Characterizing bitterness: identification of key structural features and development of a classification model

This work describes the first approach in the development of a comprehensive classification method for bitterness of small molecules. The data set comprises 649 bitter and 13 530 randomly selected molecules from the MDL Drug Data Repository (MDDR) which are analyzed by circular fingerprints (MOLPRINT 2D) and information-gain feature selection. The feature selection proposes substructural features which are statistically correlated to bitterness. Classification is performed on the selected features via a na?ve Bayes classifier. The substructural features upon which the classification is based are able to discriminate between bitter and random compounds, and thus we propose they are also functionally responsible for causing the bitter taste. Such substructures include various sugar moieties as well as highly branched carbon scaffolds. Cynaropicrine contains a number of the substructural features found to be statistically associated with bitterness and thus was correctly predicted to be bitter by our model. Alternatively, both promethazine and saccharin contain fewer of these substructural features, and thus the bitterness in these compounds was not identified. Two different classes of bitter compounds were identified, namely those which are larger and contain mainly oxygen and carbon and often sugar moieties, and those which are rather smaller and contain additional nitrogen and/or sulfur fragments. The classifier is able to predict 72.1% of the bitter compounds. Feature selection reduces the number of false-positives while also increasing the number of false negatives to 69.5% of bitter compounds correctly predicted. Overall, the method presented here presents both one of the largest databases of bitter compounds presently available as well as a relatively reliable classification method.     

A general strategy for creating "inactive-conformation" abl inhibitors

Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydrophobic site immediately adjacent to the ATP pocket made accessible by a conformational rearrangement of the activation loop (type II). To date, all type II inhibitors were discovered by using structure-activity-guided optimization strategies. Here, we describe a general pharmacophore model of type II inhibition that enables a rational "hybrid-design" approach whereby a 3-trifluoromethylbenzamide functionality is appended to four distinct type I scaffolds in order to convert them into their corresponding type II counterparts. We demonstrate that the designed compounds function as type II inhibitors by using biochemical and cellular kinase assays and by cocrystallography with Abl.     

Synthetic and structural comparisons of bismuth(III) carboxylates synthesised under solvent-free and reflux conditions

Two synthetic approaches to the formation of bismuth(III) carboxylates have been explored and compared. Ph(3)Bi was reacted with a series of carboxylic acids (RCO(2)H) of varying pK(a) and functionality (R = PhCH[double bond, length as m-dash]CH, o-MeOC(6)H(4), m-MeOC(6)H(4), o-H(2)NC(6)H, o-O(2)NC(6)H(4), p-O(2)NC(6)H(4), 2-(C(5)H(4)N)) under reflux conditions in toluene and solvent-free. The thermochemical profiles of the solvent-free reactions were also studied by DSC-TGA. All reactions produced the tri-substituted bismuth carboxylates in comparable yields and purity with the exceptions of picolinic acid and p-nitrobenzoic acid. 2-Picolinic acid exclusively formed the di-substituted complex, [PhBi(2-(C(5)H(4)N)CO(2))(2)](4), by both methods, while p-nitrobenzoic acid gave the tri-substituted complex through reflux and the di-substituted complex under solvent-free conditions. Two of the complexes were structurally authenticated by single crystal X-ray diffraction: [PhBi(2-(C(5)H(4)N)CO(2))(2)](4) is tetrameric formed through five membered chelate rings involving the pyridyl N and O(-C) rather than the less stable carboxylate (-CO(2)) chelates, while [Bi(o-MeOC(6)H(4)CO(2))(3)](infinity), is a polymer in which dimeric units, constructed around two chelating and one unsymmetrical bridging carboxylate on each Bi centre, are then joined together through longer intermolecular Bi-O bridging bonds.     

Excited-state structural dynamics of 5-fluorouracil

5-Fluorouracil is an analogue of thymine and uracil, nucleobases found in DNA and RNA, respectively. The photochemistry of thymine is significant; UV-induced photoproducts of thymine in DNA lead to skin cancer and other diseases. In previous work, we have suggested that the differences in the excited-state structural dynamics of thymine and uracil arise from the methyl group in thymine acting as a mass barrier, localizing the vibrations at the photochemical active site. To further test this hypothesis, we have measured the resonance Raman spectra of 5-fluorouracil at wavelengths throughout its 267 nm absorption band. The spectra of 5-fluorouracil and thymine are very similar. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism suggests that, at most, 81% of the reorganization energy upon excitation is directed along photochemically relevant modes. This compares well with what was found for thymine, supporting the mass barrier hypothesis.     

