Structure and Dynamics of Oligonucleotides in the Gas Phase

By combining ion‐mobility mass spectrometry experiments with sub‐millisecond classical and ab initio molecular dynamics we fully characterized, for the first time, the dynamic ensemble of a model nucleic acid in the gas phase under electrospray ionization conditions. The studied oligonucleotide unfolds upon vaporization, loses memory of the solution structure, and explores true gas‐phase conformational space. Contrary to our original expectations, the oligonucleotide shows very rich dynamics in three different timescales (multi‐picosecond, nanosecond, and sub‐millisecond). The shorter timescale dynamics has a quantum mechanical nature and leads to changes in the covalent structure, whereas the other two are of classical origin. Overall, this study suggests that a re‐evaluation on our view of the physics of nucleic acids upon vaporization is needed.     

Identification of Structure–Activity Relationships from Screening a Structurally Compact DNA‐Encoded Chemical Library

Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA‐encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL‐100K, a DNA‐encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA‐sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate‐specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small‐molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding.     

Stabilization of Titanium Dioxide Nanoparticles at the Surface of Carbon Nanomaterials Promoted by Microwave Heating

TiO₂ is frequently combined with carbon materials, such as reduced graphene oxide (RGO), to produce composites with improved properties, for example for photocatalytic applications. It is shown that heating conditions significantly affect the interface and photocatalytic properties of TiO₂@C, and that microwave irradiation can be advantageous for the synthesis of carbon‐based materials. Composites of TiO₂ with RGO or amorphous carbon were prepared from reaction of titanium isopropoxide with benzyl alcohol. During the synthesis of the TiO₂ nanoparticles, the carbon is involved in reactions that lead to the covalent attachment of the oxide, the extent of which depends on the carbon characteristics, heating rate, and mechanism. TiO₂ is more efficiently stabilized at the surface of RGO than amorphous carbon. Rapid heating of the reaction mixture results in a stronger coupling between the nanoparticles and carbon, more uniform coatings, and smaller particles with narrower size distributions. The more efficient attachment of the oxide leads to better photocatalytic performance.     

Charge mapping in 3(10)-helical peptide chains by oxidation of the terminal ferrocenyl group

Two series of 3(10)-helical peptides of different lengths and rigidity, based on the strongly foldameric α-aminoisobutyric acid and containing a terminal ferrocenyl unit, have been synthesized. Oxidation-state sensitive spectroscopic tags of helical peptides, the N-H groups, allowed mapping of the charge delocalization triggered by oxidation of the terminal ferrocenyl moiety and were monitored by IR spectroelectrochemistry.     

Densely Functionalized 2-Methylideneazetidines: Evaluation as Antibacterials

Twenty-two novel, variously substituted nitroazetidines were designed as both sulfonamide and urethane vinylogs possibly endowed with antimicrobial activity. The compounds under study were obtained following a general procedure recently developed, starting from 4-nitropentadienoates deriving from a common β-nitrothiophenic precursor. While being devoid of any activity against fungi and Gram-negative bacteria, most of the title compounds performed as potent antibacterial agents on Gram-positive bacteria (E. faecalis and three strains of S. aureus), with the most potent congener being the 1-(4-chlorobenzyl)-3-nitro-4-(p-tolyl)azetidine 22, which displayed potency close to that of norfloxacin, the reference antibiotic (minimum inhibitory concentration values 4 and 1–2 μg/mL, respectively). Since 22 combines a relatively efficient activity against Gram-positive bacteria and a cytotoxicity on eucharyotic cells only at 4-times higher concentrations (inhibiting concentration on 50% of the cultured eukaryotic cells: 36 ± 10 μM, MIC: 8.6 μM), it may be considered as a promising hit compound for the development of a new series of antibacterials selectively active on Gram-positive pathogens. The relatively concise synthetic route described herein, based on widely available starting materials, could feed further structure–activity relationship studies, thus allowing for the fine investigation and optimization of the toxico-pharmacological profile.     

Groups with many normal or self-normalizing subgroups

In this paper groups in which the set Σ of the normal or self-normalizing subgroups is large will be studied. In particular it will be characterized locally graded groups satisfying the minimal condition on subgroups which do not belong to Σ and locally finite groups for which the set Σ is dense in the lattice of all subgroups.     

Computing spin networks

We expand a set of notions recently introduced providing the general setting for a universal representation of the quantum structure on which quantum information stands. The dynamical evolution process associated with generic quantum information manipulation is based on the (re)coupling theory of SU (2) angular momenta. Such scheme automatically incorporates all the essential features that make quantum information encoding much more efficient than classical: it is fully discrete; it deals with inherently entangled states, naturally endowed with a tensor product structure; it allows for generic encoding patterns. The model proposed can be thought of as the non-Boolean generalization of the quantum circuit model, with unitary gates expressed in terms of 3nj coefficients connecting inequivalent binary coupling schemes of n + 1 angular momentum variables, as well as Wigner rotations in the eigenspace of the total angular momentum. A crucial role is played by elementary j-gates (6j symbols) which satisfy algebraic identities that make the structure of the model similar to “state sum models” employed in discretizing topological quantum field theories and quantum gravity. The spin network simulator can thus be viewed also as a Combinatorial QFT model for computation. The semiclassical limit (large j) is discussed.     

Energy loss measurements and electronic properties of thianthren

Summary The dielectric and electronic properties of thianthren (C₆H₄(S)₂H₄C₆) are determined by means of optical reflectivity, absorption measurements and reflection electron energy loss spectroscopy. The experimental results are interpreted on the basis of a Complete Neglect of Differential Overlap (CNDO) calculation used in three different parametrization schemes. Emphasis is laid on the discussion of the problems which generally affect the analysis of electron energy loss spectra, and a procedure to obtain the complex dielectric function from electron energy loss measurements performed in the reflection mode is suggested. Work partially supported by the MURST through the GNSM.     

Efficient organocatalysis with a calix[4]pyrrole derivative

The 10α,20β-bis(4-nitrophenyl)-calix[4]pyrrole was found to act as an effective organocatalyst for the hetero Diels-Alder reaction of Danishefsky’s diene with aromatic aldehydes. This discovery is the first reported case of a calixpyrrole that exhibits organocatalytic activity.