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).

An acid-base-controllable [c2]daisy chain

Abstract: Artificial molecular-based muscles, which can convert chemical, electrochemical, or photochemical energy into mechanical motion, have attracted attention as a result of their potential for spawning nanoelectromechanical systems (NEMS). Several materials, such as conducting polymers, single-walled carbon nanotubes, and dielectric elastomers, have been developed which exhibit muscle-like behavior at the nanoscale level. However, all these systems rely upon the response of a bulk substance, rather than on the behavior of individual molecules. Recently, artificial muscles have been designed on a molecular scale by taking advantage of conformational changes exerted by electrochemical stimuli. For example, oligothiophene-calix[4]arene copolymers and thiophene-fused annulenes exhibit molecular actuating behavior under redox control while crown-etherannelated oligothiophenes and polyheterocyclic strands have ion-triggered muscle-like properties. Nanoscale molecular motions, based on artificial molecular machines, offer alternative opportunities to design artificial muscle-like materials. Bistable rotaxanes are a promising component for such materials, because relative linear mechanical translocation of the ring and dumbbell components can be achieved upon activation by chemical, electrical, or light irradiation stimuli. Converting such internal molecular motions into practical actuating materials requires relocating these internal motions into components, which, when taken together, exhibit linear expansion and contraction. Sauvage et al. have reported a linear molecular muscle, based on a transition-metal templated, doubly threaded rotaxane, which can undergo the required expansion and contraction motions on the addition or removal of metal ions. On the other hand, we have reported a switchable, palindromically constituted, doubly bistable [3]rotaxane which can be selfassembled onto gold-coated microcantilevers with disulfideterminated tethers emanating from its two rings in such a manner that they can be moved towards and away from each other under redox control. Controllable and reversible deflection of the microcantilevers can be achieved when the integrated system is exposed to the addition of oxidants or reductants (or subjected to oxidizing or reducing electrochemical potentials). Acid–base controllable, bistable, rotaxane-based molecular shuttles have been reported in which a dibenzo[24]crown-8 (DB24C8) ring switches under acid–base control between two different recognition sites on a dumbbell component, where one of the sites is a secondary dialkylammonium (R2NH2 ) center and the other site, an N,N’dialkylated-4,4’-bipyridinium (Bpym) unit. Although this switching has subsequently been employed in the design of more complex machines, such as nanoscale elevators, the mechanical motions are still only relative internal movements, that is to say, there is no contraction/expansion in their overall molecular dimensions. Herein, a bistable molecular architecture incorporating a two-component [c2]daisy chain topology is designed and synthesized (Scheme 1), wherein two mechanically interlocked filaments glide along one another through the terminal crown ether rings and in which the end of each filament is attached to bulky stoppers to prevent

Supramolecular nanovalves controlled by proton abstraction and competitive binding

Abstract: A functional integrated nanosystem for trapping and releasing molecules under deliberate control is prepared. The openings to nanosized pores in silica particles are regulated by gatekeeper supermolecules that are controlled by pH stimulation and competitive binding. Controlled release of fluorescent probe molecules is demonstrated using (i) organic bases, (ii) fluorodialkylammonium ions, and (iii) metal ions as actuators. The rate of the release of the probe molecules depends on the size of the base, the dimension of the probe molecules, and the binding affinity of the metal/fluorodialkylammonium cations employed.

Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment.

Abstract: Bistable [2]rotaxanes display controllable switching properties in solution, on surfaces, and in devices. These phenomena are based on the electrochemically and electrically driven mechanical shuttling motion of the ring-shaped component, cyclobis(paraquat-p-phenylene) (CBPQT4+) (denoted as the ring), between a tetrathiafulvalene (TTF) unit and a 1,5-dioxynaphthalene (DNP) ring system located along a dumbbell component. When the ring is encircling the TTF unit, this co-conformation of the rotaxane is the most stable and thus designated the ground-state co-conformer (GSCC), whereas the other co-conformation with the ring surrounding the DNP ring system is less favored and so designated the metastable-state co-conformer (MSCC). We report here the structure and properties of self-assembled monolayers (SAMs) of a bistable [2]rotaxane on Au (111) surfaces as a function of surface coverage based on atomistic molecular dynamics (MD) studies with a force field optimized from DFT calculations and we report several...

Chromatography in a single metal-organic framework (MOF) crystal

Abstract: Millimeter-sized single MOF-5 crystals are used as “chromatographic columns” to effectively separate mixtures of organic dyes. Remarkably, owing to the nanoscopic pore dimensions and the molecular-level interactions between the migrating molecules and the MOF scaffold, the separations occur over a distance of only a few hundred micrometers which is unambiguously confirmed by fluorescence confocal microscopy.

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.