Born-Oppenheimer Molecular Dynamics Research Articles

Mechanism for the promotional formation of NH4+ by SO2 on different mineral dust surfaces

Ammonium is an important atmospheric particulate component that dictates many environmental processes. The promotion of the heterogeneous conversion of NH3 to NH4+ by SO2 on different mineral dust surfaces displays remarkable discrepancies, especially on MgO and α-Fe2O3 surfaces, however, the underlying mechanisms are not well known. Here, using periodic density functional theory (DFT) calculation and Born-Oppenheimer molecular dynamics (BOMD) simulation, we explored the heterogeneous adsorption of NH3 on MgO (110) and α-Fe2O3 (001) surfaces in the presence and absence of SO2. The results show that on MgO (110) surface, hydrogen-bonding interactions of NH3 on both adsorbed hydroxyl or bisulfite/bisulfate sites are observed no matter whether SO2 is present or not. While, on the α-Fe2O3 (001) surface, significant conversion of NH3 to NH4+ occurs with the coexistence of SO2, which is due to the hydrogen transfer reaction from surface HSO4 to N in NH3. The fundamental reason may be that the stronger electron affinity of Fe3+ than Mg2+ results in adsorbed bisulfate and/or bisulfite with greater acidity on α-Fe2O3 surface than MgO surface. Our results give a molecular-level explanation for the heterogeneous conversion of NH3 to NH4+ on different mineral dust surfaces under complex air pollution conditions. Considering the fact that ammonium is abundant in secondary particulates, this work would help in understanding the rapid conversion of ammonia to ammonium and in developing classification governance policies for the key precursor pollutants in China.

Density Embedding Method for Nanoscale Molecule-Metal Interfaces.

In this work, we extend the applicability of standard Kohn-Sham DFT (KS-DFT) to model realistically sized molecule-metal interfaces where the metal slabs venture into the tens of nanometers in size. Employing state-of-the-art noninteracting kinetic energy functionals, we describe metallic subsystems with orbital-free DFT and combine their electronic structure with molecular subsystems computed at the KS-DFT level resulting in a multiscale subsystem DFT method. The method reproduces within a few millielectronvolts the binding energy difference of water and carbon dioxide molecules adsorbed on the top and hollow sites of an Al(111) surface compared to KS-DFT of the combined supersystem. It is also robust for Born-Oppenheimer molecular dynamics simulations. Very large system sizes are approached with standard computing resources thanks to a parallelization scheme that avoids accumulation of memory at the gather-scatter stage. The results as presented are encouraging and open the door to ab initio simulations of realistically sized, mesoscopic molecule-metal interfaces.

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.

Understanding Explosive Sensitivity with Effective Trigger Linkage Kinetics.

We present a simple linear model for ranking the drop weight impact sensitivity of organic explosives that is based explicitly on chemical kinetics. The model is parameterized to specific heats of explosion, Q, and Arrhenius kinetics for the onset of chemical reactions that are obtained from gas-phase Born-Oppenheimer molecular dynamics simulations for a chemically diverse set of 24 molecules. Reactive molecular dynamics simulations sample all possible decomposition pathways of the molecules with the appropriate probabilities to provide an effective reaction barrier. In addition, the calculations of effective trigger linkage kinetics can be accomplished without prior physical intuition of the most likely decomposition pathways. We found that the specific heat of explosion tends to reduce the effective barrier for decomposition in accordance with the Bell-Evans-Polanyi principle, which accounts naturally for the well-known correlations between explosive performance and sensitivity. Our model indicates that sensitive explosives derive their properties from a combination of weak trigger linkages that react at relatively low temperatures and large specific heats of explosion that further reduce the effective activation energy.

