Alkyne Difunctionalization by Dual Gold/Photoredox Catalysis

Highly selective tandem nucleophilic addition/cross‐coupling reactions of alkynes have been developed using visible‐light‐promoted dual gold/photoredox catalysis. The simultaneous oxidation of Au^I and coordination of the coupling partner by photo‐generated aryl radicals, and the use of catalytically inactive gold precatalysts allows for high levels of selectivity for the cross‐coupled products without competing hydrofunctionalization or homocoupling. As demonstrated in representative arylative Meyer–Schuster and hydration reactions, this work expands the scope of dual gold/photoredox catalysis to the largest class of substrates for gold catalysts and benefits from the mild and environmentally attractive nature of visible‐light activation.     

New ruthenium(II) complexes with enantiomerically pure bis- and tris(pinene)-fused tridentate ligands. Synthesis, characterization and stereoisomeric analysis

A new set of Ru-Cl complexes containing either the pinene[5,6]bpea ligand (L1) or the C3 symmetric pinene[4,5]tpmOMe (L2) tridentate ligand in combination with the bidentate (B) 2,2'-bipyridine (bpy) or 1,2-diphenylphosphinoethane (dppe) with general formula [RuCl(L1 or L2)(B)](+) have been prepared and thoroughly characterized. In the solid state, X-ray diffraction analysis techniques have been used. In solution, cyclic voltammetry (CV) and 1D and 2D NMR spectroscopy have been employed. DFT calculations have been also performed on these complexes and their achiral analogues previously reported in our group, to interpret and complement experimental results. Whereas isomerically pure complexes ([Ru(II)Cl(L2)(bpy)](BF4), 5 and [Ru(II)Cl(L2)(dppe)](BF4), 6) are obtained when starting from the highly symmetric [Ru(III)Cl3(L2)], 2, isomeric mixtures of cis, fac-[Ru(II)Cl(L1)(bpy)](BF4) (3b/3b'), trans,fac- (3a) and up/down,mer- (3c, 3d) isomers are formed when bpy is added to the less symmetric [Ru(III)Cl3(L1)], 1, in contrast to the case of the bulky dppe ligand that, upon coordination to 1, leads to the trans,fac-[Ru(II)Cl(L1)(dppe)](BF4) (4a) complex as a sole isomer due to steric factors.     

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch

The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.     

Exchange frequency in replica exchange molecular dynamics

The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.     

Gas-phase fragmentation of long-lived cysteine radical cations formed via no loss from protonated S-nitrosocysteine

In this work, we describe two different methods for generating protonated S-nitrosocysteine in the gas phase. The first method involves a gas-phase reaction of protonated cysteine with t-butylnitrite, while the second method uses a solution-based transnitrosylation reaction of cysteine with S-nitrosoglutathione followed by transfer of the resulting S-nitrosocysteine into the gas phase by electrospray ionization mass spectrometry (ESI-MS). Independent of the way it was formed, protonated S-nitrosocysteine readily fragments via bond homolysis to form a long-lived radical cation of cysteine (Cys^•+), which fragments under collision-induced dissociation (CID) conditions via losses in the following relative abundance order: •COOH ≫ CH₂S > •CH₂SH-H₂S. Deuterium labeling experiments were performed to study the mechanisms leading to these pathways. DFT calculations were also used to probe aspects of the fragmentation of protonated S-nitrosocysteine and the radical cation of cysteine. NO loss is found to be the lowest energy channel for the former ion, while the initially formed distonic Cys^•+ with a sulfur radical site undergoes proton and/or H atom transfer reactions that precede the losses of CH₂S, •COOH, •CH₂SH, and H₂S.     

New method to measure packing densities of self-assembled thiolipid monolayers

For a monolayer of 2,3-di-phytanyl-sn-glycerol-1-tetraethylene glycol-D,L-a-lipoic acid ester lipid (DPTL) self-assembled (SAM) at a gold electrode surface we propose a new method to determine the charge number per adsorbed molecule and the packing density (area per molecule) in the monolayer. The method relies on chronocoulometry to measure the charge density at the SAM covered gold electrode surface. Two series of measurements have to be performed. In the first series, charge densities are measured for a monolayer transferred from the air-solution to the metal-solution interface using the Langmuir-Blodgett (LB) technique. This series of measurements allows one to determine charge numbers per adsorbed DPTL molecule. The second series is performed using a gold electrode covered with a self-assembled monolayer. The charge densities obtained in this series are then used to calculate the packing density with the help of charge numbers per adsorbed DPTL determined in the first series. The area per adsorbed molecule determined by the new method was compared to the area per molecule determined by the popular reductive desorption method. The molecular area determined with the new method is about 20% larger than the area calculated from the van der Waals model, which is a physically reasonable result. In contrast, the popular reductive desorption method gives an area per molecule 20% lower than the minimum estimated based on a van der Waals model. This is a physically unreasonable result. It is also shown that the charge numbers per adsorbed molecule depend on the electrode potential and may assume values smaller than the number of electrons participating in the reductive desorption step. An explanation of the origin of the "partial charge numbers" is provided. We recommend the new method be used in future studies of thiol adsorption at metal surfaces.     

Theoretical study of the isomerization mechanism of azobenzene and disubstituted azobenzene derivatives

A series of azobenzenes was studied using ab initio methods to determine the substituent effects on the isomerization pathways. Energy barriers were determined from three-dimensional potential energy surfaces of the ground and electronically excited states. In the ground state (S(0)), the inversion pathway was found to be preferred. Our results show that electron donating substituents increase the isomerization barrier along the inversion pathway, whereas electron withdrawing substituents decrease it. The inversion pathway of the first excited state (S(1)) showed trans --> cis barriers with no curve crossing between S(0) and S(1). In contrast, a conical intersection was found between the ground and first excited states along the rotation pathway for each of the azobenzenes studied. No barriers were found in this pathway, and we therefore postulate that after n --> pi (S(1) <-- S(0)) excitation, the rotation mechanism dominates. Upon pi --> pi (S(2) <-- S(0)) excitation, there may be sufficient energy to open an additional pathway (concerted-inversion) as proposed by Diau. Our potential energy surface explains the experimentally observed difference in trans-to-cis quantum yields between S(1) and S(2) excitations. The concerted inversion channel is not available to the remaining azobenzenes, and so they must employ the rotation pathway for both n --> pi and pi --> pi excitations.