Showing papers in "Accounts of Chemical Research in 2001"

Modular chemistry: secondary building units as a basis for the design of highly porous and robust metal-organic carboxylate frameworks.

Abstract: Secondary building units (SBUs) are molecular complexes and cluster entities in which ligand coordination modes and metal coordination environments can be utilized in the transformation of these fragments into extended porous networks using polytopic linkers (1,4-benzenedicarboxylate, 1,3,5,7-adamantanetetracarboxylate, etc.). Consideration of the geometric and chemical attributes of the SBUs and linkers leads to prediction of the framework topology, and in turn to the design and synthesis of a new class of porous materials with robust structures and high porosity.

The Development of L2X2RuCHR Olefin Metathesis Catalysts: An Organometallic Success Story

Abstract: In recent years, the olefin metathesis reaction has attracted widespread attention as a versatile carbon−carbon bond-forming method. Many new applications have become possible because of major advances in catalyst design. State-of-the-art ruthenium catalysts are not only highly active but also compatible with most functional groups and easy to use. This Account traces the ideas and discoveries that were instrumental in the development of these catalysts, with particular emphasis on (PCy3)2Cl2RuCHPh and its derivatives. The discussion includes an analysis of trends in catalyst activity, a description of catalysts coordinated with N-heterocyclic carbene ligands, and an overview of ongoing work to improve the activity, stability, and selectivity of this family of L2X2RuCHR complexes.

Some interesting properties of metals confined in time and nanometer space of different shapes.

Abstract: The properties of a material depend on the type of motion its electrons can execute, which depends on the space available for them (i.e., on the degree of their spatial confinement). Thus, the properties of each material are characterized by a specific length scale, usually on the nanometer dimension. If the physical size of the material is reduced below this length scale, its properties change and become sensitive to its size and shape. In this Account we describe some of the observed new chemical, optical, and thermal properties of metallic nanocrystals when their size is confined to the nanometer length scale and their dynamical processes are observed on the femto- to picosecond time scale.

Mimicking photosynthetic solar energy transduction

Abstract: Increased understanding of photosynthetic energy conversion and advances in chemical synthesis and instrumentation have made it possible to create artificial nanoscale devices and semibiological hybrids that carry out many of the functions of the natural process. Artificial light-harvesting antennas can be synthesized and linked to artificial reaction centers that convert excitation energy to chemical potential in the form of long-lived charge separation. Artificial reaction centers can form the basis for molecular-level optoelectronic devices. In addition, they may be incorporated into the lipid bilayer membranes of artificial vesicles, where they function as components of light-driven proton pumps that generate transmembrane proton motive force. The proton gradient may be used to synthesize adenosine triphosphate via an ATP synthase enzyme. The overall energy transduction process in the liposomal system mimics the solar energy conversion system of a photosynthetic bacterium. The results of this research illustrate the advantages of designing functional nanoscale devices based on biological paradigms.

Dendrimer-Encapsulated Metal Nanoparticles: Synthesis, Characterization, and Applications to Catalysis

Abstract: This Account reports the synthesis and characterization of dendrimer-encapsulated metal nanoparticles and their applications to catalysis. These materials are prepared by sequestering metal ions within dendrimers followed by chemical reduction to yield the corresponding zerovalent metal nanoparticle. The size of such particles depends on the number of metal ions initially loaded into the dendrimer. Intradendrimer hydrogenation and carbon−carbon coupling reactions in water, organic solvents, biphasic fluorous/organic solvents, and supercritical CO2 are also described.

Catalytic functionalization of arenes and alkanes via C-H bond activation.

Abstract: Several novel synthetic reactions of arenes and alkanes discovered and investigated in our laboratory are summarized here. These include olefin arylation, hydroarylation of alkynes, hydroxylation of arenes, carboxylation of arenes and alkanes, and aminomethylation and acetoxylation of alkanes. Most of these reactions are catalyzed by highly electrophilic transition metal cationic species generated in situ in an acid medium, involving electrophilic metalation of C−H bonds of arenes and alkanes which lead to the formation of aryl−metal and alkyl−metal σ-complexes.

