Oppenheimer Molecular Dynamics Simulations Research Articles

Reaction of SO3 with H2SO4 and its implications for aerosol particle formation in the gas phase and at the air–water interface

Abstract. The reactions between SO3 and atmospheric acids are indispensable in improving the formation of aerosol particles. However, relative to those of SO3 with organic acids, the reaction of SO3 with inorganic acids has not received much attention. Here, we explore the atmospheric reaction between SO3 and H2SO4, a typical inorganic acid, in the gas phase and at the air–water interface using quantum chemical (QC) calculations and Born–Oppenheimer molecular dynamics simulations. We also report the effect of H2S2O7, the product of the reaction between SO3 and H2SO4, on new particle formation (NPF) in various environments using the Atmospheric Cluster Dynamics Code (ACDC) kinetic model and QC calculations. The present findings show that the gas-phase reactions of SO3 + H2SO4 without and with water molecules are both low-energy-barrier processes. With the involvement of interfacial water molecules, H2O induced the formation of the S2O72-⋯H3O+ ion pair, HSO4- mediated the formation of the HSO4-⋯H3O+ ion pair, and the deprotonation of H2S2O7 was observed and proceeded on the picosecond timescale. The present findings suggest the potential contribution of the SO3–H2SO4 reaction to NPF and aerosol particle growth, showing that (i) although H2S2O7 is easily hydrolyzed with water to form H2SO4, it can directly participate in H2SO4–NH3-based cluster formation and can present a more obvious enhancement effect on SA–A-based cluster formation, and (ii) the formed interfacial S2O72- can attract candidate species from the gas phase to the water surface and, thus, accelerate particle growth.

Surface electronic structure and photo activity of double perovskite Ba[formula omitted]PrBiO[formula omitted]: First-principles investigations

Double perovskite Ba2PrBiO6 exhibits photo catalytic activity in the visible light range with the observed optical band gap of ∼1.0 eV. On the other hand, density functional theory (DFT) calculations predict a larger bulk band gap of 2.0 eV even with the standard Perdew–Burke–Ernzerhof (PBE) functional, which is known to underestimate the band gap of semiconductors. Much larger bulk band gap of 3.13 eV is predicted with a hybrid functional treatment for the exchange–correlation, which generally gives better descriptions for them. This discrepancy between experiment and theory implies the presence of unknown mechanism which effectively reduces the band gap of Ba2PrBiO6 and thereby gains the sensitivity to the visible light. The first finding is that the surface band gaps of Ba2PrBiO6 calculated using an appropriate hybrid functional are smaller than the bulk band gaps and are 2.49 eV and 2.85 eV for the Pr–Bi and Ba–O polar surfaces, respectively. We also find that work function is quite sensitive to the surface structures and its accurate calculations are essential to show that the reduction and oxidation levels are fit to the gap region. When a substitutional defect PrBi, in which Bi is substituted by Pr, is introduced into the Pr–Bi polar surface, surface band gap is further reduced to 0.93 eV, being very close to the experimental value. For the Ba–O polar surface, similar reduction to 1.59 eV is found but not substantial as compared to the Pr–Bi polar surface. These narrow surface band gaps may be the origin of the photo activity of Ba2PrBiO6 in the visible light region. We also performed Born–Oppenheimer molecular dynamics simulations to clarify the reactivity of the polar surfaces to water. We find that two hydroxyl groups were created in the adsorption of a single H2O molecule. The decomposition of water molecule in the adsorption indicates that the polar surfaces provide a promising stage for the photo catalytic activity. Further adsorption of H2O molecules leads to their diffusion on the surface.

The reaction mechanism of SO3 with the multifunctional compound ethanolamine and its atmospheric implications.

