Optimization problem solving with auctions in Cultural Algorithms

In this paper we investigate the role that the competition among knowledge sources plays in the problem solving behavior of a population as the complexity of the optimization problem solving landscapes increases. We employ a type of game theoretic mechanism, auctions, in our study. Our main goal is to determine whether it matters if knowledge sources competed for individuals using auction mechanisms or weighted majority win mechanisms as the landscape complexity increased. The weighted majority win situation allows the Knowledge Sources to make predictions about future success whereas the Auction mechanism allows them to invest in their future by using tokens earned from recent performance. This latter approach allows contextual Knowledge Sources such as Situational Knowledge to play a larger role. Although the results are preliminary, it appears that the auction mechanism is more efficient when solving a problem in situations where contextual information is available. In that case, it is easier for the knowledge sources to make judicial bids or investments. However, once the landscapes become chaotic there is less contextual information available and correspondingly little advantage to the auction mechanism over the weighted majority win situation in terms of the number of generations needed to achieve a solution.     

A Metal–Organic Framework with Cooperative Phosphines That Permit Post‐Synthetic Installation of Open Metal Sites

PCM‐101 is a phosphine coordination material comprised of tris(p‐carboxylato)triphenylphosphine and secondary pillaring groups coordinated to [M₃(OH)]⁵⁺ nodes (M=Co, Ni). PCM‐101 has a unique topology in which R₃P: sites are arranged directly trans to one another, with a P???P separation distance dictated by the pillars. Post‐synthetic coordination of soft metals to the P: sites proceeds at room temperature to provide X‐ray quality crystals that permit full structural resolution. Addition of AuCl groups forces a large distortion of the parent framework. In contrast, CuBr undergoes insertion directly between the trans‐P sites to form dimers that mimic solution‐phase complexes, but that are geometrically strained due to steric pressure exerted by the MOF scaffold. The metalated materials are active in heterogeneous hydroaddition catalysis under mild conditions, yielding different major products compared to their molecular counterparts.     

The crystal and molecular structures of isoperezone, aminoperezone, and isoaminoperezone: a comparative study of their crystal packing

The crystal structures of isoperezone (1), aminoperezone (2), and isoaminoperezone (3) have been determined by single-crystal X-ray diffraction. Compound (1) yields orange crystals, orthorhombic space group P2₁2₁2₁ with unit cell dimensions a = 6.271(6), b = 30.373(7), c = 7.257(1) Å, and Z = 4; compound (2) yields purple crystals, orthorhombic space group P2₁2₁2₁ with unit cell dimensions a = 6.498(3), b = 7.500(1) c = 29.200(6) Å, and Z = 4; compound (3) yields purple crystals, monoclinic space group P2₁ with unit cell dimensions a = 7.354(1), b = 7.511(1), c = 13.283(1) Å, = 102,07(1)°, and Z = 2. The side chains in (1)–(3) are oriented out of the plane of the quinone ring at an angle of 124, 144, and 97°, respectively. The molecules in the crystal are held together by hydrogen-bonding networks and van der Waals interactions.     

Simplified syntheses of complex multifunctional nanomaterials

Multifunctional probes are synthesized in a single step using peptide scaffold-based multifunctional single-attachment-point (MSAP) reagents.     

Elucidation of the Streptomyces coelicolor pathway to 2-undecylpyrrole, a key intermediate in undecylprodiginine and streptorubin B biosynthesis

The red gene cluster of Streptomyces coelicolor directs production of undecylprodiginine. Here we report that this gene cluster also directs production of streptorubin B and show that 2-undecylpyrrole (UP) is an intermediate in the biosynthesis of undecylprodiginine and streptorubin B. The redPQRKL genes are involved in UP biosynthesis. RedL and RedK are proposed to generate UP from dodecanoic acid or a derivative. A redK(-) mutant produces a hydroxylated undecylprodiginine derivative, whereas redL(-) and redK(-) mutants require addition of chemically synthesized UP for production of undecylprodiginine and streptorubin B. Fatty acid biosynthetic enzymes can provide dodecanoic acid, but efficient and selective prodiginine biosynthesis requires RedPQR. Deletion of redP, redQ, or redR leads to an 80%-95% decrease in production of undecylprodiginine and an array of prodiginine analogs with varying alkyl chains. In a redR(-) mutant, the ratio of these can be altered in a logical manner by feeding various fatty acids.     

Toward a consistent treatment of polarization in model QM/MM calculations

The concept of model chemistries within hybrid QM/MM calculations has been addressed through analysis of the polarization energy determined by two distinct approaches based on (i) induced charges and (ii) induced dipoles. The quantum mechanical polarization energy for four configurations of the water dimer has been determined for a range of basis sets using Morokuma energy decomposition analysis. This benchmark value has been compared to the fully classical polarization energy determined using the induced dipole approach, and the molecular mechanics polarization energy calculated using induced charges within the MM region of hybrid QM/MM calculations. From the water dimer calculations, it is concluded that the induced charge approach is consistent with medium sized basis set calculations whereas the induced dipole approach is consistent with large basis set calculations. This result is highly relevant to the concept of QM/MM model chemistries.