Handbook of Chalcogen Chemistry Volume 2

New Perspectives in Sulfur, Selenium and Tellurium

By Francesco Antonio Devillanova, Wolf-Walther du Mont

The Royal Society of Chemistry

Copyright © 2013 The Royal Society of Chemistry
All rights reserved.
ISBN: 978-1-84973-624-4

Contents

Introduction F. A. Devillanova and W.-W. duMont, 1,
Volume 1,
Chapter 1 Compounds Containing Boron–Chalcogen Bonds Michael A. Beckett, 5,
Compounds Containing the Carbon-Chalcogen Bond (E = S, Se, Te),
Chapter 2.1 Thiolates, Selenolates, and Tellurolates M. Concepción Gimeno, 37,
Chapter 2.2 Thioamides, Thioureas, and Related Selenium and Tellurium Compounds Mamoru Koketsu, 94,
Chapter 2.3 Chalcogenone C=E Compound (E=S, Se, Te) Gaetano Verani and Alessandra Garau, 118,
Chapter 3 Compounds Having Both a Single Bond and a Double Bond (Heavy Ketones) between Si, Ge, or Sn and Chalcogens (S, Se, and Te) Nobuhiro Takeda and Norihiro Tokitoh, 160,
Chapter 4 Recent Developments in Chalcogen–Nitrogen Chemistry Tristram Chivers and Risto Laitinen, 191,
Chapter 5 Chalcogen–Phosphorus (and Heavier Congener) Compounds Rob Davies and Laura Patel, 238,
Chapter 6 Compounds Containing the Chalcogen Oxygen E–O Bond (E=S, Se, Te) Mathias S. Wickleder and Christian Logemann, 307,
Compounds Containing the Chalcogen–Chalcogen E–E Bond (E=S, Se, Te),
Chapter 7.1 Structure and Bonding of the Neutral Chalcogens and Their Polyatomic Cations Ingo Krossing, 349,
Chapter 7.2 Organochalcogen Multication Species Valentine G. Nenajdenko, Nikolay E. Shevchenko, Elizabeth S. Balenkova and Igor V. Alabugin, 382,
Compounds Containing the Halogen–Chalcogen X–E Bond (X=F, Cl, Br, I; E=S, Se, Te),
Chapter 8.1 Recent Developments in Binary Halogen–Chalcogen Compounds, Polyanions, and Polycations Jing Wang and Zhengtao Xu, 425,
Chapter 8.2 Charge-Transfer Adducts and Related Compounds Vito Lippolis and Francesco Isaia, 448,
Metal Chalcogenides,
Chapter 9.1 Metal Chalcogenides: Clusters, Layers, Nanotubes Maxim N. Sokolov, 475,
Chapter 9.2 Polychalcogenides William S. Sheldrick, 514,
Subject Index, 546,
Volume 2,
Introduction F. A. Devillanova and W.-W. duMont, 1,
Biological Chemistry,
Chapter 10.1 Metal–Sulfur Clusters as the Model for the Active Sites of Metalloenzymes Yasushi Mizobe and Hidetake Seino, 7,
Chapter 10.2 Current Research on Mimics and Models of Selenium-Containing Antioxidants Bhaskar J. Bhuyan, Devappa S. Lamani, Govindasamy Mugesh and Thomas Wirth, 25,
Chapter 10.3 The Role of Sulfur and Selenium Species in the Thyroid Surendar Reddy Jakka and Govindasamy Mugesh, 47,
Material Chemistry,
Chapter 11.1 Stable Chalcogen Radicals Jeremy M. Rawson and John J. Hayward, 69,
Chapter 11.2 Chalcogen-Rich Compounds as Electron Donors Diego Cortizo-Lacalle, Peter J. Skabara and Thomas D. Westgate, 99,
Chapter 11.3 1,2-Dichalcogenolene Ligands and Related Metal Complexes Massimiliano Arca, M. Carla Aragoni and Anna Pintus, 127,
Chapter 11.4 II–VI Semiconductors and Their Device Applications Bin He and Wenjun Zhang, 180,
Chapter 11.5 Nanoparticles and Quantum Dots Lihui Yuwen and Lianhui Wang, 232,
Miscellaneous Aspects,
Chapter 12.1 Supramolecular Structures Based on Chalcogen–Halogen Secondary Bonds Wolf-Walther du Mont and Cristian George Hrib, 273,
Chapter 12.2 Synthesis and Stereochemistry of Optically Active Chalcogen Compounds Toshio Shimizu, 317,
Chapter 12.3 Hypervalent Chalcogen Compounds Satoko Hayashi and Waro Nakanishi, 335,
Chapter 12.4 Theoretical Calculations and NMR Spectroscopy Waro Nakanishi and Satoko Hayashi, 373,
Subject Index, 433,

