ETS NOCV description of σ hole bonding

Transcription

1 ETS NOCV description of σ hole bonding an insight based on the natural orbitals for chemical valence (NOCV) combined with extended transition state method (ETS) Karol Dyduch, Mariusz Mitoraj, Artur Michalak PHD student Department of Theoretical Chemistry Faculty of Chemistry Jagiellonian University ul. R. Ingardena 3; Krakow, Poland e mail: dyduch@chemia.uj.edu.pl

2 Outline introduction: definition of HB, experimental data, Politzer works, theoretical description of HB theory: MEP, deformation density, ETS, NOCV, ETS NOCV methodology & model systems fragments definition, plot constructions results conclusions

3 introduction halogen bonding does it exist? weak, noncovalent interactions of halogen atoms R X

4 introduction halogen bonding does it exist? weak, noncovalent interactions of halogen atoms Electrophile R X close contacts with electrophiles occurred at angles of with the C X bond

5 introduction halogen bonding does it exist? weak, noncovalent interactions of halogen atoms Electrophile R X Nucleophile R X near linear interactions with nucleophiles are known as halogen bonding. close contacts with electrophiles occurred at angles of with the C X bond

6 introduction experimental data biomolecular crystal structures 4,5,6,7 tetrabromobenzotriazole displaces charged ATP from its binding site on phospho CDK2 cyclin A some bromine recognition sites have sufficient features to direct specificity, other sites have weak specificity (...) that accounts for the differential binding of TBB to pcdk2 and CK2 Ennifar, E., Bernacchi, S., Wolff, P. & Dumas, P. (2007) RNA, 13,

7 introduction experimental data superconductor Au(CN) 4 Metrangolo P, Neukirch H, Pilati T, Resnati G (2005) Acc Chem Res 38:

8 introduction experimental data superconductor Au(CN) 4 halogen bonding Metrangolo P, Neukirch H, Pilati T, Resnati G (2005) Acc Chem Res 38:

9 introduction experimental data superconductor organic conductor Ɵ (DIETS) 2 [Au(CN) 4 ] superconductor Tc= 8.6 K the highest value among the known superconductors based on unsymmetrical organic ð donors. Metrangolo P, Neukirch H, Pilati T, Resnati G (2005) Acc Chem Res 38:

10 introduction Politzer works origin of halogen bonding Molecular Electrostatic Potential (MEP) for CF 3 Br 10 anisotrophy of the charge 15 Politzer P, Lane P, Concha MC, Ma Y, Murray JS (2007) J Mol Model 13:

11 introduction Politzer and Clark origin of halogen bonding X NBO charge on X Halogen population in the σ CX NBO (%) F Cl Br I σ hole Molecular Electrostatic Potential (MEP) for CF 3 I Clark T, Hennemann M, Murray JS,Politzer P, (2007) J Mol Model 13:

12 introduction σ hole concept How does the σ hole size and depth vary for diffrent halogen atoms? How can it be described? Can halogen σ hole be alternated by different alkyl substituents on halogen atom? Does σ hole exist for other elements of periodic table?

13 theory deformation density Mitoraj, M., Michalak, A. (2007) Journal of Molecular Modeling 13 (2), pp

14 theory NOCV Natural Orbitals for Chemichal Valence ψ i = i C ij * λ i PC i = v i C i ; i =1,M ρ(r) = M /2 v k [ ψ 2 2 k (r) +ψ k (r)] = ρ k (r) k=1 M /2 k=1 Mitoraj, M., Michalak, A. (2007) Journal of Molecular Modeling 13 (2), pp

15 theory NOCV applications

16 theory ETS NOCV Mitoraj, M.P., Michalak, A., Ziegler, T. (2009) J. Chem. Theory Comput. 5 (4), pp

17 methodology DFT calculations based on the Amsterdam Density Functional (ADF2009) program in which ETS NOCV scheme was implemented. The Becke Perdew exchange correlation functional (BP86) with an inclusion of the dispersion correction (BP86 D) triple zeta STO basis containing two sets of polarization functions, based on the frozen core approximation, was adopted for all of the elements (TZ2P) Relativistic effects were included using the ZORA formalism

