Unusual Bond Research Articles

Ring-expansion and desulfurisation of thiophenes with an aluminium(I) reagent.

Reactions of thiophene, 2-methylthiophene, 2-methoxythiophene, 2,3-dimethylthiophene, and benzothiophene with the aluminium(I) complex [{ArNC(Me)2H}Al] (Ar = 2,6-di-isopropylphenyl) are reported. In all cases, carbon-sulfur bond activation and ring-expansion of the heterocycle is observed. For thiophene, we identify a reaction network for desulfurisation that includes an unusual second carbon-sulfur bond activation step.

New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenase.

[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O2-sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.

The Rebbe and the Poet on Yom Kippur 1973

Abstract: Avot Yeshurun's poem, "The Tsaddik of Modzitz," highlights the unusual bond between two polar opposite personalities from the 1970s Tel Aviv scene: the secular poet Avot Yeshurun, and the ultraorthodox Rabbi Shmuel Eliyahu Taub, the Rebbe of Modzitz, who transcended his non-Zionist circles, gaining the admiration of Israelis of all walks of life. This relationship reaches a dramatic climax on a cataclysmic day in Israel's history, Yom Kippur 1973, when the surprising outbreak of a war shook Israelis' sense of invincibility and some of their Zionist creeds. At the heart of the poem is the Rebbe's luminous personality and demeanor during the services, and their impact on the poet. In his poetry, Yeshurun had revealed a conflicted personality, unable to reconcile between the vanished old world and the new reality, between the Zionist dream of his youth and the current Israeli geopolitical and ethical dilemmas. The Rebbe represents wholeness, finding in the ancient liturgy about the animals that were led to slaughter in the Temple an opportunity to subtly communicate his grief over the human sacrifices in Jewish recent past as well as at that very moment. The Rebbe's compassionate presence and his stirring niggunim eventually comfort the troubled poet. The Rebbe's words, with which Yeshurun closes his poem, reassure the poet of the validity of the State of Israel and appear to align with the paradigm of religious Zionism, viewing Israel as an essential moment in the Jewish journey toward redemption.

Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy.

The refinement of predicted 3D models aims to bring them closer to the native structure by fixing errors including unusual bonds and torsion angles and irregular hydrogen bonding patterns. Refinement approaches based on molecular dynamics (MD) simulations using different types of restraints have performed well since CASP10. ReFOLD, developed by the McGuffin group, was one of the many MD-based refinement approaches, which were tested in CASP 12. When the performance of the ReFOLD method in CASP12 was evaluated, it was observed that ReFOLD suffered from the absence of a reliable guidance mechanism to reach consistent improvement for the quality of predicted 3D models, particularly in the case of template-based modelling (TBM) targets. Therefore, here we propose to utilize the local quality assessment score produced by ModFOLD6 to guide the MD-based refinement approach to further increase the accuracy of the predicted 3D models. The relative performance of the new local quality assessment guided MD-based refinement protocol and the original MD-based protocol ReFOLD are compared utilizing many different official scoring methods. By using the per-residue accuracy (or local quality) score to guide the refinement process, we are able to prevent the refined models from undesired structural deviations, thereby leading to more consistent improvements. This chapter will include a detailed analysis of the performance of the local quality assessment guided MD-based protocol versus that deployed in the original ReFOLD method.

Bond Energy Assists Accurate Molecule Property Prediction

Molecule property prediction is a fundamental problem in many fields. To accurate and rapid prediction of molecules properties, molecule characterization and representation are key operations in the pretreatment stage. Generally, we represent molecule as graph based on different features such as element type, bond type, etc. The features we select could have the ability of enough representation and discrimination. However, in terms of bond embedding, one-hot coding is the most common processing method in the current research which means the features we used are discrete and could not distinguish different single or double bonds in a molecule. Here we add predicted bond energy feature as an extra chemical bond descriptor and compare three popular GNN models on two different datasets. The experiment shows that supplying additional unusual bond features—bond energy will improve the model performance significantly. The PDN model with bond energy has best performance among three model. Finally, we discuss the experimental result.

Aspertaichunol A, an Immunomodulatory Polyketide with an Uncommon Scaffold from the Insect-Derived Endophytic Aspergillus taichungensis SMU01.

