Car-Parrinello Molecular Dynamics Simulations Research Articles

Does Pb2+ Form Holodirected or Hemidirected Solvation Geometries in Water?

The hydration properties of the Pb2+ ion in aqueous solution have been investigated by using a synergic approach based on Classical and Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. A definite answer has been given to the main question on the Pb2+ hydration structure, which concerns the formation of either holodirected or hemidirected solvation geometries, such terms referring to the arrangements of the ligands that can be directed either throughout the surface of an encompassing globe around Pb2+ or throughout only part of the globe, respectively. Our CPMD results show that the Pb2+ ion in water forms a hemidirected 4-fold cluster with a well-defined distorted pyramidal geometry. This cluster is directed throughout one side of the first shell globe, while the other side contains either two or three very mobile water molecules that do not form a well-defined geometry around the Pb2+ ion. The Pb2+ first shell structural arrangement determined from the CPMD simulation was confirmed by the EXAFS experimental results. A homodirected Pb2+ first shell complex like the 8-fold SAP structure obtained from the classical MD simulations cannot be reconciled with the EXAFS experimental data. These findings represent a significant step forward in the understanding of the solvation chemistry of the Pb2+ ion, which is fundamental to improving the efficiency of lead removal procedures that are crucial to the safety of water resources.

Very Strong Hydrogen Bond in Nitrophthalic Cocrystals.

This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine and N,N-dimethyl-4-pyridinamine complexes with aim to obtain a VSHB. The four synthesized complexes were studied by experimental X-ray, IR, and Raman methods, as well as theoretical Car-Parrinello Molecular Dynamics (CP-MD) and Density Functional Theory (DFT) simulations. By variation of the steric repulsion and basicity of the complex' components, a very short intramolecular hydrogen bond was achieved. The potential energy curves calculated by the DFT method were characterized by a low barrier (0.7 and 0.9 kcal/mol) on proton transfer in the OHN intermolecular hydrogen bond for 3-nitrophthalic acid with either 2,4,6-collidine or N,N-dimethyl-4-pyridinamine cocrystals. Moreover, the CP-MD simulations exposed very strong bridging proton dynamics in the intermolecular hydrogen bonds. The accomplished crystallographic and spectroscopic studies indicate that the OHO intramolecular hydrogen bond in 4-nitrophthalic cocrystals is VSHB. The influence of a strong steric effect on the geometry of the studied cocrystals and the stretching vibration bands of the carboxyl and carboxylate groups was elaborated.

Ab Initio Molecular Dynamics Investigation on the Permeation of Sodium and Chloride Ions Through Nanopores in Graphene and Hexagonal Boron Nitride Membranes.

Nanoporous membranes promise energy-efficient water desalination. Hexagonal boron nitride (h-BN), like graphene, exhibits outstanding physical and chemical properties, making it a promising candidate for water treatment. We employed Car-Parrinello molecular dynamics simulations to establish an accurate modeling of Na+ and Cl- permeation through hydrogen passivated nanopores in graphene and h-BN membranes. We demonstrate that ion separation works well for the h-BN system by imposing a barrier of 0.13 eV and 0.24 eV for Na+ and Cl- permeation, respectively. In contrast, for permeation of the graphene nanopore, the Cl- ion faces a minimum of energy of 0.68 eV in the nanopore plane and is prone toward blockade of the nanopore, while the Na+ ion experiences a slight minimum of 0.03 eV. Overall, the desalination performance of h-BN nanopores surpasses that of their graphene counterparts.

Binding of Carbon Monoxide to Hemoglobin in an Oxygen Environment: Force Field Development for Molecular Dynamics.

Carbon monoxide (CO) is a byproduct of the incomplete combustion of carbon-based fuels, such as wood, coal, gasoline, or natural gas. As incomplete combustion in a fire accident or in an engine, massively produced CO leads to a serious life threat because CO competes with oxygen (O2) binding to hemoglobin and makes people suffer from hypoxia. Although there is hyperbaric O2 therapy for patients with CO poisoning, the nanoscale mechanism of CO dissociation in the O2-rich environment is not completely understood. In this study, we construct the classical force field parameters compatible with the CHARMM for simulating the coordination interactions between hemoglobin, CO, and O2, and use the force field to reveal the impact of O2 on the binding strength between hemoglobin and CO. Density functional theory and Car-Parrinello molecular dynamics simulations are used to obtain the bond energy and equilibrium geometry, and we used machine learning enabled via a feedforward neural network model to obtain the classical force field parameters. We used steered molecular dynamics simulations with a force field to characterize the mechanical strength of the hemoglobin-CO bond before rupture under different simulated O2-rich environments. The results show that as O2 approaches the Fe2+ of heme at a distance smaller than ∼2.8 Å, the coordination bond between CO and Fe2+ is reduced to 50% bond strength in terms of the peak force observed in the rupture process. This weakening effect is also shown by the free energy landscape measured by our metadynamics simulation. Our work suggests that the O2-rich environment around the hemoglobin-CO bond effectively weakens the bonding, so that designing of O2 delivery vector to the site is helpful for alleviating CO binding, which may shed light on de novo drug design for CO poisoning.

Double-proton transfer triggering mechanism of nitromethane caused by intermolecular hydrogen bonding at low temperature

The initial triggering mechanism of nitromethane is investigated by first-principles molecular dynamics simulations and temperature-dependent Raman spectroscopy experiment. The Raman spectra at different temperature are obtained by Car-Parrinello molecular dynamics simulation to explore the activated vibration modes caused by low-temperature heat. The temperature-dependent Raman spectra experiment is constructed to compare with the theoretical data. Each possible initial reaction path caused by the activated vibration mode is analyzed to reveal the triggering mechanism of the initial chemical bond breaking for nitromethane. The results show that the intermolecular double-proton transfer is the first reaction step which is triggered by the intermolecular hydrogen bond reinforced with the active C–H stretching vibration (near 3000 cm−1), which is not reported before. The scanning energy barrier related to the increase of C–H bond lengths is about 60 kcal/mol, which is consistent with the calculated activation barrier (59.8 kcal/mol) of intermolecular proton transfer reaction. This proves the reliability of our conclusions. The results provide a new interpretation for the long-debated initial decomposition mechanism of nitromethane.

Electric field-driven up-and-down motion of the flexible tail of Al13+ cluster system-a nano-scale flipper.

Dynamic metal nanoclusters have become a hot area of research in the field of nanoscience and nanotechnology due to their potential applications in micro devices. One such dynamic cluster is a quasi-planar ground state (GS) Al13+ cluster which exhibits anelectric field driven up and down flipping motion of the flexible tail which oscillates with respect to the mean plane. A Car-Parrinello molecular dynamics (CPMD) simulation has been carried out to understand the nature of dynamics of the cluster. CPMD simulation study reveals that the flexible tail region of the Al13+ isomeric system (two ground states M1, M2 and a transition state TS connecting them) can be engaged in a systematic up down flipping motion by the application of a transverse electric field. A saw tooth electric field of amplitude 5.19V/nm is sufficient to induce the up-and-down flipping oscillation of the cluster, which has an average oscillation frequency of around 20 THz. AIM, NICS and AdNDP analyses also have been carried out to understand the fluxional nature of the cluster from the electronic structural perspective. Electronic structural analysis of selected optimized intermediate states in the presence of transverse electric field has also been analyzed to correlate the electronic structure with the dynamic nature of the cluster. Single-point energies of all intermediate states between two minima of Al13+ clusters connected through a transition state cluster. Optimized geometries of Al13+ clusters in the presence of electric field of different strengths have been carried out by using the Gaussian 03 package. 6-311 + G(d) basis set and B3LYP hybrid density functional have been utilized for these studies. To establish the flipping motion, Car-Parrinello molecular dynamics (CPMD) has been performed using the cp.x module of the Quantum ESPRESSO 6.3.0 program package using the Perdew-Burke-Ernzerhof (PBE) functional, plane-wave basis set and ultrasoft pseudopotentials. ORTEP-3 and POV ray-3.7 software packages have been used for visualization and graphics generation. Atoms in molecule (AIM), Adaptive Natural Density Partitioning (AdNDP) analysis have been carried out using Multiwfn 3.7 program package.

Enabling High-Performance All-Solid-State Batteries via Guest Wrench in Zeolite Strategy.

