Density Functional Tight-binding Molecular Dynamics Research Articles

Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations.

The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.

Density-functional tight-binding molecular dynamics study on fixation reaction of CO2 to styrene oxide catalyzed by Mg-MOF-74 metal-organic framework

Abstract Carbon capture and utilization is a strategy to reduce CO2 emissions by utilizing them to synthesize fine chemicals. Mg-MOF-74 exhibits exceptional CO2 adsorption capacity and functions as a catalyst in styrene carbonate synthesis from CO2 and styrene oxide. We examined the structural properties and energetics of styrene carbonate synthesis in Mg-MOF-74 at the third-order density-functional tight-binding level. A novel reaction mechanism via the formation of a seven-membered ring intermediate was found to exhibit a lower Gibbs activation energy than the previously proposed mechanism.

Towards hybrid quantum mechanical/molecular mechanical simulations of Li and Na intercalation in graphite - force field development and DFTB parametrisation.

In this work a previously established QM/MM simulation protocol for the treatment of solid-state interfaces was extended towards the treatment of layered bulk materials enabling for instance investigation of metal intercalation in graphitic carbon materials. In order to study the intercalation of Li in graphite, new density functional tight binding (DFTB) parameters for Li have been created. Molecular dynamics (MD) simulations at constant temperatures (273.15, 298.15 and 323.15 K) have been carried out to assess the performance of the presented DFTB MD simulation approach. The intercalation of variable lithium and sodium content was investigated via z-distribution functions and analysis of the diffusivity in the direction parallel to the graphene plane. Both the calculated diffusion coefficients and the activation energy in case of lithium are in good agreement with experimental data. The comparison of the QM/MM MD simulation results provide detailed insights into the structural and dynamical properties of intercalated metal ions.

Copper Site Motion Promotes Catalytic NOx Reduction under Zeolite Confinement.

Ammonia-mediated selective catalytic reduction (NH3-SCR) is currently the key approach to abate nitrogen oxides (NOx) emitted from heavy-duty lean-burn vehicles. The state-of-art NH3-SCR catalysts, namely, copper ion-exchanged chabazite (Cu-CHA) zeolites, perform rather poorly at low temperatures (below 200 °C) and are thus incapable of eliminating effectively NOx emissions under cold-start conditions. Here, we demonstrate a significant promotion of low-temperature NOx reduction by reinforcing the dynamic motion of zeolite-confined Cu sites during NH3-SCR. Combining complex impedance-based in situ spectroscopy (IS) and extended density-functional tight-binding molecular dynamics simulation, we revealed an environment- and temperature-dependent nature of the dynamic Cu motion within the zeolite lattice. Further coupling in situ IS with infrared spectroscopy allows us to unravel the critical role of monovalent Cu in the overall Cu mobility at a molecular level. Based on these mechanistic understandings, we elicit a boost of NOx reduction below 200 °C by reinforcing the dynamic Cu motion in various Cu-zeolites (Cu-CHA, Cu-ZSM-5, Cu-Beta, etc.) via facile postsynthesis treatments, either in a reductive mixture at low temperatures (below 250 °C) or in a nonoxidative atmosphere at high temperatures (above 450 °C).

Hydrogenation of Hexa-peri-hexabenzocoronene: An Entry to Nanographanes and Nanodiamonds.

The fabrication of atomically precise nanographanes is a largely unexplored frontier in carbon-sp3 nanomaterials, enabling potential applications in phononics, photonics and electronics. One strategy is the hydrogenation of prototypical nanographene monolayers and multilayers under vacuum conditions. Here, we study the interaction of atomic hydrogen, generated by a hydrogen source and hydrogen plasma, with hexa-peri-hexabenzocoronene on gold using integrated time-of-flight mass spectrometry, scanning tunneling microscopy and Raman spectroscopy. Density functional tight-binding molecular dynamics is employed to rationalize the conversion to sp3 carbon atoms. The resulting hydrogenation of hexa-peri-hexabenzocoronene molecules is demonstrated computationally and experimentally, and the potential for atomically precise hexa-peri-hexabenzocoronene-derived nanodiamond fabrication is proposed.

Achieving Boron-Carbon-Nitrogen Heterostructures by Collision Fusion of Carbon Nanotubes and Boron Nitride Nanotubes.

