DFT/TDDFT Exploration of the Potential Energy Surfaces of the Ground State and Excited States of Fe2(S2C3H6)(CO)6: A Simple Functional Model of the [FeFe] Hydrogenase Active Site

Probing the performance of DFT in the structural characterization of [FeFe] hydrogenase models

In this work, a series of DFT and DFT-D methods is combined with double-ζ basis sets to benchmark their performance in predicting the structures of five newly synthesized hexacarbonyl diiron complexes with a bridging ligand featuring a μ-S2C3 motif in a ring-containing unit functionalized with aromatic groups. Such complexes have been considered as [FeFe] hydrogenase catalytic site models with potential for eco-friendly energetic applications. According to this assessment, r2SCAN is identified as the density functional recommended for the reliable description of the molecular and crystal structures of the herein studied models. However, the butterfly (μ-S)2Fe2 core of the models demonstrates a minor deformation of its optimized geometry obtained from both molecular and periodic calculations. The FeFe bond length is slightly underestimated while the FeS bonds tend to be too long. Adding the D3(BJ) correction to r2SCAN does not lead to any improvement in the calculated structures.

The Photochemistry of Fe2(S2C3H6)(CO)6(µ-CO) and Its Oxidized Form, Two Simple [FeFe]-Hydrogenase CO-Inhibited Models. A DFT and TDDFT Investigation

FeIFeI Fe2(S2C3H6)(CO)6(µ-CO) (1a–CO) and its FeIFeII cationic species (2a+–CO) are the simplest model of the CO-inhibited [FeFe] hydrogenase active site, which is known to undergo CO photolysis within a temperature-dependent process whose products and mechanism are still a matter of debate. Using density functional theory (DFT) and time-dependent density functional theory (TDDFT) computations, the ground state and low-lying excited-state potential energy surfaces (PESs) of 1a–CO and 2a+–CO have been explored aimed at elucidating the dynamics of the CO photolysis yielding Fe2(S2C3H6)(CO)6 (1a) and [Fe2(S2C3H6)(CO)6]+ (2a+), two simple models of the catalytic site of the enzyme. Two main results came out from these investigations. First, a–CO and 2a+–CO are both bound with respect to any CO dissociation with the lowest free energy barriers around 10 kcal mol−1, suggesting that at least 2a+–CO may be synthesized. Second, focusing on the cationic form, we found at least two clear excited-state channels along the PESs of 2a+–CO that are unbound with respect to equatorial CO dissociation.

Catalytic H2 evolution/oxidation in [FeFe]-hydrogenase biomimetics: account from DFT on the interplay of related issues and proposed solutions

A DFT overview on selected issues regarding diiron catalysts related to [FeFe]-hydrogenase biomimetic research, with implications for both energy conversion and storage strategies.

Preparation and Protonation of Fe2(pdt)(CNR)6, Electron-Rich Analogues of Fe2(pdt)(CO)6

The complexes Fe2(pdt)(CNR)6 (pdt(2-) = CH2(CH2S(-))2) were prepared by thermal substitution of the hexacarbonyl complex with the isocyanides RNC for R = C6H4-4-OMe (1), C6H4-4-Cl (2), Me (3). These complexes represent electron-rich analogues of the parent Fe2(pdt)(CO)6. Unlike most substituted derivatives of Fe2(pdt)(CO)6, these isocyanide complexes are sterically unencumbered and have the same idealized symmetry as the parent hexacarbonyl derivatives. Like the hexacarbonyls, the stereodynamics of 1-3 involve both turnstile rotation of the Fe(CNR)3 as well as the inversion of the chair conformation of the pdt ligand. Structural studies indicate that the basal isocyanide has nonlinear CNC bonds and short Fe-C distances, indicating that they engage in stronger Fe-C π-backbonding than the apical ligands. Cyclic voltammetry reveals that these new complexes are far more reducing than the hexacarbonyls, although the redox behavior is complex. Estimated reduction potentials are E1/2 ≈ -0.6 ([2](+/0)), -0.7 ([1](+/0)), and -1.25 ([3](+/0)). According to DFT calculations, the rotated isomer of 3 is only 2.2 kcal/mol higher in energy than the crystallographically observed unrotated structure. The effects of rotated versus unrotated structure and of solvent coordination (THF, MeCN) on redox potentials were assessed computationally. These factors shift the redox couple by as much as 0.25 V, usually less. Compounds 1 and 2 protonate with strong acids to give the expected μ-hydrides [H1](+) and [H2](+). In contrast, 3 protonates with [HNEt3]BAr(F)4 (pKa(MeCN) = 18.7) to give the aminocarbyne [Fe2(pdt)(CNMe)5(μ-CN(H)Me)](+) ([3H](+)). According to NMR measurements and DFT calculations, this species adopts an unsymmetrical, rotated structure. DFT calculations further indicate that the previously described carbyne complex [Fe2(SMe)2(CO)3(PMe3)2(CCF3)](+) also adopts a rotated structure with a bridging carbyne ligand. Complex [3H](+) reversibly adds MeNC to give [Fe2(pdt)(CNR)6(μ-CN(H)Me)](+) ([3H(CNMe)](+)). Near room temperature, [3H](+) isomerizes to the hydride [(μ-H)Fe2(pdt)(CNMe)6](+) ([H3](+)) via a first-order pathway.

