Molecular Dynamics Simulation of Shock Response of CL-20 Co-crystals Containing Void Defects

To investigate the effect of void defects on the shock response of hexanitrohexaazaisowurtzitane(CL-20)co-crystals,shock responses of CL-20 co-crystals with energetic materials ligands trinitrotoluene(TNT),1,3-dinitrobenzene(DNB),solvents ligands dimethyl carbonate(DMC) and gamma-butyrolactone(GBL)with void were simulated,using molecular dynamics method and reactive force field.It is found that the CL-20 co-crystals with void defects will form hot spots when impacted,significantly affecting the decomposition of molecules around the void.The degree of molecular fragmentation is relatively low under the reflection velocity of 2 km/s,and the main reactions are the formation of dimer and the shedding of nitro groups.The existence of voids reduces the safety of CL-20 co-crystals,which induced the sensitivity of energetic co-crystals CL-20/TNT and CL-20/DNB to increase more significantly.Detonation has occurred under the reflection velocity of 4 km/s,energetic co-crystals are easier to polymerize than solvent co-crystals,and are not obviously affected by voids.The results show that the energy of the wave decreases after sweeping over the void,which reduces the chemical reaction frequency downstream of the void and affects the detonation performance,especially the solvent co-crystals.

Hugoniot curve calculation of nitromethane decomposition mixtures:A reactive force field molecular dynamics approach

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics （MD） simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition.

Effect of an external electric field on liquid water using molecular dynamics simulation with a flexible potential

Molecular dynamics simulations of liquid water were performed at 258 K and density of 1.0 g/cm^3 under different strengths of an external electric field, ranging from 0 to 8.0×10^9V/m, to investigate the influence of an external field on structural and dynamic properties of water. The flexible simple point charge model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bond structure. With increasing field strength, water system has a more perfect structure, which is shnilar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected because of a too large self-diffusion coefficient. The self-diffusion coefficient decreases remarkably with increasing strength of electric field, and the self-diffusion coefficient is anisotropic.

Quantitative prediction and ranking of the shock sensitivity ofexplosives via reactive molecular dynamics simulations

A deep understanding of explosive sensitivities and their factors is important for safe and reliable applications.However,quantitative prediction of the sensitivities is difficult.Here,reactive molecular dynamics simulation models for high-speed piston impacts on explosive supercells were established.Simulations were also performed to investigate shock-induced reactions of various high-energy explosives.The fraction of reacted explosive molecules in an initial supercell changed linearly with the propagation distance of the shock-wave front.The corresponding slope could be used as a reaction rate for a specific shock-loading velocity.Reaction rates that varied with the shock-loading pressure exhibited two-stage linearities with different slopes.The two inflection points corresponded to the initial and accelerated reactions,which respectively correlated to the thresholds of shock-induced ignition and detonation.Therefore,the ignition and detonation critical pressures could be determined.The sensitivity could then be a quantitative prediction of the critical pressure.The accuracies of the quantitative shock sensitivity predictions were verified by comparing the impact and shock sensitivities of common explosives and the characteristics of anisotropic shock-induced reactions.Molecular dynamics simulations quantitatively predict and rank shock sensitivities by using only crystal structures of the explosives.Overall,this method will enable the design and safe use of explosives.

Early Stage of Oxidation on Titanium Surface by Reactive Molecular Dynamics Simulation

Understanding of metal oxidation is very critical to corrosion control,catalysis synthesis,and advanced materials engineering.Metal oxidation is a very complex phenomenon,with many different processes which are coupled and involved from the onset of reaction.In this work,the initial stage of oxidation on titanium surface was investigated in atomic scale by molecular dynamics(MD)simulations using a reactive force field(ReaxFF).We show that oxygen transport is the dominant process during the initial oxidation.Our simulation also demonstrate that a compressive stress was generated in the oxide layer which blocked the oxygen transport perpendicular to the Titanium(0001)surface and further prevented oxidation in the deeper layers.The mechanism of initial oxidation observed in this work can be also applicable to other self-limiting oxidation.

Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation

Two-state folding and down-hill folding are two kinds of protein folding dynamics for small single domain proteins.Here we apply molecular dynamics(MD)simulation to the two-state protein GB1 and down-hill folding protein gpW to reveal the relationship of their free energy landscape and folding/unfolding dynamics.Results from the steered MD simulations show that gpW is much less mechanical resistant than GB1,and the unfolding process of gpW has more variability than that of GB1 according to their force-extension curves.The potential of mean force(PMF)of GB1 and gpW obtained by the umbrella sampling simulations shows apparent difference:PMF of GB1 along the coordinate of extension exhibits a kink transition point where the slope of PMF drops suddenly,while PMF of gpW increases with extension smoothly,which are consistent with two-state folding dynamics of GB1 and downhill folding dynamics of gpW,respectively.Our results provide insight to understand the fundamental mechanism of different folding dynamics of twostate proteins and downhill folding proteins.

Molecular dynamics simulation study on behaviors of liquid 1,2-dichioroethane under external electric fields

Molecular dynamics simulation was carried out to study the behavior of liquid 1,2-dichloroethane molecules under external electric fields including direct current field, alternating current field and positive-half-period cosin field. The maximum applied field strength was 10^8 V/m , the maximum frequency of the alternating current field and that of the positive-half-period cosine field was 10^12 Hz . The simulation revealed that the field type and field strength act on the population of the molecular configuration. In the strong direct current field, all trans forms converted completely into gauche forms. Order parameter and the correlation of the system torsion angle were also investigated. The results suggested that these two dynamical parameters depended also on the field type and the field strength. The maximum of order parameter was found to be at 0.6in the strong direct current field.

Modification of short-range repulsive interactions in ReaxFF reactive force field for Fe–Ni–Al alloy

The short-range repulsive interactions of any force field must be modified to be applicable for high energy atomic collisions because of extremely far from equilibrium state when used in molecular dynamics(MD)simulations.In this work,the short-range repulsive interaction of a reactive force field(ReaxFF),describing Fe-Ni-Al alloy system,is well modified by adding a tabulated function form based on Ziegler-Biersack-Littmark(ZBL)potential.The modified interaction covers three ranges,including short range,smooth range,and primordial range.The short range is totally predominated by ZBL potential.The primordial range means the interactions in this range is the as-is ReaxFF with no changes.The smooth range links the short-range ZBL and primordial-range ReaxFF potentials with a taper function.Both energies and forces are guaranteed to be continuous,and qualified to the consistent requirement in LAMMPS.This modified force field is applicable for simulations of energetic particle bombardments and reproducing point defects'booming and recombination effectively.

Saturated sodium chloride solution under an external static electric field: A molecular dynamics study

The behavior of saturated aqueous Na Cl solutions under a constant external electric field（E） was studied by molecular dynamics（MD） simulation. Our dynamic MD simulations indicated that the irreversible nucleation process towards crystallization is accelerated by a moderate E but retarded or even prohibited under a stronger E, which can be understood by the competition between self-diffusion and drift motion. The former increases with E, thereby accelerating the nucleation process, whereas the latter pulls oppositely charged ions apart under a stronger E, thereby decelerating nucleation.Additionally, our steady-state MD simulations indicated that a first-order phase transition occurs in saturated solutions at a certain threshold Ec. The magnitude of Ec increases with concentration because larger clusters form more easily when the solution is more concentrated and require a stronger E to dissociate.

Molecular simulation studies of hydrocarbon and carbon dioxide adsorption on coal

Sorption isotherms of hydrocarbon and carbon dioxide （CO2） provide crucial information for designing processes to sequester CO2 and recover natural gas from unmineable coal beds. Methane （CH4）, ethane （C2H6）, and CO2 adsorption isotherms on dry coal and the temperature effect on their maximum sorption capacity have been studied by performing combined Monte Carlo （MC） and molecular dynamics （MD） simulations at temperatures of 308 and 370 K （35 and 97 ~C） and at pressures up to 10 MPa. Simulation results demonstrate that absolute sorption （expressed as a mass basis） divided by bulk gas density has negligible temperature effect on CH4, C2H6, and CO2 sorption on dry coal when pressure is over 6 MPa. CO2 is more closely packed due to stronger interaction with coal and the stronger interaction between CO2 mole- cules compared, respectively, with the interactions between hydrocarbons and coal and between hydrocarbons. The results of this work suggest that the ＂a＂ constant （pro- portional to TcPc） in the Peng-Robinson equation of state is an important factor affecting the sorption behavior of hydrocarbons. CO2 injection pressures of lower than 8 MPa may be desirable for CH4 recovery and CO2 sequestration. This study provides a quantitative under- standing of the effects of temperature on coal sorptioncapacity for CH4, C2H6, and CO2 from a microscopic perspective.

