Showing papers in "Chemical Reviews in 2005"

Quantum mechanical continuum solvation models.

Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

Chemistry and properties of nanocrystals of different shapes.

Abstract: The interest in nanoscale materials stems from the fact that new properties are acquired at this length scale and, equally important, that these properties * To whom correspondence should be addressed. Phone, 404-8940292; fax, 404-894-0294; e-mail, mostafa.el-sayed@ chemistry.gatech.edu. † Case Western Reserve UniversitysMillis 2258. ‡ Phone, 216-368-5918; fax, 216-368-3006; e-mail, burda@case.edu. § Georgia Institute of Technology. 1025 Chem. Rev. 2005, 105, 1025−1102

Nanostructures in Biodiagnostics

Abstract: In the last 10 years the field of molecular diagnostics has witnessed an explosion of interest in the use of nanomaterials in assays for gases, metal ions, and DNA and protein markers for many diseases. Intense research has been fueled by the need for practical, robust, and highly sensitive and selective detection agents that can address the deficiencies of conventional technologies. Chemists are playing an important role in designing and fabricating new materials for application in diagnostic assays. In certain cases assays based upon nanomaterials have offered significant advantages over conventional diagnostic systems with regard to assay sensitivity, selectivity, and practicality. Some of these new methods have recently been reviewed elsewhere with a focus on the materials themselves or as subclassifications in more generalized overviews of biological applications of nanomaterials.1-7 We intend to review some of the major advances and milestones in the field of detection systems based upon nanomaterials and their roles in biodiagnostic screening for nucleic acids, * To whom correspondence should be addressed. Phone: 847-4913907. Fax: 847-467-5123. E-mail: chadnano@northwestern.edu. Nathaniel L. Rosi earned his B.A. degree at Grinnell College (1999) and his Ph.D. degree from the University of Michigan (2003), where he studied the design, synthesis, and gas storage applications of metal−organic frameworks under the guidance of Professor Omar M. Yaghi. In 2003 he began postdoctoral studies as a member of Professor Mirkin’s group at Northwestern University. His current research focuses on the rational assembly of DNA-modified nanostructures into larger-scale materials.

Nucleus-independent chemical shifts (NICS) as an aromaticity criterion.

Abstract: A comprehensive review is presented on nucleus-independent chem. shift as a criterion for aromaticity. [on SciFinder (R)]

Organic Reactions in Aqueous Media with a Focus on Carbon−Carbon Bond Formations: A Decade Update

Abstract: 4.2.8. Reductive Coupling 3109 5. Reaction of Aromatic Compounds 3110 5.1. Electrophilic Substitutions 3110 5.2. Radical Substitution 3111 5.3. Oxidative Coupling 3111 5.4. Photochemical Reactions 3111 6. Reaction of Carbonyl Compounds 3111 6.1. Nucleophilic Additions 3111 6.1.1. Allylation 3111 6.1.2. Propargylation 3120 6.1.3. Benzylation 3121 6.1.4. Arylation/Vinylation 3121 6.1.5. Alkynylation 3121 6.1.6. Alkylation 3121 6.1.7. Reformatsky-Type Reaction 3122 6.1.8. Direct Aldol Reaction 3122 6.1.9. Mukaiyama Aldol Reaction 3124 6.1.10. Hydrogen Cyanide Addition 3125 6.2. Pinacol Coupling 3126 6.3. Wittig Reactions 3126 7. Reaction of R,â-Unsaturated Carbonyl Compounds 3127

Structure and Chemistry of Cytochrome P450

Abstract: Two decades have passed since the discovery in liver microsomes of a haemprotein that forms a reduced-CO complex with the absorptive maximum of the Soret at 450 nm (Klingenberg, 1958; Garfinkel, 1958) and the identification of this protein as a new cytochrome: pigment cytochrome, P-450 (Omura and Sato, 1962, 1964a). In the intervening years, the study of cytochrome P-450 dependent monoxygenases has expanded exponentially. From the first crude attempts to solubilise a P-450 (Omura and Sato, 1963, 1964b) to the determination of the primary, secondary, and tertiary structure of cytochrome P-450cam by amino acid sequencing (Haniu et al., 1982a,b) and x-ray crystallography (Poulos et al., 1984) our understanding of this unique family of proteins has been advancing on all fronts. Since, perhaps, the greatest understanding of the structure and mechanism of P-450s has come from concentrated study of P-450cam of the Pseudomonas putida camphor-5-exo-hydroxylase, this review will concentrate on findings with P-450cam; attention will be drawn to parallel and contrasting examples from other P-450s as appropriate.

