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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 2010 Feb 10;107(9):3994–3997. doi: 10.1073/pnas.0913399107

A model for the CO-inhibited form of [NiFe] hydrogenase: synthesis of (CO)3Fe(μ-StBu)3Ni{SC6H3-2,6-(mesityl)2} and reversible CO addition at the Ni site

Yasuhiro Ohki 1, Kazunari Yasumura 1, Masaru Ando 1, Satoko Shimokata 1, Kazuyuki Tatsumi 1,1
PMCID: PMC2840173  PMID: 20147622

Abstract

A [NiFe] hydrogenase model compound having a distorted trigonal-pyramidal nickel center, (CO)3Fe(μ-StBu)3Ni(SDmp), 1 (Dmp = C6H3-2,6-(mesityl)2), was synthesized from the reaction of the tetranuclear Fe-Ni-Ni-Fe complex [(CO)3Fe(μ-StBu)3Ni]2(μ-Br)2, 2 with NaSDmp at -40 °C. The nickel site of complex 1 was found to add CO or CNtBu at -40 °C to give (CO)3Fe(StBu)(μ-StBu)2Ni(CO)(SDmp), 3, or (CO)3Fe(StBu)(μ-StBu)2Ni(CNtBu)(SDmp), 4, respectively. One of the CO bands of 3, appearing at 2055 cm-1 in the infrared spectrum, was assigned as the Ni-CO band, and this frequency is comparable to those observed for the CO-inhibited forms of [NiFe] hydrogenase. Like the CO-inhibited forms of [NiFe] hydrogenase, the coordination of CO at the nickel site of 1 is reversible, while the CNtBu adduct 4 is more robust.

Keywords: iron, nickel, thiolates

Biological hydrogen evolution and uptake are mediated by hydrogenase enzymes (1–7). The most prevalent family are the [NiFe] hydrogenases, and various forms have been identified (8–15). A unique feature of the [NiFe] hydrogenase is the common organometallic dinuclear Ni-Fe frame at the active site (Fig. 1), which has attracted inorganic and organometallic chemists attempting to model both the structure and physicochemical properties. Thiolate-bridged Ni-Fe complexes have been synthesized as structural models of the active site (16–26), and sulfur-ligated mono- and dinuclear transition metal complexes have been reported to promote H2 activation mimicking the function of [NiFe] hydrogenase (27–41). However, synthesis of better structural/functional models remains challenging.

Fig. 1.

Fig. 1.

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The active site of [NiFe] hydrogenase (left: oxidized form, X = OH or O. right: CO-inhibited form).

One interesting aspect of the [NiFe] hydrogenase is the reversible inhibition of the active site by CO. According to a crystallographic analysis of the CO-inhibited form of the [NiFe] hydrogenase obtained from Desulfovibrio vulgaris Miyazaki F (D. v. Miyazaki F), a CO molecule is coordinated at the nickel center (42). It has been suggested that this nickel-bound CO can be liberated and the catalytic activity recovered, upon flushing with a stream of N2 (43), or by white-light irradiation at 20 K (44). Herein we report the synthesis of a thiolate-bridged dinuclear Ni-Fe complex (CO)3Fe(μ-StBu)3Ni(SDmp), 1, carrying a bulky thiolate SDmp (Dmp = C6H3-2,6-(mesityl)2) at Ni, and its CO and CNtBu adducts, (CO)3Fe(StBu)(μ-StBu)2Ni(CO)(SDmp), 3, and (CO)3Fe(StBu)(μ-StBu)2Ni(CNtBu)(SDmp), 4. The reaction of 1 with CO occurs reversibly to give 3, while the analogous CNtBu adduct 4 is robust. We also report the x-ray crystal structures of 1, 3, and 4.

Results and Discussion

Synthesis and Structure of (CO)3Fe(μ-StBu)3Ni(SDmp), 1.

