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.

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.

Close-Packed Ices in Nanopores.

Water molecules in any of the ice polymorphs organize themselves into a perfect four-coordinated hydrogen-bond network at the expense of dense packing. Even at high pressures, there seems to be no way to reconcile the ice rules with the close packing. Here, we report several close-packed ice phases in carbon nanotubes obtained from molecular dynamics simulations of two different water models. Typically they are in plastic states at high temperatures and are transformed into the hydrogen-ordered ice, keeping their close-packed structures at lower temperatures. The close-packed structures of water molecules in carbon nanotubes are identified with those of spheres in a cylinder. We present design principles of hydrogen-ordered, close-packed structures of ice in nanotubes, which suggest many possible dense ice forms with or without nonzero polarization. In fact, some of the simulated ices are found to exhibit ferroelectric ordering upon cooling.

Metal-organic framework template-guided electrochemical lithography on substrates for SERS sensing applications.

The templating method holds great promise for fabricating surface nanopatterns. To enhance the manufacturing capabilities of complex surface nanopatterns, it is important to explore new modes of the templates beyond their conventional masking and molding modes. Here, we employed the metal-organic framework (MOF) microparticles assembled monolayer films as templates for metal electrodeposition and revealed a previously unidentified guiding growth mode enabling the precise growth of metallic films exclusively underneath the MOF microparticles. The guiding growth mode was induced by the fast ion transportation within the nanochannels of the MOF templates. The MOF template could be repeatedly used, allowing for the creation of identical metallic surface nanopatterns for multiple times on different substrates. The MOF template-guided electrochemical growth mode provided a robust route towards cost-effective fabrication of complex metallic surface nanopatterns with promising applications in metamaterials, plasmonics, and surface-enhanced Raman spectroscopy (SERS) sensing fields.

Solvent-derived defects suppress adsorption in MOF-74.

Defects in metal-organic frameworks (MOFs) have great impact on their nano-scale structure and physiochemical properties. However, isolated defects are easily concealed when the frameworks are interrogated by typical characterization methods. In this work, we unveil the presence of solvent-derived formate defects in MOF-74, an important class of MOFs with open metal sites. With multi-dimensional solid-state nuclear magnetic resonance (NMR) investigations, we uncover the ligand substitution role of formate and its chemical origin from decomposed N,N-dimethylformamide (DMF) solvent. The placement and coordination structure of formate defects are determined by 13C NMR and density functional theory (DFT) calculations. The extra metal-oxygen bonds with formates partially eliminate open metal sites and lead to a quantitative decrease of N2 and CO2 adsorption with respect to the defect concentration. In-situ NMR analysis and molecular simulations of CO2 dynamics elaborate the adsorption mechanisms in defective MOF-74. Our study establishes comprehensive strategies to search, elucidate and manipulate defects in MOFs.

The packing parameter of bare surfactant does not necessarily indicate morphological changes.

Morphological changes of surfactant in water are believed to rely on the packing parameter of individual molecules. However, its validity has not been well examined due to the difficulties in both experiments and simulations. Herein, we perform all-atom molecular dynamics simulations, combined with the heavy hydrogen atom method, for aqueous mixtures of non-ionic surfactant, pentaethylene glycol monododecyl ether. We demonstrate the spontaneous self-reorganization from hexagonal to lamellar phase and quantify the variation of the packing parameter, hydration manner, and thermodynamic components during the process. The results clearly show that the packing parameter of bare surfactant is almost identical between these phases; thus, it does not function as an indicator. Instead, the consideration of hydration shell is likely to be necessary to account for the effective head group. We also find that the water molecules disturbed by surfactant aggregates are depleted during the hexagonal-to-lamellar transformation and subsequently correlate the dehydration to an increase in surfactant-related entropy, which is the dominant thermodynamic factor for the morphological transformation.

Relationship between Structure and Properties of Nonstoichiometric Protic Ionic Liquids: n-Butylammonium Butyrate System.

Nonstoichiometric protic ionic liquids have drawn much attention in applications, including fuel cells, batteries, and reaction media. An understanding of the relationship between their structure and properties is instructive for further applications. However, there are only a few studies on nonstoichiometric protic ionic liquids. Herein, the density, viscosity, and conductivity of nonstoichiometric n-butylammonium butyrate protic ionic liquids were measured, and we used small/wide-angle scattering (S/WAXS), electron paramagnetic resonance (EPR), and molecular dynamics (MD) simulation to explore the effect of mesostructure on their properties. It is found that the hydrogen bonds drive excess N-butyric acid (PrCOOH) molecules to wrap around ion clusters, resulting in the higher density and viscosity of PrCOOH-rich PILs. The microenvironments around various radicals differ significantly in BuNH2-rich and PrCOOH-rich PILs because of the distinct molecular arrangements. This research provided a link between the physicochemical properties and structures of nonstoichiometric PILs, which is essential for their applications in electrolytes and organic reactions.

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).

Breaking the nanoparticle's dispersible limit via rotatable surface ligands.

