On the Mechanism of Copper(I)‐Catalyzed Azide–Alkyne Cycloaddition

The copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) reaction regiospecifically produces 1,4‐disubstituted‐1,2,3‐triazole molecules. This heterocycle formation chemistry has high tolerance to reaction conditions and substrate structures. Therefore, it has been practiced not only within, but also far beyond the area of heterocyclic chemistry. Herein, the mechanistic understanding of CuAAC is summarized, with a particular emphasis on the significance of copper/azide interactions. Our analysis concludes that the formation of the azide/copper(I) acetylide complex in the early stage of the reaction dictates the reaction rate. The subsequent triazole ring‐formation step is fast and consequently possibly kinetically invisible. Therefore, structures of substrates and copper catalysts, as well as other reaction variables that are conducive to the formation of the copper/alkyne/azide ternary complex predisposed for cycloaddition would result in highly efficient CuAAC reactions. Specifically, terminal alkynes with relatively low pK_a values and an inclination to engage in π‐backbonding with copper(I), azides with ancillary copper‐binding ligands (aka chelating azides), and copper catalysts that resist aggregation, balance redox activity with Lewis acidity, and allow for dinuclear cooperative catalysis are favored in CuAAC reactions. Brief discussions on the mechanistic aspects of internal alkyne‐involved CuAAC reactions are also included, based on the relatively limited data that are available at this point.     

Chemical data mining of the NCI human tumor cell line database

The NCI Developmental Therapeutics Program Human Tumor cell line data set is a publicly available database that contains cellular assay screening data for over 40 000 compounds tested in 60 human tumor cell lines. The database also contains microarray assay gene expression data for the cell lines, and so it provides an excellent information resource particularly for testing data mining methods that bridge chemical, biological, and genomic information. In this paper we describe a formal knowledge discovery approach to characterizing and data mining this set and report the results of some of our initial experiments in mining the set from a chemoinformatics perspective.     

Web service infrastructure for chemoinformatics

The vast increase of pertinent information available to drug discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future.     

Euler–Poincaré Flows on <Emphasis Type="Italic">sl</Emphasis><Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> Opers and Integrability

We consider the action of vector field Vect(S ¹) on the space of an sl _n - opers on S ¹, i.e., a space of nth order differential operator . This action takes the sections of Ω ^–(n–1)/2 to those of Ω ^(n+1)/2, where Ω is the cotangent bundle on S ¹. In this paper we study Euler–Poincaré (EP) flows on the space of sl _n opers, in particular, we demonstrate explicitly EP flows on the space of third and fourth order differential operators (or sl ₃ and sl ₄ opers) and its relation to Drienfeld–Sokolov, Hirota–Satsuma and other coupled KdV type systems. We also discuss the Boussinesq equation associated with the third order operator. The solutions of the sl _n oper defines an immersion in homogeneous coordinates. We derive the Schwarzian KdV equation as an evolution of the solution curve associated to Δ ⁽ⁿ⁾, we study the factorization of higher order operators and its compatibility with the action of Vect(S ¹). We obtain the generalized Miura transformation and its connection to the modified Boussinesq equation for sl ₃ oper. We also study the eigenvalue problem associated to sl ₄ oper. We discuss flows on the special higher order differential operators for all u _i = f(u,u _x ,u _xx ⋯) and its connection to KdV equation. Finally we explore a relation between projective vector field equation and generalized Riccati equations.      

Kinetic and redox characteristics of phenoxyl radicals of eugenol and isoeugenol: A pulse radiolysis study

The phenoxyl radicals of eugenol (EgOH) and isoeugenol (iEgOH) were generated by the specific one‐electron oxidant N₃^· using pulse radiolysis technique, and were characterized by their absorption spectra, decay and formation kinetics, and one‐electron reduction potential (E₇¹) values. Reactivities of eugenol phenoxyl radical with the biologically important molecule, trolox C (analogue of vitamin E, α‐tocopheral), were determined. Reactions of OH with these phenols were studied at different pHs and suitable mechanisms for these reactions were suggested. Scavenging abilities of the phenols toward highly damaging Br^·, NO₂^·, and CCl₃O₂^· radicals were evaluated. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 17–23, 2000     

On dynamics of velocity vector potential in incompressible fluids

An elegant quaternionic formulation is given for the Lagrangian advection equation for velocity vector potential in fluid dynamics. At first we study the topological significance of a restricted conserved quantity viz., stream-helicity and later more realistic configuration of open streamlines is figured out. Also, using Clebsch parameterisation of the velocity vector potential yet another physical significance for the stream-helicity is provided. Finally we give a Nambu-Poisson formalism of the Lagrangian advection equation for velocity vector potential.     

Accelerating molecular dynamic simulation on the cell processor and Playstation 3

Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors.     

On the Jacobi Last Multiplier, integrating factors and the Lagrangian formulation of differential equations of the Painlevé–Gambier classification

We use a formula derived almost seventy years ago by Madhav Rao connecting the Jacobi Last Multiplier of a second-order ordinary differential equation and its Lagrangian and determine the Lagrangians of the Painlevé equations. Indeed this method yields the Lagrangians of many of the equations of the Painlevé–Gambier classification. Using the standard Legendre transformation we deduce the corresponding Hamiltonian functions. While such Hamiltonians are generally of non-standard form, they are found to be constants of motion. On the other hand for second-order equations of the Liénard class we employ a novel transformation to deduce their corresponding Lagrangians. We illustrate some particular cases and determine the conserved quantity (first integral) resulting from the associated Noetherian symmetry. Finally we consider a few systems of second-order ordinary differential equations and deduce their Lagrangians by exploiting again the relation between the Jacobi Last Multiplier and the Lagrangian.     

Adsorption behavior of rhodamine B on Rhizopus oryzae biomass

The removal of a carcinogenic dye rhodamine B (C. I. 45170) from wastewater by biomass of different moulds and yeasts is described. Among all of the fungal species tested, the biomass of Rhizopus oryzae MTCC 262 is found to be the most effective. Dye adsorption reaches maximum with the biomass harvested from the early stationary phase of growth. The optimum temperature and pH for adsorption are observed to be 40 degrees C and 7.0, respectively. The adsorption rate is very fast initially and attains equilibrium after 5 h. The adsorption isotherm follows the Langmuir isotherm model satisfactorily within the studied dye concentration range. Of the different metabolic inhibitors tested, 2,4-ditrophenol (DNP) and N,N'-dicyclohexylcarbodiimide (DCCD) decrease dye adsorption by approximately 30% suggesting the role of energy metabolism in the process. Spectrophotometric study indicates that the removal of rhodamine B by R. oryzae biomass involves an adsorption process. Scanning (SEM) and transmission (TEM) electron microscopic investigations have been carried out to understand the probable mechanism of the dye-biomass interaction.