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).

Evaluation of synthetic linear motor-molecule actuation energetics.

Abstract: By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of experimental force spectroscopy and theoretical computational modeling has revealed that the repulsive electrostatic interaction, which is responsible for the molecular actuation, is as high as 65 kcal·mol−1, a result that is supported by ab initio calculations.

Modular synthesis and dynamics of a variety of donor-acceptor interlocked compounds prepared by click chemistry.

Abstract: A series of donor-acceptor (2)-, (3)-, and (4)rotaxanes and self- complexes ((1)rotaxanes) have been synthesized by a threading-followed- by-stoppering approach, in which the precursor pseudorotaxanes are fixed by using Cu I -catalyzed Huisgen 1,3-dipolar cycloaddition to attach the required stoppers. This alternative approach to forming rotaxanes of the donor-accept- or type, in which the donor is a 1,5-di- oxynaphthalene unit and the acceptor is the tetracationic cyclophane cyclo- bis(paraquat-p-phenylene), proceeds with enhanced yields relative to the tried and tested synthetic strategies, which involve the clipping of the cyclo- phane around a preformed dumbbell containing p-electron-donating recogni- tion sites. The new synthetic approach is amenable to application to highly convergent sequences. To extend the scope of this reaction, we constructed (2)rotaxanes in which one of the phen- ylene rings of the tetracationic cyclo- phane is perfluorinated, a feature which significantly weakens its associa- tion with p-electron-rich guests. The activation barrier for the shuttling of the cyclophane over a spacer contain- ing two triazole rings was determined to be (15.5 � 0.1) kcal mol � 1 for a de- generate two-station (2)rotaxane, a value similar to that previously mea- sured for analogous degenerate com- pounds containing aromatic or ethyl- ene glycol spacers. The triazole rings do not seem to perturbthe shuttling process significantly; this property bodes well for their future incorpora- tion into bistable molecular switches.

Mechanical bond-induced radical stabilization

Abstract: A homologous series of [2]rotaxanes, in which cyclobis(paraquat-p-phenylene) (CBPQT4+) serves as the ring component, while the dumbbell components all contain single 4,4′-bipyridinium (BIPY2+) units centrally located in the midst of oligomethylene chains of varying lengths, have been synthesized by taking advantage of radical templation and copper-free azide–alkyne 1,3-dipolar cycloadditions in the formation of their stoppers. Cyclic voltammetry, UV/vis spectroscopy, and mass spectrometry reveal that the BIPY•+ radical cations in this series of [2]rotaxanes are stabilized against oxidation, both electrochemically and by atmospheric oxygen. The enforced proximity between the BIPY2+ units in the ring and dumbbell components gives rise to enhanced Coulombic repulsion, destabilizing the ground-state co-conformations of the fully oxidized forms of these [2]rotaxanes. The smallest [2]rotaxane, with only three methylene groups on each side of its dumbbell component, is found to exist under ambient conditions in ...

Single-walled carbon nanotubes under the influence of dynamic coordination and supramolecular chemistry.

Abstract: A dynamic coordinative-directed solubilization of single-walled carbon nanotubes (SWNTs) in aqueous solutions has been achieved through a combination of a Zn(II) metalloporphyrin complex and a cis-protected Pd(II) complex, which are believed to form charged acyclic and/or cyclic adducts on or around the side walls of SWNTs. The solubilization of SWNTs in aqueous solution only occurs when these acyclic and/or cyclic complexes are allowed to enter simultaneously into a self-assembly process with SWNTs under mild conditions. The aqueous solubility properties that these dynamic complexes confer upon SWNTs are believed to involve noncovalent bonding interactions between the two entities. They have been probed in solution using ultraviolet and visible absorption spectroscopy and in thin films using high-resolution transmission electron microscopy. The supramolecular electronic effects that the individual components of their acyclic and/or cyclic complexes impart upon a single semiconducting SWNT have been probed within a nanotube field-effect transistor device.

Recognition of Bipyridinium-Based Derivatives by Hydroquinone-and/or Dioxynaphthalene-Based Macrocyclic Polyethers: From Inclusion Complexes to the Self-Assembly of [2]Catenanes

Abstract: A range of pi-electron-rich macrocyclic polyethers incorporating dioxybenzene (hydroquinone) and/or dioxynaphthalene units have been synthesized in good yields by simple two-step procedures. These macrocycles are able to bind bipyridinium-based guests as a result of a series of cooperative noncovalent bonding interactions. These molecular recognition events can be extended to the self-assembly of [2]catenanes incorporating the bipyridinium-based cyclophane, cyclobis(paraquat-p-phenylene), and the macrocyclic polyethers incorporating dioxybenzene and -naphthalene units. The efficiencies of these self-assembly processes were found to depend upon the stereoelectronic features of the pi-electron-rich macrocycles-namely, the nature and the substitution pattern of the aromatic units. X-ray crystallographic analysis of some of these [2]catenanes proved unequivocally the relative geometries of the interlocked components. In addition, in the case of those asymmetric [2]catenanes incorporating two different aromatic units within their macrocyclic polyether components, only one of the expected two translational isomers was observed in the solid state. In particular, in all the structures examined, the 1,4-dioxybenzene and 1,5-dioxynaphthalene units are located within the cavity of the tetracationic cyclophane component in preference to other regioisomeric dioxynaphthalene units that reside alongside. Variable-temperature (1)H NMR spectroscopic investigation of the geometries adopted by these [2]catenanes in solution revealed the same selectivity that was observed for one translational isomer over another in the solid state.

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.