Asymmetric internal

The 2.8 A resolution crystal structure of an aptamer that binds to the chromo-phore malachite green shows the binding site as an asymmetric internal loop flanked by a pair of helices. There are several tiers of stacked nucleotides arranged in pairs, triples and a novel quadruple that encapsulates the ligand. 

In order to know whether the Pd ions or complexes are anchored to the zeolite framework or not, the IR framework vibrations of Pd-H-ZSM-5(0.49) were investigated (Figure 5). After activation under O2, a weak band at 930 cm" forms. Upon NO adsorption, the 930 cm band disappear while a new band appears at 980 cm". These bands are attributed to asymmetric internal stretching vibrations of T-O-T bonds (T = Si or Al) perturbed by Pd ions. The higher the perturbation, the lower the frequency. Therefore, the 930 cm band could be related to anchored Pd(II) ions or complexes formed upon decomposition of exchanged complexes, and the 980 cm band could be due to Pd(I) nitrosyl entities formed upon NO contact. Similar observations were found on Cu-ZSM-5 catalysts (34). 

Durig JR, Wang A, Beshir W, Little TS. Barrier to asymmetric internal-rotation, conformational stability, vibrational-spectra and assignments, and ab initio calculations of normal-butane-DO, normal-butane-D5 and normal-butane-DlO. J Raman Spectrosc 1991 22 683-704. 

RNA double helices are frequently interrupted by short sequences of nucleotides on both strands which cannot form standard Watson-Crick base pairs. These regions which connect two Watson-Crick helices are historically referred to as internal loops in analogy to hairpin loops which coimect the ends of helices. A symmetric internal loop has an equal number of nucleotides on opposing strands, while an asymmetric internal loop has a different number of nucleotides on the two strands. Figure 1 schematically defines internal loops. 

Figure 7. Calculation of interhelical angle and displacement in helices bounding an internal loop. An asymmetric internal loop from the P4-P6 domain of a group I intron is shovm as an example, a) The helical axes for the Watson-Crick regions are indicated by straight lines. The angle is calculated as the dot product, b) The molecule is rotated by 90° to show the translational displacement between helix axes. The displacement is the minimum displacement between the skew lines.

The NMR constructs for domain IV RNA are depicted in Figure 1. Recent low resolution models (12, 13) suggest that domain IV folds back on domain II making tertiary interactions, which would require domain IV to make a U-turn. The flexibility for this turn could be associated with the asymmetrical internal loop. Besides determining the structure of the fairly large 43 nucleotide RNA, it seemed prudent to also study the structure of domain IV by isolating the two internal loops and thus their contribution to a potential bend. 

Figure 1. Schematic drawings of typical RNA secondary structure elements. The arrows indicate the 5 to 3 direction. Bars denote Watson-Crick base pairs and dots phosphodiesters linking helices. (1) An RNA helix (2) An RNA hairpin with four unpaired residues (3) An asymmetric internal bidge between two helices (4) Two stacked helices (5) A three-way junction with one single-stranded region (6) A three-way junction with two single-stranded regions (7) A four-way junction (8) A four-way junction with two single-stranded regions.

Co2(CO)6 i-PhC2CC(0)Me)], IC02(CO)4 ii-PhC5CC(O)Me)3l and. in addition, the symmetrical trimer [PhCCC(0)Me]3 which represents the first example of the stepwise synthesis of a symmetrical benzene firom an asymmetrical internal alkyne. 

A rhodium-catalyzed one-pot synthesis of substituted pyridine derivatives from a,(3-unsaturated ketoximes and alkynes was developed in 2008 by Cheng and coworkers [99], Good yields of the desired pyri-dines can be obtained (Scheme 3.48). The reaction was proposed to proceed via rhodium-catalyzed chelation-assisted activation of the (3—C—H bond of a,(3-unsaturated ketoximes and subsequent reaction with alkynes followed by reductive elimination, intramolecular electro-cyclization, and aromatization to give highly substituted pyridine derivatives finally [100]. Later on, in their further studies, substituted isoquinolines and tetrahydroquinoline derivatives can be prepared by this catalyst system as well [101]. Their reaction mechanism was supported by isolation of the ort/jo-alkenylation products. Here, only asymmetric internal alkynes can be applied. 

In Ni(i) dinuclear complexes, the subtle factors that favor the asymmetric internally disproportionated Ni(0)-Ni(ii) structure over the symmetric Ni(i)-Ni(i) A-frame structure have not been identified completely. Oxidative addition of phenylisocyanide dichloride (PhNGGl2) to Ni(cod)2 in the presence of dppm gave the complex NizifJ z-GNPh)Gl2(dppm)2 which was found by X-ray diffraction to have an A-frame type structure with a long Ni-Ni... 

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