Ab Initio Molecular Dynamics Approach Research Articles

Amorphization of MXenes: Boosting Electrocatalytic Hydrogen Evolution.

The emergence of amorphous 2D materials has opened up new avenue for materials science and nanotechnology in the recent years. Their unique disordered structure, excellent large-area uniformity, and low fabrication cost make them important for various industrial applications. However, there have no reports on the amorphous MXene materials. In this work, the amorphous Ti2C-MXene (a-Ti2C-MXene) model is built by ab initio molecular dynamics (AIMD) approach. This model is a unique amorphous model, which is totally different from continuous random network (CRN) model for silicate glass and amorphous model for amorphous 2D BN and graphene. The structure analysis shows that the a-Ti2C-MXene composited by [Ti5C] and [Ti6C] cluster, which are surrounded by the region of mixed cluster [TixC], [Ti-Ti] cluster, and [C-C] cluster. There is a high chemical activity for hydrogen evolution reaction (HER) in a-Ti2C-MXene with |ΔGH| 0.001eV, implying that they serve as the potential boosting HER performance. The work provides insights that can pave the way for future research on novel MXene materials, leading to their increased applications in various fields.

Pyridinic Dominance N-Doped Graphene: A Potential Material for SO2 Gas Detection.

The sensors based on graphene have shown great promise in the detection of toxic air pollutants that are detrimental to nature and create risks to human health. Many recent experimental and computational efforts have been dedicated to sensor concepts incorporating pure graphene, graphene oxide, and doped graphene. Herein, a combination of spin-polarized density functional theory (DFT) with van der Waals correction and ab initio molecular dynamics (AIMD) approaches are utilized to assess the gas sensing potential of pyridinic dominance N-doped graphene (PNG) toward SO2 detection. The potential of PNG systems as SO2 sensing can be explored through an in-depth analysis of adsorption energies, electronic parameters, charge transfer, selectivity, and thermal stability. It is further demonstrated that external strains and the modulation of external electric fields are two effective ways to modify the adsorption strength. In light of these findings, our studies suggest that PNG monolayers have the potential to be an essential substrate for the detection of SO2.

An investigation into the adsorption mechanism of n-butanol by ZIF-8: a combined experimental and ab initio molecular dynamics approach.

The zeolitic imidazolate framework, ZIF-8, has been shown by experimental methods to have a maximum saturation adsorption capacity of 0.36 g g-1 for n-butanol from aqueous solution, equivalent to a loading of 14 butanol molecules per unit cell or 7 molecules per sodalite β-cage. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) shows the presence of hydrogen bonding between adsorbed butanol molecules within the cage; the presence of three different O-H stretching modes indicates the formation of butanol clusters of varying size. Ab initio molecular dynamics simulations show the formation of intermolecular hydrogen bonding between the butanol molecules, with an average hydrogen-bond coordination number of 0.9 after 15 ps simulation time. The simulations also uniquely demonstrate the presence of weaker interactions between the alcohol O-H group and the π-orbital of the imidazole ring on the internal surface of the cage during early stages of adsorption. The calculated adsorption energy per butanol molecule is -33.7 kJ mol-1, confirming that the butanol is only weakly bound, driven primarily by the hydrogen bonding. Solid-state MAS NMR spectra suggest that the adsorbed butanol molecules possess a reasonable degree of mobility in their adsorbed state, rather than being rigidly held in specific sites. 2D 13C-1H heteronuclear correlation (HETCOR) experiments show interactions between the butanol aliphatic chain and the ZIF-8 framework experimentally, suggesting that O-H interactions with the π-orbital are only short lived. The insight gained from these results will allow the design of more efficient ways of recovering and isolating n-butanol, an important biofuel, from low-concentration solutions.

Formation Mechanism of Odd- and Even-Numbered Hydrogen Cluster Cations Using the Direct Ab Initio Molecular Dynamics Approach.