Aspertaichunol A (1), a polyketide with a novel scaffold, was isolated from the medicinal insect (Periplaneta americana)-derived endophytic Aspergillus taichungensis SMU01. Its structure was assigned on the basis of spectroscopic data and quantum chemical computational methods. Notably, 1 possesses an uncommon tricyclo[6.2.0.02,6]decane motif and an unusual bridgehead double bond (anti-Bredt system). A plausible biosynthetic pathway, involving a key intramolecular [2+2] cycloaddition and a reductive cyclization, is postulated. Finally, the immunomodulatory activity of 1 at 20 nM was evaluated by promoting Th9 cell differentiation from naive CD4+CD62L+ T cells.

Electronic Structures and Unusual Chemical Bonding in Actinyl Peroxide Dimers [An2O6]2+ and [(An2O6)(12-crown-4 ether)2]2+ (An = U, Np, and Pu).

As known, actinyl peroxides play important roles in environmental transport of actinides, and they have strategic importance in the application of nuclear industry. Compared to the most studied uranyl peroxides, the studies of transuranic counterparts are still few, and more information about these species is needed. In this work, experimentally inspired actinyl peroxide dimers ([An2O6]2+, An = U, Np, and Pu) have been studied and analyzed by using density functional theory and multireference wave function methods. This study determines that the three [An2O6]2+ have unique electronic structures and oxidation states, as [(UVIO2)2(O2)2-]2+, [(NpVIIO2)2(O2-)2]2+, and mixed-valent [(PuVI/VO2)2(O2)1-]2+. This study demonstrates the significance of two bridging oxo ligands with at most four electron holes availability in ionically directing actinyl and resulting in the unusual multiradical bonding in [(PuVI/VO2)2(O2)1-]2+. In addition, thermodynamically stable 12-crown-4 ether (12C4) chelated [(An2O6)(12C4)2]2+ complexes have been predicted, that could maintain these unique electronic structures of [An2O6]2+, where the An ← O12C4 dative bonding shows a trend in binding capacity of 12C4 from κ4 (U) to κ3 (Np) and κ4 (Pu). This study reveals the interesting electronic character and bonding feature of a series of early actinide elements in peroxide complexes, which can provide insights into the intrinsic stability of An-containing species.

Reversible Glutamate Coordination to High-Valent Nickel Protects the Active Site of a [NiFe] Hydrogenase from Oxygen.

NAD+-reducing [NiFe] hydrogenases are valuable biocatalysts for H2-based energy conversion and the regeneration of nucleotide cofactors. While most hydrogenases are sensitive toward O2 and elevated temperatures, the soluble NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus (HtSH) is O2-tolerant and thermostable. Thus, it represents a promising candidate for biotechnological applications. Here, we have investigated the catalytic activity and active-site structure of native HtSH and variants in which a glutamate residue in the active-site cavity was replaced by glutamine, alanine, and aspartate. Our biochemical, spectroscopic, and theoretical studies reveal that at least two active-site states of oxidized HtSH feature an unusual architecture in which the glutamate acts as a terminal ligand of the active-site nickel. This observation demonstrates that crystallographically observed glutamate coordination represents a native feature of the enzyme. One of these states is diamagnetic and characterized by a very high stretching frequency of an iron-bound active-site CO ligand. Supported by density-functional-theory calculations, we identify this state as a high-valent species with a biologically unprecedented formal Ni(IV) ground state. Detailed insights into its structure and dynamics were obtained by ultrafast and two-dimensional infrared spectroscopy, demonstrating that it represents a conformationally strained state with unusual bond properties. Our data further show that this state is selectively and reversibly formed under oxic conditions, especially upon rapid exposure to high O2 levels. We conclude that the kinetically controlled formation of this six-coordinate high-valent state represents a specific and precisely orchestrated stereoelectronic response toward O2 that could protect the enzyme from oxidative damage.

Real space study of local bonding for zinc structure based on temperature-dependent x-ray pair distribution function analysis

Zinc metal has a hexagonal close packing hcp structure with an unusual axial ratio c/a. This work presents the local atomic structure analysis of elemental zinc using the x-ray atomic pair distribution function (PDF) method and total synchrotron x-ray scattering in the temperature range of 100–300 K. In this PDF study, we determined the evolution of local bonding in zinc structure in the temperature range of 100–300 K by fitting the first two peaks in the radial distribution function (RDF), R(r), with two Gaussian peaks. Our local structure results reveal a piece of evidence for unusual bond length behavior at low temperatures. The PDF analysis revealed that the a-axis varies linearly from 300 to 160 K and remains constant below 160 K. This local structural result indicates that at temperatures below 160 K, the Zn–Zn bonds are no longer thermally contractible in the ab plane, in agreement with standard crystallographic analysis [J. Nuss et al., Z. Anorg. Allg. Chem. 636, 309 (2010)]. Another significant observation is that the local thermal expansion for the a-axis was found to be three times larger than the one obtained using conventional crystallographic methods [U. Wedig et al., Z. Anorg. Allg. Chem. 639, 2036 (2013)]. This PDF result shows the advantage of total scattering PDF methods in studying the local structural features in elemental zinc, which cannot be captured by the crystallographic model. In addition, this PDF study demonstrates that multiple RDF-peak fitting is a useful approach for interpreting the local structural features of such a non-ideal hcp structure.

