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).

A Mechanically Interlocked Bundle

Abstract: The prototype of an artificial molecular machine consisting of a tris- ammonium tricationic component in- terlocked with a tris(crown ether) com- ponent to form a molecular bundle with averaged C3v symmetry has been designed and synthesized.The system is based on noncovalent interactions, which include 1) N + H¥¥¥O hydrogen bonds; 2) CH¥¥¥O interactions be- tween the CH2NH2 + CH2 protons on three dibenzylammonium-ion-contain- ing arms, which are attached symmetri- cally to a benzenoid core, and three di- benzo(24)crown-8 macrorings fused onto a triphenylene core; and 3) p¥¥¥p stacking interactions between the aro- matic cores.The template-directed syn- thesis of the mechanically interlocked, triply threaded bundle involves post- assembly covalent modification, that is, the efficient conversion of three azide functions at the ends of the arms of the bound and threaded trication into bulky triazole stoppers, after 1,3-dipo- lar cycloaddition with di-tert-butylacet- ylenedicarboxylate to the extremely strong 1:1 adduct that is formed in di- chloromethane/acetonitrile (3:2), on account of a cluster effect associated with the paucivalent adduct.Evidence for the averaged C3v symmetry of the molecular bundle comes from absorp- tion and luminescence data, as well as from electrochemical experiments, 1 H NMR spectroscopy, and mass spec- trometry.The photophysical properties of the mechanically interlocked bundle are very similar to those of the super- bundle that precedes the formation of the bundle in the process of supra- molecular assistance to covalent syn- thesis.Although weak non-nucleophilic bases (e.g., nBu3N and iPr2NEt) fail to deprotonate the bundle, the strong tBuOK does, as indicated by both lumi- nescence and 1 H NMR spectroscopy. While deprotonation undoubtedly loos- ens up the interlocked structure of the molecular bundle by replacing relative- ly strong N + H¥¥¥O hydrogen bonds by much weaker NH¥¥¥O ones, the p¥¥¥p stacking interactions ensure that any structural changes are inconsequential, particularly when the temperature of the solution of the neutral molecular bundle in dichloromethane is cooled down to considerably below room tem- perature.

The self-assembly of [n]pseudorotaxanes

Abstract: An acyclic oligomeric polyether in which four tetraethylene glycol units are located between five hydroquinol rings, with the two terminal rings carrying benzyl ether groups, self-assembles in solution with one and two molar equivalents of a tetracationic cyclobis(paraquat-p-phenylene) macrocycle to afford, respectively and selectively, a [2]pseudorotaxane and a [3]pseudorotaxane.

Heterogeneous Catalysis of a Copper-Coated Atomic Force Microscopy Tip for Direct-Write Click Chemistry

Abstract: We report a constructive scanning probe lithography method that uses heterogeneous copper-coated atomic force microscopy tips to catalyze azide–alkyne cycloadditions (CuAAC) between solvated terminal alkyne molecules and azide-terminated self-assembled monolayers on silicon surfaces. Spatially controlled surface functionalization was carried out successfully with 50 mM ethanolic solutions of small molecules bearing terminal alkyne groups—propargylamine, 4-pentynoic acid, and an alkynyl-oligoethyleneoxide. We observed that reaction occurs only where the copper tip is in contact with an azide-terminated surface resulting in features with linewidths on the order of 50 nm. The extent of surface functionalization, as measured by changes in surface topography and lateral force microscopy, depends on the scanning force (31–350 nN) and scanning speed, with significant surface patterning observed even at speeds as high as 64 μm/s. In contrast with related SPL techniques, this approach affords a direct-write lithographic approach to modifying and patterning surfaces constructively at the nanoscale without the need for auxiliary reagents. All that is required is (1) an azide surface (2) a solution of a terminal alkyne and (3) a copper-coated AFM tip. These advantages allow the direct attachment of a potentially limitless library of molecules that bear terminal alkyne functionalities—including biomolecules—under relatively mild conditions, with sub-100 nm spatial resolution.

Simple molecular-level machines. Interchange between different threads in pseudorotaxanes

Abstract: In suitably designed supramolecular systems, composed of a macrocycle and two different thread-like compounds, it is possible to choose, by means of chemical inputs, which thread enters the macrocycle's cavity, and it is also possible to cause reversible interchange between the two threads. Two such systems are described. In one of them, the macrocyclic component is 1,5-dinaphtho-38-crown-10, the potential threads are 1,1′-dibenzyl-4,4′-bipyridinium and 2,7-dibenzyldiazapyrenium dications, and the chemical input used is amine/acid. In the other system, the macrocyclic component is the tetracationic cyclophane, cyclobis(paraquat-p-phenylene), the potential threads are tetrathiafulvalene and a 1,5-dioxynaphthalene derivative, and the input is reduction/oxidation. These systems are examples of chemically driven molecular-level mechanical machines.

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.