Proton as the simplest of all catalysts for [2 + 2] cycloadditions: DFT study of acid-catalyzed imine metathesis

The mechanism of imine metathesis was studied as a prototype reaction for the impact that heteroatom substitution has on thermally forbidden [2 + 2] addition reactions using high-level density functional theory in combination with a continuum solvation model. The intuitively expected high activation barriers were confirmed for N-alkyl- and N-aryl-substituted imine reactants with transition state free energies of 78.8 and 68.5 kcal/mol, respectively, in benzene. The computed reaction energy profiles were analyzed to discover possible strategies for lowering the transition state energy. Protonation of the imine nitrogen was proposed as a possible catalytic route and was explicitly modeled. The computed reaction energy profile shows that protonation of one of the imine reactants has an enormous effect on the overall rate of metathesis and lowers the activation barrier by as much as 37.3 and 30.6 kcal/mol for the N-alkyl and N-aryl reactants, respectively. These results suggest that acid-catalyzed imine metathesis should be amenable at elevated temperatures. Furthermore, the protonation of both reactants of the metathesis reaction is predicted to be not productive owing to electrostatic repulsion of the reactants, thus suggesting that there should be an optimum pH for the catalytic turnover. A detailed analysis of the catalytic mechanism is presented, and the primary driving force for the catalysis is identified. Upon protonation of the imine nitrogen, the key [2 + 2]-addition step becomes asynchronous and one of the two intermolecular N-C bonds is formed before traversing the transition state, resulting in a substantial net decrease of the overall energy requirement. The general applicability of this intuitively understandable mechanism for designing structural features for lowering the energy of transition state structures is explored.     

Computational chemistry at Janssen

Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.     

Four-component gas/water/oil displacements in one dimension: part II,example solutions

In this article analytical solutions are constructed for a system of conservation laws modeling compositional flow of four components in three phases using the method of characteristics (MOC). Every component partitions between all phases present, and the equilibrium volume ratios of the components in each phase are fixed. Riemann problems modeling the injection of carbon dioxide and water in a depleted oil reservoir are studied, and the sensitivity of the solutions to changes in boundary conditions is analyzed. Finally the MOC solutions are compared to simulated displacements.     

Effect of low intensity laser interaction with human skin fibroblast cells using fiber-optic nano-probes

Over the past forty years, many efforts have been devoted to study low power laser light interactions with biological systems. Some of the investigations were performed in-vitro, on bulk cell populations. Our present work was undertaken to apply specially engineered fiber-optic based nano-probes for the precise delivery of laser light on to a single cell and to observe production of low power laser light induced reactive oxygen species (ROS). A normal human skin fibroblast (NHF) cell line was utilized in this investigation and the cells were irradiated under two different schemes of exposure: (1) an entire NHF cell population within a Petri dish using a fan beam methodology, and (2) through the precise delivery of laser energy on to a single NHF cell using fiber-optic nano-probe. Photobiostimulative studies were conducted through variation of laser intensity, exposure time, and the energy dose of exposure. Laser irradiation induced enhancement in the rate of cell proliferation was observed to be dependent on laser exposure parameters and the method of laser delivery. The total energy dose (fluence) had a greater influence on the enhancement in the rate of cellular proliferation than compared to laser intensity. The enhancement in the growth rate was observed to have a finite life-time of several days after the initial laser exposure. Fluorescent life-time imaging of ROS was performed during the nano-based single cell exposure method. The kinetics of ROS generation was found to depend strongly on the laser fluence and not on the laser intensity.     

Evolution of a protecting-group-free total synthesis: studies en route to the neuroactive marine macrolide (-)-palmyrolide A

A full account of our synthetic work toward the first total synthesis of the neuroactive marine macrolide (-)-palmyrolide A is described. Our first-generation approach aimed to unlock the unknown C(5)-C(7) stereochemical relationship via the synthesis of four diastereomers of palmyrolide A aldehyde, a known degradation product. When these efforts provided inconclusive results, recourse to synthesizing all possible stereocombinations of the 15-membered macrolide was undertaken. These studies were critical in confirming the absolute stereochemistry, yielding the first total synthesis of (+)-ent-palmyrolide A. Subsequent to this work, the first protecting-group-free total synthesis of natural (-)-palmyrolide A is also reported.     

Branchpoint expansion in a fully complementary three-way DNA junction

Branched nucleic acid molecules serve as key intermediates in DNA replication, recombination, and repair; architectural elements in RNA; and building blocks and functional components for nanoscience applications. Using a combination of high-resolution single-molecule FRET, time-resolved spectroscopy, and molecular modeling, we have probed the local and global structure of a DNA three-way junction (3WJ) in solution. We found that it adopts a Y-shaped, pyramidal structure, in which the bases adjacent to the branchpoint are unpaired, despite the full Watson-Crick complementarity of the molecule. The unpairing allows a nanoscale cavity to form at the junction center. Our structure accounts for earlier observations made of the structure, flexibility, and reactivity of 3WJs. We anticipate that these results will guide the development of new DNA-based supramolecular receptors and nanosystems.     

Nonviral gene delivery using poly‐D/L aspartate‐diethylenetriamine cationic polymers and polyethylene glycol: A two‐step approach

Cationic polymers have received much attention as promising nonviral vectors for gene transfer. However, development of polymers with low cell toxicities and high transfection efficiencies continue to be a significant problem and a major hurdle to their success. Poly‐D /L aspartate‐diethylenetriamine poly(D /L Asp‐DET) polymers were synthesized and evaluated as nonviral gene delivery agents. Poly(D /L Asp‐DET) polymers display endosome buffering capacity. The polymers condense plasmid DNA above N:P ratios of 1 and form polyplex particles of ～50–100 nm, with zeta potentials between neutral and +40 mV. Transmission electron microscopy shows the polyplexes to be uniform in size and shape. Polyplexes maintain the structural integrity of DNA following incubation in nucleases and also show high transfection efficiencies with minimal toxicity in both HCT‐116 and PC‐3 cell culture. However, it is found that these poly(D /L Asp‐DET)/DNA polyplexes immediately aggregate in salt and serum conditions, making them unsuitable for use in vivo. Therefore, the polyplexes were further modified by covalent addition of polyethylene glycol (PEG). Introduction of this second step produces PEG‐polyplexes of uniform size (below 100 nm), with neutral zeta potentials that are also stable in both salt and serum conditions. These results suggest poly(D /L Asp‐DET) cationic polymers as potentially safe and efficient nonviral gene delivery agents. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012