Cyclooctyne-based reagents for uncatalyzed click chemistry: A computational survey

With the goal of identifying alkyne-like reagents for use in click chemistry, but without Cu catalysts, we used B3LYP density function theory (DFT) to investigate the trends in activation barriers for the 1,3-dipolar cycloadditions of azides with various cyclooctyne, dibenzocyclooctyne, and azacyclooctyne compounds. Based on these trends, we find monobenzocyclooctyne-based reagents that are predicted to have dramatically improved reactivity over currently employed reagents

Lancifodilactone G : insights about an unusually stable enol

From quantum mechanics calculations we confirm that the naturally occurring enol lancifodilactone G is stable over the keto form (by 2.6 kcal/mol in water), the only known stable aliphatic enol (devoid of conjugated or bulky aromatics and lacking a 1,3-diketone structural motif known to stabilize enols). We determine architectural elements responsible for the enol stabilization and find a mechanism for keto-enol conversion in solution. In addition, we correct previously reported computational results that were performed on the misinterpreted structure demonstrating that the enol form of this natural product is more stable than previously thought

Solution-phase synthesis of pyrrole-imidazole polyamides

Pyrrole−imidazole polyamides are DNA-binding molecules that are programmable for a large repertoire of DNA sequences. Typical syntheses of this class of heterocyclic oligomers rely on solid-phase methods. Solid-phase methodologies offer rapid assembly on a micromole scale sufficient for biophysical characterizations and cell culture studies. In order to produce gram-scale quantities necessary for efficacy studies in animals, polyamides must be readily synthesized in solution. An 8-ring hairpin polyamide 1, which targets the DNA sequence 5′-WGWWCW-3′, was chosen for our synthesis studies as this oligomer exhibits androgen receptor antagonism in cell culture models of prostate cancer. A convergent solution-phase synthesis of 1 from a small set of commercially available building blocks is presented which highlights principles for preparing gram quantities of pyrrole−imidazole oligomers with minimal chromatography

Scholar Week

ONU Scholar Week #2

Oligomerization Route to Py-Im Polyamide Macrocycles

Cyclic eight-ring pyrrole−imidazole polyamides are sequence-specific DNA-binding small molecules that are cell permeable and can regulate endogenous gene expression. Syntheses of cyclic polyamides have been achieved by solid-phase and solution-phase methods. A rapid solution-phase oligomerization approach to eight-ring symmetrical cyclic polyamides yields 12- and 16-membered macrocycles as well. A preference for DNA binding by the 8- and 16-membered oligomers was observed over the 12-ring macrocycle, which we attributed to a conformational constraint not present in the smaller and larger systems

Scholar Week

ONU\u27s Scholar Week flyer #3

Scholar Week

ONU Scholar Week #2

Initiation mechanisms and kinetics of pyrolysis and combustion of JP-10 hydrocarbon jet fuel

In order to investigate the initiation mechanisms and kinetics associated with the pyrolysis of JP-10 (exo-tricyclo[5.2.1.0^2,6]decane), a single-component hydrocarbon jet fuel, we carried out molecular dynamics (MD) simulations employing the ReaxFF reactive force field. We found that the primary decomposition reactions involve either (1) dissociation of ethylene from JP-10, resulting in the formation of a C8 hydrocarbon intermediate, or (2) the production of two C5 hydrocarbons. ReaxFF MD leads to good agreement with experiment for the product distribution as a function of temperature. On the basis of the rate of consumption of JP-10, we calculate an activation energy of 58.4 kcal/mol for the thermal decomposition of this material, which is consistent with a strain-facilitated C−C bond cleavage mechanism in JP-10. This compares well with the experimental value of 62.4 kcal/mol. In addition, we carried out ReaxFF MD studies of the reactive events responsible for oxidation of JP-10. Here we found overall agreement between the thermodynamic energies obtained from ReaxFF and quantum-mechanical calculations, illustrating the usefulness of ReaxFF for studying oxidation of hydrocarbons. The agreement of these results with available experimental observations demonstrates that ReaxFF can provide useful insights into the complicated thermal decomposition and oxidation processes of important hydrocarbon fuels

Cyclic pyrrole-imidazole polyamides targeted to the androgen response element

Hairpin pyrrole−imidazole (Py-Im) polyamides are a class of cell-permeable DNA-binding small molecules that can disrupt transcription factor−DNA binding and regulate endogenous gene expression. The covalent linkage of antiparallel Py-Im ring pairs with an γ-amino acid turn unit affords the classical hairpin Py-Im polyamide structure. Closing the hairpin with a second turn unit yields a cyclic polyamide, a lesser-studied architecture mainly attributable to synthetic inaccessibility. We have applied our methodology for solution-phase polyamide synthesis to cyclic polyamides with an improved high-yield cyclization step. Cyclic 8-ring Py-Im polyamides 1−3 target the DNA sequence 5′-WGWWCW-3′, which corresponds to the androgen response element (ARE) bound by the androgen receptor transcription factor to modulate gene expression. We find that cyclic Py-Im polyamides 1−3 bind DNA with exceptionally high affinities and regulate the expression of AR target genes in cell culture studies, from which we infer that the cycle is cell permeable