Quantum Molecular Dynamics Method Research Articles

A model of ionization-induced reactions in CH4/N2 clusters in Titan's atmosphere: theoretical insights into mono- and divalent states

Abstract We propose a model for ionization-induced reactions between N2 and CH4, the main components of Titan's atmosphere, and examine their mechanism using quantum mechanical and molecular dynamics methods. Bimolecular CH4–N2 clusters form through collision, and their conformation depends on the encounter cross section due to weak intermolecular interaction. These clusters acquire a driving force through vertical ionization because the vertically ionized structure is not situated at the minimum of the potential energy surface in the ionized state. This leads to multiple reactions, overcoming energy barriers in the process. In the divalent state, a robust attractive interaction occurs between CH4 and N2 through charge transfer. Subsequently, the H4C–N2 covalent bond forms prior to reactions, resulting in the production of N2H+, CH3+, CH3N2+, and CH2N2+; otherwise only N2H+, CH3+, and CH2+ are generated. In contrast, when ionized to a monovalent state, although dissociation of N2H+ and isomerization to CH3NHN+ and CH3NNH+ occurs, a significant portion dissociates into CH4+ and N2 without undergoing further reactions. Additionally, the generation of N2H+ and CH3+ is limited in the monovalent state, primarily due to a lower driving force and the absence of Coulombic explosion. Our computational results highlight the pivotal role of divalent reactions within Titan's atmosphere, which are more efficient than monovalent reactions.

Dynamic Effects on the Ionization-Induced Reactions of Methyl Halides: Quantum Mechanical and Molecular Dynamics Studies.

The mechanisms of the ionization-induced fragmentation and H migration of methyl halides CH3X (X = F, Cl, Br) have been examined by quantum mechanical and molecular dynamics methods. When CH3X (X = F, Cl, Br) is vertically ionized into a divalent cation, it can obtain enough excess energy to overcome the energy barrier of subsequent reaction channels for the formation of H+, H2+, and H3+ species and intramolecular H migration. The product distributions of these species greatly depend on the halogen atoms. The H+ formation decreases in the order of F > Cl > Br, which is inversely proportional to the increase in the magnitude of the energy barrier in the order of Br > Cl > F. This is attributable to the change in the charge distribution of the entire molecule by the halogen atoms. Meanwhile, the small H migration ratio for Cl and Br, despite their low energy barriers, was explained by the small sum of states at the transition state based on the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The H3+ formation ratio is unexpectedly smaller despite its low energy barrier. This is attributed to the dynamic effects of the H2 roaming that always occur prior to the reaction in question. Molecular dynamics simulations showed that the H2 roaming was restricted in a certain area due to an initially produced driving force on the hydrogen atoms in a certain direction by vertical ionization; this phenomenon suppresses the formation of H3+, which requires the hydrogen atoms to be in motion over a relatively wide range to enter the transition state region. Thus, the low proportion of the observed H3+ can be explained by the dynamical probability of the transition state structure formation.

Machine learning nonequilibrium electron forces for spin dynamics of itinerant magnets

We present a generalized potential theory for conservative as well as nonconservative forces for the Landau-Lifshitz magnetization dynamics. Importantly, this formulation makes possible an elegant generalization of the Behler-Parrinello machine learning (ML) approach, which is a cornerstone of ML-based quantum molecular dynamics methods, to the modeling of force fields in adiabatic spin dynamics of out-of-equilibrium itinerant magnetic systems. We demonstrate our approach by developing a deep-learning neural network that successfully learns the electron-mediated exchange fields in a driven s-d model computed from the nonequilibrium Green’s function method. We show that dynamical simulations with forces predicted from the neural network accurately reproduce the voltage-driven domain-wall propagation. Our work also lays the foundation for ML modeling of spin transfer torques and opens a avenue for ML-based multi-scale modeling of nonequilibrium dynamical phenomena in itinerant magnets and spintronics.

Real-time hydrogen molecular dynamics satisfying the nuclear spin statistics of a quantum rotor

Apparent presence of the nuclear-spin species of a hydrogen molecule, para-hydrogen and ortho-hydrogen, associated with the quantum rotation is a manifestation of the nuclear quantum nature of hydrogen, governing not only molecular structures but also physical and chemical properties of hydrogen molecules. It has been a great challenge to observe and calculate real-time dynamics of such molecularized fermions. Here, we developed the non-empirical quantum molecular dynamics method that enables real-time molecular dynamics simulations of hydrogen molecules satisfying the nuclear spin statistics of the quantum rotor. While reproducing the species-dependent quantum rotational energy, population ratio, specific heat, and H-H bond length and frequency, we found that their translational, orientational and vibrational dynamics becomes accelerated with the higher rotational excitation, concluding that the nuclear quantum rotation stemmed from the nuclear spin statistics can induce various kinds of dynamics and reactions intrinsic to each hydrogen species.