Cyclodextrin-based molecular machines.

Abstract: Cyclodextrins have been used as a cyclic component in the construction of supramolecular architectures. Recently they have been studied as a component in the construction of rotaxanes and catenanes. A cyclodextrin ring can translocate in some rotaxane and catenane structures. Therefore, much attention has been given to cyclodextrins as a component of molecular shuttles, motors, and machines. Attempts to design and synthesize molecular-level machines using cyclodextrins as a cyclic component are described.

Supramolecular arrays based on dimetal building units.

Abstract: Supramolecular chemistry is today a major thrust area, a significant part of which is based on the use of metal atoms or ions as key elements in promoting the assembly of and dictating the main structural features of the supramolecular products. Most of the work has been done with single metal atoms or ions in this role, but considerable success has already been achieved by employing M−M bonded dimetal entities instead. We review here the work done in our laboratory. Metal−metal bonded cationic complexes of the [M2(DAniF)n(MeCN)8-2n](4-n)+ type, where M = Mo or Rh and DAniF is an N,N‘-di-p-anisylformamidinate anion, have been used as subunit precursors and then linked by various equatorial and axial bridging groups such as polycarboxylate anions, polypyridyls, and polynitriles. Characterization of the products by single-crystal X-ray diffraction, CV, DPV, NMR, and other spectroscopic techniques has revealed the presence of discrete tetranuclear (pairs or loops), hexanuclear (triangles), octanuclear (squar...

Reactions of electron-deficient alkynes and allenes under phosphine catalysis.

Abstract: The development of some new synthetic reactions derived from nucleophilic addition of phosphines to electron-deficient carbon-carbon triple bonds is described. These reactions show that the phosphine plays the role of a nucleophile as well as an excellent leaving group. The central problem is to generate a 1,3-dipole from alkynoates or allenoates (2,3-butadienoates) by interaction with various phosphines. This study illuminates the unusual phenomena and shows how this understanding allows control of the reaction.

Synthetic chemistry for ultrapure, processable, and high-mobility organic transistor semiconductors.

Abstract: An essential aspect of the development of organic-based electronics is the synthetic chemistry devised for the preparation of the semiconductor materials responsible for the activity of organic field-effect transistors. Access to organic semiconductors in sufficient purity and variety has led to breakthroughs in solid-state physics and circuit realization. In this Account, we review the synthetic methods that have been most useful for preparing a range of semiconductors, including thiophene-based oligomers, several kinds of fused rings, and polymers. The tradeoff between process efficiency and target purity is emphasized.

The depth of chemical time and the power of enzymes as catalysts.

Abstract: The fastest known reactions include reactions catalyzed by enzymes, but the rate enhancements that enzymes produce had not been fully appreciated until recently. In the absence of enzymes, these same reactions are among the slowest that have ever been measured, some with half-times approaching the age of the Earth. This difference provides a measure of the proficiencies of enzymes as catalysts and their relative susceptibilities to inhibition by transition-state analogue inhibitors. Thermodynamic comparisons between spontaneous and enzyme-catalyzed reactions, coupled with structural information, suggest that in addition to electrostatic and H-bonding interactions, the liberation of water molecules from an enzyme's active site into bulk solvent sometimes plays a prominent role in determining the relative binding affinities of the altered substrate in the ground state and transition state. These comparisons also indicate a high level of synergism in the action of binding determinants of both the substrate a...

New materials in hydrothermal synthesis.

Abstract: In this Account we describe the hydrothermal synthesis of some new materials including microporous crystals, ionic conductors, complex oxides and fluorides, low-dimensional aluminophosphates, inorganic-organic hybrid materials, and particularly condensed materials such as diamond and inorganic helical chains. Hydrothermal synthesis in biology and environment sciences is also introduced. The increasing interest in hydrothemal synthesis derives from its advantages in terms of high reactivity of reactants, easy control of solution or interface reactions, formation of metastable and unique condensed phases, less air pollution, and low energy consumption.

