On the Necessity of Nucleobase Protection for 2-Thiouracil for Fmoc-Based Pseudo-Complementary Peptide Nucleic Acid Oligomer Synthesis.

A selection of benzyl-based protecting groups for thiouracil (SU) for the synthesis of pseudo-complementary peptide nucleic acid (PNA) has been evaluated. The 4-methoxybenzyl-protecting group that has found use for SU during Boc-based oligomerization is also suitable for Fmoc-based oligomerization. Furthermore, it is demonstrated that SU protection is unnecessary for the successful synthesis of thiouracil-containing PNA. The new 2-thiothymine (ST) PNA monomer has also been prepared and incorporated into an oligomer and its binding to complementary PNA evaluated.

Readily functionalized AAA-DDD triply hydrogen-bonded motifs.

Herein we present a new, readily functionalized AAA-DDD hydrogen bond array. A novel AAA monomeric unit (3a-b) was obtained from a two-step synthetic procedure starting with 2-aminonicotinaldehyde via microwave radiation (overall yield of 52-66%). 1H NMR and fluorescence spectroscopy confirmed the complexation event with a calculated association constant of 1.57 × 107 M-1. Likewise, the usefulness of this triple hydrogen bond motif in supramolecular polymerization was demonstrated through viscosity measurements in a crosslinked supramolecular alternating copolymer.

Supramolecular Polymers Based on Non-Coplanar AAA-DDD Hydrogen-Bonded Complexes.

Non-coplanar triple-hydrogen-bond arrays are connected as telechelic groups to alkyl chains and their properties as AA/BB type supramolecular polymers are examined. Viscosity studies at three temperatures are used to study the ring-chain equilibrium and determine the critical concentrations where polymer chains are formed. It is observed that neither the temperature range studied nor the alkyl chain length of one component significantly affect the polymerization properties in this system.

Addressing the Nature of Phosphinidene Sulfides via the Synthesis of P-S Heterocycles.

The phosphorus-sulfur heterocycles 1,2-thiaphosphetenes and phosphirene sulfides have been prepared, and represent the first structurally characterized derivatives for either class of compound. These strained P-S ring systems are formed by the reaction of a phosphinidene sulfide and alkyne. Using an internal alkyne, only the 3-membered PV , phosphirene sulfide was produced, whereas a terminal alkyne yielded a mixture of phosphirene sulfide and 1,2-thiaphosphetene (PIII ). Detailed computational analysis revealed that for numerous derivatives of alkynes, the corresponding 4-membered rings are always more stable than the 3-membered isomers. The electronic nature of "free" phosphinidene sulfides (R-P=S) is discussed based on computational results.

Unusual C7- versus Normal 5'-O-Dimethoxytritylation of 6-Arylpyrrolocytidine Analogs.

Fluorescent deoxynucleosides possessing the modified bases 6-(2-benzo[b]furyl)- and 6-(2-furyl)pyrrolocytosine (BFpC and FpC) have been synthesized along with the quencher nucleosides possessing 6-{4-[(4-dimethylamino)azo]phenyl}pyrrolocytosine (DABCYLpC) and 6-(p-nitrophenyl)pyrrolocytosine (p-NO2-PhpC) nucleobase analogs. Standard treatment of BFpC, FpC, DABCYLpC, and p-NO2-PhpC with dimethoxytrityl chloride (DMT-Cl) led to the unusual substitution on the C7 of the pyrrolocytosine skeleton. The desired 5'-O-DMT-protected nucleoside analogs were synthesized from suitably protected 5'-O-DMT cytidines. Subsequent phosphitylation smoothly afforded BFpC-, FpC-, DABCYLpC-, and p-NO2-PhpC-derived monomers suitable for standard oligonucleotide synthesis.

A rare case of dual emission in a neutral heteroleptic iridium(III) complex.

