Ion‐Mobility Mass Spectrometry for the Rapid Determination of the Topology of Interlocked and Knotted Molecules

A rapid screening method based on traveling‐wave ion‐mobility spectrometry (TWIMS) combined with tandem mass spectrometry provides insight into the topology of interlocked and knotted molecules, even when they exist in complex mixtures, such as interconverting dynamic combinatorial libraries. A TWIMS characterization of structure‐indicative fragments generated by collision‐induced dissociation (CID) together with a floppiness parameter defined based on parent‐ and fragment‐ion arrival times provide a straightforward topology identification. To demonstrate its broad applicability, this approach is applied here to six Hopf and two Solomon links, a trefoil knot, and a [3]catenate.     

Reducing the computational cost of NMR crystallography of organic powders at natural isotopic abundance with the help of 13C-13C dipolar couplings

Structure determination of functional organic compounds remains a formidable challenge when the sample exists as a powder. Nuclear magnetic resonance crystallography approaches based on the comparison of experimental and Density Functional Theory (DFT)-computed ¹H chemical shifts have already demonstrated great potential for structure determination of organic powders, but limitations still persist. In this study, we discuss the possibility of using ¹³C-¹³C dipolar couplings quantified on powdered theophylline at natural isotopic abundance with the help of dynamic nuclear polarization, to realize a DFT-free, rapid screening of a pool of structures predicted by ab initio random structure search. We show that although ¹³C-¹³C dipolar couplings can identify structures possessing long range structural motifs and unit cell parameters close to those of the true structure, it must be complemented with other data to recover information about the presence and the chemical nature of the supramolecular interactions.     

The Crystal Structure of Ba3Cu2Al2F16: a Relative of Ba4Cu2Al3F21

Ba₃Cu₂Al₂F₁₆ is monoclinic: a = 7.334(1)Å, b = 5.320(2)Å, c = 16.022(1)Å, β = 96.34(1)°, Z = 2. Its crystal structure was solved in the space group P2₁ (No. 4) from synchrotron X‐ray single crystal data using 2685 unique reflections (2639 with F_o/σ(F_o) > 4). The final R factor is 0.044. The structure consists of a succession along the c‐axis of the cell of three layers of two different kinds of sheets developing in the (a, b) plane. The first one, formulated [(AlF₅)₂]_∞^4— and hereafter named A, is built up from infinite cis‐chains of aluminium‐fluorine octahedra [AlF₆], linked by two vertices and distanced by a. The second one, formulated [Cu₂AlF₁₁]_∞^4— and named B, is bidimensional. It is constituted of distorted copper‐fluorine octahedra [CuF₆], linked by edges, which form infinite chains interconnected by three vertices of isolated [AlF₆] octahedra. The stacking sequence of the sheets is (A, B, B)_∞. The barium ions, 12‐coordinated, are inserted between the sheets. The crystal structure of Ba₃Cu₂Al₂F₁₆ is closely related to that of Ba₄Cu₂Al₃F₂₁. Only the proportion and the stacking sequence of the two kinds of sheets in the c‐direction differ, according to two different compositions and two different symmetries.     

A new Na/Mg inverse crown ether

A `missing' member of the inverse crown ether family, namely μ₄‐oxo‐tetrakis(μ‐2,2,6,6‐tetra­methyl­piperidinido)­di­mag­nes­ium­(II)­disodium(I), [Na₂Mg₂O(C₉H₁₈N)₄], has been synthesized by blocking the alternative aromatic metallation route via the use of sterically hindered 1,3,5‐mesityl­ene as a solvent. [Na₂Mg₂O(NR₂)₄] (NR₂ is 2,2,6,6‐tetra­methyl­piperidinide) is shown to form a cationic planar eight‐membered ring with alternating metal and N atoms, which captures at its core an oxide guest that lies on an inversion centre [principal dimensions: Na—O = 2.2405 (11) Å, Na—N = 2.445 (3) and 2.572 (3) Å, Mg—O = 1.8673 (9) Å, and Mg—N = 2.032 (2) and 2.063 (2) Å].     

