The influence of the purine 2-amino group on DNA conformation and stability-II: Synthesis and physical characterization of d[CGT(2-NH2)ACG], d[CGU(2-NH2)ACG], and d[CGT(2-NH2)AT(2-NH2)ACG]

Synthesis of an N-protected derivative of 2-amino-2'-deoxyadenosine (dA') from 2'-deoxyguanosine is reported. The syntheses of several oligodeoxynucleotides containing this modified nucleoside are described, together with physical characterization via melting studies and CD conformational analysis. As expected, the 2-amino group is seen to add to the duplex stability. Although the sequence d(TA')₃ was found to undergo a salt-induced conformational transition, mixed sequences such as d(CGTA'CG) did not display this behavior. All guanine residues present in these sequences were O⁶ protected, either with the cyanoethyl group or the 4-nitrophenylethyl group, to eliminate guanine degradation during phosphorylation and condensation reactions. Procedures for the introduction and removal of these O⁶ protecting groups are described.     

Differential binding of Mg2+, Zn2+, and Cd2+ at two sites in a hammerhead ribozyme motif, determined by 15N NMR

A decamer duplex model of Domain II of the hammerhead ribozyme was synthesized with [8-13C-1,7,NH2-15N3]-guanosine at the known metal binding site, G10.1 and, for comparison, [2-13C-1,7,NH2-15N3]-guanosine at G16.2. The 15N NMR chemical shifts of the labeled N7s monitored during addition of Mg2+, Cd2+, and Zn2+ showed the same preference for binding at G10.1 over G16.2 for each metal. These results demonstrate that 15N labeling can be used to evaluate the binding of different metals, including Mg2+, to a given nitrogen, as well as to compare the binding potential of different sites.     

Synthesis of O-6-alkylated deoxyguanosine nucleosides

A general route for synthesis of 6-$\text{O}$-alkyl-2∝deoxyguanosine nucleosides is described. The key step is conversion of the 6-$\text{O}$-TPS derivative $\text{2}$ to the 6-trimethylamino compound $\text{3}$. The trimethylamino group is readily displaced by alcohols in the presence of DBU. Using this route the 6-$\text{O}$-methyl, ethyl and n-butyl 2∝-deoxyguanosine derivatives $\text{5a-c}$ have been prepared in excellent overall yields.     

The effect of alcoholic mobile phase modifiers on retention and stereoselectivity on a commercially available cellulose-based HPLC chiral stationary phase: An unexpected reversal in enantiometric elution order

Summary High pressure liquid chromatographic methods for the determination of diphenylmethane-4,4-diisocyanate (MDI) and toluene diisocyanate (TDI) in chemical products are described. The MDI- and TDI monomers were determined as their urea derivative formed by the reaction with 9-(methyl aminomethyl)-anthracene. Using these methods MDI- and TDI monomer concentrations have been determined in 55 chemical products: sealing waxes, insulating- and adhesive foam, hardener, primer, adhesives and surface coatings. The recovery of both MDI and TDI monomers from various types of chemical product was found to be 92–97%, and the relative standard deviations of the methods was <5% for all types of products.     

Topography of Nucleic Acid Helices in Solutions

A number of reporter molecules of the structure R-(CH₂)_n-N⁺(CH₃)₂(CH₂)_mN⁺(CH₃)₃·2Br^?, where R is a chromophore absorbing in the 300–500 mp region, have been synthesized. The effect of DNA and RNA on the absorption, induced circular dichroism, and proton magnetic resonance spectra is reported. A red shift and a hypochromic effect on the absorption spectra of the bound chromophore is observed. In all cases where R is an “unsymmetrical” 4-nitroaniline chromophore, it is found that DNA and RNA induce an opposite CD in the absorption band of the bound reporter molecules. These results together with PMR studies are interpreted in terms of the structure of the nucleic acid systems in solutions.     

Stigmergy in comparative settlement choice and palaeoenvironment simulation

Decisions on settlement location in the face of climate change and coastal inundation may have resulted in success, survival or even catastrophic failure for early settlers in many parts of the world. In this study, we investigate various questions related to how individuals respond to a palaeoenvironmental simulation, on an interactive tabletop device where participants have the opportunity to build a settlement on a coastal landscape, balancing safety, and access to resources, including sea and terrestrial foodstuffs, while taking into consideration the threat of rising sea levels. The results of the study were analyzed to consider whether decisions on settlement were predicated to be near to locations where previous structures were located, stigmergically, and whether later settler choice would fare better, and score higher, as time progressed. The proximity of settlements was investigated and the reasons for clustering were considered. The interactive simulation was exhibited to thousands of visitors at the 2012 Royal Society Summer Science Exhibition at the “Europe's Lost World” exhibit. 347 participants contributed to the simulation, providing a sufficiently large sample of data for analysis. © 2014 Wiley Periodicals, Inc. Complexity 21: 59–73, 2016     

Hot Branching Dynamics in a Light‐Harvesting Iron Carbene Complex Revealed by Ultrafast X‐ray Emission Spectroscopy

Iron N‐heterocyclic carbene (NHC) complexes have received a great deal of attention recently because of their growing potential as light sensitizers or photocatalysts. We present a sub‐ps X‐ray spectroscopy study of an Fe^IINHC complex that identifies and quantifies the states involved in the deactivation cascade after light absorption. Excited molecules relax back to the ground state along two pathways: After population of a hot ³MLCT state, from the initially excited ¹MLCT state, 30 % of the molecules undergo ultrafast (150 fs) relaxation to the ³MC state, in competition with vibrational relaxation and cooling to the relaxed ³MLCT state. The relaxed ³MLCT state then decays much more slowly (7.6 ps) to the ³MC state. The ³MC state is rapidly (2.2 ps) deactivated to the ground state. The ⁵MC state is not involved in the deactivation pathway. The ultrafast partial deactivation of the ³MLCT state constitutes a loss channel from the point of view of photochemical efficiency and highlights the necessity to screen transition‐metal complexes for similar ultrafast decays to optimize photochemical performance.     

EPR Spectroscopic Studies of Lipoxygenases

Polyunsaturated fatty acids are sources of diverse natural, and chemically designed products. The enzyme lipoxygenase selectively oxidizes fatty acid acyl chains using controlled free radical chemistry; the products are regio‐ and stereo‐chemically unique hydroperoxides. A conserved structural fold of ≈600 amino acids harbors a long and narrow substrate channel and a well‐shielded catalytic iron. Oxygen, a co‐substrate, is blocked from the active site until a hydrogen atom is abstracted from substrate bis‐allylic carbon, in a non‐heme iron redox cycle. EPR spectroscopy of ferric intermediates in lipoxygenase catalysis reveals changes in the metal coordination and leads to a proposal on the nature of the reactive intermediate. Remarkably, free radicals are so well controlled in lipoxygenase chemistry that spin label technology can be applied as well. The current level of understanding of steps in lipoxygenase catalysis, from the EPR perspective, will be reviewed.     

Hydrogen bond dynamics probed with ultrafast infrared heterodyne-detected multidimensional vibrational stimulated echoes

Hydrogen bond dynamics are explicated with exceptional detail using multidimensional infrared vibrational echo correlation spectroscopy with full phase information. Probing the hydroxyl stretch of methanol-OD oligomers in CCl4, the dynamics of the evolving hydrogen bonded network are measured with ultrashort (<50 fs) pulses. The data along with detailed model calculations demonstrate that vibrational relaxation leads to selective hydrogen bond breaking on the red side of the spectrum (strongest hydrogen bonds) and the production of singly hydrogen bonded photoproducts.