Functional Theory-based Molecular Dynamics Simulations Research Articles

Electrical conductivity of hydrogen plasmas: Low-density benchmarks and virial expansion including e–e collisions

An improved virial expansion for the low-density limit of the electrical conductivity σ(T,n) of hydrogen as the simplest ionic plasma is presented. Quantum statistical methods provide exact values for the lowest virial coefficients, which serve as a benchmark for analytical approaches to electrical conductivity as well as for numerical results from density functional theory-based molecular dynamics simulations (DFT-MD) or path-integral Monte Carlo simulations. The correction factor introduced by Reinholz et al. [Phys. Rev. E 91, 043105 (2015)] is applied to describe the inclusion of electron–electron collisions in DFT-based calculations of transport coefficients. As a benchmark, the first virial coefficient is correctly described with this approach. The value of the second virial coefficient is discussed, and questions about its value according to DFT-MD simulations are addressed.

Self-Catalytic Ternary Compounds for Efficient Synthesis of High-Quality Boron Nitride Nanotubes.

The large-scale synthesis of high-quality boron nitride nanotubes (BNNTs) has attracted considerable interests due to their applications in nanocomposites, thermal management, and so on. Despite decades of development, efficient preparation of high-quality BNNTs, which relies on the effective design of precursors and catalysts and deep insights into the catalytic mechanisms, is still urgently needed. Here, a self-catalytic process is designed to grow high-quality BNNTs using ternary W-B-Li compounds. W-B-Li compounds provide boron source and catalyst for BNNTs growth. High-quality BNNTs are successfully obtained via this approach. Density functional theory-based molecular dynamics (DFT-MD) simulations demonstrate that the Li intercalation into the lattice of W2 B5 promotes the formation of W-B-Li liquid and facilitates the compound evaporation for efficient BNNTs growth. This work demonstrates a high-efficient self-catalytic growth of high-quality BNNTs via ternary W-B-Li compounds, providing a new understanding of high-quality BNNTs growth.

Three-Electron Two-Centered Bond and Single-Electron Transfer Mechanism of Water Splitting via a Copper–Bipyridine Complex

We report the atomistic and electronic details of the mechanistic pathway of the oxygen-oxygen bond formation catalyzed by a copper-2,2'-bipyridine complex. Density functional theory-based molecular dynamics simulations and enhanced sampling methods were employed for this study. The thermodynamics and electronic structure of the oxygen-oxygen bond formation are presented in this study by considering the cis-bishydroxo, [CuIII(bpy)(OH)2]+, and cis-(hydroxo)oxo, [CuIV(bpy)(OH)(═O)]+, complexes as active catalysts. In the cis-bishydroxo complex, the hydroxide transfer requires a higher kinetic barrier than the proton transfer process. In the case of [CuIV(bpy)(OH)(═O)]+, the proton transfer requires a higher free energy than the hydroxide one. The peroxide bond formation is thermodynamically favorable for the [CuIV(bpy)(OH)(═O)]+ complex compared with the other. The hydroxide ion is transferred to one of the Cu-OH moieties, and the proton is transferred to the solvent. The free energy barrier for this migration is higher than that for the former transfer. From the analysis of molecular orbitals, it is found that the electron density is primarily present on the water molecules near the active sites in the highest occupied molecular orbital (HOMO) state and lowest unoccupied molecular orbital (LUMO) of the ligands. Natural bond orbital (NBO) analysis reveals the electron transfer process during the oxygen-oxygen bond formation. The σ*Cu(dxz)-O(p) orbitals are involved in the oxygen-oxygen bond formation. During the bond formation, three-electron two-centered (3e--2C) bonds are observed in [CuIII(bpy)(OH)2]+ during the transfer of the hydroxide before the formation of the oxygen-oxygen bond.