Teaching Old Indicators New Tricks

Abstract: Most synthetic sensors are designed with covalent attachment between a receptor and a reporter moiety. In this report, we describe the current progress of our use of noncovalently attached indicators to signal binding of analytes. With these systems, analyte binding leads to indicator displacement from the binding cavity, which in turn yields an optical signal modulation. We include previous examples, the strategies involved in our development, and the advantages as well as disadvantages of this method. Finally, our latest research in this field is briefly presented.

Switching devices based on interlocked molecules.

Abstract: An architectural rationale and an experimental program aimed at the development of molecular electronics switching devices for memory and computing applications are discussed. Two-terminal molecular switch tunnel junctions are identified as the critical device components of molecular electronics-based circuitry. They can be tiled in two dimensions and are tolerant of manufacturing defects. Singly and multiply configurable solid-state switching devices that are based upon electrochemically switchable molecular and supramolecular systems are discussed in terms of both the synthesis of the molecular components and the fabrication and performance of the devices.

Shuttles and muscles: linear molecular machines based on transition metals.

Abstract: Transition-metal-containing rotaxanes can behave as linear motors at the molecular level. The molecules are set into motion either by an electrochemical reaction or using a chemical signal. In a first example, a simple rotaxane is described that consists of a ring threaded by a two-coordination-site axle. The ring contains a bidentate ligand, coordinated to a copper center. The axle incorporates both a bidentate and a terdentate ligand. By oxidizing or reducing the copper center to Cu(II) or Cu(I) respectively, the ring glides from a given position on the axle to another position and vice versa. By generalizing the concept to a rotaxane dimer, whose synthesis involves a quantitative double-threading reaction triggered by copper(I) complexation, a molecular assembly reminiscent of a muscle is constructed. By exchanging the two metal centers of the complex (copper(I)/zinc(II)), a large-amplitude movement is generated, which corresponds to a contraction/stretching process. The copper(I)-containing rotaxane d...

In control of motion: from molecular switches to molecular motors.

Abstract: The design of molecular systems in which controlled linear and rotary motion can be achieved under the influence of an external signal is a major endeavor toward future nanoscale machinery. In this Account we describe the development of molecular switches and the discoveries that culminated in the first light-driven molecular motor. Various chiral optical molecular switches and their use as trigger elements to control organization and functions will be discussed. The construction of the first and second generation molecular motors is presented.

Sapphyrins: versatile anion binding agents.

Abstract: Sapphyrin was the first expanded porphyrin to be reported in the literature and remains among the most extensively studied. Much of the interest in this macrocycle reflects its ability to bind anions, a phenomenon that has been examined in solution and in the solid state by a wide range of experimental techniques. In this Account, we summarize these studies while also outlining strategies that may be used to synthesize sapphyrins.

Metric Engineering of Soft Molecular Host Frameworks

Abstract: The self-assembly and solid-state structures of host-guest inclusion compounds with lamellar architectures based on a common building block, a resilient hydrogen-bonded sheet consisting of guanidinium ions and sulfonate moieties of organodisulfonate "pillars", are described. The pillars connect adjacent sheets to generate galleries with molecular-scale cavities occupied by guest molecules. The size, shape, and physicochemical character of the inclusion cavities can be systematically adjusted by interchanging framework components while maintaining the lamellar architecture, enabling prediction and control of crystal lattice metrics with a precision that is unusual for "crystal engineering". The reliability of the lamellar architecture is a direct consequence of conformational flexibility exhibited by these hosts that, unlike rigid systems, enables them to achieve optimal packing with guest molecules. The adaptability of these hosts is further reflected by an architectural isomerism that is driven by guest templating during assembly of the inclusion compounds. Host frameworks constructed with various pillars display metric interdependences among specific structural features that reveal a common mechanism by which these soft frameworks adapt to different guests. This unique feature facilitates structure prediction and provides guidance for the design of inclusion compounds based on these hosts.

Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins.