Quantum simulation in the semi-classical regime

Solving the time-dependent Schrödinger equation is an important application area for quantum algorithms. We consider Schrödinger's equation in the semi-classical regime. Here the solutions exhibit strong multiple-scale behavior due to a small parameterℏ, in the sense that the dynamics of the quantum states and the induced observables can occur on different spatial and temporal scales. Such a Schrödinger equation finds many applications, including in Born-Oppenheimer molecular dynamics and Ehrenfest dynamics. This paper considers quantum analogues of pseudo-spectral (PS) methods on classical computers. Estimates on the gate counts in terms ofℏand the precisionεare obtained. It is found that the number of required qubits,m, scales only logarithmically with respect toℏ. When the solution has bounded derivatives up to orderℓ, the symmetric Trotting method has gate complexityO((εℏ)−12polylog(ε−32ℓℏ−1−12ℓ)),provided that the diagonal unitary operators in the pseudo-spectral methods can be implemented withpoly(m)operations. When physical observables are the desired outcomes, however, the step size in the time integration can be chosen independently ofℏ. The gate complexity in this case is reduced toO(ε−12polylog(ε−32ℓℏ−1)),withℓagain indicating the smoothness of the solution.

Structure, Diffusion, and Stability of Lithium Salts in Aprotic Dimethyl Sulfoxide and Acetonitrile Electrolytes

The development of lithium batteries, including lithium-ion batteries and lithium-air batteries, is the key technological breakthrough in the field of renewable energy storage. However, to date, it is still challenging to design a lithium battery with both high specific power and stability. Specifically, the solvation structure and thermodynamic stability of various electrolytes, mostly Li salts and aprotic solvents, have not been systematically studied from an atomic viewpoint. In this paper, we studied the solution chemistry of three most common inorganic Li salts (LiClO4, LiBF4, and LiPF6) and O2 in two aprotic (dimethyl sulfoxide (DMSO) and acetonitrile (CH3CN)) solvents. The Born–Oppenheimer molecular dynamics simulations and enhanced free energy samplings are employed to obtain their solvation structures, diffusion coefficients, and stability performances at room temperature. As a result, the tetrahedral Li(DMSO)4+ and Li(CH3CN)4+ are obtained as the stable solvation shells of Li+ in DMSO and CH3CN solvents, respectively. Among the three inorganic Li salts, the stability performances are found in the order of LiClO4 > LiBF4 > LiPF6 in both DMSO and CH3CN solvents. Compared with CH3CN, DMSO provides a more stable environment for the long-term usage of Li salts for that increases the energetic barriers of the degradation reactions of solvated Li+ components. However, DMSO shows a weaker ability (than CH3CN) to transport the main redox species (solvated Li+ and O2) in the electrolyte, which limits the discharging and charging rate in the batteries.

Multiple evaluations of atmospheric behavior between Criegee intermediates and HCHO: Gas-phase and air-water interface reaction

Given the high abundance of water in the atmosphere, the reaction of Criegee intermediates (CIs) with (H2O)2 is considered to be the predominant removal pathway for CIs. However, recent experimental findings reported that the reactions of CIs with organic acids and carbonyls are faster than expected. At the same time, the interface behavior between CIs and carbonyls has not been reported so far. Here, the gas-phase and air-water interface behavior between Criegee intermediates and HCHO were explored by adopting high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations. Quantum chemical calculations evidence that the gas-phase reactions of CIs + HCHO are submerged energy or low energy barriers processes. The rate ratios speculate that the HCHO could be not only a significant tropospheric scavenger of CIs, but also an inhibitor in the oxidizing ability of CIs on SOx in dry and highly polluted areas with abundant HCHO concentration. The reactions of CH2OO with HCHO at the droplet's surface follow a loop structure mechanism to produce i) SOZ (▪), ii) BHMP (HOCH2OOCH2OH), and iii) HMHP (HOCH2OOH). Considering the harsh reaction conditions between CIs and HCHO at the interface (i.e., the two molecules must be sufficiently close to each other), the hydration of CIs is still their main atmospheric loss pathway. These results could help us get a better interpretation of the underlying CIs-aldehydes chemical processes in the global polluted urban atmospheres.

Calculation of electric field gradients for CdI2 in the gas phase using BOMD simulations

The nuclear quadrupole interaction (NQI) of quadrupolar nuclei in molecules in the gas phase has recently been quantified experimentally by the technique of Perturbed Angular Correlation (PAC) spectroscopy. Interpretation of the NQI data must rely on high-level electronic structure methods for the calculation of the electric field gradient (EFG). These calculations commonly omit contributions from anharmonicity, rovibrational coupling and (if applicable) decay-induced nuclear recoil to the molecular structure and the response of the EFG. Here we choose an alternative approach, conducting Born–Oppenheimer molecular dynamics (BOMD) simulations, and account for the effects of molecular motion on the EFG. We apply this approach to the analysis of PAC spectroscopic data recorded for gas phase CdI2 (Haas et al., 2021). With this methodology, we obtain a value of the nuclear quadrupole moment Q(111Cd, 5/2+) = 0.656(7) b.

