Quantum-based Molecular Dynamics Research Articles

The base versus tip growth mode of carbon nanotubes by catalytic hydrocarbon cracking: Review, challenges and opportunities

Hydrogen gas production using catalytic hydrocarbon cracking on metal nanoparticles has become a vital bridge technology, as this process, unlike the traditional methane-based reforming process, does not co-produce carbon gasses (e.g., CO, CO2). The major benefit of direct catalytic methane cracking using a nanostructured catalyst is the formation of solid carbon in high-value products, such as carbon nanotubes (CNTs) or filaments. This solid carbon can then be removed physically and valorized. However, it is challenging to design a catalyst capable of sustaining its activity after solid carbon has started to deposit and grow, meanwhile preventing the formation of coke. For CNTs, in particular, the base growth mode of CNTs is the desired pathway, as the catalyst can then be regenerated and re-used. If the CNTs are formed under the tip-growth mode, the catalyst particle will be lifted off the support of the regeneration and reusability is lost. Therefore, the study of CNTs growth modes is a vital topic, both experimentally and theoretically, of designing appropriate catalysts. To date, enormous efforts have been made to investigate conditions where the CNTs base growth mode can be maintained during the carbon deposition process. Several possible correlations and mechanisms regarding the base growth mode have been explored and established. Theoretical calculations and numerical simulations across length scales were conducted to investigate the nucleation mechanism and growth of CNTs. Density functional theory (DFT), classical and quantum-based molecular dynamics (MD) and Monte Carlo (MC) simulations were also carried out to study the initial CNT cap formation and its encapsulation during the catalytic hydrocarbon cracking process. A thermodynamics-based nucleation formula of CNTs for both the base and tip growth modes was also established. However, there is still no consensus on what determines the CNT growth modes and what the roles are of the various influencing factors such as the nanoparticle size, the oxidation state of the catalyst, the mechanical properties of CNT, and the catalyst-support interaction. This paper reviews the current status of CNT's growth mechanism development. The benefits and limitations of theory and modeling approaches concerning CNT growth modes are discussed.

The Structure Properties of Carbon Materials Formed in 2,4,6-Triamino-1,3,5-Trinitrobenzene Detonation: A Theoretical Insight for Nucleation of Diamond-like Carbon.

The structure and properties of nano-carbon materials formed in explosives detonation are always a challenge, not only for the designing and manufacturing of these materials but also for clearly understanding the detonation performance of explosives. Herein, we study the dynamic evolution process of condensed-phase carbon involved in 2,4,6-Triamino-1,3,5-trinitrobenzene (TATB) detonation using the quantum-based molecular dynamics method. Various carbon structures such as, graphene-like, diamond-like, and "diaphite", are obtained under different pressures. The transition from a C sp2- to a sp3-hybrid, driven by the conversion of a hexatomic to a non-hexatomic ring, is detected under high pressure. A tightly bound nucleation mechanism for diamond-like carbon dominated by a graphene-like carbon layer is uncovered. The graphene-like layer is readily constructed at the early stage, which would connect with surrounding carbon atoms or fragments to form the tetrahedral structure, with a high fraction of sp3-hybridized carbon. After that, the deformed carbon layers further coalesce with each other by bonding between carbon atoms within the five-member ring, to form the diamond-like nucleus. The complex "diaphite" configuration is detected during the diamond-like carbon nucleation, which illustrates that the nucleation and growth of detonation nano-diamond would accompany the intergrowth of graphene-like layers.

Reaction mechanism and electronic properties of host-guest energetic material CL-20/HA under high pressure by quantum-based molecular dynamics simulations.

