Born-Oppenheimer Molecular Dynamics Research Articles

Nucleoside Cation Radicals: Generation, Radical-Induced Hydrogen Atom Migrations, and Ribose Ring Cleavage in the Gas Phase.

Nucleoside ions that were furnished on ribose with a 2'-O-acetyl radical group were generated in the gas phase by multistep collision-induced dissociation of precursor ions tagged with radical initiator groups, and their chemistry was investigated in the gas phase. 2'-O-Acetyladenosine cation radicals were found to undergo hydrogen transfer to the acetoxyl radical from the ribose ring positions that were elucidated using specific deuterium labeling of 1'-H, 2'-H, and 4'-H and in the N-H and O-H exchangeable positions, favoring 4'-H transfer. Ion structures and transition-state energies were calculated by a combination of Born-Oppenheimer molecular dynamics and density functional theory and used to obtain unimolecular rate constants for competitive hydrogen transfer and loss of the acetoxyl radical. Migrations to the acetoxyl radical of ribose hydrogens 1'-H, 2'-H, 3'-H, and 4'-H were all exothermic, but product formation was kinetically controlled. Both Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations indicated preferential migration of 4'-H in a qualitative agreement with the deuterium labeling results. The hydrogen migrations displayed substantial isotope effects that along with quantum tunneling affected the relative rate constants and reaction branching ratios. UV-vis action spectroscopy indicated that the cation radicals from 2'-O-acetyladenosine consisted of a mixture of isomers. Radical-driven dissociations were also observed for protonated guanosine, cytosine, and thymidine conjugates. However, for those nucleoside ions and cation radicals, the dissociations were dominated by the loss of the nucleobase or formation of protonated nucleobase ions.

Relaxation of the 2a1 ionized water dimer: An interplay of intermolecular Coulombic decay (ICD) and proton transfer processes.

This article investigates the relaxation dynamics of the ionized 2a1 state of a water molecule within a water dimer. The study was motivated by findings from two previous pieces of research that focused on the relaxation behaviors of the inner-valence ionized water dimer. The present study discloses an observation indicating that water dimers display specific fragmentation patterns following inner-valence ionization, depending on the position of the vacancy. Vacancies were created in the 2a1 state of the proton-donating water molecule (PDWM) and proton-accepting water molecule (PAWM). Utilizing Born-Oppenheimer molecular dynamics simulations, the propagation of the 2a1 ionized state was carried out for both scenarios. The results revealed proton transfer occurred when the vacancy resided in the PDWM, accompanied by the closing of decay channels for O-H bond distance (RO-H) > 1.187Å (matching Richter et al.'s findings). Conversely, when vacancy was on PAWM, we observed no closing of decay channels (aligning with Jahnke et al.'s findings). This difference translates to distinct fragmentation pathways. In PDWM cases, 2a1 state ionization leads to H3O+ -OH• formation. In contrast, PAWM vacancies result in decay pathways leading to H2O+-H2O+ products.

Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene.

We show herein that 1,10-dicyano substitution restricts the paragon fluxionality of bullvalene to just 14 isomers which isomerize along a single cycle. The restricted fluxionality of 1,10-dicyanobullvalene (DCB) is investigated by means of: (i) Bonding analyses of the isomer structures using the adaptive natural density partitioning (AdNDP). (ii) Quantum dynamical simulations of the isomerizations along the cyclic intrinsic reaction coordinate of the potential energy surface (PES). The PES possesses 14 equivalent potential wells supporting 14 isomers which are separated by 14 equivalent potential barriers supporting 14 transition states. Accordingly, at low temperatures, DCB appears as a hindered molecular rotor, without any delocalization of the wavefunction in the 14 potential wells, without any nuclear spin isomers, and with completely negligible tunneling. These results are compared and found to differ from those for molecular boron rotors. (iii) Born-Oppenheimer molecular dynamics (BOMD) simulations of thermally activated isomerizations. (iv) Calculations of the rate constants in the frame of transition state theory (TST) with reasonable agreement achieved with the BOMD results. (v) Simulations of the equilibration dynamics using rate equations for the isomerizations with TST rate coefficients. Accordingly, in the long-time limit, isomerizations of the 14 isomers, each with Cs symmetry, approach the "14 Cs → C7v" thermally averaged structure. This is a superposition of the 14 equally populated isomer structures with an overall C7v symmetry. By extrapolation, the results for DCB yield working hypotheses for so far un-explored properties e.g. for the equilibration dynamics of C10H10.

