Random Copolymers Based on 2-Ethylhexyl Acrylate Exhibit Unusual Glass Transition Breadth and Facile Autonomous Self-Healing over a Broad Composition Range.

Statistical copolymers are commercially important because their properties can be tuned by comonomer selection and composition. Rubbery-state styrene (S)/n-butyl acrylate (nBA) copolymers have previously been reported to exhibit facile, autonomous self-healing over a narrow composition band (47/53 to 53/47 mol%). The need for a narrow composition band is explained by alternating comonomer sequences that accommodate interchain secondary bonding. It is hypothesized that copolymers that achieve interchain secondary bonding without alternating sequences can exhibit facile self-healing over a broad composition range. 2-ethylhexyl acrylate (EHA) is identified as yielding sequence-independent secondary bonding interactions. For these interactions it is tested experimentally by glass transition breadth in rubbery-state S/EHA copolymers, with S/n-hexyl acrylate (nHA) and S/nBA copolymers as controls. The n-alkyl acrylate random copolymers exhibit enhanced glass transition breadths over narrow composition bands that correspond to autonomous self-healing. In contrast, S/EHA copolymers exhibit much greater glass transition breadths than S/nHA and S/nBA copolymers at all compositions tested as well as self-healing of damage over a broad composition range with full tensile-property recovery, often in 3-10 h. Characterization of glass transition breadth may serve as a simple screening tool for identifying copolymers that exhibit broad-composition-range, facile, autonomous self-healing and contribute to polymer resilience and sustainability.

Anharmonicity Reveals the Tunability of the Charge Density Wave Orders in Monolayer VSe2.

VSe2 is a layered compound that has attracted great attention due to its proximity to a ferromagnetic state that is quenched by its charge density wave (CDW) phase. In the monolayer limit, unrelated experiments have reported different CDW orders with different transition temperatures, making this monolayer very controversial. Here we perform first-principles nonperturbative anharmonic phonon calculations in monolayer VSe2 in order to estimate the CDW order and the corresponding transition temperature. They reveal that monolayer VSe2 develops two independent charge density wave orders that compete as a function of strain. Variations of only 1.5% in the lattice parameter are enough to stabilize one order or the other. Moreover, we analyze the impact of external Lennard-Jones interactions, showing that these can act together with anharmonicity to suppress the CDW orders. Our results solve previous experimental contradictions, highlighting the high tunability and substrate dependency of the CDW orders of monolayer VSe2.

Energetic basis of hydrogen bond formation in aqueous solution.

The thermodynamic forces driving the formation of H-bonds in macromolecules have long been the subject of speculation, theory and experiment. Comparison of the energetic parameters of AT and GC base pairs in DNA duplexes has recently led to the realisation that formation of a 'naked' hydrogen bond, i.e. without other accompanying Van der Waals close contacts, is a non-enthalpic process driven by the entropy increase resulting from release of tightly bound water molecules from the component polar groups. This unexpected conclusion finds a parallel in the formation of ionic bonds, for example between the amino groups of DNA binding proteins and the oxygens of DNA phosphate groups that are also non-enthalpic and entropy driven. The thermodynamic correspondence between these two types of polar non-covalent bonding implies that the non-enthalpic nature of base pairing in DNA is not particular to that specific structural circumstance.

Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms.

The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards ß-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.

Towards Predicting the Sequential Appearance of Zeolitic Imidazolate Frameworks Synthesized by Mechanochemistry.

We use computational materials methods to study the sequential appearance of zinc-based zeolitic imidazolate frameworks (ZIFs) generated in the mechanochemical conversion process. We consider nine ZIF topologies, namely RHO, ANA, QTZ, SOD, KAT, DIA, NEB, CAG and GIS, combined with the two ligands 2-methylimidazolate and 2-ethylimidazolate. Of the 18 combinations obtained, only six (three for each ligand) were actually observed during the mechanosynthesis process. Energy and porosity calculations based on density functional theory, in combination with the Ostwald rule of stages, were found to be insufficient to distinguish the experimentally observed ZIFs. We then show, using classical molecular dynamics, that only ZIFs withstanding quasi-hydrostatic pressure P ≥ 0.3 GPa without being destroyed were observed in the laboratory. This finding, along with the requirement that successive ZIFs be generated with decreasing porosity and/or energy, provides heuristic rules for predicting the sequences of mechanically generated ZIFs for the two ligands considered.