Machine learning for molecular thermodynamics

Thermodynamic properties of complex systems play an essential role in developing chemical engineering processes.It remains a challenge to predict the thermodynamic properties of complex systems in a wide range and describe the behavior of ions and molecules in complex systems.Machine learning emerges as a powerful tool to resolve this issue because it can describe complex relationships beyond the capacity of traditional mathematical functions.This minireview will summarize some fundamental concepts of machine learning methods and their applications in three aspects of the molecular thermodynamics using several examples.The first aspect is to apply machine learning methods to predict the thermodynamic properties of a broad spectrum of systems based on known data.The second aspect is to integer machine learning and molecular simulations to accelerate the discovery of materials.The third aspect is to develop machine learning force field that can eliminate the barrier between quantum mechanics and all-atom molecular dynamics simulations.The applications in these three aspects illustrate the potential of machine learning in molecular thermodynamics of chemical engineering.We will also discuss the perspective of the broad applications of machine learning in chemical engineering.

Potentials of classical force fields for interactions between Na^+ and carbon nanotubes

Carbon nanotubes （CNTs） have long been expected to be excellent nanochannels for use in desalination membranes and other bio-inspired human-made channels owing to their experimentally confirmed ultrafast water flow and theoretically predicted ion rejection. The correct classical force field potential for the interactions between cations and CNTs plays a cru- cial role in understanding the transport behaviors of ions near and inside the CNT, which is key to these expectations. Here, using density functional theory calculations, we provide classical force field potentials for the interactions of Na＋/hydrated Na＋ with （7,7）, （8,8）, （9,9）, and （10,10）-type CNTs. These potentials can be directly used in current popular classical soft- ware such as nanoscale molecular dynamics （NAMD） by employing the tclBC interface. By incorporating the potential of hydrated cation-g interactions to classical all-atom force fields, we show that the ions will move inside the CNT and accu- mulate, which will block the water flow in wide CNTs. This blockage of water flow in wide CNTs is consistent with recent experimental observations. These results will be helpful for the understanding and design of desalination membranes, new types of nanofluidic channels, nanosensors, and nanoreactors based on CNT platforms.

Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme

A protein may exist as an ensem-ble of di erent conformations in solution,which cannot be repre-sented by a single static structure.Molecular dy-namics(MD)simulation has become a useful tool for sampling protein conformations in solution,but force elds and water models are important issues.This work presents a case study of the bacteriophage T4 lysozyme(T4L).We have found that MD simulations using a classic AMBER99SB force eld and TIP4P water model cannot well describe hinge-bending domain motion of the wild-type T4L at the timescale of one microsecond.Other combinations,such as a residue-speci c force eld called RSFF2+and a dispersion-corrected water model TIP4P-D,are able to sample reasonable solution conformations of T4L,which are in good agreement with experimental data.This primary study may provide candidates of force elds and water models for further investigating conformational transition of T4L.

Validation of the CHARMM27 force field for nucleic acids using 2D nuclear overhauser effect spectroscopy

Nuclear magnetic resonance spectroscopy offers a powerful method for validation of molecular dynamics simulations as it provides information on the molecular structure and dynamics in solution. We performed 10 ns MD simulations using the CHARMM27 force field of four palindromic oligonucleotides and compared the results with experimental NOESY data using the full relaxation matrix formalism. The correlation coefficients between theoretical and experimental data for the four molecular species under study ranged from 0.82 to 0.98 confirming the high quality of the selected force field and providing a valid basis for the identification of force field imperfections. Hence, we observed an unsatisfactory treatment of deoxyribose conformational equilibrium, which resulted in the overrepresentation of the energetically favorable C3'-endo conformation in the MD trajectory. Our developed approach for force field validation based on NMR NOESY spectral data is applicable to a wide range of molecular systems and appropriate force fields.

