Algorithm for generating defective graphene sheets

An algorithm is presented for the generation of molecular models of defective graphene fragments, containing a majority of 6-membered rings with a small number of 5- and 7-membered rings as defects. The structures are generated from an initial random array of points in 2D space, which are then subject to Delaunay triangulation. The dual of the triangulation forms a Voronoi tessellation of polygons with a range of ring sizes. An iterative cycle of refinement, involving deletion and addition of points followed by further triangulation, is performed until the user-defined criteria for the number of defects are met. The array of points and connectivities are then converted to a molecular structure and subject to geometry optimization using a standard molecular modeling package to generate final atomic coordinates. On the basis of molecular mechanics with minimization, this automated method can generate structures, which conform to user-supplied criteria and avoid the potential bias associated with the manual building of structures. One application of the algorithm is the generation of structures for the evaluation of the reactivity of different defect sites. Ab initio electronic structure calculations on a representative structure indicate preferential fluorination close to 5-ring defects.

Abrupt climate change: ice sheets and oceans in action

Large temperature variations on land, in the air, and at the ocean surface, and highly variable flux of ice-rafted debris (IRD) delivered to the North Atlantic Ocean show that rapid climate fluctuations took place during the last glacial period. These quasi-periodic, high-amplitude climate variations followed a sequence of events recognized as a rapid warming, followed by a phase of gradual cooling, and terminating with more rapid cooling and increased flux of IRD to the north Atlantic Ocean. Each cycle lasted ˜1500 years, and was followed by an almost identical sequence. These cycles are referred to as Dansgaard/Oechger cycles (D/O cycles), and approximately every fourth cycle culminated in a more pronounced cooling with a massive discharge of IRD into the north Atlantic Ocean over an interval of ˜500 years. These massive discharges of IRD are known as Heinrich layers. “Heinrich events” are thus characterized as a rapid transfer of IRD from a “source,” the bed of the Laurentide Ice Sheet (LIS), to a “sink,” the North Atlantic.

The formation of large-scale current sheets within magnetic clouds

Magnetic clouds are a class of interplanetary coronal mass ejections (CME) predominantly characterised by a smooth rotation in the magnetic field direction, indicative of a magnetic flux rope structure. Many magnetic clouds, however, also contain sharp discontinuities within the smoothly varying magnetic field, suggestive of narrow current sheets. In this study we present observations and modelling of magnetic clouds with strong current sheet signatures close to the centre of the apparent flux rope structure. Using an analytical magnetic flux rope model, we demonstrate how such current sheets can form as a result of a cloud’s kinematic propagation from the Sun to the Earth, without any external forces or influences. This model is shown to match observations of four particular magnetic clouds remarkably well. The model predicts that current sheet intensity increases for increasing CME angular extent and decreasing CME radial expansion speed. Assuming such current sheets facilitate magnetic reconnection, the process of current sheet formation could ultimately lead a single flux rope becoming fragmented into multiple flux ropes. This change in topology has consequences for magnetic clouds as barriers to energetic particle propagation.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Amyloid-like fibril-forming supramolecular beta-sheets from a beta-turn forming tripeptide containing non-coded amino acids: the crystallographic signature

The crystal structure of a terminally protected tripeptide Boc-Leu-Aib-beta-Ala-OMe 1 containing non-coded amino acids reveals that it adopts a beta-turn structure, which sell-assembles to form a supramolecular beta-sheet via non-covalent interactions. The SEM image of peptide 1 exhibits amyloid-like fibrillar morphology in the solid state. (C) 2002 Elsevier Science Ltd. All rights reserved.

Stepwise self-assembly of a tripeptide from molecular dimers to supramolecular beta-sheets in crystals and amyloid-like fibrils in the solid state

The terminally protected tripeptide Boc-Ala(1)-Leu(2)-Ala(3)-OMe 1 forms antiparallel hydrogen-bonded dimers of two different conformers in the asymmetric unit and the individual dimers then self-associate to form supramolecular beta-sheet structures in crystals and amyloid-like fibrils in the solid state.