Computational design of a self-assembling β-peptide oligomer

The first computationally designed self-assembling oligomer consisting of exclusively β-amino acids (βAAs) is presented. The packing of a β-3(14) helix into coiled-coils of varying stoichiometries as a function of amino acid sequence is examined. β-Peptides with hVal repeating every third residue in the sequence appeared to have a strong propensity to pack into hexameric bundles. The designed sequence was synthesized and characterized with CD spectroscopy, NMR, and analytical ultracentrifugation, suggesting that the peptide adopts a well-folded hexameric structure.     

Photoelectron imaging of tetrahydrofuran cluster anions (THF)(n) (-) (1≤n≤100)

Anionic tetrahydrofuran clusters (THF)(n) (-) (1≤n≤100) are studied with photoelectron imaging as gas-phase precursors for electrons solvated in THF. Photoelectron spectra of clusters up to n=5 show two peaks, one of which is attributed to a solvated open chain radical anion and the other to the closed THF ring. At n=6, the spectra change shape abruptly, which become more characteristic of (THF)(n) (-) clusters containing solvated electrons. From n=6-100, the vertical detachment energies (VDEs) of these solvated electron clusters increase from 1.96 to 2.71 eV, scaling linearly with n(-1/3). For fully deuterated (THF-d8)(n) (-) clusters, the apparent transition to a solvated electron cluster is delayed to n=11. Extrapolation of the VDEs to infinite cluster size yields a value of 3.10 eV for the bulk photoelectric threshold. The relatively large VDEs at onset and small stabilization with increasing cluster size compared to other solvated electron clusters may reflect the tendency of the bulk solvent to form preexisting voids that can readily solvate a free electron.     

A Study of Ion-Neutral Collision Cross Section Values for Low Charge States of Peptides, Proteins, and Peptide/Protein Complexes

Here, we report ion-helium collision cross sections (CCS) for a number of peptide, small protein, and peptide/protein ionic complexes. The CCS values reported here are compared to previously reported results.[1, 2] We also compare values for low charge state species, i.e., [M + H](+) and [M + 2H](2+), formed by MALDI with values for high charge state species formed by ESI, and the measured CCSs are compared with predicted CCS for solid-state and solution phase structures and calculated structures obtained by using a protein-protein structure algorithm generator, based on a combined Biomolecular complex Generation with Global Evaluation and Ranking[3] and Multi Dimensional Scaling[4].     

Dual functional polyelectrolyte multilayer coatings for implants: permanent microbicidal base with controlled release of therapeutic agents

Here we present a new bifunctional layer-by-layer (LbL) construct made by combining a permanent microbicidal polyelectrolyte multilayered (PEM) base film with a hydrolytically degradable PEM top film that offers controlled and localized delivery of therapeutics. Two degradable film architectures are presented: (1) bolus release of an antibiotic (gentamicin) to eradicate initial infection at the implant site, or (2) sustained delivery of an anti-inflammatory drug (diclofenac) to cope with inflammation at the site of implantation due to tissue injury. Each degradable film was built on top of a permanent base film that imparts the implantable device surface with microbicidal functionality that prevents the formation of biofilms. Controlled-delivery of gentamicin was demonstrated over hours and that of diclofenac over days. Both drugs retained their efficacy upon release. The permanent microbicidal base film was biocompatible with A549 epithelial cancer cells and MC3T3-E1 osteoprogenitor cells, while also preventing bacteria attachment from turbid media for the entire duration of the two weeks studied. The microbicidal base film retains its functionality after the biodegradable films have completely degraded. The versatility of these PEM films and their ability to prevent biofilm formation make them attractive as coatings for implantable devices.     

Enantioselective epoxide polymerization using a bimetallic cobalt catalyst

A highly active enantiopure bimetallic cobalt complex was explored for the enantioselective polymerization of a variety of monosubstituted epoxides. The polymerizations were optimized for high rates and stereoselectivity, with s-factors (k(fast)/k(slow)) for most epoxides exceeding 50 and some exceeding 300, well above the threshold for preparative utility of enantiopure epoxides and isotactic polyethers. Values for mm triads of the resulting polymers are typically greater than 95%, with some even surpassing 98%. In addition, the use of a racemic catalyst allowed the preparation of isotactic polyethers in quantitative yields. The thermal properties of these isotactic polyethers are presented, with many polymers exhibiting high T(m) values. This is the first report of the rapid synthesis of a broad range of highly isotactic polyethers via the enantioselective polymerization of racemic epoxides.     