CHAPTER 1

Metal–Sulfur Clusters as the Model for the Active Sites of Metalloenzymes

YASUSHI MIZOBE AND HIDETAKE SEINO

Institute of Industrial Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505, Japan

10.1.1 Introduction

Nitrogen is one of the essential elements for all living things and a significant part of the nitrogen needed on Earth is supplied in the form of ammonia produce from atmospheric nitrogen by biological nitrogen fixation. This highly important reaction, converting a quite inert N2 molecule into ammonia through coupled protonation and electronation, is known to proceed under ambient conditions by the catalysis of the metalloenzyme nitrogenase. This presents a sharp contrast to industrial nitrogen fixation, i.e. the Haber–Bosch process, which requires an extremely drastic condition to produce ammonia from gaseous nitrogen and hydrogen in the presence of an Fe-based heterogeneous catalyst. From the 1970s, certain Mo–Fe–S aggregates had been proposed as the active site structure of nitrogenase mainly on the basis of EXAFS data. It was in 1992 that the first report appeared about the results of the single-crystal X-ray diffraction study (2.7 Å resolution) for the most common nitrogenase, viz. Mo nitrogenase, which disclosed the surprising MoFe7S9 mixed-metal sulfido core present at the active site. From higher-resolution (1.16 Å) crystallographic results of in 2002, one light atom X (C, N, or O) was found to be at the centre of this core, as depicted in Figure 10.1.1. Although nitrogen was proposed to be most probable for the interstitial atom X at that time, it was characterized as carbon in more recent studies (2011) by using crystal structure at the stage of more accurate resolution (1.0 Å) and X-ray emission spectroscopy.

Owing to the remarkable progress in single-crystal X-ray analysis techniques, detailed structures have recently been clarified for a number of enzymes, which include several metalloenzymes containing the cluster cores with sulfur-bridged multimetallic centres at their active sites such as hydrogenase, sulfite reductase, and carbon monoxide hydrogenase/acetyl-CoA synthase (Figure 10.1.2), as well as nitrogenase. It is likely that the high catalytic activities of these enzymes result from the cooperation of two or more metal centres in proximity, making sulfur ligands such as sulfides and thiolates the choice as the bridges to maintain these multimetallic cores intact during catalysis. This is presumably because of the characteristics of the S atom, i.e. its strong affinity with transition metals and high bridging ability. However, although X-ray crystallographic analyses have successfully disclosed the active site structures of these enzymes in the resting state, the structures during catalytic turnover may possibly be different. Furthermore, their function mechanisms are essentially unknown. It is difficult to observe directly what is occurring at active sites embedded within huge proteins, so studies to synthesize model compounds and clarify their reactivity are of much importance. In this chapter, recent advances in the chemistry of metal–sulfur clusters as synthetic analogues to natural enzymes are briefly summarized.

10.1.2 Metal–Sulfur Clusters in Metalloenzymes and Syntheses of Their Structural Models

Iron–sulfur proteins are ubiquitous in all life forms, and at their active sites they most commonly contain the Fe2S2, Fe3S4, and Fe4S4 cluster cores shown in Figure 10.1.3 to mediate the electron transfer as their predominant role. In the early 1970s a synthetic approach to these iron–sulfur cluster sites was initiated, and analogues of these rhombic, incomplete cubane-type, and cubane-type Fe clusters having certain thiolate groups as ancillary ligands in place of the cysteinyl residues have already been successfully prepared.

On the other hand, such approaches to the metalloenzymes shown in Figures 10.1.1 and 10.1.2 are still under way. Thus, the model clusters reproducing precisely their complex metal–sulfur assemblies in the native form have not yet been isolated. In this section, studies aiming at the syntheses of the model compounds of two clusters in nitrogenase, FeMo cofactor (FeMo-co) and P cluster, are surveyed. The choice of these clusters as the representatives of the metal–sulfur clusters in metalloenzymes arises from the fact that these are the largest and most complicated metal–sulfur clusters known at present among those observed in natural enzymes.

