Single Covalent Bond Research Articles

Eu11Zn4Sn2As12: A Ferromagnetic Zintl Semiconductor with a Layered Structure Featuring Extended Zn4As6 Sheets and Ethane-like Sn2As6 Units

We report the synthesis, structure, and magnetic properties of a new Zintl phase and structure type, Eu11Zn4Sn2As12. The structure and composition of this phase have been established by single-crystal X-ray diffraction and electron microprobe analysis. Eu11Zn4Sn2As12 crystallizes in monoclinic space group C2/c (No. 15) with the following lattice parameters: a = 7.5679(4) A, b = 13.0883(6) A, c = 31.305(2) A, and β = 94.8444(7)° [R1 = 0.0398; wR2 = 0.0633 (all data)]. The anisotropic structural features staggered ethane-like [Sn2As6]12– units and infinite ∞2[Zn2As3]5– sheets extended in the a–b plane. Eu cations fill the space between these anionic motifs. Temperature-dependent magnetic properties and magnetoresistance of this Zintl phase have been studied, and the electronic structure and chemical bonding were elucidated using first-principles quantum chemical calculations (TB-LMTO-ASA). Quantum chemical calculations show that the ethane-like units can be considered as consisting of covalent single bonds;...

Structures and properties of large supramolecular coordination complexes predicted with the generalized energy-based fragmentation method.

The generalized energy-based fragmentation (GEBF) method has been extended to facilitate ab initio calculations of large supramolecular coordination complexes. For metal-containing coordination complexes, a special fragmentation scheme is proposed for GEBF calculations, in which coordinate bonds between metal ions and ligands are kept intact, and only single covalent bonds in organic ligands are cut into fragments. A simple strategy is exploited for the determination of the ground-state spin multiplicity of each metal ion so that the total spin of all metal-containing subsystems is assigned automatically. With this fragmentation scheme, the GEBF method is demonstrated to provide reliable energies, optimized geometry, nuclear magnetic resonance (NMR) properties and the infrared spectrum for a medium-sized supramolecular coordination complex, which are very consistent with those from the full-system quantum chemistry calculations. The GEBF method is then applied to two large supramolecular coordination complexes to illustrate its capability. For the trimetallic coordination complex Fe2Zn2(RuL2)2 (with 618 atoms), the calculated 1H chemical shifts from GEBF calculations with the B97-2 functional can account well for the experimental NMR spectrum. For the cage-guest complex Pd4L8(BF4-)3, the computed infrared spectrum obtained with the GEBF-M06-2X method can help assign the experimental peaks to the corresponding vibrational motions. The GEBF method combining with advanced electronic structure methods is expected to be a useful tool to understand and interpret structural and spectroscopic information of various supramolecular coordination complexes.

Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role

Oxidation of halides and thiocyanate by heme peroxidases to antimicrobial oxidants is an important cornerstone in the innate immune system of mammals. Interestingly, phylogenetic and physiological studies suggest that homologous peroxidases are already present in mycetozoan eukaryotes such as Dictyostelium discoideum. This social amoeba kills bacteria via phagocytosis for nutrient acquisition at its single-cell stage and for antibacterial defense at its multicellular stages. Here, we demonstrate that peroxidase A from D. discoideum (DdPoxA) is a stable, monomeric, glycosylated, and secreted heme peroxidase with homology to mammalian peroxidases. The first crystal structure (2.5 Å resolution) of a mycetozoan peroxidase of this superfamily shows the presence of a post-translationally-modified heme with one single covalent ester bond between the 1-methyl heme substituent and Glu-236. The metalloprotein follows the halogenation cycle, whereby compound I oxidizes iodide and thiocyanate at high rates (>108 m−1 s−1) and bromide at very low rates. It is demonstrated that DdPoxA is up-regulated and likely secreted at late multicellular development stages of D. discoideum when migrating slugs differentiate into fruiting bodies that contain persistent spores on top of a cellular stalk. Expression of DdPoxA is shown to restrict bacterial contamination of fruiting bodies. Structure and function of DdPoxA are compared with evolutionary-related mammalian peroxidases in the context of non-specific immune defense.

Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals.

Protein crystals are porous self-assembling materials that can be rapidly evolved by mutagenesis. We aimed to develop scaffold assisted crystallography techniques in an engineered protein crystal with large pores (>13 nm). Guest molecules were installed via a single covalent bond to attempt to reduce the conformational freedom and achieve high-occupancy structures. We used four different conjugation strategies to attach guest molecules to three different cysteine sites within pre-existing protein crystals. In all but one case, the presence of the adduct was obvious in the electron density. Structure determination of larger guest molecules may be feasible due to the large pores of the engineered scaffold crystals.

Regioselective para-Carboxylation of Catechols with a Prenylated Flavin Dependent Decarboxylase.

The utilization of CO2 as a carbon source for organic synthesis meets the urgent demand for more sustainability in the production of chemicals. Herein, we report on the enzyme‐catalyzed para‐carboxylation of catechols, employing 3,4‐dihydroxybenzoic acid decarboxylases (AroY) that belong to the UbiD enzyme family. Crystal structures and accompanying solution data confirmed that AroY utilizes the recently discovered prenylated FMN (prFMN) cofactor, and requires oxidative maturation to form the catalytically competent prFMNiminium species. This study reports on the in vitro reconstitution and activation of a prFMN‐dependent enzyme that is capable of directly carboxylating aromatic catechol substrates under ambient conditions. A reaction mechanism for the reversible decarboxylation involving an intermediate with a single covalent bond between a quinoid adduct and cofactor is proposed, which is distinct from the mechanism of prFMN‐associated 1,3‐dipolar cycloadditions in related enzymes.

Crystal structures, DFT calculations, and Hirshfeld surface analyses of two new copper(II) and nickel(II) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

Two new Ni(II) and Cu(II) complexes of a tetradentate Schiff base ligand (1 and 2, respectively), derived from the condensation of meso-1,2-diphenyl-1,2-ethylenediamine with 2-hydroxy-6-methoxy benzaldehyde, were synthesized and characterized by IR, UV–Vis, 1H NMR spectroscopy, and X-Ray crystallography. The central metal ions in both complexes are coordinated via the N2O2 coordination sphere of the ligand with square-planar geometry. DFT results revealed that the MN and MO interactions (M = Ni, Cu) are weaker than the typical covalent single bond indicating that ionic and electrostatic interactions are dominated in MN and MO bonds. Hirshfeld surface (HS) analyses of the studied structures 1 and 2 have been performed. The study using 3D HSs and 2D fingerprint plots (FPs) highlighted the dominant contacts H⋯H, C⋯H/H⋯C and O⋯H/H⋯O in both structures, and H⋯Cl in 2. The molecular assemblies held by C⋯O/O⋯C (in 1) and C⋯C (in 1 and 2) type dipole–dipole interactions are also found in the crystal packing contributing towards stability. The significant contributions arising from the mentioned interactions in crystal packing are also revealed from the Hirshfeld surface FPs showing a major contribution to total HS area for the H⋯H contacts for both structures.

Reaction of the Tricyanoborate Dianion [B(CN)3]2- with HgCl2.

