Quantum Mechanical Study of Protonation of Oxygen Ligands in the Laccase Active Site Based on X-Ray Structures of Subatomic Resolution

Laccases are enzymes catalyzing oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Previously studies of oxygen reduction by laccases have recently been reported. They were based on single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution, As a result, coordinates of all non-hydrogen atoms of the active site have been determined with high precision for both oxidized and reduced states of the enzyme. Those data can be used to clarify the mechanism of molecular oxygen reduction by laccases. However, the X-ray data lack information about protonation states of the oxygen ligands involved. Applying quantum mechanical calculations, in the present work protonation of oxygen ligands in the active site of laccase was determined for both reduced and oxidized states of the enzyme (the stable states observed in experiments at reduction of molecular oxygen in laccase). The high precision of X-ray-determined atom coordinates allowed us to simplify preliminary calculations of molecular mechanics for models used in the quantum mechanical calculations.

Dramatic differences in the conformational equilibria of chalcogen-bridged compounds: the case of diallyl ether versus diallyl sulfide

Rotational spectroscopy and quantum mechanical calculations reveal a significant change in conformational landscapes when oxygen is substituted with sulfur: observation of features from nine conformers of diallylether versus one of the sulfide.

Детерминизм локального атомного упорядочения в монослоях золота в формировании их электронной структуры

The total and partial densities of electronic states of gold monolayer structures of different symmetry are calculated by the quantum mechanical calculations methods in the DFT approximation. It is shown that the first coordination sphere is determinant in the formation of the fine structure and the extent of the valence bands of the monolayer gold structures under study. The peaks splitting of the TDOS curve, which leads to its finer structure, is influenced not only by the lengths of interatomic bonds but also by the mutual arrangement of atoms. The influence of long-range interactions on the electronic structure of gold monolayers has been established. For example, for the (110) plane, a change in the atomic ordering in the third coordination sphere as a result of the introduction of a vacancy leads to noticeable changes in the TDOS curve, which indicates either a significant role of the atoms of the third coordination sphere or a significant redistribution of the interaction of d-orbitals of different symmetries of close neighbours. A correlation between the packing density, as well as the number of neighbours in the first coordination sphere, and the width of the energy band of gold monolayers has been established.

Molecular Structure, Vibrational Spectral Studies, NLO Properties and frontier molecular investigations of 2-Chloro-6-Fluoro Benzaldehyde by DFT

Benzaldehyde and its derivatives are the simplest in aromatic aldehydes and have wide range of use in different industries. Due to this reason, there exist a vast field of study of substituted benzaldehydes. Quantum mechanical calculations of geometries, energies, vibrational wave numbers and thermodynamic constants have been performed with Gaussian 09 program package using the beece-3-Lee-Yang-Parr- (B3LYP) functional supplemented with the standard 6-31G (DP). The optimized geometrical parameters obtained by computational methods. The thermodynamic properties as heat capacity, entropy and enthalpy of the titled compounds are derived also dipole moment, Polarizability and hyperpolarizability are calculated along with brief study of HOMO-LUMO is done.

CalcUS: An Open-Source Computational Chemistry Web Platform

Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed CalcUS, an open-source platform to streamline computational chemistry studies. Its objective is to democratize access to computational chemistry by providing a user-friendly web interface to simplify running and analyzing quantum mechanical calculations. It is freely available, expandable and customizable. It promotes connectivity to multiple software packages and algorithms, thus providing state-of-the-art techniques to all practitioners. We propose CalcUS as a standalone tool and infrastructure to support other open-source packages.

Real Structure of Benzene Molecule and the Thickness of Graphene

The problem of benzene molecular structure has not been solved for more than 100 years. This research proposes a new concept of covalent bond based on the existing theory: each electron shared by multiple atom nuclei corresponds to a half-valent bond. The half-valent bond can be formed between the spacer carbon atoms of the benzene ring. In this way, a new theory was established. Quantum mechanical calculations can quantitatively explain experimental results, such as the hydrogenation heat and ultraviolet spectrum of benzene. Using the dotted line to indicate the half-valent bond, benzene molecular structural forms and chemical reaction formulas as will as its dozens of homologues and derivatives are designed easily. The method not only has a wide range of adaptability, but can also record the chemical reaction process. If several stacked benzene rings can form a benzene tube under the guidance of the new theory, calculated thickness of the three-layer benzene tube is very close to the thickness of graphene. Therefore, referring to other characteristics of graphene, it is considered to be more like a three-layer structure.

Kinetic Study on the Reactivity of Azanone (HNO) toward Cyclic C-Nucleophiles

Azanone (HNO) is an elusive electrophilic reactive nitrogen species of growing pharmacological and biological significance. Here, we present a comparative kinetic study of HNO reactivity toward selected cyclic C-nucleophiles under aqueous conditions at pH 7.4. We applied the competition kinetics method, which is based on the use of a fluorescein-derived boronate probe FlBA and two parallel HNO reactions: with the studied scavenger or with O2 (k = 1.8 × 104 M−1s−1). We determined the second-order rate constants of HNO reactions with 13 structurally diverse C-nucleophiles (k = 33–20,000 M−1s−1). The results show that the reactivity of HNO toward C-nucleophiles depends strongly on the structure of the scavenger. The data are supported with quantum mechanical calculations. A comprehensive discussion of the HNO reaction with C-nucleophiles is provided.