Structure and rotational dynamics of water around hydrogen peroxide

The density functional theory-based molecular dynamics simulations were induced to study various properties of water around different solvation pockets around hydrogen peroxide(H2O2). Our study aims to understand water behavior in the vicinity of H2O2 molecule through analyzing structure, hydrogen bond statistics, orientational and non-diffusive jump profile. A water-like peroxide molecule can form four hydrogen bonds with nearby water molecules: two as a proton donor and two as a proton acceptor, which must disturb the local structure and dynamics of the surrounding water. The presence of two different peak maxima in radial distribution function (RDF) allows us to resolve the solvation environment into three solvation sites: solvation shell I, solvation shell II, and bulk. The probability distribution of the average distance of central water molecule from 4 nearest water molecules shows a shift in the peak for solvation shell I water molecules towards a ∼0.3Å higher value compared to two other solvation shells. This further affects tetrahedral order parameters as water molecules shift from the regular tetrahedron. For the first solvation layer, the water molecules lose their tetrahedrality to a significant extent as qtet probability distribution peaks at 0.5 and broaden in the higher values of qtet without any shoulder. For the second solvation layer, we find the qtet peak at 0.87 with a minor shoulder appearing at qtet = 0.55, a sign of slight loss of tetrahedrality in the unstructured water compared to undisturbed water. Loss of tetrahedrality hints at the change of orientation of H2O molecules in the vicinity of H2O2 and affects the water-water hydrogen bond (HB) formation. A noteworthy reduction in the HB donor/acceptor account and per water HB count shows interference of H2O2. The water molecules prefer H2O2 compared to neighboring water molecules for HB formation. The orientation autocorrelation function provides the rotational pace of water molecules in the different solvation layers. The reorientation time constant difference in the solvation shells I and II fluctuate by mere 0.20 ps, showcasing the trivial nature of hydrogen peroxide and water HBs. Using the HB descriptors, we also report the non-diffusive jump profile involving vicinal water molecules of H2O2. The jump angle profile of solvation shell water molecules is in line with bulk water.

Mechanistic Insight on the Solid Electrolyte Interphase (SEI) Formed By a Superconcentrated [Li][TFSI] in Acetonitrile Electrolyte Near Lithium Metal

Superconcentrated salt solutions are promising alternatives to conventional electrolytes in Li-ion batteries because of their enhanced redox stability and tendency to form a stable and rigid solid electrolyte interphase (SEI). Herein, we performed density functional theory-based molecular dynamics (DFT-MD) simulations to understand the initial electrode reactions between the Li metal and superconcentrated electrolyte solution of Li bis(trifluoromethanesulfonyl)imide ([Li][TFSI]) in acetonitrile (AN). We thoroughly analyzed the structure and composition of the SEI formed near the Li metal. We show that reductive decomposition of the TFSI anions contributes majorly in the initial SEI formation and the AN molecules are relatively stable against the redox processes occurring near the Li metal. The atomized C, O, F, and S atoms contributed by the TFSI anions forms the stable inorganic layer leading to highly structured and inhomogeneous SEI. The AN molecules and undissociated N–SO2–CF3 fragments are mostly aligned away from the Li layers. Figure 1

Virial expansion of the electrical conductivity of hydrogen plasmas.

The low-density limit of the electrical conductivity σ(n,T) of hydrogen as the simplest ionic plasma is presented as a function of the temperature T and mass density n in the form of a virial expansion of the resistivity. Quantum statistical methods yield exact values for the lowest virial coefficients which serve as a benchmark for analytical approaches to the electrical conductivity as well as for numerical results obtained from density functional theory-based molecular dynamics simulations (DFT-MD) or path-integral Monte Carlo simulations. While these simulations are well suited to calculate σ(n,T) in a wide range of density and temperature, in particular, for the warm dense matter region, they become computationally expensive in the low-density limit, and virial expansions can be utilized to balance this drawback. We present new results of DFT-MD simulations in that regime and discuss the account of electron-electron collisions by comparison with the virial expansion.

Solvation of anthraquinone and TEMPO redox-active species in acetonitrile using a polarizable force field.

