Prediction of spectroscopic parameters for bio-organic and bio-inorganic intermediates in complex systems
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1 Prediction of spectroscopic parameters for bio-organic and bio-inorganic intermediates in complex systems Erik Donovan Hedegård Department of Physics, Chemistry and Pharmacy University of Southern Denmark October 11, 2013 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
2 Acknowledgements University of Southern Denmark, Odense, Denmark Jacob Kongsted and Hans Jørgen Aagaard Jensen Jógvan Magnus Haugaard Olsen Nanna Holmgaard List Morten Nørby Pedersen Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland Stefan Knecht CNRS, Université de Strasbourg, Strasbourg, France Emmanuel Fromager Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
3 Topics Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
4 Topics Part I Polarizable Embedding with multireference wave functions Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
5 Topics Part I Polarizable Embedding with multireference wave functions Part II Structures and spectroscopy of [Fe]-hydrogenase Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
6 Topics Part I Polarizable Embedding with multireference wave functions Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
7 Polarizable Embedding: General Ideas Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
8 Polarizable Embedding: General Ideas Split up the total system Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
9 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
10 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Parameters from first principles Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
11 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Parameters from first principles DFT and CC problems Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
12 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Parameters from first principles DFT and CC problems Multireference character Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
13 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Parameters from first principles DFT and CC problems Multireference character Double Excitations (DFT) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
14 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Parameters from first principles DFT and CC problems Multireference character Double Excitations (DFT) MCSCF problems Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
15 Polarizable Embedding: General Ideas Split up the total system QM region: until now: DFT or CC Environment: Parameterized Parameters from first principles DFT and CC problems Multireference character Double Excitations (DFT) MCSCF problems Lack of dynamical correlation Overestimation of excitation energies Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
16 When do we need MCSCF wave functions? Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
17 When do we need MCSCF wave functions? Large mixing of several electronic configurations Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
18 When do we need MCSCF wave functions? Large mixing of several electronic configurations Example: Carotenoid derivatives Kato et al., Nature, (2012), 482, 369. Slamovits et al., Nature Comm., (2011), 2, 183. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
19 When do we need MCSCF wave functions? Large mixing of several electronic configurations Example: Carotenoid derivatives Kato et al., Nature, (2012), 482, 369. Slamovits et al., Nature Comm., (2011), 2, 183. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
20 When do we need MCSCF wave functions? Large mixing of several electronic configurations Example: Carotenoid derivatives Kato et al., Nature, (2012), 482, 369. Slamovits et al., Nature Comm., (2011), 2, 183. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
21 When do we need MCSCF wave functions? Large mixing of several electronic configurations Example: Carotenoid derivatives Kato et al., Nature, (2012), 482, 369. Slamovits et al., Nature Comm., (2011), 2, 183. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
22 When do we need MCSCF wave functions? Large mixing of several electronic configurations Example: Carotenoid derivatives Kato et al., Nature, (2012), 482, 369. Slamovits et al., Nature Comm., (2011), 2, 183. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
23 Scaling in quantum chemistry HF scales as N 4 with number of basis functions Channel-rhodopsin: 5000 atoms basis functions (6-31G ) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
24 Outline (part I) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
25 Outline (part I) Embedding with MCSCF wave functions Incorporation of embedding operators in MCSCF ansatz E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, N. H. List, H. J. Aa. Jensen, J Kongsted and E. D. Hedegård, Advances in Quantum Chemistry, (2013), 66, 195. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
