Density functional calculations for modeling the active site of nickel-iron hydrogenases. 2. Predictions for the unready and ready States and the corresponding activation processes

ZORA relativistic DFT calculations are presented which aim to model the geometric and electronic structure of the active site of NiFe hydrogenases in its EPR-active oxidized states Ni-A (unready state) and Ni-B (ready state). Starting coordinates are taken from the X-ray structure of a mutant of Desulfovibrio fructosovorans hydrogenase refined at 1.81 A resolution. Nine possible candidates for Ni-A and Ni-B are analyzed in terms of their geometric and electronic structure. Comparison of calculated geometric and magnetic resonance parameters with available experimental data indicates that both oxidized states have a micro-hydroxo bridge between the two metal centers. The different electronic structures of both forms can be explained by a modification of a terminal cysteine in Ni-B, best modeled by protonation of the sulfur atom. A possible mechanism for the activation of both oxidized forms is presented.     

Hydride-containing models for the active site of the nickel-iron hydrogenases

The [NiFe]-hydrogenase model complex NiFe(pdt)(dppe)(CO)(3) (1) (pdt = 1,3-propanedithiolate) has been efficiently synthesized and found to be robust. This neutral complex sustains protonation to give the first nickel-iron hydride [1H]BF(4). One CO ligand in [1H]BF(4) is readily substituted by organophosphorus ligands to afford the substituted derivatives [HNiFe(pdt)(dppe)(PR(3))(CO)(2)]BF(4), where PR(3) = P(OPh)(3) ([2H]BF(4)); PPh(3) ([3H]BF(4)); PPh(2)Py ([4H]BF(4), where Py = 2-pyridyl). Variable temperature NMR measurements show that the neutral and protonated derivatives are dynamic on the NMR time scale, which partially symmetrizes the phosphine complex. The proposed stereodynamics involve twisting of the Ni(dppe) center, not rotation at the Fe(CO)(2)(PR(3)) center. In MeCN solution, 3, which can be prepared by deprotonation of [3H]BF(4) with NaOMe, is about 10(4) stronger base than is 1. X-ray crystallographic analysis of [3H]BF(4) revealed a highly unsymmetrical bridging hydride, the Fe-H bond being 0.40 ? shorter than the Ni-H distance. Complexes [2H]BF(4), [3H]BF(4), and [4H]BF(4) undergo reductions near -1.46 V vs Fc(0/+). For [2H]BF(4), this reduction process is reversible, and we assign it as a one-electron process. In the presence of trifluoroacetic acid, proton reduction catalysis coincides with this reductive event. The dependence of i(c)/i(p) on the concentration of the acid indicates that H(2) evolution entails protonation of a reduced hydride. For [2H](+), [3H](+), and [4H](+), the acid-independent rate constants are 50-75 s(-1). For [2H](+) and [3H](+), the overpotentials for H(2) evolution are estimated to be 430 mV, whereas the overpotential for the N-protonated pyridinium complex [4H(2)](2+) is estimated to be 260 mV. The mechanism of H(2) evolution is proposed to follow an ECEC sequence, where E and C correspond to one-electron reductions and protonations, respectively. On the basis of their values for its pK(a) and redox potentials, the room temperature values of ΔG(H?) and ΔG(H-) are estimated as respectively as 57 and 79 kcal/mol for [1H](+).     

Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin

The hydrolysis of adenosine 5'-triphosphate (ATP) at the active site of actin has been studied using density functional calculations. The active site is modeled by the triphosphate tail of ATP, an Mg cation, surrounding water molecules, and the nearby protein residues. Four reaction paths have been followed by constraining coordinates that allow phosphate stretching, nucleophilic attack of the catalytic water, and OH(-) formation via water deprotonation. The lowest-energy barrier (21.0 kcal/mol) is obtained for a dissociative reaction where the terminal phosphate breaks on approaching the catalytic water, followed by proton release via a proton wire mechanism. A higher barrier (39.6 kcal/mol) results for an associative reaction path where OH(-) is formed first, with a pentacoordinated phosphorus atom (P-O distances 2.1 A). Stretching the terminal bridging P-O bond results in bond rupture at 2.8 A with an energy barrier of 28.8 kcal/mol. The residues Gln137 and His161 are not important in the reactions, but insight into their roles in vivo has been obtained. The favored coordination of the end products H(2)PO(4)(-) and ADP(3-) includes a hydrogen bond and an O-Mg-O bridge between the phosphates as well as a hydrogen bond between H(2)PO(4)(-) and the Ser14 side chain. The total energy is 2.1 kcal/mol lower than in the initial reactants. Classical simulations of ATP- and ADP.P(i)-actin show few hydrolysis-induced differences in the protein structure, indicating that phosphate migration is necessary for a change in conformation.     

