Dinuclear diazene iron and ruthenium complexes as models for studying nitrogenase activity

Uncovering Redox Non-innocent Hydrogen-Bonding in Cu(I)-Diazene Complexes

The life-sustaining reduction of N₂ to NH₃ is thermoneutral yet kinetically challenged by high-energy intermediates such as N₂H₂. Exploring intramolecular H-bonding as a potential strategy to stabilize diazene intermediates, we employ a series of [^xHetTpCu]₂(μ-N₂H₂) complexes that exhibit H-bonding between pendant aromatic N-heterocycles (^xHet) such as pyridine and a bridging trans-N₂H₂ ligand at copper(I) centers. X-ray crystallography and IR spectroscopy clearly reveal H-bonding in [^pyMeTpCu]₂(μ-N₂H₂) while low-temperature ¹H NMR studies coupled with DFT analysis reveals a dynamic equilibrium between two closely related, symmetric H-bonded structural motifs. Importantly, the ^xHet pendant negligibly influences the electronic structure of ^xHetTpCu^I centers in ^xHetTpCu(CNAr^2,6-Me₂) complexes that lack H-bonding as judged by nearly indistinguishable ν(CN) frequencies (2113-2117 cm^-1). Nonetheless, H-bonding in the corresponding [^xHetTpCu]₂(μ-N₂H₂) complexes results in marked changes in ν(NN) (1398-1419 cm^-1) revealed through resonance Raman studies. Due to the closely matched N-H BDEs of N₂H₂ and the pyH⁰ cation radical, the aromatic N-heterocyclic pendants may encourage partial H-atom transfer (HAT) from N₂H₂ to ^xHet through redox-non-innocent H-bonding in [^xHetTpCu]₂(μ-N₂H₂). DFT studies reveal modest thermodynamic barriers for concerted transfer of both H-atoms of coordinated N₂H₂ to the ^xHet pendants to generate tautomeric [^xHetHTpCu]₂(μ-N₂) complexes, identifying metal-assisted concerted dual HAT as a thermodynamically favorable pathway for N₂/N₂H₂ interconversion.

Exploring secondary-sphere interactions in Fe-N x H y complexes relevant to N2 fixation

Hydrogen bonding and other types of secondary-sphere interactions are ubiquitous in metalloenzyme active sites and are critical to the transformations they mediate. Exploiting secondary sphere interactions in synthetic catalysts to study the role(s) they might play in biological systems, and to develop increasingly efficient catalysts, is an important challenge. Whereas model studies in this broad context are increasingly abundant, as yet there has been relatively little progress in the area of synthetic catalysts for nitrogen fixation that incorporate secondary sphere design elements. Herein we present our first study of Fe-N x H y complexes supported by new tris(phosphine)silyl ligands, abbreviated as [SiPNMe3] and [SiPiPr2PNMe], that incorporate remote tertiary amine hydrogen-bond acceptors within a tertiary phosphine/amine 6-membered ring. These remote amine sites facilitate hydrogen-bonding interactions via a boat conformation of the 6-membered ring when certain nitrogenous substrates (e.g., NH3 and N2H4) are coordinated to the apical site of a trigonal bipyramidal iron complex, and adopt a chair conformation when no H-bonding is possible (e.g., N2). Countercation binding at the cyclic amine is also observed for anionic {Fe-N2}- complexes. Reactivity studies in the presence of proton/electron sources show that the incorporated amine functionality leads to rapid generation of catalytically inactive Fe-H species, thereby substantiating a hydride termination pathway that we have previously proposed deactivates catalysts of the type [EPR3]FeN2 (E = Si, C).

Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment

JMJD2A catalyses the demethylation of di- and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O2 , using a combination of quantum and classical simulations. O2 binding to this histone demethylase is computed to occur preferentially as an end-on superoxo radical bound to a high-spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O2 binding. Charge separation in the superoxo-intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition.

Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures

In this work, we employ density functional theory to assign vibrational signatures of [FeFe]-hydrogenase intermediates to molecular structures. For this purpose, we perform an exhaustive analysis of structures and harmonic vibrations of a series of CN and CO containing model clusters of the [FeFe]-hydrogenase enzyme active site considering also different charges, counterions, and solvents. The pure density functional BP86 in combination with a triple-ζ polarized basis set produce reliable molecular structures as well as harmonic vibrations. Calculated CN and CO stretching vibrations are analyzed separately. Scaled vibrational frequencies are then applied to assign intermediates in [FeFe]-hydrogenase's reaction cycle. The results nicely complement the previous studies of Darensbourg and Hall, and Zilberman et al. The infrared spectrum of the H(ox) form is in very good agreement with the calculated spectrum of the Fe(I)Fe(II) model complex featuring a free coordination site at the distal Fe atom, as well as, with the calculated spectra of the complexes in which H(2) or H(2)O are coordinated at this site. The spectrum of H(red) measured from Desulfovibrio desulfuricans is compatible with a mixture of a Fe(I)Fe(I) species with all terminal COs, and a Fe(I)Fe(I) species with protonated dtma ligand, while the spectrum of H(red) recently measured from Chlamydomonas reinhardtii is compatible with a mixture of a Fe(I)Fe(I) species with a bridged CO, and a Fe(II)Fe(II) species with a terminal hydride bound to the Fe atom.

Estimating the hydrogen bond energy

First, different approaches to detect hydrogen bonds and to evaluate their energies are introduced newly or are extended. Supermolecular interaction energies of 256 dimers, each containing one single hydrogen bond, were correlated to various descriptors by a fit function depending both on the donor and acceptor atoms of the hydrogen bond. On the one hand, descriptors were orbital-based parameters as the two-center or three-center shared electron number, products of ionization potentials and shared electron numbers, and the natural bond orbital interaction energy. On the other hand, integral descriptors examined were the acceptor-proton distance, the hydrogen bond angle, and the IR frequency shift of the donor-proton stretching vibration. Whereas an interaction energy dependence on 1/r(3.8) was established, no correlation was found for the angle. Second, the fit functions are applied to hydrogen bonds in polypeptides, amino acid dimers, and water cluster, thus their reliability is demonstrated. Employing the fit functions to assign intramolecular hydrogen bond energies in polypeptides, several side chain CH...O and CH...N hydrogen bonds were detected on the fly. Also, the fit functions describe rather well intermolecular hydrogen bonds in amino acid dimers and the cooperativity of hydrogen bond energies in water clusters.

Quantum Chemical Calculation of Raman Intensities for Large Molecules: The Photoisomerization of [{Fe‘S4’(PR3)}2(N2H2)] (‘S4’2− = 1,2-bis(2-Mercaptophenylthio)-Ethane(2−))

Since Raman spectra of isolated large molecules are hardly accessible by present day quantum chemical methods, we demonstrate how Raman intensities for selected vibrational normal modes can be calculated by extension of a semi-numerical, very flexible approach to the calculation of vibrational spectra [see J. Neugebauer et al., J. Comp. Chem. 23 (2002) 895–910]. The methodology is applied to a Ci -symmetric dinuclear diazene iron–sulfur complex with relevance to the biological nitrogen fixation problem. The accuracy of the vibrational spectra allows us to use the spectra for structure determination and assignment of bands to isomeric structures, which were conjectured to be generated by a photoisomerization process. We can in turn support the photoisomerization hypothesis.

Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Computational insights into the O2-evolving complex of photosystem II

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies.

Low-cost evaluation of the exchange Fock matrix from Cholesky and density fitting representations of the electron repulsion integrals

The authors propose a new algorithm, "local K" (LK), for fast evaluation of the exchange Fock matrix in case the Cholesky decomposition of the electron repulsion integrals is used. The novelty lies in the fact that rigorous upper bounds to the contribution from each occupied orbital to the exchange Fock matrix are employed. By formulating these inequalities in terms of localized orbitals, the scaling of computing the exchange Fock matrix is reduced from quartic to quadratic with only negligible prescreening overhead and strict error control. Compared to the unscreened Cholesky algorithm, the computational saving is substantial for systems of medium and large sizes. By virtue of its general formulation, the LK algorithm can be used also within the class of methods that employ auxiliary basis set expansions for representing the electron repulsion integrals.