原油-CO_(2)相互作用机理分子动力学模拟研究

CO_(2)的众多驱油机理已经被广泛认同,但受油藏因素影响,不同油藏条件下CO_(2)驱的效果差异较大。因此,需要进一步深化研究CO_(2)与原油的微观相互作用机理,明确不同油藏条件下CO_(2)的驱油方式,最大限度挖潜CO_(2)驱的潜力。利用分子动力学模拟方法研究了组分、温度、压力对油滴-CO_(2)相互作用的影响。求取动力学参数,量化表征油滴-CO_(2)间的相互作用,厘清了不同条件下二者的微观相互作用规律。模拟结果显示,色散力是主导CO_(2)-烷烃分子相互作用的主要作用能,二者相互作用主要包含两方面:一是CO_(2)分子克服烷烃分子间的位阻作用向油滴内部溶解扩散,二是CO_(2)分子对油滴外层分子的萃取吸引作用。随着烷烃分子链长减小、温度降低和压力增加,油滴溶解度参数和CO_(2)配位数增加,油滴外层分子的弯曲度减小,二者的相互作用增强。研究结果认为,在温度较低、压力较高的轻质和中轻质油藏中,应尽可能地实现CO_(2)混相驱和近混相驱,在温度较高、压力较低的中质和重质油藏中,应充分发挥CO_(2)非混相驱的溶解降黏、膨胀原油体积和补充能量的优势。研究结果能够为室内研究和现场实施CO_(2)驱油提供理论指导。

冲击作用下CL⁃20含能共晶的反应分子动力学模拟

共晶技术是降低六硝基六氮杂异伍兹烷(CL‐20)感度的有效方法之一,研究冲击作用下CL‐20共晶的化学反应,有助于理解CL‐20共晶的冲击反应机制,对炸药安全评价分析具有重要意义。本研究采用ReaxFF‐lg反应力场的分子动力学方法,同时结合非平衡加载方法,对CL‐20/2,5‐二硝基甲苯(DNT)、CL‐20/1,3‐二硝基苯(DNB)和CL‐20/1‐甲基‐3,5‐二硝基‐1,2,4‐三唑(MDNT)三种共晶在2~5 km·s^(-1)冲击速度下的冲击压缩过程进行了分子动力学模拟,获得了含能共晶在冲击作用后的热力学演化特征、初始化学反应路径和产物信息,并与CL‐20的情况进行了对比分析。研究发现:CL‐20/DNT、CL‐20/DNB和CL‐20/MDNT 3种共晶都有一定程度的降低冲击感度作用,3种共晶的冲击感度顺序依次为CL‐20/MDNT>CL‐20/DNB>CL‐20/DNT。3种共晶的分解反应均是从CL‐20分解开始,且CL‐20的分解速度比DNT、DNB和MDNT快。在2 km·s^(-1)冲击速度下,CL‐20共晶首先发生聚合反应,CL‐20与共晶配体分子间的聚合反应早于CL‐20分子间的聚合,且反应频次远高于CL‐20分子之间聚合。在3 km·s^(-1)的冲击条件下,CL‐20首先发生了N—N以及C—N键断裂,笼型结构被破坏,同时生成NO_(2),CL‐20初步断键后的结构及产物NO_(2)会进一步与共晶配体分子DNT、DNB、MDNT结合,降低CL‐20反应中间产物的浓度,达到降感作用。在4,5 km·s^(-1)冲击条件下,CL‐20中的环状骨架结构会直接遭到破坏,发生C—N键断裂,产生小分子碎片,直接生成N2,同时有NO_(2)、H_(2)、CO_(2)、H_(2)O等产物生成。

