Bimetallic carbonyl thiolates as functional models for Fe-only hydrogenases

The anion [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3))](-) (2(-)) is protonated by sulfuric or toluenesulfonic acid to give HFe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3)) (2H), the structure of which has the hydride bridging the Fe atoms with the PMe(3) and CN(-) trans to the same sulfur atom. (1)H, (13)C, and (31)P NMR spectroscopy revealed that HFe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3)) is stereochemically rigid on the NMR time scale with four inequivalent carbonyl ligands. Treatment of 2(-) with (Me(3)O)BF(4) gave Fe(2)(S(2)C(3)H(6))(CNMe)(CO)(4)(PMe(3)) (2Me). The Et(4)NCN-induced reaction of Fe(2)(S(2)C(3)H(6))(CO)(6) with P(OMe)(3) gave [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)[P(OMe)(3)]](-) (4). Spectroscopic and electrochemical measurements indicate that 2H can be further protonated at nitrogen to give [HFe(2)(S(2)C(3)H(6))(CNH)(CO)(4)(PMe(3))](+) (2H(2)(+)). Electrochemical and analytical data show that reduction of 2H(2)(+) gives H(2) and 2(-). Parallel electrochemical studies on [HFe(2)(S(2)C(3)H(6))(CO)(4)(PMe(3))(2)](+) (3H(+)) in acidic solutions led also to catalytic proton reduction. The 3H(+)/3H couple is reversible, whereas the 2H(2)(+)/2H(2) couple is not, because of the efficiency of the latter as a proton reduction catalyst. Proton reduction is proposed to involve protonation of reduced diiron hydrides. DFT calculations establish that the regiochemistry of protonation is subtly dependent on the coligands but is more favorable to occur at the Fe-Fe bond for [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PMe(3))](-) than for [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)(PH(3))](-) or [Fe(2)(S(2)C(3)H(6))(CN)(CO)(4)[P(OMe)(3)]](-). The Fe(2)H unit stabilizes the conformer with eclipsed CN and PMe(3) because of an attractive electrostatic interaction between these ligands.     

Diferrous cyanides as models for the Fe-only hydrogenases

The first systematic study of diferrous dicyano dithiolates is described. Oxidation of [Fe2(S2C2H4)(CN)2(CO)4](2-) in the presence of cyanide and tertiary phosphines and of Fe2(S2C2H4)(CO)4(PMe3)2 in the presence of cyanide affords a series of diferrous cyanide derivatives that bear a stoichiometric, structural, and electronic relationship to the H(ox)(air) state of the Fe-only hydrogenases. With PPh3 as the trapping ligand, we obtained an unsymmetrical isomer of Fe2(S2C2H4)(mu-CO)(CN)2(PPh3)2(CO)2, as confirmed crystallographically. This diferrous cyanide features the semibridging CO-ligand, with Fe-muC bond lengths of 2.15 and 1.85 A. Four isomers of Fe2(S2C2H4)(mu-CO)(CN)2(PMe3)2(CO)2 were observed, the initial product again being unsymmetrical but more stable isomers being symmetrical. DFT calculations confirm that the most stable isomers of Fe2(S2C2H4)(mu-CO)(CN)2(PMe3)2(CO)2 have cyanide trans to mu-CO. Oxidative decarbonylation also afforded the new tetracyanide [Fe2(S2C2H4)(mu-CO)(CN)4(CO)2]2-. Insights into the oxidative decarbonylation mechanism of these syntheses come from the spectroscopic characterization of the tetracarbonyl [Fe2(S2C2H4)(mu-CO)(CN)3(CO)3](-). This species reacts with PEt3 to produce the stable adduct [Fe2(S2C2H4)(mu-CO)(CN)3(CO)2(PEt3)](-).     

