Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation

Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody binding free energy (ΔΔG) induced by amino acid substitution at each position in epitope B of the H3N2 influenza hemagglutinin, the key target for antibody. A substitution with positive ΔΔG value decreases the antibody binding constant. On average an uncharged to charged amino acid substitution generates the highest ΔΔG values. Also on average, substitutions between small amino acids generate ΔΔG values near to zero. The 21 sites in epitope B have varying expected free energy differences for a random substitution. Historical amino acid substitutions in epitope B for the A/Aichi/2/1968 strain of influenza A show that most fixed and temporarily circulating substitutions generate positive ΔΔG values. We propose that the observed pattern of H3N2 virus evolution is affected by the free energy landscape, the mapping from the free energy landscape to virus fitness landscape, and random genetic drift of the virus. Monte Carlo simulations of virus evolution are presented to support this view.     

Template–Framework Interactions in Tetraethylammonium‐Directed Zeolite Synthesis

Zeolites, having widespread applications in chemical industries, are often synthesized using organic templates. These can be cost‐prohibitive, motivating investigations into their role in promoting crystallization. Herein, the relationship between framework structure, chemical composition, synthesis conditions and the conformation of the occluded, economical template tetraethylammonium (TEA⁺) has been systematically examined by experimental and computational means. The results show two distinct regimes of occluded conformer tendencies: 1) In frameworks with a large stabilization energy difference, only a single conformer was found (BEA, LTA and MFI). 2) In the frameworks with small stabilization energy differences (AEI, AFI, CHA and MOR), less than the interconversion of TEA⁺ in solution, a heteroatom‐dependent (Al, B, Co, Mn, Ti, Zn) distribution of conformers was observed. These findings demonstrate that host–guest chemistry principles, including electrostatic interactions and coordination chemistry, are as important as ideal pore‐filling.     

Selective Homogeneous Palladium(0)-Catalyzed Hydrogenation of Alkynes to (Z)-Alkenes

Zero-valent palladium precatalysts containing rigid bidentate bis(arylimino)acenaphthene ligands (shown schematically) facilitate the highly stereoselective homogeneous catalytic hydrogenation of alkynes to (Z)-alkenes. Internal, terminal, aryl-substituted, and cyclic alkynes are suitable substrates, as are some enynes, which are chemoselectively hydrogenated to dienes. E=CO(2)Me; R(1), R(2)=4-OCH(3), 4-CH(3), 2,6-(CH(3))(2).     

Synthesis of a Specified,Silica Molecular Sieve by Using Computationally Predicted Organic Structure‐Directing Agents

Crystalline molecular sieves are used in numerous applications, where the properties exploited for each technology are the direct consequence of structural features. New materials are typically discovered by trial and error, and in many cases, organic structure‐directing agents (OSDAs) are used to direct their formation. Here, we report the first successful synthesis of a specified molecular sieve through the use of an OSDA that was predicted from a recently developed computational method that constructs chemically synthesizable OSDAs. Pentamethylimidazolium is computationally predicted to have the largest stabilization energy in the STW framework, and is experimentally shown to strongly direct the synthesis of pure‐silica STW. Other OSDAs with lower stabilization energies did not form STW. The general method demonstrated here to create STW may lead to new, simpler OSDAs for existing frameworks and provide a way to predict OSDAs for desired, theoretical frameworks.     

Differential transport of DNA by a rectified Brownian motion device

An interdigitated electrode array (IDEA) device has been designed and used to transport DNA based on a Brownian ratchet mechanism. This migration is produced by the periodic formation of an asymmetric sawtooth electric field in the device. Oligonucleotides of 25, 50, and 100 bases in length were tested using two different array geometries. DNA transport as a function of DNA size, electric field frequency, and array geometry is shown to be in qualitative agreement with theory. Such a device could provide for DNA separations over a broad size range, and can be readily scaled as a component in a microfabricated DNA analysis system.     

A critical investigation of the effects of the radio frequency potential on the trapping of externally injected ions in ion trap mass spectrometry

The sensitivity of all ion trap mass spectrometry (ITMS) methods is dependent on the trapping efficiency of the instrument. For ITMS instruments utilizing external ion sources, such as laser desorption, trapping efficiency is known to depend on the phase and amplitude of the radio frequency (RF) potential applied to the ring electrode at the time of ion introduction. It is remarkable that, in a considerable body of literature, no consensus exists regarding the effects of these parameters on the efficacy of trapping externally generated ions. In this paper, a summary of the literature is presented in order to highlight significant discrepancies. New laser desorption ion trap mass spectrometry (LD-ITMS) data are also presented, from which conclusions are drawn in our effort to clarify some of the confusion. Copyright 1999 John Wiley & Sons, Ltd.     

A Brownian-ratchet DNA pump with applications to single-nucleotide polymorphism genotyping

We have fabricated a micron-scale device capable of transporting DNA oligomers using Brownian ratchets. The ratchet potential is generated by applying a voltage difference to interdigitated electrodes. Cycling between the charged state and a discharged, free-diffusion state rectifies the Brownian motion of charged particles. The observed macroscopic transport properties agree with the transport rate predicted from microscopic parameters including the DNA diffusivity, the dimensions of the ratchet potential, and the cycling time. Applications to human genetics, primarily genotyping of single-nucleotide polymorphisms (SNPs), are discussed. Received: 7 November 2001 / Accepted: 14 January 2002 / Published online: 22 April 2002     

Photoelastic determination of stresses in multiple-pin connectors

The design, fabrication, and testing of photoelastic models of double-lap, multiple-pin connectors are discussed. Interest is in the stresses in the inner laps. These stresses are determined by constructing models with photoelastic inner laps and transparent-acrylic outer laps. The connectors have two pins, in tandem, parallel to the load direction. A photoelastic-isotropic point is shown to permit the evaluation of load sharing between the two pins. A numerical scheme, utilizing the isochromatic- and isoclinic-photoelastic data and a finite-difference representation of the planestress equilibrium equations, is used to compute the stresses around the two pins. Representative stress distributions and stress-concentration factors are shown.