Chongqin Zhu

Transport behavior of water molecules through two-dimensional nanopores

Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

A new phase diagram of water under negative pressure: The rise of the lowest-density clathrate s-III

Researchers predict a new ice clathrate structure as the most stable ice polymorph with the lowest density in a negative-pressure region. Ice and ice clathrate are not only omnipresent across polar regions of Earth or under terrestrial oceans but also ubiquitous in the solar system such as on comets, asteroids, or icy moons of the giant planets. Depending on the surrounding environment (temperature and pressure), ice alone exhibits an exceptionally rich and complicated phase diagram with 17 known crystalline polymorphs. Water molecules also form clathrate compounds with inclusion of guest molecules, such as cubic structure I (s-I), cubic structure II (s-II), hexagonal structure H (s-H), tetragonal structure T (s-T), and tetragonal structure K (s-K). Recently, guest-free clathrate structure II (s-II), also known as ice XVI located in the negative-pressure region of the phase diagram of water, is synthesized in the laboratory and motivates scientists to reexamine other ice clathrates with low density. Using extensive Monte Carlo packing algorithm and dispersion-corrected density functional theory optimization, we predict a crystalline clathrate of cubic structure III (s-III) composed of two large icosihexahedral cavities (8668412) and six small decahedral cavities (8248) per unit cell, which is dynamically stable by itself and can be fully stabilized by encapsulating an appropriate guest molecule in the large cavity. A new phase diagram of water ice with TIP4P/2005 (four-point transferable intermolecular potential/2005) model potential is constructed by considering a variety of candidate phases. The guest-free s-III clathrate with ultralow density overtakes s-II and s-H phases and emerges as the most stable ice polymorph in the pressure region below −5834 bar at 0 K and below −3411 bar at 300 K.

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.

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.

Ion-specific ice recrystallization provides a facile approach for the fabrication of porous materials

Ice recrystallization is of great importance to both fundamental research and practical applications, however understanding and controlling ice recrystallization processes remains challenging. Here, we report the discovery of an ion-specific effect on ice recrystallization. By simply changing the initial type and concentration of ions in an aqueous solution, the size of ice grains after recrystallization can be tuned from 27.4±4.1 to 277.5±30.9u2009μm. Molecular dynamics simulations show that the ability of the ion to be incorporated into the ice phase plays a key role in the ultimate size of the ice grains after recrystallization. Moreover, by using recrystallized ice crystals as templates, 2D and 3D porous networks with tuneable pore sizes could be prepared from various materials, for example, NaBr, collagen, quantum dots, silver and polystyrene colloids. These porous materials are suitable for a wide range of applications, for example, in organic electronics, catalysis and bioengineering.

Interfaces Select Specific Stereochemical Conformations: The Isomerization of Glyoxal at the Liquid Water Interface

Interfacial chemistry involving glyoxal at aerosol surfaces is postulated to catalyze aerosol growth. This chemistry remains speculative due to a lack of detailed information concerning the physicochemical behavior of glyoxal at the interface of atmospheric aerosols. Here, we report results from high-level electronic structure calculations as well as both classical and Born-Oppenheimer ab initio molecular dynamics simulations of glyoxal solvation at the air/liquid water interface. When compared to the gas phase, the trans to cis isomerization of glyoxal at the liquid water interface is found to be catalyzed; additionally, the trans conformation is selectively solvated within the bulk to a greater degree than is the cis conformation. These two processes, i.e., the catalytic effect at the water interface and the differentially selective solvation, act to enhance the concentration of the cis isomer of glyoxal at the water interface. This has important consequences for the interpretation of experiments and for the modeling of glyoxal chemistry both at the interface of water clouds and at aerosols. Broader implications of this work relate to describing the role of interfaces in selecting specific stereo molecular structures at interfacial environments.

A molecular perspective for global modeling of upper atmospheric NH3 from freezing clouds

Significance The retentions of gases upon freezing of water from available studies are conflicting. Using molecular dynamic simulations, we have revealed that the retention efficiency of NH3 upon freezing cloud is close to 0 rather than 1 during deep convection. Our results further provide theoretical framework to explain the first-ever satellite-observed high concentration of NH3 in the upper troposphere and lower stratosphere (UTLS). As NH3 emission continues to increase, this study calls upon the emergent need to assess the role of NH3 in UTLS chemistry especially in the deep convective regions. Methodologically, the molecular dynamics simulation is demonstrated as a tool for improving parameterization of interactions between trace gases and cloud (including ice) particles in global atmospheric models. Ammonia plays a key role in the neutralization of atmospheric acids such as sulfate and nitrates. A few in situ observations have supported the theory that gas-phase NH3 concentrations should decrease sharply with altitude and be extremely low in the upper troposphere and lower stratosphere (UTLS). This theory, however, seems inconsistent with recent satellite measurements and is also not supported by the aircraft data showing highly or fully neutralized sulfate aerosol particles by ammonium in the UTLS in many parts of the world. Here we reveal the contributions of deep convective clouds to NH3 in the UTLS by using integrated cross-scale modeling, which includes molecular dynamic simulations, a global chemistry transport model, and satellite and aircraft measurements. We show that the NH3 dissolved in liquid cloud droplets is prone to being released into the UTLS upon freezing during deep convection. Because NH3 emission is not regulated in most countries and its future increase is likely persistent from agricultural growth and the warmer climate, the effect of NH3 on composition and phase of aerosol particles in the UTLS can be significant, which in turn can affect cirrus cloud formation, radiation, and the budgets of NOx and O3.

Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations

Significance This contribution resolves a long-standing puzzle of the nitrous acid (HONO) formation mechanism from NO+ motif and water clusters in the ionosphere (key layer for radio signal transmission). From previous studies, massive different isomer structures have been identified. However, an explanation of how the low-lying isomers channel through the high-lying ones to form HONO species has been elusive. A clear understanding of the mechanism was only possible through molecular dynamics simulation. This work identifies the critical isomer that is key to linking the network of all the low-lying isomers together. This finding provides, to our knowledge, the first solid theoretical evidence for the formation of HONO in the ionosphere. Solar emission produces copious nitrosonium ions (NO+) in the D layer of the ionosphere, 60 to 90 km above the Earth’s surface. NO+ is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200–220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates—tetrahydrate NO+(H2O)4 and pentahydrate NO+(H2O)5—are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO+(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO+(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO+(H2O)4 and NO+(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation.