Multiscale coarse-graining of ionic liquids

A recently developed multiscale coarse-graining (MS-CG) approach for obtaining coarse-grained force fields from fully atomistic molecular dynamics simulation is applied to the challenging case of the EMIM+NO3- ionic liquid. The force-matching in the MS-CG methodology is accomplished with an explicit separation of bonded and nonbonded forces. While the nonbonded forces are adopted from this force-matching approach, the bonded forces are obtained from fitting the statistical configurational data from the atomistic simulations. The many-body electronic polarizability is also successfully broken into effective pair interactions. With a virial constraint fixing the system pressure, the MS-CG models rebuild satisfactory structural and thermodynamic properties for different temperatures. The MS-CG model developed from a modest atomistic simulation is therefore suitable for simulating much larger systems, because the coarse-grained models show significant time integration efficiency. This approach is expected to be general for coarse-graining other ionic liquids, as well as many other liquid-state systems. The limitations of the present coarse-graining procedure are also discussed.     

TOF-SIMS evidence of intercalated molecular gases and diffusion-limited reaction kinetics in an alpha particle-irradiated PTFE matrix

The chemical evolution of poly(tetrafluoroethylene) (PTFE) that is brought about by increasing levels of irradiation with alpha particles is accompanied by the emergence and proliferation of functionalized moieties. Families of reaction products specifically identified in the alpha-irradiated polymer matrix include hydride-, hydroxide-, and oxide-functionalized fluorocarbons. The data also indicate the emergence of hydrogen peroxide (H2O2) and hydrazine (N2H4), but no distinct evidence suggesting the formation of perfluorinated amines, amides, or cyanogens is found. In this article we substantiate the speciation of emergent species and reveal evidence of intercalated molecular gases with which alpha particle-generated radicals may react to form the observed products. Furthermore, we present evidence to suggest that the kinetics of alpha particle-induced reaction is limited by the diffusion of radicals within the polymer matrix. That is to say, chemical additives in the polymer matrix are shown to be scavengers of H*, O*, and F* radicals and limit the rates of reaction that produce functionalized fluorocarbon moieties. Above a threshold dose of alpha particles, the concentration of radicals exceeds that of the scavenger species, and free radical diffusion commences as evidenced by a sudden increase in the yield of reaction products. Samples of PTFE were irradiated to alpha doses in the range of 10(7) to 5 x 10(10) rad with 5.5 MeV 4He2+ ions from a tandem accelerator. Residual gas analysis (RGA) was utilized to monitor the liberation of molecular gases from PTFE during alpha particle irradiation of samples in vacuum. Static time-of-flight SIMS (TOF-SIMS), equipped with a 20 keV C60+ source, was employed to probe chemical changes as a function of alpha particle irradiation. Chemical images and high-resolution mass spectra were collected in both the positive and negative polarities.     

Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion

The solvation and transport properties of the sulfonate-hydronium ion pair have been studied in hydrated Nafion through molecular dynamics simulation. Explicit proton and charge delocalization of the excess proton transport, via the Grotthuss hopping mechanism, were treated using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. The nature of the sulfonate-hydronium ion pair was characterized through analysis of free-energy profiles. It was found that, in general, the excess proton is solvated between two water molecules of a Zundel moiety while in the contact ion pair position, but then it transitions to an Eigen-like configuration in the solvent-separated pair position. Furthermore, the positive charge associated with the excess proton passes between the contact and solvent-separated ion pair positions through the Grotthuss mechanism rather than simple vehicular diffusion. The total proton diffusion was decomposed into vehicular and Grotthuss components and were found to be of the same relative magnitude, but with a strong negative correlation resulting in a smaller overall diffusion. Correlated motions between the ion pair were examined through the distinct portion of the van Hove correlation function, and a characteristic time scale of approximately 425 ps was observed. Additionally, the association of the hydrated proton with the hydrophobic polymer backbone suggests its amphiphile-like behavior (see Acc. Chem. Res. 2006, 39, 143; Phys. Rev. 1954, 95, 249; J. Chem. Phys. 2005, 123, 084309).     