Theoretical investigation on remote-control photocycloreversion of dithienylethene driven by azobenzene chromophores

When adding two azobenzene chromophores on a dithienylethene molecule, the irradiation at 450 nm can effectively arouse the cycloreversion reaction of the ring-closed dithienylethene. We investigated the frontier molecular orbitals and absorption properties of such series of molecules and inferred the mechanism of the ring-opening reaction. The 450 nm light sensed by the side azobenzene groups can excite the whole molecule to a high excited state, and through electronic transition and energy transfer the active electron may centre on the dithienylethene ring part, then the ring-opening happens. While for the ring-open form, the energy of the 450 nm light is not high enough to promote the electron to the exact molecular orbital occupying the central dithienylethene ring, so it cannot cause the ring-closing reaction.

Atomic partitioning of M-H2 bonds in [NiFe] hydrogenase--a test case of concurrent binding

The possibility of simultaneous addition of η(2)-H2 to both the metals (Ni and Fe) in the active site of the as isolated state of the enzyme (Ni-SI) is examined here by an atom-by-atom electronic energy partitioning based on the QTAIM method. Results show that the 4LS state prefers H2 removal than addition. Destabilization of the atomic basins of the thiolate bridges and decrease of the electrophilicity of the Fe and Ni, resulting in poor back donation to the CO ligand, are the bottlenecks that hamper dihydrogen activation simultaneously. The study helps to understand why such states are seldom accessed in the activation of dihydrogen. Moreover, Ni has been found to be the natural choice for the dihydrogen binding.

Properties of atoms in electronically excited molecules within the formalism of TDDFT

The topological analysis of the electron density for electronic excited states under the formalism of the quantum theory of atoms in molecules using time-dependent density functional theory (TDDFT) is presented. Relaxed electron densities for electronic excited states are computed by solving a Z-vector equation which is obtained by means of the Sternheimer interchange method. This is in contrast to previous work in which the electron density for excited states is obtained using DFT instead of TDDFT, that is, through the imposition of molecular occupancies in accordance with the electron configuration of the excited state under consideration. Once the electron density of the excited state is computed, its topological characterization and the properties of the atoms in molecules are obtained in the same manner that for the ground state. The analysis of the low-lying π→π* singlet and triplet vertical excitations of CO and C6H6 are used as representative examples of the application of this methodology. Altogether, it is shown how this procedure provides insights on the changes of the electron density following photoexcitation and it is our hope that it will be useful in the study of different photophysical and photochemical processes.

Quantum mechanical methods for the investigation of metalloproteins and related bioinorganic compounds

It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.

Excited state properties of diiron dithiolate hydrides: implications in the unsensitized photocatalysis of H2 evolution

