Compound set enrichment: a novel approach to analysis of primary HTS data

The main goal of high-throughput screening (HTS) is to identify active chemical series rather than just individual active compounds. In light of this goal, a new method (called compound set enrichment) to identify active chemical series from primary screening data is proposed. The method employs the scaffold tree compound classification in conjunction with the Kolmogorov-Smirnov statistic to assess the overall activity of a compound scaffold. The application of this method to seven PubChem data sets (containing between 9389 and 263679 molecules) is presented, and the ability of this method to identify compound classes with only weakly active compounds (potentially latent hits) is demonstrated. The analysis presented here shows how methods based on an activity cutoff can distort activity information, leading to the incorrect activity assignment of compound series. These results suggest that this method might have utility in the rational selection of active classes of compounds (and not just individual active compounds) for followup and validation.     

Experimental charge density of octafluoro-1,2-dimethylenecyclobutane: atomic volumes and charges in a perfluorinated hydrocarbon

Octafluoro-1,2-dimethylenecyclobutane, mp. 238 K, was crystallized in situ on a SMART 1000-CCD diffractometer, and high order X-ray diffraction data were collected at 100 K for a charge density determination. A topological analysis was applied and a partitioning of the molecule into atomic regions making use of Bader's zero flux surfaces yielded atomic volumes and charges. Corresponding atomic properties were also derived theoretically from B3LYP/6-311++G(3df,3pd) wavefunctions. While for carbon the volumes and charges are largely dependent on their bonding environment, fluorine has an almost constant atomic volume around 16-17 A3 and a charge between -0.6 and -0.7e, not only in the title compound, but also in two further perfluorinated hydrocarbons, of which the charge densities were determined earlier.     

The relaxation-time limit in the quantum hydrodynamic equations for semiconductors

The relaxation-time limit from the quantum hydrodynamic model to the quantum drift-diffusion equations in R³ is shown for solutions which are small perturbations of the steady state. The quantum hydrodynamic equations consist of the isentropic Euler equations for the particle density and current density including the quantum Bohm potential and a momentum relaxation term. The momentum equation is highly nonlinear and contains a dispersive term with third-order derivatives. The equations are self-consistently coupled to the Poisson equation for the electrostatic potential. The relaxation-time limit is performed both in the stationary and the transient model. The main assumptions are that the steady-state velocity is irrotational, that the variations of the doping profile and the velocity at infinity are sufficiently small and, in the transient case, that the initial data are sufficiently close to the steady state. As a by-product, the existence of global-in-time solutions to the quantum drift-diffusion model in R³ close to the steady-state is obtained.     

MultiMCS: a fast algorithm for the maximum common substructure problem on multiple molecules

Several efficient correspondence graph-based algorithms for determining the maximum common substructure (MCS) of a pair of molecules have been published in the literature. The extension of the problem to three or more molecules is however nontrivial; heuristics used to increase the efficiency in the two-molecule case are either inapplicable to the many-molecule case or do not provide significant speedups. Our specific algorithmic contribution is two-fold. First, we show how the correspondence graph approach for the two-molecule case can be generalized to obtain an algorithm that is guaranteed to find the optimum connected MCS of multiple molecules, and that runs fast on most families of molecules using a new divide-and-conquer strategy that has hitherto not been reported in this context. Second, we provide a characterization of those compound families for which the algorithm might run slowly, along with a heuristic for speeding up computations on these families. We also extend the above algorithm to a heuristic algorithm to find the disconnected MCS of multiple molecules and to an algorithm for clustering molecules into groups, with each group sharing a substantial MCS. Our methods are flexible in that they provide exquisite control on various matching criteria used to define a common substructure.     

Surprisingly Different Reaction Behavior of Alkali and Alkaline Earth Metal Bis(trimethylsilyl)amides toward Bulky N‐(2‐Pyridylethyl)‐N′‐(2,6‐diisopropylphenyl)pivalamidine

N‐(2,6‐Diisopropylphenyl)‐N′‐(2‐pyridylethyl)pivalamidine (Dipp‐N=C(tBu)‐N(H)‐C₂H₄‐Py) ( 1 ), reacts with metalation reagents of lithium, magnesium, calcium, and strontium to give the corresponding pivalamidinates [(tmeda)Li{Dipp‐N=C(tBu)‐N‐C₂H₄‐Py}] ( 6 ), [Mg{Dipp‐N=C(tBu)‐N‐C₂H₄‐Py}₂] ( 3 ), and heteroleptic [{(Me₃Si)₂N}Ae{Dipp‐N=C(tBu)‐N‐C₂H₄‐Py}], with Ae being Ca ( 2 a ) and Sr ( 2 b ). In contrast to this straightforward deprotonation of the amidine units, the reaction of 1 with the bis(trimethylsilyl)amides of sodium or potassium unexpectedly leads to a β‐metalation and an immediate deamidation reaction yielding [(thf)₂Na{Dipp‐N=C(tBu)‐N(H)}] ( 4 a ) or [(thf)₂K{Dipp‐N=C(tBu)‐N(H)}] ( 4 b ), respectively, as well as 2‐vinylpyridine in both cases. The lithium derivative shows a similar reaction behavior to the alkaline earth metal congeners, underlining the diagonal relationship in the periodic table. Protonation of 4 a or the metathesis reaction of 4 b with CaI₂ in tetrahydrofuran yields N‐(2,6‐diisopropylphenyl)pivalamidine (Dipp‐N=C(tBu)‐NH₂) ( 5 ), or [(thf)₄Ca{Dipp‐N=C(tBu)‐N(H)}₂] ( 7 ), respectively. The reaction of AN(SiMe₃)₂ (A=Na, K) with less bulky formamidine Dipp‐N=C(H)‐N(H)‐C₂H₄‐Py ( 8 ) leads to deprotonation of the amidine functionality, and [(thf)Na{Dipp‐N=C(H)‐N‐C₂H₄‐Py}]₂ ( 9 a ) or [(thf)K{Dipp‐N=C(H)‐N‐C₂H₄‐Py}]₂ ( 9 b ), respectively, are isolated as dinuclear complexes. From these experiments it is obvious, that β‐metalation/deamidation of N‐(2‐pyridylethyl)amidines requires bases with soft metal ions and also steric pressure. The isomeric forms of all compounds are verified by single‐crystal X‐ray structure analysis and are maintained in solution.