(Invited) Simulating Dynamic Excitons Via Quantum Molecular Dynamics: A Case Study in Lead Halide Perovskites

The ultrafast electronic and structural dynamics invoked by photoexcitation, i.e., “dynamic exciton” phenomena, not only are important in the context of practical applications such as solar cells, but also raise many questions from the viewpoint of fundamental science. Experimental measurement, computational simulations, and theoretical interpretation will be the three pillars for deciphering the dynamic exciton phenomena.From the viewpoint of computational simulations, molecular dynamics (MD) techniques combined with quantum chemical calculations, i.e., quantum molecular dynamics (QMD), has been the popular tool to simulate the dynamic exciton phenomena. The quantum chemical calculations, which are typically conducted on the basis of the density-functional theory (DFT), require the large computational resources and time. These have been the limiting factors for the accessible spatial and time scales by the QMD simulations.To extend the coverage of simulations to more complex, large-scale systems, we have developed efficient excited-state QMD methods that can include nonadiabatic effects. Our method combines the density-functional tight binding (DFTB) method, which is an approximate DFT, and the surface hopping method, which is a theoretical framework to incorporate the nonadiabatic effects into the QMD simulations. The method was further improved to be suitable for condensed-phase simulations explicitly including the environment, i.e., solvent, by using a “divide-and-conquer” style quantum chemical calculation technique. These theoretical framework enables us to simulate the coupled electronic–structural dynamics in excited states of systems consisting of 102–103 atoms[1,2,3].In addition, using the developed method, we conducted the real-time simulations of the ultrafast processes invoked by photoexcitation of lead iodide perovskites, which are known as the key materials for perovskite solar cells. The dissociation of the exciton into the positive and negative charge carriers was observed. Moreover, the hot carrier cooling, where the charge carriers dissipate excess energy via the electron–phonon coupling and relax to the band edges, was also tracked. Finally, the direct evidence of the polaron formation, where the structural deformation is induced by the presence of charge carriers, was observed. These results highlight the importance of the coupling between electronic and structural degrees of freedom.In the talk, recent improvements in the methodology and future perspectives will also be presented[5].

Flow-Induced Autonomic Ordering of Hydrogen Molecules under a Non-Equilibrium Flow.

A non-equilibrium molecular flow through a carbon nanotube (CNT) serves as a key system for revealing molecular transport and establishing nanofluidics. It has been challenging to simulate a non-equilibrium flow of hydrogen molecules exhibiting strong nuclear quantumness. Taking advantage of the quantum molecular dynamics method that can calculate real-time trajectories of hydrogen molecules even under a non-equilibrium flow, we found that the non-equilibrium flow makes hydrogen molecules more condensed and accelerates their adsorption near a CNT surface, letting the molecules flow more smoothly by propagating velocity momenta more efficiently along the CNT axis and by suppressing transverse molecular dynamics on the CNT cross section. Such flow-induced autonomic ordering indicates the importance of monitoring and investigating dynamics and adsorption of hydrogen molecules under a non-equilibrium circumstance as well as in a quiet equilibrium state, opening a new strategy for efficient hydrogen liquefaction and storage.

A Boron-Containing Compound Acting on Multiple Targets Against Alzheimer's Disease. Insights from Ab Initio and Molecular Dynamics Simulations.

Given the multifactorial nature and pathogenesis of Alzheimer's disease, therapeutic strategies are addressed to combine the benefits of every single-target drug into a sole molecule. Quantum mechanics and molecular dynamics (MD) methods were employed here to investigate the multitarget action of a boron-containing compound against Alzheimer's disease. The antioxidant activity as a radical scavenger and metal chelator was explored by means of density functional theory. The most plausible radical scavenger mechanisms, which are hydrogen transfer, radical adduct formation, and single-electron transfer in aqueous and lipid environments, were fully examined. Metal chelation ability was investigated by considering the complexation of Cu(II) ion, one of the metals that in excess can even catalyze the β-amyloid (Aβ) aggregation. The most probable complexes in the physiological environment were identified by considering both the stabilization energy and the shift of the λmax induced by the complexation. The excellent capability to counteract Aβ aggregation was explored by performing MD simulations on protein-ligand adducts, and the activity was compared with that of curcumin, chosen as a reference.

