Incubation period in the 2,2,4,4‐tetramethyl‐1‐piperidinyloxy‐mediated thermal autopolymerization of styrene: Kinetics and simulations

Mechanisms and simulations of the induction period and the initial polymerization stages in the nitroxide‐mediated autopolymerization of styrene are discussed. At 120–125 °C and moderate 2,2,4,4‐tetramethyl‐1‐piperidinyloxy (TEMPO) concentrations (0.02–0.08 M), the main source of radicals is the hydrogen abstraction of the Mayo dimer by TEMPO [with the kinetic constant of hydrogen abstraction (k_h)]. At higher TEMPO concentrations ([N?] > 0.1 M), this reaction is still dominant, but radical generation by the direct attack against styrene by TEMPO, with kinetic constant of addition k_ad, also becomes relevant. From previous experimental data and simulations, initial estimates of k_h ≈ 1 and k_ad ≈ 6 × 10^?7 L mol^?1 s^?1 are obtained at 125 °C. From the induction period to the polymerization regime, there is an abrupt change in the dominant mechanism generating radicals because of the sudden decrease in the nitroxide radicals. Under induction‐period conditions, the simulations confirm the validity of the quasi‐steady‐state assumption (QSSA) for the Mayo dimer in this regime; however, after the induction period, the QSSA for the dimer is not valid, and this brings into question the scientific basis of the well‐known expression k_th[M]³ (where [M] is the monomer concentration and k_th is the kinetic constant of autoinitiation) for the autoinitiation rate in styrene polymerization. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6962‐6979, 2006     

Theoretical and computational studies of vectorial processes in biomolecular systems

Efficient vectorial processes such as the transduction of bioenergy and signals are characteristics that strikingly distinguish living systems from inanimate materials. Recent developments in biophysical and biochemical techniques have provided new information about the structure, dynamics and interaction of biomolecules involved in vectorial life processes at multiple length and temporal scales. This wealth of data makes it possible to carry out theoretical and computational studied of key mechanistic questions associated with complex life processes at an unprecedented level. Using two “vectorial biomolecular machines”, myosin and cytochrome c oxidase, as examples, we discuss the identification of interesting and biologically relevant questions that require thorough theoretical analysis. Technical challenges and recent progress related to these theoretical investigations are briefly summarized     

Superdegenerate point in FCC phase diagram: CVM and Monte Carlo investigations

We investigate the topology of the phase diagram of binary alloys on the fee lattice with first-neighbor antiferromagnetic interactions around the superdegenerate point, where the L1₀ and L1₂ phases meet. We treat the system as a hard-constraint lattice gas, following a procedure previously described by Lebowitzet al. We perform cluster variation method calculations in theT0 limit and Monte Carlo simulations directly atT=0 K on the ground states of the superdegenerate point. We find that: (i) there is no disordered phase in the neighborhood of this point; (ii) a phase L for which two of the four cubic sublattices have the same average occupancy and each of the two others are different appears between L1₀ and L1₂; (iii) the transition L/L1₂ is of first order.     

多晶顺磁共振谱的拟合

对电子自旋1/2≤S<3.5,核自旋1/2≤I<4.5和配体少于10个的顺磁体系的多晶EPR谱的拟合进行研究。在VAX-11/785计算机上用FORTRAN语言建立EPR谱模拟程序包,计算了多个例子,获得较为满意的结果。     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins

Hybrid quantum mechanical-molecular mechanics (dynamics) were performed on flavin reductase (Fre) and flavodoxin reductase (Fdr), both from Escherichia coli. Each was complexed with riboflavin (Rbf) or flavin mononucleotide (FMN). During 50 ps trajectories, the relative energies of the fluorescing state (S₁) of the isoalloxazine ring and the lowest charge transfer state (CT) were assessed to aid prediction of fluorescence lifetimes that are shortened due to quenching by electron transfer from tyrosine. The simulations for the four cases display a wide range in CT–S₁ energy gap caused by the presence of phosphate, other charged and polar residues, water, and by intermolecular separation between donor and acceptor. This suggests that the Gibbs energy change (ΔG₀) and reorganization energy (λ) for the electron transfer may differ in different flavoproteins.     

Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

Molecular Dynamics Simulations of Energetic Solids

A continuing objective in the area of energetic materials is to reduce sensitivity toward impact and shock. One approach is to develop a better understanding of how factors related to the crystal lattice, e.g., defects, influence the initiation and propagation of detonation. Molecular dynamics is a useful tool for this purpose. This paper presents an overview of molecular dynamics treatments of energetic solids. Some of these have simulated initiation and propagation in idealized systems; others have focused on developing a satisfactory procedure for describing molecular crystals of practical significance. Our emphasis in this discussion is on the progress that has been made along the second lines.     

Monte Carlo Simulation of the Assembly of bis‐Biotinylated DNA and Streptavidin

We present Monte Carlo simulations of the self‐assembly of bivalent bis‐biotinylated DNA molecules with the tetravalent biotin‐binding protein streptavidin (STV). By fitting the STV binding probabilities for the four possible valencies, the modelling correctly reproduces the dependencies of various network parameters experimentally observed in an earlier study. The combined results from the experimental and theoretical studies suggest that the binding probability for divalent STV formation is about 50 times larger than for the formation of trivalent and about 200 times larger than for tetravalent STV. In accordance with the experimental results, the modelling also indicates that the mixture of an equimolar ratio of DNA and STV leads to a maximum in size of the oligomeric DNA–STV clusters formed. Furthermore, we found a percolation transition in which the DNA cluster size increases rapidly with increasing DNA concentration resulting in the formation of a single supercluster at elevated concentrations. This behaviour coincides with the occurrence of an immobile band previously observed in electrophoretic experiments, indicating the formation of extremely large DNA–STV aggregate networks.