The very reactive [B(CN)3]2- dianion has a strongly nucleophilic boron atom and can be used for the synthesis of tricyanoborates, which otherwise are difficult to access. Herein the reaction of this anion with HgCl2 is reported. The main product is the anionic mercury complex [Hg(B(CN)3)2]2-. Heteronuclear NMR spectroscopic experiments shows that the reaction proceeds via the intermediate [ClHgB(CN)3]2-. Even though [Hg(B(CN)3)2]2- is the main product, it is difficult to obtain it in pure form, because it slowly decomposes in the presence of water and air to [(NC)HgB(CN)3]-. All three anions were fully characterized by hetereonuclear NMR spectroscopy (11B, 13C, and 199Hg). Single-crystal X-ray diffraction studies of the salts K[ClHgB(CN)3], [Ph4P]2[Hg(B(CN)3)2], K[(NC)HgB(CN)3], and [Ph4P][(NC)HgB(CN)3] revealed linear coordination environments around mercury for all anions. The Hg-B bonds range from 2.219(5) Å in [Hg(B(CN)3)2]2- to 2.148(11) Å in [ClHgB(CN)3]-, are in accord with the sum of the covalent radii of mercury and boron, and can be described as covalent single bonds. A comparison with related complexes indicates that the [B(CN)3]2- dianion is a stronger ligand than chloride, cyanide, or carbenes. [Hg(B(CN)3)2]2- hydrolyses in solution only in the presence of oxygen. It is suggested that cis-[Hg(OH)2(B(CN)3)2]2- is formed as a very unstable intermediate, which decomposes very fast to [(NC)HgB(CN)3]- and other products. The anion cis-[Hg(OH)2(B(CN)3)2]2- would contain mercury in the unusual oxidation state +IV. Quantum-chemical calculations were performed to support this assumption.

Sterically protected organophosphorus compounds of unusual structures

Abstract The character of bis(2,4,6-tri-tert-butylphenyl)diphosphene is described experimentally and theoretically. The diphosphene is stabilized by steric protection and the structure can be characterized by spectroscopic as well as crystallographic analyses. Theoretical calculation on the diphosphene strongly suggests that the P=P bond is an isolated double bond and that the P–C bonds are single covalent bond. The reactivity has been investigated including photolysis, oxidation, sulfurization, selenation, transition-metal complex formation, and carbene addition. Plausible mechanistic scheme for the reaction of the diphosphene with 3,4,5,6-tetrachlorocyclohexa-3,5-diene-1,2-dione (or tetrachloro-o-benzoquinone) to a pentavalent spiro product is discussed based on the product analysis.

Bivalent IAP antagonists, but not monovalent IAP antagonists, inhibit TNF-mediated NF-\u03baB signaling by degrading TRAF2-associated cIAP1 in cancer cells

The inhibitor of apoptosis (IAP) proteins have pivotal roles in cell proliferation and differentiation, and antagonizing IAPs in certain cancer cell lines results in induction of cell death. A variety of IAP antagonist compounds targeting the baculovirus IAP protein repeat 3 (BIR3) domain of cIAP1have advanced into clinical trials. Here we sought to compare and contrast the biochemical activities of selected monovalent and bivalent IAP antagonists with the intent of identifying functional differences between these two classes of IAP antagonist drug candidates. The anti-cellular IAP1 (cIAP1) and pro-apoptotic activities of monovalent IAP antagonists were increased by using a single covalent bond to combine the monovalent moieties at the P4 position. In addition, regardless of drug concentration, treatment with monovalent compounds resulted in consistently higher levels of residual cIAP1 compared with that seen following bivalent compound treatment. We found that the remaining residual cIAP1 following monovalent compound treatment was predominantly tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2)-associated cIAP1. As a consequence, bivalent compounds were more effective at inhibiting TNF-induced activation of p65/NF-κB compared with monovalent compounds. Moreover, extension of the linker chain at the P4 position of bivalent compounds resulted in a decreased ability to degrade TRAF2-associated cIAP1 in a manner similar to monovalent compounds. This result implied that specific bivalent IAP antagonists but not monovalent compounds were capable of inducing formation of a cIAP1 E3 ubiquitin ligase complex with the capacity to effectively degrade TRAF2-associated cIAP1. These results further suggested that only certain bivalent IAP antagonists are preferred for the targeting of TNF-dependent signaling for the treatment of cancer or infectious diseases.