Heterostructures may exhibit completely new physical properties that may be otherwise absent in their individual component materials. However, how to precisely grow or assemble desired complex heterostructures is still a significant challenge. In this work, the collision dynamics of a carbon nanotube and a boron nitride nanotube under different collision modes were investigated using the self-consistent-charge density-functional tight-binding molecular dynamics method. The energetic stability and electronic structures of the heterostructure after collision were calculated using the first-principles calculations. Five main collision outcomes are observed, that is, two nanotubes can (1) bounce back, (2) connect, (3) fuse into a defect-free BCN heteronanotube with a larger diameter, (4) form a heteronanoribbon of graphene and hexagonal boron nitride and (5) create serious damage after collision. It was found that both the BCN single-wall nanotube and the heteronanoribbon created by collision are the direct band-gap semiconductors with the band gaps of 0.808 eV and 0.544 eV, respectively. These results indicate that collision fusion is a viable method to create various complex heterostructures with new physical properties.

Role of Graphitic Bowls in Temperature Dependent Fullerene Formation.

Fullerenes are used extensively in organic electronics as electron acceptors among other uses; however, there are still several key mysteries regarding their formation such as the importance of graphitic intermediates and the thermokinetics of initial cage formation. To this end, we have conducted density functional tight binding molecular dynamics (DFTB-MD) calculations on disintegrated Ih-C60 to investigate the formation mechanisms of fullerenes at high temperature conditions. From the results of these DFTB-MD calculations we were able to develop a thermokinetic model to describe the free energies and kinetics of fullerene formation at a range of temperatures. Direct observation of the mechanism revealed fullerenes readily forming in nanosecond times between 2000 and 3000 K but were hindered above this temperature window. Analysis revealed temperature dependent formation mechanisms where at low temperatures (<2750K) flat graphitic bowls play an important part as metastable intermediates while highly curved bowls follow a direct fast transformation. Meanwhile at higher temperatures (>2750 K), flat bowls become the transitory structure between chains and fullerene. Free energy analysis from our thermokinetic model shows this change in graphitic bowls to being transitory hinders fullerene formation at high temperatures compared to lower temperatures, essentially kinetically trapping C60 as chain networks. This investigation gives new key insights into the formation mechanisms of C60 fullerenes and highlights important intermediates while also illuminating the temperature window for fullerene formation, facilitating better optimization of experimental methods.

Thermal decomposition mechanisms of energetic CL-20-based co-crystals: quantum molecular dynamics simulations.

The decomposition mechanisms of energetic CL-20:2,4-dinitro-2,4-diazapentane (DNP) and CL-20:2,4-dinitro-2,4-diazaheptane (DNG) co-crystals at high temperatures (1000, 2000, and 3000K) were studied by density functional tight-binding molecular dynamics (DFTB-MD) simulations. At different temperatures, their decomposition mechanisms are very different. At 1000K, conformational changes are observed only for the CL-20:DNG co-crystal, in which the CL-20 changes from β-CL-20 to γ-CL-20. When the temperature is increased to 2000K, CL-20, DNP, and DNG begin to decompose, and there are five paths for the main initial mechanisms. Further increasing the temperature to 3000K promotes a more complete decomposition. The initial reactions of CL-20 in the two co-crystals have two channels. There are two initial decomposition channels in the DNP molecule and only one channel in the DNG molecule. As the temperature increases, the decomposition products of the two co-crystals are different. Our work may provide the in-depth understanding of the decomposition mechanisms of high-energy CL-20-based co-crystals at high temperatures.

Thermal decomposition of cocrystal BTF/TNB nanoparticles simulated using density functional tight-binding molecular dynamics

To understand the nano effect on the thermal decomposition of cocrystal explosives, this study simulated the initial decomposition of cocrystal BTF/TNB nanoparticles (NPs) with diameters of 2.2–3.0 ​nm at high temperatures of 2400–3000 ​K using density functional tight-binding molecular dynamics (DFTB-MD) with dispersion corrections. As indicated by the simulation results, the volume expansion of the nanoparticles competed with its decomposition, and smaller nanoparticles promoted the diffusion of the molecules and products in the nanoparticles. Moreover, the nanoparticles had a higher decomposition rate at higher temperatures, and smaller nanoparticles were associated with a higher decomposition rate and weaker interactions between intermediates and lattice. The number of clusters first increased and then decreased during the decomposition of the nanoparticles. The results of this study may help in understanding the effects of temperature and particle size on the thermal decomposition mechanisms of cocrystal explosives.

