Parallel replica dynamics with a heterogeneous distribution of barriers: application to n-hexadecane pyrolysis

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of E(a) = 79.7 kcal/mol and log A/s(-1) = 14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.     

Molecular theory and cooperative mechanism of shock waves-induced detonations in energetic molecular crystals

At a microscopic level, two molecular models, respectively one- and two-dimensional, for describing the shock-induced detonationmechanism of an energetic crystal have been previously successively presented (after initiation). We put together, here, their characteristic features, and we discuss their respective contributions inorder to define the molecular and crystalline conditions that a crystal fulfills to sustain a shock induced wave detonation. The two-dimensional model which allows longitunal but also transversal atomic motions, has enabled us to elicit the crystalline structure in relation with the existence of a wave detonation propagation in the crystal or not. By comparison to detonation experiments the coherence of the models is performed. It may thus be possible to form an idea as to why a molecular compound can detonate through a shock wave.     

Micellar polymerization: Computer simulations by dissipative particle dynamics

Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events. Influence of initiation probability and different termination processes on final conversion and molecular‐weight distribution are presented. We demonstrate that prolonged initiation leads to increasing in polymer average molecular weight, and surface termination events play major role in conversion limitation, in comparison with recombination. © 2018 Wiley Periodicals, Inc.     

氢键准则在DMSO水溶液中应用的评价

利用分子动力学模拟方法, 分别采用几何准则和能量准则分析了不同浓度下的二甲基亚砜(DMSO)水溶液的氢键统计和动力学等特性. 结果显示, 两种氢键准则可以很好地反映出溶液的氢键性质随浓度的变化趋势. 通过分析比较发现, 由于几何准则不能有效地排除具有弱对势能的分子对, 因此其统计的氢键数量要大于能量准则的结果.此外, 能量准则对于分子间相对取向的区分存在不足, 进而引起氢键寿命的计算结果偏大.因此,为使氢键分析更加准确, 本文建议使用几何-能量混合型氢键准则.     

A link between impact sensitivity of energetic compounds and their activation energies of thermal decomposition

A new relationship is introduced between impact sensitivity of energetic compounds and their activation energies of thermal decomposition. In this relationship, the impact sensitivity of an energetic compound with general formula C_aH_bN_cO_d is a function of its activation energy of thermal decomposition as well as the ratio of \( \left( {\frac{{n_{\text{H}} }}{{n_{\text{O}} }}} \right) \) and the contribution of specific molecular structural parameters. The new correlation can help us to elucidate the mechanism of initiation of energetic materials by impact. It can be used to predict the magnitude of impact sensitivity of new energetic materials. The new correlation has the root mean square and the average deviations of 2.22 and 1.79 J, respectively, for 40 energetic compounds with different molecular structures. The proposed new method is also tested for 11 energetic compounds, which have complex molecular structures, e.g., 4,10-dinitro-2,6,8,12-tetraoxa-4,10-diazaisowurtzitane and 1,3,7,9-tetranitrophenoxazine.     

Reactive ligand influence on initiation in phenylene catalyst‐transfer polymerization

Synthesizing conjugated polymers via catalyst‐transfer polymerization (CTP) has led to unprecedented control over polymer sequence and molecular weight. Yet many challenges remain, including broadening the monomer scope and narrowing the molecular weight dispersities. Broad polymer dispersities can arise from nonliving pathways as well as slow initiation. Previously, slow initiation was observed in Ni‐mediated CTP of phenylene monomers. Although precatalysts with faster initiation rates have been reported, the rates still do not exceed propagation. Herein a second‐ and third‐generation of reactive ligands are described, along with a simple method for measuring initiation rates. A precatalyst with an initiation rate that exceeds propagation is now reported, however, the resulting polymer samples still exhibit broad dispersities, suggesting that slow initiation is not the most significant contributing factor in Ni‐mediated phenylene polymerizations. In addition, initiation rates measured under authentic polymerization conditions revealed that both exogenous triphenylphosphine and an ortho‐trifluoroethoxy substituent on the reactive ligand have a strong influence. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 1530–1535     

A novel method for risk assessment of electrostatic sensitivity of nitroaromatics through their activation energies of thermal decomposition

