J. Fraser Stoddart

Bio: J. Fraser Stoddart is an academic researcher from Northwestern University. The author has contributed to research in topics: Catenane & Supramolecular chemistry. The author has an hindex of 147, co-authored 1239 publications receiving 96083 citations. Previous affiliations of J. Fraser Stoddart include Zhejiang University & Northwest University (United States).

The Burgeoning of Mechanically Interlocked Molecules in Chemistry

Abstract: Mechanically interlocked molecules (MIMs), such as rotaxanes, catenanes, and molecular knots, have attracted significant interest because of their unique properties originating from their mechanically bonded components. Recently, MIMs have been employed in increasingly diverse architectures thanks to the tools of rational molecular design and the ability to incorporate functions in a precise manner. Here, we discuss advances in MIM synthesis, the fundamental understanding of their working processes, and applications exploiting their singular behavior. This review covers some of the most recent studies demonstrating the widespread interest in MIMs by scientists pursuing the ultimate goal of designing functional molecular machines that surpass their natural analogs or exhibit unprecedented properties.

ExTzBox: A Glowing Cyclophane for Live-Cell Imaging

Abstract: The ideal fluorescent probe for live-cell imaging is bright and non-cytotoxic and can be delivered easily into the living cells in an efficient manner. The design of synthetic fluorophores having all three of these properties, however, has proved to be challenging. Here, we introduce a simple, yet effective, strategy based on well-established chemistry for designing a new class of fluorescent probes for live-cell imaging. A box-like hybrid cyclophane, namely ExTzBox·4X (6·4X, X = PF6−, Cl−), has been synthesized by connecting an extended viologen (ExBIPY) and a dipyridyl thiazolothiazole (TzBIPY) unit in an end-to-end fashion with two p-xylylene linkers. Photophysical studies show that 6·4Cl has a quantum yield ΦF = 1.00. Furthermore, unlike its ExBIPY2+ and TzBIPY2+ building units, 6·4Cl is non-cytotoxic to RAW 264.7 macrophages, even with a loading concentration as high as 100 μM, presumably on account of its rigid box-like structure which prevents its intercalation into DNA and may inhibit other intera...

Cyclobis(Paraquat-4,4′-Biphenylene)–an Organic Molecular Square

Abstract: Template-directed syntheses of cyclobis(paraquat-4,4′-biphenylene) (1)– a Molecular square–have been achieved by use of π-electron-rich macrocyclic hydroquinone-based and acyclic ferrocene-based templates. In particular, the use of a polyether-disubstituted ferrocene derivative as a template permits synthesis of 1 (which is accessible only in very low yields without templates) on a preparative scale. Furthermore, the use of a macrocyclic hydroquinone-based polyether template in corporating an ester function in one polyether chain–an (oriented) macrocycle–affords a 1 : 1 mixture of two topologically stereoisomeric [3]catenanes. Ester hydrolysis of the π-electron-rich macrocyclic components mechanically interlocked with 1 within the catenated structures releases the tetracationic cyclophane in quantitative yield as a result of the degradation of the [3]catenanes. The molecular square has been characterized by X-ray crystallography, FAB mass spectrometry, 1H NMR and 13C NMR spectroscopies, and elemental analysis. The binding properties of 1 and of the smaller cyclophane cyclobis(paraquat-p-phenylene) toward a series of π-electronrich guests have also been investigated with the above techniques and UV/VIS spectroscopy. The self-assembly of the resulting supramolecular complexes in solution and in the solid state is driven mainly by π–π stacking interactions and hydrogen-bonding interactions, as well as by edge-to-face T-type interactions. In particular, the complexation of ferrocene or a ferrocene-based derivative within the cavity of 1 suggests the possibility of constructing functioning ferrocene-based molecular and supramolecular devices that can be controlled electrochemically in the form of catenanes, rotaxanes, and pseudorotaxanes.

Assembly of polygonal nanoparticle clusters directed by reversible noncovalent bonding interactions.

Abstract: The reversible molecular template-directed self-assembly of gold nanoparticles (AuNPs), a process which relies solely on noncovalent bonding interactions, has been demonstrated by high-resolution transmission electron microscopy (HR-TEM). By employing a well-known host-guest binding motif, the AuNPs have been systemized into discrete dimers, trimers, and tetramers. These nanoparticulate twins, triplets, and quadruplets, which can be disassembled and reassembled either chemically or electrochemically, can be coalesced into larger, permanent polygonal structures by thermal treatment using a focused HR-TEM electron beam.

Slippage—an alternative method for assembling [2]rotaxanes

Abstract: The exploitation of size-complementarity between the macrocyclic component and the stoppers of the dumbbell component of a [2]rotaxane, together with stabilising noncovalent bonding interactions that create a thermodynamic trap, have permitted the development of an alternative method, which can be termed slippage, for the syntheses of [2]rotaxanes in good yields.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology.

Abstract: Although gold is the subject of one of the most ancient themes of investigation in science, its renaissance now leads to an exponentially increasing number of publications, especially in the context of emerging nanoscience and nanotechnology with nanoparticles and self-assembled monolayers (SAMs). We will limit the present review to gold nanoparticles (AuNPs), also called gold colloids. AuNPs are the most stable metal nanoparticles, and they present fascinating aspects such as their assembly of multiple types involving materials science, the behavior of the individual particles, size-related electronic, magnetic and optical properties (quantum size effect), and their applications to catalysis and biology. Their promises are in these fields as well as in the bottom-up approach of nanotechnology, and they will be key materials and building block in the 21st century. Whereas the extraction of gold started in the 5th millennium B.C. near Varna (Bulgaria) and reached 10 tons per year in Egypt around 1200-1300 B.C. when the marvelous statue of Touthankamon was constructed, it is probable that “soluble” gold appeared around the 5th or 4th century B.C. in Egypt and China. In antiquity, materials were used in an ecological sense for both aesthetic and curative purposes. Colloidal gold was used to make ruby glass 293 Chem. Rev. 2004, 104, 293−346

The Chemistry and Applications of Metal-Organic Frameworks

Abstract: Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.