Density functional calculations on the binding of dinitrogen to the FeFe cofactor in Fe-only nitrogenase: FeFeco(mu 6-N2) as intermediate in nitrogen fixation

The geometries and stabilities of the FeFe cofactor at different oxidation states and its complexes with N(2) have been determined by density functional calculations. These calculations support an EPR-inactive resting state of the FeFe cofactor with four Fe(2+) and four Fe(3+) sites (4Fe(2+)4Fe(3+)). FeFeco(mu(6)-N(2)) with a central dinitrogen ligand is predicted to be the most stable complex of the FeFe cofactor with N(2). It is easily formed by penetration of N(2) into the trigonal Fe(6) prism of the FeFe cofactor with an approximate barrier of 4 kcal mol(-1). The present DFT results suggest that an FeFeco(mu(6)-N(2)) entity is a plausible intermediate in dinitrogen fixation by nitrogenase. CO is calculated to bind even more strongly than N(2) to the FeFe cofactor so that CO may inhibit the reduction of nitrogen by Fe-only nitrogenase.     

Ammonia production at the FeMo cofactor of nitrogenase: results from density functional theory

Biological nitrogen fixation has been investigated beginning with the monoprotonated dinitrogen bound to the FeMo cofactor of nitrogenase up to the formation of the two ammonia molecules. The energy differences of the relevant intermediates, the reaction barriers, and potentially relevant side branches are presented. During the catalytic conversion, nitrogen bridges two Fe atoms of the central cage, replacing a sulfur bridge present before dinitrogen binds to the cofactor. A transformation from cis- to trans-diazene has been found. The strongly exothermic cleavage of the dinitrogen bond takes place, while the Fe atoms are bridged by a single nitrogen atom. The dissociation of the second ammonia from the cofactor is facilitated by the closing of the sulfur bridge following an intramolecular proton transfer. This closes the catalytic cycle.     

Activation and protonation of dinitrogen at the FeMo cofactor of nitrogenase

The protonation of N2 bound to the active center of nitrogenase has been investigated using state-of-the-art density-functional theory calculations. Dinitrogen in the bridging mode is activated by forming two bonds to Fe sites, which results in a reduction of the energy for the first hydrogen transfer by 123 kJ/mol. The axial binding mode with open sulfur bridge is less reactive by 30 kJ/mol and the energetic ordering of the axial and bridged binding modes is reversed in favor of the bridging dinitrogen during the first protonation. Protonation of the central ligand is thermodynamically favorable but kinetically hindered. If the central ligand is protonated, the proton is transferred to dinitrogen following the second protonation. Protonation of dinitrogen at the Mo site does not lead to low-energy intermediates.     

Enzymatic and catalytic reduction of dinitrogen to ammonia: Density functional theory characterization of alternative molybdenum active sites

We used density functional calculations to model dinitrogen reduction by a FeMo cofactor containing a central nitrogen atom and by a Mo‐based catalyst. Plausible intermediates, reaction pathways, and relative energetics in the enzymatic and catalytic reduction of N₂ to ammonia at a single Mo center are explored. Calculations indicate that the binding of N₂ to the Mo atom and the subsequent multiple proton–electron transfer to dinitrogen and its protonated species involved in the conversion of N₂ are feasible energetically. In the reduction of N₂ the Mo atom experiences a cycled oxidation state from Mo(IV) to Mo(VI) by nitrogenase and from Mo(III) to Mo(VI) by the molybdenum catalyst, respectively, tuning the gradual reduction of N₂. Such a wide range of oxidation states exhibited by the Mo center is crucial for the gradual reduction process via successive proton–electron transfer. Present results suggest that the Mo atom in the N‐centered FeMo cofactor is a likely alternative active site for dinitrogen binding and reduction under mild conditions once there is an empty site available at the Mo site. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A photochemical activation scheme of inert dinitrogen by dinuclear Ru(II) and Fe(II) 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.     

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.     

Modeling the nitrogenase FeMo cofactor with high‐spin Fe8S9X+ (XN,C) clusters. Is the first step for N2 reduction to NH3 a concerted dihydrogen transfer?

