Synthesis and reactivity of unique heterocyclic structures en route to substituted diamines

Rhodium-catalyzed oxidative cyclization of allylic hydroxylamine-derived sulfamate esters furnishes a novel family of bicyclic aziridines that serve as functional precursors to substituted diamines. Investigations with the N4-Troc form of these heterocycles have led to manifold improvements in reaction performance and scope and have revealed unique differences in the stability and reactivity of such compounds dictated by the choice of N4-protecting group.     

Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models

We provide an assessment of a computational strategy for protein structure refinement that combines self‐guided Langevin dynamics with umbrella‐potential biasing replica exchange using the radius of gyration as a coordinate (R_g‐ReX). Eight structurally nonredundant proteins and their decoys were examined by sampling conformational space at room temperature using the CHARMM22/GBMV2 force field to generate the ensemble of structures. Two atomic statistical potentials (RWplus and DFIRE) were analyzed for structure identification and compared to the simulation force‐field potential. The results show that, while the R_g‐ReX simulations were able to sample conformational basins that were more structurally similar to the X‐ray crystallographic structures than the starting first‐order ranked decoys, the potentials failed to detect these basins from refinement. Of the three potential functions, RWplus yielded the highest accuracy for recognition of structures that refined to an average of nearly 20% increase in native contacts relative to the starting decoys. The overall performance of R_g‐ReX is compared to an earlier study of applying temperature‐based replica exchange to refine the same decoy sets and highlights the general challenge of achieving consistently the sampling and detection threshold of 70% fraction of native contacts. © 2013 Wiley Periodicals, Inc.     

Comprehensive Analysis of LC/MS Data Using Pseudocolor Plots

We have developed new applications of the pseudocolor plot for the analysis of LC/MS data. These applications include spectral averaging, analysis of variance, differential comparison of spectra, and qualitative filtering by compound class. These applications have been motivated by the need to better understand LC/MS data generated from analysis of human biofluids. The examples presented use data generated to profile steroid hormones in urine extracts from a Cushing’s disease patient relative to a healthy control, but are general to any discovery-based scanning mass spectrometry technique. In addition to new visualization techniques, we introduce a new metric of variance: the relative maximum difference from the mean. We also introduce the concept of substructure-dependent analysis of steroid hormones using precursor ion scans. These new analytical techniques provide an alternative approach to traditional untargeted metabolomics workflow. We present an approach to discovery using MS that essentially eliminates alignment or preprocessing of spectra. Moreover, we demonstrate the concept that untargeted metabolomics can be achieved using low mass resolution instrumentation.      

A multistate switchable [3]rotacatenane

Rotacatenanes are exotic molecular compounds that can be visualized as a unique combination of a [2]catenane and a [2]rotaxane, thereby combining both the circumrotation of the ring component (rotary motion) and the shuttling of the dumbbell component (translational motion) in one structure. Herein, we describe a strategy for the synthesis of a new switchable [3]rotacatenane and the investigation of its switching properties, which rely on the formation of tetrathiafulvalene (TTF) radical π-dimer interactions-namely, the mixed-valence state (TTF(2) )(+.) and the radical-cation dimer state (TTF(+.) )(2) -under ambient conditions. A template-directed approach, based on donor-acceptor interactions, has been developed, resulting in an improved yield of the key precursor [2]catenane, prior to rotacatenation. The nature of the binding between the [2]catenane and selected π-electron-rich templates has been elucidated by using X-ray crystallography and UV/Vis spectroscopy as well as isothermal titration microcalorimetry. The multistate switching mechanism of the [3]rotacatenane has been demonstrated by cyclic voltammetry and EPR spectroscopy. Most notably, the radical-cation dimer state (TTF(+.) )(2) has been shown to enter into an equilibrium by forming the co-conformation in which the two 1,5-dioxynaphthalene (DNP) units co-occupy the cavity of tetracationic cyclophane, thus enforcing the separation of TTF radical-cation dimer (TTF(+.) )(2) . The population ratio of this equilibrium state was found to be 1:1. We believe that this research demonstrates the power of constructing complex molecular machines using template-directed protocols, enabling us to make the transition from simple molecular switches to their multistate variants for enhancing information storage in molecular electronic devices.     

Supporting evidence for reverse cochlear traveling waves

As a result of the cochlea's nonlinear mechanics, stimulation by two tones results in the generation of distortion products (DPs) at frequencies flanking the primary tones. DPs are measurable in the ear canal as oto-acoustic emissions, and are used to noninvasively explore cochlear mechanics and diagnose hearing loss. Theories of DP emissions generally include both forward and reverse cochlear traveling waves. However, a recent experiment failed to detect the reverse-traveling wave and concluded that the dominant emission path was directly through the fluid as a compression pressure [Ren, 2004, Nat. Neurosc.7, 333-334]. To explore this further, we measured intracochlear DPs simultaneously with emissions over a wide frequency range, both close to and remote from the basilar membrane. Our results support the existence of the reverse-traveling wave: (1) They show spatial variation in DPs that is at odds with a compression pressure. (2) Although they confirm a forward-traveling character of intraocochlear DPs in a broad frequency region of the best frequency, this behavior does not refute the existence of reverse-traveling waves. (3) Finally, the results show that, in cases in which it can be expected, the DP emission is delayed relative to the DP in a way that supports reverse-traveling-wave theory.