Novel All-Nitrogen Molecular Crystals Composed of Tetragonal N4 Molecules.

A computational study promises insight into molecular crystals consisting of the tetrahedral form of N molecules (Td-N). Here, our efforts are focused on theoretically predicting the existence of the molecular crystals consisting of Td-N molecules. On the basis of the first principles of Born–Oppenheimer molecular dynamics under constant temperature and pressure, and geometry optimizations under hydrostatic pressures without any constrained parameters, molecular crystals consisting of Td-N molecules were confirmed to be dynamically and thermally metastable. Our analysis shows that, with high detonation performance and high stability, these Td-N molecular crystals can indeed be potential candidates as high-energy density explosives.

Radical Cascade Dissociation Pathways to Unusual Nucleobase Cation Radicals.

We report unusual dissociations of protonated RNA nucleosides tagged with radical initiator groups at ribose 5'-O and furnished with a 2',3'-O-isopropylidene protecting group. The ions undergo collision-induced radical cascade dissociations starting at the radical initiator that break down the dioxolane ring and trigger the formation of nucleobase cations and cation radicals. The adenine cation radical that was formed by radical cascade dissociations was identified by MS5 UV-vis photodissociation action spectroscopy to be a higher-energy N-3-H tautomer of the canonical ionized nucleobase. The guanine cation radical was formed by radical cascade dissociations as the N-7-H tautomer. In contrast to adenosine and guanosine, radical cascade dissociations of the tagged ribocytidine ion produced protonated cytosine, whereas tagged ribothymidine showed yet different dissociations resulting in predominant thymine loss. Reaction mechanisms were suggested for the cascade dissociations that were based on Born-Oppenheimer molecular dynamics and density functional theory calculations that were used to map the relevant parts of the potential energy surfaces for adenosine, guanosine, and cytidine radical ions. The reported radical cascade dissociations represent a new, nonredox approach to nucleobase and nucleoside cation radicals that has the potential of being expanded to the generation of various oligonucleotide cation radicals.

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization.

Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.

Isomerization Reactions of the Cu15V+ Cluster: A Density Functional Theory Study.

The investigation of the chemical reactivity of complex systems such as transition metal clusters is a very complicated task because often the structures of the corresponding transition states are far from being intuitive. Bimetallic transition metal clusters represent a particular class of complex systems. In this work, density functional theory (DFT) is applied to study the isomerization reactions of the Cu15V+ cluster. Full geometry optimizations of dozens of initial structures taken along Born-Oppenheimer molecular dynamics (BOMD) trajectories were performed using a quasi-Newton method in a reduced space Cartesian coordinate system that works considering the internal degrees of freedom. Harmonic frequencies calculations were performed at the optimized structures. To study the isomerization reactions between the obtained stable isomers, a hierarchical transition state algorithm has been applied to locate the transition states of this cluster. The found transition states were than connected with the corresponding minimum structures by calculating the intrinsic reaction coordinates. This work demonstrates the capability of the applied method to study non-intuitive rearrangement mechanisms in complex finite systems and to create networks between minima and transition state structures on their potential energy surface.

Water Clusters in Interaction with Corannulene in a Rare Gas Matrix: Structures, Stability and IR Spectra

The interaction of polycyclic aromatic hydrocarbons (PAHs) with water is of paramount importance in atmospheric and astrophysical contexts. We report here a combined theoretical and experimental study of corannulene-water interactions in low temperature matrices and of the matrix’s influence on the photoreactivity of corannulene with water. The theoretical study was performed using a mixed density functional based tight binding/force field approach to describe the corannulene-water clusters trapped in an argon matrix, together with Born-Oppenheimer molecular dynamics to determine finite-temperature IR spectra. The results are discussed in the light of experimental matrix isolation FTIR spectroscopic data. We show that in the solid phase, π isomers of (C20H10)(H2O)n, with n = 2 or 3, are energetically favored. These π complexes are characterized by small shifts in corannulene vibrational modes and large shifts in water bands. These π structures, particularly stable in the case of the water trimer where the water cluster is trapped “inside” the corannulene bowl, may account for the difference in photoreactivity of non-planar–compared to planar–PAHs with water. Indeed, planar PAHs such as pyrene and coronene embedded in H2O:Ar matrices form σ isomers and react with water to form alcohols and quinones under low energy UV irradiation, whereas no photoreactivity was observed for corannulene under the same experimental conditions.

