Triesterase and Promiscuous Diesterase Activities of a Di‐CoII‐Containing Organophosphate Degrading Enzyme Reaction Mechanisms

The reaction mechanism for the hydrolysis of trimethyl phosphate and of the obtained phosphodiester by the di‐Co^II derivative of organophosphate degrading enzyme from Agrobacterium radiobacter P230(OpdA), have been investigated at density functional level of theory in the framework of the cluster model approach. Both mechanisms proceed by a multistep sequence and each catalytic cycle begins with the nucleophilic attack by a metal‐bound hydroxide on the phosphorus atom of the substrate, leading to the cleavage of the phosphate‐ester bond. Four exchange‐correlation functionals were used to derive the potential energy profiles in protein environments. Although the enzyme is confirmed to work better as triesterase, as revealed by the barrier heights in the rate‐limiting steps of the catalytic processes, its promiscuous ability to hydrolyze also the product of the reaction has been confirmed. The important role played by water molecules and some residues in the outer coordination sphere has been elucidated, while the binuclear Co^II center accomplishes both structural and catalytic functions. To correctly describe the electronic configuration of the d shell of the metal ions, high‐ and low‐spin arrangement jointly with the occurrence of antiferromagnetic coupling, have been herein considered.     

Experimental and Theoretical Studies on the Rearrangement of 2‐Oxoazepane α,α‐Amino Acids into 2′‐Oxopiperidine β2,3,3‐Amino Acids: An Example of Intramolecular Catalysis

Enantiopure β‐amino acids represent interesting scaffolds for peptidomimetics, foldamers and bioactive compounds. However, the synthesis of highly substituted analogues is still a major challenge. Herein, we describe the spontaneous rearrangement of 4‐carboxy‐2‐oxoazepane α,α‐amino acids to lead to 2′‐oxopiperidine‐containing β^2,3,3‐amino acids, upon basic or acid hydrolysis of the 2‐oxoazepane α,α‐amino acid ester. Under acidic conditions, a totally stereoselective synthetic route has been developed. The reordering process involved the spontaneous breakdown of an amide bond, which typically requires strong conditions, and the formation of a new bond leading to the six‐membered heterocycle. A quantum mechanical study was carried out to obtain insight into the remarkable ease of this rearrangement, which occurs at room temperature, either in solution or upon storage of the 4‐carboxylic acid substituted 2‐oxoazepane derivatives. This theoretical study suggests that the rearrangement process occurs through a concerted mechanism, in which the energy of the transition states can be lowered by the participation of a catalytic water molecule. Interestingly, it also suggested a role for the carboxylic acid at position 4 of the 2‐oxoazepane ring, which facilitates this rearrangement, participating directly in the intramolecular catalysis.     

TDPAC and first-principles study of electronic and structural properties of a Pd-vacancy complex in undoped germanium

Pd is one of the metals suitable for inducing low-temperature crystallization in Ge. However, it is not clear how residual Pd atoms are integrated into the Ge lattice. Therefore, time-differential γ–γ perturbed angular correlations (TDPAC) technique using the ¹⁰⁰Pd(→¹⁰⁰Rh) nuclear probe produced by recoil implantation has been applied to study the hyperfine interactions of this probe in single-crystalline undoped Ge. A Pd-vacancy complex aligned along the <111> crystallographic direction with a unique interaction frequency of 8.4(5) Mrad/s has been identified. This complex was measured to have a maximum relative fraction of about 76(4)% following annealing at 350 ^°C. Further annealing at higher temperatures reduced this fraction, possibly via dissociation of the complex. Calculations suggest dissociation energy of 1.94(5) eV for the complex. DFT calculations performed in this work are in reasonable good agreement with the experimental values for the electric-field gradient of the defect complex in Ge and Si for comparison. The calculations predict a split-vacancy configuration with the Pd on a bond-centred interstitial site having a nearest-neighbour semi-vacancy on both sides (V-Pd_BI-V) in Ge and Si.     

Mechanistic Aspects of a Highly Active Dinuclear Zinc Catalyst for the Co‐polymerization of Epoxides and CO2

The dinuclear zinc complex reported by us is to date the most active zinc catalyst for the co‐polymerization of cyclohexene oxide (CHO) and carbon dioxide. However, co‐polymerization experiments with propylene oxide (PO) and CO₂ revealed surprisingly low conversions. Within this work, we focused on clarification of this behavior through experimental results and quantum chemical studies. The combination of both results indicated the formation of an energetically highly stable intermediate in the presence of propylene oxide and carbon dioxide. A similar species in the case of cyclohexene oxide/CO₂ co‐polymerization was not stable enough to deactivate the catalyst due to steric repulsion.     