A high-spin Fe(8)S(9)X(+) (X=N, C) cluster is used to model the reduction of molecular nitrogen to ammonia by the nitrogenase FeMo cofactor at the B3LYP/6-311G(d,p)/ECP(Fe,SDD) level of theory. A total of seventy-three structures were optimized (including three transition state optimizations) to explore the structure and energetic of N(2), C(2)H(2), and CO coordination to the Fe(8)S(9)X(+) cluster. After three protonation-reduction (PR) steps (modeled by addition of hydrogen atoms), N(2), C(2)H(2), and CO are predicted to bind to a Fe atom in the exo (cage does not open) position with binding energies of 7.6, 14.7, and 11.7 kcal/mol. With additional PR steps the coordination number of the core nitrogen atom is reduced from six to five and the bridging thiol group becomes a terminal SH(2) group. The fifth and sixth PR steps occur on the core nitrogen and the open Fe site. Coordination of N(2) is enhanced after six PR steps to give an intermediate ideally suited for a concerted dihydrogen transfer from the Fe and core nitrogen atoms to the coordinated N(2). The identity of the central atom (nitrogen or carbon) has only a minor effect on the reaction steps.     

On the origin of dinitrogen hydrogenation promoted by [(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2)

The origin of the hydrogenation of the dinitrogen ligand in [(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2) has been investigated by a combined computational and experimental study. Density functional theory calculations on the zirconocene dinitrogen complex demonstrate significant imido character in the zirconium nitrogen bonds, arising from effective pi-back-bonding from the low-valent zirconium and the side-on bound N2 ligand. The twisted ground-state structure of the N2 complex is a key requirement for nitrogen hydrogenation, as calculations on the model complex [(eta5-C5H5)2Zr]2(mu2,eta2,eta2-N2) reveal reduced overlap as the dihedral angle between the zirconocene wedges approaches 0 degrees . Experimentally, isotopic labeling studies on the microscopic reverse are consistent with a 1,2-addition mechanism for nitrogen hydrogenation.     

How do azoles inhibit cytochrome P450 enzymes? A density functional study

To examine how azole inhibitors interact with the heme active site of the cytochrome P450 enzymes, we have performed a series of density functional theory studies on azole binding. These are the first density functional studies on azole interactions with a heme center and give fundamental insight into how azoles inhibit the catalytic function of P450 enzymes. Since azoles come in many varieties, we tested three typical azole motifs representing a broad range of azole and azole-type inhibitors: methylimidazolate, methyltriazolate, and pyridine. These structural motifs represent typical azoles, such as econazole, fluconazole, and metyrapone. The calculations show that azole binding is a stepwise mechanism whereby first the water molecule from the resting state of P450 is released from the sixth binding site of the heme to create a pentacoordinated active site followed by coordination of the azole nitrogen to the heme iron. This process leads to the breaking of a hydrogen bond between the resting state water molecule and the approaching inhibitor molecule. Although, formally, the water molecule is released in the first step of the reaction mechanism and a pentacoordinated heme is created, this does not lead to an observed spin state crossing. Thus, we show that release of a water molecule from the resting state of P450 enzymes to create a pentacoordinated heme will lead to a doublet to quartet spin state crossing at an Fe-OH(2) distance of approximately 3.0 A, while the azole substitution process takes place at shorter distances. Azoles bind heme with significantly stronger binding energies than a water molecule, so that these inhibitors block the catalytic cycle of the enzyme and prevent oxygen binding and the catalysis of substrate oxidation. Perturbations within the active site (e.g., a polarized environment) have little effect on the relative energies of azole binding. Studies with an extra hydrogen-bonded ethanol molecule in the model, mimicking the active site of the CYP121 P450, show that the resting state and azole binding structures are close in energy, which may lead to chemical equilibrium between the two structures, as indeed observed with recent protein structural studies that have demonstrated two distinct azole binding mechanisms to P450 heme.     

Electrochemical activation of molecular nitrogen at the Ir/YSZ interface

Nitrogen is often used as an inert background atmosphere in solid state studies of electrode and reaction kinetics, of solid state studies of transport phenomena, and in applications e.g. solid oxide fuel cells (SOFC), sensors and membranes. Thus, chemical and electrochemical reactions of oxides related to or with dinitrogen are not supposed and in general not considered. We demonstrate by a steady state electrochemical polarisation experiments complemented with in situ photoelectron spectroscopy (XPS) that at a temperature of 450 °C dinitrogen can be electrochemically activated at the three phase boundary between N(2), a metal microelectrode and one of the most widely used solid oxide electrolytes--yttria stabilized zirconia (YSZ)--at potentials more negative than E = -1.25 V. The process is neither related to a reduction of the electrolyte nor to an adsorption process or a purely chemical reaction but is electrochemical in nature. Only at potentials more negative than E = -2 V did new components of Zr 3d and Y 3d signals with a lower formal charge appear, thus indicating electrochemical reduction of the electrolyte matrix. Theoretical model calculations suggest the presence of anionic intermediates with delocalized electrons at the electrode/electrolyte reaction interface. The ex situ SIMS analysis confirmed that nitrogen is incorporated and migrates into the electrolyte beneath the electrode.     

