The role of organic fluorine in directing alkylation reactions via lithium chelation

The fluorine of a fluoromethyl group displays a measurable chelation effect to lithium during α-methylation of an ester with lithium diisopropylamide (LDA) and methyl iodide. A series of esters is compared with F, H and O, and the resultant diastereoselectivity is consistent with the intermediate capacity of F to chelate lithium relative to H and O. In a second system which involved comparing a tertiary organic fluorine with hydrogen, no such effect is apparent, most probably due to adverse steric effects. The absolute and relative stereochemistry of the predominant diastereoisomers are confirmed by X-ray crystallography of suitable crystalline derivatives in each case. It is concluded that there is a potential role for organic-bound fluorine to become involved in lithium chelation in well-designed enolate alkylation systems.     

The role of zinc finger linkers in zinc finger protein binding to DNA

Journal of Computer-Aided Molecular Design - Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains...     

DNA mediated assembly of single walled carbon nanotubes: role of DNA linkers and annealing

With the high demand for nanoelectronic devices, extensive research has focused on the use of single walled carbon nanotubes (CNTs) due to their high electron carrier mobility, large tensile strength, and single nanometer dimensions. Despite their promise, however, their applicability has been greatly hindered by the inherent difficulties of both separating nanotubes of different chiralities and diameters and positioning them from metallic tubes and positioning them in a precise location on a surface. In recent years, single stranded DNA (ssDNA) has been identified as a potential solution for both of these problems since DNA can be used to both separate the different types of CNTs as well as direct their organization. We demonstrate here the first principles on how to guide CNT assembly directly on surfaces from solution by specific DNA hybridization. It was found that the specific DNA sequence used to disperse the carbon nanotubes greatly influences the adsorption and specificity of nanotube binding to the surface. Furthermore, we demonstrate here that thermal annealing can correct misaligned tubes or incorrect binding. These studies provide an excellent foundation for employing two-dimensional DNA templates for CNT organization for nanoelectronic logic and memory based applications. Furthermore, using a single biomaterial to both sort and place CNTs in minimal steps would greatly help the throughput, manufacturability, and cost of such devices.     

Removable directing groups in organic synthesis and catalysis

Directing groups have been widely used in recent years to achieve control over all aspects of reaction selectivity in a wide range of transformations involving transition-metal catalysis and organometallic reagents. In cases when the existing functional group within a substrate is unsuited to achieve efficient intramolecular delivery of a reagent or catalyst, the specific introduction of an appropriately designed removable reagent-directing group can be a solution to this problem. In this Review we give an overview of the state of the art in this area, including the stoichiometric and catalytic use of directing groups.     

Tunable capsule space: self-assembly of hemispherical cavitands with hydrogen-bonding linkers

Fine and/or drastic tuning of capsule space has been attained by alteration of the hydrogen-bonding linker and/or hemispherical cavitand, respectively. Two molecules of tetracarboxyl-cavitand 1 or tetrakis(4-carboxyphenyl)-cavitand 2 as a hemisphere and four molecules of 2-aminopyrimidine (2-AP) or tetrahydro-2-pyrimidinone (THP) as an equatorial hydrogen-bonding linker self-assemble into a capsule [(1)2.(2-AP)4] (3), [(1)2.(THP)4] (4), [(2)2.(2-AP)4] (5), or [(2)2.(THP)4] (6), respectively, via 16 hydrogen bonds. These capsules provide isolated nanospace and can encapsulate one guest molecule (7-13) in solution. Each capsule has a different cavity size and shows particular guest selectivity on the competitive encapsulation experiments.     

The role of solvent models in stabilizing nonclassical ions

A molecular dynamics simulation is performed for a system of classical and nonclassical 2-norbornyl cations surrounded by a model solvent. Comparison of the energies of stabilization of the two ions due to the model solvent medium indicates that the difference in stabilization energies of the two ions is less than 1 kcal/mol.     

