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By using first principles calculations, we show that fine tuning of both p- and n-type doping can be realized on single-wall carbon nanotubes (SWNTs) by tuning the electron affinity or ionization potential of the organic and organometallic molecules encapsulated inside SWNTs. This novel type of SWNT-based material offers great promise for molecular electronics because of its air stability, synthetic simplicity and the abundance of organic and organometallic molecules.

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The conductance of a single 4,4 bipyridine (44BPD) molecule connected to two gold electrodes is calculated using a density functional theory based Green function method. The atomic geometry of such a molecular junction is constructed from the optimized structure of a gold trimer-44BPD-gold trimer complex. Resonant conduction is the main feature of its transport properties. The magnitude of the transmission coefficient at the Fermi level is determined to be T = 1.01 × 10(-2), which is in excellent agreement with the experimental value. The dependence of the transmission on the Au-N bond length and the torsion angle is also discussed.

A self-consistent ab initio approach for calculating electron transport through molecular electronic devices is developed. It is based on density functional theory (DFT) calculations and the Green's function technique employing a finite basis of local orbitals. The device is rigorously separated into the extended molecule region and the electrode region. In the DFT part calculating the Hamiltonian matrix of the extended molecule from its density matrix, the electrostatic correction induced by electrodes and the exchange-correlation correction due to the spatial diffuseness of localized basis functions are included. Our approach is efficient and accurate, with a controllable error to deal with such open systems. A one-dimensional infinite gold monatomic chain, whose electronic structure can be known from conventional DFT calculations with periodic boundary conditions (PBCs), is employed to validate the accuracy of our approach. With both corrections, our result for the gold chain at equilibrium is in excellent agreement with the PBC DFT result. We find that, for the gold chain, the exchange-correlation correction is more significant than the electrostatic correction.

␣-Amylase inhibitor (AAI), a 32-residue miniprotein from the Mexican crop plant amaranth (Amaranthus hypochondriacus), is the smallest known ␣-amylase inhibitor and is specific for insect ␣-amylases (ChagollaLopez, A., Blanco-Labra, A., Patthy, A., Sanchez, R., and Pongor, S. (1994) J. Biol. Chem. 269, 23675-23680). Its disulfide topology was confirmed by Edman degradation, and its three-dimensional solution structure was determined by two-dimensional 1 H NMR spectroscopy at 500 MHz. Structural constraints (consisting of 348 nuclear Overhauser effect interproton distances, 8 backbone dihedral constraints, and 9 disulfide distance constraints) were used as an input to the X-PLOR program for simulated annealing and energy minimization calculations. The final set of 10 structures had a mean pairwise root mean square deviation of 0.32 Å for the backbone atoms and 1.04 Å for all heavy atoms. The structure of AAI consists of a short triple-stranded ␤-sheet stabilized by three disulfide bonds, forming a typical knottin or inhibitor cystine knot fold found in miniproteins, which binds various macromolecular ligands. When the first intercystine segment of AAI (sequence IPKWNR) was inserted into a homologous position of the spider toxin Huwentoxin I, the resulting chimera showed a significant inhibitory activity, suggesting that this segment takes part in enzyme binding. Plant seeds produce a large variety of enzyme inhibitors that are thought to provide protection against insects and microbial pathogens. As plant seed inhibitors are often species specific, i.e. they inhibit enzymes of a well defined group of pathogenic organisms but do not affect the mammalian counterpart, they make attractive candidates for conferring pest resistance to transgenic plants (for a review see Ref. 1).The ␣-amylase inhibitors vary considerably in their structures. Many of their structural relatives, e.g. proteinase inhibitors, osmotin, and salt-induced proteins (Table I), play roles in plant stress response. The smallest of the known ␣-amylase inhibitors, AAI, 1 is found in the seeds of Amaranthus hypochondriacus, a variety of the Mexican crop plant amaranth or Prince's feather (2). AAI is a 32-residue polypeptide with three disulfide bridges, which has no significant sequence similarity to other proteins in the data bases. It has a spurious sequence similarity to various members of the so-called knottin (3) or "inhibitor-type cystine knot" (4) family, which includes various proteinase inhibitors and toxins. AAI is species specific; it inhibits ␣-amylase of several pathogenic insect larvae (Tribolium castaneum, Prostaphanus truncatus, Periplaneta americana, and Tenebrio mollitor) but not the mammalian ␣-amylases.Here we report the three-dimensional structure of AAI as determined by NMR spectroscopy and show via amino acid replacement and chimera construction that a short segment of the first loop of AAI is involved in enzyme inhibition. EXPERIMENTAL PROCEDURES MaterialsAAI was prepared as described (5). Sephadex G-75 and DEAE-Sepharose CL6B ...

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