Joseph S. Francisco

Near-Barrierless Ammonium Bisulfate Formation via a Loop-Structure Promoted Proton-Transfer Mechanism on the Surface of Water

In the atmosphere, a well-known and conventional pathway toward the formation of ammonium sulfate is through the neutralization of sulfuric acid with ammonia (NH3) in water droplets. Here, we present direct ab initio molecular dynamics simulation evidence of the formation of ammonium bisulfate (NH4HSO4) from the hydrated NH3 and SO3 molecules in a water trimer as well as on the surface of a water droplet. This reaction suggests a new mechanism for the formation of ammonium sulfate in the atmosphere, especially when the concentration of NH3 is high (e.g., ∼10 μg m(-3)) in the air. Contrary to the water monomer and dimer, the water trimer enables near-barrierless proton transfer via the formation of a unique loop structure around the reaction center. The formation of the loop structure promotes the splitting of a water molecule in the proton-transfer center, resulting in the generation a NH4(+)/HSO4(-) ion pair. The loop-structure promoted proton-transfer mechanism is expected to be ubiquitous on the surface of cloud droplets with adsorbed NH3 and SO3 molecules and, thus, may play an important role in the nucleation of aerosol particles (e.g., fine particles PM2.5) in water droplets.

New Mechanistic Pathways for Criegee-Water Chemistry at the Air/Water Interface

Understanding Criegee chemistry has become one of central topics in atmospheric research recently. The reaction of Criegee intermediates with gas-phase water clusters has been widely viewed as a key Criegee reaction in the troposphere. However, the effect of aerosols or clouds on Criegee chemistry has received little attention. In this work, we have investigated the reaction between the smallest Criegee intermediate, CH2OO, and water clusters in the gas phase, as well as at the air/water surface using ab initio quantum chemical calculations and adaptive buffered force quantum mechanics/molecular mechanics (QM/MM) dynamics simulations. Our simulation results show that the typical time scale for the reaction of CH2OO with water at the air/water interface is on the order of a few picoseconds, 2-3 orders of magnitude shorter than that in the gas phase. Importantly, the adbf-QM/MM dynamics simulations suggest several reaction pathways for the CH2OO + water reaction at the air/water interface, including the loop-structure-mediated mechanism and the stepwise mechanism. Contrary to the conventional gas-phase CH2OO reaction, the loop-structure is not a prerequisite for the stepwise mechanism. For the latter, a water molecule and the CH2OO at the air/water interface, upon their interaction, can result in the formation of (H3O)(+) and (OH)CH2(OO)(-). Thereafter, a hydrogen bond can be formed between (H3O)(+) and the terminal oxygen atom of (OH)CH2(OO)(-), leading to direct proton transfer and the formation of α-hydroxy methylperoxide, HOCH2OOH. The mechanistic insights obtained from this simulation study should motivate future experimental studies of the effect of water clouds on Criegee chemistry.

Unraveling the mechanism of selective ion transport in hydrophobic subnanometer channels

Significance Ion channels facilitate diffusion of ions across biological membranes. It has been a longstanding puzzle as to why the larger-sized K+ ion can diffuse across the narrow potassium channel, whereas the smaller Na+ cannot. Recently synthesized nanopores also possess ion selectivity, suggesting different mechanisms for the selective ion transport. Here, we employ ab initio molecular dynamics simulation to investigate structural and dynamical properties of aqua Na+ and K+ ions in hydrophobic nanochannels. We find that the aqua-Na+ ion has a smaller-sized but more structured and robust hydration shell, leading to low diffusivity in subnanometer channels. We predict that the (8, 8) carbon nanotube is possibly the best artificial K+-selective channel and may give rise to the highest K+ transportation rate. Recently reported synthetic organic nanopore (SONP) can mimic a key feature of natural ion channels, i.e., selective ion transport. However, the physical mechanism underlying the K+/Na+ selectivity for the SONPs is dramatically different from that of natural ion channels. To achieve a better understanding of the selective ion transport in hydrophobic subnanometer channels in general and SONPs in particular, we perform a series of ab initio molecular dynamics simulations to investigate the diffusivity of aqua Na+ and K+ ions in two prototype hydrophobic nanochannels: (i) an SONP with radius of 3.2 Å, and (ii) single-walled carbon nanotubes (CNTs) with radii of 3–5 Å (these radii are comparable to those of the biological potassium K+ channels). We find that the hydration shell of aqua Na+ ion is smaller than that of aqua K+ ion but notably more structured and less yielding. The aqua ions do not lower the diffusivity of water molecules in CNTs, but in SONP the diffusivity of aqua ions (Na+ in particular) is strongly suppressed due to the rugged inner surface. Moreover, the aqua Na+ ion requires higher formation energy than aqua K+ ion in the hydrophobic nanochannels. As such, we find that the ion (K+ vs. Na+) selectivity of the (8, 8) CNT is ∼20× higher than that of SONP. Hence, the (8, 8) CNT is likely the most efficient artificial K+ channel due in part to its special interior environment in which Na+ can be fully solvated, whereas K+ cannot. This work provides deeper insights into the physical chemistry behind selective ion transport in nanochannels.