Anionic N18 Macrocycles and a Polynitrogen Double Helix in Novel Yttrium Polynitrides YN6 and Y2N11 at 100 GPa

AbstractTwo novel yttrium nitrides, YN6 and Y2N11, were synthesized by direct reaction between yttrium and nitrogen at 100 GPa and 3000 K in a laser‐heated diamond anvil cell. High‐pressure synchrotron single‐crystal X‐ray diffraction revealed that the crystal structures of YN6 and Y2N11 feature a unique organization of nitrogen atoms—a previously unknown anionic N18 macrocycle and a polynitrogen double helix, respectively. Density functional theory calculations, confirming the dynamical stability of the YN6 and Y2N11 compounds, show an anion‐driven metallicity, explaining the unusual bond orders in the polynitrogen units. As the charge state of the polynitrogen double helix in Y2N11 is different from that previously found in Hf2N11 and because N18 macrocycles have never been predicted or observed, their discovery significantly extends the chemistry of polynitrides.

Anionic N18 Macrocycles and a Polynitrogen Double Helix in Novel Yttrium Polynitrides YN6 and Y2 N11 at 100 GPa.

Two novel yttrium nitrides, YN6 and Y2N11, were synthesized by direct reaction between yttrium and nitrogen at 100 GPa and 3000 K in a laser‐heated diamond anvil cell. High‐pressure synchrotron single‐crystal X‐ray diffraction revealed that the crystal structures of YN6 and Y2N11 feature a unique organization of nitrogen atoms—a previously unknown anionic N18 macrocycle and a polynitrogen double helix, respectively. Density functional theory calculations, confirming the dynamical stability of the YN6 and Y2N11 compounds, show an anion‐driven metallicity, explaining the unusual bond orders in the polynitrogen units. As the charge state of the polynitrogen double helix in Y2N11 is different from that previously found in Hf2N11 and because N18 macrocycles have never been predicted or observed, their discovery significantly extends the chemistry of polynitrides.

HUMAN AND GHOST ATTACHMENT IN HANNA ALKAF’S THE GIRL AND THE GHOST

For centuries, authors of literary works have sought to bewitch and enchant readers with accounts of supernatural elements such as monsters, spirits and ghosts. Ghosts especially are often depicted as representations of evil and the polar opposite of mankind. In Hanna Alkaf’s The Girl and The Ghost (2020) the adolescent protagonist, Suraya, develops an unusual bond with a ghost, Pink. This is indeed refreshing, considering the human-ghost relationship in the local literary scene is often represented as antagonistic, opposing forces, resulting in ghosts being portrayed as evil, vengeful creatures set to taunt, haunt and wreck humans’ lives. Critical examination of the human-ghost bond in the local literary-critical practice is lacking. This research aims to fill this gap by examining the human-ghost bond in The Girl and The Ghost and how this bond contributes to the (human) protagonist’s personal development. In this paper, The Girl and The Ghost is read using John Bowlby’s theory of attachment due to its robust approach to understanding human beings' emotional bond, or attachment, with their attachment figures. We argue the human-ghost bond in The Girl and The Ghost sets the novel apart from other local ghost stories filled with wicked, destructive ghosts. The findings suggest other possibilities of attachment figures when the relationship between a mother and child grows apart. The unusual but enduring relationship between Suraya and Pink demonstrates that a child’s secure attachment need not be limited to motherly figures.
 Keywords: Malaysian literature in english, the girl and the ghost, hanna alkaf, ghost tales, attachment theory

30-norlanostane triterpenoids and steroid derivatives from the endophytic fungus Aspergillus nidulans