A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases

Fe-only hydrogenases are enzymes that catalyze dihydrogen production or oxidation, due to the presence of an unusual Fe(6)S(6) cluster (the so-called H-cluster) in their active site, which is composed of a Fe(2)S(2) subsite, directly involved in catalysis, and a classical Fe(4)S(4) cubane cluster. Here, we present a hybrid quantum mechanical and molecular mechanical (QM/MM) investigation of the Fe-only hydrogenase from Desulfovibrio desulfuricans, in order to unravel key issues regarding the activation of the enzyme from its completely oxidized inactive state (Hoxinact) and the influence of the protein environment on the structural and catalytic properties of the H-cluster. Our results show that the Fe(2)S(2) subcluster in the Fe(II)Fe(II) redox state - which is experimentally observed for the completely oxidized form of the enzyme - binds a water molecule to one of its metal centers. The computed QM/MM energy values for water binding to the diferrous subsite are in fact over 70 kJ mol(-1); however, the affinity toward water decreases by 1 order of magnitude after a one-electron reduction of H(ox)(inact), thus leading to the release of coordinated water from the H-cluster. The investigation of a catalytic cycle of the Fe-only hydrogenase that implies formation of a terminal hydride ion and a di(thiomethyl)amine (DTMA) molecule acting as an acid/base catalyst indicates that all steps have reasonable reaction energies and that the influence of the protein on the thermodynamic profile of H(2) production catalysis is not negligible. QM/MM results show that the interactions between the Fe(2)S(2) subsite and the protein environment could give place to structural rearrangements of the H-cluster functional for catalysis, provided that the bidentate ligand that bridges the iron atoms in the binuclear subsite is actually a DTMA residue.     

Proton reduction and dihydrogen oxidation on models of the [2Fe]H cluster of [Fe] hydrogenases. A density functional theory investigation

Density functional theory was used to compare reaction pathways for H2 formation and H+ reduction catalyzed by models of the binuclear cluster found in the active site of [Fe] hydrogenases. Terminal H+ binding to an Fe(I)-Fe(I) form, followed by monoelectron reduction and protonation of the di(thiomethyl)amine ligand, can conveniently lead to H2 formation and release, suggesting that this mechanism could be operative within the enzyme active site. However, a pathway that implies the initial formation of Fe(II)-Fe(II) mu-H species and release of H2 from an Fe(II)-Fe(I) form is characterized by only slightly less favored energy profiles. In both cases, H2 formation becomes less favored when taking into account the competition between CN and amine groups for H+ binding, an observation that can be relevant for the design of novel synthetic catalysts. H2 cleavage can take place on Fe(II)-Fe(II) redox species, in agreement with previous proposals [Fan, H.-J.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828] and, in complexes characterized by terminal CO groups, does not need the involvement of an external base. The step in H2 oxidation characterized by larger energy barriers corresponds to the second H+ extraction from the cluster, both considering Fe(II)-Fe(II) and Fe(II)-Fe(III) species. A comparison of the different reaction pathways reveals that H2 formation could involve only Fe(I)-Fe(I), Fe(II)-Fe(I), and Fe(II)-Fe(II) species, whereas Fe(III)-Fe(II) species might be relevant in H2 cleavage.     

Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers

The mechanism of the enzymatic hydrogen bond forming/breaking (2H(+) + 2e<==>H(2)) and the plausible charge and spin states of the catalytic diiron subcluster [FeFe](H) of the H cluster in Fe-only hydrogenases are probed computationally by the density functional theory. It is found that the active center [FeFe](H) can be rationally simulated as [[H](CH(3)S)(CO)(CN(-))Fe(p)(CO(b))(mu-SRS)Fe(d)(CO)(CN(-))L], where the monovalence [H] stands for the [4Fe4S](H)(2+) subcluster bridged to the [FeFe](H) moiety, (CH(3)S) represents a Cys-S, and (CO(b)) represents a bridging CO. L could be a CO, H(2)O, H(-), H(2), or a vacant coordination site on Fe(d). Model structures of possible redox states are optimized and compared with the X-ray crystallographic structures and FTIR experimental data. On the basis of the optimal structures, we study the most favorable path of concerted proton transfer and electron transfer in H(2)-forming/breaking reactions at [FeFe](H). Previous mechanisms derived from quantum chemical computations of Fe-only hydrogenases (Cao, Z.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3734; Fan, H.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828) involved an unidentified bridging residue (mu-SRS), which is either a propanedithiolate or dithiomethylamine. Our proposed mechanism, however, does not require such a ligand but makes use of a shuttle of oxidation states of the iron atoms and a reaction site between the two iron atoms. Therefore, the hydride H(b)(-) (bridged to Fe(p) and Fe(d)) and eta(2)-H(2) at Fe(p) or Fe(d) most possibly play key roles in the dihydrogen reversible oxidation at the [FeFe](H) active center. This suggested way of H(2) formation/splitting is reminiscent of the mechanism of [NiFe] hydrogenases and therefore would unify the mechanisms of the two related enzymes.     