SO3 is an important reactive species in sulfur cycle and sulfuric acid formation processes and its reactions with some functional group substances, such as H2O, NH3, CH3OH, and organic and inorganic acids, have been extensively studied. However, its loss mechanism with multifunctional species is still lacking in detail. Herein, the reaction mechanism between SO3 and monoethanolamide (MEA) was investigated in the gas phase and on water droplets. The quantum chemical calculations indicate that the gas-phase reactions of SO3 with the OH and NH2 moieties of MEA hardly occur as their reaction energy barriers are up to 21.9-29.4 kcal mol-1. When a single water molecule is added into the SO3 + MEA reaction, it not only decreases the reaction barrier by at least 15.0 kcal mol-1 and thus enhances the rate obviously, but can also lead to the main product changing from HOCH2CH2NHSO3H to NH2CH2CH2OSO3H. The Born Oppenheimer molecular dynamics simulations on a water droplet show that the routes of the NH2CH2CH2OSO3-⋯H3O+ ion pair, HSO4- and HOCH2CH2NH3+ ions and zwitterionic formations of HOCH2CH2NH2+-SO3- and SO3--OCH2CH2NH3+ occur through a loop-structure route or chain reaction process, and can be finished within several picoseconds. Interestingly, the nucleation simulations show that the products of HOCH2CH2NHSO3H and NH2CH2CH2OSO3H have a potential ability to participate in the formation of new particles as they can form larger clusters with H2SO4, NH3 and H2O molecules within 20 ns. Thus, the present study will not only give new insight into the reaction between SO3 and multifunctional compounds, but also provide a new potential formation mechanism for particles resulting from the loss of SO3.

Planar tetracoordinate beryllium compounds with a partially covalent Be-Ng bond.

An analysis of the thermodynamic and kinetic stability and the nature of the chemical bond in hypercoordinated compounds with the formula BeH3Ng+ (Ng = He-Rn) through high-level calculations is presented in this work. Thermochemical calculations show that, for the heavier noble gases (Ar-Rn), these systems are thermodynamically stable at room temperature; however, this stability decreases due to a weakening of the Be-H2 interaction, while the Be-Ng bond strengthens going down the periodic table. These results are complemented by Born Oppenheimer molecular dynamics simulations, in which the increasing tendency to dissociate the Be-H2 bond is evidenced. The nature of the chemical bonding depends on the analysis performed. On the one hand, the interacting quantum atoms method indicates that the covalent contribution is around 25 to 30%. On the other hand, the electron density topology indicates a covalent nature for compounds with Kr-Rn, while Hirshfeld population analysis in conjunction with Mayer's bond order establishes polar covalent behavior. The geometrical parameters and natural energy decomposition analysis (NEDA) indicate a covalent nature, allowing us to consider that the Be-Ng bond has a partially covalent character.

First results from the interaction between hydroxyl radicals and condensed water droplets: A spin-polarized DFT-MD study

The formation of clouds results from condensation of water vapor into liquid water droplets. These water droplets form on the surface of tiny particles that are suspended in the air, like dust. Atmospheric chemistry relies heavily on the hydroxyl radical (OH*), which is highly reactive and prone to combining with hydrogen atoms in other compounds. Despite previous studies concerning liquid, solid, and gas phase interactions, how hydroxyl radicals interact with condensed water droplets is still unknown. OH*-condensed droplet interactions show unique behavior, according to our studies. Several hydrogen transfers were detected during the interaction process. It takes approximately 3.5 kcal/mol of energy to initiate hydrogen transfer. Moreover, we revealed the dominant structures of hydrated radicals during the mobility of OH* into condensed droplets using Born–Oppenheimer molecular dynamics simulations. In contrast to our previous studies, the hemibond doesn't significantly affect the stability of OH*(H2O)n structures in condensed droplets. Our results showed that condensed droplets hinder the mobility of OH*, causing its diffusion coefficient to decrease. Moreover, several analyses were carried out to investigate condensed droplet surfaces, bonding patterns, and the position of OH* in conjunction with water molecules, including mobility analyses, radial distribution functions, coordination analyses, and population analyses.

