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.

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.

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.

Electronic nonequilibrium effect in ultrafast-laser-irradiated solids

This paper describes the effects of electronic nonequilibrium in a simulation of ultrafast laser irradiation of materials. The simulation scheme based on tight-binding molecular dynamics, in which the electronic populations are traced with a combined Monte Carlo and Boltzmann equation, enables the modeling of nonequilibrium, nonthermal, and nonadiabatic (electron-phonon coupling) effects simultaneously. The electron-electron thermalization is described within the relaxation-time approximation, which automatically restores various known limits such as instantaneous thermalization (the thermalization time τe−e→0 ) and Born-Oppenheimer (BO) approximation ( τe−e→∞ ). The results of the simulation suggest that the non-equilibrium state of the electronic system slows down electron-phonon coupling with respect to the electronic equilibrium case in all studied materials: metals, semiconductors, and insulators. In semiconductors and insulators, it also alters the damage threshold of ultrafast nonthermal phase transitions induced by modification of the interatomic potential due to electronic excitation. It is demonstrated that the models that exclude electron-electron thermalization (using the assumption of τe−e→∞, such as BO or Ehrenfest approximations) may produce qualitatively different results, and a reliable model should include all three effects: electronic nonequilibrium, nonadiabatic electron-ion coupling, and nonthermal evolution of interatomic potential.

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.

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.

Thermal stability and decomposition mechanisms of hexatetracarbon: Tight-binding molecular dynamics and density functional theory study

In this work, we carry out molecular dynamics and ab initio modeling to determine the thermal decomposition channels and thermal stability of the recently proposed 2D carbon allotrope, hexatetracarbon (HTC). To take into account the role of edges in the initialization of decay, we considered finite size cluster models of HTC passivated by hydrogen. Four models were selected for the study: [Formula: see text], [Formula: see text] [Formula: see text] and [Formula: see text]. Molecular dynamics and hyperdynamics was carried out using the NTBM non-orthogonal tight-binding model. For ab initio calculations, we used the electron density functional theory with the B3LYP three-parameter hybrid functional and the 6-311G[Formula: see text] electronic basis set. Prismane [Formula: see text] demonstrated the highest stability due to the high energy barrier of 1.5 eV preserving its decomposition. Larger clusters possessed lower barriers in the 0.65–0.9 eV range. We concluded that the HTC edges are unstable at room temperatures. However, the destruction of some interlayer bonds can result in strain relaxation and increase of stability. We believe that HTC could exist at room temperatures in the form of nanosized quantum dots that appeared from bilayer graphene under high pressure.

Thermal Stability and Vibrational Properties of the 6,6,12-Graphyne-Based Isolated Molecules and Two-Dimensional Crystal

We report the geometry, kinetic energy, and some optical properties of the 6,6,12-graphyne-based systems. We obtained the values of their binding energies and structural characteristics such as bond lengths and valence angles. Moreover, using nonorthogonal tight-binding molecular dynamics, we carried out a comparative analysis of the thermal stability of 6,6,12-graphyne-based isolated fragments (oligomer) and two-dimensional crystals constructed on its basis in a wide temperature range from 2500 to 4000 K. We found the temperature dependence of the lifetime for the finite graphyne-based oligomer as well as for the 6,6,12-graphyne crystal using a numerical experiment. From these temperature dependencies, we obtained the activation energies and frequency factors in the Arrhenius equation that determine the thermal stability of the considered systems. The calculated activation energies are fairly high: 1.64 eV for the 6,6,12-graphyne-based oligomer and 2.79 eV for the crystal. It was confirmed that the thermal stability of the 6,6,12-graphyne crystal concedes only to traditional graphene. At the same time, it is more stable than graphene derivatives such as graphane and graphone. In addition, we present data on the Raman and IR spectra of the 6,6,12-graphyne, which will help distinguish it from the other carbon low-dimensional allotropes in the experiment.

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.

Molecular Mechanisms of Phosphoester Bond Formation in Water Using Tight-Binding Ab Initio Molecular Dynamics.

Phosphate groups are ubiquitous in biomolecules and are usually incorporated through phosphoester bonds between alcohol groups and orthophosphate. The formation of this bond is exceptionally difficult, with associated barriers of 30-45 kcal/mol in the absence of catalysts. In abiotic conditions, polymerizing nucleic acids without enzymes remains very challenging and is still a partly unsolved problem that severely questions the RNA World hypothesis for the origins of life. Offering a solution to this problem would involve a detailed knowledge of the reaction energetics and mechanisms, yet these remain not fully understood at a molecular level, especially because of the very slow reaction rates that represent a significant challenge for the experiments. The number of involved reaction coordinates and the possible role of the solvent in assisting the reaction are challenging for computational studies. Here, we use extensive ab initio molecular dynamics simulations using semiempirical tight-binding methods and enhanced sampling to address these issues. We first show that the choice of the tight-binding method is greatly limited by the instability of the water liquid phase for most DFTB generations and parameter sets that are widely available. We then focus on a model reaction involving methanol and orthophosphate, for which the two protonation states (mono- and dianionic) that are dominant around neutral pH are considered. We compare different proton coordinates that enable (or not) the participation of solvent water molecules. Our simulations suggest that in all cases, a dissociative associative mechanism, with an intermediate metaphosphate, is favored. The main difference between the two phosphate species is that reaction with the monoanion is assisted by the substrate, while that with the dianion involves solvent water molecules. Our results are in agreement with early experimental measurements, but the reaction barriers are underestimated in our framework. We believe that our approach provides an interesting perspective on how to sample the reaction phase space efficiently, but it calls for future studies using more accurate descriptions of chemical reactivity.

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.

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.