Recent developments in the non-cyclopentadienyl organometallic and related chemistry of scandium

Up to the early to mid 1990s the organometallic chemistry of scandium was dominated by cyclopentadienyl derivatives. This present article highlights advances in the synthesis and reactivity of non-cyclopentadienyl organometallic and related compounds of scandium. These include: compounds containing arene and other eta(x)-CxRx ligands; compounds with macrocyclic and fac-L3 ligands; compounds with polydentate ligands that incorporate amide donors; compounds with bidentate, monoanionic N,N' donor ligands; and compounds with iminophenolate, bis(phenoxide) and some other anionic O-donor ligands.     

Synthesis of chiral sulfonamide/Schiff base ligands

We report a facile two step synthesis of chiral ligands for bonding to transition metals. The ligands are easily prepared from trans-1,2-diaminocyclohexane by reaction with sulfonyl chlorides to give amino-sulfonamide compounds. These intermediates are then condensed with salicylaldehyde derivatives to provide sulfonamide/Schiff base compounds which represent a new class of chiral ligands.     

Challenges in quantitative analyses for volatile organic compounds bound to lipocalins

In this communication, I describe the challenges in quantitative analyses for volatile organic compounds in mouse urine, which are primarily caused by the presence of the major urinary proteins, a lipocalin subfamily, that sequester volatile ligands. The analyses of volatile compounds in mouse urine have been performed since the late 1970s. However, none of them considered the binding interactions of the quantified compounds with the urinary proteins. Some volatile ligands are tightly bound to the proteins and may not be extracted completely by organic solvents. The amounts of volatile ligands measured by external standard calibration represent those of the unbound ligands in the headspace, not the total amounts in urine. Addition of internal standards displaces ligands bound to the proteins, resulting in a completely different volatile profile. Normalization of volatile compounds using relative peak area (or height) ratios may not be used in the conditions where displacement of ligands bound to the proteins occurs. Because of the unique chemical properties of mouse urine, I have not been able to find a good quantification method for the volatile compounds released from mouse urine. I hope that the identification of these issues will stimulate others to come up with novel approaches.     

Ge4Br4[Mn(CO)5]4 and Ge6Br2[Mn(CO)5]6: first germanium cluster compounds containing Mn(CO)5 ligands

Cluster compounds of germanium exhibiting germanium-germanium bonds, where the germanium atoms are additionally bound to transition metal ligands, are rare. Here a synthetic pathway to such cluster compounds is described, starting from metastable Ge I halide solutions leading to the two cluster compounds Ge4Br4[Mn(CO)5]4 and Ge6Br2[Mn(CO)5]6, being the first examples of germanium cluster compounds bearing Mn(CO)5 ligands. The Ge6 compound exhibits a novel arrangement of germanium atoms that has not been previously observed in ligand stabilized cluster compounds of germanium, neither with organic nor with transition metal ligands. The bonding situation inside the cluster compounds is discussed, together with a possible reaction pathway that opens the way to metalloid cluster compounds of germanium exhibiting Mn(CO)5 ligands.     

An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands

A new method has been developed to design a focused library based on available active compounds using protein-compound docking simulations. This method was applied to the design of a focused library for cytochrome P450 (CYP) ligands, not only to distinguish CYP ligands from other compounds but also to identify the putative ligands for a particular CYP. Principal component analysis (PCA) was applied to the protein-compound affinity matrix, which was obtained by thorough docking calculations between a large set of protein pockets and chemical compounds. Each compound was depicted as a point in the PCA space. Compounds that were close to the known active compounds were selected as candidate hit compounds. A machine-learning technique optimized the docking scores of the protein-compound affinity matrix to maximize the database enrichment of the known active compounds, providing an optimized focused library.     

配合物稳定性与配位体酸碱强度间的直线自由能关系 III:N-(间取代苯基)氨基乙酸的铜(II)、镍(II)配合物稳定性及热力学性质的研究

The stepwise formation constants of complex compounds formed from N-(m-substituted-phenyl) glycines (m-RC6H4NHCH2COOH(m-RPhG), R = H, CH3, CH3O, Cl, NO2) with Cu(II) and Ni(II) were determined by pH method at 15, 25 35`C in 30% (V/V) ethanol solution in the presence of 0.1m NaClO4. Their thermodynamical parameters were calculated. It was found that the N-(m-substituted-phenyl) glycine complexes also showed linear free energy relationships between the stability of complex compounds and the base strength of the ligands just as the para-substituted isomers reported previously. Linear relationships not only existed between their thermodynamical parameters and the base strength of the ligands but also existed between the formation enthalpy of complex compounds and the neutralization enthalpy of the ligands and between the formation entropy of complex compounds and neutralization entropy of the ligands as well.     