We have reported that a linear tetranuclear Fe-Ni-Ni-Fe complex [(CO)3Fe(μ-StBu)3Ni]2(μ-Br)2, 2, which was synthesized from FeBr2(CO)4 + Na(StBu) + NiBr2(EtOH)4 (1∶2 ∼ 3∶1), serves as a convenient precursor for the synthesis of thiolate-bridged dinuclear Ni-Fe complexes (17). The penta-coordinate nickel centers in 2 are bridged by two bromides, and substitution of the bromides with Na{S(CH2)2SMe} and ortho-NaS(C6H4)SR (R = Me, tBu) promotes the splitting of the Fe-Ni-Ni-Fe array generating (CO)3Fe(StBu)(μ-StBu)2Ni{S(CH2)2SMe} and (CO)3Fe(StBu)(μ-StBu)2Ni{S(C6H4)SR}, respectively. In these dinuclear Ni-Fe complexes, the Ni(II) centers assume a normal square-planar geometry. In order to expand the scope of our model study for [NiFe] hydrogenase, we have introduced a bulky thiolate, SDmp, at the Ni site of the dinuclear Ni-Fe frame, anticipating that the bulkiness of SDmp induces a distorted coordination geometry and reactivity at Ni (45–47). Thus, 2 was treated with NaSDmp in THF at -40 °C, and the dark red residue was extracted with hexane/HMDSO (hexamethyldisiloxane), from which the dinuclear Ni-Fe complex 1 was isolated in 41% yield as dark red crystals (Scheme 1). Complex 1 was characterized by IR and elemental analysis, and its molecular structure was determined by x-ray analysis, while the 1H NMR spectrum is not straightforward due to the paramagnetic nature of the complex. The IR spectrum, measured in THF at -40 °C, is shown on the left side of Fig. 2. The two strong signals appearing at 2079 and 2022 cm-1 are comparable to those found in the IR spectra of 2 (2065 and 2015 cm-1 in THF) (17). The cyclic voltammetry (CV) of 1 measured at -40 °C exhibited one irreversible oxidation wave and one redox couple at Epa = 0.48 V and E1/2 = 0.91 V vs Ag/Ag+, respectively, and one irreversible reduction wave at Epc = -1.48 V.

Scheme 1.

Scheme 1

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Fig. 2.

Fig. 2.

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The infrared spectra of 1 (left), 3 (Right, Dashed Line), and 3-13CO (Right, Solid Line) measured in THF at -40 °C. The spectrum of 3-13CO is superimposed upon that of 3.

Complex 1 crystallizes with hexane and HMDSO as crystal solvents, and the molecular structure of 1 is shown in Fig. 3 with selected bond distances and angles in the captions. The octahedral iron geometry of 2 is carried over to 1, and the Fe-μ-StBu bond lengths are comparable, 1 (av. 2.341 Å) vs. 2 (av. 2.342 Å). The Fe(II)-Ni(II) distances are long for both 1 (3.0121(13) Å) and 2 (3.0898(6), 3.0935(8) Å). An interesting aspect of the structure of 1 is that the coordination geometry of nickel is approximately trigonal-pyramidal. One of the bridging sulfur atoms, namely S1, occupies the apical site. The nickel atom is nearly coplanar with the remaining bridging sulfurs and the SDmp sulfur, where the maximum deviation from planarity occurs at the SDmp sulfur (0.1035(8) Å). This unusual coordination geometry is probably caused by the steric bulk of the SDmp ligand, and in fact one Dmp mesityl group bends toward the nickel site from the bottom of the trigonal plane. However, no direct bonding interactions are discernible between the mesityl group and nickel. The Ni-S1 bond length is shorter by 0.02–0.03 Å than Ni-S bonds with the other μ-StBu sulfurs, while the Fe-S1 bond length is 0.02 Å longer than Fe-S2 and Fe-S3 bonds.

Fig. 3.

Fig. 3.

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Molecular structure of 1 with thermal ellipsoids at the 50% probability level. Selected bond distances (Å) and angles (°): Fe-Ni 3.0121(13), Fe-S1 2.3361(17), Fe-S2 2.3343(18), Fe-S3 2.354(2), Ni-S1 2.3290(17), Ni-S2 2.3154(16), Ni-S3 2.3022(19), Ni-S4 2.1848(18), Fe-C1 1.786(7), Fe-C2 1.776(7), Fe-C3 1.783(7), Fe-S1-Ni 80.43(5), Fe-S2-Ni 80.75(5), Fe-S3-Ni 80.60(6), S1-Ni-S2 82.86(5), S2-Ni-S4 144.13(6), S4-Ni-S1 104.91(6).

Reactions of 1 with CO and CNtBu.