单一应力下义马原煤热解产物演变规律及动力学模拟

以义马原煤为研究对象,构造晶胞,在ReaxFF力场中施加5×10^(9)s^(-1)的应变率,模拟1000K,1500K,2000K,2500K,3000K终温下义马原煤热解演化过程,分析单一应力对褐煤热解的作用效果。结果表明:不同模拟终温下,不同方向上的应力是上下波动的,在允许一定误差下,应力范围保持在±70GPa之间,即此应力对褐煤热解的作用受温度的影响较弱。模拟过程中,在26ps~33ps之间分子数出现极小值点而种类数出现极大值点,义马原煤热解模拟起始温度点不变,但缩聚反应的温度区间前移,表明反应前期单一应力作用效果优于温度作用效果,应力促进了整体的反应进程。受缩聚反应的影响,CO,CH_(4),H_(2)O和NH_(3)含量先升后降,符合热解一般规律,说明应力没有改变反应的最终趋势。H_(2)和·H的数量随反应进行持续上升,说明缩聚反应过程中,此应力作用促进焦油裂解生成的·H的数量大于缩聚反应消耗的·H的数量;同时,·H和H_(2)含量升高,促进·SH与·H结合,提高了H_(2)S的产率。

基于亚稳态液膜空化的长程疏水力作用机制

疏水力作为胶体物理化学及生物大分子体系中重要作用力,具有典型的多尺度作用程特征,其中亚稳态液膜空化气泡桥接诱发长程疏水力和固液界面水分子重排熵效应诱导短程疏水力假说占据着当前学术主流,但仍缺少系统理论研究.为进一步阐明基于亚稳态液膜空化的长程疏水力作用机制,借助原子力显微镜(AFM)及分子动力学模拟对全氟辛基三氯硅烷疏水化颗粒与表面间长程疏水力进行了系统研究.AFM力测试结果表明:长程疏水力作用程随接近次数增加而逐渐增大并逐渐趋于稳定,第十次接触时进针曲线跳入黏附距离达到502.01 nm,退针曲线中观察到了预示空化气泡毛细桥断裂的台阶.此外,发现经典毛细力数学模型可以较好地拟合进针曲线,通过计算得到毛细桥体积约为0.30μm^(3),从理论角度直接验证了亚稳态液膜空化气泡毛细桥的存在.进一步借助GROM ACS(GROningen M A chine for Chemical Simulations)大尺度牵引分子动力学模拟从分子尺度探索疏水颗粒分离过程中空化气泡毛细桥产生、演化过程与力学行为的内在关联机制,结果表明:疏水颗粒从基板表面跳出分离瞬间,产生的局部压降吸引氮气分子向液膜内部扩散从而形成空化气泡毛细桥,同时,在毛细桥断裂时刻在计算弹簧势力曲线中观察到了力跳跃行为.最后研究了溶液气体含量对长程疏水力的影响规律,发现气体分子含量和空化气泡毛细桥体积增长速率与毛细桥拉伸断裂长度呈现正相关关系,进一步表明了长程疏水力的气体浓度依赖效应.基于亚稳态液膜空化的长程疏水力作用机制的揭示有助于进一步完善胶体物理化学及生物大分子间相互作用理论体系,同时对调控实际矿物浮选过程具有重要指导意义.

生物质焦油模化物的热裂解ReaxFF模拟研究

实现热裂解过程中焦油的有效脱除是生物质热利用技术中亟待解决的问题。通过密度泛函理论研究生物质焦油3种典型模型化合物(甲苯、苯酚和萘)的分子结构性质,并基于ReaxFF反应力场对焦油模型化合物的热裂解过程进行分子动力学模拟研究,从分子层面对焦油热裂解的复杂反应过程进行深入研究。探索反应温度对热裂解特性的影响,详细研究甲苯、苯酚和萘的热裂解机理及中间自由基、气体产物的演化过程。结果表明:C—H键的Mayer键级小于C—C键,易于断裂,芳香环侧链结构中氢的Mulliken电荷数大,具有更强的活性;3种焦油模型化合物的热稳定性依次为:萘>苯酚>甲苯,其中苯酚具有高活性的含氧官能团,二次裂解易生成气体产物,而甲苯和萘二次裂解易生成稠环芳烃;甲苯、苯酚和萘的一级反应动力学热解表观活化能分别为314.03、362.39、396.74 kJ/mol。