 2013, 19, F F I F Electrostatic potential picture ETS-NOV perspective, σ-hole σ-hole F F F I ETS-NOV picture σ(-f) bond

36 ands-on-session agenda Exercise1. Getting started with the simple bond formed between ammonia and borane typical donor acceptor bond 3 N B 3. Exercise2. Why ammonia (with one lone electron pair) can form the bond with iodine (containing three lone pairs)? ( 3 N IF 3 ) Exercise4. Analysis of carbon carbon bond in ethane Exercise 5. Analysis of = bond in ethene Exercise 6. Analysis of quadruple bond between Re atoms in [l 4 ReRel 4 ] 2- (l 4 Re + Re l 4 ) (otton Re complex). Exercise7. Analysis of weak homopolar dihydrogen interaction formed between closed shell two dodecahedran hydrocarbon units:

37 Exercise8. Interaction between four monomers of tetra-hydroxoquinoline bonded via O O hydrogen bonds. All necessary input files (quin1.in, quin2.in, quin3.in, quin4.in and Quin-tetramer- NOV.in) are in the directory /home/baw/baw-workshop/mitoraj/exercise8. ompare the most important NOV-deformation density channels to the experimental picture of bonding emerging from the tunneling microscope: (Science, 2013, 342, )

38 Thank You very much for Your Attention! Bonding Analysis Workshop 2015, 05, 18-22, Marburg