Possible Roles of Transition Metal Cations in the Formation of Interstellar Benzene via Catalytic Acetylene Cyclotrimerization.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous interstellar molecules. However, the formation mechanisms of PAHs and even the simplest cyclic aromatic hydrocarbon, benzene, are not yet fully understood. Recently, we reported the statistical and dynamical properties in the reaction mechanism of Fe+-catalyzed acetylene cyclotrimerization, whereby three acetylene molecules are directly converted to benzene. In this study, we extended our previous work and explored the possible role of the complex of other 3d transition metal cations, TM+ (TM = Sc, Ti, Mn, Co, and Ni), as a catalyst in acetylene cyclotrimerization. Potential energy profiles for bare TM+-catalyst (TM = Sc and Ti), for TM+NC--catalyst (TM = Sc, Ti, Mn, Co, and Ni), and for TM+-(H2O)8-catalyst (TM = Sc and Ti) systems were obtained using quantum chemistry calculations, including the density functional theory levels. The calculation results show that the scandium and titanium cations act as efficient catalysts in acetylene cyclotrimerization and that reactants, which contain an isolated acetylene and (C2H2)2 bound to a bare (ligated) TM cation (TM = Sc and Ti), can be converted into a benzene-metal-cation product complex without an entrance barrier. We found that the number of electrons in the 3d orbitals of the transition metal cation significantly contributes to the catalytic efficiency in the acetylene cyclotrimerization process. On-the-fly Born-Oppenheimer molecular dynamics (BOMD) simulations of the Ti+-NC- and Ti+-(H2O)8 complexes were also performed to comprehensively understand the nuclear dynamics of the reactions. The computational results suggest that interstellar benzene can be produced via acetylene cyclotrimerization reactions catalyzed by transition metal cation complexes.

Born–Oppenheimer molecular dynamics study on collective protein dynamics invoked by ultrafast photoisomerization of retinal chromophore in bacteriorhodopsin

Large-scale quantum-chemistry-based Born–Oppenheimer molecular dynamics simulations of collective protein dynamics of bacteriorhodopsin initiated by photoinduced all-trans→ 13-cis isomerization of retinal Schiff base chromophore compensate for missing information from time-resolved serial femtosecond X-ray crystallography measurements in terms of electronic states, energy transfer, and details of structural dynamics.

Reversible Hydrogen Storage by Planar Hypercoordinate Carbon Clusters

Planar hypercoordinate carbon clusters show a high capacity of hydrogen storage with better stability, as revealed by using density functional theory. The interaction energy of H2 with the cluster lies in between chemisorption and physisorption (0.11–0.19 eV). Topological analysis indicates closed shell-type interaction of H2 with the clusters. The clusters remain stable before and after adsorption. The gravimetric densities are found to be 25.6, 39.7, and 13.5 wt % for planar tetracoordinate, pentacoordinate, and hexacoordinate clusters, respectively. Furthermore, Born–Oppenheimer molecular dynamics simulations indicate the reversibility of adsorption. The clusters can accommodate a large number of H2 molecules and can be released at an elevated temperature (400 K). Our computation reveals that the planar clusters may be used as ideal 2D materials for energy storage.

Hydrogen Storage in a Ti-Functionalized Metal Carbyne Framework: Insights from a First-Principles Study

Hydrogen (H2) has the ability to be a future green-energy source for the automotive industry due to its versatility, clean nature, and efficiency as an energy carrier. The biggest obstacle to achieving hydrogen as a potential energy source is the nonavailability of effective hydrogen storage materials. In this proposed work, the hydrogen storage capacity and reversibility of a Ti-functionalized metal carbyne framework (MCF) having carbyne as an organic linker and Mg4O as an inorganic moiety are explored. All structural relaxation and simulation calculations are performed by employing the dispersion-corrected density functional theory computation. In this Ti-functionalized MCF, each Ti can adsorb up to five H2 molecules via the Kubas mechanism, with adsorption energy lying between 0.33 and 0.44 eV, which falls within the range outlined by the U.S. Department of Energy (DOE). For a detailed study of the thermal stability of framework, hydrogen reversibility, and mechanism of hydrogen sorption, Born–Oppenheimer molecular dynamics (BOMD) simulations are carried out at various temperatures. From the findings of BOMD simulations, the Ti-functionalized MCF can reversibly adsorb the H2 molecules with a high gravimetric density of about 9.4 wt %. This proposed Ti-functionalized MCF stands out as a potential hydrogen storage medium meeting the standards established by the DOE.