Herein we describe the synthesis and characterization of a neutral heteroleptic iridium complex bearing an unusual 2-pyridyl-6-methylthiazine dioxide ligand (pythdo). X-ray crystallographic analysis reveals that in the complex, the pythdo ligand is twisted and puckered, resulting in very low photoluminescent quantum efficiency. The emission profile is structured. Excited state lifetime measurements along with oxygen quenching studies point to a rare case of dual emission from different excited states whereby the high energy bands possess significant ligand-centered ((3)LC) character while the lower energy bands are predominantly characterized as a mixture of charge transfer ((3)CT) states. A detailed computational analysis corroborates the unusual photophysical behavior.

Importance of secondary interactions in twisted doubly hydrogen bonded complexes.

Three model hydrogen bond arrays that form complexes with large twist angles between their heterocyclic rings were synthesized differing only in the sequence of their hydrogen bond donors and acceptors. The complementary and self-complementary association of the arrays to form complexes was studied computationally and in solution. The analysis reveals the significant impact secondary interactions have on complex stability in such an arrangement despite the very different topology in comparison to typical planar arrays.

Synthesis and self-association of double-helical AADD arrays.

The design and syntheses of four self-complementary oligomers that contain an underlying AADD hydrogen bond sequence are presented, and their self-association was examined in the solution and solid state. The molecular recognition between the two strands is highly sensitive to substitutions of their component heterocycles. Substitution with electron-donating and -withdrawing groups and the influence of preorganization has a large effect on the overall stabilities of the complexes studied. In particular, a wide range (>10(5) M(-1)) of stabilities with respect to substitutions at various positions in the AADD oligomers was demonstrated. In the most extreme case, the dimerization constant measured (K(dimer) ≥4.5×10(7) M(-1)) is comparable to the most stable homodimers of neutral AADD arrays reported to date.

Substituent effects in double-helical hydrogen-bonded AAA-DDD complexes.

Two series of DDD and AAA hydrogen-bond arrays were synthesized that form triply-hydrogen-bonded double-helical complexes when combined in CDCl(3) solution. Derivatization of the DDD arrays with electron-withdrawing groups increases the complex association constants by up to a factor of 30 in those arrays examined. Derivatization of the AAA arrays with electron donating substituents reveals a similar magnitude effect on the complex stabilities. The effect of substitution on both types of arrays are modeled quite satisfactorily (R(2) > 0.96 in all cases) as free energy relationships with respect to the sums of their Hammett substituent constants. In all, the complex stabilities can be manipulated over more than three orders of magnitude (>20 kJ mol(-1)) using this type of modification.

2,6-Diamino-pyridinium tetra-phenyl-borate-1,2-bis-(5,7-dimethyl-1,8-naphthyridin-2-yl)diazene (1/1).

In the title compound, C(5)H(8)N(3) (+)·C(24)H(20)B(-)·C(20)H(18)N(6), the 1,2-bis-(5,7-dimethyl-1,8-naphthyridin-2-yl)diazene mol-ecule is essentially planar (r.m.s. deviation = 0.0045 Å) and aligned in nearly coplanar manner with the 2,6-diamino-pyridinium ion, making a dihedral angle of 5.19 (5)°. The diamino-pyridine mol-ecule is protonated on the central pyridine N atom and the B atom bears the counter-charge. The amine groups of the diamino pyridinium cation form intra-molecular N-H⋯N hydrogen bonds, resulting in linear and bent inter-actions with the naphthyridine ring system.

Minimal complementary hydrogen-bonded double helices.

Molecular strands incorporating three hydrogen bond donor (D) or acceptor (A) heterocycles form highly stable double helical complexes through a complementary AAA-DDD array structure.

Anion receptors containing thiazine-1,1-dioxide heterocycles as hydrogen bond donors.