26 Outline (part I) Embedding with MCSCF wave functions Incorporation of embedding operators in MCSCF ansatz E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, N. H. List, H. J. Aa. Jensen, J Kongsted and E. D. Hedegård, Advances in Quantum Chemistry, (2013), 66, 195. Dynamical correlation with DFT-MCSCF hybrid (MC-srDFT) Benchmark studies in vacuum. Can this method be used? E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
27 Outline (part I) Embedding with MCSCF wave functions Incorporation of embedding operators in MCSCF ansatz E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, N. H. List, H. J. Aa. Jensen, J Kongsted and E. D. Hedegård, Advances in Quantum Chemistry, (2013), 66, 195. Dynamical correlation with DFT-MCSCF hybrid (MC-srDFT) Benchmark studies in vacuum. Can this method be used? E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) MC-srDFT with polarizable embedding What is the effect from the protein in the retinal chromophore? E. D. Hedegård, S. Knecht, J. M. H. Olsen, H. J. Aa. Jensen, J. Kongsted, JCP, (in prep.) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
28 Polarizable Embedding energy contributions Total interaction energy for a polarizable embedded system E tot = E QM + E pe Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
29 Polarizable Embedding energy contributions Polarizable Embedding energy E pe = E es + E ind V es = q(r s) r r s γ ( ) 1 µ γ γ r r s + Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
30 Polarizable Embedding energy contributions Polarizable Embedding energy E pe = E es + E ind V es = q(r s) r r s γ ( ) 1 µ γ γ r r s + Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
31 Polarizable Embedding energy contributions Polarizable Embedding energy E pe = E es + E ind V es = q(r s) r r s γ ( ) 1 µ γ γ r r s + E ind = 1 2 ˆF R ˆF Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
32 Polarizable Embedding effective operator Total interaction energy for a polarizable embedded system E tot = E QM + E pe Polarizable Embedding Energy E pe = E es + E ind Definition The polarizable embedding potential ˆv pe = ˆV e + R 0 ˆF 0 ˆF e R = J. M. Olsen, K. Aidas and J. Kongsted, JCTC, (2010), 6, a 1 11 T (2) 1S.... T (2) 1S a 1 SS Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
33 Polarizable Embedding for proteins Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
34 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
35 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
36 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
37 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
38 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
39 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
40 Polarizable Embedding for proteins Proteins: Amino acids linked by peptide bonds Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
41 The additional PE contributions ˆv pe = ˆV e + R 0 ˆF 0 ˆF e Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
42 The additional PE contributions Definition ˆv pe = ˆV e + R 0 ˆF 0 ˆF e The electronic gradient vector (g) and Hessian (H) matrix Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
43 The additional PE contributions Definition ˆv pe = ˆV e + R 0 ˆF 0 ˆF e The electronic gradient vector (g) and Hessian (H) matrix g g tot = g vac + g pe Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
44 The additional PE contributions Definition ˆv pe = ˆV e + R 0 ˆF 0 ˆF e The electronic gradient vector (g) and Hessian (H) matrix g g tot = g vac + g pe H H tot = H vac + H pe Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
45 The additional PE contributions Definition The electronic gradient vector (g) and Hessian (H) matrix g g tot = g vac + g pe H H tot = H vac + H pe Definition The response function Â, ˆV ω = A [1] ( E [2] ωs [2]) 1 V ω[1] E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
46 The additional PE contributions Definition The electronic gradient vector (g) and Hessian (H) matrix g g tot = g vac + g pe H H tot = H vac + H pe Definition The response function Â, ˆV ω = A [1] ( E [2] ωs [2]) 1 V ω[1] ( E [2] E [2] tot = E[2] vac + E [2] pe E [2] A B vac = B A ) E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
47 Proof-of-principle calculation: Uracil Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
48 Proof-of-principle calculation: Uracil 238 water molecules (714 atoms) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
49 Proof-of-principle calculation: Uracil 238 water molecules (714 atoms) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
50 Proof-of-principle calculation: Uracil 238 water molecules (714 atoms) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
51 Proof-of-principle calculation: Uracil 238 water molecules (714 atoms) 120 MD snapshots Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
52 Proof-of-principle calculation: Uracil 238 water molecules (714 atoms) 120 MD snapshots Vertical excitation energies (in ev) for uracil. Environment CAS(10,10) CAM-B3LYP Exp. π π Gas phase Water Shift n π Gas phase Water n.r. Shift L. B. Clark, G. G. Peschel, I. Tinoco Jr., JCP, (1965), 69, M. Daniels, W. Hauswirth, Science, (1971), 171, 675. M. Fujii, T. Tamura, N. Mikami, M. Ito, CPL, (1986), 126, 583. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