Optical and physical properties of hydrocarbons with metal impurities in the warm dense matter regime

The hydrocarbon (CH) polymer is often chosen as the converter material with potential applications to Z-pinch driven dynamic hohlraum implosion experiments. Its physical and optical properties in the warm dense matter regime are important for dynamic hohlraum platform designs. Using the quantum molecular dynamics (QMD) method, we have obtained the equation of state, absorption coefficient, and reflectivity of hydrocarbon and Al–CH mixtures with the temperature and density ranging from 104–106 K and 0.1–0.9 g/cm3, respectively. The QMD-predicted principal Hugoniot data are compared with experiments as well as the theoretical calculations, and both show good agreement. The optical reflectivity from the corresponding dielectric functions is calculated using the corrected refraction index of the ambient (n0 = 1.59). Besides, we have further analyzed the atomic structure and bond dissociation process of polystyrene and Al–CH mixture systems using a bond tracking method with the temperature ranging from 1000 K to 10 000 K. The Al impurities have a slightly promoting effect on the initial stage of polystyrene pyrolysis. The calculation results can be helpful for future theoretical and experimental studies in high energy density physics research.

Mobility of small molecules in membrane materials based on copolyimide P84

Dynamics of small molecules in copolyimide P84, which is an important membrane material for separation and purification technologies, have been analyzed using quantum chemistry and molecular dynamics methods. The most significant factors determining the membrane properties and the molecular motion of gases and liquids in the P84 membranes are both the size and dipole moment of these molecules as well as the charge state of sorption centers in the polymer.

Capturing the nuclear quantum effects in molecular dynamics for lattice thermal conductivity calculations: Using ice as example.

Molecular dynamics (MD) is a powerful (and the most viable) tool to compute the thermal conductivities of solid disordered materials. However, conventional classical MD fails to describe the nuclear quantum effects (NQEs), so it may give inaccurate results for light materials at low temperatures. While the importance of NQE has been widely acknowledged, yet we do not have a fully reliable method to account for NQE in the MD thermal conductivity calculations. In this work, we will investigate and analyze the performances of a number of path-integral-based quantum MD methods, using ordered ice as a test case. To establish the validity of these methods, we will compare the MD results with the lattice dynamics results, in both classical and quantum limits. Through such a comparison, we will show that methods such as ring polymer MD stand as a good approach for a complex solid with short phonon lifetimes but could be problematic when describing long-living acoustic phonons. In addition, we will show that the rigid water model, which is the state-of-the-art model in the studies of ice/water systems, fails to capture most of the NQEs in ice thermal conductivity. Neglecting librational and translational NQEs leads to essential errors, which clearly demonstrates the importance of a true quantum simulation method that treats all modes at a consistent quantum level.

Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions.

We describe the development of a reactive force field for C/O systems under extreme temperatures and pressures, based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model, which targets carbon condensation under thermodynamic conditions of 6500 K and 2.5 g cm-3, affords a balance between model accuracy, complexity, and training set generation expense. We show that the model recovers much of the accuracy of density functional theory for the prediction of structure, dynamics, and chemistry when applied to dissociative condensed phase systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 104 increase in efficiency for the same system size (i.e., 128 atoms) and a linear system size scalability over standard quantum molecular dynamics methods, allowing the simulation of significantly larger systems than previously possible. We find that the model captures the condensed-phase reaction-coupled formation of carbon clusters implied by recent experiments, and that this process is susceptible to strong finite size effects. Overall, we find the present ChIMES model to be well suited for studying chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a broader high pressure-high temperature force-field for condensed phase chemistry in organic materials.

Polymerization Effects on the Decomposition of a Pyrazolo-Triazine at high Temperatures and Pressures.