Complex 1 is a promising [NiFe] hydrogenase model having a distorted trigonal-pyramidal nickel center, and high reactivity at the nickel site may be anticipated. In fact, when a THF solution of 1 was exposed to 1 atm of CO at -40 °C, the color of the solution immediately turned from dark red to dark brown. Monitoring of the reaction mixture in THF by IR at -40 °C indicated the addition of CO at the Ni site (Fig. 2 Right, Dashed Line), as a new band at 2055 cm-1 appeared in addition to the signals at 2072 and 2012 cm-1 that are similar to those arising from the Fe(CO)3 units of 1. However, this nickel-bound CO is labile, and complex 1 was recovered in high yield when a solution of 3 was evaporated under reduced pressure. Nevertheless, a small amount of crystals formed from a concentrated solution under a CO atmosphere. According to the x-ray analysis, the product is (CO)3Fe(StBu)(μ-StBu)2Ni(CO)(SDmp) (3) (Scheme 2). Whereas facile loss of CO prevented the isolation of bulk 3, an analogous reaction of 1 with 1 equiv of CNtBu at -40 °C led to the isolation of the isocyanide adduct (CO)3Fe(StBu)(μ-StBu)2Ni(CNtBu)(SDmp) (4) in 83 % yield as crystals. In contrast to the CO adduct 3, the CNtBu ligand in 4 remained bound to Ni under reduced pressure. The CV measurement on 4 at -40 °C in CH2Cl2 gave one redox couple (oxidation) and one irreversible reduction wave at E1/2 = 0.10 V and Epc = -1.77 V vs Ag/Ag+, respectively.

Scheme 2.

Scheme 2

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Molecular structures of 3 and 4 as determined by x-ray analysis are similar, and a perspective view of 3 is shown in Fig. 4. One of the bridging StBu ligands in 1 dissociates from nickel, becoming a terminal ligand on Fe, during the formation of 3 or 4, and a slight elongation of the Fe-Ni distance in 3 (3.1728(9) Å) and 4 (3.2676(12) Å) occurs as compared with those in 1 and 2. The nickel center adopts a slightly folded square-planar geometry with three thiolates and a terminally bound CO or CNtBu, with dihedral angles between the Ni-S2-S3 and Ni-C1-S4 planes of 8.3° (3) and 3.4° (4). Whereas the bond between Ni and S1 is broken when 1 is transformed into 3, the S1 atom remains bound to Fe and cannot move too far from Ni. Indeed in 3, the Ni–S1 distance is as short as 2.6963(14) Å, and S1 is well placed to recoordinate to Ni, thereby facilitating the dissociation of CO. On the other hand, the Ni–S1 distance in 4 is somewhat longer, 3.0232(19) Å.

Fig. 4.

Fig. 4.

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Molecular structure of 3 with thermal ellipsoids at the 50% probability level. Selected bond distances (Å) and angles (°): Fe-Ni 3.1728(9), Fe-S1 2.3427(14), Fe-S2 2.3149(12), Fe-S3 2.3407(14), Ni-S1 2.6963(14), Ni-S2 2.2247(14), Ni-S3 2.2720(12), Ni-S4 2.2337(16), Fe-C1 1.788(5), Fe-C2 1.792(5), Fe-C3 1.792(6), Ni-C4 1.769(5), Fe-S2-Ni 88.66(4), Fe-S3-Ni 86.91(4), S2-Ni-S3 80.53(4), S3-Ni-S4 91.36(5), S4-Ni-C4 90.0(2), C4-Ni-S2 97.5(2).

In order to ascertain that the new IR band at 2055 cm-1 arises from incoming CO, we conducted an isotope-labeling experiment by charging 13CO to a THF solution of 1. The IR spectrum of the resulting 13CO adduct, 3-13CO, is superimposed upon that of 3 on the right side of Fig. 2. Of the three intense bands observed for compound 3, the band at 2072 cm-1 remains unchanged, while the one at 2055 cm-1 is greatly reduced in intensity. The band at 2010 cm-1 of 3-13CO is slightly more intense and broader than the 2012 cm-1 signal of 3. This indicates that the band at 2055 cm-1 moves to a lower frequency upon 13CO labeling and happens to overlap the band at 2012 cm-1 observed for 3, which may arise from the Fe(CO)3 fragment. In fact the observed shift, 45 cm-1, is in accord with the shift, 2055 cm-1 → 2009 cm-1, which is calculated for the replacement of 12CO by 13CO.

