Comments on the article "Evaluation of pK(a) estimation methods on 211 druglike compounds"

The recent article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds" ( Manchester, J.; et al. J. Chem Inf. Model. 2010, 50, 565-571 ) reports poor results for the program Epik. Here, we highlight likely sources for the poor performance and describe work done to improve the performance. Running Epik in the mode intended to calculate pK(a) values for sequentially adding/removing protons, as needed to reproduce the experimental conditions, improves the root mean squared error (RMSE) from 3.0 to 2.18 for the 85 public compounds available from the paper. Despite this improvement, there are still other programs in the Manchester paper that outperform Epik. The primary reason is that the public portion of the data set is not diverse and Epik is missing a few key functional groups in this data set that are heavily represented. We show that incorporation of these missing functional groups into the Epik training set improves the RMSE for the public compounds to 1.04. Furthermore, these enhancements help improve the overall performance of Epik on a large druglike test set.     

Optimization-based heuristics for underground mine scheduling

Underground mine production scheduling possesses mathematical structure similar to and yields many of the same challenges as general scheduling problems. That is, binary variables represent the time at which various activities are scheduled. Typical objectives seek to minimize costs or some measure of production time, or to maximize net present value; two principal types of constraints exist: (i) resource constraints and (ii) precedence constraints. In our setting, we maximize “discounted metal production” for the remaining life of an underground lead and zinc mine that uses three different underground methods to extract the ore. Resource constraints limit the grade, tonnage, and backfill paste (used for structural stability) in each time period, while precedence constraints enforce the sequence in which extraction (and backfill) is performed in accordance with the underground mining methods used. We tailor exact and heuristic approaches to reduce model size, and develop an optimization-based decomposition heuristic; both of these methods transform a computationally intractable problem to one for which we obtain solutions in seconds, or, at most, hours for problem instances based on data sets from the Lisheen mine near Thurles, Ireland.     

Crystallographic and magnetic characterisation of the brownmillerite Sr2Co2O5

Sr₂Co₂O₅ with the perovskite-related brownmillerite structure has been synthesised via quenching, with the orthorhombic unit cell parameters a=5.4639(3) Å, b=15.6486(8) Å and c=5.5667(3) Å based on refinement of neutron powder diffraction data collected at 4 K. Electron microscopy revealed L-R-L-R-intralayer ordering of chain orientations, which require a doubling of the unit cell along the c-parameter, consistent with the assignment of the space group Pcmb. However, on the length scale pertinent to NPD, no long-range order is observed and the disordered space group Imma appears more appropriate. The magnetic structure corresponds to G-type order with a moment of 3.00(4) μ_B directed along [1 0 0].     

Design and performance of an ultra‐high‐vacuum‐compatible artificial channel‐cut monochromator

The design and performance of a novel ultra‐high‐vacuum‐compatible artificial channel‐cut monochromator that has been commissioned at undulator beamline 8‐ID‐I at the Advanced Photon Source are presented. Details of the mechanical and optical design, control system implementation and performance of the new device are given. The monochromator was designed to meet the challenging stability and optical requirements of the X‐ray photon correlation spectroscopy program hosted at this beamline. In particular, the device incorporates a novel in‐vacuum sine‐bar drive mechanism for the combined pitch motion of the two crystals and a flexure‐based high‐stiffness weak‐link mechanism for fine‐tuning the pitch and roll of the second crystal relative to the first crystal. The monochromator delivers an exceptionally uniform and stable beam and thereby improved brilliance preservation.     

ChemInform Abstract: Thermochemistry of N3O2‐

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