All-solid-state batteries with a high energy density and safety are desirable candidates for next-generation energy storage applications. However, conventional solid electrolytes for all-solid-state batteries encounter limitations such as poor ionic conduction, interfacial compatibility, instability, and high cost. Herein, taking advantage of the ingenious capability of zeolite to incorporate functional guests in its void space, we present an innovative ionic activation strategy based on the "guest wrench" mechanism, by introducing a pair of cation and anion of LiTFSI-based guest species (GS) into the supercage of the LiX zeolite, to fabricate a zeolite membrane (ZM)-based solid electrolyte (GS-ZM) with high Li ionic conduction and interfacial compatibility. The restriction of zeolite frameworks toward the framework-associated Li ions is significantly reduced through the dynamic coordination of Li ions with the "oxygen wrench" of TFSI- at room temperature as shown by experiments and Car-Parrinello molecular dynamics simulations. Consequently, the GS-ZM shows an ∼100% increase in ionic conductivity compared with ZM and an outstanding Li+ transference number of 0.97. Remarkably, leveraging the superior ionic conduction of GS-ZM with the favorable interface structure between GS-ZM and electrodes, the assembled all-solid-state Li-ion and Li-air batteries based on GS-ZM exhibit the best-level electrochemical performance much superior to batteries based on liquid electrolytes: a capacity retention of 99.3% after 800 cycles at 1 C for all-solid-state Li-ion batteries and a cycle life of 909 cycles at 500 mA g-1 for all-solid-state Li-air batteries. The mechanistic discovery of a "guest wrench" in zeolite will significantly enhance the adaptability of zeolite-based electrolytes in a variety of all-solid-state energy storage systems with high performance, high safety, and low cost.

Competitive adsorption between sodium citrate and naphthenic acids on alumina surfaces: Experimental and computational study

The adsorption of naphthenic acids (NAs) on clay surfaces induces an increase in surface hydrophobicity, which is detrimental to crude oil recovery and froth quality. Sodium citrate (Na3Cit), with more functional groups than NAs, is expected to compete with NAs for adsorption on mineral surfaces. The adsorption of NAs on alumina surfaces was quantified in the presence and absence of Na3Cit at pH 8 ± 0.1. An increase in hydrophobicity of the alumina surface was observed after the adsorption of NAs without Na3Cit. However, adding Na3Cit significantly reduced NAs adsorption and protected the surface wettability. The viscoelasticity and electrokinetic properties of adsorbed materials indicate Na3Cit was preferentially covered on alumina surfaces and repelled NAs by its negative charges. The competition between Na3Cit and NAs for adsorption sites was explained using ab initio Car-Parrinello molecular dynamics (CPMD) simulation and periodic plane-wave density functional theory (DFT) to calculate inner-sphere adsorption and outer-sphere adsorption, respectively. Favourable adsorption of sodium citrate than NAs representatives on aluminum (hydr)oxide cluster and the basal and edge planes of gibbsite were observed from the perspective of free energy barrier and adsorption energy, respectively.

Unraveling the Ag+ ion coordination and solvation thermodynamics in the 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid

The solvation of the Ag+ ion in the 1-butyl-3-methylimidazolium tetrafluoroborate ([C4mim][BF4]) ionic liquid (IL) has been studied by means of experimental and theoretical methods with the aim of elucidating the cation coordination structure and thermodynamic properties. Car-Parrinello molecular dynamics (CPMD) simulations showed that the Ag+ ion is coordinated by an average number of four [BF4]− anions in a pseudo-tetrahedral geometry. A high configurational disorder of the first solvation sphere is found, where the anions can be found both in mono- and bidentate coordination mode around the Ag+ ion. Also, a solvational equilibrium is observed as due to [BF4]− anion dissociation along the trajectory. The analysis of X-ray absorption spectroscopy data confirmed the picture provided by the CPMD simulation. Classical molecular dynamics simulations were carried out to obtain the single-ion solvation thermodynamic parameters. The negative water → IL free energy of transfer suggests that the Ag+ ion is more favorably solvated in the [C4mim][BF4] IL than in water. This behavior is due to a balance between the enthalpic and entropic contributions, which allows to find a rationale to the strong solvation capabilities of BF4-based ILs towards Ag+.

