Key roles of metallo-organic complexes:from photovoltaics materials

to enzymatic structures

P. Giannozzi

Dip. Chimica Fisica Ambiente, Universita di Udine, Italy, and

IOM-Democritos, Trieste

ISM Montelibretti, 12 Novembre 2013

Work done in collaboration with a lot of people (see next slide)

– Typeset by FoilTEX –

About this talkThe two subjects presented here:

1. Hybrid heterostructures for photovoltaic applicationsin collaboration with: G. Mattioli, P. Alippi, F. Filippone, A. Amore Bonapasta(ISM); M.I. Saba, G. Malloci, C. Melis, A.Mattoni, (IOM Cagliari) S. Ben Dkhil,A. Thakur, M. Gaceur, O. Margeat, A. K. Diallo, Ch. Videlot-Ackermann, J.Ackermann (CNRS Marseille)

2. Metal-induced aggregation processes in β-amyloids peptidesin collaboration with K. Jansen (DESY), G. La Penna (ICCOM), V. Minicozzi,S. Morante, G. C. Rossi, F. Stellato (Roma II)

are quite different but they have something more in common than Zn atoms, DFTsimulations, and a collaboration with people from Rome:

• both are joint experimental and theoretical investigations, and

• on the theory side, in both cases complementary theoretical techniques: classicalor tight-binding MD + first-principle DFT, have been used.

New hybrid materials for solar cells

Hybrid photovoltaic cells: organic molecule or π−conjugated polymer acting asdye (light absorber) and electron donor, on inorganic substrate acting as acceptor.Hold great promises for the realization of cheap and high-yield solar cells.

Good dye and donor candidates:(on the right) polymers such as P3HT,poly(3-hexylthiophene-2,5-diyl);Phtalocyanines (Pc) (on the left, ZnPc)

Good substrate candidate: metal oxide nanoparticles,typically TiO2, with ZnO emerging as alternativematerial (both are cheap and nontoxic). ZnO is a highmobility wide gap (3.4 eV) material with wurtzitestructure. On the right, the (1010) surface of ZnO,the most common surface in ZnO nanoparticles

Model systems

In the past, both P3HT/ZnO and ZnPc/ZnO hybrid systems have been proposedand studied. In this work, the idea is to increase the efficiency of such systemsby introducing ternary heterostructures such as P3HT/ZnPc/ZnO. Hopefully, theymay provide better efficiency via

• Increased optical absorption over a wider spectrum, and

• Reduced electron-hole recombination

Problems for a first-principle theoretical approach:

• Very large supercells (hundreds of atoms) even for simplest model structures(few layers of a surface, or a very small nanoparticle): big calculations!

• Hard problem in a Density-Functional Theory (DFT) framework, due to

– Long-range dispersion (van der Waals) interactions– Strongly correlated 3d states in Zn (correct energy level alignement is crucial)– Need for reliable (or not too wrong) excited states: band gap, optical spectra

Theoretical Methods

Theoretical solutions adopted:

• Model Potential Molecular Dynamics allows relatively quick selection ofpotentially stable structures, followed by Density-Functional Theory refinements

• Usage of advanced DFT functionals:

– DFT+U corrects the worst failures of DFT in correlated materials– vdw-DF allows to include van der Waals forces– tests with hybrid functionals to gain confidence in the results

• Usage of Time-Dependent DF(P)T for calculation of optical spectra (good formolecules, much less so for solids)

DFT calculations performed on HPC machines (mostly on the SP at Cineca) using

the parallel algorithms of the QUANTUM Espresso distribution.

Model P3HT/ZnPc/ZnO: structure, stability

ZnPc on (1010) ZnO surface forms stable layer (Eb = 2.2 eV/molecule)

8-unit P3HT binds with Eb = 0.6 eV/unit to ZnPc/ZnO (vs 0.4 eV/unit to ZnO)

Electronic states, energies

CS (charge-separated) states: e− is in ZnO CBM (Conduction Band Minimum),

h+ is in molecular HOMO. The ZnPc layer raises P3HT LUMO to a more favorable

position for e− transfer to ZnPc and ZnO, improving charge separation at interface

Electronic states, localization in space

Electron-hole recombination made less likely by ZnPc layer: e− and h+ densities

in charge-separated state are more spacially separated and have smaller overlap

Simulated TD-DFPT optical spectra

A. ZnPc/ZnO absorption: split Q-bandsat 1.7 and 1.9 eV, Soret band at 3.1 eV.

B. P3HT/ZnPc/ZnO: superpositionof ZnPc/ZnO peaks and of theblue-shifted (2.3 eV) peak of P3HT.

C. 4-unit P3HT on ZnO: absorptionpeak at 2.15 eV.

(Contribution from ZnO substrate is subtracted out)

Experiments: optical spectra, ZnPc on ZnO

ZnPc on glass: two peaks (Q bands) at 622 nm and 711 nm

ZnPc on ZnO: additional peaks due to molecule-substrate interactions

appear at 674 nm (blue arrow) and at 742 nm (light blue arrow)

Experiments: optical spectra, P3HT/ZnPc/ZnO

ZnPc film thickness: black dots 4 nm, blue dots 15 nm. Up: The spectrum

of P3HT/ZnPc/ZnO exhibits absorption peaks of P3HT and of ZnPc, plus the

new optical features of ZnPc/ZnO interface. Down: External Quantum Efficiency

(EQE) shows that the new band at 674 nm contributes additional photocurrent.