18 methodology The ETS NOCV analysis was applied to describe the σ hole in a series of halogen compounds (X=F, Cl, Br, I) germanium based systems GeXH 3, X=F, Cl, H. Further to characterize bonding with ammonia for these systems e.g. FC 3 X HGe 3 X (CH 3 )H n 3-n C X

19 results deformation density of dominating NOCV channel (Δρ 1 )

20 results deformation density of dominating NOCV channel (Δρ 1 )

21 results deformation density of dominating NOCV channel (Δρ 1 ) X I Br Cl F ΔE tot energy values in kcal/mol

22 results deformation density of dominating NOCV channel (Δρ 1 ) X I Br Cl F ΔE tot ΔE elstat ΔE orb energy values in kcal/mol

23 results deformation density of dominating NOCV channel (Δρ 1 ) X I Br Cl F ΔE tot ΔE elstat ΔE orb ΔE orb energy values in kcal/mol

24 results deformation density of dominating NOCV channel (Δρ 1 ) X I Br Cl F ΔE tot ΔE elstat ΔE orb ΔE Pauli ΔE disp energy values in kcal/mol

25 results deformation density of dominating NOCV channel (Δρ 1 ) X I Br Cl F ΔE tot ΔE elstat ΔE orb ΔE Pauli ΔE disp energy values in kcal/mol

26 results deformation density of dominating NOCV channel (Δρ 1 ) formation of carbon halogen σ bond

27 results deformation density of dominating NOCV channel (Δρ 1 )

28 results deformation density of dominating NOCV channel (Δρ 1 ) ΔE tot = 6.94 kcal/mol ΔE tot = 4.34 kcal/mol ΔE tot = 2.59 kcal/mol ΔE tot = 0.13 kcal/mol

29 results

30 results

31 results

32 results

33 results deformation density of dominating NOCV channel (Δρ 1 )

34 results deformation density of dominating NOCV channel (Δρ 1 )

35 results deformation density of dominating NOCV channel (Δρ 1 )

36 results deformation density of dominating NOCV channel (Δρ 1 ) X F Cl H ΔE tot

37 results deformation density of dominating NOCV channel (Δρ 1 ) X F Cl H ΔE tot ΔE elstat ΔE orb

38 results deformation density of dominating NOCV channel (Δρ 1 ) X F Cl H ΔE tot ΔE elstat ΔE orb ΔE orb

39 results deformation density of dominating NOCV channel (Δρ 1 ) X F Cl H ΔE tot ΔE elstat ΔE orb ΔE Pauli ΔE disp

40 results

41 results

42 conclusions

43 conclusions dominating contribution to the deformation density, Δρ 1 exhibits the negative value area (σ hole area) with a minimum. "size" (spatial extension of negative value) and "depth" (minium value) of the σ hole varies for different elements and is strongly affected by substituens "size" and "depth" of the ETS NOCV representation of σ hole by Δρ1 corresponds qualitatively to the positive MEP area at the extension of σ hole generating bond. σ hole bonding with ammonia is dominated by electrostatic component. However, both ΔE orb1 and Δρ 1, indicate a non negligible covalent contribution.

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46 molecule σ hole minimum (10 3 ) minimum distance MEP at minimum distance (10 2 ) CF 3 I CF 3 Br CF 3 Cl CF

47 molecule σ hole minimum (10 3 ) minimum distance MEP at minimum distance (10 2 ) C H 3 I C(CH 3 )H 2 I C(CH 3 ) 2 HI C(CH 3 ) 3 I

48 molecule σ hole min (10 3 ) minimum distance MEP at minimum distance (10 2 ) GeH 3 F GeH 3 Cl GeH

49 molecule ΔE tot ΔE disp ΔE elstat ΔE Pauli ΔE orb ΔE 1 orb F 3 C I... NH F 3 C Br... NH 3 F 3 C Cl... NH F 3 C F... NH 3 (Repulsive interaction energy; no halogen bond minimum found) H 3 C I... NH H 2 (CH 3 )C I... NH 3 H(CH 3 ) 2 C I... NH 3 (CH 3 ) 3 C I... NH

50 (DIETS ) diiodo(ethylenedithio) diselenadithiafulvalene)

51 ETS energy decomposition scheme A B

52 ETS energy decomposition scheme A B A B

53 ETS energy decomposition scheme A B A B

54 ETS energy decomposition scheme A B A B

55 ETS energy decomposition scheme A B A B