53 MC-srDFT vacuum benchmark: Organic dyes O 1 H O 1 O O 1 H O 3 C 1 N1 C 2 N 2 C 1 N1 C 2 N2 C 1 N1 C 2 N 2 C 3 N 3 H O 2 H H O 2 H Dipeptide β-dipeptide Tripeptide N NC N HCl N-phenylpyrrole (PP) 4-(N,N-dimethylamino) benzonitrile (DMABN) Hydrogen chloride Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
54 MC-srDFT vacuum benchmark: Organic dyes Split the electronic repulsion in a short-range and a long-range part W ee = W sr,µ ee + W lr,µ ee W lr,µ ee = erf(µr 12) r 12 E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
55 MC-srDFT vacuum benchmark: Organic dyes Split the electronic repulsion in a short-range and a long-range part W ee = W sr,µ ee + W lr,µ ee W lr,µ ee = erf(µr 12) r 12 Area (normalized) 2,0 1,5 1,0 0,5 TD-CAM-B3LYP TD-B3LYP TD-MC-srPBE 0, Av. Error (ev) E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
56 MC-srDFT vacuum benchmark: Organic dyes Split the electronic repulsion in a short-range and a long-range part W ee = W sr,µ ee + W lr,µ ee W lr,µ ee = erf(µr 12) r 12 Area (normalized) 2,0 1,5 1,0 0,5 TD-CAM-B3LYP TD-B3LYP TD-MC-srPBE TD-MC-sr B3LYP CAM-B3LYP Mean MAD Results from total 24 excitations Comparison with CASPT2 0, Av. Error (ev) E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
57 MC-srDFT vacuum benchmark calculations (cont.) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
58 MC-srDFT vacuum benchmark calculations (cont.) N H Excitation E (ev) Osc. Str. Exp. S 0 S S 0 S Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
59 MC-srDFT vacuum benchmark calculations (cont.) N H Excitation E (ev) Osc. Str. Exp. S 0 S S 0 S Config. 3: Double excitation between HOMO-LUMO π π Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
60 The retinal chromophore: Influence of the protein Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
61 The retinal chromophore: Influence of the protein What is the effect of the protein on the excitation? Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
62 The retinal chromophore: Influence of the protein What is the effect of the protein on the excitation? Excitation Environment E (ev) Osc. Str. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
63 The retinal chromophore: Influence of the protein What is the effect of the protein on the excitation? Excitation Environment E (ev) Osc. Str. S 0 S 1 Gas-phase N H Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
64 The retinal chromophore: Influence of the protein What is the effect of the protein on the excitation? Excitation Environment E (ev) Osc. Str. S 0 S 1 Gas-phase Protein (m2p0) N H Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
65 The retinal chromophore: Influence of the protein What is the effect of the protein on the excitation? Environment important to fine-tune absorption range Excitation Environment E (ev) Osc. Str. S 0 S 1 Gas-phase Protein (m2p0) N H Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
66 The retinal chromophore: Influence of the protein What is the effect of the protein on the excitation? Environment important to fine-tune absorption range Excitation Environment E (ev) Osc. Str. S 0 S 1 Gas-phase Protein (m2p0) N H Experimental value: 2.70 ev Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
67 Conclusions (part I) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
68 Conclusions (part I) Embedding with MCSCF wave functions Embedding operators have been described in an MCSCF framework (implemented in DALTON) E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, N. H. List, H. J. Aa. Jensen, J Kongsted and E. D. Hedegård, Advances in Quantum Chemistry, (2013), 66, 195. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
69 Conclusions (part I) Embedding with MCSCF wave functions Embedding operators have been described in an MCSCF framework (implemented in DALTON) E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, N. H. List, H. J. Aa. Jensen, J Kongsted and E. D. Hedegård, Advances in Quantum Chemistry, (2013), 66, 195. Dynamical correlation with MC-srDFT Significant improvement of excitation energies E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
70 Conclusions (part I) Embedding with MCSCF wave functions Embedding operators have been described in an MCSCF framework (implemented in DALTON) E. D. Hedegård, N. H. List, H. J. Aa. Jensen and J. Kongsted, JCP, (2013), 139, N. H. List, H. J. Aa. Jensen, J Kongsted and E. D. Hedegård, Advances in Quantum Chemistry, (2013), 66, 195. Dynamical correlation with MC-srDFT Significant improvement of excitation energies E. D. Hedegård, F. Heiden, S. Knecht, E. Fromager, H. J. Aa. Jensen, JCP, (Accepted) MC-srDFT with polarizable embedding Protein effects can now be studied for multiconfigurational systems and for double excitations E. D. Hedegård, S. Knecht, J. M. H. Olsen, H. J. Aa. Jensen, J. Kongsted, JCP, (in prep.) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
71 Topics Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
72 Topics Part II Structures and spectroscopy of [Fe]-hydrogenase Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
73 Hydrogenase Enzymes (Collaboration with Ulf Ryde) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
74 Hydrogenase Enzymes (Collaboration with Ulf Ryde) H 2 H + + H Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
