Using circularly polarized luminescence to probe exciton coherence in disordered helical aggregates

Circularly polarized emission from helical MOPV4 aggregates is studied theoretically based on a Hamiltonian including excitonic coupling, exciton phonon coupling, and site disorder. The latter is modeled via a Gaussian distribution of site energies. The frequency dependence of the circularly polarized luminescence dissymmetry g(lum)(omega) contains structural information about the low-energy-neutral (excitonic) polaron from which emission originates. Near the 0-0 emission frequency, g(lum)(omega) provides a measure of the exciton coherence length, while at lower energies, in the vicinity of the sideband frequencies, g(lum)(omega) probes the polaron radius. The present work focuses on how the 0-0 dissymmetry, g(lum)(0-0), relates to the emitting exciton's coherence function, from which the coherence length is deduced. In the strong disorder limit where the exciton is localized on a single chromophore, g(lum)(0-0) is zero. As disorder is reduced and the coherence function expands, /g(lum)(0-0)/ increases more rapidly than the sideband dissymmetries, resulting in a pronounced surge in g(lum)(omega) near the 0-0 transition frequency. The resulting spectral shape of g(lum)(omega) is in excellent agreement with recent experiments on MOPV4 aggregates. In the limit of very weak disorder, corresponding to the motional narrowing regime, the coherence function extends over the entire helix. In this region, g(lum)(0-0) undergoes a surprising sign reversal but only for helices which are between n+12 and n+1 complete turns (n = 0,1,...). This unusual sign change is due to the dependence of the rotational line strength on long-range exciton coherences which are also responsible for a heightened sensitivity of g(lum)(omega) to long-range excitonic coupling.     

Highly selective tritium-from-deuterium isotope separation by pulsed NH3 laser multiple-photon dissociation of chloroform

Infrared multiple-photon dissociation of CTCl₃ was investigated using a pulsed CO₂ laser-pumped NH₃ laser at 12.08 μm. No evidence of any CDCl₃ depletion or decomposition product was observed in photolyzed CTCl₃/CDCl₃ mixtures. A lower limit of the single-step T/D enrichment factor, β, was found to be ≈ 165, based on the sensitivity in measuring CDCl₃ depletion. The low-fluene CTCl₃/CDCl₃ optical selectivity in absorptions is > 9000 at the 835 cm^?1 CTCl₃ ν₄ peak.     

Lindemann measures for the solid-liquid phase transition

A set of Lindemann measures, based on positional deviations or return distances, defined with respect to mechanically stable inherent structure configurations, is applied to understand the solid-liquid phase transition in a Lennard-Jones-type system. The key quantity is shown to be the single-particle return distance-squared distribution. The first moment of this distribution is related to the Lindemann parameter which is widely used to predict the melting temperature of a variety of solids. The correlation of the single-particle return distance and local bond orientational order parameter in the liquid phase provides insights into mechanisms for melting. These generalized Lindemann measures, especially the lower order moments of the single-particle return distance distribution, show clear signatures of the transition of the liquid from the stable to the metastable, supercooled regime and serve as landscape-based indicators of the thermodynamic freezing transition for the Lennard-Jones-type system investigated.     

Electron transfer dissociation in the hexapole collision cell of a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer

Electron transfer dissociation (ETD) of proteins is demonstrated in a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer (Qh-FTICRMS). Analyte ions are selected in the mass analyzing quadrupole, accumulated in the hexapole linear ion trap, reacted with fluoranthene reagent anions, and then analyzed via an FTICR mass analyzer. The hexapole trap allows for a broad fragment ion mass range and a high ion storage capacity. Using a 3 T FTICRMS, resolutions of 60 000 were achieved with mass accuracies averaging below 1.4 ppm. The high resolution, high mass accuracy ETD spectra provided by FTICR obviates the need for proton transfer reaction (PTR) charge state reduction of ETD product ions when analyzing proteins or large peptides. This is demonstrated with the ETD of ubiquitin and apomyoglobin yielding sequence coverages of 37 and 20%, respectively. We believe this represents the first reported successful combination of ETD and a FTICRMS.     