Understanding the mechanism of the sulfur mustard hydrolysis reaction on the atomistic level from experiment and first-principles simulations

After World War II, the Baltic Sea was contaminated by dumping unused sulfur mustard (SM) and other chemical warfare agents (CWAs), which now constitutes a huge environmental hazard. We use both experimental and theoretical methods to understand the reactivity of SM in water, in particular the hydrolysis, which is one of the chemical reactions leading to the neutralization of SM. Real conditions present in the Baltic Sea are represented by performing Car-Parrinello molecular dynamics simulations for sulfur mustard in explicit water solution at finite temperature. We study the relative occurrence and stability of various SM conformers in water and analyze the solute–solvent interactions, with special focus on the formation of intra- and intermolecular hydrogen bonds and their lifetime. A missing piece toward the understanding of the sulfonium cation formation and SM hydrolysis reaction is provided by obtaining the activation energy for SM decomposition in water solution from gas chromatography–mass spectrometry (GC-MS) experiments. The complex mechanism of SM hydrolysis is also studied by umbrella sampling simulations to obtain the free energy barrier for the sulfonium cation formation and to provide an atomistic view of the reaction process.

Quantitative and structural analysis of water association in water-lithium bromide-1,3-dimethylimidazolium chloride mixtures

In this work we report on the quantitative and structural analysis of the water association in water-lithium bromide-1,3-dimethylimidazolium chloride mixtures using multivariate curve resolution based on alternating least squares (MCR-ALS) of Near Infrared (NIR) spectra and Molecular Dynamics (MD) simulations. (NIR + MCR) methodology was used to determine the bulk water amount, as well as the mole ratio between the H2O/absorbent of the solvated structures. Measurements were performed for ternary mixtures prepared with absorbent mole fraction (LiBr + [Dmim][Cl]) from 0 to 0.5987 and the MD simulations were carried out at selected compositions within this concentration range. The results revealed the existence of three water chemical environments: bulk water in absence of solutes, bulk water coexisting with solvated water and solvated water. The comparative analysis of results with those obtained for binary mixtures (H2O + LiBr) and (H2O + [Dmim][Cl]) evidenced that the water amount that remains as bulk water in ternary solutions is higher than in binary mixtures. Classical MD simulations for five different concentrations of absorbent confirmed that water environment evolves from being essentially coordinated with other water molecules in the most diluted system, to being mainly surrounded by monoatomic ions for the most concentrated mixture. Furthermore, higher interaction between the ions appears with increasing the absorbent mole fraction, which is confirmed by Car-Parrinello MD simulations.

Using Car-Parrinello simulations and microscopic order descriptors to reveal two locally favored structures with distinct molecular dipole moments and dynamics in ambient liquid water

Water is essential for life and technological applications, mainly for its unique thermodynamic and dynamic properties, often anomalous or counterintuitive. These anomalies result from the hydrogen-bonds fluctuations, as evidenced by studies for supercooled water. However, it is difficult to characterize these fluctuations under ambient conditions. Here, we fill this knowledge gap thanks to the Car-Parrinello ab initio molecular dynamics (MD) simulation technique. We calculate the local structural order parameter ζ, quantifying the coordination shells separation, and find two locally-favored structures or states: High-ζ and Low-ζ. On average, High-ζ molecules have a tetrahedral arrangement, with four hydrogen bonds, and the first and the second coordination shell well separated. The Low-ζ molecules are less connected, partially merging the first and the second shells. The appearance of isosbestic points in the radial distribution functions and the collective density fluctuations at different length scales and timescales reveal that the two-state model, consistent with available experimental data for supercooled water, also holds under ambient conditions, as we confirm by analyzing the vibrational spectrum of both types of water molecules. Significant consequences of the structural differences between the two states are that High-ζ molecules have a dipole moment 6 % higher than Low-ζ. At the same time, Low-ζ structures are more disordered and with more significant angular fluctuations. These differences are also reflected in the dynamics under ambient conditions. The Low-ζ molecules decorrelate their reorientation faster than High-ζ and merge their coordination shells within 0.2 ps, while the High-ζ preserve the shell separation for longer times. Our analysis shows that first-principle calculations make predictions under ambient conditions calling for new and definitive experiments confirming the two-state model.

Enhanced Selectivity of the Propylene Epoxidation Reaction on a Cu Monolayer Surface via Eley-Rideal Mechanism.