Shadow energy functionals and potentials in Born-Oppenheimer molecular dynamics.

In Born-Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born-Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born-Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born-Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born-Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original "zeroth-level" shadow energy functionals and potentials used in extended Lagrangian BOMD [Niklasson, Eur. Phys. J. B 94, 164 (2021)]. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree-Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.

Geometric structures and hydrogen storage properties of M2B7 (M=Be, Mg, Ca) clusters

Based on the density functional theory, we investigate the electronic properties of the clusters M2B7 (M = Be, Mg, Ca) and their hydrogen storage properties systematically in this paper. Extensive global search results show that the global minimal structures of the three systems (Be2B7, Mg2B7 and Ca2B7) are heptagonal biconical structure, and the two alkaline earth metals are located at the top of the biconical. Chemical bonding analyses show that M2B7 clusters have 6σ and 6π delocalized electrons, which are doubly aromatic. At the wB97XD level, the three systems have good hydrogen storage capabilities. The hydrogen storage density of Be2B7 is as high as 23.03 wt%, while Mg2B7 and Ca2B7 also far exceed the hydrogen storage target set by the U.S. Department of Energy in 2017. Their average adsorption energies of H2 molecules all ranged from 0.1 eV/H2 to 0.48 eV/H2, which is fall in between physisorption and chemisorption. Extensive Born Oppenheimer molecular dynamics (BOMD) simulations show that the H2 molecules of the three systems can be completely released at a certain temperature. Therefore, M2B7 systems can achieve reversible adsorption of H2 molecules at normal temperature and pressure. It can be seen that the B7 clusters modified by alkaline earth metals may become a promising new nano-hydrogen storage material.

CAl4X4 (X = Te, Po): Double Aromatic Molecular Stars Containing Planar Tetracoordinate Carbon Atoms

Planar tetracoordinate carbon (ptC) species are scarce and exotic. Introducing four peripheral Te/Po auxiliary atoms is an effective strategy to flatten the tetrahedral structure of CAl4 (Td, 1A1). Neutral CAl4X4 (X = Te, Po) clusters possess quadrangular star structures containing perfect ptC centers. Unbiased density functional theory (DFT) searches and high-level CCSD(T) calculations suggest that these ptC species are the global minima on the potential energy surfaces. Bonding analyses indicate that 40 valence-electron (VE) is ideal for the ptC CAl4X4 (X = Te, Po): one delocalized π and three σ bonds for the CAl4 core; four lone pairs (LPs) of four X atoms, eight localized Al-X σ bonds, and four delocalized Al-X-Al π bonds for the periphery. Thus, the ptC CAl4X4 (X = Te, Po) clusters possess the stable eight electron structures and 2π + 6σ double aromaticity. Born-Oppenheimer molecular dynamics (BOMD) simulations indicate that neutral ptC CAl4X4 (X = Te, Po) clusters are robust.

Explainable Artificial Intelligence Approach to Identify the Origin of Phonon‐Assisted Emission in WSe2 Monolayer

The application of explainable artificial intelligence in nanomaterial research has emerged in the past few years, which has facilitated the discovery of novel physical findings. However, a fundamental question arises concerning the physical insights presented by deep neural networks; the model interpretation results have not been carefully evaluated. Herein, explainable artificial intelligence and quantum mechanical calculations is bridged to investigate the correlation between light scattering and emission in a WSe2 monolayer. Convolutional neural networks using light scattering and emission data are first trained, while expecting the networks to determine the relationships between them. The trained models are interpreted and the specific phonon contribution during the exciton relaxation process is derived. Finally, the findings are independently evaluated through quantum mechanical calculations, such as the Born–Oppenheimer molecular dynamics simulation and density functional perturbation theory. The study provides reliable fundamental physical insight by evaluating the results of neural networks and suggests a novel methodology that can be applied in materials science.