Stabilization of DNA duplexes by covalently-linked peptides

The hybridization properties of various peptide-oligonucleotide hybrids were assessed from UV thermal denaturation experiments. Analysis of these and other published data suggests that peptide chains, both hydrophobic and positively charged, generally have a clear stabilizing effect on short-chain oligonucleotide duplexes.     

Structure factor calculations of various DNA duplexes

Based upon a stereochemical guideline, both right- and left-handed duplexes were generated for A, B, and D forms of DNA using a mononucleotide as the repeat. Structure factor amplitudes were computed following two methods: (i) one employed an infinite helix as the motif and (ii) the other had an exact crystallographic repeat (e.g., 10 b.p. for B-DNA) as the motif. Both the procedures showed that DNA in either handedness for A, B, and D forms of DNA are consistent with the observed fiber data. This observation is attributed to the fact that fibre pattern (resolved only upto 3 Å) only gives the image of the gross structure of the molecule. Thus, when the gross structure is suitably fitted to match the observed pattern, it is immaterial as to what the precise stereochemistry of the repeating unit (fine structure) and handedness of a model are. Sequence specific helical conformations were obtained using dinucleotide as the repeating unit. Helices fell into two classes: (i) right-handed uniform (RU ) and (ii) left-handed zig-zag (LZ ) structures. A few aspects concerning the scattering profile of these helices are discussed.     

Geometric self-sorting in DNA self-assembly

Two types of DNA star motifs (tiles) can recognize and associate with like tiles to form 2D arrays but exclude unlike tiles even though the local interactions between any two tiles are exactly the same.     

MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes

The very specific binding of the HgII ion unexpectedly and significantly stabilizes naturally occurring thymine-thymine base mispairing in DNA duplexes. Following this finding, we prepared DNA duplexes containing metal-mediated base pairs at the desired sites, as well as novel double helical architectures consisting only of thymine-HgII-thymine pairs.     

The role of heterogeneous nucleation in the self-assembly of oligothiophenes

The cooperative self-assembly of oligothiophenes can be characterized by heterogeneous nucleation caused by trace amounts of impurities leading to a manifold of supramolecular arrangements.     

Theoretical study on self-assembly in organic materials

Theoretical work related to the self-assembly of organic materials was dealt with, and the various mechanisms leading to self-assembly, such as transition metal mediated self-assembly, constraint induced self-assembly, covalent bond based self-assembly and van der Waals interaction driven self-assembly, etc., were discussed. The formation of ordered structures could be attributed to the competition between short range attractive forces and long-range repulsion, which was arising from dipole interaction or may result from a different mechanism based on a purely repulsive isotropic short-range pair potential with two characteristic length scales. Such mechanism could be exploited in the study of self-assembly process. First principles SAPT(DFT) interaction energy calculations, combined with the Williams-Stone-Misquitta method, offer the ability to improve the molecular dynamics (MD) accuracy which could in turn be used in the prediction of crystal structures and self-assembly tendency. The combination of experimental and theoretical studies could open new breakthroughs over the design, synthesis, and characterization of self-assembled materials.     

The role of cooling rate in crystallization-driven block copolymer self-assembly

Self-assembly of crystalline-coil block copolymers (BCPs) in selective solvents is often carried out by heating the mixture until the sample appears to dissolve and then allowing the solution to cool back to room temperature. In self-seeding experiments, some crystallites persist during sample annealing and nucleate the growth of core-crystalline micelles upon cooling. There is evidence in the literature that the nature of the self-assembled structures formed is independent of the annealing time at a particular temperature. There are, however, no systematic studies of how the rate of cooling affects self-assembly. We examine three systems based upon poly(ferrocenyldimethylsilane) BCPs that generated uniform micelles under typical conditions where cooling took pace on the 1–2 h time scale. For example, several of the systems generated elongated 1D micelles of uniform length under these slow cooling conditions. When subjected to rapid cooling (on the time scale of a few minutes or faster), branched structures were obtained. Variation of the cooling rate led to a variation in the size and degree of branching of some of the structures examined. These changes can be explained in terms of the high degree of supersaturation that occurs when unimer solutions at high temperature are suddenly cooled. Enhanced nucleation, seed aggregation, and selective growth of the species of lowest solubility contribute to branching. Cooling rate becomes another tool for manipulating crystallization-driven self-assembly and controlling micelle morphologies.

