Tight-binding Molecular Dynamics Research Articles

Symmetrical Linkage in Porphyrin Nanoring Suppressed the Electron–Hole Recombination Demonstrated by Nonadiabatic Molecular Dynamics

Macromolecular porphyrin nanorings are receiving significant attention because of their excellent optoelectronic properties. However, their efficiencies as potential solar materials are significantly affected by nonradiative charge recombination. To understand the recombination mechanism by alternating structural parameters and using tight-binding nonadiabatic molecular dynamics, we demonstrate that charge recombination depends strongly on the mode of the linker in the porphyrin nanoring. The nanoring having all-butadiyne-linkage (pristine-P8) inhibits carrier relaxation. In contrast, a partially fused nanoring (fused-P8) expedites the rate of quantum transition. An extension of the lifetime by a factor of 4 is due to the larger optical gap in pristine-P8 that reduces the NA coupling by decreasing the overlap between band edge states. Additionally, an intense phonon peak in the low-frequency region and rapid coherence loss within the electronic subsystem favors prolonging the carrier lifetime. This study provides an atomistic realization for the design of macromolecular porphyrin nanorings for the potential use in photovoltaic materials.

Electron-Phonon Coupling and Nonthermal Effects in Gold Nano-Objects at High Electronic Temperatures.

Laser irradiation of metals is widely used in research and applications. In this work, we study how the material geometry affects electron–phonon coupling in nano-sized gold samples: an ultrathin layer, nano-rod, and two types of gold nanoparticles (cubic and octahedral). We use the combined tight-binding molecular dynamics Boltzmann collision integral method implemented within XTANT-3 code to evaluate the coupling parameter in irradiation targets at high electronic temperatures (up to Te~20,000 K). Our results show that the electron–phonon coupling in all objects with the same fcc atomic structure (bulk, layer, rod, cubic and octahedral nanoparticles) is nearly identical at electronic temperatures above Te~7000 K, independently of geometry and dimensionality. At low electronic temperatures, reducing dimensionality reduces the coupling parameter. Additionally, nano-objects under ultrafast energy deposition experience nonthermal damage due to expansion caused by electronic pressure, in contrast to bulk metal. Nano-object ultrafast expansion leads to the ablation/emission of atoms and disorders the inside of the remaining parts. These nonthermal atomic expansion and melting are significantly faster than electron–phonon coupling, forming a dominant effect in nano-sized gold.

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.

Mechanism of alcohol chemical vapor deposition growth of carbon nanotubes: Catalyst oxidation

Alcohol chemical vapor deposition (ACVD) was established as one of the most promising methods for single-walled carbon nanotube (SWCNT) growth almost two decades ago however the mechanisms behind its success remain elusive. To unveil the mechanism of SWCNT growth via ACVD, we employed density functional tight binding molecular dynamics simulations, supplying ethanol to a Fe nanoparticle. Here we demonstrate the oxidation of the Fe catalyst with varying supply rates of ethanol and how the catalyst composition is controlled by the reaction pathways mediated by the hydroxyl OH radical. Following ethanol dissociation on Fe and subsequent O dissolution, the catalyst becomes oxidized and the mobility and availability of Fe to bond with C are reduced. However, SWCNT growth is promoted via the key reaction pathways of the hydroxyl H; controlling the catalyst composition through the formation and release of H2O and H2. These reaction pathways also demonstrate how active growth species such as ethylene can be formed preferentially to ethane from ethanol dissociation. This work provides important insight into the mechanism of how the catalyst composition changes during ACVD and can be extended to understand the catalyst nature during other O-assisted SWCNT growth processes such as H2O-assisted supergrowth and CO/CO2-promoted growth.

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.

Structural stability and initial decomposition mechanisms of BTF crystals induced by vacancy defects: a computational study

Density functional tight binding (DFTB) and DFTB-based molecular dynamics (DFTB-MD) were used to study the effects of vacancy defects on the structure, stability, and initial decomposition mechanisms of condensed phase benzotrifuroxan (BTF).

Inducing a topological transition in graphene nanoribbon superlattices by external strain.

