Functional Tight-binding Molecular Dynamics Research Articles

Carborane-Cluster-Wrapped Copper Cluster with Cyclodextrin-like Cavities for Chiral Recognition.

Chiral atomically precise metal clusters, known for their remarkable chiroptical properties, hold great potential for applications in chirality recognition. However, advancements in this field have been constrained by the limited exploration of host-guest chemistry, involving metal clusters. This study reports the synthesis of a chiral Cu16(C2B10H10S2)8 (denoted as Cu16@CB8, where C2B10H12S2H2 = 9,12-(HS)2-1,2-closo-carborane) cluster by an achiral carboranylthiolate ligand. The chiral R-/S-Cu16@CB8 cluster features chiral cavities reminiscent of cyclodextrins, which are surrounded by carborane clusters, yet they crystallize in a racemate. These cyclodextrin-like cavities demonstrated the specific recognition of amino acids, as indicated by the responsive output of circular dichroism and circularly polarized luminescence signals of Cu16 moieties of the Cu16@CB8 cluster. Notably, a quantitative chiroptical analysis of amino acids in a short time and a concomitant deracemization of Cu16@CB8 were achieved. Density functional tight-binding molecular dynamics simulation and noncovalent interaction analysis further unraveled the great importance of the cavities and binding sites for chiral recognition. Dipeptide, tripeptide, and polypeptide containing the corresponding amino acids (Cys, Arg, or His residues) display the same chiral recognition, showing the generality of this approach. The functional synergy of dual clusters, comprising carborane and metal clusters, is for the first time demonstrated in the Cu16@CB8 cluster, resulting in the valuable quantification of the enantiomeric excess (ee) value of amino acids. This work opens a new avenue for chirality sensors based on chiral metal clusters with unique chiroptical properties and inspires the development of carborane clusters in host-guest chemistry.

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.

Interfacial properties of a ZnO/PTFE composite from density functional tight-binding simulations.

Metal-oxide-reinforced plastic nanocomposites are widely used in high-tech industries, but the reinforcement mechanism of the metal oxide is not fully understood. Here we investigate the interfacial properties of a zinc-oxide-reinforced amorphous polytetrafluoroethylene (a-PTFE) composite as a prototype for such composites using superlattice modeling and density functional tight-binding molecular dynamics simulations. To study the ZnO/a-PTFE composites, the superlattice supercells are built using a ZnO (112̄0) surface supercell and a-PTFE layer with an experimental density of 1.8 g cm-3 and various thicknesses. Our calculations demonstrate that the binding energy between ZnO and a-PTFE is negative, indicating their attractive binding, and electron accumulation occurs in the middle space between ZnO and a-PTFE, as well as around ZnO, evidencing that the newly formed interfacial chemical bonds are partially covalent. We further reveal that the tensile stress and elastic moduli of the ZnO/a-PTFE superlattice increases with increasing ZnO fraction, with values placed between those of ZnO and a-PTFE, which confirms the enhancement of the mechanical strength of the composites by incorporating ZnO into the a-PTFE matrix. This work provides a design guideline for developing high-performance metal-oxide-reinforced plastic composites.

High-Throughput Aqueous Electrolyte Structure Prediction Using IonSolvR and Equivariant Graph Neural Network Potentials.

Neural network potentials have recently emerged as an efficient and accurate tool for accelerating ab initio molecular dynamics (AIMD) in order to simulate complex condensed phases such as electrolyte solutions. Their principal limitation, however, is their requirement for sufficiently large and accurate training sets, which are often composed of Kohn-Sham density functional theory (DFT) calculations. Here we examine the feasibility of using existing density functional tight-binding (DFTB) molecular dynamics trajectory data available in the IonSolvR database in order to accelerate the training of E(3)-equivariant graph neural network potentials. We show that the solvation structure of Na+ and Cl- in aqueous NaCl solutions can be accurately reproduced with remarkably small amounts of data (i.e., 100 MD frames). We further show that these predictions can be systematically improved further via an embarrassingly parallel resampling approach.

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.

Metallic water: Transient state under ultrafast electronic excitation.

The modern means of controlled irradiation by femtosecond lasers or swift heavy ion beams can transiently produce such energy densities in samples that reach collective electronic excitation levels of the warm dense matter state, where the potential energy of interaction of the particles is comparable to their kinetic energies (temperatures of a few eV). Such massive electronic excitation severely alters the interatomic potentials, producing unusual nonequilibrium states of matter and different chemistry. We employ density functional theory and tight binding molecular dynamics formalisms to study the response of bulk water to ultrafast excitation of its electrons. After a certain threshold electronic temperature, the water becomes electronically conducting via the collapse of its bandgap. At high doses, it is accompanied by nonthermal acceleration of ions to a temperature of a few thousand Kelvins within sub-100fs timescales. We identify the interplay of this nonthermal mechanism with the electron-ion coupling, enhancing the electron-to-ions energy transfer. Various chemically active fragments are formed from the disintegrating water molecules, depending on the deposited dose.

Structural Properties of Metal-Organic Frameworks at Elevated Thermal Conditions via a Combined Density Functional Tight Binding Molecular Dynamics (DFTB MD) Approach.

The performance of different density functional tight binding (DFTB) methods for the description of six increasingly complex metal-organic framework (MOF) compounds have been assessed. In particular the self-consistent charge density functional tight binding (SCC DFTB) approach utilizing the 3ob and matsci parameter sets have been considered for a set of four Zn-based and two Al-based MOF systems. Moreover, the extended tight binding for geometries, frequencies, and noncovalent interactions (GFN2-xTB) approach has been considered as well. In addition to the application of energy minimizations of the respective unit cells, molecular dynamics (MD) simulations at constant temperature and pressure conditions (298.15 K, 1.013 bar) have been carried out to assess the performance of the different DFTB methods at nonzero thermal conditions. In order to obtain the XRD patterns from the MD simulations, a flexible workflow to obtain time-averaged XRD patterns from (in this study 5000) individual snapshots taken at regular intervals over the simulation trajectory has been applied. In addition, the comparison of pair-distribution functions (PDFs) directly accessible from the simulation data shows very good agreement with experimental reference data obtained via measurements employing synchrotron radiation in case of MOF-5. The comparison of the lattice constants and the associated X-ray diffraction (XRD) patterns with the experimental reference data demonstrate, that the SCC DFTB approach provides a highly efficient and accurate description of the target systems.

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.

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).

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.

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).

Mechanisms of Al3+ Dimerization in Alkaline Solutions.

The molecular speciation of aluminum (Al3+) in alkaline solutions is fundamental to its precipitation chemistry within a number of industrial applications that include ore refinement and industrial processing of Al wastes. Under these conditions, Al3+ is predominantly Al(OH)4-, while at high [Al3+] dimeric species are also known to form. To date, the mechanism of dimer formation remains unclear and is likely influenced by complex ion···ion interactions. In the present work, we investigate a suite of potential dimerization pathways and the role of ion pairing on energetics using static DFT calculations and DFT and density functional tight binding molecular dynamics. Specific cation effects imparted by the background electrolyte cations Na+, Li+, and K+ have been examined. Our simulations predict that, when the Al species are ion-paired with either cation, the formation of the oxo-bridged Al2O(OH)62- is favored with respect to the dihydroxo-bridged Al2(OH)82-, in agreement with previous spectroscopic work. The formation of both dimers first proceeds by bridging of two monomeric units via one hydroxo ligand, leading to a labile Al2(OH)82- isomer. The effect of contact ion pairing of Li+ and K+ on the dimerization energetics is distinctly more favorable than that of Na+, which may have an effect on further oligomerization.

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.