Redox-active molecules are of interest in many fields, such as medicine, catalysis, or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is often required, but few force fields are developed ad hoc for these molecules. Moreover, they do not include polarization effects, which can lead to inaccurate solvation and dynamical properties. In this work, we developed polarizable force fields for redox-active species anthraquinone (AQ) and 2,2,6,6-tetra-methylpiperidinyl-1-oxyl (TEMPO) in their oxidized and reduced states as well as for acetonitrile. We validate the structural properties of AQ, AQ•-, AQ2-, TEMPO•, and TEMPO+ in acetonitrile against density functional theory-based molecular dynamics simulations and we study the solvation of these redox molecules in acetonitrile. This work is a first step toward the characterization of the role played by AQ and TEMPO in electrochemical and catalytic devices.

Graphene–Ionic Liquid Interfacial Potential Drop from Density Functional Theory-Based Molecular Dynamics Simulations

Ionic liquids (IL) are promising electrolytes for electrochemical applications due to their remarkable stability and high charge density. Molecular dynamics simulations are essential for better understanding the complex phenomena occurring at the electrode-IL interface. In this work, we have studied the interface between graphene and 1-ethyl-3-methyl-imidazolium tetrafluoroborate IL, using density functional theory-based molecular dynamics simulations at variable surface charge densities. We have disassembled the electrical double layer potential drop into two main components: one involving atomic charges and the other - dipoles. The latter component arises due to the electronic polarisation of the surface and is related to concepts hotly debated in the literature, such as the Thomas-Fermi screening length, effective surface charge plane, and quantum capacitance.

A silicate dynamo in the early Earth

The Earth’s magnetic field has operated for at least 3.4 billion years, yet how the ancient field was produced is still unknown. The core in the early Earth was surrounded by a molten silicate layer, a basal magma ocean that may have survived for more than one billion years. Here we use density functional theory-based molecular dynamics simulations to predict the electrical conductivity of silicate liquid at the conditions of the basal magma ocean: 100–140 GPa, and 4000–6000 K. We find that the electrical conductivity exceeds 10,000 S/m, more than 100 times that measured in silicate liquids at low pressure and temperature. The magnetic Reynolds number computed from our results exceeds the threshold for dynamo activity and the magnetic field strength is similar to that observed in the Archean paleomagnetic record. We therefore conclude that the Archean field was produced by the basal magma ocean.

Hydration interactions beyond the first solvation shell in aqueous phenolate solution.

We investigate the orientational dynamics of water molecules solvating phenolate ions using ultrafast vibrational spectroscopy and density functional theory-based molecular dynamics simulations. To assess the roles of the hydrophobic and hydrophilic parts of the anion, we also perform experiments and simulations on solutions of phenol. The experiments show that phenolate immobilizes (τor > 10 ps) 6.2 ± 0.5 water molecules beyond the first solvation shell of its oxygen atom, whereas phenol immobilizes only ∼2 water molecules, including the water molecules in its first solvation shell. The simulations reproduce the experiments very well, and show that phenolate causes a local ordering of the hydrogen-bond structure that extends beyond the first solvation shell, thus explaining the experimental observations. The comparison with phenol solution shows that the solvation interaction of phenolate beyond its first solvation shell is due to the high charge density of its negatively charged oxygen atom.

Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays

It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.

Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water–Air Interface

Density functional theory-based molecular dynamics simulations are increasingly being used for simulating aqueous interfaces. Nonetheless, the choice of the appropriate density functional, critically affecting the outcome of the simulation, has remained arbitrary. Here, we assess the performance of various exchange–correlation (XC) functionals, based on the metrics relevant to sum-frequency generation spectroscopy. The structure and dynamics of water at the water–air interface are governed by heterogeneous intermolecular interactions, thereby providing a critical benchmark for XC functionals. We find that the XC functionals constrained by exact functional conditions (revPBE and revPBE0) with the dispersion correction show excellent performance. The poor performance of the empirically optimized density functional (M06-L) indicates the importance of satisfying the exact functional condition. Understanding the performance of different XC functionals can aid in resolving the controversial interpretation of the interfacial water structure and direct the design of novel, improved XC functionals better suited to describing the heterogeneous interactions in condensed phases.

Ethene Dimerization on Zeolite-Hosted Ni Ions: Reversible Mobilization of the Active Site.