The photoreaction of hydrogen clusters caused by cosmic-ray irradiations plays a crucial role in interstellar molecular clouds because the reaction of molecules takes place in these surrounding clusters. Previous gas-phase experiments introduced the reaction products after the ionization of the neutral hydrogen cluster. In the experiments, the odd-numbered hydrogen cluster cation, H+(H2)m, was the main product, while the even-numbered cluster cation, (H2)n+, was the minor product. However, the formation yield of (H2)n+ was significantly low. Despite many theoretical calculations and experiments, the formation mechanism of odd- and even-numbered cluster ions from ionized hydrogen clusters is still unclear. In this study, the direct ab initio molecular dynamics (AIMD) method was applied to the reaction of the hydrogen cluster cation (H2)n+ to understand the abovementioned formation mechanism. The trajectories of (H2)n+ following the vertical ionization of the neutral cluster were calculated. Direct AIMD calculations indicated that odd-numbered cluster cations, H3+(H2)n-2 + H (dissociation), were formed directly as the main product after the ionization of (H2)n. An even-numbered cluster, (H2)n+, was temporally formed when an H-shaped complex composed of three H2 molecules existed within a neutral cluster. However, it was rapidly dissociated to an odd-numbered cluster. Static ab initio calculations suggested that the odd-numbered cluster complex, H3+(H2)n-2-H, could be transferred to even-numbered ions via a transition state with a low energy barrier. The even-numbered cluster cation was formed stepwise from the odd-numbered cluster cation. The formation mechanism of odd- and even-numbered cluster cations is discussed based on these results.

The chemistry of AlF and CaF production in buffer gas sources.

In this work, we explore the role of chemical reactions on the properties of buffer gas cooled molecular beams. In particular, we focus on scenarios relevant to the formation of AlF and CaF via chemical reactions between the Ca and Al atoms ablated from a solid target in an atmosphere of a fluorine-containing gas, in this case, SF6 and NF3. Reactions are studied following an ab initio molecular dynamics approach, and the results are rationalized following a tree-shaped reaction model based on Bayesian inference. We find that NF3 reacts more efficiently with hot metal atoms to form monofluoride molecules than SF6. In addition, when using NF3, the reaction products have lower kinetic energy, requiring fewer collisions to thermalize with the cryogenic helium. Furthermore, we find that the reaction probability for AlF formation is much higher than for CaF across a broad range of kinetic temperatures.

Relationship between local coordinates and thermal conductivity in amorphous carbon

To determine the correlation between local structure and thermal conductivity of amorphous carbon, we investigated heat conduction in 216-atom systems with different densities (2.0–3.4 g/cm3) using the ab initio molecular dynamics approach. By applying the Allen–Feldman theory with interatomic force constants from ab initio calculations, we report a significant correlation between the thermal conductivity and the density. To clarify which structural characteristics in the high- and low-density cases determine the magnitude of thermal conductivity, we performed geometrical and topological analyses. Coordination number analysis and ring statistics revealed that the sp/sp2/sp3 bond ratios and topological characteristics correlate with density. We also demonstrated that these structural characteristics can be quantified using persistent homology analysis, providing a predictive model of thermal conductivity.

Phonon–phonon interaction assisted electron–hole recombination in WSe2/hBN van der Waals heterostructure

Photogenerated charge carrier dynamics at the WSe2/hBN van der Waals interface play an important role in optical device applications. The carrier behavior has been argued to be related to the interlayer phonon–phonon interaction in the heterostructure. However, the effect of the interlayer coupling on the electron–hole recombination dynamics is still unclear. Using the ab initio nonadiabatic molecular dynamics approach, we investigate the photoexcited electron dynamics at the interface, which has a type I energy alignment. The out-of-plane phonon of hBN is found to strongly couple with the WSe2 out-of-plane A′1 phonon, enhancing the electron–phonon interaction and accelerating the electron–hole recombination compared to pristine WSe2. Our work provides valuable guidance on the design of novel two-dimensional optoelectronic and opto-phononic devices.

Investigating Tunneling-Controlled Chemical Reactions through Ab Initio Ring Polymer Molecular Dynamics.