Palladium-catalyzed arylation of bis(4-bromo-2-methylinden-1-yl)dimethylsilane and related compounds

A new procedure was developed for the synthesis of a broad range of ansa-zirconocenes containing bis(2-methyl-4-arylindenyl)dimethylsilane ligands. The method is based on the palladium-catalyzed reaction of halogen-substituted bis(indenyl)dimethylsilanes with various organozinc compounds. The aryl-substituted bridging ligands thus prepared serve as the starting compounds for the synthesis of ansa-zirconocenes, which can be used as components of promising catalysts for propylene polymerization.     

Recent advances on carborane-based ligands in low-valent group 13 and group 14 elements chemistry

Carboranes are a class of polyhedral boron-carbon molecular clusters, they can serve as versatile ligands in stabilizing low-valent main group element compounds, due to their exceptionally thermal and chemical stabilities, easy modifications at the cage carbon vertices, as well as large spherical steric effects. These carborane-based ligands provide interesting opportunities for the synthesis of low-valent main group element compounds with novel structure and reactivity, which indeed enrich the chemistry of low-valent element main group compounds. This review summarizes the recent advances in the chemistry of low-valent group 13 and group 14 element compounds supported by carborane-based ligands. Achievements and perspectives in this new and flourishing field are discussed in this review.     

One-step multi-electron transfer mechanism of polynuclear copper complexes for molecular conversions

The oxidative coupling reaction of 2,6-dimethylphenol may result in either a desired polymeric substance (i.e. the polyphenylene ether, PPE) or the undesired “dimeric” species diphenoquinone, DPQ. The relative amounts of each product depend on the experimental conditions and the used catalytic system. Usually copper amine compounds are used as a catalyst for the oxidative coupling reactions. They have the advantage of easy access and produce high yields of high molecular PPE; however, other metal coordination compounds, like those of Mn, may also be used as catalysts. The present paper focuses on mechanistic studies with various copper (aliphatic and aromatic) amine compounds as catalysts. Owing to the steric constraints of the amine ligands, dinuclear Cu(II) compounds, with small bridging anionic ligands, are easily formed. Such species are believed to be the catalyst precursors. Upon addition of a base (1:1 on copper) and excess phenol, phenolate ligands coordinate as bridging ligands to copper. After a two-electron transfer reaction, the resulting phenoxonium ligand, which is a rather poor ligand, remains attached to the Cu(I), probably coordinating via its aromatic ring. Nucleophilic attack by a phenol to the phenoxonium ion at the 4-position is likey to be most important to the coupling reaction. In the beginning of the reaction the undesired side product DPQ is also formed via a C–C coupling reaction. With copper(II) compounds containing imidazole-type chelating ligands, good activity was obtained; in the case of pyrazole-based and bridging S-donor chelating ligands, that no or very weak activity was found. In a study of the mechanism of the propagation reaction the rate-determining reaction was thought to be probably a one-step, two-electron transfer, during which the two Cu(II) ions in the dinuclear complex oxidize the phenolate to phenoxonium. After the phenoxium ion is formed the bonding with the (then) Cu(I) species is weakened and the reactions with phenolic end groups can take place. The effect of the amine ligands appears to be both steric and electronic. With certain ligands the reoxidationof the reduced catalyst is not possible.     

Interplay and Competition Between Two Different Types of Redox-Active Ligands in Cobalt Complexes: How to Allocate the Electrons?

The field of molecular transition metal complexes with redox-active ligands is dominated by compounds with one or two units of the same redox-active ligand; complexes in which different redox-active ligands are bound to the same metal are uncommon. This work reports the first molecular coordination compounds in which redox-active bisguanidine or urea azine (biguanidine) ligands as well as oxolene ligands are bound to the same cobalt atom. The combination of two different redox-active ligands leads to mono- as well as unprecedented dinuclear cobalt complexes, being multiple (four or six) center redox systems with intriguing electronic structures, all exhibiting radical ligands. By changing the redox potential of the ligands through derivatisation, the electronic structure of the complexes could be altered in a rational way.     