Diversifying Nanoparticle Superstructures and Functions Enabled by Translative Templating from Supramolecular Polymerization.

Biology exploits a transcription-translation approach to deliver structural information from DNA to the protein-building machines with high precision. Here, we show how the structural information of small synthetic molecules could be used to guide the assembly of inorganic nanoparticles into diversified yet long-range ordered superstructures, enabling the information transfer across four or five orders of magnitude in length scale. We designed three perylene diimide (PDI) based isomers differing by their site-specific substitutions of the methyl group, which were able to supramolecularly polymerize into diverse structures. Importantly, coassembly of these PDI isomers with nanoparticles (NPs) could produce diverse long-range ordered nanoparticle superstructures, including one-dimensional NPs chains, double helical NPs assemblies and two-dimensional NPs superlattices. Equally important, we demonstrate that the information originated from small molecules could diversify the functions of the self-assembled nanocomposites.

Novel van der Waals Deep-UV Nonlinear Optical Materials.

Van der Waals (vdW) deep-UV (DUV) nonlinear optical (NLO) crystal is an important material system recently developed. Herein, we review its concept and original intention, and then summarized the discovery process of related materials, including the role of A-site cations and the resulting two-/one-dimensional vdW DUV NLO systems. Finally, we evaluate the practical DUV NLO performance and prospected the opportunities and challenges.

Thermodynamic basis of the α-helix and DNA duplex.

Analysis of calorimetric and crystallographic information shows that the α-helix is maintained not only by the hydrogen bonds between its polar peptide groups, as originally supposed, but also by van der Waals interactions between tightly packed apolar groups in the interior of the helix. These apolar contacts are responsible for about 60% of the forces stabilizing the folded conformation of the α-helix and their exposure to water on unfolding results in the observed heat capacity increment, i.e. the temperature dependence of the melting enthalpy. The folding process is also favoured by an entropy increase resulting from the release of water from the peptide groups. A similar situation holds for the DNA double helix: calorimetry shows that the hydrogen bonding between conjugate base pairs provides a purely entropic contribution of about 40% to the Gibbs energy while the enthalpic van der Waals interactions between the tightly packed apolar parts of the base pairs provide the remaining 60%. Despite very different structures, the thermodynamic basis of α-helix and B-form duplex stability are strikingly similar. The general conclusion follows that the stability of protein folds is primarily dependent on internal atomic close contacts rather than the hydrogen bonds they contain.

Perfluorination of Aromatic Compounds Reinforce Their van der Waals Interactions with Rare Gases: The Rotational Spectrum of Pentafluoropyridine-Ne.

The rotational spectrum of the pentafluoropyridine-Ne complex, generated in a supersonic jet, has been investigated using chirped-pulse microwave Fourier transform spectroscopy in the 2-8 GHz range. The spectra of the 20Ne and 22Ne species have been observed, and the rotational constants have been used to determine the structure of the complex. This structure, and those of the previously experimentally studied complexes benzene-Ne and pyridine-Ne, are an excellent benchmark for the theoretical calculations on these adducts. These complexes and hexafluorobenzene-Ne have been investigated at the CCSD/6-311++G(2d,p) level. The calculations reproduce the experimental structures well and show how the van der Waals complexes are stronger for the perfluorinated compound.

Chiral Metal Nanoparticle Superlattices Enabled by Porphyrin-Based Supramolecular Structures.

Herein, we show that chiral metal nanoparticle superlattices can be produced through coassembly of achiral metal nanoparticles and porphyrin-based organic molecules. This chirality transfer from molecules to nanoparticle superstructures across three orders of magnitude in length scale is enabled by the hetero chain-chain van der Waals interactions. As far as we know, these are the first chiral nanoparticle assemblies based on chirality transfer through weak van der Waals forces. The dimensionality of the nanoparticle superlattices (1D chiral chains, 2D chiral sheets (cones), and 3D chiral particles) can be controlled based on a same synthetic chiral porphyrin molecule. Metalation of these porphyrin molecules with zinc cations results in the switching of molecular packing from J-type to H-type, which thereby produces 1D chiral nanoparticle chains. Functionalization of these zinc porphyrins with oleylamine can induce the assembly of nanoparticles into 2D chiral nanoparticle sheets.