Achieving versatile dispersion of nanoparticles in a broad range of solvents (e.g., water, oil, and biofluids) without repeatedly recourse to chemical modifications are desirable in optoelectronic devices, self-assembly, sensing, and biomedical fields. However, such a target is limited by the strategies used to decorate nanoparticle's surface properties, leading to a narrow range of solvents for existing nanoparticles. Here we report a concept to break the nanoparticle's dispersible limit via electrochemically anchoring surface ligands capable of sensing the surrounding liquid medium and rotating to adapt to it, immediately forming stable dispersions in a wide range of solvents (polar and nonpolar, biofluids, etc.). Moreover, the smart nanoparticles can be continuously electrodeposited in the electrolyte, overcoming the electrode surface-confined low throughput limitation of conventional electrodeposition methods. The anomalous dispersive property of the smart Ag nanoparticles enables them to resist bacteria secreted species-induced aggregation and the structural similarity of the surface ligands to that of the bacterial membrane assists them to enter the bacteria, leading to high antibacterial activity. The simple but massive fabrication process and the enhanced dispersion properties offer great application opportunities to the smart nanoparticles in diverse fields.

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.

Solubility of Hydrophobes into Macrocyclic Hosts.

The intrinsic nature of macrocyclic molecules to preferentially absorb a specific solute has been opening up supramolecular chemistry. Nevertheless, the determinant factor with molecular perspectives in promoting host-guest complexations remains inconclusive, due to the lack of rigorous thermodynamic examination on the guest solubility inside the host. Here, we quantify the solute-solvent energetic and entropic contributions between the end states and on the docking route during inclusion of noble gases in cucurbit[5]uril, cucurbit[6]uril, and α-cyclodextrin, using molecular dynamics simulations in combination with the potential distribution theorem. Results show that in all of the pairs examined both the solute-solvent energy and entropy favor the inclusion, while the former is rather dominant. The frequency of interior drying, which pertains to the entropic contribution, differs between the hosts and is controlled by the existence of lid water at portal and the flexibility of host framework. Moreover, the hosts exhibit various types of absorption manners, involving non-, single-, and double-free-energy barriers.

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.

Less-Ordered Hydration Shell around Poly(N,N-diethylacrylamide) Is Insensitive to the Clouding Transition.

Raman multivariate curve resolution (Raman-MCR) is applied to examine how the hydration shell around poly(N,N-diethylacrylamide) (PDEAM) changes upon heating, in comparison with poly(N-isopropylacrylamide) (PNIPAM), both of which undergo a clouding transition near room temperature. We report that PDEAM possesses a less-ordered and smaller hydration shell than PNIPAM. Furthermore, the PDEAM hydration-shell structure is insensitive to the occurrence of clouding, indicating the coil-globule transition and aggregation of multiple chains can be achieved without the hydration-shell structural transformation.

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.

On-Off of Co-non-solvency for Poly(N-vinylcaprolactam) in Alcohol-Water Mixtures: A Molecular Dynamics Study.

Poly(N-vinylcaprolactam) (PVCL) exhibits co-non-solvency in aqueous solutions of 2-propanol but not in methanol. What distinguishes the impact of these two cosolvents on the polymer conformational stability? We report a molecular dynamics simulation study on PVCL 50-mer and monomers dissolved in methanol-water and 2-propanol-water mixtures. We show that the alcohol-concentration dependence of the effective attraction between a pair of PVCL monomers closely resembles the conformational changes in a single PVCL 50-mer as well as the experimentally observed behavior for PVCL chains. We also found that, at the co-non-solvency maximum, the monomer-monomer attraction works over a long-range beyond the solvent-separated distance. Then, we correlate the long-range attraction to the appearance of a dense alcohol concentration accumulated between the monomers. Furthermore, we distinctly demonstrate that the co-non-solvency of PVCL monomers can be switched on/off by artificially tuning the alcohol size while keeping the energetic parameters. Thus, we conclude that the magnitude of the excluded volume effect in alcohol accompanying the gain in translational entropy of the solvent is crucial to the occurrence of PVCL polymer co-non-solvency.

Hyperstable De Novo Protein with a Dimeric Bisecting Topology.

Recently, we designed and assembled protein nanobuilding blocks (PN-Blocks) from an intermolecularly folded dimeric de novo protein called WA20. Using this dimeric 4-helix bundle, we constructed a series of self-assembling supramolecular nanostructures including polyhedra and chain-type complexes. Here we describe the stabilization of WA20 by designing mutations that stabilize the helices and hydrophobic core. The redesigned proteins denature with substantially higher midpoints, with the most stable variant, called Super WA20 (SUWA), displaying an extremely high midpoint (Tm = 122 °C), much higher than the Tm of WA20 (75 °C). The crystal structure of SUWA reveals an intermolecularly folded dimer with bisecting U topology, similar to the parental WA20 structure, with two long α-helices of a protomer intertwined with the helices of another protomer. Molecular dynamics simulations demonstrate that the redesigned hydrophobic core in the center of SUWA significantly suppresses the deformation of helices observed in the same region of WA20, suggesting this is a critical factor stabilizing the SUWA structure. This hyperstable de novo protein is expected to be useful as nanoscale pillars of PN-Block components in new types of self-assembling nanoarchitectures.

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.

Temperature-Dependent Structural Changes in Liquid Benzene.

Benzene is the simplest aromatic molecule with intermolecular π-π interactions. Because ordered liquids are key structures used to study chemical and biological phenomena in the liquid state, ordered structures of benzene confined in nanopores have been extensively studied, whereas those in the liquid state are still unknown. In this study, we address fundamental questions regarding whether ordered structures of benzene are formed in the liquid state by using carbon K-edge X-ray absorption spectroscopy (XAS) as a sensitive local probe. By comparing unexpected temperature behaviors of the π* peak in XAS spectra with model calculations, we have investigated temperature-dependent changes of ordered structures in liquid benzene caused by the increase in abundance of the parallel sandwich orientation relative to parallel displaced structures for the higher temperature. These results are confirmed by infrared spectroscopy with additional support of vibrational mode calculations.

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.