Theoretical Study of the Photochemical Reaction Mechanism of Bicyclo [4.1.0 ] heptane

IntroductionPhotochemical reactions, which involve a three-membered ring, have been of great interest to experi-mental photochemists[1—10]. A main reason for thisphenomenon is that the cyclopropane ring exhibits somereaction characteristics of double bon…     

Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification

Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of target DNA, annealing of sequence-specific oligonucleotide primers and the enzyme-catalyzed elongation of the annealed complex (primer:DNA:polymerase). The denaturation step separates the double strands of DNA; this model assumes denaturation is complete. The annealing step describes the formation of a primer-fragment complex followed by the attachment of the polymerase to form a ternary complex. This step is complicated by competitive annealing between primers and incomplete fragments including primer-primer reactions. The elongation step is modeled by a stochastic method. Species that compete during the elongation step are deoxynucleotide triphosphates dCTP, dATP, dTTP, dGTP, dUTP, and pyrophosphate. Thermal deamination of dCTP to form dUTP is included in the model. The probability for a species to arrive at the active site is based on its molar fraction. The number of random insertion events depends on the average processing speed of the polymerase and the elongation time of the simulation. The numerical stochastic experiment is repeated a sufficient number of times to construct a probability density distribution (PDF). The moment of the PDF and the annealing step products provide the product distribution at the end of the elongation step. The overall yield is compared to six experimental values of the yield. In all cases the comparisons are very good.     

Retention of ionizable compounds on HPLC. Modelling retention for neutral and ionizable compounds by linear solvation energy relationships

Summary A global LSER model that relates HPLC retention to mobile phase composition and pH is tested for a varied group of solutes, both neutral and ionizable, in a polymeric column and methanol-water mobile phases. It is compared to the local LSER model developed only for a given mobile phase, i.e., a fixed organic modifier content, and to the global LSER model set only for neutral solutes. The global LSER model for neutral and ionizable solutes requires a few supplementary parameters over the other models tested, but it accounts for retention under any experimental conditions for a given column and methanol-water mobile phases, describing properly the interactions established in the HPLC system (hydrophobicity, hydrogen-bond acidity and basicity, dipolarity/polarizability…). This paper is number 13 of a series with the same general title: “Retention of Ionizable Compounds on HPLC” published in various journals.     

Application of a chemical equilibrium model to thermodynamic functions of transfer of alcohols from water to aqueous surfactants

In ternary aqueous solutions, hydrophobic solutes such as alcohols tend to aggregate with surfactants to form mixed micelles. These systems can be studied by meas of the functions of transfer of hydrophobic solutes from water to aqueous solutions of surfactant. These thermodynamic functions often go through extrema in the critical micellar concentration (CMC) region of the surfactant. A simple model based on interactions between surfactant and hydrophobic solute monomers, on the distribution of the hydrophobic solute between water and the micelles and on the shift in the CMC induced by the hydrophobic solute, can simulate the magnitude and trends of the transfer functions using parameters which are mostly derived from the binary systems. In order to check the model more quantitatively, volumes and heat capacities of transfer of alcohols from water to aqueous solutions of a nonionic surfactant, octyldimethylamine oxide, were measured. A quantitative agreement was achieved with three adjustable parameters. Good fits are also obtained for the transfers to the ionic surfactants, octylamine hydrobromide and sodium dodecylsulfate. When the equilibrium displacement contribution is small, the distribution constants and the partial molar properties of the alcohols in the micellar phase agree well with the parameters obtained with similar models.     

Model networks of end-linked polydimethylsiloxane chains

Summary Elastomeric networks of high extensibility were prepared by end-linking mixtures of vinyl-terminated polydimethylsiloxane chains having molecular weights of approximately 600 and 11,000 g mol^–1, with silanes chosen to give junction functionalities ranging from 3 to 8. The resulting bimodal networks were studied in elongation, at 25 °C, to their rupture points, and in swelling equilibrium in benzene at room temperature. The elongation moduli [f ^*] were found to be in satisfactory agreement with previous results obtained by end-linking hydroxyl-terminated polydimethylsiloxane chains. Values of [f ^*] at low and moderate deformations gave relatively low values of the ratio of elasticity constants 2C ₂/2C ₁, which is a measure of the extent to which the elongation changes from approximately affine to nonaffine as the elongation increases. The low values obtained for this ratio are presumably due to diminished interpenetration of configurational domains in the case of very short chains. In spite of its small magnitude, 2C ₂/2C ₁ does show some decrease with increase in , as predicted by the recent molecular theory of rubberlike elasticity developed by Flory. The swelling equilibrium results were also found to be in satisfactory agreement with theory. The elongation moduli increased significantly at high elongations, and the values of the elongation at which the upturn was first discernible were very nearly independent of , This is consistent with the interpretation of this anomalous behaviour in terms of limited chain extensibility. The maximum extensibility generally decreased somewhat with increase in and this caused a decrease in both the ultimate strength and the toughness of the elastomer, as measured by the energy required for rupture.     

