(2‐Aminopyrimidine‐κN1)aqua(pyridine‐2,6‐dicarboxylato‐κ3O2,N,O6)copper(II): X‐ray and DFT calculated structure

In the title compound, [Cu(C₇H₃N₂O₄)(C₄H₅N₂)(H₂O)], (I), pyridine‐2,6‐dicarboxylate (pydc²⁻), 2‐aminopyrimidine and aqua ligands coordinate the Cu^II centre through two N atoms, two carboxylate O atoms and one water O atom, respectively, to give a nominally distorted square‐pyramidal coordination geometry, a common arrangement for copper complexes containing the pydc²⁻ ligand. Because of the presence of Cu...X_bridged contacts (X = N or O) between adjacent molecules in the crystal structures of (I) and three analogous previously reported compounds, and the corresponding uncertainty about the effective coordination number of the Cu^II centre, density functional theory (DFT) calculations were used to elucidate the degree of covalency in these contacts. The calculated Wiberg and Mayer bond‐order indices reveal that the Cu...O contact can be considered as a coordination bond, whereas the amine group forming a Cu...N contact is not an effective participant in the coordination environment.     

Structures and energetics of complexation of metal ions with ammonia,water, and benzene: A computational study

Quantum chemical calculations have been performed at CCSD(T)/def2‐TZVP level to investigate the strength and nature of interactions of ammonia (NH₃), water (H₂O), and benzene (C₆H₆) with various metal ions and validated with the available experimental results. For all the considered metal ions, a preference for C₆H₆ is observed for dicationic ions whereas the monocationic ions prefer to bind with NH₃. Density Functional Theory–Symmetry Adapted Perturbation Theory (DFT‐SAPT) analysis has been employed at PBE0AC/def2‐TZVP level on these complexes (closed shell), to understand the various energy terms contributing to binding energy (BE). The DFT‐SAPT result shows that for the metal ion complexes with H₂O electrostatic component is the major contributor to the BE whereas, for C₆H₆ complexes polarization component is dominant, except in the case of alkali metal ion complexes. However, in case of NH₃ complexes, electrostatic component is dominant for s‐block metal ions, whereas, for the d and p‐block metal ion complexes both electrostatic and polarization components are important. The geometry (M⁺–N and M⁺–O distance for NH₃ and H₂O complexes respectively, and cation–π distance for C₆H₆ complexes) for the alkali and alkaline earth metal ion complexes increases down the group. Natural population analysis performed on NH₃, H₂O, and C₆H₆ complexes shows that the charge transfer to metal ions is higher in case of C₆H₆ complexes. © 2016 Wiley Periodicals, Inc.     

Protein environmental effects on iron‐sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres

The structural properties and reactivity of iron‐sulfur proteins are greatly affected by interactions between the prosthetic groups and the surrounding amino acid residues. Thus, quantum chemical investigations of the structure and properties of protein‐bound iron‐sulfur clusters can be severely limited by truncation of computational models. The aim of this study was to identify, a priori, significant interactions that must be included in a quantum chemical model. Using the [2Fe‐2S] accessory cluster of the FeFe‐hydrogenase as a demonstrative example with rich electronic structural features, the electrostatic and covalent effects of the surrounding side chains, charged groups, and backbone moieties were systematically mapped through density functional theoretical calculations. Electron affinities, spin density differences, and delocalization indexes from the quantum theory of atoms in molecules were used to evaluate the importance of each interaction. Case studies for hydrogen bonding and charged side‐chain interactions were used to develop selection rules regarding the significance of a given protein environmental effect. A set of general rules is proposed for constructing quantum chemical models for iron‐sulfur active sites that capture all significant interactions from the protein environment. This methodology was applied to our previously used models in galactose oxidase and the 6Fe‐cluster of FeFe‐hydrogenase. © 2016 Wiley Periodicals, Inc.     