An ab initio study on the equilibrium structure and torsional potential energy function of dinitrogen tetroxide

The molecular parameters of dinitrogen tetroxide, N₂O₄, have been determined in large-scale ab initio calculations using the multiconfigurational second-order perturbation method, CASSCF/CASPT2, and basis sets of double- to quadruple-zeta quality. With the largest basis set employed, cc-pVQZ for nitrogen and cc-pVTZ for oxygen, the structural equilibrium parameters are determined to be r(NN) = 1.7940 Å, r(NO) = 1.1906 Å and (NNO) = 112.55°. The potential energy barrier at the staggered conformation of the molecule is found to be 2313 cm⁻¹, and the binding energy of the NN bond is calculated to be 4616 cm⁻¹ (13.2 kcal/mol).     

Electronic and magnetic properties of endohedrally doped fullerene Mn@C(60): a total energy study

We perform total energy calculations on a manganese atom encapsulated inside a C(60) cage using density functional theory with the generalized gradient approximation through three optimization schemes and along four paths inside the cage. We find that when Mn is located in the central region, its electronic and magnetic properties are not exactly the same as those of a free Mn atom due to weak coupling between Mn and the cage. As Mn is shifted toward to the edge, the total energy and spin start to change significantly when Mn is situated about one-third of the way between the cage center and edge, and the total energy reaches a local minimum. Finally the interaction between Mn and the cage turns repulsive as Mn approaches the edge. We also find that, along the lowest energy path, there exist three consecutive local energy minima and each of these has a different spin M. The ground state has the lowest M=3, Mn is located about 1.6 A away from the cage center, and the binding energy is 0.08 eV. We attribute the decrease in total energy and spin to Mn and C hybridization.     

Binding modes for the first coupled electron and proton addition to FeMoco of nitrogenase

A combined broken-symmetry density functional and electrostatics approach has been used to model the one-electron reduced and protonated state of the iron-molybdenum cofactor active site of nitrogenase. The active site of the protein contains Fe, Mo, S, N, and O atoms, and many possible sites for protonation have been examined. A novel hydridic proton asymmetrically located in the central cavity created by six Fe sites is most favored from the calculations. Under physiological turnover conditions of low electron flux, the formation of this iron-hydride intermediate may represent a first step towards cofactor liberation of dihydrogen in the absence of dinitrogen.     

Dynamic interplay between diffusion and reaction: nitrogen recombination on Rh{211} in car exhaust catalysis

The adsorption and diffusion of atomic nitrogen on Rh{211} as well as formation and desorption of molecular nitrogen from this surface have been investigated by means of density functional theory (DFT) calculations. The elementary step reaction mechanism derived from this comprehensive DFT study forms the foundation of a detailed microkinetic model including diffusion, recombination, and desorption of nitrogen species. It will be shown that nitrogen formation on a stepped rhodium surface is a dynamic interplay of atomic nitrogen diffusion and reaction. Moreover, evidence will be presented that not one but several on-step recombination reactions are responsible for dinitrogen formation and desorption.     

Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: implications to reactivity and relevance to the nitrogenase problem

Dinitrogen complexes of transition metals exhibit different binding geometries of N2 (end-on terminal, end-on bridging, side-on bridging, side-on end-on bridging), which are investigated by spectroscopy and DFT calculations, analyzing their electronic structure and reactivity. For comparison, a bis(mu-nitrido) complex, where the N--N bond has been split, has been studied as well. Most of these systems are highly covalent, and have strong metal-nitrogen bonds. In the present review, particular emphasis is put on a consideration of the activation of the coordinated dinitrogen ligand, making it susceptible to protonation, reactions with electrophiles or cleavage. In this context, theoretical, structural, and spectroscopic data giving informations on the amount of charge on the N2 unit are presented. The orbital interactions leading to a charge transfer from the metals to the dinitrogen ligand and the charge distribution within the coordinated N2 group are analyzed. Correlations between the binding mode and the observed reactivity of N2 are discussed.     

硼/氮掺杂富勒烯C20的结构和稳定性

应用密度泛函理论(DFT)的B3LYP/6-31G*方法, 对C_20-2nX_2n(X=B, N; n=1、2、3、4)各异构体进行几何构型全优化和振动频率计算, 确定了基态结构, 对它们的取代方式、电子结构、张力和芳香性进行了研究. 氮掺杂不能显著降低分子的张力, C₁₂N₈的张力甚至比C₂₀的还要大, 极不稳定. C₁₈B₂的两个最稳定异构体1,14-C₁₈B₂和1,3-C₁₈B₂都有比较大的能隙和结合能, 具有很强的芳香性, 其张力与C₂₀的相比均显著降低. 1,14-C₁₈B₂ 和1,3-C₁₈B₂具有较高的稳定性, 可以用红外光谱区分这两个构型异构体.     