This study presents a novel relationship between electric spark sensitivity of nitroaromatic energetic compounds and their activation energies of thermal decomposition. The new correlation can help to elucidate the mechanism of initiation of energetic materials by electric spark. It can be used to predict the magnitude of electric spark sensitivity of new nitroaromatics, which is difficult to measure. The methodology assumes that electric spark sensitivity of a nitroaromatic energetic compound with general formula C_aH_bN_cO_d can be expressed as a function of its activation energy of thermal decomposition as well as optimized elemental composition and the contribution of specific molecular structural parameters. The new correlation has the root mean square and the average deviations of 1.43 and 1.17 J, respectively, for 22 nitroaromatic energetic compounds with different molecular structures. The proposed new method is also tested for eight nitroaromatic energetic compounds, which have complex molecular structures, e.g., 1,3,7,9-tetranitrophenoxazine, 2,4,6-tris(2,4,6-trinitrophenyl)-1,3,5-triazine, and 1-(2,4,6-trinitrophenyl)-5,7-dinitrobenzotriazole.     

Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen‐storage catalyst: A classical and ab initio molecular simulation study

Classical and ab initio, density functional theory‐ and semiempirical‐based molecular simulation, including molecular dynamics, have been carried out to compare and contrast the effect of explicit and implicit solvation representation of tetrahydrofuran (THF) solvent on the structural, energetic, and dynamical properties of a novel bifunctional arene ruthenium catalyst embedded therein. Particular scrutiny was afforded to hydrogen‐bonding and energetic interactions with the THF liquid. It was found that the presence of explicit THF solvent molecules is required to capture an accurate picture of the catalyst's structural properties, particularly in view of the importance of hydrogen bonding with the surrounding THF molecules. This has implications for accurate modeling of the reactivity of the catalyst. © 2014 Wiley Periodicals, Inc.     

Modeling stable free-radical polymerization

A kinetic model has been developed for stable free-radical polymerization (SFRP) processes by using the method of moments. This model predicts monomer conversion, number-average molecular weight, and polydispersity of molecular weight distribution. The effects of the concentrations of initiator, stable radical, and monomer, as well as the rate constants of initiation, propagation, termination, transfer, and the equilibrium constant between active and dormant species, are systematically investigated by using this model. It is shown that the ideal living-radical polymerization having a linear relationship between number-average molecular weight and conversion and a polydispersity close to unity is the result of fast initiation, slow propagation, absence of radical termination, and a high level of dormant species. Increasing stable radical concentration helps to reduce polydispersity but also decreases polymerization rate. Thermal initiation significantly broadens molecular weight distribution. Without the formation of dormant species, the model predicts a conventional free-radical polymerization. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2692–2704, 1999     

Modeling of molecular weight development in atom transfer radical polymerization

A kinetic model has been developed for atom transfer radical polymerization processes using the method of moments. This model predicts monomer conversion, number‐average molecular weight and polydispersity of molecular weight distribution. It takes into account the effects of side reactions including bimolecular radical termination and chain transfers. The determining parameters include the ratios of the initiator, catalyst and monomer concentrations, as well as the ratios of the rate constants of propagation, termination, transfer and the equilibrium constant between radicals and their dormant species. The effects of these parameters on polymer chain properties are systematically simulated. The results show that an ideal living radical polymerization exhibiting a linear relationship between number‐average molecular weight versus conversion and polydispersity approaching unity is only achievable under the limiting condition of slow monomer propagation and free of radical termination and transfers. Improving polymerization rate usually accompanies a loss of this linearity and small polydispersity. For polymerization systems having a slow initiation, the dormant species exercise a retention effect on chain growing and tend to narrow the molecular weight distribution. Increasing catalyst concentration accelerates the initiation rate and thus decreases the polydispersities. It is also shown that for a slow initiation system, delaying monomer addition helps to reduce the polydispersities. Radical termination and transfers not only slow down the monomer conversion rates but also broaden polymer molecular weight distributions. Under the limiting conditions of fast propagation and termination and slow initiation, the model predicts the conventional free radical polymerization behaviors.     