Synthesis and functionalization of indoles through palladium-catalyzed reactions

Abstract: The substituted indole nucleus [indole is the acronym from indigo (the natural dye) and oleum (used for the isolation)] is a structural component of a vast number of biologically active natural and unnatural compounds. The synthesis and functionalization of indoles has been the object of research for over 100 years, and a variety of well-established classical methods are now available, to name a few of them, the Fisher indole synthesis, the Gassman synthesis of indoles from N-halo-anilines, the Madelung cyclization of N-acyl-o-toluidines, the Bischler indole synthesis, the Batcho-Leimgruber synthesis of indoles from o-nitrotoluenes and dimethylformamide acetals, and the reductive cyclization of o-nitrobenzyl ketones.1 In the last 40 years or so, however, palladiumcatalyzed reactions, generally tolerant of a wide range of functionalities and therefore applicable to complex molecules, have achieved an important place in the arsenal of the practicing organic chemist. Since the invention of an industrial process for the palladium-catalyzed production of acetaldehyde from ethylene in the presence of PdCl2 and CuCl2, an everincreasing number of organic transformations have been based on palladium catalysis. Almost every area of the organic synthesis has been deeply influenced by the profound potential of this versatile transition metal, modifying the way organic chemists design and realize synthetic processes.2,3 Because of its catalytic nature, palladium-catalyzed synthesis can provide access to fine chemicals, agrochemical and pharmaceutical intermediates, and active ingredients in fewer steps and with less waste than classical † In memory of Prof. Bianca Rosa Pietroni, a colleague and very close friend. * To whom correspondence should be addressed. Phone: + 39 (06) 4991-2785. Fax: + 30 (06) 4991-2780. E-mail: sandro.cacchi@ uniroma1.it. 2873 Chem. Rev. 2005, 105, 2873−2920

Self-Assembled Nanoreactors

Abstract: An overview of the wide range of nanoreactors that have been constructed from synthetic and biological building blocks using both covalent and noncovalent approaches is given. Focus is on self-assembled systems, varying in size from a few nanometers to tens of micrometers. The review is divided into several sections that cover the development of tailor-made nanoreactors, starting from small organic molecular containers expanding to large compartment-containing assemblies. First, the construction of capsules from low molecular weight compounds by means of covalent synthesis and self-assembly by highly directive and pre-designed interactions is discussed. Second, nanocapsules based on micellar and vesicular assemblies that are built up frow low molecular weight molecules are described. Finally, the construction of nanoreactors from macromolecular building blocks, as well as recent developments in the use of viruses as nanocontainers and reactors are outlined.

Mechanochemistry: the mechanical activation of covalent bonds.

Abstract: Regarding the activation of chemical reactions, today’s chemist is used to thinking in terms of thermochemistry, electrochemistry, and photochemistry, which is reflected in the organization and content of the standard physical chemistry textbooks. The fourth way of chemical activation, mechanochemistry, is usually less well-known. The purpose of the present review is to give a survey of the classical works in mechanochemistry and put the key mechanochemical phenomena into perspective with recent results from atomic force microscopy and quantum molecular dynamics simulations. A detailed historical account on the development of mechanochemistry, with an emphasis on the mechanochemistry of solids, was recently given by Boldyrev and Tkáčová.1 The first written document of a mechanochemical reaction is found in a book by Theophrastus of Ephesus (371-286 B.C.), a student of Aristotle, “De Lapidibus” or “On stones”. If native cinnabar is rubbed in a brass mortar with a brass pestle in the presence of vinegar, metallic mercury is obtained. The mechanochemical reduction probably follows the reaction:1-3 * To whom correspondence should be addressed. Telephone: ++49-89-289-13417. Fax: ++49-89-289-13416. E-mail: martin.beyer@ch.tum.de (M.K.B.); Telephone: ++49-89-12651417. Fax: ++49-89-1265-1480. E-mail: clausen-schaumann@ fhm.edu (H.C.-S.). † Technische Universität München. ‡ Institut für Strahlenschutz. § Current address: Munich University of Applied Sciences. HgS + Cu f Hg + CuS (1) Volume 105, Number 8

Ag(I) N-Heterocyclic Carbene Complexes: Synthesis, Structure, and Application

Abstract: Öfele and Wanzlick first pioneered the metalation of imidazol-2-ylidenes, better known as N-heterocyclic carbenes (NHCs), from imidazolium salts in 1968.1,2 Lappert and co-workers followed this work with the investigation of N-heterocyclic carbene complexes synthesized from electron-rich olefins.3,4 However, it was not until the isolation of the first free carbene by Arduengo, in 1991, that significant interest was given to the area.5 Since then the complexation chemistry of these new ligands has become a major area of research.6-10 This new class of ligand has shown to equal, if not exceed, phosphines in their ability to bind to a variety of metals. Complexes of N-heterocyclic carbenes with virtually every transition metal and many main group elements have been reported.1-10 N-Heterocyclic carbenes bind to both hard and soft metals making it a very versatile ligand system. NHCs bond to metals primarily through σ donation of the carbene lone pair to the metal. The bonding of the carbene was believed to have been purely σ donation in nature; however, recent evidence suggests that some degree of backdonation may occur.11,12 The bond strength of Nheterocyclic carbenes, as mentioned earlier, has been shown to rival phosphines. Due to this bonding * To whom correspondence should be addressed. Phone: (330)972-5362. E-mail: youngs@uakron.edu. 3978 Chem. Rev. 2005, 105, 3978−4008

Advances in Homogeneous and Heterogeneous Catalytic Asymmetric Epoxidation

Abstract: Laboratory for Advanced Materials and New Catalysis, School of Chemistry and Materials Science, Hubei University, Wuhan 430062, China,Laboratory of Natural Gas Utilization and Applied Catalysis, Dalian Institute of Chemical Physics of Chinese Academy of Sciences, Dalian 116023,China, and Jingmen Technological College, Jingmen 448000, ChinaReceived June 30, 2004

Intramolecular dipolar cycloaddition reactions of azomethine ylides.