Quartic force field-derived vibrational frequencies and spectroscopic constants for the isomeric pair SNO and OSN and isotopologues

The SNO and OSN radical isomers are likely to be of significance in atmospheric and astrochemistry, but very little is known about their gas phase spectroscopic properties. State-of-the-art ab initio composite quartic force fields are employed to analyze the rovibrational features for both systems. Comparison to condensed-phase experimental data for SNO has shown that the 1566.4 cm(-1) ν1 N-O stretch is indeed exceptionally bright and likely located in this vicinity for subsequent gas phase experimental analysis. The OSN ν1 at 1209.4 cm(-1) is better described as the antisymmetric stretch in this molecule and is also quite bright. The full vibrational, rotational, and rovibrational data are provided for SNO and OSN and their single (15)N, (18)O, and (34)S isotopic substitutions in order to give a more complete picture as to the chemical physics of these molecules.

Interaction of the NH2 Radical with the Surface of a Water Droplet

We present a comprehensive computational study of NH2 (radical) solvation in a water nanodroplet. The ab initio Born-Oppenheimer molecular dynamics simulation shows that NH2 tends to accumulate at the air-water interface. The hydrogen-bonding analysis shows that compared to the hydrogen bond of HNH··OH2, the hydrogen bond of HOH··NH2 is the dominant interaction between NH2 and water. Due to the loose hydrogen-bonding network formed between NH2 and the droplet interface, the NH2 can easily move around on the droplet surface, which speeds up the dynamics of NH2 at the air-water interface. Moreover, the structural analysis indicates that the NH2 prefers an orientation such that both N atom and one of its H atoms interact with the water droplet, while the other H atom is mostly exposed to the air. As a result, the NH2 radical becomes more accessible for reaction at the water interface. More importantly, the solvation of NH2 modifies the amplitude of vibration of the N-H bond, thereby affecting the Mulliken charges and electrophilicity of NH2. As such, reactive properties of the NH2 are altered by the droplet interface, and this can either speed up reactions or allow other reactions processes to occur in the atmosphere. Hence, the solvation of NH2 on water droplets, in chemistry of the atmosphere, may not be negligible when considering the effects of clouds.

Elemental sulfur aerosol-forming mechanism

Significance The elemental sulfur aerosols are an important constituent in the atmospheres of Earth, Mars, and Venus. There is now evidence suggesting that these aerosols have also played a role in the evolution of early life on Earth. Traditionally, the photolysis of sulfur gases by UV light is thought to be the main mechanism for the formation of sulfur particles in these atmospheres. But, in the theoretical calculations reported here, we propose a nonphotochemical mechanism for the formation of elemental sulfur aerosols that takes advantage of the interaction between sulfur oxides and hydrogen sulfide under water or sulfuric acid catalysis. These results provide a chemical framework for understanding the formation mechanism of S0 aerosols in planetary atmospheres. Elemental sulfur aerosols are ubiquitous in the atmospheres of Venus, ancient Earth, and Mars. There is now an evolving body of evidence suggesting that these aerosols have also played a role in the evolution of early life on Earth. However, the exact details of their formation mechanism remain an open question. The present theoretical calculations suggest a chemical mechanism that takes advantage of the interaction between sulfur oxides, SOn (n = 1, 2, 3) and hydrogen sulfide (nH2S), resulting in the efficient formation of a Sn+1 particle. Interestingly, the SOn + nH2S → Sn+1 + nH2O reactions occur via low-energy pathways under water or sulfuric acid catalysis. Once the Sn+1 particles are formed, they may further nucleate to form larger polysulfur aerosols, thus providing a chemical framework for understanding the formation mechanism of S0 aerosols in different environments.

Energetics, structure, and rovibrational spectroscopic properties of the sulfurous anions SNO− and OSN−

The SNO(-) and OSN(-) anions are shown in this work to be very stable negatively charged species in line with other recent work [T. Trabelsi et al., J. Chem. Phys. 143, 164301 (2015)]. Utilizing established quartic force field techniques, the structural and rovibrational data for these anions are produced. The SNO(-) anion is less linear and has weaker bonds than the corresponding neutral radical giving much smaller rotational constants. OSN(-) is largely unchanged in these regards with inclusion of the additional electron. The S-N bond is actually stronger, and the rotational constants of OSN(-) versus OSN are similar. The vibrational frequencies of SNO(-) are red-shifted from the radical while those in OSN(-) are mixed. OSN(-) has mixing of the stretching modes while the S-N and N-S stretches of SNO(-) are largely independent of one another. The ω3 stretches are much brighter in these anions than they are in the radicals, but the ω1 stretches are still the brightest.