Hidden active information in a random compound library: extraction using a pseudo-structure-activity relationship model

We propose a hypothesis that "a model of active compound can be provided by integrating information of compounds high-ranked by docking simulation of a random compound library". In our hypothesis, the inclusion of true active compounds in the high-ranked compound is not necessary. We regard the high-ranked compounds as being pseudo-active compounds. As a method to embody our hypothesis, we introduce a pseudo-structure-activity relationship (PSAR) model. Although the PSAR model is the same as a quantitative structure activity relationship (QSAR) model, in terms of statistical methodology, the implications of the training data are different. Known active compounds (ligands) are used as training data in the QSAR model, whereas the pseudo-active compounds are used in the PSAR model. In this study, Random Forest was used as a machine-learning algorithm. From tests for four functionally different targets, estrogen receptor antagonist (ER), thymidine kinase (TK), thrombin, and acetylcholine esterase (AChE), using five scoring functions, we obtained three conclusions: (1) the PSAR models significantly gave higher percentages of known ligands found than random sampling, and these results are sufficient to support our hypothesis; (2) the PSAR models gave higher percentages of known ligands found than normal scoring by scoring function, and these results demonstrate the practical usefulness of the PSAR model; and (3) the PSAR model can assess compounds failed in the docking simulation. Note that PSAR and QSAR models are used in different situations; the advantage of the PSAR model emerges when no ligand is available as training data or when one wants to find novel types of ligands, whereas the QSAR model is effective for finding compounds similar to known ligands when the ligands are already known.     

Titanium-based molecular squares and rectangles: syntheses by self-assembly reactions of titanocene fragments and aromatic N-heterocycles

This paper reports on the potential of titanium compounds as building blocks for supramolecular polygons. Self-assembly reactions of low-valent titanocene units and N-heterocyclic bridging ligands lead to novel titanium-based supramolecular squares. Pyrazine (3), 4,4'-bipyridine (4), and tetrazine (5) were used as bridging ligands, and the acetylene complexes [Cp2Ti{eta2-C2(SiMe3)2}] (1) and [(tBuCp)2Ti{eta2-C2(SiMe3)2}] (2) as sources of titanocene fragments. Molecular rectangles can be synthesized by stepwise reduction of the titanocene dichlorides [Cp(2)TiCl2] and [(tBuCp)2TiCl2] and consecutive coordination of two different bridging ligands. The resulting complexes are the first examples of molecular rectangles containing bent metallocene corner units. Single-crystal X-ray analyses of the tetranuclear compounds revealed the geometric properties of the molecular polygons in the solid state. Comparison of bond lengths and angles in coordinated and free ligands reveals the reduced state of the bridging ligand in the low-valent titanium compounds. The syntheses and properties of these novel, highly air- and moisture-sensitive compounds are discussed.     

New macrocycles derived from biphenyl for pH-switched solvent extraction

Four new fluorescent macrocyclic ligands derived from biphenyl are described. The new compounds have been used in liquid-liquid extraction experiments and the influence of pH has been studied in those ligands containing carboxylic groups. The results obtained for the latter ligands have been compared with those observed in the presence of an external acid.     

Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR

Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available Chemicals Directory (ACD) to identify ligands to bind to a TAR RNA structure using a four-step docking procedure: rigid docking first, followed by three steps of flexible docking using a pseudobrownian Monte Carlo minimization in torsion angle space with progressively more detailed conformational sampling on a progressively smaller list of top-ranking compounds. To validate the procedure, we successfully docked ligands for five RNA complexes of known structure. For ranking ligands according to binding avidity, an empirical binding free energy function was developed which accounts, in particular, for solvation, isomerization free energy, and changes in conformational entropy. System-specific parameters for the function were derived on a training set of RNA/ligand complexes with known structure and affinity. To validate the free energy function, we screened the entire ACD for ligands for an RNA aptamer which binds l-arginine tightly. The native ligand ranked 17 out of ca. 153,000 compounds screened, i.e., the procedure is able to filter out >99.98% of the database and still retain the native ligand. Screening of the ACD for TAR ligands yielded a high rank for all known TAR ligands contained in the ACD and suggested several other potential TAR ligands. Eight of the highest ranking compounds not previously known to be ligands were assayed for inhibition of the Tat-TAR interaction, and two exhibited a CD₅₀ of ca. 1 M.     

