coordination spheres
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Abstract In this work, the modeling of the sulfur interaction with substitutional impurities (Mn, P) and interstitial (C) has been carried out. All calculations were performed using the density functional theory in the WIEN2k software package. For the first two coordination spheres, there is a strong repulsion between carbon and sulfur, but in the third relative position, a slight attraction arises between the atoms. When sulfur interacts with manganese, attraction occurs only for the first coordination sphere, while the dissolution energy of both manganese and sulfur decreases. In the case of the S-P interaction, the binding energy is negative, and the dissolution energy of both sulfur and phosphorus decreases for all configurations, although the distance between phosphorus and sulfur increases. It can be assumed that the presence of phosphorus leads to the accumulation of sulfur in the material.

Abstract The capability of silver(I) cyclo-hexamethylenedithiocarbamate to concentrate gold(III) from solutions characterized by a high level of salinity (5.15 M NaCl) into the solid phase has been established. The double chloroform-solvated Au(III)–Ag(I) complex [Au{S2CN(CH2)6}2]2[AgCl2]Cl·2CHCl3 (I) was preparatively isolated as an individual form of binding of [AuCl4]– anions. The composition of the ionic structural units of compound I indicates that gold(III) binding from a solution to the solid phase is accompanied by the complete redistribution of the HmDtc ligands between the coordination spheres of Ag(I) and Au(III). Complex I characterized by IR spectroscopy, simultaneous thermal analysis, and X-ray structure analysis (CIF file CCDC no. 2051654) exhibits the supramolecular structure containing two oppositely charged pseudo-polymeric subsystems. Complex cations [Au{S2CN(CH2)6}2]+ and anions [AgCl2]– (in a ratio of 2 : 1) form a complicatedly organized cation-anionic pseudo-polymeric ribbon ({[Au(HmDtc)2]⋅⋅⋅[AgCl2]⋅⋅⋅[Au(HmDtc)2]}+)n due to secondary interactions Ag⋅⋅⋅S (3.2613 Å) and Au⋅⋅⋅Cl (3.2765 Å). The pseudo-polymeric ribbon consists of two rows of cations and a row of anions. The outer-sphere chloride ions combine the solvate chloroform molecules by two equivalent hydrogen bonds Cl⋅⋅⋅H–C yielding anion-molecular triads [Cl3CH⋅⋅⋅Cl⋅⋅⋅HCCl3]–, which are involved in the formation of the supramolecular ribbon due to the secondary Cl⋅⋅⋅Cl interactions (3.4058 Å) between the nonequivalent chlorine atoms of the nearest solvate molecules. The study of the thermal behavior of complex I makes it possible to determine the character of thermolysis and conditions for the quantitative regeneration of bound gold.

Using a dehydrogenative chemistry on the complex approach, a new polypyridine bridging ligand that bridges the gap of already existing systems is synthesized. By the usage of versatile cross-coupling reactions two different coordination spheres are included in the ligand architecture. Due to the twisted geometry of the novel ditopic ligand, the resultant division of the ligand in two distinct subunits leads to steady state as well as excited state properties of the corresponding mononuclear Ru(II) polypyridine complex resembling those of prototype [Ru(bpy)3]2+ (bpy = 2,2´-bipyridine). The localization of the initially optically excited and the nature of the long-lived excited states on the Ru-facing ligand spheres is evaluated by resonance Raman and fs-TA spectroscopy, respectively, and supported by DFT and TDDFT calculations. Coordination of a second metal (Zn or Rh) to the available bis-pyrimidyl-like coordination sphere strongly influences the frontier molecular orbitals apparent by e.g., luminescence quenching. Thus, the new bridging ligand motif offers electronic properties which can be adjusted by the nature of the second metal center. Using the heterodinuclear Ru-Rh complex, visible light-driven reduction of NAD+ to NADH was achieved, highlighting the potential of this system for photocatalytic applications.