Multisample probe for fast-atom bombardment / mass spectrometry

An inexpensive multisample fast-atom bombardment (FAB) probe assembly was designed for high-throughput analysis of samples on a VG ZAB-SE mass spectrometer. The system consists of a vacuum lock system and a FAB probe whose tip contains five or more sample wells. The probe enters the mass spectrometer source region perpendicular to the secondary ion beam axis, The probe is maintained at high voltage on contact with a spring clip attached to the screen plate of the source block. Sample throughput with the multisample probe is twice that of a coaxial probe, with about twice the sensitivity and no sample cross contamination.     

The superhydrophobicity of polymer surfaces: Recent developments

Superhydrophobicity is the extreme water repellence of highly textured surfaces. The field of superhydrophobicity research has reached a stage where huge numbers of candidate treatments have been proposed and jumps have been made in theoretically describing them. There now seems to be a move to more practical concerns and to considering the demands of individual applications instead of more general cases. With these developments, polymeric surfaces with their huge variety of properties have come to the fore and are fast becoming the material of choice for designing, developing, and producing superhydrophobic surfaces. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1203–1217, 2011     

Proton ionizable crown compounds. 18. Comparison of alkali metal transport in a H2O-CH2Cl2-H2O liquid membrane system by four proton-ionizable macrocycles containing the dialkylhydrogenphosphate moiety

The macrocycle-mediated fluxes of alkali, alkaline earth, and several transition metal cations have been determined and compared in a H₂O-CH₂Cl₂-H₂O liquid membrane system using four water-insoluble macrocycles containing a dialkylhydrogenphosphate moiety. Transport of alkali metal cations by these ligands was greatest from a source phase pH = 12 or above into an acid receiving phase (pH = 1.5). Very low fluxes were observed for the transport of the alkaline earth cations and all transition metal ions studied except Ag⁺ and Pb²⁺ which were transported reasonably well by these new macrocycles.Deceased: September 5, 1987.     

Dynamic collision-induced dissociation (DCID) in a quadrupole ion trap using a two-frequency excitation waveform: I. Effects of excitation frequency and phase angle

This study describes the application of a two-frequency excitation waveform to the end-cap electrodes of a quadrupole ion trap (QIT) during the mass acquisition period to deliberately fragment selected precursor ions. This approach obviates the need for a discrete excitation period and guarantees on-resonant excitation conditions without any requirement for resonant tuning; it is therefore faster than the conventional approach to collision-induced dissociation (CID) in QITs. The molecular ion of n-butylbenzene is used as thermometer molecule to determine the energetics of the new excitation procedure. The excitation waveform, consisting of two closely spaced sinusoidal frequencies, has an interference pattern that displays nodes and crests in the time domain. The energetics (determined by the product ion ratios of 91/92 Th) and CID efficiencies are highly dependent on the excitation amplitude, the relative position of the excitation frequencies in the Mathieu stability diagram, and whether the ions come into resonance during a node or crest of the excitation waveform. Under highly energetic conditions, ratios of 91/92 as large as 15 can be obtained at concomitant CID efficiencies of 10%, indicating internal energies in excess of 10 eV at the time of fragmentation. These extremely high internal energies far exceed the energetics achievable using conventional on-resonance excitation in QITs, indicating that the collisional heating rate is very fast in the new approach. Under less energetic conditions CID efficiencies as high as 70% are possible, which compares favorably with results obtained by conventional on-resonance excitation. Correlation analyses are used to determine the conditions that simultaneously optimize energetic and efficient fragmentation conditions.     

Enhancing the Value of Free Metals in the Synthesis of Lanthanoid Formamidinates: Is a Co‐oxidant Needed?