75 Hydrogenase Enzymes (Collaboration with Ulf Ryde) H 2 H + + H Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
76 Hydrogenase Enzymes (Collaboration with Ulf Ryde) H 2 H + + H Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
77 Hydrogenase Enzymes (Collaboration with Ulf Ryde) H 2 H + + H What is the binding site (and/or binding mode) of H 2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
78 The [Fe]-hydrogenase enzyme: The substrate Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
79 The [Fe]-hydrogenase enzyme: The substrate [Fe]-hydrogenase is the only hydrogenase which has an (additional) substrate Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
80 The [Fe]-hydrogenase enzyme: The substrate [Fe]-hydrogenase is the only hydrogenase which has an (additional) substrate Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
81 The [Fe]-hydrogenase enzyme: The substrate [Fe]-hydrogenase is the only hydrogenase which has an (additional) substrate The enzyme is inactive without this substrate Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
![The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård](/docs-images/94/118092769/images/82-0.jpg "(SDU) Fall Meeting Chemsoc (theory) October 11, 2013 20 / 28")
82 The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
83 The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
84 The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
![The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård](/docs-images/94/118092769/images/85-0.jpg "(SDU) Fall Meeting Chemsoc (theory) October 11, 2013 20 / 28")
85 The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
![The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård](/docs-images/94/118092769/images/86-0.jpg "(SDU) Fall Meeting Chemsoc (theory) October 11, 2013 20 / 28")
86 The [Fe]-hydrogenase enzyme: Mechanism Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
87 Structures from X-ray Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
88 Structures from X-ray Open form structure with active site has been obtained Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
89 Structures from X-ray Open form structure with active site has been obtained Closed form structure has also been obtained but without the active site Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
90 Structures from X-ray Open form structure with active site has been obtained Closed form structure has also been obtained but without the active site Further problems: A mutant (Cys 176 Ala 176 ) has been used and dithiotheretinol (DTT) has been added (coordinates to iron) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
91 Structures from X-ray Open form structure with active site has been obtained Closed form structure has also been obtained but without the active site Further problems: A mutant (Cys 176 Ala 176 ) has been used and dithiotheretinol (DTT) has been added (coordinates to iron) Workflow Back-mutate Ala 176 Cys 176 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
92 Structures from X-ray Open form structure with active site has been obtained Closed form structure has also been obtained but without the active site Further problems: A mutant (Cys 176 Ala 176 ) has been used and dithiotheretinol (DTT) has been added (coordinates to iron) Workflow Back-mutate Ala 176 Cys 176 Solvate (total system size atoms) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
93 Structures from X-ray Open form structure with active site has been obtained Closed form structure has also been obtained but without the active site Further problems: A mutant (Cys 176 Ala 176 ) has been used and dithiotheretinol (DTT) has been added (coordinates to iron) Workflow Back-mutate Ala 176 Cys 176 Solvate (total system size atoms) Modify active site with H 2 and perform QM/MM optimizations on open form (a) and closed form + substrate (b) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
94 Structures from X-ray Open form structure with active site has been obtained Closed form structure has also been obtained but without the active site Further problems: A mutant (Cys 176 Ala 176 ) has been used and dithiotheretinol (DTT) has been added (coordinates to iron) Workflow Back-mutate Ala 176 Cys 176 Solvate (total system size atoms) Modify active site with H 2 and perform QM/MM optimizations on open form (a) and closed form + substrate (b) MD (10 ns) on the closed form + substrate (c) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
95 The [Fe]-hydrogenase enzyme: The intermediates Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
96 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
97 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2a Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H Using B97-D/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
![The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc.](/docs-images/94/118092769/images/98-0.jpg "111 (1989), 8823. J. Am. Chem. Soc. 112 (1990), 4831. b From various sources Coord. Chem. Rev. 252 (2008), 2381. Chem. Soc. Rev. 33 (2004), 175. Bond 3a Exp. Fe N 2.085 2.006 Fe C 1.956 1.914 Fe S 2.")