Abstract: The dynamics of photoinduced charge separation and charge recombination processes in synthetic DNA hairpins have been investigated by means of femtosecond transient absorption spectroscopy. The driving force and distance dependence of charge-transfer processes involving singlet acceptors and nucleobase donors are consistent with a single-step superexchange mechanism in which the electronic coupling between the donor and acceptor is strongly distance dependent. The dynamics of reversible hole transport between a primary guanine donor and nearby GG or GGG sequences has also been determined and establishes that these sequences are very shallow hole traps.

Designer magnets containing cyanides and nitriles.

Abstract: Magnets synthesized from molecules have contributed to the renaissance in the study of magnetic materials. Three-dimensional network solids exhibiting magnetic ordering have been made from several first-row metal ions and bridging unsaturated cyanide, tricyanomethanide, and/or dicyanamide ligands. These materials possess several different structural motifs, and the shorter the bridge, the stronger the interaction (i.e., C⋮N > N⋮CN ≫ N⋮CNC⋮N = N⋮CCC⋮N). Cyanide additionally has the ability to discriminate between C- and N-bonding to form ordered heterobimetallic magnets, and the strong coupling can lead to ferro- or ferrimagnetic ordering substantially above room temperature. Tricoordination of tricyanomethanide results in spin-frustrated systems, which possess interpenetrating rutile-like networks. In contrast, single rutile-like frameworks are formed by μ3-bonded dicyanamide, which leads to ferromagnetics and weak ferromagnetics.

Artificial Molecular-Level Machines: Which Energy To Make Them Work?†

Abstract: The concept of machine can be extended to the molecular level by designing and synthesizing (supra)molecular species capable of performing mechanical movements. The energy needed to make a machine work can be supplied as chemical energy, electrical energy, or light. When a chemical “fuel” is used, waste products are formed, whereas this is not the case when suitable photochemical or electrochemical energy inputs are employed. A number of elementary functions performed by molecular-level machines are illustrated, and more complex ones are foreseen.

Theoretical Perspectives on Proton-Coupled Electron Transfer Reactions

Abstract: This Account presents a theoretical formulation for proton-coupled electron transfer reactions. The active electrons and transferring protons are treated quantum mechanically, and the free energy surfaces are obtained as functions of collective solvent coordinates corresponding to the proton and electron transfer reactions. Rate expressions have been derived in the relevant limits, and methodology for including the dynamical effects of the solvent and protein has been developed. This theoretical framework allows predictions of rates, mechanisms, and kinetic isotope effects for proton-coupled electron transfer reactions.

Wide bite angle diphosphines: xantphos ligands in transition metal complexes and catalysis.

Abstract: The reactivity of organotransition metal complexes is dependent on the ligand environment of the metal. This Account describes the development and application of new diphosphine ligands, designed to induce large P−M−P angles in transition metal complexes. Aided by computational chemistry, a homologous range of diphosphines based on rigid heterocyclic aromatic backbones of the xanthene-type with natural bite angles of ∼100−134° have been developed. The special structure of the ligands has an enormous impact on stability and reactivity of various transition metal complexes. Highly active and selective catalysts have been obtained by influencing this reactivity.

Attractive intramolecular edge-to-face aromatic interactions in flexible organic molecules.

Abstract: Recent X-ray crystallographic and NMR evidence indicates that relatively weak intramolecular edge-to-face interactions between aromatic rings can affect or determine the conformation of organic molecules in the solid state and in solution. Experimental estimates indicate that these interactions are energetically attractive by ca. 1.5 kcal mol-1 but disfavored in solution by entropic factors due to the restricted internal mobility. Hence, these interactions are more manifest at low temperature in solution or in crystal structures where conformational entropy effects are negligible.

Positive allosteric systems designed on dynamic supramolecular scaffolds: toward switching and amplification of guest affinity and selectivity.