Characterization of a diferrous terminal hydride mechanistically relevant to the Fe-only hydrogenases

Reduction of diferrous dithiolato complexes with hydride donor reagents affords the first example of the previously elusive terminal diferrous hydride, [Fe2(edt)(mu-CO)(H)(CO)(PMe3)4]PF6 (edt = S2C2H4). Crystallographic characterization shows that this model contains an asymmetrical semi-bridging CO trans to a terminal hydrido, as indicated in the Hred state in the D. desulfuricans enzyme. The model reacts with protons to yield H2 and rearranges via an intramolecular process to the isomeric mu-hydrido isomer, which is unreactive toward protons.     

Density functional study of small neutral and charged silver cluster hydrides

Small neutral, anionic, and cationic silver cluster hydrides AgnH and anionic HAgnH (n=1-7) have been studied using the PW91PW91 density functional method. It was found that the most stable structure of the AgnH complex (neutral or charged) does not always come from that of the lowest energy bare silver cluster plus an attached H atom. Among various possible adsorption sites, the bridge site is energetically preferred for the cationic and most cases of neutral Agn. For anionic Agn, the top site is preferred for smaller Agn within n相似文献   

Density functional study of the mechanism of the Beckmann rearrangement catalyzed by H-ZSM-5: a cluster and embedded cluster study

The mechanism of the Beckmann rearrangement (BR) catalyzed by the ZSM-5 zeolite has been investigated by both the quantum cluster and embedded cluster approaches at the B3LYP level of theory using the 6-31G(d,p) basis set. Single-point calculations were carried out at the MP2/6-311G(d,p) level of theory to improve energetic properties. The embedded cluster model suggests that the initial step of the Beckmann rearrangement is not the O-protonated oxime but the N-protonated oxime. The energy barriers derived from the proton shuttle of the N-bound to the O-bound isomer are determined to be approximately 99 and approximately 40 kJ/mol for the embedded cluster and quantum cluster approaches, respectively. The difference in the activation energy is due mainly to the effect of the Madelung potential from the zeolite framework. The next step is the rearrangement step, which is the transformation of the O-protonated oxime to be an enol-formed amide compound, formimidic acid. The activation energy, at the rearrangement step, is calculated to be approximately 125 and approximately 270 kJ/mol for the embedded cluster and quantum cluster approaches, respectively. The final step is the tautomerization step which transforms the enol-form to the keto-form, formamide compound. The energy barrier for tautomerization is calculated to be 123 and 151 kJ/mol for the embedded cluster and quantum cluster approaches, respectively. These calculated results suggest that the rate-determining step of the vapor phase of the Beckmann rearrangement on H-ZSM-5 is the rearrangement or tautomerization step.     

Density functional theory study of the oxidation of methanol to formaldehyde on a hydrated vanadia cluster

Density functional theory was used to study the mechanism for the oxidation of methanol to formaldehyde. A vanadium oxide cluster O?V(OH)₃ has been utilized to represent the catalytic system under hydrated conditions, i.e., in the presence of V? OH hydroxyl groups. Two types of methoxy‐intermediates have been considered: a penta‐coordinate methoxy‐intermediate (OH)₄V(OCH₃) and a tetrahedral methoxy‐intermediate (OH)₂VO(OCH₃)(H₂O). The most plausible reaction pathway corresponds to the process involving first the formation of the tetrahedral methoxide, and a subsequent rate‐limiting step where hydrogen is transferred from the methoxy groups toward the oxygen atom of the vanadyl V?O site. The reaction mechanism is a typical two‐state reactivity process due to a change of the multiplicity (reactive singlet → product triplet) along the reaction coordinate accompanied by a reduction of the vanadium center from V^V (d⁰) to V^III (d²). Minimum energy crossing points were localized and possible spin inversion processes are discussed by means of the intrinsic reaction coordinate approach to find the most favorable reaction pathways. The hydration effect is found to be mainly the destabilization of the methoxy intermediates. An alternative reaction pathway with a lower apparent barrier is presented. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Reactivation pathway of the hydrogenase H‐cluster: Density functional theory study

