Template‐Directed Copying of RNA by Non‐enzymatic Ligation

The non‐enzymatic replication of the primordial genetic material is thought to have enabled the evolution of early forms of RNA‐based life. However, the replication of oligonucleotides long enough to encode catalytic functions is problematic due to the low efficiency of template copying with mononucleotides. We show that template‐directed ligation can assemble long RNAs from shorter oligonucleotides, which would be easier to replicate. The rate of ligation can be greatly enhanced by employing a 3′‐amino group at the 3′‐end of each oligonucleotide, in combination with an N‐alkyl imidazole organocatalyst. These modifications enable the copying of RNA templates by the multistep ligation of tetranucleotide building blocks, as well as the assembly of long oligonucleotides using short splint oligonucleotides. We also demonstrate the formation of long oligonucleotides inside model prebiotic vesicles, which suggests a potential route to the assembly of artificial cells capable of evolution.     

Modeling red coral (Corallium rubrum) and African snail (Helixia aspersa) shell pigments: Raman spectroscopy versus DFT studies

Pigments from red coral (Corallium rubrum) and African snail (Helixia aspersa) shell were studied non‐invasively using Raman spectroscopy with 1064‐nm laser beam. The two observed bands because of organic pigments confined in biomineralized CaCO₃ matrix at about 1500 and 1100 cm⁻¹ were assigned to ν(CC) and ν(C―C), respectively. Both signals originate from polyene(s) of largely unknown structure, containing several conjugated CC bonds. The small peak at 1016 cm⁻¹ in the Raman spectrum of coral pigment was assigned to in‐plane ―CH₃ rocking or structural deformation of polyene chain because of spatial confinement in the mineral matrix. The organic pigments in red coral and snail shell were present in inorganic matrix containing aragonite (shell) and calcite (coral). In addition, using Raman spectroscopy, it was observed that aragonite was replaced by calcite as result of healing damaged parts of snail shell. This is an important finding which indicates a great potential of nondestructive Raman spectroscopy instead of X‐ray technique, as a diagnostic tool in environmental studies. To support analysis of the observed Raman spectra detailed calculations using density functional theory (DFT with B3LYP and BLYP density functionals) on structure and vibrations of model all‐trans polyenes were undertaken. DFT calculated CC and C―C stretching frequencies for all‐trans polyenes containing from 2 to 14 CC units were compared with the observed ν(CC) and ν(C―C) band positions of the studied coral and shell. Individual correction factors were used to better match theoretical wavenumbers with observed band positions in red coral and African snail. It was concluded that all‐trans polyene pigments of red coral and dark parts of African snail shell contain 11–12 and 14 CC double bond units, respectively. However, Raman spectroscopy cannot produce any clear information on the presence and nature of the end‐chain substituents in the studied pigments. Copyright © 2016 John Wiley & Sons, Ltd.     

Cascade-fluorescence spectroscopy on impact-excited He-atoms using level-crossing techniques

He atoms have been excited by 35 keV-Ne⁺ ions, and magnetic depolarization signals of the induced fluorescent light at 667.8nm (1s3d ¹ D-1s 2p ¹ P) have been investigated. By applying suitable electric fields in addition to the variable magnetic field, the complicated superposition structure of the depolarization signal resulting from cascade processes could be analyzed. Beside direct excitation of 1s 3d ¹ D (53%), cascade excitation through 1s4f (26%), 1s 5g (12%), and 1s5f-levels (6%) contributes significantly to the magnetic depolarization signal. From the signal widths the radiative lifetimes of the 1s4f-levels and 1s5g-levels have been deduced: τ(1s4f)=(74±3)ns, τ(1s5g)=(230±20)ns.     

Spectroscopic,structural and theoretical studies of 2‐methyl‐4‐nitroaniline (MNA) crystal. Electronic transitions in IR

Polarized FT‐IR, Raman, neutron scattering (IINS), and UV‐Vis‐NIR spectra of 2‐methyl‐4‐nitroaniline (MNA) crystal plates, powder, and solutions were measured in the 10–50 000 cm⁻¹ range. The FT‐IR spectrum of deuterated MNA (DMNA) in KBr pellet, the Raman spectrum of the DMNA powder as well as the EPR spectrum of the MNA powder were also recorded. Complete assignments of bands to normal vibrations have been proposed. Density functional theory (DFT) calculations of wavenumbers and potential energy distribution (PED) have been performed to strengthen the assignments. The analysis of vibrational and electronic spectra has revealed vibronic couplings in MNA molecules in solutions and in crystals. In the polarized FT‐IR spectra of the crystal five unusually large bands are observed in MIR and NIR regions. Their origin is discussed in terms of N H···O, C H···O, C H···H N hydrogen bonds, intermolecular charge transfers, electrostatic interactions, and ion radicals formation in the crystal. The role of a methyl group introduction to 4‐nitroaniline is analyzed. The crystal structure of MNA at the room temperature was re‐investigated. Copyright © 2008 John Wiley & Sons, Ltd.     

