Protein nanopores with covalently attached molecular adapters

Molecular adapters are crucial for the stochastic sensing of organic analytes with alpha-hemolysin (alphaHL) protein nanopores when direct interactions between analytes and the pore cannot readily be arranged by conventional protein engineering. In our earlier studies, cyclodextrin adapters were lodged noncovalently within the lumen of the alphaHL pore. In the present work, we have realized the controlled covalent attachment of a beta-cyclodextrin (betaCD) adapter in the two possible molecular orientations inside alphaHL pores prepared by genetic engineering. There are two advantages to such a covalent system. First, the adapter cannot dissociate, which means there are no gaps during stochastic detection, a crucial advance for single-molecule exonuclease DNA sequencing where the continuous presence of a molecular adapter will be essential for reading individual nucleotides. Second, the ability to orient the adapter allows analytes to bind through only one of the two entrances to the betaCD cavity. We demonstrate that the covalently attached adapters can be used to alter the ion selectivity of the alphaHL pore, examine binding events at elevated temperatures, and detect analytes with prolonged dwell times.     

Estimate of the vibrational contribution to the entropy change associated with the spin transition in the d4 systems [MnIII(pyrol)3tren] and [CrII(depe)2I2

The vibrational contribution to DeltaS of the low-spin ((3)T(1)) to high-spin ((5)E) spin transition in two 3d(4) octahedral systems [Mn(III)(pyrol)(3)tren] and [Cr(depe)(2)I(2)] have been estimated by means of DFT calculations (B3LYP/CEP-31G) of the vibrational normal-modes frequencies. The obtained value at the transition temperature for the Mn(iii) complex is DeltaS(vib)(44 K) = 6.3 J K(-1) mol(-1), which is comparable with the proposed Jahn-Teller contribution of R ln3 = 9.1 J K(-1) mol(-1) and which is approximately half of the experimentally determined 13.8 J K(-1) mol(-1). The corresponding value for the Cr(ii) complex is DeltaS(vib)(171.45 K) = 46.5 J K(-1) mol(-1), as compared to the experimental value of 39.45 J K(-1) mol(-1). The analysis of the vibrational normal modes reveals that for the d(4) systems under study, contrary to Fe(ii) d(6) systems, not all metal-ligand stretching vibrations make a contribution. For the Mn(iii) complex, the only vibration that contributes to DeltaS(vib) involve the nitrogens occupying the Jahn-Teller axis, while in the case of Cr(ii) the contributing vibrations involve the Cr-I bonds. Low-frequency modes due to ring vibrations, metal-ligand bending and movement of the molecule as a whole also contribute to the vibrational entropy associated with the spin transition.     

Alkaline‐Earth‐Catalysed Cross‐Dehydrocoupling of Amines and Hydrosilanes: Reactivity Trends,Scope and Mechanism

Alkaline‐earth (Ae=Ca, Sr, Ba) complexes are shown to catalyse the chemoselective cross‐dehydrocoupling (CDC) of amines and hydrosilanes. Key trends were delineated in the benchmark couplings of Ph₃SiH with pyrrolidine or tBuNH₂. Ae{E(SiMe₃)₂}₂ ? (THF)_x (E=N, CH; x=2–3) are more efficient than {N^N}Ae{E(SiMe₃)₂} ? (THF)_n (E=N, CH; n=1–2) complexes (where {N^N}^?={ArN(o‐C₆H₄)C(H)=NAr}^? with Ar=2,6‐iPr₂‐C₆H₃) bearing an iminoanilide ligand, and alkyl precatalysts are better than amido analogues. Turnover frequencies (TOFs) increase in the order Ca<Sr<Ba. Ba{CH(SiMe₃)₂}₂ ? (THF)₃ displays the best performance (TOF up to 3600 h^?1). The substrate scope (>30 products) includes diamines and di(hydrosilane)s. Kinetic analysis of the Ba‐promoted CDC of pyrrolidine and Ph₃SiH shows that 1) the kinetic law is rate=k[Ba]¹[amine]⁰[hydrosilane]¹, 2) electron‐withdrawing p‐substituents on the arylhydrosilane improve the reaction rate and 3) a maximal kinetic isotopic effect (k_SiH/k_SiD=4.7) is seen for Ph₃SiX (X=H, D). DFT calculations identified the prevailing mechanism; instead of an inaccessible σ‐bond‐breaking metathesis pathway, the CDC appears to follow a stepwise reaction path with N?Si bond‐forming nucleophilic attack of the catalytically competent Ba pyrrolide onto the incoming silane, followed by rate limiting hydrogen‐atom transfer to barium. The participation of a Ba silyl species is prevented energetically. The reactivity trend Ca<Sr<Ba results from greater accessibility of the metal centre and decreasing Ae?N_amide bond strength upon descending Group 2.     