The synthesis, X-ray crystal structures and anion recognition properties of two receptors containing thiazine-1,1-dioxide heterocycles as hydrogen bond donating subunits are reported. The newly synthesized receptors display much different anion selectivities in acetone-d6 than N,N'-diphenyl-1,3-disulfonamidobenzene that was used as a comparison. The selectivity exhibited by one of the new receptors for chloride anions can be attributed to greater steric demand in the cleft formed, in part, by its terminal phenyl rings; an effect that is absent in the comparison receptor.

Stability of [2]pseudorotaxanes templated through second-sphere coordination.

A series of nine trans-dichlorobis(pyridine)palladium(II) complexes were prepared (2a-i), containing different 4-substituted pyridine co-ligands. The association constants between these Pd-complexes and 1 were measured, and their values plotted against corresponding sigma(p) degrees values. Measurement of the hydrogen bond acceptor capability of the chloride co-ligands revealed the presence of a linear free energy relationship between the electronic induction of a given 4-substituted pyridine co-ligand and the subsequent complexation strength in [2]pseudorotaxane formation. These trends also extended to trans-dibromobis(pyridine)palladium(II) (3a-e) and trans- dichlorobis(pyridine)platinum(II) complexes (5a-e) when plotted against sigma(p) degrees values. In addition, solid-state structures of three [2]pseudorotaxanes (1.2h, 1.2i, and 1.5e) were determined by single crystal X-ray diffraction further confirming the viability of this template in forming interpenetrated molecular architectures.

[2]Pseudorotaxane and [2]rotaxane molecular shuttles: self-assembly through second-sphere coordination of thiocyanate ligands.

A Pd(Py)(2)(SCN)(2) complex is shown to form a [2]pseudorotaxane complex with a macrocyclic tetralactam, which binds in the solid state through an unexpected complexation geometry. The intermolecular complexation is further applied to template the formation of a [2]rotaxane. The interlocked product acts as a degenerate molecular shuttle in solution, which is consistent with the co-conformation observed in the solid state.

A self-associating ADADA hydrogen-bonded double helix.

We report the design, synthesis, and characterization of an oligomer which incorporates a non-coplanar ADADA (hydrogen bond donor/acceptor) array within its structure. The molecule associates through self-complementary hydrogen bonding to form a dimeric double-helical complex.

Synthesis of a [2]rotaxane through first- and second-sphere coordination.

In an effort to expand the application of a new template from interpenetrated to interlocked molecular species, we report the synthesis of a new [2]rotaxane by means of both first- and second-sphere coordination of a palladium(II) dichloride subunit.

Anion-templated assembly of [2]rotaxanes.

Anion templation is used to develop a general method for rotaxane synthesis. The anion-templated synthesis of three new [2]rotaxanes containing positively charged pyridinium axles and neutral isophthalamide macrocyclic components is described. The incorporation of electron withdrawing substituents, such as the nitro group, into the 5-position of an isophthalamide bis-vinyl acyclic precursor results in a significant improvement in [2]rotaxane assembly yields. Rotaxane anion binding strengths are also enhanced whilst the rotaxane's unique interlocked binding domain ensures selectivity for chloride--the templating anion--is maintained.

A versatile template for the formation of [2]pseudorotaxanes. 1,2-Bis(pyridinium)ethane axles and 24-crown-8 ether wheels.

Linear 1,2-bis(pyridinium)ethane 'axles' and macrocyclic 24-membered crown ether 'wheels' (, and ) combine to form [2]pseudorotaxanes. These interpenetrated adducts are held together by N+...O ion-dipole interactions, a series of C-H...O hydrogen bonds and pi-stacking between electron-poor pyridinium rings of the axle and electron-rich catechol rings of the wheel. 1H NMR spectroscopy was used to identify the structural details of the interaction and to determine the thermodynamics of the binding process in solution. Analysis of nine of these adducts by single crystal X-ray crystallography allowed a detailed study of the non-covalent interactions in the solid state. A wide variety of structural changes could be made to the system. The versatility and potential of the template for the construction of permanently interlocked structures such as rotaxanes and catenanes is discussed.