Organic Chemistry with a Biological Emphasis

I. Organic structureII. Structure determinationIII. Introduction to organic reactionsIV. Acid-base chemistryV. Nucleophilic substitution reactionsVI. Phosphoryl group transfer reactionsVII. Nucleophilic addition to carbonyls and iminesVIII. Acyl substitution reactionsIX. Alpha-carbon reactionsX. Electrophilic reactionsXI. Redox reactionsXII. Radical reactionsXIII. Coenzyme-mediated reactionsA free, open-access organic chemistry textbook in which the main focus is on relevance to biology and medicine. This is a PDF version of a wiki project called Chemwiki at the University of California, Davis

p-Sulfonic acid calixarenes as efficient and reusable organocatalysts for the synthesis of 3,4-dihydropyrimidin-2(1H)-ones/-thiones

AbstractA new and efficient methodology is proposed for obtaining 3,4-dihydropyrimidin-2(1H)-ones/-thiones through Biginelli reactions. It is based on the use of less than the stoichiometric amount of p-sulfonic acid calixarenes as organocatalysts. A number of aromatic aldehydes as well as urea or thiourea can be employed for successfully synthesizing the corresponding Biginelli adducts. The described methodology is devoid of metal-containing catalysts, which in turn is very attractive for safely producing 3,4-dihydropyrimidin-2-(1H)-ones/-thiones of pharmacological interest. In addition, the catalyst efficiency is not compromised after its successive use in reactions. This is the first report about the application of calixarenes as catalysts in the multicomponent Biginelli reaction

Velocity fluctuations of noisy reaction fronts propagating into a metastable state: testing theory in stochastic simulations

The position of a reaction front, propagating into a metastable state, fluctuates because of the shot noise of reactions and diffusion. A recent theory [B. Meerson, P.V. Sasorov, and Y. Kaplan, Phys. Rev. E 84, 011147 (2011)] gave a closed analytic expression for the front diffusion coefficient in the weak noise limit. Here we test this theory in stochastic simulations involving reacting and diffusing particles on a one-dimensional lattice. We also investigate a small noise-induced systematic shift of the front velocity compared to the prediction from the spatially continuous deterministic reaction-diffusion equation.Comment: 5 pages, 5 figure

Theory of Branching and Annihilating Random Walks

A systematic theory for the diffusion--limited reaction processes $A + A \to 0$ and $A \to (m+1) A$ is developed. Fluctuations are taken into account via the field--theoretic dynamical renormalization group. For $m$ even the mean field rate equation, which predicts only an active phase, remains qualitatively correct near $d_c = 2$ dimensions; but below $d_c' \approx 4/3$ a nontrivial transition to an inactive phase governed by power law behavior appears. For $m$ odd there is a dynamic phase transition for any $d \leq 2$ which is described by the directed percolation universality class.Comment: 4 pages, revtex, no figures; final version with slight changes, now accepted for publication in Phys. Rev. Let

Retrofit self-optimizing control of Tennessee Eastman process

This paper considers near-optimal operation of the Tennessee Eastman (TE) process by using a retrofit self-optimizing control (SOC) approach. Motivated by the factor that most chemical plants in operation have already been equipped with a workable control system for regulatory control, we propose to improve the economic performance by controlling some self-optimizing controlled variables (CVs). Different from traditional SOC methods, the proposed retrofit SOC approach improves economic optimality of operation through newly added cascaded SOC loops, where carefully selected SOC CVs are maintained at constant by adjusting set-points of the existing regulatory control loops. To demonstrate the effectiveness of the retrofit SOC proposed, we adopted measurement combinations as the CVs for the TE process, so that the economic cost is further reduced comparing to existing studies where single measurements are controlled. The optimality of the designed control architecture is validated through both steady state analysis and dynamic simulations

Signatures of dense hadronic matter in ultrarelativistic heavy ion reactions

The behavior of hadronic matter at high baryon densities is studied within Ultrarelativistic Quantum Molecular Dynamics (URQMD). Baryonic stopping is observed for Au+Au collisions from SIS up to SPS energies. The excitation function of flow shows strong sensitivities to the underlying equation of state (EOS), allowing for systematic studies of the EOS. Dilepton spectra are calculated with and without shifting the $\rho$ pole. Except for S+Au collisions our calculations reproduce the CERES data.Comment: Invited talk at RHIC-theory workshop at BNL july 8-1

Structure of exotic nuclei from direct reactions

Expérience GANILInternational audienc