Formation pathways of formic acid (HCOOH) in regions with methanol ices

We modeled the collisions between OH^+ projectiles with kinetic energies ranging from 10 to 22 eV and an amorphous cold (CH3OH)_10 substrate using Born-Oppenheimer molecular dynamics (BOMD) simulations. We conducted the simulations for a collision time of 400 femtoseconds (fs), during which we followed multiple bond-forming and breaking reactions. Here, we report four new pathways for the formation of formic acid HCOOH . We find new precursors such as CH3(OH)2+ HC(OH)2^+ CH2OH^+ and CH2(OH)2 which are essential in these pathways for the formation of formic acid. The methanodiol CH2(OH)2 and hydroxymethyl CH2OH^+ cations have previously been identified as key precursors of formaldehyde. These pathways suggest new ways to form formic acid in methanol ice mantles on dust grains, offering alternative mechanisms leading to the formation of complex organic molecules (COMs) in space.

Molecular mechanisms and atmospheric implications of the simplest criegee intermediate and hydrochloric acid chemistry in the gas phase and at the aqueous interfaces

The atmospheric chemistry of Criegee Intermediates has become a frontier research point in environmental pollution in recent years. In this work, quantum chemical calculations and Born-Oppenheimer Molecular Dynamics (BOMD) simulations were employed to explore the gas phase and aqueous interface behavior of the simplest Criegee Intermediate (sCI, CH2OO) and hydrochloric acid (HCl) reaction. Quantum chemical calculations have revealed that the product of ClCH2OOH (CMHP) formation from the CH2OO + HCl reaction without and with water molecule undergoes a barrierless or near barrierless process in the gas phase. The results of the rate coefficients calculated by the master equation indicate that the gas-phase CMHP formation from the reaction of CH2OO + HCl could compete with the hydrolysis of CH2OO with (H2O)2 at the altitude of 15 km. BOMD simulations at the aqueous interfaces show that the CH2OO + HCl reaction occurs through stepwise mechanisms that are distinct from those in the gas phase. Three different interfacial reaction channels were identified: i) CMHP direct formation, ii) water-mediated CMHP formation, and iii) HCl-mediated hydroxymethyl hydroperoxide (HMHP) formation, and completed in picosecond time scales. Considering the harsh reaction conditions between CH2OO and HCl at the interface (i.e., the two molecules must be sufficiently close to form the CH2OO-HCl complex), the route of HMHP formation via the hydrolysis of CH2OO remains the main atmospheric loss pathway of CH2OO at the aqueous interfaces. Interestingly, molecular dynamic simulations in nanosecond time scales reveal that the formed CMHP in the gas phase has a tendency to aggregate with sulfuric acids, ammonia, and water molecules to form stable clusters within 213–278 K. The present results for the CMHP and HMHP formations from the sCI-HCl chemistry in the atmosphere will enhance our comprehension of the atmospheric behavior of Criegee intermediates in urban and marine pollution areas.

Adsorption behaviors of ethyltriethoxysilane on the calcium silicate hydrate surface: Effect of Ca/Si ratio and adsorption sites

Silane coupling agents (SCAs) are utilized to enhance the impermeability of concrete surfaces, whose adhesion force is affected by the interfacial interactions in between that remain unclear. In this study, we probe the adsorption tendencies of ethyltriethoxysilane (ETES) onto C-S-H surfaces by employing density functional theory (DFT) calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations. Results suggest that significant chemisorption occurs at the CaOH(1.5), SiOH(1.0), Ca(1.0) sites C-S-H surfaces. Electronic structures analysis proved that the chemisorption of hydroxyl sites arises from the overlap of H and O atomic orbitals, resulting in the formation of hydrogen bonds. The chemisorption of the Ca(1.0) site is caused by electrostatic adsorption between calcium and oxygen. Adsorption energy results show: ECaOH(1.5) > ECa(1.0) > ESiOH(1.0). Moreover, ETES remains transverse adsorption on low Ca/Si C-S-H surfaces, while displaying longitudinal adsorption on high. Interaction analysis illustrates the configuration discrepancy arising from the absence of bridge silicon-oxygen tetrahedrons which possess vdW interactions with ethyl. Notably, transverse adsorption covers a wider area on the C-S-H surface thereby enhancing the hydrophobic effect. In summary, the utilization of ETES presents notable advantages within the context of low Ca/Si ratio cement. This study contributes valuable insights into the design and application of silane coatings.

