A density functional theory analysis for the adsorption of the amine group on graphene and boron nitride nanosheets

In this paper first principles total energy calculations to study the adsorption of amine group (NH₂) on graphene (G) and boron nitride (hBN) nanosheets are developed; the density functional theory, within the local density approximation and Perdew-Wang functional was employed. The sheets were modeled with a sufficiently proved C_nH_m-like cluster with armchair edge. The optimized geometry was obtained following the minimum energy criterion, searching on four positions for each nanosheet: perpendicular to the carbon atom, on the hexagon, inside the hexagon and on the bridge C–C, for the G-amine interaction; and, perpendicular to the B, perpendicular to the N, on the hexagon, and inside the hexagon, for the hBN-amine interaction. A physisorption, with amine parallel to the C–C–C bond with a distance graphene-amine of 2.56 Å, was found. For the case of BN a B–N bond, with bond length equal to 1.56 Å, was found; the amine lies perpendicular to the nanosheet. When the graphene is doped with B and Al atoms a chemisorption with B–N (1.57 Å) and Al–N (1.78 Å) bonds is observed; the bond angle in the amine group is also incremented, 5.5° and 8.1°, respectively. In the presence of point defects (monovacancies) of B in the hBN-amine and C in the G-amine, there exists chemisorption, increasing the reactivity of the sheets.     

Influence of point defects on the electronic properties of boron nitride nanosheets

Density functional theory was utilized to study the electronic properties of boron nitride (BN) sheets, taking into account the presence of defects. The structure considered consisted of a central hexagon surrounded by alternating pentagons (three) and heptagons (three). The isocoronene cluster model with an armchair edge was used with three different chemical compositions. In the first structure, three B–B bonds were formed where one B in the dimer was part of the central hexagon. In the second structure, three N–N–N bonds were formed at the periphery of the cluster, around the central hexagon. In the third structure, three N–N bonds were formed in a similar fashion to the first model. Our results indicated that the third structure was the most stable configuration; this exhibited planar geometry, semiconductor behavior, and ionic character. To explore the effects of doping, we replaced B and N atoms with C atoms, considering different atomic positions in the central hexagon. When an N atom was replaced with a C atom, the new structure was a semiconductor, but when a B atom was replaced with a C atom, the new structure was a semimetal. At the same time, the polarity increased, inducing covalent behavior. Replacing two N atoms with two C atoms also resulted in a semiconductor, while replacing two B atoms with two C atoms yielded a semimetal; in both cases the bonding was covalent. When three B (three N) atoms of the central hexagon were replaced with three C atoms, the new structure exhibited a transition to a conductor (remained a semiconductor) with low polarity. When monovacancies (N) and divacancies (B and N) were inserted into the lattice, the system was transformed into a covalent semiconductor. Finally, the electrostatic potential surface was calculated in order to explore intermolecular properties such as the charge distribution, which showed how the reactivity of the boron nitride sheets was affected by doping and orbital hybridization.     

On the influence of point defects on the structural and electronic properties of graphene-like sheets: a molecular simulation study

The influence of vacancies and substitutional defects on the structural and electronic properties of graphene, graphene oxide, hexagonal boron nitride, and boron nitride oxide two-dimensional molecular models was studied using density functional theory (DFT) at the level of local density approximation (LDA). Bond length, dipole moment, HOMO–LUMO energy gap, and binding energy were calculated for each system with and without point defects. The results obtained indicate that the formation of a point defect does not necessary lead to structural instability; nevertheless, surface distortions and reconstruction processes were observed, mainly when a vacancy-type defect is generated. For graphene, it was found that incorporation of a point defect results in a semiconductor–semimetal transition and also increases notably its polar character. As with graphene, the formation of a point defect in a hexagonal boron nitride sheet reduces its energy gap, although its influence on the resulting dipole moment is not as dramatic as in graphene. The influence of point defects on the structural and electronic properties of graphene oxide and boron nitride oxide sheets were found to be mediated by the chemisorbed species.     

