Tight-binding Molecular Dynamics Simulations 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.

Exploring the adsorption of five emerging pollutants on activated carbon: A theoretical approach

The identification and management of contaminants of emerging concern (CECs) in water systems is crucial for protecting public and environmental health. This paper reports a theoretical approach to studying the adsorption of five CECs: Atrazine (ATZ), Caffeine (CAF), Carbamazepine (CBZ), Sulfamethoxazole (SMX), and Ibuprofen (IBU) - onto Activated Carbon (AC). A set of computational methods, including electrostatic molecular potential maps, conceptual density functional theory, Fukui functions, thermodynamic analysis, and tight-binding molecular dynamics simulations, were employed to analyze the electronic/energetic interactions and mechanisms involved in the adsorption of CECs on AC. The theoretical methodology offered valuable predictions on reactivity sites, stability, and binding mechanisms. Results showed that adsorption primarily occurred through non-covalent interactions like π-π electron donor-acceptor interactions, van der Waals forces, and hydrophobic interactions. Thermodynamic properties suggested the adsorption process was spontaneous and exothermic. However, for the AC/SMX system, the Gibbs free energy reveals that adsorption may be unfavorably compared to the other study systems. Molecular dynamics simulations validated the kinetic stability in the following order CAF (0.13 Å)>CBZ (0.23 Å)>ATZ (0.75 Å)> IBU (1.28 Å)>SMX (1.54 Å). This exploratory theoretical study provides a deep understanding of the interactions between AC and five CECs, aiding in the rational design and optimization of AC-based treatment systems for environmental and industrial applications.

Assessment of Hydrazone Derivatives for Enhanced Steel Corrosion Resistance in 15 wt.% HCl Environments: A Dual Experimental and Theoretical Perspective.

This study evaluates the corrosion inhibition capabilities of two novel hydrazone derivatives, (E)-2-(5-methoxy-2-methyl-1H-indol-3-yl)-N'-(4-methylbenzylidene)acetohydrazide (MeHDZ) and (E)-N'-benzylidene-2-(5-methoxy-2-methyl-1H-indol-3-yl)acetohydrazide (HHDZ), on carbon steel in a 15 wt.% HCl solution. A comprehensive suite of analytical techniques, including gravimetric analysis, potentiodynamic polarization (PDP), electrochemical impedance spectroscopy (EIS), and scanning electron microscopy (SEM), demonstrates their significant inhibition efficiency. At an optimal concentration of 5 × 10-3 mol/L, MeHDZ and HHDZ achieve remarkable inhibition efficiencies of 98% and 94%, respectively. EIS measurements reveal a dramatic reduction in effective double-layer capacitance (from 236.2 to 52.8 and 75.3 µF/cm2), strongly suggesting inhibitor adsorption on the steel surface. This effect is further corroborated by an increase in polarization resistance and a significant decrease in corrosion current density at optimal concentrations. Moreover, these inhibitors demonstrate sustained corrosion mitigation over extended exposure durations and maintain effectiveness even under elevated temperatures, highlighting their potential for diverse operational conditions. The adsorption process of these inhibitors aligns well with the Langmuir adsorption isotherm, implying physicochemical interactions at the carbon steel surface. Density functional tight-binding (DFTB) calculations and molecular dynamics simulations provide insights into the inhibitor-surface interaction mechanism, further elucidating the potential of these hydrazone derivatives as highly effective corrosion inhibitors in acidic environments.

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).

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.

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.

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.

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.

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.

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.

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).

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.

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.

Electronic structure and tight-binding molecular dynamics simulations for calcium and strontium

Alkaline earth metals, Calcium and Strontium, are soft materials with a stable fcc crystal structure. In this work we have applied the Naval Research Laboratory Tight-Binding (NRL-TB) method to these materials using total energies and energy bands inputs generated by the Linearized Augmented Plane Wave (LAPW) method using the Generalized Gradient Approximation (GGA) for treatment of exchange and correlation. Accurate TB Hamiltonians have been obtained for Ca and Sr that fit very well the LAPW results of the fcc, bcc and sc structures for the total energy and band structure. Also, properties that were not fitted including elastic constants and phonon frequencies reproduce well the measured values, as well as producing total energies for the evaluation of structural differences. In addition, our model is successful in performing molecular dynamics (MD) simulations to derive quantities such as mean-squared displacements, vacancy formation energies and thermal expansion coefficients. Finally, we have shown that Sr which is known to have semi-metallic behavior can be turned into a semiconductor (possibly a topological insulator) upon applying spin-orbit interaction.