Armchair graphene nanoribbons, when forming a superlattice, can be classified into different topological phases, with or without edge states. By means of tight-binding and classical molecular dynamics (MD) simulations, we studied the electronic and mechanical properties of some of these superlattices. MD shows that fracture in modulated superlattices is brittle, as for unmodulated ribbons, and occurs at the thinner regions, with staggered superlattices achieving a larger fracture strain than inline superlattices. We found a general mechanism to induce a topological transition with strain, related to the electronic properties of each segment of the superlattice, and by studying the sublattice polarization we were able to characterize the transition and the response of these states to the strain. For the cases studied in detail here, the topological transition occurred at ∼3-5% strain, well below the fracture strain. The topological states of the superlattice - if present - are robust to strain even close to fracture. The topological transition was characterized by means of the sublattice polarization of the states.

IRMPD spectroscopy of a PAH cation using FELICE: The infrared spectrum and photodissociation of dibenzo[a,l]pyrene

We present the experimental InfraRed Multiple Photon Dissociation (IRMPD) spectrum and fragmentation mass spectrum of the irregular, cationic PAH dibenzo[a,l]pyrene (C24H14+) in the 6–40μm/250–1650 cm−1 range. The use of the Free-Electron Laser for IntraCavity Experiments (FELICE) enabled us to record its Far-InfraRed (FIR) spectrum for the first time. We aim to understand how irregularity affects the infrared spectrum and fragmentation chemistry of PAHs. Dibenzo[a,l]pyrene is an asymmetric, non-planar molecule, for which all vibrational modes are in principle IR-active. Calculated harmonic Density Function Theory (DFT) and anharmonic Density Functional based Tight Binding Molecular Dynamics (DFTB-MD) spectra show a large wealth of bands, which match the experiment well, but with a few differences. The periphery of the molecule contains several edge geometries, but out of all possible modes in the 11–14μm out-of-plane CH bending region, only one band at 13.5μm is prominent. This fact and the richness of the CC stretching range make irregular PAHs a possible contributor to D-class interstellar spectra. The fragmentation mass spectra reveal facile 2H-loss and no [2C, 2H]-loss, which is attributed to the sterically hindered, non-planar cove region, which could protect irregular PAHs from radiation damage.

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.

Atom-by-Atom and Sheet-by-Sheet Chemical Mechanical Polishing of Diamond Assisted by OH Radicals: A Tight-Binding Quantum Chemical Molecular Dynamics Simulation Study.

Ultraflat and damage-free single-crystal diamond is a promising material for use in electronic devices such as field-effect transistors. Diamond surfaces are conventionally prepared by the chemical mechanical polishing (CMP) method, although the CMP efficiency remains a critical issue owing to the extremely high hardness of diamond. Recently, OH radicals have been demonstrated to be potentially useful for improving the CMP efficiency for diamond; however, the underlying mechanisms are still elusive. In this work, we applied our previously developed CMP-specialized tight-binding quantum chemical molecular dynamics simulator to comprehensively elucidate the CMP mechanisms of diamond assisted by OH radicals. Our simulation results indicate that the diamond surface is oxidized by reactions with OH radicals and then a concomitant surface reconstruction takes place due to the distorted and unstable nature of the oxidized diamond surface structure. Furthermore, we interestingly reveal that the reconstruction of the diamond surface ultimately leads to two distinct removal mechanisms: (i) gradual atom-by-atom removal through the desorption of gaseous molecules (e.g., CO2 and H2CO3) and (ii) drastic sheet-by-sheet removal through the exfoliation of graphitic ring structures. Hence, we propose that promoting the oxidation-induced graphitization of the diamond surface may provide a route to further improving the CMP efficiency.