Significant influence of water molecules on the SO3 + HCl reaction in the gas phase and at the air-water interface.

The products resulting from the reactions between atmospheric acids and SO3 have a catalytic effect on the formation of new particles in aerosols. However, the SO3 + HCl reaction in the gas-phase and at the air-water interface has not been considered. Herein, this reaction was explored exhaustively by using high-level quantum chemical calculations and Born Oppenheimer molecular dynamics (BOMD) simulations. The quantum calculations show that the gas-phase reaction of SO3 + HCl is highly unlikely to occur under atmospheric conditions with a high energy barrier of 22.6 kcal mol-1. H2O and (H2O)2 play obvious catalytic roles in reducing the energy barrier of the SO3 + HCl reaction by over 18.2 kcal mol-1. The atmospheric lifetimes of SO3 show that the (H2O)2-assisted reaction dominates over the H2O-assisted reaction within the altitude range of 0-5 km, whereas the H2O-assisted reaction is more favorable within an altitude range of 10-50 km. BOMD simulations show that H2O-induced formation of the ClSO3-⋯H3O+ ion pair and HCl-assisted formation of the HSO4-⋯H3O+ ion pair were identified at the air-water interface. These routes followed a stepwise reaction mechanism and proceeded at a picosecond time scale. Interestingly, the formed ClSO3H in the gas phase has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters within 40 ns simulation time, while the interfacial ClSO3- and H3O+ can attract H2SO4, NH3, and HNO3 for particle formation from the gas phase to the water surface. Thus, this work will not only help in understanding the SO3 + HCl reaction driven by water molecules in the gas-phase and at the air-water interface, but it will also provide some potential routes of aerosol formation from the reaction between SO3 and inorganic acids.

Understanding the thermal stability of a 3d, 4d, and 5d element doped aluminium nanocluster through BOMD simulations

ABSTRACT Endohedrally doped atomic clusters have generated considerable interest among computational chemists on account of their tunable chemical properties that mimic a super atom. Such endohedrally doped clusters have also been experimentally realised in the more recent past. The present work explores the practical existence of 3d, 4d and 5d doped aluminium clusters, more specifically doped cluster, by evaluating systematically their structural stability through the first principle molecular dynamical simulations. Born–Oppenheimer Molecular Dynamics (BOMD) simulations have been carried out on atomic clusters where X = Ti, V, Fe, Co, Ni, Cu, Zn, Y, Mo, Ru, Rh and W are in endohedral position. The thermal stability of such endohedrally doped clusters is quantified through parameters such as , MSD and . Electronic structure calculations reveal that endohedral doping of only Rh, Cu and Zn is preferred in the cluster. Other dopants prefer to remain on the surface positions. However, finite temperature calculations reveal that the Zn cluster undergoes surface modifications from 300K leading to a distorted icosahedral structure. Cu cluster in quartet spin state is the only thermally stable cluster with Cu remaining in the endohedral position and structure retaining icosahedral confirmation till 700K.

Trapping the Transition State in a [2,3]-Sigmatropic Rearrangement by Applying Pressure.

Transition states are of central importance in chemistry. While they are, by definition, transient species, it has been shown before that it is possible to "trap" transition states by applying stretching forces. We here demonstrate that the task of transforming the transition state of a chemical reaction into a minimum on the potential energy surface can be achieved using hydrostatic pressure. We apply the computational extended hydrostatic compression force field (X-HCFF) approach to the educt of a [2,3]-sigmatropic rearrangement in both static and dynamic calculations and find that the five-membered cyclic transition state of this reaction becomes a minimum at pressures in the range between 100 and 150 GPa. Born-Oppenheimer molecular dynamics (BOMD) simulations suggest that slow decompression leads to a 70:30 mix of the product and the educt of the sigmatropic rearrangement. Our findings are discussed in terms of geometric parameters and electronic rearrangements throughout the reaction. To provide reference data for experimental investigations, we simulated the IR, Raman, and time-resolved UV/vis absorption spectra for the educt, transition state, and product. We speculate that the trapping of transition states by using pressure is generally possible if the transition state of a chemical reaction has a more condensed geometry than both the educt and the product, which paves the way for new ways of initiating chemical reactions.