Experiments: current density-voltage curves

Measured performances:

Voc Jsc PCEno ZnPc 0.71 0.17 0.064 nm ZnPc 0.61 0.26 0.0915 nm ZnPc 0.60 0.07 0.07

Open-circuit voltage Voc in V,short-circuit density current Jscin mA/cm2, Power ConversionEfficiency (PCE) in %

Experiments: transient open circuit voltage decay

Blue: P3HT/ZnPc/ZnO, Red: P3HT/ZnO. Illumination is suppressed with circuit

open (no current flowing) and the decay time of carriers is measured. Carrier

lifetime as a function of the open circuit voltage, in the region Voc < 0.48 V, is a

measure of recombination in the heterostructure region, showing improved lifetime

for P3HT/ZnPc/ZnO.

Discussion and conclusions (1)

Theoretical predictions on the ternary P3HT/ZnPc/ZnO system:

• The system is thermodynamically stable

• Light absorption from both P3HT and ZnPc covering a wide spectrum

• Increased charge separation due to ZnPc layer reduces recombination

• The P3HT HOMO is shifted by the ZnPc layer to higher energies, leading to areduction of Voc of ∼ 0.1 V.

Experimental data on actual samples, produced and measured at CNRS Marseille,confirm all of the above findings.

Aggregation of peptides induced by metal ions

Very nasty degenerative illnesses are caused

by aggregation of naturally present proteins or

peptides into toxic amyloid fibrils and plaques

In Alzheimer disease, the main components of

plaques are β-amyloids peptides (Aβ): chains

of 39 to 43 aminoacids, obtained by cleavage

of a precursor protein

(in the figure: Aβ40 peptide in water)

There is experimental evidence that transition metal ions Cu, Zn, Fe

play a role in the processes of Aβ aggregation and plaque formation

The details of the metal-Aβ binding are thus subject of intense study

β-amyloids binding with Cu and Zn: state of the art

• The structure of Aβ binding with Cu is relatively well characterized,

with Cu having a stable intra-peptide coordination

• Aβ binding with Zn is not as clear. Competing structural models

– from XAS: inter-peptide Zn2+ bridge between three or more

histidines (His) belonging to different peptides. Rather peculiar

and infrequent: hallmark of peptide aggregation?

– from NMR: intra-peptide binding to three His and either the

N-terminus or a residue (Glu11)

• Competition for peptide binding between Cu and Zn ions likely

Goal of this work: to find, using numerical simulations, realistic

configurations for Aβ chains coordinated by Zn2+, fitting XAS results

Simulation procedure

• Initial configurations generated with graphical tools (VMD),

optimized with Amber force fields and Monte Carlo Random Walk

• Selected configurations truncated (aminoacids 1-10 removed),

optimized, set into an orthorhombic cell filled with water molecules,

thermalized with classical MD, optimized with Tight-Binding MD

• Finally, first-principle (i.e. from electronic structure) Car-Parrinello

Molecular Dynamics runs are performed to check the stability and

refine the structure of the various binding configurations

The last step is by far the most time-consuming, requiring parallel

execution on big computer facilities, including the BG/P

(courtesy of DEISA DECI and of John von Neumann Institute for Computing)

Choosing the starting configurations

Four good starting models (generated for Aβ16) compatible with XAS

data (many more turned out to be bad and were discarded):

• S1: Zn bound to four

histidines

• S2: Zn bound to three

histidines

• S3: two Zn ions, bound

to four histidines

• S4: two Zn ions, bound

to three peptides

Car-Parrinello Molecular Dynamics

Introduce fictitious dynamics on the electronic orbitals φv:

L = µ∑v

∫|φv(~r)|2d~r +

1

2

∑I

MI∇2~RI− E[φ,R]

(µ = fictitious electronic mass), subject to orthonormality constraints

on the orbitals, implemented via Lagrange multipliers Λij. The above

Lagrangian generates the following equations of motion:

µφi = −δEδφi

+∑ij

Λijφj MI~RI = −∇~RI

E[φ,R]

(nuclear motion is classical). These equations can be integrated

(i.e. solved) for both electrons and nuclei using classical Molecular

Dynamics algorithms. The combined electronic and nuclear dynamics

keeps electrons close to the ground state.

Technical details

• Perdew-Burke-Erzerhof (PBE) exchange-correlation functionals

• Ultrasoft (Vanderbilt) pseudopotentials with 25 Ry (orbitals) or

250 Ry (charge density) kinetic energy cutoff for plane waves

• Simulation cell size:

– S1: 1351 atoms, 21.291×35.193×23.241A3

– S2: 1204 atoms, 21.976×27.947×22.881A3

– S3: 1349 atoms, cell as S1

– S4: 2347 atoms, 32.083×31.01×23.14A3:

Tight-Binding MD only, too big for Car-Parrinello MD

• At least 3.6 ps simulation time

Results

Structures for S1,

S2, S3 models

before and after

CP-MD. Note the

fourth His leaving

the Zn site in

S1, while in S3

model Zn keeps

a stable fourfold

coordination

Results: a nice cover picture...

PG, K. Jansen, G. La Penna,V. Minicozzi, S. Morante, G. C.Rossi, F. Stellato, Metallomics 4,156-165 (2012)

(S4 model)

More serious results: simulated XAS spectra

Similar structures in other biological systems?

Comparison of the Zna site in S4 model (green: fit to XAS) with the

Zn site in the reduced bovine superoxide-dismutase (SOD) enzyme

Only residues involved in binding with Zn are shown

Discussion and conclusions

• XAS yields information on short-range structure (up to 5÷6A) only

• First-principle techniques can take into account both the peculiar

chemical binding of metals with peptides and the electrostatic

interactions between peptides

• Structures (S3 and S4) in which Zn is bound in a stable ways to

four His have been identified...

• ...but their structure is not trivial, requiring a second Zn and/or a

third peptide chain; in the simpler S1 structure Zn loses a His and

a satisfactory XAS fit is not obtained

• S4 model reminiscent of the Zn site of bovine SOD