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951.
The local spin formalism ( 3 ) for computing expectation values 〈SA · SB〉 that appear in the Heisenberg spin model has been extended to semiempirical single determinant wave functions. An alternative derivation of expectation values in restricted and unrestricted cases is given that takes advantage of the zero differential overlap (ZDO) approximation. A formal connection between single determinant wave functions (which are not in general spin eigenfunctions) and the Heisenberg spin model was established by demonstrating that energies of single determinants that are eigenfunctions of the local spin operators with eigenvalues corresponding to high‐spin radical centers are given by the same Heisenberg coupling constants {JAB} that describe the true spin states of the system. Unrestricted single determinant wave functions for transition metal complexes are good approximations of local spin eigenfunctions when the metal d orbitals are local in character and all unpaired electrons on each metal have the same spin (although spins on different metals might be reversed). Good approximations of the coupling constants can then be extracted from local spin expectation values 〈SA · SB〉 energies of the single determinant wave functions. Once the coupling constants are obtained, diagonalization of the Heisenberg spin Hamiltonian provides predictions of the energies and compositions of the spin states. A computational method is presented for obtaining coupling constants and spin‐state energies in this way for polynuclear transition metal complexes using the intermediate neglect of differential overlap Hamiltonian parameterized for optical spectroscopy (INDO/S) in the ZINDO program. This method is referred to as ZILSH, derived from ZINDO, Davidson's local spin formalism, and the Heisenberg spin model. Coupling constants and spin ground states obtained for 10 iron complexes containing from 2 to 6 metals are found to agree well with experimental results in most cases. In the case of the complex [Fe6O3(OAc)9(OEt)2(bpy)2]+, a priori predictions of the coupling constants yield a ground‐state spin of zero, in agreement with variable‐temperature magnetization data, and corroborate spin alignments proposed earlier on the basis of structural considerations. This demonstrates the potential of the ZILSH method to aid in understanding magnetic interactions in polynuclear transition metal complexes. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003 相似文献
952.
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. 相似文献
953.
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. 相似文献
954.
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. 相似文献
955.
Dr. M. A. Llorente Dr. A. L. Andrady Professor J. E. Mark 《Colloid and polymer science》1981,259(11):1056-1061
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. 相似文献
956.
Muñoz-Muriedas J Perspicace S Bech N Guccione S Orozco M Luque FJ 《Journal of computer-aided molecular design》2005,19(6):401-419
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. 相似文献
957.
Mordvintsev DY Polyak YL Levtsova OV Tourleigh YV Kasheverov IE Shaitan KV Utkin YN Tsetlin VI 《Computational Biology and Chemistry》2005,29(6):398-411
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. 相似文献
958.
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 λa and oxygen λc stoichiometries. In this Letter, we analyze the general case of arbitrary λa and λc. In the case of λa > λc current may occupy finite domain of the cell surface. Asymptotic solution for the case of λa λc shows, that the size of this domain is proportional to oxygen stoichiometry. In the opposite limit of λa λc local current exponentially decreases with the distance along the channel. Asymptotic solutions suggest that the bridge forms regardless of the relationship between λa and λc. 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. 相似文献
959.
The electron beam process has proved to be an efficient method for the removal of inorganic pollutants from flue gas. Since it simulates natural processes which occur in the atmospheric photochemistry, it appeared attractive to investigate the potential of the e-beam process to clean off-gases which contain hydrocarbon and inorganic trace components. Such emissions arise from industrial processes and from automobile tunnels. Commercial solvents were vaporized in air and irradiated with energetic electrons (300 keV). CO, CO2 and aerosol particles were found as products and were determined quantitatively. The aerosol particles can be collected by a gravel bed filter and can be removed by combustion or biological degradation. From experiments and model calculations it was found that the e-beam process is a very economic tool to remove hydrocarbons from large off-gas volumes at initial concentrations of 50–100 mg C/m3, and that NOx can be removed very efficiently from tunnel off-gas. 相似文献
960.
Michael J. Monteiro 《Journal of polymer science. Part A, Polymer chemistry》2005,43(15):3189-3204
Living radical polymerization has allowed complex polymer architectures to be synthesized in bulk, solution, and water. The most versatile of these techniques is reversible addition–fragmentation chain transfer (RAFT), which allows a wide range of functional and nonfunctional polymers to be made with predictable molecular weight distributions (MWDs), ranging from very narrow to quite broad. The great complexity of the RAFT mechanism and how the kinetic parameters affect the rate of polymerization and MWD are not obvious. Therefore, the aim of this article is to provide useful insights into the important kinetic parameters that control the rate of polymerization and the evolution of the MWD with conversion. We discuss how a change in the chain‐transfer constant can affect the evolution of the MWD. It is shown how we can, in principle, use only one RAFT agent to obtain a polymer with any MWD. Retardation and inhibition are discussed in terms of (1) the leaving R group reactivity and (2) the intermediate radical termination model versus the slow fragmentation model. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3189–3204, 2005 相似文献