Application of NMR SHAPES screening to an RNA target

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.     

A note on the nonexistence of Barker sequences

A Barker sequence is a sequence with elements ±1 such that all out-of-phase aperiodic autocorrelation coefficients are 0, 1 or -1. It is known that if a Barker sequence of length s > 13 exists then s = 4N ² for some odd integer N 55, and it has long been conjectured that no such sequence exists. We review some previous attempts to improve the bound on N which, unfortunately, contain errors. We show that a recent theorem of Eliahou et al. [5] rules out all but six values of N less than 5000, the smallest of which is 689.     

Swallowtail porphyrins: synthesis, characterization and incorporation into porphyrin dyads

The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid.     

Experimental and computational studies of trialkylaluminum and alkylaluminum chloride reactions with silica

Reactions of trimethylaluminum, triethylaluminum, and diethylaluminum chloride and ethylaluminum dichloride with silica gel have been studied experimentally by infrared spectroscopy and elemental analysis. The silica gel was subjected to different pretreatments to alter surface functionalities prior to reaction. In all cases the extent of surface modification reaction follows the trend unmodified > 600 degrees C pretreated > hexamethyldisilazane (HMDZ) pretreated > 600 degrees C/HMDZ pretreated. All of the aluminum compounds studied completely react non-hydrogen-bonded silanols, while also reacting with hydrogen-bonded silanols and siloxanes. Primarily monomeric surface species result from the surface modification reaction. Ethylaluminum chlorides preferentially react with silanols through cleavage of the Al-C bond rather than the Al-Cl bond. Singly bonded Si(s)-O-AlCl(2) surface species are readily synthesized by reaction of ethylaluminum dichloride with HMDZ-pretreated silica gel. Bridged bonded (Si(s)-O)(2)-AlCl surface species are readily synthesized by reaction of diethylaluminum chloride with HMDZ-pretreated silica gel. Computational ab initio studies of the cluster Si(4)O(6)(OH)(4) as a model to study the reaction of monomeric and dimeric methylaluminum dichloride with a silica silanol are also described. Comparison of the potential energy surface (PES) of monomer and dimer indicates that the energetics favor monomer reaction, consistent with experimental results. The energy cost in the dimer reaction is primarily from cleavage of a bridged Al-Cl bond upon adsorption. This does not occur when the monomer adsorbs. A comparison of the PES for the two reaction pathways resulting from cleavage of either an Al-Cl or Al-C bond indicates that while the former reaction is slightly kinetically favored (E(a) = 23.1 kJ/mol for Al-Cl bond cleavage versus E(a) = 31.1 kJ/mol for Al-C bond cleavage), the latter is strongly thermodynamically favored with an overall free energy difference between the two reaction pathways of 135 kJ/mol favorable to Al-C bond cleavage. These reactions are thermodynamically controlled.     

Side-chain crystallinity. III. Influence of side-chain crystallinity on the glass transition temperatures of selected copolymers incorporating n-octadecyl acrylate or vinyl stearate

The influence of side-chain crystallinity on the glass transition temperatures of selected copolymers was investigated. The copolymers were selected, in part, from those whose crystallinity was treated in the preceding paper. These included the lower amorphous acrylate esters, such as methyl, ethyl, n-butyl, and 2-ethylhexyl acrylates, together with methyl methacrylate and acrylonitrile, each copolymerized with n-octadecyl acrylate over the range of composition. The decline in the glass transition temperature was linear with increasing weight fraction of n-octadecyl acrylate for all systems in the composition range where the copolymers were essentially amorphous. The extrapolated T_g for the amorphous state of poly(n-octadecyl acrylate), and for amorphous poly(oleyl acrylate), was close to ?111°C. This coincided with a value previously obtained by an extrapolation of data on homologs. Beyond a critical fraction of octadecyl acrylate (0.3 to 0.5), developing side-chain crystallinity in n-octadecyl acrylate raised the glass temperature steadily for all systems, up to a value of 17-C, obtained for the crystalline homopolymer. Crystallinity did not develop in stiff copolymers until T_g was about 30°C below the melting point of the most perfect crystals. In compositionally heterogeneous copolymers incorporating vinyl stearate, blocks of crystalline units appeared to be dispersed in a glassy matrix of amorphous co-units. An empirical equation was derived which fitted the experimental data for random copolymers, over all composition ranges, with fair accuracy.     

