Further cautionary tales on thermostatting in molecular dynamics: Energy equipartitioning and non-equilibrium processes in gas-phase simulations

Molecular dynamics (MD) simulations of gas-phase chemical reactions are typically carried out on a small number of molecules near thermal equilibrium by means of various thermostatting algorithms. Correct equipartitioning of kinetic energy among translations, rotations, and vibrations of the simulated reactants is critical for many processes occurring in the gas phase. As thermalizing collisions are infrequent in gas-phase simulations, the thermostat has to efficiently reach equipartitioning in the system during equilibration and maintain it throughout the actual simulation. Furthermore, in non-equilibrium simulations where heat is released locally, the action of the thermostat should not lead to unphysical changes in the overall dynamics of the system. Here, we explore issues related to both obtaining and maintaining thermal equilibrium in MD simulations of an exemplary ion-molecule dimerization reaction. We first compare the efficiency of global (Nosé-Hoover and Canonical Sampling through Velocity Rescaling) and local (Langevin) thermostats for equilibrating a system of flexible compounds and find that of these three only the Langevin thermostat achieves equipartition in a reasonable simulation time. We then study the effect of the unphysical removal of latent heat released during simulations involving multiple dimerization events. As the Langevin thermostat does not produce the correct dynamics in the free molecular regime, we only consider the commonly used Nosé-Hoover thermostat, which is shown to effectively cool down the reactants, leading to an overestimation of the dimerization rate. Our findings underscore the importance of thermostatting for the proper thermal initialization of gas-phase systems and the consequences of global thermostatting in non-equilibrium simulations.

The missing base molecules in atmospheric acid-base nucleation

Transformation of low-volatility gaseous precursors to new particles affects aerosol number concentration, cloud formation and hence the climate. The clustering of acid and base molecules is a major mechanism driving fast nucleation and initial growth of new particles in the atmosphere. However, the acid–base cluster composition, measured using state-of-the-art mass spectrometers, cannot explain the measured high formation rate of new particles. Here we present strong evidence for the existence of base molecules such as amines in the smallest atmospheric sulfuric acid clusters prior to their detection by mass spectrometers. We demonstrate that forming (H₂SO₄)₁(amine)₁ is the rate-limiting step in atmospheric H₂SO₄-amine nucleation and the uptake of (H₂SO₄)₁(amine)₁ is a major pathway for the initial growth of H₂SO₄ clusters. The proposed mechanism is very consistent with measured new particle formation in urban Beijing, in which dimethylamine is the key base for H₂SO₄ nucleation while other bases such as ammonia may contribute to the growth of larger clusters. Our findings further underline the fact that strong amines, even at low concentrations and when undetected in the smallest clusters, can be crucial to particle formation in the planetary boundary layer.

Shells in CO2 clusters

Abundance spectra of (CO₂)_N clusters up to N ≈ 500 acquired under a wide range of adiabatic expansion conditions are analyzed within the evaporative ensemble framework. The analysis reveals that the cluster stability functions display a strikingly universal pattern for all expansion conditions. These patterns reflect the inherent properties of individual clusters. From this analysis the size-dependent cluster binding energies are determined, shell and subshell closing sizes are identified, and cuboctahedral packing ordering for sizes above N ≈ 130 is confirmed. It is demonstrated that a few percent variation in the dissociation energies translates into significant abundance variations, especially for the larger clusters.

New Particle Formation from the Vapor Phase: From Barrier-Controlled Nucleation to the Collisional Limit

Studies of vapor phase nucleation have largely been restricted to one of two limiting cases-nucleation controlled by a substantial free energy barrier or the collisional limit where the barrier is negligible. For weakly bound systems, exploring the transition between these regimes has been an experimental challenge, and how nucleation evolves in this transition remains an open question. We overcome these limitations by combining complementary Laval expansion experiments, providing new particle formation data for carbon dioxide over a uniquely broad range of conditions. Our experimental data together with a kinetic model using rate constants from high-level quantum chemical calculations provide a comprehensive picture of new particle formation as nucleation transitions from a barrier-dominated process to the collisional limit.