4‐amino‐3‐aminopyrazole‐8‐trinitropyrazolo‐[5, 1‐c] [1, 2, 4]triazine (PTX, C5H2N8O6) has good detonation performance, thermal stability and low mechanical sensitivity, which endow it with good development prospects in insensitive ammunition applications. To study the effects of polymerization on the decomposition of PTX, the reaction processes of PTX at different conditions were simulated by quantum chemistry and molecular dynamics methods. In this paper, the effects of polymerization on the decomposition of PTX were studied in terms of species information, reaction path of PTX, bond formation and bond cleavage, evolution of small molecules and clusters, and kinetic parameters at different stages. The results show that under the high‐temperature and high‐pressure conditions, the initial reaction path of unimolecular PTX in the thermal decomposition is mainly the cleavage of C−NO2 bonds. At the same time, there are many polymerization reactions in thermal decomposition process, which may greatly affect the reaction rate and path. The higher the degree of polymerization, the larger equilibrium value of potential energy, the less energy release of thermal decomposition. Compared with the activation energy of other explosives, the activation energy of PTX is higher than that of β‐HMX and lower than that of TNT.

Why Purine Nucleoside Phosphorylase Ribosylates 2,6-Diamino-8-azapurine in Noncanonical Positions? A Molecular Modeling Study.

Protein nucleoside phosphorylase (PNP) is an enzyme that catalyzes a reversible conversion process (ribosylation and phosphorolysis) between nucleobases (purines) and their nucleosides. Experimental studies showed that calf PNP ribosylates purine analogues in specific positions: 2,6-diamino-8-azapurine in position 7 or 8 and 8-azaguanine in position 9 of the triazole ring. The reason for this phenomenon can be a result of different expositions of purine substrates to the channel leading to the binding site. This hypothesis was verified by the application of molecular modeling techniques to two complexes of purine analogues 2,6-diamino-azapurine, calf PNP (pdb-code: 1LVU), and 8-azaguanine, calf PNP (pdb-code: 2AI1). The results obtained with a combination of quantum chemistry, docking, and molecular dynamics methods showed qualitative validity of our hypothesis. Binding free energies of protein-ligand systems showed that most probable binding poses expose N8 nitrogen for 2,6-diamino-8-azapurine and N9 nitrogen for 8-azaguanine into the binding channel and ruled out the exposition of N9 for 2,6-diamino-8-azapurine and N7 for 8-azaguanine, partially in agreement with the experimental data. The other important result obtained in this study is a significantly higher population of the protonated form of crucial residue Glu-201 present in the binding pocket, compared to the standard protonation of free glutamic acid in solution. This result combined with populations of tautomeric forms of both investigated systems strongly suggests that 2,6-diamino-8-azapurine and 8-azaguanine are recognized by proteins with deprotonated and protonated Glu-201 residues, respectively. A comparison of computed binding poses of the investigated ligands to the inhibitors present in crystal structures suggests that the modification of the (S)-PMPDAP inhibitor, in which a 2-(phosphonomethoxy)propyl chain is attached at position 8 instead of position 9, might increase its binding affinity.

Metastable Conducting Crystalline Hydrogen at High Pressure

The quantum molecular dynamics method within the density functional theory has been used to calculate the equation of state, pair correlation function, and static electrical conductivity of solid hydrogen in the region of formation of a conducting phase. Hysteresis has been revealed on the density dependence of the pressure at a temperature of 100 K under compression and subsequent tension. The overlapping of branches of the isotherms of the molecular and nonmolecular phases of solid hydrogen corresponds to the region of existence of metastable states. The width of this region is 275 GPa. It has been shown that conducting crystalline nonmolecular hydrogen with P21/c symmetry can exist at extension to a pressure of 350 GPa.

Accurate quantum molecular dynamics for multidimensional systems by the basis expansion leaping multi-configuration Gaussian (BEL MCG) method.

Quantum phenomena are quite often of critical importance in chemical reactions. Thus the development of quantum molecular dynamics approaches is required to study the role of quantum effects such as tunnelling in chemical processes. The basis expansion leaping multi-configuration Gaussian (BEL MCG) method has been developed to obtain time-propagated wave packets describing reactive molecular systems. Here we examine the applicability of BEL MCG to double well problems in several dimensions. We pay particular attention to what is required to yield highly accurate dynamics with respect to several key features of the BEL MCG propagation. The importance of using basis functions of a width appropriate to the nature of the potential energy surface in the region of configuration space where each basis function is located is highlighted, which has implications for virtually all quantum molecular dynamics methods utilising Gaussian basis functions.