One-step synthesis of oxazoline and dihydrooxazine libraries

The reactions of 1,2- and 1,3-hydroxyalkyl azides and aldehydes in the presence of Lewis acid result in the one-step construction of oxazolines and dihydrooxazines, respectively. The reaction was adapted to parallel synthesis using a polymer-bound phosphine to scavenge excess hydroxyalkyl azide. Thus, a 60-member library of various disubstituted oxazolines and di- and trisubstituted dihydrooxazines was generated.     

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.     

Under-three minute PCR: probing the limits of fast amplification

Nucleic acid amplification is enormously useful to the biotechnology and clinical diagnostic communities; however, to date point-of-use PCR has been hindered by thermal cycling architectures and protocols that do not allow for near-instantaneous results. In this work we demonstrate PCR amplification of synthetic SARS respiratory pathogenic targets and bacterial genomic DNA in less than three minutes in a hardware configuration utilizing convenient sample loading and disposal. Instead of sample miniaturization techniques, near-instantaneous heating and cooling of 5 μL reaction volumes is enabled by convective heat transfer of a thermal fluid through porous media combined with an integrated electrical heater. This method of rapid heat transfer has enabled 30 cycles of PCR amplification to be completed in as little as two minutes and eighteen seconds. Surprisingly, multiple enzymes have been shown to work at these breakthrough speeds on our system. A tool for measuring enzyme kinetics now exists and can allow polymerase optimization through directed evolution studies. Pairing this instrument technology with modified polymerases should result in a new paradigm for high-throughput, ultra-fast PCR and will hopefully improve our ability to quickly respond to the next viral pandemic.     

N-heterocyclic carbene-catalyzed cross-coupling of aromatic aldehydes with activated alkyl halides

N-Heterocyclic carbene-catalyzed umpolung of aldehydes followed by their interception with diarylbromomethanes has been reported. This conceptually novel transition-metal-free cross-coupling of aldehydes with alkyl halides works well at low catalyst loadings and under mild reaction conditions leading to the formation of diaryl acetophenone derivatives in good yields. In addition, α-halo ketones and esters can also be used as aldehyde reaction partners.     

Importance of the diamine reactant in the production of polyphosphonamides by the interfacial technique

The stirred interfacial polycondensation of phenylphosphonic dichloride and 1,6-hexanediamine has been studied as a function of several reaction variables. The reaction is rapid, being completed in less than 1 min. When organic solvent is varied and reactant molar ratio is varied with an excess of the acid chloride, yield is constant. When reactant molar ratio is varied polymer yield increases with increase in amine concentration. When reactant concentration is increased yield increases. With the addition of a soluble salt in the aqueous phase yield is increased. The above indicates that the diffusion of the amine to the reaction zone is of primary importance in determining polymerization rate and that the diffusion of the acid chloride is relatively unimportant. Polymer yield was found to be dependent on the pH of the amine in the aqueous phase. The observed trend is related to the apparent solubility of the amine in the aqueous phase such that the greater the apparent solubility of the amine, the less the polymer yield. Polymer molecular weight is found to be independent of reaction variables tested. Polymer was also formed from the condensation of phenylphosphonic dichloride with p-phenylenediamine, H₂N-D-NH₂ (where D is a 36-carbon hydrocarbon chain), 1,3-di-4-piperidylpropane, and 4-aminomethylpiperidine; phenyl phosphorodichloridate with 1,6-hexanediamine; chloromethyl phosphonic dichloride with 1,6-hexanediamine.     

Mössbauer and molecular orbital study of the myoglobin-CO complex

Experimental Mössbauer spectra of the Fe⁵⁷-enriched CO complex of sperm whale myoglobin (MbCO) at T= 4.2 K with and without applied magnetic field (H⊥γ) were measured to derive the sign of the electric field gradient (EFG), the quadrupole splitting ΔE _Q, and the isomer shift δ of the heme iron. We find a positive EFG, δE _Q = 0.363 mm/sec, and δ + 0.266 mm/sec. Molecular orbital calculations were carried out to obtain theoretical estimates of EFG and ΔE _Q for several steric arrangements of the CO ligand relative to the heme group. Our results are most consistent with the conclusion that the iron is situated in the heme plane, and that a bent geometry with a Fe-C-O angle of about 135 ° is more favorable than a more symmetric structure with a linear Fe-C-O geometry.