Abstract: It was in 1963 that Huisgen laid out the classification of 1,3-dipoles and the concepts for 1,3-dipolar cycloaddition reactions, although it was not until 1976 that the first intramolecular 1,3-dipolar cycloaddition reaction of an azomethine ylide was reported. Since then, impressive developments have been described in this area, with the establishment of various useful methods for the formation of azomethine ylides and the determination of the requirements for a successful intramolecular cycloaddition reaction. Use of this methodology for the synthesis of pyrrolidineand pyrrole-containing natural products has been expanding rapidly. This review aims to describe the background and mechanisms of azomethine ylide formation and intramolecular cycloaddition, giving a critical account including the very first example and covering to early 2005. It is hoped that this review will be a useful resource for chemists interested in cycloaddition reactions and will inspire further exciting developments in this area. Cycloaddition reactions are one of the most important class of reactions in synthetic chemistry. Within * Corresponding author. Tel: +44 (0)114 222 9428. Fax: +44 (0)114 222 9346. E-mail: i.coldham@sheffield.ac.uk. † University of Sheffield. ‡ Tripos Discovery Research Ltd. Iain Coldham (b. 1965) is a Reader in Organic Chemistry at the University of Sheffield. He obtained his undergraduate degree and Ph.D. from the University of Cambridge, completing his Ph.D. in 1989 under the supervision of Stuart Warren. After postdoctoral studies at the University of Texas with Philip Magnus, he joined the staff in 1991 at the University of Exeter, U.K. In 2003, he moved to the University of Sheffield where he is involved in research on chiral organolithium compounds and on dipolar cycloaddition reactions in synthetic organic chemistry.

Toward intelligent molecular machines: directed motions of biological and artificial molecules and assemblies.

Abstract: In the last two decades, considerable progress has been made in the field of molecular biology, which has enabled a molecular-level understanding of a number of interesting biological events. In particular, the discovery of a family of moving proteins and their assemblies has attracted particular attention not only of biologists but also of chemists and physicists.1-5 In response to certain biological stimuli, these proteins perform directed or programmed motions, similar to many tools and machines used in our daily life. Such biological molecular machines play essential roles in a wide variety of biological events, particularly those related to the activities of cells,1 and realize specific functions through their stimuliresponsive mechanical motions. Cytoplasmic proteins such as myosins, kinesins, and dyneins are called “molecular motors” and are the most extensively studied molecular machines.2-5 These protein-based supramolecular conjugates are known to switch back and forth along linear tracks of actin filaments or microtubules and transport substrates at the expense of adenosine triphosphate (ATP) as fuel. The flagellum is a huge protein conjugate that controls the swimming motion of bacteria.6 The bacterial flagellar motor consists of (1) flagellar filaments that are 15 μm long and 120-250 Å in diameter and a (2) motor domain that rotates the flagellar filaments alternately in clockwise and anticlockwise directions. This unique behavior of rotation allows bacteria to swim desirably. ATP synthase is a different type of a molecular machine, which synthesizes and hydrolyzes ATP through its rotary motion.7-9 ATP synthase is built up of two different machinery components, that is, F1 and F0, where the rotation of the former is driven by the free energy released from the hydrolysis of ATP to adenosine diphosphate (ADP); the latter rotates by a flux of ions passing through a membrane and synthesizes ATP. This huge protein complex has a shaft, which rotates just like real rotary motors. Since the rotary motion of ATP synthase occurs in a stepwise manner in response to the hydrolysis of ATP, it is regarded as a biological stepping motor. In addition to these molecular motors, some other biological machines are known, where the hydrolysis of ATP triggers different types of mechanical motions. Representative examples include the family of chap† The University of Tokyo. ‡ PRESTO. 1377 Chem. Rev. 2005, 105, 1377−1400

Water Dynamics in the Hydration Layer around Proteins and Micelles

Abstract: This review deals with dynamics of water molecules in the hydration layer that surrounds self-assemblies and proteins in aqueous solutions. This topic has not only seen a vigorous upsurge of interest in the past decade but also has been a subject of investigation for almost half a century now. The basic motivation behind such studies is that they provide valuable information regarding the structure and dynamics of hydration layers and also about the dynamics of self-assemblies and biomolecules themselves. Perhaps the perception about this problem was aptly voiced by Robinson et al. a few years ago when they observed that this "is the most important problem in science that hardly anyone wants to see solved. While one may certainly argue over the superlative used and the skepticism voiced, the need for a better understanding of this important problem was apparent. Fortunately, considerable progress has been made in recent years by the combination of a host of experimental, theoretical, and computer simulation techniques. We aim to review a part of this progress. Because the existing literature is huge, my review may not be exhaustive but I hope to address at least some of the key issues.