Mechanism of poly(N-isopropylacrylamide) cononsolvency in aqueous methanol solutions explored via oxygen K-edge X-ray absorption spectroscopy.

The cononsolvency mechanism of poly(N-isopropylacrylamide) (PNIPAM), dissolving in pure methanol (MeOH) and water (H2O) but being insoluble in MeOH-H2O mixtures, was investigated by O K-edge X-ray absorption spectroscopy (XAS). The cononsolvency emerges from the aggregation of PNIPAM with MeOH clusters, leading to the collapse of the hydrophobic hydration of PNIPAM.

Hydrogen-bond linking is crucial for growing ice VII embryos.

We use molecular dynamics simulations to examine the homogeneous nucleation of ice VII from metastable liquid water. An unsupervised machine learning classification identifies two distinct local structures composing Ice VII nuclei. The seeding method, combined with the classical nucleation theory (CNT), predicts the solid-liquid interfacial free energy, consistent with the value from the mold integration method. Meanwhile, the nucleation rates estimated from the CNT framework and brute force spontaneous nucleations are inconsistent, and we discuss the reasons for this discrepancy. Structural and dynamical heterogeneities suggest that the potential birthplace for an ice VII embryo is relatively ordered, although not necessarily relatively immobile. Moreover, we demonstrate that without the formation of hydrogen-bond links, ice VII embryos do not grow.

A tiny charge-scaling in the OPLS-AA + L-OPLS force field delivers the realistic dynamics and structure of liquid primary alcohols.

We carry out molecular dynamics simulations for pure liquid primary alcohols ranging from methanol to 1-decanol under ambient conditions. Based on the OPLS-AA force field with the L-OPLS correction, we demonstrate that a few % increases in the partial charges deliver the realistic dynamics (self-diffusion coefficient and shear viscosity) and structure (density and X-ray scattering intensity) as well as enthalpy of vaporization and isothermal compressibility. The validity against thermal expansion coefficient, isobaric heat capacity, and static dielectric constant are also discussed.

Advanced Buffering Acidic Aqueous Electrolytes for Ultra-Long Life Aqueous Zinc-Ion Batteries.

Mild aqueous Zn batteries have attracted increasing attention for energy storage due to the advantages of high safety and low cost; however, the rechargeability of Zn anodes is one major issue for practical applications. In this work, an effective approach is proposed to improve the reversibility and stability of Zn anodes using advanced acidic electrolytes. A trace amount of acetic acid (HAc) is employed as a buffering agent to provide a stable pH environment in aqueous Zn electrolytes, and thus suppress passivation from precipitation reactions on Zn electrodes. Meanwhile, tetramethylene sulfone (TMS) is introduced as the critical component to stabilize the Zn anodes in the acidic electrolyte. TMS greatly strengthens the hydrogen-bonding network with reduced H2 O activity and extends the electrochemical window of acidic electrolytes. With the optimal 3 m Zn(OTF)2 in (H2 O-HAc)/TMS acidic electrolyte (pH 1.6), the Zn electrode exhibits a coulombic efficiency of >99.8% and smooth Zn deposition. The Zn-V2 O5 full cell demonstrates ultra-stable cycling over 20 000 cycles with a low decay rate of 0.0009% for each cycle at a negative/postive capacity ratio of 6.5. This work provides an insightful perspective to stabilize Zn electrodes by regulating the pH environment and limiting the H2 O activity simultaneously for long-life Zn anodes.

Transcription Factor SrsR (YgfI) Is a Novel Regulator for the Stress-Response Genes in Stationary Phase in Escherichia coli K-12.

Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI is an uncharacterized LysR family transcription factor in Escherichia coli. To identify the function of YgfI, the genomic SELEX (gSELEX) screening was performed for YgfI regulation targets on the E. coli genome. In addition, regulatory and phenotypic analyses were performed. A total of 10 loci on the E. coli genome were identified as the regulatory targets of YgfI with the YgfI binding activity. These predicted YgfI target genes were involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance, many of which were expressed in the stationary phase. The TCAGATTTTGC sequence was identified as an YgfI box in in vitro gel shift assay and DNase-I footprinting assays. RT-qPCR analysis in vivo revealed that the expression of YgfI increased in the stationary phase. Physiological analyses suggested the participation of YgfI in biofilm formation and an increase in the tolerability against hydrogen peroxide. In summary, we propose to rename ygfI as srsR (a stress-response regulator in stationary phase).

Absorption of mechanical energy via formation of ice nanotubes in zeolites.

