Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficients

This paper evaluates the effectiveness of various similarity coefficients for 2D similarity searching when multiple bioactive target structures are available. Similarity searches using several different activity classes within the MDL Drug Data Report and the Dictionary of Natural Products databases are performed using BCI 2D fingerprints. Using data fusion techniques to combine the resulting nearest neighbor lists we obtain group recall results which, in many cases, are a considerable improvement on standard average recall values obtained for individual structures. It is shown that the degree of improvement can be related to the structural diversity of the activity class that is searched for, the best results being found for the most diverse groups. The group recall of active compounds using subsets of the class is also investigated: for highly self-similar activity classes, the group recall improvement saturates well before the full activity class size is reached. A rough correlation is found between the relative improvement using the group recall and the square of the number of unique compounds available in all of the merged lists. The Tanimoto coefficient is found unambiguously to be the best coefficient to use for the recovery of active compounds using multiple targets. Furthermore, when using the Tanimoto coefficient, the "MAX" fusion rule is found to be more effective than the "SUM" rule for the combination of similarity searches from multiple targets. The use of group recall can lead to improved enrichment in database searches and virtual screening.     

Synthesis of β3‐Homophenylalanine‐Derived Amino Acids and Peptides by Suzuki Coupling in Solution and on Solid Support

β‐Peptides and, to a certain extent, also mixed α,β‐peptides, are resistant to degradation by a variety of proteolytic enzymes that rapidly degrade natural α‐peptides. This is one of many characteristics that make β‐peptides an attractive class of compounds for drug‐discovery studies. On the other hand, modern organometallic reactions such as the Suzuki–Miyaura cross‐coupling have become standard tools in industry laboratories to derivatize side chains of α‐peptidic compounds to build up libraries of unnatural peptides. Combining both features, we prepared (4‐bromo)‐β³‐homophenylalanine derivatives 3 – 5 and 12 as precursors for Suzuki–Miyaura couplings. From these bromo compounds, we synthesized biaryl‐substituted β‐homoamino acids 6 , and analogs 13 and 15 of the anti‐AIDS drug Saquinavir.     

Coordination Chemistry of Acrylamide 4. Crystal Structures and IR Spectroscopic Properties of Acrylamide Complexes with CoII,NiII, and ZnII nitrates

Acrylamide complexes of metal nitrates: [M(O‐OC(NH₂)CHCH₂)_n(H₂O)_m][NO₃]₂ (M = Co( 1 ), Ni( 2 ) (n = 6 and m = 0) and Zn( 3 ) (n = 4 and m = 2)) have been determined by using single crystal X‐ray diffraction analysis. All complexes crystallize in the triclinic space group . The structures of 1 and 2 represent octahedral species [M(AAm)₆]²⁺ (AAm = O‐OC(NH₂)CHCH₂ and M = Co or Ni) and uncoordinated nitrate ions. The structure of 3 involves the octahedral cation [Zn(AAm)₄(H₂O)₂]²⁺ in which the Zn²⁺ environment includes oxygen atoms of four acrylamide and two water molecules that are stabilized using ionic nitrate ions. The observations of the solid‐state IR spectroscopic vibrational frequencies of these acrylamide complexes are in agreement with the crystal structures.     

Density fluctuations in amorphous and semicrystalline polymers

Summary The small-angle scattering of amorphous and semicrystalline polymers contains an intensity component due to density fluctuations within the crystalline and amorphous domains.For amorphous polymers, the density fluctuations aboveT _g correspond to the theoretical value for a fluid system in thermodynamic equilibrium. BelowT _g , a temperature dependence proportional to T is observed over a range of about 50°. At lower temperatures, a linear relationship with a smaller slope has been found which extrapolates to a non-zero value at 0 °K. This value corresponds to the frozen-in disorder, the slope at low temperatures is related to thermal vibrations and can be evaluated in terms of photon-phonon scattering.Semicrystalline polymers show a temperature dependence of the density fluctuation similar to that of the amorphous polymers. At constant temperature the density fluctuations vary linearly with crystallinity.Natural rubber shows an increase of the density fluctuations with increasing cross-linking densities from which information on the density changes in the vicinity of a cross-link and on the statistics of the distribution of cross-linking can be obtained.

