Synthesis of sugar nucleotides by application of phosphoramidites

A new method for the construction of pyrophosphates is reported based on the coupling of a sugar phosphate and a nucleoside phosphoramidite. The in situ formed phosphate-phosphite intermediate was subsequently oxidized with tBuOOH. Three UDP-N-acetylglucosamine derivatives were prepared using this one-pot procedure in good yields.     

Theoretical analysis of the intermolecular interaction effects on the excitation energy of organic pigments: solid state quinacridone

Quinacridones (QAs) are organic hydrogen-bonded pigments, which are yellow in solution and become reddish to violet in solid phase depending on the crystal structure. We have carried out regular and fragment molecular orbital (FMO) based time-dependent density functional theory (TDDFT) calculations of the alpha (I), beta, and gamma crystalline phases of QA to examine the origin of the spectral shift in the solid phase. On the basis of the TDDFT calculations, we have found that the spectral shift from gas to solid phase in QA is dominated by the interplay of the structural deformation, electrostatic potential (crystal field), and intermolecular interactions, and each contribution is of the same order of magnitude. The spectral shift induced by the structural deformation is mainly caused by the stretch of the CO bond. The individual intermolecular interactions contribute to bathochromic and hypsochromic shifts depending on the spatial orientation, and their sums result in the bathochromic shift overall.     

On the design of algebraic flux correction schemes for quadratic finite elements

A fully algebraic approach to the design of nonlinear high-resolution schemes is revisited and extended to quadratic finite elements. The matrices resulting from a standard Galerkin discretization are modified so as to satisfy sufficient conditions of the discrete maximum principle for nodal values. In order to provide mass conservation, the perturbation terms are assembled from skew-symmetric internodal fluxes which are redefined as a combination of first- and second-order divided differences. The new approach to the construction of artificial diffusion operators is combined with a node-oriented limiting strategy. The resulting algorithm is applied to _P1$P_1$ and _P2$P_2$ approximations of stationary convection–diffusion equations in 1D/2D.     

Pseudo-conformal quaternionic CR structure on (4n + 3)-dimensional manifolds

We study an integrable, nondegenerate codimension 3-subbundle ${\mathcal{D}}We study an integrable, nondegenerate codimension 3-subbundle on a (4n + 3)-manifold M whose fiber supports the structure of 4n-dimensional quaternionic vector space. It is thought of as a generalization of quaternionic CR structure. We single out an -valued 1-form ω locally on a neighborhood U such that and construct the curvature invariant on (M, ω) whose vanishing gives a uniformization to flat quaternionic CR geometry. The invariant obtained on M has the same formula as that of pseudo-quaternionic K?hler 4n-manifolds. From this viewpoint, we exhibit a quaternionic analogue of Chern-Moser’s CR structure. The authors are grateful to ESI for financial support and hospitality during the preparation of this work. The first author acknowledge the support by Grant FWF Project P17108-N04 (Vienna) and Grant N MSM 0021622409 of the Ministry of Education, Youth and Sports (Brno).     

Anisotropy in the crystal growth of hexagonal ice, I(h)

Growth of ice crystals has attracted attention because ice and water are ubiquitous in the environment and play critical roles in natural processes. Hexagonal ice, I(h), is the most common form of ice among 15 known crystalline phases of ice. In this work we report the results of an extensive and systematic molecular dynamics study of the temperature dependence of the crystal growth on the three primary crystal faces of hexagonal ice, the basal {0001} face, the prism {1010} face, and the secondary prism {1120} face, utilizing the TIP4P-2005 water model. New insights into the nature of its anisotropic growth are uncovered. It is demonstrated that the ice growth is indeed anisotropic; the growth and melting of the basal face are the slowest of the three faces, its maximum growth rates being 31% and 43% slower, respectively, than those of the prism and the secondary prism faces. It is also shown that application of periodic boundary conditions can lead to varying size effect for different orientations of an ice crystal caused by the anisotropic physical properties of the crystal, and results in measurably different thermodynamic melting temperatures in three systems of similar, yet moderate, size. Evidence obtained here provides the grounds on which to clarify the current understanding of ice growth on the secondary prism face of ice. We also revisit the effect of the integration time step on the crystal growth of ice in a more thorough and systematic way. Careful evaluation demonstrates that increasing the integration time step size measurably affects the free energy of the bulk phases and shifts the temperature dependence of the growth rate curve to lower temperatures by approximately 1 K when the step is changed from 1 fs to 2 fs, and by 3 K when 3 fs steps are used. A thorough investigation of the numerical aspects of the simulations exposes important consequences of the simulation parameter choices upon the delicate dynamic balance that is involved in ice crystal growth.     

Efficient quantum-classical method for computing thermal rate constant of recombination: application to ozone formation

Efficient method is proposed for computing thermal rate constant of recombination reaction that proceeds according to the energy transfer mechanism, when an energized molecule is formed from reactants first, and is stabilized later by collision with quencher. The mixed quantum-classical theory for the collisional energy transfer and the ro-vibrational energy flow [M. Ivanov and D. Babikov, J. Chem. Phys. 134, 144107 (2011)] is employed to treat the dynamics of molecule + quencher collision. Efficiency is achieved by sampling simultaneously (i) the thermal collision energy, (ii) the impact parameter, and (iii) the incident direction of quencher, as well as (iv) the rotational state of energized molecule. This approach is applied to calculate third-order rate constant of the recombination reaction that forms the (16)O(18)O(16)O isotopomer of ozone. Comparison of the predicted rate vs. experimental result is presented.     

Fully automated sequential solid phase approach towards viral RNA-nucleopeptides

The synthesis of two ribonucleoprotein fragments of unprecedented complexity is reported. These hybrid biomolecules are prepared combining the use of an automated solid phase peptide and oligonucleotide synthesizer on a single solid support.