SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Chemical bond

166

Until now, few sp carbon materials simultaneously exhibit superior performance for specific surface area (SSA) and electrical conductivity at bulk state. Thus, it is extremely important to make such materials at bulk scale with those two outstanding properties combined together. Here, we present a simple and green but very efficient approach using two standard and simple industry steps to make such three-dimensional graphene-based porous materials at the bulk scale, with ultrahigh SSA (3523 m/g) and excellent bulk conductivity. We conclude that these materials consist of mainly defected/wrinkled single layer graphene sheets in the dimensional size of a few nanometers, with at least some covalent bond between each other. The outstanding properties of these materials are demonstrated by their superior supercapacitor performance in ionic liquid with specific capacitance and energy density of 231 F/g and 98 Wh/kg, respectively, so far the best reported capacitance performance for all bulk carbon materials.

Concepts: Fundamental physics concepts, Density, Water, Chemical bond, Physical quantities, Ionic bond, Specific surface area, Porous media

149

In this data article we provide topologies and force field parameters files for molecular dynamics simulations of lipids in the OPLS-aa force field using the GROMACS package. This is the first systematic parameterization of lipid molecules in this force field. Topologies are provided for four phosphatidylcholines: saturated DPPC, mono-cis unsaturated POPC and DOPC, and mono-trans unsaturated PEPC. Parameterization of the phosphatidylcholines was achieved in two steps: first, we supplemented the OPLS force field parameters for DPPC with new parameters for torsion angles and van der Waals parameters for the carbon and hydrogen atoms in the acyl chains, as well as new partial atomic charges and parameters for torsion angles in the phosphatidylcholine and glycerol moieties [1]. Next, we derived parameters for the cis and trans double bonds and the neighboring them single bonds [2]. Additionally, we provide GROMACS input files with parameters describing simulation conditions (md.mdp), which are strongly recommended to be used with these lipids models. The data are associated with the research article “Cis and trans unsaturated phosphatidylcholine bilayers: a molecular dynamics simulation study” [2] and provided as supporting materials.

Concepts: Molecular dynamics, Atom, Chemical bond, Lipid, Lipid bilayer, Lecithin, GROMACS, OPLS

96

The search for new hard materials is often challenging, but strongly motivated by the vast application potential such materials hold. Ti3Au exhibits high hardness values (about four times those of pure Ti and most steel alloys), reduced coefficient of friction and wear rates, and biocompatibility, all of which are optimal traits for orthopedic, dental, and prosthetic applications. In addition, the ability of this compound to adhere to ceramic parts can reduce both the weight and the cost of medical components. The fourfold increase in the hardness of Ti3Au compared to other Ti-Au alloys and compounds can be attributed to the elevated valence electron density, the reduced bond length, and the pseudogap formation. Understanding the origin of hardness in this intermetallic compound provides an avenue toward designing superior biocompatible, hard materials.

Concepts: Electron, Chemical bond, Materials science, Alloy, Intermetallics, Steel, Friction, Hardness

64

Glutathione S-transferase pi 1 (GSTP1), is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased glutathione (GSH). This data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at PLs C7-C8 olefin, while PLs C2-C3 olefin was postulated to react with GSH. However, direct evidence for this mechanism has been lacking. To investigate, we solved the x-ray crystal structure of GSTP1 bound to PL and GSH at 1.1 Angstrom resolution to rationalize previously reported structure activity relationship studies. Surprisingly, the structure showed a hydrolysis product of PL (hPL) was conjugated to glutathione at the C7-C8 olefin, and this complex was bound to the active site of GSTP1; No covalent bond formation between hPL and GSTP1 was observed. Mass spectrometric (MS) analysis of reactions between PL and GSTP1 confirmed that PL does not label GSTP1. Moreover, MS data also indicated that nucleophilic attack on PL at the C2-C3 olefin led to PL hydrolysis. Although hPL inhibits GSTP1 enzymatic activity in vitro, treatment of cells susceptible to PL with hPL did not have significant anti-proliferative effects, suggesting hPL is not membrane permeable. Altogether, our data suggest a model wherein PL is a prodrug whose intracellular hydrolysis initiates the formation of the hPL:GSH conjugate, which blocks the active site of and inhibits GSTP1 and thereby cancer cell proliferation.

Concepts: Cancer, Cell division, Chemical bond, Disulfide bond, Glutathione, Covalent bond, Electrophile, Pi bond

46

Graphene oxide membranes show exceptional molecular permeation properties, with promise for many applications. However, their use in ion sieving and desalination technologies is limited by a permeation cutoff of ∼9 Å (ref. 4), which is larger than the diameters of hydrated ions of common salts. The cutoff is determined by the interlayer spacing (d) of ∼13.5 Å, typical for graphene oxide laminates that swell in water. Achieving smaller d for the laminates immersed in water has proved to be a challenge. Here, we describe how to control d by physical confinement and achieve accurate and tunable ion sieving. Membranes with d from ∼9.8 Å to 6.4 Å are demonstrated, providing a sieve size smaller than the diameters of hydrated ions. In this regime, ion permeation is found to be thermally activated with energy barriers of ∼10-100 kJ mol(-1) depending on d. Importantly, permeation rates decrease exponentially with decreasing sieve size but water transport is weakly affected (by a factor of <2). The latter is attributed to a low barrier for the entry of water molecules and large slip lengths inside graphene capillaries. Building on these findings, we demonstrate a simple scalable method to obtain graphene-based membranes with limited swelling, which exhibit 97% rejection for NaCl.