H2 and CO adsorption ability of cationic lithiated carbenes: A computational study

Quantum chemical calculations have been carried out to investigate the hydrogen and carbon monoxide adsorption characteristics of cationic lithiated carbene complexes. Through the computation of electron density and electron−density−based reactivity descriptors, the nature of interactions related to the bonding between carbene and lithium as well as that between lithium and adsorbed H2 and CO are examined. Calculations reveal that the carbene−Li + complexes can absorb a maximum of four H2 molecules reaching a maximum gravimetric density of 8.8 wt%, whereas, it is found to reach a maximum of 41.3 wt% for the absorption of four CO molecules. The fate of H2 absorption in a carbene−Li+ complex has been studied in the course of a 2000 fs time evolution through Born−Oppenheimer Molecular Dynamics simulation at different temperatures. The outcomes reveal that the H2 molecules are strongly bound at 77 K and get slowly released at elevated temperature.

Evidence of Formation of Monolayer Hydrated Salts in Nanopores.

Despite much effort being devoted to the study of ionic aqueous solutions at the nanoscale, our fundamental understanding of the microscopic kinetic and thermodynamic behaviors in these systems remains largely incomplete. Herein, we reported the first 10 μs molecular dynamics simulation, providing evidence of the spontaneous formation of monolayer hexagonal honeycomb hydrated salts of XCl2·6H2O (X = Ba, Sr, Ca, and Mg) from electrolyte aqueous solutions confined in an angstrom-scale slit under ambient conditions. By using both the classical molecular dynamics simulations and the first-principles Born-Oppenheimer molecular dynamics simulations, we further demonstrated that the hydrated salts were stable not only at ambient temperature but also at elevated temperatures. This phenomenon of formation of hydrated salt in water is contrary to the conventional view. The free energy calculations and dehydration analyses indicated that the spontaneous formation of hydrated salts can be attributed to the interplay between ion hydration and Coulombic attractions in the highly confined water. In addition to providing molecular-level insights into the novel behavior of ionic aqueous solutions at the nanoscale, our findings may have implications for the future exploration of potential existence of water molecules in the saline deposits on hot planets.

Si6C18: A bispentalene derivative with two planar tetracoordinate carbons

AbstractHere we show that substituting the ten protons in the dianion of a bispentalene derivative (C18H102−) by six Si2+ dications produces a minimum energy structure with two planar tetracoordinate carbons (ptC). In Si6C18, the ptCs are embedded in the terminal C5 pentagonal rings and participate in a three‐center, two‐electron (3c‐2e) Si‐ptC‐Si σ‐bond. Our exploration of the potential energy surface identifies a triphenylene derivative as the putative global minimum. Nevertheless, robustness to Born–Oppenheimer molecular dynamics (BOMD) simulations at 900 and 1500 K supports bispentalene derivative kinetic stability. Chemical bonding analysis reveals ten delocalized π‐bonds, which, according to Hückel's 4n + 2 π‐electron rule, would classify it as an aromatic system. Magnetically induced current density analysis reveals the presence of intense local paratropic currents and a weakly global diatropic current, the latter agreeing with the possible global aromatic character of this specie.

The quest for negative methane: The CH4− anion

In this review, we present the recent discovery and confirmation of a new negative molecular ion, the [Formula: see text] anion. The experimental identification of this high-spin exciplex was difficult because it overlaps with the negative oxygen ion commonly present as a contaminant in vacuum systems and with the same mass-spectrometric signature. Born–Oppenheimer molecular dynamics (BOMD) simulations finally reveal that this anion is a quartet ([Formula: see text]) metastable species, which leads to the formation of a molecular ([Formula: see text] excited complex.