Comparative study of machine-learning and chemometric tools for analysis of in-vivo high-throughput screening data

High-throughput screening (HTS) has become a central tool of many pharmaceutical and crop-protection discovery operations. If HTS screening is carried out at the level of the intact organism, as is commonly done in crop protection, this strategy has the potential of uncovering a completely new mechanism of actions. The challenge in running a cost-effective HTS operation is to identify ways in which to improve the overall success rate in discovering new biologically active compounds. To this end, we describe our efforts directed at making full use of the data stream arising from HTS. This paper describes a comparative study in which several machine learning and chemometric methodologies were used to develop classifiers on the same data sets derived from in vivo HTS campaigns and their predictive performances compared in terms of false negative and false positive error profiles.     

Dynamic nuclear polarization and nuclear magnetic resonance in the vicinity of edge states of a 2DES in GaAs quantum wells

Nuclear magnetic resonance is detected via the in-plane conductivity of a two-dimensional electron system at unity Landau level filling factor in the regime of the quantum Hall effect in narrow and wide quantum wells. The NMR is spatially selective to nuclei with a coupling to electrons in the current carrying edge states at the perimeter of the 2DES. Interpretation of the electron-nuclear double resonance signals is facilitated by numerical simulations. A new RF swept method for conductivity-detected NMR is introduced which offers more efficient signal averaging. The method is applied to the study of electric quadrupole interactions, weakly allowed overtone transitions, and evaluation of the extent of electron wave function delocalization in the wide quantum well.     

Vibrational spectra of methane clathrate hydrates from molecular dynamics simulation

Molecular dynamics simulations were performed on methane clathrate hydrates at ambient conditions. Thermal expansion results over the temperature range 60-300 K show that the unit cell volume increases with temperature in agreement with experiment. Power spectra were obtained at 273 K from velocity autocorrelation functions for selected atoms, and normal modes were assigned. The spectra were further classified according to individual atom types, allowing the assignment of contributions from methane molecules located in small and large cages within the structure I unit cell. The symmetric C-H stretch of methane in the small cages occurs at a higher frequency than for methane located in the large cages, with a peak separation of 14 cm(-1). Additionally, we determined that the symmetric C-H stretch in methane gas occurs at the same frequency as methane in the large cages. Results of molecular dynamics simulations indicate the use of power spectra obtained from the velocity autocorrelation function is a reliable method to investigate the vibrational behavior of guest molecules in clathrate hydrates.     

Reactive carbon-chain molecules: synthesis of 1-diazo-2,4-pentadiyne and spectroscopic characterization of triplet pentadiynylidene (H-C[triple bond]C-:C-C[triple bond]C-H)

1-Diazo-2,4-pentadiyne (6a), along with both monodeuterio isotopomers 6b and 6c, has been synthesized via a route that proceeds through diacetylene, 2,4-pentadiynal, and 2,4-pentadiynal tosylhydrazone. Photolysis of diazo compounds 6a-c (lambda > 444 nm; Ar or N2, 10 K) generates triplet carbenes HC5H (1) and HC5D (1-d), which have been characterized by IR, EPR, and UV/vis spectroscopy. Although many resonance structures contribute to the resonance hybrid for this highly unsaturated carbon-chain molecule, experiment and theory reveal that the structure is best depicted in terms of the dominant resonance contributor of penta-1,4-diyn-3-ylidene (diethynylcarbene, H-C[triple bond]C-:C-C[triple bond]C-H). Theory predicts an axially symmetric (D(infinity h)) structure and a triplet electronic ground state for 1 (CCSD(T)/ANO). Experimental IR frequencies and isotope shifts are in good agreement with computed values. The triplet EPR spectrum of 1 (absolute value(D/hc) = 0.6157 cm(-1), absolute value(E/hc) = 0.0006 cm(-1)) is consistent with an axially symmetric structure, and the Curie law behavior confirms that the triplet state is the ground state. The electronic absorption spectrum of 1 exhibits a weak transition near 400 nm with extensive vibronic coupling. Chemical trapping of triplet HC5H (1) in an O2-doped matrix affords the carbonyl oxide 16 derived exclusively from attack at the central carbon.     

Influence of lattice interactions on the Jahn-Teller distortion of the [Cu(H2O)6]2+ ion: dependence of the crystal structure of K2[Cu(H2O)6](SO4)(2x)(SeO4)(2-2x) upon the sulfate/selenate ratio

The temperature dependence of the structure of the mixed-anion Tutton salt K2[Cu(H2O)6](SO4)(2x)(SeO4)(2-2x) has been determined for crystals with 0, 17, 25, 68, 78, and 100% sulfate over the temperature range of 85-320 K. In every case, the [Cu(H2O)6]2+ ion adopts a tetragonally elongated coordination geometry with an orthorhombic distortion. However, for the compounds with 0, 17, and 25% sulfate, the long and intermediate bonds occur on a different pair of water molecules from those with 68, 78, and 100% sulfate. A thermal equilibrium between the two forms is observed for each crystal, with this developing more readily as the proportions of the two counterions become more similar. Attempts to prepare a crystal with approximately equal amounts of sulfate and selenate were unsuccessful. The temperature dependence of the bond lengths has been analyzed using a model in which the Jahn-Teller potential surface of the [Cu(H2O)6]2+ ion is perturbed by a lattice-strain interaction. The magnitude and sign of the orthorhombic component of this strain interaction depends on the proportion of sulfate to selenate. Significant deviations from Boltzmann statistics are observed for those crystals exhibiting a large temperature dependence of the average bond lengths, and this may be explained by cooperative interactions between neighboring complexes.     

The Role of Organic Glasses in cis/trans Photoisomerization at Low Temperatures

Into the looking glass! Low temperature photoisomerization studies on some arenes have been studied in different organic glasses. The results are consistent with a possible softening of the glass and offer an explanation for the mechanism of photoisomerization in a confined medium.

     

Single-shot measurement of triplet-singlet relaxation in a Si/SiGe double quantum dot

We investigate the lifetime of two-electron spin states in a few-electron Si/SiGe double dot. At the transition between the (1,1) and (0,2) charge occupations, Pauli spin blockade provides a readout mechanism for the spin state. We use the statistics of repeated single-shot measurements to extract the lifetimes of multiple states simultaneously. When the magnetic field is zero, we find that all three triplet states have equal lifetimes, as expected, and this time is ~10 ms. When the field is nonzero, the T(0) lifetime is unchanged, whereas the T- lifetime increases monotonically with the field, reaching 3 sec at 1 T.