Ultrafast spectroscopy and computational study of the photochemistry of diphenylphosphoryl azide: direct spectroscopic observation of a singlet phosphorylnitrene

The photochemistry of diphenylphosphoryl azide was studied by femtosecond transient absorption spectroscopy, by chemical analysis of light-induced reaction products, and by RI-CC2/TZVP and TD-B3LYP/TZVP computational methods. Theoretical methods predicted two possible mechanisms for singlet diphenylphosphorylnitrene formation from the photoexcited phosphoryl azide. (i) Energy transfer from the (π,π*) singlet excited state, localized on a phenyl ring, to the azide moiety, thereby leading to the formation of the singlet excited azide, which subsequently loses molecular nitrogen to form the singlet diphenylphosphorylnitrene. (ii) Direct irradiation of the azide moiety to form an excited singlet state of the azide, which in turn loses molecular nitrogen to form the singlet diphenylphosphorylnitrene. Two transient species were observed upon ultrafast photolysis (260 nm) of diphenylphosphoryl azide. The first transient absorption, centered at 430 nm (lifetime (τ) ～ 28 ps), was assigned to a (π,π*) singlet S(1) excited state localized on a phenyl ring, and the second transient observed at 525 nm (τ ～ 480 ps) was assigned to singlet diphenylphosphorylnitrene. Experimental and computational results obtained from the study of diphenyl phosphoramidate, along with the results obtained with diphenylphosphoryl azide, supported the mechanism of energy transfer from the singlet excited phenyl ring to the azide moiety, followed by nitrogen extrusion to form the singlet phosphorylnitrene. Ultrafast time-resolved studies performed on diphenylphosphoryl azide with the singlet nitrene quencher, tris(trimethylsilyl)silane, confirmed the spectroscopic assignment of singlet diphenylphosphorylnitrene to the 525 nm absorption band.     

An ion mobility spectrometer sensor system for subsurface use

An ion mobility spectrometer (IMS) probe system for real-time, subsurface soil-gas sampling applications is presented. The system includes an IMS and supporting electronics encased in a 51 mm diameter stainless steel probe housing. The IMS was challenged in the laboratory with 2,6-di-tert-butylpyridine (DtBP) and tetrachloroethylene (PCE) in zero air yielding reduced ion mobility constants (K_o) values of 1.42 cm²/Vs (n = 3) and 1.79 ± 0.01 cm²/Vs (n = 3), respectively. A resolving power of 38 and 31 was obtained for DtBP and PCE, respectively. The system was deployed at a PCE-contaminated site to demonstrate its performance under field conditions. PCE was detected in the vapor samples as evidenced by peaks with a K_o value of 1.80 ± 0.01 cm²/Vs for two measurements that were taken 6 min apart. The presence of PCE at the contaminated site was confirmed by GC-MS analysis of a gas sample at an EPA-certified laboratory, suggesting that this IMS system can be used to detect PCE under field conditions.     

Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface

The authors present an integrated approach to "alchemical" free energy simulation, which permits efficient calculation of the free energy difference on rugged energy surface. The method is designed to obtain efficient canonical sampling for rapid free energy convergence. The proposal is motivated by the insight that both the exchange efficiency in the presently designed dual-topology alchemical Hamiltonian replica exchange method (HREM), and the confidence of the free energy determination using the overlap histogramming method, depend on the same criterion, viz., the overlaps of the energy difference histograms between all pairs of neighboring states. Hence, integrating these two techniques can produce a joint solution to the problems of the free energy convergence and conformational sampling in the free energy simulations, in which lambda parameter plays two roles to simultaneously facilitate the conformational sampling and improve the phase space overlap for the free energy determination. Specifically, in contrast with other alchemical HREM based free energy simulation methods, the dual-topology approach can ensure robust conformational sampling. Due to these features (a synergistic solution to the free energy convergence and canonical sampling, and the improvement of the sampling efficiency with the dual-topology treatment), the present approach, as demonstrated in the model studies of the authors, is highly efficient in obtaining accurate free energy differences, especially for the systems with rough energy landscapes.     

Click Functionalization of a Dibenzocyclooctyne‐Containing Conjugated Polyimine

A conjugated poly(phenyl‐co‐dibenzocyclooctyne) Schiff‐base polymer, prepared through polycondensation of dibenzocyclooctyne bisamine (DIBO‐(NH₂)₂) with bis(hexadecyloxy)phenyldialdehyde, is reported. The resulting polymer, which has a high molecular weight (M_n>30 kDa, M_w>60 kDa), undergoes efficient strain‐promoted alkyne–azide cycloaddition reactions with a series of azides. This enables quantitative modification of each repeat unit within the polymer backbone and the rapid synthesis of a conjugated polymer library with widely different substituents but a consistent degree of polymerization (DP). Kinetic studies show a second‐order reaction rate constant that is consistent with monomeric dibenzocyclooctynes. Grafting with azide‐terminated polystyrene and polyethylene glycol monomethyl ether chains of varying molecular weight resulted in the efficient syntheses of a series of graft copolymers with a conjugated backbone and maximal graft density.