The aerobic oxidation of propylene to selectively achieve propylene oxide (PO) is a challenging reaction in catalysis. Therefore, an active catalyst which shows enhanced PO selectivity is extremely desired. In the present investigation, an attempt has been made to explore the catalytic activity of a mono-atomically thin two-dimensional (2D) hexagonal (HX) Cu layer for selective propylene epoxidation using molecular O2 with the aid of density functional theory calculations. The results reveal that the conversion of propylene to PO via Eley-Rideal mechanism is an exoergic and barrierless reaction on the O2 pre-adsorbed Cu monolayer. The Pauli energy component plays a decisive role for barrierless reaction whereas the electrostatic and orbital contribution governs the energetic stability of PO. Car-Parrinello molecular dynamics (CPMD) simulation reinforces the outcomes of climbing image nudged elastic band (CI-NEB) calculation. Further, the formation of oxametallacycle OMC-2 (0.47 eV) is kinetically favourable over OMC-1 (0.87 eV) and AHS (0.50 eV) on O pre-adsorbed 2D HX Cu. Interestingly, the energy barrier for the conversion of OMC-2 to PO (0.70 eV) is considerably low in comparison with the acetone formation (0.90 eV). Therefore, it is worth to mention that the 2D HX Cu surface provides a promising platform for selective propylene epoxidation.

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives.

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car–Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion—the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.

From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases.

The amyloid β-protein is an intrinsically disordered protein that has the potential to assemble into myriad structures, including oligomers and fibrils. These structures are neurotoxic and are thought to initiate a cascade of events leading to Alzheimer's disease. Understanding this pathogenetic process and elucidating targets for drug therapy depends on elucidation of the structural dynamics of Aβ assembly. In this chapter, we describe work packages required to determine the three-dimensional structures of Aβ and of smaller bioactive fragments thereof, which may be important in AD pathogenesis. These packages include density functional theory, Car-Parrinello molecular dynamics simulations, temperature-dependent replica exchange molecular dynamics simulations, disorder predictors based on bioinformatics, and neural network deep learning.

Exoergic pathways triggered by O/H radicals in different metallic carbohydrazide perchlorates (M2+ = Mn2+, Fe2+, Co2+, Ni2+, Zn2+ and Cd2+).

Metallic carbohydrazide perchlorates (M[(N2H3)2C = O](ClO4)2, M2+ = Mn2+, Fe2+, Co2+, Ni2+, Zn2+ and Cd2+, simplified as MCPs) are a series of energetic primary explosives, among which ZnCP and CdCP are already applied in civilian/military fields. The six MCPs possess similar structures but demonstrate different energetic performances in their decomposition, which are obviously determined by their different central metals. Here, we apply DFT and Car-Parrinello molecular dynamics (CPMD) to understand the electronic structures and decomposition pathways of the MCPs. Based on the results, the crystal MCPs with larger electronic band gaps show lower impact sensitivity. However, the friction sensitivity of MCPs is dominated by the strength of their intermolecular O⋯H interactions. In the CPMD simulations, we obtained a different conclusion from the traditional viewpoint, where the decomposition is spontaneous from the cleavage of M-N bonds. Indeed, there are two stages in the decomposition of the MCPs, based on our calculations: (I) nonspontaneous 3-step departure of the CHZ groups and (II) spontaneous exoergic decomposition pathways of the CHZ groups triggered by the transfer of O/H radicals. Our study provides a systematic study of the MCP family, which also affords a new route for understanding the relationship between the energetic properties and electronic structures of energetic metal complexes.

Combined ReaxFF and Ab Initio MD Simulations of Brown Coal Oxidation and Coal-Water Interactions.

In this manuscript, we use a combination of Car–Parrinello molecular dynamics (CPMD) and ReaxFF reactive molecular dynamics (ReaxFF-MD) simulations to study the brown coal–water interactions and coal oxidation. Our Car–Parrinello molecular dynamics simulation results reveal that hydrogen bonds dominate the water adsorption process, and oxygen-containing functional groups such as carboxyl play an important role in the interaction between brown coal and water. The discrepancy in hydrogen bonds formation between our simulation results by ab initio molecular dynamics (CPMD) and that by ReaxFF-MD indicates that the ReaxFF force field is not capable of accurately describing the diffusive behaviors of water on lignite at low temperatures. The oxidations of brown coal for both fuel rich and fuel lean conditions at various temperatures were investigated using ReaxFF-MD simulations through which the generation rates of major products were obtained. In addition, it was observed that the density decrease significantly enhances the generation of gaseous products due to the entropy gain by reducing system density. Although the ReaxFF-MD simulation of complete coal combustion process is limited to high temperatures, the combined CPMD and ReaxFF-MD simulations allow us to examine the correlation between water adsorption on brown coal and the initial stage of coal oxidation.