Density functional theory (DFT) and time-dependent DFT (TDDFT) have been used to investigate how visible light photons can excite an asymmetrically substituted diiron hydride, [Fe2(pdt)(μ-H)(CO)4dppv](+) (1(+), dppv = cis-1,2-C2H2(PPh2)2; pdt = 1,3-propanedithiolate), as well as the symmetric species [Fe2(pdt)(μ-H)(CO)4(PMe3)2](+) (2(+)), which are the first photocatalysts of proton reduction operating without employing sensitizers (Wang, W.; Rauchfuss, T. B.; Bertini, L.; Zampella, G.; J. Am. Chem. Soc., 2012, 134, 4525). Theoretical results illustrate that the peculiar reactivity associated to the excited states of 1(+) and 2(+) is compatible with three different scenarios: (i) it can arise from the movement of the hydride ligand from fully bridging to semibridging/terminal coordination, which is expected to be more reactive toward protons; (ii) reactivity could be related to cleavage of a Fe-S bond, which implies formation of a transient Fe penta-coordinate species that would trigger a facile turnstile hydride isomerization, if lifetime excitation is long enough; (iii) also in line with a Fe-S bond cleavage is the possibility that after excited state decay, a highly basic S center is protonated so that a species simultaneously containing S-H(δ+) and Fe-H(δ-) moieties is formed and, once reduced by a suitable electron donor, it can readily afford H2 plus an unprotonated form of the FeFe complex. This last possibility is consistent with (31)P NMR and IR solution data. All the three possibilities are compatible with the capability of 1(+) and 2(+) to perform photocatalysis of hydrogen evolving reaction (HER) without sensitizer. Moreover, even though it turned out difficult to discriminate among the three scenarios, especially because of the lack of experimental excitation lifetimes, it is worth underscoring that all of the three pathways represent a novelty regarding diiron carbonyl photoreactivity, which is usually associated with CO loss. Results provide also a rationale to the experimental observations which showed that the simultaneous presence of donor ligands (dppv in the case of 1(+)) and a H ligand in the coordination environment of diiron complexes is a key factor to prevent CO photodissociation and catalyze HER. Finally, the comparison of photoexcitation behavior of 1(+) and 2(+) allows a sort of generalization about the functioning of such hydride species.

Towards [NiFe]-hydrogenase biomimetic models that couple H2 binding with functionally relevant intramolecular electron transfers: a quantum chemical study

[FeFe]- and [NiFe]-hydrogenases are dihydrogen-evolving metalloenzymes that share striking structural and functional similarities, despite being phylogenetically unrelated. Most notably, they are able to combine substrate binding and redox functionalities, which has important bearings on their efficiency. Model complexes of [FeFe]-hydrogenases that are able to couple H2 binding with a substrate-dependent intramolecular electron transfer promoting dihydrogen activation were recently shown to reproduce the complex redox chemistry of the all-iron enzyme. Notably, coupling of H2 binding and intramolecular redox events was proposed to have a key role also in [NiFe]-hydrogenases, but this feature is not reproduced in currently available nickel-iron biomimetic compounds. In the present study, we exploit dedicated density functional theory approaches to show that H2 binding and activation on a NiFe core can be favored by the installment of conveniently substituted isocyanoferrocenes, thanks to their ability to undergo intramolecular reduction upon substrate binding. Our results support the concept that a unified view on hydrogenase chemistry is a key element to direct future efforts in the modeling of microbial H2 metabolism.

H2 binding and splitting on a new-generation [FeFe]-hydrogenase model featuring a redox-active decamethylferrocenyl phosphine ligand: a theoretical investigation

[FeFe]-hydrogenases are dihydrogen-evolving metalloenzymes that are able to combine substrate binding and redox functionalities, a feature that has important bearing on their efficiency. New-generation bioinspired systems such as Fe(2)[(SCH(2))(2)NBn](CO)(3)(Cp*Fe(C(5)Me(4)CH(2)PEt(2)))(dppv) were shown to mimic H(2) oxidation and splitting processes performed by the [FeFe]-hydrogenase/ferredoxin system, and key mechanistic aspects of such reaction are theoretically investigated in the present contribution. We found that H(2) binding and heterolytic cleavage take place concomitantly on DFT models of the synthetic catalyst, due to a substrate-dependent intramolecular redox process that promotes dihydrogen activation. Therefore, formation of an iron-dihydrogen complex as a reaction intermediate is excluded in the biomimetic system, at variance with the case of the enzyme. H(2) uptake at the synthetic system also requires an energetically disfavored isomerization of the amine group acting as a base during splitting. A possible strategy to stabilize the conformation competent for H(2) binding is proposed, along with an analysis of the reactivity of a triiron complex in which di(thiomethyl)amine--the chelating group naturally occurring in [FeFe]-hydrogenases--substitutes the benzyl-containing dithiolate ligand.