Molecular dynamics simulations are carried out for a heterogeneous system composed of bulk water and pure-silica zeolites of the AFI type. My simulations show, for the first time, the spontaneous crystallization of water in hydrophobic zeolite channels by compression, while the water outside remains liquid. The formation of ice nanotubes results in a molecular bumper behavior in the absence of chemical reactions, although the mechanism has been explained by the appearance of silanol defects. In contrast, the same zeolite-water system exhibits a weak shock-absorber behavior at higher temperatures. My study shows that the phase transitions of confined water dramatically change its intrusion/extrusion behavior and alter the energetic performance by varying the temperature alone. The results offer a new perspective for a better design of hydrophobic nanoporous materials utilized with water.

Reduction of water-mediated repulsion drives poly(N-vinylcaprolactam) collapse upon heating.

Upon heating, thermo-sensitive aqueous polymers undergo the coil-to-globule transition, where drastic chemical and structural transformations occur that are of great interest for academia and applications. Although it is widely believed that the disruption of the clathrate-like hydration shell drives this polymer collapse, no decisive evidence has yet been provided. Here, we demonstrate, using all-atom molecular dynamics simulations, that poly(N-vinylcaprolactam) in water has a less ordered hydration structure than the bulk liquid and undergoes the coil-to-globule transition without remarkable hydration shell depletion or qualitative transformation. Furthermore, our free energy analyses show that water strongly pushes the "hydrophobic" caprolactam groups apart rather than bringing them together. We find that the reduction of this water-mediated repulsion, arising from the change in free energies for cavity formation, drives the polymer collapse upon heating.

Defect pair separation as the controlling step in homogeneous ice melting.

On being heated, ice melts into liquid water. Although in practice this process tends to be heterogeneous, it can occur homogeneously inside bulk ice. The thermally induced homogeneous melting of solids is fairly well understood, and involves the formation and growth of melting nuclei. But in the case of water, resilient hydrogen bonds render ice melting more complex. We know that the first defects appearing during homogeneous ice melting are pairs of five- and seven-membered rings, which appear and disappear repeatedly and randomly in space and time in the crystalline ice structure. However, the accumulation of these defects to form an aggregate is nearly additive in energy, and results in a steep free energy increase that suppresses further growth. Here we report molecular dynamics simulations of homogeneous ice melting that identify as a crucial first step not the formation but rather the spatial separation of a defect pair. We find that once it is separated, the defect pair--either an interstitial (I) and a vacancy (V) defect pair (a Frenkel pair), or an L and a D defect pair (a Bjerrum pair)--is entropically stabilized, or 'entangled'. In this state, defects with threefold hydrogen-bond coordination persist and grow, and thereby prepare the system for subsequent rapid melting.

Antifreeze Glycoproteins Bind Reversibly to Ice via Hydrophobic Groups.

Antifreeze molecules allow organisms to survive in subzero environments. Antifreeze glycoproteins (AFGPs), produced by polar fish, are the most potent inhibitors of ice recrystallization. To date, the molecular mechanism by which AFGPs bind to ice has not yet been elucidated. Mutation experiments cannot resolve whether the binding occurs through the peptide, the saccharides, or both. Here, we use molecular simulations to determine the mechanism and driving forces for binding of AFGP8 to ice, its selectivity for the primary prismatic plane, and the molecular origin of its exceptional ice recrystallization activity. Consistent with experiments, AFGP8 in simulations preferentially adopts the PPII helix secondary structure in solution. We show that the segregation of hydrophilic and hydrophobic groups in the PPII helix is vital for ice binding. Binding occurs through adsorption of methyl groups of the peptide and disaccharides to ice, driven by the entropy of dehydration of the hydrophobic groups as they nest in the cavities at the ice surface. The selectivity to the primary prismatic plane originates in the deeper cavities it has compared to the basal plane. We estimate the free energy of binding of AFGP8 and the longer AFGPs4-6, and find them to be consistent with the reversible binding demonstrated in experiments. The simulations reveal that AFGP8 binds to ice through a myriad of conformations that it uses to diffuse through the ice surface and find ice steps, to which it strongly adsorbs. We interpret that the existence of multiple, weak binding sites is the key for the exceptional ice recrystallization inhibition activity of AFGPs.

Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy.

Recently, we proposed a reference-modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard-sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard-sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard-sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high-temperature and high-pressure unfolding of the protein. © 2017 Wiley Periodicals, Inc.

Multiple binding modes of a moderate ice-binding protein from a polar microalga.