Toward efficient enantioseparation of ibuprofen isomers using chiral BNNTs: Dispersion corrected DFT calculations and DFTB molecular dynamic simulations

The separation of drug enantiomers in pharmaceutical industry is one of great importance since most organic compounds are chiral. In this study, the separation of ibuprofen enantiomers and the interaction between right-handed (R) and left-handed (S) isomers of ibuprofen with the outer surface as well as internal sidewall of a chiral boron nitride nanotube (BNNT(10,5)) was evaluated. The geometry optimizations and total energy calculations were performed with DFT–D3/revPBE-GGA method for various adsorption configurations. Our first-principles findings showed that interaction strength of the incorporated enantiomers into the BNNTs was higher than ones adsorbed onto the outer surface of nanotube. Also, the interaction energy difference between two enantiomers interacting with inside and outside of the BNNT was about 0.63 and 1.25 kcal/mol, respectively. This finding indicated the more ability of outer surface of BNNT in efficient enantioseparation of Ibuprofen isomers rather than inner site. Furthermore, in order to model a realistic system, tight-binding density functional molecular dynamics (DFTB–MD) simulation was performed at room temperature, and the results were consisted with the DFT–D3 findings. The nudged elastic band (NEB) method was also used to evaluate the activation energy barrier for incorporation of ibuprofen into the BNNT cavity. Our molecular simulation findings are reliable to offer beneficial information about the potential application of chiral BNNTs in enantiomer molecules adsorption and separation.

Contribution of inter- and intraband transitions into electron\u2013phonon coupling in metals

We recently developed an approach for calculation of the electron–phonon (electron–ion in a more general case) coupling in materials based on tight-binding molecular dynamics simulations. In the present work, we utilize this approach to study partial contributions of inter- and intraband electron scattering events into total electron–phonon coupling in Al, Au, and Cu elemental metals and in AlCu alloy. We demonstrate that the interband scattering plays an important role in the electron–ion energy exchange process in Al and AlCu, whereas intraband d–d transitions are dominant in Au and Cu. Moreover, inter- and intraband transitions exhibit qualitatively different dependencies on the electron temperature. Our findings should be taken into account for the interpretation of experimental results on the electron–phonon coupling parameter.Graphic abstract

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.

Peculiar diffusion behavior of AlCl4 intercalated in graphite from nanosecond-long molecular dynamics simulations* *Project supported by the National Key Research and Development Program of China (Grant No. 2016YFB0201202) and the National Natural Science Foundation of China (Grant Nos. 11874335 and 11774327).

The diffusion property of the intercalated species in the graphite materials is at the heart of the rate performance of graphite-based metal-ion secondary battery. Here we study the diffusion process of a AlCl4 molecule within graphite — a key component of a recently reported aluminum ion battery with excellent performance — via molecular dynamics (MD) simulations. Both ab-initio MD (AIMD) and semiempirical tight-binding MD simulations show that the diffusion process of the intercalated AlCl4 molecule becomes rather inhomogeneous, when the simulation time exceeds approximately 100 picoseconds. Specifically, during its migration in between graphene layers, the intercalated AlCl4 molecule may become stagnant occasionally, and then recovers its normal (fast) diffusion behavior after halting for a while. When this phenomenon occurs, the linear relationship of the mean squared displacement (MSD) versus the duration time is not fulfilled. We interpret this peculiar behavior as a manifestation of inadequate sampling of rare event (the stagnation of the molecule), which does not yet appear in short-time MD simulations. We further check the influence of strains present in graphite intercalated compounds (GIC) on the diffusion properties of AlCl4, and find that their presence in general slows down the diffusion of the intercalated molecule, and is detrimental to the rate performance of the GIC-based battery.

Role of OH Termination in Mitigating Friction of Diamond-like Carbon under High Load: A Joint Simulation and Experimental Study.

Diamond-like carbon (DLC) has recently attracted much attention as a promising solid-state lubricant because it exhibits low friction, low abrasion, and high wear resistance. Although we previously reported the reason why H-terminated DLC exhibits low friction based on a tight-binding quantum chemical molecular dynamics (TB-QCMD) simulation, experimentally, the low-friction state of H-terminated DLC is not stable, limiting its application. In the present work, our TB-QCMD simulations suggest that H/OH-terminated DLC could give low friction even under high loads, whereas H-terminated DLC could not. By using gas-phase friction experiments, we confirm that OH termination can indeed provide much more stable lubricity than H termination, validating the predictions from simulations. We conclude that H/OH-terminated DLC is a new low-friction material with high load capacity and high stable lubricity that may be suitable for practical use in industrial applications.

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.

Bispropylurea bridged polysilsesquioxane: A microporous MOF-like material for molecular recognition

Microporous organosilicas assembled from polysilsesquioxane (POSS) building blocks are promising materials that are yet to be explored in-depth. Here, we investigate the processing and molecular structure of bispropylurea bridged POSS (POSS-urea), synthesised through the acidic condensation of 1,3-bis(3-(triethoxysilyl)propyl)urea (BTPU). Experimentally, we show that POSS-urea has excellent functionality for molecular recognition toward acetonitrile with an adsorption level of 74 mmol/g, which compares favourably to MOFs and zeolites, with applications in volatile organic compounds (VOC). The acetonitrile adsorption capacity was 132-fold higher relative to adsorption capacity for toluene, which shows the pores are highly selective towards acetonitrile adsorption due to their size and arrangement. Theoretically, our tight-binding density functional and molecular dynamics calculations demonstrated that this BTPU based POSS is microporous with an irregular placement of the pores. Structural studies confirm maximal pore sizes of ∼1 nm, with POSS cages possessing an approximate edge length of ∼3.16 Å.

Parametrization of the Fe-Owater cross-interaction for a more accurate Fe3O4/water interface model and its application to a spherical Fe3O4 nanoparticle of realistic size.

The accurate description of iron oxides/water interfaces requires reliable force field parameters that can be developed through comparison with sophisticated quantum mechanical calculations. Here, a set of CLASS2 force field parameters is optimized to describe the Fe-Owater cross-interaction through comparison with hybrid density functional theory (HSE06) calculations of the potential energy function for a single water molecule adsorbed on the Fe3O4 (001) surface and with density functional tight binding (DFTB+U) molecular dynamics simulations for a water trilayer on the same surface. The performance of the new parameters is assessed through the analysis of the number density profile of a water bulk (12 nm) sandwiched between two magnetite slabs of large surface area. Their transferability is tested for water adsorption on the curved surface of a spherical Fe3O4 nanoparticle of realistic size (2.5 nm).

Cooperative roles of chemical reactions and mechanical friction in chemical mechanical polishing of gallium nitride assisted by OH radicals: tight-binding quantum chemical molecular dynamics simulations.

Chemical mechanical polishing (CMP) is a key manufacturing process for applying gallium nitride (GaN), especially the Ga-face GaN, to semiconductor devices such as laser diodes. However, the CMP efficiency for GaN is very low due to its high hardness and chemical stability. Experimentally, OH radicals appear able to improve the CMP efficiency of GaN polished by a SiO2 abrasive grain, whereas the mechanisms of the OH-radical-assisted CMP process remain unclear because experimental elucidation of the complex chemical reactions occurring among GaN substrate, abrasive grain, and OH radicals is difficult. In this work, we used our previously developed tight-binding quantum chemical molecular dynamics simulator to study the OH-radical-assisted CMP process of the widely employed Ga-face GaN substrate polished by an amorphous SiO2 abrasive grain in an effort to understand how OH radicals assist the CMP process and then aid the development of next-generation CMP techniques. Our simulations revealed that the OH-radical-assisted CMP process of GaN occurs via the following three basic reaction steps: (i) first, all hydrogen terminations on the GaN surface are replaced by OH terminations through continuous reactions with OH radicals; (ii) after the substrate is fully terminated by OH, the hydrogen atoms of these OH terminations are removed by reacting with newly added OH radicals, which forms H2O molecules and leaves energetic oxygen atoms with dangling bonds on the surface; and (iii) finally, these energetic oxygen atoms intrude inside the substrate with concomitant dissociation of Ga-N bonds and the generation of N2 and gallium hydroxide molecules, which accumulatively lead to the removal of N and Ga atoms from the substrate.

Localized electronic and vibrational states in amorphous diamond.

Amorphous diamond structures are generated by quenching high-density high-temperature liquid carbon using tight-binding molecular-dynamics simulations. We show that the generated amorphous diamond structures are predominated by strong tetrahedral bonds with the sp3 bonding fraction as high as 97%, thus exhibit an ultra-high incompressibility and a wide band gap close to those of crystalline diamond. A small amount of sp2 bonding defects in the amorphous sample contributes to localized electronic states in the band gap while large local strain gives rise to localization of vibrational modes at both high and low frequency regimes.