A Multifunctional Dysprosium-Carboxylato 2D Metall-Organic Framework.

We report the microwave assisted synthesis of a bidimensional (2D) MOF of formula [Dy(MeCOO)(PhCOO)2 ]n (1) and its magnetically diluted analogue [La0.9 Dy0.1 (MeCOO)(PhCOO)2 ] (1 d). 1 is a 2D material with single-ion-magnet (SIM) behaviour and 1 d is a multifunctional, magnetic and luminescent 2D material. 1 can be exfoliated into stable nanosheets by sonication.

Accurately Regulating the Electronic Structure of Nix Sey @NC Core-Shell Nanohybrids through Controllable Selenization of a Ni-MOF for pH-Universal Hydrogen Evolution Reaction.

N-doped carbon-encapsulated transition metal selenides (TMSs) have garnered increasing attention as promising electrocatalysts for hydrogen evolution reaction (HER). Accurately regulating the electronic structure of these nanohybrids to reveal the underlying mechanism for enhanced HER performances is still challenging and thus requires deep excavation. Herein, a series of pomegranate-like Nix Sey @NC core-shell nanohybrids (including Ni0.85 Se @ NC, NiSe2 @NC, and NiSe@NC) through controllable selenization of a Ni-MOF precursor is reported. The component of the nanohybrids can be fine-tuned by tailoring the selenization temperature and feed ratio, through which the electronic structure can be synchronously regulated. Among these nanohybrids, the Ni0.85 Se @ NC exhibits the optimum pH-universal HER performance with overpotentials of 131, 135, and 183 mV in 0.5 m H2 SO4 , 1.0 m KOH, and 1.0 m PBS, respectively, at 10 mA cm-2 , which are attributed to the increased partial density of state at the Fermi level and effective van der Waals interactions between Ni0.85 Se and NC matrix explained by density functional theory calculations.

How van der Waals interactions determine the unique properties of water.

Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.

A Three-Dimensional Dynamic Supramolecular "Sticky Fingers" Organic Framework.

Engineering high-recognition host-guest materials is a burgeoning area in basic and applied research. The challenge of exploring novel porous materials with advanced functionalities prompted us to develop dynamic crystalline structures promoted by soft interactions. The first example of a pure molecular dynamic crystalline framework is demonstrated, which is held together by means of weak "sticky fingers" van der Waals interactions. The presented organic-fullerene-based material exhibits a non-porous dynamic crystalline structure capable of undergoing single-crystal-to-single-crystal reactions. Exposure to hydrazine vapors induces structural and chemical changes that manifest as toposelective hydrogenation of alternating rings on the surface of the [60]fullerene. Control experiments confirm that the same reaction does not occur when performed in solution. Easy-to-detect changes in the macroscopic properties of the sample suggest utility as molecular sensors or energy-storage materials.

A self-consistent structural perturbation approach for determining the magnitude and extent of allosteric coupling in proteins.

Elucidating the extent of energetic coupling between residues in single-domain proteins, which is a fundamental determinant of allostery, information transfer and folding cooperativity, has remained a grand challenge. While several sequence- and structure-based approaches have been proposed, a self-consistent description that is simultaneously compatible with unfolding thermodynamics is lacking. We recently developed a simple structural perturbation protocol that captures the changes in thermodynamic stabilities induced by point mutations within the protein interior. Here, we show that a fundamental residue-specific component of this perturbation approach, the coupling distance, is uniquely sensitive to the environment of a residue in the protein to a distance of ∼15 Å. With just the protein contact map as an input, we reproduce the extent of percolation of perturbations within the structure as observed in network analysis of intra-protein interactions, molecular dynamics simulations and NMR-observed changes in chemical shifts. Using this rapid protocol that relies on a single structure, we explain the results of statistical coupling analysis (SCA) that requires hundreds of sequences to identify functionally critical sectors, the propagation and dissipation of perturbations within proteins and the higher-order couplings deduced from detailed NMR experiments. Our results thus shed light on the possible mechanistic origins of signaling through the interaction network within proteins, the likely distance dependence of perturbations induced by ligands and post-translational modifications and the origins of folding cooperativity through many-body interactions.