Dissociative Adsorption of H2 S on Li(110) Surface Using Density Functional Theory Calculations and Car-Parrinello Molecular Dynamics Simulations.

The information concerning dissociative adsorption of H2 S on Li surface is inadequate and the mechanistic insight for its complete dissociation is yet to be explored. The present investigation aims to scrutinize the dissociative adsorption of H2 S on Li(110) surface using density functional theory calculations. The climbing image nudged elastic band calculation was employed to unveil the relative energy profiles for S-H dissociation. To elucidate the components of interaction energy responsible for stabilizing the adsorbed moieties on the surface, periodic energy decomposition analysis was performed. A Car-Parrinello molecular dynamics (CPMD) simulation was performed to understand the dynamic behaviour of H2 S on Li(110). Results vividly demonstrates: (i) partially dissociated product with perpendicular S-H is comparatively stable than the parallel SH, (ii) completely dissociated moieties H/H/S are the most stable among all, (iii) dissociation of first S-H is barrierless and the second S-H dissociation is a low energy barrier reaction, (iv) complete dissociation of H2 S occurs in a stepwise manner, (v) orbital and electrostatic contributions of the interaction energy plays a vital role in stabilizing the dissociated moieties, and (vi) stepwise dissociation of H2 S was further reinforced by CPMD.

Gas sensing behavior and adsorption mechanism on χ3 borophene surface

Following the demands to find high sensitivity sensors for pollutant gases with compact size, we investigate the adsorption mechanism and detecting capability of χ3 borophene, based on the density functional theory (DFT) calculations. Except for HCN, the overall structure of adsorbed molecules is maintained during the adsorption on the χ3 borophene surface. The obtained adsorption energies vary from −0.20 to −2.45 eV. While the CO2 molecule has a weak interaction with the surface, other molecules, notably CO, NO, NO2, SO, SO2, and SO3 adsorb strongly to the surface. The minimum-energy path and energy barrier for dissociation of the HCN molecule on the surface were studied in detail through the CI-NEB method. Plots of charge density difference and electron localization function demonstrated the covalent character of the formed bonds between N or S-containing gases and the surface. Our investigations of surface and adsorbate band alignments clearly justify the amount of charge transfer in the gap between the Fermi level of χ3 borophene and the LUMO of gas molecules. Furthermore, the surface sensitivity to adsorption was confirmed by analyzing the changes in the transmission coefficient, calculated with the non-equilibrium Green’s function approach. In terms of recovery time, SO, SO3, and NO2 molecules diminish the surface sensing performance, but the χ3 borophene surface is suitable for their removal from the environment. Accordingly, the thermal stability and adsorption capacity of these gases was investigated by Car-Parrinello molecular dynamics simulations. Our study not only clarifies the mechanism of the adsorption of various gas molecules on the χ3 borophene surface, but also reveals the benefit of χ3 in the sensing and removal of these gas species.

Phase-transition behavior of (H2O) n=1-4 few-body systems from Car–Parrinello molecular dynamics

ABSTRACT Car–Parrinello molecular dynamics simulations were applied to investigate phase-transition behavior of (HO) few-body system for n=1−4 at BLYP-GGA level of density-functional theory. A number of important indicators including Lindemann index, ionic mean square displacements, radial distribution function, and shape deformation parameter were accordingly calculated as functions of temperature from 5 to 2000 K. All the four systems exhibited high thermal stabilities compared to bulk water with melting points estimated at , and 700 K for n=2,3, and 4, respectively. No obvious melting behavior was also observed for n=1 due to strong O–H covalent bonds. These values were also found to obey a decreasing trend as the size of the system increases, showing that a minimum size value can also be estimated for which characteristics of liquid water at the thermodynamic limit would consequently appear, in case of studying larger systems with .