Effect of Vacancy Defects on the Young's Modulus and Fracture Strength of Graphene: A Molecular Dynamics Study

The Young's modulus of graphene with various rectangular and circular vacancy defects is investigated by molecular dynamics simulation. By comparing with the results calculated from an effective spring model, it is demonstrated that the Young's modulus of graphene is largely correlated to the size of vacancy defects perpendicular to the stretching direction. And a linear reduction of Young's modulus with the increasing concentration of mono‐atomic‐vacancy defects (i.e., the slope of ?0.03) is also observed. The fracture behavior of graphene, including the fracture strength, crack initiation and propagation are then studied by the molecular dynamics simulation, the effective spring model, and the quantized fracture mechanics. The blunting effect of vacancy edges is demonstrated, and the characterized crack tip radius of 4.44 Å is observed.     

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study

Molecular dynamics (MD) simulation is the standard computational technique used to obtain information on the time evolution of the conformations of proteins and many other molecular systems. However, for most biological systems of interest, the time scale for slow conformational transitions is still inaccessible to standard MD simulations. Several sampling methods have been proposed to address this issue, including the accelerated molecular dynamics method. In this work, we study the extent of sampling of the phi/psi space of alanine dipeptide in explicit water using accelerated molecular dynamics and present a framework to recover the correct kinetic rate constant for the helix to beta-strand transition. We show that the accelerated MD can drastically enhance the sampling of the phi/psi conformational phase space when compared to normal MD. In addition, the free energy density plots of the phi/psi space show that all minima regions are accurately sampled and the canonical distribution is recovered. Moreover, the kinetic rate constant for the helix to beta-strand transition is accurately estimated from these simulations by relating the diffusion coefficient to the local energetic roughness of the energy landscape. Surprisingly, even for such a low barrier transition, it is difficult to obtain enough transitions to accurately estimate the rate constant when one uses normal MD.     

Flash ignition and initiation of explosives-nanotubes mixture

Optical ignition and initiation of energetic materials could thus far be only accomplished through lasers, with specific characteristics of high power, pulse length, wavelength, and a small target area that greatly inhibit their applications. Here, we report that an ignition and an initiation process, further leading to actual detonation, does occur for energetic materials in lax contact with carbon nanotubes that are prone to opto-thermal activity via a conventional flashbulb. Our results show that, for the first time, optical initiation of energetic materials is possible on a large surface area and using ordinary light intensity of several W/cm2. The implication is that energetic materials mixed with optically active nanotubes could be new ideal candidates for safety apparatus, such as the firing of bolts on space shuttle rockets and aircraft exit doors.     

The role of dislocations in the solid-state polymerization of monomers having conjugated triple bonds: A study of 2,4-hexadiyne-1,6-diol bis(p-toluene sulfonate)

The crystal structure of the monomer bis(p-toluene sulfonate) ester of 2,4-hexadiyne-1,6-diol (pT) is conducive from the viewpoint of both the separation distances and molecular configuration, to polymerization, irrespective of whether initiation is thermal, photochemical, or mechanical. The dislocations present in the monomer and polymer structures have been characterized by employing optical microscopic techniques. The slip system (102)[010] is found to be present in both monomer and polymer crystals but the (010)[001] system is found only in the monomer. On this basis a crystal structure for the monomer is proposed based on existing crystallographic information relating to the structure of the polymer. Dislocations are thought, on energetic grounds, to facilitate nucleation of product in the thermal polymerization but have no observable influence on the photoinduced reaction which proceeds homogeneously through the bulk.     

