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.     

Insight into Mechanical Properties of CH3SiO3/2 Film

Young's modulus and stress-optical coefficient of self-sustained gel film of CH₃SiO_3/2 were measured. Young's modulus varied from 1.1 to 1.5 GPa, depending on the structural state of the film. It increased with an increase in the degree of polymerization that was induced by heat treatments, and also increased with subsequent exposure to the ambient condition. The stress-optical coefficient was 6.3 × 10^–12 Pa^–1 for a sample treated at 120°C. The compliance of the film seems to depend mainly on the intermolecular structure of Si–CH₃...CH₃–Si as well as hydrogen bonding due to silanols and adsorbed water.     

Polarised vibrational spectra of KH2PO3 single crystal

Polarised IR and Raman spectra for KH₂PO₃ single crystal samples were measured at room temperature. Additionally, the IR spectra for the Xb(Z) sample were also measured at low temperatures (300–14 K). The spectra are discussed on the basis of oriented gas model and group theory. The stretching νOH vibrations of the hydrogen bonds with the OO distances of 2.547 and 2.529 Å give characteristic broad ABC-type bands in the IR (polarised parallel to the X and to the b(Z) directions) and Raman (xx, xz and yx) spectra. The Davydov-type (correlation field or factor group) splitting is not observed for the νOH modes. The presence of two independent hydrogen bonds in the crystal is manifested by splitting of the C band into two (C′, C″) components and by the different frequencies of the out-of-plane bending γOH vibrations. The in-plane bending modes δOH are strongly mixed/coupled with the stretching vibrations of the PO₃ groups.

The C bands (C′ and C″) change into quite sharp bands on lowering of the temperature. Various simplified models for internal vibrations of the phosphite anions are applied for finding a correlation between the crystal structure and polarised vibrational spectra. The stretching vibrations of the νPH groups manifest their unequivalence in two symmetry-independent hydrogenphosphite anions.     

磁场对含稀土铝锂合金断裂特征的影响

以含铈铝锂合金为研究对象，研究了磁场对含稀土铝锂合金时效过程的影响，从断裂特征及微观组织两方面分析了磁场作用规律。实验结果表明：未加磁场时，合金的断裂特征以理断裂为主；扁平晶粒厚度不匀，在磁场作用下，此合金的断裂特征与微观组织发生明显改观，随磁感应强度增强，合金主断裂面上准解理断裂特征减弱，同时二次裂纹增多，分层比较升高；扁平晶粒厚度变薄，尺寸趋于均匀。用少体物理理论，探讨了磁场对含稀土合金原子扩散过程的影响，为进一步研究稀土元素在磁场中的行为及其局域效应提供了一定的实验依据。     

Organometallic Allene [(μ-C)(Fe(CO)4)2]: Bridging Carbon Showing Transformation from Classical Electron-Sharing Bonding to Double σ-Donor and Double π-Acceptor Ligation

Allenes (R₂C=C=CR₂) have been traditionally perceived to feature localized orthogonal π-bonds between the carbon centres. We have carried out quantum-mechanical studies of the organometallic allenes envisioned by the isolobal replacement of the terminal CH₂ groups by the d⁸ Fe(CO)₄ fragment. Our studies have identified two organometallic allenes viz. D_2d symmetric [(μ-C)(Fe(CO)₄)₂] ( 2 ) and D₃ symmetric [(μ-C)(Fe(CO)₄)₂] ( 3 ) with trigonal bipyramidal coordination at the Fe atoms. Compound 2 features the bridging carbon atom in an equatorial position with respect to the ligands on the TM centre, while 3 features the central carbon atom in an axial position. The bis-pseudoallylic anionic delocalisation proposed in the C2-C1-C3 spine of organic allene is retained in the organometallic allene 2 , and is transformed to a typical three-centre bis-allylic anionic delocalisation in the organometallic allene 3 . The topological analysis of electron density also indicates a bis-allylic anionic type delocalisation in the organometallic allenes. The quantitative bonding analysis using the EDA-NOCV method suggests a transition from classical electron-sharing bonding between the central carbon atom and the terminal groups in 1 to donor-acceptor bonding in 3 . Meanwhile, both electron-sharing and donor-acceptor bonding models are found to be probable heuristic bonding representations in the organometallic allene 2 .     

Triel Bond Formed by Malondialdehyde and Its Influence on the Intramolecular H-Bond and Proton Transfer

Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX₃ (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central carbon atoms of MDA act as the electron donors, respectively. A H···X secondary interaction coexists with the TrB in the former two types of complexes. The carbonyl O forms a stronger TrB than the hydroxyl O, and both of them are better electron donors than the central carbon atom. The TrB formed by the hydroxyl O enhances the intramolecular H-bond in MDA and thus promotes proton transfer in MDA-BX₃ (X = Cl and Br) and MDA-AlX₃ (X = halogen), while a weakening H-bond and the inhibition of proton transfer are caused by the TrB formed by the carbonyl O. The TrB formed by the central carbon atom imposes little influence on the H-bond. The BH₂ substitution on the central C-H bond can also realise the proton transfer in the triel-bonded complexes between the hydroxyl O and TrH₃ (Tr = B and Al).     

Molecular assemblies from imidazolyl-containing haloalkenes and haloalkynes: competition between halogen and hydrogen bonding

The structural characterization of molecular assemblies constructed from imidazolyl-containing haloalkenes and haloalkynes is reported. 1-(3-Iodopropargyl)imidazole (2) and 1-(2,3,3-triiodoallyl)imidazole (5) were synthesized from 1-propargylimidazole (1). In the solid state, these wholly organic modules self-assemble through N...I halogen-bonding interactions, thus giving rise to polymeric chains. The N...I interaction observed in 2 (d(N...I)=2.717 A, angle-spherical C(sp)-I...N=175.8 degrees) is quite strong relative to previously reported data. The N...I interaction in 5 (d(N...I)=2.901 A, angle-spherical C(sp2)-I...N=173.6 degrees) is weaker, in accordance with the order C(sp)-X<--base>C(sp2)-X<--base. Compound 5 was found to give a 1:1 cocrystal 4 with morpholinium iodide (6). In the X-ray crystal studies of 4, N...I halogen-bonding interactions similar to those observed in 5 were shown not to be present, as the arrangement of the molecules is governed by two interwoven hydrogen-bonding networks. The first network involves N-H...O interactions between nearby morpholinium cations, and the second network is based on N-H...N hydrogen bonding between morpholinium cations and imidazolyl groups. Both hydrogen-bonding schemes are charge-assisted. Halogen bonding is not completely wiped out, however, as the triiodoalkene fragment forms a halogen bond with an iodide anion in its vicinity (d(I...I)=3.470 A, angle-spherical C(sp2)-I...I=170.7 degrees). X-ray crystal studies of 6 show a completely different arrangement from that observed in 4, namely, N-H...O interactions are not present. In crystalline 6, morpholinium cations are interconnected through C-H...O bridges (d(H...O)=2.521 and 2.676 A), and the NH2+ groups interact with nearby iodide anions (d(H...I)=2.633 and 2.698 A).     

Dipyrrinone imines: controlling self-association

We report the synthesis of three new dipyrrinone imine analogues and the characterisation of their self-association properties. Based on vapour pressure osmometry and nuclear magnetic resonance studies, placing the imine functional group at C(9) of the dipyrrinone disrupts the native self-association of the dipyrrinone core in a manner that correlates with the conformational A-value of the imine N-substituent.