Solvation and Hydrolysis Reaction of Isocyanic Acid at the Air-Water Interface: A Computational Study.

Isocyanic acid (HNCO) is known to be inert to strong oxidants and photolysis in the atmosphere but often appears in different forms of smoke; therefore, it is linked to various smoke-related illnesses due to tobacco usage or wildfire events. To date, the major loss pathway of HNCO is believed to be through its uptake on aerosol droplets. However, the molecular mechanisms underlying such an uptake process are still incompletely understood. Herein, we use the Born-Oppenheimer molecular dynamics (BOMD) simulations to study solvation and hydrolysis reactions of HNCO on water droplets at ambient temperature. The BOMD simulations indicate that the scavenging of HNCO by water droplets is largely attributed to the preferential adsorption of HNCO at the air-water interface, rather than inside bulk water. Specifically, the H atom of HNCO interacts with the O atom of interfacial water, leading to the formation of a hydrogen bond (H-bond) of (HNCO)H···O(H2O), which prevents HNCO from evaporating. Moreover, the interfacial water can act as H-bond acceptors/donors to promote the proton transfer during the HNCO hydrolysis reaction. Compared to the gas phase, the activation barrier is lowered from 45 to 14 kcal·mol-1 on the water surface, which facilitates the formation of the key intermediate of NH2COOH. This intermediate eventually decomposes into NH3 and CO2, consistent with the previous study [ Atmos. Chem. Phys. 2016, 16, 703-714]. The new molecular insight into HNCO solvation and reaction on the water surface improves our understanding of the uptake of HNCO on aerosols.

OH + HCl Reaction on the Surface of Ice: An Ab Initio Molecular Dynamics Study.

We have investigated the OH + HCl reaction on the surface of ice using Born-Oppenheimer molecular dynamics (BOMD) simulation. The present work revealed that the OH + HCl reaction becomes ∼1 order of magnitude faster on the ice surface compared to the bare reaction. The BOMD simulation also indicates that the Cl radical formed on the ice surface through the title reaction can form two hydrogen bonds at a time with the water molecules present on the ice surface; hence, the Cl radical cannot escape from the ice surface easily.

Fluctuation-induced quantum friction in nanoscale water flows.

The flow of water in carbon nanochannels has defied understanding thus far1, with accumulating experimental evidence for ultra-low friction, exceptionally high water flow rates and curvature-dependent hydrodynamic slippage2-5. In particular, the mechanism of water-carbon friction remains unknown6, with neither current theories7 nor classical8,9 or ab initio molecular dynamics simulations10 providing satisfactory rationalization for its singular behaviour. Here we develop a quantum theory of the solid-liquid interface, which reveals a new contribution to friction, due to the coupling of charge fluctuations in the liquid to electronic excitations in the solid. We expect that this quantum friction, which is absent in Born-Oppenheimer molecular dynamics, is the dominant friction mechanism for water on carbon-based materials. As a key result, we demonstrate a marked difference in quantum friction between the water-graphene and water-graphite interface, due to the coupling of water Debye collective modes with a thermally excited plasmon specific to graphite. This suggests an explanation for the radius-dependent slippage of water in carbon nanotubes4, in terms of the electronic excitations of the nanotubes. Our findings open the way for quantum engineering of hydrodynamic flows through the electronic properties of the confining wall.