Metal complexes of biological active 2-aminothiazole derived ligands

The most imperative outcomes of extensive sterdies (synthesis, spectral, structural characterization and biological applications) of metal complexes with thiazole derived ligands are reviewed. A large number of coordination compounds are known but still there is a need of new compounds to develop various efforts in different fields for biomedical applications. The synthesis of Schiff base ligands is very important, and it has recently drawn the attention of numerous research groups, making this area constantly evolve. Authors are also synthesizing some novel biologically potent ligands and their unique complexes and complexes found more biological active agents than that of ligands against bacteria, fungi and herbs. Highlights: Schiff bases and their metal chelates catalyze reactions; Schiff bases derived from sulfane thiadiazole show toxicities against insects; Schiff bases of thiadiazole have good plant regulator activity; Phenyl ring attached to the thiazole group showed interesting structure activity.     

Computer Graphics in the Study of Metal Cluster Compounds

Polynuclear carbonylmetal compounds provide convenient molecular analogues for the reactions occurring at metal surfaces during catalytic processes. Many properties of these cluster compounds are determined by the type and distribution of the ligands covering the metal polyhedral surface. Computer simulated space-filling models of these complicated molecules provide readily assimilated information about the arrangement of surface ligands, and in many cases lead to conclusions not readily deduced from other approaches.     

Preparation and evaluation of a hydrolytically stable amide-embedded stationary phase

We have developed a new hydrolytically stable amide-embedded stationary phase via a simple and effective synthetic method. The preparation of the new phase involves the synthesis of multifunctional silane ligands and the surface modification of porous silica particles via multiple attachments of these ligands to the silica surface. A hydrolytically stable coating was produced as a result of multiple covalent linkages formed between silane ligands and the silica surface, and cross-linking between adjacent ligands. The resulting amide-embedded stationary phase showed excellent hydrolytic stability over a wide pH range. Like other existing amide-embedded columns, this new stationary phase exhibits higher retention for polar compounds and different selectivity as compared to conventional C18 columns. The new phase is compatible with 100% aqueous mobile phases, and also provides high column efficiency and good peak shapes for both acidic and basic compounds.     

Synthesis, structure, and spectroscopy of phenylacetylenylene rods incorporating meso-substituted dipyrrin ligands

The synthesis, structure, and spectroscopic characterization of a series of phenylacetylenylene rodlike molecules containing dipyrromethene (dipyrrin) ligands are described. The combination of the phenylacetylenylene groups with the porphyrinogenic dipyrrin moieties results in a rich absorption spectroscopy for these compounds, although the fluorescence of the phenylacetylenylene moiety is quenched by presence of the dipyrrin chelator. The Cu(2+) and Fe(3+) complexes of these ligands have been prepared and three of these compounds have been structurally characterized by using single-crystal X-ray diffraction. Unlike other octahedral metal-dipyrrin complexes described to date, one of the iron complexes demonstrates ideal threefold symmetry in the solid-state. The elongated structure and high symmetry of these complexes suggests the use of these meso-substituted phenylacetylenylene ligands as an interesting class of extended, branched molecules for the construction of supramolecular architectures.     

Preparation of mononuclear, homodinuclear, and heterotrinuclear complexes by salicylaldiminato-functionalized imidazolium salt: approach to multifunctional catalysts

A salicylaldiminato imidazolium salt that bears both a Schiff base and imidazolium salt moiety was used to synthesize heterometallic compounds that could serve as multifunctional catalysts in certain reactions. The successful preparation of seven mononuclear compounds with a variety of transition metals (Pd, Ir, Ru, Zn, Ni) illustrated the high versatility of this class of ligands, which is crucial for the design of catalysts. Synthesis of homodinuclear compounds and heterotrinuclear compounds provided practical methods to connect multiple metal fragments through these ligands. The heterotrinuclear complex (Ni/Ir) was employed as a catalyst in the reaction of dehalogenation/transfer hydrogenation of halo-acetophenones. The preliminary catalytic study showed that this heterometallic species is more active than a combination of the corresponding monometallic species.