The novel host-guest material 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20)/hydroxylamine (HA) improves the detonation energy of CL-20 explosives without compromising its safety. However, the reaction mechanism of CL-20/HA under high pressure is not yet fully understood for the complex host-guest structure. A multiscale shock simulation technique by quantum-based molecular dynamics was performed to investigate the reaction mechanism of CL-20/HA under shock with different velocities along different directions, focusing on charge transfer, electronic properties, reaction path and product evolution. The structural changes caused by both insertion of HA and charge overlap between CL-20 and HA are responsible for the electronic changes and gap decrease. Directional charge transfer was observed between CL-20 and HA molecular fragments during shock in all shock loading directions, causing the CL-20 molecular group to become electrically non-neutral. The C-N bond in the CL-20 cage then broke, leading to the release of nitro and nitrous oxide at high temperatures and pressures. The HA molecules or free H atoms from HA could bond with the O atom in the nitro group, leading to the N-O bond cleavage. Some free H atoms could act as an intermediary, connecting two CL-20 molecules and forming dimeric molecules briefly. Compared with the pure CL-20 system, HA can inhibit the reaction of CL-20 in the CL-20/HA system to some extent during the initial shock stage. A further understanding of the chemical reaction mechanism and energy release in dense host-guest materials can be advanced by focusing on the microscopic internal effects of the guest molecule on the host molecule reactions.

Reaction mechanism and kinetics properties of β-HMX under different thermodynamics States: A theoretical study for thermal decomposition

The thermolysis of β-HMX under different thermodynamics states are investigated using quantum-based molecular dynamics method. The reaction is mainly initiated with molecular ring breaking and alkyl dehydrogenation. The cleavages of N-N and C-N bonds are impeded under high pressure, while that of C-H bond is significantly enhanced. NO3 is more favorably produced under low pressure, which can promote the hydrogen transfer to form H2O or OH. The reaction kinetics constants reflect that the initial endothermic reaction is really slower under high pressure, but the following exothermic reaction is significantly accelerated with a larger reaction heat of 368.05 cal·g−1.

Anisotropic Reaction Properties for Different HMX/HTPB Composites: A Theoretical Study of Shock Decomposition.

Plastic-bonded explosives (PBXs) consisting of explosive grains and a polymer binder are commonly synthesized to improve mechanical properties and reduce sensitivity, but their intrinsic chemical behaviors while subjected to stress are not sufficiently understood yet. Here, we construct three composites of β-HMX bonded with the HTPB binder to investigate the reaction characteristics under shock loading using the quantum-based molecular dynamics method. Six typical interactions between HMX and HTPB molecules are detected when the system is subjected to pressure. Although the initial electron structure is modified by the impurity states from HTPB, the metallization process for HMX does not significantly change. The shock decompositions of HMX/HTPB along the (100) and (010) surface are initiated by molecular ring dissociation and hydrogen transfer. The initial oxidations of C and H within HTPB possess advantages. As for the (001) surface, the dissociation is started with alkyl dehydrogenation oxidation, and a stronger hydrogen transfer from HTPB to HMX is detected during the following process. Furthermore, considerable fragment aggregation is observed, which mainly derives from the formation of new C−C and C−N bonds under high pressure. The effect of cluster evolution on the progression of the following reaction is further studied by analyzing the bonded structure and displacement rate.

Polymer degradation through chemical change: a quantum-based test of inferred reactions in irradiated polydimethylsiloxane

Chemical reaction schemes are key conceptual tools for interpreting the results of experiments and simulations, but often carry implicit assumptions that remain largely unverified for complicated systems. Established schemes for chemical damage through crosslinking in irradiated silicone polymers comprised of polydimethylsiloxane (PDMS) date to the 1950's and correlate small-molecule off-gassing with specific crosslink features. In this regard, we use a somewhat reductionist model to develop a general conditional probability and correlation analysis approach that tests these types of causal connections between proposed experimental observables to reexamine this chemistry through quantum-based molecular dynamics (QMD) simulations. Analysis of the QMD simulations suggests that the established reaction schemes are qualitatively reasonable, but lack strong causal connections under a broad set of conditions that would enable making direct quantitative connections between off-gassing and crosslinking. Further assessment of the QMD data uncovers a strong (but nonideal) quantitative connection between exceptionally hard-to-measure chain scission events and the formation of silanol (Si-OH) groups. Our analysis indicates that conventional notions of radiation damage to PDMS should be further qualified and not necessarily used ad hoc. In addition, our efforts enable independent quantum-based tests that can inform confidence in assumed connections between experimental observables without the burden of fully elucidating entire reaction networks.

Bringing discrete-time Langevin splitting methods into agreement with thermodynamics.