Kinetics and thermodynamics of silicon carbide physical vapor transport reactions: A quantum chemistry and kinetic Monte Carlo approach

The thermodynamics and chemical kinetics of silicon carbide sublimation and lateral interaction reactions are two vital branches that aid in understanding silicon carbide crystal growth, in the Physical Vapor Transport process (PVT). Whilst the former determines the feasibility of the processes and gives an idea about end products and their stability, kinetics explains the dynamism of the reactions and the contribution of species to crystal growth. The potential energy surfaces of the reactions are first determined via Born Oppenheimer Molecular Dynamics observation of the reaction kinetics. By employing an atomic basis set of split-valence double-zeta coupled with Becke’s three-parameter hybrid method with LYP correction function, the trajectory of different reactant configurations confirming minimum energy molecules, end products, and potential energy surface is established. Various structural possibilities for the reactant, intermediates, and product of each reaction are investigated by means of geometry optimization and utilization of second-order Moller-Plesset level of theory with electron correlation and a basis set of split-valence triple-zeta polarization. Reaction paths are ascertained via QST2 transition state calculation and their mechanism is confirmed by intrinsic reaction coordinate (IRC). Rate constants for forward and reverse processes are estimated using appropriate and applicable theories, adequate to capture the scenarios. Sublimation of silicon carbide source powder is solved thermodynamically at equilibrium using the equation of Gibbs free chemical reaction isotherm, and the equilibrium partial pressures of species in ideal conditions and Kinetic Monte Carlo evolution of the PVT reactions species, were used in determining the most dominant gaseous molecules around the substrate.

Benchmarking Plane Waves Quantum Mechanical Calculations of Iron(II) Tris(2,2′-bipyridine) Complex by X-ray Absorption Spectroscopy

In this work, we used, for the first time, a computational Self-Consistent Field procedure based on plane waves to describe the low and high spin conformational states of the complex [Fe(bpy)3]2+. The results obtained in the study of the minimum energy structures of this complex, a prototype of a wide class of compounds called Spin Cross Over, show how the plane wave calculations are in line with the most recent studies based on gaussian basis set functions and, above all, reproduce within acceptable errors the experimental spectra of X-ray absorption near-edge structure spectroscopy (XANES). This preliminary study shows the capabilities of plane wave methods to correctly describe the molecular structures of metal-organic complexes of this type and paves the way for future even complex computational simulations based on the energy gradient, such as Nudge Elastic Band or ab-initio Born-Oppenheimer molecular dynamics.

Automatic Approach to Explore the Multireaction Mechanism for Medium-Sized Bimolecular Reactions via Collision Dynamics Simulations and Transition State Searches

We develop a broadly applicable computational method for the automatic exploration of the bimolecular multireaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation and the successive reaction pathway construction. Several computational tricks are introduced, which include the selection of the reactive regions based on the electronic structure calculations and the employment of the virtual collision dynamics simulations with the monitoring of the atomic distance before the BOMD simulation. These prescreening steps largely reduce the number of trajectories in the BOMD simulations and significantly save the computational cost. The hidden Markov model combined with the modified atomic connectivity matrix is used for the detection of reaction events in each BOMD trajectory. Starting from several geometries close to the reaction events, the further intermediate optimization and transition state searches are conducted. The proposed method allows us to build the complicated multireaction mechanism of medium-sized bimolecular systems automatically. Here, we examine the feasibility and efficiency of the current method by its performance in searching the mechanisms of two prototype reactions in environmental science, which are the penicillin G anion + H2O and penicillin G anion + OH radical reactions. The result indicates that the proposed theoretical method is a powerful protocol for the automatic search of the bimolecular reaction mechanisms for medium-sized compounds.

A multiple time step algorithm for trajectory surface hopping simulations.

A multiple time step (MTS) algorithm for trajectory surface hopping molecular dynamics has been developed, implemented, and tested. The MTS scheme is an extension of the ab initio implementation for Born-Oppenheimer molecular dynamics presented in the work of Liberatore et al. [J. Chem. Theory Comput. 14, 2834 (2018)]. In particular, the MTS algorithm has been modified to enable the simulation of non-adiabatic processes with the trajectory surface hopping (TSH) method and Tully's fewest switches algorithm. The specificities of the implementation lie in the combination of Landau-Zener and Tully's transition probabilities during the inner MTS time steps. The new MTS-TSH method is applied successfully to the photorelaxation of protonated formaldimine, showing that the important characteristics of the process are recovered by the MTS algorithm. A computational speed-up between 1.5 and 3 has been obtained compared to standard TSH simulations, which is close to the ideal values that could be obtained with the computational settings considered.