Selenium-bridged diiron hexacarbonyl complexes as biomimetic models for the active site of Fe-Fe hydrogenases

Three N-substituted selenium-bridged diiron complexes [{(mu-SeCH2)2NC6H4R}Fe2(CO)6] (R = 4-NO2, 7; R = H, 8; R = 4-CH3, 9) were firstly prepared as biomimetic models for the Fe-Fe hydrogenases active site. Models could be generated by the convergent reaction of [(mu-HSe)2Fe2(CO)6] (6) with N,N-bis(hydroxymethyl)-4-nitroaniline (1), N,N-bis(hydroxymethyl)aniline (2), and N,N-bis(hydroxymethyl)-4-methylaniline (3) in 46-52% yields. All the new complexes were characterized by IR, 1H and 13C NMR and HRMS spectra and their molecular structures were determined by single-crystal X-ray analysis. The redox properties of and their dithiolate analogues [{(mu-SCH2)2NC6H4R}Fe2(CO)6] (R = 4-NO2, 7s; R = H, 8s; R = 4-CH3, 9s ) were evaluated by cyclic voltammograms. The electrochemical proton reduction by and were investigated in the presence of p-toluenesulfonic acid (HOTs) to evaluate the influence of changing the coordinating S atoms of the bridging ligands to Se atoms on the electrocatalytic activity for proton reduction.     

Density functional studies of oxidized and reduced methane monooxygenase. Optimized geometries and exchange coupling of active site clusters

The conflicting protein crystallography data for the oxidized form (MMOH(ox)) of methane monooxygenase present a dilemma regarding the identity of the solvent-derived bridging ligands within the active site: do they comprise a diiron unit bridged by 1H2O and 1OH(-) as postulated for Methylococcus capsulatus or 2OH(-) ligands as suggested for Methylosinus trichosporium? Using models derived explicitly from the M. capsulatus and M. trichosporium protein data, spin-unrestricted density functional methods have been used to study two structurally characterized forms of the hydroxylase component of methane monooxygenase. The active site geometries of the oxidized (MMOH(ox)) and two-electron-reduced (MMOH(red)) states have been geometry optimized using several quantum cluster models which take into account the antiferromagnetic (AF) and ferromagnetic (F) coupling of electron spins. Trends in cluster geometries, energetics, and Heisenberg J values have been evaluated. For the majority of models, calculated geometries are in good agreement with the X-ray analyses and appear relatively insensitive to the F or AF alignment of electron spins on adjacent Fe sites. Discrepancies between calculation and experiment appear in the orientation of the coordinated His and Glu amino acid side chains for both MMOH(ox) and MMOH(red) and also in unexpected intramolecular proton transfer in the MMOH(ox) cluster models. There is additional dispersion between (and among) calculated and experimental Fe(3+)-OH(-) distances with relevance to the correct protonation state of the solvent-derived ligands. In an accompanying paper (Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5267), a comparison of the related energetics of the active site models examined herein is further evaluated in the full protein and solvent environment.     

Fe-S complexes containing five-membered heterocycles: novel models for the active site of hydrogenases with unusual low reduction potential

Three biomimetic 2Fe2S complexes [{(micro-SCH2)2NCH2(2-C4H3O)}](Fe2(CO)6), [{(micro-SCH2)2 NCH2(2-C4H3S)}](Fe2(CO)6) and [{(micro-SCH2)2NCH2(5-Br-2-C4H2S)}Fe2(CO)6] were prepared as models for the active site of Fe-only hydrogenase by the convergent process from [(micro-S2)Fe2(CO)6] and N,N-bis(hydromethyl)-2-furan and thiophene. The structures of these complexes were identified spectroscopically and crystallographically. The electrochemical behavior of the complexes and was unique as they showed catalytic proton reduction with a low reduction potential at -1.13 and -1.09 V vs Fc/Fc+, respectively, in the presence of HClO4.     

Density functional calculations for predicting structures and vibrational frequencies of aluminum chloride-fluoride complexes

Quantum chemical calculations are used to study AlCl_y−xF_x^3−y (y = 5 or 6, x = 0,…,y) species that can occur in aluminum electrorefining melts. These theoretical studies are included in a wider research program concerning the chemical instabilities in the bulk of molten salts during the refinement process. Stabilization energies, equilibrium geometries and vibrational frequencies of the complexes are calculated using the Delley functional methodology described in Ref. [1] (B. Delley, J. Chem. Phys., 92 (1990) 508). These computational simulations, discussed and compared with the experimental results demonstrate that density functional calculations can be reliably used in the study of complexes existing in molten salts. Quantum chemical calculations are accurate tools for theoretically predicting structures, physical and chemical properties and vibrational frequencies of known entities as well as unknown compounds.     