Significantly, the Ni-CO stretching frequency for 3 (2055 cm-1) is comparable to those observed for the CO-inhibited forms of [NiFe] hydrogenases from C. vinosum and Desulfovibrio fructosovorans, which exhibit the nickel-bound CO band in the 2055–2060 cm-1 range (44, 48). This similarity suggests that the electronic properties of the nickel centers in 3 and the CO-inhibited forms of the [NiFe] hydrogenases are similar. In contrast, these frequencies are notably higher than those reported for Ni(II)-CO thiolate complexes such as Inline graphic (2029 cm-1, Inline graphic) (49) and [Ni(CO)(SePh)(SPh)2]- (2032 cm-1) (50), in which the CO ligands are strongly bound to nickel. For both 3 and the corresponding [NiFe] hydrogenases, π-back donation to CO is weak, and the weak Ni-CO bond contributes to the reversibility of CO coordination.

Concluding Remarks

The thiolate-bridged dinulear Ni-Fe complex 1 was synthesized as a new class of [NiFe] hydrogenase models, which consists of a Fe(CO)3 unit and an intriguing trigonal-pyramidal Ni center. Reversible coordination of CO was found to occur at this nickel site, and the resulting CO adduct, (CO)3Fe(StBu)(μ-StBu)2Ni(CO)(SDmp) (3), models the structure and properties of the CO-inhibited form of [NiFe] hydrogenase from C. vinosum and Desulfovibrio fructosovorans. The S atom of the Fe-bound thiolate approaches the square-planar nickel center with a Ni-S distance of 2.6963(14) Å, and therefore the Ni coordination environment of 3 does not differ much from that of the penta-coordinate nickel of the CO-inhibited form of the protein from D. v. Miyazaki F (42). Complex 3 also reproduces reversibility of CO coordination and the CO-stretching frequency of the CO-inhibited form of [NiFe] hydrogenase. On the other hand, some discrepancies are found in the number of thiolates between metals (three for 3 and two for hydrogenase) and the diatomic ligands on iron (Fe(CO)3 for 3 and Fe(CO)(CN)2 for hydrogenase). Furthermore, the Ni-Fe distance in 3 (3.17 Å) is substantially longer than those in the protein (2.61–2.62 Å) (42). Perhaps the oxidation states of Fe and/or Ni of 3 are different from those of the structurally characterized CO-inhibited form of [NiFe] hydrogenase. Two distinct CO-inhibited states of [NiFe] hydrogenase have been reported, namely a paramagnetic Ni-CO state and an EPR-silent Ni-CO state (51), but it is not clear to which state the CO-inhibited form of the protein from D. v. Miyazaki F belongs.

Materials and Methods

All reactions and the manipulations were performed under a nitrogen atmosphere using standard Schlenk techniques. Solvents were dried, degassed, and distilled from CaH2 (CH2Cl2) under nitrogen. Hexane, HMDSO (hexamethyldisiloxane), and THF were purified by columns of activated alumina and a supported copper catalyst supplied by Hansen & Co. Ltd.

All experimental conditions and procedures, spectroscopic data, and details of characterization of complexes are given in SI Text, which is published on the PNAS web site. Molecular structure of 4 is given in Fig. S1. Infrared spectra of 1–4 are given in Figs. S2–S5, respectively.

Supplementary Material

Supporting Information
supp_107_9_3994__index.html (976B, html)

Acknowledgments.

We thank Professor Roger E. Cramer (University of Hawaii) for fruitful discussion and careful reading of the manuscript. We also thank Mr. Koshi Onishi, Miss Nonoka Oshima, Professors Hiroshi Shinokubo and Satoru Hiroto (Nagoya University) for technical assistance. We are grateful to Dr. Rie Suizu and Professors Hirofumi Yoshikawa, Michio Matsushita, and Kunio Awaga (Nagoya University), for aiding us in the SQUID measurements. This research was financially supported by Grant-in-Aids for Scientific Research (nos. 18GS0207, 18064009, and 20613004) from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

Footnotes

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The atomic coordinates have been deposited with the Cambridge Crystallographic Data Centre, Cambridge CB2 1EK, UK (CSD reference nos. 755051-755053).

This article contains supporting information online at www.pnas.org/cgi/content/full/0913399107/DCSupplemental.

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