In light of the recently published complete set of statistically correct Grønbech-Jensen (GJ) methods for discrete-time thermodynamics, we revise a differential operator splitting method for the Langevin equation in order to comply with the basic GJ thermodynamic sampling features, namely, the Boltzmann distribution and Einstein diffusion, in linear systems. This revision, which is based on the introduction of time scaling along with flexibility of a discrete-time velocity attenuation parameter, provides a direct link between the ABO splitting formalism and the GJ methods. This link brings about the conclusion that any GJ method has at least weak second order accuracy in the applied time step. It further helps identify a novel half-step velocity, which simultaneously produces both correct kinetic statistics and correct transport measures for any of the statistically sound GJ methods. Explicit algorithmic expressions are given for the integration of the new half-step velocity into the GJ set of methods. Numerical simulations, including quantum-based molecular dynamics (QMD) using the QMD suite Los Alamos Transferable Tight-Binding for Energetics, highlight the discussed properties of the algorithms as well as exhibit the direct application of robust, time-step-independent stochastic integrators to QMD.

Understanding the behaviour of carnosine in aqueous solution: an experimental and quantum-based computational investigation on acid–base properties and complexation mechanisms with Ca2+and Mg2+

Thermodynamic parameters together with unprecedented quantum-based molecular dynamics simulations contribute to the macroscopic and microscopic understanding of the mechanisms of action of carnosine in aqueous solution.

A Quantum-Based Approach to Predict Primary Radiation Damage in Polymeric Networks.

Initial atomistic-level radiation damage in chemically reactive materials is thought to induce reaction cascades that can result in undesirable degradation of macroscale properties. Ensembles of quantum-based molecular dynamics (QMD) simulations can accurately predict these cascades, but extracting chemical insights from the many underlying trajectories is a labor-intensive process that can require substantial a priori intuition. We develop here a general and automated graph-based approach to extract all chemically distinct structures sampled in QMD simulations and apply our approach to predict primary radiation damage of polydimethylsiloxane (PDMS), the main constituent of silicones. A postprocessing protocol is developed to identify underlying polymer backbone structures as connected components in QMD trajectories. These backbones form a repository of radiation-damaged structures. A scheme for extracting and updating a library of isomorphically distinct structures is proposed to identify the spanning set and aid chemical interpretation of the repository. The analyses are applied to ensembles of cascade QMD simulations in which the four element types in PDMS are selectively excited in primary knock-on atom events. Our approach reveals a much higher degree of combinatorial complexity in this system than was inferred through radiolysis experiments. Probabilities are extracted for radiation-induced network changes including formation of branch points, carbon linkages, cycles, bond scissions, and carbon uptake into the Si-O siloxane backbone network. The general analysis framework presented here is readily extendable to modeling chemical degradation of other polymers and molecular materials and provides a basis for future quantum-informed multiscale modeling of radiation damage.

Initial Decomposition of Condensed-Phase 1,3,5-Triamino-2,4,6-trinitrobenzene under High Temperature

ABSTRACT We have performed quantum-based molecular dynamics (MD) simulations to investigate the initial chemical processes of the TATB under different temperatures. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed.The results show that a large number of clusters (such as C12H12O8N10, C12H12O12N12, C12H12O6N9, C18H18O16N17) formed in the initial reaction process, which indicates that the initial heating mainly results in the binding of TATB adjacent molecules rather than their decomposition. Moreover, the stability sequence of bonds is C-C > N-H > C-NH2 > C-NO2 in our research, C-NO2 is the main reaction path at 1500 K, and C-NO2 and C-NH2 are the main reaction path at 2000 K. When temperature increase to 2500 K and 3000 K, the homolytic cleavage of the N-NO2 and C-NH2 bonds is suppressed, and the C-H bond dissociation becomes the primary pathway for TATB decomposition in its early stages.

Graphics Processing Unit-Accelerated Semiempirical Born Oppenheimer Molecular Dynamics Using PyTorch.

A new open-source high-performance implementation of Born Oppenheimer molecular dynamics based on semiempirical quantum mechanics models using PyTorch called PYSEQM is presented. PYSEQM was designed to provide researchers in computational chemistry with an open-source, efficient, scalable, and stable quantum-based molecular dynamics engine. In particular, PYSEQM enables computation on modern graphics processing unit hardware and, through the use of automatic differentiation, supplies interfaces for model parameterization with machine learning techniques to perform multiobjective training and prediction. The implemented semiempirical quantum mechanical methods (MNDO, AM1, and PM3) are described. Additional algorithms include a recursive Fermi-operator expansion scheme (SP2) and extended Lagrangian Born Oppenheimer molecular dynamics allowing for rapid simulations. Finally, benchmark testing on the nanostar dendrimer and a series of polyethylene molecules provides a baseline of code efficiency, time cost, and scaling and stability of energy conservation, verifying that PYSEQM provides fast and accurate computations.