Difference in Number of Electrons in Inner Shells of Charged or Uncharged Elements in Organic and Inorganic Chemistry: Compatibility with the Even-Odd Rule

The recently introduced even-odd rule has been shown to successfully represent chemical structures of ions and molecules. While comparing available drawings in the scientific literature with the list of compounds predicted by the even-odd rule, it became however obvious that existing compounds are fewer than expected. Several predicted compounds involving many covalent bonds have apparently never been experimentally observed. Neutral oxygen for instance is expected to have 6 valence electrons, whereas oxygen can only build a maximum of two bonds, as in water. This specificity is observed for elements in the top-right corner of the periodic table. For compounds to contain only single covalent bonds, and thus follow the even-odd rule, further explanations are necessary. The present paper proposes that those specific elements experience a transfer of electrons from the valence shell into the inner shell, making them unavailable for further bonding. These elements will be described as organic, hereby providing a clear and hopefully unifying definition of the term. In opposition, inorganic elements have a constant inner shell no matter their electrical state or the number of bonds they maintain. More than 70 compounds involving 11 elements of the main group are studied, revealing a progression from fully inorganic elements at the left of the periodic table to fully organic elements. The transition between inorganic or organic elements is made of few elements that take an organic form when negatively charged; they are labelled semi-organic. The article concludes that the fully organic elements of the main group are Oxygen and Fluorine, whereas semi-organic elements are more numerous: C, N, S, Cl, Se, Br and I. Thus, the even-odd rule becomes fully compatible with scientific knowledge of compounds in liquid or gaseous phase.

Significance of Ethanol Product of Gmelina arborea

This work covers the process of making Ethanol from wood dust instead of starchy biomass which could be meant for food or instead of overdependence on hydrocarbon source. The saw dust of Gmelina arborea was collected in a saw mill in Ore, Ondo State, Nigeria and it was used to produce ethanol by hydrolysis and fermentation processes. The density of the wood species was 570 kg/m3. The ionic constituents of the ethanol from the wood biomass were analyzed using Fourier Transform Infrared Spectrometric Analyzer (FTIR) and Atomic Absorption Spectrometric Analyzer (AAS). The AAS result shows that the ethanol obtained from the wood species contains transition metals like Copper (Cu), Zinc (Zn), Cadmium (Cd) and Chromium (Cr) while the FTIR results show the presence of ethanol functional groups such as OH, Carbon to carbon single covalent bond which and these are normal components of ethanol in the conventional ethanol.

Anticancer Effects of a New Aminosugar-conjugated Platinum Complex Agent Against Cisplatin-resistant Gastric Cancer.

Resistance against cisplatin is a problem for the success of gastric cancer chemotherapy. Herein, we evaluated the antitumor effect of a new aminosugar-conjugated, mono-functional platinum complex (Pt-Oqn), which forms a single covalent bond with DNA. We compared the cytotoxicity of Pt-Oqn to that of cisplatin (CDDP), oxaliplatin (L-OHP) and carboplatin (CBDCA). We also compared Pt-Oqn and cisplatin for DNA double-strand breaks based on phosphorylated histone H2AX levels in cancer cells and antitumor effects in xenograft models. The resistance factor (RF) for Pt-Oqn was low among the four drugs, indicating the potential of Pt-Oqn for overcoming CDDP-induced resistance. In MKN45-R cells, γ-H2AX protein increased following treatment with Pt-Oqn, but not with cisplatin. Finally, Pt-Oqn, but not cisplatin, showed significant antitumor effects in MKN45-R xenografts. This new aminosugar-conjugated platinum complex is a promising candidate agent for overcoming the drug resistance of cisplatin-resistant stomach cancer.

Matrix Infrared Spectra and Quantum Chemical Calculations of Ti, Zr, and Hf Dihydride Phosphinidene and Arsinidene Molecules.

Laser ablated Ti, Zr, and Hf atoms react with phosphine during condensation in excess argon or neon at 4 K to form metal hydride insertion phosphides (H2P-MH) and metal dihydride phosphinidenes (HP═MH2) with metal phosphorus double bonds, which are characterized by their intense metal-hydride stretching frequencies. Both products are formed spontaneously on annealing the solid matrix samples, which suggests that both products are relaxed from the initial higher energy M-PH3 intermediate complex, which is not observed. B3LYP (DFT) calculations show that these phosphinidenes are strongly agostic with acute H-P═M angles in the 60° range, even smaller than those for the analogous methylidenes (carbenes) (CH2═MH2) and in contrast to the almost linear H-N═Ti subunit in the imines (H-N═TiH2). Comparison of calculated agostic and terminal bond lengths and covalent bond radii for HP═TiH2 with computed bond lengths for Al2H6 finds that these strong agostic Ti-H bonds are 18% longer than single covalent bonds, and the bridged bonds in dialane are 10% longer than the terminal Al-H single bonds, which show that these agostic bonds can also be considered as bridged bonds. The analogous arsinidenes (HAs═MH2) have 4° smaller agostic angles and almost the same metal-hydride stretching frequencies and double bond orders. Calculations with fixed H-P-Ti and H-As-Ti angles (170.0°) and Cs symmetry find that electronic energies increased by 36 and 44 kJ/mol, respectively, which provide estimates for the agostic/bridged bonding energies.