Dynamic Optical Tuning of Interlayer Interactions in the Transition Metal Dichalcogenides.

Modulation of weak interlayer interactions between quasi-two-dimensional atomic planes in the transition metal dichalcogenides (TMDCs) provides avenues for tuning their functional properties. Here we show that above-gap optical excitation in the TMDCs leads to an unexpected large-amplitude, ultrafast compressive force between the two-dimensional layers, as probed by in situ measurements of the atomic layer spacing at femtosecond time resolution. We show that this compressive response arises from a dynamic modulation of the interlayer van der Waals interaction and that this represents the dominant light-induced stress at low excitation densities. A simple analytic model predicts the magnitude and carrier density dependence of the measured strains. This work establishes a new method for dynamic, nonequilibrium tuning of correlation-driven dispersive interactions and of the optomechanical functionality of TMDC quasi-two-dimensional materials.

The H2 S Dimer is Hydrogen-Bonded: Direct Confirmation from Microwave Spectroscopy.

Ice and solid H2 S look as different as pears and oranges, leading Pauling to conclude that H2 O has hydrogen bonds and H2 S has van der Waals interactions. Now it is shown that the H2 S dimer, like the H2 O dimer, is indeed hydrogen-bonded.

A combinatorial scoring function for protein-RNA docking.

Protein-RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near-native structures from the incorrect ones. To solve the problem, we have constructed a knowledge-based residue-nucleotide pairwise potential with secondary structure information considered for nonribosomal protein-RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics-based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics-based method derived potential ITScore-PR, and the united atom-based statistical potentials QUASI-RNP and DARS-RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near-native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long-range electrostatic attractive energy plays an important role in distinguishing near-native structures from the incorrect ones. This work can be helpful for the development of protein-RNA docking methods and for the understanding of protein-RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741-752. © 2016 Wiley Periodicals, Inc.

The van der Waals Interactions of n-Alkanethiol-Covered Surfaces: From Planar to Curved Surfaces.

The van der Waals (vdW) interactions of n-alkanethiols (ATs) adsorbed on planar Au(111) and Au(100) surfaces and curved Au nanoparticles of different diameters are reported. By means of electrochemical measurements and molecular dynamic calculations, the increase in the average geometrical curvature of the surface influences the global interactions, that is, decreasing vdW interactions between neighboring molecules. Small NPs do not present the same electrochemical behavior as planar surfaces. The transition between nanoparticle to flat surface electrochemical response is estimated to occur at a circa 13-20 nm diameter range.

Behavior of Halogen Bonds of the Y-X⋠⋠⋠π Type (X, Y=F, Cl, Br, I) in the Benzene π System, Elucidated by Using a Quantum Theory of Atoms in Molecules Dual-Functional Analysis.

The nature of halogen bonds of the Y-X-✶-π(C6 H6 ) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual-functional analysis (QTAIM-DFA), which we proposed recently. Asterisks (✶) emphasize the presence of bond-critical points (BCPs) in the interactions in question. Total electron energy densities, Hb (rc ), are plotted versus Hb (rc )-Vb (rc )/2 [=(h(2) /8m)∇(2) ρb (rc )] for the interactions in QTAIM-DFA, in which Vb (rc ) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θp , κp ) for those that contained the perturbed structures; θp corresponds to the tangent line of the plot and κp is the curvature. Whereas (R, θ) corresponds to the static nature, (θp , κp ) represents the dynamic nature of the interactions. All interactions in Y-X-✶-π(C6 H6 ) are classified by pure closed-shell interactions and characterized to have vdW nature, except for Y-I-✶-π(C6 H6 ) (Y=F, Cl, Br) and F-Br-✶-π(C6 H6 ), which have typical hydrogen-bond nature without covalency. I-I-✶-π(C6 H6 ) has a borderline nature between the two. Y-F-✶-π(C6 H6 ) (Y=Br, I) were optimized as bent forms, in which Y-✶-π interactions were detected. The Y-✶-π interactions in the bent forms are predicted to be substantially weaker than those in the linear F-Y-✶-π(C6 H6 ) forms.