Efficient Synthesis of Diaryl Ketones by Nickel‐Catalyzed Negishi Cross‐Coupling of Amides by Carbon–Nitrogen Bond Cleavage at Room Temperature Accelerated by a Solvent Effect

The first Negishi cross‐coupling of amides for the synthesis of versatile diaryl ketones by selective C?N bond activation under exceedingly mild conditions is reported. The cross‐coupling was accomplished with bench‐stable, inexpensive precatalyst [Ni(PPh₃)₂Cl₂] that shows high functional‐group tolerance and enables the synthesis of highly functionalized diaryl ketone motifs. The coupling occurred with excellent chemoselectivity favoring the ketone (cf. biaryl) products. Notably, this process represents the mildest conditions for amide N?C bond activation accomplished to date (room temperature, <10 min). Considering the versatile role of polyfunctional biaryl ketone linchpins in modern organic synthesis, availability, and excellent functional‐group tolerance of organozinc reagents, this strategy provides a new platform for amide N?C bond/organozinc cross‐coupling under mild conditions.     

Synthesis of Biaryls through Nickel‐Catalyzed Suzuki–Miyaura Coupling of Amides by Carbon–Nitrogen Bond Cleavage

The first Ni‐catalyzed Suzuki–Miyaura coupling of amides for the synthesis of widely occurring biaryl compounds through N?C amide bond activation is reported. The reaction tolerates a wide range of electron‐withdrawing, electron‐neutral, and electron‐donating substituents on both coupling partners. The reaction constitutes the first example of the Ni‐catalyzed generation of aryl electrophiles from bench‐stable amides with potential applications for a broad range of organometallic reactions.     

C?X⋅⋅⋅O Halogen Bonding: Interactions of Trifluoromethyl Halides with Dimethyl Ether

The formation of weakly bound molecular complexes between dimethyl ether (DME) and the trifluoromethyl halides CF₃Cl, CF₃Br and CF₃I dissolved in liquid argon and in liquid krypton is investigated, using Raman and FTIR spectroscopy. For all halides evidence is found for the formation of C? X???O halogen‐bonded 1:1 complexes. At higher concentrations of CF₃Br, a weak absorption due to a 1:2 complex is also observed. Using spectra recorded at temperatures between 87 and 125 K, the complexation enthalpies for the complexes are determined to be ?6.8(3) kJ mol^?1 (DME?CF₃Cl), ?10.2(1) kJ mol^?1 (DME?CF₃Br), ?15.5(1) kJ mol^?1 (DME?CF₃I), and ?17.8(5) kJ mol^?1 [DME(?CF₃Br)₂]. Structural and spectral information on the complexes is obtained from ab initio calculations at the MP2/ 6‐311++G(d,p) and MP2/6‐311++G(d,p)+LanL2DZ* levels. By applying Monte Carlo free energy perturbation calculations to account for the solvent influences, and statistical thermodynamics to estimate the zero‐point vibrational and thermal influences, the ab initio complexation energies are converted into complexation enthalpies for the solutions in liquid argon. The resulting values are compared with the experimental data deduced from the cryosolutions.     

In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors

There is a great demand for the discovery of new therapeutic molecules that combine the high specificity and affinity of biologic drugs with the bioavailability and lower cost of small molecules. Small, natural-product-like peptides hold great promise in bridging this gap; however, access to libraries of these compounds has been a limitation. Since ribosomal peptides may be subjected to in vitro selection techniques, the generation of extremely large libraries (>10(13)) of highly modified macrocyclic peptides may provide a powerful alternative for the generation and selection of new useful bioactive molecules. Moreover, the incorporation of many non-proteinogenic amino acids into ribosomal peptides in conjunction with macrocyclization should enhance the drug-like features of these libraries. Here we show that mRNA-display, a technique that allows the in vitro selection of peptides, can be applied to the evolution of macrocyclic peptides that contain a majority of unnatural amino acids. We describe the isolation and characterization of two such unnatural cyclic peptides that bind the protease thrombin with low nanomolar affinity, and we show that the unnatural residues in these peptides are essential for the observed high-affinity binding. We demonstrate that the selected peptides are tight-binding inhibitors of thrombin, with K(i)(app) values in the low nanomolar range. The ability to evolve highly modified macrocyclic peptides in the laboratory is the first crucial step toward the facile generation of useful molecular reagents and therapeutic lead molecules that combine the advantageous features of biologics with those of small-molecule drugs.     

Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for both monomers and templates for efficient copying. However, RNA monomers are predominantly in the C2'-endo conformation when free in solution, except for cytidine, which is approximately equally distributed between the C2'-endo and C3'-endo conformations. We hypothesized that ribonucleotides undergo a switch in sugar pucker upon binding to an A-type template and that this conformational switch allows or enhances subsequent polymerization. We used transferred nuclear Overhauser effect spectroscopy (TrNOESY), which can be used for specific detection of the bound conformation of small-molecule ligands with relatively weak affinity to receptors, to study the interactions between nucleotide 5'-phosphorimidazolides and single-stranded oligonucleotide templates. We found that the sugar pucker of activated ribonucleotides switches from C2'-endo in the free state to C3'-endo upon binding to an RNA template. This switch occurs only on RNA and not on DNA templates. Furthermore, activated 2'-deoxyribonucleotides maintain a C2'-endo sugar pucker in both the free and template-bound states. Our results provide a structural explanation for the observations that activated ribonucleotides are superior to activated deoxyribonucleotides and that RNA templates are superior to DNA templates in template-directed nonenzymatic primer-extension reactions.