This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H‐cluster, the active site of Fe‐only hydrogenases. The H‐cluster is a dimetal complex, Fe–Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H₂O, and OH^?, are bound to the distal iron (Fe_d). Density functional theory (DFT) calculations on the native and ruthenium‐modified H‐cluster have been performed using the B3LYP functional with 6‐31+G** and 6‐311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH^? inhibited H‐cluster, which proceeds by an initial protonation of the Fe_d–OH^? complex. The proposed reaction pathway has all its intermediate reactions ensue exothermically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Density functional theory study of an all ferrous 4Fe-4S cluster

The all-ferrous, carbene-capped Fe(4)S(4) cluster, synthesized by Deng and Holm (DH complex), has been studied with density functional theory (DFT). The geometry of the complex was optimized for several electronic configurations. The lowest energy was obtained for the broken-symmetry (BS) configuration derived from the ferromagnetic state by reversing the spin projection of one of the high spin (S(i) = 2) irons. The optimized geometry of the latter configuration contains one unique and three equivalent iron sites, which are both structurally and electronically clearly distinguishable. For example, a distinctive feature of the unique iron site is the diagonal Fe···S distance, which is 0.3 ? longer than for the equivalent irons. The calculated (57)Fe hyperfine parameters show the same 1:3 pattern as observed in the M?ssbauer spectra and are in good agreement with experiment. BS analysis of the exchange interactions in the optimized geometry for the 1:3, M(S) = 4, BS configuration confirms the prediction of an earlier study that the unique site is coupled to the three equivalent ones by strong antiferromagnetic exchange (J > 0 in J Σ(j<4)?(4)·?(j)) and that the latter are mutually coupled by ferromagnetic exchange (J' < 0 in J' Σ(i相似文献   

Density functional study on the sensing properties of nano-sized BeO tube toward H2S

Using density functional calculations, we have investigated the adsorption of a H₂S molecule on the pristine and Si-doped BeO nanotubes (BeONT). It was found that the H₂S molecule is physically adsorbed on the pristine BeONT with adsorption energies ranging from 3.0 to 4.2 kcal/mol. Substituting a Be or O atom of the tube by Si increases the adsorption energy to 6.9–17.2 kcal/mol. We found that substituting an O atom by Si makes the electronic properties of the BeONT strongly sensitive to the H₂S molecule. Therefore, the process of Si doping provides a good strategy for improving the sensitivity of BeONT to toxic H₂S, which cannot be trapped and detected by the pristine BeONT. Also, the emitted electron current density from the Si_O–BeONT will be significantly increased after the H₂S adsorption.     

Spectroscopic and crystallographic evidence for the N-protonated FeIFeI azadithiolate complex related to the active site of Fe-only hydrogenases

The complex [{(mu-SCH2)2N(CH2C6H4-2-Br)}Fe2(CO)6] and its N-protonated species, as structural models of the Fe-only hydrogenase active site, were identified spectroscopically and crystallographically, and their molecular structures show the 0.04-0.1 A lengthening of the three N-C bonds and an intramolecular HBr contact (2.82 Angstroms) in the crystalline state of the N-protonated species.     

Density functional theory study of eight-atom germanium clusters: effect of electron count on cluster geometry

Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge8z(z=-6, -4, -2, 0, +2, +4) using nine initial geometries. For Ge8(2-) the D2d bisdisphenoid structure predicted by the Wade-Mingos rules is not computed to be the global minimum but instead lies 3.9 kcal mol-1 above the Td tetracapped tetrahedron global minimum predicted to exhibit spherical aromaticity. The hyperelectronic clusters Ge(8)4- and Ge8(6-) have nido B8H12 and square antiprism structures, respectively, as global minima in accord with the Wade-Mingos rules and experimental data on E(8)2+(E=Sb, Bi) cations. Hypoelectronic eight-vertex clusters isoelectronic and isolobal with Ge8, Ge8(2+) and Ge(8)4+ are not known experimentally. Their computed structures include smaller polyhedra having one or more capped triangular faces as well as more open non-polyhedral structures.     