Analysis of serotonin release from single neuron soma using capillary electrophoresis and laser-induced fluorescence with a pulsed deep-UV NeCu laser

The use of capillary electrophoresis (CE) with laser-induced fluorescence excited by ultraviolet (UV) lasers in the range 200–300 nm has been restricted by the available wavelengths and expense of UV lasers. The integration of a NeCu deep UV laser operating at 248.6 nm with a single channel CE system with post-column sheath flow detection allows detection limits for serotonin and tryptophan of 3.9×10^-8 M and 4.5×10^-8 M respectively. Single cell analysis of serotonergic metacerebral cells from the sea slug Aplysia californica yields a value of 800±85 fmol of serotonin in each cell soma. For the first time, serotonin is directly detected in electrically stimulated release from single metacerebral cell soma, with approximately 4% of the serotonin contained in the soma released from a semi-intact preparation with a 2 min electrical stimulation.     

Structural studies of ammonia and metallic lithium-ammonia solutions

The technique of hydrogen/deuterium isotopic substitution has been used to extract detailed information concerning the solvent structure in pure ammonia and metallic lithium-ammonia solutions. In pure ammonia we find evidence for approximately 2.0 hydrogen bonds around each central nitrogen atom, with an average N-H distance of 2.4 A. On addition of alkali metal, we observe directly significant disruption of this hydrogen bonding. At 8 mol % metal there remains only around 0.7 hydrogen bond per nitrogen atom. This value decreases to 0.0 for the saturated solution of 21 mol % metal, as all ammonia molecules have then become incorporated into the tetrahedral first solvation spheres of the lithium cations. In conjunction with a classical three-dimensional computer modeling technique, we are now able to identify a well-defined second cationic solvation shell. In this secondary shell the nitrogen atoms tend to reside above the faces and edges of the primary tetrahedral shell. Furthermore, the computer-generated models reveal that on addition of alkali metal the solvent molecules form voids of approximate radius 2.5-3.0 A. Our data therefore provide new insight into the structure of the polaronic cavities and tunnels, which have been theoretically predicted for lithium-ammonia solutions.     

Increased Affinity of 2′‐O‐(2‐Methoxyethyl)‐Modified Oligonucleotides to RNA through Conjugation of Spermine at Cytidines

Structural modification at the 2′‐O‐position of riboses in oligonucleotide therapeutics is of critical importance for their use as drugs. To date, the methoxyethyl (MOE) substituent is the most important and features in dozens of antisense oligonucleotides that have been tested in clinical trials. Yet, the search for new improved modifications continues in a quest for increased oligonucleotide potency, improved transport in vivo and favorable metabolism. Recently, we described how the conjugation of spermine groups to pyrimidines in oligonucleotides vastly increases their affinity for complementary RNAs through accelerated binding kinetics. Here we describe how spermines can be linked to the exocyclic amino groups of cytidines in MOE‐oligonucleotides employing a straightforward ‘convertible nucleoside approach’ during solid phase synthesis. Singly‐ or doubly‐modified oligonucleotides show greatly enhanced affinity for complementary RNA, with potential for a new generation of MOE‐based oligonucleotide drugs.     

Mirror-Image Oligonucleotides: History and Emerging Applications

As chiral molecules, naturally occurring d -oligonucleotides have enantiomers, l -DNA and l -RNA, which are comprised of l -(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d -counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l -oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d -oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d - and l -oligonucleotides to form contiguous Watson–Crick base pairs with each other has ultimately led to the perception that l -oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l -oligonucleotides, while overcoming (and even exploiting) their inability to Watson–Crick base pair with the natural polymer. Herein, a brief history of l -oligonucleotide research is presented and emerging l -oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.