Two undescribed 30-norlanostane triterpenoids, named nidulanoids A and B, one ergostane-type steroid with an unusual double bond between C-17 and C-20 designated (17E,22E,24R)-3β,5α-dihydroxyergosta-7,17,22-trien-6,16-dione, and one pregnane, (7Z,9Z,17Z)-,2α,3β-dihydroxypregna-7,9,17 (20)-trien-18-al, along with six known steroids were isolated from the extract of the fungus Aspergillus nidulans. Among them, nidulanosides A and B represents the first example of naturally occurred 30-norlanostane triterpenoids featuring a C9 side-chain moiety at C-17 and a hemiacetal system formed between C-3 and C-19, as an intermediate between lanostane and the regular steriods; the structure of (17E,22E,24R)-3β,5α-dihydroxyergosta-7,17,22-trien-6,16-dione possesses an untypical Δ17,20 double bond; meanwhile, (7Z,9Z,17Z)-,2α,3β-dihydroxypregna-7,9,17 (20)-trien-18-al represents the first example of C-21 steroid with an aldehyde group at C-13. Their structures and absolute stereochemistry were elucidated based on spectroscopic data, electronic circular dichroism (ECD) calculations, and single-crystal X-ray diffraction analysis. (7Z,9Z,17Z)-,2α,3β-dihydroxypregna-7,9,17 (20)-trien-18-al showed moderate inhibitory activities against rat brain cancer (PC12) cell lines, with IC50 value of 7.34 μM. This study enriches the diversified structures of triterpenoids and steroids analogues from A. nidulans and indicated (7Z,9Z,17Z)-,2α,3β-dihydroxypregna-7,9,17(20)-trien-18-al to be a promising lead compound against PC12 cell lines.

Collective interactions among organometallics are exotic bonds hidden on lab shelves

Recent discovery of an unusual bond between Na and B in NaBH3− motivated us to look for potentially similar bonds, which remained unnoticed among systems isoelectronic with NaBH3−. Here, we report a novel family of collective interactions and a measure called exchange-correlation interaction collectivity index (ICIXC; {ICI}in left[{{{{mathrm{0,1}}}}}right]) to characterize the extent of collective versus pairwise bonding. Unlike conventional bonds in which ICIXC remains close to one, in collective interactions ICIXC may approach zero. We show that collective interactions are commonplace among widely used organometallics, as well as among boron and aluminum complexes with the general formula [Ma+AR3]b− (A: C, B or Al). In these species, the metal atom interacts more efficiently with the substituents (R) on the central atoms than the central atoms (A) upon forming efficient collective interactions. Furthermore, collective interactions were also found among fluorine atoms of XFn systems (X: B or C). Some of organolithium and organomagnesium species have the lowest ICIXC among the more than 100 studied systems revealing the fact that collective interactions are rather a rule than an exception among organometallic species.

Atomic Clusters with Unusual Structure, Bonding and Reactivity: Theoretical Approaches, Computational Assessment and Applications

d-Glucose derived synthon 4 was successfully utilized for the synthesis of (2S,3R)-β-hydroxyornithine 1, (2S,3R)-β-hydroxylysine 2 and tetrahydroazepine core of balanol 3.

Berberine bridge enzyme-like oxidase-catalysed double bond isomerization acts as the pathway switch in cytochalasin synthesis

Cytochalasans (CYTs), as well as their polycyclic (pcCYTs) and polymerized (meCYTs) derivatives, constitute one of the largest families of fungal polyketide-nonribosomal peptide (PK-NRP) hybrid natural products. However, the mechanism of chemical conversion from mono-CYTs (moCYTs) to both pcCYTs and meCYTs remains unknown. Here, we show the first successful example of the reconstitution of the CYT core backbone as well as the whole pathway in a heterologous host. Importantly, we also describe the berberine bridge enzyme (BBE)-like oxidase AspoA, which uses Glu538 as a general acid biocatalyst to catalyse an unusual protonation-driven double bond isomerization reaction and acts as a switch to alter the native (for moCYTs) and nonenzymatic (for pcCYTs and meCYTs) pathways to synthesize aspochalasin family compounds. Our results present an unprecedented function of BBE-like enzymes and highly suggest that the isolated pcCYTs and meCYTs are most likely artificially derived products.

Stimuli Responsive Materials Supported by Orthogonal Hydrogen and Halogen Bonding or I···Alkene Interaction.

Smart materials represent an elegant class of (macro)-molecules endowed with the ability to react to chemical/physical changes in the environment. Herein, we prepared new photo responsive azobenzenes possessing halogen bond donor groups. The X-ray structures of two molecules highlight supramolecular organizations governed by unusual noncovalent bonds. In azo dye I-azo-NO2, the nitro group is engaged in orthogonal H···O···I halogen and hydrogen bonding, linking the units in parallel undulating chains. As far as compound I–azo–NH–MMA is concerned, a non-centrosymmetric pattern is formed due to a very rare I···π interaction involving the alkene group supplemented by hydrogen bonds. The Cambridge Structural Database contains only four structures showing the same I···CH2=C contact. For all compounds, an 19F-NMR spectroscopic analysis confirms the formation of halogen bonds in solution through a recognition process with chloride anion, and the reversible photo-responsiveness is demonstrated upon exposing a solution to UV light irradiation. Finally, the intermediate I–azo–NH2 also shows a pronounced color change due to pH variation. These azobenzenes are thereby attractive building blocks to design future multi-stimuli responsive materials for highly functional devices.