A new high‐pressure strontium germanate,SrGe2O5

The Sr–Ge–O system has an earth‐scientific importance as a potentially good low‐pressure analog of the Ca–Si–O system, one of the major components in the constituent minerals of the Earth's crust and mantle. However, it is one of the germanate systems that has not yet been fully examined in the phase relations and structural properties. The recent findings that the SrGeO₃ high‐pressure perovskite phase is the first Ge‐based transparent electronic conductor make the Sr–Ge–O system interesting in the field of materials science. In the present study, we have revealed the existence of a new high‐pressure strontium germanate, SrGe₂O₅. Single crystals of this compound crystallized as a co‐existent phase with SrGeO₃ perovskite single crystals in the sample recovered in the compression experiment of SrGeO₃ pseudowollastonite conducted at 6 GPa and 1223 K. The crystal structure consists of germanium–oxygen framework layers stacked along [001], with Sr atoms located at the 12‐coordinated cuboctahedral site; the layers are formed by the corner linkages between GeO₆ octahedra and between GeO₆ octahedra and GeO₄ tetrahedra. The present SrGe₂O₅ is thus isostructural with the high‐pressure phases of SrSi₂O₅ and BaGe₂O₅. Comparison of these three compounds leads to the conclusion that the structural responses of the GeO₆ and GeO₄ polyhedra to cation substitution at the Sr site are much less than that of the SrO₁₂ cuboctahedron to cation substitution at the Ge sites. Such a difference in the structural response is closely related to the bonding nature.     

Energy Spectrum and Its Pressure-Induced Shift and g Factor of ZnS:Mn2+

By using strong-field scheme, the complete d⁵ energy matrix with D_2d symmetry has been constructed. Then, by diagonalization of this matrix at normal and various pressures,the whole energy spectrum [including the ground-state zero-field-splitting (GSZFS)], its PS and the g factor of the ground state for zns:Mn²⁺ have uniformly been calculated. According to the eigenfunctions and PS, the new assignments of five absorption bands have been given.The variation of tetragonal field with pressure makes a main contribution to the pressureinduced shift (PS) of GSZFS of zns:Mn²⁺, which supports the existence of tetragonal Jahn-Teller distortion in zns:Mn²⁺. It is found that when P≥62 kbar, t₂⁴(³T₁)e⁴T₁ merges with t₂e^{4 2}T₂, which has to be taken into account in the calculation of PS of the fifth band in the range of 1 bar ~ 95 kbar. It is demonstrated that the Mn²⁺ ions in ZnS:Mn²⁺ have tetrahedral coordination, and the difference between ζ and ζ' caused by the covalency effect is very important for GSZFS. The physical essentials of typical levels, GSZFS and their PS have been revealed. By taking into account the influence of covalency on t₂³(⁴A₂)e²(³A₂)⁴A₁ and t₂³(²E)e²(³A₂)⁴E, the positon of the third absorption band at normal pressure has been estimated.     

Structural elucidation of transition metal complex by single crystal EPR study

Single crystal EPR studies of Mn(II) doped hexaaquazincdiaquabis(malonato) zincate [Zn(H₂O)₆][Zn(mal)₂(H₂O)₂] have been carried out at room temperature using X-band spectrometer to identify the location of the dopant. Single crystal rotations along the three orthogonal axes show more than 30 line pattern EPR spectra indicating the presence of two types of dopant ions in the host lattice, with intensity ratio of 6:1. However, the latter could not be followed due to its low intensity during crystal rotations. The spin-Hamiltonian parameters, estimated from the three mutually orthogonal crystal rotations are: g_xx = 1.972, g_yy = 2.000, g_zz = 2.023, A_xx = 8.95, A_yy = 9.48, A_zz = 9.93 mT, D_xx = −34.49, D_yy = −3.26, D_zz = 37.74 mT and E = 15.6 mT. The direction cosines of one of the principal values of g match with that of Zn-O bond in the host lattice, suggesting that the Mn(II) ion entered the lattice substitutionally. The large value of E is indicative of low symmetry of the substitutional site, in accordance with the crystal structure of the isomorphous [Zn(H₂O)₆][Cu(mal)₂(H₂O)₂]. Covalency of Mn-O bond, estimated from Matamura’s plot, is 9%. Various admixture coefficients, bonding and optical parameters have also been calculated.     

Modification of Lytle’s theory: Interpretation of the extended fine structure associated with LIII absorption discontinuity of some ytterbium systems

In Lytle’s theory for the extended fine structure in x-ray absorption spectra, the potential at the boundary of the ‘equivalent sphere’ around the absorbing atom, having volume equal to that of the Wigner-Seitz cell is considered to be infinite. It has been observed that Lytle’s theory is applicable only in the case of metals and metallic systems. In the present paper the extended fine structure associated with the L_III absorption spectra of some systems of ytterbium is interpreted on the basis of Lytle’s model, modified by using a finite potential instead of an infinite one at the boundary of the equivalent sphere. The values of this potential are estimated for eight systems of ytterbium. It has been shown that there exists a correlation between the potentials and covalency of the compounds.