We use the ab initio ring polymer molecular dynamics (RPMD) approach to investigate tunneling-controlled reactions in methylhydroxycarbene. Nuclear tunneling effects enable molecules to overcome the barriers which cannot be overcome classically. Under low-temperature conditions, intrinsic quantum tunneling effects can facilitate the chemical reaction in a pathway that is favored neither thermodynamically nor kinetically. This behavior is referred to as the tunneling-controlled chemical reaction and is regarded as the third paradigm of chemical reaction controls. In this work, we use the ab initio RPMD approach to incorporate the tunneling effects in our quantum dynamics simulations and investigate the reaction kinetics of two competitive reaction pathways at various temperatures. The reaction rate constants obtained here agree extremely well with the experimentally measured rates. We demonstrate the feasibility of using ab initio RPMD rate calculations in a realistic molecular system and provide an interesting and important example for future investigations of reaction mechanisms dominated by quantum tunneling effects.

A polarizability driven ab initio molecular dynamics approach to stimulating Raman activity: Application to C20

We describe a novel variant of the driven molecular dynamics (DMD) method derived for probing Raman active vibrations. The method is an extension of the conventional μ-DMD formulation for simulating IR activity by means of coupling an oscillating electric field to the molecule’s dipole moment, μ, and inducing absorption of energy via tuning the field to a resonant frequency. Presently, we modify the above prescription to invoke Raman activity by coupling two electric fields, i.e. a ‘Pump’ photon of frequency ωP and a Stokes photon of frequency ωS to the molecule’s polarizability tensor, α, with the difference in the frequencies ω = ωP – ωS corresponding to the Stokes Raman shift. If ω is close to a Raman active vibrational frequency, energy absorption ensues. Varying ω allows identifying and assigning all Raman active vibrational modes, including anharmonic corrections, by means of trajectory analysis. We show that only one element of the full polarizability tensor, and its nuclear derivative, is needed for an α-DMD trajectory, making this method well suited for ab initio dynamics implementation. Numerical results using first-principles calculations are presented and discussed for the vibrational fundamentals, combination bands, overtones of H2O, CH4, and the C20 fullerene.

Effect of temperature on the structure of Pd8 and Pd7Au1 clusters: an Ab initio molecular dynamics approach

Effect of temperature on the structure of Pd8 and Pd7Au1 clusters: an Ab initio molecular dynamics approach

Stoichiometric amorphous boron carbide (BC)

In this work, a stoichiometric amorphous boron carbide (a-BC) network is constructed via an ab initio molecular dynamics approach. Its structural, electrical and mechanical features are reconnoitered in details and compared with those of turbostratic BC and some important graphite-like amorphous materials. Our computer-generated structure exhibits strong chemical disorder as seen in turbostratic BC. However, it has mixed sp2 and sp3 hybridizations and the average coordination number of B and C atoms is projected to be $$\sim$$ 3.22 and 3.46, correspondingly. Consequently, a-BC appears to be structurally different from turbostratic BC and graphite-like amorphous systems. a-BC is semiconductor having a theoretical band gap of $$\sim$$ 0.20 eV. The bulk, Young’s and shear moduli are estimated as $$\sim$$ 105, 142 and 56 GPa, respectively. Its Vickers hardness is calculated to be about 7–8.5 GPa. a-BC is anticipated to be electronically and mechanically parallel to amorphous boron carbonitride.

Atomic ordering at the interfaces between liquid Al and solid MgO: An Ab Initio molecular dynamics study

ABSTRACTMagnesia (MgO) particles inevitably exist in Al-Mg based alloys and can act as potential nucleation sites during solidification processing. In this paper we investigated the effect of MgO substrates on the atomic ordering in the liquid Al adjacent to the liquid Al/solid MgO interfaces using an ab initio molecular dynamics approach. We found that at thermal equilibrium, on the O-terminated MgO{1 1 1} surface forms an Al-terminating layer that contains vacancies and is thus atomically rough. In contrast, we found that both Mg-terminating MgO{1 1 1} and MgO{0 0 1} substrates are stable in liquid Al. The analysis suggests that the MgO{1 1 1} substrate with a new Al-terminating layer has much less templating power for atomic ordering in the liquid Al compared with that of the Mg-terminated MgO{1 1 1} substrate. In addition, there is also little atomic ordering in the liquid Al adjacent to the MgO{0 0 1} substrate due to the chemical interaction between the substrate surface and the liquid Al.

