On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.     

A Facile Method for the Separation of Methionine Sulfoxide Diastereomers,Structural Assignment,and DFT Analysis

Methionine (Met) oxidation is an important biological redox node, with hundreds if not thousands of protein targets. The process yields methionine oxide (MetO). It renders the sulfur chiral, producing two distinct, diastereomerically related products. Despite the biological significance of Met oxidation, a reliable protocol to separate the resultant MetO diastereomers is currently lacking. This hampers our ability to make peptides and proteins that contain stereochemically defined MetO to then study their structural and functional properties. We have developed a facile method that uses supercritical CO₂ chromatography and allows obtaining both diastereomers in purities exceeding 99 %. ¹H NMR spectra were correlated with X-ray structural information. The stereochemical interconversion barrier at sulfur was calculated as 45.2 kcal mol⁻¹, highlighting the remarkable stereochemical stability of MetO sulfur chirality. Our protocol should open the road to synthesis and study of a wide variety of stereochemically defined MetO-containing proteins and peptides.     

Comparative reactivity of TpRu(L)(NCMe)Ph (L = CO or PMe3): impact of ancillary ligand l on activation of carbon-hydrogen bonds including catalytic hydroarylation and hydrovinylation/oligomerization of ethylene

Complexes of the type TpRu(L)(NCMe)R [L = CO or PMe3; R = Ph or Me; Tp = hydridotris(pyrazolyl)borate] initiate C-H activation of benzene. Kinetic studies, isotopic labeling, and other experimental evidence suggest that the mechanism of benzene C-H activation involves reversible dissociation of acetonitrile, reversible benzene coordination, and rate-determining C-H activation of coordinated benzene. TpRu(PMe3)(NCMe)Ph initiates C-D activation of C6D6 at rates that are approximately 2-3 times more rapid than that for TpRu(CO)(NCMe)Ph (depending on substrate concentration); however, the catalytic hydrophenylation of ethylene using TpRu(PMe3)(NCMe)Ph is substantially less efficient than catalysis with TpRu(CO)(NCMe)Ph. For TpRu(PMe3)(NCMe)Ph, C-H activation of ethylene, to ultimately produce TpRu(PMe3)(eta3-C4H7), is found to kinetically compete with catalytic ethylene hydrophenylation. In THF solutions containing ethylene, TpRu(PMe3)(NCMe)Ph and TpRu(CO)(NCMe)Ph separately convert to TpRu(L)(eta3-C4H7) (L = PMe3 or CO, respectively) via initial Ru-mediated ethylene C-H activation. Heating mesitylene solutions of TpRu(L)(eta3-C4H7) under ethylene pressure results in the catalytic production of butenes (i.e., ethylene hydrovinylation) and hexenes.     

Bioorthogonal Chemical Reporters for Selective In Situ Probing of Mycomembrane Components in Mycobacteria

The global pathogen Mycobacterium tuberculosis and other species in the suborder Corynebacterineae possess a distinctive outer membrane called the mycomembrane (MM). The MM is composed of mycolic acids, which are either covalently linked to an underlying arabinogalactan layer or incorporated into trehalose glycolipids that associate with the MM non‐covalently. These structures are generated through a process called mycolylation, which is central to mycobacterial physiology and pathogenesis and is an important target for tuberculosis drug development. Current approaches to investigating mycolylation rely on arduous analytical methods that occur outside the context of a whole cell. Herein, we describe mycobacteria‐specific chemical reporters that can selectively probe either covalent arabinogalactan mycolates or non‐covalent trehalose mycolates in live mycobacteria. These probes, in conjunction with bioorthogonal chemistry, enable selective in situ detection of the major MM components.     

Enhanced relaxation of nanoparticle-bound supercoiled DNA in X-ray radiation

A therapeutic methodology was developed based on the large X-ray absorption cross-section of gold nanoparticles at high photon energies (>81 keV). Experimental results showed that the amounts of the relaxed circular supercoiled DNA (scDNA) for gold nanoparticle-bound scDNA were more than doubled compared to that for free scDNA under otherwise identical radiation conditions.     

Antioxidant inhibition of porphyrin-induced cellular phototoxicity.

