Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Comprehensive inter‐laboratory calibration of reference materials for δ18O versus VSMOW using various on‐line high‐temperature conversion techniques

Internationally distributed organic and inorganic oxygen isotopic reference materials have been calibrated by six laboratories carrying out more than 5300 measurements using a variety of high‐temperature conversion techniques (HTC) a in an evaluation sponsored by the International Union of Pure and Applied Chemistry (IUPAC). To aid in the calibration of these reference materials, which span more than 125‰, an artificially enriched reference water (δ¹⁸O of +78.91‰) and two barium sulfates (one depleted and one enriched in ¹⁸O) were prepared and calibrated relative to VSMOW2 b and SLAP reference waters. These materials were used to calibrate the other isotopic reference materials in this study, which yielded:

Cohomology with coefficients for operadic coalgebras

Corepresentations of a coalgebra over a quadratic operad are defined, and various characterizations of them are given. Cohomology of such an operadic coalgebra with coefficients in a corepresentation is then studied.     

Products of Jacobians as Prym-Tyurin varieties

Let X ₁, ..., X _m denote smooth projective curves of genus g _i ≥ 2 over an algebraically closed field of characteristic 0 and let n denote any integer at least equal to . We show that the product JX ₁ × ... × JX _m of the corresponding Jacobian varieties admits the structure of a Prym-Tyurin variety of exponent n ^m-1. This exponent is considerably smaller than the exponent of the structure of a Prym-Tyurin variety known to exist for an arbitrary principally polarized abelian variety. Moreover it is given by explicit correspondences.      

Locating a minisum circle in the plane

We consider the problem of locating a circle with respect to existing facilities in the plane such that the sum of weighted distances between the circle and the facilities is minimized, i.e., we approximate a set of given points by a circle regarding the sum of weighted distances. If the radius of the circle is a variable we show that there always exists an optimal circle passing through two of the existing facilities. For the case of a fixed radius we provide characterizations of optimal circles in special cases. Solution procedures are suggested.     

Artificial transfer hydrogenases based on the biotin-(strept)avidin technology: fine tuning the selectivity by saturation mutagenesis of the host protein

Incorporation of biotinylated racemic three-legged d6-piano stool complexes in streptavidin yields enantioselective transfer hydrogenation artificial metalloenzymes for the reduction of ketones. Having identified the most promising organometallic catalyst precursors in the presence of wild-type streptavidin, fine-tuning of the selectivity is achieved by saturation mutagenesis at position S112. This choice for the genetic optimization site is suggested by docking studies which reveal that this position lies closest to the biotinylated metal upon incorporation into streptavidin. For aromatic ketones, the reaction proceeds smoothly to afford the corresponding enantioenriched alcohols in up to 97% ee (R) or 70% (S). On the basis of these results, we suggest that the enantioselection is mostly dictated by CH/pi interactions between the substrate and the eta6-bound arene. However, these enantiodiscriminating interactions can be outweighed in the presence of cationic residues at position S112 to afford the opposite enantiomers of the product.     

Comparative studies on the DNA-binding properties of linear and angular dibenzoquinolizinium ions

The interaction of the linear dibenzo[b,g]quinolizinium (5a) and the angular dibenzo[a,f]quinolizinium (6) with DNA was studied in detail in order to evaluate the influence of the shape of polycyclic quinolizinium ions on their DNA-binding properties. First, the synthesis and the thermally induced dimerization of 5a were reinvestigated because the preparation and isolation of the bromide salt of 5a according to literature procedures turned out to be problematic. The dibenzo[b,g]quinolizinium bromide [5a(Br)] tends to dimerize in solution with a highly selective and unprecedented formation of the corresponding anti-head-to-head dimer. Nevertheless, it was observed that careful exclusion of bromide ions from the reaction mixture suppresses the formation of the dimer. Moreover, the dimer may be transformed to the monomer by a remarkably rapid photoinduced electron-transfer reaction with 1-methoxynaphthalene. The association of 5a and 6 with nucleic acids was investigated by spectrophotometric and spectrofluorimetric DNA titrations, CD and LD spectroscopy, DNA thermal denaturation studies, and competition-dialysis techniques. Both dibenzoquinolizinium ions 5a and 6 exhibit an intercalative mode of binding to double-stranded DNA with moderate binding constants (K = 1-7 x 10(5) M(-1)) and a slight preference for association with GC-rich DNA regions. The structures of the intercalation complexes were calculated by molecular modeling methods. Competition-dialysis studies reveal that the isomers 5a and 6 bind selectively to triple-helical DNA (poly[dA]-poly[dT]2) as compared to selected synthetic and native double-stranded nucleic acids. Notably, the selectivity of the linear dibenzo[b,g]quinolizinium 5a toward triplex DNA is higher than the one of the angular derivative 6. In contrast, the DNA thermal denaturation studies reveal a higher stabilization of triple-helical DNA in the presence of 6 (DeltaTm3-->2 = 28 degrees C at r = 0.5) as compared to the stabilization by 5a (DeltaTm3-->2 = 14 degrees C at r = 0.5). This comparison emphasizes the importance of the extended pi system for the interaction of annelated quinolizinium ions with DNA. Moreover, the comparison between 5a and 6 demonstrates the significant influence of the shape of the pi system on the duplex- and triplex-stabilizing properties of the dibenzoquinolizinium ions.     

Static secondary ion mass spectrometry (S-SIMS) for the characterization of surface components in mineral particulates

The feasibility of static secondary ion mass spectrometry (S-SIMS) for the detection of molecule specific information from complex materials, such as natural clay and soil samples, has been investigated. Ion trap (IT), as well as triple quadrupole (TQ) instruments, have been used for mass analysis. Secondary ion images have been acquired using time-of-flight (TOF) S-SIMS. The generation of molecular adduct ions from thin and thick layers on the mineral substrates has been investigated using KBr as a simple model system. Results show that molecular adducts of KBr can be indeed detected from the spiked materials. However, the concentrations of the spiking solutions have to be significantly larger than expected from the surface area measured by gas adsorption techniques. In addition imaging analysis has evidenced that the detection of adduct ions in the mass spectra directly relates to the presence of local micro-crystallites.