The importance of the composite mechanisms with two transition states in the F- + NH2I SN2 reaction.

The dynamics of the bimolecular nucleophilic substitution (SN2) reactions at nitrogen are less understood than those of their corresponding reactions at carbon. In this paper, we report an ab initio molecular dynamics approach to investigate the reaction mechanisms of the F- + NH2I SN2 reaction at nitrogen. We found not only the one-transition-state mechanisms, but also the composite mechanisms with two and three transition states. For the two-transition-state mechanisms, the double inversion mechanism and the proton-abstraction roundabout followed by the backside-attack reaction mechanism have been reported before; but we discovered that there is also a new, front-side attack followed by the backside-attack Walden-inversion mechanism. Furthermore, a composite mechanism with three transition states also shows up in the reactive trajectories. Our results show that, as the collision energy increases, the SN2 reactivity decreases, and the proton-abstraction reactivity increases. The two-transition-state mechanisms, especially the double-inversion mechanism, make the largest contribution to the SN2 reactivity, followed then by the one-transition-state mechanisms, with the three-transition-state mechanism contributing the least. The potential energy profiles of the reaction mechanisms are characterized at the CCSD(T)/aug-cc-pVTZ(PP) level of theory. The analysis on stationary points shows that the proton-abstraction inversion transition state is ∼12.4 kcal mol-1 lower than the Walden-inversion transition state in contrast to the corresponding reaction at carbon F- + CH3I, in which the former is ∼26.1 kcal mol-1 higher than the latter. This might explain why the composite mechanism of the double inversion mechanism contributes the most to the SN2 reactivity in the F- + NH2I reaction.

Methanol synthesis from CO2/H2 on Cu (1 0 0): Two-tier ab initio molecular dynamics study

We carried out a two-tier ab initio molecular dynamics approach to investigate the molecular-level mechanism of methanol synthesis from CO2/H2 on a Cu (1 0 0) surface. The first-tier calculations were performed with the surface covered with the maximum number of adsorbates, and the second-tier calculations only with one set of the reactant species. A novel intermediate HCOHOH* was discovered, resulting in two reaction routes to form methanol. The first route is the attack on HCOHOH* by H2 molecule, and the second is a proton transfer reaction between two adjacent HCOHOH*s. This finding confirms the existence of the HCOHOH* intermediate suggested in an experimental study. The proposed two reaction paths have the same largest barrier of 0.68 eV for the rate-limiting step, which agrees with the mean activation energy at 0.77 ± 0.06 eV determined experimentally.

Ab initio surface hopping excited-state molecular dynamics approach on the basis of spin-orbit coupled states: An application to the A-band photodissociation of CH3 I.

Ab initio molecular dynamics approach has been extended to multi-state dynamics on the basis of the spin-orbit coupled electronic states that are obtained through diagonalization of the spin-orbit coupling matrix with the multi-state second-order multireference perturbation theory energies in diagonal elements and the spin-orbit coupling terms at the state-averaged complete active space self-consistent field level in off-diagonal elements. Nonadiabatic transitions over the spin-orbit coupled states were taken into account explicitly by a surface hopping scheme with utilizing the nonadiabatic coupling terms calculated by numerical differentiation of the spin-orbit coupled wavefunctions and analytical nonadiabatic coupling terms. The present method was applied to the A-band photodissociation of methyl iodide, CH3 I + hv → CH3 + I (2 P3/2 )/I* (2 P1/2 ), for which a pioneering theoretical work was reported by Amatatsu, Yabushita, and Morokuma. The present results reproduced well the experimental branching ratio and energy distributions in the dissociative products. © 2018 Wiley Periodicals, Inc.