New insight into the helium-induced damage in MAX phase Ti3AlC2 by first-principles studies

In the present work, the behavior of He in the MAX phase Ti3AlC2 material is investigated using first-principle methods. It is found that, according to the predicted formation energies, a single He atom favors residing near the Al plane in Ti3AlC2. The results also show that Al vacancies are better able to trap He atoms than either Ti or C vacancies. The formation energies for the secondary vacancy defects near an Al vacancy or a C vacancy are strongly influenced by He impurity content. According to the present results, the existence of trapped He atoms in primary Al vacancy can promote secondary vacancy formation and the He bubble trapped by Al vacancies has a higher tendency to grow in the Al plane of Ti3AlC2. The diffusion of He in Ti3AlC2 is also investigated. The energy barriers are approximately 2.980 eV and 0.294 eV along the c-axis and in the ab plane, respectively, which means that He atoms exhibit faster migration parallel to the Al plane. Hence, the formation of platelet-like bubbles nucleated from the Al vacancies is favored both energetically and kinetically. Our calculations also show that the conventional spherical bubbles may be originated from He atoms trapped by C vacancies. Taken together, these results are able to explain the observed formation of bubbles in various shapes in recent experiments. This study is expected to provide new insight into the behaviors of MAX phases under irradiation from electronic structure level in order to improve the design of MAX phase based materials.

Distinct ice patterns on solid surfaces with various wettabilities

Significance Ice growth is essential to the final shape of ice crystals; therefore, it is of significant relevance to rich varieties of practical applications and fundamental research. A correlation between the surface wettability and ice growth has not been established, although ice often forms on solid surfaces. We discover experimentally that ice grows along surface when the contact angle of water drops on solid surfaces is below a critical value, and ice grows off surface when the contact angle is above this critical value. Our molecular dynamics simulation analysis reveals that the presence/absence of bilayer ice on solid surfaces of different surface wettabilities dictates the ice growth and therefore provides the molecular mechanism of ice growth on solid surfaces. No relationship has been established between surface wettability and ice growth patterns, although ice often forms on top of solid surfaces. Here, we report experimental observations obtained using a process specially designed to avoid the influence of nucleation and describe the wettability-dependent ice morphology on solid surfaces under atmospheric conditions and the discovery of two growth modes of ice crystals: along-surface and off-surface growth modes. Using atomistic molecular dynamics simulation analysis, we show that these distinct ice growth phenomena are attributable to the presence (or absence) of bilayer ice on solid surfaces with different wettability; that is, the formation of bilayer ice on hydrophilic surface can dictate the along-surface growth mode due to the structural match between the bilayer hexagonal ice and the basal face of hexagonal ice (ice Ih), thereby promoting rapid growth of nonbasal faces along the hydrophilic surface. The dramatically different growth patterns of ice on solid surfaces are of crucial relevance to ice repellency surfaces.

Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network

Significance Quantitative characterization of hydrophobicity of amino acid side chains in protein environment has important implications to the understanding of the hydrophobic effects and their role in protein folding. Numerous parameters were developed previously to determine hydrophobicity of amino acid residues. However, these hydrophobicity scales are not always correlated consistently. Here, we constructed artificial planar peptide networks composed of unified amino acid side chains, considering both the primary and β-sheet secondary structure of the protein. Using molecular dynamics simulation, we computed the contact angle of a water nanodroplet on the peptide networks for all 20 types of amino acids. Our simulations offer a bridge that can connect thermodynamic hydrophobic data of amino acid residues and contact angle measurement widely used in engineering fields. Hydrophobicity of macroscopic planar surface is conventionally characterized by the contact angle of water droplets. However, this engineering measurement cannot be directly extended to surfaces of proteins, due to the nanometer scale of amino acids and inherent nonplanar structures. To measure the hydrophobicity of side chains of proteins quantitatively, numerous parameters were developed to characterize behavior of hydrophobic solvation. However, consistency among these parameters is not always apparent. Herein, we demonstrate an alternative way of characterizing hydrophobicity of amino acid side chains in a protein environment by constructing a monolayer of amino acids (i.e., artificial planar peptide network) according to the primary and the β-sheet secondary structures of protein so that the conventional engineering measurement of the contact angle of a water droplet can be brought to bear. Using molecular dynamics simulations, contact angles θ of a water nanodroplet on the planar peptide network, together with excess chemical potentials of purely repulsive methane-sized Weeks−Chandler−Andersen solute, are computed. All of the 20 types of amino acids and the corresponding planar peptide networks are studied. Expectedly, all of the planar peptide networks with nonpolar amino acids are hydrophobic due to θ > 90°, whereas all of the planar peptide networks of the polar and charged amino acids are hydrophilic due to θ < 90°. Planar peptide networks of the charged amino acids exhibit complete-wetting behavior due to θ = 0°. This computational approach for characterization of hydrophobicity can be extended to artificial planar networks of other soft matter.