Synthesis of Boltorn 1,2,3‐triazole dendrimers by click chemistry

Second‐, third‐, and fourth‐generation hyperbranched aliphatic polyols namely Boltorn® H20, Boltorn H30, and Boltorn H40 were endcapped with azido and activated acetylenic groups in good to excellent yields (75–95%) following an acid catalyzed procedure. The resultant terminally functionalized dendritic azido and acetylenic groups undergo 1,3‐dipolar cycloaddition using methyl (or ethyl) propiolate and benzyl azide, respectively, under catalytic or noncatalytic conditions below 40 °C to yield 1,2,3‐triazole dendrimeric polymers in 82–95% yield, under extremely mild conditions that could be applied for compounds sensitive to acid, base, or heat. The dendritic azido and activated acetylenic derivatives may act as novel scaffolds to tune the mechanical properties of different polymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3748–3756, 2009     

Non-nucleoside building blocks for copper-assisted and copper-free click chemistry for the efficient synthesis of RNA conjugates

Novel non-nucleoside alkyne monomers compatible with oligonucleotide synthesis were designed, synthesized, and efficiently incorporated into RNA and RNA analogues during solid-phase synthesis. These modifications allowed site-specific conjugation of ligands to the RNA oligonucleotides through copper-assisted (CuAAC) and copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) reactions. The SPAAC click reactions of cyclooctyne-oligonucleotides with various classes of azido-functionalized ligands in solution phase and on solid phase were efficient and quantitative and occurred under mild reaction conditions. The SPAAC reaction provides a method for the synthesis of oligonucleotide-ligand conjugates uncontaminated with copper ions.     

Relativity and the lead-acid battery

The energies of the solid reactants in the lead-acid battery are calculated ab?initio using two different basis sets at nonrelativistic, scalar-relativistic, and fully relativistic levels, and using several exchange-correlation potentials. The average calculated standard voltage is 2.13?V, compared with the experimental value of 2.11?V. All calculations agree in that 1.7-1.8?V of this standard voltage arise from relativistic effects, mainly from PbO2 but also from PbSO4.     

Dynamical approach to spectator fragmentation in Au+Au reactions at 35 MeV/A

The characteristics of fragment emission in peripheral ¹⁹⁷Au+¹⁹⁷Au collisions 35 MeV/A are studied using the two clusterization approaches within framework of quantum molecular dynamics model. Our model calculations using minimum spanning tree (MST) algorithm and advanced clusterization method namely simulated annealing clusterization algorithm (SACA) showed that fragment structure can be realized at an earlier time when spectators contribute significantly toward the fragment production even at such a low incident energy. Comparison of model predictions with experimental data reveals that SACA method can nicely reproduce the fragment charge yields and mean charge of the heaviest fragment. This reflects suitability of SACA method over conventional clusterization techniques to investigate spectator matter fragmentation in low energy domain.     

Post-buckling of cantilever columns having variable cross-section under a combined load

Post-buckling of a cantilever column is examined under a combined load consisting of a tip-concentrated load and a distributed axial load, through dynamic formulation. The formulation of the problem is based on the moment–curvature relationship. The two-point boundary value problem described by the governing equations is dependent on the frequency parameter and the two load parameters. The buckling loads are those loads at which the eigencurve, namely, the load versus frequency curve of the column meets the load axis. A simple and reliable iterative procedure to convert the two-point boundary value problem into an initial value problem is followed and solved the non-linear differential equations utilizing a fourth-order Runge–Kutta integration scheme. To demonstrate the potentiality of the adopted numerical scheme, linear vibration frequencies of truncated, tapered cantilever wedges and cones are determined and compared with the published analytical and test results. Buckling and post-buckling loads of a simply supported stepped column are obtained and compared with the published test results. The loads and deflections of non-uniform cantilever columns are obtained for various slopes at the tip. The interaction of load parameters for a free–free truncated conical column has also been examined. The numerical results indicate that the path represented by the two load parameters turns out to be nearly a straight line.     

N‐Alkoxyheterocycles As Irreversible Photooxidants

Irreversible photooxidation based on N–O bond fragmentation is demonstrated for N‐methoxyheterocycles in both the singlet and triplet excited state manifolds. The energetic requirements for bond fragmentation are studied in detail. Bond fragmentation in the excited singlet manifold is possible for ππ* singlet states with energies significantly larger than the N–O bond dissociation energy of ca 55 kcal mol^?1. For the nπ* triplet states, N–O bond fragmentation does not occur in the excited state for orbital overlap and energetic reasons. Irreversible photooxidation occurs in the singlet states by bond fragmentation followed by electron transfer. Irreversible photooxidation occurs in the triplet states via bimolecular electron transfer to the donor followed by bond fragmentation. Using these two sensitization schemes, donors can be irreversibly oxidized with oxidation potentials ranging from ca 1.6–2.2 V vs SCE. The corresponding N‐ethylheterocycles are characterized as conventional reversible photooxidants in their triplet states. The utility of these sensitizers is demonstrated by irreversibly generating the guanosine radical cation in buffered aqueous solution.     

Diagnosing the Protonation Site of <Emphasis Type="BoldItalic">b</Emphasis><Subscript><Emphasis Type="BoldItalic">2</Emphasis></Subscript> Peptide Fragment Ions using IRMPD in the X–H (X = O,N, and C) Stretching Region

Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b ₂ ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800–3800 cm^–1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO₂ laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm^–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH₂ group, is a distinct vibrational signature of the ring-protonated oxazolone structure.     

The mechanism of the reduction of [AnO2]2+ (An = U, Np, Pu) in aqueous solution, and by Fe(II) containing proteins and mineral surfaces, probed by DFT calculations

The fate of actinyl species in the environment is closely linked to oxidation state, since the reduction of An(VI) to An(IV) greatly decreases their mobility due to the precipitation of the relatively insoluble An(IV) species. Here we study the mechanism of the reduction of [AnO(2)](2+) (An = U, Np, Pu) both in aqueous solution and by Fe(II) containing proteins and mineral surfaces, using density functional theory calculations. We find a disproportionation mechanism involving a An(V)-An(V) cation-cation complex, and we have investigated how these complexes are formed in the different environments. We find that the behaviour of U and Pu complexes are similar, but the reduction of Np(V) to Np(IV) would seems to be more difficult, in line with the experimental finding that Np(V) is generally more stable than U(V) or Pu(V). Although the models we have used are somewhat idealised, our calculations suggest that there are strong similarities between the biotic and abiotic reduction pathways.     

A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate

We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.