Born-Oppenheimer Molecular Dynamics Simulations Research Articles

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.

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.

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.

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.

Dissociation of H2O2 on water surfaces (ice and water droplets).

OH radicals are an important constituent of the atmosphere. Therefore, all reactions that act as a source of OH radicals are important. It is known that photo-dissociation of H2O2 is an important source of OH radicals in the atmosphere. In the present study, using Born-Oppenheimer molecular dynamics simulations, we have shown that the H2O2 molecule can dissociate thermally on water droplets, as well as on the surface of ice, to form OH radicals. Furthermore, the dissociation of H2O2 was found to be very fast (less than 50 fs) on the ice surface compared with on the water droplets. We believe this route for the formation of OH radicals could be more critical than photo-dissociation, as it can take place both during the day and at night, but further studies with more sophisticated theoretical approaches or experiments are required to confirm this hypothesis.

Barrierless reactions of C2 Criegee intermediates with H2SO4 and their implication to oligomers and new particle formation

The formation of oligomeric hydrogen peroxide triggered by Criegee intermediate maybe contributes significantly to the formation and growth of secondary organic aerosol (SOA). However, to date, the reactivity of C2 Criegee intermediates (CH3CHOO) in areas contaminated with acidic gas remains poorly understood. Herein, high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations are used to explore the reaction of CH3CHOO and H2SO4 both in the gas phase and at the air-water interface. In the gas phase, the addition reaction of CH3CHOO with H2SO4 to generate CH3HC(OOH)OSO3H (HPES) is near-barrierless, regardless of the presence of water molecules. BOMD simulations show that the reaction at the air-water interface is even faster than that in the gas phase. Further calculations reveal that the HPES has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters, meanwhile the oligomerization reaction of CH3CHOO with HPES in the gas phase is both thermochemically and kinetically favored. Also, it is noted that the interfacial HPES− ion can attract H2SO4, NH3, (COOH)2 and HNO3 for particle formation from the gas phase to the water surface. Thus, the results of this work not only elucidate the high atmospheric reactivity of C2 Criegee intermediates in polluted regions, but also deepen our understanding of the formation process of atmospheric SOA induced by Criegee intermediates.

Wetting of a Hydrophobic Surface: Far-IR Action Spectroscopy and Dynamics of Microhydrated Naphthalene.

The interaction of water and polycyclic aromatic hydrocarbons is of fundamental importance in areas as diverse as materials science and atmospheric and interstellar chemistry. The interplay between hydrogen bonding and dipole-π interactions results in subtle dynamics that are challenging to describe from first principles. Here, we employ far-IR action vibrational spectroscopy with the infrared free-electron laser FELIX to investigate naphthalene with one to three water molecules. We observe diffuse bands associated with intermolecular vibrational modes that serve as direct probes of the loose binding of water to the naphthalene surface. These signatures are poorly reproduced by static DFT or Møller-Plesset computations. Instead, a rationalization is achieved through Born-Oppenheimer Molecular Dynamics simulations, revealing the active mobility of water over the surface, even at low temperatures. Therefore, our work provides direct insights into the wetting interactions associated with shallow potential energy surfaces while simultaneously demonstrating a solid experimental-computational framework for their investigation.

Can Ozone Dissociate at the Surface of Water (Water Droplet and Ice) without Light?

Ozone is a major source of OH radicals in the troposphere. It is well-known that photodissociation of ozone is key for the conversion of ozone into OH radicals. In the present study, using Born-Oppenheimer molecular dynamics simulation, we have shown that on the surface of the droplet and ice, ozone can dissociate without light. In addition, the dissociation time of ozone is found to be much less on the ice surface than the same time on the water droplet. As the dissociation of ozone on the water surface can happen during the day as well as in the night time, we believe this route of forming OH radicals can be even more important than the photodissociation. The present study suggests that the cloud and ice surface can enhance the oxidizing power of the troposphere.

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.

A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born-Oppenheimer Molecular Dynamics.

This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in Born-Oppenheimer Molecular Dynamics (BOMD) simulations. The method shows excellent results on four large molecular systems that are representative of real-life production applications, ranging from 21 to 94 atoms simulated with Kohn-Sham (KS) density functional theory surrounded with a classical environment with 6k to 16k atoms. Namely, it clearly reduces the number of self-consistent field iterations while at the same time achieving energy-conserving simulations, resulting in a considerable speed-up of BOMD simulations even when tight convergence of the KS equations is required.

Distinctive Heterogeneous Reaction Mechanism of ClNO2 on the Air-Water Surface Containing Cl.

The heterogeneous reaction of nitryl chloride (ClNO2) on the air-water surface plays a significant role in the chloride lifecycle. The air-water surface is ubiquitous on ice surfaces under supercooled conditions, affecting the uptake and heterogeneous reaction processes of trace gases. Previous studies suggest that ClNO2 is formed on Cl-doped ice surfaces following the N2O5 uptake. Herein, a distinctive heterogeneous reaction mechanism of ClNO2 is suggested on an air-water surface containing Cl under supercooled conditions using combined classic molecular dynamics (MD) and Born-Oppenheimer MD simulations. It is found that N2O5 dissociates into a NO2+ and NO3- ionic pair on the top air-water surface. In the top layer of the surface containing barely any Cl-, NO2+ proceeds through hydrolysis and produces H3O+ and HNO3. Thus, surface acidification appears because of H3O+ yields. With NO2+ diffusion to the deep layer of the surface, NO2+ reacts with Cl- and forms ClNO2. Note that ClNO2 formation competes with NO2+ hydrolysis, and the rate of ClNO2 formation is 27.7[Cl-] larger than that of NO2+ hydrolysis. Afterward, the reaction of ClNO2 with Cl- becomes barrierless with the catalysis by H3O+, which is not feasible on a neutral surface. Cl2 is thus generated and escapes into the atmosphere (low solubility of Cl2), contributing to the Cl radical. The proposed mechanism bolsters the current understanding of ClNO2's fate and its role in Cl chemistry in extremely cold environments like the Arctic and other high-latitude regions in wintertime.

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.

Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B12 Derivatives?

Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.

Planar hexacoordinate phosphorous and arsenic

Here the first planar hexacoordinate phosphorous and arsenic (phP and phAs) atoms are reported. Neutral 18 valence electron EBe3Li3H6 clusters (E = P, As) adopt planar D3h symmetry in their lowest energy singlet state. Chemical bonding reveals partial double bond character in P(As)-Be bonds and single bond character in P(As)-Li bonds. Born-Oppenheimer molecular dynamics simulation as well as their reluctance towards decomposition reveals high kinetic stability of these clusters.