All‐Surface‐Atomic‐Metal Chalcogenide Sheets for High‐Efficiency Visible‐Light Photoelectrochemical Water Splitting

Artificial all‐surface‐atomic 2D sheets can trigger breakthroughs in tailoring the physical and chemical properties of advanced functional materials. Here, the conceptually new all‐surface‐atomic semiconductors of SnS and SnSe freestanding sheets are realized using a scalable strategy. As an example, all‐surface‐atomic SnS sheets undergo surface atomic elongation and structural disordering, which is revealed by X‐ray absorption fine structure spectroscopy and first‐principles calculations, endowing them with high structural stability and an increased density of states at the valence band edge. These exotic atomic and electronic structures make the all‐surface‐atomic SnS sheet‐based photoelectrode exhibit an incident photon‐to‐current conversion efficiency of 67.1% at 490 nm, much higher than the efficiencies of other visible‐light‐driven water splitting. A photocurrent density of 5.27 mA cm^‐2, which is two orders of magnitude higher than that of the bulk counterpart, is also achieved for the all‐surface‐atomic SnS sheets‐based photoelectrode. This will allow the manipulation of the basic properties of advanced materials on the atomic scale, thus paving the way for innovative applications.     

Clathrin lattice reorganization: theoretical considerations

We wish to postulate a mechanism by which flat hexagonal lattices of clathrin trimers transform into coated pits. Using an established model for packing trimers into lattices, we explored the assembly process by single addition of trimers to form polygons. Subject to favorable conditions, removal of a single trimer from a hexagon could lead to the formation of a pentagon. Elimination of trimers from polygonal sheets can occur either at the center of the network or at the edges. Removal of a trimer from the center of these adjacent polygons, "hub transformation," is possible in very few instances, whereas removal from the edges of a polygonal sheet, "fringe transformation," is possible in a host of cases. These hypothetical constructs can be used effectively to explain intermediate structures actually observed in flat hexagonal lattices. The geometry of a purely hexagonal lattice seems to dictate that the first step in transformation must be a "fringe transformation," which then will allow subsequent "hub transformation" to take place leading to the introduction of pentagons into the center of the lattice and ultimately to the curvature of the clathrin lattice.     

Polymorphism of Crystals of Salmonella minnesota Re and Ra Lipopolysaccharides

Salmonella minnesota Re and Ra lipopolysaccharides (LPSs) formed three-dimensional crystals when they were precipitated by the addition of 2 volumes of 95% ethanol containing 375 mM MgCl₂ and incubated in 70% ethanol containing 250 mM MgCl₂ at 4 C. Besides typical shapes of crystals, hexagonal plates and solid columns, which were already reported (J. Bacteriol. 172: 1516–1528 (1990)), the LPSs thus treated formed crystals possessing various shapes such as square or rectangular plate, lozenge plate, discoid, and truncated hexangular pyramid forms. Electron diffraction patterns from all these crystals except square or rectangular plate crystals obtained by electron irradiation from the direction perpendicular to the basal plane were essentially the same as those from hexagonal plate crystals, indicating that they consist of hexagonal lattices with the lattice constant of 4.62 Å. From these results as well as the results of electron microscopic observations of these crystals, it was concluded that all these crystals except square or rectangular plate crystals are composed of hexagonal plate sheets as the basic structural units. Square or rectangular crystals were assumed to correspond to the {1011} planes of solid hexagonal column crystals.     

First principles studies of the graphene-phenol interactions

Studies of the interaction between phenol and intrinsic graphene, as well as phenol and aluminum doped graphene layer are performed using first principles total energy calculations within the periodic density functional theory. A 4x4 periodic structure is used to explore the adsorption of a phenol molecule on the intrinsic graphene and on aluminum doped graphene layer. The electron-ion interactions are modeled using ultra-soft pseudo-potentials, and the exchange-correlation energies are treated according to the generalized gradient approximation (GGA) with the PBE parameterization. We consider different molecule orientations: parallel and perpendicular to the graphene layer to relax the atomic structure. To explain the optimized atomic geometry we determine binding energies for all cases and the density of states (DOS) and partial DOS for the most relevant configurations. Results indicate that the direct interaction of oxygen with aluminum yields the ground state geometry with the phenol molecule adsorbed on the graphene layer. Binding energies and DOS structures also demonstrate that the ground state configuration is that where the O and Al atoms interact with a separation distance of 1.97 ?.     