Porphyrins such as protoporphyrin IX (PP IX) and uroporphyrin I (UP I) can be phototoxic to human cells. To study the protective ability of antioxidants (beta-carotene, lycopene, ascorbic acid and alpha-tocopherol), against such porphyrin phototoxicity, membrane destruction experiments (Jurkat cells) and human cell cultures (fibroblasts) were performed. Both beta-carotene and lycopene and also the combination of beta-carotene, ascorbic acid and alpha-tocopherol offered cell protection against PP IX phototoxicity. Investigations of both cell membrane protection and of cell growth showed differences in terms of the protection afforded by the anti-oxidants. Thus, for PP IX, carotenoids alone, and in combination with ascorbic acid and alpha-tocopherol, showed higher protection factors in general than UP I. However, for membrane protection there was significant protection against UP I by the combination of beta-carotene, ascorbic acid and alpha-tocopherol but not by any of these anti-oxidants alone. The membrane protection against PP IX by beta-carotene, and especially lycopene, is significant presumably because of the high lipophilicity of all these molecules. However, the hydrophilic UP I will cause phototoxicity mainly via H(2)O(2), radical or singlet oxygen production in the aqueous phase, and these reactive species may be generated some distance from the cell membrane. This may lead to the little or no protection observed for UP I by the individual antioxidants. Nevertheless, a combination of beta-carotene, ascorbic acid and alpha-tocopherol offers membrane protection against the phototoxicity of both porphyrins. This is believed to occur as a result of synergistic processes. Our results suggest that the treatment of porphyria cutanea tarda and erythropoietic protoporphyria may be improved by the use of a combination of the antioxidants studied.     

Nonlinear Parameter Identification of a Mechanical Interface Based on Primary Wave Scattering

We study stress-wave propagation in an impulsively forced split Hopkinson bar system incorporating a threaded interface. We first consider only primary transmission and reflection and reduce the problem to a first-order, strongly nonlinear ordinary differential equation governing the displacement across the interface, called the primary-pulse model. The interface is modeled as an adjusted-Iwan element, which is characterized by matching experimental and numerical eigenfrequencies as well as primary pulse amplitudes. We find that the adjusted-Iwan element parameters are dependent on preload and impact velocity (input force). A high-order finite element model paired with the identified adjusted-Iwan element is used to simulate multiple transmissions and reflections across the interface. We find that the finite element simulation reproduces the experimental results in both the wavelet and Fourier domains, validating the identification method. Our findings demonstrate that the primary-pulse model can be used for experimental parameter identification of nonlinear interfaces in waveguides.     

N-doping and coalescence of carbon nanotubes: synthesis and electronic properties

Self-assembly pyrolytic routes to large arrays (<2.5 cm²) of aligned CN_x nanotubes (15–80 nm OD and <100 μm in length) are presented. The method involves the thermolysis of ferrocene/melamine mixtures (5:95) at 900–1000 °C in the presence of Ar. Electron energy loss spectroscopy (EELS) reveals that the N content varies from 2–10%, and can be bonded to C in two different fashions (double-bonded and triple-bonded nitrogen). The electronic densities of states (DOS) of these CN_x nanotubes, using scanning tunneling spectroscopy (STS), are presented. The doped nanotubes exhibit strong features in the conduction band close to the Fermi level (0.18 eV). Using tight-binding and ab initio calculations, we confirm that pyridine-like (double-bonded) N is responsible for introducing donor states close to the Fermi Level. These electron-rich structures are the first example of n-type nanotubes. Finally, it will be shown that moderate electron irradiation at 700–800 °C is capable of coalescing single-walled nanotubes (SWNTs). The process has also been studied using tight-binding molecular dynamics (TBMD). Vacancies induce the coalescence via a zipper-like mechanism, which has also been observed experimentally. These vacancies trigger the organization of atoms on the tube lattices within adjacent tubes. These results pave the way to the fabrication of nanotube heterojunctions, robust composites, contacts, nanocircuits and strong 3D composites using N-doped tubes as well as SWNTs. Received: 10 October 2001 / Accepted: 3 December 2001 / Published online: 4 March 2002     

Spectral functions at small energies and the electrical conductivity in hot quenched lattice QCD

In lattice QCD, the maximum entropy method can be used to reconstruct spectral functions from Euclidean correlators obtained in numerical simulations. We show that at finite temperature the most commonly used algorithm, employing Bryan's method, is inherently unstable at small energies and gives a modification that avoids this. We demonstrate this approach using the vector current-current correlator obtained in quenched QCD at finite temperature. Our first results indicate a small electrical conductivity above the deconfinement transition.