How Mutations Affecting the Ligand-receptor Interactions:a Combined MD and QM/MM Calculation on CYP2E1 and Its Two Mutants

Cytochrome P450(CYP) 2E1 is a dual function monoxygenase with a crucial role in the metabolism of 6% of drugs on the market at present. The enzyme is of tremendous interest for its association with alcohol consumption, diabetes, obesity and fasting. Despite the abundant experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activity deficiencies have not been rationalized at the atomic level. In this regard, we have investigated the effects of mutation on the structural and energetic characteristics upon single point mutations in CYP2E1, N219D and S366C. The molecular dynamics(MD) simulation combined with quantum mechanics/molecular mechanics(QM/MM) and noncovalent interaction(NCI) analysis was carried out on CYP2E1 and its two mutants. The results highlight the critical role of Phe207, which is responsible for both structural flexibility and energetic variation, shortening the gap between the theory and the experimentally observed results of enzymatic activity decrease. The underlying molecular mechanism of the enzymatic activity deficiencies for mutants may be attributed to the changes of spatial position of Phe207 in the two mutants. This work provides particular explanations to how mutations affect ligand-receptor interactions based on combined MD and QM/MM calculations. Furthermore, the mutational effects on the activity of CYP2E1 obtained in the present study are beneficial to both the experimental and the computational works of CYPs and may allow researchers to achieve desirable changes in enzymatic activity.     

What does zeolitic water look like?: Modelization by molecular dynamics simulations

In this paper, we present Monte Carlo and molecular dynamics simulations of water molecules inside a ferrierite-type framework. Detailed analyses of the energetic, structural, and dynamical properties are carried out and compared with liquid water results in order to study the influence of the framework on the physisorbed water molecules.     

Adsorption of catechol on a wet silica surface: density functional theory study

Marine mussel proteins adhere permanently to diverse wet surfaces via their catechol (1, 2-dihydroxybenzene) functionality. To elucidate the molecular mechanism underlying this water-resistant adhesion, we performed density functional theory calculations for the competitive adsorption of catechol and water on a wet silica surface. Results show the energetic spontaneity of the reaction; catechol displaces water molecules and adheres directly to the surface. This result was subsequently corroborated by our molecular dynamics simulation.     

Polymerization molecular dynamics simulations. I. Cross-linked atomistic models for poly(methacrylate) networks

A methodology to build cross-linked atomistic structures for poly(methacrylates) is presented. The methodology is based on a polymerization molecular dynamics (MD) scheme in which monomers are allowed to react with each other during an MD simulation. The criteria for forming chemical bonds is based on distances between prespecified reactive centres on the monomers and growing polymer chains. The simulated rate of monomer diffusion is increased through the use of scaled charges and approximations in non-bond energy calculations. Local energetic stresses caused by bond formation are relaxed through the use of an explicit velocity rescaling molecular dynamics algorithm. An example network consisting of a typical dental resin is constructed and presented.     

高压下β-HMX热分解机理的ReaxFF反应分子动力学模拟

采用ReaxFF反应分子动力学方法研究了不同压缩态β-HMX晶体(ρ=1.89、2.11、2.22、2.46、2.80、3.20 g·cm^-3)在T=2500 K时的热分解机理, 分析了压力对初级和次级化学反应速率的影响、高压与低压下初始分解机理的区别以及造成反应机理发生变化的原因. 发现HMX的初始分解机理与压力(或密度)相关. 低压下(ρ<2.80 g·cm^-3)以分子内反应为主, 即N－NO₂键的断裂、HONO的生成以及分子主环的断裂(C－N键的断裂). 高压下(ρ≥2.80 g·cm^-3)分子内反应被显著地抑制, 而分子间反应得到促进, 生成了较多的O₂、HO等小分子和大分子团簇. 初始分解机理随压力的变化导致不同密度下的反应速率和势能也有所不同. 本文在原子水平对高压下HMX反应机理的深入研究对于认识含能材料在极端条件下的起爆、化学反应的发展以及爆轰等具有重要意义.     

Thermodynamic features and environmental effects in a two-states molecular device under strict electrochemical control

The thermodynamic features of a synthetic molecular thread, recently proposed acting as an electrochemically-driven two-states molecular device, have been systematically investigated by means of nanoseconds time-scale classical molecular dynamics (MD) simulations and basic statistical mechanics relations. Results clearly suggest that the accessible conformational space of such a potential molecular switch shows a strong environmental dependence: the reversible molecular switching mechanism observed in liquid solution is effectively suppressed when the synthetic thread is hypothesized working in vacuo. Such a result has been related to a subtle energetic/entropic balance experienced by the whole system (solute and solvent) during the intramolecular conformational transition of the molecular thread, in presence and in absence of the solvent.