Regulating levels of the neuromodulator d-serine in human brain: structural insight into pLG72 and d-amino acid oxidase interaction.

The human flavoenzyme d-amino acid oxidase (hDAAO) degrades the NMDA-receptor modulator d-serine in the brain. Although hDAAO has been extensively characterized, little is known about its main modulator pLG72, a small protein encoded by the primate-specific gene G72 that has been associated with schizophrenia susceptibility. pLG72 interacts with neosynthesized hDAAO, promoting its inactivation and degradation. In this work, we used low-resolution techniques to characterize the surface topology of the hDAAO-pLG72 complex. By using limited proteolysis coupled to mass spectrometry, we could map the exposed regions in the two proteins after complex formation and highlighted an increased sensitivity to proteolysis of hDAAO in complex with pLG72. Cross-linking experiments by using bis(sulfosuccinimidyl)suberate identified the single covalent bond between T182 in hDAAO and K62 in pLG72. In order to validate the designed mode of interaction, three pLG72 variants incrementally truncated at the C terminus, in addition to a form lacking the 71 N-terminal residues, were produced. All variants were dimeric, folded, and interacted with hDAAO. The strongest decrease in affinity for hDAAO (as well as for the hydrophobic drug chlorpromazine) was apparent for the N-terminally deleted pLG72(72-153) form, which lacked K62. On the other hand, eliminating the disordered C-terminal tail yielded a more stable pLG72 protein, improved the binding to hDAAO, although giving lower enzyme inhibition. Elucidation of the mode of hDAAO-pLG72 interaction now makes it possible to design novel molecules that, by targeting the protein complex, can be therapeutically advantageous for diseases related to impairment in d-serine metabolism.

High Pseduo-Stoke's Shift of a Naphthalene-Bisindolylmaleimide Dye.

An energy transfer cassette was reported with energy donor and acceptor incorporated in one molecular. The two units (naphthalene and bisindolylmaleimide) were connected by covalent single bond. The intramolecular repulsion twisted the molecular conformation, thereby forcing the two units act as independent chromophores. Upon photoexcitation (λ = 280 nm), bright emission peak was observed around 583 nm. The intramolecular cascade energy transfer from the naphthalene moiety to the bisindolylmaleimide framework is efficient and the efficiency is estimated to be 86%, providing large pseudo-Stoke's shift (303 nm). At such a short separation, the orbital overlap interaction was completely isolated between chromophoric units. Computational study was carried out based on DFT. Further analysis of optimized structure and FMOs supports the efficient energy transfer in NBM. Favorable photophysical properties, such as efficient energy transfer, strong emission, and large Stoke's shift make it an attractive functional dye.

The Even-Odd and the Isoelectronicity Rules Applied to Single Covalent Bonds in Ionic, Double-Face-Centered Cubic and Diamond-Like Crystals

Although atom configuration in crystals is precisely known thanks to imaging techniques, there is no experimental way to know the exact location of bonds or charges. Many different representations have been proposed, yet no theory to unify conceptions. The present paper describes methods to derive bonds and charge location in double-face-centered cubic crystals with 4 and 6 atoms per unit cell using two novel rules introduced in earlier works: the even-odd and the isoelectronicity rules. Both of these rules were previously applied to ions, molecules and some solids, and the even-odd rule was also tested on two covalent crystal structures: centered-cubic and single-face-centered cubic crystals. In the present study, the diamond-like structure was subjected to the isoelectronicity rule in order to derive Zinc-blende structures. Rock-salt-like crystals were derived from each other using both rules. These structures represent together more than 230 different crystals. Findings for these structures are threefold: both rules describe a very sure method to obtain valid single covalent-bonded structures; single covalent structures can be used in every case instead of the classical ionic model; covalent bonds and charges positions do not have any relation with the valence number given in the periodic table.