Concepts: Ammonia, Water, Molecule, Atom, Chemical bond, Sodium chloride, Ion, Sodium

43

Graphene is increasingly explored as a possible platform for developing novel separation technologies. This interest has arisen because it is a maximally thin membrane that, once perforated with atomic accuracy, may allow ultrafast and highly selective sieving of gases, liquids, dissolved ions and other species of interest. However, a perfect graphene monolayer is impermeable to all atoms and molecules under ambient conditions: even hydrogen, the smallest of atoms, is expected to take billions of years to penetrate graphene’s dense electronic cloud. Only accelerated atoms possess the kinetic energy required to do this. The same behaviour might reasonably be expected in the case of other atomically thin crystals. Here we report transport and mass spectroscopy measurements which establish that monolayers of graphene and hexagonal boron nitride (hBN) are highly permeable to thermal protons under ambient conditions, whereas no proton transport is detected for thicker crystals such as monolayer molybdenum disulphide, bilayer graphene or multilayer hBN. Protons present an intermediate case between electrons (which can tunnel easily through atomically thin barriers) and atoms, yet our measured transport rates are unexpectedly high and raise fundamental questions about the details of the transport process. We see the highest room-temperature proton conductivity with monolayer hBN, for which we measure a resistivity to proton flow of about 10 Ω cm(2) and a low activation energy of about 0.3 electronvolts. At higher temperatures, hBN is outperformed by graphene, the resistivity of which is estimated to fall below 10(-3) Ω cm(2) above 250 degrees Celsius. Proton transport can be further enhanced by decorating the graphene and hBN membranes with catalytic metal nanoparticles. The high, selective proton conductivity and stability make one-atom-thick crystals promising candidates for use in many hydrogen-based technologies.

Concepts: Electron, Electric charge, Fundamental physics concepts, Hydrogen, Proton, Chemistry, Atom, Chemical bond

38

Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power.

Concepts: DNA, Protein, Oxygen, Hydrogen, Atom, Chemical bond, Hydrogen bond, Drug discovery

37

Just over a century ago, Lewis published his seminal work on what became known as the covalent bond, which has since occupied a central role in the theory of making organic molecules. With the advent of covalent organic frameworks (COFs), the chemistry of the covalent bond was extended to two- and three-dimensional frameworks. Here, organic molecules are linked by covalent bonds to yield crystalline, porous COFs from light elements (boron, carbon, nitrogen, oxygen, and silicon) that are characterized by high architectural and chemical robustness. This discovery paved the way for carrying out chemistry on frameworks without losing their porosity or crystallinity, and in turn achieving designed properties in materials. The recent union of the covalent and the mechanical bond in the COF provides the opportunity for making woven structures that incorporate flexibility and dynamics into frameworks.

Concepts: Electron, Oxygen, Molecule, Chemistry, Atom, Chemical bond, Chemical element, Carbon

36

We show that the different bond orders of individual carbon-carbon bonds in polycyclic aromatic hydrocarbons and fullerenes can be distinguished by noncontact atomic force microscopy (AFM) with a carbon monoxide (CO)-functionalized tip. We found two different contrast mechanisms, which were corroborated by density functional theory calculations: The greater electron density in bonds of higher bond order led to a stronger Pauli repulsion, which enhanced the brightness of these bonds in high-resolution AFM images. The apparent bond length in the AFM images decreased with increasing bond order because of tilting of the CO molecule at the tip apex.

Concepts: Electron, Atom, Chemical bond, Carbon, Polycyclic aromatic hydrocarbon, Benzene, Quantum chemistry, Bond order

33

After decades of vituperative debate over the classical or nonclassical structure of the 2-norbornyl cation, the long-sought x-ray crystallographic proof of the bridged, nonclassical geometry of this prototype carbonium ion in the solvated [C7H11](+)[Al2Br7](-) • CH2Br2 salt has finally been realized. This achievement required exceptional treatment. Crystals obtained by reacting norbornyl bromide with aluminum tribromide in CH2Br2 undergo a reversible order-disorder phase transition at 86 kelvin due to internal 6,1,2-hydride shifts of the 2-norbornyl cation moiety. Cooling with careful annealing gave a suitably ordered phase. Data collection at 40 kelvin and refinement revealed similar molecular structures of three independent 2-norbornyl cations in the unit cell. All three structures agree very well with quantum chemical calculations at the MP2(FC)/def2-QZVPP level of theory.

Concepts: Crystal, Crystallography, Molecule, Chemistry, Atom, Chemical bond, Solid, Crystallographic database