The active site in ethene oligomerization catalyzed by Ni-zeolites is proposed to be a mobile Ni(II) complex, based on density functional theory-based molecular dynamics (DFT-MD) simulations corroborated by continuous-flow experiments on Ni-SSZ-24 zeolite. The results of the simulations at operating conditions show that ethene molecules reversibly mobilize the active site as they exchange with the zeolite as ligands on Ni during reaction. Microkinetic modeling was conducted on the basis of free-energy profiles derived with DFT-MD for oligomerization on these mobile [(ethene)2-Ni-alkyl]+ species. The model reproduces the experimentally observed high selectivity to dimerization and indicates that the mechanism is consistent with the observed second-order rate dependence on ethene pressure.

Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations.

The enol form of dibenzoylmethane has been the subject of many experimental and theoretical studies, yet the symmetry and the spectral response of the OHO intramolecular hydrogen bond remains mysterious due to conflicting assignments. In order to qualitatively understand the complex proton dynamics, it is necessary to probe the neighborhood of stationary points on the potential energy landscape. Here, we employ density functional theory-based molecular dynamics (DFT-MD) simulations to sample the coupling between the intermolecular proton transfer and all other molecular modes. To account for the quantum nature of the proton motion, we employ the path integral formalism within the DFT-MD simulations. Our results reveal that the hydrogen-bonded proton is delocalized between two oxygen atoms with sightly higher probability to be observed in the asymmetric than the symmetric position. The simulated infrared spectrum is found to be in a reasonably good agreement with the experimental spectrum. The computed νOH band is remarkably broad and centered around 2640 cm-1. The origin of the discrepancy between the simulated and experimental intensities of the νOH band is discussed.

Bonding in the metallic molecular solid α-Gallium

ABSTRACTSolid, liquid and alloyed phases of gallium play a role in a variety of important technological applications. While many of the gallium phases involved in these applications are metallic, some have been proposed or are known to contain covalently bound Ga dimers. Thus, understanding the nature of bonding in Ga is crucial to the development of Ga-based materials. The solid phase of gallium at ambient conditions, α-Ga, is metallic and composed of molecular dimers, and can serve as a testing ground for studying gallium bonding with electronic structure calculations. We use density functional theory-based molecular dynamics simulations in conjunction with maximally localised Wannier functions to examine the nature of chemical bonding in α-Ga. We propose a geometric criterion for defining various bonding environments, which enables the quantification of covalent and weak bonds in solid gallium. We additionally connect the bonding structure of α-Ga to its phonon density of states and discuss similarities and differences with diatomic halogen crystals.

Research Update: Ca doping effect on the Li-ion conductivity in NASICON-type solid electrolyte LiZr2(PO4)3: A first-principles molecular dynamics study

In this work, we used a density functional theory-based molecular dynamics simulation to investigate the Ca content-dependent Li-ion conductivity of NASICON-type Li1+2xCaxZr2-x(PO4)3 (LCZP) solid electrolytes (0.063 ≤ x ≤ 0.375) which exhibit a Li-excess chemical composition. The LCZP systems show a higher room temperature Li-ion conductivity and a lower activation energy than pristine LiZr2(PO4)3 (LZP), and the tendencies of those properties agree with the experimental results. In addition, the Li-ion conduction mechanisms in LCZP were clarified by analyzing the radial distribution functions and site displacement functions obtained from our molecular dynamics simulations. For minimal Ca substitution for LZP, the Li-ion conductivity is enhanced because of the creation of interstitial Li ions by Ca doping in the LCZP systems; the frequency of collisions with Li ions dramatically increases. For substantial Ca substitution for LZP, the Li-ion conductivity gradually worsened because some Li ions were trapped at the M1 (most stable) and M2 (metastable) sites near Ca atoms.