In the self-assembly of crystalline-coil block copolymers in solution, heating followed by different cooling rates can lead to different structures.     

Asymmetric charge partitioning upon dissociation of DNA duplexes

Upon collisional activation, a series of DNA duplexes exhibited a significant degree of asymmetric dissociation with respect to charge partitioning among the single strands. That is, the charge states of the single strand product ions did not equal q/2 for even precursor charge states or (q + 1)/2 and (q − 1)/2 for odd precursor charge states (where q is the charge of the precursor). The factors that affect this asymmetric charge partitioning were assessed. The smaller, lower charged duplexes resulted in more symmetric dissociation compared with larger duplexes in higher charge states, which displayed a high degree of asymmetry upon dissociation. The composition of the duplexes influenced charge partitioning, with those containing a greater number of A/T base pairs showing more symmetric dissociation relative to the more G/C rich duplexes. The use of higher collisional energies resulted in significantly more asymmetric dissociation. Comparisons were made with the dissociation behavior previously studied for protein noncovalent complexes and past studies of the gas-phase conformations and dissociation of DNA complexes.     

The role of a liquid crystal oligomer in stabilizing blue phases

A novel liquid crystal oligomer, 4‐(4‐cyanophenyl)phenyl 4‐octyloxy‐2‐{7‐{4‐[4‐(4‐hexylphenyl)‐2,3‐difluorophenyl]phenyloxy}heptanoyloxy}benzoate, was prepared and found to exhibit a wide temperature range of a nematic phase in spite of being far from a rod‐like structure. Furthermore, the compound induced blue phases in the mixture with a chiral smectic liquid crystal. The molecular shape and its 2,3‐difluorophenyl unit play a role in stabilizing the blue phases.     

Combinatorial self-assembly of DNA nanostructures

Here we report a modular design of self-assembly of DNA nanostructures in a combinatorial approach; a square with approximately 25 nm cavity dimension, a chair with approximately 80 nm in height and a line with approximately 100 nm in length are formed through combinations of four cross-shaped DNA tiles which are kept constant and six variable linker tiles.     

Duplex stability of DNA.DNA and DNA.RNA duplexes containing 3'-S-phosphorothiolate linkages

3'-S-Phosphorothiolate (3'-SP) linkages have been incorporated into the DNA strand of both a DNA.RNA duplex and a DNA.DNA duplex. Thermal melting (T(m)) studies established that this modification significantly stabilises the DNA.RNA duplex with an average increase in T(m) of about 1.4 degrees C per modification. For two or three modifications, the increase in T(m) was larger for an alternating, as compared to the contiguous, arrangement. For more than three modifications their arrangement had no effect on T(m). In contrast to the DNA.RNA duplex, the 3'-S-phosphorothiolate linkage destabilised the DNA.DNA duplex, irrespective of the arrangement of the 3'-SP linkages. The effect of ionic strength on duplex stability was similar for both the phosphorothiolate-substituted and the unmodified RNA.DNA duplexes. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and comparisons are also drawn between the current study and those previously conducted with other modifications that have a similar conformational effect.     

The stability of intramolecular DNA quadruplexes with extended loops forming inter- and intra-loop duplexes

We have examined the formation of intramolecular quadruplex DNA structures in which the loops have been extended so as to generate short DNA duplexes. Fluorescence melting and DNase I cleavage studies show that duplexes can be formed within each loop, but that duplexes between the loops are not stable.