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).

Experimentally-based recommendations of density functionals for predicting properties in mechanically interlocked molecules.

Abstract: Mechanically interlocked molecules (rotaxanes and catenanes) have already revolutionized molecular electronics and have the promise of a similar impact in other areas of nanotechnology, ranging from nanoactuators to in vivo drug nanocarriers. However, it would be most useful to have quantitative criteria for predicting structures, binding, and excitation energies for use in designing molecules with mechanical bonds. We assess here the use of density functional theory (DFT) to a noncovalently bound complex and find that no density functional is fully satisfactory. However, we find that the new M06-suite of density functionals, which include attractive medium-range interactions, leads to dramatic improvements in the structures (error of 0.04 A in the interplanar distances for M06-L compared to 0.42 A for B3LYP) and excitation energies (within 0.08 eV for TD-M06-HF without empirical correction compared to 2.2 eV error for TD-B3LYP). However, M06 predicts the complex to be too strongly bound by 22.6 kcal mol−...

Semiconducting single crystals comprising segregated arrays of complexes of C60.

Abstract: Although pristine C60 prefers to adopt a face-centered cubic packing arrangement in the solid state, it has been demonstrated that noncovalent-bonding interactions with a variety of molecular receptors lead to the complexation of C60 molecules, albeit usually with little or no control over their long-range order. Herein, an extended viologen-based cyclophane—ExBox24+—has been employed as a molecular receptor which, not only binds C60 one-on-one, but also results in the columnar self-assembly of the 1:1 inclusion complexes under ambient conditions. These one-dimensional arrays of fullerenes stack along the long axis of needle-like single crystals as a consequence of multiple noncovalent-bonding interactions between each of the inclusion complexes. The electrical conductivity of these crystals is on the order of 10–7 S cm–1, even without any evacuation of oxygen, and matches the conductivity of high-quality, unfunctionalized C60-based materials that typically require stringent high-temperature vaporization ...

The self-assembly of fullerene-containing [2]pseudorotaxanes: formation of a supramolecular C60 dimer

Abstract: With its unique chemical and physical properties, C60 is an attractive molecule to be incorporated into molecular assemblies and supramolecular arrays. This paper reports the syntheses of a C60 derivative with the macrocyclic polyether dibenzo-24-crown-8 (DB24C8) attached to the carbon sphere and of a C60 adduct with a dibenzylammonium salt covalently bonded to the carbon allotrope. The C60 DB24C8 conjugate forms a stable, pseudorotaxane-like 1∶1 complex (ΔG° = –16.6 kJ mol–1, T = 298 K, CDCl3–CD3CN 1∶1) with dibenzylammonium hexafluorophosphate. Evidence for this superstructure was provided by 1H NMR spectroscopic studies in solution and by mass spectrometric investigations in the gas phase. Equally, the C60 dibenzylammonium conjugate threads through the cavity of DB24C8 to form a 1∶1 complex with a pseudorotaxane-like geometry (ΔG° = –23.3 kJ mol–1, CDCl3). Furthermore, the C60 DB24C8 adduct and the C60 dibenzylammonium conjugate interact with each other by means of hydrogen bonding and ion–dipole interactions to form the first supramolecular C60 dimer (ΔG° = –17.0 kJ mol–1, CDCl3–CD3CN 90∶10). In all three cases, the dibenzylammonium component is threaded through the cavity of the crown ether macrocycle. When DB24C8 is complexed to the C60 dibenzylammonium conjugate, the luminescence associated with the catechol rings of the crown ether is partially quenched upon complex formation. We have profited from this special feature to monitor reversible, acid–base induced dethreading/rethreading processes.

Functionalized Defects through Solvent-Assisted Linker Exchange: Synthesis, Characterization, and Partial Postsynthesis Elaboration of a Metal–Organic Framework Containing Free Carboxylic Acid Moieties

Abstract: Intentional incorporation of defect sites functionalized with free carboxylic acid groups was achieved in a paddlewheel-based metal-organic framework (MOF) of rht topology, NU-125. Solvent-assisted linker exchange (SALE) performed on a mixed-linker derivative of NU-125 containing isophthalate (IPA) linkers (NU-125-IPA) led to the selective replacement of the IPA linkers in the framework with a conjugate base of trimesic acid (H3BTC). Only two of the three carboxylic acid moieties offered by H3BTC coordinate to the Cu2 centers in the MOF, yielding a rare example of a MOF decorated with free -COOH groups. The presence of the -COOH groups was confirmed by diffuse reflectance infrared Fourier-transformed spectroscopy (DRIFTS); moreover, these groups were found to be available for postsynthesis elaboration (selective monoester formation). This work constitutes an example of the use of SALE to obtain otherwise challenging-to-synthesize MOFs. The resulting MOF, in turn, can serve as a platform for accomplishing selective organic transformations, in this case, exclusive monoesterification of trimesic acid.

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.