The First Photoexcitation Step of Ruthenium-Based Models for Artificial Photosynthesis Highlighted by Resonance Raman Spectroscopy

Ruthenium-polypyridine and related complexes play an important role as models for light-harvesting antenna systems to be employed in artificial photosynthesis. In this theoretical and experimental work, the first photoexcitation step of a tetranuclear [Ru2Pd2] complex composed of two ruthenium-bipyridyl subunits and two palladium-based fragments, {[(tbbpy)2Ru(tmbi)]2[Pd(allyl)]2}2+ (tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine, tmbi = 5,6,5',6'-tetramethyl-2,2'-bibenzimidazolate), is investigated by means of experimental and theoretical resonance Raman spectroscopy. The calculated spectra, which were obtained within the short-time approximation combined with time-dependent density functional theory (TDDFT), reproduce the experimental spectrum with excellent agreement. We also compared calculations on off-resonance Raman spectra, for which a completely different theoretical approach has to be used, to experimental ones and again found very good agreement. The [Ru2Pd2] complex represents the probably largest system for which a quantum chemical frequency analysis and a calculation of conventional Raman as well as resonance Raman spectra with reasonable basis sets have been performed. A comparison between the resonance Raman spectra of the [Ru2Pd2] complex and its mononuclear [Ru] building block [(tbbpy)2Ru(tmbi)]2+ and a normal-mode analysis reveal that the [Ru2Pd2] resonance Raman spectrum is composed uniquely from peaks arising from the [Ru] fragment. This observation and an analysis of the Kohn-Sham orbitals mainly involved in the initial electronic excitation in the TDDFT description of the [Ru2Pd2] system support the hypothesis that the initial photoexcitation step of [Ru2Pd2] is a charge-transfer excitation from the ruthenium atoms to the adjacent butyl-2,2'-bipyridine ligands.

Computational approaches to shed light on molecular mechanisms in biological processes

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.

Hydrogen Bond Detection

In this Article we extend the idea of detecting a hydrogen bond solely on one single quantum chemically determined descriptor. We present an improvement of the method introduced by Reiher et al. (Theor. Chim. Acta 2001, 106, 379), who mapped the strength of the hydrogen bond onto an easily accessible quantity, namely, the two-center shared-electron number sigma(HA). First, we show that the linear dependence between the interaction energy from the supermolecular approach and sigma(HA) is valid for a test set of about 120 hydrogen-bonded complexes. Furthermore, we demonstrate that a classification according to acceptor atoms of the hydrogen-bonded complexes can give more accurate results. We thus recommend to detect hydrogen bonds with a specific acceptor atom according to our subset linear regression analysis. Case studies on alcohols and isolated base pairs and trimers from RNA and DNA show the utility of the detection criterion. The shared-electron number method yields that the strength of the N1...N3 hydrogen bond is in the range of 30 kJ/mol. Furthermore the A-U pair is indeed stronger bound than the A-T complex if environmental effects are incorporated in the calculations.

Nitrogen Fixation under Mild Ambient Conditions: Part I—The Initial Dissociation/Association Step at Molybdenum Triamidoamine Complexes

In several recent studies Schrock and collaborators demonstrated for the first time how molecular dinitrogen can be catalytically transformed under mild and ambient conditions to ammonia by a molybdenum triamidoamine complex. In this work, we investigate the geometrical and electronic structures involved in this process of dinitrogen activation with quantum chemical methods. Density functional theory (DFT) has been employed to calculate the coordination energies of ammonia and dinitrogen relevant for the dissociation/association step in which ammonia is substituted by dinitrogen. In the DFT calculations the triamidoamine chelate ligand has been modeled by a systematic hierarchy of increasingly complex substituents at the amide nitrogen atoms. The most complex ligand considered is an experimentally known ligand with an HMT = 3,5-(2,4,6-Me3C6H2)2C6H3 substituent. Several assumptions by Schrock and collaborators on key reaction steps are confirmed by our calculations. Additional information is provided on many species not yet observed experimentally. Particular attention is paid to the role of the charge of the complexes. The investigation demonstrates that dinitrogen coordination is enhanced for the negatively charged metal fragment, that is, coordination is more favorable for the anionic metal fragment than for the neutral species. Coordination of N2 is least favorable for the cationic metal fragment. Furthermore, ammonia abstraction from the cationic complex is energetically unfavorable, while NH3 abstraction is less difficult from the neutral and easily feasible from the anionic low-spin complex.