Interaction of CO2 with TiO2/reduced graphene oxide as superior catalysts: Dispersion-corrected density functional theory simulation

Interaction of CO2 with the anatase TiO2 slab, nano-TiO2 cluster and nano-TiO2/reduced graphene oxide (rGO) was explored by density functional theory simulations. Two orientations, namely (001) and (100) directions, were examined for an approaching CO2 molecule to the surfaces. The energetically favorable state corresponds to a CO2 molecule adsorbed in the (001) direction for all the considered substrates. The interaction energies of adsorbed CO2 on the TiO2 slab, nano-TiO2 cluster, and nano-TiO2-rGO (on the nano-TiO2 cluster attached to the rGO) surfaces were determined to be about −5.007, −11.643, and −13.025 kcal/mol, respectively. Interaction properties were identified by the high-level MP2 calculations and the AIM theory analysis. Finally, for the adsorbed CO2 on the nano-TiO2-rGO, density-functional tight-binding (DFTB) molecular dynamics simulation were carried out and the results showed that CO2 absorption strength was enhanced on the (001) nano-TiO2 at room temperature by bonding of either O atom or C atom to the surface Ti and O atoms. It is found that nano-TiO2-rGO was more effective for CO2 adsorption than both the bulk TiO2 slab and free nano-TiO2 cluster.

Annihilation dynamics of a dislocation pair in graphene: Density-functional tight-binding molecular dynamics simulations and first principles study

The time evolution of a dislocation pair in graphene is investigated by performing subnanosecond-scale molecular dynamics simulations based on the density-functional tight-binding method. The simulations show the self-healing behavior of the graphene lattice, resulting in complete annihilation of dislocations, that is, the formation of the pristine graphene structure. To understand the mechanism of the structural developments, first principles calculations are performed for the principal dislocation structures observed in the density-functional tight-binding/molecular dynamics simulations. We reveal the characteristic bonding states in the area around the dislocation structures by bond analyses based on the Wiberg bond index and crystal orbital Hamilton population approaches. The unusual local bonding states mainly originate from geometrical features of the out-of-plane deformation of the dislocation structures. The annihilation processes of dislocations in graphene are discussed in relation to the local bonding states of the dislocation structures.

A DFTB-Based Molecular Dynamics Investigation of an Explicitly Solvated Anatase Nanoparticle

We performed a self-consistent charge density functional tight-binding molecular dynamics (SCC DFTB-MD) simulation of an explicitly solvated anatase nanoparticle. From the 2 ps trajectory, we were able to calculate both dynamic and static properties, such as the energies of interaction and the formation of water layers at the surface, and compare them to the observed behaviour reported elsewhere. The high degree of agreement between our simulation and other sources, and the additional information gained from employing this methodology, highlights the oft-overlooked viability of DFTB-based methods for electronic structure calculations of large systems.

Investigating the Accuracy of Water Models through the Van Hove Correlation Function.

We present molecular-simulation-based calculations of the Van Hove correlation function (VHF) of water using multiple modeling approaches: classical molecular dynamics with simple three-site nonpolarizable models, with a polarizable model, and with a reactive force field; density functional tight-binding molecular dynamics; and ab initio molecular dynamics. Due to the many orders of magnitude difference in the computational cost of these approaches, we investigate how small and short the simulations can be while still yielding sufficiently accurate and interpretable results for the VHF. We investigate the accuracy of the different models by comparing them to recently published inelastic X-ray scattering measurements of the VHF. We find that all of the models exhibit qualitative agreement with the experiments, and in some models and for some properties, the agreement is quantitative. This work lays the foundation for future simulation approaches to calculating the VHF for aqueous solutions in bulk and under nanoconfinement.

Thermal decomposition mechanisms of benzotrifuroxan:2,4,6-trinitrotoluene cocrystal using quantum molecular dynamics simulations

Density functional tight-binding molecular dynamics simulations with dispersion corrections were performed to study the thermal decomposition mechanisms of benzotrifuroxan: 2,4,6-trinitrotoluene (BTF:TNT) cocrystal at 2400 and 2700 K. The TNT molecules are easier to decompose, which promotes the initial decomposition of the cocrystal. The furoxan ring opening by the NO bond cleavage is the initial reaction step of BTF, while the CNO2 homolysis and NO2 rearrangement of TNT are the main decomposition paths. The rate constants of the BTF and TNT decomposition were obtained by analyzing the decomposition kinetics of the cocrystal using the first order rate model.