Density functional study of ammonia activation by late first-row transition metal cations

Density functional theory (DFT) in its B3LYP implementation is used to investigate the reaction of ammonia with the late (Co(+), Ni(+), and Cu(+)) first-row transition metal cations in both high- and low-spin states. The potential energy surfaces (PES's) leading to three different exit channels are closely examined. The binding energies for the reaction products are calculated and compared with the corresponding experimental values. A comparison with our earlier works covering the reactivity of the Sc-Fe series of cations is made in order to underline similarities and differences of the reaction mechanisms as well as to establish trends along the row.     

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.     

Density functional theory study of nine-atom germanium clusters: effect of electron count on cluster geometry

Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge(9)(z) clusters (z = -6, -4, -3, -2, 0, +2, and +4) starting from three different initial configurations. Double-zeta quality LANL2DZ basis functions extended by adding one set of polarization (d) and one set of diffuse (p) functions were used. The global minimum for Ge(9)(2)(-) is the tricapped trigonal prism expected by Wade's rules for a 2n + 2 skeletal electron structure. An elongated tricapped trigonal prism is the global minimum for Ge(9)(4)(-) similar to the experimentally found structure for the isoelectronic Bi(9)(5+). However, the capped square antiprism predicted by Wade's rules for a 2n + 4 skeletal electron structure is only 0.21 kcal/mol above this global minimum indicating that these two nine-vertex polyhedra have very similar energies in this system. Tricapped trigonal prismatic structures are found for both singlet and triplet Ge(9)(6)(-), with the latter being lower in energy by 3.66 kcal/mol and far less distorted. The global minimum for the hypoelectronic Ge(9) is a bicapped pentagonal bipyramid. However, a second structure for Ge(9) only 4.54 kcal/mol above this global minimum is the C(2)(v)() flattened tricapped trigonal prism structure found experimentally for the isoelectronic Tl(9)(9)(-). For the even more hypoelectronic Ge(9)(2+), the lowest energy structure consists of an octahedron fused to two trigonal bipyramids. For Ge(9)(4+), the global minimum is an oblate (squashed) pentagonal bipyramid with two pendant Ge vertices.     

Density functional calculation of transition metal cluster energy surfaces

A quantum field mechanics of an electron subsystem in 3D physical space as the topology of compact atomic clusters with spontaneously broken local canonical symmetry is used for investigation of different types of microdefects in the condensed state of transition metals. The theory is illustrated with results of calculation of small compact Fe_n clusters (n = 2, 6, 14).     

Density functional theory study of enantiospecific adsorption at chiral surfaces

Density functional theory calculations are carried out for the adsorption of a chiral molecule, (S)- and (R)-HSCH(2)CHNH(2)CH(2)P(CH(3))(2), on a chiral surface, Au(17 11 9)(S)(). The S-enantiomer is found to bind more strongly than the R-enantiomer by 8.8 kJ/mol, evidencing that the chiral nature of the kink sites at the Au(17 11 9) surface leads to enantiospecific binding. The adsorption of two related chiral molecules, HSCH(2)CHNH(2)COOH ("cysteine") and HSCH(2)CHNH(2)CH(2)NH(2), does not, however, lead to enantiospecific binding. The results of the density functional calculations are broken down into a local binding model in which each of the chiral molecule's three contact points with the surface provides a contribution to the overall adsorption bond strength. The enantiospecific binding is demonstrated to originate from the simultaneous optimization of these three local bonds. In the model, the deformation energy costs of both the molecule and the surface are further included. The model reveals that the molecule may undergo large deformations in the attempt to optimize the three bonds, while the surface deforms to a lesser extent. The most favorable binding configurations of each enantiomer are, however, characterized by small deformation energies only, justifying a local binding picture.