Born-Oppenheimer Molecular Dynamics with a Linear Combination of Atomic Orbitals and Hybrid Functionals for Condensed Matter Simulations Made Possible. Theory and Performance for the Microcanonical and Canonical Ensembles.

The implementation of an original Born-Oppenheimer molecular dynamics module is presented, which is able to perform simulations of large and complex condensed phase systems for sufficiently long time scales at the level of density functional theory with hybrid functionals, in the microcanonical (NVE) and canonical (NVT) ensembles. The algorithm is fully integrated in the Crystal code, a program for quantum mechanical simulations of materials, whose peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals to describe the wave function. The corresponding efficiency in the evaluation of the exact Fock exchange series has led to the implementation of a rich variety of hybrid density functionals at a low computational cost. In addition, the molecular dynamics implementation benefits also from the effective MPI parallelization of the code, suited to exploit high-performance computing resources available on current generation supercomputer architectures. Furthermore, the information contained in the trajectory of the dynamics is extracted through a series of postprocessing algorithms that provide the radial distribution function, the diffusion coefficient and the vibrational density of states. In this work, we present a detailed description of the theoretical framework and the algorithmic implementation, followed by a critical evaluation of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach, when ice and liquid water simulations are performed in the microcanonical and canonical ensembles.

Predicting the photodynamics of cyclobutanone triggered by a laser pulse at 200nm and its MeV-UED signals-A trajectory surface hopping and XMS-CASPT2 perspective.

This work is part of a prediction challenge that invited theoretical/computational chemists to predict the photochemistry of cyclobutanone in the gas phase, excited at 200nm by a laser pulse, and the expected signal that will be recorded during a time-resolved megaelectronvolt ultrafast electron diffraction (MeV-UED). We present here our theoretical predictions based on a combination of trajectory surface hopping with XMS-CASPT2 (for the nonadiabatic molecular dynamics) and Born-Oppenheimer molecular dynamics with MP2 (for the athermal ground-state dynamics following internal conversion), coined (NA+BO)MD. The initial conditions were sampled from Born-Oppenheimer molecular dynamics coupled to a quantum thermostat. Our simulations indicate that the main photoproducts after 2ps of dynamics are CO + cyclopropane (50%), CO + propene (10%), and ethene and ketene (34%). The photoexcited cyclobutanone in its second excited electronic state S2 can follow two pathways for its nonradiative decay: (i) a ring-opening in S2 and a subsequent rapid decay to the ground electronic state, where the photoproducts are formed, or (ii) a transfer through a closed-ring conical intersection to S1, where cyclobutanone ring opens and then funnels to the ground state. Lifetimes for the photoproduct and electronic populations were determined. We calculated a stationary MeV-UED signal [difference pair distribution function-ΔPDF(r)] for each (interpolated) pathway as well as a time-resolved signal [ΔPDF(r,t) and ΔI/I(s,t)] for the full swarm of (NA+BO)MD trajectories. Furthermore, our analysis provides time-independent basis functions that can be used to fit the time-dependent experimental UED signals [both ΔPDF(r,t) and ΔI/I(s,t)] and potentially recover the population of photoproducts. We also offer a detailed analysis of the limitations of our model and their potential impact on the predicted experimental signals.

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.

Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce4-xNixO8- x (x = 1, 2, 3).

Ni-CeO2 nanoparticles (NPs) are promising nanocatalysts for water splitting and water gas shift reactions due to the ability of ceria to temporarily donate oxygen to the catalytic reaction and accept oxygen after the reaction is completed. Therefore, elucidating how different properties of the Ni-Ceria NPs relate to the activity and selectivity of the catalytic reaction, is of crucial importance for the development of novel catalysts. In this work the active learning (AL) method based on machine learning regression and its uncertainty is used for the global optimization of Ce(4-x)NixO(8-x) (x = 1, 2, 3) nanoparticles, employing density functional theory calculations. Additionally, further investigation of the NPs by mass-scaled parallel-tempering Born-Oppenheimer molecular dynamics resulted in the same putative global minimum structures found by AL, demonstrating the robustness of our AL search to learn from small datasets and assist in the global optimization of complex electronic structure systems.

