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).

C-h...o interactions as a control element in supramolecular complexes : experimental and theoretical evaluation of receptor affinities for the binding of bipyridinium-based guests by catenated hosts

Abstract: Macrocyclic receptors incorporating two facing π-electron-rich aromatic surfaces, held at a distance of approximately 7 A by polyether spacers, bind bipyridinium-based guests. This recognition motif, which is dictated by π−π stacking and [C−H···O] hydrogen-bonding interactions, has led to the development of efficient template-directed syntheses of mechanically interlocked molecules, such as catenanes and rotaxanes. By employing a supramolecularly assisted synthetic methodology based on these interactions, we have self-assembled two novel [3]catenanes, each incorporating two 1,5-dioxynaphtho-38-crown-10 components and one bipyridinium-based tetracationic cyclophane component. Single-crystal X-ray analyses of these [3]catenanes revealed that they possess internal cavities bounded on two opposite sites by π-electron-rich 1,5-dioxynaphthalene units separated by a distance of approximately 7−8 A. Despite the presence of apparently ideal “binding pockets”, these mechanically interlocked compounds steadfastly re...

Controllable donor-acceptor neutral [2]rotaxanes

Abstract: In pursuit of a neutral bi- stable (2)rotaxane made up of two tetra- arylmethane stoppers—both carrying one isopropyl and two tert-butyl groups located at the para positions on each of three of the four aryl rings—known to permit the slippage of the p-electron- donating 1,5-dinaphtho(38)crown-10 (1/5DNP38C10) at the thermodynamic instigation of p-electron-accepting rec- ognition sites, in this case, pyromellitic diimide (PmI) and 1,4,5,8-naphthalene- tetracarboxylate diimide (NpI) units separated from each other along the rod section of the rotaxaneFs dumbbell component, and from the para posi- tions of the fourth aryl group of the two stoppers by pentamethylene chains, a modular approach was em- ployed in the synthesis of the dumb- bell-shaped compound NpPmD, as well as of its two degenerate counterparts, one (PmPmD) which contains two PmI units and the other (NpNpD) which contains two NpI units. The bistable (2)rotaxane NpPmR, as well as its two degenerate analogues PmPmR and NpNpR, were obtained from the corre- sponding dumbbell-shaped compounds NpPmD, PmPmD, and NpNpD and 1/5DNP38C10 by slippage. Dynamic 1 H NMR spectroscopy in CD 2Cl2 revealed that shuttling of the 1/5DNP38C10 ring occurs in NpNpR and PmPmR, with activation barriers of 277 K of 14.0 and 10.9 kcal mol 1 , re- spectively, reflecting a much more pro- nounced donor-acceptor stabilizing in- teraction involving the NpI units over the PmI ones. The photophysical and electrochemical properties of the three neutral (2)rotaxanes and their dumb- bell-shaped precursors have also been investigated in CH2Cl2. Interactions be- tween 1/5DNP38C10 and PmI and NpI units located within the rod section of the dumbbell components of the (2)ro- taxane give rise to the appearance of charge-transfer bands, the energies of which correlate with the electron-ac- cepting properties of the two diimide moieties. Comparison between the po- sitions of the visible absorption bands in the three (2)rotaxanes shows that, in NpPmR, the major translatio- nal isomer is the one in which 1/5DNP38C10 encircles the NpI unit. Correlations of the reduction potentials for all the compounds studied confirm that, in this non-degenerate (2)ro- taxane, one of the translational isomers predominates. Furthermore, after deac- tivation of the NpI unit by one-electron reduction, the 1/5DNP38C10 macrocy- cle moves to the PmI unit. Li + ions have been found to strengthen the in- teraction between the electron-donat- ing crown ether and the electron-ac- cepting diimide units, particularly the PmI one. Titration experiments show that two Li + ions are involved in the strengthening of the donor-acceptor in- teraction. Addition of Li + ions to NpPmR induces the 1/5DNP38C10 macrocycle to move from the NpI to the PmI unit. The Li + -ion-promoted switching of NpPmR in a 4:1 mixture of CD2Cl2 and CD3COCD3 has also been shown by 1 H NMR spectroscopy to involve the mechanical movement of the 1/5DNP38C10 macrocycle from the NpI to the PmI unit, a process that can be reversed by adding an excess of (12)crown-4 to sequester the Li + ions.

A redox-driven multicomponent molecular shuttle.

Abstract: A multicomponent [2]rotaxane designed to operate as a molecular shuttle driven by light energy has been constructed, and its properties have been investigated. The system is composed of (1) a light-fueled power station, capable of using the photon energy to create a charge-separated state, and (2) a mechanical switch, capable of utilizing such a photochemically generated driving force to bring about controllable molecular shuttling motions. The light-fueled power station is, in turn, a dyad comprising (i) a pi-electron-accepting fullerene (C60) component and (ii) a light-harvesting porphyrin (P) unit which acts as an electron donor in the excited state. The mechanical switch is a redox-active bistable [2]rotaxane moiety that consists of (i) a tetrathiafulvalene (TTF) unit as an efficient pi-electron-donor station, (ii) a dioxynaphthalene (DNP) unit as a second pi-electron-rich station, and (iii) a tetracationic cyclobis(paraquat-p-phenylene) (CBPQT4+) pi-electron-acceptor cyclophane, which encapsulates the better pi-electron-donating TTF station. Diethylene glycol spacers were conveniently introduced between the electroactive components in the dumbbell-shaped thread to facilitate the template-directed synthesis of the [2]rotaxane. A modular synthetic approach was undertaken for the overall synthesis of this multicomponent bistable [2]rotaxane, beginning with the syntheses of the P-C60 dyad unit and the two-station TTF-DNP-based [2]rotaxane separately, using conventional synthetic methodologies. These two components were finally stitched together by an esterification to afford the target rotaxane. Its structure was characterized by 1H NMR spectroscopy and mass spectrometry as well as by UV-vis-NIR absorption spectroscopy and voltammetry. The observations reflect remarkable electronic interactions between the various units, pointing to the existence of folded conformations in solution. The redox-driven shuttling process of the CBPQT4+ ring between the two competitive electron-rich recognition units, namely, TTF and DNP, was investigated by electrochemistry and spectroelectrochemistry as a means to verify its operational behavior prior to the photophysical studies related to light-driven operation. The oxidation process of the TTF unit is dramatically hampered in the rotaxane, thereby reducing the efficiency of the shuttling motion. These results confirm that, as the structural complexity increases, the overall function of the system no longer depends simply on its "primary" structure but also on higher-level effects which are reminiscent of the secondary and tertiary structures of biomolecules.

Flexible ferroelectric organic crystals.

Abstract: Flexible organic materials possessing useful electrical properties, such as ferroelectricity, are of crucial importance in the engineering of electronic devices. Up until now, however, only ferroelectric polymers have intrinsically met this flexibility requirement, leaving small-molecule organic ferroelectrics with room for improvement. Since both flexibility and ferroelectricity are rare properties on their own, combining them in one crystalline organic material is challenging. Herein, we report that trisubstituted haloimidazoles not only display ferroelectricity and piezoelectricity-the properties that originate from their non-centrosymmetric crystal lattice-but also lend their crystalline mechanical properties to fine-tuning in a controllable manner by disrupting the weak halogen bonds between the molecules. This element of control makes it possible to deliver another unique and highly desirable property, namely crystal flexibility. Moreover, the electrical properties are maintained in the flexible crystals.

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.