Ice-binding proteins (IBPs) produced by cold-tolerant organisms interact with ice and strongly control crystal growth. The molecular basis for the different magnitudes of activity displayed by various IBPs (moderate and hyperactive) has not yet been clarified. Previous studies questioned whether the moderate activity of some IBPs relies on their weaker binding modus to the ice surface, compared to hyperactive IBPs, rather than relying on binding only to selected faces of the ice crystal. We present the structure of one moderate IBP from the sea-ice diatom Fragilariopsis cylindrus (fcIBP) as determined by X-ray crystallography and investigate the protein's binding modes to the growing ice-water interface using molecular dynamics simulations. The structure of fcIBP is the IBP-1 fold, defined by a discontinuous ß-solenoid delimitated by three faces (A, B and C-faces) and braced by an α-helix. The fcIBP structure shows capping loops on both N- and C-terminal parts of the solenoid. We show that the protein adsorbs on both the prism and the basal faces of ice crystals, confirming experimental results. The fcIBP binds irreversibly to the prism face using the loop between the B and the C-faces, involving also the B-face in water immobilization despite its irregular structure. The α-helix attaches the protein to the basal face with a partly reversible modus. Our results suggest that fcIBP has a looser attachment to ice and that this weaker binding modus is the basis to explain the moderate activity of fcIBP.

Solid-liquid critical behavior of water in nanopores.

Nanoconfined liquid water can transform into low-dimensional ices whose crystalline structures are dissimilar to any bulk ices and whose melting point may significantly rise with reducing the pore size, as revealed by computer simulation and confirmed by experiment. One of the intriguing, and as yet unresolved, questions concerns the observation that the liquid water may transform into a low-dimensional ice either via a first-order phase change or without any discontinuity in thermodynamic and dynamic properties, which suggests the existence of solid-liquid critical points in this class of nanoconfined systems. Here we explore the phase behavior of a model of water in carbon nanotubes in the temperature-pressure-diameter space by molecular dynamics simulation and provide unambiguous evidence to support solid-liquid critical phenomena of nanoconfined water. Solid-liquid first-order phase boundaries are determined by tracing spontaneous phase separation at various temperatures. All of the boundaries eventually cease to exist at the critical points and there appear loci of response function maxima, or the Widom lines, extending to the supercritical region. The finite-size scaling analysis of the density distribution supports the presence of both first-order and continuous phase changes between solid and liquid. At around the Widom line, there are microscopic domains of two phases, and continuous solid-liquid phase changes occur in such a way that the domains of one phase grow and those of the other evanesce as the thermodynamic state departs from the Widom line.

Promotion of Homogeneous Ice Nucleation by Soluble Molecules.

Atmospheric aerosols nucleate ice in clouds, strongly impacting precipitation and climate. The prevailing consensus is that ice nucleation is promoted heterogeneously by the surface of ice nucleating particles in the aerosols. However, recent experiments indicate that water-soluble molecules, such as polysaccharides of pollen and poly(vinyl alcohol) (PVA), increase the ice freezing temperature. This poses the question of how do flexible soluble molecules promote the formation of water crystals, as they do not expose a well-defined surface to ice. Here we use molecular simulations to demonstrate that PVA promotes ice nucleation through a homogeneous mechanism: PVA increases the nucleation rate by destabilizing water in the solution. This work demonstrates a novel paradigm for understanding ice nucleation by soluble molecules and provides a new handle to design additives that promote crystallization.

Influence of co-non-solvency on hydrophobic molecules driven by excluded volume effect.

We demonstrate by molecular dynamics simulation that co-non-solvency manifests itself in the solvent-induced interaction between three hydrophobes, methane, propane and neopentane, in methanol-water mixtures. Decomposition of the potential of mean force, based on the potential distribution theorem, clearly shows that the solute-solvent entropic change is responsible for stabilizing the aggregation of these hydrophobic molecules. Furthermore, we show that the entropic change pertains to the excluded volume effect.

Influence of Cononsolvency on the Aggregation of Tertiary Butyl Alcohol in Methanol-Water Mixtures.

The term cononsolvency has been used to describe a situation in which a polymer is less soluble (and so is more likely to collapse and aggregate) in a mixture of two cosolvents than it is in either one of the pure solvents. Thus, cononsolvency is closely related to the suppression of protein denaturation by stabilizing osmolytes. Here, we show that cononsolvency behavior can also influence the aggregation of tertiary butyl alcohol in mixtures of water and methanol, as demonstrated using both Raman multivariate curve resolution spectroscopy and molecular dynamics simulations. Our results imply that cononsolvency results from the cosolvent-mediated enhancement of the attractive (solvophobic) mean force between nonpolar groups, driven by preferential solvation of the aggregates, in keeping with Wyman-Tanford theory.

Cononsolvency behavior of hydrophobes in water + methanol mixtures.