Anticorrosion potential of domperidone on copper in different concentration of hydrochloric acid solution

The inhibition performance of domperidone on the corrosion of copper in different concentration of HCl solution has been investigated by electrochemical, weight loss, and surface analysis, and theoretical calculation methods. Results indicate that domperidone was found to be an effective inhibitor with the inhibition efficiency as high as 98.5% when the HCl concentration was 0.01 M, and the corrosion rate of copper increased with the increment of HCl concentration from 0.001 to 1 M. The potentiodynamic polarization results revealed that domperidone can be seen as a mixed type inhibitor when the HCl concentration was high (1 and 0.1 M), while it acted as a cathodic inhibitor for copper at low HCl concentrations (0.01 and 0.001 M). The potentiodynamic polarization results revealed that domperidone can be seen as mixed-type or cathodic inhibitor as the HCl concentration changes. Scanning electron microscopy studies indicated the formation of protective films of inhibitor molecule on copper surface. Besides, density functional theory-based quantum chemical calculations and molecular dynamics simulations showed the electronic structure of domperidone and its optimized adsorption configuration on copper surface, which could account for the experimental findings.

Dynamic Stabilization of Metal Oxide-Water Interfaces.

The interaction of water with metal oxide surfaces plays a crucial role in the catalytic and geochemical behavior of metal oxides. In a vast majority of studies, the interfacial structure is assumed to arise from a relatively static lowest energy configuration of atoms, even at room temperature. Using hematite (α-Fe2O3) as a model oxide, we show through a direct comparison of in situ synchrotron X-ray scattering with density functional theory-based molecular dynamics simulations that the structure of the (11̅02) termination is dynamically stabilized by picosecond water exchange. Simulations show frequent exchanges between terminal aquo groups and adsorbed water in locations and with partial residence times consistent with experimentally determined atomic sites and fractional occupancies. Frequent water exchange occurs even for an ultrathin adsorbed water film persisting on the surface under a dry atmosphere. The resulting time-averaged interfacial structure consists of a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Surface pKa prediction based on bond valence analysis suggests that water exchange will influence the proton-transfer reactions underlying the acid/base reactivity at the interface. Our findings provide important new insights for understanding complex interfacial chemical processes at metal oxide-water interfaces.

Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics

The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O−) and doubly protonated oxygens (-OH) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.

Ab initio molecular dynamics study for C–Br dissociation within BrH2C–C≡C(ads) adsorbed on an Ag(111) surface: a short-time Fourier transform approach

The reaction dynamics for C–Br dissociation within BrH2C–C≡CH(ads) adsorbed on an Ag(111) surface has been investigated by combining density functional theory-based molecular dynamics simulations with short-time Fourier transform (STFT) analysis of the dipole moment autocorrelation function. Two possible reaction pathways for C–Br scission within BrH2C–C≡CH(ads) have been proposed on the basis of different initial structural models. Firstly, the initial perpendicular orientation of adsorbed BrH2C–C≡CH(ads) with a stronger C–Br bond will undergo dynamic rotation leading to the final parallel orientation of BrH2C–C≡CH(ads) to cause the C–Br scission, namely, an indirect dissociation pathway. Secondly, the initial parallel orientation of adsorbed BrH2C–C≡C(ads) with a weaker C–Br bond will directly cause the C–Br scission within BrH2C–C≡CH(ads), namely, a direct dissociation pathway. To further investigate the evolution of different vibrational modes of BrH2C–C≡CH(ads) along these two reaction pathways, the STFT analysis is performed to illustrate that the infrared (IR) active peaks of BrH2C–C≡CH(ads) such as vCH2 [2956 cm−1(s) and 3020 cm−1(as)], v≡CH (3320 cm−1) and vC≡C (2150 cm−1) gradually vanish as the rupture of C–Br bond occurs and then the resulting IR active peaks such as C=C=C (1812 cm−1), ω-CH2 (780 cm−1) and δ-CH (894 cm−1) appear due to the formation of H2C=C=CH(ads) which are in a good agreement with experimental reflection adsorption infrared spectrum (RAIRS) at temperatures of 110 and 200 K, respectively. Finally, the total energy profiles indicate that the reaction barriers for the scission of C–Br within BrH2C–C≡CH(ads) along both direct and indirect dissociation pathways are very close due to a similar rupture of C–Br bond leading to a similar transition state.