Rotational Dynamics of Water at the Phospholipid Bilayer Depending on the Head Groups Studied by Molecular Dynamics Simulations

Hydration states are a crucial factor that affect the self-assembly and properties of soft materials and biomolecules. Although previous experiments have revealed that the hydration state strongly depends on the chemical structure of lipid molecules, the mechanisms at the molecular level remain unknown. Classical and density-functional tight-binding (DFTB) molecular dynamics (MD) simulations are employed to determine the mechanisms underlying dissimilar water dynamics between lipid membranes with phosphatidylcholine (PC) and phosphatidylethanolamine (PE) head groups. The classical MD simulation shows that rotational relaxations of water are faster on the PE lipid than on the PC lipid, which is consistent with a previous experimental study using terahertz spectroscopy. Furthermore, DFTB-MD simulation of N(CH3)4+ and NH4+ ions, which correspond to the different head groups in PC and PE, respectively, shows qualitative agreement with the classical MD simulation. Remarkably, the PE lipids and the NH4+ ions break hydrogen bonds between water molecules in the secondary hydration shell. In contrast, the PC lipids and the N(CH3)4+ ions bind water molecules weakly in both the primary and secondary hydration shells and increase hydrogen bonds between water. Our atomistic simulations show that these changes in the hydrogen-bond network of water molecules cause the different rotational relaxation of water molecules between the two lipids.

Coupling effect of high temperature and pressure on the decomposition mechanism of crystalline HMX

The coupling effect of temperature and pressure plays a significant role in the behavior of energetic materials. Energetic materials present extremely complex behavior at high temperatures. Handling difficulties and safety risks have restricted detailed experimental studies on their decomposition mechanisms, especially for less-stable configurations of energetic materials. This has necessitated theoretical studies particularly under the coupling effect. A combinational strategy based on density functional tight-binding molecular dynamics (DFTB-MD) simulations and the density functional theory (DFT) was applied to study the effects of temperature and pressure on the initial decomposition and reaction activation barrier of α-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and δ-HMX. A comprehensive analysis of HMX in each system indicated that while the initial decomposition mechanism was not dependent on pressure at high temperatures, the initial reaction rate and activation barrier were highly dependent on pressure. The initial decomposition mechanisms of α-HMX at 1500 ​K and δ-HMX at 1200 ​K under pressures of 1–3 ​GPa involved unimolecular C–H bond breakage and N–NO2 homolysis, respectively. Pressure inhibited the decomposition of α-HMX, but accelerated that of δ-HMX. The decompositions of α-HMX and δ-HMX occurred via first-order reactions. The classical Arrhenius form indicated that pressure (1–3 ​GPa) increased and decreased the decomposition barriers of α-HMX at 1500 ​K and δ-HMX at 1200 ​K, respectively. These findings provide a new understanding of the thermal decomposition and reaction mechanisms of HMX under the coupling effect of temperature and varying pressures.

Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations.

Massively parallel divide-and-conquer density functional tight-binding (DC-DFTB) molecular dynamics and metadynamics simulations are efficient approaches for describing various chemical reactions and dynamic processes of large complex systems via quantum mechanics. In this study, DC-DFTB simulations were combined with multi-replica techniques. Specifically, multiple walkers metadynamics, replica exchange molecular dynamics, and parallel tempering metadynamics methods were implemented hierarchically into the in-house Dcdftbmd program. Test simulations in an aqueous phase of the internal rotation of formamide and conformational changes of dialanine showed that the newly developed extensions increase the sampling efficiency and the exploration capabilities in DC-DFTB configuration space.

Conformational Changes and Decomposition Mechanisms of HMX-Based Cocrystal Explosives at High Temperatures

The cocrystallization effect plays a prominent role in improving the performance of energetic materials. A combinational strategy based on density functional tight-binding molecular dynamics (DFTB-...

Mechanisms and kinetics of initial pyrolysis and combustion reactions of 1,1-diamino-2,2-dinitroethylene from density functional tight-binding molecular dynamics simulations

The density functional tight-binding molecular dynamics approach was used to study the mechanisms and kinetics of initial pyrolysis and combustion reactions of isolated and multi-molecular FOX-7. Based on the thermal cleavage of bridge bonds, the pyrolysis process of FOX-7 can be divided into three stages. However, the combustion process can be divided into five decomposition stages, which is much more complex than the pyrolysis reactions. The vibrations in the mean temperature contain nodes signifying the formation of new products and thereby the transitions between the various stages in the pyrolysis and combustion processes. Activation energy and pre-exponential factor for the pyrolysis and combustion reactions of FOX-7 were obtained from the kinetic analysis. It is found that the activation energy of its pyrolysis and combustion reactions are very low, making both take place fast. Our simulations provide the first atomic-level look at the full dynamics of the complicated pyrolysis and combustion process of FOX-7.

Artificial neural network correction for density-functional tight-binding molecular dynamics simulations

Abstract