Using a dehydrogenative chemistry on the complex approach, a new polypyridine bridging ligand that bridges the gap of already existing systems is synthesized. By the usage of versatile cross-coupling reactions two different coordination spheres are included in the ligand architecture. Due to the twisted geometry of the novel ditopic ligand, the resultant division of the ligand in two distinct subunits leads to steady state as well as excited state properties of the corresponding mononuclear Ru(II) polypyridine complex resembling those of prototype [Ru(bpy)3]2+ (bpy = 2,2´-bipyridine). The localization of the initially optically excited and the nature of the long-lived excited states on the Ru-facing ligand spheres is evaluated by resonance Raman and fs-TA spectroscopy, respectively, and supported by DFT and TDDFT calculations. Coordination of a second metal (Zn or Rh) to the available bis-pyrimidyl-like coordination sphere strongly influences the frontier molecular orbitals apparent by e.g., luminescence quenching. Thus, the new bridging ligand motif offers electronic properties which can be adjusted by the nature of the second metal center. Using the heterodinuclear Ru-Rh complex, visible light-driven reduction of NAD+ to NADH was achieved, highlighting the potential of this system for photocatalytic applications.

Ca2+-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we applied two new scoring schemes enabling the user to manipulate the binding affinities of such proteins. We specifically designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues of the loop based on the scoring scheme. We worked on the N-terminal domain of Entamoeba histolytica calcium-binding protein1 (NtEhCaBP1), and used site-directed mutagenesis to incorporate the designed loop sequence into the second EF hand motif of this protein. The binding isotherms calculated using ITC calorimetry showed a ~500-fold greater association constant (Ka) for the mutant. The crystal structure of the mutant was also determined, and displayed more compact Ca2+-coordination spheres in both of its EF loops than did the structure of the wildtype protein, consistent with the greater calcium-binding affinities of the mutant. The NtEhCaBP1 mutant was also shown to form a hexamer rather than just a trimer, and this hexamer formation was attributed to the position of the last helix of the mutant having been changed as a result of the strong calcium coordination. Further dynamic correlation analysis revealed that the mutation in the second EF loop changed the entire residue network of the monomer, resulting in a stronger coordination of Ca2+.

Designing the perfect sensor is the dream of any chemist. Since decades, a wide diversity of synthetic receptors targeting analytes has been explored in chemistry. Their chemical optimization is hard and with no guarantee of success. In this context, we propose a fast and self assembling colorimetric bio-chemical receptor coined Enzyvitand. It consists only of commercial chemicals. It relies on the reunification of combinatorial chemistry , first and second coordination spheres interactions and indicators displacement assays. All harbored within a protein cavity. The sensor is highly modular, cheap and evolvable. Thanks to its solved X-ray structure, we rationally designed it for the selectiv naked-eye recognition of dopamine over other neutrotransmitters through second coordination sphere. Hence, our sensor imitates a biological receptor for the recognition of neurotransmitters. Finally, it works in complex samples such as urine. Its immediate high versatility and evolvability is valuable for the selective detection of a wide assortment of analytes from small molecules up to micro-organisms. For the future, we anticipate new biotechnological or immunotherapeutic applications of our synthetic oligomer.

The article deals with computer modeling of responses of multicomponent semiconductor nanoelectromechanical systems of arsenides to an attosecond radiation pulse at cryogenic (T1=77 K) and standard temperatures (T2=298 K). Kinetic curves of relaxation processes in ternary semiconductor nanolayers CdSiAs2, CdGeAs2, ZnSiAs2, ZnGeAs2, and nanolayers of variable composition CdSi1-xGex As2, ZnSi1-xGexAs2, Cd1-xZnxSiAs2 и Cd1-xZnxGeAs2 are obtained. This research reveals the differences in the average relaxation energy of nanolayers that depend on temperature and the amplitudes of energy fluctuations, and the time of reaching the plateau. A comparison with relaxation processes taking place at absolute zero temperatures is demonstrated. The radial distribution functions of atoms in the system before and after relaxation processes caused by impulsive action on the system of atoms in the semiconductor layer are considered. The modification of the peaks corresponding to the coordination spheres of atomic distribution depending on the composition of the nanolayer is described. The regularities of relaxation changes of the first order coordination spheres, as well as the regularities of relaxation destructions of the second and the third order coordination spheres at cryogenic and standard temperatures are revealed.

An algorithm is proposed for constructing curves of thermal cooling and ordering kinetics with a monotonic decrease in temperature for alloys to stoichiometric composition. Modeling is carried out by the Monte Carlo method in the model of a rigid crystal lattice and pair interatomic interactions. The application of the algorithm is illustrated by the example to a square lattice, taking into account interatomic interactions in the first two coordination spheres for alloys with the composition AB, A3B, and A3B5. The proposed model makes it possible to calculate individual sections of the phase diagrams to the state for binary alloys.