High Explosive Ignition through Chemically Activated Nanoscale Shear Bands.

Shock initiation and detonation of high explosives is considered to be controlled through hot spots, which are local regions of elevated temperature that accelerate chemical reactions. Using classical molecular dynamics, we predict the formation of nanoscale shear bands through plastic failure in shocked 1,3,5-triamino-2,4,6-trinitrobenzene high explosive crystal. By scale bridging with quantum-based molecular dynamics, we show that shear bands exhibit lower reaction barriers. While shear bands quickly cool, they remain chemically activated and support increased reaction rates without the local heating typically evoked by the hot spot paradigm. We describe this phenomenon as chemical activation through shear banding.

A quantum-based molecular dynamics study of the ICM-102/HNO3 host–guest reaction at high temperatures

The contradiction between energy and safety of explosives is better balanced by the host-guest inclusion strategy. Understanding the reaction mechanism of the host-guest explosive is necessary. To deeply analyze the role of the small guest molecules in the host-guest system, a quantum-based molecular dynamics method was used to calculate the initial decomposition reaction of the new host-guest explosive ICM-102/HNO3 against the pure ICM-102 at several high temperatures. The incorporation of HNO3 had no significant influence on the initial decomposition step of ICM-102. Conversely, the earliest intramolecular hydrogen transfer reaction is delayed partly because the H and O atoms of HNO3 connect with the O and H atoms of ICM-102, respectively. As the reaction proceeds, guest molecules get heavily involved in the reaction and increase the reaction rate. The generation rate and quantity of the small oxidizing molecules in the final product were increased significantly in the ICM-102/HNO3 system. These mechanisms revealed that HNO3 molecules inhibit the early stages of the initial decomposition of ICM-102 to some extent, and play an important role in accelerating the decomposition subsequently.

Ranking the Drop-Weight Impact Sensitivity of Common Explosives Using Arrhenius Chemical Rates Computed from Quantum Molecular Dynamics Simulations.

Drop-weight impact tests are used routinely to characterize the handling safety of explosives. Numerous studies have sought to connect various physical and chemical properties of the energetic molecules and materials to their measured impact sensitivities. Wenograd in the early 1960s demonstrated that there is a strong dependency of the drop-heights on the critical temperatures required for explosives to undergo prompt reactions. Reactive quantum molecular dynamics simulations with the lanl31 density functional tight binding model have been used to compute the delay time before the thermal explosion of the secondary explosives erythritol tetranitrate (ETN), pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), cyclotetramethylene tetranitramine (HMX), trinitrotolune (TNT), and 3,3'-diamino-4,4'-azoxyfurazan (DAAF) as a function of the initial temperature and pressure. The delay time to explosion data are consistent with Arrhenius chemical kinetics, which is expected for thermally activated processes in materials and in accord with experimental measurements. The critical temperatures required for the materials to undergo prompt explosions display the same dependence on drop height as was observed by Wenograd. Hence, quantum-based reactive molecular dynamics simulations are potentially a tool for ranking the drop-weight impact sensitivity and handling safety of explosives.

Parallel replica dynamics simulations of reactions in shock compressed liquid benzene.

The study of the long-term evolution of slow chemical reactions is challenging because quantum-based reactive molecular dynamics simulation times are typically limited to hundreds of picoseconds. Here, the extended Lagrangian Born-Oppenheimer molecular dynamics formalism is used in conjunction with parallel replica dynamics to obtain an accurate tool to describe the long-term chemical dynamics of shock-compressed benzene. Langevin dynamics has been employed at different temperatures to calculate the first reaction times in liquid benzene at pressures and temperatures consistent with its unreacted Hugoniot. Our coupled engine runs for times on the order of nanoseconds (one to two orders of magnitude longer than traditional techniques) and is capable of detecting reactions that are characterized by rates significantly slower than we could study before. At lower pressures and temperatures, we mainly observe Diels-Alder metastable reactions, whereas at higher pressures and temperatures we observe stable polymerization reactions.

