Francesco Buda

Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes

Chlorosomes are the largest and most efficient light-harvesting antennae found in nature, and they are constructed from hundreds of thousands of self-assembled bacteriochlorophyll (BChl) c, d, or e pigments. Because they form very large and compositionally heterogeneous organelles, they had been the only photosynthetic antenna system for which no detailed structural information was available. In our approach, the structure of a member of the chlorosome class was determined and compared with the wild type (WT) to resolve how the biological light-harvesting function of the chlorosome is established. By constructing a triple mutant, the heterogeneous BChl c pigment composition of chlorosomes of the green sulfur bacteria Chlorobaculum tepidum was simplified to nearly homogeneous BChl d. Computational integration of two different bioimaging techniques, solid-state NMR and cryoEM, revealed an undescribed syn-anti stacking mode and showed how ligated BChl c and d self-assemble into coaxial cylinders to form tubular-shaped elements. A close packing of BChls via π–π stacking and helical H-bonding networks present in both the mutant and in the WT forms the basis for ultrafast, long-distance transmission of excitation energy. The structural framework is robust and can accommodate extensive chemical heterogeneity in the BChl side chains for adaptive optimization of the light-harvesting functionality in low-light environments. In addition, syn-anti BChl stacks form sheets that allow for strong exciton overlap in two dimensions enabling triplet exciton formation for efficient photoprotection.

Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods?

We perform a thorough comparative investigation of the excitation energies of the anionic and neutral forms of the green fluorescent protein (GFP) chromophore in the gas phase using a variety of first-principle theoretical approaches commonly used to access excited state properties of photoactive molecules. These include time-dependent density functional theory (TDDFT), complete-active-space second-order perturbation theory (CASPT2), equation-of-motion coupled cluster (EOM-CC), and quantum Monte Carlo (QMC) methods. We find that all approaches give roughly the same vertical excitation for the anionic form, while TDDFT predicts an excitation for the neutral chromophore significantly lower than the highly correlated methods. Our findings support the picture emerging from the extrapolation of the Kamlet-Taft fit of absorption experimental data in solution and indicate that the protein gives rise to a considerable bathochromic shift with respect to vacuum. These results also open some questions on the interpretation of photodestruction spectroscopy experiments in the gas phase as well as on the accuracy of previous theoretical calculations in the more complex protein environment.

DFT Study of the Active Intermediate in the Fenton Reaction

Density functional theory has been used to investigate the nature of the oxidizing agent in the Fenton reaction. Starting from the primary intermediate [FeII(H2O)5H2O2]2+, we show that the oxygen-oxygen bond breaking mechanism has a small activation energy and could therefore demonstrate the catalytic effect of the metal complex. The O-O bond cleavage of the coordinated H2O2, however, does not lead to a free hydroxyl radical. Instead, the leaving hydroxyl radical abstracts a hydrogen from an adjacent coordinated water leading to the formation of a second Fe-OH bond and of a water molecule. Along this reaction path the primary intermediate transforms into the [FeIV(H2O)4(OH)2]2+ complex and in a second step into a more stable high valent ferryl-oxo complex [FeIV(H2O)5O]2+. We show that the energy profile along the reaction path is strongly affected by the presence of an extra water molecule located near the iron complex. The alternative intermediate [FeII(H2O)4(OOH-)(H3O+)]2+ suggested in the literature has been also investigated, but it is found to be unstable against the primary intermediate. Our results support a picture in which an FeIV-oxo complex is the most likely candidate as the active intermediate in the Fenton reaction, as indeed first proposed by Bray and Gorin already in 1932.

Zinc chlorins for artificial light-harvesting self-assemble into antiparallel stacks forming a microcrystalline solid-state material

We introduce a concept to solve the structure of a microcrystalline material in the solid-state at natural abundance without access to distance constraints, using magic angle spinning (MAS) NMR spectroscopy in conjunction with X-ray powder diffraction and DFT calculations. The method is applied to a novel class of materials that form (semi)conductive 1D wires for supramolecular electronics and artificial light-harvesting. The zinc chlorins 3-devinyl-31-hydroxymethyl-132-demethoxycarbonylpheophorbide a (3′,5′-bis-dodecyloxy)benzyl ester zinc complex 1 and 3-devinyl-31-methoxymethyl-132-demethoxycarbonylpheophorbide a (3′,5′-bis-dodecyloxy)benzyl ester zinc complex 2, self-assemble into extended excitonically coupled chromophore stacks. 1H-13C heteronuclear dipolar correlation MAS NMR experiments provided the 1H resonance assignment of the chlorin rings that allowed accurate probing of ring currents related to the stacking of macrocycles. DFT ring-current shift calculations revealed that both chlorins self-assemble in antiparallel π-stacks in planar layers in the solid-state. Concomitantly, X-ray powder diffraction measurements for chlorin 2 at 80 °C revealed a 3D lattice for the mesoscale packing that matches molecular mechanics optimized aggregate models. For chlorin 2 the stacks alternate with a periodicity of 0.68 nm and a 3D unit cell with an approximate volume of 6.28 nm3 containing 4 molecules, which is consistent with space group P21221.

Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches

We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophore-protein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore.

Crystallographic evidence of theoretically novel anion–π interactions

The reaction of Cu(NO3)2·3H2O with the multidentate ligand N,N′,N″,N‴-tetrakis{2,4-bis(di-2-pyridylamino)-1,3,5-triazin-6-yl} triethylenetetramine (dpatta) in acetonitrile at high temperature and pressure results in the formation of the tetranuclear coordination compound [Cu4(dpatta)(NO3)4](NO3)4·12H2O (1), whose crystal structure exhibits remarkable anion–π interactions which have been calculated, considering the unexpected position of the anion toward the aromatic ring.

Anion−π and π−π Cooperative Interactions Regulating the Self-Assembly of Nitrate−Triazine−Triazine Complexes

We theoretically investigate the cooperative enhancement of the interactions between anions and electron-deficient aromatics by pi-pi stacking, focusing on the recent crystallographic observation of anion-pi-pi interactions in a synthesized coordination compound based on 1,3,5-triazine moieties. Using a combination of state-of-the-art dispersion-corrected density functional and quantum Monte Carlo calculations, we rationalize the unusual structural features observed in this nitrate-triazine-triazine complex. We show that the triazine rings are staggered and bent and slip with respect to each other with the nitrate bound off-center in a T-like configuration. Our results indicate that this pi-pi stacking is not simply enforced by the coordination of the triazines within the particular crystal structure but is regulated by cooperative anion-pi and pi-pi interactions. In the nitrate-triazine-triazine complex, this cooperative effect amounts to 6% of the total binding energy. Ways to further increase this energetic enhancement in the design of anion-host architectures are discussed.

Chemical Involvement of Solvent Water Molecules in Elementary Steps of the Fenton Oxidation Reaction We gratefully acknowledge the helpful discussions with Michiel Gribnau (Unilever-Vlaardingen) and we thank the Netherlands Organization for Scientific Research (NWO) for support through the PPM-CMS program and the NCF for providing computer time

The spontaneous formation of the contested ferryl ion is evident in ab initio molecular dynamics calculations on the FeII /H2 O2 system in aqueous solution (Fenton reagents). Not only is the ferryl ion preferred over the hydroxyl radical as the active oxidative species, but the solvent water molecules play a crucial role in the mechanism. The picture shows the unit cell containing the iron complex surrounded by solvent water molecules 1.8 ps after the start of the simulation, when the ferryl ion is being formed (blue: iron, red: oxygen, white: hydrogen).

Excitations in photoactive molecules from quantum Monte Carlo

Despite significant advances in electronic structure methods for the treatment of excited states, attaining an accurate description of the photoinduced processes in photoactive biomolecules is proving very difficult. For the prototypical photosensitive molecules, formaldimine, formaldehyde, and a minimal protonated Schiff base model of the retinal chromophore, we investigate the performance of various approaches generally considered promising for the computation of excited potential energy surfaces. We show that quantum Monte Carlo can accurately estimate the excitation energies of the studied systems if one constructs carefully the trial wave function, including in most cases the reoptimization of its determinantal part within quantum Monte Carlo. While time-dependent density functional theory and quantum Monte Carlo are generally in reasonable agreement, they yield a qualitatively different description of the isomerization of the Schiff base model. Finally, we find that the restricted open shell Kohn-Sham method is at variance with quantum Monte Carlo in estimating the lowest-singlet excited state potential energy surface for low-symmetry molecular structures.

Ab Initio Molecular Dynamics Study of Water Oxidation Reaction Pathways in Mono-Ru Catalysts

Ab initio molecular dynamics simulations with an adaptive biasing potential are carried out to study the reaction path in mononuclear Ru catalysts for water oxidation of the type [(Ar)Ru(X)(bpy)](+) with different aromatic ligands (Ar). The critical step of the O-O bond formation in the catalytic cycle starting from the [(Ar)Ru(O)(bpy)](2+) intermediate is analyzed in detail. It is shown that an explicit inclusion of the solvent environment is essential for a realistic description of the reaction path. Clear evidence is presented for a concerted reaction in which the O-O bond formation is quickly followed by a proton transfer leading to a Ru-OOH intermediate and a hydronium ion. An alternative path in which the approaching water first coordinates to the metal centre is also investigated, and it is found to induce a structural instability of the catalyst with the breaking of the aromatic ligand coordination bond.