An Electronic Perspective on the Reduction of an N?N Double Bond at a Conserved Dimolybdenum Core

Density functional theory has been used to assess the role of the bimetallic core in supporting reductive cleavage of the N=N double bond in [Cp2Mo2(mu-SMe)3(mu-eta1:eta1-HN=NPh)]+. The HOMO of the complex, the Mo-Mo delta orbital, plays a key role as a source of high-energy electrons, available for transfer into the vacant orbitals of the N=N unit. As a result, the metal centres cycle between the Mo(III) and Mo(IV) oxidation states. The symmetry of the Mo-Mo delta "buffer" orbital has a profound influence on the reaction pathway, because significant overlap with the redox-active orbital on the N=N unit (pi* or sigma*) is required for efficient electron transfer. The orthogonality of the Mo-Mo delta and N-N sigma* orbitals in the eta1:eta1 coordination mode ensures that electron transfer into the N-N sigma bond is effectively blocked, and a rate-limiting eta1:eta1-->eta1 rearrangement is a necessary precursor to cleavage of the bond.

A Photochemical Activation Scheme of Inert Dinitrogen by Dinuclear RuII and FeII Complexes

A general photochemical activation process of inert dinitrogen coordinated to two metal centers is presented on the basis of high-level DFT and ab initio calculations. The central feature of this activation process is the occupation of an antibonding pi* orbital upon electronic excitation from the singlet ground state S0 to the first excited singlet state S1. Populating the antibonding LUMO weakens the triple bond of dinitrogen. After a vertical excitation, the excited complex may structurally relax in the S1 state and approaches its minimum structure in the S1 state. This excited-state minimum structure features the dinitrogen bound in a diazenoid form, which exhibits a double bond and two lone pairs localized at the two nitrogen atoms, ready to be protonated. Reduction and de-excitation then yield the corresponding diazene complex; its generation represents the essential step in a nitrogen fixation and reduction protocol. The consecutive process of excitation, protonation, and reduction may be rearranged in any experimentally appropriate order. The protons needed for the reaction from dinitrogen to diazene can be provided by the ligand sphere of the complexes, which contains sulfur atoms acting as proton acceptors. These protonated thiolate functionalities bring protons close to the dinitrogen moiety. Because protonation does not change the pi*-antibonding character of the LUMO, the universal and well-directed character of the photochemical activation process makes it possible to protonate the dinitrogen complex before it is irradiated. The pi*-antibonding LUMO plays the central role in the activation process, since the diazenoid structure was obtained by excitation from various occupied orbitals as well as by a direct two-electron reduction (without photochemical activation) of the complex; that is, the important bending of N2 towards a diazenoid conformation can be achieved by populating the pi*-antibonding LUMO.

A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site

We have applied density functional theory, using both pure (BP86) and hybrid (B3LYP and B3LYP*) functionals, to investigate structural parameters and reaction energies for nickel(II)-sulfur coordination compounds, as well as for small cluster models of the Ni-SI and Ni-R redox state of [NiFe] hydrogenases. Results obtained investigating experimentally well-characterized complexes show that BP86 is well suited to describe the structural features of this class of compounds. However, the singlet-triplet energy splitting and even the computed ground state are strongly dependent on the applied functional. Results for the cluster models of [NiFe] hydrogenases lead to the conclusion that in the reduced protein structures characterized by X-ray diffraction a hydride bridges the two metal centres. The energy splitting of the singlet and triplet states in Ni-R and Ni-SI models is calculated to be very small and may be overcome at room temperature to allow a spin crossover. Moreover, the relative stability of the Ni-SI and Ni-R structures adopted in the present investigation is fully compatible with their involvement in the reversible heterolytic cleavage of H(2).