Abstract: Positive homotropic allosterism appears in important information transduction processes where chemical and physical signals are efficiently amplified. The phenomena are ubiquitous in nature, but the general methodology for the design of such allosteric systems is not yet established in an artificial system. This account reviews such artificial receptors that can bind guest ions and molecules in a positive allosteric manner and discusses what kinds of factors are indispensable as scaffolds in the design of this novel class of allosteric systems and what common factors are needed to realize the cooperativity. It has been shown that the scaffolds are mostly dynamic and are skillfully combined with the molecular recognition systems so that the subsequent guest binding can occur more favorably than the first guest binding. In addition, it has been suggested that positive homotropic allosterism can be utilized as a new strategy to attain high guest selectivity and guest affinity which cannot be attained by conv...

On the way to rotaxane-based molecular motors: studies in molecular mobility and topological chirality.

Abstract: ATP synthase represents a machine at the molecular level which couples the rotation of an axle in a wheel with the endergonic production of ATP, the general source of chemical energy in the cell. The natural system prototypically bears all features of a macroscopic motor: a rotor within a stator held by a membrane and fueled by a difference in chemical potential in the form of a proton gradient combined with a machine for ATP production. The assembly of axle and wheel to a rotor device reminds one very much of a rotaxane. In this Account, we discuss some important features of motors and their (potential) realization in simpler artificial model systems, that is, the molecular mobility of mechanically bound molecules, the importance of chirality for unidirectional motion, the sources of energy for driving the rotation, and the potential of using membranes and surfaces for ordering a large number of devices to achieve macroscopic effects.

Aufbau principle of complex open-framework structures of metal phosphates with different dimensionalities.

Abstract: Open-framework metal phosphates occur as one-dimensional (1D) chains or ladders, two-dimensional (2D) layers, and complex three-dimensional (3D) structures. Zero-dimensional monomers have also been isolated recently. These materials are traditionally prepared by hydrothermal means, in the presence of organic amines, but the reactions of amine phosphates with metal ions provide a facile route for the synthesis, and also throw some light on the mode of formation of these fascinating architectures. Careful studies of the transformations of monophasic zinc phosphates of well-characterized structures show that the 1D structures transform to 2D and 3D structures, while the 2D structures transform to 3D structures. The zero-dimensional monomers transform to 1D, 2D, and 3D structures. There is reason to believe that the 0D monomers, comprising four-membered rings, are the most basic structural units of the open-framework phosphates and that after an optimal precursor state, such as the ladder structure, is formed, further building may occur spontaneously. Evidence for the occurrence of self-assembly in the formation of complex structures is provided by the presence of the structural features of the one-dimensional starting material in the final products. These observations constitute the beginning of our understanding of the building-up principle of such complex structures.

The physics of molecular motors.

Abstract: Molecular motors convert chemical energy into mechanical force and movement. Operating at energies just above those of the thermal bath, these motors experience large fluctuations, and their physical description must be necessarily stochastic. Here, motor operation is described as a biased diffusion on a potential energy surface defined by the interactions of the motor with its track and its fuel. These ideas are illustrated with a model of the rotary movement of the Fo motor.

Targeting RNA with small-molecule drugs: therapeutic promise and chemical challenges.

Abstract: Researchers' increasing awareness of the essential role played by RNA in many biological processes and in the progression of disease makes the discovery of new RNA targets an emerging field in drug discovery Since most existing pharmacologically active compounds bind proteins, RNA provides nearly untapped opportunities for pharmacological development The elucidation of the structure of the ribosome and other cellular and viral RNA motifs creates the opportunity for discovering new drug-like compounds that inhibit RNA function However, further advances in understanding the chemistry and structure of RNA recognition are needed before these promises are fulfilled

Chiral autocatalysis, spontaneous symmetry breaking, and stochastic behavior.

Abstract: During the past decade, chirally autocatalytic systems that exhibit unusual and interesting phenomena, such as spontaneous chiral symmetry breaking and stochastic behavior, have been identified. In this Account we outline the context in which chiral autocatalysis is of interest, summarize recent advances, and discuss our current understanding of the underlying kinetics and mechanisms. In addition, we note some fundamental aspects of amplification of enantiomeric excess and sensitivity of symmetry breaking transitions to asymmetric factors.