Treatment of N,N′‐bis(aryl)formamidines (ArFormH), N,N′‐bis(2,6‐difluorophenyl)formamidine (DFFormH) or N,N′‐bis(2,6‐diisopropylphenyl)formamidine (DippFormH), with europium metal in CH₃CN is an efficient synthesis of the divalent complexes: [{Eu(DFForm)₂(CH₃CN)₂}₂] ( Eu1 ) or [Eu(DippForm)₂(CH₃CN)₄] ( Eu2 ). The synthetic method was extended to ytterbium, but the metal required activation by addition of Hg⁰. With DFFormH in CH₃CN, [{Yb(DFForm)₂(CH₃CN)}₂] ( Yb1 ) was obtained in good yield, and [Yb(DFForm)₂(thf)₃] ( Yb3 ) was obtained from a synthesis in CH₃CN/THF. Thus, this synthetic method completely circumvents the use of either salt metathesis, or redox transmetallation/protolysis (RTP) protocols to prepare divalent rare‐earth formamidinates. Heating Yb1 in PhMe/C₆D₆ resulted in decomposition to trivalent products, including one from a CH₃CN activation process. For a synthetic comparison, divalent ytterbium DFForm and DippForm complexes were synthesised by RTP reactions between Yb⁰, Hg(R)₂ (R=Ph, C₆F₅), and ArFormH in THF, leading to the isolation of either [Yb(DFForm)₂(thf)₃] ( Yb3 ), or the first five coordinate rare‐earth formamidinate complex [Yb(DippForm)₂(thf)] ( Yb4 b ), and, from adjustment of the stoichiometry, trivalent [Yb(DFForm)₃(thf)] ( Yb6 ). Oxidation of Yb3 with benzophenone (bp), or halogenating agents (TiCl₄(thf)₂, Ph₃CCl, C₂Cl₆) gave [Yb(DFForm)₃(bp)] or [Yb(DFForm)₂Cl(thf)₂], respectively. Furthermore, the structural chemistry of divalent ArForm complexes has been substantially broadened. Not only have the highest and lowest coordination numbers for divalent rare‐earth ArForm complexes been achieved in Eu2 and Yb4 b , respectively, but also dimeric Eu1 and Yb1 have highly unusual ArForm bridging coordination modes, either perpendicular μ‐1κ(N:N′):2κ(N:N′) in Eu1 , or the twisted μ‐1κ(N:N′):2κ(N′:F′) DFForm coordination in Yb1 , both unprecedented in divalent rare‐earth ArForm chemistry and in the wider divalent rare‐earth amidinate field.     

Single and double hydrogen migration in the fragmentation of 3-methyl-2-butyl trifluoroacetate

Three of the main oxygen-containing fragments resulting from 3-methyl-2-butyl trifluoroacetate (11) had been identified previously as the 1-triflnoroacetoxyethyl cation (m/z 141, 12, product of simple cleavage), and the products of single (m/z 142) and double hydrogen transfer (m/z 143, protonated ethyl trifluoroacetate). Collisionally activated dissociation of m/z 142 and the isotopomers resulting from 11-2-d, 11-1-d₃, 11-5,6-d₆, and 11-¹⁸O₂ has established that m/z 142 is the oxygen protonated 1-trifluoroacetoxyethyl free radical (17) formed by hydrogen shift irom a γ-methyl group to oxygen in the molecular ion, rather than in a complex (18) between 12 and the 2-propyl free radical, as expected based on a mechanistic model existing in the literature. The second hydrogen transferred originates in the other γ-methyl group; its migration may occur, but does not have to, in the complex between 17 and a molecule of propene, prior to dissociation of the two fragments. Collision-activated dissociation has now shown that the m/z 140 ion observed in the spectrum is the molecular ion of vinyl trifluoroacetate, possibly formed by a hydrogen transfer from 12 to the 2-propyl radical in the complex 18. The hydrogen migration to oxygen exhibits no isotope effect, whereas the transfers to carbon atoms exhibit small primary and α secondary kinetic isotope effects. Exclusive migration of the tertiary hydrogen from C(3) occurs in the formation of 2-methylbutene cation radical (m/z 70) from the molecular ion. The hydrocarbon ion fragments and the heteroatom-containing fragments are formed from 11 by disjoint pathways.