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Zusammenfassung Die Kleinwinkelstreuung amorpher und teilkristalliner Polymere besitzt eine Intensitätskomponente, die von Dichtefluktuationen innerhalb der kristallinen und amorphen Bezirke herrührt. Für amorphe Polymere entspricht die Dichtefluktuation oberhalb vonT _g dem theoretischen Wert für ein fluides System im thermodynamischen Gleichgewicht. UnterhalbT _g wird eine Temperaturabhängigkeit proportional zuT über einen Bereich von etwa 50° beobachtet. Bei tieferen Temperaturen wird eine lineare Beziehung mit einer geringeren Steigung gefunden, welche zu einem endlichen Wert bei 0 °K extrapoliert werden kann. Dieser Wert bezieht sich auf die eingefrorene Fehlordnung, die Steigung bei tiefen Temperaturen ist auf thermische Schwingungen zurückzuführen und kann als Photon-Phonon-Streuung ausgewertet werden.Teilkristalline Polymere zeigen eine Temperaturabhängigkeit der Dichtefluktuation, die der von amorphen Polymeren ähnlich ist. Bei konstanter Temperatur ändert sich die Dichtefluktuation linear mit der Kristallinität.Naturkautschuk zeigt eine mit der Vernetzungsdichte ansteigende Dichtefluktuation, aus der man Information über die Dichteänderung in der Umgebung eines Netzpunktes und die Statistik der Netzpunktverteilung erhalten kann.

     

Growth and characterization of Mn- and Co-doped ZnO nanowires

A flow injection chemiluminescence method is proposed for the determination of cobalt, based on the strong catalytic effect of Cobalt(II) (1,10-phenanthroline)₃ complex on the lucigenin-periodate reaction in alkaline medium. Under the optimum experimental conditions, the chemiluminescence signal responded linearly to the concentration of cobalt(II) in the 1.0 × 10⁻⁹–3.0 × 10⁻⁷ g mL⁻¹ range with a detection limit of 4.4 × 10⁻¹⁰ g mL⁻¹ cobalt(II). The relative standard deviation for the determination of 5.0 × 10⁻⁸ g mL⁻¹ of cobalt was 2.3% in eleven replicated measurements. The method was successfully applied to the determination of cobalt(II) in pharmaceutical preparations.     

A novel method for the filterless preconcentration of iron

A novel method of analysis of iron by filterless preconcentration is presented. This is the first example of efficient preconcentration of a refractory transition metal where coprecipitation and columns were omitted. The method applies a manifold of flow injection analysis (FIA) to iron species that are preconcentrated on the inner walls of a tubular reactor. It was found that the adsorption of iron species to the walls was particularly pronounced in reactors of nylon material and enrichment factors of 30-35 could be attained, as dependent on the length of the reactor and on the time of preconcentration. In the preconcentration step of the FIA accessory, the optimum efficacy was obtained when the acidity of the samples was adjusted by HCl to pH = 2.5 whereas the ammonia preconcentration buffer should be kept alkaline at pH = 9.8. After being preconcentrated on the tubular reactor, the iron species were eluted by hydrochloric acid and analysed by flame atomic absorption spectrometry (FAAS). An unprecedented low limit of detection (LOD, 3sigma) of 1.8 microg L(-1) was thus obtained for the analysis of iron by FAAS, and the calibration line was linear up to 100 microg L(-1). A high sampling frequency of 40 per hour was obtained and the protocol allowed analysis of small amounts of iron in drinking water, in digested samples and in saline water. The major influence of interferences originated from ligands that are known to complex strongly to iron species. The method thus developed was uncomplicated in operation and it exhibited an excellent long-term stability and a high selectivity. Further, it was environmentally safe owing to production of non-toxic waste disposals. Equally high enrichment factors (EF) were obtained for Fe(ii) and Fe(iii), which is explained by the very low solubility product of both species.     

Application of the method of images on electrostatic phenomena in aqueous Al2O3 and ZrO2 suspensions

A new solution for the Poisson equation for the diffuse part of the double layer around spherical particles will be presented. The numerical results are compared with the solution of the well-known DLVO theory. The range of the diffuse layer differs considerably in the two theories. Also, the inconsistent representation of the surface and diffuse layer charge in the DLVO theory do not occur in the new theory. Experimental zeta potential measurements were used to determine the charge of colloidal Al2O3 and ZrO2 particles. It is shown that the calculated charge can be interpreted as a superposition of independent H+ and OH- adsorption isotherms. The corresponding Langmuir adsorption isotherms are taken to model the zeta potential dependence on pH. In the vicinity of the isoelectric point the model fits well with the experimental data, but at higher ion concentrations considerable deviations occur. The deviations are discussed. Furthermore, the numerical results for the run of the potential in the diffuse part of the double layer were used to determine the electrostatic interaction potential between the particles in correlation with the zeta potential measurements. The corresponding total interaction potentials, including the van der Waals attraction, were taken to calculate the coagulation half-life for a suspension with a particle loading of 2 vol%. It is shown that stability against coagulation is maintained for Al2O3 particles in the pH region between 3.3 and 7 and for ZrO2 only around pH 5. Stability against flocculation can be achieved in the pH regime between 4.5 and 7 for Al2O3, while the examined ZrO2 particles are not stable against flocculation in aqueous suspensions.