Structures and binding energies of the (dibenzoylmethanato)boron difluoride complexes with aromatic hydrocarbons in the ground and excited states. Density functional theory calculations

Structures of the (dibenzoylmethanato)boron difluoride molecule (DBMBF2) and its complexes with a series of aromatic hydrocarbons (benzene; toluene; o-, m-, and p-xylenes, naphthalene; anthracene; and pyrene) in the ground and the first singlet excited states have been calculated. The calculations have been performed by the density functional theory (DFT) and time-dependent density functional theory (TDDFT) for the ground and excited states, respectively, with the empirical dispersion correction. It has been shown that the complexes in the ground and excited states have similar stacking structures and are characterized by short contacts between the F atom of DBMBF2 and H atoms of the hydrocarbon molecule, which decrease on transition from the ground to the excited state. The calculated binding energies in the complexes in the excited state are two to three times higher than those in the ground state. The charge transfer in the ground state of the complexes is insignificant and directed from DBMBF2 to the ligand, while in the excited state it is 0.6–0.8 e and directed from the ligand to DBMBF2.     

Synthesis and structural characterization of diiron azadithiolate complexes relevant to the active site of [FeFe] hydrogenases

Two N-functionally substituted diiron azadithiolate complexes, [(µ-SCH₂)₂NCH₂CH₂OC(O)C₆H₄I-p]Fe₂(CO)₆ (1) and {[(µ-SCH₂)₂NCH₂CH₂OC(O)C₆H₄I-p]Fe₂(CO)₅Ph₂PCH}₂ (2) as models for the active site of [FeFe] hydrogenases, have been prepared and fully characterized. Complex 1 was prepared by the reaction of [(µ-SCH₂)₂NCH₂CH₂OH]Fe₂(CO)₆ with p-iodobenzoic acid in the presence of 4-dimethylaminopyridine (DMAP) and N,N′-dicyclohexylcarbodiimide (DCC) in 78% yield. Further treatment of 1 with 1 equiv. of Me₃NO?·?2H₂O followed by 0.5 equiv. of trans-1,2-bis(diphenylphosphino)ethylene (dppe) affords 2 in 60% yield. The new complexes 1 and 2 were characterized by IR and ¹H (¹³C, ³¹P) NMR spectroscopic techniques and their molecular structures were confirmed by X-ray diffraction analysis. The molecular structure of 1 has two conformational isomers, in one isomer its N-functional substituent is axial to its bridged nitrogen and in the other isomer its N-functional substituent is equatorial. The crystal structure of 2 revealed that its N-functional substituents are equatorial to its nitrogens and dppe occupies the two apical positions of the square-pyramidal irons.     

Density functional calculations of 9-diphenylaminoacridine fluorescent indicator and its interactions with analyte molecules: I. Structures of complexes in the ground electronic states and absorption spectra

The interaction of 9-diphenylaminoacridine dye (indicator) with several small analyte molecules (methanol, acetonitrile, acetone, tetrahydrofuran, benzene, ammonia, formaldehyde, and acetaldehyde) has been theoretically studied in relation to the problem of the development of optical chemosensors based on organic dyes. The structures of the resulting complexes and the absorption spectra of 9-diphenylaminoacridine and its complexes with analytes were calculated using density functional theory (DFT) with the PBE0 functional and the 6-31G(d,p) basis set. It was demonstrated that complexes of two types with different mutual arrangements of molecules corresponding to the lateral and stacking structures can be formed for each analyte. The calculated absorption spectrum only weakly changes upon complex formation, which is in agreement with experimental data on the absorption spectra of 2,7-dimethyl-9-ditolylaminoacridine in solutions of corresponding solvents. The method for the calculation of excited states that was used in this work can be applied to the calculation of the fluorescence spectra of 9-diphenylaminoacridine complexes.     