Chemical Degradation Pathways in Siloxane Polymers Following Phenyl Excitations.

We use ensembles of quantum-based molecular dynamics simulations to predict the chemical reactions that follow radiation-induced excitations of phenyl groups in a model copolymer of polydimethylsiloxane and polydiphenylsiloxane. Our simulations span a wide range of highly porous and condensed phase densities and include both wet and dry conditions. We observe that in the absence of water, excited phenyl groups tend to abstract hydrogen from other methyl or phenyl side groups to produce benzene, with the under-hydrogenated group initiating subsequent intrachain cyclization reactions. These systems also yield minor products of diphenyl moieties formed by the complete abstraction of both phenyl groups from a single polydiphenylsiloxane subunit. In contrast, we find that the presence of water promotes the formation of free benzene and silanol side groups, reduces the likelihood for intrachain cyclization reactions, and completely suppresses the formation of diphenyl species. In addition, we predict that water plays a critical role in chain scission reactions, which indicates a possible synergistic effect between environmental moisture and radiation that could promote alterations of a larger polymer network. These results could have impact in interpreting accelerated aging experiments, where polymer decomposition reactions and network rearrangements are thought to have a significant effect on the ensuing mechanical properties.

Theoretical study for anisotropic responses of the condensed-phase RDX under shock loadings

We have performed quantum-based molecular dynamics (MD) simulations in conjunction with multiscale shock technique (MSST) to investigate the initial chemical processes and the anisotropy of shock sensitivity of the RDX under shock loading applied along the different directions. The results show that there is a difference between x (or y)-direction and z-direction in the response to a shock wave velocity of 12 km/s. It was shown that detonation temperature and pressure in the z-direction lags behind that of x-direction (or y-direction). Moreover, from the time evolution of the population of various key fragments, we also observe that along with z-direction significantly later than that of x (or y)-direction, which the reaction rate is also slower. Thus, we draw a conclusion that sensitive for shock propagation along x or y-direction, but less sensitive for shock propagation along z-direction.

Next generation extended Lagrangian first principles molecular dynamics.

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Initial Decomposition of Condensed-Phase 1,3,5-Triamino-2,4,6-trinitrobenzene under Shock Loading

We study the intrinsic shock decomposition mechanism of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) via quantum-based multiscale molecular dynamics methods. Some distinctive and novel insights are obtained based on our simulation results. The reaction is always initiated by hydrogen transfer both in intra- and intermolecular conditions. The carbon atom is mostly oxidized by nitro O directly. The earliest gas product NO2 is produced with the cleavage of C-NO2. The initial N2 mainly derives from the interaction between NO and TATB molecular residues. More intriguingly, we detect 28 kinds of heterocyclic structures involved in the TATB decomposition process. Most of the newly formed C–N heterocycles possess high stability, which obviously inhibit the further reaction toward releasing C oxides and N2. These results reveal not only the early shock decomposition properties of TATB but also the different reaction mechanisms between sensitive and insensitive explosives.

Task-based Parallel Computation of the Density Matrix in Quantum-based Molecular Dynamics using Graph Partitioning

Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms. These constraints arise due to expensive self-consistent ground-state electronic structure calculations that can often scale cubically with the number of atoms. Linearly scaling methods depend on computing the density matrix P from the Hamiltonian matrix H by exploiting the sparsity in both matrices. The second-order spectral projection (SP2) algorithm is an O(N) algorithm that computes P with a sequence of 40-50 matrix-matrix multiplications. In this paper, we present task-based implementations of a recently developed data-parallel graph-based approach to the SP2 algorithm, G-SP2. We represent the density matrix P as an undirected graph and use graph partitioning techniques to divide the computation into smaller independent tasks. The partitions thus obtained are generally not of equal size and give rise to undesirable load imbalances in standard MPI-based implementations. This load-balancing challenge can be mitigated by dynamically scheduling parallel computations at runtime using task-based programming models. We develop task-based implementations of the data-parallel G-SP2 algorithm using both Intel's Concurrent Collections (CnC) as well as the Charm++ programming model and evaluate these implementations for future use. Scaling and performance results of our implementations are investigated for representative segments of QMD simulations for solvated protein systems containing more than 10,000 atoms.