Dust Motions in Magnetized Turbulence: Source of Chemical Complexity

Abstract In addition to the manufacture of complex organic molecules from impacting cometary and icy planet surface analogs, which is well-established, dust grain–grain collisions driven by turbulence in interstellar or circumstellar regions may represent a parallel chemical route toward the shock synthesis of prebiotically relevant species. Here we report on a study, based on the multi-scale shock-compression technique combined with ab initio molecular dynamics approaches, where the shock-wave-driven chemistry of mutually colliding isocyanic acid (HNCO) containing icy grains has been simulated by first principles. At the shock-wave velocity threshold triggering the chemical transformation of the sample (7 km s−1), formamide is the first synthesized species, thus being the springboard for the further complexification of the system. Also, upon increasing the shock impact velocity, formamide is formed in progressively larger amounts. More interestingly, at the highest velocity considered (10 km s−1), impacts drive the production of diverse carbon–carbon bonded species. In addition to glycine, the building block of alanine (i.e., ethanimine) and one of the major components of a plethora of amino acids including, e.g., asparagine, cysteine, and leucine (i.e., vinylamine), have been detected after shock compression of samples containing the most widespread molecule in the universe (H2) and the simplest compound bearing all of the primary biogenic elements (HNCO). The present results indicate novel chemical pathways toward the chemical complexity typical of interstellar and circumstellar regions.

Atomic diffusion in liquid nickel: First-principles modeling.

Self- and impurity diffusion coefficients are assessed in the liquid nickel system by the fundamental ab initio molecular dynamics approach. The impurity diffusion coefficients in the Ni-X systems (X=C, Co, N, Nb, Ta, Ti, W) are mostly not available in the current literature. The simulations are performed at four temperatures, in the range from 1903 to 2303 K, which allows to extract activation energies and frequency factors for the temperature dependent diffusion coefficient assuming an Arrhenius-type behavior in the liquid. In addition to the temperature dependence, the concentration-dependent impurity diffusion was investigated for the Ni-Co system. The data are of relevance for the development of the state-of-the art Ni-based superalloys and alternative binder systems in cemented carbides. The obtained theoretical results are in very good agreement with the limited experimental data for the diffusion in liquid Ni systems.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH)2 and (DCOOH)2, using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm-1. Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm-1. In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

(Invited) Modeling Glassy Electrolytes for All-Solid-State Sodium Ion Batteries

Solid-state sodium ion batteries, a relatively safe and potentially cost-effective technology for electrical grid-scale energy storage, has attracted significant scientific attention in recent times. However, identifying solid electrolytes with high ionic conductivity at room temperature is a requirement in order to commercialize solid state sodium ion batteries. Amorphous sulfide glasses are considered as promising candidates with relatively high ionic conductivity. However, the properties of these electrolytes are highly sensitive to the chemical composition. We present a multiscale approach, which employs atomistic simulations coupled with mesoscale modeling, to analyze and evaluate transport properties of solid glassy electrolytes. As a model system, we studied sodium sulfide – silicon sulfide [xNa2S – (1-x)SiS2] based electrolytes with varying compositions. We determined the ionic conductivities and activation energies for sodium ion hops using ab initio and classical molecular dynamics (MD) approach. These simulations provide fundamental insights into ion conduction mechanisms as well as help to correlate ionic conductivity with glass structure and composition. We further developed a Monte Carlo model to scale up our calculations to a much larger length-scales that are inaccessible by molecular dynamics simulations. Crucial inputs such as Na+ ions distribution and migration energies obtained from classical and ab initio MD served as key inputs to the Monte Carlo model. This model accurately predicts the ionic conductivity of the glasses in agreement with experimental values. Overall, the multiscale model shows excellent promise in identifying optimal glassy electrolytes for sodium ion batteries.

Computational Study of Surface Reactivity and Metal Dissolution in LixNi0.5Mn1.5O4-Δ

Understanding surface chemistry of Li-ion battery (LIB) cathode materials is crucial for improving their performance. Decomposition of electrolyte and dissolution of transition metal species are interfacial processes both playing key roles in the formation of solid electrolyte interphase (SEI) and contributing to LIB degradation. Here, we focus on spinel LixNi0.5Mn1.5O4-δ as a promising high-voltage cathode material for LIB. By employing a combination of static DFT and enhanced ab initio molecular dynamics (AIMD) approaches we investigate adsorption/decomposition of electrolyte species (e.g., dimethylcarbonate) and kinetics/mechanism of Mn and Ni dissolution into the electrolyte solution. Specifically, we analyze the roles of surface disproportionation reactions and transition metal oxidation states, lithiation/delithiation and formation of oxygen vacancies to identify factors controlling adsorption and dissolution processes.