Unusual polymethylene-interrupted, Δ5 monounsaturated and omega-3 fatty acids in sea urchin (Arbacia punctulata) from the Gulf of Mexico identified by solvent mediated covalent adduct chemical ionization mass spectrometry

Sea urchin (class Echinoidea) gonads are a prized delicacy in Japan and many other world cultures. The complexity of its fatty acid (FA) profile, particularly minor FA, presents a formidable analytical challenge. We applied solvent mediated (SM) covalent adduct chemical ionization (CACI) tandem mass spectrometry to comprehensive de novo structural and quantitative characterization of the FA profile of Gulf of Mexico Atlantic sea urchin (Arbacia punctulata). >100 FA were detected including many with unusual double bond structure. Gulf sea urchin gonad lipids are rich in Δ5 monounsaturated FA 20:1(5Z) at 2.7% and the polymethylene-interrupted (PMI) diene 20:2(5Z,11Z) at 4.9%, as well as common omega-3 eicosapentaenoic acid (EPA; 5Z, 8Z, 11Z, 14Z, 17Z) at 9.8%±3.1% and arachidonic acid (AA; 5Z, 8Z, 11Z, 14Z) at 6.1%±2.1%. We propose plausible desaturation/elongation-based biochemical pathways for the endogenous production of unusual unsaturates. Unusual unsaturates may modify mammalian signaling and present novel bioactivities.

Two-band conduction and nesting instabilities in superconducting Ba2CuO3+δ : First-principles study

First principles investigations of the high temperature superconducting system Ba$_2$CuO$_{3+\delta}$, recently discovered at $\delta\approx0.2$ at $T_c=70$ K, are applied to demonstrate the effects of oxygen ordering on the electronic and magnetic properties. The observed `highly over-doped' superconducting phase displays stretched Cu-planar oxygen O$_{\rm P}$ distances and anomalously shortened Cu-apical O$_{\rm A}$ separations compared with other cuprates. The stoichiometric system $\delta=0$, with its strongly one-dimensional (1D) Cu-O$_{\rm P}$ chain structure, when nonmagnetic shows 1D Fermi surfaces that lead, within density functional theory, to antiferromagnetic Cu-O$_{\rm P}$ chains (a spin-Peierls instability). Accounting for 1D fluctuations and small interchain coupling according to the theory of Schulz indicates this system, like Sr$_2$CuO$_3$, is near the 1D Luttinger-liquid quantum critical phase. The unusual Cu-O bond lengths per se have limited effects on other properties for $\delta$=0. We find that a `doubled bilayer' structure of alternating Cu-O$_{\rm P}$ chains and wide rung Cu$_3$O$_4$ ladders is the energetically preferred one of three possibilities where the additional oxygen ions bridge Cu-O$_{\rm P}$ chains in the superconducting phase $\delta=1/4$. Nominal formal valences of the three Cu sites are discussed. The six-fold (octahedral) site is the most highly oxidized, accepting somewhat more holes in the $d_{z^2}$ orbital than in the $d_{x^2-y^2}$ orbital. The implication is that two-band physics is involved in the pairing mechanism and the superconducting carriers. The Fermi surfaces of this metallic bilayer structure show both 1D and 2D strong (incipient) nesting instabilities, possibly accounting for the lack of clean single-phase samples based on this structure and suggesting importance for the pairing mechanism.

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Abstract Human manganese superoxide dismutase (MnSOD) is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers (CPETs) are used by the enzyme to rid the mitochondria of O 2 •− , a precursor to other harmful reactive oxygen and nitrogen species. The mechanisms of CPET-utilizing enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules involved in catalysis while controlling the redox state of the enzyme. Here, neutron diffraction of redox-controlled MnSOD crystals revealed the all-atom structures of Mn 3+ SOD and Mn 2+ SOD delivering unique data on sites of differential protonation. A novel mechanism is proposed from the direct observation of glutamine deprotonation, the involvement of Tyr and His with altered pK a s, and three unusual strong-short hydrogen bonds that change with the oxidation state of the metal. Quantum calculations provide insight into the electronic modulation of the observed structures.