Bridging Efficiency within Multinuclear Homogeneous Catalysts in the Photocatalytic Reduction of Carbon Dioxide

AbstractA trinuclear complex consisting of one [Ru(dmb)3]2+ (dmb=4,4′‐dimethyl‐2,2′‐bipyridine) (Ru) and two [Re(dmb)(CO)3Cl] (Re) building blocks, [Re(CO)3Cl(dmb−dmb)Ru(dmb)(dmb−dmb)Re(CO)3Cl](PF6)2 (Re−Ru−Re), is presented. Photophysical properties of Re−Ru−Re and the individual components with different or no covalent linkages are thoroughly investigated and compared. To elucidate the role of the single covalent bonds, photocatalytic reduction of CO2 is performed with the trinuclear complex and a series of model systems featuring systematic absence of linkages between the metal centers. Photoluminescence spectra and quantum yields reveal efficient energy transfer from the excited state of Re to Ru if these fragments are covalently linked. Moreover, intramolecular electron transfer from the one‐electron reduced species of Ru to Re occurs if there is covalent bonding, leading to a higher photostability and thus the highest turnover number in photocatalytic CO2 reduction of 199 for the trinuclear complex Re−Ru−Re within the systems under investigation. Optimized experimental conditions reveal the highest turnover number (315) reported to date for ReI/RuII‐based homogeneous catalysts in photocatalytic CO2 reduction.

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.

An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

The large variation in acidity of diethyl ether cation induced by internal rotation about a single covalent bond.

In the IR spectrum of the diethyl ether cation, an extraordinarily intense band, with an extremely broad bandwidth, was observed at 2700 cm(-1), much lower frequency than normal CH stretch frequencies. This band is assigned to the stretch band of the CH bond, which is hyperconjugated with the singly occupied molecular orbital of the oxygen atom. The hyperconjugation causes the delocalization of the σ electron of the CH bond so that it enhances the acidity of the CH bond as well as the CH stretch band intensity. Theoretical simulation shows that the strength of hyperconjugation varies greatly with internal rotation of the ethyl group, and this is reflected in the large width of the observed CH stretch band. These results indicate that the DEE cation drastically changes its property from aprotic to highly acidic by the rotational isomerization of the ethyl group.

How the Even-Odd Rule, by Defining Electrons Pairs and Charge Positions, Can Be Used as a Substitute to the Langmuir-Octet Rule in Understanding Interconnections between Atoms in Ions and Molecules

In the course of time, numerous rules were proposed to predict how atoms connect through covalent bonds. Based on the classification of elements in the periodic table, the rule of eight was first proposed to draw formulas of organic compounds. The later named octet rule exhibited shortcomings when applied to inorganic compounds. Another rule, the rule of two, using covalent bonds between atoms, was proposed as an attempt to unify description of organic and inorganic molecules. This rule unfortunately never managed to expand the field of application of the octet rule to inorganic compounds. In order to conciliate organic and inorganic compounds, the recently put forward even-odd and the isoelectronicity rules suggest the creation of one group of compounds with pairs of electrons. These rules compass the rule of two for covalent bonds as well as the octet rule for organic compounds and suggest transforming bonds of multi-bonded compounds in order to unify representations of both groups of compounds. The aim of the present paper is fourfold: to extend the rule of two to every atom shells; to replace the well-known octet rule by the even-odd rule; to apply the isoelectronicity rule to each atom and to reduce the influence range of the charge of an atom in a compound. According to both rules, the drawing of one atom with its single-covalent bonds is described with electron pairs and charge positions. To illustrate the rules, they are applied to 3D configurations of clusters.