Full Dynamical and Ab Initio Investigation of the Electron Transfer-Mediated Decay Mechanism of He+ in the Presence of Heavier Alkali Dimers.

We have studied the electron transfer-mediated decay (ETMD) process for the 1s ionized state of the He atom in the presence of a heavier alkali homonuclear dimer (Na2, K2, and Rb2) as well as heteronuclear dimer (LiNa, NaK, and KRb). In our computation, we have considered all the alkali dimers being in the singlet electronic ground state. The electron transfer from the alkali dimer to He (1s-1) leads to the emission of another electron from the alkali dimer into the continuum. We have investigated the impact of the distance of the He atom from the center of mass of the alkali dimer on the ETMD decay width. We also performed the Born-Oppenheimer molecular dynamics simulation to understand the impact of nuclear dynamics on the ETMD process.

XB2Bi2 (X = Si, Ge, Sn, Pb): Penta-Atomic Planar Tetracoordinate Si/Ge/Sn/Pb Clusters with 20 Valence Electrons.

Planar tetracoordinate silicon, germanium, tin, and lead (ptSi/Ge/Sn/Pb) species are scarce and exotic. Here, we report a series of penta-atomic ptSi/Ge/Sn/Pb XB2Bi2 (X = Si, Ge, Sn, Pb) clusters with 20 valence electrons (VEs). Ternary XB2Bi2 (X = Si, Ge, Sn, Pb) clusters possess beautiful fan-shaped structures, with a Bi-B-B-Bi chain surrounding the central X core. The unbiased density functional theory (DFT) searches and high-level CCSD(T) calculations reveal that these ptSi/Ge/Sn/Pb species are the global minima on their potential energy surfaces. Born-Oppenheimer molecular dynamics (BOMD) simulations indicate that XB2Bi2 (X = Si, Ge, Sn, Pb) clusters are robust. Bonding analyses indicate that 20 VEs are perfect for the ptX XB2Bi2 (X = Si, Ge, Sn, Pb): two lone pairs of Bi atoms; one 5c-2e π, and three σ bonds (two Bi-X 2c-2e and one B-X-B 3c-2e bonds) between the ligands and X atom; three 2c-2e σ bonds and one delocalized 4c-2e π bond between the ligands. The ptSi/Ge/Sn/Pb XB2Bi2 (X = Si, Ge, Sn, Pb) clusters possess 2π/2σ double aromaticity, according to the (4n + 2) Hückel rule.

Enticing a Proton using Single Ammonia Molecule as Bait.

In microhydrated acid-solvent clusters, deprotonation of an acid is assisted by a critical number of solvent molecules and a solvent electric field. Born-Oppenheimer molecular dynamics simulations reveal that trifluoroacetic acid undergoes spontaneous proton transfer in water clusters, with the critical number being five. Acetic acid and phenol, on the other hand, do not dissociate even in the presence of a large number of water molecules (in excess of 40). The addition of a single ammonia molecule to the water cluster, which interacts directly with the protic group, lowers the critical number of solvent water molecules required for proton transfer to three and seven in the case of acetic acid and phenol, respectively. The population of the undissociated and the proton-transferred structures get dispersed to form separate islands on the electric field versus the O-H distance representation with the cusp representing the critical values. The critical electric fields for the spontaneous proton transfer are around 254, 237, and 318 MV cm-1 for trifluoroacetic acid, acetic acid, and phenol, respectively. In the case of phenol, the free energy profiles suggest that proton transfer to the ammonia moiety embedded in water promotes proton transfer efficiently due to the higher basicity of ammonia and enhanced hydrogen bonding network of solvent water, vis-à-vis phenol-ammonia clusters.

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.

Pd8 Cluster: Too Small to Melt? A BOMD Study.