Density functional calculations of 9-diphenylaminoacridine fluorescent indicator and its interactions with analyte molecules: II. Structures of complexes in the excited electronic states and emission spectra

Structures of the 9-diphenylaminoacridine (DPAA) dye and its complexes with several small analyte molecules (methanol, acetonitrile, acetone, tetrahydrofuran, benzene, ammonia, formaldehyde, and acetaldehyde) in the first excited singlet state and positions of emission bands in these systems were calculated using time-dependent density functional theory (TDDFT) with the PBE0 functional and the 6–31G(d, p) basis set. It was demonstrated that in the first excited singlet state, as well as in the ground state, complexes of two types with different mutual arrangements of molecules corresponding to the lateral and stacking structures can be formed for each analyte. These structures are very similar to the structures found for the complexes in the ground state. For the majority of the complexes in the excited state, stacking structures are more stable than lateral structures. It was found that for stacking structures, shifts of the DPAA emission band caused by complex formation correlate with the experimental solvatochromic effect in the corresponding solvent, whereas this correlation was not observed for lateral structures.     

Synthetic modeling of the active site of native metalloenzymes by trimethylacetatozinc complexes

Synthetic approaches are discussed to a preparation of binuclear trimethylacetatozinc complexes containing an M₂(μ-OOCR)₂L₄ binuclear fragment, which is found in the active site of native metalloenzymes.     

Density functional calculations of NMR shielding tensors for paramagnetic systems with arbitrary spin multiplicity: validation on 3d metallocenes

The calculation of nuclear shieldings for paramagnetic molecules has been implemented in the ReSpect program, which allows the use of modern density functional methods with accurate treatments of spin-orbit effects for all relevant terms up to order Omicron(alpha4) in the fine structure constant. Compared to previous implementations, the methodology has been extended to compounds of arbitrary spin multiplicity. Effects of zero-field splittings in high-spin systems are approximately accounted for. Validation of the new implementation is carried out for the 13C and 1H NMR signal shifts of the 3d metallocenes 4VCp2, 3CrCp2, 2MnCp2, 6MnCp2, 2CoCp2, and 3NiCp2. Zero-field splitting effects on isotropic shifts tend to be small or negligible. Agreement with experimental isotropic shifts is already good with the BP86 gradient-corrected functional and is further improved by admixture of Hartree-Fock exchange in hybrid functionals. Decomposition of the shieldings confirms the dominant importance of the Fermi-contact shifts, but contributions from spin-orbit dependent terms are frequently also non-negligible. Agreement with 13C NMR shift tensors from solid-state experiments is of similar quality as for isotropic shifts.     

Protonation, electrochemical properties and molecular structures of halogen-functionalized diiron azadithiolate complexes related to the active site of iron-only hydrogenases

Diiron complexes [{(micro-SCH2)2NCH2C6H4X}{Fe(CO)2L}2] (L = CO, X = 2-Br, 1; 2-F, 2; 3-Br, 3; L = PMe(3), X = 2-Br, 4) were prepared as biomimetic models of the iron-only hydrogenase active site. The N-protonated species [(NH)]+ClO(4)(-), [(NH)](+)ClO(4)(-) and the micro-hydride diiron complex [4(FeHFe)]+PF(6)(-) were obtained in the presence of proton acids and well characterized. The protonation process of 4 was studied by in-situ IR and NMR spectroscopy, which suggests the formation of the diprotonated species [4(NH)(FeHFe)](2+) in the presence of an excess of proton acid. The molecular structures of 1, [(NH)]+ClO(4)(-), 4 and [4(FeHFe)]+PF(6)(-) were determined by X-ray crystallography. The single-crystal X-ray analysis reveals that an intramolecular H...Br contact (2.82 A) in the crystalline state of [1(NH)]+ClO(4)(-). In the presence of 1-6 equiv of the stronger acid HOTf, complex 1 is readily protonated on the bridged-N atom and can electrochemically catalyze the proton reduction at a relatively mild potential (ca.-1.0 V). Complex 4 is also electrocatalytic active at -1.4 V in the presence of HOTf with formation of the micro-hydride diiron species.     

Density functional calculations of ATP systems. 1. Crystalline ATP hydrates and related molecules

Adenosine 5'-triphosphate (ATP) is an essential energy carrier in mammalian and other cells, and its hydrolysis to the diphosphate (ADP) in the presence of metal cations (e.g., Mg(2+) or Ca(2+)) is one of the most prevalent biochemical reactions. We describe here density functional (DF) calculations on closely related systems and compare the results with other calculations and available experimental data: Na(H2O)n +, Mg(H2O)n 2+, and Ca(H2O)n 2+ clusters (n = 1, 4-7), the crystalline pyrophosphates Mg(2)P(2)O(7).6H2O and alpha-CaNa(2)P(2)O(7).4H2O, and crystalline Na(2)ATP.3H2O. The last of these comprises asymmetric units of ATP dimers (monomers A and B) in a double-protonated state H(2)(ATP)(2-). The calculated structures agree well with available measurements and provide additional information, including the location of the H atoms. Analysis of the dipole moments of individual ATP monomers and their dimers shows that the crystal comprises blocks of opposing dipoles. Replacing one Na+ ion with Mg2+ or Ca2+ results in a significant elongation of the terminal bridging P-O bond. The calculations provide benchmarks for the use of DF methods in ATP systems and are used in the companion paper to study the hydrolysis of ATP at the active site of the protein actin.     