Difference in Conversions Between Dimethyl Sulfide and Methanethiol in a Cold Plasma Environment

This study compared the conversion of two malodorous substances, dimethyl sulfide (CH₃SCH₃, DMS) and methanethiol (CH₃SH) in a cold plasma reactor. The DMS and CH₃SH were successfully destroyed at room temperature. DMS decomposed less than CH₃SH at the same conditions. In oxygen-free condition, CS₂ and hydrocarbons were the major products, while SO₂ and CO_x were main compounds in oxygen-rich environments. The DMS/Ar plasma yielded more hydrocarbons and less CS₂ than that of CH₃SH/Ar plasma. In the CH₃SH/O₂/Ar plasma, rapid formation of SO and CO resulted in the yields much more amounts of SO₂ and CO₂ than those in the DMS/O₂/Ar plasma; and remained only a trace of total hydrocarbons, CH₂O, CH₃OH, CS₂, and OCS. The major differences between the reaction mechanisms of DMS and CH₃SH were also proposed and discussed.     

Condensed tetrazolo-1,3,5-triazines. 4. Synthesis of salts of 5-aminotetrazolo[1,5-a]-1,3,5-triazin-7-one

2-Amino-4-azido-1,3,5-triazin-6(1H)-ones were synthesized by successive substitution of the trinitromethyl groups in 2-amino-4,6-bis(trinitromethyl)-1,3,5-triazines under the influence of azide and nitrite ions. Interaction of 2-amino-4-azido-1,3,5-triazin-6(1H)-ones with bases led to the azido-tetrazole tautomeric conversion give salts of 5-aminotetrazolo[1,5-a]-1,3,5-triazin-7-one. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1211–1219, August, 2006.     

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.     

A model for short alpha-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica: comparison with long-chain alpha-neurotoxins and alpha-conotoxins

Short-chain alpha-neurotoxins from snakes are highly selective antagonists of the muscle-type nicotinic acetylcholine receptors (nAChR). Although their spatial structures are known and abundant information on topology of binding to nAChR is obtained by labeling and mutagenesis studies, the accurate structure of the complex is not yet known. Here, we present a model for a short alpha-neurotoxin, neurotoxin II from Naja oxiana (NTII), bound to Torpedo californica nAChR. It was built by comparative modeling, docking and molecular dynamics using 1H NMR structure of NTII, cross-linking and mutagenesis data, cryoelectron microscopy structure of Torpedo marmorata nAChR [Unwin, N., 2005. Refined structure of the nicotinic acetylcholine receptor at 4A resolution. J. Mol. Biol. 346, 967-989] and X-ray structures of acetylcholine-binding protein (AChBP) with agonists [Celie, P.H., van Rossum-Fikkert, S.E., van Dijk, W.J., Brejc, K., Smit, A.B., Sixma, T.K., 2004. Nicotine and carbamylcholine binding to nicotinic acetylcholine receptors as studied in AChBP crystal structures. Neuron 41 (6), 907-914] and antagonists: alpha-cobratoxin, a long-chain alpha-neurotoxin [Bourne, Y., Talley, T.T., Hansen, S.B., Taylor, P., Marchot, P., 2005. Crystal structure of Cbtx-AChBP complex reveals essential interactions between snake alpha-neurotoxins and nicotinic receptors. EMBO J. 24 (8), 1512-1522] and alpha-conotoxin [Celie, P.H., Kasheverov, I.E., Mordvintsev, D.Y., Hogg, R.C., van Nierop, P., van Elk, R., van Rossum-Fikkert, S.E., Zhmak, M.N., Bertrand, D., Tsetlin, V., Sixma, T.K., Smit, A.B., 2005. Crystal structure of nicotinic acetylcholine receptor homolog AChBP in complex with an alpha-conotoxin PnIA variant. Nat. Struct. Mol. Biol. 12 (7), 582-588]. In complex with the receptor, NTII was located at about 30 A from the membrane surface, the tip of its loop II plunges into the ligand-binding pocket between the alpha/gamma or alpha/delta nAChR subunits, while the loops I and III contact nAChR by their tips only in a 'surface-touch' manner. The toxin structure undergoes some changes during the final complex formation (for 1.45 rmsd in 15-25 ps according to AMBER'99 molecular dynamics simulation), which correlates with NMR data. The data on the mobility and accessibility of spin- and fluorescence labels in free and bound NTII were used in MD simulations. The binding process is dependent on spontaneous outward movement of the C-loop earlier found in the AChBP complexes with alpha-cobratoxin and alpha-conotoxin. Among common features in binding of short- and long alpha-neurotoxins is the rearrangement of aromatic residues in the binding pocket not observed for alpha-conotoxin binding. Being in general very similar, the binding modes of short- and long alpha-neurotoxins differ in the ways of loop II entry into nAChR.     

1D + 1D model of a DMFC: localized solutions and mixedpotential

Our 1D + 1D model of DMFC reveals a new effect. At infinitely small total current in the cell, near the channel inlet forms a “bridge”, a narrow region with finite local current density. The bridge short-circuits the electrodes, thus reducing cell open-circuit voltage. In our previous work the effect is described for the case of equal methanol λ^a and oxygen λ^c stoichiometries. In this Letter, we analyze the general case of arbitrary λ^a and λ^c. In the case of λ^a > λ^c current may occupy finite domain of the cell surface. Asymptotic solution for the case of λ^a  λ^c shows, that the size of this domain is proportional to oxygen stoichiometry. In the opposite limit of λ^a  λ^c local current exponentially decreases with the distance along the channel. Asymptotic solutions suggest that the bridge forms regardless of the relationship between λ^a and λ^c. In all cases local current density in the bridge increases with the rate of methanol crossover and decreases with the growth of the “rate-determining” stoichiometry. The expression for voltage loss at open-circuit is derived.