Transient palladadiphosphanylcarbenes: singlet carbenes with an "inverse" electronic configuration (p(pi)2 instead of sigma2) and unusual transannular metal-carbene interactions (piC-->Pd donation and sigmaPd-->C back-donation)

Upon treatment with [PdCl(allyl)]2, asymmetrically substituted alpha,alpha'-diphosphanyl diazo compounds eliminate dinitrogen to afford C-chlorodiphosphanylmethanide complexes in high yields. In the presence of a chloride-abstracting agent, such as sodium tetraphenylborate, the C-chlorodiphosphanylmethanide complexes react with pyridine and trimethylphosphine, readily affording the corresponding nitrogen and phosphorus ylides. The postulated intermediate in this process, namely palladadiphosphanylcarbenes, could not be spectroscopically characterized, but their transient formation was chemically supported further by a Lewis base exchange reaction between pyridine and 4-dimethylaminopyridine. This hypothesis has also been substantiated by computing the corresponding dissociation energy using two model systems featuring methyl groups at the phosphorus. Of particular interest, density functional theory calculations reveal that these palladadiphosphanylcarbenes have a singlet ground state with an "inverse" ppi2 electronic configuration and a distorted geometry associated with unusual transannular metal-carbene interactions (piC-->Pd donation and sigmaPd-->C back-donation).     

Molybdenum-catalyzed reduction of molecular dinitrogen into ammonia under ambient reaction conditions

Synthesis of transition metal–dinitrogen complexes and stoichiometric transformations of their coordinated dinitrogen into ammonia and hydrazine have so far been well investigated in order to achieve a novel nitrogen fixation under ambient conditions. As an extension of our study, the dimolybdenum–dinitrogen complex bearing PNP pincer ligands has been found to work as an effective catalyst for the formation of ammonia from dinitrogen, where 52 equiv of ammonia are produced based on the catalyst (26 equiv of ammonia are produced based on the molybdenum atom of the catalyst). This is the most effective catalytic reaction system for the formation of ammonia from molecular dinitrogen catalyzed by transition metal–dinitrogen complexes as catalysts under ambient reaction conditions. Herein, we describe recent results concerning the catalytic reaction, including the proposed reaction pathway.     

Mechanism of nitrite reduction at T2Cu centers: electronic structure calculations of catalysis by copper nitrite reductase and by synthetic model compounds

The mechanism of nitrite reduction at the Cu(II) center of both copper nitrite reductase and a number of corresponding synthetic models has been investigated by using both QM/MM and cluster calculations employing density functional theory methods. The mechanism in both cases is found to be very similar. Initially nitrite is bound in a bidentate fashion to the Cu(II) center via the two oxygen atoms. Upon reduction of the copper center, the two possible coordination modes of the protonated nitrite, by either nitrogen or a single oxygen atom, are close in energy, with nitrogen coordination probably preferred. Further protonation of this species leads to N-O bond cleavage, and an electron transfer from the Cu(I) center to the N-O+ ligand, resulting in loss of NO and regeneration of the resting state of the enzyme having a bound water molecule.     

Why vanadium complexes perform poorly in comparison to related molybdenum complexes in the catalytic reduction of dinitrogen to ammonia (Schrock cycle): a theoretical study

Energetics and mechanistic details for the conversion of dinitrogen to ammonia mediated by vanadium triamidoamine has been studied theoretically involving various mechanistic possibilities. For most of the cases, protonation at the amido nitrogen atom is more favorable compared to the terminal one. Further, the most important steps of the mechanism were compared with the well established chemistry of nitrogen fixation mediated by molybdenum. Such a comparison helps in understanding why vanadium triamidoamine complex performs poorly compared to molybdenum. The main factors responsible for the poor performance of the vanadium complex toward NH(3) production are identified as low exergonic cleavage of the N-N bond and limitation of the ligand exchange step via a dissociative mechanism at the end of the cycle to only one possible pathway. A major aspect of the failure of the vanadium complex to mediate the reduction of N(2) to ammonia is the fact that the protonation steps involve major barriers, which cannot be surmounted thermally. Moreover, unlike molybdenum, the associative mechanism with vanadium triamidoamine complex is not likely to operate during the NH(3)/N(2) exchange step.