Molecular reorganization in the hexagon to star transition of the baseplate of bacteriophage T4

The baseplate of bacteriophage T4 is a complex structure containing at least 14 different structural proteins. It undergoes a transition from a hexagonal to a star-shaped configuration during infection of the host bacterial cell. We have used a combination of genetics and image processing of electron micrographs to analyse both the wild-type structure and a series of mutant structures lacking specific gene products. Besides describing the basic anatomy of the hexagon and star configurations, we have been able to locate the products of genes 9, 11 and 12.Gene 9 product occupies a peripheral position in hexagons and stars consistent with its providing a binding site for the long tail fibres. Gene 11 product in the hexagon forms the distal part of the tail pin, which folds out to form the point of the hexagram in the star configuration. Gene 12 product is visualized as an extended 350 Å fibre in stars and broken baseplates but appears to have a more compact configuration in hexagons and intact phage.We demonstrate the structural relationship between the hexagonal and starshaped configurations and show how the positions of the specific gene products alter as a result of the structural transition. We suggest a speculative model for the role of gene 9 and gene 12 products in triggering the rearrangement of the baseplate and tail contraction.     

Structures of single‐layer β‐sheet proteins evolved from β‐hairpin repeats

Free‐standing single‐layer β‐sheets are extremely rare in naturally occurring proteins, even though β‐sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single‐layer, anti‐parallel β‐sheet proteins, comprised of three or four twisted β‐hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β‐sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent‐exposed tyrosine residues, was identified on the concave surface of the β‐sheet. These new modular single‐layer β‐sheet proteins may serve as a new model system for studying folding and design of β‐rich proteins.     

Structure of polyglycine I: a comparison of the antiparallel pleated and antiparallel rippled sheets

Packing energy calculations are made for two possible sheet structures of polyglycine I, i.e. the antiparallel pleated and rippled sheets. They indicate that the rippled sheet is the more stable structure and that its calculated lattice parameters are close to those experimentally determined. Furthermore, the results on the packing of pleated sheets of polyglycine improve understanding of the well-known model of silk fibroin structure of Marsh et al. (1955). They also suggest that the sheet structures of l-polypeptides with short side-chains should pack in monoclinic unit cells rather than the orthorhombic ones which are observed. A possible origin of this discrepancy is discussed.     

Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase

A systematic analysis of the hydrogen-bonding geometry in helices and beta sheets has been performed. The distances and angles between the backbone carbonyl O and amide N atoms were correlated considering more than 1500 protein chains in crystal structures determined to a resolution better than 1.5 A. They reveal statistically significant trends in the H-bond geometry across the different secondary structural elements. The analysis has been performed using Secbase, a modular extension of Relibase (Receptor Ligand Database) which integrates information about secondary structural elements assigned to individual protein structures with the various search facilities implemented into Relibase. A comparison of the mean hydrogen-bond distances in alpha helices and 3(10) helices of increasing length shows opposing trends. Whereas in alpha helices the mean H-bond distance shrinks with increasing helix length and turn number, the corresponding mean dimension in 3(10) helices expands in a comparable series. Comparing similarly the hydrogen-bond lengths in beta sheets there is no difference to be found between the mean H-bond length in antiparallel and parallel beta sheets along the strand direction. In contrast, an interesting systematic trend appears to be given for the hydrogen bonds perpendicular to the strands bridging across an extended sheet. With increasing number of accumulated strands, which results in a growing number of back-to-back piling hydrogen bonds across the strands, a slight decrease of the mean H-bond distance is apparent in parallel beta sheets whereas such trends are obviously not given in antiparallel beta sheets. This observation suggests that cooperative effects mutually polarizing spatially well-aligned hydrogen bonds are present either in alpha helices and parallel beta sheets whereas such influences seem to be lacking in 3(10) helices and antiparallel beta sheets.     

X-ray structural study of noncrystalline regenerated Bombyx mori silk fibroin

X-ray diffraction measurements of regenerated Bombyx mori silk fibroin were carried out to determine its structural characteristic from an analysis of differential radial distribution functions (DRDFs). The temperature dependence of X-ray diffraction patterns from noncrystalline and crystal structures of regenerated silk fibroin was investigated using a high temperature furnace. Time resolved X-ray diffraction profiles were also obtained to construct kinematical models of structural changes caused by the addition of water. DRDFs, calculated from the experimental data, were compared with the DRDFs simulated on the basis of the Monte Carlo method. In order to model the noncrystalline structures, structural units were assumed to be parts of the crystalline structure of silk and those with appropriate structural defects reported previously. From the comparison of experimental and simulated DRDFs, it was determined that noncrystalline regenerated silk consisted of locally ordered atomic sheets similar to the atomic arrangement in the silk I crystal (Type-I sheets), and the final state of the structural change was noncrystalline, consisting of small crystallites, the structure of which is similar to that of silk II (Type-II crystallites). Time resolved DRDFs were also qualitatively interpreted by both the ordering of Type-I sheets and structural changes from Type-I to Type-II. The formation of the small Type-II crystallites obtained in this study was consistent with the nucleation of silk II by birefringence measurements of silk glands and the spinneret of Bombyx mori silkworm reported previously. X-ray diffraction should be a useful technique to understand the structural characteristics of noncrystalline organic materials.     