Titanium-hydrogen interaction at high pressure

The process of transport of metal particles (ejecta) in gases is the subject of recent works in the field of nuclear energetics. We studied the process of dissolution of titanium ejecta in warm dense hydrogen at hundred GPa pressure. Thermodynamic and kinetic properties of the process were investigated using classical and quantum molecular dynamics methods. We estimated the dissolution time of ejecta, the saturation limit of titanium atoms with hydrogen, and the heat of dissolution. It was found that particles with a radius of 1 μm dissolve in hydrogen in a time of 1.5×10−2 μs, while the process of mixing can be described by diffusion law. The presented approach demonstrates the final state of the titanium-hydrogen system as a homogenized fluid with completely dissolved titanium particles. This result can be generalized to all external conditions under which titanium and hydrogen are atomic fluids.

Theoretical Study of Oil Desulfuration by Ammonium-Based Deep Eutectic Solvents

A theoretical study using quantum chemistry and molecular dynamics methods is reported on the properties of deep eutectic solvent prepared by tetrabutylammonium bromide and formic acid regarding oil desulfurization. The objective of the work is to obtain molecular level insights into the mechanisms of extractive desulfuration by deep eutectic solvents for designing suitable processes for deep desulfuration purposes. The intermolecular interactions of solvent molecules and relevant organosulfur compounds (thiophene, benzothiophene, and dibenzothiophene) are analyzed together with the liquid structure of solvent + sulfur compounds as a function of organosulfur content. Interfacial properties between the solvent and model oil (n-octane) with different contents of organosulfur compounds are also studied to analyze the molecular level mechanism of liquid–liquid equilibria. Likewise, free energies of solvation in the solvent and in n-octane are calculated to justify the partition of organosulfur compounds betwe...

Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer.

We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

Ab Initio Nonadiabatic Quantum Molecular Dynamics.

The Born-Oppenheimer approximation underlies much of chemical simulation and provides the framework defining the potential energy surfaces that are used for much of our pictorial understanding of chemical phenomena. However, this approximation breaks down when the dynamics of molecules in excited electronic states are considered. Describing dynamics when the Born-Oppenheimer approximation breaks down requires a quantum mechanical description of the nuclei. Chemical reaction dynamics on excited electronic states is critical for many applications in renewable energy, chemical synthesis, and bioimaging. Furthermore, it is necessary in order to connect with many ultrafast pump-probe spectroscopic experiments. In this review, we provide an overview of methods that can describe nonadiabatic dynamics, with emphasis on those that are able to simultaneously address the quantum mechanics of both electrons and nuclei. Such ab initio quantum molecular dynamics methods solve the electronic Schrödinger equation alongside the nuclear dynamics and thereby avoid the need for precalculation of potential energy surfaces and nonadiabatic coupling matrix elements. Two main families of methods are commonly employed to simulate nonadiabatic dynamics in molecules: full quantum dynamics, such as the multiconfigurational time-dependent Hartree method, and classical trajectory-based approaches, such as trajectory surface hopping. In this review, we describe a third class of methods that is intermediate between the two: Gaussian basis set expansions built around trajectories.

Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair.

The fluorescent non-natural 4-aminophthalimide (4AP) base, when paired to the complementary 2,4-diaminopyrimidine (DAP) nucleobase, is accommodated in a B-DNA duplex being efficiently recognized and incorporated by DNA polymerases. To complement the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM calculations were initially focused on the geometry and energetics of the 4AP:DAP non-natural pair and of H-bonded base pairs between 4AP and all the natural bases in their classical Watson-Crick geometries. The QM calculations indicate that the 4AP:DAP pair, despite the fact that it can form 3 H-bonds in a classic Watson-Crick geometry, has a stability comparable to the A:T pair. Then, we extended the study to reverse Watson-Crick geometries, characteristic of parallel strands. MD simulations were carried out on two 13-mer DNA duplexes, featuring a central 4AP:DAP or A:T pair, respectively. No major structural deformation of the duplex was observed during the MD simulation. Snapshots from the MD simulations were subjected to QM calculations to investigate the 4AP:DAP interaction energy when embedded into a duplex structure, and to investigate the impact of the two non-natural bases on the stacking interactions with adjacent bases in the DNA duplex. We found a slight increase in stacking interactions involving the 4AP:DAP pair, counterbalanced by a moderate decrease in H-bonding interactions of the 4AP:DAP and of the adjacent base pairs in the duplex. The results of our study are in agreement with experimental data and complement them by providing an insight into which factors contribute positively and which factors contribute negatively to the structural compatibility of the fluorescent 4AP:DAP pair with a B-DNA structure.