Time-dependent Ginzburg–Landau equations for multi-gap superconductors

We numerically solve the time-dependent Ginzburg–Landau equations for two-gap superconductors using the finite-element technique. The real-time simulation shows that at low magnetic field, the vortices in small-size samples tend to form clusters or other disorder structures. When the sample size is large, stripes appear in the pattern. These results are in good agreement with the previous experimental observations of the intriguing anomalous vortex pattern, providing a reliable theoretical basis for the future applications of multi-gap superconductors.     

Definition and detection of data-based uniqueness in evaluating bilinear (two-way) chemical measurements

Multivariate curve resolution methods, frequently used in analyzing bilinear data sets, result in ambiguous decomposition in general. Implementing the adequate constraints may lead to reduce the so-called rotational ambiguity drastically, and in the most favorable cases to the unique solution. However, in some special cases, non-negativity constraint as minimal information of the system is a sufficient condition to resolve profiles uniquely. Although, several studies on exploring the uniqueness of the bilinear non-negatively constrained multivariate curve resolution methods have been made in the literature, it has still remained a mysterious question. In 1995, Manne published his profile-based theorems giving the necessary and sufficient conditions of the unique resolution. In this study, a new term, i.e., data-based uniqueness is defined and investigated in details, and a general procedure is suggested for detection of uniquely recovered profile(s) on the basis of data set structure in the abstract space. Close inspection of Borgen plots of these data sets leads to realize the comprehensive information of local rank, and these argumentations furnish a basis for data-based uniqueness theorem. The reported phenomenon and its exploration is a new stage (it can be said fundament) in understanding and describing the bilinear (matrix-type) chemical data in general.     

Photoisomerisation in Aminoazobenzene‐Substituted Ruthenium(II) Tris(bipyridine) Complexes: Influence of the Conjugation Pathway

Transition‐metal complexes containing stimuli‐responsive systems are attractive for applications in optical devices, photonic memory, photosensing, as well as luminescence imaging. Amongst them, photochromic metal complexes offer the possibility of combining the specific properties of the metal centre and the optical response of the photochromic group. The synthesis, the electrochemical properties and the photophysical characterisation of a series of donor–acceptor azobenzene derivatives that possess bipyridine groups connected to a 4‐dialkylaminoazobenzene moiety through various linkers are presented. DFT and TD‐DFT calculations were performed to complement the experimental findings and contribute to their interpretation. The position and nature of the linker (ethynyl, triazolyl, none) were engineered and shown to induce different electronic coupling between donor and acceptor in ligands and complexes. This in turn led to strong modulations in terms of photoisomerisation of the ligands and complexes.     

Semilinear wave models with friction and viscoelastic damping

In this paper, we study the global (in time) existence of small data solutions to the Cauchy problem for the semilinear wave equation with friction, viscoelastic damping, and a power nonlinearity. We are interested in the connection between regularity assumptions for the data and the admissible range of exponents p in the power nonlinearity.     

A new study of associating inhomogeneous fluids with classical density functional theory

ABSTRACT

A new density functional for the study of associating inhomogeneous fluids based on Wertheim's first-order thermodynamic perturbation theory is presented and compared to the most currently used associating density functionals. This functional is developed using the weighted density approximation in the range of association of hard spheres. We implement this functional within the framework of classical density functional theory together with modified fundamental measure theory to account for volume exclusion of hard spheres. This approach is tested against molecular simulations from literature of pure associating hard spheres and mixtures of non-associationg and associating hard spheres with different number of bonding sites close to a hard uniform wall. Furthermore, we compare and review our results with the performance of associating functionals from literature, one based on fundamental measure theory and the inhomogeneous version of Wertheim's perturbation theory. Results obtained with classical DFT and the three functionals show excellent agreement with molecular simulations in systems with one hard wall. For the cases of small pores where only one or two layers of fluid are allowed discrepancies between results with classical DFT and molecular simulations were found.     

Spectral estimates for saddle point matrices arising in weak constraint four‐dimensional variational data assimilation

We consider the large sparse symmetric linear systems of equations that arise in the solution of weak constraint four‐dimensional variational data assimilation, a method of high interest for numerical weather prediction. These systems can be written as saddle point systems with a 3 × 3 block structure but block eliminations can be performed to reduce them to saddle point systems with a 2 × 2 block structure, or further to symmetric positive definite systems. In this article, we analyse how sensitive the spectra of these matrices are to the number of observations of the underlying dynamical system. We also obtain bounds on the eigenvalues of the matrices. Numerical experiments are used to confirm the theoretical analysis and bounds.