Three-dimensional structure of gap junctions in fragmented plasma membranes from rat liver.

Gap junctions forming extensive hexagonal crystalline sheets (unit cell dimension, a = 89 A) were obtained by mild mechanical disruption of plasma membranes from rat liver. The sheets were analysed in three dimensions by negative stain electron microscopy and Fourier image processing. The crystallographic symmetry was shown to approximate to the two-sided plane group p622, indicating that the sheets are composed of two equivalent, oppositely-facing membrane assemblies. The structure of the connexon in these near-to-native junctions is essentially the same as that found in detergent-extracted junctions, the subunits appearing slightly tilted tangential to the central six-fold axis and aligned almost perpendicular to the membrane plane.     

The structure of rabbit muscle phosphoglucomutase at intermediate resolution

The three-dimensional structure of rabbit phosphoglucomutase has been determined to 2.7 A resolution by a combination of isomorphous and molecular replacement techniques. Heavy atom positions were found by using vector search and difference Fourier methods. The two molecules in the asymmetric unit form a dimer with its 2-fold axis perpendicular to and intersecting with a crystallographic 4(1) axis. Thus, the dimers are arranged so that they form fibers that are coincident with the 4(1) axes. A polypeptide model, corresponding with the known residue sequence, has been fitted to the electron density map to produce a structure that consists of four domains. All four have an alpha/beta structure; the first three have a somewhat similar topology that is based on a mixed parallel/antiparallel beta sheet, whereas the fourth is based on an antiparallel sheet. The active site lies between the four domains, with the phosphoserine residue in the first domain and some of the probable substrate-binding residues in the fourth and final domain. The carboxyl edges of all four sheets are directed towards the active site region, which lies in a deep crevice.     

Structure of the tubulin dimer in zinc-induced sheets

The structure of tubulin has been studied in projection by minimum beam electron microscopy and image processing of negatively stained zinc-induced sheets. The reconstructed images include data to 15 Å resolution.We report here a clear and reproducible 82 Å repeat arising from the arrangement of heterodimers in sheet aggregates of tubulin. This repeat is only observed in diffraction patterns from images recorded by minimum beam methods (10 to 20 e/Ų) and arises from small, but consistent, structural differences between two similar subunits believed to represent the two chemical species of tubulin monomer (M_r, 55,000). At higher electron doses (100 to 200 e/Ų), the additional information is lost or very much reduced, and only a repeat of 41 Å is observed, owing to the loss of distinction between monomers in the tubulin heterodimer.The sheets are composed of 49 Å wide, polar protofilaments, similar to those observed in microtubules; however, the interprotofilament packing is completely different in the two structures. In these sheets, adjacent protofilaments point and face in opposite directions; i.e. they are related by dyad-screw axes normal to the protofilament axes and in the plane of the sheet. Thus, the zinc-induced sheets are crystals of space group P2₁, with cell dimensions of about 97 Å × 82 Å, containing one tubulin heterodimer per asymmetric unit.Reconstructed images of four individual sheets, and their average, show the arrangement and shapes of the two heterodimers contained in each unit cell. The structure and packing of heterodimers in sheets are compared to those in opened out microtubules where all protofilaments point and face in the same direction.     

Lamellar lubrication in vivo and vitro: friction testing of hexagonal boron nitride

Phospholipid molecules (PLs) in vivo and graphite, molybdenum disulfide, tungsten disulfide and hexagonal boron nitride (h-BN) in vitro are good examples of frictionless lubricants. PLs and solid materials have the ability to form multi-bilayer or layered structures similar to lamellate solid. It has been confirmed experimentally that PLs as lamellar lubricants protect the surface of joints against wear while acting as frictionless lubricant. An experimental study has been conducted on the friction properties of h-boron nitride on porous non-full journal bearings. The porous non-full journal bearings were a mixture of 97.5 wt.% Fe and 2.5 wt.% Cu powder, and compressed to a density of 5.9 g/cm(3). The porosity of non-full journal bearings were 15.5 and 27.8 wt.% and were impregnated with vaseline and vaseline+5 wt.% h-BN. Additionally, the two additives SFR NLGI #2 (or SFR 2522) grease and graphite grease were used for comparison to h-BN. The tribological tests were performed on a four-ball machine under load of 49 daN, and a friction tribotester. The above experiment strongly suggested that h-BN has the ability to lubricate under load with very low friction coefficient comparable to phospholipids. Relatively low surface energy and low adhesion between the crystallites are giving the additives low friction coefficient. The results of the experimental studies showed that h-BN as an additive in vaseline possesses friction reducing properties, and excellent anti-wear properties.     