10.1.2.1 Preparation and Reactions of the FeMo Cofactor Model Clusters

The most common nitrogenase is composed of two proteins, Mo–Fe protein and Fe protein, both of which contain metal–sulfur clusters. The former protein contains two kinds of clusters: FeMo-co, a Mo–Fe–S cluster which is believed to be the site for N2 activation and reduction, and P cluster, a Fe–S cluster mediating the transfer of electrons for N2 reduction from Fe protein to FeMo-co, while the latter protein has the Fe4S4 cluster. Before its elucidation by crystallography, the structure of FeMo-co had been proposed mostly based on the EXAFS results, and a cubane-type MoFe3S4 core was one of those suggested as its partial structure using the data around Mo in 1978. Synthesis of the MoFe3S4 clusters was reported in the same year, and their reactivity toward nitrogenase substrates has been investigated since then. Importantly, this led not only to the isolation of clusters with these substrate molecules bonded to the Mo site but also the demonstration of the reaction systems containing the MoFe3S4 clusters that can reduce nitrogenase substrates. Although it is now known that, as shown in Figure 10.1.1, the Mo–Fe–S aggregate present in FeMo-co does not have the cubane-type MoFe3S4 fragment but an incomplete cubane-type MoFe3(μ3-S)3 chromophore that is connected by one μ6-C and three μ2-S ligands to the Fe4(μ3-S)3 unit, these studies nevertheless represent one of the most successful examples of the synthetic approach mimicking the metalloenzyme system.

The cubane-type MoFe3S4 cluster was first prepared in the form of the double cubane clusters [Mo2Fe6S8(SR)9] and [Mo2Fe6S9(SEt)8] which contain two cubanes connected at each Mo site by three μ2-SR bridges or one μ2-S and two μ2-SEt bridges (Figure 10.1.4, left). These clusters were obtained by self-assembly reactions using tetrathiomolybdate, FeCl3, and thiols. The [Mo2Fe6S8(SR)9]3- cluster undergoes chemical and electrolytic, one- and two-electron reductions to give the clusters [Mo2Fe6S8(SR)9]n- (n = 4 and 5). Hydrogen evolution by treatment of these reduced clusters with PhSH or Et3NH+ in solution was demonstrated as the model of hydrogenase function observed for nitrogenase. Reduction of acetylene to ethylene and of hydrazine or N2 to ammonia was also attained under electrolytic conditions, e.g. in THF–MeOH by using [Mo2Fe6S8(SPh)9]3- as catalyst precursor. However, the efficiencies were still poor and the mechanism operating in these substrate reductions is uncertain. It is noteworthy that the cluster contains only coordinately saturated Mo and Fe centres, even in the reduced form [Mo2Fe6S8(SPh)9]3-.

The synthesis of MoFe3S4 single cubane clusters having the potential substrate-binding site was also attempted, which provided more sophisticated models for FeMo-co than the above-mentioned double cubane with two Mo atoms each surrounded by six sulfur ligands. By starting from the Fe(SEt)6-bridged double cubane cluster [Mo2Fe7S8(SEt)12]3- (Figure 10.1.4, right), the desired single cubane clusters [MoFe3S4(SR)3(cat)(L)]n- (cat = substituted catecholate; n = 2, 3) were able to be derivatized, in which not only the RS- and RO- anions but also nitrogenase substrates such as MeCN, N2H4, N3-, and CN- can bind to the Mo site as L (Figure 10.1.5). Hydrazine-bridged double cubane clusters [FORMULA OMITTED] (Cl4-cat = tetrachlorocatecholate) and [FORMULA OMITTED] were also isolated. By the use of [FORMULA OMITTED] as catalyst, reduction of acetylene to ethylene, cis-dimethyldiazene to methylamine, and hydrazine to ammonia were attained at room temperature in the system using 2,6-lutidinium chloride ([LutH]Cl) and cobaltocene as external proton and electron sources, respectively.