The molecular origin of cononsolvency behavior is explored using molecular dynamics simulations. Cononsolvency behavior in aggregations of methane molecules and conformational changes of those clusters dissolved in water + methanol mixtures are confirmed by re-entrant changes in the solvent-mediated interactions with increasing methanol concentration. The results indicate that the cononsolvency behavior arises from the solute-solute hydrophobic interactions rather than other interactions such as solute-solvent hydrophilic interactions. Furthermore, we show that even the van der Waals interaction is not necessary to induce the cononsolvency behavior by investigating the dimerization process of repulsive cavities. The non-monotonic change of the solvent-mediated interaction results from the difference in the concentration dependencies of excess chemical potentials between an isolated methane and methane clusters. The concentration dependencies of the excess chemical potentials are decomposed into contributions from various intermolecular effective interactions through the framework of the Kirkwood-Buff theory, and then we show that the change of the relative magnitude between hydrophobe-methanol and hydrophobe-water effective interactions with increasing methanol concentration is responsible for the cononsolvency behavior.

Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) in water.

Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) (PNiPA) in water are investigated by performing extensive molecular dynamics simulations. First, we observe that the model short oligomer of PNiPA with a modified OPLS-AA force field in water shrinks with increasing pressure. At varying pressures, the potentials of mean force (PMFs) between a pair of N-isopropylpropionamide (NiPPA) molecules, the repeating unit of PNiPA, are obtained and decomposed into the nonpolar and Coulombic contributions. The nonpolar contribution is the PMF between the hypothetical nonpolar NiPPA molecules in the solvent, which is mainly due to the molecular volume effect. The attractive force between NiPPA molecules is enhanced at higher pressures in agreement with the behavior of PNiPA. This pressure dependence of the PMF is caused by the growing nonpolar contribution at higher pressures. In contrast, the Coulombic contribution to the PMF becomes higher overall, making the mean force less attractive or more repulsive, with increasing pressure. The strength of the aggregation and its pressure dependence of the nonpolar contribution in water are closely reproduced even in nonpolar solvents. The degree of the pressure dependence is explained by the isothermal compressibility or the tightness of the solvation shell around an isolated solute, without regard to the existence and variation of hydrogen bond networks in a solvent. The role of hydrogen bonds in the aggregation of NiPPA and PNiPA molecules is also discussed.

Water-mediated aggregation of 2-butoxyethanol.

Water plays an important role in mediating hydrophobic interactions, and yet open questions remain regarding the magnitude, and even the sign, of water-mediated contributions to the potential of mean force between a pair of oily molecules dissolved in water. Here, the water-mediated interaction between 2-butoxyethanol (BE) molecules dissolved in water is quantified using Raman multivariate curve resolution (Raman-MCR), molecular dynamics (MD) simulations, and random mixing (RM) predictions. Our results indicate that the number of contacts between BE molecules at concentrations between 0.2 M and 1 M exceeds RM predictions, but is less than some MD predictions. Moreover, the potential of mean force between BE molecules in water has a well depth that is shallower than the direct interaction between 1-ethoxybutane chains in the gas phase, and thus the water-mediated contribution to BE aggregation is repulsive, as it pulls BE molecules apart rather than pushing them together.

Solid-liquid critical behavior of a cylindrically confined Lennard-Jones fluid.

Extensive molecular dynamics simulations have been performed to study the phase behavior of Lennard-Jones particles confined in a quasi-one-dimensional hydrophobic nanopore. We provide unambiguous evidence for a solid-liquid critical point by investigating (i) isotherms in the pressure-volume plane, (ii) the spontaneous solid-liquid phase separation below a certain temperature, (iii) diverging heat capacity and isothermal compressibility as a certain point is approached, (iv) continuous change of dynamical and structural properties above the point, (v) the finite-size scaling analysis of the density distribution below and above the point. The result combined with earlier studies of confined water suggests that the solid-liquid critical point is not uncommon in quasi-one- and quasi-two-dimensional fluids.

Diversity of transition pathways in the course of crystallization into ice VII.

We report various types of pathways emerging in the course of freezing into a high pressure ice VII by large-scale molecular dynamics (MD) simulations at 10 GPa, 425 K. Some trajectories showed an apparently stepwise transition via the unique metastable "phase" in accordance with Ostwald's step rule. The metastable structure was identified as one of the tetrahedrally close-packed structures having the nature of a rotator phase (plastic phase). The unit cell consists of 21 water molecules that has not yet been reported by simulation or by experiments. Structure analysis of numerous trajectories reveals that the nucleation of ice VII easily occurs at the grain boundaries of the metastable embryos, known as epitaxy-mediated transformation in line with Ostwald's step rule. The size of the grain boundaries is thus responsible for the lifetime of the metastable phase. On the other hand, once the embryo of ice VII appears prior to that of the metastable phase in liquid, direct transition to ice VII takes place. We also show that the plastic behavior of the metastable phase is not uniform but is sensitive to the interaction strength of adjacent molecules and the local structure, thus we call "partially plastic ice".