PackHelix: a tool for helix-sheet packing during protein structure prediction

The three‐dimensional structure of a protein is organized around the packing of its secondary structure elements. Predicting the topology and constructing the geometry of structural motifs involving α‐helices and/or β‐strands are therefore key steps for accurate prediction of protein structure. While many efforts have focused on how to pack helices and on how to sample exhaustively the topologies and geometries of multiple strands forming a β‐sheet in a protein, there has been little progress on generating native‐like packings of helices on sheets. We describe a method that can generate the packing of multiple helices on a given β‐sheet for αβα sandwich type protein folds. This method mines the results of a statistical analysis of the conformations of αβ₂ motifs in protein structures to provide input values for the geometric attributes of the packing of a helix on a sheet. It then proceeds with a geometric builder that generates multiple arrangements of the helices on the sheet of interest by sampling through these values and performing consistency checks that guarantee proper loop geometry between the helices and the strands, minimal number of collisions between the helices, and proper formation of a hydrophobic core. The method is implemented as a module of ProteinShop. Our results show that it produces structures that are within 4–6 Å RMSD of the native one, regardless of the number of helices that need to be packed, though this number may increase if the protein has several helices between two consecutive strands in the sequence that pack on the sheet formed by these two strands. Proteins 2011; Published 2011 Wiley‐Liss, Inc.     

Density functional studies of the stepwise substitution of pyridine,pyridazine, pyrimidine,pyrazine, and 1,3,5-triazine with BCO

Ozone (O₃) adsorption on pristine Stone–Wales (SW) defective BC₃ graphene-like sheets was investigated using density functional calculations. It was found that O₃ is weakly adsorbed on the pristine sheet. Two types of SW-defective sheets were studied, SW-CC and SW-BC, in which a defect is formed by rotating a C–C or B–N bond, respectively. O₃ molecules were found to be more reactive on SW-BC defective sheets. It was predicted that O₃ molecules are reduced to O₂ molecules on SW-BC sheets, overcoming an energy barrier of 34.2 kcal/mol^?1 at the B3LYP level of theory and 27.2 kcal/mol^?1 at the BP98 level of theory. Therefore, SW-BC sheets could potentially be employed as a metal-free catalyst for O₃ reduction. The HOMO–LUMO gap of a SW-BC sheet decreases from 2.16 to 1.21 eV after O₃ dissociation on its surface in the most stable state.     

DNA and the origins of life in micaceous clay

Reproducible imaging of DNA by atomic force microscopy was a useful predecessor to Ned Seeman’s DNA nanotechnology. Many of the products of DNA nanotechnology were imaged in the atomic force microscope. The mica substrate used in this atomic force microscopy research formed the inspiration for the hypothesis that micaceous clay was a likely habitat for the origins of life. Montmorillonite clay has been a successful substrate for the polymerization of amino acids and nucleotides into peptides and DNA oligomers in research on life’s origins. Mica and montmorillonite have the same anionic lattice, with a hexagonal spacing of 0.5 nm. Micas are nonswelling clays, with potassium ions (K⁺) holding the crystal sheets together, providing a stable environment for the processes and molecular complexes needed for the emergence of living cells. Montmorillonite crystal sheets are held together by smaller sodium ions (Na⁺), which results in swelling and shrinking during wet-dry cycles, providing a less stable environment. Also, the cells in all types of living systems have high intracellular K⁺ concentrations, which makes mica a more likely habitat for the origins of life than montmorillonite. Finally, moving mica sheets provides mechanical energy at the split edges of the sheets in mica “books.” This mechanical energy of mica sheets, moving open and shut, in response to fluid flow, may have preceded chemical energy at life’s origins, powering early prebiotic processes, such as the formation of covalent bonds, the interactions of molecular complexes, and the budding off of protocells before the molecular mechanism of cell division had developed.