Active-site models for the nickel-iron hydrogenases: effects of ligands on reactivity and catalytic properties

Described are new derivatives of the type [HNiFe(SR)(2)(diphosphine)(CO)(3)](+), which feature a Ni(diphosphine) group linked to a Fe(CO)(3) group by two bridging thiolate ligands. Previous work had described [HNiFe(pdt)(dppe)(CO)(3)](+) ([1H](+)) and its activity as a catalyst for the reduction of protons (J. Am. Chem. Soc. 2010, 132, 14877). Work described in this paper focuses on the effects on properties of NiFe model complexes of the diphosphine attached to nickel as well as the dithiolate bridge, 1,3-propanedithiolate (pdt) vs 1,2-ethanedithiolate (edt). A new synthetic route to these Ni-Fe dithiolates is described, involving reaction of Ni(SR)(2)(diphosphine) with FeI(2)(CO)(4) followed by in situ reduction with cobaltocene. Evidence is presented that this route proceeds via a metastable μ-iodo derivative. Attempted isolation of such species led to the crystallization of NiFe(Me(2)pdt)(dppe)I(2), which features tetrahedral Fe(II) and square planar Ni(II) centers (H(2)Me(2)pdt = 2,2-dimethylpropanedithiol). The new tricarbonyls prepared in this work are NiFe(pdt)(dcpe)(CO)(3) (2, dcpe = 1,2-bis(dicyclohexylphosphino)ethane), NiFe(edt)(dppe)(CO)(3) (3), and NiFe(edt)(dcpe)(CO)(3) (4). Attempted preparation of a phenylthiolate-bridged complex via the FeI(2)(CO)(4) + Ni(SPh)(2)(dppe) route gave the tetrametallic species [(CO)(2)Fe(SPh)(2)Ni(CO)](2)(μ-dppe)(2). Crystallographic analysis of the edt-dcpe compund [2H]BF(4) and the edt-dppe compound [3H]BF(4) verified their close resemblance. Each features pseudo-octahedral Fe and square pyramidal Ni centers. Starting from [3H]BF(4) we prepared the PPh(3) derivative [HNiFe(edt)(dppe)(PPh(3))(CO)(2)]BF(4) ([5H]BF(4)), which was obtained as a ～2:1 mixture of unsymmetrical and symmetrical isomers. Acid-base measurements indicate that changing from Ni(dppe) (dppe = Ph(2)PCH(2)CH(2)PPh(2)) to Ni(dcpe) decreases the acidity of the cationic hydride complexes by 2.5 pK(a)(PhCN) units, from ～11 to ～13.5 (previous work showed that substitution at Fe leads to more dramatic effects). The redox potentials are more strongly affected by the change from dppe to dcpe, for example the [2](0/+) couple occurs at E(1/2) = -820 for [2](0/+) vs -574 mV (vs Fc(+/0)) for [1](0/+). Changes in the dithiolate do not affect the acidity or the reduction potentials of the hydrides. The acid-independent rate of reduction of CH(2)ClCO(2)H by [2H](+) is about 50 s(-1) (25 °C), twice that of [1H](+). The edt-dppe complex [2H](+) proved to be the most active catalyst, with an acid-independent rate of 300 s(-1).     

Density functional theory calculations for endohedral complexes of non-pi C60H60 cage with small guest molecules

Hybrid density-functional theory (B3LYP) calculations were carried out to determine the structures and energies of endohedral complexes of non-pi C(60)H(60) with H(2), CO, and LiH. It was demonstrated that the endohedral complexes of C(60)H(60) with the above three guest molecules are more stable than the corresponding complexes with C(60). Furthermore, the interaction between C(60)H(60) and the inside H(2) or CO is negligible, but the formation of the LiH-C(60)H(60) complex is exothermic with a stabilization energy of -6.0 kcal/mol. While the bond lengths of H(2) and CO changed a little when placed inside the cages, that of the LiH molecule increased and decreased inside C(60)H(60) and C(60), respectively.     

High level ab initio and DFT calculations of models of the catalytically active Ni-Fe hydrogenases

Multi-reference M?ller-Plesset calculations of a model of the Ni-SI state of nickel-iron hydrogenase predict a singlet rather than a triplet state for this species, and show that it is better described with a BP86 rather than a B3LYP functional.