A fast parallel clustering algorithm for molecular simulation trajectories

We implemented a GPU‐powered parallel k‐centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370‐residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k‐centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc.     

Harnessing the Flexibility of Peptidic Scaffolds to Control their Copper(II)‐Coordination Properties: A Potentiometric and Spectroscopic Study

Designing small peptides that are capable of binding Cu²⁺ ions mainly through the side‐chain functionalities is a hard task because the amide nitrogen atoms strongly compete for Cu²⁺ ion coordination. However, the design of such peptides is important for obtaining biomimetic small systems of metalloenyzmes as well as for the development of artificial systems. With this in mind, a cyclic decapeptide, C‐Asp, which contained three His residues and one Asp residue, and its linear derivative, O‐Asp, were synthesized. The C‐Asp peptide has two Pro? Gly β‐turn‐inducer units and, as a result of cyclization, and as shown by CD spectroscopy, its backbone is constrained into a more defined conformation than O‐Asp, which is linear and contains a single Pro? Gly unit. A detailed potentiometric, mass spectrometric, and spectroscopic study (UV/Vis, CD, and EPR spectroscopy) showed that at a 1:1 Cu²⁺/peptide ratio, both peptides formed a major [CuHL]²⁺ species in the pH range 5.0–7.5 (C‐Asp) and 5.5–7.0 (O‐Asp). The corrected stability constants of the protonated species (log K*_CuH(O?Asp)=9.28 and log K*_CuH(C?Asp)=10.79) indicate that the cyclic peptide binds Cu²⁺ ions with higher affinity. In addition, the calculated value of K_eff shows that this higher affinity for Cu²⁺ ions prevails at all pH values, not only for a 1:1 ratio but even for a 2:1 ratio. The spectroscopic data of both [CuHL]²⁺ species are consistent with the exclusive coordination of Cu²⁺ ions by the side‐chain functionalities of the three His residues and the Asp residue in a square‐planar or square‐pyramidal geometry. Nonetheless, although these data show that, upon metal coordination, both peptides adopt a similar fold, the larger conformational constraints that are present in the cyclic scaffold results in different behaviour for both [CuHL]²⁺ species. CD and NMR analysis revealed the formation of a more rigid structure and a slower Cu²⁺‐exchange rate for [CuH(C‐Asp)]²⁺ compared to [CuH(O‐Asp]²⁺. This detailed comparative study shows that cyclization has a remarkable effect on the Cu²⁺‐coordination properties of the C‐Asp peptide, which binds Cu²⁺ ions with higher affinity at all pH values, stabilizes the [CuHL]²⁺ species in a wider pH range, and has a slower Cu²⁺‐exchange rate compared to O‐Asp.     

Mechanistic Dichotomy in the Asymmetric Allylation of Aldehydes with Allyltrichlorosilanes Catalyzed by Chiral Pyridine N‐Oxides

Detailed kinetic and computational investigation of the enantio‐ and diastereoselective allylation of aldehydes 1 with allyltrichlorosilanes 5 , employing the pyridine N‐oxides METHOX ( 9 ) and QUINOX ( 10 ) as chiral organocatalysts, indicate that the reaction can proceed through a dissociative (cationic) or associative (neutral) mechanism: METHOX apparently favors a pentacoordinate cationic transition state, while the less sterically demanding QUINOX is likely to operate via a hexacoordinate neutral complex. In both pathways, only one molecule of the catalyst is involved in the rate‐ and selectivity‐determining step, which is supported by both experimental and computational data.     

Nanoparticles from conventional cellulose esters: evaluation of preparation methods

Nano-scaled particles were obtained from two different cellulose acetates, cellulose acetate propionate, and cellulose acetate butyrate using the emulsification solvent evaporation procedure and the low energy methods of solvent displacement (dialysis and controlled precipitation). The relationship between the formulation parameters and the particle properties were evaluated in case of the emulsification-evaporation technique. For the solvent displacement procedures, the influence of the formulation parameters, and the intrinsic polymer properties like the hydrophilic-hydrophobic balance was evaluated. Comparing the methods, it could be shown that large amounts of small and uniform nanoparticles can be obtained by the emulsification solvent evaporation procedure. The solvent displacement techniques turned out to be very easy to use and to yield narrowly distributed particles as well.     

CuI/glycerol mediated stereoselective synthesis of 1,2-bis-chalcogen alkenes from terminal alkynes: synthesis of new antioxidants

(E)-1,2-Bis-chalcogen alkenes were stereoselectively prepared in good yields by the addition of diorganyl dichalcogenides to terminal alkynes using CuI/Zn/glycerol as a recyclable catalytic system. The antioxidant activity in vitro of four (E)-1,2-bis-chalcogen alkenes synthesized was evaluated and (E)-1,2-bis-(4-methoxyphenylselanyl)styrene 3b presented excellent activity. The catalytic system used in the synthesis was recovered and used directly up to 5 cycles without loss of activity.