Upon elucidation of the presence of a homocitrato ligand at the Mo atom in FeMo-co, synthesis of the MoFe3S4 cubane clusters with a polycarboxylato ligand was subsequently attempted, which led to the isolation of the clusters [FORMULA OMITTED] (L1 = oxalate and L2 = Cl, CN; L1/L2 = methyliminodiacetate, thiodiglycolate). Interestingly, a series of the clusters of this type consisting of the tridentate ligands at the Mo site can catalyse the reduction of hydrazine into ammonia under conditions analogous to those described above, for which reduction of hydrazine is presumed to proceed on the single Mo site. Other routes to the MoFe3S4 single cubanes have been developed recently, which use [TpMoS(S4)]- (Tp = hydrotris(pyrazol-1-yl) borate) or [Cp*Mo(StBu)3] (Cp* = η5-C5Me5) as synthetic precursors. The Mo atom of the resulting clusters, [TpMoFe3S4Cl3]- or [Cp*MoFe3 S4(StBu)3]-, is tightly capped by Tp or Cp*, and only the Fe sites undergo ligand substitution and substrate coordination.

The Mo–Fe–S clusters containing the cores other than the MoFe3S4 cubane are also known. These include, for example, [Mo2Fe6S6L6 (CO)6]3- (L = Cl, Br, OR) with the bicapped prismatic core and [MoFe5S6 (CO)6L3]n- (L = PEt3, n = 0; L = I, n = 2), which consists of a MoFe3S4 cubane and a Fe2S2 unit (Figure 10.1.6). The cuboidal (defect cubane) MoFe3S3 clusters such as [FORMULA OMITTED](pyridine)] are of much interest as the model of the MoFe3S3 fragment in FeMo-co. In [FORMULA OMITTED], a cuboidal Fe4S3 fragment is connected to a Mo atom by three μ2-S atoms. Relevantly, the cubane-type Fe4S3N and Fe4S2N2 clusters were synthesized recently as a partial representation of FeMo-co, in which the interstitial μ6-X atom is postulated to be N.

By treatment of the single cubane cluster [FORMULA OMITTED] with PEt3, the edge-fused double cubane cluster [FORMULA OMITTED] was obtained, which was converted upon reaction with [Et4N]SH to the higher-nuclearity cluster [FORMULA OMITTED] containing the Mo2Fe6S9 fragments relating topologically to the PN cluster core in nitrogenase described below. Similarly, a Mo2Fe6S9 core was also found in the relating cluster [FORMULA OMITTED] that is derivatized from [FORMULA OMITTED] by an analogous route, as depicted in Figure 10.1.7.

10.1.2.2 Preparation of PN Cluster Models

X-ray analysis disclosed the structures of the P cluster in the dithionite-reduced state (PN cluster) and the oxidized state (POX cluster) (Figure 10.1.8). The PN cluster core has a corner-shared double cubane structure connected further by two cysteinyl μ-S atoms. As described above, the Mo2Fe6S9 fragments observed in [FORMULA OMITTED] and [FORMULA OMITTED] closely resembled the metal–sulfur connecting scheme of the PN cluster, and analogous clusters having W2Fe6S9, V2Fe6S9, and Mo2Fe4Cu2S9 cores of the same topology are known. Apparently, the core structures of FeMo-co and the P cluster are mutually intimately related: two incomplete cubane-type M4S3 cores are connected by either μ6-X or μ6-S, respectively.

The all-iron corner-shared Fe8S7 core itself has been constructed by a self-assembly reaction using [FORMULA OMITTED], tetramethylthiourea, 2,4,6-triisopropylbenzenethiol, and elemental sulfur. The product [FORMULA OMITTED] contains two cuboidal Fe4S3 cores bridged by one μ6-sulfide and two μ2-bis(trimethylsilyl)amides (Figure 10.1.9, left). The thiourea and terminal amide ligands in this cluster are replaceable by thiolate ligands. The amide-free clusters [FORMULA OMITTED] or [FORMULA OMITTED] have been isolated under modified reaction conditions. The topology of these clusters (Figure 10.1.9, right), with three μ2-S atoms connecting two cuboidal Fe4S3 units, closely resembles that of FeMo-co.

(Continues…)Excerpted from Handbook of Chalcogen Chemistry Volume 2 by Francesco Antonio Devillanova, Wolf-Walther du Mont. Copyright © 2013 The Royal Society of Chemistry. Excerpted by permission of The Royal Society of Chemistry.
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