98 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 3a Exp. Fe N Fe C Fe S Fe CO Fe H b Fe H - - H H - - Using B97-D/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
99 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2b Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using B97-D/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
100 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2b Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using B97-D/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
101 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2b Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using B97-D/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
102 Vacuum calculations for the active site Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
103 Vacuum calculations for the active site Optimize 2a structure in vacuum Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
104 Vacuum calculations for the active site Optimize 2a structure in vacuum 2a Fe H Fe H B3LYP TPSS TPSSh PBE PBE B97-D N.A. N.A. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
105 Vacuum calculations for the active site Optimize 2a structure in vacuum 2a Fe H Fe H B3LYP TPSS TPSSh PBE PBE B97-D N.A. N.A. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
106 Vacuum calculations for the active site Optimize 2a structure in vacuum 2a Fe H Fe H B3LYP TPSS TPSSh PBE PBE B97-D N.A. N.A. With B97-D the H 2 ligand floats away Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
107 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
108 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
109 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2b Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using TPSSh/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
110 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2c Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using TPSSh/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
111 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2c Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using TPSSh/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
![The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc.](/docs-images/94/118092769/images/112-0.jpg "111 (1989), 8823. J. Am. Chem. Soc. 112 (1990), 4831. b From various sources Coord. Chem. Rev. 252 (2008), 2381. Chem. Soc. Rev. 33 (2004), 175. Bond 2c Exp. Fe N 2.037 2.006 Fe C 1.903 1.914 Fe S 2.")
112 The [Fe]-hydrogenase enzyme: The intermediates a b c Configuration Open Closed Closed Substrate No Yes Yes MD No No Yes a From Fe(H2 )(H)(dppe) 2 ] + and Fe(H 2 )(H) 2 (PEtPh 2 ) 2 J. Am. Chem. Soc. 111 (1989), J. Am. Chem. Soc. 112 (1990), b From various sources Coord. Chem. Rev. 252 (2008), Chem. Soc. Rev. 33 (2004), 175. Bond 2c Exp. Fe N Fe C Fe S Fe CO Fe H a Fe H a H H - - Using TPSSh/SV(P)-def2 Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
113 Conclusions (part II) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
114 Conclusions (part II) Structures of [Fe]-hydrogenase intermediates A series of structures in both open and closed configurations have been optimized E. D. Hedegård, U. Ryde, J. Kongsted, Angew. Chem. Int. Ed., (to be submitted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
115 Conclusions (part II) Structures of [Fe]-hydrogenase intermediates A series of structures in both open and closed configurations have been optimized E. D. Hedegård, U. Ryde, J. Kongsted, Angew. Chem. Int. Ed., (to be submitted) Functional dependence of structural parameters The dispertion corrected B97-D functional becomes problematic for η 2 -bonded (side-on) H 2 E. D. Hedegård, U. Ryde, J. Kongsted, Angew. Chem. Int. Ed., (to be submitted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
116 Conclusions (part II) Structures of [Fe]-hydrogenase intermediates A series of structures in both open and closed configurations have been optimized E. D. Hedegård, U. Ryde, J. Kongsted, Angew. Chem. Int. Ed., (to be submitted) Functional dependence of structural parameters The dispertion corrected B97-D functional becomes problematic for η 2 -bonded (side-on) H 2 E. D. Hedegård, U. Ryde, J. Kongsted, Angew. Chem. Int. Ed., (to be submitted) Further studies Spectroscopic parameters (Mössbauer, NMR) Environmental effects Relativistic effects E. D. Hedegård, S. Knecht, U. Ryde, J. Kongsted, T. Saue, Phys. Chem. Chem. Phys., (to be submitted) Erik Donovan Hedegård (SDU) Fall Meeting Chemsoc (theory) October 11, / 28
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