Upper domination and upper irredundance perfect graphs

Let β(G), Γ(G) and IR(G) be the independence number, the upper domination number and the upper irredundance number, respectively. A graph G is called Γ-perfect if β(H) = Γ(H), for every induced subgraph H of G. A graph G is called IR-perfect if Γ(H) =IR(H), for every induced subgraph H of G. In this paper, we present a characterization of Γ-perfect graphs in terms of a family of forbidden induced subgraphs, and show that the class of Γ-perfect graphs is a subclass of IR-perfect graphs and that the class of absorbantly perfect graphs is a subclass of Γ-perfect graphs. These results imply a number of known theorems on Γ-perfect graphs and IR-perfect graphs. Moreover, we prove a sufficient condition for a graph to be Γ-perfect and IR-perfect which improves a known analogous result.     

Self‐Immolative Poly(4,5‐dichlorophthalaldehyde) and its Applications in Multi‐Stimuli‐Responsive Macroscopic Plastics

End‐capped poly(4,5‐dichlorophthalaldehyde) (PCl₂PA), which is a new self‐immolative CD_r polymer with the unique capability of depolymerizing continuously and completely in the solid state when an end cap is cleaved from the polymer by reaction with a specific molecular signal, is described. End‐capped poly(4,5‐dichlorophthalaldehyde) is sufficiently stable to enable patterning of three‐dimensional macroscopic polymeric materials by selective laser sintering. These unique materials are capable of 1) autonomously amplifying macroscopic changes in the material in response to specific molecular inputs, and 2) altering their responses depending on the identity of the applied signal. Thus, not only does end‐capped PCl₂PA provide new and unique capabilities compared to the small subset of existing CD_r polymers, but it also provides access to a new class of stimuli‐responsive materials.     

A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.     

Cyclic maps in rational homotopy theory

The notion of a cyclic map g:AX is a natural generalization of a Gottlieb element in _n(X). We investigate cyclic maps from a rational homotopy theory point of view. We show a number of results for rationalized cyclic maps which generalize well-known results on the rationalized Gottlieb groups.Mathematics Subject Classification (2000): 55P62, 55Q05     

A concise synthesis of (S)-N-ethoxycarbonyl-alpha-methylvaline

A practical and efficient protocol for the three-step synthesis of (S)-N-ethoxycarbonyl-alpha-methylvaline 3 is described which utilizes readily available commercial starting materials. The key transformations involve resolution-crystallization of tartrate salt 6 followed by a one-pot procedure for the preparation of 3 which is isolated as the dicyclohexylamine salt in 45% overall yield and in 91-95% ee.     

Spectroscopic characterization of hydroxylated nanoballs in methanol

In this report, the photophysical properties of self-assembled [Cu(2)(5-OH-bdc)(2)L(2)](12) [where (5-OH-bdc)(2-) = 5-hydroxybenzene-1,3-dicarboxylate and L is a dimethyl sulfoxide, methanol, or water ligand] hydroxylated nanoballs (OH-nanoball) were examined in methanol using optical absorption and steady-state and time-resolved fluorescence methods. The optical spectrum of the OH-nanoball is dominated by ligand absorbance at 305 nm and a weaker Cu(2+)-to-ligand charge-transfer transition at approximately 695 nm, which are distinct from the absorption of either the free ligand (approximately 312 nm) or Cu(2+)(NO(3))(2) (>750 nm) in methanol. The corresponding emission spectrum of the OH-nanoball originates from the emission of the ligand and is centered at approximately 360 nm with a shoulder at approximately 390 nm. The emission from the OH-nanoball is significantly quenched relative to the free ligand [Phi(5-OH-H(2)bdc) = 0.014 and Phi(OH-nanoball) = (5.6 +/- 0.5) x 10-5]. The addition of bases such as imidazole results in an increase in the emission intensity of the OH-nanoball solution, indicating dissociation of the [Cu(2)(5-OH-bdc)(2)L(2)](12) units. Although the mechanism of (5-OH-bdc)(2-) quenching within the OH-nanoball is not clear, it is likely due to interactions between the ligand pi system and the Cu d orbitals. Fluorescence polarization studies further suggest that the OH-nanoball retains a spherical shape in solution. This is evident by the fact that the fluorescence anisotropy of the nanoball is nearly identical with that of the free ligand, suggesting rapid energy transfer (homogeneous fluorescence resonance energy transfer) between ligands within the OH-nanoball.