Enabling drug discovery project decisions with integrated computational chemistry and informatics

Computational chemistry/informatics scientists and software engineers in Genentech Small Molecule Drug Discovery collaborate with experimental scientists in a therapeutic project-centric environment. Our mission is to enable and improve pre-clinical drug discovery design and decisions. Our goal is to deliver timely data, analysis, and modeling to our therapeutic project teams using best-in-class software tools. We describe our strategy, the organization of our group, and our approaches to reach this goal. We conclude with a summary of the interdisciplinary skills required for computational scientists and recommendations for their training.     

Implicit QR algorithms for palindromic and even eigenvalue problems

In the spirit of the Hamiltonian QR algorithm and other bidirectional chasing algorithms, a structure-preserving variant of the implicit QR algorithm for palindromic eigenvalue problems is proposed. This new palindromic QR algorithm is strongly backward stable and requires less operations than the standard QZ algorithm, but is restricted to matrix classes where a preliminary reduction to structured Hessenberg form can be performed. By an extension of the implicit Q theorem, the palindromic QR algorithm is shown to be equivalent to a previously developed explicit version. Also, the classical convergence theory for the QR algorithm can be extended to prove local quadratic convergence. We briefly demonstrate how even eigenvalue problems can be addressed by similar techniques. D. S. Watkins partly supported by Deutsche Forschungsgemeinschaft through Matheon, the DFG Research Center Mathematics for key technologies in Berlin.     

Complete Quenching of the Pd3(dppm)3(CO)2+ Cluster Emission Via Electrostatic Host–Guest Assemblies with Carboxylate-Containing Tetraphenylporphyrins of Ni(II) and Fe(III)

The title cluster is luminescent at 77?K and exhibits an unsaturated site for binding anions when the counter ion is PF₆ ^?. A series of five non-luminescent metalloporphyrins exhibiting carboxylate anchoring groups were synthesized and characterized. These are the sodium salts of the 5-carboxyphenyl-tri-10,15,20-tolyl-, trans-di-5,10-carboxyphenyl-di-15,20-tolyl-, and tetra-5,10,15,20-carboxyphenyl(metallo)porphyrin (metallo?=?chloroiron(III), nickel(II)) anions. Evidence for supramolecular assemblies between the carboxylates and the cluster is provided by ³¹P NMR and UV?Cvis spectroscopy. The binding constant, K_1n, extracted from the UV?Cvis data via Benesi-Hildebrand, Scott and Scatchard plots are approximately 21,000?±?5,000?M^?1 for the nickel(II) species, in agreement with the previously reported zinc(II) ones (K₁₁?=?20,000?±?2,000?M^?1), but those for the chloroiron(III) are measured to be lower (12,500?±?3,500?M^?1). This association is accompanied by a complete quenching of the luminescence of the cluster which can only be due to an efficient energy transfer to the d?Cd states of the chloroiron(III) and nickel(II) species but an electron transfer from the nickel(II)-containing chromophore to the cluster is also possible. This work demonstrates the profound effect that supramolecular interactions may have on the photophysical properties despite the long donor?Cacceptor separation.     

Positron spectroscopy analysis in metallocene propylene/1‐octadecene copolymers: Parameters dependence on monoclinic and mesomorphic polymorphs

Copolymers of propylene and 1‐octadecene synthesized by a metallocene catalyst were characterized by PALS, WAXD, DSC, and density measurements. The change in the sizes and the number density of free‐volume holes as a function of the 1‐octadecene content were compared to the master laws published for copolymers of propylene with α‐olefins of shorter lengths. It was found that the samples were separated into two groups. The first set of samples obeyed the master laws while the second group deviated. This behavior was explained by the difference in the copolymer structure. The WAXD analysis confirmed the separation as well. The deviation was explained as due to the mesomorphic crystalline structure of the second group of samples, in contrast to the monoclinic one for the first group, which was a result of the relatively fast cooling from the molten state and from the high comonomer molar content. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1994–2002, 2010