Creation and comparison of MS/MS spectral libraries using quadrupole ion trap and triple-quadrupole mass spectrometers

Searchable libraries of MS/MS spectra, obtained using liquid chromatography/tandem mass spectrometry (LC/MS/MS) with data-dependent scan mode switching on both quadrupole ion trap and triple-quadrupole mass spectrometers in conjunction with electrospray ionization, are presented. The effects on library search scores of changing the parameters for producing collision-induced dissociation (CID) on both instrument types are systematically evaluated. These observations serve as a basis for determining a universal set of conditions for building MS/MS libraries. A group of 19 closely related steroids was used. The ability to obtain library-searchable spectra at low concentrations is demonstrated for the analysis of a sample of progesterone spiked with hydroxyprogesterone impurities at 0.1 and 0.01%.     

Macrophage-targeting oligopeptides from Mortierella alpina

The realm of natural products of early diverging fungi such as Mortierella species is largely unexplored. Herein, the nonribosomal peptide synthetase (NRPS) MalA catalysing the biosynthesis of the surface-active biosurfactants, malpinins, has been identified and biochemically characterised. The investigation of the substrate specificity of respective adenylation (A) domains indicated a substrate-tolerant enzyme with an unusual, inactive C-terminal NRPS module. Specificity-based precursor-directed biosynthesis yielded 20 new congeners produced by a single enzyme. Moreover, MalA incorporates artificial, click-functionalised amino acids which allowed postbiosynthetic coupling to a fluorophore. The fluorescent malpinin conjugate penetrates mammalian cell membranes via an phagocytosis-mediated mechanism, suggesting Mortierella oligopeptides as carrier peptides for directed cell targeting. The current study demonstrates substrate-specificity testing as a powerful tool to identify flexible NRPS modules and highlights basal fungi as reservoir for chemically tractable compounds in pharmaceutical applications.

Specificity profiling of a nonribosomal peptide synthetase of an early diverging fungus revealed high substrate flexibility. Feeding studies with click-functionalised amino acids enabled the production of fluorescent peptides targeting macrophages.     

MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations

The use of machine learning techniques in computational chemistry has gained significant momentum since large molecular databases are now readily available. Predictions of molecular properties using machine learning have advantages over the traditional quantum mechanics calculations because they can be cheaper computationally without losing the accuracy. We present a new extrapolatable and explainable molecular representation based on bonds, angles and dihedrals that can be used to train machine learning models. The trained models can accurately predict the electronic energy and the free energy of small organic molecules with atom types C, H N and O, with a mean absolute error of 1.2 kcal mol⁻¹. The models can be extrapolated to larger organic molecules with an average error of less than 3.7 kcal mol⁻¹ for 10 or fewer heavy atoms, which represent a chemical space two orders of magnitude larger. The rapid energy predictions of multiple molecules, up to 7 times faster than previous ML models of similar accuracy, has been achieved by sampling geometries around the potential energy surface minima. Therefore, the input geometries do not have to be located precisely on the minima and we show that accurate density functional theory energy predictions can be made from force-field optimised geometries with a mean absolute error 2.5 kcal mol⁻¹.

New representations and machine learning calculate DFT minima from force field geometries.     

Cationic molybdenum oxo alkylidenes stabilized by N-heterocyclic carbenes: from molecular systems to efficient supported metathesis catalysts

Cationic d⁰ group 6 olefin metathesis catalysts have been recently shown to display in most instances superior activity in comparison to their neutral congeners. Furthermore, their catalytic performance is greatly improved upon immobilization on silica. In this context, we have developed the new family of molecular cationic molybdenum oxo alkylidene complexes stabilized by N-heterocyclic carbenes of the general formula [Mo(O)(CHCMe₃)(IMes)(OR)[X⁻]] (IMes = 1,3-dimesitylimidazol-2-ylidene; R = 1,3-dimesityl-C₆H₃, C₆F₅; X⁻ = B(3,5-(CF₃)₂C₆H₃)₄⁻, B(Ar^F)₄, tetrakis(perfluoro-t-butoxy)aluminate (PFTA)). Immobilization of [Mo(O)(CHCMe₃)(IMes)(O-1,3-dimesityl-C₆H₃)⁺B(Ar^F)₄⁻] on silica via surface organometallic chemistry yields an active alkene metathesis catalyst that shows the highest productivity towards terminal olefins amongst all existing molybdenum oxo alkylidene catalysts.

The first cationic molybdenum oxo complexes were synthesized and immobilized on partially dehydroxylated silica. Vastly enhanced catalytic activity for terminal olefins was found compared to their neutral congeners.     

Nearly invariant subspaces for shift semigroups

Let{T (t)}_t≥0 be a C₀-semigroup on an infinite-dimensional separable Hilbert space; a suitable definition of near{T (t)~*}_t≥0 invariance of a subspace is presented in this paper. A series of prototypical examples for minimal nearly{S(t)~*}t≥0 invariant subspaces for the shift semigroup{S(t)}_t≥0 on L²(0,∞) are demonstrated, which have close links with near T~*_θ invariance on Hardy spaces of the unit disk for an inner function θ. Especially, ...