The question of whether a solid-liquid phase transition occurs in small clusters poses a fundamental challenge. In this study, we attempt to elucidate this phenomenon through a thorough examination of the thermal behavior and structural stability of Pd8 clusters employing ab initio simulations. Initially, a systematic global search is carried out to identify the various isomers of the Pd8 cluster. This is accomplished by employing an ab initio basin-hopping algorithm and using the PBE/SDD scheme integrated in the Gaussian code. The resulting isomers are further refined through reoptimization using the deMon2k package. To ensure the structural firmness of the lowest-energy isomer, we calculated normal modes. The structural stability as a function of temperature is analyzed through the Born-Oppenheimer molecular dynamics (BOMD) approach. Multiple BOMD trajectories at distinct simulated temperatures are examined with data clustering analysis to determine cluster isomers. This analysis establishes a connection between the potential energy landscape and the simulated temperature. To address the question of cluster melting, canonical parallel-tempering BOMD runs are performed and analyzed with the multiple-histogram method. A broad maximum in the heat capacity curve indicates a melting transition between 500 and 600 K. To further examine this transition, the mean-squared displacement and the pair-distance distribution function are calculated. The results of these calculations confirm the existence of a solid-liquid phase transition, as indicated by the heat capacity curve.

Mechanistic insights into Criegee intermediates with benzoic acid at gas-phase and air-water interface and nucleation of product

Since the detection of Criegee intermediates (CIs) in the gas phase, there has been a growing recognition of the important role of CIs in atmospheric oxidation. Further mechanistic investigations are required to fully elucidate the bimolecular reactions of CIs with atmospheric species, such as OH, RO2/HO2, and carbonyl compounds. This article primarily focused on the reactions of benzoic acid (BA) with syn- and anti- CH3CHOO (C2 CI) in both gas-phase and gas-liquid interface using density functional theory (DFT) and Born-Oppenheimer molecular dynamics (BOMD). The results reveal that the reactions of BA and anti-CH3CHOO represent the principal pathway in the gaseous phase, whereas the water-involved reactions exhibit higher energy barriers, rendering them less favorable for occurrence. At the air-water interface, the reactions of BA and C2 CI as well as the BA-catalyzed hydration take place on the picosecond scale, conforming to the stepwise mechanism. The direct reaction between BA and anti- CH3CHOO remains the main sink for C2 CI at the gas-liquid interface. Molecular dynamics (MD) simulations were employed to investigate the nucleation capabilities of the reaction products and to examine the influence of temperature and water molecules on the nucleation process. The product molecules of BA and C2 CI can form stable clusters with sulfuric acid, ammonia molecules, and water molecules within 30 ns? The nucleation ability tends to decrease with the elevation of temperature, and the presence of water molecules promotes the new particles formation (NPF). Therefore, BA and its products with CIs affect the budget of secondary organic aerosols (SOAs).

Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid.

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.

Shell-dependent photofragmentation dynamics of a heavy-atom-containing bifunctional nitroimidazole radiosensitizer.

Radiation therapy uses ionizing radiation to break chemical bonds in cancer cells, thereby causing DNA damage and leading to cell death. The therapeutic effectiveness can be further increased by making the tumor cells more sensitive to radiation. Here, we investigate the role of the initial halogen atom core hole on the photofragmentation dynamics of 2-bromo-5-iodo-4-nitroimidazole, a potential bifunctional radiosensitizer. Bromine and iodine atoms were included in the molecule to increase the photoionization cross-section of the radiosensitizer at higher photon energies. The fragmentation dynamics of the molecule was studied experimentally in the gas phase using photoelectron-photoion-photoion coincidence spectroscopy and computationally using Born-Oppenheimer molecular dynamics. We observed significant changes between shallow core (I 4d, Br 3d) and deep core (I 3d) ionization in fragment formation and their kinetic energies. Despite the fact, that the ions ejected after deep core ionization have higher kinetic energies, we show that in a cellular environment, the ion spread is not much larger, keeping the damage well-localized.

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.

Combining stochastic density functional theory with deep potential molecular dynamics to study warm dense matter

In traditional finite-temperature Kohn–Sham density functional theory (KSDFT), the partial occupation of a large number of high-energy KS eigenstates restricts the use of first-principles molecular dynamics methods at extremely high temperatures. However, stochastic density functional theory (SDFT) can overcome this limitation. Recently, SDFT and the related mixed stochastic–deterministic density functional theory, based on a plane-wave basis set, have been implemented in the first-principles electronic structure software ABACUS [Q. Liu and M. Chen, Phys. Rev. B 106, 125132 (2022)]. In this study, we combine SDFT with the Born–Oppenheimer molecular dynamics method to investigate systems with temperatures ranging from a few tens of eV to 1000 eV. Importantly, we train machine-learning-based interatomic models using the SDFT data and employ these deep potential models to simulate large-scale systems with long trajectories. Subsequently, we compute and analyze the structural properties, dynamic properties, and transport coefficients of warm dense matter.