Toward the Rational Design of Galactosylated Glycoclusters That Target Pseudomonas aeruginosa Lectin A (LecA): Influence of Linker Arms That Lead to Low‐Nanomolar Multivalent Ligands

Anti‐infectious strategies against pathogen infections can be achieved through antiadhesive strategies by using multivalent ligands of bacterial virulence factors. LecA and LecB are lectins of Pseudomonas aeruginosa implicated in biofilm formation. A series of 27 LecA‐targeting glycoclusters have been synthesized. Nine aromatic galactose aglycons were investigated with three different linker arms that connect the central mannopyranoside core. A low‐nanomolar (K_d=19 nm , microarray) ligand with a tyrosine‐based linker arm could be identified in a structure–activity relationship study. Molecular modeling of the glycoclusters bound to the lectin tetramer was also used to rationalize the binding properties observed.     

Alkaline Earth–Olefin Complexes with Secondary Interactions

Strontium and calcium (alkaline earth: Ae) olefin complexes stabilised by secondary Ae???F?C and β‐agostic Ae???H?Si interactions are presented. Olefin coordination onto the alkaline earths is plain in the solid state, and it is thermodynamically favoured over the coordination of THF. The existence of the Ae???olefin interactions is corroborated by solution NMR data and DFT computations. The coordination mode of the olefin varies with steric effects and, if enforced, olefin dissociation can be compensated by the other non‐covalent interactions, as supported by DFT computations.     

Gas‐Phase Infrared Spectroscopy of Substituted Cyanobutadiynes: Roles of the Bromine Atom and Methyl Group as Substituents

The IR spectra of 5‐bromo‐2,4‐pentadiynenitrile (Br?C≡C?C≡C?CN) and 2,4‐hexadiynenitrile (CH₃?C≡C?C≡C?CN), a compound of interstellar interest, have been recorded within the 4000–500 cm^?1 spectral region and calculated by means of high‐level ab initio and density functional calculations. Although the calculated structures of both compounds are rather similar, there are very subtle differences, mainly in the strength of the C≡C bond not directly bound to the substituent. These subtle bonding differences are reflected in small, but not negligible, differences in the electron density at the corresponding bond critical points, and, more importantly, are reflected in the IR spectra. Indeed, the IR spectrum for the bromine derivative presents two well‐differentiated strong bands around 2250 cm^?1, whereas for the methyl derivative both absorptions coalesce in a single band. These bands correspond in both cases to the coupling between C≡C and C≡N stretching displacements. A third, very weak, band also associated with C≡C and C≡N coupled stretches is observed for the bromine derivative, but not for the methyl one, owing to its extremely low intensity.     

Infrared and Raman Spectroscopy of Methylcyanodiacetylene (CH3C5N)

A spectroscopic study combining IR absorption and Raman scattering is presented for methylcyanodiacetylene (CH₃C₅N). Gas‐phase, cryogenic matrix‐isolated, and pure solid‐phase substance was analyzed. Out of 16 normal vibrational modes, 14 were directly observed. The analysis of the spectra was assisted by quantum chemical calculations of vibrational frequencies, IR absorption intensities, and Raman scattering activities at density functional theory and ab initio levels. Previous assignments of gas‐phase IR absorption bands were revisited and extended.     

Reactivity study of 1H-thieno[3,2-d][1,3]oxazine-2,4-dione toward the synthesis of bicyclic 3,4-dihydro-1H-thieno[3,2-e][1,4]diazepine-2,5-dione analogues

A series of 10 optically pure 3,4-dihydro-1H-thieno[3,2-e][1,4]diazepine-2,5-dione derivatives has been synthesized in 41-75% yields on treatment of 1H-thieno[3,2-d][1,3]oxazine-2,4-dione with different natural alpha-amino acids.     

Selective thin-layer chromatography of 4-R-1,2,4-triazoles

A convenient and selective TLC of 4-R-1,2,4-triazoles (Rtrz) and nitrogen containing aromatic rings is presented (molecules 1-11). This simple revelation method implies a complexation of heterocycles to Co(II) ions on a TLC plate, followed by a subsequent modification of the reduction potential which enables oxidation of Co(II) by permanganate.