Conformation/Tautomerization effect on the pKa values of lumazine and 6‐thienyllumazine

Density functional theory [B3LYP/6‐311+G(d,p)] was used in combination with the conductor‐like polarizable continuum model (CPCM) solvation model to investigate the relative stability and site‐specific values of neutral and ionized tautomers of lumazine (LM) and 6‐thienylLM (TLM). Two types of populations should be taken into consideration when calculating the , tautomers, and conformers. The major tautomer of neutral LM in aqueous solution is 13‐LM (the 13 notation refers to the acidic protons being in positions 1 and 3 of LM) TLM has decreased acidity at N₈ relative to LM. Further, the trans conformer of TLM is more acidic than cis. Similar to the case of LM, for TLM, N₁ is more acidic than N₃ in the uracil part. However, N₈ is predicted to be a stronger acid than N₁ for TLM. This acidity enhancement is essentially because of a specific stabilization of the anion when the thienyl group replaces H. Two factors are responsible for the acidity strength of N₈: The thienyl ring upon deprotonation acts inductively as an electron‐withdrawing group, and the excess electron density is dispersed better when the system is trans and contains second‐row atoms. Accurate pK_a calculation requires that all conformers/tautomers be included into the calculation. Copyright © 2014 John Wiley & Sons, Ltd.     

Approximation of weak adjoints by reverse automatic differentiation of BDF methods

We shed light on the relation between the discrete adjoints of multistep backward differentiation formula (BDF) methods and the solution of the adjoint differential equation. To this end, we develop a functional-analytic framework based on a constrained variational problem and introduce the notion of weak adjoint solutions of ordinary differential equations. We devise a Petrov-Galerkin finite element (FE) interpretation of the BDF method and its discrete adjoint scheme obtained by reverse internal numerical differentiation. We show how the FE approximation of the weak adjoint is computed by the discrete adjoint scheme and prove its convergence in the space of normalized functions of bounded variation. We also show convergence of the discrete adjoints to the classical adjoints on the inner time interval. Finally, we give numerical results for non-adaptive and fully adaptive BDF schemes. The presented framework opens the way to carry over techniques on global error estimation from FE methods to BDF methods.     

Korn’s second inequality and geometric rigidity with mixed growth conditions

Geometric rigidity states that a gradient field which is $L^p$ -close to the set of proper rotations is necessarily $L^p$ -close to a fixed rotation, and is one key estimate in nonlinear elasticity. In several applications, as for example in the theory of plasticity, energy densities with mixed growth appear. We show here that geometric rigidity holds also in $L^p+L^q$ and in $L^{p,q}$ interpolation spaces. As a first step we prove the corresponding linear inequality, which generalizes Korn’s inequality to these spaces.     

On the topology of synchrony optimized networks of a Kuramoto-model with non-identical oscillators

We study synchrony optimized networks. In particular, we focus on the Kuramoto model with non-identical native frequencies on a random graph. In a first step, we generate synchrony optimized networks using a dynamic breeding algorithm, whereby an initial network is successively rewired toward increased synchronization. These networks are characterized by a large anti-correlation between neighbouring frequencies. In a second step, the central part of our paper, we show that synchrony optimized networks can be generated much more cost efficiently by minimization of an energy-like quantity E and subsequent random rewires to control the average path length. We demonstrate that synchrony optimized networks are characterized by a balance between two opposing structural properties: A large number of links between positive and negative frequencies of equal magnitude and a small average path length. Remarkably, these networks show the same synchronization behaviour as those networks generated by the dynamic rewiring process. Interestingly, synchrony-optimized network also exhibit significantly enhanced synchronization behaviour for weak coupling, below the onset of global synchronization, with linear growth of the order parameter with increasing coupling strength. We identify the underlying dynamical and topological structures, which give rise to this atypical local synchronization, and provide a simple analytical argument for its explanation.     

Aircraft noise: accounting for changes in air traffic with time of day

Aircraft noise contours are estimated using model calculations and, due to their impact on land use planning, they need to be highly accurate. During night time, not only the number and dominant types of aircraft may differ from daytime but also the flight paths flown may differ. To determine to which detail these variations in flight paths need to be considered, calculations were performed exemplarily for two airports using all available radar data over 1 year, taking into account their changes over the day. The results of this approach were compared with results of a simpler approach which does not consider such changes. While both calculations yielded similar results for the day and close to the airport, differences increased with distance as well as with the period of day (day相似文献   

Comment on "Strong signature of the active Sun in 100 years of terrestrial insolation data" by W. Weber

An analysis of ground-based observations of solar irradiance was recently published in this journal, reporting an apparent increase of solar irradiance on the ground of the order of 1% between solar minima and maxima [1]. Since the corresponding variations in total solar irradiance on top of the atmosphere are accurately determined from satellite observations to be of the order of 0.1% only [2], the one order of magnitude stronger effect in the terrestrial insolation data was interpreted as evidence for cosmic-ray induced aerosol formation in the atmosphere. In my opinion, however, this result does not reflect reality. Using the energy budget of Earth's surface, I show that changes of ground-based insolation with the solar cycle of the order of 1% between solar minima and maxima would result in large surface air temperature variations which are inconsistent with the instrumental record. It would appear that the strong variations of terrestrial irradiance found by [1] are due to the uncorrected effects of volcanic or local aerosols and seasonal variations. Taking these effects into account, I find a variation of terrestrial insolation with solar activity which is of the same order as the one measured from space, bringing the surface energy budget into agreement with the solar signal detected in temperature data.     

Structural fine-tuning of a multifunctional cytochrome P450 monooxygenase

AurH is a unique cytochrome P450 monooxygenase catalyzing the stepwise formation of a homochiral oxygen heterocycle, a key structural and pharmacophoric component of the antibiotic aureothin. The exceptional enzymatic reaction involves a tandem oxygenation process including a regio- and stereospecific hydroxylation, followed by heterocyclization. For the structural and biochemical basis of this unparalleled sequence, four crystal structures of AurH variants in different conformational states and in complex with the P450 inhibitor ancymidol were solved, which represent the first structures of the CYP151A group. Structural data in conjunction with computational docking, site-directed mutagenesis, and chemical analyses unveiled a switch function when recognizing the two substrates, deoxyaureothin and the hydroxylated intermediate, thus allowing the second oxygenation-heterocyclization step. Furthermore, we were able to modify the chemo- and regioselectivity of AurH, yielding mutants that catalyze the regioselective six-electron transfer of a nonactivated methyl group to a carboxylic acid via hydroxyl and aldehyde intermediates.     

Not Guilty on Every Count: The “Non‐Innocent” Nitrosyl Ligand in the Framework of IUPAC′s Oxidation‐State Formalism

Nitrosyl–metal bonding relies on the two interactions between the pair of N–O‐π* and two of the metal's d orbitals. These (back)bonds are largely covalent, which makes their allocation in the course of an oxidation‐state determination ambiguous. However, apart from M‐N‐O‐angle or net‐charge considerations, IUPAC′s “ionic approximation” is a useful tool to reliably classify nitrosyl metal complexes in an orbital‐centered approach.