MBO(N)D: A multibody method for long‐time molecular dynamics simulations

A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body‐based modes. This approach allows for the elimination of the high‐frequency harmonic motion while capturing the low‐frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5‐ to 30‐fold over atomistic simulations have been realized in various applications of the method. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 159–184, 2000     

Silica hydride intermediate for octadecylsilica and phenyl bonded phase preparation via heterogeneous hydrosilation in supercritical carbon dioxide

Investigations into the preparation of silica hydride intermediate in supercritical carbon dioxide (sc-CO(2)) that avoids the use of organic solvents such as toluene or dioxane are described. The effects of reaction temperature, pressure and time on the surface coverage of the supercritical fluid generated silica hydride intermediate were studied. Under optimised supercritical conditions of 120°C, 483 bar and 3 h reaction time, silica hydride (Si-H) conversion efficiencies of ca. 40% were achieved for the hydride intermediate prepared from a monofunctional silane reagent (dimethylmethoxysilane). Si-H conversion efficiencies (as determined from (29)Si CP-MAS NMR spectral analysis) for the hydride intermediate prepared from triethoxysilane (TES) in sc-CO(2) were found to be comparable to those obtained using a TES silanisation approach in an organic solvent. (13)C and (29)Si CP-MAS-NMR spectroscopy was employed to provide a complete structural assignment of the silica hydride intermediates. Furthermore, supercritical CO(2) was subsequently employed as a reaction medium for the heterogenous hydrosilation of silica hydride with octadecene and with styrene, in the presence of a free radical initiator. These supercritical fluid generated reversed-phase materials were prepared in a substantially reduced reaction time (3 h) compared to organic solvent based methods (100 h reaction time). Silica functionalisation in sc-CO(2) presents an efficient and clean alternative to organic solvent based methods for the preparation of important silica hydride intermediate and silica bonded stationary phases via a hydrosilation approach.     

Anaerobic digestion of municipal solid waste

Tuna processing wastes (sludges high in fat, oil, and grease [FOG]) and municipal solid waste (MSW) generated on Tutuila Island, American Samoa, represent an ongoing disposal challenge. The biological conversion of the organic fraction of these wastes to useful products, including methane and fertilizer-grade residue, through anaerobic high-solids digestion is currently in scale-up development. The suitability of the anaerobic digestion residues as a soil amendment was evaluated through extensive chemical analysis and greenhouse studies using corn as an indicator crop. Additionally, native Samoan soil was used to evaluate the specific application rates for the compost. Experiments established that anaerobic residues increase crop yields in direct proportion to increases in the application rate. Additionally, nutrient saturation was not demonstrated within the range of application rates evaluated for the Samoan soil. Beyond nutrient supplementation, organic residue amendment to Samoan soil imparts enhanced water- and nutrient-binding capacities.     

Understanding the DNA binding of novel non-symmetrical guanidinium/2-aminoimidazolinium derivatives

Biophysical studies have been carried out on a family of asymmetric guanidinium-based diaromatic derivatives to assess their potential as DNA minor groove binding agents. To experimentally assess the binding of these compounds to DNA, solution phase biophysical studies have been performed. Thus, surface plasmon resonance, UV-visible spectroscopy and circular and linear dichroism have been utilized to evaluate binding constants, stoichiometry and mode of binding. In addition, the thermodynamics of the binding process have been determined by using isothermal titration calorimetry. These results show significant DNA binding affinity that correlates with the expected 1?:?1 binding ratio usually observed for minor groove binders. Moreover, a simple computational approach has been devised to assess the potential as DNA binders of this family of compounds.     

Cesium effect: high chemoselectivity in direct N-alkylation of amines

A novel method for the mono-N-alkylation of primary amines, diamines, and polyamines was developed using cesium bases in order to prepare secondary amines efficiently. A cesium base not only promoted alkylation of primary amines but also suppressed overalkylations of the produced secondary amines. Various amines, alkyl bromides, and alkyl sulfonates were examined, and the results demonstrated this methodology was highly chemoselective to favor mono-N-alkylation over dialkylation. In particular, use of either sterically demanding substrates or amino acid derivatives afforded the secondary amines exclusively, offering wide applications in peptidomimetic syntheses.     

Charge transfer and intraligand excited state interactions in platinum-sensitized dithienylethenes

The photophysical behavior for two photochromic Pt-terpyridine acetylide complexes containing pendant dithienylethenes (DTEs) bound to the metal through the alkynyl linkage is presented. Selective excitation of the Pt complex with visible light resulted in the metal-sensitized ring closing of the DTE unit. The central purpose of this study was to understand how excited state interactions govern the photophysics by correlating differences in the linkage of the two components with differences in the intramolecular energy transfer processes that occur between the Pt complex and the DTE. A series of model complexes without photochromic ligands were prepared and studied to elucidate the contributions of the triplet metal-to-ligand charge transfer and triplet intraligand states. It is demonstrated that reducing the orbital overlap of the metal-based and intraligand states by lengthening the linkage and eliminating a conjugated pathway is effective at dramatically decreasing the efficiency of intramolecular energy transfer. This is evidenced by the appearance of Pt-terpyridine based phosphorescence and a significant decrease in the observed rate of metal-sensitized ring closing of the DTE.     

Antifungal cyclopentenediones from Piper coruscans

Coruscanones A and B, two new antifungal cyclopentenedione derivatives, have been isolated from Piper coruscans and their structures elucidated by spectroscopic and chemical methods. Coruscanone A exhibits significant antifungal activity against Candida albicans and its azole-resistant strains and may serve as a template for a new class of antifungal agents.     

Dijet production by double pomeron exchange at the fermilab tevatron

We report the first observation of dijet events with a double Pomeron exchange topology produced in &pmacr;p collisions at sqrt[s] = 1800 GeV. The events are characterized by a leading antiproton, two jets in the central pseudorapidity region, and a large rapidity gap on the outgoing proton side. We present results on jet kinematics and production rates, compare them with corresponding results from single diffractive and inclusive dijet production, and test factorization.     

Compositionally asymmetrical multiquantum wells: “Pseudo-molecules” for giant optical nonlinearities in the infrared (9–11 μm)

Intersubband transitions in quantum well have extremely large oscillator strengths and induce strong nonlinear effects in structures where inversion symmetry is broken, realized by growing AlGaAs quantum wells with asymmetrical A1 gradients. These compositionally asymmetrical multiquantum wells may thus be viewed as giant “quasimolecules” optimized for optimal nonlinearities in the mid infrared. Optical rectification as well as second harmonic generation have been measured in those structures using a continuous CO₂ laser. At 10.6 μm the nonlinear coefficients are more than 3 orders of magnitude higher in these samples than for bulk GaAs (i.e. χ₀⁽²⁾ = 5.3 × 10⁻⁶m/V, χ_2ω⁽²⁾ = 7.2 × 10⁻⁷ m/V) and are in good agreement with theoretical predictions. We present more complex “pseudo-molecules” involving weakly coupled quantum wells. The optical rectification effects in these devices are so large χ₀⁽²⁾ = 1.6 × 10⁻³ m/V) that application to infrared detection may be envisioned.