Homogeneous nucleation of carbon dioxide in supersonic nozzles II: molecular dynamics simulations and properties of nucleating clusters

Large scale molecular dynamics simulations of the homogeneous nucleation of carbon dioxide in an argon atmosphere were carried out at temperatures between 75 and 105 K. Extensive analyses of the nucleating clusters' structural and energetic properties were performed to quantify these details for the supersonic nozzle experiments described in the first part of this series [Dingilian et al., Phys. Chem. Chem. Phys., 2020, 22, 19282-19298]. We studied ten different combinations of temperature and vapour pressure, leading to nucleation rates of 10²³-10²⁵ cm^-3 s^-1. Nucleating clusters possess significant excess energy from monomer capture, and the observed cluster temperatures during nucleation - on both sides of the critical cluster size - are higher than that of the carrier gas. Despite strong undercooling with respect to the triple point, most clusters are clearly liquid-like during the nucleation stage. Only at the lowest simulation temperatures and vapour densities, clusters containing over 100 molecules are able to undergo a second phase transition to a crystalline solid. The formation free energies retrieved from the molecular dynamics simulations were used to improve the classical nucleation theory by introducing a Tolman-like term into the classical liquid-drop model expression for the formation free energy. This simulation-based theory predicts the simulated nucleation rates perfectly, and improves the prediction of the experimental rates compared to self-consistent classical nucleation theory.

Homogeneous nucleation of carbon dioxide in supersonic nozzles I: experiments and classical theories

We studied the homogeneous nucleation of carbon dioxide in the carrier gas argon for concentrations of CO2 ranging from 2 to 39 mole percent using three experimental methods. Position-resolved pressure trace measurements (PTM) determined that the onset of nucleation occurred at temperatures between 75 and 92 K with corresponding CO2 partial pressures of 39 to 793 Pa. Small angle X-ray scattering (SAXS) measurements provided particle size distributions and aerosol number densities. Number densities of approximately 1012 cm-3, and characteristic times ranging from 6 to 13 μs, resulted in measured nucleation rates on the order of 5 × 1017 cm-3 s-1, values that are consistent with other nucleation rate measurements in supersonic nozzles. Finally, we used Fourier transform infrared (FTIR) spectroscopy to identify that the condensed CO2 particles were crystalline cubic solids with either sharp or rounded corners. Molecular dynamics simulations, however, suggest that CO2 forms liquid-like critical clusters before transitioning to the solid phase. Furthermore, the critical clusters are not in thermal equilibrium with the carrier gas. Comparisons with nucleation theories were therefore made assuming liquid-like critical clusters and incorporating non-isothermal correction factors.

Deviation from equilibrium conditions in molecular dynamic simulations of homogeneous nucleation

We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].

Atmospheric Fate of Monoethanolamine: Enhancing New Particle Formation of Sulfuric Acid as an Important Removal Process

Monoethanolamine (MEA), a potential atmospheric pollutant from the capture unit of a leading CO₂ capture technology, could be removed by participating H₂SO₄-based new particle formation (NPF) as simple amines. Here we evaluated the enhancing potential of MEA on H₂SO₄-based NPF by examining the formation of molecular clusters of MEA and H₂SO₄ using combined quantum chemistry calculations and kinetics modeling. The results indicate that MEA at the parts per trillion (ppt) level can enhance H₂SO₄-based NPF. The enhancing potential of MEA is less than that of dimethylamine (DMA), one of the strongest enhancing agents, and much greater than methylamine (MA), in contrast to the order suggested solely by their basicity (MEA < MA < DMA). The unexpectedly high enhancing potential is attributed to the role of -OH of MEA in increasing cluster binding free energies by acting as both a hydrogen bond donor and acceptor. After the initial formation of one H₂SO₄ and one MEA cluster, the cluster growth mainly proceeds by first adding one H₂SO₄, and then one MEA, which differs from growth pathways in H₂SO₄-DMA and H₂SO₄-MA systems. Importantly, the effective removal rate of MEA due to participation in NPF is comparable to that of oxidation by hydroxyl radicals at 278.15 K, indicating NPF as an important sink for MEA.

Formation of atmospheric molecular clusters consisting of sulfuric acid and C8H12O6 tricarboxylic acid

We present the structures and thermochemical properties of (MBTCA)₁₋₃(H₂SO₄)₁₋₄ atmospheric molecular clusters.

Indoor radon concentrations caused by construction materials in 23 workplaces

The aim of this study was to compare the measured and the calculated concentrations of indoor radon caused by building materials at 23 workplaces. The measured concentrations of radon were clearly higher than the calculated radon concentrations from the building materials, which indicated that the main source of indoor radon was the soil under and around the buildings. The highest means of continuously (933 Bq m(-3)) and integrated (169 Bq m(-3)) measured and calculated (from 70 to 169 Bq m(-3)) concentrations of radon were found in hillside locations. On the other hand, the median (27 and 43 Bq m(-3)) and maximum (626 and 1002 Bq m(-3)) values of calculated indoor radon concentrations exhaled from construction materials were the highest at the ground level places. On average, only 7-19% of the radon seemed to originate from the construction materials.